ClustID MergedIDs Count AvgDissim Members M33 295 3 0.53 hek-i_NM_004622_193,hek-i_NM_000194_118,hek-i_NM_004136_72 Best CMs (by avg z-score): 1. (Z = 1.90) H19_3 - H19_conserved_region_3 2. (Z = 1.86) ctRNA_pGA1 - ctRNA 3. (Z = 1.83) HIV-1_SD - Human_immunodeficiency_virus_type_1_major_splice_donor 4. (Z = 1.82) TCV_Pr - Turnip_crinkle_virus_(TCV)_core_promoter_hairpin_(Pr) 5. (Z = 1.70) RydC - RydC_RNA 6. (Z = 1.62) P37 - Pseudomonas_sRNA_P37 7. (Z = 1.56) suhB - suhB 8. (Z = 1.55) SAH_riboswitch - S-adenosyl-L-homocysteine_riboswitch 9. (Z = 1.52) VrrA - Vibrio_regulatory_RNA_of_OmpA 10. (Z = 1.48) 23S-methyl - 23S_methyl_RNA_motif Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM33.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM33_global.out/ --free-endgaps --indel=-100 --threads=4 .....(((.(((((....))))).)))...((..................)).... MFE = -21.01 (Covariance contribution: -15.58) RNAz stats: MPI: 42.51, SCI: 0.67, ZSCORE: -0.6 Full summary: Sequences: 3 Columns: 56 Reading direction: forward Mean pairwise identity: 42.51 Shannon entropy: 0.80934 G+C content: 0.61017 Mean single sequence MFE: -12.70 Consensus MFE: -8.49 Energy contribution: -6.17 Covariance contribution: -2.33 Combinations/Pair: 2.00 Mean z-score: -0.60 Structure conservation index: 0.67 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 2.29 SVM RNA-class probability: 0.987817 Prediction: RNA Multiple alignment from mlocarna: hek-i_NM_004622_193 ~GCGGCCGUUGCGAUUGAUUGCGCUGGUUGCCUGCGGCGUCCACUUCCUUG~~~~~ hek-i_NM_004136_72 ~~~~~CUCUCGCGAUAU-UUGCGCGAGCCUGCUUCCUUCUUUCCUCCCUUGCCAGU hek-i_NM_000194_118 CGCGCGGCGCCGCCUCU-UGCUGCGCCUCCGCCUCCUCCUCUGCUCC---GCCA~~ // ClustID MergedIDs Count AvgDissim Members M32 416 3 0.56 hek-i_NM_002812_472,hek-i_NM_001078172_203,hek-i_NM_002798_239 Best CMs (by avg z-score): 1. (Z = 2.69) CRISPR-DR41 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.31) sR60 - Small_nucleolar_RNA_sR60 3. (Z = 1.76) SNORD125 - Small_nucleolar_RNA_SNORD125 4. (Z = 1.70) H19_2 - H19_conserved_region_2 5. (Z = 1.56) MIR2907 - microRNA_MIR2907 6. (Z = 1.54) SNORD35 - Small_nucleolar_RNA_SNORD35 7. (Z = 1.49) SBWMV1_UPD-PKh - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 8. (Z = 1.48) CRISPR-DR53 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.47) snoZ248 - Small_nucleolar_RNA_Z248 10. (Z = 1.41) SNORD12 - Small_nucleolar_SNORD12/SNORD106 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM32.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM32_global.out/ --free-endgaps --indel=-100 --threads=4 ......................((((((.......)))).)).((...))........................... MFE = -7.87 (Covariance contribution: -10.11) RNAz stats: MPI: 28.14, SCI: 0.52, ZSCORE: 1.04 Full summary: Sequences: 3 Columns: 77 Reading direction: forward Mean pairwise identity: 28.14 Shannon entropy: 1.04261 G+C content: 0.36461 Mean single sequence MFE: -6.90 Consensus MFE: -3.57 Energy contribution: -1.13 Covariance contribution: -2.44 Combinations/Pair: 3.00 Mean z-score: 1.04 Structure conservation index: 0.52 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.32 SVM RNA-class probability: 0.071318 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_002812_472 ~~~~~~~~~~~UGGAGCUCAACUUCUUGCCAACCACAGG-GACCAAGCUGACCAAACAGCAG~~~~~~~~~~~~~~~ hek-i_NM_001078172_203 ~~~~~~~~~~~~~~~~~~~~~~~~GGAACC--CGAUUCCCUUUC-CCGAGACGUUUGACGGAGAUACCGACCGACUC hek-i_NM_002798_239 AGAACAACCACUGGGUCCUA--CAUCGCCAAUCGAGUGACUGACAAGCUGAC~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M31 1492 3 0.55 hek-i_NM_006801_112,hek-i_NM_005969_312,hek-i_NM_001660_243 Best CMs (by avg z-score): 1. (Z = 2.21) mir-877 - microRNA_mir-877 2. (Z = 2.02) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 3. (Z = 1.90) TB10Cs5H3 - Trypanosomatid_snoRNA_TB10Cs5H3 4. (Z = 1.85) mir-650 - microRNA_mir-650 5. (Z = 1.79) SAH_riboswitch - S-adenosyl-L-homocysteine_riboswitch 6. (Z = 1.76) TB10Cs2H1 - Trypanosomatid_snoRNA_TB10Cs2H1 7. (Z = 1.74) mir-214 - microRNA_mir-214 8. (Z = 1.71) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.69) mir-328 - microRNA_mir-328 10. (Z = 1.49) MIAT_exon5_2 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM31.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM31_global.out/ --free-endgaps --indel=-100 --threads=4 ..(((...(((((.....(((..((....))....)))....)))))....))).......... MFE = -8.59 (Covariance contribution: -11.66) RNAz stats: MPI: 35.64, SCI: -0.00, ZSCORE: 2.12 Full summary: Sequences: 3 Columns: 64 Reading direction: forward Mean pairwise identity: 35.64 Shannon entropy: 0.91671 G+C content: 0.52028 Mean single sequence MFE: -8.30 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 2.12 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -9.12 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_006801_112 CCCGGAGCGGAGCGCACCUAG--GGUCCCUC----UUCCGUCCCCCCAGCCCAGCU~~~~~~~~ hek-i_NM_005969_312 ~~~~~~~~~~~~~~UACAGGAGCGACUUGACAAUGUCCCUCACACCCCUUCCAGCUACAUCGAA hek-i_NM_001660_243 ~~CGGCACAGGGGCCACUGAGACGUUUCUGC----CUCCCUCUUUCUUCCUCCGCU~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M30 937 3 0.54 hek-i_NM_017812_97,hek-i_NM_016404_44,hek-i_NR_003287_4975 Best CMs (by avg z-score): 1. (Z = 2.55) TB9Cs4H2 - Trypanosomatid_snoRNA_TB9Cs4H2 2. (Z = 2.54) MIR2907 - microRNA_MIR2907 3. (Z = 2.32) 5S_rRNA - 5S_ribosomal_RNA 4. (Z = 2.31) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.17) TB11Cs3H1 - Trypanosomatid_snoRNA_TB11Cs3H1 6. (Z = 2.16) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 7. (Z = 2.04) mir-1180 - microRNA_mir-1180 8. (Z = 1.79) mir-280 - microRNA_mir-280 9. (Z = 1.62) P13 - Pseudomonas_sRNA_P13 10. (Z = 1.59) SAM-IV - S-adenosyl_methionine_(SAM)_riboswitch, Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM30.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM30_global.out/ --free-endgaps --indel=-100 --threads=4 ....................(((((((.(((.(((....))).))).))))))).............. MFE = -22.53 (Covariance contribution: -13.07) RNAz stats: MPI: 30.88, SCI: 0.66, ZSCORE: 2.33 Full summary: Sequences: 3 Columns: 68 Reading direction: forward Mean pairwise identity: 30.88 Shannon entropy: 1.00394 G+C content: 0.49569 Mean single sequence MFE: -14.90 Consensus MFE: -9.85 Energy contribution: -9.87 Covariance contribution: 0.02 Combinations/Pair: 1.92 Mean z-score: 2.33 Structure conservation index: 0.66 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.93 SVM RNA-class probability: 0.023128 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_017812_97 ~~~~~~~~~~~~~~~~UCCAGGCCCUUCCACGCGCGU--GUGGGUGCGGGGGCCCCGAAGUGCUCGUG hek-i_NM_016404_44 UGUCUCUCCGGUUCCGGCCUGGCGAGAGUUUGUGCGGCGACAUGAAACUG~~~~~~~~~~~~~~~~~~ hek-i_NR_003287_4975 ~~~~~~~~~~~~~~~~CGCCCGUCACGCACCGCACGUUCGUGGGGAACCUGGCGCUAAACCAUUCG~~ // ClustID MergedIDs Count AvgDissim Members M5 1345 5 0.63 hek-i_NM_000983_85,hek-i_NM_003543_45,hek-i_NM_006013_323,hek-i_NM_014225_625,hek-i_NM_003089_655 Best CMs (by avg z-score): 1. (Z = 2.12) SNORD15 - Small_nucleolar_RNA_SNORD15 2. (Z = 1.96) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 3. (Z = 1.86) TB10Cs1H2 - Trypanosomatid_snoRNA_TB10Cs1H2 4. (Z = 1.76) mir-597 - microRNA_mir-597 5. (Z = 1.66) snoZ242 - Small_nucleolar_RNA_Z242 6. (Z = 1.63) mir-515 - microRNA_mir-515 7. (Z = 1.60) mir-124 - mir-124_microRNA_precursor_family 8. (Z = 1.59) mir-638 - microRNA_mir-638 9. (Z = 1.55) HIV_PBS - HIV_primer_binding_site_(PBS) 10. (Z = 1.52) sR53 - Small_nucleolar_RNA_sR53 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM5.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM5_global.out/ --free-endgaps --indel=-100 --threads=4 .......(((.((((((((..................))))).))))))............ MFE = -20.61 (Covariance contribution: -13.21) RNAz stats: MPI: 31.58, SCI: 0.56, ZSCORE: -0.22 Full summary: Sequences: 5 Columns: 61 Reading direction: forward Mean pairwise identity: 31.58 Shannon entropy: 1.32082 G+C content: 0.49909 Mean single sequence MFE: -12.70 Consensus MFE: -7.15 Energy contribution: -3.63 Covariance contribution: -3.52 Combinations/Pair: 2.82 Mean z-score: -0.22 Structure conservation index: 0.56 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.88 SVM RNA-class probability: 0.842074 Prediction: RNA Multiple alignment from mlocarna: hek-i_NM_000983_85 CCGCUGCCGC-CAUGGCU--CC--------UGUGAAAAAGCUUGUGGUGAAGGGGGGCAAA hek-i_NM_003543_45 ~~~~~~UGCU-CAUGUCUGGCCGUGGUAAAGGUGGAAAAGGUU-UGGGUAAGGGAGGA~~~ hek-i_NM_003089_655 ~~~~~~CUCCAACUCGUGCUG-AAACCCGAGAGGAGCGCAUGGAGAGGAAAAGACGG~~~~ hek-i_NM_014225_625 ~~~~~~AGUCGCUGGCCACAGUGGAGGAG----ACA-GUGGUGCGGGACAAGGCAGUGGAG hek-i_NM_006013_323 ~CCAAGAUUCGCAUUUUUGACCUGGGGCGGAAAAAGGCAAAA-GUGGAUGAG~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M4 668 3 0.55 hek-i_NM_001123375_189,hek-i_NM_003531_204,hek-i_NM_003536_199 Best CMs (by avg z-score): 1. (Z = 2.50) sR32 - Small_nucleolar_RNA_sR32 2. (Z = 2.38) sR39 - Small_nucleolar_RNA_sR39 3. (Z = 2.32) H19_2 - H19_conserved_region_2 4. (Z = 2.05) CRISPR-DR61 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.76) TCV_Pr - Turnip_crinkle_virus_(TCV)_core_promoter_hairpin_(Pr) 6. (Z = 1.69) sR8 - Small_nucleolar_RNA_sR8 7. (Z = 1.53) mir-1180 - microRNA_mir-1180 8. (Z = 1.52) MIAT_exon5_2 - Myocardial_infarction_associated_transcript_exon_5_conserved_region_2 9. (Z = 1.48) sR3 - Small_nucleolar_RNA_sR3 10. (Z = 1.48) group-II-D1D4-1 - Group_II_catalytic_intron_D1-D4-1 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM4.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM4_global.out/ --free-endgaps --indel=-100 --threads=4 .............((((.((.(((.(..(.......).)))).)).))))............... MFE = -15.44 (Covariance contribution: -13.04) RNAz stats: MPI: 63.59, SCI: 0.33, ZSCORE: 2.63 Full summary: Sequences: 3 Columns: 65 Reading direction: forward Mean pairwise identity: 63.59 Shannon entropy: 0.51111 G+C content: 0.47692 Mean single sequence MFE: -10.87 Consensus MFE: -3.63 Energy contribution: -4.30 Covariance contribution: 0.67 Combinations/Pair: 1.20 Mean z-score: 2.63 Structure conservation index: 0.33 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.91 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001123375_189 UGGCUCUGCGGGAGAUCCGGCGCUACCAGAAGUCUACGGAGCUGCUGAUC~~~~~~~~~~~~~~~ hek-i_NM_003531_204 ~~~~~~~~~~~~~~~UCCGUCGCUACCAGAAGUCCACCGAGCUGCUGAUCCGGAAGCUGCCGUUC hek-i_NM_003536_199 UGGCUCUCCGCGAGAUUCGCCGCUACCAGAAGUCCACCGAGCUGCUGAUC~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M7 397 3 0.55 hek-i_NM_001207067_522,hek-i_NM_014679_175,hek-i_NM_001839_348 Best CMs (by avg z-score): 1. (Z = 2.87) ykkC-III - ykkC-III_RNA 2. (Z = 2.62) SNORA22 - Small_nucleolar_RNA_SNORA22 3. (Z = 2.45) TLS-PK4 - Pseudoknot_of_tRNA-like_structure 4. (Z = 2.19) Rubella_3 - Rubella_virus_3'_cis-acting_element 5. (Z = 2.16) Tombus_5 - Tombusvirus_5'_UTR 6. (Z = 2.16) TLS-PK3 - Pseudoknot_of_tRNA-like_structure 7. (Z = 2.14) sucA - SucA_RNA_motif 8. (Z = 2.06) GIR1 - GIR1_branching_ribozyme 9. (Z = 2.05) TLS-PK2 - Pseudoknot_of_tRNA-like_structure 10. (Z = 2.02) Archaea_SRP - Archaeal_signal_recognition_particle_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM7.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM7_global.out/ --free-endgaps --indel=-100 --threads=4 ..........(((((.((......))..)))))((((....))))................ MFE = -19.29 (Covariance contribution: -14.76) RNAz stats: MPI: 33.33, SCI: 0.47, ZSCORE: 1.48 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 33.33 Shannon entropy: 0.97273 G+C content: 0.46623 Mean single sequence MFE: -11.93 Consensus MFE: -5.56 Energy contribution: -2.13 Covariance contribution: -3.42 Combinations/Pair: 2.27 Mean z-score: 1.48 Structure conservation index: 0.47 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.76 SVM RNA-class probability: 0.004760 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001207067_522 GCAAAAGCCAACGCUAUCA-----GGCCAGCGUUUUAAAACUAGAAAAAGAGAUG~~~~~~ hek-i_NM_014679_175 ~~~~~~~~~AGGGUCCCCGCUGGUGGGCGGCUCCCG-AGUCUUGGAGAAGAGCACGAGAA~ hek-i_NM_001839_348 ~~~~~~~ACAAGGGCCCUUCCUAUGG--GCUCUCGGCCGAAGUCAAGAACA--AGAUUGCU // ClustID MergedIDs Count AvgDissim Members M6 1264 4 0.63 hek-i_NM_002271_366,hek-i_NM_001034996_658,hek-i_NM_001415_1377,hek-i_NM_000986_283 Best CMs (by avg z-score): 1. (Z = 2.41) sR44 - Small_nucleolar_RNA_sR44 2. (Z = 2.12) snopsi28S-3316 - Small_nucleolar_RNA_psi28S-3316 3. (Z = 2.03) SCARNA1 - Small_Cajal_body_specific_RNA_1 4. (Z = 1.88) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.78) Antizyme_FSE - Antizyme_RNA_frameshifting_stimulation_element 6. (Z = 1.75) PK-G12rRNA - Pseudoknot_of_the_domain_G(G12)_of_23S_ribosomal_RNA 7. (Z = 1.72) bxd_4 - Bithoraxoid_conserved_region_4 8. (Z = 1.71) L10_leader - Ribosomal_protein_L10_leader 9. (Z = 1.71) mir-320 - microRNA_mir-320 10. (Z = 1.67) mir-999 - microRNA_mir-999 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM6.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM6_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ...............................(((.....)))............... MFE = -2.12 (Covariance contribution: -3.49) RNAz stats: MPI: 44.51, SCI: -0.00, ZSCORE: 0.53 Full summary: Sequences: 4 Columns: 57 Reading direction: forward Mean pairwise identity: 44.51 Shannon entropy: 0.94371 G+C content: 0.42929 Mean single sequence MFE: -6.80 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: -6.85 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_002271_366 AGGCAGAGGAAACCUAUGAGAAUAUCCC--AGGCC---AGUCAAAGAUCACAUUC~~ hek-i_NM_001034996_658 ~~~CUAAAGUUCCAGCAAAAAAGAUCACC---GCCGCGAGUAAAAAGGCUCCAGCC~ hek-i_NM_000986_283 ~CGGAAGAAAUUCAAAAGAAAAGAACCC---GCCGAGCAGUCAAAUUCCAGAGG~~~ hek-i_NM_001415_1377 ~~~~~~~AGGUAGGAGAAAAAAUUGCCCUUAGCCGAAGAGUUGAAAAACACUGGCGU // ClustID MergedIDs Count AvgDissim Members M1 1142 3 0.51 hek-i_NR_002312_26,hek-i_NM_001034996_145,hek-i_NM_018509_239 Best CMs (by avg z-score): 1. (Z = 2.53) IRES_IGF2 - Insulin-like_growth_factor_II_IRES 2. (Z = 2.36) Pseudomon-groES - Pseudomon-groES_RNA 3. (Z = 2.35) MIR1846 - microRNA_MIR1846 4. (Z = 2.24) mir-593 - microRNA_mir-593 5. (Z = 2.17) mir-1208 - microRNA_mir-1208 6. (Z = 2.02) IRES_FGF2 - FGF-2_internal_ribosome_entry_site_(IRES) 7. (Z = 2.00) b55 - M._tuberculosis_B11 8. (Z = 1.99) ApoB_5_CRE - Apolipoprotein_B_(apoB)_5'_UTR_cis-regulatory_element 9. (Z = 1.96) mir-484 - microRNA_mir-484 10. (Z = 1.95) RNase_MRP - RNase_MRP Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM1.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM1_global.out/ --free-endgaps --indel=-100 --threads=4 ....(((((((....((.(((.(.(....)))))..))...)))))))............. MFE = -31.68 (Covariance contribution: -20.88) RNAz stats: MPI: 30.05, SCI: 0.76, ZSCORE: 0.84 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 30.05 Shannon entropy: 1.02469 G+C content: 0.62732 Mean single sequence MFE: -19.53 Consensus MFE: -14.84 Energy contribution: -11.07 Covariance contribution: -3.77 Combinations/Pair: 2.22 Mean z-score: 0.84 Structure conservation index: 0.76 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.57 SVM RNA-class probability: 0.746449 Prediction: RNA Multiple alignment from mlocarna: hek-i_NR_002312_26 ~~~~UCCCUCCAGUUCCCCGG-----GCCCGCCAUAGGGC-GGAGGGA-AGCUCAUCAGUG hek-i_NM_001034996_145 ~~GAGGCGCCGAACGGCUCCCAGAGGGUCCCGGGAAGCGCAUGGUGUUCAGG~~~~~~~~~ hek-i_NM_018509_239 UCACCCGCCGGAACCCCGGAGCCGGGGCCCGCUCA-----GCCGGCGUUACCAUG~~~~~~ // ClustID MergedIDs Count AvgDissim Members M3 607 3 0.53 hek-i_NM_015051_154,hek-i_NR_002183_73,hek-i_NM_145808_251 Best CMs (by avg z-score): 1. (Z = 2.13) H19_3 - H19_conserved_region_3 2. (Z = 2.06) SAH_riboswitch - S-adenosyl-L-homocysteine_riboswitch 3. (Z = 1.87) suhB - suhB 4. (Z = 1.76) Rhizobiales-2 - Rhizobiales-2_RNA 5. (Z = 1.68) 6C - 6C_RNA 6. (Z = 1.65) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.50) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 8. (Z = 1.50) TUG1_3 - Taurine_upregulated_gene_1_conserved_region_3 9. (Z = 1.48) F6 - F6_TB_sRNA 10. (Z = 1.44) HIV_FS2 - ribosomal_frameshift_site Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM3.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM3_global.out/ --free-endgaps --indel=-100 --threads=4 .......(((((..(....)..))))).............................. MFE = -17.67 (Covariance contribution: -12.37) RNAz stats: MPI: 41.52, SCI: 0.49, ZSCORE: -0.66 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 41.52 Shannon entropy: 0.84921 G+C content: 0.59211 Mean single sequence MFE: -10.70 Consensus MFE: -5.26 Energy contribution: -4.60 Covariance contribution: -0.66 Combinations/Pair: 1.67 Mean z-score: -0.66 Structure conservation index: 0.49 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.45 SVM RNA-class probability: 0.939011 Prediction: RNA Multiple alignment from mlocarna: hek-i_NM_015051_154 ~~~~~~UCCGCUGCCGUCGGCUCCCGGAGCCCAGC-CCUUUCCUAACCCAACCCAAC hek-i_NR_002183_73 CCUGGAACCGGGCCG-CAGCCCCCCGGCUUCGCCCACCAUCUCCCUACCAU~~~~~~ hek-i_NM_145808_251 ~~~~~AACUGCCUCGCCCGCCUGGCAGCCUAACCCUCCUUCUCUUCUUCUCCUCU~~ // ClustID MergedIDs Count AvgDissim Members M2 1164 3 0.55 hek-i_NM_005861_864,hek-i_NM_003932_626,hek-i_NR_002604_123 Best CMs (by avg z-score): 1. (Z = 3.48) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 2. (Z = 2.92) MIR820 - microRNA_MIR820 3. (Z = 2.89) mir-322 - microRNA_mir-322 4. (Z = 2.76) mir-150 - microRNA_mir-150 5. (Z = 2.76) MIR476 - microRNA_MIR476 6. (Z = 2.71) mir-202 - microRNA_mir-202 7. (Z = 2.70) SNORA56 - Small_nucleolar_RNA_SNORA56 8. (Z = 2.67) SNORA74 - Small_nucleolar_RNA_SNORA74 9. (Z = 2.59) mir-452 - microRNA_mir-452 10. (Z = 2.59) mir-431 - microRNA_mir-431 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM2.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM2_global.out/ --free-endgaps --indel=-100 --threads=4 ..((((.(((((.(((((.....))))).....)))))))))............... MFE = -34.88 (Covariance contribution: -21.32) RNAz stats: MPI: 37.06, SCI: 0.94, ZSCORE: -1.52 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 37.06 Shannon entropy: 0.90924 G+C content: 0.51444 Mean single sequence MFE: -18.63 Consensus MFE: -17.56 Energy contribution: -13.47 Covariance contribution: -4.10 Combinations/Pair: 2.25 Mean z-score: -1.52 Structure conservation index: 0.94 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 3.04 SVM RNA-class probability: 0.997095 Prediction: RNA Multiple alignment from mlocarna: hek-i_NM_005861_864 ~~UCCCCAGCGCUCUUCGAAUCGCGAAGAAGAAGCGCUGGAAC--AGCAUUGAG~~~ hek-i_NM_003932_626 ~CUCGCUUGGCCAUUUUGUAUGCCAAGAG----GGCCAGUGUCUUCG--UCAAAUUA hek-i_NR_002604_123 CUUCCCAGGGCUGUUGUCUGCCUGGCGG--GAAGGUCCUGGGCAAAGGAUCA~~~~~ // ClustID MergedIDs Count AvgDissim Members M9 976 3 0.52 hek-i_NM_175055_301,hek-i_NM_003519_303,hek-i_NM_003651_995 Best CMs (by avg z-score): 1. (Z = 2.92) SAH_riboswitch - S-adenosyl-L-homocysteine_riboswitch 2. (Z = 2.25) IRES_mnt - Mnt_IRES 3. (Z = 2.15) IRES_IGF2 - Insulin-like_growth_factor_II_IRES 4. (Z = 2.11) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 5. (Z = 2.02) UPD-PK2 - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 6. (Z = 1.91) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.80) CC3664 - caulobacter_sRNA_CC3664 8. (Z = 1.73) C4 - C4_antisense_RNA 9. (Z = 1.67) CRISPR-DR23 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.66) snoZ178 - Small_nucleolar_RNA_Z178 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM9.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM9_global.out/ --free-endgaps --indel=-100 --threads=4 .........((((........))))(((((..........)))))................ MFE = -19.27 (Covariance contribution: -10.77) RNAz stats: MPI: 50.56, SCI: 0.60, ZSCORE: 0.49 Full summary: Sequences: 3 Columns: 61 Reading direction: forward Mean pairwise identity: 50.56 Shannon entropy: 0.67331 G+C content: 0.57356 Mean single sequence MFE: -12.00 Consensus MFE: -7.22 Energy contribution: -5.90 Covariance contribution: -1.32 Combinations/Pair: 1.67 Mean z-score: 0.49 Structure conservation index: 0.60 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.08 SVM RNA-class probability: 0.109401 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_175055_301 ~~~~~~~~GAGGCCU---CCCGCCUGGCACACUACAACAAGCGCUCCACCAUCACGUCCCG hek-i_NM_003519_303 ~~~~~~~~GAGGCUU---CCCGCCUGGCGCACUACAACAAGCGCUCGACCAUCACCUCCAG hek-i_NM_003651_995 CGGCGGUUCCCGCCUUACCACGUGGGACAGACC------UUUGACCGUCGCUCACG~~~~~ // ClustID MergedIDs Count AvgDissim Members M8 231 4 0.57 hek-i_NM_006601_74,hek-i_NM_005999_117,hek-i_NM_006887_163,hek-i_NM_014184_251 Best CMs (by avg z-score): 1. (Z = 1.80) RydC - RydC_RNA 2. (Z = 1.70) H19_3 - H19_conserved_region_3 3. (Z = 1.29) Yfr1 - Cyanobacterial_functional_RNA_1 4. (Z = 1.18) IRES_mnt - Mnt_IRES 5. (Z = 1.17) mir-248 - microRNA_mir-248 6. (Z = 1.16) Arthropod_7SK - Arthropod_7SK_RNA 7. (Z = 1.15) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.11) Pseudomon-Rho - Pseudomon-Rho_RNA 9. (Z = 1.07) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.06) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM8.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM8_global.out/ --free-endgaps --indel=-100 --threads=4 ..........((.(((......))).))......((...........)).............. MFE = -8.59 (Covariance contribution: -10.69) RNAz stats: MPI: 39.95, SCI: 0.47, ZSCORE: 1.48 Full summary: Sequences: 4 Columns: 63 Reading direction: forward Mean pairwise identity: 39.95 Shannon entropy: 1.04326 G+C content: 0.50000 Mean single sequence MFE: -5.45 Consensus MFE: -2.58 Energy contribution: -0.20 Covariance contribution: -2.38 Combinations/Pair: 3.00 Mean z-score: 1.48 Structure conservation index: 0.47 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.69 SVM RNA-class probability: 0.005414 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_006601_74 ~~~~~~~~UUUGCACGCACGCACGUUCAUUCUCCG-----UCCUCGCGCCCCUUUUCCUACAC hek-i_NM_006887_163 ~GGACCCUCCCGCCGGCCCGCGCCGCUGCA-CUCGCCCUCUCCUCUCGCCCC~~~~~~~~~~~ hek-i_NM_005999_117 ~~~GUUUUCCCAGGUUCCCUC-GGCCUGUACCUCGCGCACUCCUCUUGCUCCAG~~~~~~~~~ hek-i_NM_014184_251 UUGUCACUGUAUUACU-GCUCAUGUCAUUGCACUGGUUCAUCUUCCUUCUC~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M28 1285 4 0.59 hek-i_NM_001174097_540,hek-i_NM_001009186_875,hek-i_NM_001102667_643,hek-i_NM_002074_378 Best CMs (by avg z-score): 1. (Z = 3.46) snoZ169 - Small_nucleolar_RNA_Z169 2. (Z = 3.23) CRISPR-DR6 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.10) sR18 - Small_nucleolar_RNA_sR18 4. (Z = 2.99) SNORD29 - Small_nucleolar_RNA_SNORD29 5. (Z = 2.85) sR20 - Small_nucleolar_RNA_sR20 6. (Z = 2.84) sR5 - Small_nucleolar_RNA_sR5 7. (Z = 2.83) sR58 - Small_nucleolar_RNA_sR58 8. (Z = 2.81) snoZ163 - Small_nucleolar_RNA_Z163/Z177_family 9. (Z = 2.75) snoMe28S-Cm2645 - Small_nucleolar_RNA_Me28S-Cm2645 10. (Z = 2.73) snoR114 - small_nucleolar_RNA_snoR114 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM28.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM28_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ........................................................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 37.55, SCI: -0.00, ZSCORE: 1.29 Full summary: Sequences: 4 Columns: 91 Reading direction: forward Mean pairwise identity: 37.55 Shannon entropy: 1.06736 G+C content: 0.20870 Mean single sequence MFE: -5.71 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.29 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.58 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001174097_540 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AUGUUUUGGAAGAUAAGCUU-AAAGGAGAAAUG-AUGGAUCUGCAGCAUGGG~ hek-i_NM_001009186_875 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UCAUUGAAGAUAGGGUUAAAAAAAUAAUAGAACUGAAAAGGAAAGUCUGU hek-i_NM_002074_378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UUGAAGGUGGCAUUGAAGAGCAC--UAAGAUCGGAAGAUGAGUGAGCUUGAC~~~~~~~ hek-i_NM_001102667_643 CUGUGUCAAUGUUGAAACAAGACUAUAAAGAAGGAGAAAUGACCUUGAAG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M29 781 4 0.61 hek-i_NM_003347_143,hek-i_NM_000981_392,hek-i_NM_006009_1383,hek-i_NM_006600_527 Best CMs (by avg z-score): 1. (Z = 3.53) sR30 - Small_nucleolar_RNA_sR30 2. (Z = 2.91) sR4 - Small_nucleolar_RNA_sR4 3. (Z = 2.73) enod40 - Early_nodulin_40 4. (Z = 2.30) sR45 - Small_nucleolar_RNA_sR45 5. (Z = 2.26) sR36 - Small_nucleolar_RNA_sR36 6. (Z = 2.20) sR9 - Small_nucleolar_RNA_sR9 7. (Z = 2.16) sR23 - Small_nucleolar_RNA_sR23 8. (Z = 2.15) sR55 - Small_nucleolar_RNA_sR55 9. (Z = 2.15) sR13 - Small_nucleolar_RNA_sR13 10. (Z = 2.03) sR43 - Small_nucleolar_RNA_sR42 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM29.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM29_global.out/ --free-endgaps --indel=-100 --threads=4 .........((((.(((......(((((((..........)))))))...))).)))). MFE = -20.28 (Covariance contribution: -11.91) RNAz stats: MPI: 33.05, SCI: 0.71, ZSCORE: 0.77 Full summary: Sequences: 4 Columns: 59 Reading direction: forward Mean pairwise identity: 33.05 Shannon entropy: 1.12039 G+C content: 0.47066 Mean single sequence MFE: -10.00 Consensus MFE: -7.10 Energy contribution: -4.85 Covariance contribution: -2.25 Combinations/Pair: 2.43 Mean z-score: 0.77 Structure conservation index: 0.71 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.47 SVM RNA-class probability: 0.708817 Prediction: RNA Multiple alignment from mlocarna: hek-i_NM_003347_143 GGCUGAUGAAGGAGCUUGAAGAAAUCCGCAAAU------GUG-GGAUGAAAAACUUC~~ hek-i_NM_000981_392 ~~~~~~~~CAUGGAUGAGGAGAAUGAGGAUUUUGCGCCGGCUGCUCAGAAGAUACCGU~ hek-i_NM_006009_1383 ~~~GGAUGGAGGAAGGU----GAGUUUUCAGAG--GCCCGUGAGGACAUGGCUGCCCUU hek-i_NM_006600_527 ~~AGAA--AAAGGAUGCAGAGAAUCAUGAG--G--CCCAGCUCAAGAACGGCAGCCUU~ // ClustID MergedIDs Count AvgDissim Members M24 120 4 0.58 hek-i_NM_018715_172,hek-i_NM_001080469_2895,hek-i_NM_006743_192,hek-i_NM_018122_80 Best CMs (by avg z-score): 1. (Z = 2.49) suhB - suhB 2. (Z = 1.66) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 3. (Z = 1.58) rnk_pseudo - Pseudomonas_rnk_leader 4. (Z = 1.52) AMV_RNA1_SL - Alfalfa_mosaic_virus_RNA_1_5'_UTR_stem-loop 5. (Z = 1.52) Corona_SL-III - Coronavirus_SL-III_cis-acting_replication_element_(CRE) 6. (Z = 1.42) snoU97 - Small_nucleolar_RNA_U97 7. (Z = 1.41) InvR - Invasion_gene-associated_RNA 8. (Z = 1.31) VrrA - Vibrio_regulatory_RNA_of_OmpA 9. (Z = 1.31) U1_yeast - Yeast_U1_spliceosomal_RNA 10. (Z = 1.31) SNORD111 - Small_Nucleolar_RNA_SNORD111 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM24.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM24_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ........................................................................................................ MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 33.65, SCI: -0.00, ZSCORE: -0.38 Full summary: Sequences: 4 Columns: 104 Reading direction: forward Mean pairwise identity: 33.65 Shannon entropy: 1.13405 G+C content: 0.23798 Mean single sequence MFE: -7.85 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.38 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.92 SVM RNA-class probability: 0.000001 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_018715_172 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CCGUCUUUUAGUUGCUUCUCUUCCUUUUUUCUCUCCGGUUUCUCAUCACU~~~~~ hek-i_NM_001080469_2895 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CAGGCAUUUUGGUCUGGGGUAUUUUUGUUUGUUCUCUCUGUUUUUUGUUU~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_006743_192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UCCGGCGCAGCCCCGUCCCUGUUUUUUGUGCUCCUCCGAGCUCGCUGUUC hek-i_NM_018122_80 CCAGCGGCGAUCUGUGUUUGGGUUCGCGCUCUGGGAGAAUUUUGGCUUUG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M25 75 3 0.47 hek-i_NM_080596_282,hek-i_NM_003517_282,hek-i_NM_001151_404 Best CMs (by avg z-score): 1. (Z = 3.04) mir-692 - microRNA_mir-692 2. (Z = 2.59) SBRMV1_UPD-PKd - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 3. (Z = 2.48) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.16) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 5. (Z = 2.01) CRISPR-DR23 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.77) H19_2 - H19_conserved_region_2 7. (Z = 1.61) CRISPR-DR8 - CRISPR_RNA_direct_repeat_element 8. (Z = 1.57) SBWMV2_UPD-PKk - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 9. (Z = 1.51) CRISPR-DR10 - CRISPR_RNA_direct_repeat_element 10. (Z = 1.47) mir-1280 - microRNA_mir-1280 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM25.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM25_global.out/ --free-endgaps --indel=-100 --threads=4 ................((((..........((....))........))))..... MFE = -10.01 (Covariance contribution: -8.34) RNAz stats: MPI: 60.00, SCI: 0.35, ZSCORE: -0.47 Full summary: Sequences: 3 Columns: 55 Reading direction: forward Mean pairwise identity: 60.00 Shannon entropy: 0.54183 G+C content: 0.57697 Mean single sequence MFE: -8.97 Consensus MFE: -3.13 Energy contribution: -2.14 Covariance contribution: -1.00 Combinations/Pair: 1.50 Mean z-score: -0.47 Structure conservation index: 0.35 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.91 SVM RNA-class probability: 0.003576 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001151_404 ~~~~~UCCCCACCCAAGCUCUCAACUUCGCCUUCAAGGACAAGUACAAGCAGCUC hek-i_NM_003517_282 GCAUCAUCCCUCGUCACCUC-CAGCU----GGCCAUCCGCAACGACGAGGAACUG hek-i_NM_080596_282 GUAUCAUCCCGCGUCACCUC-CAACU----GGCCAUCCGCAACGACGAGGAGCUC // ClustID MergedIDs Count AvgDissim Members M26 260 4 0.45 hek-i_NM_021062_151,hek-i_NM_003523_156,hek-i_NM_003525_154,hek-i_NM_003524_150 Best CMs (by avg z-score): 1. (Z = 2.30) mir-101 - mir-101_microRNA_precursor_family 2. (Z = 2.29) Corona_SL-III - Coronavirus_SL-III_cis-acting_replication_element_(CRE) 3. (Z = 2.25) mir-375 - microRNA_mir-375 4. (Z = 2.13) mir-80 - microRNA_mir-80 5. (Z = 2.06) SNORD101 - Small_nucleolar_RNA_SNORD101 6. (Z = 2.00) SAM-II_long_loops - SAM-II_long_loops 7. (Z = 2.00) SNORA70 - Small_nucleolar_RNA_SNORA70 8. (Z = 1.97) CRISPR-DR57 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.91) mir-378 - microRNA_mir-378 10. (Z = 1.85) MIR2907 - microRNA_MIR2907 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM26.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM26_global.out/ --free-endgaps --indel=-100 --threads=4 ....((((.....))))..............((..(((...)))..))........ MFE = -10.73 (Covariance contribution: -7.73) RNAz stats: MPI: 78.57, SCI: 0.46, ZSCORE: 1.56 Full summary: Sequences: 4 Columns: 56 Reading direction: forward Mean pairwise identity: 78.57 Shannon entropy: 0.34012 G+C content: 0.46429 Mean single sequence MFE: -8.75 Consensus MFE: -3.99 Energy contribution: -4.18 Covariance contribution: 0.19 Combinations/Pair: 1.27 Mean z-score: 1.56 Structure conservation index: 0.46 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -8.00 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_021062_151 ~CAAGGAGAGCUAUUCUAUCUAUGUGUACAAGGUUCUGAAGCAGGUCCACC~~~~~ hek-i_NM_003523_156 ~~~~~~AGAGCUACUCCGUAUACGUGUACAAGGUGCUGAAACAGGUCCACCCCGAC hek-i_NM_003525_154 ~~~~GGAGAGCUAUUCCGUGUACGUGUACAAGGUGCUGAAGCAGGUCCACCCCG~~ hek-i_NM_003524_150 GCAAGGAGAGCUACUCCGUAUACGUUUACAAGGUGCUGAAGCAAGUCCAC~~~~~~ // ClustID MergedIDs Count AvgDissim Members M27 168 5 0.42 hek-i_NR_002756_85,hek-i_NR_002753_84,hek-i_NR_002755_83,hek-i_NR_002754_83,hek-i_NR_002757_85 Best CMs (by avg z-score): 1. (Z = 3.36) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 2. (Z = 3.22) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 3. (Z = 3.18) Hammerhead_1 - Hammerhead_ribozyme_(type_I) 4. (Z = 3.01) snoR130 - small_nucleolar_RNA_snoR130 5. (Z = 3.00) snoZ159 - Small_nucleolar_RNA_Z159/U59 6. (Z = 2.93) SNORD74 - Small_nucleolar_RNA_SNORD74 7. (Z = 2.77) SNORD36 - Small_nucleolar_RNA_SNORD36 8. (Z = 2.76) SNORD26 - Small_nucleolar_RNA_SNORD26 9. (Z = 2.70) CRISPR-DR33 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.65) U5 - U5_spliceosomal_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM27.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM27_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((....))))......)))..((((..((....))..)))).... MFE = -7.74 (Covariance contribution: -7.90) RNAz stats: MPI: 85.80, SCI: 0.39, ZSCORE: 0.52 Full summary: Sequences: 5 Columns: 50 Reading direction: forward Mean pairwise identity: 85.80 Shannon entropy: 0.27016 G+C content: 0.42000 Mean single sequence MFE: -6.86 Consensus MFE: -2.70 Energy contribution: -2.70 Covariance contribution: 0.00 Combinations/Pair: 1.00 Mean z-score: 0.52 Structure conservation index: 0.39 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.58 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NR_002756_85 CGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACAACUCUGAGUCUUAACC hek-i_NR_002753_84 CGCCUUUUACUAAAGAUUUCCGUGGAGAAAAACAACUAUGAGUUUAUGGU hek-i_NR_002755_83 CGCCUUUUACUAAAGAUUUCCGUGGAGAGAAACCGUUUUGAGUUUCAAGC hek-i_NR_002754_83 CGCCUUUUACUAAAGAUUUCCGUGGAGAGAAACGAGUGUGAGUCUGAAAC hek-i_NR_002757_85 CGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACAACUCUGAGUCUUAAGC // ClustID MergedIDs Count AvgDissim Members M20 756 3 0.29 hek-i_NM_001199456_1694,hek-i_NM_001144966_4955,hek-i_NM_001144970_5003 Best CMs (by avg z-score): 1. (Z = 5.56) plasmodium_snoR11 - small_nucleolar_RNA_snoR11 2. (Z = 5.17) ceN115 - C._elegans_sRNA_ceN115 3. (Z = 5.05) rox2 - Drosophila_rox2_ncRNA 4. (Z = 4.70) MIR812 - microRNA_MIR812 5. (Z = 4.63) mycoplasma_FSE - mycoplasma_ribosomal_frameshift_element 6. (Z = 4.52) mir-981 - microRNA_mir-981 7. (Z = 4.36) CyaR_RyeE - CyaR/Rye_RNA 8. (Z = 4.35) plasmodium_snoR30 - small_nucleolar_RNA_snoR30 9. (Z = 4.34) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element 10. (Z = 4.29) mir-320 - microRNA_mir-320 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM20.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM20_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ....................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 66.06, SCI: -0.00, ZSCORE: 0.16 Full summary: Sequences: 3 Columns: 55 Reading direction: forward Mean pairwise identity: 66.06 Shannon entropy: 0.47504 G+C content: 0.16970 Mean single sequence MFE: -0.23 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: -8.57 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001199456_1694 ~~~~~CCAAGCCCAAGAGGAAAAGAGAGAAAAAAGAGAAAAAGAAGAAACGGAAG hek-i_NM_001144966_4955 UGCUAUGUAACUAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAU~~~~~ hek-i_NM_001144970_5003 ~~CUAUGUAACUAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUUC~~~ // ClustID MergedIDs Count AvgDissim Members M21 713 4 0.54 hek-i_NR_003285_141,hek-i_NR_003287_4045,hek-i_NM_005009_34,hek-i_NM_001039690_103 Best CMs (by avg z-score): 1. (Z = 3.31) P35 - Pseudomonas_sRNA_P35 2. (Z = 3.05) P13 - Pseudomonas_sRNA_P13 3. (Z = 2.86) HBV - HBV_RNA_encapsidation_signal_epsilon 4. (Z = 2.65) DsrA - DsrA_RNA 5. (Z = 2.57) suhB - suhB 6. (Z = 2.53) C4 - C4_antisense_RNA 7. (Z = 2.48) mir-484 - microRNA_mir-484 8. (Z = 2.45) MIR2907 - microRNA_MIR2907 9. (Z = 2.44) mir-1180 - microRNA_mir-1180 10. (Z = 2.43) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM21.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM21_global.out/ --free-endgaps --indel=-100 --threads=4 ...............((((((((((((.(((.....))))))))..)))))))....... MFE = -31.40 (Covariance contribution: -16.60) RNAz stats: MPI: 35.57, SCI: 0.43, ZSCORE: -0.28 Full summary: Sequences: 4 Columns: 60 Reading direction: forward Mean pairwise identity: 35.57 Shannon entropy: 1.08080 G+C content: 0.66167 Mean single sequence MFE: -25.88 Consensus MFE: -11.09 Energy contribution: -10.65 Covariance contribution: -0.44 Combinations/Pair: 2.15 Mean z-score: -0.28 Structure conservation index: 0.43 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.50 SVM RNA-class probability: 0.720628 Prediction: RNA Multiple alignment from mlocarna: hek-i_NR_003285_141 CGACACUUCGAACGCACUUGCGGCCCC-GGGUUCCUCCCGGGGCUACGCCU~~~~~~~~~ hek-i_NR_003287_4045 ~~~~~CCCCG--CGAGGGGCCCGGGGC-GGGGUCCGCCGGCCCUGCGGGCCGCCGGUG~~ hek-i_NM_005009_34 ~~UUACAGCUCUUUUAGACGCGCUCACAGCGGCCCGCGGGCCGGGCGUCAUG~~~~~~~~ hek-i_NM_001039690_103 ~~~~~~UUCG--GUUGUCGCCCGUUGGCCGCG--CGGCGCCGCGCUCGGCGGCCGCCAUU // ClustID MergedIDs Count AvgDissim Members M22 440 3 0.33 hek-i_NM_018064_535,hek-i_NM_005796_556,hek-i_NM_005875_103 Best CMs (by avg z-score): 1. (Z = 1.99) suhB - suhB 2. (Z = 1.98) CRISPR-DR45 - CRISPR_RNA_direct_repeat_element 3. (Z = 1.90) H19_3 - H19_conserved_region_3 4. (Z = 1.51) BLV_package - Bovine_leukaemia_virus_RNA_packaging_signal 5. (Z = 1.47) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.34) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 7. (Z = 1.19) bxd_6 - Bithoraxoid_conserved_region_6 8. (Z = 1.16) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 9. (Z = 1.06) CRISPR-DR27 - CRISPR_RNA_direct_repeat_element 10. (Z = 0.97) NEAT1_2 - Nuclear_enriched_abundant_transcript_1_conserved_region_2 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM22.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM22_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .......((((....))))........................................... MFE = -0.30 (Covariance contribution: -2.47) RNAz stats: MPI: 40.86, SCI: -0.00, ZSCORE: -0.35 Full summary: Sequences: 3 Columns: 62 Reading direction: forward Mean pairwise identity: 40.86 Shannon entropy: 0.86148 G+C content: 0.49755 Mean single sequence MFE: -1.50 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.35 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.54 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_018064_535 UCUCCUCGAGUUCCCGCUCUUCACC----CCUUC-CCUCACCCUCUUCUUUCGUC~~~~~~~ hek-i_NM_005796_556 ~~~~~~~~~~~~GCUGUUUCCUCCUCCCUCCUCUUCCCAAUACUAUUCCCACUCCUCCAGAU hek-i_NM_005875_103 ~~~~~~~~GCGCCCUCGCCUCUUCCUCCGCCUCCUCCUUCGCCUCUUCCUGCCUCCUC~~~~ // ClustID MergedIDs Count AvgDissim Members M23 1331 3 0.48 hek-i_NM_003537_120,hek-i_NM_014633_55,hek-i_NM_003536_130 Best CMs (by avg z-score): 1. (Z = 3.80) IRES_Hsp70 - Heat_shock_protein_70_(Hsp70)_internal_ribosome_entry_site_(IRES) 2. (Z = 3.25) sucA - SucA_RNA_motif 3. (Z = 3.07) Cyano-2 - Cyano-2_RNA 4. (Z = 2.91) p27_CRE - p27_cis-regulatory_element 5. (Z = 2.83) TLS-PK3 - Pseudoknot_of_tRNA-like_structure 6. (Z = 2.70) TLS-PK2 - Pseudoknot_of_tRNA-like_structure 7. (Z = 2.46) flg-Rhizobiales - flg-Rhizobiales_RNA 8. (Z = 2.43) snoZ242 - Small_nucleolar_RNA_Z242 9. (Z = 2.43) ykkC-III - ykkC-III_RNA 10. (Z = 2.41) HIV-1_SD - Human_immunodeficiency_virus_type_1_major_splice_donor Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM23.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM23_global.out/ --free-endgaps --indel=-100 --threads=4 .(((...((.((....((.((((((....)))))))).))..)).)))...... MFE = -30.77 (Covariance contribution: -19.77) RNAz stats: MPI: 52.50, SCI: 0.59, ZSCORE: -1.01 Full summary: Sequences: 3 Columns: 54 Reading direction: forward Mean pairwise identity: 52.50 Shannon entropy: 0.66158 G+C content: 0.66453 Mean single sequence MFE: -21.90 Consensus MFE: -12.85 Energy contribution: -12.30 Covariance contribution: -0.55 Combinations/Pair: 1.46 Mean z-score: -1.01 Structure conservation index: 0.59 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 1.73 SVM RNA-class probability: 0.963709 Prediction: RNA Multiple alignment from mlocarna: hek-i_NM_003537_120 AGGCUGCUCGCA-AGAGCGCGCCGG-CUACCGGCGGCGUGAAAAAGCCUCAC~~ hek-i_NM_014633_55 ~~~~GGAGAAGCCAGAGCUCCAGCGGCGCCGCGGGGCGGCAGUCAAGACCAGAG hek-i_NM_003536_130 AGGCGGCUCGGA-AGAGCGCUCCGG-CCACCGGCGGUGUCAAGAAGCCCCAU~~ // ClustID MergedIDs Count AvgDissim Members M11 691 4 0.61 hek-i_NM_001164722_1837,hek-i_NM_004146_353,hek-i_NM_004356_265,hek-i_NM_003769_548 Best CMs (by avg z-score): 1. (Z = 2.43) mir-1180 - microRNA_mir-1180 2. (Z = 2.26) mir-458 - microRNA_mir-458 3. (Z = 2.26) 5S_rRNA - 5S_ribosomal_RNA 4. (Z = 1.96) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 5. (Z = 1.88) SAM-IV - S-adenosyl_methionine_(SAM)_riboswitch, 6. (Z = 1.86) mir-692 - microRNA_mir-692 7. (Z = 1.84) mir-639 - microRNA_mir-639 8. (Z = 1.84) mir-593 - microRNA_mir-593 9. (Z = 1.68) ovine_lenti_FSE - ribosomal_frameshift_element 10. (Z = 1.63) mir-199 - mir-199_microRNA_precursor Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM11.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM11_global.out/ --free-endgaps --indel=-100 --threads=4 ...((((....(((((....((.......))))).))))))..................... MFE = -20.26 (Covariance contribution: -15.09) RNAz stats: MPI: 36.44, SCI: 0.27, ZSCORE: 1.31 Full summary: Sequences: 4 Columns: 62 Reading direction: forward Mean pairwise identity: 36.44 Shannon entropy: 1.05811 G+C content: 0.56307 Mean single sequence MFE: -13.92 Consensus MFE: -3.75 Energy contribution: -2.75 Covariance contribution: -1.00 Combinations/Pair: 2.36 Mean z-score: 1.31 Structure conservation index: 0.27 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.79 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001164722_1837 ~~~CCUGUAGUCCCAGCUACUCAGGA---GGCUGAGGCAGGAGAAU-CGCUUGAACC~~~~~ hek-i_NM_004146_353 ACUUCCU----GGCCUGCAAGCAGGAGCGGCACGACUGGGACUACUGCGAGCAC~~~~~~~~ hek-i_NM_004356_265 ~~~CCCGCCGCCCGC-----GCCGCCAUGGGAGU-GGAGGGCUGCACCAAGUGCAUCAA~~~ hek-i_NM_003769_548 ~~UUCCUCCGUCAGGC---AGCUGGCA--GGACC-UGAAGGAU----CACAUGCGAGAAGCU // ClustID MergedIDs Count AvgDissim Members M10 1052,435 7 0.78 hek-i_NM_003542_57,hek-i_NM_003543_75,hek-i_NM_199440_1698,hek-i_NM_003538_75,hek-i_NM_003546_85,hek-i_NM_003542_84,hek-i_NM_003545_85 Best CMs (by avg z-score): 1. (Z = 2.10) blv_FSE - ribosomal_frameshift_site 2. (Z = 1.80) CRISPR-DR12 - CRISPR_RNA_direct_repeat_element 3. (Z = 1.74) flg-Rhizobiales - flg-Rhizobiales_RNA 4. (Z = 1.69) TB10Cs1H1 - Trypanosomatid_snoRNA_TB10Cs1H1 5. (Z = 1.46) Pseudomon-groES - Pseudomon-groES_RNA 6. (Z = 1.45) UPD-PKib - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 7. (Z = 1.44) snoTBR17 - Small_nucleolar_RNA_TBR17 8. (Z = 1.42) flpD - flpD_RNA 9. (Z = 1.41) RF_site5 - Ma3_gene_ribosomal_frameshift_signal 10. (Z = 1.34) snoZ169 - Small_nucleolar_RNA_Z169 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM10.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM10_global.out/ --free-endgaps --indel=-100 --threads=4 ................................((.((((((.....)))))).))........................... MFE = -15.55 (Covariance contribution: -8.72) RNAz stats: MPI: 52.47, SCI: 0.58, ZSCORE: 1.78 Full summary: Sequences: 7 Columns: 82 Reading direction: forward Mean pairwise identity: 52.47 Shannon entropy: 0.92809 G+C content: 0.35178 Mean single sequence MFE: -13.26 Consensus MFE: -7.73 Energy contribution: -7.34 Covariance contribution: -0.38 Combinations/Pair: 1.75 Mean z-score: 1.78 Structure conservation index: 0.58 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -2.29 SVM RNA-class probability: 0.011575 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_003542_57 GUCGCGGCAAAGGCGGAAAAGGCUUGGGGAAGGGUGGUGCU----AAGCGCCAU~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003545_85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~UAAAGGAGGCGCU----AAGCGUCACCGUAAGGUCCUGCGAGAUAACAUCCAGG hek-i_NM_003542_84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~GGAAGGGUGGUGCU----AAGCGCCAUCGUAAGGUGCUCCGGGAUAACAUCCAG~ hek-i_NM_003543_75 ~~~~~~~~~~~~~~~~~~AAGGUUUGGGUAAGGGAGGAGCU----AAGCGUCAUCGCAAGGUUUUGCGCGAU~~~~~~~~~~ hek-i_NM_003538_75 ~~~~~~~~~~~~~~~~~~AGGGUUUGGGUAAGGGGGGUGCC----AAGCGCCACCGCAAGGUGUUGCGUGAC~~~~~~~~~~ hek-i_NM_199440_1698 ~~~~~~~~~~UGAAUAUGGUGGAAAAAGGAAUCAUUGACCCAACAAAGGUUGUGAGAACU~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003546_85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~GCAAAGGAGGCGCU----AAGCGCCACCGCAAAGUUCUGCGCGACAACAUUCAG~ // ClustID MergedIDs Count AvgDissim Members M13 405 3 0.49 hek-i_NM_006275_122,hek-i_NM_022066_68,hek-i_NM_014188_257 Best CMs (by avg z-score): 1. (Z = 2.52) P10 - Pseudomonas_sRNA_P10 2. (Z = 2.42) Rubella_3 - Rubella_virus_3'_cis-acting_element 3. (Z = 2.10) isrG - isrG_Hfq_binding_RNA 4. (Z = 2.09) CRISPR-DR20 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.78) Pseudomon-Rho - Pseudomon-Rho_RNA 6. (Z = 1.77) RydC - RydC_RNA 7. (Z = 1.71) mir-484 - microRNA_mir-484 8. (Z = 1.58) Pxr - Pxr_regulatory_sRNA 9. (Z = 1.57) Moco-II - Moco-II_RNA 10. (Z = 1.48) IRES_mnt - Mnt_IRES Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM13.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM13_global.out/ --free-endgaps --indel=-100 --threads=4 .((((.((.((....))....)).))..))..(((((...))).))........... MFE = -26.09 (Covariance contribution: -24.09) RNAz stats: MPI: 36.53, SCI: 0.21, ZSCORE: 1.47 Full summary: Sequences: 3 Columns: 57 Reading direction: forward Mean pairwise identity: 36.53 Shannon entropy: 0.90482 G+C content: 0.68689 Mean single sequence MFE: -13.03 Consensus MFE: -2.77 Energy contribution: -0.67 Covariance contribution: -2.10 Combinations/Pair: 2.00 Mean z-score: 1.47 Structure conservation index: 0.21 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: hek-i_NM_006275_122 CGUGUUCGGGCUCUUGC----CGUCCCCGCA-CCCG--CACCGCGGUUACUGGCUUG hek-i_NM_022066_68 ~UCGCCGCCGCUGUCGCCGCCGCCGCCCGAGACUCGCGCAGAGCAGUUAUG~~~~~~ hek-i_NM_014188_257 ~~GCGCCGUCGU-UUCG----CGUCGCCCGCUUCCGGCCACCGCGGCCGCCAUUUUG // ClustID MergedIDs Count AvgDissim Members M12 1058 3 0.55 hek-i_NM_001415_45,hek-i_NM_006924_2031,hek-i_NM_003486_807 Best CMs (by avg z-score): 1. (Z = 2.69) CRISPR-DR52 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.62) TB11Cs2H1 - Trypanosomatid_snoRNA_TB11Cs2H1 3. (Z = 2.56) MIR476 - microRNA_MIR476 4. (Z = 2.55) SAM_alpha - SAM_riboswitch_(alpha-proteobacteria) 5. (Z = 2.40) CRISPR-DR34 - CRISPR_RNA_direct_repeat_element 6. (Z = 2.38) mir-597 - microRNA_mir-597 7. (Z = 2.21) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 8. (Z = 2.16) MIR815 - microRNA_MIR815 9. (Z = 2.10) mir-932 - microRNA_mir-932 10. (Z = 2.07) SNORA70 - Small_nucleolar_RNA_SNORA70 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM12.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM12_global.out/ --free-endgaps --indel=-100 --threads=4 ......................(((.(((..((((((....))))))))).)))............ MFE = -12.67 (Covariance contribution: -9.50) RNAz stats: MPI: 30.30, SCI: 0.29, ZSCORE: 0.89 Full summary: Sequences: 3 Columns: 66 Reading direction: forward Mean pairwise identity: 30.30 Shannon entropy: 1.01663 G+C content: 0.32605 Mean single sequence MFE: -9.87 Consensus MFE: -2.81 Energy contribution: -2.17 Covariance contribution: -0.65 Combinations/Pair: 1.92 Mean z-score: 0.89 Structure conservation index: 0.29 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.77 SVM RNA-class probability: 0.000001 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001415_45 ~~~~~~~~~~~~~~~CUGAUUUUCCUUCCU-CUUUUGGCAACAUGGCGGGCGGAGAAGCUGGAGUG hek-i_NM_006924_2031 ~~~~AAAGACUUUAAUUUACAAAUUAAAUUGCAAAUGGGAGCAUUAGAUUUAGU~~~~~~~~~~~~ hek-i_NM_003486_807 CCAACUUCUCAUUUGAAG--GCACCAAACUGGAUGUGGG-GAACAUUGUGCUG~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M15 1399 4 0.55 hek-i_NM_003113_2649,hek-i_NM_005527_951,hek-i_NM_057175_89,hek-i_NM_015920_209 Best CMs (by avg z-score): 1. (Z = 3.04) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.60) PK-SPCSV - 3'-terminal_pseudoknot_in_SPCSV 3. (Z = 2.54) REN-SRE - Renin_stability_regulatory_element_(REN-SRE) 4. (Z = 2.50) SNORD26 - Small_nucleolar_RNA_SNORD26 5. (Z = 2.44) plasmodium_snoR11 - small_nucleolar_RNA_snoR11 6. (Z = 2.42) sR43 - Small_nucleolar_RNA_sR42 7. (Z = 2.33) CRISPR-DR9 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.32) SCARNA1 - Small_Cajal_body_specific_RNA_1 9. (Z = 2.27) SNORA57 - Small_nucleolar_RNA_SNORA57 10. (Z = 2.23) PK-PYVV - 3'-terminal_pseudoknot_in_PYVV Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM15.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM15_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ............................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 47.62, SCI: -0.00, ZSCORE: 0.8 Full summary: Sequences: 4 Columns: 63 Reading direction: forward Mean pairwise identity: 47.62 Shannon entropy: 0.90025 G+C content: 0.35788 Mean single sequence MFE: -5.75 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: -7.53 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_003113_2649 ~~~~~~~~~~~~AGAAGGCUGCAAAGCUGAAGGAAAAAUACAAAAAGGAUAUU-GCUGCAUAU hek-i_NM_005527_951 ~~~~~~UGAGCCACUUCGUGGAGGAGUUCAAGAGGAAACACAAAAAGGACAUCAGC~~~~~~~ hek-i_NM_057175_89 ~~~~~~UGGGGGAGGCGGCGGCAGCGUUAAGUGAGAAAGGAAAAAAGACAACGAGG~~~~~~~ hek-i_NM_015920_209 UACAUCCGUCCU------UGGAAGAGGAAAAGAAAAAACAUAAAAAGAAACGCCUA~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M14 1444 4 0.40 hek-i_NM_003542_189,hek-i_NM_003545_189,hek-i_NM_003539_189,hek-i_NM_003538_189 Best CMs (by avg z-score): 1. (Z = 3.59) snoPyro_CD - Pyrococcus_C/D_box_small_nucleolar_RNA 2. (Z = 3.57) sR51 - Small_nucleolar_RNA_sR51 3. (Z = 3.37) sR4 - Small_nucleolar_RNA_sR4 4. (Z = 3.21) sR28 - Small_nucleolar_RNA_sR28 5. (Z = 2.83) sR40 - Small_nucleolar_RNA_sR40 6. (Z = 2.54) SECIS_1 - Selenocysteine_insertion_sequence_1 7. (Z = 2.51) Trp_leader - Tryptophan_operon_leader 8. (Z = 2.50) rnk_pseudo - Pseudomonas_rnk_leader 9. (Z = 2.30) ROSE_2 - Repression_of_heat_shock_gene_expression_(ROSE)_element 10. (Z = 2.10) PSLVbeta_UPD-PK2 - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM14.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM14_global.out/ --free-endgaps --indel=-100 --threads=4 ...(((((....(((.((((....)))).)))..)))...))........ MFE = -13.91 (Covariance contribution: -8.34) RNAz stats: MPI: 80.67, SCI: 0.79, ZSCORE: -0.53 Full summary: Sequences: 4 Columns: 50 Reading direction: forward Mean pairwise identity: 80.67 Shannon entropy: 0.31603 G+C content: 0.48500 Mean single sequence MFE: -12.75 Consensus MFE: -10.06 Energy contribution: -9.50 Covariance contribution: -0.56 Combinations/Pair: 1.50 Mean z-score: -0.53 Structure conservation index: 0.79 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.10 SVM RNA-class probability: 0.104218 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_003542_189 UUUCCGGUCUUAUCUAUGAGGAGACUCGAGGUGUGCUUAAGGUUUUCUUA hek-i_NM_003538_189 UCUCUGGUCUGAUCUACGAGGAGACUCGCGGGGUGCUCAAGGUGUUUUUG hek-i_NM_003539_189 UUUCUGGCCUCAUUUAUGAGGAAACUCGCGGAGUGCUGAAAGUUUUCCUG hek-i_NM_003545_189 UUUCUGGUCUCAUCUACGAGGAGACUCGCGGGGUUCUGAAGGUGUUUCUG // ClustID MergedIDs Count AvgDissim Members M17 329 3 0.37 hek-i_NM_003542_145,hek-i_NM_003545_145,hek-i_NM_003544_144 Best CMs (by avg z-score): 1. (Z = 3.39) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 2. (Z = 3.17) PtaRNA1 - Plasmid_transferred_anti-sense_RNA 3. (Z = 2.77) ROSE_2 - Repression_of_heat_shock_gene_expression_(ROSE)_element 4. (Z = 2.72) mir-298 - microRNA_mir-298 5. (Z = 2.37) P37 - Pseudomonas_sRNA_P37 6. (Z = 2.20) mir-1180 - microRNA_mir-1180 7. (Z = 2.13) TB9Cs1H2 - Trypanosomatid_snoRNA_TB9Cs1H2 8. (Z = 2.07) SAM-IV - S-adenosyl_methionine_(SAM)_riboswitch, 9. (Z = 2.06) TB11Cs5H1 - Trypanosomatid_snoRNA_TB11Cs5H1 10. (Z = 1.99) ykkC-III - ykkC-III_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM17.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM17_global.out/ --free-endgaps --indel=-100 --threads=4 ...((((.....))))...((((.(((((....))))).))))........ MFE = -25.07 (Covariance contribution: -12.63) RNAz stats: MPI: 73.20, SCI: 0.57, ZSCORE: 0.34 Full summary: Sequences: 3 Columns: 51 Reading direction: forward Mean pairwise identity: 73.20 Shannon entropy: 0.38133 G+C content: 0.63843 Mean single sequence MFE: -16.43 Consensus MFE: -9.29 Energy contribution: -9.30 Covariance contribution: 0.01 Combinations/Pair: 1.42 Mean z-score: 0.34 Structure conservation index: 0.57 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.19 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_003542_145 ~ACCGGCUAUUCGCCGUUUGGCUCGGCGCGGUGGCGUCAAGCGCAUUUCCG hek-i_NM_003545_145 GCCUGCC-AUCCGGCGCCUUGCUCGUCGCGGGGGUGUCAAGCGCAUUUCUG hek-i_NM_003544_144 AACCGGCCAUUCGGCGCCUUGCUAGGCGUGGUGGGGUUAAGCGAAUUUCC~ // ClustID MergedIDs Count AvgDissim Members M16 1293 4 0.56 hek-i_NM_021134_112,hek-i_NM_017813_105,hek-i_NM_023936_41,hek-i_NM_001013_323 Best CMs (by avg z-score): 1. (Z = 3.50) CRISPR-DR23 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.67) WLE3 - Wingless_localisation_element_3_(WLE3) 3. (Z = 2.65) TB8Cs2H1 - Trypanosomatid_snoRNA_TB8Cs2H1 4. (Z = 2.59) mir-632 - microRNA_mir-632 5. (Z = 2.53) HIV-1_SD - Human_immunodeficiency_virus_type_1_major_splice_donor 6. (Z = 2.34) mir-639 - microRNA_mir-639 7. (Z = 2.32) CRISPR-DR28 - CRISPR_RNA_direct_repeat_element 8. (Z = 2.14) mir-574 - microRNA_mir-574 9. (Z = 2.09) TB11Cs5H1 - Trypanosomatid_snoRNA_TB11Cs5H1 10. (Z = 2.04) CC3513 - caulobacter_sRNA_CC3513 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM16.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM16_global.out/ --free-endgaps --indel=-100 --threads=4 ......................((((..((((......))))........)))).................... MFE = -14.03 (Covariance contribution: -10.58) RNAz stats: MPI: 36.65, SCI: 0.17, ZSCORE: 3.24 Full summary: Sequences: 4 Columns: 74 Reading direction: forward Mean pairwise identity: 36.65 Shannon entropy: 1.04359 G+C content: 0.50245 Mean single sequence MFE: -19.30 Consensus MFE: -3.26 Energy contribution: -7.07 Covariance contribution: 3.81 Combinations/Pair: 1.50 Mean z-score: 3.24 Structure conservation index: 0.17 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -7.16 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_021134_112 ~~~~CGCGGACCCCGGAAGCGCGCGUGGCCGCCAUGGCGCGGAAU--GUGGUGUAC~~~~~~~~~~~~~~~~~~ hek-i_NM_017813_105 ~~~~~~~~~~~~~~~~~~~CUAGAGCGCGCUGCCUGGCGAGUCAG-----GCGCGCGGGGCGGCGUUGGUGGUC hek-i_NM_023936_41 ACAAGCCUCGCUGAGGA----CGCGGACCCGCCAUGGCGCGGAAGAAGGUGCGU~~~~~~~~~~~~~~~~~~~~ hek-i_NM_001013_323 ~~~~~~~~~~~~~~~~~~~~~~AAGGCAACGCCCUGCUGCGGCGGCUGGUCCGCAUUGGGGUGCUGGAUGAG~~ // ClustID MergedIDs Count AvgDissim Members M19 634 4 0.57 hek-i_NM_002229_65,hek-i_NR_003286_302,hek-i_NM_000075_158,hek-i_NM_001037495_69 Best CMs (by avg z-score): 1. (Z = 2.47) IRES_L-myc - L-myc_internal_ribosome_entry_site_(IRES) 2. (Z = 2.41) mir-632 - microRNA_mir-632 3. (Z = 2.40) CC3513 - caulobacter_sRNA_CC3513 4. (Z = 2.31) HIV-1_DIS - Human_immunodeficiency_virus_type_1_dimerisation_initiation_site 5. (Z = 2.15) mir-1180 - microRNA_mir-1180 6. (Z = 2.07) mir-639 - microRNA_mir-639 7. (Z = 1.97) sR40 - Small_nucleolar_RNA_sR40 8. (Z = 1.89) snoZ6 - Z6_small_nucleolar_RNA 9. (Z = 1.83) Prion_pknot - Prion_pseudoknot 10. (Z = 1.74) SNORA70 - Small_nucleolar_RNA_SNORA70 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM19.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM19_global.out/ --free-endgaps --indel=-100 --threads=4 ....(((.(((((((((.(((((.....)))))..))))))))).)))............... MFE = -30.14 (Covariance contribution: -15.34) RNAz stats: MPI: 33.95, SCI: 0.75, ZSCORE: 0.97 Full summary: Sequences: 4 Columns: 63 Reading direction: forward Mean pairwise identity: 33.95 Shannon entropy: 1.11769 G+C content: 0.58210 Mean single sequence MFE: -19.53 Consensus MFE: -14.71 Energy contribution: -15.28 Covariance contribution: 0.56 Combinations/Pair: 2.11 Mean z-score: 0.97 Structure conservation index: 0.75 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.29 SVM RNA-class probability: 0.630236 Prediction: RNA Multiple alignment from mlocarna: hek-i_NM_002229_65 ~~~~~~~~~~CCUCGGAGCCAGCAGGGAGCUGGGAGCUGGGGG---AAACGACGCCAGGAAAG hek-i_NR_003286_302 ~~~~~~~~~~~~CCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAA~ hek-i_NM_000075_158 ~~~~UCCAGCUGCUCCGG-ACCGAGCUCGGGUGUAUGGGGCCGUAGGAACCGGCU~~~~~~~~ hek-i_NM_001037495_69 CUGAGCA-CUAGGCGGCG-GCG--GCUGGCGUGGGGCUGCUUAGAUGCGCCACG~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M18 1407 3 0.47 hek-i_NM_003472_406,hek-i_NM_001136232_615,hek-i_NR_023344_32 Best CMs (by avg z-score): 1. (Z = 2.70) U6atac - U6atac_minor_spliceosomal_RNA 2. (Z = 2.40) Bacillus-plasmid - Bacillus-plasmid_RNA 3. (Z = 2.34) U6 - U6_spliceosomal_RNA 4. (Z = 2.31) sR36 - Small_nucleolar_RNA_sR36 5. (Z = 2.12) sR52 - Small_nucleolar_RNA_sR52 6. (Z = 2.07) snoZ163 - Small_nucleolar_RNA_Z163/Z177_family 7. (Z = 2.01) sR44 - Small_nucleolar_RNA_sR44 8. (Z = 1.97) mir-23 - microRNA_mir-23 9. (Z = 1.90) SCARNA4 - Small_Cajal_body_specific_RNA_4 10. (Z = 1.85) RF_site5 - Ma3_gene_ribosomal_frameshift_signal Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM18.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_50/bgDinucWT/hek-i_50_structs/clustM18_global.out/ --free-endgaps --indel=-100 --threads=4 ........................((((((..(((...........))).))))))....................... MFE = -9.06 (Covariance contribution: -6.56) RNAz stats: MPI: 24.57, SCI: 0.30, ZSCORE: 2.8 Full summary: Sequences: 3 Columns: 79 Reading direction: forward Mean pairwise identity: 24.57 Shannon entropy: 1.07226 G+C content: 0.31663 Mean single sequence MFE: -5.59 Consensus MFE: -1.65 Energy contribution: -0.22 Covariance contribution: -1.44 Combinations/Pair: 2.40 Mean z-score: 2.80 Structure conservation index: 0.30 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: hek-i_NM_003472_406 AAGGCAAGAGGGAAAAGAAAAAAGUAGAGAGGUUGACAAU-----GCAAGUCUCU~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NR_023344_32 ~~~~~~~CCUGCGGAGGAGACGAGGGUGUUGUAUGAAAGGAGAGAAGGUUAGCACUC~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_001136232_615 ~~~~~~~~~~~~~~~~~~~~~~~~CUUACACCGGGGAAGG-----CCAAUGGGAAGUAAAGAAGAUCAACAACGCUCAC //