ClustID MergedIDs Count AvgDissim Members M5 136 6 0.51 novel-3hp_9,novel-3hp_17,novel-3hp_14,novel-3hp_30,novel-3hp_24,novel-1hp_38 Best CMs (by avg z-score): 1. (Z = 7.02) mir-625 - microRNA_mir-625 2. (Z = 6.07) mir-934 - microRNA_mir-934 3. (Z = 6.03) mir-548 - microRNA_mir-548 4. (Z = 5.79) mir-3179 - microRNA_mir-3179 5. (Z = 5.65) mir-942 - microRNA_mir-942 6. (Z = 5.63) mir-452 - microRNA_mir-452 7. (Z = 5.60) MIR1151 - microRNA_MIR1151 8. (Z = 5.38) mir-185 - microRNA_mir-185 9. (Z = 5.33) mir-370 - microRNA_mir-370 10. (Z = 5.32) mir-574 - microRNA_mir-574 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM5.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM5_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((....)))))((((((...))))))(((((....))))))))))))))))))) MFE = -82.67 (Covariance contribution: -48.27) RNAz stats: MPI: 29.39, SCI: 1.18, ZSCORE: -8.6 Full summary: Sequences: 6 Columns: 71 Reading direction: forward Mean pairwise identity: 29.39 Shannon entropy: 1.45712 G+C content: 0.50704 Mean single sequence MFE: -44.32 Consensus MFE: -52.15 Energy contribution: -36.95 Covariance contribution: -15.20 Combinations/Pair: 3.13 Mean z-score: -8.60 Structure conservation index: 1.18 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.71 SVM RNA-class probability: 0.198104 Prediction: OTHER Multiple alignment from mlocarna: novel-3hp_9 UUUAGGAGAAGAACACGUAUGGAUACGUGUUUUUACUGAAAACGGCAAGUCCUUGCCGUUCUUCUCCUAAA novel-3hp_17 CUGAUGAAGUCAGUCUACUCUGCAGUAGGAUAUCGCUAAUAUCGUUACGUUCGUAACACUGACUUCAUCAG novel-3hp_14 GGUGAGCUGGUUGGUCGUUAGAGAACGAGAUGAACGAUUCAUCAACUCGGUGGAGUUCCAACCAGCUCACC novel-3hp_30 GGCAGGAUCACUGAGAGACACCCGUCUCGUCCUACGGUAGGACGACCGAUCACGGUCUCAGUGAUCCUGCC novel-3hp_24 AGGGUGGCAGCCGUUACGCAGAUGCGUAGCGACCAUAGGUCGCAACUGUAUGCAGUUACGGCUGCCACCCU novel-1hp_38 AAGAUGGGUGUCAGGGUAUGAAUGCAGUGGCAUUGGUGAUGCCACUGCAUUCAUACCCUGACACCCAUCUU // ClustID MergedIDs Count AvgDissim Members M4 111 5 0.22 novel-1hp_32,novel-1hp_24,novel-1hp_10,novel-1hp_45,novel-1hp_4 Best CMs (by avg z-score): 1. (Z = 16.29) mir-625 - microRNA_mir-625 2. (Z = 16.13) mir-934 - microRNA_mir-934 3. (Z = 16.00) mir-642 - microRNA_mir-642 4. (Z = 15.80) mir-296 - microRNA_mir-296 5. (Z = 14.82) mir-944 - microRNA_mir-944 6. (Z = 14.41) mir-885 - microRNA_mir-885 7. (Z = 14.06) mir-607 - microRNA_mir-607 8. (Z = 13.51) mir-548 - microRNA_mir-548 9. (Z = 13.40) mir-942 - microRNA_mir-942 10. (Z = 12.98) mir-876 - microRNA_mir-876 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM4.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM4_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((((((((((((((((.....))))))))))))))))))))))))))))))))) MFE = -118.46 (Covariance contribution: -57.60) RNAz stats: MPI: 29.58, SCI: 1.31, ZSCORE: -15.96 Full summary: Sequences: 5 Columns: 71 Reading direction: forward Mean pairwise identity: 29.58 Shannon entropy: 1.34068 G+C content: 0.46761 Mean single sequence MFE: -61.04 Consensus MFE: -79.70 Energy contribution: -60.98 Covariance contribution: -18.72 Combinations/Pair: 2.82 Mean z-score: -15.96 Structure conservation index: 1.31 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.42 SVM RNA-class probability: 0.059917 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_32 CCGAACCUGGGCUUCGCCCUUGUAGAAACCACAACCGAUGUGGUUUCUACAAGGGCGAAGCCCAGGUUCGG novel-1hp_24 UGUGGUACUGUCCACGCUUUAAGAAGAACCCAAACGGAUUGGGUUCUUCUUAAAGCGUGGACAGUACCACA novel-1hp_10 AGAUGGCCUCGUGAAACCUACAUUACAAUAAUUUCAGUAAUUAUUGUAAUGUAGGUUUCACGAGGCCAUCU novel-1hp_4 UACAGGCGGUCGGUCUUAGUCUGUAGACCAACGAGUUCCGUUGGUCUACAGACUAAGACCGACCGCCUGUA novel-1hp_45 AAGUAUUCCGCGGCGUCACCUUAAAAUUCUAAUACCAUAUUAGAAUUUUAAGGUGACGCCGCGGAAUACUU // ClustID MergedIDs Count AvgDissim Members M7 175,33,21 17 0.47 novel-1hp_48,novel-1hp_28,novel-1hp_43,novel-3hp_7,novel-1hp_44,novel-1hp_30,novel-1hp_39,novel-3hp_20,novel-3hp_2,novel-3hp_22,novel-1hp_31,novel-1hp_11,novel-3hp_37,novel-1hp_18,novel-1hp_7,novel-1hp_34,novel-2hp_12 Best CMs (by avg z-score): 1. (Z = 12.05) mir-625 - microRNA_mir-625 2. (Z = 11.37) mir-934 - microRNA_mir-934 3. (Z = 10.67) mir-944 - microRNA_mir-944 4. (Z = 10.61) mir-642 - microRNA_mir-642 5. (Z = 10.56) mir-296 - microRNA_mir-296 6. (Z = 10.37) mir-548 - microRNA_mir-548 7. (Z = 10.17) mir-607 - microRNA_mir-607 8. (Z = 10.12) mir-885 - microRNA_mir-885 9. (Z = 9.76) mir-185 - microRNA_mir-185 10. (Z = 9.52) mir-3179 - microRNA_mir-3179 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM7.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM7_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((((((((((((((((.....)))))))))))))....................)))))))))))))))))))) MFE = -92.32 (Covariance contribution: -40.97) RNAz stats: MPI: 25.92, SCI: 1.14, ZSCORE: -12.85 Full summary: Sequences: 17 Columns: 91 Reading direction: forward Mean pairwise identity: 25.92 Shannon entropy: 1.51446 G+C content: 0.46579 Mean single sequence MFE: -53.68 Consensus MFE: -61.38 Energy contribution: -45.69 Covariance contribution: -15.70 Combinations/Pair: 4.06 Mean z-score: -12.85 Structure conservation index: 1.14 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.48 SVM RNA-class probability: 0.281095 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_48 GUCGUUGCGGAAAGUACGAUAGUAAGCGAUAGGAGUUACCUAUCGCUUACU--------------------AUCGUACUUUCCGCAACGAC novel-1hp_28 CCGCCGGAGCGAAAAAACAAAUGAAGAGCGAGCGCUUCGCUCGCUCUUCAU--------------------UUGUUUUUUCGCUCCGGCGG novel-3hp_20 GCCUGUCCUGGAAGGUUAACCAAUUAACAUGGGCGCUUCCCAUUAAACACU--------------------CGUUUACUUCCAGGACAGGC novel-1hp_43 UAGUCCUGCUAAAAACCAAGAGUGUAUGUAUGUGUACAACAUACAUACACU--------------------CUUGGUUUUUAGCAGGACUA novel-3hp_7 AGGGGUGUCGGCGACGAGCGGAGGCUCGGCUUAGGACCUAAGCUCAACUUA--------------------UGUUGAUCGCCGACACCCCU novel-3hp_2 GACUCCCCUUACAUGUAACGAGUGUUACAUGUGCCCGACACAUAAGUCACU--------------------CGACUUAUGUAAGGGGAGUC novel-1hp_44 UCCUCAUUUGGGUAUCCAUCGAGCGAGUUGGGAAGGCCUCCCAACUCGCUC--------------------GAUGGAUACCCAAAUGAGGA novel-3hp_22 CCCUGAUACAUUAUUGGAUGAAUAUCCAUAUGAAAUCAUCAUAGUUUUACA--------------------UAAAACAUAAUGUAUCAGGG novel-1hp_30 GACCCGGCGACGAUCCCCACCAGACCUCAAAGCUGAAGGCUUUGAGGUCUG--------------------GUGGGGAUCGUCGCCGGGUC novel-1hp_31 CGUCUUGGUCCUCAGGAGCAUUAAGGUCCGUGGUACGGCCACGGACCUUAA--------------------UGCUCCUGAGGACCAAGACG novel-2hp_12 ~~~~~~~~~~CAGCCAGCGGGAGGUUUGUUGAAGUAGGUUCAACAAACCUCCGUUCUCUCGGUAGAGAACGCCGCUGGCUG~~~~~~~~~~ novel-1hp_11 CCGAGCACCUGAUCGACAACCUUGAUGAUGCUAUUCCCUAGCAUCAUCAAG--------------------GUUGUCGAUCAGGUGCUCGG novel-1hp_34 UAGGUACGUCCACUAAAAUAUGAUAAAGCAUGUUCAUUACAUGCUUUAUCA--------------------UAUUUUAGUGGACGUACCUA novel-3hp_37 UCCUAGUGGGCAAACAGACAUCCGUCUGUGAUGAUACGCAUCAUUCAAUCG--------------------UUUGAAUUUGCCCACUAGGA novel-1hp_39 ACCGAGUUGGUAAUUAAAGAGAAAUCGACGCACACAUUGUGCGUCGAUUUC--------------------UCUUUAAUUACCAACUCGGU novel-1hp_18 GGCAUAUCGGCUAGCAUAGUAAUGUUCGUGUUUCUUUAAAACACGAACAUU--------------------ACUAUGCUAGCCGAUAUGCC novel-1hp_7 GUGAGCUGUGCAAUAAAAAUACAUAUAGUGUCUGCUAGAGACACUAUAUGU--------------------AUUUUUAUUGCACAGCUCAC // ClustID MergedIDs Count AvgDissim Members M6 177 8 0.51 novel-2hp_33,novel-2hp_30,novel-2hp_37,novel-2hp_35,novel-1hp_40,novel-2hp_47,novel-3hp_13,novel-2hp_19 Best CMs (by avg z-score): 1. (Z = 6.12) mir-642 - microRNA_mir-642 2. (Z = 5.92) mir-625 - microRNA_mir-625 3. (Z = 5.87) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 4. (Z = 5.78) mir-885 - microRNA_mir-885 5. (Z = 5.67) mir-548 - microRNA_mir-548 6. (Z = 5.57) mir-607 - microRNA_mir-607 7. (Z = 5.39) mir-934 - microRNA_mir-934 8. (Z = 4.84) mir-942 - microRNA_mir-942 9. (Z = 4.84) mir-3179 - microRNA_mir-3179 10. (Z = 4.75) mir-299 - microRNA_mir-299 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM6.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM6_global.out/ --free-endgaps --indel=-100 --threads=4 ...(((((((((((......((((((((((((((...))))))))))))))((((((((....)))))))))))))))))))... MFE = -77.43 (Covariance contribution: -40.56) RNAz stats: MPI: 27.02, SCI: 1.19, ZSCORE: -9.83 Full summary: Sequences: 8 Columns: 85 Reading direction: forward Mean pairwise identity: 27.02 Shannon entropy: 1.55614 G+C content: 0.44036 Mean single sequence MFE: -46.39 Consensus MFE: -55.13 Energy contribution: -39.91 Covariance contribution: -15.22 Combinations/Pair: 3.29 Mean z-score: -9.83 Structure conservation index: 1.19 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.69 SVM RNA-class probability: 0.204200 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_33 ~~~~UAUGAAAUAG------UUUAGGGUAGCAGACCCACUGCUACCCUAAAGUACGACAGCUGUGUCGUACCUAUUUCAUA~~~~ novel-2hp_30 ~~~~UGCGAUAAGU------AAUAGAGGGCUUCUGACCGAAGCCCUCUAUUGGGUAGCCCCCUGGCUACCCACUUAUCGCA~~~~ novel-2hp_37 ~~~~UACUGUACGG------GUUAGGGUAAGCGCGCCGCGCUUACCCUAACUCAAGGACGGCGGUCCUUGACCGUACAGUA~~~~ novel-2hp_35 ~~~~UGAGGGGAAU------CCUUAGCGUUAAAGGCCGUUUAACGCUAAGGCGUGCGGAAGGGUCCGCACGAUUCCCCUCA~~~~ novel-1hp_40 UGUGGCAAUUAUUAGCUCCAAGAUAUUCCUUUUACUCUAAAAGGAAUAUCUUGG--------------AGCUAAUAAUUGCCACA novel-3hp_13 UCACAAUGACUUUGGAUAGUUGACUAUCGUCUACCCCGUAGACCGGAGAUAACU--------------CCGCAAAGUCAUUGUGA novel-2hp_47 ~~~~GACAUAGUUG------AUCAUUGGGGGCUCGAAGAGCCCCCAAUGAUCGGCUACGGUACCGUAGCCGCAACUAUGUC~~~~ novel-2hp_19 ~~~~GAAAUAUAAU------AGUGGGUUCAUUGUGCGGCAAUGAACCCACUUAGUACGCCCAUGCGUACUAAUUAUAUUUC~~~~ // ClustID MergedIDs Count AvgDissim Members M1 218 3 0.32 novel-2hp_40,novel-2hp_48,novel-2hp_3 Best CMs (by avg z-score): 1. (Z = 8.07) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 2. (Z = 6.47) Bacteria_large_SRP - Bacterial_large_signal_recognition_particle_RNA 3. (Z = 6.28) P36 - Pseudomonas_sRNA_P36 4. (Z = 5.86) mir-642 - microRNA_mir-642 5. (Z = 5.54) Clostridiales-1 - Clostridiales-1_RNA 6. (Z = 5.44) RRE - HIV_Rev_response_element 7. (Z = 5.17) 5S_rRNA - 5S_ribosomal_RNA 8. (Z = 5.10) mir-607 - microRNA_mir-607 9. (Z = 5.02) RNAI - RNAI 10. (Z = 4.95) traJ-II - traJ-II_RNA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM1.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM1_global.out/ --free-endgaps --indel=-100 --threads=4 ((((((((((((((((((((((((...))))))))))))))((((((((....)))))))))))))))))) MFE = -113.60 (Covariance contribution: -61.70) RNAz stats: MPI: 25.35, SCI: 1.29, ZSCORE: -10.44 Full summary: Sequences: 3 Columns: 71 Reading direction: forward Mean pairwise identity: 25.35 Shannon entropy: 1.10130 G+C content: 0.57277 Mean single sequence MFE: -54.37 Consensus MFE: -70.25 Energy contribution: -54.27 Covariance contribution: -15.98 Combinations/Pair: 2.31 Mean z-score: -10.44 Structure conservation index: 1.29 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.99 SVM RNA-class probability: 0.020530 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_40 CGUGCACGGCUGUGAGUCGUGGGUCUCGCCCACGACUCACAACAGACCCUUGAGGGUCUGUGCCGUGCACG novel-2hp_48 UCGUCUGCAGUAUUAUCUGGCGCGCGUCGCGCCAGAUAAUAUCAAGAGAUAGCUCUCUUGACUGCAGACGA novel-2hp_3 GGGCGCCAGUACGACAGGACAGGGGUACCCUGUCCUGUCGUAAAAACGAGUUAUCGUUUUUACUGGCGCCC // ClustID MergedIDs Count AvgDissim Members M3 116 6 0.51 novel-2hp_37,novel-1hp_28,novel-2hp_42,novel-2hp_38,novel-1hp_32,novel-2hp_12 Best CMs (by avg z-score): 1. (Z = 8.95) mir-625 - microRNA_mir-625 2. (Z = 8.72) mir-642 - microRNA_mir-642 3. (Z = 8.62) mir-934 - microRNA_mir-934 4. (Z = 7.88) mir-607 - microRNA_mir-607 5. (Z = 7.58) mir-944 - microRNA_mir-944 6. (Z = 7.35) mir-548 - microRNA_mir-548 7. (Z = 7.00) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 8. (Z = 6.94) mir-885 - microRNA_mir-885 9. (Z = 6.73) mir-296 - microRNA_mir-296 10. (Z = 6.61) mir-299 - microRNA_mir-299 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM3.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM3_global.out/ --free-endgaps --indel=-100 --threads=4 .((((((((((((((((((((((((((((((((.....)))))))))))))((((((((....))))))))))))))))))))))))))). MFE = -82.01 (Covariance contribution: -43.74) RNAz stats: MPI: 24.46, SCI: 1.19, ZSCORE: -10.48 Full summary: Sequences: 6 Columns: 91 Reading direction: forward Mean pairwise identity: 24.46 Shannon entropy: 1.53941 G+C content: 0.44970 Mean single sequence MFE: -54.17 Consensus MFE: -64.50 Energy contribution: -49.75 Covariance contribution: -14.75 Combinations/Pair: 2.76 Mean z-score: -10.48 Structure conservation index: 1.19 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.70 SVM RNA-class probability: 0.202087 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_37 ~~~~~~~~~~UACUGUACGGGUUAGGGUAAGCGCGCCGCGCUUACCCUAACUCAAGGACGGCGGUCCUUGACCGUACAGUA~~~~~~~~~~ novel-1hp_28 CCGCCGGAGCGAAAAAACAAAUGAAGAGCGAGCGCUUCGCUCGCUCUUCAU--------------------UUGUUUUUUCGCUCCGGCGG novel-2hp_42 ~~~~~~~~~~CGACUGGGCCUAUGUAAAGGUUUAUAUAAAACCUUUACAUACCGUCGUCAUCGGACGACGGGGCCCAGUCG~~~~~~~~~~ novel-2hp_38 ~~~~~~~~~~GCUACUUGGGUAAUCGAAUCUAUUGUGUAUAGAUUCGAUUAUGUCUUACAAUUGUAAGACACCCAAGUAGC~~~~~~~~~~ novel-1hp_32 CCGAACCUGGGCUUCGCCCUUGUAGAAACCACAACCGAUGUGGUUUCUACA--------------------AGGGCGAAGCCCAGGUUCGG novel-2hp_12 ~~~~~~~~~~CAGCCAGCGGGAGGUUUGUUGAAGUAGGUUCAACAAACCUCCGUUCUCUCGGUAGAGAACGCCGCUGGCUG~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M2 271 8 0.29 novel-1hp_26,novel-1hp_46,novel-1hp_14,novel-1hp_3,novel-1hp_36,novel-3hp_40,novel-1hp_4,novel-1hp_19 Best CMs (by avg z-score): 1. (Z = 15.65) mir-625 - microRNA_mir-625 2. (Z = 15.14) mir-934 - microRNA_mir-934 3. (Z = 14.21) mir-642 - microRNA_mir-642 4. (Z = 14.03) mir-296 - microRNA_mir-296 5. (Z = 13.94) mir-944 - microRNA_mir-944 6. (Z = 13.63) mir-885 - microRNA_mir-885 7. (Z = 13.56) mir-607 - microRNA_mir-607 8. (Z = 12.90) mir-548 - microRNA_mir-548 9. (Z = 12.49) mir-942 - microRNA_mir-942 10. (Z = 12.22) mir-185 - microRNA_mir-185 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM2.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM2_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((((((((((((((((.....))))))))))))))))))))))))))))))))) MFE = -119.48 (Covariance contribution: -56.53) RNAz stats: MPI: 32.29, SCI: 1.29, ZSCORE: -15.15 Full summary: Sequences: 8 Columns: 71 Reading direction: forward Mean pairwise identity: 32.29 Shannon entropy: 1.48126 G+C content: 0.52113 Mean single sequence MFE: -62.74 Consensus MFE: -81.23 Energy contribution: -62.65 Covariance contribution: -18.58 Combinations/Pair: 3.36 Mean z-score: -15.15 Structure conservation index: 1.29 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.17 SVM RNA-class probability: 0.093244 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_26 UACGCAACGUAAGACGGAUAGGCACGUGGGUCGAUUACCGACCCACGUGCCUAUCCGUCUUACGUUGCGUA novel-1hp_46 GUCACGCAAAGAUUCGGUCCGUCUCUAUAGACACUAUAUGUCUAUAGAGACGGACCGAAUCUUUGCGUGAC novel-1hp_14 GCUACGCGAGACGAGGCAGCUACCACAAUAAUGUUGUCCAUUAUUGUGGUAGCUGCCUCGUCUCGCGUAGC novel-1hp_3 ACGGUUACGAGGAACUGCGCAUCAUGCCCAUCGGUCUACGAUGGGCAUGAUGCGCAGUUCCUCGUAACCGU novel-1hp_36 AGUACGAAAUUCUAGGUAGCGUCGUGUUCGACUGAUCCAGUCGAACACGACGCUACCUAGAAUUUCGUACU novel-3hp_40 GACCAGAGAAUACUUGGUGUAUUCACCACGGCAGGCGGUGCCGCGGUAAGCGUACCGAGUAUUCUCUGGUC novel-1hp_4 UACAGGCGGUCGGUCUUAGUCUGUAGACCAACGAGUUCCGUUGGUCUACAGACUAAGACCGACCGCCUGUA novel-1hp_19 CCCCGAGGAUGGGCUGCUACAUCAAAUUCAAGUCAUUAACUUGAAUUUGAUGUAGCAGCCCAUCCUCGGGG // ClustID MergedIDs Count AvgDissim Members M9 87 7 0.26 novel-1hp_14,novel-1hp_23,novel-1hp_2,novel-1hp_30,novel-1hp_17,novel-1hp_6,novel-1hp_19 Best CMs (by avg z-score): 1. (Z = 16.46) mir-625 - microRNA_mir-625 2. (Z = 16.18) mir-642 - microRNA_mir-642 3. (Z = 15.93) mir-934 - microRNA_mir-934 4. (Z = 15.86) mir-296 - microRNA_mir-296 5. (Z = 15.26) mir-944 - microRNA_mir-944 6. (Z = 15.10) mir-885 - microRNA_mir-885 7. (Z = 13.96) mir-607 - microRNA_mir-607 8. (Z = 13.48) mir-548 - microRNA_mir-548 9. (Z = 13.46) mir-299 - microRNA_mir-299 10. (Z = 13.13) mir-942 - microRNA_mir-942 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM9.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM9_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((((((((((((((((.....))))))))))))))))))))))))))))))))) MFE = -122.80 (Covariance contribution: -58.12) RNAz stats: MPI: 29.31, SCI: 1.31, ZSCORE: -15.75 Full summary: Sequences: 7 Columns: 71 Reading direction: forward Mean pairwise identity: 29.31 Shannon entropy: 1.52131 G+C content: 0.50503 Mean single sequence MFE: -65.06 Consensus MFE: -84.92 Energy contribution: -65.06 Covariance contribution: -19.86 Combinations/Pair: 3.30 Mean z-score: -15.75 Structure conservation index: 1.31 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.12 SVM RNA-class probability: 0.101389 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_2 AGUGCCAGUUGAAGCUCUCUUACAUCCUAUAUGUUGCACAUAUAGGAUGUAAGAGAGCUUCAACUGGCACU novel-1hp_23 CCCUCAAGAGAGGAGAUCUUCCCGUGUAAGUGGCAGAUCCACUUACACGGGAAGAUCUCCUCUCUUGAGGG novel-1hp_14 GCUACGCGAGACGAGGCAGCUACCACAAUAAUGUUGUCCAUUAUUGUGGUAGCUGCCUCGUCUCGCGUAGC novel-1hp_30 GACCCGGCGACGAUCCCCACCAGACCUCAAAGCUGAAGGCUUUGAGGUCUGGUGGGGAUCGUCGCCGGGUC novel-1hp_17 ACUAGUGAGCUGGACGUUCGAACCCCGGGUAACAAUUUGUUACCCGGGGUUCGAACGUCCAGCUCACUAGU novel-1hp_6 ACUUGCUUGGAUUGAAGUUCAACACAGCAAAAUAUUCCAUUUUGCUGUGUUGAACUUCAAUCCAAGCAAGU novel-1hp_19 CCCCGAGGAUGGGCUGCUACAUCAAAUUCAAGUCAUUAACUUGAAUUUGAUGUAGCAGCCCAUCCUCGGGG // ClustID MergedIDs Count AvgDissim Members M8 119 5 0.20 novel-1hp_25,novel-1hp_15,novel-1hp_47,novel-1hp_11,novel-1hp_42 Best CMs (by avg z-score): 1. (Z = 16.62) mir-625 - microRNA_mir-625 2. (Z = 15.75) mir-934 - microRNA_mir-934 3. (Z = 15.30) mir-885 - microRNA_mir-885 4. (Z = 14.64) mir-642 - microRNA_mir-642 5. (Z = 14.44) mir-548 - microRNA_mir-548 6. (Z = 14.31) mir-296 - microRNA_mir-296 7. (Z = 13.96) mir-607 - microRNA_mir-607 8. (Z = 13.81) mir-944 - microRNA_mir-944 9. (Z = 12.94) mir-185 - microRNA_mir-185 10. (Z = 12.85) mir-3179 - microRNA_mir-3179 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM8.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM8_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((((((((((((((((.....))))))))))))))))))))))))))))))))) MFE = -124.09 (Covariance contribution: -60.93) RNAz stats: MPI: 32.82, SCI: 1.28, ZSCORE: -16.12 Full summary: Sequences: 5 Columns: 71 Reading direction: forward Mean pairwise identity: 32.82 Shannon entropy: 1.29565 G+C content: 0.49577 Mean single sequence MFE: -63.94 Consensus MFE: -81.56 Energy contribution: -63.88 Covariance contribution: -17.68 Combinations/Pair: 2.82 Mean z-score: -16.12 Structure conservation index: 1.28 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.47 SVM RNA-class probability: 0.054099 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_25 CGUAUUUUGCGACGCAUAGGCUGGUGUAUUUGUAUUGGACAAAUACACCAGCCUAUGCGUCGCAAAAUACG novel-1hp_15 GCCGUCUUACGGUUGUCAGGAUAGGCAGUGCAGUAUGGCUGCACUGCCUAUCCUGACAACCGUAAGACGGC novel-1hp_47 GUAUACAUGGUAUCAUUAGGCUGGAGAUCAUGCCUCUGGCAUGAUCUCCAGCCUAAUGAUACCAUGUAUAC novel-1hp_11 CCGAGCACCUGAUCGACAACCUUGAUGAUGCUAUUCCCUAGCAUCAUCAAGGUUGUCGAUCAGGUGCUCGG novel-1hp_42 CAUAGUGAUUGCACGGAAGAGCUGGGUCUGCAACAUACUUGCAGACCCAGCUCUUCCGUGCAAUCACUAUG // ClustID MergedIDs Count AvgDissim Members M24 110 4 0.59 novel-3hp_31,novel-3hp_50,novel-1hp_47,novel-3hp_36 Best CMs (by avg z-score): 1. (Z = 6.99) mir-625 - microRNA_mir-625 2. (Z = 6.73) mir-934 - microRNA_mir-934 3. (Z = 6.36) mir-452 - microRNA_mir-452 4. (Z = 5.73) mir-942 - microRNA_mir-942 5. (Z = 5.66) mir-885 - microRNA_mir-885 6. (Z = 5.60) mir-3179 - microRNA_mir-3179 7. (Z = 5.29) mir-548 - microRNA_mir-548 8. (Z = 5.28) MIR815 - microRNA_MIR815 9. (Z = 5.26) MIR821 - microRNA_MIR821 10. (Z = 5.05) mir-744 - microRNA_mir-744 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM24.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM24_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((....)))))((((((...))))))(((((....))))))))))))))))))) MFE = -73.32 (Covariance contribution: -45.65) RNAz stats: MPI: 33.10, SCI: 1.01, ZSCORE: -9.12 Full summary: Sequences: 4 Columns: 71 Reading direction: forward Mean pairwise identity: 33.10 Shannon entropy: 1.15638 G+C content: 0.44014 Mean single sequence MFE: -40.30 Consensus MFE: -40.72 Energy contribution: -28.98 Covariance contribution: -11.75 Combinations/Pair: 2.41 Mean z-score: -9.12 Structure conservation index: 1.01 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.00 SVM RNA-class probability: 0.500000 Prediction: OTHER Multiple alignment from mlocarna: novel-3hp_31 GGAUACGUAGUCUUGAGUCACCCGACUCCGGUUUUAGGAACCGACAGGCCAUCCUGUAAGACUACGUAUCC novel-3hp_50 GAGUUGUUCUGAAAUUCUGCACGCAGAACCUUAUCGCGUAAGGGUAUAAAGGUAUACUUUCAGAACAACUC novel-1hp_47 GUAUACAUGGUAUCAUUAGGCUGGAGAUCAUGCCUCUGGCAUGAUCUCCAGCCUAAUGAUACCAUGUAUAC novel-3hp_36 UACGAUAUAUUUAGCACUGACUCCAGUGCAUACGGACAGUAUGAACGGAUAGCCGUUCUAAAUAUAUCGUA // ClustID MergedIDs Count AvgDissim Members M20 31 4 0.40 novel-1hp_49,novel-1hp_40,novel-1hp_37,novel-3hp_7 Best CMs (by avg z-score): 1. (Z = 13.49) mir-625 - microRNA_mir-625 2. (Z = 13.15) mir-934 - microRNA_mir-934 3. (Z = 12.20) mir-885 - microRNA_mir-885 4. (Z = 11.91) mir-944 - microRNA_mir-944 5. (Z = 11.91) mir-642 - microRNA_mir-642 6. (Z = 11.51) mir-296 - microRNA_mir-296 7. (Z = 11.34) mir-548 - microRNA_mir-548 8. (Z = 11.11) mir-607 - microRNA_mir-607 9. (Z = 10.92) mir-185 - microRNA_mir-185 10. (Z = 10.85) mir-3179 - microRNA_mir-3179 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM20.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM20_global.out/ --free-endgaps --indel=-100 --threads=4 ((((((((((((((((((((((((((((((((((...)))))))))))))))))))))))))))))))))) MFE = -107.82 (Covariance contribution: -51.30) RNAz stats: MPI: 27.23, SCI: 1.27, ZSCORE: -13.59 Full summary: Sequences: 4 Columns: 71 Reading direction: forward Mean pairwise identity: 27.23 Shannon entropy: 1.29205 G+C content: 0.47183 Mean single sequence MFE: -55.45 Consensus MFE: -70.62 Energy contribution: -55.25 Covariance contribution: -15.37 Combinations/Pair: 2.73 Mean z-score: -13.59 Structure conservation index: 1.27 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.43 SVM RNA-class probability: 0.057953 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_49 AUUACGUCUUCGACCUAGAAAAGAUUGCUCUGGCUCUCCCAGAGCAAUCUUUUCUAGGUCGAAGACGUAAU novel-1hp_40 UGUGGCAAUUAUUAGCUCCAAGAUAUUCCUUUUACUCUAAAAGGAAUAUCUUGGAGCUAAUAAUUGCCACA novel-1hp_37 AUCCAACCAGUCAGAGCCCUUAAGUUCUGCUCUGCCCUAGAGCAGAACUUAAGGGCUCUGACUGGUUGGAU novel-3hp_7 AGGGGUGUCGGCGACGAGCGGAGGCUCGGCUUAGGACCUAAGCUCAACUUAUGUUGAUCGCCGACACCCCU // ClustID MergedIDs Count AvgDissim Members M21 30 6 0.39 novel-2hp_42,novel-2hp_43,novel-2hp_40,novel-2hp_47,novel-2hp_18,novel-2hp_16 Best CMs (by avg z-score): 1. (Z = 7.54) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 2. (Z = 6.48) P36 - Pseudomonas_sRNA_P36 3. (Z = 6.14) mir-642 - microRNA_mir-642 4. (Z = 5.89) Bacteria_large_SRP - Bacterial_large_signal_recognition_particle_RNA 5. (Z = 5.27) yybP-ykoY - yybP-ykoY_leader 6. (Z = 5.27) mir-607 - microRNA_mir-607 7. (Z = 5.15) mir-934 - microRNA_mir-934 8. (Z = 5.11) mir-625 - microRNA_mir-625 9. (Z = 5.08) traJ-II - traJ-II_RNA 10. (Z = 5.07) RRE - HIV_Rev_response_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM21.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM21_global.out/ --free-endgaps --indel=-100 --threads=4 ((((((((((((((((((((((((...))))))))))))))((((((((....)))))))))))))))))) MFE = -105.89 (Covariance contribution: -56.29) RNAz stats: MPI: 27.79, SCI: 1.35, ZSCORE: -11.13 Full summary: Sequences: 6 Columns: 71 Reading direction: forward Mean pairwise identity: 27.79 Shannon entropy: 1.49829 G+C content: 0.53286 Mean single sequence MFE: -51.87 Consensus MFE: -69.93 Energy contribution: -51.50 Covariance contribution: -18.43 Combinations/Pair: 3.19 Mean z-score: -11.13 Structure conservation index: 1.35 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.15 SVM RNA-class probability: 0.096854 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_42 CGACUGGGCCUAUGUAAAGGUUUAUAUAAAACCUUUACAUACCGUCGUCAUCGGACGACGGGGCCCAGUCG novel-2hp_43 ACCUACACGUCAAUUUAAGGCGAGAACCUCGCCUUAAAUUGAGCGAUCAUCUGUGAUCGCUACGUGUAGGU novel-2hp_40 CGUGCACGGCUGUGAGUCGUGGGUCUCGCCCACGACUCACAACAGACCCUUGAGGGUCUGUGCCGUGCACG novel-2hp_47 GACAUAGUUGAUCAUUGGGGGCUCGAAGAGCCCCCAAUGAUCGGCUACGGUACCGUAGCCGCAACUAUGUC novel-2hp_18 CGCAAGAGUCCGGUGCUAGGGGUGGGAAACCCCUAGCACCGCAAUCACCUCGUGGUGAUUGGACUCUUGCG novel-2hp_16 GUCAAGAGUAUGCUGCGAUACGUUUGAUACGUAUCGCAGCAUGAGCUAUUCAUAUAGCUCAUACUCUUGAC // ClustID MergedIDs Count AvgDissim Members M22 246 8 0.51 novel-2hp_36,novel-2hp_39,novel-2hp_41,novel-1hp_15,novel-2hp_11,novel-2hp_10,novel-2hp_13,novel-2hp_17 Best CMs (by avg z-score): 1. (Z = 6.66) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 2. (Z = 6.58) mir-642 - microRNA_mir-642 3. (Z = 6.54) mir-885 - microRNA_mir-885 4. (Z = 5.99) mir-607 - microRNA_mir-607 5. (Z = 5.74) mir-625 - microRNA_mir-625 6. (Z = 5.71) mir-934 - microRNA_mir-934 7. (Z = 5.45) mir-944 - microRNA_mir-944 8. (Z = 5.43) gyrA - gyrA_RNA 9. (Z = 5.41) mir-296 - microRNA_mir-296 10. (Z = 5.13) P36 - Pseudomonas_sRNA_P36 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM22.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM22_global.out/ --free-endgaps --indel=-100 --threads=4 .........(((((((((((((((((((((((((...))))))))))))))((((((((....)))))))))))))))))))......... MFE = -92.35 (Covariance contribution: -48.75) RNAz stats: MPI: 38.38, SCI: 1.26, ZSCORE: -9.37 Full summary: Sequences: 8 Columns: 91 Reading direction: forward Mean pairwise identity: 38.38 Shannon entropy: 1.39115 G+C content: 0.40833 Mean single sequence MFE: -51.14 Consensus MFE: -64.57 Energy contribution: -49.22 Covariance contribution: -15.34 Combinations/Pair: 2.80 Mean z-score: -9.37 Structure conservation index: 1.26 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.19 SVM RNA-class probability: 0.090438 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_36 ~~~~~~~~~~UGAAGUUGGUGCACCAUCUUACGCUGGGCGUAAGAUGGUGCGAGCGCGGAGGGCCGCGCUCACCAACUUCA~~~~~~~~~~ novel-2hp_39 ~~~~~~~~~~GUUUCCAGCUGGUUUGAGACUUCCUGGGGAAGUCUCAAACCGGACUCGGUAUUCCGAGUCCAGCUGGAAAC~~~~~~~~~~ novel-2hp_41 ~~~~~~~~~~GCUUGGGGAUUUAUACCCAUUUCCCACGGAAAUGGGUAUAAGUCCGACGUGUGCGUCGGACAUCCCCAAGC~~~~~~~~~~ novel-1hp_15 GCCGUCUUACGGUUGUCAGGAUAGGCAGUGCAGUAUGGCUGCACUGCCUAU--------------------CCUGACAACCGUAAGACGGC novel-2hp_11 ~~~~~~~~~~AUUACUUGUUUUAGGCCCGUCGAGGUUAUCGACGGGCCUAAGUUGACAGCGGGCUGUCAACAACAAGUAAU~~~~~~~~~~ novel-2hp_10 ~~~~~~~~~~UGUUUUCGUGAUUUUUAUAUCUUCGUCAAAGAUAUAAAAAUGACAGACGACCGCGUCUGUCCACGAAAACA~~~~~~~~~~ novel-2hp_13 ~~~~~~~~~~UCUGACGUAUCCUACAAAACUCCUCGCGGGAGUUUUGUAGGGAGUACAUUAGUAUGUACUCAUACGUCAGA~~~~~~~~~~ novel-2hp_17 ~~~~~~~~~~GAAUCAUUUCGUCUGACCCCCGACUCUAUCGGGGGUCAGACGCAGUCAAAAGGUUGACUGCGAAAUGAUUC~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M23 57 5 0.52 novel-1hp_9,novel-3hp_43,novel-3hp_13,novel-3hp_40,novel-3hp_19 Best CMs (by avg z-score): 1. (Z = 8.20) mir-625 - microRNA_mir-625 2. (Z = 7.24) mir-548 - microRNA_mir-548 3. (Z = 6.80) mir-934 - microRNA_mir-934 4. (Z = 6.60) mir-296 - microRNA_mir-296 5. (Z = 6.54) mir-3179 - microRNA_mir-3179 6. (Z = 6.40) mir-452 - microRNA_mir-452 7. (Z = 6.37) mir-944 - microRNA_mir-944 8. (Z = 6.32) mir-607 - microRNA_mir-607 9. (Z = 6.24) mir-942 - microRNA_mir-942 10. (Z = 6.20) mir-885 - microRNA_mir-885 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM23.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM23_global.out/ --free-endgaps --indel=-100 --threads=4 ((((((((((((((.(((((((.((((.(((((.....))))).)))).))))))).)))))))))))))) MFE = -76.93 (Covariance contribution: -39.39) RNAz stats: MPI: 30.70, SCI: 1.09, ZSCORE: -9.22 Full summary: Sequences: 5 Columns: 71 Reading direction: forward Mean pairwise identity: 30.70 Shannon entropy: 1.32441 G+C content: 0.50986 Mean single sequence MFE: -45.06 Consensus MFE: -49.02 Energy contribution: -37.22 Covariance contribution: -11.80 Combinations/Pair: 2.83 Mean z-score: -9.22 Structure conservation index: 1.09 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.35 SVM RNA-class probability: 0.333207 Prediction: OTHER Multiple alignment from mlocarna: novel-3hp_40 GACCAGAGAAUACUUGGUGUAUUCACCACGGCAGGCGGUGCCGCGGUAAGCGUACCGAGUAUUCUCUGGUC novel-1hp_9 GACGCGGACAGCAUGCGGGGAUUAUGCAGAUGCGUCCUGCAUCUGCAUAAUCCCCGCAUGCUGUCCGCGUC novel-3hp_13 UCACAAUGACUUUGGAUAGUUGACUAUCGUCUACCCCGUAGACCGGAGAUAACUCCGCAAAGUCAUUGUGA novel-3hp_43 AUAUCCGGAAAAUUGGCUGUGUACAGCCUCGUUAGCAGAACGACUCUGCAUGCAGAGAAUUUUCCGGAUAU novel-3hp_19 AGGUUCUGAAAGUGUGCUCUGGCGAGCAUCGUUGAAAGAACGAGAGACAUAGGUCUCCACUUUCAGAACCU // ClustID MergedIDs Count AvgDissim Members M11 20 4 0.52 novel-1hp_1,novel-3hp_34,novel-3hp_28,novel-3hp_42 Best CMs (by avg z-score): 1. (Z = 6.58) mir-625 - microRNA_mir-625 2. (Z = 6.34) mir-934 - microRNA_mir-934 3. (Z = 6.22) mir-452 - microRNA_mir-452 4. (Z = 5.86) mir-944 - microRNA_mir-944 5. (Z = 5.76) mir-3179 - microRNA_mir-3179 6. (Z = 5.71) mir-607 - microRNA_mir-607 7. (Z = 5.61) mir-942 - microRNA_mir-942 8. (Z = 5.59) MIR1151 - microRNA_MIR1151 9. (Z = 5.53) mir-160 - mir-160_microRNA_precursor_family 10. (Z = 5.50) mir-200 - microRNA_mir-200 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM11.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM11_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((....)))))(((((.....)))))(((((....))))))))))))))))))) MFE = -77.99 (Covariance contribution: -47.49) RNAz stats: MPI: 28.40, SCI: 1.09, ZSCORE: -9.47 Full summary: Sequences: 4 Columns: 71 Reading direction: forward Mean pairwise identity: 28.40 Shannon entropy: 1.23650 G+C content: 0.44366 Mean single sequence MFE: -42.58 Consensus MFE: -46.35 Energy contribution: -31.85 Covariance contribution: -14.50 Combinations/Pair: 2.59 Mean z-score: -9.47 Structure conservation index: 1.09 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.48 SVM RNA-class probability: 0.278418 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_1 GUGGAUCACAAUUACAAUCCCCAGGCUGUCUAGGCUAUCUAGACAGCCUGGGGAUUGUAAUUGUGAUCCAC novel-3hp_28 CAUGCACUACCAUGGGCCUUUGGAGGCCGGACCGAAUGGGUCCAUUAAUAAAUUAAUCAUGGUAGUGCAUG novel-3hp_34 GCAUGACAAACUCAGUCUAGCGGUAGACGUAAGGAAUACUUACCUUAUUCAGAUAAGUGAGUUUGUCAUGC novel-3hp_42 GAAACAAGCUCACUCGACGGAUCCGUCGAAGACAAUCUGUCUUUUAAAUCGUUUUAAAGUGAGCUUGUUUC // ClustID MergedIDs Count AvgDissim Members M10 255,296 8 0.47 novel-3hp_29,novel-3hp_32,novel-3hp_25,novel-3hp_11,novel-3hp_8,novel-3hp_16,novel-3hp_45,novel-3hp_41 Best CMs (by avg z-score): 1. (Z = 4.88) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 2. (Z = 4.36) yybP-ykoY - yybP-ykoY_leader 3. (Z = 4.36) RCNMV_TE_DR1 - 3'TE-DR1_translation_enhancer_element 4. (Z = 4.32) MIR1151 - microRNA_MIR1151 5. (Z = 4.16) mir-708 - microRNA_mir-708 6. (Z = 4.06) mir-160 - mir-160_microRNA_precursor_family 7. (Z = 4.02) mir-934 - microRNA_mir-934 8. (Z = 3.88) mir-452 - microRNA_mir-452 9. (Z = 3.87) MIR820 - microRNA_MIR820 10. (Z = 3.86) MIR815 - microRNA_MIR815 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM10.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM10_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((....)))))(((((.....)))))(((((....))))))))))))))))))) MFE = -88.09 (Covariance contribution: -50.71) RNAz stats: MPI: 28.07, SCI: 1.44, ZSCORE: -7.48 Full summary: Sequences: 8 Columns: 71 Reading direction: forward Mean pairwise identity: 28.07 Shannon entropy: 1.57790 G+C content: 0.52113 Mean single sequence MFE: -39.96 Consensus MFE: -57.35 Energy contribution: -39.29 Covariance contribution: -18.06 Combinations/Pair: 3.34 Mean z-score: -7.48 Structure conservation index: 1.44 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.85 SVM RNA-class probability: 0.158736 Prediction: OTHER Multiple alignment from mlocarna: novel-3hp_8 UAACUGACUUAACCGGCGGGAACCCGCCAGGGAAUACCUCCCUCCCACUUCAGUGGGGGUUAAGUCAGUUA novel-3hp_16 GUAUCAACUGGGCGUACUUAUGCAAGUAGAAAAUACACUUUUCGCCCAAGAAUGGGCCGCCCAGUUGAUAC novel-3hp_11 UCUAUCGUGGCCCCCAACUUCACAGUUGAACAGUUUAUCUGUUCGGCCUUCCGGCCGGGGGCCACGAUAGA novel-3hp_45 GUCAAUUGAGACUAUCCCGGGGCCGGGAAAGAAAGGCCUUCUUACGGUUCCGACCGUUAGUCUCAAUUGAC novel-3hp_32 AUUCAAUCGCUCGGCGCGUUCCUACGCGUAGAGUGAAGCUCUAACACGACCACGUGUCCGAGCGAUUGAAU novel-3hp_41 GAUUUGAUACCGGCGUACCACAGGGUACAAGAGCCGACCUCUUCUGCACGUGUGCAGGCCGGUAUCAAAUC novel-3hp_25 CUGAUGUGCCGUCCCUACUAUUUAGUAGAGGGUCGAGAACCCUAGGUACGGAUACCUGGACGGCACAUCAG novel-3hp_29 UUUCGUUACUCCAGUAUGUUACCACAUAUGCAGCUAGGCUGCAGGCAUAAACAUGCCCUGGAGUAACGAAA // ClustID MergedIDs Count AvgDissim Members M13 182 4 0.45 novel-2hp_16,novel-1hp_20,novel-2hp_44,novel-2hp_2 Best CMs (by avg z-score): 1. (Z = 7.75) mir-642 - microRNA_mir-642 2. (Z = 7.56) mir-625 - microRNA_mir-625 3. (Z = 7.28) mir-934 - microRNA_mir-934 4. (Z = 7.27) mir-885 - microRNA_mir-885 5. (Z = 7.25) mir-607 - microRNA_mir-607 6. (Z = 6.66) mir-299 - microRNA_mir-299 7. (Z = 6.30) mir-548 - microRNA_mir-548 8. (Z = 6.30) mir-944 - microRNA_mir-944 9. (Z = 6.17) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 10. (Z = 6.13) mir-577 - microRNA_mir-577 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM13.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM13_global.out/ --free-endgaps --indel=-100 --threads=4 .........((((((((((((((((((((((((.....)))))))))))))((((((((....)))))))))))))))))))......... MFE = -85.10 (Covariance contribution: -46.22) RNAz stats: MPI: 28.02, SCI: 1.19, ZSCORE: -10.66 Full summary: Sequences: 4 Columns: 91 Reading direction: forward Mean pairwise identity: 28.02 Shannon entropy: 1.28052 G+C content: 0.38226 Mean single sequence MFE: -49.77 Consensus MFE: -59.28 Energy contribution: -46.40 Covariance contribution: -12.88 Combinations/Pair: 2.27 Mean z-score: -10.66 Structure conservation index: 1.19 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.04 SVM RNA-class probability: 0.115710 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_2 ~~~~~~~~~~AAUCAGGCAGGCUUCGUUGUUCUUUAUGAGAACAACGAAGCACGAGUUUUCAAAAACUCGUCUGCCUGAUU~~~~~~~~~~ novel-1hp_20 GGCUUAAAGAGCGGACAAUUUGUGUUCACACGCACGCGGCGUGUGAACACA--------------------AAUUGUCCGCUCUUUAAGCC novel-2hp_44 ~~~~~~~~~~GAAGAUGAGACGGGUACGAUCAGAUAACCUGAUCGUACCCGGGCUAUUACACAUAAUAGCCUCUCAUCUUC~~~~~~~~~~ novel-2hp_16 ~~~~~~~~~~GUCAAGAGUAUGCUGCGAUACGUUUGAUACGUAUCGCAGCAUGAGCUAUUCAUAUAGCUCAUACUCUUGAC~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M12 41,281 14 0.51 novel-3hp_23,novel-2hp_29,novel-2hp_46,novel-1hp_32,novel-2hp_9,novel-1hp_11,novel-2hp_6,novel-2hp_14,novel-2hp_32,novel-2hp_49,novel-2hp_34,novel-2hp_28,novel-3hp_46,novel-2hp_15 Best CMs (by avg z-score): 1. (Z = 6.20) mir-607 - microRNA_mir-607 2. (Z = 6.02) mir-625 - microRNA_mir-625 3. (Z = 5.98) mir-642 - microRNA_mir-642 4. (Z = 5.82) mir-885 - microRNA_mir-885 5. (Z = 5.80) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 6. (Z = 5.57) mir-296 - microRNA_mir-296 7. (Z = 5.43) mir-934 - microRNA_mir-934 8. (Z = 5.25) Bacteria_large_SRP - Bacterial_large_signal_recognition_particle_RNA 9. (Z = 5.03) mir-944 - microRNA_mir-944 10. (Z = 5.01) mir-200 - microRNA_mir-200 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM12.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM12_global.out/ --free-endgaps --indel=-100 --threads=4 ..........(((((((((((((((((((((((.....)))))))))....))))((((((((....)))))))))))))))))).......... MFE = -83.00 (Covariance contribution: -43.91) RNAz stats: MPI: 36.04, SCI: 1.09, ZSCORE: -9.06 Full summary: Sequences: 14 Columns: 95 Reading direction: forward Mean pairwise identity: 36.04 Shannon entropy: 1.53612 G+C content: 0.41328 Mean single sequence MFE: -49.81 Consensus MFE: -54.19 Energy contribution: -37.63 Covariance contribution: -16.57 Combinations/Pair: 3.75 Mean z-score: -9.06 Structure conservation index: 1.09 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.22 SVM RNA-class probability: 0.390085 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_32 ~~~~~~~~~~CGAAUUCCACUGAGGUCUCCGUAUACCGUACGGAGAC----CUCAUUAAUGUGAGUCCACAUUAAGUGGAAUUCG~~~~~~~~~~ novel-2hp_49 ~~~~~~~~~~UUACUUCAAGAAAUGCCUGUGAAUACGAUUCACAGGC----AUUUAAGCACCAGCCCUGGUGCUUCUUGAAGUAA~~~~~~~~~~ novel-2hp_34 ~~~~~~~~~~AUUUAAGCAGUGCCCACCCUUAAUAGGUUUAAGGGUG----GGCAAGCAUGGGCGCGCCCAUGCUCUGCUUAAAU~~~~~~~~~~ novel-2hp_28 ~~~~~~~~~~CUAUUUUAACGCUCUCCACUGAAUACGCUUCAGUGGA----GAGCUAACGCACAGAUGUGCGUUAGUUAAAAUAG~~~~~~~~~~ novel-2hp_29 ~~~~~~~~~~ACGUACCUUAACUUCGCCGGUAAUUAGUUUACCGGCG----AAGUGUGACCUGUAAUCAGGUCACUAAGGUACGU~~~~~~~~~~ novel-2hp_46 ~~~~~~~~~~UCGGUCCUGACCUAUUCCCUGCGUAACGCGCAGGGAA----UAGGUGCAACUUGCUGAAGUUGCAUCAGGACCGA~~~~~~~~~~ novel-3hp_23 ~~~~~~~~~CUAGGACUUUA-----AGGCACAUU-CUCAUGUGCCGGGGAAUACCCGGAACGUAUCGACGUUCCUUAAAGUCCUAG~~~~~~~~~ novel-3hp_46 ~~~~~~~~~CAUUGUCCGAC-----UAGGUCCUU-CGCAGGACCUAACUUAAUGUUAGCACUGUAACCAGUGCUAGUCGGACAAUG~~~~~~~~~ novel-2hp_9 ~~~~~~~~~~UUGUGUUUGUACCUGGUUCUUUGUAAGUCAAAGAACC----AGGUUACCAACUUGUGAGUUGGUAACAAACACAA~~~~~~~~~~ novel-1hp_11 CCGAGCACCUGAUCGACAACCUUGAUGAUGCUAUUCCCUAGCAUCAU----CAAG--------------------GUUGUCGAUCAGGUGCUCGG novel-1hp_32 CCGAACCUGGGCUUCGCCCUUGUAGAAACCACAACCGAUGUGGUUUC----UACA--------------------AGGGCGAAGCCCAGGUUCGG novel-2hp_6 ~~~~~~~~~~CGACUCUUGGACCCGAAUCUGCUAAUGAAGCAGAUUC----GGGUAAUAACGUUUCCACGUUAUUCCAAGAGUCG~~~~~~~~~~ novel-2hp_15 ~~~~~~~~~~CCGCGGCUAGAAUAGCCAUCCGGACGUCCCGGAUGGC----UAUUCACUGCGGACGCCCGCAGUGCUAGCCGCGG~~~~~~~~~~ novel-2hp_14 ~~~~~~~~~~GCGUGUCUAGGCCACUCCACGUGAAUCCCACGUGGAG----UGGCCUCCACCGGAGCCGGUGGAGCUAGACACGC~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M15 260 5 0.52 novel-3hp_4,novel-3hp_49,novel-3hp_47,novel-1hp_31,novel-3hp_15 Best CMs (by avg z-score): 1. (Z = 7.05) mir-625 - microRNA_mir-625 2. (Z = 6.32) mir-452 - microRNA_mir-452 3. (Z = 6.31) mir-934 - microRNA_mir-934 4. (Z = 6.23) mir-3179 - microRNA_mir-3179 5. (Z = 6.21) mir-885 - microRNA_mir-885 6. (Z = 6.16) mir-708 - microRNA_mir-708 7. (Z = 5.94) mir-136 - microRNA_mir-136 8. (Z = 5.79) MIR815 - microRNA_MIR815 9. (Z = 5.76) mir-607 - microRNA_mir-607 10. (Z = 5.70) MIR1151 - microRNA_MIR1151 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM15.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM15_global.out/ --free-endgaps --indel=-100 --threads=4 ((((((((((((((((((((......)))))(((((.....)))))(((((....)))))))))))))))))))) MFE = -79.61 (Covariance contribution: -46.17) RNAz stats: MPI: 33.20, SCI: 1.10, ZSCORE: -8.6 Full summary: Sequences: 5 Columns: 75 Reading direction: forward Mean pairwise identity: 33.20 Shannon entropy: 1.26646 G+C content: 0.45796 Mean single sequence MFE: -42.86 Consensus MFE: -47.00 Energy contribution: -37.12 Covariance contribution: -9.88 Combinations/Pair: 2.72 Mean z-score: -8.60 Structure conservation index: 1.10 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.50 SVM RNA-class probability: 0.270950 Prediction: OTHER Multiple alignment from mlocarna: novel-3hp_4 ~GGACAUUCCAAACACAUCAA--GCAUGAUGGGCGCAUUGAGCGCCCGGCUCCUCAGCCGUGUUUGGAAUGUCC~ novel-3hp_47 ~ACAUCCAUACUCGU-AUAUUUGGAAAUAU-ACAGCACAUGGCUGUGAUAUGUUGAUAUCACGAGUAUGGAUGU~ novel-3hp_15 ~UGAGAGUUCGCUUUAAUUUC--AAAAAAUUCUUGCAUGACGCAAGGAUCUAGAAAGAUCAAAGCGAACUCUCA~ novel-3hp_49 ~AUCUCAUCCCUCAGGAUUUA--UUGAAAUCCACGGAGGUCCCGUGCAAAUGGCUAUUUGCUGAGGGAUGAGAU~ novel-1hp_31 CGUCUUGGUCCUCAGGAGCAU--UAAGGUCCGUGGUAC--GGCCACGGACCUUAAUGCUCCUGAGGACCAAGACG // ClustID MergedIDs Count AvgDissim Members M14 146 4 0.44 novel-3hp_39,novel-3hp_33,novel-3hp_36,novel-3hp_19 Best CMs (by avg z-score): 1. (Z = 4.58) tRNA-Sec - Selenocysteine_transfer_RNA 2. (Z = 3.92) mir-160 - mir-160_microRNA_precursor_family 3. (Z = 3.79) MIR162_2 - microRNA_MIR162_2 4. (Z = 3.70) MIR821 - microRNA_MIR821 5. (Z = 3.57) mir-284 - microRNA_mir-284 6. (Z = 3.53) mir-156 - mir-156_microRNA_precursor 7. (Z = 3.50) mir-317 - microRNA_mir-317 8. (Z = 3.36) Clostridiales-1 - Clostridiales-1_RNA 9. (Z = 3.33) MIR815 - microRNA_MIR815 10. (Z = 3.33) mir-541 - microRNA_mir-541 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM14.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM14_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((....)))))(((((.....)))))(((((....))))))))))))))))))) MFE = -83.49 (Covariance contribution: -49.86) RNAz stats: MPI: 25.35, SCI: 1.46, ZSCORE: -6.81 Full summary: Sequences: 4 Columns: 71 Reading direction: forward Mean pairwise identity: 25.35 Shannon entropy: 1.30082 G+C content: 0.44014 Mean single sequence MFE: -34.22 Consensus MFE: -49.92 Energy contribution: -33.42 Covariance contribution: -16.50 Combinations/Pair: 2.72 Mean z-score: -6.81 Structure conservation index: 1.46 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.00 SVM RNA-class probability: 0.125412 Prediction: OTHER Multiple alignment from mlocarna: novel-3hp_39 UCUGAAUUUAGUACCUGCGGGAUCGCAGUUCGUUGGUUACGAAAGAUCUUCAGAUCUGUACUAAAUUCAGA novel-3hp_33 GACACGAUUAGCAUCCUCCUUGCGGAGGCACUGAGGUUCAGUGGAUUAAGCAUAAUCAUGCUAAUCGUGUC novel-3hp_36 UACGAUAUAUUUAGCACUGACUCCAGUGCAUACGGACAGUAUGAACGGAUAGCCGUUCUAAAUAUAUCGUA novel-3hp_19 AGGUUCUGAAAGUGUGCUCUGGCGAGCAUCGUUGAAAGAACGAGAGACAUAGGUCUCCACUUUCAGAACCU // ClustID MergedIDs Count AvgDissim Members M17 169 6 0.31 novel-1hp_26,novel-1hp_23,novel-1hp_3,novel-1hp_13,novel-1hp_9,novel-2hp_15 Best CMs (by avg z-score): 1. (Z = 14.73) mir-625 - microRNA_mir-625 2. (Z = 13.70) mir-934 - microRNA_mir-934 3. (Z = 13.60) mir-642 - microRNA_mir-642 4. (Z = 13.20) mir-296 - microRNA_mir-296 5. (Z = 13.19) mir-885 - microRNA_mir-885 6. (Z = 12.76) mir-944 - microRNA_mir-944 7. (Z = 12.64) mir-607 - microRNA_mir-607 8. (Z = 12.21) mir-185 - microRNA_mir-185 9. (Z = 11.67) mir-548 - microRNA_mir-548 10. (Z = 11.22) mir-3179 - microRNA_mir-3179 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM17.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM17_global.out/ --free-endgaps --indel=-100 --threads=4 (((((((((((((((((((((((((((((((((.....)))))))))))))....................)))))))))))))))))))) MFE = -116.89 (Covariance contribution: -54.89) RNAz stats: MPI: 24.81, SCI: 1.10, ZSCORE: -14.05 Full summary: Sequences: 6 Columns: 91 Reading direction: forward Mean pairwise identity: 24.81 Shannon entropy: 1.33114 G+C content: 0.56444 Mean single sequence MFE: -66.75 Consensus MFE: -73.50 Energy contribution: -56.72 Covariance contribution: -16.78 Combinations/Pair: 3.00 Mean z-score: -14.05 Structure conservation index: 1.10 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.41 SVM RNA-class probability: 0.309439 Prediction: OTHER Multiple alignment from mlocarna: novel-1hp_26 UACGCAACGUAAGACGGAUAGGCACGUGGGUCGAUUACCGACCCACGUGCC--------------------UAUCCGUCUUACGUUGCGUA novel-1hp_23 CCCUCAAGAGAGGAGAUCUUCCCGUGUAAGUGGCAGAUCCACUUACACGGG--------------------AAGAUCUCCUCUCUUGAGGG novel-1hp_3 ACGGUUACGAGGAACUGCGCAUCAUGCCCAUCGGUCUACGAUGGGCAUGAU--------------------GCGCAGUUCCUCGUAACCGU novel-1hp_13 GCCACGAGGCAUCGAUGAUCCCAAUCUGGACUCGCCCCGAGUCCAGAUUGG--------------------GAUCAUCGAUGCCUCGUGGC novel-1hp_9 GACGCGGACAGCAUGCGGGGAUUAUGCAGAUGCGUCCUGCAUCUGCAUAAU--------------------CCCCGCAUGCUGUCCGCGUC novel-2hp_15 ~~~~~~~~~~CCGCGGCUAGAAUAGCCAUCCGGACGUCCCGGAUGGCUAUUCACUGCGGACGCCCGCAGUGCUAGCCGCGG~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M16 241 4 0.37 novel-2hp_7,novel-2hp_1,novel-2hp_22,novel-2hp_17 Best CMs (by avg z-score): 1. (Z = 6.89) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 2. (Z = 5.44) mir-885 - microRNA_mir-885 3. (Z = 5.41) mir-607 - microRNA_mir-607 4. (Z = 5.10) mir-642 - microRNA_mir-642 5. (Z = 4.86) P36 - Pseudomonas_sRNA_P36 6. (Z = 4.82) 23S-methyl - 23S_methyl_RNA_motif 7. (Z = 4.79) Bacteria_large_SRP - Bacterial_large_signal_recognition_particle_RNA 8. (Z = 4.74) mir-625 - microRNA_mir-625 9. (Z = 4.68) Clostridiales-1 - Clostridiales-1_RNA 10. (Z = 4.66) yybP-ykoY - yybP-ykoY_leader Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM16.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM16_global.out/ --free-endgaps --indel=-100 --threads=4 ((((((((((((((((((((((((...))))))))))))))((((((((....)))))))))))))))))) MFE = -96.83 (Covariance contribution: -52.73) RNAz stats: MPI: 22.54, SCI: 1.39, ZSCORE: -10.73 Full summary: Sequences: 4 Columns: 71 Reading direction: forward Mean pairwise identity: 22.54 Shannon entropy: 1.38532 G+C content: 0.45775 Mean single sequence MFE: -46.23 Consensus MFE: -64.32 Energy contribution: -46.08 Covariance contribution: -18.25 Combinations/Pair: 2.87 Mean z-score: -10.73 Structure conservation index: 1.39 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.33 SVM RNA-class probability: 0.070589 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_22 CCAGGGGUCUUUCCGCAUAUCUCAUACUGAGAUAUGCGGAAUUAUUAUCGCUGGAUAAUAAAGACCCCUGG novel-2hp_1 AGUAUAGAGUUCUACCAACGAUACUUUGUAUCGUUGGUAGAAGAACUCUCGUCAGAGUUCUACUCUAUACU novel-2hp_7 CGCAGACGGUUGACUUUGACCCGCAGCUCGGGUCAAAGUCAGAUAAUAUGUUGAUAUUAUCACCGUCUGCG novel-2hp_17 GAAUCAUUUCGUCUGACCCCCGACUCUAUCGGGGGUCAGACGCAGUCAAAAGGUUGACUGCGAAAUGAUUC // ClustID MergedIDs Count AvgDissim Members M19 220 8 0.43 novel-2hp_20,novel-2hp_31,novel-2hp_50,novel-2hp_39,novel-1hp_31,novel-2hp_9,novel-2hp_8,novel-2hp_5 Best CMs (by avg z-score): 1. (Z = 7.34) mir-642 - microRNA_mir-642 2. (Z = 6.50) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 3. (Z = 5.87) mir-885 - microRNA_mir-885 4. (Z = 5.75) mir-607 - microRNA_mir-607 5. (Z = 5.72) Bacteria_large_SRP - Bacterial_large_signal_recognition_particle_RNA 6. (Z = 5.45) mir-934 - microRNA_mir-934 7. (Z = 5.30) mir-625 - microRNA_mir-625 8. (Z = 5.17) P36 - Pseudomonas_sRNA_P36 9. (Z = 4.87) mir-548 - microRNA_mir-548 10. (Z = 4.84) mir-486 - microRNA_mir-486 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM19.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM19_global.out/ --free-endgaps --indel=-100 --threads=4 .........(((((((((((((((((((((((((...))))))))))))))((((((((....)))))))))))))))))))......... MFE = -94.82 (Covariance contribution: -48.38) RNAz stats: MPI: 34.62, SCI: 1.28, ZSCORE: -8.94 Full summary: Sequences: 8 Columns: 91 Reading direction: forward Mean pairwise identity: 34.62 Shannon entropy: 1.50072 G+C content: 0.43207 Mean single sequence MFE: -53.11 Consensus MFE: -68.10 Energy contribution: -51.29 Covariance contribution: -16.81 Combinations/Pair: 3.02 Mean z-score: -8.94 Structure conservation index: 1.28 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.11 SVM RNA-class probability: 0.103940 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_20 ~~~~~~~~~~UGCCGAGCGCACACCCCUAGCAUUUCUGAUGCUAGGGGUGUUCGGAGUCGUGGGACUCCGAGCGCUCGGCA~~~~~~~~~~ novel-2hp_31 ~~~~~~~~~~UCUCGAACCUCUGAGUCCGUAGAACUCGUCUACGGACUCAGUGCUACCCACACGGGUAGCAAGGUUCGAGA~~~~~~~~~~ novel-2hp_50 ~~~~~~~~~~GCUUGCUAGCGACCGAACUCGAACCGUUUUCGAGUUCGGUCUCUCCAACAGGUGUUGGAGAGCUAGCAAGC~~~~~~~~~~ novel-2hp_39 ~~~~~~~~~~GUUUCCAGCUGGUUUGAGACUUCCUGGGGAAGUCUCAAACCGGACUCGGUAUUCCGAGUCCAGCUGGAAAC~~~~~~~~~~ novel-1hp_31 CGUCUUGGUCCUCAGGAGCAUUAAGGUCCGUGGUACGGCCACGGACCUUAA--------------------UGCUCCUGAGGACCAAGACG novel-2hp_9 ~~~~~~~~~~UUGUGUUUGUACCUGGUUCUUUGUAAGUCAAAGAACCAGGUUACCAACUUGUGAGUUGGUAACAAACACAA~~~~~~~~~~ novel-2hp_8 ~~~~~~~~~~UCACGAUCUACCGUAUUAUACUGUCAGGCAGUAUAAUACGGAUCUCUGAGCCUUCAGAGAUUAGAUCGUGA~~~~~~~~~~ novel-2hp_5 ~~~~~~~~~~GUGCGCUGCCGCUAGAAUGCCGCACGACGCGGCAUUCUAGCCACACUUAUGCCUAAGUGUGGGCAGCGCAC~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M18 164 7 0.46 novel-2hp_50,novel-2hp_26,novel-1hp_41,novel-2hp_14,novel-2hp_45,novel-2hp_15,novel-2hp_40 Best CMs (by avg z-score): 1. (Z = 7.16) Archaea_SRP - Archaeal_signal_recognition_particle_RNA 2. (Z = 6.75) mir-642 - microRNA_mir-642 3. (Z = 6.34) mir-625 - microRNA_mir-625 4. (Z = 6.03) mir-607 - microRNA_mir-607 5. (Z = 6.01) mir-185 - microRNA_mir-185 6. (Z = 5.85) mir-934 - microRNA_mir-934 7. (Z = 5.74) mir-885 - microRNA_mir-885 8. (Z = 5.66) mir-296 - microRNA_mir-296 9. (Z = 5.61) Bacteria_large_SRP - Bacterial_large_signal_recognition_particle_RNA 10. (Z = 5.36) mir-574 - microRNA_mir-574 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM18.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/novel-71nt_dinuc500/1-2-3hp/novel-1-2-3hp_structs/clustM18_global.out/ --free-endgaps --indel=-100 --threads=4 .........((((((((((((((((((((((((.....)))))))))))))((((((((....)))))))))))))))))))......... MFE = -100.78 (Covariance contribution: -51.33) RNAz stats: MPI: 35.69, SCI: 1.23, ZSCORE: -9.23 Full summary: Sequences: 7 Columns: 91 Reading direction: forward Mean pairwise identity: 35.69 Shannon entropy: 1.39231 G+C content: 0.48438 Mean single sequence MFE: -57.10 Consensus MFE: -70.20 Energy contribution: -54.71 Covariance contribution: -15.48 Combinations/Pair: 2.70 Mean z-score: -9.23 Structure conservation index: 1.23 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -1.05 SVM RNA-class probability: 0.115361 Prediction: OTHER Multiple alignment from mlocarna: novel-2hp_50 ~~~~~~~~~~GCUUGCUAGCGACCGAACUCGAACCGUUUUCGAGUUCGGUCUCUCCAACAGGUGUUGGAGAGCUAGCAAGC~~~~~~~~~~ novel-2hp_26 ~~~~~~~~~~CUCAGGUUGAAGCGAGGCUCUGAGCCGUUCAGAGCCUCGCUCCUCUUUUUACCAAAAGAGGUCAACCUGAG~~~~~~~~~~ novel-2hp_40 ~~~~~~~~~~CGUGCACGGCUGUGAGUCGUGGGUCUCGCCCACGACUCACAACAGACCCUUGAGGGUCUGUGCCGUGCACG~~~~~~~~~~ novel-2hp_45 ~~~~~~~~~~GGUGGAAAGUGAGCCUCUGUAGAGUUUCUCUACAGAGGCUCCCCUCAAGAGCACUUGAGGGACUUUCCACC~~~~~~~~~~ novel-1hp_41 UGGUGAGACUGGCUCUCGAGGUAACAGUGGGUGCUACCCACCCACUGUUAC--------------------CUCGAGAGCCAGUCUCACCA novel-2hp_15 ~~~~~~~~~~CCGCGGCUAGAAUAGCCAUCCGGACGUCCCGGAUGGCUAUUCACUGCGGACGCCCGCAGUGCUAGCCGCGG~~~~~~~~~~ novel-2hp_14 ~~~~~~~~~~GCGUGUCUAGGCCACUCCACGUGAAUCCCACGUGGAGUGGCCUCCACCGGAGCCGGUGGAGCUAGACACGC~~~~~~~~~~ //