ClustID MergedIDs Count AvgDissim Members M55 6669 3 0.34 Dync1i1.30809072_4,Nrgn.38790596_6,Pklr.181222231_1 Best CMs (by avg z-score): 1. (Z = 2.40) H19_3 - H19_conserved_region_3 2. (Z = 2.22) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 3. (Z = 2.17) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 4. (Z = 2.01) PRINS - PRINS_RNA 5. (Z = 1.64) CC0196 - Cauldobacter_sRNA_CC0196 6. (Z = 1.50) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.49) CRISPR-DR55 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.34) sbrA - Listeria_sRNA_sbrA 9. (Z = 1.28) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.18) mir-1937 - microRNA_mir-1937 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM55.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM55_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ............................................................ MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 44.69, SCI: 0.00, ZSCORE: 0.47 Full summary: Sequences: 3 Columns: 60 Reading direction: forward Mean pairwise identity: 44.69 Shannon entropy: 0.79564 G+C content: 0.45165 Mean single sequence MFE: 0.00 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.47 Structure conservation index: 0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.46 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Dync1i1.30809072_4 ~~~~~~~~~~UCCCCAUAUCCUCCCCAUGUACCCUACUCACCCGAAAUCCACCACAGCAU Nrgn.38790596_6 UCGCCUUUUCUCUCCACCCUCGUCCCAAACCCCAUACUC-CCAAAAAUGUC~~~~~~~~~ Pklr.181222231_1 ~~~~~~UUUCUUUCAACCCACACCCC---UCCCAUAGUC-CUACAUCUGCCAUCUAGCCC // ClustID MergedIDs Count AvgDissim Members M54 3279 3 0.48 Fmr1.154791521_12,Appbp2.73460120_93,Usp9x.21606330_96 Best CMs (by avg z-score): 1. (Z = 2.74) suhB - suhB 2. (Z = 2.56) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.47) Pseudomon-1 - Pseudomon-1_RNA 4. (Z = 2.44) GcvB - GcvB_RNA 5. (Z = 2.36) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.27) DPB - Stem_loopII_regulatory_element_in_POLB 7. (Z = 2.26) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop 8. (Z = 2.26) RsaD - RNA_Staph._aureus_D 9. (Z = 2.20) MicF - MicF_RNA 10. (Z = 2.16) mir-644 - microRNA_mir-644 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM54.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM54_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((....((.....))....))..((((.........))))............... MFE = -5.41 (Covariance contribution: -10.71) RNAz stats: MPI: 49.21, SCI: -0.00, ZSCORE: 0.57 Full summary: Sequences: 3 Columns: 66 Reading direction: forward Mean pairwise identity: 49.21 Shannon entropy: 0.69053 G+C content: 0.27427 Mean single sequence MFE: -2.20 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.57 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.14 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Fmr1.154791521_12 ~~~~~~~~~~UCAUGUCCUGUGUCAGUUUAUGUUUUGGUCCGCUUUUCCAGUAUUUUAGU~~~~~~ Appbp2.73460120_93 ~~~~~~~UUACCA--CCUUUUUUUAAUAUAUGUUUUCCCC------UAGAGU-UUUUAGCCUUGCU Usp9x.21606330_96 CAGGUUUUUAUUA-GUGUUUUUCCAGGUUAUGUUUUUCCC-----AUGAACU-UUUU~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M57 1853 4 0.46 Vegfa.10534185_46,Stmn2.95284903_3,Cdh2.8048920_32,Pcdh17.66481698_8 Best CMs (by avg z-score): 1. (Z = 4.85) Rhino_CRE - Human_rhinovirus_internal_cis-acting_regulatory_element_(CRE) 2. (Z = 4.35) snoR15 - small_nucleolar_RNA_snoR15 3. (Z = 4.30) snoR25 - small_nucleolar_RNA_snoR25 4. (Z = 4.24) plasmodium_snoR11 - small_nucleolar_RNA_snoR11 5. (Z = 4.01) ceN115 - C._elegans_sRNA_ceN115 6. (Z = 3.99) SCARNA1 - Small_Cajal_body_specific_RNA_1 7. (Z = 3.96) sR6 - sR6_snoRNA 8. (Z = 3.90) rli43 - Listeria_sRNA_rli43 9. (Z = 3.86) snoMe28S-U3344 - Small_nucleolar_RNA_Me28S-U3344 10. (Z = 3.85) rox2 - Drosophila_rox2_ncRNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM57.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM57_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ........................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 52.12, SCI: -0.00, ZSCORE: 0.41 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 52.12 Shannon entropy: 0.80666 G+C content: 0.16299 Mean single sequence MFE: -0.29 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.41 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.30 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Vegfa.10534185_46 ~~~~~~UAUAUGUAAAAACAAAACGAGAAAAAAUAG-AGAAUUCUACAUACUAAAUC~~ Stmn2.95284903_3 GAACUCAUUAUGAAAAAAAAACAGAAUCAAAAAUAAAAUAAAUCAAUGCG~~~~~~~~~ Cdh2.8048920_32 ~~~~~~~~UUUUAAAAAACAAAAC-AAACAAACAAAAAAAAUUAAUAAAGAGAAAAAAA Pcdh17.66481698_8 ~~~~~~~UUAGUCAGAAGCAAAAG-AAAAAAAAUGUAAUAAUAACAAAACAGAAAAAA~ // ClustID MergedIDs Count AvgDissim Members M56 2544 3 0.51 Gng7.10269272_39,Sept9.107478216_17,Dpysl2.46346413_17 Best CMs (by avg z-score): 1. (Z = 2.78) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 2. (Z = 2.73) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 3. (Z = 2.11) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.06) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.93) IRES_APC - APC_internal_ribosome_entry_site_(IRES) 6. (Z = 1.90) mir-BART2 - mir-BART2_microRNA_precursor_family 7. (Z = 1.90) BsrC - BsrC 8. (Z = 1.78) TB10Cs3H2 - Trypanosomatid_snoRNA_TB10Cs3H2 9. (Z = 1.75) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 10. (Z = 1.74) mir-432 - microRNA_mir-432 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM56.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM56_global.out/ --free-endgaps --indel=-100 --threads=4 ..................(((..((((((((((......))))))....)))))))... MFE = -14.35 (Covariance contribution: -11.81) RNAz stats: MPI: 38.42, SCI: 0.17, ZSCORE: 1.24 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 38.42 Shannon entropy: 0.88695 G+C content: 0.44722 Mean single sequence MFE: -10.23 Consensus MFE: -1.79 Energy contribution: -2.47 Covariance contribution: 0.68 Combinations/Pair: 1.60 Mean z-score: 1.24 Structure conservation index: 0.17 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.38 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Gng7.10269272_39 ~~~~~GAGACUCCAGUUACCUCUUUCUCCUGCCGGAUCAGUGUGGGAGCAGAAAU~~~~ Sept9.107478216_17 ~~~~~~AAGAACUAGUCGCCU---CUUCCCAAAUGUCCCUUUGGGUGAAAAGCAGGGAC Dpysl2.46346413_17 UGUCUGUAUCACCCAUC-CCUUACUCUUCCGGG---UCAGCUGUUGAGAAGAGA~~~~~ // ClustID MergedIDs Count AvgDissim Members M51 6900 3 0.50 Dlg4.56889789_7,Ntrk2.11676658_66,Cyfip2.31321000_56 Best CMs (by avg z-score): 1. (Z = 2.14) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 2. (Z = 1.58) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 3. (Z = 1.57) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 4. (Z = 1.52) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 5. (Z = 1.40) H19_3 - H19_conserved_region_3 6. (Z = 1.32) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.22) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 8. (Z = 1.19) IRES_mnt - Mnt_IRES 9. (Z = 1.18) 6C - 6C_RNA 10. (Z = 1.05) P10 - Pseudomonas_sRNA_P10 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM51.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM51_global.out/ --free-endgaps --indel=-100 --threads=4 ...(.(((((.....)))))).................................... MFE = -8.67 (Covariance contribution: -6.13) RNAz stats: MPI: 37.43, SCI: 0.35, ZSCORE: 0.42 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 37.43 Shannon entropy: 0.93108 G+C content: 0.56139 Mean single sequence MFE: -4.37 Consensus MFE: -1.54 Energy contribution: -0.77 Covariance contribution: -0.77 Combinations/Pair: 2.20 Mean z-score: 0.42 Structure conservation index: 0.35 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.18 SVM RNA-class probability: 0.014312 Prediction: OTHER Multiple alignment from mlocarna: Dlg4.56889789_7 ~~AGCCCUUGCUCCUUAGGACCCCUACCCCCGCCCGC---CCCCAUGCACACAUA~~ Ntrk2.11676658_66 CCUGCGAACUCUCCUCGUUCCCUCUGCCUACCACUGACAGCUGCACUUAA~~~~~~~ Cyfip2.31321000_56 ~~~~~CCGCCUUCCUGGCAGCUCAUCCCUCCUCCCCUGUACUCCUG--ACCCCAACA // ClustID MergedIDs Count AvgDissim Members M50 6380 3 0.47 Atp2b2.149655651_52,Atp2a2.35312505_10,Gnb1.172386440_5 Best CMs (by avg z-score): 1. (Z = 4.50) REN-SRE - Renin_stability_regulatory_element_(REN-SRE) 2. (Z = 3.54) UPD-PKib - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 3. (Z = 3.16) mir-23 - microRNA_mir-23 4. (Z = 3.05) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 5. (Z = 3.04) mir-515 - microRNA_mir-515 6. (Z = 2.69) isrD - isrD_Hfq_binding_RNA 7. (Z = 2.65) mir-190 - microRNA_mir-190 8. (Z = 2.64) Trp_leader - Tryptophan_operon_leader 9. (Z = 2.53) class_I_RNA - Class_I_RNA 10. (Z = 2.50) mir-124 - mir-124_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM50.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM50_global.out/ --free-endgaps --indel=-100 --threads=4 ..(((..(((((....((((((((........)))....))))).....)))))))) MFE = -20.56 (Covariance contribution: -15.83) RNAz stats: MPI: 32.12, SCI: 0.45, ZSCORE: -1.05 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 32.12 Shannon entropy: 0.95315 G+C content: 0.35831 Mean single sequence MFE: -8.83 Consensus MFE: -3.97 Energy contribution: -1.87 Covariance contribution: -2.10 Combinations/Pair: 2.20 Mean z-score: -1.05 Structure conservation index: 0.45 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.19 SVM RNA-class probability: 0.985053 Prediction: RNA Multiple alignment from mlocarna: Atp2b2.149655651_52 ~~UGACCGGUGGUGUCCCGUGCUUUGAGGAAAAC---CAAACAC--UUUCCGCCUCA Atp2a2.35312505_10 ~AAAU--GAAUGUGUGUGGUUUUUAAAAGAAAAAA----AACUAAAUAGCAUGUAUU Gnb1.172386440_5 AAGAG--AAGGAUCUCUGUGCUGUAAACUAAAACAAAUUGUGCA-----UUUUUCUG // ClustID MergedIDs Count AvgDissim Members M53 5609 3 0.80 Cyfip2.31321000_20,Atrn.118696808_124,Atf3.107191620_23 Best CMs (by avg z-score): 1. (Z = 1.62) snoZ152 - Small_nucleolar_RNA_Z152/R70/R12/ 2. (Z = 1.60) PK-BYV - 3'-terminal_pseudoknot_in_BYV 3. (Z = 1.57) snoZ6 - Z6_small_nucleolar_RNA 4. (Z = 1.56) IRES_FGF2 - FGF-2_internal_ribosome_entry_site_(IRES) 5. (Z = 1.56) SNORD62 - Small_nucleolar_RNA_SNORD62 6. (Z = 1.55) HIV-1_SL3 - HIV-1_stem-loop_3_Psi_packaging_signal 7. (Z = 1.53) RyeB - RyeB_RNA 8. (Z = 1.51) sR13 - Small_nucleolar_RNA_sR13 9. (Z = 1.45) Plant_U3 - Plant_small_nucleolar_RNA_U3 10. (Z = 1.43) SNORD29 - Small_nucleolar_RNA_SNORD29 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM53.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM53_global.out/ --free-endgaps --indel=-100 --threads=4 .......................................................................(((((..........((....)))))))........ MFE = -1.54 (Covariance contribution: -4.41) RNAz stats: MPI: 25.55, SCI: -0.00, ZSCORE: 0.72 Full summary: Sequences: 3 Columns: 107 Reading direction: forward Mean pairwise identity: 25.55 Shannon entropy: 1.00705 G+C content: 0.24193 Mean single sequence MFE: -8.63 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.72 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.89 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Cyfip2.31321000_20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UUGUGAAACCACACU-GAGUGGAAGUAGGGGAGAAGAUGCCAGGGCCUGCU~~~~~~~~ Atrn.118696808_124 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CCUUCUGAAAUAAAAGUAGAUCUGGUAAA-----------GCAAGGGCCUUUGUGAUGACG Atf3.107191620_23 UAGGACUCCACACUCAGUGACAGGGCAGGAAGAGCCAAGGAUUCUCCGUU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M52 5496 4 0.70 Eif4a2.79950592_9,Pcdh17.66481698_16,Usp9x.21606330_25,Syn2.151412465_15 Best CMs (by avg z-score): 1. (Z = 3.53) RMST_10 - Rhabdomyosarcoma_2_associated_transcript_conserved_region_10 2. (Z = 3.22) K10_TLS - K10_transport/localisation_element_(TLS) 3. (Z = 3.17) veev_FSE - venezuelan_equine_encephalitis_virus_ribosomal_frameshift_element 4. (Z = 3.12) snoZ267 - Small_nucleolar_RNA_Z267 5. (Z = 3.05) rspL - rpsL_sRNA 6. (Z = 2.97) mir-3 - microRNA_mir-3 7. (Z = 2.89) mir-999 - microRNA_mir-999 8. (Z = 2.86) mir-BART7 - microRNA_mir-BART7 9. (Z = 2.83) Plasmid_R1162 - R1162-like_plasmid_antisense_RNA 10. (Z = 2.80) mir-15 - mir-15_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM52.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM52_global.out/ --free-endgaps --indel=-100 --threads=4 ...............(((((((((....((((...........))))....)))))))))................... MFE = -7.29 (Covariance contribution: -7.46) RNAz stats: MPI: 32.97, SCI: 0.07, ZSCORE: 0.39 Full summary: Sequences: 4 Columns: 79 Reading direction: forward Mean pairwise identity: 32.97 Shannon entropy: 1.06183 G+C content: 0.21092 Mean single sequence MFE: -8.00 Consensus MFE: -0.57 Energy contribution: 0.92 Covariance contribution: -1.50 Combinations/Pair: 2.25 Mean z-score: 0.39 Structure conservation index: 0.07 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.30 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Eif4a2.79950592_9 ~CUUGUGGACUAAAAGAUAUAAGU---GCUGUA-----UAAAAUCAG--CCAAUUAUGUUA~~~~~~~~~~~~~~~~~~ Pcdh17.66481698_16 ~~~~~~~~~~~~~~~~~~~~~~UCAUUGAGUAG-----UA--AUACUGAGAGAAAAUUAACAUAACUAAAAUGUUUUAC Usp9x.21606330_25 CUUGG-----UAAUGGGAAUUUUGAAAGAUUUA-----AAACAAAAUAAGCAAAAAUUUG~~~~~~~~~~~~~~~~~~~ Syn2.151412465_15 ~~~~~~~~~~~~GGAGGUCAAGU--UCCUUGUGACUGUUUGAAACAAGAGAACAAGGAUCCACA~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M177 3782 4 0.56 Dpysl2.46346413_25,Slc7a8.32800927_43,Syn2.151412465_14,Olfm1.7194336_11 Best CMs (by avg z-score): 1. (Z = 3.21) mir-484 - microRNA_mir-484 2. (Z = 2.41) MIR2907 - microRNA_MIR2907 3. (Z = 2.18) Corona_SL-III - Coronavirus_SL-III_cis-acting_replication_element_(CRE) 4. (Z = 2.15) MIR403 - microRNA_MIR403 5. (Z = 2.13) mir-2241 - microRNA_mir-2241 6. (Z = 1.92) lin-4 - lin-4_microRNA_precursor 7. (Z = 1.90) F6 - F6_TB_sRNA 8. (Z = 1.76) mraW - mraW_RNA 9. (Z = 1.74) sbrA - Listeria_sRNA_sbrA 10. (Z = 1.71) mir-248 - microRNA_mir-248 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM177.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM177_global.out/ --free-endgaps --indel=-100 --threads=4 ............(((((((((((.........))))))....)))))............ MFE = -17.24 (Covariance contribution: -10.89) RNAz stats: MPI: 31.36, SCI: 0.51, ZSCORE: 0.14 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 31.36 Shannon entropy: 1.21041 G+C content: 0.50620 Mean single sequence MFE: -12.17 Consensus MFE: -6.21 Energy contribution: -4.78 Covariance contribution: -1.44 Combinations/Pair: 2.27 Mean z-score: 0.14 Structure conservation index: 0.51 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.19 SVM RNA-class probability: 0.584020 Prediction: RNA Multiple alignment from mlocarna: Olfm1.7194336_11 UCUCCCCACCCACAGCCCCCAGCCCCCGUGGCGCUCGGUGUAGGCUGCUU~~~~~~~~~ Dpysl2.46346413_25 ~~~~~~~~~ACCCUAGUUUUGACCCCCACUCCAUAGUUUUGUGCUAGCCUGGUGUCUGU Syn2.151412465_14 ACAUUCACC---UGACCCUGCACUCCCUAGAC-UGCUGUGGAGGUCAAGUUCCU~~~~~ Slc7a8.32800927_43 ~~~UCCCACCUAGCUCACCCUACCCCUAACUGGUGAGAGGC-UGAGUUUGGGCU~~~~~ // ClustID MergedIDs Count AvgDissim Members M59 429 3 0.48 Dynll1.42582642_6,Stmn2.95284903_10,Atp1b2.56418323_32 Best CMs (by avg z-score): 1. (Z = 3.32) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.76) suhB - suhB 3. (Z = 2.67) potC - potC_RNA 4. (Z = 2.56) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.27) rhtB - rhtB_sRNA 6. (Z = 2.22) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.21) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.16) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 9. (Z = 2.04) RsaD - RNA_Staph._aureus_D 10. (Z = 2.02) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM59.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM59_global.out/ --free-endgaps --indel=-100 --threads=4 ..............((.(((...(((...))).........)))...)).................. MFE = -8.30 (Covariance contribution: -12.80) RNAz stats: MPI: 33.33, SCI: 0.39, ZSCORE: 0.59 Full summary: Sequences: 3 Columns: 67 Reading direction: forward Mean pairwise identity: 33.33 Shannon entropy: 0.89445 G+C content: 0.32667 Mean single sequence MFE: -1.10 Consensus MFE: -0.43 Energy contribution: 0.57 Covariance contribution: -1.00 Combinations/Pair: 2.33 Mean z-score: 0.59 Structure conservation index: 0.39 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.14 SVM RNA-class probability: 0.015654 Prediction: OTHER Multiple alignment from mlocarna: Dynll1.42582642_6 CUUCUGUACCCCCAUUUUUUUCUCCCUUAGGUCAUUCCUUUAAAAUAAAU~~~~~~~~~~~~~~~~~ Stmn2.95284903_10 ~~~~~~~UCCCCCAUGUUGAACUCAGUCCCUGC---CCUUUUCAUUCCACCC------AAAAAUGA~ Atp1b2.56418323_32 ~~~~~~~~~~~~~~GAAUUUCUUGGCUCCGCCU---CCUUCAAACUCUUUCCCCUUUAAAAAACAAA // ClustID MergedIDs Count AvgDissim Members M58 5317 3 0.50 Gria2.172265159_35,Vegfa.10534185_51,Bdnf.977114_76 Best CMs (by avg z-score): 1. (Z = 3.82) SNORA20 - Small_nucleolar_RNA_SNORA20 2. (Z = 3.80) S_pombe_snR3 - small_nucleolar_RNA_snR3 3. (Z = 3.37) SCARNA24 - Small_Cajal_body_specific_RNA_24 4. (Z = 3.35) veev_FSE - venezuelan_equine_encephalitis_virus_ribosomal_frameshift_element 5. (Z = 3.22) PK-PYVV - 3'-terminal_pseudoknot_in_PYVV 6. (Z = 3.07) SCARNA14 - Small_Cajal_body_specific_RNA_14 7. (Z = 3.06) RsaF - RNA_Staph._aureus_F 8. (Z = 3.06) mir-315 - microRNA_mir-315 9. (Z = 3.05) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 10. (Z = 3.03) MIR162_2 - microRNA_MIR162_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM58.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM58_global.out/ --free-endgaps --indel=-100 --threads=4 ..............(((((((((.................)))))))..))............... MFE = -11.68 (Covariance contribution: -9.45) RNAz stats: MPI: 28.57, SCI: 0.94, ZSCORE: 0.12 Full summary: Sequences: 3 Columns: 66 Reading direction: forward Mean pairwise identity: 28.57 Shannon entropy: 1.03055 G+C content: 0.21863 Mean single sequence MFE: -5.57 Consensus MFE: -5.21 Energy contribution: -2.33 Covariance contribution: -2.88 Combinations/Pair: 2.43 Mean z-score: 0.12 Structure conservation index: 0.94 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.50 SVM RNA-class probability: 0.944507 Prediction: RNA Multiple alignment from mlocarna: Gria2.172265159_35 ~~~~~~~~~~~~~~CUGCUCUUGAAGUAUUUAAGGUUGUGUAGGAGC--AGUAAUCAAUAUAGAUA Vegfa.10534185_51 UUCCGUAGUACAUAUUUAUUUUUAAACA-----GCAACAAAGAAAUACAGAUAUA~~~~~~~~~~~ Bdnf.977114_76 ~~~~~~~~~~~~CUCUCUAUGGUAAAGAUAU----UAUUCACCAUGUAAAACAAGAAAAAUAUUUA // ClustID MergedIDs Count AvgDissim Members M176 78 4 0.47 Ddn.137572548_2,Cyfip2.31321000_33,Grb2.105722014_7,Sdcbp.19848126_27 Best CMs (by avg z-score): 1. (Z = 3.37) suhB - suhB 2. (Z = 2.56) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.34) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.10) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.73) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.72) snoU97 - Small_nucleolar_RNA_U97 7. (Z = 1.68) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.68) KCNQ1DN - KCNQ1_downstream_neighbour 9. (Z = 1.63) RydC - RydC_RNA 10. (Z = 1.63) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM176.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM176_global.out/ --free-endgaps --indel=-100 --threads=4 .........................(((((....................)))))............ MFE = -1.74 (Covariance contribution: -3.11) RNAz stats: MPI: 36.50, SCI: -0.00, ZSCORE: 0.96 Full summary: Sequences: 4 Columns: 67 Reading direction: forward Mean pairwise identity: 36.50 Shannon entropy: 1.09292 G+C content: 0.35512 Mean single sequence MFE: -2.04 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.96 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.90 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Ddn.137572548_2 ~~~CCUCUCUCCAGGCUUC--GUUUGCUUCCUUUUCUUCUUUCCUA-CCUGUACCU~~~~~~~~~~~ Cyfip2.31321000_33 UCUUUUGCUCUCAACUUCC-----UGGUCUCUUCCUUUUGCUCAAGCCCCGUGCU~~~~~~~~~~~~ Grb2.105722014_7 ~~~~~~~~UUCCUGUGUCCUUUUUUCGCG---UUCUUUCUUUCCUGUCCAGUGCAUGAUGU~~~~~~ Sdcbp.19848126_27 ~~~~~~~~~~~~~~~~~GUUUCCCUAGUCAUCUCAGUUUGUUCCAUUUUCUGACUCUAUCCUGCAAA // ClustID MergedIDs Count AvgDissim Members M151 5199 3 0.49 Ddn.137572548_33,Ntrk2.11676658_51,Mapre3.25496282_13 Best CMs (by avg z-score): 1. (Z = 3.77) suhB - suhB 2. (Z = 3.66) Arthropod_7SK - Arthropod_7SK_RNA 3. (Z = 3.58) Qrr - Qrr_RNA 4. (Z = 2.82) sbrA - Listeria_sRNA_sbrA 5. (Z = 2.68) 23S-methyl - 23S_methyl_RNA_motif 6. (Z = 2.67) RyhB - RyhB_RNA 7. (Z = 2.61) ctRNA_p42d - ctRNA 8. (Z = 2.55) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.49) mir-354 - microRNA_mir-354 10. (Z = 2.37) OmrA-B - OmrA-B_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM151.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM151_global.out/ --free-endgaps --indel=-100 --threads=4 ...((.(((........))).))(((((........)))))................. MFE = -12.38 (Covariance contribution: -10.11) RNAz stats: MPI: 36.21, SCI: 0.57, ZSCORE: 0.23 Full summary: Sequences: 3 Columns: 58 Reading direction: forward Mean pairwise identity: 36.21 Shannon entropy: 0.94669 G+C content: 0.41885 Mean single sequence MFE: -9.00 Consensus MFE: -5.16 Energy contribution: -3.83 Covariance contribution: -1.33 Combinations/Pair: 2.33 Mean z-score: 0.23 Structure conservation index: 0.57 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.64 SVM RNA-class probability: 0.772936 Prediction: RNA Multiple alignment from mlocarna: Ddn.137572548_33 AUCCACGCCUACC----GGUUUGAGACUGACAUUCAAGUCUUUUUUUUUUUUUG~~~~ Ntrk2.11676658_51 ~~~~~UUUAAGCCCCCAGGACUGCCGU---CAGCAACACGGCUUUUCUUUCCCAUGGU Mapre3.25496282_13 ~~~CCCUAGAGCCCAGACUGGGGCAGGACUCACCAAUUCUUAUUUAUUUUGUC~~~~~ // ClustID MergedIDs Count AvgDissim Members M150 4519 4 0.70 Appbp2.73460120_32,Gria2.172265159_54,Fmr1.154791521_32,Pabpn1.32998239_2 Best CMs (by avg z-score): 1. (Z = 3.12) RMST_10 - Rhabdomyosarcoma_2_associated_transcript_conserved_region_10 2. (Z = 2.84) BsrC - BsrC 3. (Z = 2.77) mir-15 - mir-15_microRNA_precursor_family 4. (Z = 2.75) DdR18 - D._discoideum_snoRNA_DdR18 5. (Z = 2.66) SCARNA15 - Small_Cajal_body_specific_RNA_15 6. (Z = 2.62) isrI - isrI_Hfq_binding_RNA 7. (Z = 2.57) Nkx2-2as - Nkx2-2_antisense 8. (Z = 2.57) SCARNA8 - Small_Cajal_body_specific_RNA_8 9. (Z = 2.56) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.56) IRES_Cripavirus - Cripavirus_internal_ribosome_entry_site_(IRES) Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM150.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM150_global.out/ --free-endgaps --indel=-100 --threads=4 ...............(((.....)))................((((....))))........... MFE = -8.08 (Covariance contribution: -9.20) RNAz stats: MPI: 37.92, SCI: -0.00, ZSCORE: 0.39 Full summary: Sequences: 4 Columns: 65 Reading direction: forward Mean pairwise identity: 37.92 Shannon entropy: 1.01407 G+C content: 0.23408 Mean single sequence MFE: -3.65 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.39 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.22 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Appbp2.73460120_32 ~~~~~~~CAUUUUAACUGACAUCCAGGACUUCAAU--------GGAAAAAUCCUCCAGUUACAAU Gria2.172265159_54 CAUUA-----CUCAUCAGGGAUGCUGGAGGUACAUUUUAAGUUUUAAUAAUAAAU~~~~~~~~~~ Fmr1.154791521_32 AAUGUAUAAGCAGAACUGAAAAACAGGCCUACAAUU-----AGUUAAAAAUAAUU~~~~~~~~~~ Pabpn1.32998239_2 ~~~~~~~~~~~~~~AAAGAAAAACAGAAGAUGACCUUGAUGGAAAAAAAAUAUUUAAAAAAAAA~ // ClustID MergedIDs Count AvgDissim Members M153 5936 4 0.51 Fmr1.154791521_6,Ccni.16459077_25,Map1b.30415235_74,Canx.35850944_71 Best CMs (by avg z-score): 1. (Z = 3.37) Arthropod_7SK - Arthropod_7SK_RNA 2. (Z = 2.91) suhB - suhB 3. (Z = 2.83) Qrr - Qrr_RNA 4. (Z = 2.79) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.79) rimP - Enterobacteria_rnk_leader 6. (Z = 2.77) sbrA - Listeria_sRNA_sbrA 7. (Z = 2.73) GcvB - GcvB_RNA 8. (Z = 2.64) L10_leader - Ribosomal_protein_L10_leader 9. (Z = 2.59) MicF - MicF_RNA 10. (Z = 2.49) RyeB - RyeB_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM153.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM153_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ................................................................................................ MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 27.26, SCI: -0.00, ZSCORE: 0.57 Full summary: Sequences: 4 Columns: 96 Reading direction: forward Mean pairwise identity: 27.26 Shannon entropy: 1.17953 G+C content: 0.15423 Mean single sequence MFE: -3.50 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.57 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.71 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Fmr1.154791521_6 ~UUAAGUACACUUAACACUUCAGGGCAGGAUUUUACUU---UAUUUUUUAAAAA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Ccni.16459077_25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AUUCAGUACCCUAGUUUUAUAUUGCGCUA-UUAGGAUUUUCUUUAUAAGGA Map1b.30415235_74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AGUUCUACAGCUUAAAUUUAUUUAGCCUUUUAUAUUAUUUUGUUUUAAAG~~ Canx.35850944_71 UGCUCUAGCACUGAGCUACAC---CCUGUUCUCCUAGAUAAUAUUCUUUAAGA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M152 6418 3 0.43 Stxbp1.11762105_35,Atp1b2.56418323_35,Glt25d1.18822081_25 Best CMs (by avg z-score): 1. (Z = 2.26) suhB - suhB 2. (Z = 2.25) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 3. (Z = 1.61) H19_3 - H19_conserved_region_3 4. (Z = 1.59) bxd_6 - Bithoraxoid_conserved_region_6 5. (Z = 1.48) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.48) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.26) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.24) mir-188 - microRNA_mir-188 9. (Z = 1.21) CC0196 - Cauldobacter_sRNA_CC0196 10. (Z = 1.21) RsaE - RNA_Staph._aureus_E Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM152.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM152_global.out/ --free-endgaps --indel=-100 --threads=4 .....((......))............(((((.(..........).))))).... MFE = -10.66 (Covariance contribution: -11.56) RNAz stats: MPI: 43.03, SCI: -0.00, ZSCORE: 0.92 Full summary: Sequences: 3 Columns: 55 Reading direction: forward Mean pairwise identity: 43.03 Shannon entropy: 0.80736 G+C content: 0.51841 Mean single sequence MFE: -5.11 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.92 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.14 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Stxbp1.11762105_35 UGUCCGGUGCCCUCCUCCCUUCCUGCCUCUAGAG-UUCUCCUCUCCUUAGU~~~~ Atp1b2.56418323_35 ~~~~~CGCCUGUACCAAGUUUUCUUCCACCAUAGCUGCGUUUUCCUCUGGUCUCU Glt25d1.18822081_25 ~~~~GGCUCCCUUGCCCACCCCUGGUUUCCAGAGCUUCUCCCUGCCUUUGUGUC~ // ClustID MergedIDs Count AvgDissim Members M155 1617 4 0.66 Arc.112771937_18,Vegfa.10534185_22,Vgf.20905861_3,Shank3.127875955_44 Best CMs (by avg z-score): 1. (Z = 2.32) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 2. (Z = 1.86) F6 - F6_TB_sRNA 3. (Z = 1.80) P10 - Pseudomonas_sRNA_P10 4. (Z = 1.79) isrD - isrD_Hfq_binding_RNA 5. (Z = 1.74) g2 - G2 6. (Z = 1.68) 6C - 6C_RNA 7. (Z = 1.57) IRES_mnt - Mnt_IRES 8. (Z = 1.46) mir-689 - microRNA_mir-689 9. (Z = 1.36) snoU2-25 - Small_nucleolar_RNA_U2-25 10. (Z = 1.31) CC3664 - caulobacter_sRNA_CC3664 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM155.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM155_global.out/ --free-endgaps --indel=-100 --threads=4 .....................(((....(((......)))......)))................ MFE = -6.79 (Covariance contribution: -6.11) RNAz stats: MPI: 41.24, SCI: -0.00, ZSCORE: 1.1 Full summary: Sequences: 4 Columns: 65 Reading direction: forward Mean pairwise identity: 41.24 Shannon entropy: 1.01682 G+C content: 0.55076 Mean single sequence MFE: -10.59 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.10 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.50 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Arc.112771937_18 ~~~~~~~~~~~~~~UUCUGA-CAGAUCCCCCACCCUGUGCCCCUGCCAGCCCCCACAGGUUUAUU Vegfa.10534185_22 UCCCCACUAGAUUCUGCAAGAGCACCCUGCCCCUCUGGGCACUGCCUGGA~~~~~~~~~~~~~~~ Vgf.20905861_3 ~~~~~~~~~~CGGCUGCCGCCCGGCCCCGCCCCACAAGGCCCCGCCCCG--GGUUCUGUCAG~~~ Shank3.127875955_44 ~~~~~~~~~~UCUGUGCCCACCCGCCCCGCCCCACCCUGGCCCA--CCG--GCCCCAUUCCUUA~ // ClustID MergedIDs Count AvgDissim Members M154 6415 4 0.53 Canx.35850944_25,Opcml.28508230_17,Marcksl1.148671604_4,Fgf13.144199535_13 Best CMs (by avg z-score): 1. (Z = 3.04) Arthropod_7SK - Arthropod_7SK_RNA 2. (Z = 2.66) suhB - suhB 3. (Z = 2.16) Pseudomon-Rho - Pseudomon-Rho_RNA 4. (Z = 2.08) U2 - U2_spliceosomal_RNA 5. (Z = 2.05) GcvB - GcvB_RNA 6. (Z = 1.90) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 7. (Z = 1.83) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.83) RydC - RydC_RNA 9. (Z = 1.83) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 10. (Z = 1.83) SraG - SraG_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM154.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM154_global.out/ --free-endgaps --indel=-100 --threads=4 ..................((((...((((.......)))).))..))................ MFE = -8.86 (Covariance contribution: -7.53) RNAz stats: MPI: 35.68, SCI: 0.56, ZSCORE: 0.82 Full summary: Sequences: 4 Columns: 63 Reading direction: forward Mean pairwise identity: 35.68 Shannon entropy: 1.08474 G+C content: 0.34496 Mean single sequence MFE: -3.90 Consensus MFE: -2.17 Energy contribution: -0.92 Covariance contribution: -1.25 Combinations/Pair: 2.00 Mean z-score: 0.82 Structure conservation index: 0.56 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.53 SVM RNA-class probability: 0.259489 Prediction: OTHER Multiple alignment from mlocarna: Canx.35850944_25 UCCUCAUGCAUCUCCUCAGUCC--CUAGCUUUCUCUGCUAUGC--AUUUUCUUC~~~~~~~~~ Opcml.28508230_17 ~~UUUUACCAUCUUCUCUGGCCAUUCUGCUUAAUCUGCAUUUUUUCCACUAG~~~~~~~~~~~ Marcksl1.148671604_4 ~~~~~~~~~~UCUUCUCCCUCC--UGUGGAUUCUC-CCAUCAGCCAUUUGGUCUUACUAUUAG Fgf13.144199535_13 ~~~~~UCUUGGCUUCGUGUUUU--CUAUCUCUGCUUGAUUCAA--AUGUACUCUUUACU~~~~ // ClustID MergedIDs Count AvgDissim Members M157 3100 6 0.64 Tmem30a.84827711_3,Appbp2.73460120_6,Fmr1.154791521_20,Usp9x.21606330_88,Atp2a2.35312505_7,Morf4l1.91235629_4 Best CMs (by avg z-score): 1. (Z = 3.55) ctRNA_pT181 - ctRNA 2. (Z = 3.29) rli61 - Listeria_sRNA_rli61 3. (Z = 3.19) mir-48 - microRNA_mir-48 4. (Z = 3.01) sbrA - Listeria_sRNA_sbrA 5. (Z = 2.94) LhrC - Listeria_Hfq_binding_LhrC 6. (Z = 2.94) mir-70 - microRNA_mir-70 7. (Z = 2.83) DPB - Stem_loopII_regulatory_element_in_POLB 8. (Z = 2.82) L10_leader - Ribosomal_protein_L10_leader 9. (Z = 2.78) Chlorobi-RRM - Chlorobi-RRM_RNA 10. (Z = 2.78) GcvB - GcvB_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM157.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM157_global.out/ --free-endgaps --indel=-100 --threads=4 .............(((((.((......)))))....))................................ MFE = -3.65 (Covariance contribution: -4.44) RNAz stats: MPI: 40.28, SCI: -0.00, ZSCORE: 0.49 Full summary: Sequences: 6 Columns: 70 Reading direction: forward Mean pairwise identity: 40.28 Shannon entropy: 1.16753 G+C content: 0.22062 Mean single sequence MFE: -5.60 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.49 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.62 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Tmem30a.84827711_3 ~~~~~~~~~~~~~~~~~~~ACAUAACAAAAAACAGCCU-UUGUUCUUUGCUUCUUACAUAUGGAUGACUU Appbp2.73460120_6 ~~~~~~~~~~~~~ACCCUAGUAGAACAACAGGAAACGUUUUUUUUUUUUCUUUUUAAAAAAUA~~~~~~~ Fmr1.154791521_20 CUUAGGCAGUAUAAAGAA-UA-GGACUUGUUU----UUCGUUUUUGUU--UUGUUGCA~~~~~~~~~~~~ Usp9x.21606330_88 ~~AAUACAAGCAUAAACAUAUAUGGGCUUUGU-----UUCUUUUUGUUGAUUUUUCU~~~~~~~~~~~~~ Atp2a2.35312505_7 ~~~GUAGAUGAAAAAAGC-AU-GUACAGUGUU----CUGUUUCAUACUCAUACUUGUAC~~~~~~~~~~~ Morf4l1.91235629_4 ~~~~~~AAAUA-AAAGGA-GU-UAACUGCUCC----UUUUUUCUUUCU--UUUUUUCAUUUCAAA~~~~~ // ClustID MergedIDs Count AvgDissim Members M156 4929 3 0.44 Pcdh17.66481698_22,Sdcbp.19848126_30,Gria2.172265159_31 Best CMs (by avg z-score): 1. (Z = 4.38) mir-140 - microRNA_mir-140 2. (Z = 4.35) mtDNA_ssA - Mitochondrial_DNA_control_region_secondary_structure_A 3. (Z = 4.11) mir-BART2 - mir-BART2_microRNA_precursor_family 4. (Z = 3.83) mir-15 - mir-15_microRNA_precursor_family 5. (Z = 3.72) SprD - Small_pathogenicity_island_RNA_D 6. (Z = 3.71) K10_TLS - K10_transport/localisation_element_(TLS) 7. (Z = 3.61) mir-154 - microRNA_mir-154 8. (Z = 3.53) RUF1 - Plasmodium_RNA_of_unkown_function_RUF1 9. (Z = 3.50) Lacto-rpoB - Lacto-rpoB_RNA 10. (Z = 3.50) mir-286 - microRNA_mir-286 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM156.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM156_global.out/ --free-endgaps --indel=-100 --threads=4 .........(((((((((..(((((((((......))).)))))).))))))))).... MFE = -15.50 (Covariance contribution: -12.90) RNAz stats: MPI: 44.63, SCI: 0.36, ZSCORE: 0.15 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 44.63 Shannon entropy: 0.79783 G+C content: 0.14479 Mean single sequence MFE: -4.13 Consensus MFE: -1.47 Energy contribution: -0.27 Covariance contribution: -1.21 Combinations/Pair: 1.71 Mean z-score: 0.15 Structure conservation index: 0.36 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.03 SVM RNA-class probability: 0.019051 Prediction: OTHER Multiple alignment from mlocarna: Pcdh17.66481698_22 ~~~~~~AAUUGUUGAGUG-UAUAAGAGCUAUAUUGUGUAUUUUAUUAAAUUAAUAUA~~ Sdcbp.19848126_30 ~~~~~~~~UUAUUAUUUUAUGUGAUAUUAUCCUAUUAAAUG-UAUAAAAAUAUUAAAUA Gria2.172265159_31 UCUAUGUAAAGCUAUUUUUUCUGU--ACAUCAUACUGUAUAAUAGUAAAAUA~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M159 3972 4 0.56 Myo5b.71580455_9,Grb2.105722014_46,Tmeff1.65356245_27,Gria2.172265159_38 Best CMs (by avg z-score): 1. (Z = 4.23) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 2. (Z = 4.06) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.91) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.83) K10_TLS - K10_transport/localisation_element_(TLS) 5. (Z = 3.66) mir-1302 - microRNA_mir-1302 6. (Z = 3.60) mir-577 - microRNA_mir-577 7. (Z = 3.50) mir-BART2 - mir-BART2_microRNA_precursor_family 8. (Z = 3.42) snoCD11 - Small_nucleolar_RNA_CD11 9. (Z = 3.30) snopsi28S-3316 - Small_nucleolar_RNA_psi28S-3316 10. (Z = 3.28) snR36 - Small_nucleolar_RNA_snR36 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM159.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM159_global.out/ --free-endgaps --indel=-100 --threads=4 ......((((((.((((..((........))..))))..)))))).............. MFE = -10.39 (Covariance contribution: -10.44) RNAz stats: MPI: 36.31, SCI: 0.82, ZSCORE: 0.72 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 36.31 Shannon entropy: 1.07258 G+C content: 0.21237 Mean single sequence MFE: -2.41 Consensus MFE: -1.98 Energy contribution: 0.52 Covariance contribution: -2.50 Combinations/Pair: 2.33 Mean z-score: 0.72 Structure conservation index: 0.82 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.86 SVM RNA-class probability: 0.838102 Prediction: RNA Multiple alignment from mlocarna: Myo5b.71580455_9 ~~~~GUAUAUAACUUAAGA---AUG--UUCAAACUAAGAUUAUAUUAAAAACACAUGAC Grb2.105722014_46 UUUGUGUGUAUA-UAUUUAAAGAUCAGUGUUUAAAUAAAAAAACAAACCUA~~~~~~~~ Tmeff1.65356245_27 ~~AGC-CAGUCA-AAAUUAUGCA----UGUAGAAUUUAAAGACUAUGUUUAAACUUAA~ Gria2.172265159_38 ~~~~~CUGUAAUCUAAGUAUGCAUC--UUCAGUUUUAAAAUUAUAAAAACCAACAUC~~ // ClustID MergedIDs Count AvgDissim Members M158 956 4 0.55 Map1b.30415235_49,Canx.35850944_39,Gng7.10269272_21,Usp9x.21606330_61 Best CMs (by avg z-score): 1. (Z = 2.46) CRISPR-DR24 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.45) whalefall-1 - Whalefall-1_RNA 3. (Z = 2.36) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.28) rli49 - Listeria_sRNA_rli49 5. (Z = 2.23) PtaRNA1 - Plasmid_transferred_anti-sense_RNA 6. (Z = 2.20) CRISPR-DR53 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.16) CRISPR-DR66 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.96) MIR815 - microRNA_MIR815 9. (Z = 1.96) P4 - Pseudomonas_sRNA_P4 10. (Z = 1.93) U7 - U7_small_nuclear_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM158.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM158_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((((((((((....)))))))))).(((((((......)))))))..... MFE = -24.15 (Covariance contribution: -13.75) RNAz stats: MPI: 36.99, SCI: 0.87, ZSCORE: -0.01 Full summary: Sequences: 4 Columns: 61 Reading direction: forward Mean pairwise identity: 36.99 Shannon entropy: 1.09077 G+C content: 0.36432 Mean single sequence MFE: -11.70 Consensus MFE: -10.14 Energy contribution: -9.32 Covariance contribution: -0.81 Combinations/Pair: 2.35 Mean z-score: -0.01 Structure conservation index: 0.87 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.86 SVM RNA-class probability: 0.971713 Prediction: RNA Multiple alignment from mlocarna: Map1b.30415235_49 UCCUUUCAAGAUUUUUUCACCGUGAGGUGGAAGAGCCAAGUUCAGA----AGCA~~~~~~~ Canx.35850944_39 ~~~~~~~~~GUUUUGUUUUUCAUGUGGAAUGCAGAUGGGUGCUAGAGGAGGCUCUCCCA~~ Gng7.10269272_21 ~~~~~~~~AGAUUUAAUUAUCUUGAGGUGAUUGAGAAGGACC--GAUG-GGGUUCUCCAUC Usp9x.21606330_61 ~~UUUUUUAAAGUUCUUCA---AGUAGUGAAGUAGGUUGGCUUUG-UUUGGACCAG~~~~~ // ClustID MergedIDs Count AvgDissim Members M174 4795 3 0.54 Map1b.30415235_60,Pou4f2.31390818_16,Fmr1.154791521_33 Best CMs (by avg z-score): 1. (Z = 3.76) tp2 - tp2 2. (Z = 3.51) Vault - Vault_RNA 3. (Z = 3.29) DPB - Stem_loopII_regulatory_element_in_POLB 4. (Z = 3.28) snoR110 - Small_nucleolar_RNA_snoR110 5. (Z = 3.24) Phe_leader - Phenylalanine_leader_peptide 6. (Z = 3.08) MicF - MicF_RNA 7. (Z = 3.07) GcvB - GcvB_RNA 8. (Z = 3.06) RyhB - RyhB_RNA 9. (Z = 3.05) ctRNA_pT181 - ctRNA 10. (Z = 2.95) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM174.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM174_global.out/ --free-endgaps --indel=-100 --threads=4 .......((((.....)))).........(((((....))))).............. MFE = -6.38 (Covariance contribution: -7.28) RNAz stats: MPI: 46.20, SCI: 1.27, ZSCORE: -0.46 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 46.20 Shannon entropy: 0.76292 G+C content: 0.20816 Mean single sequence MFE: -3.03 Consensus MFE: -3.85 Energy contribution: -1.63 Covariance contribution: -2.21 Combinations/Pair: 2.40 Mean z-score: -0.46 Structure conservation index: 1.27 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.09 SVM RNA-class probability: 0.538981 Prediction: RNA Multiple alignment from mlocarna: Map1b.30415235_60 UAUUUCAAAAGU-UACAUUUUAGUUUACUUUUCGUCUGUGAAGUCUAUGUU~~~~~~ Pou4f2.31390818_16 ~~~~~~~AUAUUAUAUAUAUAUUUUUAUUGUGGUUCUUAUCGCUUUCUUCCUUCUCU Fmr1.154791521_33 UAGUUAAAAAUAAUUCAUU--UUUUUCCUUUUGAUGUGUCAAGUCUUAUUUU~~~~~ // ClustID MergedIDs Count AvgDissim Members M168 619 6 0.57 Rnf111.74909360_24,Irgm.34132512_9,Dync1i1.30809072_14,Adcy5.67290968_16,Aco2.120266024_24,Gyg1.105264657_16 Best CMs (by avg z-score): 1. (Z = 3.48) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.26) snR36 - Small_nucleolar_RNA_snR36 3. (Z = 3.21) CRISPR-DR38 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.15) SCARNA8 - Small_Cajal_body_specific_RNA_8 5. (Z = 3.11) ceN46 - C._elegans_snoRNA_ceN46 6. (Z = 3.08) PK-PYVV - 3'-terminal_pseudoknot_in_PYVV 7. (Z = 3.01) K10_TLS - K10_transport/localisation_element_(TLS) 8. (Z = 3.01) snoZ242 - Small_nucleolar_RNA_Z242 9. (Z = 2.99) GIR1 - GIR1_branching_ribozyme 10. (Z = 2.97) Lnt - Lnt_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM168.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM168_global.out/ --free-endgaps --indel=-100 --threads=4 ..........................(((((....)))))..................................... MFE = -3.54 (Covariance contribution: -3.02) RNAz stats: MPI: 38.28, SCI: 0.29, ZSCORE: -0.1 Full summary: Sequences: 6 Columns: 77 Reading direction: forward Mean pairwise identity: 38.28 Shannon entropy: 1.20756 G+C content: 0.19196 Mean single sequence MFE: -4.93 Consensus MFE: -1.45 Energy contribution: -0.20 Covariance contribution: -1.25 Combinations/Pair: 3.00 Mean z-score: -0.10 Structure conservation index: 0.29 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.41 SVM RNA-class probability: 0.060163 Prediction: OTHER Multiple alignment from mlocarna: Rnf111.74909360_24 ~~~~~~~~~~~~~~~UAGCUGGA--UUGUAUAUACUUGCAGAUUUAAAAAAAUAGGGAAAUUGAAAA~~~~~~~~~~ Irgm.34132512_9 ~~~~~GGAUGUAUAUGCAG---CA-GAGCAC--UCAUAUAU--UAAAUAAAUAAACUUUAAAA~~~~~~~~~~~~~~ Dync1i1.30809072_14 ~~~~~~~~~~~~~~~~~~~UUGUA-ACGUGC---UGCAUGGAACAUAUU----UAUUUGAAAGCAUUAAAAUAAACG Adcy5.67290968_16 ~~~~~~~~~~~~~~~~~~~~GGCA-AGGAGCAGUGGCUCUGAGCAAAAGAAAAUAUUUAUUA--AAUAAAACA~~~~ Aco2.120266024_24 ~~~~~~~~~~~~~~GACAGCUACA-GUGUAC--UUAUAUAUAAUAAAUGAAUAAAUCUUAAAAAAAU~~~~~~~~~~ Gyg1.105264657_16 UAGCUGUGGAAGCACUGUGUAUAACAAAUAAAGACUUAUUGACAUACUAA~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M48 6608 4 0.51 Dlg4.56889789_12,Gng7.10269272_27,Irgm.34132512_3,Arc.112771937_1 Best CMs (by avg z-score): 1. (Z = 2.22) TLS-PK6 - Pseudoknot_of_tRNA-like_structure 2. (Z = 2.13) Yfr1 - Cyanobacterial_functional_RNA_1 3. (Z = 2.09) 6C - 6C_RNA 4. (Z = 1.79) CRISPR-DR16 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.78) sbrA - Listeria_sRNA_sbrA 6. (Z = 1.71) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 7. (Z = 1.70) snoU82P - Small_nucleolar_RNA_U82P 8. (Z = 1.50) CC3552 - Cauldobacter_sRNA_CC3552 9. (Z = 1.46) snoM1 - Small_nucleolar_RNA_snoM1 10. (Z = 1.45) mir-650 - microRNA_mir-650 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM48.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM48_global.out/ --free-endgaps --indel=-100 --threads=4 ..((..((((......))))...)).......(((............)))...... MFE = -15.31 (Covariance contribution: -14.61) RNAz stats: MPI: 43.28, SCI: 0.31, ZSCORE: 0.5 Full summary: Sequences: 4 Columns: 56 Reading direction: forward Mean pairwise identity: 43.28 Shannon entropy: 0.97943 G+C content: 0.55471 Mean single sequence MFE: -11.31 Consensus MFE: -3.51 Energy contribution: -4.08 Covariance contribution: 0.56 Combinations/Pair: 1.25 Mean z-score: 0.50 Structure conservation index: 0.31 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.77 SVM RNA-class probability: 0.004699 Prediction: OTHER Multiple alignment from mlocarna: Dlg4.56889789_12 ~~GGCUGGGGU--CACCCCUGCCCCAUCAUAACUCCCCAUGCCAUUUGAGUUCU~~ Gng7.10269272_27 CUAGACGGGGCUCCACCCCUGACCACGCCCCAGUCCCC-CAUUGAGGGAUU~~~~~ Irgm.34132512_3 UAGUCAUGAUGGACUCAUCCCCCCCCCA------CCCAGACUCUAAUGUAUUGUUC Arc.112771937_1 ~UGGAAGGGGUACCACCCCAGCACCAGCACCG-UCCCCUCCUCUCUUGAAGC~~~~ // ClustID MergedIDs Count AvgDissim Members M49 397 4 0.61 Pebp1.40495174_10,Map1b.30415235_107,Atp5c1.79761059_2,Dlgap4.147175874_0 Best CMs (by avg z-score): 1. (Z = 3.48) K10_TLS - K10_transport/localisation_element_(TLS) 2. (Z = 3.16) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.61) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 4. (Z = 2.55) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.48) DdR18 - D._discoideum_snoRNA_DdR18 6. (Z = 2.29) rli37 - Listeria_sRNA_rli37 7. (Z = 2.29) CRISPR-DR2 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.22) CRISPR-DR16 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.20) mir-449 - microRNA_mir-449 10. (Z = 2.19) snR82 - Small_nucleolar_RNA_snR82 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM49.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM49_global.out/ --free-endgaps --indel=-100 --threads=4 ..........(((.......)))(((((((.......)))))))................ MFE = -13.54 (Covariance contribution: -10.14) RNAz stats: MPI: 35.14, SCI: 0.71, ZSCORE: 0.94 Full summary: Sequences: 4 Columns: 60 Reading direction: forward Mean pairwise identity: 35.14 Shannon entropy: 1.10690 G+C content: 0.33502 Mean single sequence MFE: -6.40 Consensus MFE: -4.57 Energy contribution: -1.32 Covariance contribution: -3.25 Combinations/Pair: 2.80 Mean z-score: 0.94 Structure conservation index: 0.71 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.20 SVM RNA-class probability: 0.588829 Prediction: RNA Multiple alignment from mlocarna: Pebp1.40495174_10 ~~AGCAAAGGUCACCGGAGUUGCUGGGCGUGUUA---AACCUCAUCAAAUACAAA~~~~~ Map1b.30415235_107 ~~~~GCACCGCGCUUUGGUAGCGAUUAGGUUUUAUUCACCUGGUAUUAAAACUA~~~~~~ Atp5c1.79761059_2 ~~~CACAAAGACAGCAGG-AUGUUUGUAAAUUAU---CUUACAAU---AAACAACUUAAG Dlgap4.147175874_0 GGCCACAAAGGAGAAAGC-ACUCAUUUUAAAUCA---UUAAAAACUCAAUGCAA~~~~~~ // ClustID MergedIDs Count AvgDissim Members M169 5282 4 0.65 Rab5c.89652340_5,Calm2.10951142_15,Fmr1.154791521_39,Pcp4.36889112_6 Best CMs (by avg z-score): 1. (Z = 3.61) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.99) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.81) sbrA - Listeria_sRNA_sbrA 4. (Z = 2.77) RybB - RybB_RNA 5. (Z = 2.75) suhB - suhB 6. (Z = 2.75) InvR - Invasion_gene-associated_RNA 7. (Z = 2.75) snoR99 - Small_nucleolar_RNA_snoR99 8. (Z = 2.74) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.72) RsaD - RNA_Staph._aureus_D 10. (Z = 2.70) snoR110 - Small_nucleolar_RNA_snoR110 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM169.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM169_global.out/ --free-endgaps --indel=-100 --threads=4 .........................((((((.(((......)))....))))))................... MFE = -8.25 (Covariance contribution: -6.83) RNAz stats: MPI: 33.33, SCI: 0.47, ZSCORE: 0.55 Full summary: Sequences: 4 Columns: 73 Reading direction: forward Mean pairwise identity: 33.33 Shannon entropy: 1.13645 G+C content: 0.19550 Mean single sequence MFE: -3.40 Consensus MFE: -1.61 Energy contribution: 1.45 Covariance contribution: -3.06 Combinations/Pair: 2.75 Mean z-score: 0.55 Structure conservation index: 0.47 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.88 SVM RNA-class probability: 0.151520 Prediction: OTHER Multiple alignment from mlocarna: Calm2.10951142_15 ~~~~~~~~~~~UGGCACAAUUUGCCUCAAAUCCAUUCCAAGUUG-UAUAUUUGUUUUCCAAU~~~~~~~~~~~ Rab5c.89652340_5 UGUACAAAUACUAAUUCAAUUUUAAGUCUUA--AGUCACUUUUU----UAAUAUAU~~~~~~~~~~~~~~~~~ Fmr1.154791521_39 ~~~~~~~~~~~~~~~~~~~~~~~UUUGUGAAUUUGUUUCUUUGAAUUUUUCAUUUUUCAUUUAGUUUUCCUUG Pcp4.36889112_6 ~~~~~~~~~~CCAUUACAAUUCCUCUGCAACGAUUUUCCUCGAU----GUUGUAAUAAAAAGGA~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M42 1669 4 0.45 Atp2b2.149655651_53,Mapre3.25496282_1,Ntrk2.11676658_19,Pklr.181222231_0 Best CMs (by avg z-score): 1. (Z = 2.02) suhB - suhB 2. (Z = 2.00) LhrC - Listeria_Hfq_binding_LhrC 3. (Z = 1.87) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.80) H19_3 - H19_conserved_region_3 5. (Z = 1.59) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.58) NrrF - NrrF_RNA 7. (Z = 1.55) 6C - 6C_RNA 8. (Z = 1.43) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 9. (Z = 1.42) sbrA - Listeria_sRNA_sbrA 10. (Z = 1.38) MIAT_exon5_3 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_3 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM42.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM42_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ..................(((((..............)))))................................. MFE = -6.14 (Covariance contribution: -4.92) RNAz stats: MPI: 33.10, SCI: 0.55, ZSCORE: -0.45 Full summary: Sequences: 4 Columns: 75 Reading direction: forward Mean pairwise identity: 33.10 Shannon entropy: 1.10036 G+C content: 0.38885 Mean single sequence MFE: -1.60 Consensus MFE: -0.88 Energy contribution: 0.56 Covariance contribution: -1.44 Combinations/Pair: 2.80 Mean z-score: -0.45 Structure conservation index: 0.55 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.86 SVM RNA-class probability: 0.972129 Prediction: RNA Multiple alignment from mlocarna: Atp2b2.149655651_53 ACACUUUCCGCCUCACUUGUGAACUCCAUCC------UUCACUCUCUCCCUUC--UCA~~~~~~~~~~~~~~~~~ Mapre3.25496282_1 ~~~~~~~~~CCCACCCCGACUCUGCCCACCCCACAUUAUAGUCCUUUCCUUUCAGCCAG~~~~~~~~~~~~~~~~ Ntrk2.11676658_19 ~~~~~~~~~~~~~UCCCCGCUAGCAAUCCCC------AUGGCC--CCCAACCACUCCCCACUUGAUUCUGA~~~~ Pklr.181222231_0 ~~~~~~~~~~~~~~~~~~~AAUGCCUCUCCC------CAUUCUGACCCAGUUACACCCUAUUUCUUUCAACCCAC // ClustID MergedIDs Count AvgDissim Members M43 4483 3 0.50 Usp9x.21606330_24,Usp9x.21606330_108,Glra1.40922867_7 Best CMs (by avg z-score): 1. (Z = 2.55) SCARNA16 - Small_Cajal_body_specific_RNA_16 2. (Z = 2.48) SBWMV2_UPD-PKb - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 3. (Z = 2.48) SBWMV1_UPD-PKb - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 4. (Z = 2.37) mir-197 - microRNA_mir-197 5. (Z = 2.33) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.24) rli22 - Listeria_sRNA_rli22 7. (Z = 2.24) K10_TLS - K10_transport/localisation_element_(TLS) 8. (Z = 2.23) Entero_OriR - Enteroviral_3'_UTR_element 9. (Z = 2.21) CRISPR-DR50 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.18) SNORA20 - Small_nucleolar_RNA_SNORA20 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM43.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM43_global.out/ --free-endgaps --indel=-100 --threads=4 ...(((((((.........))....)))))..(((((((.....))))..)))... MFE = -14.80 (Covariance contribution: -14.70) RNAz stats: MPI: 36.53, SCI: 0.07, ZSCORE: 0.89 Full summary: Sequences: 3 Columns: 56 Reading direction: forward Mean pairwise identity: 36.53 Shannon entropy: 0.92098 G+C content: 0.36913 Mean single sequence MFE: -5.93 Consensus MFE: -0.43 Energy contribution: 1.33 Covariance contribution: -1.77 Combinations/Pair: 2.14 Mean z-score: 0.89 Structure conservation index: 0.07 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.86 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Usp9x.21606330_24 CUCUGGGUGGAAUAAAGAAC-----ACUUAAACUUAACAACUUG-GUAAUGGGAAU Usp9x.21606330_108 ~GUAAGGGGGAAAGGUGAACCACA--UUUUAAAGUCACUAA-UGAGUGCAAUUU~~ Glra1.40922867_7 ~~~GAGGGGAUUGGGAAAAUCACAGCUUUCAAAAUUCAAGUCCAUUGG--GUUGA~ // ClustID MergedIDs Count AvgDissim Members M40 2396 5 0.58 Rnf111.74909360_5,Slc25a4.49356988_4,Ccni.16459077_22,Gng7.10269272_19,Gria2.172265159_45 Best CMs (by avg z-score): 1. (Z = 3.09) SNORA22 - Small_nucleolar_RNA_SNORA22 2. (Z = 3.07) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.77) snR85 - Small_nucleolar_RNA_snR85 4. (Z = 2.72) snoR110 - Small_nucleolar_RNA_snoR110 5. (Z = 2.57) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop 6. (Z = 2.57) MIR1444 - microRNA_MIR1444 7. (Z = 2.54) rli36 - Listeria_sRNA_rli36 8. (Z = 2.50) MIR478 - microRNA_MIR478 9. (Z = 2.47) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.42) lincRNA-p21_2 - LincRNA-p21_conserved_region_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM40.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM40_global.out/ --free-endgaps --indel=-100 --threads=4 .........................(((((..........................)))))............. MFE = -5.59 (Covariance contribution: -5.99) RNAz stats: MPI: 35.54, SCI: 0.14, ZSCORE: 0.11 Full summary: Sequences: 5 Columns: 74 Reading direction: forward Mean pairwise identity: 35.54 Shannon entropy: 1.16720 G+C content: 0.21833 Mean single sequence MFE: -4.94 Consensus MFE: -0.71 Energy contribution: 1.37 Covariance contribution: -2.08 Combinations/Pair: 2.83 Mean z-score: 0.11 Structure conservation index: 0.14 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.55 SVM RNA-class probability: 0.000003 Prediction: OTHER Multiple alignment from mlocarna: Rnf111.74909360_5 ~~~~~~~~~~~~~~~~~~GAUGU--AUUUA---UAAAAGCUUUUGUGUU-UUUUUCUAGAUUUGACAUUACUUC Slc25a4.49356988_4 ~~~~~~~~~~~~~~~~CAAAAGUAUUUUGUAUUUAUUUUACAUUUAGAUUCCCACAGCAAACAGAA~~~~~~~~ Ccni.16459077_22 ~~~~~~UAUAAGUAGAUUUUUGUAACUGAU---CU----GUUUUCACUCAUUUAUAAUCAGUA~~~~~~~~~~~ Gng7.10269272_19 ~~~~~~~~~~~~GAUCCAUGUGUUCAUUGG---UGA---CUCCU-CGUU-UUUCUCCCAGUU--ACACAGAU~~ Gria2.172265159_45 UUCAUUAAAAUGCCU-UUUAUUUUUAUUUC---CA----CUAAUGUGU------UCCAAAUGAG~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M41 411 4 0.53 Atp2b2.149655651_36,Shank3.127875955_52,Canx.35850944_85,Usp9x.21606330_89 Best CMs (by avg z-score): 1. (Z = 4.18) suhB - suhB 2. (Z = 3.34) Qrr - Qrr_RNA 3. (Z = 3.28) VrrA - Vibrio_regulatory_RNA_of_OmpA 4. (Z = 3.20) ctRNA_pND324 - ctRNA 5. (Z = 3.12) GadY - GadY 6. (Z = 3.11) L10_leader - Ribosomal_protein_L10_leader 7. (Z = 3.02) GcvB - GcvB_RNA 8. (Z = 2.97) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 9. (Z = 2.91) sbrA - Listeria_sRNA_sbrA 10. (Z = 2.87) rimP - Enterobacteria_rnk_leader Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM41.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM41_global.out/ --free-endgaps --indel=-100 --threads=4 ..........(((((((((........))))).))))......................... MFE = -12.27 (Covariance contribution: -8.19) RNAz stats: MPI: 36.09, SCI: 0.72, ZSCORE: 0.08 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 36.09 Shannon entropy: 1.08930 G+C content: 0.26768 Mean single sequence MFE: -5.72 Consensus MFE: -4.11 Energy contribution: -2.05 Covariance contribution: -2.06 Combinations/Pair: 2.67 Mean z-score: 0.08 Structure conservation index: 0.72 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.71 SVM RNA-class probability: 0.962702 Prediction: RNA Multiple alignment from mlocarna: Atp2b2.149655651_36 GUGUUCAGAUAUCACA-GA---UGCUAUUGUGUUGAUUUUUUUUUUUUUUUAGU~~~~~~~~ Shank3.127875955_52 ~~~~~~~CCUGACGUUGUGAUACACCCCACAGAGAUCUAUGUUUCUUAUAUUAUUAU~~~~~ Canx.35850944_85 ~~~~~~~~GCAACUCCCUU---CACCAAAGGG-AGUUUUUAUUUUGUUUUUAUUUUUACUGC Usp9x.21606330_89 ~~~UUUGUU--GAUUUUUC---UCAGUGAUGAUUUCCCAGCUUUUUUUUUUUGUCUCU~~~~ // ClustID MergedIDs Count AvgDissim Members M46 195 4 0.50 Bdnf.977114_71,Ntrk2.11676658_72,Apba1.227308605_16,Map1b.30415235_103 Best CMs (by avg z-score): 1. (Z = 2.64) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 2. (Z = 2.54) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.19) suhB - suhB 4. (Z = 2.16) RybB - RybB_RNA 5. (Z = 2.09) snoU97 - Small_nucleolar_RNA_U97 6. (Z = 2.07) KCNQ1DN - KCNQ1_downstream_neighbour 7. (Z = 2.02) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.89) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.87) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 10. (Z = 1.86) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM46.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM46_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ...................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 45.96, SCI: -0.00, ZSCORE: 0.88 Full summary: Sequences: 4 Columns: 54 Reading direction: forward Mean pairwise identity: 45.96 Shannon entropy: 0.93010 G+C content: 0.36765 Mean single sequence MFE: -0.77 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.88 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.53 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Bdnf.977114_71 UUAAAAUCUCUCCUCUGUUUCUGUUCGUU--CUGUUUCCG-UCCUGUUCUGUU~ Ntrk2.11676658_72 ~UAAAUACUUUCCUC-UGUUCUUUCCCUU--CUCUCCAAGCUCCAUGUCUUCUG Apba1.227308605_16 ~~~AAAUCCCUUCCCUAGUUUCUUUUAGUUGCAAUGUGUGUGCUAAUUCAGGC~ Map1b.30415235_103 ~UAAUGACGUUCCUUCUCUCCUUUUUUUUUCCUUUCAUACUUCAGAUUUAG~~~ // ClustID MergedIDs Count AvgDissim Members M47 4583 3 0.45 Tmeff1.65356245_28,Gria2.172265159_91,Gnai1.12494046_10 Best CMs (by avg z-score): 1. (Z = 4.88) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 2. (Z = 4.33) mir-597 - microRNA_mir-597 3. (Z = 4.32) K10_TLS - K10_transport/localisation_element_(TLS) 4. (Z = 3.96) mir-335 - microRNA_mir-335 5. (Z = 3.83) Pox_AX_element - Poxvirus_AX_element_late_mRNA_cis-regulatory_element 6. (Z = 3.74) mir-576 - microRNA_mir-576 7. (Z = 3.69) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 8. (Z = 3.67) mir-802 - microRNA_mir-802 9. (Z = 3.65) tp2 - tp2 10. (Z = 3.64) snR85 - Small_nucleolar_RNA_snR85 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM47.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM47_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((((((.((((....)))).))))))........................ MFE = -15.26 (Covariance contribution: -12.09) RNAz stats: MPI: 30.94, SCI: 1.20, ZSCORE: -0.35 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 30.94 Shannon entropy: 0.99871 G+C content: 0.18942 Mean single sequence MFE: -4.67 Consensus MFE: -5.58 Energy contribution: -2.37 Covariance contribution: -3.22 Combinations/Pair: 2.00 Mean z-score: -0.35 Structure conservation index: 1.20 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.41 SVM RNA-class probability: 0.683677 Prediction: RNA Multiple alignment from mlocarna: Gria2.172265159_91 ~~~~~~~~~CUAACUUUCACAUAAAUUUGUCAAAGUUUUAUAUUUAAAUGUAUCAGGUA~~ Tmeff1.65356245_28 UAUGUUUAAACUUAAAU-AUUAAUUUUAAUAAUUUGAU--UUGGAAAAGCAUG~~~~~~~~ Gnai1.12494046_10 ~~AUGUUUACUUAUACUCAUAAAAUGUUAUUUGUAUA---------AACGUUGCACAGACU // ClustID MergedIDs Count AvgDissim Members M44 824 4 0.48 Pabpn1.32998239_20,Morf4l1.91235629_11,Grina.114279801_5,Pabpn1.32998239_8 Best CMs (by avg z-score): 1. (Z = 3.52) mir-500 - microRNA_mir-500 2. (Z = 3.09) mir-202 - microRNA_mir-202 3. (Z = 3.00) mir-154 - microRNA_mir-154 4. (Z = 2.98) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.95) mir-135 - mir-135_microRNA_precursor_family 6. (Z = 2.90) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 7. (Z = 2.85) mir-204 - microRNA_mir-204 8. (Z = 2.69) TB10Cs1H2 - Trypanosomatid_snoRNA_TB10Cs1H2 9. (Z = 2.68) tp2 - tp2 10. (Z = 2.66) mir-223 - microRNA_mir-223 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM44.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM44_global.out/ --free-endgaps --indel=-100 --threads=4 ...........(((((((..((((((((...........))))))))))))))).... MFE = -20.60 (Covariance contribution: -11.18) RNAz stats: MPI: 32.28, SCI: 0.70, ZSCORE: -0.08 Full summary: Sequences: 4 Columns: 58 Reading direction: forward Mean pairwise identity: 32.28 Shannon entropy: 1.17533 G+C content: 0.43870 Mean single sequence MFE: -14.75 Consensus MFE: -10.35 Energy contribution: -7.97 Covariance contribution: -2.38 Combinations/Pair: 2.54 Mean z-score: -0.08 Structure conservation index: 0.70 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.75 SVM RNA-class probability: 0.965611 Prediction: RNA Multiple alignment from mlocarna: Pabpn1.32998239_20 UUUUUCCUUUACCUUUUUUUUUCCCUUU------UAUUUGGAGGGAAUGGGAGGAA~~ Morf4l1.91235629_11 ~~~ACUCAUCCAUCUGUGCUCUUUUUUUUUUAAAAUGGUGCUUAAAGAGCCCA~~~~~ Grina.114279801_5 ~~~~~~CAUG-GCCCCCUU-UAUCCCUUUUGCCCUUGCCAAGGGGUGACAGGGCUGCA Pabpn1.32998239_8 ~~~~~CCCUG-CUCCCCUUCAUCCUCUUUGGGCCUGCUCA--AGGGUAGGUGGGCACG // ClustID MergedIDs Count AvgDissim Members M45 6857 2 0.19 Bdnf.977114_47,Ntrk2.11676658_41 Best CMs (by avg z-score): 1. (Z = 5.10) PreQ1 - PreQ1_riboswitch 2. (Z = 4.23) mir-999 - microRNA_mir-999 3. (Z = 4.05) mir-981 - microRNA_mir-981 4. (Z = 3.95) lsrR - Antisense_RNA_which_regulates_isiA_expression 5. (Z = 3.81) Rhino_CRE - Human_rhinovirus_internal_cis-acting_regulatory_element_(CRE) 6. (Z = 3.78) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 7. (Z = 3.75) glmS - glmS_glucosamine-6-phosphate_activated_ribozyme 8. (Z = 3.68) RNAIII - RNAIII 9. (Z = 3.60) DnaX - DnaX_ribosomal_frameshifting_element 10. (Z = 3.59) plasmodium_snoR11 - small_nucleolar_RNA_snoR11 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM45.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM45_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ........................................................ MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 69.64, SCI: 0.00, ZSCORE: 0.0 Full summary: Sequences: 2 Columns: 56 Reading direction: forward Mean pairwise identity: 69.64 Shannon entropy: 0.30357 G+C content: 0.28151 Mean single sequence MFE: 0.00 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.00 Structure conservation index: 0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -9.08 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Bdnf.977114_47 GAAAAAAGAAAGAAG-----AAAAC-AAACAAACAAAACCAGAAAAAGCACCAAAA Ntrk2.11676658_41 ~GAAAAAGAAAAAAUCCCCCAAAACAAAACAAACAAA--CAAAAAAACC-CCAA~~ // ClustID MergedIDs Count AvgDissim Members M170 3624 3 0.45 Grb2.105722014_19,Opcml.28508230_13,Gria2.172265159_57 Best CMs (by avg z-score): 1. (Z = 3.51) mir-248 - microRNA_mir-248 2. (Z = 3.45) K10_TLS - K10_transport/localisation_element_(TLS) 3. (Z = 3.14) CyaR_RyeE - CyaR/Rye_RNA 4. (Z = 3.13) rli34 - Listeria_sRNA_rli34 5. (Z = 3.08) RsaC - RNA_Staph._aureus_C 6. (Z = 2.97) isrD - isrD_Hfq_binding_RNA 7. (Z = 2.95) ceN105 - C._elegans_snoRNA_ceN105 8. (Z = 2.95) rli36 - Listeria_sRNA_rli36 9. (Z = 2.94) UPSK - UPSK_RNA 10. (Z = 2.91) SNORA20 - Small_nucleolar_RNA_SNORA20 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM170.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM170_global.out/ --free-endgaps --indel=-100 --threads=4 ..........(((((...((((.....)))).....))))).................. MFE = -7.67 (Covariance contribution: -8.84) RNAz stats: MPI: 35.03, SCI: 0.31, ZSCORE: 0.68 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 35.03 Shannon entropy: 0.95474 G+C content: 0.19770 Mean single sequence MFE: -2.10 Consensus MFE: -0.66 Energy contribution: 1.00 Covariance contribution: -1.66 Combinations/Pair: 2.25 Mean z-score: 0.68 Structure conservation index: 0.31 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.21 SVM RNA-class probability: 0.000012 Prediction: OTHER Multiple alignment from mlocarna: Grb2.105722014_19 ~~~~~CUUUUUUAUUUUUUUAAAUAAGUUAAA----GAUAGUCCAGAGCUUUUCAGUUG Opcml.28508230_13 UAAGUUUUCAAUAAGACAGUUUAAAAAGAGCACAUCCUUAUCCCUAUGUU~~~~~~~~~ Gria2.172265159_57 ~~~~~~~UUUAAAAAUUAUUUUAAAAAAAGA-UGACUAUAUACAAUCAAUGCUAUUUA~ // ClustID MergedIDs Count AvgDissim Members M124 1622 3 0.17 Appbp2.73460120_97,Appbp2.73460120_70,Pklr.181222231_15 Best CMs (by avg z-score): 1. (Z = 3.88) mir-296 - microRNA_mir-296 2. (Z = 3.04) SraH - SraH_RNA 3. (Z = 3.03) CRISPR-DR41 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.91) snoR109 - Small_nucleolar_RNA_snoR109 5. (Z = 2.65) HIV-1_DIS - Human_immunodeficiency_virus_type_1_dimerisation_initiation_site 6. (Z = 2.50) snoU89 - Small_nucleolar_RNA_U89 7. (Z = 2.46) sroD - sroD_RNA 8. (Z = 2.44) mir-689 - microRNA_mir-689 9. (Z = 2.29) HCV_SLIV - Hepatitis_C_stem-loop_IV 10. (Z = 2.26) CRISPR-DR29 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM124.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM124_global.out/ --free-endgaps --indel=-100 --threads=4 .(((((.......)))))((....((((((((...))))))))....)).. MFE = -37.62 (Covariance contribution: -14.72) RNAz stats: MPI: 89.54, SCI: 1.02, ZSCORE: -1.35 Full summary: Sequences: 3 Columns: 51 Reading direction: forward Mean pairwise identity: 89.54 Shannon entropy: 0.14405 G+C content: 0.64052 Mean single sequence MFE: -21.43 Consensus MFE: -21.91 Energy contribution: -21.80 Covariance contribution: -0.11 Combinations/Pair: 1.13 Mean z-score: -1.35 Structure conservation index: 1.02 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.53 SVM RNA-class probability: 0.947175 Prediction: RNA Multiple alignment from mlocarna: Pklr.181222231_15 GCUGGGGACCGAACCCAGGGCCUUGUGCUUGCUAGGCAAGCGCUCUACCA~ Appbp2.73460120_70 ~CUGGGGACUGAACCCAGGGCCUUGCGCUUGCUAGGCAAGUGCUCUACCGC Appbp2.73460120_97 ~CUGGGGACCGAACCCAGGGCCUUGCGCUCGCUAGGCAAGCGCUCUUCCAC // ClustID MergedIDs Count AvgDissim Members M125 13 3 0.46 Bdnf.977114_17,Sept9.107478216_18,Grin1.3453776_2 Best CMs (by avg z-score): 1. (Z = 3.07) mir-197 - microRNA_mir-197 2. (Z = 2.88) mir-625 - microRNA_mir-625 3. (Z = 2.75) mir-185 - microRNA_mir-185 4. (Z = 2.71) Glycine - Glycine_riboswitch 5. (Z = 2.62) mir-942 - microRNA_mir-942 6. (Z = 2.55) mir-188 - microRNA_mir-188 7. (Z = 2.35) Intron_gpII - Group_II_catalytic_intron 8. (Z = 2.31) mir-337 - microRNA_mir-337 9. (Z = 2.30) mir-451 - microRNA_mir-451 10. (Z = 2.26) s2m - Coronavirus_3'_stem-loop_II-like_motif_(s2m) Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM125.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM125_global.out/ --free-endgaps --indel=-100 --threads=4 ...((.((((......))))))((((((((((((.....))..)))))))))). MFE = -36.42 (Covariance contribution: -22.56) RNAz stats: MPI: 34.16, SCI: 0.83, ZSCORE: -1.38 Full summary: Sequences: 3 Columns: 54 Reading direction: forward Mean pairwise identity: 34.16 Shannon entropy: 0.97046 G+C content: 0.56012 Mean single sequence MFE: -20.40 Consensus MFE: -16.89 Energy contribution: -12.90 Covariance contribution: -3.99 Combinations/Pair: 2.25 Mean z-score: -1.38 Structure conservation index: 0.83 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.62 SVM RNA-class probability: 0.999062 Prediction: RNA Multiple alignment from mlocarna: Bdnf.977114_17 ~~~UUAGUUCCACCCGGAGUAGGGAUGGAGAAAAU-UUCUUCACUCUCCAUUCU Sept9.107478216_18 GUGAAAAGCAGGGACGUGCU-GGAGAGGGGGAAAU-GUCUUU-UCUCCCUCAC~ Grin1.3453776_2 GAGCC-CCGGAGCACGACGGGGUCGGGGGAGGAGCACUCCCAGCCUCCCCC~~~ // ClustID MergedIDs Count AvgDissim Members M126 3202 3 0.14 Rhobtb1.20089811_43,Canx.35850944_38,Rnf111.74909360_10 Best CMs (by avg z-score): 1. (Z = 4.56) suhB - suhB 2. (Z = 3.90) GcvB - GcvB_RNA 3. (Z = 3.72) rimP - Enterobacteria_rnk_leader 4. (Z = 3.29) InvR - Invasion_gene-associated_RNA 5. (Z = 3.28) snoU97 - Small_nucleolar_RNA_U97 6. (Z = 3.05) snoR17 - Small_nucleolar_RNA_snoR17 7. (Z = 3.01) RybB - RybB_RNA 8. (Z = 2.98) VrrA - Vibrio_regulatory_RNA_of_OmpA 9. (Z = 2.82) MicC - MicC_RNA 10. (Z = 2.73) snoZ107_R87 - Small_nucleolar_RNA_Z107/R87 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM126.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM126_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 75.82, SCI: -0.00, ZSCORE: -0.29 Full summary: Sequences: 3 Columns: 51 Reading direction: forward Mean pairwise identity: 75.82 Shannon entropy: 0.33718 G+C content: 0.21085 Mean single sequence MFE: -0.77 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.29 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.49 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Rhobtb1.20089811_43 UUUGGGUUUAUUUUGUUUUUUGUUUUGUUUUGUUUUGUUUUGUUUUCUCU~ Canx.35850944_38 UUUAGGGCU-UUUUGUUUUGGUUUUUGUUUGUUUUUGUUUUGUUUUUCAUG Rnf111.74909360_10 UUUGGUUUUGUUUUGUUUUGUUUUUUGUUUUUUGUUUUUUUUUUUUUUAC~ // ClustID MergedIDs Count AvgDissim Members M127 1039 4 0.48 Rnf111.74909360_21,Ntrk2.11676658_52,Rnf111.74909360_6,Usp9x.21606330_16 Best CMs (by avg z-score): 1. (Z = 3.08) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.92) suhB - suhB 3. (Z = 2.77) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.62) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.39) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.32) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.22) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.19) DicF - DicF_RNA 9. (Z = 2.19) U2 - U2_spliceosomal_RNA 10. (Z = 2.17) snoU97 - Small_nucleolar_RNA_U97 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM127.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM127_global.out/ --free-endgaps --indel=-100 --threads=4 ........................((((((............)))))).................. MFE = -1.53 (Covariance contribution: -1.56) RNAz stats: MPI: 35.96, SCI: -0.00, ZSCORE: 1.18 Full summary: Sequences: 4 Columns: 66 Reading direction: forward Mean pairwise identity: 35.96 Shannon entropy: 1.06202 G+C content: 0.29426 Mean single sequence MFE: -2.63 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.18 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.43 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Rnf111.74909360_21 ACUGCUGUUCUGACCCUAUUUAUCUCUGCCAUU-----U---GGAACUUUAUCCCUAA~~~~~~~~ Ntrk2.11676658_52 ~~~~~~~~~~~~~~~~UUUCUUUCCCAUGGUCUUCCUAUUAUCCUUGGCUUUCUUUGAUCCCCCCC Rnf111.74909360_6 ~~~~~~~~AUUUGACAUUACUUCCUGUAUCAUU-----UUACUGUAUUUUUGCAUGAUUCCUU~~~ Usp9x.21606330_16 ~CUAUGUUUCUAGGUCUU--UUUCAUUGCCUUU-----UUAUUCUGAUGUUAGGUUAA~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M120 6482 4 0.62 Higd2a.16083853_6,Appbp2.73460120_58,Lypla1.14882196_8,Gria2.172265159_93 Best CMs (by avg z-score): 1. (Z = 3.41) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.82) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.54) MIR171_1 - microRNA_MIR171_1 4. (Z = 2.51) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.51) mir-154 - microRNA_mir-154 6. (Z = 2.44) CRISPR-DR11 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.43) LhrC - Listeria_Hfq_binding_LhrC 8. (Z = 2.42) NrrF - NrrF_RNA 9. (Z = 2.42) K10_TLS - K10_transport/localisation_element_(TLS) 10. (Z = 2.42) snoR99 - Small_nucleolar_RNA_snoR99 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM120.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM120_global.out/ --free-endgaps --indel=-100 --threads=4 ..............................(((((...............)))))......................... MFE = -1.47 (Covariance contribution: -3.69) RNAz stats: MPI: 36.88, SCI: -0.00, ZSCORE: 0.53 Full summary: Sequences: 4 Columns: 80 Reading direction: forward Mean pairwise identity: 36.88 Shannon entropy: 1.07356 G+C content: 0.19816 Mean single sequence MFE: -3.54 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.53 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.19 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Higd2a.16083853_6 ~~~~~~~~~GAUGCGUCCCCUUAAUUACUUAAUAAAACCUUAUUA--CACUUGUAUGUGAU~~~~~~~~~~~~~~~~~~~ Appbp2.73460120_58 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CAAGUUUCCACAUGAAUUAUUUUUAUUUAAUCUGCAUCUUUGGUGGUGUG Lypla1.14882196_8 ~~~~~~~~~~AGAUAACACAAGCAGAGUUUUAUUACAUCAUUUCAAUUACUAGUAUGCUC~~~~~~~~~~~~~~~~~~~~ Gria2.172265159_93 GCGAAUCUGCUUAAAAUACAGUAA----UUUUACA-----UUUCUAAU-CUGUAAGUACU~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M121 2957 3 0.48 Map1b.30415235_71,Stmn2.95284903_27,Cyfip2.31321000_6 Best CMs (by avg z-score): 1. (Z = 3.62) Vault - Vault_RNA 2. (Z = 3.34) CyaR_RyeE - CyaR/Rye_RNA 3. (Z = 2.86) snopsi28S-3316 - Small_nucleolar_RNA_psi28S-3316 4. (Z = 2.76) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.75) GlmY_tke1 - Glm_Y_RNA_activator_of_glmS_mRNA 6. (Z = 2.71) rli34 - Listeria_sRNA_rli34 7. (Z = 2.71) Entero_CRE - Enterovirus_cis-acting_replication_element 8. (Z = 2.69) Bacteroidales-1 - Bacteroidales-1_RNA 9. (Z = 2.63) PreQ1 - PreQ1_riboswitch 10. (Z = 2.62) Hairpin - Hairpin_ribozyme Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM121.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM121_global.out/ --free-endgaps --indel=-100 --threads=4 ..((((..............))))...(((((.....))))).......... MFE = -11.64 (Covariance contribution: -9.70) RNAz stats: MPI: 44.23, SCI: 0.82, ZSCORE: 0.81 Full summary: Sequences: 3 Columns: 52 Reading direction: forward Mean pairwise identity: 44.23 Shannon entropy: 0.80411 G+C content: 0.37029 Mean single sequence MFE: -5.11 Consensus MFE: -4.18 Energy contribution: -2.30 Covariance contribution: -1.88 Combinations/Pair: 2.40 Mean z-score: 0.81 Structure conservation index: 0.82 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.14 SVM RNA-class probability: 0.562579 Prediction: RNA Multiple alignment from mlocarna: Map1b.30415235_71 UGGGUUGGUCCACACA-AUACACUCAAAGAGAAACAGUUUCUAGCCUUCUU~ Stmn2.95284903_27 ~~UGUUGCAUUAAACACACAAACGAAAUCACAAACACUGUGGACUUUUACUC Cyfip2.31321000_6 ~AGUGUAAAUGAAAAAAACAACAAAAACACAGGGCAG-UGUGUGCUUUCUUC // ClustID MergedIDs Count AvgDissim Members M122 1501 9 0.57 Spag7.57543647_5,Gria2.172265159_98,Spag7.57543647_7,Calm2.10951142_37,Calm2.10951142_36,Fhod1.35144280_2,Fhod1.35144280_3,Calm2.10951142_39,Calm2.10951142_38 Best CMs (by avg z-score): 1. (Z = 4.77) snoU90 - Small_nucleolar_RNA_U90 2. (Z = 2.33) snoZ188 - Small_nucleolar_RNA_Z188 3. (Z = 2.04) snoZ112 - Small_nucleolar_RNA_Z112 4. (Z = 1.72) HIV-1_SL4 - HIV-1_stem-loop_4_packaging_signal 5. (Z = 1.54) snoU6-53 - Small_nucleolar_RNA_U6-53/MBII-28 6. (Z = 1.50) snoU2-25 - Small_nucleolar_RNA_U2-25 7. (Z = 1.45) SNORD94 - Small_Nucleolar_RNA_SNORD94 8. (Z = 1.37) rnk_pseudo - Pseudomonas_rnk_leader 9. (Z = 1.18) Tombus_3_III - Tombus_virus_defective_interfering_(DI)_RNA_region_3 10. (Z = 1.18) snoR126 - small_nucleolar_RNA_snoR126 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM122.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM122_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .................................................................................. MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 53.39, SCI: -0.00, ZSCORE: -0.06 Full summary: Sequences: 9 Columns: 82 Reading direction: forward Mean pairwise identity: 53.39 Shannon entropy: 1.03238 G+C content: 0.29825 Mean single sequence MFE: -7.34 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.06 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.19 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Spag7.57543647_5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GUGUGUGUGUGUGUGUGUG-UGUGUGUGUGAGAGAGAGAGAGAGAGAGAGA Gria2.172265159_98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~AGUGUACGUAUGUGUGUGCCUGCUGUGGGAAUGUGCCAGUGAGUGCAGGU~~~~ Spag7.57543647_7 ~GAGAGAGAGAGAAUGCAUGUGUGUAAAUGUGUGAGUGUGUAAAUGUGUGA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Calm2.10951142_37 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GUGUGUGUGUGUGUGUGUGUG-UGUGUGUGUGUUUAGGCACUGCUAACUCU~~ Calm2.10951142_36 ~~~~~~~~~~GCUACAUAGAGGGGUGUGUGUGUGUGUGUGUGUGUGUGUG-UGUGUGUGUG~~~~~~~~~~~~~~~~~~~~~ Fhod1.35144280_2 AGAAACCAGCAUUGUGAACAGUAUUAGGGGUGUGUGUGUGUGUGUGUGUG-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Fhod1.35144280_3 ~~~~~~~~~~~~~~~~~~~~~GUGUGUGUGUGUGUGUGUGUGUGUGUGUG-UGUGUGUGUGUACACAUACAU~~~~~~~~~~ Calm2.10951142_39 ~~~~~~~~~~~~UGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUG-UGUGUGUGUGUU~~~~~~~~~~~~~~~~~~~ Calm2.10951142_38 ~~~~~~~GGCACUGCUAACUCUGCUCAGUCUGUGUGUGUGUGUGUGUGUG-UGUGUGU~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M123 161 4 0.52 Morf4l1.91235629_4,Dlg4.56889789_17,Opcml.28508230_2,Dpysl2.46346413_52 Best CMs (by avg z-score): 1. (Z = 4.28) VrrA - Vibrio_regulatory_RNA_of_OmpA 2. (Z = 3.77) GcvB - GcvB_RNA 3. (Z = 3.74) RyhB - RyhB_RNA 4. (Z = 3.68) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 5. (Z = 3.62) suhB - suhB 6. (Z = 3.56) snoU97 - Small_nucleolar_RNA_U97 7. (Z = 3.44) rimP - Enterobacteria_rnk_leader 8. (Z = 3.41) ctRNA_pT181 - ctRNA 9. (Z = 3.40) mir-48 - microRNA_mir-48 10. (Z = 3.02) LhrC - Listeria_Hfq_binding_LhrC Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM123.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM123_global.out/ --free-endgaps --indel=-100 --threads=4 ....((((((((((.....)))))))))).............................. MFE = -10.40 (Covariance contribution: -5.83) RNAz stats: MPI: 43.75, SCI: 1.06, ZSCORE: -0.59 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 43.75 Shannon entropy: 0.96353 G+C content: 0.22296 Mean single sequence MFE: -5.15 Consensus MFE: -5.44 Energy contribution: -4.25 Covariance contribution: -1.19 Combinations/Pair: 2.44 Mean z-score: -0.59 Structure conservation index: 1.06 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.52 SVM RNA-class probability: 0.945954 Prediction: RNA Multiple alignment from mlocarna: Morf4l1.91235629_4 AAAUAAAAGGAGUUAAC--UGCUCCUUUUUUCUUUCUU--UUUUUCAUUUCAAA~~~~~ Dlg4.56889789_17 ~~~~~GGAAGGUCUAACUGUGGCUUUUUUUUUUUUCCUGGGAUUUUAUUUUAUUU~~~~ Opcml.28508230_2 GGCAAACCAGUUUGGGCUUCUUUUUGGUUAUUUUU-UUGUUCUUCUUGACU~~~~~~~~ Dpysl2.46346413_52 ~~~~~AUUGGAAAACACAUUUUUUUAUUUUAUUUUAUU----UUUUAUUUUUUUUUUGG // ClustID MergedIDs Count AvgDissim Members M128 6751 3 0.49 Stxbp1.11762105_7,Fmnl1.92383698_9,Lypla1.14882196_16 Best CMs (by avg z-score): 1. (Z = 2.03) 23S-methyl - 23S_methyl_RNA_motif 2. (Z = 1.89) mir-64 - microRNA_mir-64 3. (Z = 1.87) g2 - G2 4. (Z = 1.80) Arthropod_7SK - Arthropod_7SK_RNA 5. (Z = 1.71) RsaC - RNA_Staph._aureus_C 6. (Z = 1.70) VrrA - Vibrio_regulatory_RNA_of_OmpA 7. (Z = 1.60) mir-2774 - microRNA_mir-2774 8. (Z = 1.59) OmrA-B - OmrA-B_family 9. (Z = 1.58) mir-577 - microRNA_mir-577 10. (Z = 1.56) Qrr - Qrr_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM128.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM128_global.out/ --free-endgaps --indel=-100 --threads=4 ..............................(((.(((.......))))))................... MFE = -14.99 (Covariance contribution: -9.62) RNAz stats: MPI: 30.58, SCI: 0.60, ZSCORE: 2.84 Full summary: Sequences: 3 Columns: 69 Reading direction: forward Mean pairwise identity: 30.58 Shannon entropy: 0.99668 G+C content: 0.40931 Mean single sequence MFE: -8.47 Consensus MFE: -5.06 Energy contribution: -3.07 Covariance contribution: -1.99 Combinations/Pair: 2.17 Mean z-score: 2.84 Structure conservation index: 0.60 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.40 SVM RNA-class probability: 0.009520 Prediction: OTHER Multiple alignment from mlocarna: Stxbp1.11762105_7 ACACUGCAGAAGCAUCAGAACUCUG-GACCGAGUGGA----CUCUCCCUUAUUUA~~~~~~~~~~~~~~ Fmnl1.92383698_9 ~~~~~~~~~~CACCUCGCCGCCGCCCUAACUCG-GAGGACUCUCCUUGGACCUUAUUUUUA~~~~~~~~ Lypla1.14882196_16 ~~~~~~~~~~~~~~~~~~CGCCCUGCUACUGGG-GGACCAGGCUUCCCCCCUUCGAUGUAACUUUUCUC // ClustID MergedIDs Count AvgDissim Members M129 4521 4 0.53 Gria2.172265159_14,Sipa1l1.106282825_4,Olfm1.7194336_20,Canx.35850944_5 Best CMs (by avg z-score): 1. (Z = 4.25) Lacto-rpoB - Lacto-rpoB_RNA 2. (Z = 3.71) SCARNA24 - Small_Cajal_body_specific_RNA_24 3. (Z = 3.46) SNORA31 - Small_nucleolar_RNA_SNORA31 4. (Z = 3.42) mir-320 - microRNA_mir-320 5. (Z = 3.39) snopsi28S-3316 - Small_nucleolar_RNA_psi28S-3316 6. (Z = 3.29) ceN72-3 - C._elegans_sRNA_ceN72-3 7. (Z = 3.25) RsaD - RNA_Staph._aureus_D 8. (Z = 3.18) mir-515 - microRNA_mir-515 9. (Z = 3.08) SNORA20 - Small_nucleolar_RNA_SNORA20 10. (Z = 3.07) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM129.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM129_global.out/ --free-endgaps --indel=-100 --threads=4 ..............................((((.(....)))))................. MFE = -8.39 (Covariance contribution: -8.59) RNAz stats: MPI: 43.60, SCI: 0.07, ZSCORE: 0.43 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 43.60 Shannon entropy: 0.93896 G+C content: 0.22401 Mean single sequence MFE: -3.47 Consensus MFE: -0.25 Energy contribution: 0.88 Covariance contribution: -1.13 Combinations/Pair: 1.75 Mean z-score: 0.43 Structure conservation index: 0.07 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.92 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Gria2.172265159_14 ~~~~~~~ACUG-CAUCAAGAUGUGACCUG-UUUU-AUAAAUAAAAAGGAAAAAAACAUUU~~ Sipa1l1.106282825_4 ~~~~~~~~~~~AUCAACAAUCAUUAUCUGCCUUU-UAUAGAAAAGAAAAAACAAAAAUCUUC Canx.35850944_5 ~~~UGCAGUUG-UAAUGUAAAGGACCCUGUUUCUGUAGAAAAGAAAACAUUUAA~~~~~~~~ Olfm1.7194336_20 AGUUUGGAUUGAUAAGUGGAUGGUUUCUG-UUUC-UAAAAAGAAAAAAAAAU~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M160 1443 3 0.64 Sdcbp.19848126_4,Pou4f2.31390818_17,Calm2.10951142_41 Best CMs (by avg z-score): 1. (Z = 3.28) TB10Cs4H2 - Trypanosomatid_snoRNA_TB10Cs4H2 2. (Z = 2.71) mir-632 - microRNA_mir-632 3. (Z = 2.66) mir-9 - mir-9/mir-79_microRNA_precursor_family 4. (Z = 2.55) TB10Cs2H2 - Trypanosomatid_snoRNA_TB10Cs2H2 5. (Z = 2.44) mir-802 - microRNA_mir-802 6. (Z = 2.42) Corona_SL-III - Coronavirus_SL-III_cis-acting_replication_element_(CRE) 7. (Z = 2.34) mir-17 - mir-17_microRNA_precursor_family 8. (Z = 2.19) mir-203 - microRNA_mir-203 9. (Z = 2.19) MIR1444 - microRNA_MIR1444 10. (Z = 2.18) PK-PYVV - 3'-terminal_pseudoknot_in_PYVV Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM160.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM160_global.out/ --free-endgaps --indel=-100 --threads=4 ........(((..(((((((....(((((....)))))..)))))))..)))...... MFE = -16.83 (Covariance contribution: -13.26) RNAz stats: MPI: 32.18, SCI: 0.93, ZSCORE: 0.1 Full summary: Sequences: 3 Columns: 58 Reading direction: forward Mean pairwise identity: 32.18 Shannon entropy: 0.99853 G+C content: 0.35834 Mean single sequence MFE: -9.27 Consensus MFE: -8.60 Energy contribution: -5.17 Covariance contribution: -3.43 Combinations/Pair: 2.33 Mean z-score: 0.10 Structure conservation index: 0.93 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.54 SVM RNA-class probability: 0.948588 Prediction: RNA Multiple alignment from mlocarna: Sdcbp.19848126_4 ~~~~~~~CCUCACUCUAUCUGAGAGCGUCUUCAGAUUUUAAGAUAGGUGUAGCCUUA~ Pou4f2.31390818_17 ~~~~~~~~CUUUCUUCCUUCUCUAAAGUGUUAAUACUUACGAAGGAGUUGCGCCUGCU Calm2.10951142_41 CACUCUAUCCCUCAAGUGAAAACUUCGUAUUAAUA-GGUGGCCAUUUGUGA~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M161 6227 3 0.49 Fmr1.154791521_40,Usp9x.21606330_87,Lypla1.14882196_7 Best CMs (by avg z-score): 1. (Z = 3.23) mir-1280 - microRNA_mir-1280 2. (Z = 2.97) CRISPR-DR4 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.96) RMST_10 - Rhabdomyosarcoma_2_associated_transcript_conserved_region_10 4. (Z = 2.94) ceN110 - C._elgans_snoRNA_ceN110 5. (Z = 2.87) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.84) ALIL - ALIL_pseudoknot 7. (Z = 2.78) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.77) SNORA23 - Small_nucleolar_RNA_SNORA23 9. (Z = 2.73) K10_TLS - K10_transport/localisation_element_(TLS) 10. (Z = 2.68) SNORA57 - Small_nucleolar_RNA_SNORA57 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM161.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM161_global.out/ --free-endgaps --indel=-100 --threads=4 .....((((...((((.......(((........))).....)))).)))).......... MFE = -8.83 (Covariance contribution: -9.36) RNAz stats: MPI: 34.62, SCI: -0.00, ZSCORE: -0.25 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 34.62 Shannon entropy: 0.94674 G+C content: 0.29136 Mean single sequence MFE: -6.85 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.25 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.26 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Fmr1.154791521_40 AUUUAGUUUUCCUUGCAUA---CAAA-UAAGCAUAUAAAAUGGCAACAAACUGC~~~~~~~ Usp9x.21606330_87 ~~~~~~~~~~~UACUGACUUCUCGUGUUUAGCAUCGCAGAGGCAGAAAUACAAGCAUAAAC Lypla1.14882196_7 ~~CUAGCUUCUUUGUCUCAAAUUAAU-UCAGCAAAAUAAGAUAACACAAGCAG~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M162 1117 4 0.61 Atf3.107191620_24,Stxbp1.11762105_0,Appbp2.73460120_83,Arhgef7.82521224_58 Best CMs (by avg z-score): 1. (Z = 2.35) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.25) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 3. (Z = 2.11) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.97) P10 - Pseudomonas_sRNA_P10 5. (Z = 1.90) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.85) IRES_mnt - Mnt_IRES 7. (Z = 1.81) MIAT_exon5_2 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_2 8. (Z = 1.75) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.70) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 10. (Z = 1.63) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM162.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM162_global.out/ --free-endgaps --indel=-100 --threads=4 .............................................((((((...............))))))....................... MFE = -2.21 (Covariance contribution: -2.89) RNAz stats: MPI: 35.15, SCI: -0.00, ZSCORE: -0.8 Full summary: Sequences: 4 Columns: 95 Reading direction: forward Mean pairwise identity: 35.15 Shannon entropy: 1.11835 G+C content: 0.26832 Mean single sequence MFE: -6.26 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.80 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.03 SVM RNA-class probability: 0.002809 Prediction: OTHER Multiple alignment from mlocarna: Atf3.107191620_24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CAAGGAUUCUCCGUUUUCCCUUCCUUCCCACCAAAAACCACAGCCCGUGG Stxbp1.11762105_0 AAUCAGCUGCCCUCCAAAACCCUGGCUCCCUUCCCACAAUGCUCUGCAGC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Appbp2.73460120_83 ~~~~~~~~~~~~~~~~~~~UUUACAUUCUUUAUAAAC--AACUCACCAGCACCCUGC-CCAGGUAUUGCUGC~~~~~~~~~~~~~~~~~~~~~~~ Arhgef7.82521224_58 ~~~~~~~~~~~~~~~~~~~~~~~AACUCCUUAUUUUCCUAUCUCACCAACACGGCUC-CCCUCAGUUCUUGGUU~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M163 1293 4 0.58 Ntrk2.11676658_43,Laptm4a.32427418_13,Pou4f2.31390818_48,Appbp2.73460120_113 Best CMs (by avg z-score): 1. (Z = 3.36) rli49 - Listeria_sRNA_rli49 2. (Z = 3.30) mir-597 - microRNA_mir-597 3. (Z = 3.29) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.11) tp2 - tp2 5. (Z = 3.06) RsaF - RNA_Staph._aureus_F 6. (Z = 3.03) mir-767 - microRNA_mir-767 7. (Z = 2.99) 23S-methyl - 23S_methyl_RNA_motif 8. (Z = 2.99) mir-248 - microRNA_mir-248 9. (Z = 2.98) U2 - U2_spliceosomal_RNA 10. (Z = 2.96) S_pombe_snR93 - small_nucleolar_RNA_snR93 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM163.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM163_global.out/ --free-endgaps --indel=-100 --threads=4 ....((((((((((((......((((........))))))))))..))....))))... MFE = -16.77 (Covariance contribution: -14.75) RNAz stats: MPI: 29.41, SCI: 0.68, ZSCORE: 0.49 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 29.41 Shannon entropy: 1.18835 G+C content: 0.23147 Mean single sequence MFE: -3.62 Consensus MFE: -2.46 Energy contribution: 0.35 Covariance contribution: -2.81 Combinations/Pair: 2.67 Mean z-score: 0.49 Structure conservation index: 0.68 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.68 SVM RNA-class probability: 0.786165 Prediction: RNA Multiple alignment from mlocarna: Ntrk2.11676658_43 ~~~~~UCUAUUUUGUUCCAUGGAGCCA--CAAGAGGAUUACGGAUUAUUUAAAGAUU~~ Laptm4a.32427418_13 GUUUUCAUCUUUGUGAUAAAAUGCUU---UAAUAAAGCUCUUAA--AUU----UGGAAU Pou4f2.31390818_48 ~UACUUUUUUCAUUAA-----AAUAU-GCUAUUAAUAUUAAAUG--ACUUUUAAAACGU Appbp2.73460120_113 ~UUUACUUUUAUGUGA-----AUGAAUGCUACAUUUUAUUAAAU--AAUACCAGGUCA~ // ClustID MergedIDs Count AvgDissim Members M39 1066 4 0.51 Morf4l1.91235629_3,Map1b.30415235_42,Bdnf.977114_25,Syt4.23805080_33 Best CMs (by avg z-score): 1. (Z = 5.80) K10_TLS - K10_transport/localisation_element_(TLS) 2. (Z = 4.31) mir-154 - microRNA_mir-154 3. (Z = 4.15) mir-BART2 - mir-BART2_microRNA_precursor_family 4. (Z = 4.09) mir-9 - mir-9/mir-79_microRNA_precursor_family 5. (Z = 3.83) mir-203 - microRNA_mir-203 6. (Z = 3.83) SNORA20 - Small_nucleolar_RNA_SNORA20 7. (Z = 3.73) mir-186 - microRNA_mir-186 8. (Z = 3.62) mir-932 - microRNA_mir-932 9. (Z = 3.58) tp2 - tp2 10. (Z = 3.57) mir-458 - microRNA_mir-458 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM39.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM39_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((((...(((((((((((((.....)))))))))))))))))........ MFE = -23.79 (Covariance contribution: -13.67) RNAz stats: MPI: 37.68, SCI: 1.04, ZSCORE: -1.23 Full summary: Sequences: 4 Columns: 61 Reading direction: forward Mean pairwise identity: 37.68 Shannon entropy: 1.02411 G+C content: 0.22525 Mean single sequence MFE: -8.40 Consensus MFE: -8.73 Energy contribution: -6.85 Covariance contribution: -1.88 Combinations/Pair: 2.25 Mean z-score: -1.23 Structure conservation index: 1.04 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.13 SVM RNA-class probability: 0.983397 Prediction: RNA Multiple alignment from mlocarna: Morf4l1.91235629_3 ~~~~~UUGAUGUUUG----UUUC-CUGUUUGA-UUUUAAACAGAGAAAAUAAAAGGAGUUA Map1b.30415235_42 UUUUUUAAUUAUUAU---UUUAAGUGUUUUGUAAGACAAAAAAAUUGAAGUUU~~~~~~~~ Bdnf.977114_25 ~~~~~~~~UUUUGGUCCCUUUCUUUUUUGUUU-UGUUUUAAGAAAGAAAAUUAAGUUGC~~ Syt4.23805080_33 ~~~~~CAGUUCGUUC-----UGAGCUGUUAUU-UUUAAGAUAGCUUAAAGAAUCGUGUCUC // ClustID MergedIDs Count AvgDissim Members M38 2996 4 0.55 Calm2.10951142_0,Cyfip2.31321000_34,Map1b.30415235_100,Mapk1.85968732_3 Best CMs (by avg z-score): 1. (Z = 2.96) mir-932 - microRNA_mir-932 2. (Z = 2.49) Corona_SL-III - Coronavirus_SL-III_cis-acting_replication_element_(CRE) 3. (Z = 2.49) isrP - isrP_Hfq_binding_RNA 4. (Z = 2.36) MIR476 - microRNA_MIR476 5. (Z = 2.24) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.22) Qrr - Qrr_RNA 7. (Z = 2.19) mir-128 - microRNA_mir-128 8. (Z = 2.18) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.10) suhB - suhB 10. (Z = 2.04) rnk_pseudo - Pseudomonas_rnk_leader Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM38.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM38_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((((((((((.(((......))).)))).)))))))................... MFE = -23.31 (Covariance contribution: -12.68) RNAz stats: MPI: 35.23, SCI: 0.75, ZSCORE: -0.35 Full summary: Sequences: 4 Columns: 61 Reading direction: forward Mean pairwise identity: 35.23 Shannon entropy: 1.08566 G+C content: 0.42748 Mean single sequence MFE: -12.70 Consensus MFE: -9.56 Energy contribution: -6.44 Covariance contribution: -3.12 Combinations/Pair: 2.82 Mean z-score: -0.35 Structure conservation index: 0.75 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.44 SVM RNA-class probability: 0.990823 Prediction: RNA Multiple alignment from mlocarna: Calm2.10951142_0 AGACCCUGUACAGAAGGUGUUA------AAUUUCUUGUACAGAACUGUUAAUUUGC~~~~~ Cyfip2.31321000_34 ~CUCAAGCCCCGUGCUGGGGUAGAGCUUCUUUCACAGGGGUG---UAUUAACGU~~~~~~~ Map1b.30415235_100 ~~~CUUAGCUCCUGGAGCGGCAC-UAC-AAUUCA-GGAGUUG---UUUUU--UCUCACCUC Mapk1.85968732_3 ~~~UGAGCCGUUCCGAGGGGCAG-UUCUGGUCGU-AGUGGCU---UUUAUACUUUCAC~~~ // ClustID MergedIDs Count AvgDissim Members M37 3240 4 0.57 Cyfip2.31321000_14,Map1b.30415235_103,Stxbp1.11762105_38,Grb2.105722014_42 Best CMs (by avg z-score): 1. (Z = 2.47) suhB - suhB 2. (Z = 2.19) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.15) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.95) snoU97 - Small_nucleolar_RNA_U97 5. (Z = 1.93) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.84) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.71) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 8. (Z = 1.62) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.49) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.37) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM37.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM37_global.out/ --free-endgaps --indel=-100 --threads=4 ...((((((..................))))))................................................ MFE = -1.37 (Covariance contribution: -2.54) RNAz stats: MPI: 37.19, SCI: -0.00, ZSCORE: 0.9 Full summary: Sequences: 4 Columns: 81 Reading direction: forward Mean pairwise identity: 37.19 Shannon entropy: 1.04563 G+C content: 0.30958 Mean single sequence MFE: -4.37 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.90 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.03 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Cyfip2.31321000_14 CUGUGGCUUC---UCCCUCCAGUGUCCUGGUCACUUCACUUCCUGCUC-UUGAU~~~~~~~~~~~~~~~~~~~~~~~~~~~ Map1b.30415235_103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UAAUGACGUUCCUUCUCUCCUUUUUUUUUCCUUUCAUACUUCAGAUUUAG Stxbp1.11762105_38 ~~CUGGUUG--GUUUCUUC---UGUAGCAGCUUCUUUUGUCCCUUCUCUCUGGUCAA~~~~~~~~~~~~~~~~~~~~~~~~ Grb2.105722014_42 ~~~CGGAGCCUGUUCCCACCCCUCCUGGUUCUGCUGCCUCUUUCCCUG-CUGAU~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M36 4738 4 0.75 Sept9.107478216_1,Sept9.107478216_0,Gng7.10269272_30,Bdnf.977114_41 Best CMs (by avg z-score): 1. (Z = 2.10) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 2. (Z = 2.03) snoM1 - Small_nucleolar_RNA_snoM1 3. (Z = 1.98) PVX_3 - Potato_virus_X_cis-acting_regulatory_element 4. (Z = 1.94) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 5. (Z = 1.82) Corona_SL-III - Coronavirus_SL-III_cis-acting_replication_element_(CRE) 6. (Z = 1.80) PRINS - PRINS_RNA 7. (Z = 1.78) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.71) RsaE - RNA_Staph._aureus_E 9. (Z = 1.60) Mg_sensor - Magnesium_Sensor 10. (Z = 1.59) U1A_PIE - U1A_polyadenylation_inhibition_element_(PIE) Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM36.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM36_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .................................................................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 37.50, SCI: -0.00, ZSCORE: 0.39 Full summary: Sequences: 4 Columns: 100 Reading direction: forward Mean pairwise identity: 37.50 Shannon entropy: 1.06488 G+C content: 0.24250 Mean single sequence MFE: -6.05 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.39 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.96 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Sept9.107478216_1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UUCAUCAUCCCUGGCCCACCCACCUACCCUGUCUUAUUUUAUAUAAUUAU~~~~~~~~~~~~~~~ Sept9.107478216_0 AUGCGUCCCGCCCCUGGACCCCACCCCCAGAUCUUUUCAUCAUCCCUGGC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gng7.10269272_30 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GGGGCUCCACCCUGACCACGCCCCCAGACCCUUACUGGUAAAUUCUAGAU~~~~~~~~~~~ Bdnf.977114_41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CCAUUUAUGGCCUCCAUCCCAUUUUAAAUAAUUAUGGAUAAAGUUGGAUU // ClustID MergedIDs Count AvgDissim Members M35 5300 3 0.51 Usp9x.21606330_35,Canx.35850944_17,Syt4.23805080_17 Best CMs (by avg z-score): 1. (Z = 3.37) snoZ163 - Small_nucleolar_RNA_Z163/Z177_family 2. (Z = 3.30) PK-SPCSV - 3'-terminal_pseudoknot_in_SPCSV 3. (Z = 3.29) SAM_V - SAM-V_riboswitch 4. (Z = 3.14) snoZ267 - Small_nucleolar_RNA_Z267 5. (Z = 3.06) SNORD127 - Small_nucleolar_RNA_SNORD127 6. (Z = 3.01) CC0734 - caulobacter_sRNA_CC0734 7. (Z = 2.99) SNORA53 - Small_nucleolar_RNA_SNORA53 8. (Z = 2.97) snoR18 - small_nucleolar_RNA_snoR18 9. (Z = 2.92) Vg1_ribozyme - Manganese_dependent_ribozyme_in_Vg1_mRNA 10. (Z = 2.91) rpsL_ricks - Rickettsia_rpsL_leader Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM35.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM35_global.out/ --free-endgaps --indel=-100 --threads=4 .............((((((........))))))................................. MFE = -6.30 (Covariance contribution: -5.53) RNAz stats: MPI: 37.37, SCI: 0.50, ZSCORE: 1.15 Full summary: Sequences: 3 Columns: 66 Reading direction: forward Mean pairwise identity: 37.37 Shannon entropy: 0.91295 G+C content: 0.21101 Mean single sequence MFE: -3.03 Consensus MFE: -1.53 Energy contribution: 0.13 Covariance contribution: -1.66 Combinations/Pair: 2.00 Mean z-score: 1.15 Structure conservation index: 0.50 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.93 SVM RNA-class probability: 0.023293 Prediction: OTHER Multiple alignment from mlocarna: Usp9x.21606330_35 UGACUGAUUAAAUUUUAGAGUAAACAAUUUGAAUAAAGAUAAAGGAAUCA~~~~~~~~~~~~~~~~ Canx.35850944_17 ~~~~~~~~~AUCAAAUUUACAUUGUAUUGAAUAGACCCAAAAAGAACUAAAAGGAGACU~~~~~~~ Syt4.23805080_17 ~~~~~~~~~AAGAAGUUGAGA----AAUUAAUUUA---UUAAAGGGCUGAAUUGAAGAACACUGUG // ClustID MergedIDs Count AvgDissim Members M34 4734 3 0.49 Pabpn1.32998239_21,Shank3.127875955_29,Dlg4.56889789_20 Best CMs (by avg z-score): 1. (Z = 1.90) pRNA - NoRC_assoicated_RNA,_pRNA 2. (Z = 1.64) Prion_pknot - Prion_pseudoknot 3. (Z = 1.63) GRIK4_3p_UTR - GRIK4_3_prime_UTR_element 4. (Z = 1.50) Bacillus-plasmid - Bacillus-plasmid_RNA 5. (Z = 1.47) mir-638 - microRNA_mir-638 6. (Z = 1.25) HIV-1_DIS - Human_immunodeficiency_virus_type_1_dimerisation_initiation_site 7. (Z = 1.19) sR21 - Small_nucleolar_RNA_sR21 8. (Z = 1.15) MIR159 - microRNA_MIR159 9. (Z = 1.14) CsrB - CsrB/RsmB_RNA_family 10. (Z = 1.14) KCNQ1OT1_4 - KCNQ1_overlapping_transcript_1_conserved_region_4 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM34.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM34_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ....................(((.........((((....).)))...)))..... MFE = -5.34 (Covariance contribution: -7.04) RNAz stats: MPI: 37.20, SCI: -0.00, ZSCORE: -0.4 Full summary: Sequences: 3 Columns: 56 Reading direction: forward Mean pairwise identity: 37.20 Shannon entropy: 0.90750 G+C content: 0.59490 Mean single sequence MFE: -6.60 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.40 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.16 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Pabpn1.32998239_21 AGGGAAUGGGAGGAAGUGGGAACAGGGU----GGUGGGGGUGGCUUUUGUUUUU~~ Shank3.127875955_29 ~~~~~UGGAUGGGUGGGAGGUUGAGGAAGCUUGCACAGGGG-UGCAUGCAUGGGUG Dlg4.56889789_20 UAUGGGAGGGGGGUGGGGGGGCAAGGGGU----CAG-GGGU-UGGGUGUCCGGGAG // ClustID MergedIDs Count AvgDissim Members M33 3430 3 0.51 Rab5c.89652340_0,Ntrk2.11676658_89,Grin1.3453776_0 Best CMs (by avg z-score): 1. (Z = 2.48) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 2. (Z = 2.43) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 3. (Z = 1.92) IRES_mnt - Mnt_IRES 4. (Z = 1.81) snoU82P - Small_nucleolar_RNA_U82P 5. (Z = 1.78) H19_2 - H19_conserved_region_2 6. (Z = 1.46) 6C - 6C_RNA 7. (Z = 1.42) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.30) snoU2-25 - Small_nucleolar_RNA_U2-25 9. (Z = 1.30) Pseudomon-Rho - Pseudomon-Rho_RNA 10. (Z = 1.12) snoZ178 - Small_nucleolar_RNA_Z178 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM33.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM33_global.out/ --free-endgaps --indel=-100 --threads=4 ...............(((...(((....(((((.............)))))....))).))). MFE = -4.22 (Covariance contribution: -6.36) RNAz stats: MPI: 34.59, SCI: -0.00, ZSCORE: 0.16 Full summary: Sequences: 3 Columns: 63 Reading direction: forward Mean pairwise identity: 34.59 Shannon entropy: 0.89552 G+C content: 0.59027 Mean single sequence MFE: -6.83 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.16 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.38 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Rab5c.89652340_0 GCCCCUUACCUGCCACUGCCCCCACUCCUCCAGCAGAAUGACCUGACUGG~~~~~~~~~~~~~ Ntrk2.11676658_89 ~CUGCUCCCUUCCCCCUCCCCCAGCU-CUCUAAA----CCGACCCCAUG-----ACUGAGA~~ Grin1.3453776_0 ~~~~~~~~~GACGCCCCGCCCGCCCUCCUCUGCC----CCUCCCCCGCAGACAGACGCACGGG // ClustID MergedIDs Count AvgDissim Members M32 3249 3 0.49 Ccni.16459077_21,Rhobtb1.20089811_28,Map1b.30415235_94 Best CMs (by avg z-score): 1. (Z = 3.08) Qrr - Qrr_RNA 2. (Z = 2.69) sbrA - Listeria_sRNA_sbrA 3. (Z = 2.68) NrrF - NrrF_RNA 4. (Z = 2.65) mir-2774 - microRNA_mir-2774 5. (Z = 2.64) 23S-methyl - 23S_methyl_RNA_motif 6. (Z = 2.59) PVX_3 - Potato_virus_X_cis-acting_regulatory_element 7. (Z = 2.53) rli52 - Listeria_sRNA_rli52 8. (Z = 2.47) Thr_leader - Threonine_operon_leader 9. (Z = 2.43) SraD - SraD_RNA 10. (Z = 2.39) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM32.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM32_global.out/ --free-endgaps --indel=-100 --threads=4 ...............(((.....))).........((((((...)))))).............. MFE = -12.94 (Covariance contribution: -11.88) RNAz stats: MPI: 30.73, SCI: 0.89, ZSCORE: 1.09 Full summary: Sequences: 3 Columns: 64 Reading direction: forward Mean pairwise identity: 30.73 Shannon entropy: 1.00929 G+C content: 0.28047 Mean single sequence MFE: -3.90 Consensus MFE: -3.48 Energy contribution: -0.60 Covariance contribution: -2.88 Combinations/Pair: 2.00 Mean z-score: 1.09 Structure conservation index: 0.89 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.29 SVM RNA-class probability: 0.631372 Prediction: RNA Multiple alignment from mlocarna: Ccni.16459077_21 ~~~~~~~~~AUCCA-GGUGCU-CACCAAAGAAACAUGUAUGUAACAUAUAAGUAGAUUUUU~~~ Rhobtb1.20089811_28 ~~~~~~~~~~~~~ACGGCCUCACACCUACAGCCAACUU-CACUUUGUAAGACAAGUAUUUGUAU Map1b.30415235_94 CCUCGCCUCAAACACCAUUUUCCAUGGAAUUCAAAAGAAAAAAAUUUUUU~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M31 3562 5 0.49 Gnb1.172386440_6,Pabpn1.32998239_14,Canx.35850944_85,Shank1.94839593_16,Rhobtb1.20089811_6 Best CMs (by avg z-score): 1. (Z = 4.12) suhB - suhB 2. (Z = 3.57) GcvB - GcvB_RNA 3. (Z = 2.99) rimP - Enterobacteria_rnk_leader 4. (Z = 2.97) VrrA - Vibrio_regulatory_RNA_of_OmpA 5. (Z = 2.89) InvR - Invasion_gene-associated_RNA 6. (Z = 2.86) GadY - GadY 7. (Z = 2.72) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.70) LhrC - Listeria_Hfq_binding_LhrC 9. (Z = 2.64) RyhB - RyhB_RNA 10. (Z = 2.50) RybB - RybB_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM31.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM31_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ..............((((.((........))....))))........................... MFE = -0.13 (Covariance contribution: -3.39) RNAz stats: MPI: 43.80, SCI: -0.00, ZSCORE: -0.45 Full summary: Sequences: 5 Columns: 66 Reading direction: forward Mean pairwise identity: 43.80 Shannon entropy: 1.06110 G+C content: 0.27878 Mean single sequence MFE: -5.03 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.45 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.17 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Gnb1.172386440_6 UUGUGCAUUUUUCUGGGGCCAU-UGUCUUUG---GUUUA-UUUUGUUUUGUUUUU~~~~~~~~~~~ Pabpn1.32998239_14 ~~~~~~~~~~CCCCUCCAGUUUGCCUGGUGAUCUAUUUUGUUUCCUUUUGUGUUUCUUUU~~~~~~ Canx.35850944_85 ~~~~~~~~~~~GCAACUCCCUU-CACCAAAG---GGAGU-UUUUAUUUUGUUUUUAUUUUUACUGC Shank1.94839593_16 ~~UCUCAGCUUCCCAACACGCUGCAUUCGGUUUUUUGUU-UUUUGUUUUGUUU~~~~~~~~~~~~~ Rhobtb1.20089811_6 ~~~~~~~~CCCUUCAGACCCAUAAUGUCCUCCCUUUUCUUUCUUUUUUUUUUUUUUUC~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M30 5514 4 0.53 Gng7.10269272_47,Slc7a8.32800927_34,Canx.35850944_47,Arhgef7.82521224_33 Best CMs (by avg z-score): 1. (Z = 3.31) mir-449 - microRNA_mir-449 2. (Z = 3.26) mir-14 - microRNA_mir-14 3. (Z = 3.08) mir-458 - microRNA_mir-458 4. (Z = 2.92) K_chan_RES - Potassium_channel_RNA_editing_signal 5. (Z = 2.85) mir-32 - microRNA_mir-32 6. (Z = 2.71) mir-574 - microRNA_mir-574 7. (Z = 2.67) mir-156 - mir-156_microRNA_precursor 8. (Z = 2.63) mir-33 - microRNA_mir-33 9. (Z = 2.52) mir-190 - microRNA_mir-190 10. (Z = 2.45) mir-134 - microRNA_mir-134 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM30.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM30_global.out/ --free-endgaps --indel=-100 --threads=4 .((((((((((((.(((((..............))))).)))))))))))).. MFE = -34.11 (Covariance contribution: -16.94) RNAz stats: MPI: 37.78, SCI: 0.89, ZSCORE: -1.33 Full summary: Sequences: 4 Columns: 53 Reading direction: forward Mean pairwise identity: 37.78 Shannon entropy: 1.06086 G+C content: 0.53827 Mean single sequence MFE: -18.95 Consensus MFE: -16.86 Energy contribution: -15.37 Covariance contribution: -1.50 Combinations/Pair: 2.25 Mean z-score: -1.33 Structure conservation index: 0.89 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.25 SVM RNA-class probability: 0.998082 Prediction: RNA Multiple alignment from mlocarna: Gng7.10269272_47 ~GGGGAGGGGCACUGCAGGUGCUAAGAGAGGACCCUGUUU-CCCCCUCCAUG~ Slc7a8.32800927_34 ~GAGGUAGGGGGA-GAAUGUUUUCUGA-AGGCCAGUUCCUCUCCCCUCCUCCA Canx.35850944_47 UUGAGGGUGG-AAUGCAUUUUUCUUCC-UGUUCAGUGCUUUAUCACCAUCUG~ Arhgef7.82521224_33 ~AGUGGGUGUGUGGAGGCCCUUUGUGC-UCUCCUUCCUCCACACUCUGGCUG~ // ClustID MergedIDs Count AvgDissim Members M5 665 4 0.64 Olfm1.7194336_21,Syt4.23805080_28,Syt4.23805080_23,Vim.87855449_1 Best CMs (by avg z-score): 1. (Z = 3.26) IS102 - IS102_RNA 2. (Z = 3.08) SCARNA13 - Small_Cajal_body_specific_RNA_13 3. (Z = 3.07) SCARNA1 - Small_Cajal_body_specific_RNA_1 4. (Z = 3.05) CyaR_RyeE - CyaR/Rye_RNA 5. (Z = 3.02) rox2 - Drosophila_rox2_ncRNA 6. (Z = 2.97) MicX - MicX_Vibrio_cholerae_sRNA 7. (Z = 2.92) Phe_leader - Phenylalanine_leader_peptide 8. (Z = 2.85) LhrC - Listeria_Hfq_binding_LhrC 9. (Z = 2.78) enod40 - Early_nodulin_40 10. (Z = 2.76) SNORA31 - Small_nucleolar_RNA_SNORA31 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM5.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM5_global.out/ --free-endgaps --indel=-100 --threads=4 .....................((((.(((................))))))).............. MFE = -10.09 (Covariance contribution: -7.74) RNAz stats: MPI: 35.86, SCI: 0.42, ZSCORE: 0.13 Full summary: Sequences: 4 Columns: 66 Reading direction: forward Mean pairwise identity: 35.86 Shannon entropy: 1.07060 G+C content: 0.26023 Mean single sequence MFE: -5.02 Consensus MFE: -2.10 Energy contribution: 0.71 Covariance contribution: -2.81 Combinations/Pair: 3.00 Mean z-score: 0.13 Structure conservation index: 0.42 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.49 SVM RNA-class probability: 0.276366 Prediction: OTHER Multiple alignment from mlocarna: Olfm1.7194336_21 ~~~~AAAAGAAAAAAAAAUCAGUGUUCGCCC---UUAUAG-----GAGACAUAGUCAAGUUC~~~~ Syt4.23805080_28 ~~ACGAAAGAAAAGAAAAGAAAAAC-UUGUG---AAAUUCAUGGUCAGGUUGAAGU~~~~~~~~~~ Syt4.23805080_23 ~~~~~~~~AAAAAAAAACAAACCUAAGCUAG---AAUUUC-----AGUUAGGAAUACAGUUGUUUU Vim.87855449_1 GCAAGAAGGAAAAAAAAAU--CGUAUCUUAGAAAAAAGAGCUUUCAAGUGCC~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M4 1262 3 0.48 Calm2.10951142_46,Arc.112771937_3,Cdh2.8048920_30 Best CMs (by avg z-score): 1. (Z = 2.39) alpha_tmRNA - Alphaproteobacteria_transfer-messenger_RNA 2. (Z = 2.39) CRISPR-DR47 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.38) CRISPR-DR46 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.36) rli59 - Listeria_sRNA_rli59 5. (Z = 2.35) sn2343 - Small_nucleolar_RNA_sn2343 6. (Z = 2.34) HIV_PBS - HIV_primer_binding_site_(PBS) 7. (Z = 2.19) CyaR_RyeE - CyaR/Rye_RNA 8. (Z = 2.12) sR24 - Small_nucleolar_RNA_sR24 9. (Z = 2.06) C0299 - C0299_RNA 10. (Z = 2.00) snoZ169 - Small_nucleolar_RNA_Z169 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM4.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM4_global.out/ --free-endgaps --indel=-100 --threads=4 ...(((((..............................))))).............. MFE = -10.07 (Covariance contribution: -8.40) RNAz stats: MPI: 46.15, SCI: -0.00, ZSCORE: 1.55 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 46.15 Shannon entropy: 0.77307 G+C content: 0.40851 Mean single sequence MFE: -5.56 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.55 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -9.11 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Calm2.10951142_46 UAACACUGAGAUACAGAAAACCGAGGAUAAAGGGAAAGCGGUGCGUGUAC~~~~~~~ Arc.112771937_3 ~GACACUUUCAAGGC--AGAGAAAAUAGGAUUACAAAGAGGAGGUGCCUGGCA~~~~ Cdh2.8048920_30 ~~ACACACACAAAUA--AAAGGAAAGAAAAGUA-AAAGGGGUG--GCCUGGUACUGG // ClustID MergedIDs Count AvgDissim Members M7 1266 4 0.55 Tmem50a.153674488_0,Pebp1.40495174_2,Arc.112771937_14,Dpysl2.46346413_6 Best CMs (by avg z-score): 1. (Z = 3.18) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 2. (Z = 2.58) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 3. (Z = 1.82) H19_3 - H19_conserved_region_3 4. (Z = 1.62) 6C - 6C_RNA 5. (Z = 1.38) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.34) PVX_3 - Potato_virus_X_cis-acting_regulatory_element 7. (Z = 1.32) PRINS - PRINS_RNA 8. (Z = 1.29) g2 - G2 9. (Z = 1.26) P10 - Pseudomonas_sRNA_P10 10. (Z = 1.24) Yfr1 - Cyanobacterial_functional_RNA_1 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM7.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM7_global.out/ --free-endgaps --indel=-100 --threads=4 ..........((...))..........((((((...............))))))...... MFE = -9.88 (Covariance contribution: -8.56) RNAz stats: MPI: 41.23, SCI: 0.52, ZSCORE: -0.61 Full summary: Sequences: 4 Columns: 60 Reading direction: forward Mean pairwise identity: 41.23 Shannon entropy: 1.02247 G+C content: 0.53399 Mean single sequence MFE: -7.25 Consensus MFE: -3.79 Energy contribution: -2.41 Covariance contribution: -1.38 Combinations/Pair: 2.67 Mean z-score: -0.61 Structure conservation index: 0.52 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.00 SVM RNA-class probability: 0.978552 Prediction: RNA Multiple alignment from mlocarna: Tmem50a.153674488_0 ~~~~~~~~~~GGACCCCCACUUCUGCAGCACAACCGCCCCACCCCCACUUCUGCAGCAUG Pebp1.40495174_2 ~~~~~~~~GUGUCCCCCCACGCCCAUCCUUCCUUCCCACCCU-CUCAUAGGGAGUUCUC~ Arc.112771937_14 UGCCCAGCUGGAACCUCAUCCAC--ACCCCAGCACCAACCAC-CUCGUGUUGG~~~~~~~ Dpysl2.46346413_6 ~~~~~~~~AUGAACACCACACCCAAGCCCAGCCACCCACCCCACACUGAGCUGCAUCC~~ // ClustID MergedIDs Count AvgDissim Members M6 1761 3 0.50 Ntrk2.11676658_121,Calm2.10951142_26,Vdac2.2515297_6 Best CMs (by avg z-score): 1. (Z = 3.56) CRISPR-DR44 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.05) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.01) CRISPR-DR41 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.88) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.72) CRISPR-DR53 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.70) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.50) SBWMV2_UPD-PKl - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 8. (Z = 2.35) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.30) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.27) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM6.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM6_global.out/ --free-endgaps --indel=-100 --threads=4 .......((((((....)))))).......(..(((((......))))))..... MFE = -12.11 (Covariance contribution: -11.58) RNAz stats: MPI: 43.56, SCI: 0.53, ZSCORE: 0.28 Full summary: Sequences: 3 Columns: 55 Reading direction: forward Mean pairwise identity: 43.56 Shannon entropy: 0.79821 G+C content: 0.33706 Mean single sequence MFE: -5.23 Consensus MFE: -2.77 Energy contribution: -2.33 Covariance contribution: -0.44 Combinations/Pair: 1.50 Mean z-score: 0.28 Structure conservation index: 0.53 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.35 SVM RNA-class probability: 0.332292 Prediction: OTHER Multiple alignment from mlocarna: Calm2.10951142_26 ~~~~CCUUCUACUAUUUAA-AGACUAGGUUGGUGCGGAUGAGUGUUUGCCCUGUA Ntrk2.11676658_121 CCUUCCCUCUCUUUUUAAAGAGAUUUUACUU--UUAAGUGCUGUUUUAACAA~~~ Vdac2.2515297_6 ~~~CCUCUACAUUAUUUAAUGUACUUAACUG--UUAAAUGUGCUACCCACCAAUG // ClustID MergedIDs Count AvgDissim Members M1 2712 4 0.54 Fgf13.144199535_29,Itpr1.144028781_6,Sdcbp.19848126_14,Canx.35850944_44 Best CMs (by avg z-score): 1. (Z = 2.94) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 2. (Z = 2.78) U1A_PIE - U1A_polyadenylation_inhibition_element_(PIE) 3. (Z = 2.74) S_pombe_snR99 - small_nucleolar_RNA_snR99 4. (Z = 2.72) 5S_rRNA - 5S_ribosomal_RNA 5. (Z = 2.63) mir-345 - microRNA_mir-345 6. (Z = 2.51) snR85 - Small_nucleolar_RNA_snR85 7. (Z = 2.51) CRISPR-DR33 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.41) mir-320 - microRNA_mir-320 9. (Z = 2.40) SNORA70 - Small_nucleolar_RNA_SNORA70 10. (Z = 2.39) snR189 - Small_nucleolar_RNA_snR189 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM1.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM1_global.out/ --free-endgaps --indel=-100 --threads=4 .....(.((((...((((((((.........))))....)))))))).)................. MFE = -11.33 (Covariance contribution: -11.03) RNAz stats: MPI: 40.93, SCI: 0.12, ZSCORE: 0.68 Full summary: Sequences: 4 Columns: 66 Reading direction: forward Mean pairwise identity: 40.93 Shannon entropy: 0.99670 G+C content: 0.28240 Mean single sequence MFE: -7.04 Consensus MFE: -0.88 Energy contribution: -0.00 Covariance contribution: -0.87 Combinations/Pair: 2.22 Mean z-score: 0.68 Structure conservation index: 0.12 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.58 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Fgf13.144199535_29 ~~~~CCCUAAACAACAUAUAUUAUACUUGCUACUGGAAAAGUGUUUAAGA-CUUA~~~~~~~~~~~ Itpr1.144028781_6 ~~~~~CUGCCA---AAAAUAUUAAA------AAUGC-CUUUUUUGGAAGG-ACUACAGAAAGUACC Sdcbp.19848126_14 ~~~~~~AUUCCACAAAAGCAUUAUACAGUUCUGUG---UAGGUGGCAAGAGACUAAUGA~~~~~~~ Canx.35850944_44 AUAAACACUCC--ACAGUGUUUAUAUUGGGGGAAU----ACUGGGAAAGA-AAUAUA~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M166 2802 3 0.39 Calm1.124484785_24,Atp2b2.149655651_7,Atrn.118696808_120 Best CMs (by avg z-score): 1. (Z = 5.70) K10_TLS - K10_transport/localisation_element_(TLS) 2. (Z = 5.69) mir-932 - microRNA_mir-932 3. (Z = 4.50) MIR476 - microRNA_MIR476 4. (Z = 4.49) mir-335 - microRNA_mir-335 5. (Z = 4.35) SNORA20 - Small_nucleolar_RNA_SNORA20 6. (Z = 4.24) tp2 - tp2 7. (Z = 4.12) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 8. (Z = 4.05) mir-9 - mir-9/mir-79_microRNA_precursor_family 9. (Z = 4.01) isrP - isrP_Hfq_binding_RNA 10. (Z = 3.91) mir-154 - microRNA_mir-154 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM166.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM166_global.out/ --free-endgaps --indel=-100 --threads=4 .....((((.((.((((((((..........))))))))..)).))))........ MFE = -12.13 (Covariance contribution: -14.46) RNAz stats: MPI: 55.21, SCI: -0.00, ZSCORE: -0.02 Full summary: Sequences: 3 Columns: 56 Reading direction: forward Mean pairwise identity: 55.21 Shannon entropy: 0.62447 G+C content: 0.17428 Mean single sequence MFE: -3.11 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.02 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.50 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Calm1.124484785_24 CUAGUCUUUUAUUUUUUUUUUCCA------AUAAAAAGACCAUUAACUUAAAUCAU Atp2b2.149655651_7 ~~~UUGUUUUUUUUUUUUUUUCCAAAACAUAAAAAAAUAAUAACGAAUUAAUU~~~ Atrn.118696808_120 ~UGCAAUUUUUGGUAUUUUUUGUA-----UUGUAAAAUAACAGCUAAUUUAAUCAG // ClustID MergedIDs Count AvgDissim Members M3 667 3 0.58 Canx.35850944_32,Appbp2.73460120_105,Fmr1.154791521_21 Best CMs (by avg z-score): 1. (Z = 2.56) snR62 - Small_nucleolar_RNA_snR62 2. (Z = 2.51) MIR824 - microRNA_MIR824 3. (Z = 2.50) CRISPR-DR11 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.50) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.46) SprD - Small_pathogenicity_island_RNA_D 6. (Z = 2.44) SAM_V - SAM-V_riboswitch 7. (Z = 2.41) S_pombe_snR36 - small_nucleolar_RNA_snR36 8. (Z = 2.40) mir-283 - microRNA_mir-283 9. (Z = 2.38) snR41 - Small_nucleolar_RNA_snR41 10. (Z = 2.34) PCA3_2 - Prostate_cancer_antigen_RNA_3_conserved_region_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM3.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM3_global.out/ --free-endgaps --indel=-100 --threads=4 ........((..((((((.((((................)))).)).))))..)).... MFE = -9.17 (Covariance contribution: -11.07) RNAz stats: MPI: 31.07, SCI: 0.53, ZSCORE: 0.73 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 31.07 Shannon entropy: 1.01274 G+C content: 0.28309 Mean single sequence MFE: -4.77 Consensus MFE: -2.52 Energy contribution: 1.24 Covariance contribution: -3.76 Combinations/Pair: 2.17 Mean z-score: 0.73 Structure conservation index: 0.53 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.62 SVM RNA-class probability: 0.229165 Prediction: OTHER Multiple alignment from mlocarna: Canx.35850944_32 AUUCAGAAUUGACUAUAAUUGAACACAGGCUAA-----AAGUAUUU-AUGGGAGGA~~~ Appbp2.73460120_105 ~~~~UGCUUUAGGAUUUA-UUAA----AUAACACUAUUGUUAAUUGCAGUCUAGGUAUC Fmr1.154791521_21 ~~~~~~~UUUUGUUUUGUUGCACUGAAGUAUGACAAAUAGUGUUAUUGGAAGGGAUG~~ // ClustID MergedIDs Count AvgDissim Members M2 5170 3 0.46 Vegfa.10534185_47,Usp9x.21606330_97,Grb2.105722014_44 Best CMs (by avg z-score): 1. (Z = 4.72) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.20) mir-154 - microRNA_mir-154 3. (Z = 3.12) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.96) U1_yeast - Yeast_U1_spliceosomal_RNA 5. (Z = 2.93) mir-186 - microRNA_mir-186 6. (Z = 2.87) SNORD111 - Small_Nucleolar_RNA_SNORD111 7. (Z = 2.84) mir-276 - microRNA_mir-276 8. (Z = 2.84) mir-302 - microRNA_mir-302 9. (Z = 2.77) CRISPR-DR11 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.72) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM2.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM2_global.out/ --free-endgaps --indel=-100 --threads=4 .............(((((..(((((................)))))..)))))........ MFE = -11.54 (Covariance contribution: -8.81) RNAz stats: MPI: 36.07, SCI: 0.62, ZSCORE: -0.26 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 36.07 Shannon entropy: 0.92489 G+C content: 0.24188 Mean single sequence MFE: -6.10 Consensus MFE: -3.79 Energy contribution: -1.69 Covariance contribution: -2.10 Combinations/Pair: 2.10 Mean z-score: -0.26 Structure conservation index: 0.62 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.87 SVM RNA-class probability: 0.972524 Prediction: RNA Multiple alignment from mlocarna: Vegfa.10534185_47 ~~~~~~~~~~~UCUACAUACUAAAUCUCUCUCCUUUUUUAAUUUUAAUAUUUGUUAUCAUU Usp9x.21606330_97 UCCCAUGAACUUUUUACUUUGUUAA---UUUUGUGG-----UUAAUUUGGUGGCUAUA~~~ Grb2.105722014_44 ~~~~~~~~~~GUUACACCUGGGCCAUUUGAUUGUUUUAUUUUGGAAUUGGUGUAUAUCAU~ // ClustID MergedIDs Count AvgDissim Members M167 200 4 0.51 Nsf.92974385_7,Ak7.129933292_14,Grb2.105722014_37,Avp.118205007_0 Best CMs (by avg z-score): 1. (Z = 3.44) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 2. (Z = 1.74) 6C - 6C_RNA 3. (Z = 1.51) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 4. (Z = 1.40) MIR2907 - microRNA_MIR2907 5. (Z = 1.27) IRES_mnt - Mnt_IRES 6. (Z = 1.26) bxd_6 - Bithoraxoid_conserved_region_6 7. (Z = 1.20) CRISPR-DR30 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.19) NrrF - NrrF_RNA 9. (Z = 1.12) snoM1 - Small_nucleolar_RNA_snoM1 10. (Z = 1.10) Yfr1 - Cyanobacterial_functional_RNA_1 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM167.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM167_global.out/ --free-endgaps --indel=-100 --threads=4 ...............................((((....)))).............. MFE = -1.28 (Covariance contribution: -1.98) RNAz stats: MPI: 43.70, SCI: -0.00, ZSCORE: -0.17 Full summary: Sequences: 4 Columns: 57 Reading direction: forward Mean pairwise identity: 43.70 Shannon entropy: 0.96887 G+C content: 0.52006 Mean single sequence MFE: -4.00 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.17 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.31 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Nsf.92974385_7 CACACCUCGCUCCCCGCCACGCCCACCCUUGGAAAACACUUGACCUACCC~~~~~~~ Ak7.129933292_14 ~~~~~~CCUGCUACCCCCACCCCACCCCUAUCACUACAAAGUGCUGAAUAUGCACC~ Grb2.105722014_37 ~~~~~UUUCUCUCCACGCA-GCCUCCUCC-CCACAGCAGAGUCAUGGCUACUCCCAG Avp.118205007_0 ~~~~~GCCAUCGCCCCCCACGCCUCCCCC-CUACAGCAUGGAAAAUAAACUUUUAA~ // ClustID MergedIDs Count AvgDissim Members M9 4785 4 0.65 Dpysl2.46346413_38,Gria2.172265159_80,Dpysl2.46346413_66,Morf4l1.91235629_16 Best CMs (by avg z-score): 1. (Z = 2.95) 23S-methyl - 23S_methyl_RNA_motif 2. (Z = 2.81) Qrr - Qrr_RNA 3. (Z = 2.56) psbNH - psbNH_RNA 4. (Z = 2.55) Trp_leader - Tryptophan_operon_leader 5. (Z = 2.51) RsaD - RNA_Staph._aureus_D 6. (Z = 2.48) isrP - isrP_Hfq_binding_RNA 7. (Z = 2.46) rimP - Enterobacteria_rnk_leader 8. (Z = 2.40) isrO - isrO_Hfq_binding_RNA 9. (Z = 2.38) rli34 - Listeria_sRNA_rli34 10. (Z = 2.36) Spot_42 - Spot_42_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM9.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM9_global.out/ --free-endgaps --indel=-100 --threads=4 .................................(((((...)))))............................................ MFE = -8.86 (Covariance contribution: -6.93) RNAz stats: MPI: 34.46, SCI: 0.36, ZSCORE: -0.31 Full summary: Sequences: 4 Columns: 90 Reading direction: forward Mean pairwise identity: 34.46 Shannon entropy: 1.07849 G+C content: 0.19671 Mean single sequence MFE: -7.28 Consensus MFE: -2.60 Energy contribution: -1.73 Covariance contribution: -0.87 Combinations/Pair: 2.00 Mean z-score: -0.31 Structure conservation index: 0.36 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.20 SVM RNA-class probability: 0.398888 Prediction: OTHER Multiple alignment from mlocarna: Gria2.172265159_80 UGCUCAGUUUGUUAGAAAAGUAUGAUAGAGUCAAGGCAGAAUGUCUUUUU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dpysl2.46346413_38 ~~~~~~~~~~~~~~~~~~~~~~~~GGGAUAAUUAGACUUCAAGUCUUUUUACAAGAGGGGCAACCC------U-AUUUUAG~~~~~~~~~ Morf4l1.91235629_16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UGCAUCAUGUAGCUACAGUUUUAUGGAAAAGU------CAAUCUUGUAGGAGUUUU Dpysl2.46346413_66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CUGUCUUAAUGGCAAGAUAAUUAUGGUAAAAUACAAGUCUCGUGUUUAUU~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M8 5656 4 0.55 Tmem30a.84827711_2,Fmr1.154791521_22,Ap2a2.201813143_1,Rhobtb1.20089811_8 Best CMs (by avg z-score): 1. (Z = 3.14) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.97) L13_leader - Ribosomal_protein_L13_leader 3. (Z = 2.96) Lacto-rpoB - Lacto-rpoB_RNA 4. (Z = 2.95) mir-154 - microRNA_mir-154 5. (Z = 2.92) eeev_FSE - eastern_equine_encephalitis_ribosomal_frameshift_element 6. (Z = 2.90) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.83) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.76) mir-BART2 - mir-BART2_microRNA_precursor_family 9. (Z = 2.76) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.74) mir-140 - microRNA_mir-140 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM8.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM8_global.out/ --free-endgaps --indel=-100 --threads=4 ................((((((..(((((((((....)))))))))))))))........ MFE = -14.06 (Covariance contribution: -10.21) RNAz stats: MPI: 34.37, SCI: 0.70, ZSCORE: 0.11 Full summary: Sequences: 4 Columns: 60 Reading direction: forward Mean pairwise identity: 34.37 Shannon entropy: 1.10470 G+C content: 0.31425 Mean single sequence MFE: -6.23 Consensus MFE: -4.38 Energy contribution: -3.50 Covariance contribution: -0.88 Combinations/Pair: 2.29 Mean z-score: 0.11 Structure conservation index: 0.70 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.58 SVM RNA-class probability: 0.952565 Prediction: RNA Multiple alignment from mlocarna: Tmem30a.84827711_2 ~~~~~~CCGAUGUCUGGUUA-GUAUGUCAUUUU---GAAGUUGGCACAUAACAAAAAACA Fmr1.154791521_22 ~UUAUUGGAAGGGAUGUGUA---AUUUUUCUGUAUAGACAGGAAAAGAAAUAAC~~~~~~ Ap2a2.201813143_1 GUCUCUCUCGUCUCUCUCGUUUGUCUUUGUACCAC--ACUGCAGAUAAACAC~~~~~~~~ Rhobtb1.20089811_8 ~~~~CACUUUAGUCCGUUAUUUUGUUCCUUUUUAU--ACAAAGACAAAACAAAGCC~~~~ // ClustID MergedIDs Count AvgDissim Members M137 2758 3 0.46 Gria2.172265159_72,Canx.35850944_73,Vegfa.10534185_36 Best CMs (by avg z-score): 1. (Z = 3.55) 23S-methyl - 23S_methyl_RNA_motif 2. (Z = 3.35) Arthropod_7SK - Arthropod_7SK_RNA 3. (Z = 3.15) RybB - RybB_RNA 4. (Z = 3.12) InvR - Invasion_gene-associated_RNA 5. (Z = 3.08) CRISPR-DR41 - CRISPR_RNA_direct_repeat_element 6. (Z = 3.04) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.95) sbrA - Listeria_sRNA_sbrA 8. (Z = 2.76) mir-644 - microRNA_mir-644 9. (Z = 2.70) snoZ119 - Small_nucleolar_RNA_Z119 10. (Z = 2.68) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM137.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM137_global.out/ --free-endgaps --indel=-100 --threads=4 .....................((((((...((((...))))...))))))........ MFE = -12.97 (Covariance contribution: -10.24) RNAz stats: MPI: 37.79, SCI: 0.95, ZSCORE: -0.43 Full summary: Sequences: 3 Columns: 58 Reading direction: forward Mean pairwise identity: 37.79 Shannon entropy: 0.90072 G+C content: 0.26842 Mean single sequence MFE: -6.70 Consensus MFE: -6.33 Energy contribution: -4.57 Covariance contribution: -1.77 Combinations/Pair: 2.00 Mean z-score: -0.43 Structure conservation index: 0.95 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.95 SVM RNA-class probability: 0.976604 Prediction: RNA Multiple alignment from mlocarna: Gria2.172265159_72 ~~~~CUUUCUACAACUUCUAUUGAAGACACUGGGAUUUCCAAUUUUUUCAUGUG~~~~ Canx.35850944_73 AUUUUUCACUAGAA--AAUUUUUCUCA------GGCUCCAUAUUUGAGGAUAUUAUUG Vegfa.10534185_36 ~UAUUUAAUUUCAACUAUUUAUGAGGA--UGCAUCUCUUGCUCUUUCUUAUUU~~~~~ // ClustID MergedIDs Count AvgDissim Members M136 1741 3 0.41 Dpysl2.46346413_12,Atp2b2.149655651_12,Grb2.105722014_4 Best CMs (by avg z-score): 1. (Z = 2.27) mir-9 - mir-9/mir-79_microRNA_precursor_family 2. (Z = 2.24) mir-23 - microRNA_mir-23 3. (Z = 2.02) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.02) CRISPR-DR11 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.97) VIS1 - Viral_integration_site_1 6. (Z = 1.91) snoZ107_R87 - Small_nucleolar_RNA_Z107/R87 7. (Z = 1.88) fstAT - Fst_antitoxin_sRNA 8. (Z = 1.80) mir-154 - microRNA_mir-154 9. (Z = 1.80) hvt-mir-H - microRNA_hvt-mir-H9 10. (Z = 1.78) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM136.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM136_global.out/ --free-endgaps --indel=-100 --threads=4 .............................(((((((.........)))))))........ MFE = -8.15 (Covariance contribution: -5.19) RNAz stats: MPI: 44.69, SCI: 0.56, ZSCORE: 1.27 Full summary: Sequences: 3 Columns: 60 Reading direction: forward Mean pairwise identity: 44.69 Shannon entropy: 0.80256 G+C content: 0.38233 Mean single sequence MFE: -6.07 Consensus MFE: -3.39 Energy contribution: -1.40 Covariance contribution: -1.99 Combinations/Pair: 2.33 Mean z-score: 1.27 Structure conservation index: 0.56 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.03 SVM RNA-class probability: 0.019211 Prediction: OTHER Multiple alignment from mlocarna: Dpysl2.46346413_12 GGACUGGGGAGGGAUGGGGGGGUGGG---AGUGUUUUU-UUUUUU-AAUACUAAA~~~~~ Atp2b2.149655651_12 ~~~~~~~~~AGGGUUAGGGAGGGGAGUUUUUUGUUUGU-UUUCUUAGGCGGGAACUGCAA Grb2.105722014_4 ~~~~~~~~~AACUUUUGGG-GGUGGGAAGGGGUGUUUGAUUUCAUAAUGCCAAAACUUAA // ClustID MergedIDs Count AvgDissim Members M135 6697,2500 7 0.52 Fmr1.154791521_34,Atp2b2.149655651_80,Canx.35850944_8,Bdnf.977114_25,Cyfip2.31321000_62,Ccni.16459077_18,Rnf111.74909360_31 Best CMs (by avg z-score): 1. (Z = 4.09) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.69) mir-101 - mir-101_microRNA_precursor_family 3. (Z = 3.67) tp2 - tp2 4. (Z = 3.65) K10_TLS - K10_transport/localisation_element_(TLS) 5. (Z = 3.58) mir-BART2 - mir-BART2_microRNA_precursor_family 6. (Z = 3.57) mir-154 - microRNA_mir-154 7. (Z = 3.48) mir-9 - mir-9/mir-79_microRNA_precursor_family 8. (Z = 3.34) mir-186 - microRNA_mir-186 9. (Z = 3.23) MIR396 - microRNA_MIR396 10. (Z = 3.20) mir-92 - mir-92_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM135.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM135_global.out/ --free-endgaps --indel=-100 --threads=4 ................(((((.((((((...................)))))).))))).............. MFE = -9.58 (Covariance contribution: -8.79) RNAz stats: MPI: 38.89, SCI: 0.08, ZSCORE: -0.3 Full summary: Sequences: 7 Columns: 73 Reading direction: forward Mean pairwise identity: 38.89 Shannon entropy: 1.20884 G+C content: 0.19434 Mean single sequence MFE: -4.45 Consensus MFE: -0.34 Energy contribution: 1.68 Covariance contribution: -2.02 Combinations/Pair: 3.33 Mean z-score: -0.30 Structure conservation index: 0.08 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.04 SVM RNA-class probability: 0.002767 Prediction: OTHER Multiple alignment from mlocarna: Ccni.16459077_18 ~~ACUAUUGUC----CUUUUU-UGUUUAU--------CU---U----GAAGCUUAAAAAUGGCA-UGUAAUUA Fmr1.154791521_34 ~~~~~~~GUCAAGUCUUAUUUUUUGUUUUUUUUCUCUUU---UUAAUGAAUGAAAUUUAC~~~~~~~~~~~~~ Canx.35850944_8 ~~~~~~~~AAAUCUUCCAGGUUUGUCUUUUUUUCCUUUU---UUUA-AAGAUACAAUGAUAG~~~~~~~~~~~ Bdnf.977114_25 ~~~~~~UUUUGGUCCCUU-UCUUUUUUGUUU----UGUU---U----UAAGAAAGAAAAUUAAGUUGC~~~~~ Rnf111.74909360_31 ~~~~~~~~~~~~~ACAUGUCUCUUGUUUUAUUUCUCUCUAAACUUGAAAACAAUAAAUCUGCA~~~~~~~~~~ Cyfip2.31321000_62 ~~~~~~~~~~~ACCCCUCUUUGAUUUUUUUUAAUGUAUU---U----AAAAAUCAAGAAAAAAGCUUA~~~~~ Atp2b2.149655651_80 UGACCAUUCAU----CUGUUUUUAUGAAU--------UU---U----UUUAUCUAGACA-AUAAUUGUAA~~~ // ClustID MergedIDs Count AvgDissim Members M134 1747 3 0.50 Canx.35850944_43,Snrpn.111570586_2,Itpr1.144028781_35 Best CMs (by avg z-score): 1. (Z = 4.05) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.49) snoM1 - Small_nucleolar_RNA_snoM1 3. (Z = 2.95) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.79) PK-PYVV - 3'-terminal_pseudoknot_in_PYVV 5. (Z = 2.64) SNORD101 - Small_nucleolar_RNA_SNORD101 6. (Z = 2.51) mir-154 - microRNA_mir-154 7. (Z = 2.50) class_I_RNA - Class_I_RNA 8. (Z = 2.45) snoR8a - Small_nucleolar_RNA_snoR8a 9. (Z = 2.37) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.34) plasmodium_snoR30 - small_nucleolar_RNA_snoR30 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM134.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM134_global.out/ --free-endgaps --indel=-100 --threads=4 ............................(((....................))).......... MFE = -2.52 (Covariance contribution: -4.89) RNAz stats: MPI: 45.21, SCI: -0.00, ZSCORE: 1.15 Full summary: Sequences: 3 Columns: 64 Reading direction: forward Mean pairwise identity: 45.21 Shannon entropy: 0.77461 G+C content: 0.26701 Mean single sequence MFE: -1.73 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.15 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.61 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Canx.35850944_43 UGUACCAAUGAUACUUUUCCUUGCA---CUGAAUAUAUAUAAACACU-CCACAG~~~~~~~~~~ Snrpn.111570586_2 ~~~~CUUUUGACCCCUCUUACUGCA---UUAACUAUAGAUAAUAAAU-ACAUAGCGCA~~~~~~ Itpr1.144028781_35 ~~~~~~~~~~~~~~UUGUAAGUGCAUACCUGAAAUUAUUUAAUAAAUGACGCAGAAUACUACAG // ClustID MergedIDs Count AvgDissim Members M133 722 4 0.66 Atrn.118696808_80,Syn2.151412465_1,Nrgn.38790596_21,Ap2a2.201813143_3 Best CMs (by avg z-score): 1. (Z = 1.74) mir-10 - mir-10_microRNA_precursor_family 2. (Z = 1.73) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 3. (Z = 1.66) MIR2907 - microRNA_MIR2907 4. (Z = 1.50) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 5. (Z = 1.48) EAV_LTH - Equine_arteritis_virus_leader_TRS_hairpin_(LTH) 6. (Z = 1.43) Cardiovirus_CRE - Cardiovirus_cis-acting_replication_element_(CRE) 7. (Z = 1.42) mir-1180 - microRNA_mir-1180 8. (Z = 1.32) lin-4 - lin-4_microRNA_precursor 9. (Z = 1.32) SNORD105 - Small_nucleolar_RNA_SNORD105 10. (Z = 1.31) IRES_Bip - bip_internal_ribosome_entry_site_(IRES) Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM133.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM133_global.out/ --free-endgaps --indel=-100 --threads=4 ....................................................(((((((.((((......................))))))))).)).. MFE = -7.03 (Covariance contribution: -5.53) RNAz stats: MPI: 34.33, SCI: 0.11, ZSCORE: -0.39 Full summary: Sequences: 4 Columns: 100 Reading direction: forward Mean pairwise identity: 34.33 Shannon entropy: 1.12809 G+C content: 0.30168 Mean single sequence MFE: -14.36 Consensus MFE: -1.61 Energy contribution: -0.93 Covariance contribution: -0.69 Combinations/Pair: 2.22 Mean z-score: -0.39 Structure conservation index: 0.11 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.85 SVM RNA-class probability: 0.003971 Prediction: OTHER Multiple alignment from mlocarna: Atrn.118696808_80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ACCCCAGGUAACCCAACACCCUCUUCUGUCCUCCUCGGGUGCCUGUGGCG Syn2.151412465_1 GAAAGGCAUCUAAGACAUUCAUCAACAGCAGUCCGCCAUGUUUGGUGGCA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nrgn.38790596_21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GCAGCCCUGACC-CUAUAGC-CUCUACCCCGUUGGGCUCCUGGGGUUGUGGC~ Ap2a2.201813143_3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UUCAAGGCACCUCCAGUCCUACACCUACAGCCAGCCCCUGGGUGUGGAGG~~~~~ // ClustID MergedIDs Count AvgDissim Members M132 2108 4 0.55 Calm1.124484785_3,Aco2.120266024_10,Usp9x.21606330_94,Calm2.10951142_16 Best CMs (by avg z-score): 1. (Z = 3.39) K10_TLS - K10_transport/localisation_element_(TLS) 2. (Z = 3.17) SNORA20 - Small_nucleolar_RNA_SNORA20 3. (Z = 3.01) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.99) snoZ267 - Small_nucleolar_RNA_Z267 5. (Z = 2.93) snoR10 - small_nucleolar_RNA_snoR10 6. (Z = 2.89) mir-597 - microRNA_mir-597 7. (Z = 2.70) ceN101 - C._elegans_snoRNA_ceN101 8. (Z = 2.62) rli34 - Listeria_sRNA_rli34 9. (Z = 2.61) CRISPR-DR6 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.58) Lacto-rpoB - Lacto-rpoB_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM132.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM132_global.out/ --free-endgaps --indel=-100 --threads=4 ...........(((((((((..........)))))))))(((((((.....)))))...))........... MFE = -19.67 (Covariance contribution: -14.24) RNAz stats: MPI: 38.48, SCI: 0.17, ZSCORE: 0.05 Full summary: Sequences: 4 Columns: 72 Reading direction: forward Mean pairwise identity: 38.48 Shannon entropy: 0.98976 G+C content: 0.23333 Mean single sequence MFE: -4.62 Consensus MFE: -0.80 Energy contribution: -0.30 Covariance contribution: -0.50 Combinations/Pair: 1.79 Mean z-score: 0.05 Structure conservation index: 0.17 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.64 SVM RNA-class probability: 0.000002 Prediction: OTHER Multiple alignment from mlocarna: Calm1.124484785_3 ~~~~~~~~~~~AUUCUGUUUGUAUCUAGCAAAACUGAAUGUCAAAAGUACCUUCUGUCCAC~~~~~~~~~~~ Aco2.120266024_10 ~~~~~~~~~~~~ACUUGUUC----UUAUAAGAAAAAAAAAAAGAU---CCAAAUCU---AUUGAGCGUCCUG Usp9x.21606330_94 UUAUUUGAAUUACUUUUGUA----AAAGAAAGCAACAGUCUGAAU-------AUUC---AGGUG~~~~~~~~ Calm2.10951142_16 ~~~~~~~~~~UAUUUGUUUU----CCAAUAAAAAAAAAUGACAAUUUACCCAAUUG---UUGCUCUG~~~~~ // ClustID MergedIDs Count AvgDissim Members M131 2358 4 0.51 Fmr1.154791521_14,Lypla1.14882196_17,Usp9x.21606330_46,Atrn.118696808_61 Best CMs (by avg z-score): 1. (Z = 3.15) PyrR - PyrR_binding_site 2. (Z = 2.87) mir-515 - microRNA_mir-515 3. (Z = 2.85) HOTAIR_3 - HOTAIR_conserved_region_3 4. (Z = 2.84) mir-154 - microRNA_mir-154 5. (Z = 2.78) tp2 - tp2 6. (Z = 2.69) K10_TLS - K10_transport/localisation_element_(TLS) 7. (Z = 2.68) WLE3 - Wingless_localisation_element_3_(WLE3) 8. (Z = 2.59) rli42 - Listeia_sRNA_rli42 9. (Z = 2.54) isrP - isrP_Hfq_binding_RNA 10. (Z = 2.53) mir-101 - mir-101_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM131.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM131_global.out/ --free-endgaps --indel=-100 --threads=4 ........((((...((((((....))))))))))(((((....)))))....... MFE = -13.95 (Covariance contribution: -12.62) RNAz stats: MPI: 37.54, SCI: 0.47, ZSCORE: 0.57 Full summary: Sequences: 4 Columns: 56 Reading direction: forward Mean pairwise identity: 37.54 Shannon entropy: 1.04631 G+C content: 0.30838 Mean single sequence MFE: -7.13 Consensus MFE: -3.38 Energy contribution: -2.12 Covariance contribution: -1.25 Combinations/Pair: 2.17 Mean z-score: 0.57 Structure conservation index: 0.47 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.88 SVM RNA-class probability: 0.151936 Prediction: OTHER Multiple alignment from mlocarna: Fmr1.154791521_14 ~UGUGACAUUUGUUAUUUUUGUUAGCAAAAAAGUUGUAUGA-UCUGUGCCUU~~~~ Lypla1.14882196_17 GAUGUAACUUUU----CUCCUUUCAAGAAGAAAAAGGUAGA-UUCUUUUUUGGUU~ Usp9x.21606330_46 ~AA-GUCUCAUUAAGUUUUUGUGCACAGAAAGAUGGGGUCU-UUGGCUCUUUA~~~ Atrn.118696808_61 ~~~~GAUACUGUUUAUUCU--UUAAAAAGAAGCAGAUGGCAUUUGUUUCUGCUCCU // ClustID MergedIDs Count AvgDissim Members M130 5819 4 0.56 Ccni.16459077_5,Rnf111.74909360_13,Gnb1.172386440_8,Stxbp1.11762105_41 Best CMs (by avg z-score): 1. (Z = 3.85) Bacteroid-trp - Bacteroidete_tryptophan_peptide_leader_RNA 2. (Z = 3.72) K10_TLS - K10_transport/localisation_element_(TLS) 3. (Z = 3.67) snoZ267 - Small_nucleolar_RNA_Z267 4. (Z = 3.43) mir-286 - microRNA_mir-286 5. (Z = 3.33) mir-315 - microRNA_mir-315 6. (Z = 3.30) PK-SPCSV - 3'-terminal_pseudoknot_in_SPCSV 7. (Z = 3.28) mir-15 - mir-15_microRNA_precursor_family 8. (Z = 3.20) mir-3 - microRNA_mir-3 9. (Z = 3.19) SNORA20 - Small_nucleolar_RNA_SNORA20 10. (Z = 3.16) mir-231 - microRNA_mir-231 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM130.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM130_global.out/ --free-endgaps --indel=-100 --threads=4 ......(((((.((...((((................))))...)).))))).......... MFE = -7.43 (Covariance contribution: -8.81) RNAz stats: MPI: 40.88, SCI: 0.03, ZSCORE: 0.43 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 40.88 Shannon entropy: 0.97822 G+C content: 0.19366 Mean single sequence MFE: -3.95 Consensus MFE: -0.12 Energy contribution: 1.50 Covariance contribution: -1.62 Combinations/Pair: 2.60 Mean z-score: 0.43 Structure conservation index: 0.03 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.18 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Ccni.16459077_5 GGCAUAUAUUUAUAAACUCAA-------GAUCCAAAAUAUAUU-UAAAAGUAAAGCAA~~~~ Stxbp1.11762105_41 ~~~~UAUUUAUAUAAAUAAUU-------UCUCAAAUGGAUAUU-UAAAAAAAAAGCUAGUCU Gnb1.172386440_8 ~~~~~~UUGGUCAAAUUUUUAAAGGAAAUACUACAAUAAAAAUGUUAACCAGAAGG~~~~~~ Rnf111.74909360_13 ~~~UCAAUCAUGUACUUUAGUUUA-AUGUAUAAAGAUCCUCUAGGAAAUGAUAA~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M139 150 4 0.62 Ddn.137572548_1,Lyl1.25115234_4,Camk2a.56948506_0,Calm3.77245609_0 Best CMs (by avg z-score): 1. (Z = 2.46) HCV_SLIV - Hepatitis_C_stem-loop_IV 2. (Z = 2.30) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.04) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.86) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 5. (Z = 1.84) toga_FSE - togavirus_ribosomal_frameshift_element 6. (Z = 1.83) suhB - suhB 7. (Z = 1.78) PhotoRC-I - PhotoRC-I_RNA 8. (Z = 1.66) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.63) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.62) mir-354 - microRNA_mir-354 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM139.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM139_global.out/ --free-endgaps --indel=-100 --threads=4 .............((((((((.......))))))))............................. MFE = -13.85 (Covariance contribution: -6.60) RNAz stats: MPI: 31.69, SCI: 0.66, ZSCORE: 1.58 Full summary: Sequences: 4 Columns: 65 Reading direction: forward Mean pairwise identity: 31.69 Shannon entropy: 1.16501 G+C content: 0.50282 Mean single sequence MFE: -12.25 Consensus MFE: -8.04 Energy contribution: -7.10 Covariance contribution: -0.94 Combinations/Pair: 2.62 Mean z-score: 1.58 Structure conservation index: 0.66 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.25 SVM RNA-class probability: 0.080073 Prediction: OTHER Multiple alignment from mlocarna: Ddn.137572548_1 ~~~~~~~~~~~~CGGCCCAG---CCAGCCUUGGGCUCACCGCGCUCCUUUCCUCUCUCCAGGCUU Lyl1.25115234_4 UCCCACAGCCUACUUGCAGUGGCUUUGCCAGUGUCCUCUUGCC--AGGGCCG~~~~~~~~~~~~~ Camk2a.56948506_0 ~~~~~AGGACCAGGCCAGGGU-CCCUGCGCUCUUGCUUUUUCCUAAAGUCCAUCUC~~~~~~~~~ Calm3.77245609_0 ~~~~~~~~AGGCCCGGGCAG---CUGGCCAUGCCCGUUC--UCCUGAUCUCUUCUUGCGCUCU~~ // ClustID MergedIDs Count AvgDissim Members M138 2513 3 0.52 Atp6v1b2.22320426_32,Dpysl2.46346413_15,Irgm.34132512_5 Best CMs (by avg z-score): 1. (Z = 2.65) sR8 - Small_nucleolar_RNA_sR8 2. (Z = 2.58) Plasmid_RNAIII - Plasmid_RNAIII 3. (Z = 2.36) sR35 - Small_nucleolar_RNA_sR35 4. (Z = 2.34) Xist_exon1 - X-chromosome_inactivation_gene_exon_1 5. (Z = 2.29) sR18 - Small_nucleolar_RNA_sR18 6. (Z = 2.19) sR24 - Small_nucleolar_RNA_sR24 7. (Z = 2.15) CC0734 - caulobacter_sRNA_CC0734 8. (Z = 2.07) isrA - isrA_Hfq_binding_RNA 9. (Z = 2.02) isrN - isrN_Hfq_binding_RNA 10. (Z = 2.01) plasmodium_snoR20 - small_nucleolar_RNA_snoR20 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM138.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM138_global.out/ --free-endgaps --indel=-100 --threads=4 ......................(.(((.((((((........)))).))))))....................... MFE = -13.90 (Covariance contribution: -12.13) RNAz stats: MPI: 27.68, SCI: 0.42, ZSCORE: 1.71 Full summary: Sequences: 3 Columns: 76 Reading direction: forward Mean pairwise identity: 27.68 Shannon entropy: 1.02240 G+C content: 0.30148 Mean single sequence MFE: -8.13 Consensus MFE: -3.38 Energy contribution: -0.83 Covariance contribution: -2.55 Combinations/Pair: 2.43 Mean z-score: 1.71 Structure conservation index: 0.42 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.70 SVM RNA-class probability: 0.000002 Prediction: OTHER Multiple alignment from mlocarna: Irgm.34132512_5 ~~~~UAAUGAUUAAAAAUCAAUGACUG-GGGGCUGACAAGAUGGCUCACUGGCUG~~~~~~~~~~~~~~~~~~~~~ Dpysl2.46346413_15 ~~~~~~~~~~~~~~~~~~~~~~GCAAU-UACUUAACC---AUUAAGCUGAUUCCGAGGCUGGCAGGCUACCGCCGC Atp6v1b2.22320426_32 AAAAUAAAUGUUAAAUUAAAUGGAAGGUUACACUGA----AGCCUGGUGCCUCU~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M175 3704 4 0.52 Bdnf.977114_70,Cyfip2.31321000_69,Canx.35850944_23,Ntrk2.11676658_75 Best CMs (by avg z-score): 1. (Z = 2.18) IBV_D-RNA - Infectious_bronchitis_virus_D-RNA 2. (Z = 2.17) ceN54 - C._elegans_snoRNA_ceN54 3. (Z = 2.04) bxd_7 - Bithoraxoid_conserved_region_7 4. (Z = 1.95) TUG1_2 - Taurine_upregulated_gene_1_conserved_region_2 5. (Z = 1.94) TPP - TPP_riboswitch_(THI_element) 6. (Z = 1.92) SCARNA24 - Small_Cajal_body_specific_RNA_24 7. (Z = 1.92) GcvB - GcvB_RNA 8. (Z = 1.91) U8 - U8_small_nucleolar_RNA 9. (Z = 1.86) mir-337 - microRNA_mir-337 10. (Z = 1.85) mir-9 - mir-9/mir-79_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM175.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM175_global.out/ --free-endgaps --indel=-100 --threads=4 ........((((((....))))))(((((.((((((....))))))..)))))...... MFE = -10.24 (Covariance contribution: -8.59) RNAz stats: MPI: 31.07, SCI: 0.34, ZSCORE: 1.25 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 31.07 Shannon entropy: 1.18195 G+C content: 0.34245 Mean single sequence MFE: -7.68 Consensus MFE: -2.61 Energy contribution: -2.30 Covariance contribution: -0.31 Combinations/Pair: 2.67 Mean z-score: 1.25 Structure conservation index: 0.34 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.74 SVM RNA-class probability: 0.000002 Prediction: OTHER Multiple alignment from mlocarna: Bdnf.977114_70 AUGUCGGUGGUUUAUGU--UGACCUGAGAUUGAUUUGUUAAAAUCUCUCCUC~~~~~~~ Cyfip2.31321000_69 AUUUGUAUUUUGGGGGUACCUGUGUUGAGUUGAUAAAACAUUUUCAUCUC~~~~~~~~~ Canx.35850944_23 ~~~~~~~~GCUUUUUAAGGAAGGCUGGUGUGCCUGAGUAGAUA-AUUACAUCACUUGUU Ntrk2.11676658_75 ~~~~~~~GUGUCCUUAGUAGG--CUGAUGACCCUGGGUAGUUAGAAAACAUCACCUCAA // ClustID MergedIDs Count AvgDissim Members M28 260 3 0.50 Map1b.30415235_40,Tmeff1.65356245_10,Prkch.96280653_30 Best CMs (by avg z-score): 1. (Z = 4.74) SNORA22 - Small_nucleolar_RNA_SNORA22 2. (Z = 4.71) rli36 - Listeria_sRNA_rli36 3. (Z = 4.21) RMST_10 - Rhabdomyosarcoma_2_associated_transcript_conserved_region_10 4. (Z = 4.00) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 5. (Z = 3.85) mir-624 - microRNA_mir-624 6. (Z = 3.76) CRISPR-DR41 - CRISPR_RNA_direct_repeat_element 7. (Z = 3.64) RUF1 - Plasmodium_RNA_of_unkown_function_RUF1 8. (Z = 3.58) Pox_AX_element - Poxvirus_AX_element_late_mRNA_cis-regulatory_element 9. (Z = 3.56) mir-929 - microRNA_mir-929 10. (Z = 3.49) PK-PYVV - 3'-terminal_pseudoknot_in_PYVV Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM28.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM28_global.out/ --free-endgaps --indel=-100 --threads=4 .....................(((((.(((((((......))))))..)))))).................. MFE = -13.01 (Covariance contribution: -13.08) RNAz stats: MPI: 27.44, SCI: 0.51, ZSCORE: -0.72 Full summary: Sequences: 3 Columns: 72 Reading direction: forward Mean pairwise identity: 27.44 Shannon entropy: 1.04670 G+C content: 0.18714 Mean single sequence MFE: -7.80 Consensus MFE: -4.00 Energy contribution: -2.23 Covariance contribution: -1.77 Combinations/Pair: 2.00 Mean z-score: -0.72 Structure conservation index: 0.51 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.14 SVM RNA-class probability: 0.983610 Prediction: RNA Multiple alignment from mlocarna: Map1b.30415235_40 ~~~~~~~~~~~~~~~~~~~~~UAGAU-GAACUUUCUAACGAAUGUUUUCAUUUACAGAAAAAUGCAAAGAAA Tmeff1.65356245_10 CUAAAAGUAAAGAUGUUUACAGAUUACUUUUCUUACAAAAAAGAAAAAAA~~~~~~~~~~~~~~~~~~~~~~ Prkch.96280653_30 ~~~~~ACGACAGAGGUGUACCUUUUC-AUGUGUAACCAUAUAUACAGUUGAAAAAA~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M29 3336 4 0.52 Aco2.120266024_11,Bdnf.977114_72,Atp6v1b2.22320426_13,Atp6v1b2.22320426_27 Best CMs (by avg z-score): 1. (Z = 2.51) lincRNA-p21_2 - LincRNA-p21_conserved_region_2 2. (Z = 2.09) rnk_pseudo - Pseudomonas_rnk_leader 3. (Z = 1.77) SBWMV1_UPD-PKb - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 4. (Z = 1.60) mir-554 - microRNA_mir-554 5. (Z = 1.59) mir-515 - microRNA_mir-515 6. (Z = 1.52) HCV_SLIV - Hepatitis_C_stem-loop_IV 7. (Z = 1.43) mir-84 - microRNA_mir-84 8. (Z = 1.41) suhB - suhB 9. (Z = 1.41) SNORD15 - Small_nucleolar_RNA_SNORD15 10. (Z = 1.33) sR8 - Small_nucleolar_RNA_sR8 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM29.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM29_global.out/ --free-endgaps --indel=-100 --threads=4 ..........................(((((((((......))))))))).................... MFE = -10.77 (Covariance contribution: -4.97) RNAz stats: MPI: 30.48, SCI: 0.87, ZSCORE: 0.63 Full summary: Sequences: 4 Columns: 70 Reading direction: forward Mean pairwise identity: 30.48 Shannon entropy: 1.16037 G+C content: 0.36369 Mean single sequence MFE: -7.22 Consensus MFE: -6.31 Energy contribution: -6.38 Covariance contribution: 0.06 Combinations/Pair: 2.45 Mean z-score: 0.63 Structure conservation index: 0.87 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.92 SVM RNA-class probability: 0.853122 Prediction: RNA Multiple alignment from mlocarna: Aco2.120266024_11 CUAUUGAGCGUC--CUGUCUGAGAGUGGUUGGUGUACUGUUUUAUCAGCUUG~~~~~~~~~~~~~~~~~~ Bdnf.977114_72 ~~~~~~~~~~~~~~CCGUCCUGUUCUGUUCUGUUCUGUUCUGAA-AGUCUUGCUGUGGUCUCUUU~~~~~ Atp6v1b2.22320426_13 ~ACCUGUGGGUCUGUCCUCUGCUCUGUGCAGAUGGGUUUUACUGUCUGCUU~~~~~~~~~~~~~~~~~~~ Atp6v1b2.22320426_27 ~~~~~~~~~~~~~~~~~~CUGUGUGCCUCUGCCGUG--UCUGCUGUUUGGGUCUCUGUGCUGUGUGUUCU // ClustID MergedIDs Count AvgDissim Members M24 5388 4 0.61 Ntrk2.11676658_96,Rab5c.89652340_7,Atp1b2.56418323_0,Gng7.10269272_5 Best CMs (by avg z-score): 1. (Z = 2.23) CRISPR-DR15 - CRISPR_RNA_direct_repeat_element 2. (Z = 1.62) Pseudomon-Rho - Pseudomon-Rho_RNA 3. (Z = 1.59) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 4. (Z = 1.58) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.52) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 6. (Z = 1.37) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 7. (Z = 1.37) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.35) sbrA - Listeria_sRNA_sbrA 9. (Z = 1.27) IRES_Bip - bip_internal_ribosome_entry_site_(IRES) 10. (Z = 1.20) bxd_6 - Bithoraxoid_conserved_region_6 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM24.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM24_global.out/ --free-endgaps --indel=-100 --threads=4 .................((((((((...................))))).)))......... MFE = -5.45 (Covariance contribution: -5.23) RNAz stats: MPI: 39.95, SCI: -0.00, ZSCORE: 1.35 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 39.95 Shannon entropy: 0.99557 G+C content: 0.44998 Mean single sequence MFE: -4.91 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.35 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.99 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Ntrk2.11676658_96 ~~~~AUUCGUUCACACUCUAAUUGAAACCCACUU--CCUCUUGUUUGGUCUAGACU~~~~~~ Rab5c.89652340_7 ~~~~~~~~GUUCCCUUUCUACUGCUCCCCCACUUGCCCUUUGCUGGUAG-UAGCCAUGC~~~ Atp1b2.56418323_0 ~~~~~~~~~GGCUC-CCCACCCCCUCUCACCCAUACCCUCCUGUGGAU--GCUUCUGGAAUG Gng7.10269272_5 CUAACUUUAGCCUCAUCCACCCCCUCCCGUCGAGAACCAC----UGAU--GUGACA~~~~~~ // ClustID MergedIDs Count AvgDissim Members M25 1797 4 0.58 Spag7.57543647_0,Ntrk2.11676658_16,Rab43.121980138_3,Ddn.137572548_20 Best CMs (by avg z-score): 1. (Z = 3.26) WLE3 - Wingless_localisation_element_3_(WLE3) 2. (Z = 2.80) drz-agam-1 - drz-agam-1_riboswitch 3. (Z = 2.77) SNORD105 - Small_nucleolar_RNA_SNORD105 4. (Z = 2.60) mir-202 - microRNA_mir-202 5. (Z = 2.56) mir-500 - microRNA_mir-500 6. (Z = 2.41) mir-124 - mir-124_microRNA_precursor_family 7. (Z = 2.40) mir-3179 - microRNA_mir-3179 8. (Z = 2.40) mir-367 - microRNA_mir-367 9. (Z = 2.38) mir-770 - microRNA_mir-770 10. (Z = 2.36) mir-208 - microRNA_mir-208 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM25.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM25_global.out/ --free-endgaps --indel=-100 --threads=4 ......((((((.(((((((((((........))))))...)))))...)))))).. MFE = -34.76 (Covariance contribution: -19.36) RNAz stats: MPI: 35.40, SCI: 0.85, ZSCORE: 0.44 Full summary: Sequences: 4 Columns: 57 Reading direction: forward Mean pairwise identity: 35.40 Shannon entropy: 1.09929 G+C content: 0.57330 Mean single sequence MFE: -15.88 Consensus MFE: -13.54 Energy contribution: -11.72 Covariance contribution: -1.81 Combinations/Pair: 2.29 Mean z-score: 0.44 Structure conservation index: 0.85 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.26 SVM RNA-class probability: 0.918100 Prediction: RNA Multiple alignment from mlocarna: Spag7.57543647_0 ~~GCAUCCCACCCACCUUGCUUUGACCUCCAGCAAAGC---AGGGGCAUGGAGGG~~ Ntrk2.11676658_16 ~AGCAUGCUGCCCUACCGCUGUGU----CCUGACCCAGCAGCAAAG--AGGUUGCGG Rab43.121980138_3 AGGGAUUCUGCACCCCUAGCCUGGAU-----GCUGGGUAGGAAGGGAAAUGCAGG~~ Ddn.137572548_20 ~GUCCGGUCACUGCCUCUGGCCUGCUGUGAUCCAAGCU-GGAGAGGGAAGGU~~~~~ // ClustID MergedIDs Count AvgDissim Members M26 4176 3 0.47 Arhgef7.82521224_19,Tmeff1.65356245_13,Appbp2.73460120_83 Best CMs (by avg z-score): 1. (Z = 2.94) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.90) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 3. (Z = 2.17) Vault - Vault_RNA 4. (Z = 1.98) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.96) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.95) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.94) MIAT_exon5_2 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_2 8. (Z = 1.89) IRES_mnt - Mnt_IRES 9. (Z = 1.82) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.74) CRISPR-DR11 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM26.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM26_global.out/ --free-endgaps --indel=-100 --threads=4 ............................(((((..((((....))))))))). MFE = -18.43 (Covariance contribution: -11.17) RNAz stats: MPI: 35.44, SCI: 1.10, ZSCORE: 0.27 Full summary: Sequences: 3 Columns: 53 Reading direction: forward Mean pairwise identity: 35.44 Shannon entropy: 0.91497 G+C content: 0.42306 Mean single sequence MFE: -7.70 Consensus MFE: -8.46 Energy contribution: -5.70 Covariance contribution: -2.76 Combinations/Pair: 2.22 Mean z-score: 0.27 Structure conservation index: 1.10 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.46 SVM RNA-class probability: 0.705564 Prediction: RNA Multiple alignment from mlocarna: Arhgef7.82521224_19 ~~GUUGUGUUAUUUAUUCCAUAUUCUUUAGCCG-GUGCUGCCGGGCAGGGUUU Tmeff1.65356245_13 CUGGUUUUUU-UUAGAUACUUCCCCUAUUGCAU-GAGCUGCAAAGCUGUGUG~ Appbp2.73460120_83 ~~~UUUACAUUCUUUAUAAACAACUCACCAGCACCCUGCCCAGGUAUUGCUGC // ClustID MergedIDs Count AvgDissim Members M27 6447 3 0.48 Atp2a2.35312505_1,Dpysl2.46346413_2,Map1b.30415235_78 Best CMs (by avg z-score): 1. (Z = 2.92) MIR478 - microRNA_MIR478 2. (Z = 2.83) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.73) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.72) Afu_300 - A._fumigatus_snoRNA_Afu_300 5. (Z = 2.70) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.63) 23S-methyl - 23S_methyl_RNA_motif 7. (Z = 2.59) SNORD102 - Small_nucleolar_RNA_SNORD102 8. (Z = 2.44) U1_yeast - Yeast_U1_spliceosomal_RNA 9. (Z = 2.43) snR13 - Small_nucleolar_RNA_snR13 10. (Z = 2.40) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM27.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM27_global.out/ --free-endgaps --indel=-100 --threads=4 ..............((.(.....))).(((((.((...)).)..))))......... MFE = -5.48 (Covariance contribution: -11.11) RNAz stats: MPI: 46.47, SCI: -0.00, ZSCORE: 1.09 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 46.47 Shannon entropy: 0.78035 G+C content: 0.28428 Mean single sequence MFE: -2.80 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.09 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.50 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Atp2a2.35312505_1 ~~UCAAUUAAUUUUUU-AUUGUUUAA-AGCAACUG-UCUAUUUCUGCUGAAUUUU~~ Dpysl2.46346413_2 UUCCAAUUUUUUUUUCCUUUUUUUGAGAGAGCCUGUGAUAGUUGCUGUGG~~~~~~~ Map1b.30415235_78 ~~~~AAACACUUUUUU-UUUUCAAAACUGUCACUGAUCCACU--GGCUGUGAUUCCU // ClustID MergedIDs Count AvgDissim Members M20 4988 3 0.51 Irgm.34132512_4,Atp1b2.56418323_41,Gnai1.12494046_5 Best CMs (by avg z-score): 1. (Z = 3.00) snoU6-77 - Small_nucleolar_RNA_U6-77 2. (Z = 2.99) mir-15 - mir-15_microRNA_precursor_family 3. (Z = 2.92) S_pombe_snR42 - small_nucleolar_RNA_snR42 4. (Z = 2.85) mir-515 - microRNA_mir-515 5. (Z = 2.78) SCARNA8 - Small_Cajal_body_specific_RNA_8 6. (Z = 2.75) ceN93 - C._elegans_sRNA_ceN93 7. (Z = 2.58) mir-575 - microRNA_mir-575 8. (Z = 2.55) S_pombe_snR92 - small_nucleolar_RNA_snR92 9. (Z = 2.55) mir-345 - microRNA_mir-345 10. (Z = 2.53) mir-9 - mir-9/mir-79_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM20.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM20_global.out/ --free-endgaps --indel=-100 --threads=4 ....((((..((((((((.((.......)).)))))).))))))............. MFE = -16.20 (Covariance contribution: -12.63) RNAz stats: MPI: 38.60, SCI: 0.74, ZSCORE: -0.37 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 38.60 Shannon entropy: 0.87856 G+C content: 0.31541 Mean single sequence MFE: -8.43 Consensus MFE: -6.27 Energy contribution: -3.73 Covariance contribution: -2.54 Combinations/Pair: 2.25 Mean z-score: -0.37 Structure conservation index: 0.74 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.31 SVM RNA-class probability: 0.988160 Prediction: RNA Multiple alignment from mlocarna: Irgm.34132512_4 ~~~~~UCUAAUGUAUUGUUCU--ACUGAGGAACAGGGACAAGUAAUGAUUAAAAAUC Atp1b2.56418323_41 ~~~~AUUUAAUGCCUGUGUCAGAACUACUGUAAGAGGAUAAAGUACAAUAAAAU~~~ Gnai1.12494046_5 AACUUAUG---GUCCUAGUGCGA---UGGCUUUGGGAAAACAUAACUGUUAAGUAC~ // ClustID MergedIDs Count AvgDissim Members M21 1442 3 0.44 Atp2b2.149655651_4,Grin1.3453776_20,Slc7a8.32800927_47 Best CMs (by avg z-score): 1. (Z = 2.66) Pseudomon-Rho - Pseudomon-Rho_RNA 2. (Z = 2.32) suhB - suhB 3. (Z = 2.08) Arthropod_7SK - Arthropod_7SK_RNA 4. (Z = 1.86) snoZ178 - Small_nucleolar_RNA_Z178 5. (Z = 1.82) TCV_Pr - Turnip_crinkle_virus_(TCV)_core_promoter_hairpin_(Pr) 6. (Z = 1.73) MIAT_exon5_3 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_3 7. (Z = 1.70) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.60) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.57) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.54) HCV_SLIV - Hepatitis_C_stem-loop_IV Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM21.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM21_global.out/ --free-endgaps --indel=-100 --threads=4 ................(((...)))................................... MFE = -5.39 (Covariance contribution: -5.92) RNAz stats: MPI: 39.44, SCI: -0.00, ZSCORE: 1.12 Full summary: Sequences: 3 Columns: 60 Reading direction: forward Mean pairwise identity: 39.44 Shannon entropy: 0.87908 G+C content: 0.42222 Mean single sequence MFE: -2.67 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.12 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.13 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Atp2b2.149655651_4 ACACAGACCCUUUCUCUGGCUGCCAUGCUGUUUGAACUCUUUUUCACUCC~~~~~~~~~~ Grin1.3453776_20 ~~~~~~~CCCUUCCUCCAGCGCCUGCUCUCUGCAACUUGAUUUCCACCUCUCUCCUG~~~ Slc7a8.32800927_47 ~~~~~~~~~~UUCAGCCUGCACCUGCCCCUCCUUGAAUUAUUGUCUCUCUCUCUCUUUUU // ClustID MergedIDs Count AvgDissim Members M22 3489 5 0.58 Slc7a8.32800927_42,Opcml.28508230_7,Atp1b2.56418323_28,Dlg4.56889789_15,Gng7.10269272_22 Best CMs (by avg z-score): 1. (Z = 2.42) rli32 - Listeria_sRNA_rli32 2. (Z = 1.90) H19_3 - H19_conserved_region_3 3. (Z = 1.82) Yfr1 - Cyanobacterial_functional_RNA_1 4. (Z = 1.62) snoZ178 - Small_nucleolar_RNA_Z178 5. (Z = 1.60) blv_FSE - ribosomal_frameshift_site 6. (Z = 1.60) BYDV_5_UTR - Barley_yellow_dwarf_virus_5'UTR 7. (Z = 1.56) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 8. (Z = 1.54) 6S - 6S_/_SsrS_RNA 9. (Z = 1.43) Y_RNA - Y_RNA 10. (Z = 1.37) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM22.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM22_global.out/ --free-endgaps --indel=-100 --threads=4 ....(((((.......((((........)))).........)))))................... MFE = -9.81 (Covariance contribution: -8.55) RNAz stats: MPI: 33.80, SCI: 0.33, ZSCORE: 0.39 Full summary: Sequences: 5 Columns: 65 Reading direction: forward Mean pairwise identity: 33.80 Shannon entropy: 1.23977 G+C content: 0.47076 Mean single sequence MFE: -12.67 Consensus MFE: -4.20 Energy contribution: -2.28 Covariance contribution: -1.92 Combinations/Pair: 3.00 Mean z-score: 0.39 Structure conservation index: 0.33 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.08 SVM RNA-class probability: 0.017332 Prediction: OTHER Multiple alignment from mlocarna: Slc7a8.32800927_42 ~~~~~~~~GGAACACCCAGGGGCCUUUUCCUGGUCUCCCAACUUCCCACCUAGCUCAC~~~~~~~ Opcml.28508230_7 ~GGUGGGCCCCCAAAUGGAA----UAUAUUCCUGCUACCUUGGCCUUCCUUUUCU~~~~~~~~~~ Atp1b2.56418323_28 ~~~~GGGGGGAC-UCCCUGA-G-----CCCAGAUCUACCCACCCCCAUCCUCUCUCUGGCU~~~~ Dlg4.56889789_15 ~~~~~~~~~~~~~GGGGGCUCUCCUGAGGGUCCCCUGUCUUUCACACACCU--CCCACCUUUUUU Gng7.10269272_22 AUGGGGUUCUCCAUCCCACA-UCGUGACUGUGCCUCCAGAUCCCCCUUCCU~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M23 3182 6 0.54 Sept9.107478216_18,Grb2.105722014_27,Opcml.28508230_5,Sept9.107478216_31,Pklr.181222231_7,Shank3.127875955_6 Best CMs (by avg z-score): 1. (Z = 2.02) mir-638 - microRNA_mir-638 2. (Z = 1.55) Prion_pknot - Prion_pseudoknot 3. (Z = 1.51) KCNQ1OT1_4 - KCNQ1_overlapping_transcript_1_conserved_region_4 4. (Z = 1.47) GRIK4_3p_UTR - GRIK4_3_prime_UTR_element 5. (Z = 1.47) sR60 - Small_nucleolar_RNA_sR60 6. (Z = 1.33) IRES_FGF2 - FGF-2_internal_ribosome_entry_site_(IRES) 7. (Z = 1.30) Xist_exon4 - X-chromosome_inactivation_gene_exon_4 8. (Z = 1.30) Intron_gpII - Group_II_catalytic_intron 9. (Z = 1.26) PrrB_RsmZ - PrrB/RsmZ_RNA_family 10. (Z = 1.19) snoZ206 - Small_nucleolar_RNA_Z206 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM23.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM23_global.out/ --free-endgaps --indel=-100 --threads=4 ......(((((....))))).........(((((((...((.......)).)))))))..... MFE = -22.76 (Covariance contribution: -12.65) RNAz stats: MPI: 33.52, SCI: 0.42, ZSCORE: 0.09 Full summary: Sequences: 6 Columns: 63 Reading direction: forward Mean pairwise identity: 33.52 Shannon entropy: 1.30957 G+C content: 0.51958 Mean single sequence MFE: -13.43 Consensus MFE: -5.68 Energy contribution: -2.35 Covariance contribution: -3.33 Combinations/Pair: 3.42 Mean z-score: 0.09 Structure conservation index: 0.42 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.69 SVM RNA-class probability: 0.205595 Prediction: OTHER Multiple alignment from mlocarna: Sept9.107478216_18 GUGAAAAGCAGGGACGUGCUG-----GAGAGGGGGA---AAUGU--CUUU-UCUCCCUCAC~~ Grb2.105722014_27 ~~~~~AAGGGUCAAAACACAAGGCAGGCAGGGGGGA---GCGGG--UGGCAUCCUUCCCU~~~ Opcml.28508230_5 ~~~~UUCGUUUGAAUGGACGGGGUUGGGGGUUGGGA---UGGGC--AGGG-UUCUACCAC~~~ Sept9.107478216_31 ~~~~~~~~~~UGCAAAGAGGGAGAGAUGAGGGGGUCAGAGAGGGAUAGUCGGGCUCACUC~~~ Pklr.181222231_7 ~~~UCCCAAUCAUUGGAAUGGGGGAGUGGAAACAGG---GU------GAU-CUUGUCCAAUUU Shank3.127875955_6 ~~CGGACCAGGGGG-GCUGGGUGGAAGGGGGUUGGG---GCAGG--GUGC-UCUGGCCU~~~~ // ClustID MergedIDs Count AvgDissim Members M188 686 6 0.69 Ddn.137572548_15,Nrgn.38790596_19,Marcksl1.148671604_9,Dlg4.56889789_3,Mapre3.25496282_14,Pabpn1.32998239_22 Best CMs (by avg z-score): 1. (Z = 2.28) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 2. (Z = 2.25) WLE3 - Wingless_localisation_element_3_(WLE3) 3. (Z = 2.21) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.10) CRISPR-DR66 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.04) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.98) mir-500 - microRNA_mir-500 7. (Z = 1.93) tp2 - tp2 8. (Z = 1.87) CRISPR-DR11 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.85) bxd_7 - Bithoraxoid_conserved_region_7 10. (Z = 1.82) mir-626 - microRNA_mir-626 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM188.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM188_global.out/ --free-endgaps --indel=-100 --threads=4 ....................((((.(((((((((.((......))..)))))))))))))... MFE = -13.82 (Covariance contribution: -8.60) RNAz stats: MPI: 36.52, SCI: 0.51, ZSCORE: 0.27 Full summary: Sequences: 6 Columns: 63 Reading direction: forward Mean pairwise identity: 36.52 Shannon entropy: 1.30404 G+C content: 0.37960 Mean single sequence MFE: -10.90 Consensus MFE: -5.54 Energy contribution: -3.49 Covariance contribution: -2.05 Combinations/Pair: 3.38 Mean z-score: 0.27 Structure conservation index: 0.51 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.32 SVM RNA-class probability: 0.345511 Prediction: OTHER Multiple alignment from mlocarna: Ddn.137572548_15 ~~~~~~~~~AUUCUUUUGUCCCUA-GAAUUUU--GUGAACGAGCG-AGUAGAAUUUGAGGGUU Nrgn.38790596_19 ~~~~CCCGCUCUCCUUUGUUUAUGCAAAAGCCUCCGGAGC--GCUGGGAGGCUGGC~~~~~~~ Marcksl1.148671604_9 ~~~~~~~UUCGUUUUGUUUAUCCU-GCUUCU----CAAGCCCCUG-AGCCAGAAGUGGGGCUU Dlg4.56889789_3 ~~~~~~~~~~~UCUUAUUUAUUUC-CUUUCUAACUGGAUCGAGCC-CACUGGAGGGGGGACAC Mapre3.25496282_14 ~~~~~~~~~~~~CUUAUUUAUUUUGUCUUUUGACUUCUCUCCCAGUAGUUGAGGGAAAGGCU~ Pabpn1.32998239_22 GUGGCUUUUGUUUUUAUUUUUUUAACUCAUUUCC------------AGGGGAUGGGAAUUUU~ // ClustID MergedIDs Count AvgDissim Members M189 681 4 0.53 Sdcbp.19848126_29,Itpr1.144028781_30,Usp9x.21606330_76,Grb2.105722014_17 Best CMs (by avg z-score): 1. (Z = 2.82) suhB - suhB 2. (Z = 2.80) RydC - RydC_RNA 3. (Z = 2.77) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.62) InvR - Invasion_gene-associated_RNA 5. (Z = 2.41) snoU97 - Small_nucleolar_RNA_U97 6. (Z = 2.30) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.26) MIR478 - microRNA_MIR478 8. (Z = 2.25) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.24) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.11) GcvB - GcvB_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM189.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM189_global.out/ --free-endgaps --indel=-100 --threads=4 ...........................((((............))))....((((((.........)))))).. MFE = -7.72 (Covariance contribution: -9.32) RNAz stats: MPI: 37.33, SCI: 0.06, ZSCORE: -0.12 Full summary: Sequences: 4 Columns: 74 Reading direction: forward Mean pairwise identity: 37.33 Shannon entropy: 1.05084 G+C content: 0.24273 Mean single sequence MFE: -5.33 Consensus MFE: -0.32 Energy contribution: 0.80 Covariance contribution: -1.13 Combinations/Pair: 2.00 Mean z-score: -0.12 Structure conservation index: 0.06 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.35 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Sdcbp.19848126_29 ~~~~~~~~~~~~~~~~~~~~~UAUCCUGACU-CUUUCCUUCUUAGUUUGUGCCUAUCUUAUUAUUUUAUGUG~~ Itpr1.144028781_30 CCACGUUUGGGUUUUAUUUCUUUGUCACAUGAUUUCUUUUCUGGAUGUGU~~~~~~~~~~~~~~~~~~~~~~~~ Usp9x.21606330_76 ~~~~~~~~~~~~~~~~~~~~~~AUUCUCUCAACUGAUUUCUUUUGAGCCAUAUGUUUUC-UCCUUUAAAUGUU~ Grb2.105722014_17 ~~~~~~~~~~~~~~~~CUUCAGUGUCUCACU---UGUUUUCAUAGUG----CCUUUGUC-UUAUUUCAAGGGUG // ClustID MergedIDs Count AvgDissim Members M182 1972 3 0.34 Grin1.3453776_21,Mapre3.25496282_22,Syngr1.118351457_1 Best CMs (by avg z-score): 1. (Z = 2.20) H19_3 - H19_conserved_region_3 2. (Z = 1.94) IRES_mnt - Mnt_IRES 3. (Z = 1.73) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 4. (Z = 1.33) 6C - 6C_RNA 5. (Z = 1.14) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 6. (Z = 1.00) H19_2 - H19_conserved_region_2 7. (Z = 0.99) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 8. (Z = 0.90) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 9. (Z = 0.83) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element 10. (Z = 0.82) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM182.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM182_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ........................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 48.30, SCI: -0.00, ZSCORE: 0.43 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 48.30 Shannon entropy: 0.73983 G+C content: 0.55164 Mean single sequence MFE: -0.80 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.43 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.67 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Grin1.3453776_21 ~~~~~~~UCCACCUCUCU-CCUGCUGCACCACCCUCCC-ACGACAUUUCCCCACCCCAU Mapre3.25496282_22 CAAUUCUCCCACCUCCCCACCUUUGCCCCUUGCCUCCC-ACCAGCCUGCAC~~~~~~~~ Syngr1.118351457_1 ~~~~~CUGCCCCUGCCCUUACAUCCUAGCUCCCCUCCCAAGCACCCUGCUCCCUC~~~~ // ClustID MergedIDs Count AvgDissim Members M183 6135 3 0.27 Map1b.30415235_11,Spag7.57543647_6,Map1b.30415235_9 Best CMs (by avg z-score): 1. (Z = 3.08) sR43 - Small_nucleolar_RNA_sR42 2. (Z = 2.36) Tombus_3_III - Tombus_virus_defective_interfering_(DI)_RNA_region_3 3. (Z = 2.15) CsrB - CsrB/RsmB_RNA_family 4. (Z = 2.05) sR34 - Small_nucleolar_RNA_sR34 5. (Z = 1.95) sR52 - Small_nucleolar_RNA_sR52 6. (Z = 1.92) mir-638 - microRNA_mir-638 7. (Z = 1.91) SSU_rRNA_archaea - Archaeal_small_subunit_ribosomal_RNA 8. (Z = 1.85) HIV-1_SL3 - HIV-1_stem-loop_3_Psi_packaging_signal 9. (Z = 1.83) sR21 - Small_nucleolar_RNA_sR21 10. (Z = 1.83) IRES_Bag1 - Bag-1_internal_ribosome_entry_site_(IRES) Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM183.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM183_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ............................................................ MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 59.44, SCI: -0.00, ZSCORE: -0.0 Full summary: Sequences: 3 Columns: 60 Reading direction: forward Mean pairwise identity: 59.44 Shannon entropy: 0.56901 G+C content: 0.43041 Mean single sequence MFE: -1.04 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.00 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.83 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Map1b.30415235_11 ~~~~~~~~~~GAGACUGCCGGAGAGAGAGAGAGUGAGAGUGAGAGAGGAAGAAUCAGAAA Map1b.30415235_9 UAGAGAGAGAAAGAGAGAGGGAAAGAGAGUCAGCGGGAG-GGGAGGGAGAG~~~~~~~~~ Spag7.57543647_6 ~~~~~AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAUG~~~~~ // ClustID MergedIDs Count AvgDissim Members M180 1801 3 0.41 Gria2.172265159_73,Usp9x.21606330_7,Map1b.30415235_65 Best CMs (by avg z-score): 1. (Z = 3.76) RprA - RprA_RNA 2. (Z = 3.73) 23S-methyl - 23S_methyl_RNA_motif 3. (Z = 3.71) L10_leader - Ribosomal_protein_L10_leader 4. (Z = 3.51) isrP - isrP_Hfq_binding_RNA 5. (Z = 3.44) InvR - Invasion_gene-associated_RNA 6. (Z = 3.41) ctRNA_pT181 - ctRNA 7. (Z = 3.41) Trp_leader - Tryptophan_operon_leader 8. (Z = 3.30) GcvB - GcvB_RNA 9. (Z = 3.29) Arthropod_7SK - Arthropod_7SK_RNA 10. (Z = 3.28) VrrA - Vibrio_regulatory_RNA_of_OmpA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM180.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM180_global.out/ --free-endgaps --indel=-100 --threads=4 .......((((((......))))))(((((.....)).)))................ MFE = -10.16 (Covariance contribution: -10.33) RNAz stats: MPI: 42.60, SCI: 0.59, ZSCORE: 1.07 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 42.60 Shannon entropy: 0.81412 G+C content: 0.22431 Mean single sequence MFE: -3.23 Consensus MFE: -1.91 Energy contribution: 0.87 Covariance contribution: -2.77 Combinations/Pair: 2.60 Mean z-score: 1.07 Structure conservation index: 0.59 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.33 SVM RNA-class probability: 0.070560 Prediction: OTHER Multiple alignment from mlocarna: Gria2.172265159_73 CAAUUUUUUCAUGUGU-ACUAUG-UCAGAAAAUGCUU-UUGAUUUUAUUUUUA~~~~ Usp9x.21606330_7 ~~~~AUAUUAAUGUUUGACUGUUAAUUCUUAA-GCAA-GAGACUUUUUUUUUUCUU~ Map1b.30415235_65 ~~AUAUUCUAUUUU-----UGUUAGGCGUCUCUAGGAAUGCAGCUUUUAUUUAUUUU // ClustID MergedIDs Count AvgDissim Members M181 790 4 0.62 Opcml.28508230_4,Rhobtb1.20089811_29,Calm2.10951142_13,Tmem30a.84827711_3 Best CMs (by avg z-score): 1. (Z = 3.33) sn2524 - Small_nucleolar_RNA_sn2524 2. (Z = 3.21) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.20) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.15) snoU97 - Small_nucleolar_RNA_U97 5. (Z = 2.86) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.84) mir-186 - microRNA_mir-186 7. (Z = 2.83) VrrA - Vibrio_regulatory_RNA_of_OmpA 8. (Z = 2.72) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 9. (Z = 2.68) suhB - suhB 10. (Z = 2.62) MIR478 - microRNA_MIR478 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM181.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM181_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((((...........))))...........((((....)))).............. MFE = -9.47 (Covariance contribution: -10.12) RNAz stats: MPI: 39.19, SCI: 0.47, ZSCORE: 1.55 Full summary: Sequences: 4 Columns: 67 Reading direction: forward Mean pairwise identity: 39.19 Shannon entropy: 1.01365 G+C content: 0.22587 Mean single sequence MFE: -2.50 Consensus MFE: -1.17 Energy contribution: 0.95 Covariance contribution: -2.12 Combinations/Pair: 2.00 Mean z-score: 1.55 Structure conservation index: 0.47 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.84 SVM RNA-class probability: 0.004068 Prediction: OTHER Multiple alignment from mlocarna: Opcml.28508230_4 UUCUGGGAUUUUCAA-----UUUGAUUUGAUUUUUCUUUUUUCGUUUGAAUGGAC~~~~~~~~~~~~ Rhobtb1.20089811_29 ~~~~~~~~~~GACAAGU-------AUUUGUAUUUUUUUUUUUUUAAUUUUAACUCUUCCCAGGGAAA Calm2.10951142_13 ~~~~~CCA-GAAACAUUUUCUUUUAUUGUUACUUGCUUUUUAAACUUU-GUUUAGCC~~~~~~~~~~ Tmem30a.84827711_3 ACAUAACAAAAAACAGCCU------UUGUUCUUUGCUUCUUACAUAUGGAUGACUU~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M186 6331 4 0.52 Atp1b2.56418323_37,Nrgn.38790596_14,Pebp1.40495174_2,Atp1b2.56418323_22 Best CMs (by avg z-score): 1. (Z = 2.41) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 2. (Z = 2.12) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 3. (Z = 1.94) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.57) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.46) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.35) g2 - G2 7. (Z = 1.18) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.17) CRISPR-DR44 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.14) EAV_LTH - Equine_arteritis_virus_leader_TRS_hairpin_(LTH) 10. (Z = 1.13) 6C - 6C_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM186.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM186_global.out/ --free-endgaps --indel=-100 --threads=4 .....................(((((((.......................)))))))..... MFE = -15.41 (Covariance contribution: -9.61) RNAz stats: MPI: 41.10, SCI: 0.62, ZSCORE: -0.11 Full summary: Sequences: 4 Columns: 63 Reading direction: forward Mean pairwise identity: 41.10 Shannon entropy: 0.96495 G+C content: 0.50755 Mean single sequence MFE: -7.25 Consensus MFE: -4.46 Energy contribution: -3.90 Covariance contribution: -0.56 Combinations/Pair: 2.00 Mean z-score: -0.11 Structure conservation index: 0.62 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.66 SVM RNA-class probability: 0.959041 Prediction: RNA Multiple alignment from mlocarna: Atp1b2.56418323_37 ~~~~~~~UAACCUCCCUCCUCUUCACUGCAGCCCCAUCCUGUCCUCA-----AGUGGAUUCU~ Nrgn.38790596_14 CCGCGUCUUUCCACCCUAACCUAACCUC-------AAC--CUCCUAAACCUGGGGCUAG~~~~ Pebp1.40495174_2 ~~GUGUCCCCCCACGCCCAUCCUUCCU----UCCCACCCUCUCAU-------AGGGAGUUCUC Atp1b2.56418323_22 ~~~~~~~~~~UCUUCCUAGUCCCUCCUGUCAUCCAAACAACUCCUA---CUCAGGCGGGCUUG // ClustID MergedIDs Count AvgDissim Members M187 474 3 0.50 Gng7.10269272_2,Tmeff1.65356245_11,Appbp2.73460120_8 Best CMs (by avg z-score): 1. (Z = 4.47) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.94) IS061 - IS061_RNA 3. (Z = 3.68) PVX_3 - Potato_virus_X_cis-acting_regulatory_element 4. (Z = 3.62) SCARNA1 - Small_Cajal_body_specific_RNA_1 5. (Z = 3.47) NrrF - NrrF_RNA 6. (Z = 3.41) LhrC - Listeria_Hfq_binding_LhrC 7. (Z = 3.40) snR5 - Small_nucleolar_RNA_snR5 8. (Z = 3.39) Bacteroid-trp - Bacteroidete_tryptophan_peptide_leader_RNA 9. (Z = 3.35) mir-2774 - microRNA_mir-2774 10. (Z = 3.33) IS128 - IS128_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM187.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM187_global.out/ --free-endgaps --indel=-100 --threads=4 ...............(((((..(((......(((....)))...)))...)))))........ MFE = -13.20 (Covariance contribution: -11.76) RNAz stats: MPI: 29.44, SCI: 0.31, ZSCORE: -0.9 Full summary: Sequences: 3 Columns: 63 Reading direction: forward Mean pairwise identity: 29.44 Shannon entropy: 0.97499 G+C content: 0.22055 Mean single sequence MFE: -4.00 Consensus MFE: -1.22 Energy contribution: 2.10 Covariance contribution: -3.32 Combinations/Pair: 2.09 Mean z-score: -0.90 Structure conservation index: 0.31 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.34 SVM RNA-class probability: 0.652090 Prediction: RNA Multiple alignment from mlocarna: Tmeff1.65356245_11 CAAAAAAGAAAAAAAAUCUAGAGGA------CA---CUGUG---UUUAAAUAGAUAUUCAAA~ Gng7.10269272_2 ~~~~~~~~~~~CCUGUAAGAAAAAAAUAUUUGAAUCCCUUCUACUUUGAAUUUUAAAGGAA~~ Appbp2.73460120_8 GAAAGAAAAAAAAAAGAACCCCUAA------AUAAAACUAU---UUAAGA-GUUUA---AAAG // ClustID MergedIDs Count AvgDissim Members M184 1472 4 0.53 Fmr1.154791521_27,Map1b.30415235_37,Fgf13.144199535_36,Tmeff1.65356245_8 Best CMs (by avg z-score): 1. (Z = 3.39) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.93) bxd_6 - Bithoraxoid_conserved_region_6 3. (Z = 2.71) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.58) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.45) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.37) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.29) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.27) K10_TLS - K10_transport/localisation_element_(TLS) 9. (Z = 2.23) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.19) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM184.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM184_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ....................(((((((.....)))))))................ MFE = -5.03 (Covariance contribution: -4.08) RNAz stats: MPI: 35.45, SCI: -0.00, ZSCORE: -0.07 Full summary: Sequences: 4 Columns: 55 Reading direction: forward Mean pairwise identity: 35.45 Shannon entropy: 1.11096 G+C content: 0.32178 Mean single sequence MFE: -2.05 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.07 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.74 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Tmeff1.65356245_8 GACCCACUUCAUAGUCGU--UAUAAAGUCAUACUUUCUUCCCCAAUGACCAC~~~ Map1b.30415235_37 ~~~~~GCCUUCCUUUGUCUUGCAUUGACUAUUUUAAUUUUUCCAUUAAUUCCAAC Fmr1.154791521_27 UGUCCUCCCCAAGUUUUGUCAAGUUUUUCAUUCAUAUUUUACAUUAAAGC~~~~~ Fgf13.144199535_36 ~GUAUACCCAAAUACGCACCGAAUAAACUCUUUAUAUUCAUUCAACGAACU~~~~ // ClustID MergedIDs Count AvgDissim Members M185 2226 3 0.52 Pcdh17.66481698_21,Rnf111.74909360_11,Tmeff1.65356245_0 Best CMs (by avg z-score): 1. (Z = 3.67) K10_TLS - K10_transport/localisation_element_(TLS) 2. (Z = 2.88) ALIL - ALIL_pseudoknot 3. (Z = 2.83) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.82) rli34 - Listeria_sRNA_rli34 5. (Z = 2.72) GcvB - GcvB_RNA 6. (Z = 2.70) mir-223 - microRNA_mir-223 7. (Z = 2.69) RprA - RprA_RNA 8. (Z = 2.64) Arthropod_7SK - Arthropod_7SK_RNA 9. (Z = 2.43) CRISPR-DR38 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.43) 23S-methyl - 23S_methyl_RNA_motif Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM185.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM185_global.out/ --free-endgaps --indel=-100 --threads=4 ............................(((((((.((......))))))))).. MFE = -6.48 (Covariance contribution: -5.02) RNAz stats: MPI: 38.41, SCI: 0.71, ZSCORE: 0.44 Full summary: Sequences: 3 Columns: 55 Reading direction: forward Mean pairwise identity: 38.41 Shannon entropy: 0.89976 G+C content: 0.27808 Mean single sequence MFE: -4.53 Consensus MFE: -3.22 Energy contribution: -0.10 Covariance contribution: -3.12 Combinations/Pair: 2.56 Mean z-score: 0.44 Structure conservation index: 0.71 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.92 SVM RNA-class probability: 0.851829 Prediction: RNA Multiple alignment from mlocarna: Tmeff1.65356245_0 GCUGCUGACUUUUAUAUGCACACUGACC-ACGUGA-UGUACAUUUAUUAUGU~~~ Rnf111.74909360_11 ~~~~UUUUUUUUUUUUUACAUAGUACCU-UGAAAAUUAUGAAUUUGUUUUUAUCC Pcdh17.66481698_21 ~~~~~UAUUGAUUUAUUGCAGAUUCCGUGCAUAUGAGCCAAAUUGUUGAGUGUAU // ClustID MergedIDs Count AvgDissim Members M102 3002 3 0.50 Atp2b2.149655651_35,Eif4a2.79950592_5,Atrn.118696808_19 Best CMs (by avg z-score): 1. (Z = 3.16) mir-28 - microRNA_mir-28 2. (Z = 2.99) mir-280 - microRNA_mir-280 3. (Z = 2.91) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 4. (Z = 2.64) mir-46 - mir-46/mir-47/mir-281_microRNA_precursor_family 5. (Z = 2.58) mir-340 - microRNA_mir-340 6. (Z = 2.50) SBWMV1_UPD-PKb - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 7. (Z = 2.43) mir-144 - microRNA_mir-144 8. (Z = 2.42) MIR820 - microRNA_MIR820 9. (Z = 2.42) SNORA20 - Small_nucleolar_RNA_SNORA20 10. (Z = 2.41) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM102.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM102_global.out/ --free-endgaps --indel=-100 --threads=4 ..((...((((((((((..(((.........))).))))))))))....)).... MFE = -18.22 (Covariance contribution: -12.62) RNAz stats: MPI: 39.63, SCI: 0.67, ZSCORE: -0.83 Full summary: Sequences: 3 Columns: 55 Reading direction: forward Mean pairwise identity: 39.63 Shannon entropy: 0.86797 G+C content: 0.37312 Mean single sequence MFE: -10.73 Consensus MFE: -7.17 Energy contribution: -4.30 Covariance contribution: -2.87 Combinations/Pair: 2.09 Mean z-score: -0.83 Structure conservation index: 0.67 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.91 SVM RNA-class probability: 0.996270 Prediction: RNA Multiple alignment from mlocarna: Atp2b2.149655651_35 ~AGUUGUCUUUGGCACUGUCUUUGUGAGUCAAGGUAGUGUUCAGAUAUCAC~~~~ Atrn.118696808_19 AGAGGGCUAUUCUAAAUGUCACGGU----CAAUGGAGUUAGAAUAUAGACAAAU~ Eif4a2.79950592_5 ~~UUGGCUUUAUCCUCU-UUAGAGUUAG--ACUGUUGGGGGUGGGUAUAAAAGAU // ClustID MergedIDs Count AvgDissim Members M103 5339 3 0.49 Syt4.23805080_54,Atp2b2.149655651_49,Vegfa.10534185_34 Best CMs (by avg z-score): 1. (Z = 5.47) K10_TLS - K10_transport/localisation_element_(TLS) 2. (Z = 4.84) 23S-methyl - 23S_methyl_RNA_motif 3. (Z = 4.78) MIR476 - microRNA_MIR476 4. (Z = 4.54) mir-BHRF1-2 - mir-BHRF1-2_microRNA_precursor_family 5. (Z = 4.33) rli61 - Listeria_sRNA_rli61 6. (Z = 4.29) mir-449 - microRNA_mir-449 7. (Z = 4.10) mir-335 - microRNA_mir-335 8. (Z = 4.04) mir-186 - microRNA_mir-186 9. (Z = 4.03) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 10. (Z = 3.90) mir-340 - microRNA_mir-340 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM103.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM103_global.out/ --free-endgaps --indel=-100 --threads=4 .(((.((.((((((..(((((.....))))))))))).))))).................. MFE = -23.35 (Covariance contribution: -18.31) RNAz stats: MPI: 32.60, SCI: 0.76, ZSCORE: -1.07 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 32.60 Shannon entropy: 0.95912 G+C content: 0.20065 Mean single sequence MFE: -7.53 Consensus MFE: -5.74 Energy contribution: -0.53 Covariance contribution: -5.20 Combinations/Pair: 2.06 Mean z-score: -1.07 Structure conservation index: 0.76 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.47 SVM RNA-class probability: 0.998750 Prediction: RNA Multiple alignment from mlocarna: Syt4.23805080_54 ~CUU-UUAAAAUUG--UAAA---UAGUUUUACGAUUUAAAGUGU----UUUGACGGUGUAA Atp2b2.149655651_49 ~UCAUAAAAGAACU-UUUGUAUUUAAUACAAAGUUUGCUUUGAGACUUUUCA~~~~~~~~~ Vegfa.10534185_34 CCUU-UUUAAUUAGAAAUUAAAACAGUUAAUUUAAUUAAAGAGUAGGGUUU~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M100 2973 3 0.36 Usp9x.21606330_11,Aco2.120266024_25,Atp1b2.56418323_33 Best CMs (by avg z-score): 1. (Z = 4.05) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.56) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.55) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.44) IS128 - IS128_RNA 5. (Z = 3.39) tmRNA - transfer-messenger_RNA 6. (Z = 3.34) SCARNA1 - Small_Cajal_body_specific_RNA_1 7. (Z = 3.33) snopsi18S-1854 - Small_nucleolar_RNA_psi18S-1854 8. (Z = 3.32) CyaR_RyeE - CyaR/Rye_RNA 9. (Z = 3.31) mir-214 - microRNA_mir-214 10. (Z = 3.25) HCV_ARF_SL - Hepatitis_C_alternative_reading_frame_stem-loop Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM100.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM100_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .................................................................. MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 46.39, SCI: -0.00, ZSCORE: 0.12 Full summary: Sequences: 3 Columns: 66 Reading direction: forward Mean pairwise identity: 46.39 Shannon entropy: 0.75114 G+C content: 0.23455 Mean single sequence MFE: -0.10 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.12 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.07 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Usp9x.21606330_11 GAUCACCUCCUUUACAAAAAC---AAAAAGUAAACCAACAUCAA-CAAAACAGC~~~~~~~~~~~~ Aco2.120266024_25 ~~~~~~~~~~~~~~~~AAAUCUUAAAAAAAUAAAUAAAUACAAAGUAAACAAACAAUCUAAAUCGG Atp1b2.56418323_33 ~~~~~~~~CCUUUA-AAAAAC---AAA---CAAACAAACAAAAA-CAAACAACCCCUAGAAUGCCC // ClustID MergedIDs Count AvgDissim Members M101 4105 3 0.49 Marcksl1.148671604_7,Pklr.181222231_32,Atf3.107191620_1 Best CMs (by avg z-score): 1. (Z = 2.46) mir-500 - microRNA_mir-500 2. (Z = 2.40) CRISPR-DR15 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.00) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 4. (Z = 1.91) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.85) mir-188 - microRNA_mir-188 6. (Z = 1.80) EAV_LTH - Equine_arteritis_virus_leader_TRS_hairpin_(LTH) 7. (Z = 1.69) MIAT_exon5_2 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_2 8. (Z = 1.57) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 9. (Z = 1.57) Pseudomon-Rho - Pseudomon-Rho_RNA 10. (Z = 1.52) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM101.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM101_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((...((((((((...(((..........)))..))))))))..))... MFE = -8.95 (Covariance contribution: -9.49) RNAz stats: MPI: 33.33, SCI: 0.27, ZSCORE: 0.26 Full summary: Sequences: 3 Columns: 60 Reading direction: forward Mean pairwise identity: 33.33 Shannon entropy: 0.95833 G+C content: 0.47214 Mean single sequence MFE: -6.07 Consensus MFE: -1.63 Energy contribution: -0.87 Covariance contribution: -0.76 Combinations/Pair: 2.00 Mean z-score: 0.26 Structure conservation index: 0.27 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.84 SVM RNA-class probability: 0.004037 Prediction: OTHER Multiple alignment from mlocarna: Marcksl1.148671604_7 ~~~~~~~UCCUGCCUCUCUCCUUCCCAAGCCCCAUC-CCCGCU--GAAGGCAACUGCUGG Pklr.181222231_32 CCUGCUGCCCUCCUCUUUUCACUACCUCAAUACAGCAAGUUUGAGUAUUG~~~~~~~~~~ Atf3.107191620_1 ~~CUGAAUCCUCC---UUUUCCACCCCAAACCCUGA-AGC-CA--UUGGAAAACUGGCU~ // ClustID MergedIDs Count AvgDissim Members M106 6289 4 0.64 Canx.35850944_54,Vegfa.10534185_35,Canx.35850944_36,Morf4l1.91235629_4 Best CMs (by avg z-score): 1. (Z = 3.34) mir-48 - microRNA_mir-48 2. (Z = 3.31) Arthropod_7SK - Arthropod_7SK_RNA 3. (Z = 3.19) snoU97 - Small_nucleolar_RNA_U97 4. (Z = 3.12) mir-198 - microRNA_mir-198 5. (Z = 3.04) SNORA8 - Small_nucleolar_RNA_SNORA8 6. (Z = 3.01) bxd_6 - Bithoraxoid_conserved_region_6 7. (Z = 2.97) ctRNA_pT181 - ctRNA 8. (Z = 2.93) GcvB - GcvB_RNA 9. (Z = 2.90) rseX - rseX_Hfq_binding_RNA 10. (Z = 2.88) VrrA - Vibrio_regulatory_RNA_of_OmpA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM106.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM106_global.out/ --free-endgaps --indel=-100 --threads=4 ..((((((((((((..................))..))))))))))..................... MFE = -14.41 (Covariance contribution: -9.44) RNAz stats: MPI: 33.70, SCI: 0.61, ZSCORE: -1.15 Full summary: Sequences: 4 Columns: 67 Reading direction: forward Mean pairwise identity: 33.70 Shannon entropy: 1.00307 G+C content: 0.24507 Mean single sequence MFE: -7.39 Consensus MFE: -4.50 Energy contribution: -2.43 Covariance contribution: -2.06 Combinations/Pair: 2.38 Mean z-score: -1.15 Structure conservation index: 0.61 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.48 SVM RNA-class probability: 0.998760 Prediction: RNA Multiple alignment from mlocarna: Vegfa.10534185_35 ~~UAAAGAGUAGGGU-------------UUUUUUCAGUAUUCUUGGUUAAU--AUUUAAUUUCAACU Canx.35850944_36 ~ACAAUAAAGCAGUCCUGUUCAAUUUUAUUUUAUUUUAUUUUAUUGUGGCU~~~~~~~~~~~~~~~~ Canx.35850944_54 UGUACAAUGACAGGU-------------UUAUUU-AUGUCAUUGGUGGUGUUCAUUGCCUUUCU~~~ Morf4l1.91235629_4 ~AAAUAAAAGGAGUU-------------AACUGC--UCCUUUUUUCUUUCUUUUUUUCAUUUCAAA~ // ClustID MergedIDs Count AvgDissim Members M107 6281 4 0.48 Ccni.16459077_10,Apba1.227308605_16,Opcml.28508230_12,Marcksl1.148671604_11 Best CMs (by avg z-score): 1. (Z = 2.61) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.29) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.16) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 4. (Z = 2.12) suhB - suhB 5. (Z = 2.05) UPSK - UPSK_RNA 6. (Z = 1.95) K10_TLS - K10_transport/localisation_element_(TLS) 7. (Z = 1.90) U1_yeast - Yeast_U1_spliceosomal_RNA 8. (Z = 1.85) snoU97 - Small_nucleolar_RNA_U97 9. (Z = 1.83) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.75) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM107.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM107_global.out/ --free-endgaps --indel=-100 --threads=4 .............(((((.....(((..............))).......))))).......... MFE = -1.43 (Covariance contribution: -3.83) RNAz stats: MPI: 35.42, SCI: -0.00, ZSCORE: 2.39 Full summary: Sequences: 4 Columns: 65 Reading direction: forward Mean pairwise identity: 35.42 Shannon entropy: 1.09853 G+C content: 0.33299 Mean single sequence MFE: -2.08 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 2.39 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.45 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Ccni.16459077_10 ~~~~~~~~~~~~~GUUGACCUCUUC--CUCUUGCCUUUUCUUGCCUCGGUUGAAUACUUCAUAAG Apba1.227308605_16 AAAUCCCUUCCCUAGUUUCUUUUAGU--UGCAAUGUGUGUGCUAAUU--CAGGC~~~~~~~~~~~ Opcml.28508230_12 ~~~~~~~~~~~~GAGUUGCAUCUACAUUUCCUGUUUUCUUUGUCCU---UUAAGUUUUCAAUAAG Marcksl1.148671604_11 ~~~~~~~~~~~~UCCAGCCUUUCCCU--UGUUGAAUUCUUAGUCUCUUGUGCUGUGCCCUGUGG~ // ClustID MergedIDs Count AvgDissim Members M104 1901 3 0.43 Shank3.127875955_13,Basp1.76877616_1,Vgf.20905861_1 Best CMs (by avg z-score): 1. (Z = 2.03) snoZ178 - Small_nucleolar_RNA_Z178 2. (Z = 1.98) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 3. (Z = 1.94) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.43) suhB - suhB 5. (Z = 1.34) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.28) 6C - 6C_RNA 7. (Z = 1.24) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.23) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.15) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.11) Pseudomon-Rho - Pseudomon-Rho_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM104.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM104_global.out/ --free-endgaps --indel=-100 --threads=4 .................(((.............)))............................. MFE = -1.68 (Covariance contribution: -2.92) RNAz stats: MPI: 40.51, SCI: -0.00, ZSCORE: 1.02 Full summary: Sequences: 3 Columns: 65 Reading direction: forward Mean pairwise identity: 40.51 Shannon entropy: 0.84359 G+C content: 0.49182 Mean single sequence MFE: -2.93 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.02 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.13 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Shank3.127875955_13 UGUCCGUAACAGUUCCCGCCCUCUUC-CCCUCAAGUCCUCUCGCUGGUCCC~~~~~~~~~~~~~~ Basp1.76877616_1 ~~~~~~~AACGA--CCUGUCUCACGCUCUCUCUGUCUCUCACUCUGUCCUCUCUCUGUC~~~~~~ Vgf.20905861_1 ~~~~~~~~~~~~~~CGCCACGCCCCCCCCCUCCGUGUCGCUC-CUCCUCCCUCUCGGUGUUUGCA // ClustID MergedIDs Count AvgDissim Members M105 5238 4 0.60 Vegfa.10534185_35,Gabarapl2.41889904_17,Pou4f2.31390818_15,Morf4l1.91235629_14 Best CMs (by avg z-score): 1. (Z = 3.00) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop 2. (Z = 2.95) psbNH - psbNH_RNA 3. (Z = 2.79) TB3Cs2H1 - Trypanosomatid_snoRNA_TB3Cs2H1 4. (Z = 2.66) mir-340 - microRNA_mir-340 5. (Z = 2.58) Chlorobi-RRM - Chlorobi-RRM_RNA 6. (Z = 2.57) LhrA - Listeria_Hfq_binding_LhrA 7. (Z = 2.52) rli36 - Listeria_sRNA_rli36 8. (Z = 2.52) U1A_PIE - U1A_polyadenylation_inhibition_element_(PIE) 9. (Z = 2.52) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.48) snoR110 - Small_nucleolar_RNA_snoR110 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM105.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM105_global.out/ --free-endgaps --indel=-100 --threads=4 .....((((((.(((.........))).))))))....(((((((...)))))))........... MFE = -14.06 (Covariance contribution: -10.91) RNAz stats: MPI: 39.64, SCI: 0.79, ZSCORE: 0.76 Full summary: Sequences: 4 Columns: 66 Reading direction: forward Mean pairwise identity: 39.64 Shannon entropy: 1.01842 G+C content: 0.24266 Mean single sequence MFE: -5.42 Consensus MFE: -4.28 Energy contribution: -0.65 Covariance contribution: -3.63 Combinations/Pair: 2.50 Mean z-score: 0.76 Structure conservation index: 0.79 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.76 SVM RNA-class probability: 0.809318 Prediction: RNA Multiple alignment from mlocarna: Vegfa.10534185_35 ~~UAAAGAGUAG-GG---UUUUUUUCAGUAUUC----UUGGUUAAUAUUUAAUUUCAACU~~~~~~ Gabarapl2.41889904_17 ~~AUAAAAAGGGUUG------------GUUUUUUUCAGUGGUUA--AUGUAGUCAUAGGUUCAGAU Pou4f2.31390818_15 AAAAAAAGAUGGCAGA----UUUUCUG-CAUUU-ACACUGUAUAUUAUAUAUAUAU~~~~~~~~~~ Morf4l1.91235629_14 ~~~~AAAGAAUGGUGGCUUGUUUUCAUGGUUUUUGUAUUUGUGUCUAAUGCACG~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M164 328 4 0.45 Atrn.118696808_22,Opcml.28508230_8,Atp1b2.56418323_14,Shank1.94839593_26 Best CMs (by avg z-score): 1. (Z = 2.46) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.27) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.18) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.16) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.11) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.06) H19_3 - H19_conserved_region_3 7. (Z = 1.99) tp2 - tp2 8. (Z = 1.81) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 9. (Z = 1.76) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 10. (Z = 1.72) CC0196 - Cauldobacter_sRNA_CC0196 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM164.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM164_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .................................................................. MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 46.27, SCI: -0.00, ZSCORE: 0.23 Full summary: Sequences: 4 Columns: 66 Reading direction: forward Mean pairwise identity: 46.27 Shannon entropy: 0.89821 G+C content: 0.36692 Mean single sequence MFE: -0.65 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.23 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.51 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Atrn.118696808_22 ~~~~~~~CUUCUCUUUUUUCU-----CACUCUGUCUUACA----CACAUACACACGUGCACACACA Opcml.28508230_8 ~~~~UGGCCUUCCUUUUCUCUACUUCUCUUCCUACCACCAUUAACACACAAACA~~~~~~~~~~~~ Atp1b2.56418323_14 CUAGCCGCUUUUCUUUUAUCUCUCCACACUUCUGUCACCA-UAGCCAGUAU~~~~~~~~~~~~~~~ Shank1.94839593_26 ~CCCUGCCUUCUCUAUUUUCUCU-GACACUUAGCACACCC----CUCCCACACUCG~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M108 5544 4 0.58 Cyfip2.31321000_32,Atp2b2.149655651_40,Gabarapl2.41889904_19,Ccni.16459077_26 Best CMs (by avg z-score): 1. (Z = 2.81) suhB - suhB 2. (Z = 2.74) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.61) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 4. (Z = 2.58) mir-248 - microRNA_mir-248 5. (Z = 2.54) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 6. (Z = 2.45) RsaD - RNA_Staph._aureus_D 7. (Z = 2.43) IRES_mnt - Mnt_IRES 8. (Z = 2.42) snoU97 - Small_nucleolar_RNA_U97 9. (Z = 2.40) Afu_264 - A._fumigatus_snoRNA_Afu_264 10. (Z = 2.25) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM108.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM108_global.out/ --free-endgaps --indel=-100 --threads=4 .........................((((((........))))))........................ MFE = -5.14 (Covariance contribution: -3.84) RNAz stats: MPI: 34.62, SCI: 0.15, ZSCORE: 0.82 Full summary: Sequences: 4 Columns: 69 Reading direction: forward Mean pairwise identity: 34.62 Shannon entropy: 1.11921 G+C content: 0.25774 Mean single sequence MFE: -3.94 Consensus MFE: -0.60 Energy contribution: -0.48 Covariance contribution: -0.12 Combinations/Pair: 2.33 Mean z-score: 0.82 Structure conservation index: 0.15 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.12 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Atp2b2.149655651_40 ~~~~~~~~~~~~~~~UUUUCUUUUUGAAGAAUAGCCU--UUUUUCUCUGCACUAUUUAG--AUCCGAAU Ccni.16459077_26 ~~~~~~~~~~~~~~~~~UUUUCUUUAUAAGGAAUUUUUCCCUUGUUUUUCUCUGAUUGGCUUCUGGA~~ Cyfip2.31321000_32 AUGUUGGCUACUAAAAGAUU--CUUGGAAC-----GUUUUAUUCUUUUGCUCUCAAC~~~~~~~~~~~~ Gabarapl2.41889904_19 ~~~~UUAUACUGCAAAGUCUCGCUUCUACCAC-UUUUUCUGAUCUCUGCUGCUUA~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M109 2 3 0.48 Stmn2.95284903_6,Gabarapl2.41889904_32,Arc.112771937_24 Best CMs (by avg z-score): 1. (Z = 5.49) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 4.30) mir-87 - microRNA_mir-87 3. (Z = 4.07) rli36 - Listeria_sRNA_rli36 4. (Z = 3.98) Qrr - Qrr_RNA 5. (Z = 3.93) rli34 - Listeria_sRNA_rli34 6. (Z = 3.85) snR85 - Small_nucleolar_RNA_snR85 7. (Z = 3.82) SNORA20 - Small_nucleolar_RNA_SNORA20 8. (Z = 3.71) DdR35 - D._discoideum_sRNA_DdR35 9. (Z = 3.65) tp2 - tp2 10. (Z = 3.60) S_pombe_snR90 - small_nucleolar_RNA_snR90 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM109.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM109_global.out/ --free-endgaps --indel=-100 --threads=4 ......(((.(((((....((((.((.....)).))))..))))).)))............ MFE = -8.92 (Covariance contribution: -13.25) RNAz stats: MPI: 39.33, SCI: -0.00, ZSCORE: 0.3 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 39.33 Shannon entropy: 0.85374 G+C content: 0.16041 Mean single sequence MFE: -3.17 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.30 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.87 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Stmn2.95284903_6 ~~UGUAAAUAUUUAC--AUUUUUGUU-----AAAAAA--UACAAGUAUUGCAUUAUGCAAG Gabarapl2.41889904_32 ~~~~~~AUAUACAUAAAUCUUUCUUUAAAAAAAUAAAACGUAUGUUUAUACACUGG~~~~~ Arc.112771937_24 UAUAUAUACAUAUAUAUGAUUUUGUU-----AAUAAAACUAUGAAAUUUACCUUU~~~~~~ // ClustID MergedIDs Count AvgDissim Members M191 1574 3 0.44 Slc7a8.32800927_19,Prkch.96280653_6,Gng7.10269272_45 Best CMs (by avg z-score): 1. (Z = 2.76) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 2. (Z = 2.42) MIR2907 - microRNA_MIR2907 3. (Z = 2.19) mir-500 - microRNA_mir-500 4. (Z = 2.09) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 5. (Z = 1.98) rydB - rydB_RNA 6. (Z = 1.84) CRISPR-DR30 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.71) 6C - 6C_RNA 8. (Z = 1.65) L20_leader - Ribosomal_protein_L20_leader 9. (Z = 1.61) Plasmid_R1162 - R1162-like_plasmid_antisense_RNA 10. (Z = 1.54) F6 - F6_TB_sRNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM191.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM191_global.out/ --free-endgaps --indel=-100 --threads=4 .......(((((.......)))))((((..(((((.......))))).))))...... MFE = -29.55 (Covariance contribution: -17.38) RNAz stats: MPI: 41.04, SCI: 0.45, ZSCORE: 1.49 Full summary: Sequences: 3 Columns: 58 Reading direction: forward Mean pairwise identity: 41.04 Shannon entropy: 0.85756 G+C content: 0.55964 Mean single sequence MFE: -12.23 Consensus MFE: -5.52 Energy contribution: -5.53 Covariance contribution: 0.01 Combinations/Pair: 1.77 Mean z-score: 1.49 Structure conservation index: 0.45 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.32 SVM RNA-class probability: 0.000008 Prediction: OTHER Multiple alignment from mlocarna: Prkch.96280653_6 AGACGUGCACCGCCCACCCCGGAGUCUCCAUGGCUUUCA---GGCUUGGAGUA~~~~~ Slc7a8.32800927_19 ~~~~~~GGAGGA-CUGCCCCCCUCCCCCCCAGCUC-UCAGCCAGGCUUGUGGAAUAUA Gng7.10269272_45 ~~~~~AAGGUGG-CAGCCCCCCCCCCCCCCAGUCCAUUUGAUGGAAUCAGGGAAAG~~ // ClustID MergedIDs Count AvgDissim Members M190 683 5 0.58 Map1b.30415235_48,Shank3.127875955_49,Sdcbp.19848126_0,Syn2.151412465_19,Vdac2.2515297_5 Best CMs (by avg z-score): 1. (Z = 1.96) InvR - Invasion_gene-associated_RNA 2. (Z = 1.93) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 3. (Z = 1.55) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 4. (Z = 1.53) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.52) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.51) MicF - MicF_RNA 7. (Z = 1.47) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.42) 23S-methyl - 23S_methyl_RNA_motif 9. (Z = 1.42) IRES_IGF2 - Insulin-like_growth_factor_II_IRES 10. (Z = 1.36) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM190.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM190_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ......................(((.....)))..................................... MFE = -0.28 (Covariance contribution: -1.74) RNAz stats: MPI: 33.57, SCI: -0.00, ZSCORE: 1.48 Full summary: Sequences: 5 Columns: 70 Reading direction: forward Mean pairwise identity: 33.57 Shannon entropy: 1.23771 G+C content: 0.35009 Mean single sequence MFE: -5.59 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.48 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.03 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Map1b.30415235_48 ~~~~GCUACU---GUUCAGGGUUUCACAGUGCUAUUCCCUCCUCCUUUCAAGAUUUU~~~~~~~~~~~~~ Shank3.127875955_49 UUUGGGUUUUUAACUUUA--CAGGGUCAGUUCCGCUUCAUCCCCCUUUUGUA~~~~~~~~~~~~~~~~~~ Sdcbp.19848126_0 ACCUUGUACAGUGCAUCACCGCCGAACGCUUCCAGU-CUUCCUCUUCGGCA~~~~~~~~~~~~~~~~~~~ Syn2.151412465_19 ~~~~~~~~~~~~~~~~~~UGCCGCUAUAACAGCAGUCCACCAACCUUUGUG-UUCCUC-ACCUUAUGAAU Vdac2.2515297_5 ~~~~~~~~~~~~~~GUUAUCUCGUUAU-----CAGUGCUGCCGUCGUGCGGCCUCCUCUACAUUAUUUA~ // ClustID MergedIDs Count AvgDissim Members M165 1296 3 0.47 Fmr1.154791521_15,Sdcbp.19848126_24,Usp9x.21606330_98 Best CMs (by avg z-score): 1. (Z = 3.67) veev_FSE - venezuelan_equine_encephalitis_virus_ribosomal_frameshift_element 2. (Z = 2.88) mir-154 - microRNA_mir-154 3. (Z = 2.71) P20 - Pseudomonas_sRNA_P20 4. (Z = 2.69) snR32 - Small_nucleolar_RNA_snR32 5. (Z = 2.64) isrO - isrO_Hfq_binding_RNA 6. (Z = 2.60) CRISPR-DR38 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.54) mir-248 - microRNA_mir-248 8. (Z = 2.51) InvR - Invasion_gene-associated_RNA 9. (Z = 2.50) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.46) mir-1912 - microRNA_mir-1912 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM165.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM165_global.out/ --free-endgaps --indel=-100 --threads=4 ........(((((.....(((..((((.........))).)...)))...)))))...... MFE = -13.56 (Covariance contribution: -14.06) RNAz stats: MPI: 34.64, SCI: 0.42, ZSCORE: 0.78 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 34.64 Shannon entropy: 0.93169 G+C content: 0.28669 Mean single sequence MFE: -7.35 Consensus MFE: -3.09 Energy contribution: -0.55 Covariance contribution: -2.54 Combinations/Pair: 2.25 Mean z-score: 0.78 Structure conservation index: 0.42 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.05 SVM RNA-class probability: 0.018604 Prediction: OTHER Multiple alignment from mlocarna: Fmr1.154791521_15 ~~~~~~~UAUGAUCUGUGCCUUUUUUAU----AUCUUGGCAGGUAGGAAUAUUAUAUUUGG Sdcbp.19848126_24 ~~~~~AUUUUGGAGUCUCUUUUUCACUCGUAGAUUAAGUGG-GUAAUA--UCUAAUUU~~~ Usp9x.21606330_98 AAUUUGGUGGC--UAUAUCC--UGCCUU----AUUUAGGAUUUUAGGAAAUUGCCUUU~~~ // ClustID MergedIDs Count AvgDissim Members M119 1590 5 0.59 Shank3.127875955_7,Shank3.127875955_40,Nsf.92974385_2,Vgf.20905861_6,Dnajc5.170685641_3 Best CMs (by avg z-score): 1. (Z = 2.24) Yfr1 - Cyanobacterial_functional_RNA_1 2. (Z = 2.01) TB10Cs2H1 - Trypanosomatid_snoRNA_TB10Cs2H1 3. (Z = 1.75) sbrA - Listeria_sRNA_sbrA 4. (Z = 1.70) mir-3 - microRNA_mir-3 5. (Z = 1.67) g2 - G2 6. (Z = 1.47) snoU82P - Small_nucleolar_RNA_U82P 7. (Z = 1.43) TB10Cs5H2 - Trypanosomatid_snoRNA_TB10Cs5H2 8. (Z = 1.37) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 9. (Z = 1.36) snoZ178 - Small_nucleolar_RNA_Z178 10. (Z = 1.34) 6C - 6C_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM119.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM119_global.out/ --free-endgaps --indel=-100 --threads=4 .........(((((((...........)))))))............................. MFE = -7.73 (Covariance contribution: -4.65) RNAz stats: MPI: 37.97, SCI: 0.18, ZSCORE: 1.58 Full summary: Sequences: 5 Columns: 63 Reading direction: forward Mean pairwise identity: 37.97 Shannon entropy: 1.12723 G+C content: 0.49275 Mean single sequence MFE: -9.48 Consensus MFE: -1.66 Energy contribution: -2.46 Covariance contribution: 0.80 Combinations/Pair: 2.14 Mean z-score: 1.58 Structure conservation index: 0.18 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.19 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Shank3.127875955_7 ~~~~~~~~~AGGGUGCUCUGGCCUGA-CCACCUCCUCCACAGCUCCUGGUGGCCAUUCUU~~~ Vgf.20905861_6 GUGUGGUUUGUGCGAGU-----CCC--CUUACACCCCCACUUCCUCCAGGGGCCUCG~~~~~~ Nsf.92974385_2 ~~~~~~~CUGGACUAAG-----UGAAGUGUCCACCUCCCUCUCCACAC-UCACUCUGCAUGAC Shank3.127875955_40 ~~~~~~~~~~~UGGAGUCUGGACUAAGCUCCAUCCACGUCACUCACAAGUUUCUGUUUCUA~~ Dnajc5.170685641_3 ~~~~~CGCUGUGGCUGG-----UCA--GGGCCACUCCCACCUCCUCUUAAGUCCACCCAUCU~ // ClustID MergedIDs Count AvgDissim Members M118 6800 3 0.37 Nrgn.38790596_17,Stxbp1.11762105_32,Slc7a8.32800927_21 Best CMs (by avg z-score): 1. (Z = 1.73) IRES_mnt - Mnt_IRES 2. (Z = 1.64) H19_3 - H19_conserved_region_3 3. (Z = 1.62) suhB - suhB 4. (Z = 1.52) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 5. (Z = 1.52) snoU82P - Small_nucleolar_RNA_U82P 6. (Z = 1.50) 6C - 6C_RNA 7. (Z = 1.21) Afu_254 - A._fumigatus_sRNA_Afu_254 8. (Z = 1.18) LhrC - Listeria_Hfq_binding_LhrC 9. (Z = 1.10) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 10. (Z = 1.07) snoZ178 - Small_nucleolar_RNA_Z178 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM118.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM118_global.out/ --free-endgaps --indel=-100 --threads=4 ...((.......))....((((...(...............)...)))).... MFE = -6.72 (Covariance contribution: -11.52) RNAz stats: MPI: 54.09, SCI: -0.00, ZSCORE: 1.26 Full summary: Sequences: 3 Columns: 53 Reading direction: forward Mean pairwise identity: 54.09 Shannon entropy: 0.65199 G+C content: 0.59107 Mean single sequence MFE: -2.32 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.26 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -9.24 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Nrgn.38790596_17 ~~AAGUGAAGUCCUAUCCCACACCUGCCUGUCACCCCUUUUCUCUUGAGAAC~ Stxbp1.11762105_32 AAAUGUC---CCCAGCCCAGCCCCUGCCCCUCCCUCCCUCCCGCAGACUUGUA Slc7a8.32800927_21 AGAAGCCAAGCCCUGCCCCACCCCUGCCCCUGCCUCCUGUCCUCUUGUGG~~~ // ClustID MergedIDs Count AvgDissim Members M115 1358 4 0.61 Marcksl1.148671604_16,Arhgef7.82521224_48,Pabpn1.32998239_7,Becn1.90317957_5 Best CMs (by avg z-score): 1. (Z = 1.95) snoZ178 - Small_nucleolar_RNA_Z178 2. (Z = 1.84) SNORD116 - Small_nucleolar_RNA_SNORD116 3. (Z = 1.71) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.60) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.52) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.50) InvR - Invasion_gene-associated_RNA 7. (Z = 1.49) suhB - suhB 8. (Z = 1.47) snoU83B - Small_nucleolar_RNA_U83B 9. (Z = 1.38) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 10. (Z = 1.37) MIR403 - microRNA_MIR403 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM115.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM115_global.out/ --free-endgaps --indel=-100 --threads=4 ..(((((..............((((((((....))))))))......))))).. MFE = -12.48 (Covariance contribution: -8.80) RNAz stats: MPI: 48.61, SCI: -0.00, ZSCORE: -0.17 Full summary: Sequences: 4 Columns: 54 Reading direction: forward Mean pairwise identity: 48.61 Shannon entropy: 0.88031 G+C content: 0.52868 Mean single sequence MFE: -8.38 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.17 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.80 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Marcksl1.148671604_16 ~~GAGGGAGGU-CUGUAAUGUGAAA-CAACUCCUUGUUGUCUUUCCCCCCUCCC Arhgef7.82521224_48 CGGAGCAGUCCUUUUUAAAGCUGGCACACACCCC-GUUCUCCU--CCUGCAUC~ Pabpn1.32998239_7 ~~~~GGACACAUCUCAACUGUGCAAGCUGCUCCCUGUUUCCCUGCUCCCCUUCA Becn1.90317957_5 ~~~AGAGCCCUGCCGUAGUUUGGCU-CAACCCCAUGCUGUCCUUUCCCUCUUCC // ClustID MergedIDs Count AvgDissim Members M114 2814 4 0.54 Apba1.227308605_21,Rnf111.74909360_4,Atp5j.24316748_0,Itpr1.144028781_2 Best CMs (by avg z-score): 1. (Z = 2.67) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.63) mir-280 - microRNA_mir-280 3. (Z = 2.37) RMST_10 - Rhabdomyosarcoma_2_associated_transcript_conserved_region_10 4. (Z = 2.27) rli36 - Listeria_sRNA_rli36 5. (Z = 2.22) PVX_3 - Potato_virus_X_cis-acting_regulatory_element 6. (Z = 2.19) snopsi28S-3316 - Small_nucleolar_RNA_psi28S-3316 7. (Z = 2.15) CRISPR-DR41 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.12) P27 - Pseudomonas_sRNA_P27 9. (Z = 2.10) S_pombe_snR33 - small_nucleolar_RNA_snR33 10. (Z = 2.10) snR85 - Small_nucleolar_RNA_snR85 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM114.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM114_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ................(((((.(((((...........)))))..))).)).............. MFE = -7.33 (Covariance contribution: -8.95) RNAz stats: MPI: 30.05, SCI: 0.32, ZSCORE: 1.55 Full summary: Sequences: 4 Columns: 65 Reading direction: forward Mean pairwise identity: 30.05 Shannon entropy: 1.21885 G+C content: 0.30360 Mean single sequence MFE: -5.85 Consensus MFE: -1.86 Energy contribution: -0.05 Covariance contribution: -1.81 Combinations/Pair: 2.60 Mean z-score: 1.55 Structure conservation index: 0.32 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.51 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Apba1.227308605_21 ~~~~~ACUGUCCUAACGUACU-UGCACAGGCG-CUUAUGUGUAACACACACACACAC~~~~~~~~ Rnf111.74909360_4 CGCUAGACCUACAACU-UAUG-UACACAGUUGAUUUCGAUGUAUUUAUAAAA~~~~~~~~~~~~~ Atp5j.24316748_0 ~~~~~~~~~~~~~~~GGAACAUACAAACCAUGUGGUAAUUUGUCAUGACUUAGUUGUACAAUUAA Itpr1.144028781_2 UGAUCUGCCCUCUAAGGUUAC-AUGU---GCG-CUUAGUACAUUUGUAAAUACUC~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M117 467 5 0.53 Dpysl2.46346413_64,Appbp2.73460120_6,Atp2a2.35312505_4,Stxbp1.11762105_40,Ntrk2.11676658_46 Best CMs (by avg z-score): 1. (Z = 3.49) mir-335 - microRNA_mir-335 2. (Z = 3.45) ctRNA_p42d - ctRNA 3. (Z = 3.14) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.11) L10_leader - Ribosomal_protein_L10_leader 5. (Z = 3.11) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.99) rli56 - Listeria_sRNA_rli56 7. (Z = 2.96) mir-70 - microRNA_mir-70 8. (Z = 2.90) mir-248 - microRNA_mir-248 9. (Z = 2.89) rimP - Enterobacteria_rnk_leader 10. (Z = 2.79) snoU97 - Small_nucleolar_RNA_U97 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM117.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM117_global.out/ --free-endgaps --indel=-100 --threads=4 .............((((((((((..........))))))))))................. MFE = -10.18 (Covariance contribution: -5.62) RNAz stats: MPI: 41.31, SCI: 0.60, ZSCORE: 0.07 Full summary: Sequences: 5 Columns: 60 Reading direction: forward Mean pairwise identity: 41.31 Shannon entropy: 1.03144 G+C content: 0.25549 Mean single sequence MFE: -5.36 Consensus MFE: -3.20 Energy contribution: -2.76 Covariance contribution: -0.44 Combinations/Pair: 2.30 Mean z-score: 0.07 Structure conservation index: 0.60 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.24 SVM RNA-class probability: 0.915458 Prediction: RNA Multiple alignment from mlocarna: Dpysl2.46346413_64 ~~~CAUGUGUGUAGCCAGAAAGGUACU------UCUUUCUUUUUUCUUUUUCAAAUUUU~ Appbp2.73460120_6 ACCCUAGUAGAACAACAGGAAACGUUU------UUUUUUUUUCUUUUUAAAAAAUA~~~~ Atp2a2.35312505_4 ~~~UUUCUGACUCCAGUGGGACAAGAU------UUUCCUUUUU-UUUAUACACAUAAUUA Stxbp1.11762105_40 ~CCUUGUUUGUCGAACAUGUGGGGUUU------CCUUUAUGUUAUUUAUAUAAAUAA~~~ Ntrk2.11676658_46 ~~~~~~~UUAACAGUGAGAAGAAAUGUAGGGUAAUCUUUUUAUUUUGAGAUAUAAAG~~~ // ClustID MergedIDs Count AvgDissim Members M116 5020 3 0.44 Atp1b2.56418323_43,Shank3.127875955_42,Gabarapl2.41889904_22 Best CMs (by avg z-score): 1. (Z = 3.87) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.74) Plasmid_RNAIII - Plasmid_RNAIII 3. (Z = 3.64) snR85 - Small_nucleolar_RNA_snR85 4. (Z = 2.98) SBWMV2_UPD-PKl - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 5. (Z = 2.87) SraB - SraB_RNA 6. (Z = 2.86) RsaH - RNA_Staph._aureus_H 7. (Z = 2.82) sbrA - Listeria_sRNA_sbrA 8. (Z = 2.81) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.70) rli36 - Listeria_sRNA_rli36 10. (Z = 2.66) SNORA15 - Small_nucleolar_RNA_SNORA15 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM116.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM116_global.out/ --free-endgaps --indel=-100 --threads=4 .(((((((....)))))))..........((((((((........)))))).)).. MFE = -26.38 (Covariance contribution: -18.58) RNAz stats: MPI: 42.07, SCI: 0.80, ZSCORE: -1.12 Full summary: Sequences: 3 Columns: 56 Reading direction: forward Mean pairwise identity: 42.07 Shannon entropy: 0.81226 G+C content: 0.33662 Mean single sequence MFE: -8.47 Consensus MFE: -6.73 Energy contribution: -4.30 Covariance contribution: -2.43 Combinations/Pair: 2.25 Mean z-score: -1.12 Structure conservation index: 0.80 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.14 SVM RNA-class probability: 0.997614 Prediction: RNA Multiple alignment from mlocarna: Atp1b2.56418323_43 ~AUAUAUAUAAAUGUAUAUCAAACACAGACCGCCGCC----UCCCGGCCCCAGGC~ Shank3.127875955_42 AAUAUAUAUAUAUAUAUAU--AAAAAAGACAGAAAAC----AGGUGUUUUCAUGGC Gabarapl2.41889904_22 ~~~AUAUAUAUAUAUUUUAGAAGUUAUUUUGCCUGCAUGUGUGUCUGUGGG-CG~~ // ClustID MergedIDs Count AvgDissim Members M111 988 3 0.44 Glra1.40922867_0,Rab5c.89652340_18,Glra1.40922867_6 Best CMs (by avg z-score): 1. (Z = 3.13) Prion_pknot - Prion_pseudoknot 2. (Z = 2.01) GRIK4_3p_UTR - GRIK4_3_prime_UTR_element 3. (Z = 1.83) SNORD23 - Small_nucleolar_RNA_SNORD23 4. (Z = 1.72) sR24 - Small_nucleolar_RNA_sR24 5. (Z = 1.60) sR53 - Small_nucleolar_RNA_sR53 6. (Z = 1.58) sR40 - Small_nucleolar_RNA_sR40 7. (Z = 1.58) whalefall-1 - Whalefall-1_RNA 8. (Z = 1.57) sR1 - Small_nucleolar_RNA_sR1 9. (Z = 1.53) IRES_FGF2 - FGF-2_internal_ribosome_entry_site_(IRES) 10. (Z = 1.51) sR51 - Small_nucleolar_RNA_sR51 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM111.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM111_global.out/ --free-endgaps --indel=-100 --threads=4 ............((((((...............))))))...................... MFE = -6.94 (Covariance contribution: -4.27) RNAz stats: MPI: 43.17, SCI: 0.32, ZSCORE: -0.06 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 43.17 Shannon entropy: 0.83724 G+C content: 0.55660 Mean single sequence MFE: -5.13 Consensus MFE: -1.64 Energy contribution: -1.43 Covariance contribution: -0.21 Combinations/Pair: 2.00 Mean z-score: -0.06 Structure conservation index: 0.32 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.92 SVM RNA-class probability: 0.023710 Prediction: OTHER Multiple alignment from mlocarna: Glra1.40922867_0 ~~~~~~~~~~~AGGCUCUGGGACGGGGUGGGGGGGAGCUGGGAGAGGGUGGUGGGAUGAGC Rab5c.89652340_18 CGAUGAUGAGUAUUCGG-GGGUGGG----UGGGUAAGGGGGGGGAGUGGGAGGGA~~~~~~ Glra1.40922867_6 ~~~AACUGGGGACCAUGAGGGGUGGGACAGGGGUCAGGGAGGGGAUUGGGAAA~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M110 4460 4 0.39 Sept9.107478216_2,Map1b.30415235_91,Rab5c.89652340_6,Adcy5.67290968_17 Best CMs (by avg z-score): 1. (Z = 2.73) H19_3 - H19_conserved_region_3 2. (Z = 2.69) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.67) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 4. (Z = 2.63) MicF - MicF_RNA 5. (Z = 2.52) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.47) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.45) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.43) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.31) RsaD - RNA_Staph._aureus_D 10. (Z = 2.26) IRES_mnt - Mnt_IRES Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM110.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM110_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .............(((((....)))))..................................... MFE = -0.32 (Covariance contribution: -2.09) RNAz stats: MPI: 37.50, SCI: -0.00, ZSCORE: 0.84 Full summary: Sequences: 4 Columns: 64 Reading direction: forward Mean pairwise identity: 37.50 Shannon entropy: 1.04171 G+C content: 0.29820 Mean single sequence MFE: -0.35 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.84 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.94 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Adcy5.67290968_17 ~~~~UUAUUAAAUAAAACAAAAGUUUUCUCUGCCCUUCCCAUCCAGACCCGGUG~~~~~~~~~~ Map1b.30415235_91 UCCUCCAUU--UCAAUUUUAAUCAAUUCUGUCCUCCUUUUUUCCAAACCCCG~~~~~~~~~~~~ Sept9.107478216_2 ~~~~~~~~~~~~~AUUUUAUAUA-AUUAUCUCCAUUUGUCACCUGCCUCCAUCUCUUUCCACAC Rab5c.89652340_6 ~~~~~~~~~ACUUUUUUAAUAUAUAUGAUCUUCUGCUCUUCCCUGU-----UCCCUUUCUACUG // ClustID MergedIDs Count AvgDissim Members M113 4273 3 0.50 Tmem30a.84827711_10,Cdh2.8048920_13,Appbp2.73460120_42 Best CMs (by avg z-score): 1. (Z = 2.60) VIS1 - Viral_integration_site_1 2. (Z = 2.48) mir-101 - mir-101_microRNA_precursor_family 3. (Z = 2.07) SNORD38 - Small_nucleolar_RNA_SNORD38 4. (Z = 1.89) mir-609 - microRNA_mir-609 5. (Z = 1.87) sR2 - Small_nucleolar_RNA_sR2 6. (Z = 1.86) Pseudomon-1 - Pseudomon-1_RNA 7. (Z = 1.83) HIV-1_SL4 - HIV-1_stem-loop_4_packaging_signal 8. (Z = 1.79) SNORA66 - Small_nucleolar_RNA_SNORA66 9. (Z = 1.78) sR33 - Small_nucleolar_RNA_sR33 10. (Z = 1.73) sR7 - Small_nucleolar_RNA_sR7 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM113.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM113_global.out/ --free-endgaps --indel=-100 --threads=4 ......((((((....((((................)))).....))))))... MFE = -11.11 (Covariance contribution: -8.41) RNAz stats: MPI: 42.50, SCI: 0.34, ZSCORE: 0.49 Full summary: Sequences: 3 Columns: 54 Reading direction: forward Mean pairwise identity: 42.50 Shannon entropy: 0.82068 G+C content: 0.43866 Mean single sequence MFE: -5.77 Consensus MFE: -1.96 Energy contribution: -1.19 Covariance contribution: -0.77 Combinations/Pair: 2.00 Mean z-score: 0.49 Structure conservation index: 0.34 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.90 SVM RNA-class probability: 0.003638 Prediction: OTHER Multiple alignment from mlocarna: Tmem30a.84827711_10 ~~UGUGUGCCUA--CUGUGUGAUGAAAGGGAUUAUGAGAUGUAUGAGUGUAAUG Cdh2.8048920_13 ~~UUUGUUACCUUGGGGUGGGGGGUGGGGGAUGAGACCACGAGAUAGGAAAA~~ Appbp2.73460120_42 AGCAUGCUUGUU--GGGUGAGGGGAAAGAAA-GUUAUCAUGGAGAGACAGAAA~ // ClustID MergedIDs Count AvgDissim Members M112 2683 5 0.65 Syngr1.118351457_2,Shank1.94839593_22,Pou4f2.31390818_30,Ntrk2.11676658_20,Slc7a8.32800927_26 Best CMs (by avg z-score): 1. (Z = 1.53) IRES_mnt - Mnt_IRES 2. (Z = 1.40) snoZ178 - Small_nucleolar_RNA_Z178 3. (Z = 1.30) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 4. (Z = 1.27) 6C - 6C_RNA 5. (Z = 1.24) NrrF - NrrF_RNA 6. (Z = 1.19) SraG - SraG_RNA 7. (Z = 1.12) H19_2 - H19_conserved_region_2 8. (Z = 1.10) MIAT_exon5_3 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_3 9. (Z = 1.10) H19_3 - H19_conserved_region_3 10. (Z = 1.01) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM112.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM112_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ....................(((.((((........)))).))).................... MFE = -1.82 (Covariance contribution: -3.16) RNAz stats: MPI: 36.25, SCI: -0.00, ZSCORE: 0.2 Full summary: Sequences: 5 Columns: 64 Reading direction: forward Mean pairwise identity: 36.25 Shannon entropy: 1.19857 G+C content: 0.48997 Mean single sequence MFE: -6.38 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.20 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.84 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Syngr1.118351457_2 GCACCCUGCUCCCUCCCAGGUGACCCUGCCU-CGCACAUGCUCAGCCUCCA~~~~~~~~~~~~~ Shank1.94839593_22 ~CACAUUCCC---GUAGUCCCUG-GCCACCCCUGCUCUCUGCU---CUCUCUGCACAC~~~~~~ Pou4f2.31390818_30 ~~~~~~UCCCACAUUGUCCCCCGCAGCACACGUGCUCUCUCACUCACUUUACAAGC~~~~~~~~ Ntrk2.11676658_20 ~~~~~~~CCCACUUGAUUCUGACCCGAGC-CCCUCUCUCUCGUUCACUUUGUCAUGGC~~~~~~ Slc7a8.32800927_26 ~~~~~~~~~~~~~~UCCCAGCAGCUCUGCCCACUCACAGAUCUGCCUGCCGUCCUCCUCUUUCC // ClustID MergedIDs Count AvgDissim Members M99 6168 4 0.54 Dpysl2.46346413_39,Syt4.23805080_22,Gria2.172265159_17,Map1b.30415235_120 Best CMs (by avg z-score): 1. (Z = 3.78) SNORA20 - Small_nucleolar_RNA_SNORA20 2. (Z = 3.56) S_pombe_snR93 - small_nucleolar_RNA_snR93 3. (Z = 3.49) RMST_10 - Rhabdomyosarcoma_2_associated_transcript_conserved_region_10 4. (Z = 3.42) ceN102 - C._elegans_snoRNA_ceN80 5. (Z = 3.34) SNORA27 - Small_nucleolar_RNA_SNORA27 6. (Z = 3.13) RUF1 - Plasmodium_RNA_of_unkown_function_RUF1 7. (Z = 3.08) mir-320 - microRNA_mir-320 8. (Z = 3.04) S_pombe_snR3 - small_nucleolar_RNA_snR3 9. (Z = 3.04) snR36 - Small_nucleolar_RNA_snR36 10. (Z = 3.00) SNORA79 - Small_nucleolar_RNA_SNORA79 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM99.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM99_global.out/ --free-endgaps --indel=-100 --threads=4 .(((((...(....((((....))))).......)))))................... MFE = -10.89 (Covariance contribution: -10.77) RNAz stats: MPI: 37.43, SCI: 1.01, ZSCORE: 0.73 Full summary: Sequences: 4 Columns: 58 Reading direction: forward Mean pairwise identity: 37.43 Shannon entropy: 1.06440 G+C content: 0.28566 Mean single sequence MFE: -4.99 Consensus MFE: -5.05 Energy contribution: -1.86 Covariance contribution: -3.19 Combinations/Pair: 2.78 Mean z-score: 0.73 Structure conservation index: 1.01 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.56 SVM RNA-class probability: 0.742513 Prediction: RNA Multiple alignment from mlocarna: Dpysl2.46346413_39 ~~GCAACCCU----AUUUUAGGAAAUAAUAUG--UUGUGGGAAGAAAACUAUACAAAU Syt4.23805080_22 ~CUUACCUUUGUGAAGUUGUCAGACUA---UUUAGUGGGAAAAAAAAACAAACC~~~~ Map1b.30415235_120 AAUAUCCCCU----CUUCUAUUGAGGAUAUUU--GAUGUAAAGGAAAAAAAAAAAG~~ Gria2.172265159_17 UUGCUUCCGUACUGGUUGGUUAAGACAAAUACAAAAACAAAAACAAAACA~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M98 4101 3 0.51 Map1b.30415235_117,Atf3.107191620_32,Fgf13.144199535_4 Best CMs (by avg z-score): 1. (Z = 2.81) BsrC - BsrC 2. (Z = 2.41) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 3. (Z = 2.34) CRISPR-DR44 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.25) SNORD12 - Small_nucleolar_SNORD12/SNORD106 5. (Z = 2.18) snR85 - Small_nucleolar_RNA_snR85 6. (Z = 2.14) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 7. (Z = 2.09) MicF - MicF_RNA 8. (Z = 2.04) sbrA - Listeria_sRNA_sbrA 9. (Z = 2.03) RsaD - RNA_Staph._aureus_D 10. (Z = 2.00) CRISPR-DR16 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM98.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM98_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ..................................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 38.16, SCI: -0.00, ZSCORE: 1.64 Full summary: Sequences: 3 Columns: 69 Reading direction: forward Mean pairwise identity: 38.16 Shannon entropy: 0.88784 G+C content: 0.25362 Mean single sequence MFE: -0.60 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.64 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.81 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Map1b.30415235_117 UGUCUUAUAAUCCUGCAUCACUUCCAUCCUAUCCAGUCAUAUCUAAUGUA~~~~~~~~~~~~~~~~~~~ Atf3.107191620_32 ~~~~CGUUACUUAUUUAUCCCAGUAUUCCUAGCCUGUCA-ACGUAAUAAAAUAUC~~~~~~~~~~~~~~ Fgf13.144199535_4 ~~~~~~~~~~~~~~~~~~GCCAUUAUACCUUGUUA-UCAUCCGUACUAAAGCCCCAUAAUUUAGAUUAA // ClustID MergedIDs Count AvgDissim Members M91 5970 3 0.49 Itpr1.144028781_15,Shank1.94839593_25,Atp1b2.56418323_39 Best CMs (by avg z-score): 1. (Z = 2.45) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 2. (Z = 2.35) suhB - suhB 3. (Z = 2.31) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.30) RsaD - RNA_Staph._aureus_D 5. (Z = 2.05) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.04) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.02) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.93) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.78) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.73) InvR - Invasion_gene-associated_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM91.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM91_global.out/ --free-endgaps --indel=-100 --threads=4 ........................((((((.............)))))).......................... MFE = -9.49 (Covariance contribution: -6.73) RNAz stats: MPI: 28.57, SCI: 0.64, ZSCORE: 0.85 Full summary: Sequences: 3 Columns: 75 Reading direction: forward Mean pairwise identity: 28.57 Shannon entropy: 0.98488 G+C content: 0.31252 Mean single sequence MFE: -7.27 Consensus MFE: -4.65 Energy contribution: -2.32 Covariance contribution: -2.33 Combinations/Pair: 2.40 Mean z-score: 0.85 Structure conservation index: 0.64 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.01 SVM RNA-class probability: 0.491374 Prediction: OTHER Multiple alignment from mlocarna: Itpr1.144028781_15 AUUUUGUACCUUGUAAUUAUCCUAUGGUGAUGCUGUUUCUC-GUUGCUAAU~~~~~~~~~~~~~~~~~~~~~~~~ Shank1.94839593_25 ~~~~~~~~~~~~~~~~~~~~~~~~~ACCGUUACUCUCCUUCUCAUGGUGGCACUCCUGUGCCCUGCCUUCUCUAU Atp1b2.56418323_39 ~AUCUGUAUCUCUU-----CCCUUUGGGUAUCCAGCUCUUC-CUGCCCGUUCAUCUU~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M90 1246 3 0.51 Slc7a8.32800927_53,Appbp2.73460120_57,Syt4.23805080_24 Best CMs (by avg z-score): 1. (Z = 5.00) mir-458 - microRNA_mir-458 2. (Z = 4.81) K10_TLS - K10_transport/localisation_element_(TLS) 3. (Z = 4.54) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 4. (Z = 4.49) rli36 - Listeria_sRNA_rli36 5. (Z = 4.42) mir-286 - microRNA_mir-286 6. (Z = 4.41) mir-649 - microRNA_mir-649 7. (Z = 4.39) mir-3 - microRNA_mir-3 8. (Z = 4.35) mir-190 - microRNA_mir-190 9. (Z = 4.30) mir-235 - microRNA_mir-235 10. (Z = 4.28) MIR1444 - microRNA_MIR1444 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM90.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM90_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((((((.((((.......(((........)))......)))).).)))))). MFE = -22.80 (Covariance contribution: -17.57) RNAz stats: MPI: 30.41, SCI: 1.02, ZSCORE: -1.19 Full summary: Sequences: 3 Columns: 58 Reading direction: forward Mean pairwise identity: 30.41 Shannon entropy: 1.00287 G+C content: 0.20989 Mean single sequence MFE: -7.23 Consensus MFE: -7.35 Energy contribution: -1.55 Covariance contribution: -5.79 Combinations/Pair: 2.29 Mean z-score: -1.19 Structure conservation index: 1.02 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.26 SVM RNA-class probability: 0.987015 Prediction: RNA Multiple alignment from mlocarna: Slc7a8.32800927_53 UGGAGUAUUUUCUUUUC----UCGUAAUAA--AAUUUU-AAAUGGAAAUG-AAAAUGG Syt4.23805080_24 ~~~~~GAAUACAGUUGUUUUUUAUAUAAAA--AUCUAUCAGUGUACAAGU-GUAUUUU Appbp2.73460120_57 ~~~~~~UCAUGGUAAAUUGUUUCUUAAUAAAUAUUUUAAAACAAGUUUCCACAUGA~~ // ClustID MergedIDs Count AvgDissim Members M93 5974 5 0.68 Morf4l1.91235629_13,Pabpn1.32998239_20,Syn2.151412465_11,Sdcbp.19848126_1,Pou4f2.31390818_25 Best CMs (by avg z-score): 1. (Z = 3.29) mir-154 - microRNA_mir-154 2. (Z = 2.62) K10_TLS - K10_transport/localisation_element_(TLS) 3. (Z = 2.60) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.57) mir-3 - microRNA_mir-3 5. (Z = 2.42) mir-92 - mir-92_microRNA_precursor_family 6. (Z = 2.14) Pox_AX_element - Poxvirus_AX_element_late_mRNA_cis-regulatory_element 7. (Z = 2.09) mir-101 - mir-101_microRNA_precursor_family 8. (Z = 2.09) mir-279 - microRNA_mir-279 9. (Z = 2.08) mir-449 - microRNA_mir-449 10. (Z = 2.07) mir-1912 - microRNA_mir-1912 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM93.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM93_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((((((...((((((((.......))....))))...))..)))).))........ MFE = -13.83 (Covariance contribution: -11.49) RNAz stats: MPI: 29.91, SCI: 0.11, ZSCORE: 0.83 Full summary: Sequences: 5 Columns: 67 Reading direction: forward Mean pairwise identity: 29.91 Shannon entropy: 1.23647 G+C content: 0.32514 Mean single sequence MFE: -8.55 Consensus MFE: -0.94 Energy contribution: 2.42 Covariance contribution: -3.36 Combinations/Pair: 2.90 Mean z-score: 0.83 Structure conservation index: 0.11 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.14 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Morf4l1.91235629_13 ~UUGUUCCUUAGGCAUUUUAUCUUUGCU--CAAUUGU----UAAA---GAAUGGUGGCUU~~~~~~~ Pabpn1.32998239_20 UUUUUCCUUUACCUUUUUUUUUCCCUUU--UAUUUGG----AGGG---AA-UGGGA-GGAA~~~~~~ Syn2.151412465_11 ~~~~~~~~~~~CAGUGCUACCUGUGGGAAAUAUAUUC----UUACCUUAGAAGUAU-UGUUGGCUC~ Sdcbp.19848126_1 ~~~~~UCUUCCUCUUCGGCAACUUCUCUAUUUCACCGCACAUGAAGCUUUCCCGG~~~~~~~~~~~~ Pou4f2.31390818_25 ~~~~~~~GUUCUCUUCGGCCUAGUUG----UAUAUUC----UCAC-UUUGAAUGAA-GAUUGUUUCC // ClustID MergedIDs Count AvgDissim Members M92 3252 3 0.52 Ddn.137572548_14,Shank3.127875955_31,Grb2.105722014_6 Best CMs (by avg z-score): 1. (Z = 2.31) RydC - RydC_RNA 2. (Z = 2.16) mir-248 - microRNA_mir-248 3. (Z = 1.94) suhB - suhB 4. (Z = 1.80) CRISPR-DR59 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.77) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.65) Vault - Vault_RNA 7. (Z = 1.64) KCNQ1DN - KCNQ1_downstream_neighbour 8. (Z = 1.60) InvR - Invasion_gene-associated_RNA 9. (Z = 1.60) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.58) BaMV_CRE - Bamboo_mosaic_potexvirus_(BaMV)_cis-regulatory_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM92.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM92_global.out/ --free-endgaps --indel=-100 --threads=4 ...........(((((.(.((....((((.....)).))....))).)))))....... MFE = -10.46 (Covariance contribution: -12.83) RNAz stats: MPI: 32.76, SCI: 0.42, ZSCORE: 0.45 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 32.76 Shannon entropy: 0.96327 G+C content: 0.39825 Mean single sequence MFE: -4.70 Consensus MFE: -1.96 Energy contribution: 0.47 Covariance contribution: -2.43 Combinations/Pair: 2.25 Mean z-score: 0.45 Structure conservation index: 0.42 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.28 SVM RNA-class probability: 0.076112 Prediction: OTHER Multiple alignment from mlocarna: Ddn.137572548_14 ~~~~~~~UAAUGUAAAUGUAAAACGAGCGAUUUCUGCCUCCCAUUCUUUUGUCCCUA~~ Shank3.127875955_31 GUCUUCUCCAAAGAAA---GGCUGUCCUGCU-CUUGGGUCCUGCUGUUUUCUCA~~~~~ Grb2.105722014_6 ~~~~~UUUUAUUACGG---AAUCUCGCCGCUACUCGUGUUCCCUU-CCUGUGUCCUUUU // ClustID MergedIDs Count AvgDissim Members M95 2003 3 0.50 Vegfa.10534185_33,Gria2.172265159_32,Bdnf.977114_77 Best CMs (by avg z-score): 1. (Z = 4.05) bxd_7 - Bithoraxoid_conserved_region_7 2. (Z = 3.87) rli61 - Listeria_sRNA_rli61 3. (Z = 3.78) rli42 - Listeia_sRNA_rli42 4. (Z = 3.76) mir-932 - microRNA_mir-932 5. (Z = 3.67) mir-286 - microRNA_mir-286 6. (Z = 3.64) mir-230 - microRNA_mir-230 7. (Z = 3.60) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 8. (Z = 3.56) mir-92 - mir-92_microRNA_precursor_family 9. (Z = 3.53) MIR1122 - microRNA_MIR1122 10. (Z = 3.52) rli36 - Listeria_sRNA_rli36 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM95.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM95_global.out/ --free-endgaps --indel=-100 --threads=4 ...........(((((((((..((.((((............)))).)).)))))))))......... MFE = -14.67 (Covariance contribution: -12.97) RNAz stats: MPI: 36.41, SCI: 0.91, ZSCORE: 0.74 Full summary: Sequences: 3 Columns: 67 Reading direction: forward Mean pairwise identity: 36.41 Shannon entropy: 0.88074 G+C content: 0.12930 Mean single sequence MFE: -2.93 Consensus MFE: -2.68 Energy contribution: -0.13 Covariance contribution: -2.54 Combinations/Pair: 2.00 Mean z-score: 0.74 Structure conservation index: 0.91 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.51 SVM RNA-class probability: 0.725226 Prediction: RNA Multiple alignment from mlocarna: Vegfa.10534185_33 ~~~~~~~~~~AGAAAGUGUU--UU--AUAUACGGUA---CUUAUUUAAUAGCCCUUUUUAAUUAGAA Gria2.172265159_32 UAUAAUAGUAAAAUAUUUGU--UA-AUUAAAAAGCA---UUUAAUCUAUAUAGAUA~~~~~~~~~~~ Bdnf.977114_77 ~~~~~~~~CAAGAAAAAUAUUUAUUGUAUUUUAGUAUAUUUAUAUAAUUAUGUUAUUG~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M94 4260 4 0.59 Shank3.127875955_41,Canx.35850944_75,Syt4.23805080_60,Gria2.172265159_56 Best CMs (by avg z-score): 1. (Z = 4.11) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.76) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.40) mir-154 - microRNA_mir-154 4. (Z = 3.29) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 5. (Z = 3.22) RsaD - RNA_Staph._aureus_D 6. (Z = 3.13) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 7. (Z = 3.04) snR85 - Small_nucleolar_RNA_snR85 8. (Z = 3.03) U1A_PIE - U1A_polyadenylation_inhibition_element_(PIE) 9. (Z = 3.01) mir-248 - microRNA_mir-248 10. (Z = 3.00) SprD - Small_pathogenicity_island_RNA_D Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM94.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM94_global.out/ --free-endgaps --indel=-100 --threads=4 ...........(((((....)))))...(((((.((.....)))))))........... MFE = -8.68 (Covariance contribution: -9.88) RNAz stats: MPI: 39.27, SCI: -0.00, ZSCORE: 0.59 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 39.27 Shannon entropy: 1.04507 G+C content: 0.18494 Mean single sequence MFE: -2.99 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.59 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.46 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Shank3.127875955_41 ~AAGUUUCUGUUUCUAUUUCUAGCUUUUUUUAAUAAAAUAUAUAUAUAUAU~~~~~~~~ Canx.35850944_75 UUGUGUUUUACAUUGCUUCCGGAAUUUAUAUACUACAGU--GUGUAUAUACU~~~~~~~ Syt4.23805080_60 ~~~~~~~~~CCAAUUCUGCUAAAUUUCCUGCACUGUAUUAAACAUGUAAAUUAACUUUU Gria2.172265159_56 ~~~~~~GACUAAUUAUUUCCAUAUUGUACUUAA-AAUUAGUUUUUAAAAAUUAUUUU~~ // ClustID MergedIDs Count AvgDissim Members M97 2599 4 0.54 Ppm1e.75516706_7,Prkch.96280653_2,Syt4.23805080_45,Vegfa.10534185_2 Best CMs (by avg z-score): 1. (Z = 2.64) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.49) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 3. (Z = 2.00) CC0196 - Cauldobacter_sRNA_CC0196 4. (Z = 1.92) snoM1 - Small_nucleolar_RNA_snoM1 5. (Z = 1.73) MicF - MicF_RNA 6. (Z = 1.69) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.64) RsaE - RNA_Staph._aureus_E 8. (Z = 1.63) mir-2774 - microRNA_mir-2774 9. (Z = 1.62) H19_3 - H19_conserved_region_3 10. (Z = 1.60) CRISPR-DR23 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM97.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM97_global.out/ --free-endgaps --indel=-100 --threads=4 .......................................(((((....)))).)....... MFE = -5.20 (Covariance contribution: -5.02) RNAz stats: MPI: 43.06, SCI: 0.54, ZSCORE: 0.67 Full summary: Sequences: 4 Columns: 61 Reading direction: forward Mean pairwise identity: 43.06 Shannon entropy: 0.95034 G+C content: 0.42583 Mean single sequence MFE: -3.95 Consensus MFE: -2.12 Energy contribution: -0.75 Covariance contribution: -1.38 Combinations/Pair: 3.25 Mean z-score: 0.67 Structure conservation index: 0.54 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.48 SVM RNA-class probability: 0.278324 Prediction: OTHER Multiple alignment from mlocarna: Ppm1e.75516706_7 ~~~~~~~CCUCUCCACCAUCCCUUCA-CGUCACUAGUGGAAGCUUGAAAGUUAUUCCA~~~ Vegfa.10534185_2 ~~~~~CAUGUCACCACCACACCACCAUCGUCACC-GUCGACAGAACAGUCCU-UAAU~~~~ Syt4.23805080_45 GACUUUACGCUUUCCCCACAC--UCAUCGUCAUC---CAGUGACA-AUGUCA-UCUG~~~~ Prkch.96280653_2 ~~~~~UGCCUUUUAACACCACCUUCACCUUCAC------GGAGCAAAUGUUCACAACUCUG // ClustID MergedIDs Count AvgDissim Members M96 570 4 0.59 Appbp2.73460120_39,Dpysl2.46346413_20,Pabpn1.32998239_18,Shank3.127875955_48 Best CMs (by avg z-score): 1. (Z = 2.26) suhB - suhB 2. (Z = 2.21) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.07) U1_yeast - Yeast_U1_spliceosomal_RNA 4. (Z = 1.89) RybB - RybB_RNA 5. (Z = 1.76) MIR478 - microRNA_MIR478 6. (Z = 1.75) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop 7. (Z = 1.75) InvR - Invasion_gene-associated_RNA 8. (Z = 1.70) GcvB - GcvB_RNA 9. (Z = 1.69) lincRNA-p21_2 - LincRNA-p21_conserved_region_2 10. (Z = 1.68) RydC - RydC_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM96.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM96_global.out/ --free-endgaps --indel=-100 --threads=4 .............(((((..(((((......))))).......)))))................ MFE = -9.31 (Covariance contribution: -7.44) RNAz stats: MPI: 38.02, SCI: 0.77, ZSCORE: 0.12 Full summary: Sequences: 4 Columns: 64 Reading direction: forward Mean pairwise identity: 38.02 Shannon entropy: 1.05216 G+C content: 0.35286 Mean single sequence MFE: -8.18 Consensus MFE: -6.31 Energy contribution: -4.25 Covariance contribution: -2.06 Combinations/Pair: 2.55 Mean z-score: 0.12 Structure conservation index: 0.77 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.76 SVM RNA-class probability: 0.965988 Prediction: RNA Multiple alignment from mlocarna: Appbp2.73460120_39 CCCCCUAUUUUCAGGGGCUUCUGACUUGGCUGUUAGAUGCACUGCUCCUG~~~~~~~~~~~~~~ Dpysl2.46346413_20 CUACCAUUUUUCUGUGUCUCCGGUCUGUUCUGGCUUUUUCUUCUGCACUC~~~~~~~~~~~~~~ Pabpn1.32998239_18 ~~~~~~~~~~~~~UGCACUACUUUGUUUUG-GGGAGUUUGGGGGUGUUUUUGUUUUUCAGGUGU Shank3.127875955_48 CUCACAUUUACCUGUGGGUUUUUGGUUCUGUUCAGUUUGGGUUUUUAACU~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M11 6871 3 0.50 Nrgn.38790596_7,Atrn.118696808_93,Gng7.10269272_64 Best CMs (by avg z-score): 1. (Z = 2.71) H19_3 - H19_conserved_region_3 2. (Z = 2.26) IRES_mnt - Mnt_IRES 3. (Z = 1.30) TMV_UPD-PK3 - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 4. (Z = 1.22) BYDV_5_UTR - Barley_yellow_dwarf_virus_5'UTR 5. (Z = 1.21) snoM1 - Small_nucleolar_RNA_snoM1 6. (Z = 1.20) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 7. (Z = 1.14) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.14) Yfr1 - Cyanobacterial_functional_RNA_1 9. (Z = 1.11) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.09) g2 - G2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM11.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM11_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ....................(((....((..(((....)))......))..)))................ MFE = -7.92 (Covariance contribution: -11.06) RNAz stats: MPI: 36.36, SCI: 0.06, ZSCORE: 2.37 Full summary: Sequences: 3 Columns: 70 Reading direction: forward Mean pairwise identity: 36.36 Shannon entropy: 0.91685 G+C content: 0.42865 Mean single sequence MFE: -2.70 Consensus MFE: -0.16 Energy contribution: 0.83 Covariance contribution: -1.00 Combinations/Pair: 2.33 Mean z-score: 2.37 Structure conservation index: 0.06 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.62 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Nrgn.38790596_7 ACUCCCAAAAAUGUCCUUUUGCUUCACGCCCAC----CUGUCCACGCGCCCAGC~~~~~~~~~~~~~~~~ Atrn.118696808_93 ~~~~~~~~AUAGCACUAUUUUCC-CACACCUCAGCCUCCUGUC-CCCGUCCUGGUCUUCC~~~~~~~~~~ Gng7.10269272_64 ~~~~~~~~~~~~~~~~~~~AACU-CAAAUCUGCAUCUCUGCCCACACCUCCAGUUCCCCCUCCCCGGGUG // ClustID MergedIDs Count AvgDissim Members M10 3044 2 0.51 Spag7.57543647_3,Rab5c.89652340_14 Best CMs (by avg z-score): 1. (Z = 3.56) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.25) ctRNA_pGA1 - ctRNA 3. (Z = 3.06) SNORA52 - Small_nucleolar_RNA_SNORA52 4. (Z = 3.04) SNORA77 - Small_nucleolar_RNA_SNORA77 5. (Z = 2.90) isrA - isrA_Hfq_binding_RNA 6. (Z = 2.39) mir-3 - microRNA_mir-3 7. (Z = 2.20) TB9Cs4H2 - Trypanosomatid_snoRNA_TB9Cs4H2 8. (Z = 2.19) TB10Cs1H1 - Trypanosomatid_snoRNA_TB10Cs1H1 9. (Z = 2.19) PRINS - PRINS_RNA 10. (Z = 2.09) SNORA73 - Small_nucleolar_RNA_SNORA73_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM10.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM10_global.out/ --free-endgaps --indel=-100 --threads=4 .(((.(((((((.....).)))))))))....((((.((......)))))). MFE = -41.82 (Covariance contribution: -30.37) RNAz stats: MPI: 53.85, SCI: 0.68, ZSCORE: -1.2 Full summary: Sequences: 2 Columns: 52 Reading direction: forward Mean pairwise identity: 53.85 Shannon entropy: 0.46154 G+C content: 0.55882 Mean single sequence MFE: -16.15 Consensus MFE: -11.05 Energy contribution: -10.30 Covariance contribution: -0.75 Combinations/Pair: 1.33 Mean z-score: -1.20 Structure conservation index: 0.68 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.81 SVM RNA-class probability: 0.823390 Prediction: RNA Multiple alignment from mlocarna: Spag7.57543647_3 ~CCUGCCAGCUGCCACUCAGGCUGGAGGAGAAGCAGGUGU-UUAUCACUGCU Rab5c.89652340_14 CCUCCCCAUCUGACUCCC-AGCUGGGAGAGAAACCGCAGCAUUACUUAAGC~ // ClustID MergedIDs Count AvgDissim Members M13 6479 3 0.51 Vdac2.2515297_9,Appbp2.73460120_33,Dpysl2.46346413_21 Best CMs (by avg z-score): 1. (Z = 2.68) mir-248 - microRNA_mir-248 2. (Z = 2.24) mir-228 - microRNA_mir-228 3. (Z = 2.18) Vault - Vault_RNA 4. (Z = 2.09) TB10Cs2H2 - Trypanosomatid_snoRNA_TB10Cs2H2 5. (Z = 2.05) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop 6. (Z = 1.97) GcvB - GcvB_RNA 7. (Z = 1.86) U1_yeast - Yeast_U1_spliceosomal_RNA 8. (Z = 1.86) mir-101 - mir-101_microRNA_precursor_family 9. (Z = 1.86) snosnR54 - Small_nucleolar_RNA_snR54 10. (Z = 1.86) SVLPA - Simian_virus_40_late_polyadenylation_signal_(SVLPA) Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM13.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM13_global.out/ --free-endgaps --indel=-100 --threads=4 ...............(((((((((...............)))))))))............... MFE = -13.31 (Covariance contribution: -7.45) RNAz stats: MPI: 33.33, SCI: 0.75, ZSCORE: 1.26 Full summary: Sequences: 3 Columns: 63 Reading direction: forward Mean pairwise identity: 33.33 Shannon entropy: 0.94325 G+C content: 0.32275 Mean single sequence MFE: -7.65 Consensus MFE: -5.76 Energy contribution: -4.66 Covariance contribution: -1.10 Combinations/Pair: 2.11 Mean z-score: 1.26 Structure conservation index: 0.75 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.28 SVM RNA-class probability: 0.359373 Prediction: OTHER Multiple alignment from mlocarna: Vdac2.2515297_9 CUUUUACCCUUGACUGUUGUACUGAAUGAGAUGGAU---CAGUGGAUGUUUUA~~~~~~~~~~ Appbp2.73460120_33 ~~~~~~~~~~~~~UCCUCCAGUUACAAUGUCUGUUUUACUGAUUGGGGCUUUUGGUUUUUCUA Dpysl2.46346413_21 ~UUUUCUUCUGCACUCUUGGAGAGAUUUAGAUGUUG---GUCUCCUGGUUUGUG~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M12 1524 4 0.47 Grina.114279801_11,Atp2b2.149655651_11,Slc7a8.32800927_33,Arhgef7.82521224_32 Best CMs (by avg z-score): 1. (Z = 3.19) mir-500 - microRNA_mir-500 2. (Z = 3.07) mir-1180 - microRNA_mir-1180 3. (Z = 3.07) mir-557 - microRNA_mir-557 4. (Z = 2.97) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 5. (Z = 2.66) mir-42 - microRNA_mir-42 6. (Z = 2.65) TB10Cs3H2 - Trypanosomatid_snoRNA_TB10Cs3H2 7. (Z = 2.46) mir-32 - microRNA_mir-32 8. (Z = 2.46) mir-135 - mir-135_microRNA_precursor_family 9. (Z = 2.44) mir-458 - microRNA_mir-458 10. (Z = 2.38) MIR815 - microRNA_MIR815 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM12.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM12_global.out/ --free-endgaps --indel=-100 --threads=4 ............(((((((((((.(((.....)))....)))))))))))....... MFE = -32.04 (Covariance contribution: -17.57) RNAz stats: MPI: 34.31, SCI: 0.87, ZSCORE: 0.1 Full summary: Sequences: 4 Columns: 57 Reading direction: forward Mean pairwise identity: 34.31 Shannon entropy: 1.12560 G+C content: 0.54286 Mean single sequence MFE: -19.10 Consensus MFE: -16.66 Energy contribution: -13.47 Covariance contribution: -3.19 Combinations/Pair: 2.36 Mean z-score: 0.10 Structure conservation index: 0.87 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.68 SVM RNA-class probability: 0.960213 Prediction: RNA Multiple alignment from mlocarna: Grina.114279801_11 ~~CAUGUCCCCUCCUCACCCUGCCUUCUGAG-GGGC-UUGCAGGGUGGGGUCUC~~~ Slc7a8.32800927_33 ~~~~~~~GUGCUCAUCCCUCACCCUGGGGAGACCAUGUUGGUGAGGUAGGGGGAGAA Atp2b2.149655651_11 GACACUUUUAAUCCCCUCCCUCGAUUGGUUCUUGGAGGGUUAGGGAGGGG~~~~~~~ Arhgef7.82521224_32 ~~~~~~AGCUCCUGGCCGCUCGUCCUCCGUGCAGGU-UUCUGAGUGGGUGUGUGGAG // ClustID MergedIDs Count AvgDissim Members M15 3795 2 0.24 Atp2b2.149655651_66,Atp2b2.149655651_65 Best CMs (by avg z-score): 1. (Z = 3.20) snoZ107_R87 - Small_nucleolar_RNA_Z107/R87 2. (Z = 3.15) suhB - suhB 3. (Z = 2.47) rimP - Enterobacteria_rnk_leader 4. (Z = 2.42) RybB - RybB_RNA 5. (Z = 2.28) snoR17 - Small_nucleolar_RNA_snoR17 6. (Z = 1.95) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.94) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop 8. (Z = 1.92) GcvB - GcvB_RNA 9. (Z = 1.91) snoR77Y - Small_nucleolar_RNA_snoR77Y 10. (Z = 1.84) MIR478 - microRNA_MIR478 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM15.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM15_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((((.((((((.(((........))).)))))).))))... MFE = -3.24 (Covariance contribution: -5.59) RNAz stats: MPI: 44.23, SCI: 1.13, ZSCORE: 0.62 Full summary: Sequences: 2 Columns: 52 Reading direction: forward Mean pairwise identity: 44.23 Shannon entropy: 0.55769 G+C content: 0.37877 Mean single sequence MFE: -1.60 Consensus MFE: -1.80 Energy contribution: 0.70 Covariance contribution: -2.50 Combinations/Pair: 1.64 Mean z-score: 0.62 Structure conservation index: 1.13 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.45 SVM RNA-class probability: 0.293060 Prediction: OTHER Multiple alignment from mlocarna: Atp2b2.149655651_66 ~GAUUGG-UUUGGGGGUUUUUUGGUUUUGUUUUUUUUGGGGGGGGUUUUGUU Atp2b2.149655651_65 GGAUAGGUUUUUCUUUGGGUUUUUUGUUGUUGUUUGAUUGGUUUGGGGGU~~ // ClustID MergedIDs Count AvgDissim Members M14 2325 3 0.49 Bdnf.977114_80,Atrn.118696808_122,Tmeff1.65356245_21 Best CMs (by avg z-score): 1. (Z = 4.32) mir-286 - microRNA_mir-286 2. (Z = 3.94) snopsi28S-3316 - Small_nucleolar_RNA_psi28S-3316 3. (Z = 3.91) Pox_AX_element - Poxvirus_AX_element_late_mRNA_cis-regulatory_element 4. (Z = 3.65) mir-374 - microRNA_mir-374 5. (Z = 3.56) mir-223 - microRNA_mir-223 6. (Z = 3.51) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 7. (Z = 3.47) IFN_gamma - Interferon_gamma_5'_UTR_regulatory_element 8. (Z = 3.45) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 9. (Z = 3.42) ctRNA_pND324 - ctRNA 10. (Z = 3.41) SNORA31 - Small_nucleolar_RNA_SNORA31 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM14.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM14_global.out/ --free-endgaps --indel=-100 --threads=4 ...((((...((((...((((((((((...)))))..))..))).))))))))... MFE = -24.53 (Covariance contribution: -19.17) RNAz stats: MPI: 29.09, SCI: 0.49, ZSCORE: -0.26 Full summary: Sequences: 3 Columns: 56 Reading direction: forward Mean pairwise identity: 29.09 Shannon entropy: 1.02229 G+C content: 0.25799 Mean single sequence MFE: -7.07 Consensus MFE: -3.44 Energy contribution: 1.43 Covariance contribution: -4.87 Combinations/Pair: 2.13 Mean z-score: -0.26 Structure conservation index: 0.49 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.04 SVM RNA-class probability: 0.879462 Prediction: RNA Multiple alignment from mlocarna: Bdnf.977114_80 ~CUAUUUAAGUGUACCAAUUAACAUAUAAUAUAUG--UU-UUAAAUAUAGAAUU~~ Atrn.118696808_122 GGGUCUGCAUUUUA--AAUGCAAAUGUGAAGCACU--UG--UAUAUAAACAGAAGU Tmeff1.65356245_21 ~~~CUGU---UUUCAUAUAAAUGUACAAAUUGUAUCAGUGUUUGUGAAUACAACGC // ClustID MergedIDs Count AvgDissim Members M17 4140 5 0.58 Stxbp1.11762105_12,Canx.35850944_41,Lypla1.14882196_13,Cyfip2.31321000_17,Lypla1.14882196_3 Best CMs (by avg z-score): 1. (Z = 2.74) mir-204 - microRNA_mir-204 2. (Z = 2.28) PRINS - PRINS_RNA 3. (Z = 2.25) Qrr - Qrr_RNA 4. (Z = 2.20) PK-IAV - Pseudoknot_of_influenza_A_virus_gene 5. (Z = 2.06) IS128 - IS128_RNA 6. (Z = 2.03) mir-48 - microRNA_mir-48 7. (Z = 2.02) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.00) Fungi_U3 - Fungal_small_nucleolar_RNA_U3 9. (Z = 1.98) snR36 - Small_nucleolar_RNA_snR36 10. (Z = 1.95) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM17.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM17_global.out/ --free-endgaps --indel=-100 --threads=4 .......................((((((((((........))))).)))))........ MFE = -16.63 (Covariance contribution: -8.89) RNAz stats: MPI: 36.52, SCI: 0.54, ZSCORE: -0.28 Full summary: Sequences: 5 Columns: 60 Reading direction: forward Mean pairwise identity: 36.52 Shannon entropy: 1.15836 G+C content: 0.34908 Mean single sequence MFE: -8.20 Consensus MFE: -4.44 Energy contribution: -2.80 Covariance contribution: -1.64 Combinations/Pair: 2.56 Mean z-score: -0.28 Structure conservation index: 0.54 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.36 SVM RNA-class probability: 0.931748 Prediction: RNA Multiple alignment from mlocarna: Canx.35850944_41 ~~~AUUACACCACACUGAAAUGUAUUCAGAAAC----AGAUGUUUC---AAUUUCAUUCU Lypla1.14882196_13 ~~~~AUUCACACAUACGUGAC---UGGGAUACCUAA--GAUGGUAU-UACAUCAUCCCUG Lypla1.14882196_3 ~~UGUUUUGCAAAUACAUACCAAUGAGACAGACUAAAUGAUGUCUC-CCUCAU~~~~~~~ Cyfip2.31321000_17 ~~ACUGUCAAGACAAC-AAAUGAUGCUGAAAAG----GGAUCUUUUACAGCCCCCCU~~~ Stxbp1.11762105_12 UCUCUGUCCCCAAGAUAUGACAUGCUGAGGAAGU-GAUG-UUUUUC-UCUCUA~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M16 5625 3 0.20 Appbp2.73460120_96,Pklr.181222231_14,Appbp2.73460120_69 Best CMs (by avg z-score): 1. (Z = 5.18) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.71) MIR478 - microRNA_MIR478 3. (Z = 3.58) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.33) bxd_7 - Bithoraxoid_conserved_region_7 5. (Z = 3.28) suhB - suhB 6. (Z = 3.08) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.99) DdR4 - D._discoideum_snoRNA_DdR4 8. (Z = 2.97) snoU97 - Small_nucleolar_RNA_U97 9. (Z = 2.96) snoZ159 - Small_nucleolar_RNA_Z159/U59 10. (Z = 2.86) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM16.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM16_global.out/ --free-endgaps --indel=-100 --threads=4 ...............................(((((..(...)..)))))... MFE = -9.94 (Covariance contribution: -6.78) RNAz stats: MPI: 75.47, SCI: 0.60, ZSCORE: 0.99 Full summary: Sequences: 3 Columns: 53 Reading direction: forward Mean pairwise identity: 75.47 Shannon entropy: 0.34961 G+C content: 0.37195 Mean single sequence MFE: -5.74 Consensus MFE: -3.43 Energy contribution: -3.43 Covariance contribution: 0.00 Combinations/Pair: 1.00 Mean z-score: 0.99 Structure conservation index: 0.60 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.63 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Appbp2.73460120_96 UAAGU-ACUG--AAUUUUUUUUUUUCUUUUUUUCGGAGCUGGGGACCGAACCC Pklr.181222231_14 ~~CUUUUUUUUUUUCUUUUCUUUUUCUUUUUUUCGGAGCUGGGGACCGAACC~ Appbp2.73460120_69 ~~~GCCACCGUAAUUUUUUUUUUUUCUUUUUUUCGGAGCUGGGGACUGAACCC // ClustID MergedIDs Count AvgDissim Members M19 4854 4 0.67 Atp6v1b2.22320426_32,Map1b.30415235_118,Gyg1.105264657_4,Gria2.172265159_62 Best CMs (by avg z-score): 1. (Z = 2.78) RsaH - RNA_Staph._aureus_H 2. (Z = 2.57) snoR160 - Small_nucleolar_RNA_R160 3. (Z = 2.51) IRE - Iron_response_element 4. (Z = 2.36) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.26) snoZ267 - Small_nucleolar_RNA_Z267 6. (Z = 2.26) snoZ13_snr52 - Small_nucleolar_RNA_Z13/snr52 7. (Z = 2.24) MIR477 - microRNA_MIR477 8. (Z = 2.22) snoMe28S-Am982 - Small_nucleolar_RNA_Me28S-Am982 9. (Z = 2.18) Bacteroid-trp - Bacteroidete_tryptophan_peptide_leader_RNA 10. (Z = 2.18) AdoCbl_riboswitch - AdoCbl_riboswitch Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM19.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM19_global.out/ --free-endgaps --indel=-100 --threads=4 ...........................(((((((((((....)))))))))))............. MFE = -9.22 (Covariance contribution: -5.17) RNAz stats: MPI: 36.04, SCI: 0.57, ZSCORE: 1.4 Full summary: Sequences: 4 Columns: 66 Reading direction: forward Mean pairwise identity: 36.04 Shannon entropy: 1.09032 G+C content: 0.24540 Mean single sequence MFE: -5.43 Consensus MFE: -3.08 Energy contribution: -2.33 Covariance contribution: -0.75 Combinations/Pair: 2.22 Mean z-score: 1.40 Structure conservation index: 0.57 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.55 SVM RNA-class probability: 0.046848 Prediction: OTHER Multiple alignment from mlocarna: Atp6v1b2.22320426_32 AAAAUAAAUGUUAAAUUAAAUGGA--AGGUUACACUG-AAGCCUGGUGCCUCU~~~~~~~~~~~~~ Map1b.30415235_118 ~~~~~~~~~GUCAUAUCUAAUGUAGAAAAAUUAGUUUCCAGUGAAAGUAAUAUGUAGUG~~~~~~~ Gyg1.105264657_4 ~~~~~~~~~~~~~GGGCAAAUGUU---AUUAAGUAAUAAUUCUAUUAUGUGGACAAGUGUUGUGUU Gria2.172265159_62 ~~~~~~~~~~CAAGAACAUAUAAUGUAAGAGUAUCU-CAAGUGUGGAUAAUGUUGAUUGGC~~~~~ // ClustID MergedIDs Count AvgDissim Members M18 2480 4 0.59 Lypla1.14882196_24,Tpt1.56755083_4,Fmr1.154791521_7,Rnf111.74909360_30 Best CMs (by avg z-score): 1. (Z = 3.98) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.91) SCARNA24 - Small_Cajal_body_specific_RNA_24 3. (Z = 3.41) K10_TLS - K10_transport/localisation_element_(TLS) 4. (Z = 3.33) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 5. (Z = 3.29) RUF1 - Plasmodium_RNA_of_unkown_function_RUF1 6. (Z = 3.14) mir-248 - microRNA_mir-248 7. (Z = 3.14) SNORA20 - Small_nucleolar_RNA_SNORA20 8. (Z = 3.06) snR44 - Small_nucleolar_RNA_snR44 9. (Z = 3.00) Qrr - Qrr_RNA 10. (Z = 3.00) S_pombe_snR100 - small_nucleolar_RNA_snR100 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM18.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM18_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((((((...)))))))...........(((((.......)))))................. MFE = -8.84 (Covariance contribution: -9.99) RNAz stats: MPI: 39.49, SCI: 0.46, ZSCORE: 0.69 Full summary: Sequences: 4 Columns: 67 Reading direction: forward Mean pairwise identity: 39.49 Shannon entropy: 0.99857 G+C content: 0.18256 Mean single sequence MFE: -2.70 Consensus MFE: -1.24 Energy contribution: 0.20 Covariance contribution: -1.44 Combinations/Pair: 2.80 Mean z-score: 0.69 Structure conservation index: 0.46 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.27 SVM RNA-class probability: 0.077970 Prediction: OTHER Multiple alignment from mlocarna: Lypla1.14882196_24 ~~GUUUUAUUUUUCUAUAAAAA------CUUAAAGGGUAAAUAAUAUCUUGGCGUGUU~~~~~~~~~ Tpt1.56755083_4 ~~~~UUUUUUUUUUAAAGAAAA------AAAAACAUGU------CAUGUGGG-UUGUCUAAAAAUAA Fmr1.154791521_7 ~~~~~UUUAUUUUUUAAAAAUACUAAGCAGUGAUCUUU-AUUAACUAGGA-CCAUUU~~~~~~~~~~ Rnf111.74909360_30 UUUUUUUUAUAGUUUAAAUAAAGUCAGCUGAAUCUACAUGUCUCUUGUUU~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M73 445 3 0.48 Psmb2.146121851_2,Fmr1.154791521_63,Pou4f2.31390818_41 Best CMs (by avg z-score): 1. (Z = 3.81) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.72) S_pombe_snR36 - small_nucleolar_RNA_snR36 3. (Z = 3.71) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.57) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 5. (Z = 3.36) SNORA22 - Small_nucleolar_RNA_SNORA22 6. (Z = 3.28) SNORD127 - Small_nucleolar_RNA_SNORD127 7. (Z = 3.24) ROSE_2 - Repression_of_heat_shock_gene_expression_(ROSE)_element 8. (Z = 3.06) tp2 - tp2 9. (Z = 3.02) SCARNA24 - Small_Cajal_body_specific_RNA_24 10. (Z = 3.00) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM73.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM73_global.out/ --free-endgaps --indel=-100 --threads=4 .................((((.(((.((((((....)))))).)))))))................. MFE = -11.99 (Covariance contribution: -7.85) RNAz stats: MPI: 33.67, SCI: 1.39, ZSCORE: 1.6 Full summary: Sequences: 3 Columns: 67 Reading direction: forward Mean pairwise identity: 33.67 Shannon entropy: 0.93181 G+C content: 0.21479 Mean single sequence MFE: -2.75 Consensus MFE: -3.82 Energy contribution: -1.73 Covariance contribution: -2.09 Combinations/Pair: 2.15 Mean z-score: 1.60 Structure conservation index: 1.39 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.46 SVM RNA-class probability: 0.055387 Prediction: OTHER Multiple alignment from mlocarna: Psmb2.146121851_2 ~~~~~~~~~~~~~~~~~UUGACGUUCACUCUCAAUAGAUGGUUAAUUCAAAAUAAAGCUGAACACAG Fmr1.154791521_63 GAUUGUUUAUCUUAUCUAGAU-GUAAAUUUUUAUUAAAAAGU-UGCA-CUUAU~~~~~~~~~~~~~~ Pou4f2.31390818_41 GACUGG-UACCUUCUCUAUUG-UAAAUAUUUCAUUCAAAAUG-AUGCACAUAU~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M72 301 3 0.48 Canx.35850944_87,Pou4f2.31390818_46,Becn1.90317957_7 Best CMs (by avg z-score): 1. (Z = 3.83) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.55) K10_TLS - K10_transport/localisation_element_(TLS) 3. (Z = 3.24) CRISPR-DR39 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.14) MIR478 - microRNA_MIR478 5. (Z = 3.09) eeev_FSE - eastern_equine_encephalitis_ribosomal_frameshift_element 6. (Z = 3.05) 23S-methyl - 23S_methyl_RNA_motif 7. (Z = 3.03) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 8. (Z = 3.03) TMV_UPD-PK3 - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 9. (Z = 2.72) snoU97 - Small_nucleolar_RNA_U97 10. (Z = 2.72) mir-154 - microRNA_mir-154 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM72.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM72_global.out/ --free-endgaps --indel=-100 --threads=4 .................((((((.((((......(((((....))))))))))))))).... MFE = -9.27 (Covariance contribution: -10.57) RNAz stats: MPI: 31.32, SCI: 0.76, ZSCORE: 0.81 Full summary: Sequences: 3 Columns: 62 Reading direction: forward Mean pairwise identity: 31.32 Shannon entropy: 0.98260 G+C content: 0.22986 Mean single sequence MFE: -4.20 Consensus MFE: -3.21 Energy contribution: -0.77 Covariance contribution: -2.44 Combinations/Pair: 2.20 Mean z-score: 0.81 Structure conservation index: 0.76 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.58 SVM RNA-class probability: 0.751912 Prediction: RNA Multiple alignment from mlocarna: Canx.35850944_87 ~~~~CUGUUAGCUUUUUUUCUUGUGA--------UUUUAAAAAUAAAAUUUUCGUGAACUCC Pou4f2.31390818_46 ~~~~~~~~~~GUUAUUUUGGGUGUUGUUUCAUUGUCUUUCAUCGAAGAGAUGAUUUUAAU~~ Becn1.90317957_7 UUUGCUUUGUUUUCUUUUUUAAGUUGAAUU----GACAUUAAUGUGUUUUCACU~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M71 3662 4 0.57 Sept9.107478216_19,Psma5.203848218_1,Fgf13.144199535_19,Basp1.76877616_2 Best CMs (by avg z-score): 1. (Z = 3.05) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.30) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.18) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 4. (Z = 2.18) snoU97 - Small_nucleolar_RNA_U97 5. (Z = 2.13) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.07) suhB - suhB 7. (Z = 1.93) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.87) HOTAIR_3 - HOTAIR_conserved_region_3 9. (Z = 1.84) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.70) bxd_6 - Bithoraxoid_conserved_region_6 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM71.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM71_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .............................................................. MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 43.90, SCI: -0.00, ZSCORE: 1.01 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 43.90 Shannon entropy: 0.94612 G+C content: 0.35831 Mean single sequence MFE: -3.28 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.01 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.67 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Sept9.107478216_19 ~~~~UCUUUUCUCCCUCACCCU-UCGAUUCUCUCUCCCC---UGUGCUGUAGAUAGCG~~~~ Psma5.203848218_1 CAGUUCUAAUGGCUCUUAGACUUUAUUUCCAACUCCACGUCGUGGAAAAU~~~~~~~~~~~~ Fgf13.144199535_19 ~~~~~~~~~UGUCCCUCUUCCUCUCUCUCCUUUUUCUGU---UGUCAAUUAGAACUGUAGCA Basp1.76877616_2 ~~~~~~UGUCCUCUCUCUGUCUCUCUAUCCUAUACUAACUUGUUUCAAAUUGGAAG~~~~~~ // ClustID MergedIDs Count AvgDissim Members M70 448 3 0.46 Bdnf.977114_7,Tmem30a.84827711_12,Atp5j.24316748_1 Best CMs (by avg z-score): 1. (Z = 4.16) class_I_RNA - Class_I_RNA 2. (Z = 3.94) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.61) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.61) snoMe28S-Cm3227 - Small_nucleolar_RNA_Me28S-Cm3227 5. (Z = 3.51) snR36 - Small_nucleolar_RNA_snR36 6. (Z = 3.41) snoR101 - Small_nucleolar_RNA_snoR101 7. (Z = 3.41) snoZ163 - Small_nucleolar_RNA_Z163/Z177_family 8. (Z = 3.40) SCARNA1 - Small_Cajal_body_specific_RNA_1 9. (Z = 3.39) RsaH - RNA_Staph._aureus_H 10. (Z = 3.32) DdR18 - D._discoideum_snoRNA_DdR18 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM70.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM70_global.out/ --free-endgaps --indel=-100 --threads=4 ..........((((....))))..................................... MFE = -3.64 (Covariance contribution: -4.70) RNAz stats: MPI: 38.42, SCI: 0.36, ZSCORE: 1.21 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 38.42 Shannon entropy: 0.90102 G+C content: 0.20873 Mean single sequence MFE: -1.23 Consensus MFE: -0.44 Energy contribution: 1.00 Covariance contribution: -1.44 Combinations/Pair: 2.25 Mean z-score: 1.21 Structure conservation index: 0.36 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.75 SVM RNA-class probability: 0.000001 Prediction: OTHER Multiple alignment from mlocarna: Bdnf.977114_7 ~UUGCCAAGAAUUGAAAACAAAAAGUUAAAAAAAAUAAUAAAUUGCAUGCU~~~~~~~~ Tmem30a.84827711_12 UUGGUUACAGUUCAG-AUUGAAGAAAGACUAAAUAUAAAUAAA---ACACUUCA~~~~~ Atp5j.24316748_1 ~~~~~~~~~UAGUUGUACAAUUAAUCUAAAAAAUUCAAAUAAACAUUCACUUCACAGUC // ClustID MergedIDs Count AvgDissim Members M77 1930 3 0.50 Atp1b2.56418323_13,Marcksl1.148671604_3,Shank1.94839593_24 Best CMs (by avg z-score): 1. (Z = 2.72) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.25) InvR - Invasion_gene-associated_RNA 3. (Z = 2.14) rli32 - Listeria_sRNA_rli32 4. (Z = 1.81) Yfr1 - Cyanobacterial_functional_RNA_1 5. (Z = 1.79) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.77) TMV_UPD-PK3 - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 7. (Z = 1.70) suhB - suhB 8. (Z = 1.67) rnk_pseudo - Pseudomonas_rnk_leader 9. (Z = 1.45) Y_RNA - Y_RNA 10. (Z = 1.41) mir-286 - microRNA_mir-286 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM77.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM77_global.out/ --free-endgaps --indel=-100 --threads=4 ...((.(((((.......))))).))................................... MFE = -16.55 (Covariance contribution: -11.05) RNAz stats: MPI: 43.89, SCI: 0.63, ZSCORE: 0.55 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 43.89 Shannon entropy: 0.79765 G+C content: 0.50293 Mean single sequence MFE: -8.67 Consensus MFE: -5.44 Energy contribution: -4.67 Covariance contribution: -0.77 Combinations/Pair: 1.86 Mean z-score: 0.55 Structure conservation index: 0.63 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.11 SVM RNA-class probability: 0.442169 Prediction: OTHER Multiple alignment from mlocarna: Atp1b2.56418323_13 ~~~GGGGUGAAUAUUGUUUUCCCUCCCUUUACAACGCUCUAGCCGCUUUUCUU~~~~~~~~ Marcksl1.148671604_3 ~~~GAAGGGGC--UUGUUGCCCCGUCCCAGCCA-----CGCUCC-CUCUUCUCCCUCCUGU Shank1.94839593_24 CAUACGGGG-----UCUCUUUCCGGUCUUGCCA-CCCCCAUACCGUUACUCUCCUU~~~~~ // ClustID MergedIDs Count AvgDissim Members M76 5327 4 0.64 Rab5c.89652340_12,Shank1.94839593_19,Atp1b2.56418323_26,Slc7a8.32800927_15 Best CMs (by avg z-score): 1. (Z = 3.28) mir-128 - microRNA_mir-128 2. (Z = 3.09) mir-136 - microRNA_mir-136 3. (Z = 3.06) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.03) mir-296 - microRNA_mir-296 5. (Z = 2.98) mir-942 - microRNA_mir-942 6. (Z = 2.96) mir-491 - microRNA_mir-491 7. (Z = 2.95) mir-322 - microRNA_mir-322 8. (Z = 2.92) mir-14 - microRNA_mir-14 9. (Z = 2.91) mir-675 - microRNA_mir-675 10. (Z = 2.90) mir-3179 - microRNA_mir-3179 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM76.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM76_global.out/ --free-endgaps --indel=-100 --threads=4 ........((((((((((((((((((.......))))))))))))))).))).......... MFE = -41.62 (Covariance contribution: -19.39) RNAz stats: MPI: 36.49, SCI: 1.05, ZSCORE: -0.17 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 36.49 Shannon entropy: 1.07910 G+C content: 0.51218 Mean single sequence MFE: -22.05 Consensus MFE: -23.19 Energy contribution: -19.00 Covariance contribution: -4.19 Combinations/Pair: 2.50 Mean z-score: -0.17 Structure conservation index: 1.05 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.29 SVM RNA-class probability: 0.921742 Prediction: RNA Multiple alignment from mlocarna: Slc7a8.32800927_15 ~~~~~AGGGAGCCAAAAGGCAGAGGGCUCACUUCUCUUUGCCUUCUGCACUCUGU~~~~~~~ Shank1.94839593_19 ~~~~~~~UUCUGGGGGA--GGAGGGUAUUGC--ACCCUUUAUUUCUCU-AGCUACCCUGGAC Atp1b2.56418323_26 ~~~~~GGAGCUCUGGGGGAGGGGCCGCUGUC-UUGGCUCUAUCCCCAGUGGCCACC~~~~~~ Rab5c.89652340_12 GGGCAGGCCCUGGGCUGGGGAAGGGACAGGCAGCUCUUUCCUCAGCU--GGC~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M75 5779 3 0.51 Pcdh17.66481698_15,Appbp2.73460120_66,Syt4.23805080_63 Best CMs (by avg z-score): 1. (Z = 4.14) SNORD15 - Small_nucleolar_RNA_SNORD15 2. (Z = 3.14) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.63) SNORD110 - Small_Nucleolar_RNA_SNORD110 4. (Z = 2.59) ROSE_2 - Repression_of_heat_shock_gene_expression_(ROSE)_element 5. (Z = 2.59) ceN54 - C._elegans_snoRNA_ceN54 6. (Z = 2.54) SNORD59 - Small_nucleolar_RNA_SNORD59 7. (Z = 2.41) SNORD29 - Small_nucleolar_RNA_SNORD29 8. (Z = 2.38) RF_site2 - Polymerase_ribosomal_frameshift_site 9. (Z = 2.37) SNORD28 - Small_nucleolar_RNA_SNORD28 10. (Z = 2.30) sn1185 - Small_nucleolar_RNA_sn1185 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM75.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM75_global.out/ --free-endgaps --indel=-100 --threads=4 ............................(((((((....))).)))).......... MFE = -9.50 (Covariance contribution: -7.33) RNAz stats: MPI: 35.88, SCI: 0.37, ZSCORE: 1.65 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 35.88 Shannon entropy: 0.91807 G+C content: 0.32615 Mean single sequence MFE: -4.53 Consensus MFE: -1.66 Energy contribution: -0.33 Covariance contribution: -1.32 Combinations/Pair: 2.00 Mean z-score: 1.65 Structure conservation index: 0.37 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.39 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Pcdh17.66481698_15 UGUUUUGCAUUUGAACA--GUUCUG-AA-UUAUGAGUUAUCAUUGAGUAGUAAU~~~ Appbp2.73460120_66 ~~~~~~UGCUUAGCGAUAUGACUUGAUAUGUUCUGAUUCCAGUGAAAG-UAAUGCCC Syt4.23805080_63 ~~CUGUGUGAUUCAGUGAUGACUUG-UUCUGACUUGUUGUAGUUCAGUAGUGU~~~~ // ClustID MergedIDs Count AvgDissim Members M74 589 3 0.50 Shank1.94839593_12,Stxbp1.11762105_36,Atp2b2.149655651_54 Best CMs (by avg z-score): 1. (Z = 2.08) H19_3 - H19_conserved_region_3 2. (Z = 1.79) IRES_mnt - Mnt_IRES 3. (Z = 1.61) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.42) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.17) CC1840 - caulobacter_sRNA_CC1840 6. (Z = 1.03) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.02) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.01) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 9. (Z = 0.98) H19_2 - H19_conserved_region_2 10. (Z = 0.96) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM74.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM74_global.out/ --free-endgaps --indel=-100 --threads=4 ..............((.............))........((((...))))..................... MFE = -11.41 (Covariance contribution: -10.58) RNAz stats: MPI: 38.46, SCI: 0.92, ZSCORE: 0.34 Full summary: Sequences: 3 Columns: 71 Reading direction: forward Mean pairwise identity: 38.46 Shannon entropy: 0.85699 G+C content: 0.48128 Mean single sequence MFE: -4.25 Consensus MFE: -3.91 Energy contribution: -2.13 Covariance contribution: -1.78 Combinations/Pair: 2.67 Mean z-score: 0.34 Structure conservation index: 0.92 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.00 SVM RNA-class probability: 0.870194 Prediction: RNA Multiple alignment from mlocarna: Shank1.94839593_12 GCCCCUCAGCCUUCCCA----CUCUCCUUGGCUCACUCAGCUG-CCCAGCCCCCU~~~~~~~~~~~~~~~~ Stxbp1.11762105_36 ~~~~~~~~~~~~~UCUC----CUCUCCUUAGUU--CUCAGGC--CCCGCCCCUCUCCAGUGACCCUUUCCC Atp2b2.149655651_54 ~~CUCUCUCCCUUCUCACAAUCGCUCCUCGCUCUUCAGCCUGGUCCCCAGCC~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M79 941 2 0.31 Pou4f2.31390818_1,Pabpn1.32998239_11 Best CMs (by avg z-score): 1. (Z = 2.61) IRES_mnt - Mnt_IRES 2. (Z = 2.48) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.35) suhB - suhB 4. (Z = 2.19) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 5. (Z = 2.13) sbrA - Listeria_sRNA_sbrA 6. (Z = 2.06) RydC - RydC_RNA 7. (Z = 2.04) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.57) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.56) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.52) snoZ178 - Small_nucleolar_RNA_Z178 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM79.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM79_global.out/ --free-endgaps --indel=-100 --threads=4 ...................................((((...))))................ MFE = -4.16 (Covariance contribution: -4.56) RNAz stats: MPI: 38.71, SCI: -0.00, ZSCORE: -0.5 Full summary: Sequences: 2 Columns: 62 Reading direction: forward Mean pairwise identity: 38.71 Shannon entropy: 0.61290 G+C content: 0.43139 Mean single sequence MFE: -1.75 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.50 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.69 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Pou4f2.31390818_1 ~~~~~~~~~~~~CUCUCUUUUCUAACCCCCCUCUUGUCUCUCCUGCCUCUUUUCUUUCUACU Pabpn1.32998239_11 GCUUGUUUCCUUCCCUCGUCUCU-CCCUGCCUUUUGCAGCCCCUGCCUUCC~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M78 4358 5 0.58 Pou4f2.31390818_2,Atp2b2.149655651_50,Fmr1.154791521_19,Calm2.10951142_4,Fmr1.154791521_1 Best CMs (by avg z-score): 1. (Z = 4.01) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.58) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.17) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.03) tp2 - tp2 5. (Z = 2.82) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.68) SNORD111 - Small_Nucleolar_RNA_SNORD111 7. (Z = 2.52) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.42) CRISPR-DR41 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.31) class_I_RNA - Class_I_RNA 10. (Z = 2.30) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM78.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM78_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ..................((((...((((..........)).....))..))))............... MFE = -0.72 (Covariance contribution: -6.94) RNAz stats: MPI: 40.67, SCI: -0.00, ZSCORE: 1.6 Full summary: Sequences: 5 Columns: 69 Reading direction: forward Mean pairwise identity: 40.67 Shannon entropy: 1.08098 G+C content: 0.26009 Mean single sequence MFE: -2.04 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.60 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.99 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Atp2b2.149655651_50 CUUUGAGACUUUUCAGCAUACAAUCUUUUUC-----CAUA------AACUUGUACAGUGCA~~~~~~~~ Pou4f2.31390818_2 ~~~~~~~~~~UCUUUUCUUUCU-ACUUUGGC-----UAUCAGAAACAAUUCCGGUAAAUGUGAACC~~~ Fmr1.154791521_19 ~~~~~~~~~~~~~UGCUUUCCAUAUUUUUUUCCUUACAUAAACAUCAGCUUAGGCAGUAUAAA~~~~~~ Calm2.10951142_4 ~~~~~~~~UUCCCUAUCUUCUG-UCAUUGUC-----CUUCAACCUUAUAUUAGAAAACUGAUCA~~~~~ Fmr1.154791521_1 ~~~~~~~~~~~~~~UUCCGUAAUUCUUACUC-----CAUUUUAGAAAACUUUAUUAGGCCAAAGACAAA // ClustID MergedIDs Count AvgDissim Members M179 1802 4 0.59 Ntrk2.11676658_70,Atp2a2.35312505_3,Stxbp1.11762105_5,Atrn.118696808_11 Best CMs (by avg z-score): 1. (Z = 3.07) suhB - suhB 2. (Z = 2.68) U7 - U7_small_nuclear_RNA 3. (Z = 2.36) snoU97 - Small_nucleolar_RNA_U97 4. (Z = 2.26) SNORD11 - Small_nucleolar_RNA_SNORD11 5. (Z = 2.25) tp2 - tp2 6. (Z = 2.24) mir-156 - mir-156_microRNA_precursor 7. (Z = 2.21) DPB - Stem_loopII_regulatory_element_in_POLB 8. (Z = 2.20) snR13 - Small_nucleolar_RNA_snR13 9. (Z = 2.17) MIR478 - microRNA_MIR478 10. (Z = 2.11) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM179.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM179_global.out/ --free-endgaps --indel=-100 --threads=4 .............((((((.....))))))............................. MFE = -4.71 (Covariance contribution: -4.33) RNAz stats: MPI: 36.36, SCI: 0.38, ZSCORE: 1.64 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 36.36 Shannon entropy: 1.10664 G+C content: 0.33211 Mean single sequence MFE: -4.09 Consensus MFE: -1.55 Energy contribution: -0.43 Covariance contribution: -1.12 Combinations/Pair: 2.50 Mean z-score: 1.64 Structure conservation index: 0.38 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.01 SVM RNA-class probability: 0.000001 Prediction: OTHER Multiple alignment from mlocarna: Ntrk2.11676658_70 ~~~~~~CCUUGAUGGCUUGUUCUUACAGUCUUGUCUUCUCUCCAUUCUCCAAGCAC~~~ Atp2a2.35312505_3 ~~~~~~~~~UGAAGGAGGUUUCAUAUCUAGAUUUUGUUUUGCUUUUUCUGACUCCAGUG Stxbp1.11762105_5 ~~AGUAAUGUG--UUGUUUUUUAAAAAUGAGUAUCUUCUGUAUGUAUCCCACAG~~~~~ Atrn.118696808_11 CUGAAGCUUGC--UGUCUUUUUACAAGAUGUGCUUUUACUC---UCUUCCAGGAA~~~~ // ClustID MergedIDs Count AvgDissim Members M178 3099 2 0.53 Gnai1.12494046_1,Map1b.30415235_47 Best CMs (by avg z-score): 1. (Z = 3.31) sR36 - Small_nucleolar_RNA_sR36 2. (Z = 3.24) psbNH - psbNH_RNA 3. (Z = 3.23) CRISPR-DR24 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.43) beta_tmRNA - Betaproteobacteria_transfer-messenger_RNA 5. (Z = 2.31) sR30 - Small_nucleolar_RNA_sR30 6. (Z = 2.21) mir-1275 - microRNA_mir-1275 7. (Z = 1.88) Protozoa_SRP - Protozoan_signal_recognition_particle_RNA 8. (Z = 1.84) sR20 - Small_nucleolar_RNA_sR20 9. (Z = 1.83) sR24 - Small_nucleolar_RNA_sR24 10. (Z = 1.76) sR21 - Small_nucleolar_RNA_sR21 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM178.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM178_global.out/ --free-endgaps --indel=-100 --threads=4 .(((((((.((((....................)))).))))))).................. MFE = -25.33 (Covariance contribution: -15.53) RNAz stats: MPI: 28.57, SCI: 0.79, ZSCORE: -0.59 Full summary: Sequences: 2 Columns: 63 Reading direction: forward Mean pairwise identity: 28.57 Shannon entropy: 0.71429 G+C content: 0.50654 Mean single sequence MFE: -11.70 Consensus MFE: -9.30 Energy contribution: -7.55 Covariance contribution: -1.75 Combinations/Pair: 1.60 Mean z-score: -0.59 Structure conservation index: 0.79 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.97 SVM RNA-class probability: 0.977426 Prediction: RNA Multiple alignment from mlocarna: Gnai1.12494046_1 CCUGGAGUGUGAGAGGGAGGGUUGAUGUUGAAGCUGGGGCUCUAGUGUAC~~~~~~~~~~~~~ Map1b.30415235_47 ~CCGUGCUGUUUGAGAGUGG------------GUAGGUGGCAGGGUAGGCUACUGUUCAGGGU // ClustID MergedIDs Count AvgDissim Members M88 1942 4 0.67 Atp6v1b2.22320426_29,Morf4l1.91235629_12,Grin1.3453776_25,Map1b.30415235_92 Best CMs (by avg z-score): 1. (Z = 2.18) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 2. (Z = 1.86) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 3. (Z = 1.86) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 4. (Z = 1.85) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.78) ciona-mir-92 - Ciona_microRNA_mir-92 6. (Z = 1.75) Corona_SL-III - Coronavirus_SL-III_cis-acting_replication_element_(CRE) 7. (Z = 1.65) HHBV_epsilon - Heron_HBV_RNA_encapsidation_signal_epsilon 8. (Z = 1.59) snoU6-77 - Small_nucleolar_RNA_U6-77 9. (Z = 1.52) sbrA - Listeria_sRNA_sbrA 10. (Z = 1.51) WLE3 - Wingless_localisation_element_3_(WLE3) Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM88.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM88_global.out/ --free-endgaps --indel=-100 --threads=4 .................((((((.((((...(((................)))..)))).))))))... MFE = -21.66 (Covariance contribution: -13.01) RNAz stats: MPI: 28.93, SCI: 0.65, ZSCORE: 0.57 Full summary: Sequences: 4 Columns: 69 Reading direction: forward Mean pairwise identity: 28.93 Shannon entropy: 1.13274 G+C content: 0.44025 Mean single sequence MFE: -12.55 Consensus MFE: -8.18 Energy contribution: -6.49 Covariance contribution: -1.69 Combinations/Pair: 2.31 Mean z-score: 0.57 Structure conservation index: 0.65 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.51 SVM RNA-class probability: 0.724776 Prediction: RNA Multiple alignment from mlocarna: Atp6v1b2.22320426_29 ~~~~~~~CCACUCCGAGCAUUCCACCUUCC-AGUUGUU----------UUUCUCUGAGG-GGAUGGGGG Morf4l1.91235629_12 ~~~~~~~~~~~~~~~~UGCUUAAAGAGCC--CAUCCUUUGCAAGUCAUCCAUGUUGUUCCUUAGGCAU~ Grin1.3453776_25 ~~~~~~~~~~~~~~~~GGGCUCCAGACUCCAAGAGGGCUGAGCC---UUCUCUUCUGUCCGCAGCCACA Map1b.30415235_92 UUUUUCCAAACCCCGAACCCCAU---GCAU-GCUU-UC----------CCAGUCUUGUG-AUGGGA~~~ // ClustID MergedIDs Count AvgDissim Members M89 5871 3 0.43 Atp2b2.149655651_68,Adcy5.67290968_13,Atp2b2.149655651_75 Best CMs (by avg z-score): 1. (Z = 2.89) Yfr1 - Cyanobacterial_functional_RNA_1 2. (Z = 2.17) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.14) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.10) snoZ178 - Small_nucleolar_RNA_Z178 5. (Z = 1.90) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 6. (Z = 1.87) Y_RNA - Y_RNA 7. (Z = 1.78) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.71) Pospi_RY - Pospiviroid_RY_motif_stem_loop 9. (Z = 1.71) mir-32 - microRNA_mir-32 10. (Z = 1.67) Arthropod_7SK - Arthropod_7SK_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM89.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM89_global.out/ --free-endgaps --indel=-100 --threads=4 ((((((((...(((....)))....))))))...))...................... MFE = -23.67 (Covariance contribution: -17.13) RNAz stats: MPI: 53.53, SCI: 0.71, ZSCORE: -0.49 Full summary: Sequences: 3 Columns: 58 Reading direction: forward Mean pairwise identity: 53.53 Shannon entropy: 0.63612 G+C content: 0.50749 Mean single sequence MFE: -10.93 Consensus MFE: -7.75 Energy contribution: -6.20 Covariance contribution: -1.55 Combinations/Pair: 1.78 Mean z-score: -0.49 Structure conservation index: 0.71 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.14 SVM RNA-class probability: 0.899101 Prediction: RNA Multiple alignment from mlocarna: Atp2b2.149655651_68 GGUGGGGA---GUCCUUUGUCACAUUUUUCA--UCCUACCCUCCUCCAUUCAACC~~~ Adcy5.67290968_13 ~GGAGAGAUGCGGCCUGUGCC--AUUCUCUC---CUCACA--CCUCCAUGCACACAGA Atp2b2.149655651_75 ~~GAGGGAU--AGCCUAUGCUCCAGCCCCUCGUUCUCACACUCUUCCAUACACA~~~~ // ClustID MergedIDs Count AvgDissim Members M86 3444 3 0.52 Grina.114279801_13,Shank3.127875955_10,Glt25d1.18822081_24 Best CMs (by avg z-score): 1. (Z = 2.87) TB11Cs4H3 - Trypanosomatid_snoRNA_TB11Cs4H3 2. (Z = 2.81) mir-32 - microRNA_mir-32 3. (Z = 2.66) mir-22 - microRNA_mir-22 4. (Z = 2.54) HBV - HBV_RNA_encapsidation_signal_epsilon 5. (Z = 2.52) mir-1207 - microRNA_mir-1207 6. (Z = 2.46) mir-661 - microRNA_mir-661 7. (Z = 2.32) mir-458 - microRNA_mir-458 8. (Z = 2.27) snoR114 - small_nucleolar_RNA_snoR114 9. (Z = 2.14) pRNA - NoRC_assoicated_RNA,_pRNA 10. (Z = 2.11) mir-574 - microRNA_mir-574 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM86.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM86_global.out/ --free-endgaps --indel=-100 --threads=4 ..........((((((((.....((((...((........))))))...))))))))...... MFE = -30.79 (Covariance contribution: -19.62) RNAz stats: MPI: 36.02, SCI: 0.66, ZSCORE: -0.18 Full summary: Sequences: 3 Columns: 63 Reading direction: forward Mean pairwise identity: 36.02 Shannon entropy: 0.91010 G+C content: 0.57600 Mean single sequence MFE: -20.50 Consensus MFE: -13.61 Energy contribution: -10.29 Covariance contribution: -3.32 Combinations/Pair: 2.17 Mean z-score: -0.18 Structure conservation index: 0.66 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.88 SVM RNA-class probability: 0.972750 Prediction: RNA Multiple alignment from mlocarna: Grina.114279801_13 GAGCAGAGAGGGUGGCAUGUUUCAGGG-GAGGAGGCU----CUCUU---GUGCUGCCA~~~~~ Shank3.127875955_10 ~~~~~~~GGGGAGGGGGGAGACAUUGGGGUUCUCGAUAGGGGCCAAGGAGCCCCCUG~~~~~~ Glt25d1.18822081_24 ~~~~~~GGGGGGGGGGGCG----UGUGUGUGCAGGUAGGGGCUAUG---GCUCCCUUGCCCAC // ClustID MergedIDs Count AvgDissim Members M87 1241 4 0.53 Atp2a2.35312505_11,Tmeff1.65356245_12,Syt4.23805080_8,Cdh2.8048920_22 Best CMs (by avg z-score): 1. (Z = 3.34) 23S-methyl - 23S_methyl_RNA_motif 2. (Z = 2.91) GcvB - GcvB_RNA 3. (Z = 2.87) Chlorobi-RRM - Chlorobi-RRM_RNA 4. (Z = 2.86) Arthropod_7SK - Arthropod_7SK_RNA 5. (Z = 2.84) RprA - RprA_RNA 6. (Z = 2.81) OmrA-B - OmrA-B_family 7. (Z = 2.74) rnk_pseudo - Pseudomonas_rnk_leader 8. (Z = 2.66) MIR1444 - microRNA_MIR1444 9. (Z = 2.65) ctRNA_pT181 - ctRNA 10. (Z = 2.56) rimP - Enterobacteria_rnk_leader Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM87.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM87_global.out/ --free-endgaps --indel=-100 --threads=4 ......................(((((((.......)))))))........................ MFE = -7.76 (Covariance contribution: -4.99) RNAz stats: MPI: 32.09, SCI: 0.77, ZSCORE: 0.62 Full summary: Sequences: 4 Columns: 67 Reading direction: forward Mean pairwise identity: 32.09 Shannon entropy: 1.17867 G+C content: 0.24316 Mean single sequence MFE: -6.25 Consensus MFE: -4.84 Energy contribution: -1.65 Covariance contribution: -3.19 Combinations/Pair: 3.33 Mean z-score: 0.62 Structure conservation index: 0.77 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.80 SVM RNA-class probability: 0.822488 Prediction: RNA Multiple alignment from mlocarna: Tmeff1.65356245_12 ~~~~~~~~~~~~~AAAUAGAUAUUCAAAU----GUUUUUUGAGAUUUAGUACCUGGUUUUUUUUAGA Cdh2.8048920_22 ~~~~GGAACAUGUGUAUGUAUUAUUUGGACUUUGGAUUCAGGUUUUUUG-CAUGU~~~~~~~~~~~~ Syt4.23805080_8 UCAAGUCACAGAUGUGUGUUGUGGGUGAUUUCAUUUUUUGCCUUGGUAGU~~~~~~~~~~~~~~~~~ Atp2a2.35312505_11 ~~~~~~~UAAAUAGCAUG---UAUUGUGUCUUUU--GCAUGAUUCUCUGGAUUUAAUUUGGU~~~~~ // ClustID MergedIDs Count AvgDissim Members M84 36 3 0.44 Fmr1.154791521_48,Usp9x.21606330_39,Becn1.90317957_13 Best CMs (by avg z-score): 1. (Z = 3.83) RybB - RybB_RNA 2. (Z = 3.43) rimP - Enterobacteria_rnk_leader 3. (Z = 3.41) Arthropod_7SK - Arthropod_7SK_RNA 4. (Z = 3.21) P20 - Pseudomonas_sRNA_P20 5. (Z = 3.20) U1_yeast - Yeast_U1_spliceosomal_RNA 6. (Z = 3.07) GcvB - GcvB_RNA 7. (Z = 2.99) mir-626 - microRNA_mir-626 8. (Z = 2.96) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.89) S_pombe_snR35 - small_nucleolar_RNA_snR35 10. (Z = 2.79) CRISPR-DR24 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM84.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM84_global.out/ --free-endgaps --indel=-100 --threads=4 .................(((((((.((((...............)))))))))))........ MFE = -16.01 (Covariance contribution: -12.71) RNAz stats: MPI: 29.73, SCI: 1.26, ZSCORE: 0.59 Full summary: Sequences: 3 Columns: 63 Reading direction: forward Mean pairwise identity: 29.73 Shannon entropy: 0.98698 G+C content: 0.20962 Mean single sequence MFE: -3.73 Consensus MFE: -4.71 Energy contribution: -1.06 Covariance contribution: -3.65 Combinations/Pair: 2.00 Mean z-score: 0.59 Structure conservation index: 1.26 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.54 SVM RNA-class probability: 0.256459 Prediction: OTHER Multiple alignment from mlocarna: Fmr1.154791521_48 ~~ACAGAUUGGAUUU--UAUGUUGACAUUUGUUUGGUU----AUAGUGCAAUAUAUUU~~~~~ Becn1.90317957_13 ~~~~~~~~~~~~~UACAAAAUGCUGUUUGAUACUGUUUGAGAUGUGGAAGGAUUUAAUUAUUU Usp9x.21606330_39 CAACCUACCCUAUUUAAAUAUUUUGCUGU---UUUAUU----UUAUAGAAAUUAUUU~~~~~~ // ClustID MergedIDs Count AvgDissim Members M85 2048 6 0.62 Suclg1.106601307_2,Bdnf.977114_22,Slc7a8.32800927_36,Grina.114279801_2,Atp5d.11072820_4,Mapre3.25496282_5 Best CMs (by avg z-score): 1. (Z = 2.90) mir-593 - microRNA_mir-593 2. (Z = 2.74) mir-202 - microRNA_mir-202 3. (Z = 2.59) HBV - HBV_RNA_encapsidation_signal_epsilon 4. (Z = 2.42) SNORA49 - Small_nucleolar_RNA_SNORA49 5. (Z = 2.42) mir-1180 - microRNA_mir-1180 6. (Z = 2.31) IRES_IGF2 - Insulin-like_growth_factor_II_IRES 7. (Z = 2.27) mir-488 - microRNA_mir-488 8. (Z = 2.24) MIR2907 - microRNA_MIR2907 9. (Z = 2.20) MIR476 - microRNA_MIR476 10. (Z = 2.19) mir-150 - microRNA_mir-150 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM85.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM85_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((((((((..((((((.......)))))).......))))..)))))............... MFE = -32.00 (Covariance contribution: -17.50) RNAz stats: MPI: 31.28, SCI: 0.62, ZSCORE: 0.58 Full summary: Sequences: 6 Columns: 68 Reading direction: forward Mean pairwise identity: 31.28 Shannon entropy: 1.31046 G+C content: 0.53397 Mean single sequence MFE: -18.05 Consensus MFE: -11.16 Energy contribution: -6.45 Covariance contribution: -4.71 Combinations/Pair: 3.36 Mean z-score: 0.58 Structure conservation index: 0.62 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.17 SVM RNA-class probability: 0.414162 Prediction: OTHER Multiple alignment from mlocarna: Suclg1.106601307_2 ~~~~CAGGCACCUGACCCUGGUCUCUCAGUACAGGGGAAGUCCAGGCAUGUUUU~~~~~~~~~~~~~~ Bdnf.977114_22 ~~~~CUCCCUGGUCCCCCAGGUCACUC--UUCUGGC---AUGGGUC--AGGGAAAGCUGCU~~~~~~~ Slc7a8.32800927_36 ~CCUCCUGCCAUCC-CAUUUGGGA-----CAAGAUG---ACAGGAU--GGCACUCACUUUGG~~~~~~ Grina.114279801_2 UCCCCCUCUCUGGUCCCCAGGC--AUG--GCCUGG----AG---CA--GAGGG-AGCCCCUCUC~~~~ Atp5d.11072820_4 ~~~~CUUCCAGAG---UCUGGG--AUC--CCCAGG----AUGCCUC--UGGAG-AGCUGGCCUUGAUU Mapre3.25496282_5 ~~~~CCUCUCUGGGUCCCCCAAG-------UGGCAC---UGGCCCA--GGGACGUCCAGGACCCCU~~ // ClustID MergedIDs Count AvgDissim Members M82 847 5 0.58 Laptm4a.32427418_7,Rab5c.89652340_19,Bdnf.977114_15,Morf4l1.91235629_17,Atrn.118696808_119 Best CMs (by avg z-score): 1. (Z = 2.75) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.60) frnS - Fumarate/nitrate_reductase_regulator_sRNA 3. (Z = 2.51) mir-556 - microRNA_mir-556 4. (Z = 2.33) isrP - isrP_Hfq_binding_RNA 5. (Z = 2.25) RyhB - RyhB_RNA 6. (Z = 2.23) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.21) suhB - suhB 8. (Z = 2.17) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.16) SprD - Small_pathogenicity_island_RNA_D 10. (Z = 2.14) rimP - Enterobacteria_rnk_leader Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM82.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM82_global.out/ --free-endgaps --indel=-100 --threads=4 ...((((.(((((((.((((((........)))))).))))))).))))............ MFE = -10.81 (Covariance contribution: -7.37) RNAz stats: MPI: 38.88, SCI: 0.72, ZSCORE: -0.04 Full summary: Sequences: 5 Columns: 61 Reading direction: forward Mean pairwise identity: 38.88 Shannon entropy: 1.14065 G+C content: 0.31798 Mean single sequence MFE: -7.58 Consensus MFE: -5.48 Energy contribution: -2.24 Covariance contribution: -3.24 Combinations/Pair: 3.17 Mean z-score: -0.04 Structure conservation index: 0.72 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.82 SVM RNA-class probability: 0.969834 Prediction: RNA Multiple alignment from mlocarna: Laptm4a.32427418_7 ~~~GGGUAGGGAGGGGAAGGGU----CUCUAUGUUUUCUUUUUUAACUUUGCACUUU~~~~ Rab5c.89652340_19 ~~GGGGAGUGGGAGGGAUGGAACCAACUUUUUCUGUAUUUUGUAUUGUAUGU~~~~~~~~~ Bdnf.977114_15 ~~AUGGGGAACGGGAGGGGUAG----AUUUCUGUUUGUUUUGUGUUUUAUUUCGUU~~~~~ Morf4l1.91235629_17 ~~~~~~~UCUUGUAGGAGUUUUU----UUCAGAUCUUCAAUAAAUUUUUUCUUUAAAUUUC Atrn.118696808_119 GCUGGGAUUGGUGGUGUUAUAC----AUACAUUUAGGACUGCAAUUUUUGGUAU~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M83 6420 5 0.59 Glt25d1.18822081_8,Usp9x.21606330_12,Itpr1.144028781_17,Vdac2.2515297_16,Gria2.172265159_103 Best CMs (by avg z-score): 1. (Z = 2.79) Arthropod_7SK - Arthropod_7SK_RNA 2. (Z = 2.62) 23S-methyl - 23S_methyl_RNA_motif 3. (Z = 2.58) NrrF - NrrF_RNA 4. (Z = 2.49) LhrC - Listeria_Hfq_binding_LhrC 5. (Z = 2.42) rnk_leader - Enterobacteria_rnk_leader 6. (Z = 2.19) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.08) rseX - rseX_Hfq_binding_RNA 8. (Z = 2.07) PVX_3 - Potato_virus_X_cis-acting_regulatory_element 9. (Z = 2.05) SVLPA - Simian_virus_40_late_polyadenylation_signal_(SVLPA) 10. (Z = 2.01) PrrF - PrrF_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM83.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM83_global.out/ --free-endgaps --indel=-100 --threads=4 ...............................((((..........)))).................................. MFE = -2.93 (Covariance contribution: -3.45) RNAz stats: MPI: 32.53, SCI: -0.00, ZSCORE: 0.89 Full summary: Sequences: 5 Columns: 83 Reading direction: forward Mean pairwise identity: 32.53 Shannon entropy: 1.25700 G+C content: 0.23011 Mean single sequence MFE: -3.35 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.89 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.91 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Glt25d1.18822081_8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GACUCCCCCUUAUCAGUGAUUGAUUUCAUCAUC--AGGUUUUUUUGUUCAGC Usp9x.21606330_12 ~CAUCAACAAAACAGCCCAUUCAUUCAUGUCACACCAAUAGUUUCGUGUUC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Itpr1.144028781_17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~UAGUGAUAACUCCAGGUCUGUGAACCAUUCAAACAACAUUCAUUUUUGAG~~~~~~ Vdac2.2515297_16 GCAACCAAACUCCCUGUGUCCCUAGCAUAAUCAAUCCACGAGGUCUUUGA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Gria2.172265159_103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~AACCACUGAACAAUUCUCCAGUACCAACAAUAUCAUUAAAUUUUUUUUUA~~~~~~ // ClustID MergedIDs Count AvgDissim Members M80 4356 4 0.41 Mapre3.25496282_6,Fgf13.144199535_18,Dlg4.56889789_2,Slc7a8.32800927_46 Best CMs (by avg z-score): 1. (Z = 3.41) suhB - suhB 2. (Z = 2.17) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.07) H19_3 - H19_conserved_region_3 4. (Z = 1.94) LhrC - Listeria_Hfq_binding_LhrC 5. (Z = 1.85) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.74) sbrA - Listeria_sRNA_sbrA 7. (Z = 1.73) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.56) RsaE - RNA_Staph._aureus_E 9. (Z = 1.56) RydC - RydC_RNA 10. (Z = 1.47) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM80.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM80_global.out/ --free-endgaps --indel=-100 --threads=4 .................(((.....)))......................................... MFE = -7.01 (Covariance contribution: -5.86) RNAz stats: MPI: 45.68, SCI: 0.63, ZSCORE: 0.44 Full summary: Sequences: 4 Columns: 69 Reading direction: forward Mean pairwise identity: 45.68 Shannon entropy: 0.87624 G+C content: 0.40007 Mean single sequence MFE: -2.68 Consensus MFE: -1.67 Energy contribution: -1.05 Covariance contribution: -0.62 Combinations/Pair: 2.00 Mean z-score: 0.44 Structure conservation index: 0.63 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.46 SVM RNA-class probability: 0.704176 Prediction: RNA Multiple alignment from mlocarna: Slc7a8.32800927_46 ~~~~~~~~~~~~~~~CAGGGACCACCCCUCUACCCCUU-UCCU-CCCAU--UCCUUCAGCCUGCACCUG Mapre3.25496282_6 ~~~~~~~~~~~~ACGUCCAGGACCCCUGUCCACUCCCC-UCCUAUUUAU--UUCCGUUGUCUCCA~~~~ Dlg4.56889789_2 CAAGUCCUUUGUAC-CCCAGCCUCCCUUCCCA--CCCU-UCUUAUUUAU--UUCCU~~~~~~~~~~~~~ Fgf13.144199535_18 ~~~~~~~~~~~~~~UUAAGGUUUUUCCUCUUUCUCCCUCUCCUUCCUACUGUCCCUCUUCCUCU~~~~~ // ClustID MergedIDs Count AvgDissim Members M81 6678 4 0.53 Gria2.172265159_76,Slc7a8.32800927_10,Cyfip2.31321000_32,Dpysl2.46346413_50 Best CMs (by avg z-score): 1. (Z = 3.31) suhB - suhB 2. (Z = 2.82) ctRNA_p42d - ctRNA 3. (Z = 2.70) sbrA - Listeria_sRNA_sbrA 4. (Z = 2.66) snoR110 - Small_nucleolar_RNA_snoR110 5. (Z = 2.56) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 6. (Z = 2.46) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.45) Pseudomon-1 - Pseudomon-1_RNA 8. (Z = 2.42) L10_leader - Ribosomal_protein_L10_leader 9. (Z = 2.40) mir-335 - microRNA_mir-335 10. (Z = 2.34) VrrA - Vibrio_regulatory_RNA_of_OmpA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM81.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM81_global.out/ --free-endgaps --indel=-100 --threads=4 ..............(((((((((.............))))))))).................... MFE = -8.69 (Covariance contribution: -6.57) RNAz stats: MPI: 35.38, SCI: 0.42, ZSCORE: 1.01 Full summary: Sequences: 4 Columns: 65 Reading direction: forward Mean pairwise identity: 35.38 Shannon entropy: 1.08707 G+C content: 0.25341 Mean single sequence MFE: -3.66 Consensus MFE: -1.53 Energy contribution: -0.65 Covariance contribution: -0.88 Combinations/Pair: 2.00 Mean z-score: 1.01 Structure conservation index: 0.42 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.34 SVM RNA-class probability: 0.010695 Prediction: OTHER Multiple alignment from mlocarna: Gria2.172265159_76 ~~~~~~~~~~~~~~~AAUAUGUUCUUAUAAAAUGCCAACAUCUUUUUAUUCUGUUUUUCCUCAAU Slc7a8.32800927_10 ~UUUAGGUGCCUCUAAGAAACCUGGGUUCAC---UACUGUUUCUUCUCCCUAAC~~~~~~~~~~~ Cyfip2.31321000_32 AUGUUGG---CUACUAAAAGAUUCUUGGAACGUUUUAUUCUUUUGCUCUCAAC~~~~~~~~~~~~ Dpysl2.46346413_50 ~~~~~~~~~UUUAAAAAUUGGUUGACUUAAUAUAUUUGCUCUUUUUUUUCUUACCUGCG~~~~~~ // ClustID MergedIDs Count AvgDissim Members M60 2079 3 0.63 Rnf111.74909360_35,Fmr1.154791521_51,Atrn.118696808_13 Best CMs (by avg z-score): 1. (Z = 4.29) RUF1 - Plasmodium_RNA_of_unkown_function_RUF1 2. (Z = 3.67) mir-932 - microRNA_mir-932 3. (Z = 3.51) tp2 - tp2 4. (Z = 3.51) snoMe28S-U3344 - Small_nucleolar_RNA_Me28S-U3344 5. (Z = 3.48) S_pombe_snR33 - small_nucleolar_RNA_snR33 6. (Z = 3.48) DdR2 - D._discoideum_snoRNA_DdR2 7. (Z = 3.43) K10_TLS - K10_transport/localisation_element_(TLS) 8. (Z = 3.33) snR85 - Small_nucleolar_RNA_snR85 9. (Z = 3.33) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 10. (Z = 3.31) mir-135 - mir-135_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM60.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM60_global.out/ --free-endgaps --indel=-100 --threads=4 .......((((.(((((.....)))))))))(((((...........)))))............. MFE = -19.44 (Covariance contribution: -15.14) RNAz stats: MPI: 32.63, SCI: 0.78, ZSCORE: -1.23 Full summary: Sequences: 3 Columns: 65 Reading direction: forward Mean pairwise identity: 32.63 Shannon entropy: 0.94886 G+C content: 0.17767 Mean single sequence MFE: -7.03 Consensus MFE: -5.50 Energy contribution: -0.95 Covariance contribution: -4.54 Combinations/Pair: 2.23 Mean z-score: -1.23 Structure conservation index: 0.78 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.62 SVM RNA-class probability: 0.999060 Prediction: RNA Multiple alignment from mlocarna: Rnf111.74909360_35 ~UUAAAAAUUU-UAAUUUCUAUAGUUAAGAUUUACAACAUAAUAUAGAGUAA~~~~~~~~~~~~~ Fmr1.154791521_51 ~~~~~~~GCAA-UCUUUACAAU---GAUUGCUUUUA----AAAAUUUUAAGAUAGGAAAGAAAUC Atrn.118696808_13 AUUAAUAAUGAUCUUUCUCUUUGGAAGUCAUAUCAA----AGUAUAAUUGAUGG~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M61 6197 3 0.37 Oxt.118194940_1,Nrgn.38790596_10,Ntrk2.11676658_40 Best CMs (by avg z-score): 1. (Z = 4.22) RMST_10 - Rhabdomyosarcoma_2_associated_transcript_conserved_region_10 2. (Z = 4.08) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.91) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 4. (Z = 3.85) plasmodium_snoR11 - small_nucleolar_RNA_snoR11 5. (Z = 3.77) Vg1_ribozyme - Manganese_dependent_ribozyme_in_Vg1_mRNA 6. (Z = 3.74) PreQ1 - PreQ1_riboswitch 7. (Z = 3.64) ceN115 - C._elegans_sRNA_ceN115 8. (Z = 3.60) SCARNA8 - Small_Cajal_body_specific_RNA_8 9. (Z = 3.57) CRISPR-DR55 - CRISPR_RNA_direct_repeat_element 10. (Z = 3.55) S_pombe_snR36 - small_nucleolar_RNA_snR36 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM61.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM61_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ............((....))..................................... MFE = -2.38 (Covariance contribution: -3.68) RNAz stats: MPI: 50.88, SCI: -0.00, ZSCORE: -0.47 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 50.88 Shannon entropy: 0.70576 G+C content: 0.25146 Mean single sequence MFE: -1.57 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.47 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.20 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Oxt.118194940_1 ~~~~~~~UCAUUCCCCAUGGCCACUACCAGAAAAAAUUAAAAAAAAAACAUAAAUAA Nrgn.38790596_10 GCCCAAUGCGUCGCCCAAGUACUCUCAAAAAAAAAAAAAAAAAAAAAAAA~~~~~~~ Ntrk2.11676658_40 ~~~~~~GCCAUUUGACACCAAAGGAAAAAAAAAAAGAAAAAGAAAAAGAAAAAAUC~ // ClustID MergedIDs Count AvgDissim Members M62 5843 3 0.50 Ak7.129933292_2,Adcy5.67290968_12,Appbp2.73460120_40 Best CMs (by avg z-score): 1. (Z = 3.51) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 2. (Z = 2.00) TB11Cs4H3 - Trypanosomatid_snoRNA_TB11Cs4H3 3. (Z = 1.93) mir-202 - microRNA_mir-202 4. (Z = 1.92) TB10Cs4H2 - Trypanosomatid_snoRNA_TB10Cs4H2 5. (Z = 1.71) MIR1122 - microRNA_MIR1122 6. (Z = 1.69) mir-46 - mir-46/mir-47/mir-281_microRNA_precursor_family 7. (Z = 1.67) HBV - HBV_RNA_encapsidation_signal_epsilon 8. (Z = 1.66) TB10Cs1H2 - Trypanosomatid_snoRNA_TB10Cs1H2 9. (Z = 1.64) ceN33 - C._elegans_snoRNA_ceN33 10. (Z = 1.56) S_pombe_snR93 - small_nucleolar_RNA_snR93 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM62.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM62_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((((((((.((......)).)))))))))..................... MFE = -24.83 (Covariance contribution: -13.63) RNAz stats: MPI: 37.72, SCI: 1.06, ZSCORE: 0.26 Full summary: Sequences: 3 Columns: 56 Reading direction: forward Mean pairwise identity: 37.72 Shannon entropy: 0.88235 G+C content: 0.52292 Mean single sequence MFE: -13.43 Consensus MFE: -14.27 Energy contribution: -11.50 Covariance contribution: -2.77 Combinations/Pair: 2.20 Mean z-score: 0.26 Structure conservation index: 1.06 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.62 SVM RNA-class probability: 0.765813 Prediction: RNA Multiple alignment from mlocarna: Ak7.129933292_2 AAAUGCCUUCCUAGGGGU-----UUUUUGGGGGGAGUUGGGUGGG-GGGAGUAGUG Adcy5.67290968_12 ~~~~~UAUGCCCCCUCACAACAUUUUGGGGGCAGGAACUGGGAGAGAUGCGGCCU~ Appbp2.73460120_40 ~GAUGCACUGCUCCUGGU-AUUGCUUGGAGUGGUGGAUGAGUGGGUGUGUGU~~~~ // ClustID MergedIDs Count AvgDissim Members M63 1132 5 0.61 Fmr1.154791521_23,Morf4l1.91235629_4,Syt4.23805080_44,Map1b.30415235_95,Fmr1.154791521_33 Best CMs (by avg z-score): 1. (Z = 3.60) rli61 - Listeria_sRNA_rli61 2. (Z = 3.11) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 3. (Z = 3.08) ctRNA_pT181 - ctRNA 4. (Z = 3.05) VrrA - Vibrio_regulatory_RNA_of_OmpA 5. (Z = 2.99) CopA - CopA-like_RNA 6. (Z = 2.99) Qrr - Qrr_RNA 7. (Z = 2.98) RsaE - RNA_Staph._aureus_E 8. (Z = 2.90) GcvB - GcvB_RNA 9. (Z = 2.89) leu-phe_leader - leu/phe_leader_RNA_from_Lactococcus_lactis 10. (Z = 2.82) DPB - Stem_loopII_regulatory_element_in_POLB Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM63.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM63_global.out/ --free-endgaps --indel=-100 --threads=4 ....(((((((..........)))))))........((((........)))).......... MFE = -13.62 (Covariance contribution: -12.56) RNAz stats: MPI: 36.05, SCI: 0.50, ZSCORE: -0.53 Full summary: Sequences: 5 Columns: 62 Reading direction: forward Mean pairwise identity: 36.05 Shannon entropy: 1.13137 G+C content: 0.24434 Mean single sequence MFE: -6.08 Consensus MFE: -3.06 Energy contribution: -1.62 Covariance contribution: -1.44 Combinations/Pair: 1.86 Mean z-score: -0.53 Structure conservation index: 0.50 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.61 SVM RNA-class probability: 0.954953 Prediction: RNA Multiple alignment from mlocarna: Fmr1.154791521_23 ~~AGGAAAAGAAAUAAC-U-AUCUUUUC---G----UUUGGGAGAGGCUAAAGAUGUUUUC~ Morf4l1.91235629_4 AAAUAAAAGGAGUUAACUG-CUCCUUUUUUCUUUCUUUUUUUCAUUUCAAA~~~~~~~~~~~ Syt4.23805080_44 ~UAUAAGGAGAUAUAUCUCAUUCUGUUU---GUACAAAAGACUUUACGCUUUCC~~~~~~~~ Map1b.30415235_95 ~~~~AGAAAAAAAU----U-UUUUUUCU---UAACCUUACAUAUCAUAGUGAAUGGUUUCCC Fmr1.154791521_33 UAGUUAAAAAUAAU----U-CAUUUUUU---U--CCUUUUGAUGUGUCAAGUCUUAUUUU~~ // ClustID MergedIDs Count AvgDissim Members M64 1397 4 0.48 Vegfa.10534185_44,Gria2.172265159_65,Vegfa.10534185_10,Atp2b2.149655651_20 Best CMs (by avg z-score): 1. (Z = 5.63) K10_TLS - K10_transport/localisation_element_(TLS) 2. (Z = 5.22) MIR1122 - microRNA_MIR1122 3. (Z = 5.09) mir-198 - microRNA_mir-198 4. (Z = 5.04) mir-576 - microRNA_mir-576 5. (Z = 4.86) snR85 - Small_nucleolar_RNA_snR85 6. (Z = 4.86) mir-280 - microRNA_mir-280 7. (Z = 4.86) MIR476 - microRNA_MIR476 8. (Z = 4.81) ceN81 - C._elegans_snoRNA_ceN81 9. (Z = 4.80) SNORA72 - Small_nucleolar_RNA_SNORA72 10. (Z = 4.79) mir-649 - microRNA_mir-649 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM64.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM64_global.out/ --free-endgaps --indel=-100 --threads=4 ......((.((((((((((((((......)))))))))...))))).))........... MFE = -21.35 (Covariance contribution: -15.37) RNAz stats: MPI: 44.54, SCI: 0.73, ZSCORE: -0.8 Full summary: Sequences: 4 Columns: 60 Reading direction: forward Mean pairwise identity: 44.54 Shannon entropy: 0.91115 G+C content: 0.13520 Mean single sequence MFE: -9.87 Consensus MFE: -7.22 Energy contribution: -4.72 Covariance contribution: -2.50 Combinations/Pair: 2.00 Mean z-score: -0.80 Structure conservation index: 0.73 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.05 SVM RNA-class probability: 0.997165 Prediction: RNA Multiple alignment from mlocarna: Vegfa.10534185_44 ~~~~~~~AAUAUAUAUAUAUAUAUAUGUUUAUGUAUAU---AUGUGAUUCUGAUAAAAUA Gria2.172265159_65 GCAUCAGUAUAUUGCUGUAUACAUGUGUCUGUGCAUAGAAGUGAUAAAUG~~~~~~~~~~ Vegfa.10534185_10 ~~UAUAUAUAUAUUAUAUAUAUAAAUAAAUAUAUAUGU---UUUAUAU----AUAAAAU~ Atp2b2.149655651_20 ~~UAAGUAGAUAUUAUAUAUAUAUAUACAUAUAUAUACAUGGAUAUAUAAAG~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M65 1401 4 0.52 Tpt1.56755083_4,Atrn.118696808_122,Bdnf.977114_2,Sept9.107478216_48 Best CMs (by avg z-score): 1. (Z = 3.82) mir-286 - microRNA_mir-286 2. (Z = 3.72) snopsi28S-3316 - Small_nucleolar_RNA_psi28S-3316 3. (Z = 3.63) SNORA20 - Small_nucleolar_RNA_SNORA20 4. (Z = 3.62) snoR13 - small_nucleolar_RNA_snoR13 5. (Z = 3.54) SNORA15 - Small_nucleolar_RNA_SNORA15 6. (Z = 3.50) SCARNA24 - Small_Cajal_body_specific_RNA_24 7. (Z = 3.48) RUF1 - Plasmodium_RNA_of_unkown_function_RUF1 8. (Z = 3.47) SNORD29 - Small_nucleolar_RNA_SNORD29 9. (Z = 3.45) S_pombe_snR90 - small_nucleolar_RNA_snR90 10. (Z = 3.43) SNORA31 - Small_nucleolar_RNA_SNORA31 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM65.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM65_global.out/ --free-endgaps --indel=-100 --threads=4 ...............(((((((((.....)))))))))............................... MFE = -6.31 (Covariance contribution: -5.59) RNAz stats: MPI: 38.50, SCI: 0.16, ZSCORE: -0.03 Full summary: Sequences: 4 Columns: 69 Reading direction: forward Mean pairwise identity: 38.50 Shannon entropy: 1.05289 G+C content: 0.17615 Mean single sequence MFE: -4.85 Consensus MFE: -0.80 Energy contribution: -0.55 Covariance contribution: -0.25 Combinations/Pair: 2.00 Mean z-score: -0.03 Structure conservation index: 0.16 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.37 SVM RNA-class probability: 0.000006 Prediction: OTHER Multiple alignment from mlocarna: Tpt1.56755083_4 ~~~~~~~~~~~~~~~UUUUUUUUUUAAAGAAAAAAAAACAUGUCAUGUGGGUUGUCUAAAAAUAA~~~~ Atrn.118696808_122 GGGUCUGCAUUUUAAAUGCAAAUGUGAAGCACUUGUAUAUAAACAGAAGU~~~~~~~~~~~~~~~~~~~ Bdnf.977114_2 ~~~~~~~~~~~~~~~~~UAUUCAGUUAAGAAAAAGAUA-AUUUUAUGAACUGCAUGUAUAAAUGAAGU~ Sept9.107478216_48 ~~~~~~~~~~~~~~~~UUUUUGUAUAAAUAACAAAGU---GUUGAAAUGUAUUUCCUGAAAUAAAUGUU // ClustID MergedIDs Count AvgDissim Members M66 529 3 0.41 Cdh2.8048920_19,Map1b.30415235_66,Stmn2.95284903_15 Best CMs (by avg z-score): 1. (Z = 2.82) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.82) tp2 - tp2 3. (Z = 2.70) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.65) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 5. (Z = 2.47) MIR396 - microRNA_MIR396 6. (Z = 2.38) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.37) snR85 - Small_nucleolar_RNA_snR85 8. (Z = 2.31) mir-3 - microRNA_mir-3 9. (Z = 2.24) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.13) HSUR - Herpesvirus_saimiri_U_RNA1/RNA2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM66.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM66_global.out/ --free-endgaps --indel=-100 --threads=4 ...........(((((((.....((..............))......)))))))............ MFE = -10.63 (Covariance contribution: -11.53) RNAz stats: MPI: 36.27, SCI: 0.54, ZSCORE: -0.45 Full summary: Sequences: 3 Columns: 66 Reading direction: forward Mean pairwise identity: 36.27 Shannon entropy: 0.89027 G+C content: 0.28913 Mean single sequence MFE: -2.62 Consensus MFE: -1.42 Energy contribution: 0.02 Covariance contribution: -1.44 Combinations/Pair: 1.86 Mean z-score: -0.45 Structure conservation index: 0.54 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.62 SVM RNA-class probability: 0.955376 Prediction: RNA Multiple alignment from mlocarna: Cdh2.8048920_19 CAUGUACACUUUUUUUAUUUUCUGU-----AUUUUUUCCACCUCGCUGUAAAAAU~~~~~~~~~~~ Map1b.30415235_66 ~~~~~~~~~~~GCUUUUAUUUAUUUUCCUAUUUCUUUCCAACUCG--UAAAAGCCACACAUUA~~~ Stmn2.95284903_15 ~~~~~~~ACAUUUCUCUGCUCAUAA---------UCUGCUUCCUGCCUAGAAACCACAAAGCCAGG // ClustID MergedIDs Count AvgDissim Members M67 1259 3 0.51 Canx.35850944_61,Glt25d1.18822081_22,Opcml.28508230_3 Best CMs (by avg z-score): 1. (Z = 2.83) mir-154 - microRNA_mir-154 2. (Z = 2.55) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.54) SNORD93 - Small_Nucleolar_RNA_SNORD93 4. (Z = 2.39) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.33) RybB - RybB_RNA 6. (Z = 2.31) RydC - RydC_RNA 7. (Z = 2.28) mir-186 - microRNA_mir-186 8. (Z = 2.27) suhB - suhB 9. (Z = 2.14) CRISPR-DR26 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.13) InvR - Invasion_gene-associated_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM67.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM67_global.out/ --free-endgaps --indel=-100 --threads=4 .((((...((.((..(((..............))).)).))....))))........ MFE = -6.59 (Covariance contribution: -10.29) RNAz stats: MPI: 40.72, SCI: -0.00, ZSCORE: 1.67 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 40.72 Shannon entropy: 0.83751 G+C content: 0.32757 Mean single sequence MFE: -4.56 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.67 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -9.02 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Canx.35850944_61 ~GGCCCAUAUAUUCUGAUUUUCUA--UGCUGGAUUCUUUAU----GGUUGUAAAAUA Glt25d1.18822081_22 ~GGUUCUUAUUCCCUUGGUUGACUGCUGGGUUUCAGGGUAUUCAUGACUUU~~~~~~ Opcml.28508230_3 UUGUUCUUCUUGACUGUUUAGUUUUUUGGUUUGAUUUCUGG----GAUUUUCAA~~~ // ClustID MergedIDs Count AvgDissim Members M68 2882 6 0.31 Cdh2.8048920_29,Vegfa.10534185_9,Apba1.227308605_22,Rhobtb1.20089811_38,Slc7a8.32800927_3,Slc7a8.32800927_2 Best CMs (by avg z-score): 1. (Z = 3.26) NrrF - NrrF_RNA 2. (Z = 2.96) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 3. (Z = 2.44) snoZ178 - Small_nucleolar_RNA_Z178 4. (Z = 2.21) mir-1937 - microRNA_mir-1937 5. (Z = 2.16) H19_3 - H19_conserved_region_3 6. (Z = 2.05) snR161 - Small_nucleolar_RNA_snR161 7. (Z = 1.85) CC0196 - Cauldobacter_sRNA_CC0196 8. (Z = 1.82) MIR806 - microRNA_MIR806 9. (Z = 1.72) sbrA - Listeria_sRNA_sbrA 10. (Z = 1.71) Histone3 - Histone_3'_UTR_stem-loop Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM68.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM68_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ................................................................. MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 63.90, SCI: -0.00, ZSCORE: 0.53 Full summary: Sequences: 6 Columns: 65 Reading direction: forward Mean pairwise identity: 63.90 Shannon entropy: 0.71861 G+C content: 0.32051 Mean single sequence MFE: -0.27 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.53 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.94 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Cdh2.8048920_29 ~~~~~~AUUACACACACACACACACACACACACACACACACACACACACAAAUAAA~~~~~~~~~ Vegfa.10534185_9 ~~~~~~~~~~~~~~~CUGUAGACACACCCACCCACAUACACACACAUAUAUAUAUAUAUAUUAUA Apba1.227308605_22 ~~~~~~~~~~~~AACACACACACACACACACACACACACACACACAAAUAGAUACAACCAAU~~~ Rhobtb1.20089811_38 AAUGUUACAGUAUACACACUUGCACACACACACACACACACACACAACCA~~~~~~~~~~~~~~~ Slc7a8.32800927_3 ~~~~~~~~~~~~~~~ACACACACACACACACACACACACACACACACACACACACUUCUGUUAGG Slc7a8.32800927_2 ~~~~~~AACACACACACACACACACACACACACACACUCACACACACACACACACA~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M69 1139 5 0.59 Morf4l1.91235629_3,Ntrk2.11676658_73,Bdnf.977114_46,Bdnf.977114_4,Gria2.172265159_61 Best CMs (by avg z-score): 1. (Z = 3.79) mir-802 - microRNA_mir-802 2. (Z = 3.45) mir-92 - mir-92_microRNA_precursor_family 3. (Z = 3.34) mir-154 - microRNA_mir-154 4. (Z = 3.34) TB11Cs4H1 - Trypanosomatid_snoRNA_TB11Cs4H1 5. (Z = 3.28) mir-BART2 - mir-BART2_microRNA_precursor_family 6. (Z = 3.27) K10_TLS - K10_transport/localisation_element_(TLS) 7. (Z = 3.20) mir-124 - mir-124_microRNA_precursor_family 8. (Z = 3.17) mir-1912 - microRNA_mir-1912 9. (Z = 3.16) mir-280 - microRNA_mir-280 10. (Z = 3.15) mir-199 - mir-199_microRNA_precursor Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM69.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM69_global.out/ --free-endgaps --indel=-100 --threads=4 .........(((.((.(((.....(((....)))))).....)).)))............ MFE = -9.65 (Covariance contribution: -12.47) RNAz stats: MPI: 32.26, SCI: 0.21, ZSCORE: -0.4 Full summary: Sequences: 5 Columns: 60 Reading direction: forward Mean pairwise identity: 32.26 Shannon entropy: 1.29014 G+C content: 0.26418 Mean single sequence MFE: -7.58 Consensus MFE: -1.60 Energy contribution: 0.32 Covariance contribution: -1.92 Combinations/Pair: 4.00 Mean z-score: -0.40 Structure conservation index: 0.21 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.44 SVM RNA-class probability: 0.057476 Prediction: OTHER Multiple alignment from mlocarna: Morf4l1.91235629_3 UUGAUGUUUGUU-UCCUGU-----UUGAUUUUAAACA-GA--GAAAAUAAAAGGAGUUA~ Ntrk2.11676658_73 ~~~~~GCUCCAUGUCUUCUG--GACUCUUUAGAGAGCAGAACGAGAUGAAAAAAGUC~~~ Bdnf.977114_46 ~~~UAUUUAUUUAUUUUUUUGAGACAUUUUGGUGAAAGGAAAAAAGAAAGAAG~~~~~~~ Bdnf.977114_4 ~~~~~~~~~~ACAAUCUAUUUAUUGGACAUAUCCAUGACCAGAAAGAAACAGUCAUUUGC Gria2.172265159_61 AGUUAUAUUUUCAUGUUUU-----UAUAGAUAUGACAUGA--CAAGAACAU---AUAAUG // ClustID MergedIDs Count AvgDissim Members M146 6747 3 0.35 Ccni.16459077_17,Map1b.30415235_64,Appbp2.73460120_99 Best CMs (by avg z-score): 1. (Z = 4.47) isrP - isrP_Hfq_binding_RNA 2. (Z = 4.44) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 3. (Z = 4.13) 23S-methyl - 23S_methyl_RNA_motif 4. (Z = 4.03) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 5. (Z = 3.96) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 6. (Z = 3.88) mir-252 - microRNA_mir-252 7. (Z = 3.88) SprD - Small_pathogenicity_island_RNA_D 8. (Z = 3.85) K10_TLS - K10_transport/localisation_element_(TLS) 9. (Z = 3.82) snoR110 - Small_nucleolar_RNA_snoR110 10. (Z = 3.78) rli42 - Listeia_sRNA_rli42 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM146.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM146_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((((((((..(((((........))))).)))..........))))))...... MFE = -16.13 (Covariance contribution: -17.10) RNAz stats: MPI: 41.48, SCI: 0.52, ZSCORE: -0.63 Full summary: Sequences: 3 Columns: 60 Reading direction: forward Mean pairwise identity: 41.48 Shannon entropy: 0.81241 G+C content: 0.16006 Mean single sequence MFE: -4.06 Consensus MFE: -2.12 Energy contribution: 0.53 Covariance contribution: -2.66 Combinations/Pair: 1.90 Mean z-score: -0.63 Structure conservation index: 0.52 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.48 SVM RNA-class probability: 0.942756 Prediction: RNA Multiple alignment from mlocarna: Appbp2.73460120_99 ~AAUUUUAAGAGUUUUAUUUUGUUUUA--AAAAUUAACAUUUUUCACCUCUUG~~~~~~~ Map1b.30415235_64 CAUUUUCCAAAUGUUUAAUUUUUUAAAGAAAAUUAAUAUUCUAU----UUUUGU~~~~~~ Ccni.16459077_17 ~~~~~GUCAGUCUUAUUUUAGUUUUUAGUUUAAA-AAGAUUACU----AUUGUCCUUUUU // ClustID MergedIDs Count AvgDissim Members M147 3734 5 0.57 Ddn.137572548_32,Dpysl2.46346413_55,Atp6v1b2.22320426_6,Atp2b2.149655651_39,Tpt1.56755083_3 Best CMs (by avg z-score): 1. (Z = 2.27) suhB - suhB 2. (Z = 2.09) GcvB - GcvB_RNA 3. (Z = 2.03) Chlorobi-RRM - Chlorobi-RRM_RNA 4. (Z = 1.95) RyhB - RyhB_RNA 5. (Z = 1.92) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.91) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.91) L10_leader - Ribosomal_protein_L10_leader 8. (Z = 1.83) HCV_SLIV - Hepatitis_C_stem-loop_IV 9. (Z = 1.74) Spot_42 - Spot_42_RNA 10. (Z = 1.73) rnk_pseudo - Pseudomonas_rnk_leader Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM147.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM147_global.out/ --free-endgaps --indel=-100 --threads=4 ......((((((...((((((.....))))))...........))..))))............... MFE = -12.99 (Covariance contribution: -9.39) RNAz stats: MPI: 30.91, SCI: 0.69, ZSCORE: 2.12 Full summary: Sequences: 5 Columns: 66 Reading direction: forward Mean pairwise identity: 30.91 Shannon entropy: 1.25974 G+C content: 0.38107 Mean single sequence MFE: -8.30 Consensus MFE: -5.70 Energy contribution: -3.82 Covariance contribution: -1.88 Combinations/Pair: 3.00 Mean z-score: 2.12 Structure conservation index: 0.69 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.91 SVM RNA-class probability: 0.024172 Prediction: OTHER Multiple alignment from mlocarna: Dpysl2.46346413_55 ~~~~~~UUCUUGUACGGGGCCGC--GGGCCUCUUGGUUGUUUUCG--AGCAUUUUCUUAA~~~~~~ Ddn.137572548_32 ~GACUUCUGGGGCGCGCCGAGCCCUUCUUUGUAUUAAUCCACGCCUACCGG~~~~~~~~~~~~~~~ Atp6v1b2.22320426_6 CUUUAAAGUGGCGGAGGUGAGGCUUGCUUACC---GGUGUAU--C--UAUUUGUACA~~~~~~~~~ Atp2b2.149655651_39 ~~~~~~~CUGGAUGAGGGUUGG--UACGGCUU---GCUGCU--UU--CGGUUUUUCUUUUUGAAGA Tpt1.56755083_3 ~~~~~~~~~GACCGUGAUUUAU--UUGGAGUG---GAGGCAUUGU--UUUUUUUUUUUUUUAAAGA // ClustID MergedIDs Count AvgDissim Members M144 3864 3 0.49 Pklr.181222231_24,Lypla1.14882196_27,Pdcd5.88194319_2 Best CMs (by avg z-score): 1. (Z = 3.29) CRISPR-DR42 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.17) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.84) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.78) U2 - U2_spliceosomal_RNA 5. (Z = 2.70) snoR10 - small_nucleolar_RNA_snoR10 6. (Z = 2.65) tp2 - tp2 7. (Z = 2.61) U1A_PIE - U1A_polyadenylation_inhibition_element_(PIE) 8. (Z = 2.52) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 9. (Z = 2.51) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.44) CRISPR-DR5 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM144.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM144_global.out/ --free-endgaps --indel=-100 --threads=4 .................((...((.(..((((....))))....).)).))............ MFE = -3.29 (Covariance contribution: -9.12) RNAz stats: MPI: 32.80, SCI: -0.00, ZSCORE: 1.46 Full summary: Sequences: 3 Columns: 63 Reading direction: forward Mean pairwise identity: 32.80 Shannon entropy: 0.97499 G+C content: 0.25317 Mean single sequence MFE: -1.32 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.46 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.24 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Pklr.181222231_24 UUCUUUUAAACCCAACUGUUUAGGUGCAAUUAUAAAAA---CAACUCCCACAG~~~~~~~~~~ Lypla1.14882196_27 ~~~~AGUUUACAUUUUCUGUACAUGUUAUGCUUAAAACCAAAUACUGUUCAAGA~~~~~~~~~ Pdcd5.88194319_2 ~~~~~~~~~~~~~CCCUGUCUAUAUGCCUUUUGAAAAAAAUAAACUUGUACCUCAAACUCAAA // ClustID MergedIDs Count AvgDissim Members M145 3530 4 0.57 Tmeff1.65356245_2,Slc7a8.32800927_52,Canx.35850944_37,Usp9x.21606330_98 Best CMs (by avg z-score): 1. (Z = 3.26) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.07) MIR478 - microRNA_MIR478 3. (Z = 2.95) snoR110 - Small_nucleolar_RNA_snoR110 4. (Z = 2.70) CRISPR-DR21 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.61) GcvB - GcvB_RNA 6. (Z = 2.60) SprD - Small_pathogenicity_island_RNA_D 7. (Z = 2.56) rimP - Enterobacteria_rnk_leader 8. (Z = 2.55) RyhB - RyhB_RNA 9. (Z = 2.54) DPB - Stem_loopII_regulatory_element_in_POLB 10. (Z = 2.53) HIV_FE - HIV_Ribosomal_frameshift_signal Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM145.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM145_global.out/ --free-endgaps --indel=-100 --threads=4 ...............((((((((.....)))....)))))......((((.........))))..... MFE = -8.02 (Covariance contribution: -8.42) RNAz stats: MPI: 29.59, SCI: 0.07, ZSCORE: 0.67 Full summary: Sequences: 4 Columns: 68 Reading direction: forward Mean pairwise identity: 29.59 Shannon entropy: 1.13747 G+C content: 0.22373 Mean single sequence MFE: -5.22 Consensus MFE: -0.36 Energy contribution: 1.95 Covariance contribution: -2.31 Combinations/Pair: 2.62 Mean z-score: 0.67 Structure conservation index: 0.07 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.55 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Tmeff1.65356245_2 ~~~~~~~~UAUUUAUUUCAGAGGCCUUAUUU----UUGGACAUUUUUAGUG----UAGUACUGUUG~~ Slc7a8.32800927_52 ~~UUCAUUUAGGUUUUAAAUU----UUAUUG----GUUUGUUUUAUGGAG-----UAUUUUCUUU~~~ Canx.35850944_37 ~~~~~~~~~~~UAUUUUAUUGUGGCUUGUAC----AAUU---UUUUAAGUGAAUUUAGGGCUUUUUGU Usp9x.21606330_98 AAUUUGGUGGCUAUAUCCUGCCUUAUUUAGGAUUUUAGGAAAUUGCCUUU~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M142 4272 3 0.62 Gria2.172265159_94,Stmn2.95284903_1,Tmem30a.84827711_5 Best CMs (by avg z-score): 1. (Z = 3.28) mir-17 - mir-17_microRNA_precursor_family 2. (Z = 3.15) mir-449 - microRNA_mir-449 3. (Z = 3.12) mir-92 - mir-92_microRNA_precursor_family 4. (Z = 3.09) Pox_AX_element - Poxvirus_AX_element_late_mRNA_cis-regulatory_element 5. (Z = 3.03) mir-46 - mir-46/mir-47/mir-281_microRNA_precursor_family 6. (Z = 2.92) plasmodium_snoR24 - small_nucleolar_RNA_snoR24 7. (Z = 2.87) TB6Cs1H4 - Trypanosomatid_snoRNA_TB6Cs1H4 8. (Z = 2.71) mir-286 - microRNA_mir-286 9. (Z = 2.70) mir-500 - microRNA_mir-500 10. (Z = 2.69) mir-592 - microRNA_mir-592 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM142.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM142_global.out/ --free-endgaps --indel=-100 --threads=4 ..........((((((((((((((....))))))))......))))))....... MFE = -18.98 (Covariance contribution: -14.18) RNAz stats: MPI: 26.22, SCI: 1.25, ZSCORE: -0.49 Full summary: Sequences: 3 Columns: 55 Reading direction: forward Mean pairwise identity: 26.22 Shannon entropy: 1.08181 G+C content: 0.28379 Mean single sequence MFE: -7.63 Consensus MFE: -9.52 Energy contribution: -5.10 Covariance contribution: -4.42 Combinations/Pair: 2.29 Mean z-score: -0.49 Structure conservation index: 1.25 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.20 SVM RNA-class probability: 0.591869 Prediction: RNA Multiple alignment from mlocarna: Gria2.172265159_94 ~UAAUCUGUAAGUACUAUGGAUAUUUUGAUGAUCAUGAU---GGUAUUCGGAGA~ Stmn2.95284903_1 AAUCCCCCUGCCUAUAUUAUAAUGGAU-CA-UGCGAUAUCAGUAUGGGAAAA~~~ Tmem30a.84827711_5 ~~~~UAAAAAUUAGCCAUAUUGAUUAU-AUCAAUAUUAUAACUGCUAAAAUGACA // ClustID MergedIDs Count AvgDissim Members M143 2634 3 0.45 Gria2.172265159_15,Usp9x.21606330_113,Fgf13.144199535_11 Best CMs (by avg z-score): 1. (Z = 4.70) ceN100 - C._elegans_snoRNA_ceN100 2. (Z = 4.34) MIR1444 - microRNA_MIR1444 3. (Z = 4.32) rli36 - Listeria_sRNA_rli36 4. (Z = 4.01) MIR1122 - microRNA_MIR1122 5. (Z = 3.89) MIR476 - microRNA_MIR476 6. (Z = 3.86) DdR18 - D._discoideum_snoRNA_DdR18 7. (Z = 3.86) mir-2774 - microRNA_mir-2774 8. (Z = 3.81) snR85 - Small_nucleolar_RNA_snR85 9. (Z = 3.78) MIR828 - microRNA_MIR828 10. (Z = 3.65) LhrC - Listeria_Hfq_binding_LhrC Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM143.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM143_global.out/ --free-endgaps --indel=-100 --threads=4 ......((((.((((((...((((.....))))...)))))).))))............ MFE = -12.04 (Covariance contribution: -11.94) RNAz stats: MPI: 39.66, SCI: 1.09, ZSCORE: -0.12 Full summary: Sequences: 3 Columns: 59 Reading direction: forward Mean pairwise identity: 39.66 Shannon entropy: 0.83471 G+C content: 0.18096 Mean single sequence MFE: -4.71 Consensus MFE: -5.16 Energy contribution: -2.17 Covariance contribution: -2.99 Combinations/Pair: 1.80 Mean z-score: -0.12 Structure conservation index: 1.09 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.78 SVM RNA-class probability: 0.816022 Prediction: RNA Multiple alignment from mlocarna: Gria2.172265159_15 AGGAAAAAAACAUUUAAAAUAAAA-AAAUAUUU---UUAGGUAUUUUCACAGAC~~~~~ Usp9x.21606330_113 ~~~~~~AAAAUAAAACUUUAUAAAUUAAAUUUG---GGUUUUUCUUUCAUUUAUUAACA Fgf13.144199535_11 ~~~~~~~AAACAAAACAACAAAGUUAACUGCUUAAAUGUUUUGUAGGGGCAAACAAA~~ // ClustID MergedIDs Count AvgDissim Members M140 6497 4 0.57 Spag7.57543647_8,Vegfa.10534185_38,Fhod1.35144280_3,Map1b.30415235_116 Best CMs (by avg z-score): 1. (Z = 2.94) snoU90 - Small_nucleolar_RNA_U90 2. (Z = 2.71) mir-558 - microRNA_mir-558 3. (Z = 2.39) DicF - DicF_RNA 4. (Z = 2.37) snoZ188 - Small_nucleolar_RNA_Z188 5. (Z = 2.27) mir-140 - microRNA_mir-140 6. (Z = 2.27) snoZ112 - Small_nucleolar_RNA_Z112 7. (Z = 2.07) lincRNA-p21_2 - LincRNA-p21_conserved_region_2 8. (Z = 2.03) CRISPR-DR65 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.88) mir-449 - microRNA_mir-449 10. (Z = 1.87) CRISPR-DR48 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM140.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM140_global.out/ --free-endgaps --indel=-100 --threads=4 ..................((((((((.(............)))))))))............... MFE = -3.20 (Covariance contribution: -3.58) RNAz stats: MPI: 47.91, SCI: -0.00, ZSCORE: 0.42 Full summary: Sequences: 4 Columns: 64 Reading direction: forward Mean pairwise identity: 47.91 Shannon entropy: 0.88324 G+C content: 0.31341 Mean single sequence MFE: -7.26 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.42 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.94 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Spag7.57543647_8 ~~~~~UGUGUAAAUGUGUGAGUGGGU-AUUUAAUCUGUAUUAUUCUCUAUUACCCU~~~~~~~~ Vegfa.10534185_38 ~~~~GUUUUUCUGUGUGUGUGUGUGU-AUGAAAUCUGUGUUU-CCAAUCUCUCUCU~~~~~~~~ Fhod1.35144280_3 GUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUGUAC-ACAUACAU~~~~~~~~~~~~~ Map1b.30415235_116 ~~~~~~~~~~~~~~GUGUUUGUGUCGGUCUGCCUCUGUGUAUGGUAUUAUGUCUUAUAAUCCUG // ClustID MergedIDs Count AvgDissim Members M141 6131 3 0.37 Pklr.181222231_16,Appbp2.73460120_71,Appbp2.73460120_98 Best CMs (by avg z-score): 1. (Z = 3.21) CRISPR-DR3 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.18) TLS-PK6 - Pseudoknot_of_tRNA-like_structure 3. (Z = 2.78) sbrA - Listeria_sRNA_sbrA 4. (Z = 2.74) UPSK - UPSK_RNA 5. (Z = 2.58) LhrC - Listeria_Hfq_binding_LhrC 6. (Z = 2.48) CRISPR-DR29 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.24) RsaC - RNA_Staph._aureus_C 8. (Z = 2.01) ceN65 - C._elegans_snoRNA_ceN65 9. (Z = 1.95) ceN111 - C._elegans_snoRNA_ceN111 10. (Z = 1.95) P1 - Pseudomonas_sRNA_P1 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM141.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM141_global.out/ --free-endgaps --indel=-100 --threads=4 ......((((.......)))).............................. MFE = -10.60 (Covariance contribution: -6.03) RNAz stats: MPI: 74.51, SCI: 0.97, ZSCORE: -0.98 Full summary: Sequences: 3 Columns: 51 Reading direction: forward Mean pairwise identity: 74.51 Shannon entropy: 0.37146 G+C content: 0.46405 Mean single sequence MFE: -5.57 Consensus MFE: -5.40 Energy contribution: -5.40 Covariance contribution: -0.00 Combinations/Pair: 1.00 Mean z-score: -0.98 Structure conservation index: 0.97 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.16 SVM RNA-class probability: 0.901392 Prediction: RNA Multiple alignment from mlocarna: Pklr.181222231_16 GCAAGCGCUCUACCACUGAGCUAAAUCCCCAACCCCAGCUUUUCUCUUUU~ Appbp2.73460120_71 ~CAAGUGCUCUACCGCUGAGCUAAAUCCCCAACCCCACCACCGUAAUUUUA Appbp2.73460120_98 ~CAAGCGCUCUUCCACUGAGCUAAAUCCCCAACCUGAAUUUUAAGAGUUUU // ClustID MergedIDs Count AvgDissim Members M148 4290 3 0.49 Stmn2.95284903_24,Becn1.90317957_0,Usp9x.21606330_28 Best CMs (by avg z-score): 1. (Z = 2.97) Qrr - Qrr_RNA 2. (Z = 2.95) suhB - suhB 3. (Z = 2.59) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.55) 23S-methyl - 23S_methyl_RNA_motif 5. (Z = 2.36) GcvB - GcvB_RNA 6. (Z = 2.29) ctRNA_pGA1 - ctRNA 7. (Z = 2.29) RydC - RydC_RNA 8. (Z = 2.16) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 9. (Z = 2.09) ROSE_2 - Repression_of_heat_shock_gene_expression_(ROSE)_element 10. (Z = 2.08) mir-9 - mir-9/mir-79_microRNA_precursor_family Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM148.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM148_global.out/ --free-endgaps --indel=-100 --threads=4 .........(((((((((.......)))))))))....(((...))).................... MFE = -20.23 (Covariance contribution: -13.96) RNAz stats: MPI: 29.00, SCI: 1.41, ZSCORE: 1.87 Full summary: Sequences: 3 Columns: 67 Reading direction: forward Mean pairwise identity: 29.00 Shannon entropy: 1.03507 G+C content: 0.32926 Mean single sequence MFE: -8.30 Consensus MFE: -11.68 Energy contribution: -7.47 Covariance contribution: -4.21 Combinations/Pair: 2.56 Mean z-score: 1.87 Structure conservation index: 1.41 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.48 SVM RNA-class probability: 0.053417 Prediction: OTHER Multiple alignment from mlocarna: Stmn2.95284903_24 ~~~~~~~~UUAUCUGUGG----GUGCCAUGGGUG---ACGAUGUUCGUU--UUAAGCUUUUGCCUGU Becn1.90317957_0 ~~~CUUGCUCCUUAGGGGAUAUUUGCCUUUAAGGUUUUACAUUUUGUUUGGUU~~~~~~~~~~~~~~ Usp9x.21606330_28 UUCUUUGCUAGAGCUUACUAA----GUGA-CUCUUUUCAAACUGUCCUUCUGUGC~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M149 4923 4 0.63 Rab5c.89652340_22,Dpysl2.46346413_43,Atp2a2.35312505_6,Laptm4a.32427418_8 Best CMs (by avg z-score): 1. (Z = 2.72) tp2 - tp2 2. (Z = 2.68) SNORD111 - Small_Nucleolar_RNA_SNORD111 3. (Z = 2.22) snoU97 - Small_nucleolar_RNA_U97 4. (Z = 2.19) snoR101 - Small_nucleolar_RNA_snoR101 5. (Z = 2.19) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.10) snoZ107_R87 - Small_nucleolar_RNA_Z107/R87 7. (Z = 2.09) snoR17 - Small_nucleolar_RNA_snoR17 8. (Z = 2.06) U7 - U7_small_nuclear_RNA 9. (Z = 2.00) suhB - suhB 10. (Z = 1.86) InvR - Invasion_gene-associated_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM149.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM149_global.out/ --free-endgaps --indel=-100 --threads=4 ............(((((........(((((......)))))..........)))))...... MFE = -7.67 (Covariance contribution: -6.77) RNAz stats: MPI: 37.50, SCI: -0.00, ZSCORE: 1.41 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 37.50 Shannon entropy: 1.06313 G+C content: 0.31940 Mean single sequence MFE: -5.05 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.41 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.79 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Rab5c.89652340_22 ~~~~ACCUCACACUUGUCUUC----CUCGUCUU-UCUCUGG---CAGUUUAUCAGGCCAUAC Dpysl2.46346413_43 ~~~~~~~~~~~~CAGGCUUUCACUAGCUGGCUUCUUUCUGUAUUUGCUGAUGUCUGUCAUAC Atp2a2.35312505_6 AGAGAACUAACACUAUUUU----AUGCAGAUAUUUUUUUG---UAGAUGAAAAAAGC~~~~~ Laptm4a.32427418_8 ~~~~~~UUAACUUUGCACUUUCUUUGUAUAAUGGUUUAUGUUUUGGAUGUCUGAUG~~~~~~ // ClustID MergedIDs Count AvgDissim Members M173 3351 4 0.62 Pou4f2.31390818_10,Vdac2.2515297_3,Map1b.30415235_44,Itpr1.144028781_26 Best CMs (by avg z-score): 1. (Z = 2.99) CRISPR-DR40 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.62) CRISPR-DR14 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.59) mir-672 - microRNA_mir-672 4. (Z = 2.59) mir-71 - microRNA_mir-71 5. (Z = 2.52) hvt-mir-H - microRNA_hvt-mir-H9 6. (Z = 2.50) MIR478 - microRNA_MIR478 7. (Z = 2.49) mir-3 - microRNA_mir-3 8. (Z = 2.43) DdR7 - D._discoideum_snoRNA_Dd7 9. (Z = 2.36) mir-577 - microRNA_mir-577 10. (Z = 2.27) snoCD11 - Small_nucleolar_RNA_CD11 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM173.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM173_global.out/ --free-endgaps --indel=-100 --threads=4 ..................((((((((((((((....))))))..))))).)))................. MFE = -9.73 (Covariance contribution: -8.03) RNAz stats: MPI: 36.67, SCI: 0.47, ZSCORE: 0.42 Full summary: Sequences: 4 Columns: 70 Reading direction: forward Mean pairwise identity: 36.67 Shannon entropy: 1.07612 G+C content: 0.25208 Mean single sequence MFE: -6.71 Consensus MFE: -3.17 Energy contribution: -0.80 Covariance contribution: -2.37 Combinations/Pair: 2.60 Mean z-score: 0.42 Structure conservation index: 0.47 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.57 SVM RNA-class probability: 0.246127 Prediction: OTHER Multiple alignment from mlocarna: Pou4f2.31390818_10 ~~~~~~~~~~~~~~~~GCAAGAAUGAGCAAGUAAG-AUUUGUUUUUAUU-CUUACAGACGU-CACCUUG~ Vdac2.2515297_3 ~~~~~~~~~~~~~~~~~~AAGGAUGAUUAAGCAAGAGCGUGUUUUAAAUAUUU--AGACAGUCACCCGUU Map1b.30415235_44 UGAAGCCUGAUAUUGAAGUCGUGAUGAUAUUUAUUUAAAAACC-CGUCACU~~~~~~~~~~~~~~~~~~~ Itpr1.144028781_26 ~~~~~~~~~~~~~~~~~~AUGAUGCAGUAGGUGAGAAGUUAUUAUGCAUAUAUACACAUAUACAUCCA~~ // ClustID MergedIDs Count AvgDissim Members M172 5354 6 0.61 Syt4.23805080_11,Kcnj3.37256728_0,Ccni.16459077_11,Vdac2.2515297_4,Map1b.30415235_70,Ap2a2.201813143_0 Best CMs (by avg z-score): 1. (Z = 2.22) Chlorobi-RRM - Chlorobi-RRM_RNA 2. (Z = 2.17) snoZ107_R87 - Small_nucleolar_RNA_Z107/R87 3. (Z = 2.01) DPB - Stem_loopII_regulatory_element_in_POLB 4. (Z = 1.95) SVLPA - Simian_virus_40_late_polyadenylation_signal_(SVLPA) 5. (Z = 1.93) ctRNA_pT181 - ctRNA 6. (Z = 1.90) mir-345 - microRNA_mir-345 7. (Z = 1.83) U1_yeast - Yeast_U1_spliceosomal_RNA 8. (Z = 1.78) mir-154 - microRNA_mir-154 9. (Z = 1.76) InvR - Invasion_gene-associated_RNA 10. (Z = 1.70) mir-506 - microRNA_mir-506 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM172.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM172_global.out/ --free-endgaps --indel=-100 --threads=4 ...............((.((((((((((....))))))...))))))................. MFE = -11.84 (Covariance contribution: -7.09) RNAz stats: MPI: 30.64, SCI: 0.66, ZSCORE: 0.31 Full summary: Sequences: 6 Columns: 64 Reading direction: forward Mean pairwise identity: 30.64 Shannon entropy: 1.37863 G+C content: 0.33656 Mean single sequence MFE: -9.35 Consensus MFE: -6.14 Energy contribution: -1.98 Covariance contribution: -4.16 Combinations/Pair: 4.33 Mean z-score: 0.31 Structure conservation index: 0.66 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.24 SVM RNA-class probability: 0.606656 Prediction: RNA Multiple alignment from mlocarna: Syt4.23805080_11 ~~~~~~~AAAUUAAUCCAUGUUUCUUCAGG-UUGGGGA---GAUAGGUUU--UAUUUAAAUCC~ Kcnj3.37256728_0 CAAAACACCCCAUUAGGCAUUAUUUCAUGU-UUUGAUU---UAGUUUUAGUCCA~~~~~~~~~~ Ccni.16459077_11 ~~~~~~~~UGAAUAC---UUCAUAAGUUGU-GUGCUUGU--UGAUUUGUGUAUUCUGACUUCAC Vdac2.2515297_4 ~~~~~~~AGACAGUCACCCGUUGGCUGGUU-UCUAGUUG--GAUGGUUAUCUCGUUAUCA~~~~ Map1b.30415235_70 ~~~~~~GAACACACACAAGAUGGCAAUCUCAUGGUAGC---UGUUGGGUUGGUCCACAC~~~~~ Ap2a2.201813143_0 ~~~~~UCCACAGACCAGAAGAUCAGGCUCU-UUGUUUGUGCGUCUCUCUCGUCUCU~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M171 5531 3 0.49 Gria2.172265159_87,Sirt5.27135611_6,Stmn2.95284903_5 Best CMs (by avg z-score): 1. (Z = 4.05) mir-186 - microRNA_mir-186 2. (Z = 3.79) mir-872 - microRNA_mir-872 3. (Z = 3.74) MIR1444 - microRNA_MIR1444 4. (Z = 3.58) mir-248 - microRNA_mir-248 5. (Z = 3.33) mir-802 - microRNA_mir-802 6. (Z = 3.24) snoR110 - Small_nucleolar_RNA_snoR110 7. (Z = 3.23) RsaD - RNA_Staph._aureus_D 8. (Z = 3.12) mir-190 - microRNA_mir-190 9. (Z = 3.12) mir-2 - mir-2_microRNA_precursor 10. (Z = 3.10) mir-286 - microRNA_mir-286 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM171.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-r3_50/bgDinucWT/dloc-r3_50_structs/clustM171_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((((((.((((((....(((...)))...)))))))))))))...... MFE = -14.95 (Covariance contribution: -13.95) RNAz stats: MPI: 43.83, SCI: 0.69, ZSCORE: -0.39 Full summary: Sequences: 3 Columns: 54 Reading direction: forward Mean pairwise identity: 43.83 Shannon entropy: 0.80065 G+C content: 0.23052 Mean single sequence MFE: -5.35 Consensus MFE: -3.70 Energy contribution: -1.60 Covariance contribution: -2.10 Combinations/Pair: 1.90 Mean z-score: -0.39 Structure conservation index: 0.69 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.95 SVM RNA-class probability: 0.976349 Prediction: RNA Multiple alignment from mlocarna: Gria2.172265159_87 GGUUUGAUUUUUAAAAACUGACCAUUUAUUAUUUGA--CUUAAAAAUUCUUU~~ Sirt5.27135611_6 ~~~AUUUGACCUGAAAUAUGAGUAUUUUGGAUCUGAUAUUUUGGUUAGUUACU~ Stmn2.95284903_5 GCUUGAUGUUUAAAAAAGU----ACCUUGGAUCUUAUUUUGUAAAUAUUUACAU //