ClustID MergedIDs Count AvgDissim Members M5 428 5 0.48 hek-i_NM_021062_151,hek-i_NM_003523_156,hek-i_NM_003521_189,hek-i_NM_003525_154,hek-i_NM_003524_150 Best CMs (by avg z-score): 1. (Z = 3.56) sn2417 - Small_nucleolar_RNA_sn2417 2. (Z = 2.74) sucC - sucC_RNA 3. (Z = 2.11) DnaX - DnaX_ribosomal_frameshifting_element 4. (Z = 2.10) snoZ242 - Small_nucleolar_RNA_Z242 5. (Z = 1.97) sR41 - Small_nucleolar_RNA_sR41 6. (Z = 1.79) sR38 - Small_nucleolar_RNA_sR38 7. (Z = 1.75) astro_FSE - ribosomal_frameshift_site 8. (Z = 1.70) mir-378 - microRNA_mir-378 9. (Z = 1.68) Plasmid_R1162 - R1162-like_plasmid_antisense_RNA 10. (Z = 1.64) RF_site9 - Gag/pro_ribosomal_frameshift_site Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM5.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM5_global.out/ --free-endgaps --indel=-100 --threads=4 .....................((((((((((.......))))(((.....((((........))).).......)))((((.....(((....))).))))...)).))))(((.(.......).)))...(((((((...)))...))))...................................... MFE = -51.39 (Covariance contribution: -39.15) RNAz stats: MPI: 74.81, SCI: 0.53, ZSCORE: 4.59 Full summary: Sequences: 5 Columns: 189 Reading direction: forward Mean pairwise identity: 74.81 Shannon entropy: 0.45474 G+C content: 0.44550 Mean single sequence MFE: -44.54 Consensus MFE: -23.51 Energy contribution: -24.92 Covariance contribution: 1.41 Combinations/Pair: 1.21 Mean z-score: 4.59 Structure conservation index: 0.53 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.75 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_021062_151 ~UGCCUGAACCCUCUAAGUCUGCUCCAGCCCCUAAAAAGGGUUCUAAGAAGGCUAUCACUAAGGCGCAGAAGAAGGAUGGUAAGAAGCGUAAGCGCAGCCGCAAGGAGAGCUAUUCUAUCUAUGUGUACAAGGUUCUGAAGCAGGUCCACC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003523_156 ~~~~~~GAGCCAGCGAAAUCCGCUCCCGCCCCGAAGAAGGGCUCCAAGAAGGCCGUGACCAAGGCGCAGAAGAAGGACGGCAAGAAGCGCAAGCGCAGCCGCAAGGAGAGCUACUCCGUAUACGUGUACAAGGUGCUGAAACAGGUCCACCCCGAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003521_189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GGCUCCAAGAAGGCCAUUAACAAGGCUCAGAAGAAGGAUGGAAAGAAGCGCAAACGCAGCCGCAAGGAGAGCUACUCUGUGUAUGUGUACAAGGUGCUGAAGCAGGUCCACCCCGACACCGGCAUCUCUUCCAAGGCUAUGGGAAUCAUG hek-i_NM_003525_154 ~~~~CUGAACCAGCUAAGUCAGCUCCCGCCCCGAAGAAGGGCUCCAAGAAGGCGGUGACCAAGGCACAGAAGAAGGAUGGCAAGAAGCGCAAGCGCAGCCGCAAGGAGAGCUAUUCCGUGUACGUGUACAAGGUGCUGAAGCAGGUCCACCCCG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003524_150 AUGCCUGAUCCAGCUAAGUCCGCUCCCGCCCCGAAGAAGGGCUCCAAGAAGGCGGUGACCAAGGCGCAGAAGAAGGAUGGCAAGAAGCGUAAACGCAGCCGCAAGGAGAGCUACUCCGUAUACGUUUACAAGGUGCUGAAGCAAGUCCAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M4 52 4 0.62 hek-i_NM_003529_149,hek-i_NM_001123375_189,hek-i_NM_003531_204,hek-i_NM_015681_102 Best CMs (by avg z-score): 1. (Z = 2.95) p27_CRE - p27_cis-regulatory_element 2. (Z = 2.56) mir-874 - microRNA_mir-874 3. (Z = 2.49) Pseudomon-groES - Pseudomon-groES_RNA 4. (Z = 2.21) g2 - G2 5. (Z = 2.19) sR45 - Small_nucleolar_RNA_sR45 6. (Z = 1.97) AS1890 - AS1890_sRNA 7. (Z = 1.94) ykkC-III - ykkC-III_RNA 8. (Z = 1.91) H19_1 - H19_conserved_region_1 9. (Z = 1.89) ybhL - ybhL_leader 10. (Z = 1.81) HDV_ribozyme - Hepatitis_delta_virus_ribozyme Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM4.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM4_global.out/ --free-endgaps --indel=-100 --threads=4 ..........................................................((((.((((.(....)..))).)((((.(((.((((((((((...(((((.(.(.......).).)))))...))))))....)))).))))))).((..((.((.....)).))..)).........)))).................. MFE = -63.68 (Covariance contribution: -42.83) RNAz stats: MPI: 46.97, SCI: 0.34, ZSCORE: 0.04 Full summary: Sequences: 4 Columns: 208 Reading direction: forward Mean pairwise identity: 46.97 Shannon entropy: 0.89502 G+C content: 0.48160 Mean single sequence MFE: -60.52 Consensus MFE: -20.58 Energy contribution: -18.45 Covariance contribution: -2.13 Combinations/Pair: 1.73 Mean z-score: 0.04 Structure conservation index: 0.34 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.61 SVM RNA-class probability: 0.041832 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_003529_149 UAUGGCUCGCACUAAGCAAACUGCUCGGAAGUCUACUGGUGGCAAGGCGCCACGCAAACAGUUGGCCACUAAGG-CAGC-CCGCAAAAG-CGCUCCGGCCACCGGCGGCGUGAAAAAGCCCCACCGCUACCGGCCGGGCACCGUGGCUCUGCG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_001123375_189 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GGCAAGGCCCCGAGGAAGCAGCUGGCUACCAAAG-CGGC-CCGCAAGAG-CGCGCCGGCCACGGGCGGGGUGAAGAAGCCGCACCGCUACCGGCCCGGCACCGUGGCUCUGCGGGAGAUCCGGCGCUACCAGAAGUCUACGGAGCUGCUGAUC~~~~~~~~~~~~~~~ hek-i_NM_003531_204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AAGCAGCUUGCUACUAAAG-CAGC-CCGUAAGAG-CGCUCCGGCCACCGGUGGCGUGAAGAAACCUCAUCGCUACCGCCCGGGCACCGUGGCCUUGCGCGAAAUCCGUCGCUACCAGAAGUCCACCGAGCUGCUGAUCCGGAAGCUGCCGUUC hek-i_NM_015681_102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GUCAAUGAUUGCGAUGAGCUGGUGGCCAUCAUCGCCCGCACCGACCUGCUGCGCCUGCGCAUGCCACACGCGCA-----CUCGCGUGGCCUUCGCGA--AGGUGUCGCUGCCAAGAAACGUGUCCUGCGCGCUACGCCGUCUGUUUCUAGGGCAACG~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M7 646 3 0.48 hek-i_NM_024629_289,hek-i_NM_000977_682,hek-i_NM_033251_855 Best CMs (by avg z-score): 1. (Z = 3.60) Rubella_3 - Rubella_virus_3'_cis-acting_element 2. (Z = 2.63) RF_site5 - Ma3_gene_ribosomal_frameshift_signal 3. (Z = 2.63) TB9Cs1H1 - Trypanosomatid_snoRNA_TB9Cs1H1 4. (Z = 2.60) TB9Cs3H1 - Trypanosomatid_snoRNA_TB9Cs3H1 5. (Z = 2.60) rmf - rmf_RNA 6. (Z = 2.57) NAMA_1 - MAP_kinase_and_growth_arrest_RNA_conserved_region_1 7. (Z = 2.49) g2 - G2 8. (Z = 2.42) glmS - glmS_glucosamine-6-phosphate_activated_ribozyme 9. (Z = 2.41) enod40 - Early_nodulin_40 10. (Z = 2.18) rydB - rydB_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM7.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM7_global.out/ --free-endgaps --indel=-100 --threads=4 ...........................((.((.(((((.((.((((.((.((((...........)))).))..)))).))))))).))..))(((((.((...(((.((((...(.(((.......)))..)...)))).)))...)).)))))..................... MFE = -56.95 (Covariance contribution: -37.45) RNAz stats: MPI: 49.72, SCI: 0.61, ZSCORE: 3.12 Full summary: Sequences: 3 Columns: 176 Reading direction: forward Mean pairwise identity: 49.72 Shannon entropy: 0.70430 G+C content: 0.41589 Mean single sequence MFE: -36.03 Consensus MFE: -22.01 Energy contribution: -18.60 Covariance contribution: -3.41 Combinations/Pair: 1.60 Mean z-score: 3.12 Structure conservation index: 0.61 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.61 SVM RNA-class probability: 0.000003 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_024629_289 ~~~~~~~~~~~~~UUAGAAAGAACACAUUCCAUGAAAGAUAAAGCUGGUCAA--AAGUGCAAGCCUAUUGAC-GUGUUCGACUUUCCUGAUAAUUCUGAUG----UCUCAAG-CAUUGGC----AGGCUGGGUGAAAAUGAGAAAGAUGA-AGAAACUUAUGAGACCUUUGAUCCU hek-i_NM_033251_855 GUCCGGAACGUCUAUAAGAAGGAGAAAGCUCGAGUCAUCACUGAGGAAGAGAAGAAUUUCAAAGCCUUCGCUAGUCUCCGUAUGGCCCG-UGCCAACGCCCGGCUCUUCGGCAUACGGGCAAAAAGAGCCAAGGAAGCCGCAGAACAGGAU~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_000977_682 ~~~~~~~~~~~~~AUAAGAAGGAGAAAGCUCGAGUCAUCACUGAGGAAGAGAAGAAUUUCAAAGCCUUCGCUAGUCUCCGUAUGGCCCG-UGCCAACGCCCGGCUCUUCGGCAUACGGGCAAAAAGAGCCAAGGAAGCCGCAGAACAGGAUGUUGAAAAGAAAA~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M6 521 4 0.62 hek-i_NM_003510_259,hek-i_NM_003517_282,hek-i_NM_080596_282,hek-i_NM_003513_321 Best CMs (by avg z-score): 1. (Z = 2.56) IBV_D-RNA - Infectious_bronchitis_virus_D-RNA 2. (Z = 2.38) TB6Cs1H1 - Trypanosomatid_snoRNA_TB6Cs1H1 3. (Z = 2.20) RF_site1 - Putative_RNA-dependent_RNA_polymerase_ribosomal_frameshift_site 4. (Z = 1.98) veev_FSE - venezuelan_equine_encephalitis_virus_ribosomal_frameshift_element 5. (Z = 1.96) HIV-1_DIS - Human_immunodeficiency_virus_type_1_dimerisation_initiation_site 6. (Z = 1.91) radC - radC_RNA 7. (Z = 1.87) TB10Cs3H2 - Trypanosomatid_snoRNA_TB10Cs3H2 8. (Z = 1.86) mir-138 - microRNA_mir-138 9. (Z = 1.82) VA - VA_RNA 10. (Z = 1.75) AS1890 - AS1890_sRNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM6.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM6_global.out/ --free-endgaps --indel=-100 --threads=4 .......................(((((((...((((((.....)))))).))))))).............(((.((...((((((.(((((((..(((((((.(..(....)..)..).).)))))....)).))))).)))))))))))..(((.(......).)))........................................... MFE = -68.59 (Covariance contribution: -45.76) RNAz stats: MPI: 64.70, SCI: 0.45, ZSCORE: 0.96 Full summary: Sequences: 4 Columns: 212 Reading direction: forward Mean pairwise identity: 64.70 Shannon entropy: 0.58243 G+C content: 0.46344 Mean single sequence MFE: -55.88 Consensus MFE: -25.30 Energy contribution: -26.99 Covariance contribution: 1.69 Combinations/Pair: 1.26 Mean z-score: 0.96 Structure conservation index: 0.45 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.29 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_003510_259 AGGGCAACUACGCUGAGCGGGUCGGUGCCGGAGCGCCGGUGUACCUGGCGGCGGUGUUGGAGUACCUAACCGCCGAGAUCCUGGAACUGGCUGGCAACGCGGCCCGCGACAACAAGAAGACCCGCAUCAUCCCGCGCCACUUGCAGCUGG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003517_282 ~~~~~~~~~~~~~~~~~~~~~~~GGGGCCGGCGCGCCCGUCUACAUGGCGGCGGUCCUCGAGUACCUGACCGCCGAGAUCCUGGAGCUGGCGGGCAACGCGGCUCGGGACAACAAGAAGACGCGCAUCAUCCCUCGUCACCUCCAGCUGGCCAUCCGCAACGACGAGGAACUG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003513_321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UACCUGACCGCCGAGAUCCUGGAGCUGGCGGGCAAUGCGGCCCGCGACAACAAGAAGACCCGCAUCAUCCCGCGCCACCUGCAAUUGGCCAUCCGCAAUGACGAGGAGCUUAAUAAACUCUUGGGGCGUGUGACCAUCGCGCAGGGUGGC hek-i_NM_080596_282 ~~~~~~~~~~~~~~~~~~~~~~~GGAGCCGGCGCGCCAGUGUACCUGGCUGCGGUGCUGGAGUACCUGACCGCUGAGAUCCUGGAGCUGGCUGGCAAUGCGGCCCGCGACAACAAGAAGACCCGUAUCAUCCCGCGUCACCUCCAACUGGCCAUCCGCAACGACGAGGAGCUC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M1 880 3 0.43 hek-i_NM_018046_203,hek-i_NM_033251_627,hek-i_NM_000977_454 Best CMs (by avg z-score): 1. (Z = 2.40) b55 - M._tuberculosis_B11 2. (Z = 1.88) snoU82P - Small_nucleolar_RNA_U82P 3. (Z = 1.87) eiav_FSE - ribosomal_frameshift_site 4. (Z = 1.83) SAM - SAM_riboswitch_(S_box_leader) 5. (Z = 1.82) g2 - G2 6. (Z = 1.82) mir-572 - microRNA_mir-572 7. (Z = 1.71) mir-663 - microRNA_mir-663 8. (Z = 1.70) CC1840 - caulobacter_sRNA_CC1840 9. (Z = 1.68) TCV_Pr - Turnip_crinkle_virus_(TCV)_core_promoter_hairpin_(Pr) 10. (Z = 1.62) blv_FSE - ribosomal_frameshift_site Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM1.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM1_global.out/ --free-endgaps --indel=-100 --threads=4 ..........................(((((......)))))(((.((((((.(((...((((((((((.((...(((....((((.(((((.(....).))))).))))...))))).))))).........))))).))).))).....))))))............................................. MFE = -65.44 (Covariance contribution: -38.81) RNAz stats: MPI: 44.26, SCI: 0.46, ZSCORE: 4.11 Full summary: Sequences: 3 Columns: 202 Reading direction: forward Mean pairwise identity: 44.26 Shannon entropy: 0.77070 G+C content: 0.47245 Mean single sequence MFE: -54.27 Consensus MFE: -25.13 Energy contribution: -23.93 Covariance contribution: -1.19 Combinations/Pair: 1.48 Mean z-score: 4.11 Structure conservation index: 0.46 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.54 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_018046_203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AGCUCUUCUGG-CCUCUGG------UUUUCCGACUGCUUAUCCGACGCUCCUCCCUCUGUC---UCUGUAGCUGGAGA---AGGUAGUUUCCA-----GGAAAGUUUUCCGGUUUGCAGGCCGCGCACAUCGGGCAGGGGCCAUCCUCGGUCCCCUUGCUCGUUGCUC hek-i_NM_033251_627 CUCAGGGUGGCCGGCAUUCACAAGAAGGUGGCCCGGACCAUCGGCAUUUCUGUGGAUCCGAGGAGGCGGAACAAGUCCACGGAGUCCCUGCAGGCCAACGUGCAGCGGCUGAAGGAGUACCGCUCCAAACUCAUCCUCUUCCCCAG-----GAAG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_000977_454 ~~~~~~~~~~~~~GCAUUCACAAGAAGGUGGCCCGGACCAUCGGCAUUUCUGUGGAUCCGAGGAGGCGGAACAAGUCCACGGAGUCCCUGCAGGCCAACGUGCAGCGGCUGAAGGAGUACCGCUCCAAACUCAUCCUCUUCCCCAG-----GAAGCCCUCGGCCCCCA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M3 1074 3 0.41 hek-i_NM_001144966_4955,hek-i_NM_004168_880,hek-i_NM_001144970_5003 Best CMs (by avg z-score): 1. (Z = 3.71) eeev_FSE - eastern_equine_encephalitis_ribosomal_frameshift_element 2. (Z = 3.08) Lacto-rpoB - Lacto-rpoB_RNA 3. (Z = 2.99) DdR7 - D._discoideum_snoRNA_Dd7 4. (Z = 2.89) mir-875 - microRNA_mir-875 5. (Z = 2.86) TB6Cs1H4 - Trypanosomatid_snoRNA_TB6Cs1H4 6. (Z = 2.84) rox2 - Drosophila_rox2_ncRNA 7. (Z = 2.76) rli40 - Listeria_sRNA_rli40 8. (Z = 2.69) mir-922 - microRNA_mir-922 9. (Z = 2.62) SMK_box_riboswitch - SMK_box_translational_riboswitch 10. (Z = 2.60) snoZ118 - Small_nucleolar_RNA_Z118/Z121/Z120 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM3.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM3_global.out/ --free-endgaps --indel=-100 --threads=4 ...........((((...((((((..((((....)))).(((((((..........................)))))))...)))))).))))....(((...(((((........))).))))).....((((..(((...))).))))...................................... MFE = -48.91 (Covariance contribution: -34.41) RNAz stats: MPI: 45.27, SCI: 0.77, ZSCORE: 1.19 Full summary: Sequences: 3 Columns: 188 Reading direction: forward Mean pairwise identity: 45.27 Shannon entropy: 0.70692 G+C content: 0.31132 Mean single sequence MFE: -29.70 Consensus MFE: -22.76 Energy contribution: -14.24 Covariance contribution: -8.52 Combinations/Pair: 1.74 Mean z-score: 1.19 Structure conservation index: 0.77 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.21 SVM RNA-class probability: 0.086631 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_001144966_4955 GCCUGAGGUUUCUAA---AAGAAG--GUAGAUUUCUACAGAGCUGAGU-----------------------GUUGGUUCCUUUUUCUUAUUGG----UUGAAAAUUACCUGGU--AGUG-AUCAGAAAACUUAGA-UGCUAUGUAACUAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAU~~ hek-i_NM_004168_880 GGAAGGUCUCUGCGAUAUGAUACCAGCUAU-UUUGUGGAGUAUUUUGCCUUGGAUCUCCUGAUGGAGAAUGGGGAGUGCCGUGGUGUCAUCGCACUGUGCAUAGAGGACGGGUCCAUCCAUCGCAUAAGAGCAAAGAACACUGUUGUUGCC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_001144970_5003 ~~CUGAGGUUUCUAA---AAGAAG--GUAGAUUUCUACAGAGCUGAGU-----------------------GUUGGUUCCUUUUUCUUAUUGG----UUGAAAAUUACCUGGU--AGUG-AUCAGAAAACUUAGA-UGCUAUGUAACUAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUUC // ClustID MergedIDs Count AvgDissim Members M2 1061 5 0.64 hek-i_NR_003287_4045,hek-i_NM_021134_112,hek-i_NM_052850_243,hek-i_NM_003651_995,hek-i_NM_001039690_103 Best CMs (by avg z-score): 1. (Z = 2.99) mir-572 - microRNA_mir-572 2. (Z = 2.95) mir-675 - microRNA_mir-675 3. (Z = 2.63) mir-663 - microRNA_mir-663 4. (Z = 2.61) mir-61 - microRNA_mir-61 5. (Z = 2.59) HOTAIRM1_1 - HOX_antisense_intergenic_RNA_myeloid_1_conserved_region_1 6. (Z = 2.37) Moco-II - Moco-II_RNA 7. (Z = 2.29) mir-339 - microRNA_mir-339 8. (Z = 2.22) mir-636 - microRNA_mir-636 9. (Z = 2.10) P18 - Pseudomonas_sRNA_P18 10. (Z = 2.09) MIR2907 - microRNA_MIR2907 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM2.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM2_global.out/ --free-endgaps --indel=-100 --threads=4 .....................(((....((((.(((((..............)))))...)))))))................(((..(((((......(((((((((((..(((.(..(((((((....(((.....)))....)))).)).))))).))))))...)))))))))).)))......................................... MFE = -79.81 (Covariance contribution: -47.47) RNAz stats: MPI: 32.50, SCI: 0.38, ZSCORE: 1.6 Full summary: Sequences: 5 Columns: 223 Reading direction: forward Mean pairwise identity: 32.50 Shannon entropy: 1.22364 G+C content: 0.52564 Mean single sequence MFE: -71.70 Consensus MFE: -27.25 Energy contribution: -21.98 Covariance contribution: -5.27 Combinations/Pair: 2.64 Mean z-score: 1.60 Structure conservation index: 0.38 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.96 SVM RNA-class probability: 0.000001 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NR_003287_4045 CGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAGUCUGG----CACGGUGAAGAGACAUGAGAGGUGUA-------GAAUAAGUGGGAGGCCC-----------CCGGCGC-----C--CCCCCGGUGUCCCCGC-GAGGGGC--CCGG-GGCGGGGUCCGCCGG--CCCUGCGGGCCGCCGGUG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_021134_112 ~~~~~~~~~~~~~~~~~CGGGGCCAGG-AGAGAAAGCUUUGU----------GGUUUGGUCUCAGGAAGCGAGGGGGCGCUGUGCCAGG--CGGCGGCCGUGCGGGGCGG-GCGC-G--CUGCUCCUUCCGCCUC-GCGGACCCCGGAAGCGCGCGUGGCCGCCA--UGGCGCGGAAUGUGGUGUAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_052850_243 ~~~~~~~~~~~~~~~~~GGCUACC----GGGCGCGGCCGCCCCCGCGCCGCAGGCCGGGACCCCGGUG-------GCCAGACCCCGAGGACCUCCUG-ACCCCGCGGUGGCAGCUGG--GACCGCGCUACGCGGC-UAAGCAGUUCGCGCGUUACGGCGCCGCCU--CCGGGGUGGUCCCCGGU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_001039690_103 ~~~~~~~~~~~~~~AAAAUUGCUGAAG-UAGGGGCCAGGU----------CACUGGUAG--UUAUAGUAU----GGAAAUAGUCGGAAGUGCGCAGGCAGUGCUCGCGGC--GGCG---GCGACGG--CGGCGG--GAGGUUCGGUUGU-CGCCCGUUGGCCGCG--CGGCGCCGCGCUCGGCGGCCGCCAUU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003651_995 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CGGCAGCAGUGAAGGAUUUGACCCCCCUGCCACUGAUAGGCAGUUCUCUGGGGCCCGGAAUCAGCUGCGCCGCCCCCAGUAUCGCCCUCAGUACCGGCAGCGGCGGUUCCCGCCUUACCACGUGGGACAGACCUUUGACCGUCGCUCACG // ClustID MergedIDs Count AvgDissim Members M9 31 3 0.53 hek-i_NM_175055_301,hek-i_NM_003519_303,hek-i_NM_006009_528 Best CMs (by avg z-score): 1. (Z = 2.23) IRES_IGF2 - Insulin-like_growth_factor_II_IRES 2. (Z = 1.93) sR28 - Small_nucleolar_RNA_sR28 3. (Z = 1.80) UPD-PKib - Pseudoknot_of_upstream_pseudoknot_domain_(UPD)_of_the_3'UTR 4. (Z = 1.77) EAV_LTH - Equine_arteritis_virus_leader_TRS_hairpin_(LTH) 5. (Z = 1.72) Downstream-peptide - Downstream_peptide_RNA 6. (Z = 1.58) SNORD48 - Small_nucleolar_RNA_SNORD48 7. (Z = 1.55) SAH_riboswitch - S-adenosyl-L-homocysteine_riboswitch 8. (Z = 1.51) PhotoRC-I - PhotoRC-I_RNA 9. (Z = 1.50) S_pombe_snR92 - small_nucleolar_RNA_snR92 10. (Z = 1.46) H19_1 - H19_conserved_region_1 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM9.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM9_global.out/ --free-endgaps --indel=-100 --threads=4 ..((((((((..(..((......))..)..)))).......))))...(.((((.(.((((....)))))....)))).)...(((........((((((..(((((..(((.((...)).))).)))))...........))))))........)))......................... MFE = -53.78 (Covariance contribution: -38.91) RNAz stats: MPI: 48.79, SCI: 0.42, ZSCORE: 2.45 Full summary: Sequences: 3 Columns: 183 Reading direction: forward Mean pairwise identity: 48.79 Shannon entropy: 0.70018 G+C content: 0.50444 Mean single sequence MFE: -46.03 Consensus MFE: -19.46 Energy contribution: -17.33 Covariance contribution: -2.13 Combinations/Pair: 1.38 Mean z-score: 2.45 Structure conservation index: 0.42 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.42 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NM_175055_301 CAAGGUGCUGAAGCAGGUGCACCCCGACACCGGC-------AUCUCGUCCAAGGCC-AUGG-GCAUCAUGAACUCCUUCGUCAAUGACAUCUUCGAGCGCAUCGCCA--GCGAGGCCUCC-CGCCUGGCACACUACAACAAGCGCUCCACCAUCACGUCCCG~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_003519_303 CAAGGUGCUGAAGCAGGUCCACCCCGACACCGGC-------AUCUCUUCUAAGGCC-AUGG-GAAUCAUGAACUCCUUCGUCAACGACAUCUUCGAGCGCAUCGCAA--GCGAGGCUUCC-CGCCUGGCGCACUACAACAAGCGCUCGACCAUCACCUCCAG~~~~~~~~~~~~~~~~~~~~~ hek-i_NM_006009_528 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ACAGGCAAAGAAGAUGCUGCCAAUAACUAUGCCCGAGGGCACUACACCAUUGGCAAGGAGAUCAUUGACCUCGUGUUGGACCGAAUUCGCAAGCUGGCCGACCAGUGC----ACGGGUCU-CCAGGGCUUCUUGGUUUUCCACAGCUUUGGUGGG // ClustID MergedIDs Count AvgDissim Members M8 282 5 0.57 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 = 12.72) U5 - U5_spliceosomal_RNA 2. (Z = 3.48) mir-231 - microRNA_mir-231 3. (Z = 3.43) Hammerhead_3 - Hammerhead_ribozyme_(type_III) 4. (Z = 3.21) MIR1122 - microRNA_MIR1122 5. (Z = 3.11) mir-205 - microRNA_mir-205 6. (Z = 2.91) mir-434 - microRNA_mir-434 7. (Z = 2.81) PYLIS_1 - Pyrrolysine_insertion_sequence_1 8. (Z = 2.80) mir-616 - microRNA_mir-616 9. (Z = 2.76) mir-136 - microRNA_mir-136 10. (Z = 2.68) mir-244 - microRNA_mir-244 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM8.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/hek-i_150/bgDinucWT/hek-i_150_structs/clustM8_global.out/ --free-endgaps --indel=-100 --threads=4 .....................................................................................................(...(((..(((((((((((...((...((((((((.(.......).)))))))).)))))))))))))......))))....... MFE = -55.46 (Covariance contribution: -37.06) RNAz stats: MPI: 56.73, SCI: 0.49, ZSCORE: 0.27 Full summary: Sequences: 5 Columns: 187 Reading direction: forward Mean pairwise identity: 56.73 Shannon entropy: 0.78935 G+C content: 0.37509 Mean single sequence MFE: -36.14 Consensus MFE: -17.62 Energy contribution: -17.58 Covariance contribution: -0.04 Combinations/Pair: 1.04 Mean z-score: 0.27 Structure conservation index: 0.49 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.78 SVM RNA-class probability: 0.179841 Prediction: OTHER Multiple alignment from mlocarna: hek-i_NR_002756_85 ~~~~~~~~~~~~~~~~AUGCAAGCUCUGCCUCCCAGGUUCA--------CGCCAUUCUCCUGUCUCAGCCUC----------CCAAGUAGCUGGGACUAAUA---CUCUGGUUUCUCUUCAGAUCGCAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACAACUCUGAGUCUUAACC hek-i_NR_002753_84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UUCAGAAAAAAAAUGGAGACAACUAGAGUUGAUCUGAAGAUUAUGGCAGAAUUCAAUAUUGGGGGAAUCUCUGGUUUCUCUUCAUAACGAAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAAAAACAACUAUGAGUUUAUGGU hek-i_NR_002755_83 ~~~~~~~~~~~~~~~ACCUC--A--UGCCUUGUGUAGUAAAAAAGGAUUUGGGGGU----UUUGUUUGGUUC----------CUGAGAGGGUUGUGUU-UUG---CUCUGGUUUCUCUUCAAAUCGUAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGAAACCGUUUUGAGUUUCAAGC hek-i_NR_002754_83 UAGCACUUGGCCCCAUUGUA--GAUUGCCCUGUGCAGUAAA--------CUUUCAA----GGUGUCGGCUGC----------CCCAGA---------U-UGA---CUCUGGUUUCUCUUCAAAUCGUAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGAAACGAGUGUGAGUCUGAAAC hek-i_NR_002757_85 ~~~~~~~~~~~~~~~~~~~~AUCAUUCUUCUUUUUCAUGCAUUUGUCCUUCUCCCACCCCCUUACUA--CAC----------CCUAGCAGAU--CAGCUAUA---CUCUGGUUUCUCUUCAGAUCGUAUAAAUCUUUCGCCUUUUACUAAAGAUUUCCGUGGAGAGGAACAACUCUGAGUCUUAAGC //