ClustID MergedIDs Count AvgDissim Members M5 530 8 0.88 Atrn.118669796-5,Atrn.118669796-6,Laptm4a.32414563-2,Laptm4a.32414563-3,Usp9x.21659964-3,Psmb2.146112219-0,Appbp2.73471088-1,Appbp2.73471088-0 Best CMs (by avg z-score): 1. (Z = 2.88) rox2 - Drosophila_rox2_ncRNA 2. (Z = 2.77) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.48) ceN115 - C._elegans_sRNA_ceN115 4. (Z = 2.31) mycoplasma_FSE - mycoplasma_ribosomal_frameshift_element 5. (Z = 2.23) PreQ1 - PreQ1_riboswitch 6. (Z = 2.22) SCARNA15 - Small_Cajal_body_specific_RNA_15 7. (Z = 2.22) srg1 - srg1 8. (Z = 2.21) Lacto-rpoB - Lacto-rpoB_RNA 9. (Z = 2.20) Lnt - Lnt_RNA 10. (Z = 2.14) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM5.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM5_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ................................................................................................................................................................................................................................................................................................................................................................................................................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 45.62, SCI: -0.00, ZSCORE: -0.23 Full summary: Sequences: 8 Columns: 435 Reading direction: forward Mean pairwise identity: 45.62 Shannon entropy: 1.12665 G+C content: 0.11909 Mean single sequence MFE: -27.45 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.23 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -4.30 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Atrn.118669796-5 ~~~~~AGUACACUUUUGUAAUCCCAGGAUGUGGAAGACCAACGCAGGAGGAUCACCCUGAGUUUGAGACCAUAGGAAGACCUUUUCUCAAAAAAAAAAAAAAAAAGAAAGAAAGAAAGAAAGAAAGAAAUCAAAUUGAUUGGCAUAUAGUUAUGU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Atrn.118669796-6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AAAGAAAGAAAGAAAGAAAUCAAAUUGAUUGGCAUAUAGUUAUGUGUUUAUUUUUGAGUACUUGCUAUGUAAAAGCCUUUAGAAAUACACAGUUUUAAUUAUGGAAUUGAGUAUAAAUAAAACAAGUACAUGUAUGUAACCAAUAAAGUA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Laptm4a.32414563-2 GGAAGGUGGAAGCAAGAGAAUCAGAAGUUCAUGGUAAUUCUCCACUAAAUAGAGUGCUGAGCAGGUAUGUACAAGGAUCUGACUUUACCUGUGGCACCAAAAAAAAAAAAACAAAAACAAAAACAAAAAACAAA---AAACCCUUAUGUGUAG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Laptm4a.32414563-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AAAAAACAAAAACAAAAACAAAAAACAAA---AAACCCUUAUGUGUAGGGGUGCUUUUUGAUGAGGAGAAGGAUGGAGCAGUCUUAGUCAGUAAAAUGCAUCUAGACGCUAACUUAUUACCAACUGGACAUUUGAGGUAUUCAGUAGACACUU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Usp9x.21659964-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CCAGCAACCACAUGGUGGCUCACAACCAUCUGUAAUGAGAUUCGAUGCCCUCUUCUGGUGUGUCUGAAGACAGCUACAGUGUACUC--AUAUACAAUAAAUAAAUCUUUAAAAAAAAAAAACAAAAAAAAAAAAACUUAACUACAAACAUUA Psmb2.146112219-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GGUUAAGAGCACCUGACUGCUCUUCCAGAGGUUAUGAGUUCAAUUCCCAGCAACCACAUGGUGGCUCACAACCAUCUGUAAAGAGAUCUGAUGCCCUCUUCUGGUGUAUCUGAAGACAGCUACAGUGUACUUAUAUAUAUAAUAAAUAAA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Appbp2.73471088-1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AGAGUUAAAUGACUGUGAGAGAGUAUUGCCAAUG------UUAACAGUGUUUACUGUAUAGCCCAUAGCAAAGGAAACUUUCUGGAUCUGAUUAAAAAAAAACAAAACAAAACAAAACAAAAAAAACCUGUAAUAUUUUGGAG~~~~~~ Appbp2.73471088-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GGUAAAUUUAACAACUUACAAACUUAUUGCUGAAAAAACCCACUAGUGGGUCAGACACACUCACUGGUUUAUUCCUGUCCUGUGGCUGUCUCAUGCCAGGACAGCAGAGUUAAAUGACUGUGAGAGAGUAUUGCCAAUG------UUAACAGUGUU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M4 899 8 0.83 Map1b.30419933-4,Map1b.30419933-5,Myo5a.80026797-1,Myo5a.80026797-2,Rpl6.36484470-2,Rpl6.36484470-3,Myo5a.80026480-1,Myo5a.80026480-2 Best CMs (by avg z-score): 1. (Z = 2.44) CRISPR-DR25 - CRISPR_RNA_direct_repeat_element 2. (Z = 1.88) KCNQ1DN - KCNQ1_downstream_neighbour 3. (Z = 1.78) P16 - Pseudomonas_sRNA_P16 4. (Z = 1.59) CRISPR-DR17 - CRISPR_RNA_direct_repeat_element 5. (Z = 1.51) CRISPR-DR60 - CRISPR_RNA_direct_repeat_element 6. (Z = 1.37) CRISPR-DR44 - CRISPR_RNA_direct_repeat_element 7. (Z = 1.34) PRINS - PRINS_RNA 8. (Z = 1.33) LhrC - Listeria_Hfq_binding_LhrC 9. (Z = 1.29) RsaE - RNA_Staph._aureus_E 10. (Z = 1.27) CRISPR-DR43 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM4.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM4_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ......................................................................................................................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 34.26, SCI: -0.00, ZSCORE: 0.34 Full summary: Sequences: 8 Columns: 153 Reading direction: forward Mean pairwise identity: 34.26 Shannon entropy: 1.41411 G+C content: 0.23578 Mean single sequence MFE: -11.88 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 0.34 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.94 SVM RNA-class probability: 0.000001 Prediction: OTHER Multiple alignment from mlocarna: Map1b.30419933-4 ~~~~~~~~~ACAUGAGAAACGAUCCCUAACCCAAACAGUUCUCAACACUACUGCGUUAAAAAGCCCUCAGUGAAAUUUACAGGAAUGAAAUACAAAUUCCCAGGUGAU-UCAGAUUUUAGUCUCCACCUCUUUCCCUCAAUGACCCCCCCCA~ Map1b.30419933-5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~UUUAGUCUCCACCUCUUUCCCUCAAUGACCCCCCCCA~ Rpl6.36484470-2 GUGUAGACCACUCUGGCCUCAAACUCAGAGAUCUACCUUCCCCUGCUGCUGAAAUGACAGGCAUGUGCUACCAUGCCCAGACUG-AAUCUUAACUGAUGGGUGUUAAU-UCAUCCUUUUC---AAAUGUGUUUUCCUCAUAG~~~~~~~~~~~ Myo5a.80026797-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AUAUCUUACAAUGCCGUUUGUCUUUUUUCAUAAUACCCUCAG~~~~~ Myo5a.80026797-1 ~UUUACUUUAUAGUACAUUCACUAUUUUAUAUAGGUUUAUAAUCCAUAAAUAUUUUAAUAAAAAAGUUAACUUUUUUAAAUUUUUAAUAGGAAUUUUGGUAAGAAAAUAUCUUACAAUGCCGUUUGUCUUUUUUCAUAAUACCCUCAG~~~~~ Rpl6.36484470-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~AU-UCAUCCUUUUC---AAAUGUGUUUUCCUCAUAG~~~~~~~~~~~ Myo5a.80026480-1 ~~~~~~~~~~~~~~UGUGCCCUUUGCUUCCUCCUUCCCUCUCUCCCAGCCCACCCGGGUAAAACUGAAAGGGAGGUACAGUGGUCC----UUCCCAGAUCCUGACCAG-CCAGCCUGUUUGUGAAACGUCUUUCCCU---UUUCUCUCUCCAG Myo5a.80026480-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~AACGUCUUUCCCU---UUUCUCUCUCCAG // ClustID MergedIDs Count AvgDissim Members M7 1453 5 0.71 Nsf.93003905-1,Myo5a.79965252-0,Atp5c1.79755749-0,Arl6ip5.131941412-2,Vim.87850381-0 Best CMs (by avg z-score): 1. (Z = 2.84) DicF - DicF_RNA 2. (Z = 2.46) snoU90 - Small_nucleolar_RNA_U90 3. (Z = 2.15) mir-574 - microRNA_mir-574 4. (Z = 2.03) TLS-PK2 - Pseudoknot_of_tRNA-like_structure 5. (Z = 1.97) snoZ188 - Small_nucleolar_RNA_Z188 6. (Z = 1.83) mir-14 - microRNA_mir-14 7. (Z = 1.78) purD - purD_RNA_motif 8. (Z = 1.77) snoZ112 - Small_nucleolar_RNA_Z112 9. (Z = 1.59) snoR126 - small_nucleolar_RNA_snoR126 10. (Z = 1.55) SNORD94 - Small_Nucleolar_RNA_SNORD94 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM7.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM7_global.out/ --free-endgaps --indel=-100 --threads=4 ................................((((((((...(((..............)))))..))))))........................................(((.(((((((((((((((.(((((........))))..).)))))))))))))))))).................................................. MFE = -35.95 (Covariance contribution: -20.67) RNAz stats: MPI: 38.49, SCI: 0.29, ZSCORE: -0.44 Full summary: Sequences: 5 Columns: 222 Reading direction: forward Mean pairwise identity: 38.49 Shannon entropy: 1.08770 G+C content: 0.32891 Mean single sequence MFE: -40.48 Consensus MFE: -11.91 Energy contribution: -8.27 Covariance contribution: -3.64 Combinations/Pair: 2.72 Mean z-score: -0.44 Structure conservation index: 0.29 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -0.73 SVM RNA-class probability: 0.194241 Prediction: OTHER Multiple alignment from mlocarna: Nsf.93003905-1 ~~~~~~~~~~~~~~~AGCACAUGCAAGGCCUGGUGCUCCA---UC-------------UCUAGUG--GAGUGUGUGU---------GUGUGUGUGUGUG---------UGUGUGUGUGUGUGUGUGUGUGUGAGUGUGUGUGUGUCCCCA--UGUGCACACAUGUGUGUCCCC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Myo5a.79965252-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~GAUUGCUUCCAAU---UC-------------UGU--UU--UGUUAG-UAG---------UUGUGUGUGUGUG---------UGUGUGUGUGUGUGUGUGUGU----GUGUGUGUGUGUCCCCA--CACACACAAUAAAAUGUAAUUAGAAAAGUGGACAUUGAAAGUUUAUUUGGAAUUUGGAAAGGACUAUACU Vim.87850381-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GAAUACAGGAAACAAAAAGAG-------CUUGCAUAUGUGUUAACCCUUCUGAGCGCAAUUUUAAAUGAUGUUGCAAUGUGUAUGUGUUUGUGUCUGUGUGGGUGUACAG---GGCACU----UAUGCAGGCGCGCACGAGGCCAGAAGAGGGCGUCUGAUCCA~~~~~~~~~~~~~~~~~~~~~~~~~~~ Arl6ip5.131941412-2 GCAUCCCGGACUAUAACUGCUUCCCAGAUUCUUGGACUUG---UUGGAAAA-------UGCAAUU--AGUCUUGUGUCUGGUGUGUGUGUGUGUGUGUG---------UGUGUGUGUGUGUUUUUCAUGUGU-GCCUGUGUGUUAUCGUG--UUACAAGUGUAAGUGGCUACCA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Atp5c1.79755749-0 ~~~~~~~~~~~~~~~~GUAAAUGAGACAUGUGUUCCAUGU---UCAGAAGAGUGGGAACCUGAGCGAAUGGAAGACUGAGAUA-GAGAAGUUUUUCGUGAUACAUU--------GGAGUGUUUGUGUAUACUGUGUGUUGGUUUUUACACUGUGUGUGUGCAUGGGCUCUCCUCUAUA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M6 653 5 0.62 Syt4.23808955-4,Syn2.151323233-5,Usp9x.21659964-3,Shank1.94837356-1,Arl6ip5.131941412-6 Best CMs (by avg z-score): 1. (Z = 2.75) CRISPR-DR13 - CRISPR_RNA_direct_repeat_element 2. (Z = 2.61) rox2 - Drosophila_rox2_ncRNA 3. (Z = 2.56) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.54) PK-CuYV_BPYV - 3'-terminal_pseudoknot_of_CuYV/BPYV 5. (Z = 2.54) PreQ1 - PreQ1_riboswitch 6. (Z = 2.51) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 7. (Z = 2.51) Lacto-rpoB - Lacto-rpoB_RNA 8. (Z = 2.50) mycoplasma_FSE - mycoplasma_ribosomal_frameshift_element 9. (Z = 2.39) CRISPR-DR6 - CRISPR_RNA_direct_repeat_element 10. (Z = 2.31) CRISPR-DR55 - CRISPR_RNA_direct_repeat_element Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM6.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM6_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ...................................................................................................................................................................................... MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 33.04, SCI: -0.00, ZSCORE: 1.37 Full summary: Sequences: 5 Columns: 182 Reading direction: forward Mean pairwise identity: 33.04 Shannon entropy: 1.27958 G+C content: 0.28032 Mean single sequence MFE: -18.39 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: 1.37 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -6.62 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Syt4.23808955-4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GUACCUGAAACAACCACAAGAUGGCAGGCAAUGGUUUUAAUCAUUAUGG-------AGCGG------CACAAAAGCAGUU------UCUGA-GAUUUCUUAGCCUGUUAAAAUUAAAAAAAAAAAAAAGGGAAC~~~~~~~~~~~~~~~~ Arl6ip5.131941412-6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UUUUCCAUUGUUCC----UCACCCCAGGCUUUAUUUAGACGUUC-GGU----UAGGAUCUCUGCUCCACUUGUCCAAAGUAAAAAUAGAAAAAAAAAUAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Usp9x.21659964-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CCAGCAACCACAUGGUGGCUCACAACCA-UCUGUAAUGAGAUUCGAUGCCCUCUUCUGGUGUGUCUGAAGACAGCUACAGUGUACUCAUAUACAAUAAAUAAAUCUUUAAA-AAAAAAAAACAAAAAAAAAAAAACUUAACUACAAACAUUA Shank1.94837356-1 CUGUUCUCUGUCCCCAUCCCUUCCAUCUCUCUCCCCCUUGAAAACCCACCCUCUUUUUGUUGUUGUUACGUUUG-UUUCUGUCUCCCUGUCUUCCACUCUGCUAUAACUGACCAUAACCAAAA-CAAAAAACAAACAAAAAAAAAAAAAACC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Syn2.151323233-5 AACUCAAAACUCCAGCUCAACACUAGCUGCAGGCAUUGAUGCUUCUGUGCUGUUUCCA-UUCU------GUGGUCAUGUCUUCUCC----AUGUGUACC----UCUAAGUUUUCCAUGAUGUCUCAAAGUAAAAGCUUUAAGAAAAGAAAAGAAAAAAAAAAGAA~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M1 1268 5 0.89 Slc25a4.49356080-4,Slc7a8.32858151-0,Slc25a4.49356080-3,Nsf.93029810-2,Nsf.93029810-1 Best CMs (by avg z-score): 1. (Z = 1.98) mir-1937 - microRNA_mir-1937 2. (Z = 1.76) PRINS - PRINS_RNA 3. (Z = 1.74) CRISPR-DR4 - CRISPR_RNA_direct_repeat_element 4. (Z = 1.62) PK1-TEV_CVMV - 5'-leader_pseudoknot_of_TEV/CVMV 5. (Z = 1.61) ZEB2_AS1_3 - ZEB2_antisense_RNA_1_conserved_region_3 6. (Z = 1.59) Histone3 - Histone_3'_UTR_stem-loop 7. (Z = 1.46) bxd_6 - Bithoraxoid_conserved_region_6 8. (Z = 1.37) NrrF - NrrF_RNA 9. (Z = 1.31) H19_3 - H19_conserved_region_3 10. (Z = 1.26) sbrA - Listeria_sRNA_sbrA Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM1.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM1_global.out/ --free-endgaps --indel=-100 --threads=4 --LP ....................................................................................................................(((......)))............................................................................................................................... MFE = -2.86 (Covariance contribution: -3.02) RNAz stats: MPI: 44.23, SCI: 0.02, ZSCORE: -0.05 Full summary: Sequences: 5 Columns: 255 Reading direction: forward Mean pairwise identity: 44.23 Shannon entropy: 1.02548 G+C content: 0.21319 Mean single sequence MFE: -21.00 Consensus MFE: -0.44 Energy contribution: 0.08 Covariance contribution: -0.52 Combinations/Pair: 2.00 Mean z-score: -0.05 Structure conservation index: 0.02 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -5.05 SVM RNA-class probability: 0.000000 Prediction: OTHER Multiple alignment from mlocarna: Slc25a4.49356080-4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CACACACACACGCACACACAUGUACCACCCCCAUCCCACCCCCCCAUGCACAUGCACAUACCUCAAAUGUUGGGAUUUUGGAUGACCCAAAAGUCAGACCUUUUAUUUUUUCCUCCCUAGUCUUGGGGCCUCAUCUGAGACCAGGGCUAG Slc7a8.32858151-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ACACAUACUCACACAUACACACUCAAACAUACACACACACUCACACACACAUAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Slc25a4.49356080-3 AUAGUGACUGGAAGUGUAAGUGAAAAGGAUGUUGGCCUGACCCAUCCUGCUUUGUUAGUUUCAGCUUUAUAGCUAAAAGCAUGAAACUGCCAUUCUUAAAGUUAACACACACACACGCACACACAUGUACCACCCCCAUCCCACCCCCCC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nsf.93029810-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GGCACCAGGCACACACAUGCAC--AUACACUUACAUACAUGCAAGCAAAGCGUUCAUACACAUAAAAUAAAAGUAGUAAGUC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nsf.93029810-1 ~~~UGUUCUUCCAGAGGACCUGGGUUCAAUUCCUGGUAUCCACAUAGCAGCUCAUAGUUGUCAUAACUCCAGUUUCAAGGACUCUGAUGUCCUCUUCUGCCCUCCUUAGGCACCAGGCACACACAUGCAC--AUACACUUACAUACAUGCAAGCA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M3 697 13 0.86 Stmn2.95287015-8,Opa1.73055102-1,Mapk1.85991310-1,Stxbp1.11798125-2,Grin1.3470909-0,Cdh2.8055601-3,Boll.54127808-7,Appbp2.73474168-6,App.24635748-0,Opa1.73055102-2,Boll.54127808-1,Canx.35855359-6,Atrn.118673182-9 Best CMs (by avg z-score): 1. (Z = 4.87) tRNA - tRNA 2. (Z = 2.54) mir-934 - microRNA_mir-934 3. (Z = 2.36) mir-304 - microRNA_mir-304 4. (Z = 2.19) mir-423 - microRNA_mir-423 5. (Z = 2.13) mir-625 - microRNA_mir-625 6. (Z = 2.10) TLS-PK6 - Pseudoknot_of_tRNA-like_structure 7. (Z = 1.96) mir-744 - microRNA_mir-744 8. (Z = 1.85) mir-548 - microRNA_mir-548 9. (Z = 1.73) mir-616 - microRNA_mir-616 10. (Z = 1.69) mir-489 - microRNA_mir-489 Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM3.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM3_global.out/ --free-endgaps --indel=-100 --threads=4 .........................................................................................((((((((((.(((((((.(((...((((((...................))))))...)))))))))).))))))))))........................................................................................................................... MFE = -30.57 (Covariance contribution: -13.84) RNAz stats: MPI: 53.38, SCI: 0.12, ZSCORE: -1.85 Full summary: Sequences: 13 Columns: 292 Reading direction: forward Mean pairwise identity: 53.38 Shannon entropy: 1.06664 G+C content: 0.20932 Mean single sequence MFE: -39.11 Consensus MFE: -4.61 Energy contribution: -4.03 Covariance contribution: -0.58 Combinations/Pair: 2.67 Mean z-score: -1.85 Structure conservation index: 0.12 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: 0.44 SVM RNA-class probability: 0.697634 Prediction: RNA Multiple alignment from mlocarna: Stmn2.95287015-8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CAAAAAUCUUUCCCUAGGGGUUGGGGAUUUAGCUCAGUGGUAGAGCCCUU------------GCCUAGGAAGCGCAAGGCCCUGGGUUCUGUCCCCAGCUCCGAAAA----AGAGA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Mapk1.85991310-1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CUUAAUAGUAUUCUUCCUCAAAAGUGAUAGCUAAGGGGUUGGGGAUUUAGCUCAGCGGUAGAGCACUUGCCUAGGAACUUGCCUAGGAAGUGCAAGGCCCUGGCUUCGGUCCCCAGCUCCGAAGA----AAAAGAAAAGAAAAAAAAA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Stxbp1.11798125-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AAGAUGGUGGGGCUGGGGAUUUAGCUCAGUGGUAGAGCGCUU------------ACCUAGGAAGCGCAAGGCCCUGGGUUCGGUCCCCAGCUCCGAAAA----AAAAGAACC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Grin1.3470909-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GAUUUAGCUCAGUAGUAGAGCGUUU------------ACCUAGGAAGCGCAAGGCCCUGGGUUCGGUCCCCAGCUCCGAAAA----AAAGAACCAAAAAAAAAAAAAAUAAUAAGAUCUUCACCAAGGACAGCCCUACACCAUCCUGCCUUCCUCCUUCUCUCCUG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Cdh2.8055601-3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AAGAGCACAGUGAAGGGGCUGGGGUAGUAGCUCAGUGGUAGAGCGCUU------------GCCUAGGAAGCGCAAGGCCCUGG~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Boll.54127808-7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CCAUAUGAAAUGUGAAAGG-----CUUAU-------AAUGAAAUUCAGUAAUAAAAUUCAUCUUCAGCAUGUGUAAGGCCCUGGAUUUUAUUUCUAGCAGUGUGAAAAGAAGGAAAAAAAAGGGGAAUAGGGAAAGAGAAAAGAAAGAAGAAAAGGCAGGGG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Opa1.73055102-1 GCAUAUCUAUCUUAAAAUGUUAUUUAUUUACUUGUAUUAUGAUUAACUAUUUGCAUUAUAUGCCUACUUUAAAAAUAAGAUUAAGUGGGGCUGGGGAUUUAGCUCAGUGGUAGAGCGCUU------------ACCUAGGAAGCGCAAGGCCCUGGGUUCGGU~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Appbp2.73474168-6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UAUUUAAAAGUUACUGCUUCGGGGUUGGGGAUUUAGCUCAGUGGUAGAGCGCUU------------GCCUAGCAAGCGCAAGGCCCUGGGUUCGGUCCCCAGCU~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ App.24635748-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GAAUUAUGCAAAGGCCUGGGGGAGAUGGCUUAUAGGUAGAGUGCUU------------GCCUUGCAAGCA-------UGAGGCCAGAAUCCCCAGAACGCAUU----GUCAAAAAAGC------UAAGUGAGGAGCAUAAUUGUAACCCCA-GUAUUGGGGAGGCAGAGACAG--GCAACUG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Opa1.73055102-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AGUGGUAGAGCGCUU------------ACCUAGGAAGCGCAAGGCCCUGGGUUCGGUCCCCAGCUCC~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Boll.54127808-1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AUUCUCAUCUGUUCAAAA-------U-UUA------------UUCUAAAAC-UU-------UUUUAAUAGGCUAGGAUAGU-----G----CU-----CAAUGGU-AGGAUGCUUUCAUCUAUAGUGCCCUGGGUUCCAUUUCCA--GCACC----ACACAAAC---AAAAAUCUUUACCAGUAAUUCACAAAGCCAUAUAC Canx.35855359-6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UAUACUUUGGGGUUGGGGAUU-------UAAGG------------CCCUGGGUC-CA-------GUCCCCAGCUCCGAAAAAAUGAAAAG----GAAAAAAAAAUUAUUUAUACUUUGUCAGAUUCA--AA--GGUUUCUUUCUAGCC--UUACCCUCAUCAUUCACUGUUGGAGUAUAUGUAUCUG~~~~~~~~~~~~~~~~~~ Atrn.118673182-9 ~~~~~~~~~~~~~~~~~~~~~~AUCUCCUAGUCCUGUCCCAAACAGAUCCACCAAGUGGGAAACAGACAUUAAAAUAUAUGAACCU-GGGUUGGGGAUUUGGCUCAGUGGUAGAGCGCUU------------GCCUAGCAAGCACAAGGCCCUGGGUUCGGUCCCCAACUCUGAAAA----AAA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ // ClustID MergedIDs Count AvgDissim Members M2 205 12 0.82 Opcml.28141848-2,Mapk1.85991310-2,Mapk1.85991310-1,Opcml.28141848-1,Grin1.3470909-0,Laptm4a.32414563-2,Itpr1.143854884-2,App.24539484-5,Boll.54127808-9,Shank1.94837356-1,Atp5j.24319157-7,Canx.35855359-6 Best CMs (by avg z-score): 1. (Z = 2.77) PreQ1 - PreQ1_riboswitch 2. (Z = 2.69) CRISPR-DR62 - CRISPR_RNA_direct_repeat_element 3. (Z = 2.60) CRISPR-DR7 - CRISPR_RNA_direct_repeat_element 4. (Z = 2.52) rox2 - Drosophila_rox2_ncRNA 5. (Z = 2.23) mycoplasma_FSE - mycoplasma_ribosomal_frameshift_element 6. (Z = 2.20) Afu_298 - A._fimigatus_snoRNA_Afu_298 7. (Z = 2.10) Lnt - Lnt_RNA 8. (Z = 2.07) PK-BYV - 3'-terminal_pseudoknot_in_BYV 9. (Z = 2.04) Lacto-rpoB - Lacto-rpoB_RNA 10. (Z = 2.02) SAM-II_long_loops - SAM-II_long_loops Structure and mfe from mlocarna: Command: mlocarna /home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM2.fa --tgtdir=/home/sarahmid/Project1_RNAstruct/results/dloc-rC_150/bgDinucWT/dloc-rC_150_structs/clustM2_global.out/ --free-endgaps --indel=-100 --threads=4 --LP .................................................................................................................................................................................................................................................................................................................................................................................................. MFE = 0.00 (Covariance contribution: 0.00) RNAz stats: MPI: 48.88, SCI: -0.00, ZSCORE: -0.74 Full summary: Sequences: 12 Columns: 386 Reading direction: forward Mean pairwise identity: 48.88 Shannon entropy: 1.11763 G+C content: 0.12136 Mean single sequence MFE: -23.52 Consensus MFE: 0.00 Energy contribution: 0.00 Covariance contribution: 0.00 Combinations/Pair: 0.00 Mean z-score: -0.74 Structure conservation index: -0.00 Background model: dinucleotide Decision model: sequence based alignment quality SVM decision value: -3.18 SVM RNA-class probability: 0.000014 Prediction: OTHER Multiple alignment from mlocarna: Opcml.28141848-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~UCUCAGUGAUG--ACCAAAAAGAAAGAAACAAAACAGAACAAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Mapk1.85991310-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~UCGGUCCCCAGCUCCGAAGAAAAAGAAAAGAAAAAAAAA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Mapk1.85991310-1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CUUAAUAGUAUUCUUCCUCAAAAGUGAUAGCUAAGGGGUUGGGGAUUUAGCUCAGCGGUAGAGCACUUGCCUAGGAACUUGCCUAGGAAGUGCA---AGGCCCUGGCUUCGGUCCCCAGCUCCGAAGAAAAAGAAAAGAAAAAAAAA~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Itpr1.143854884-2 ~~~~~~AUCUGAUUCAGCUUUUGGC----UUCUUGC-CUUAAAAAAAAAAAAAA----AAAAACAGGGCCACAAAGUUAUAUUCUAAGAUUUUAUUCAUUUUU-----------------AUUGCUGACACUUAGA---UUCUUGGCUUGUUUUGGAAUAUUCUAAAACAUAUUUUGAGGUAGGG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Grin1.3470909-0 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GAUUUAGCUCAGUAGUAGAGCGU------------UUACCUAGGAAGCGCA---AGGCCCUGGGUUCGGUCCCCAGCUCCGAA-AAAAAGAACCAAAAAAAAAAAAAAUAAUAAGAU-CUUCACCAAGGACAGCCCUACACCAUCCUGCCUUCCUCCUUCUCUCCUG~~~~~~~~~~~~~~~ Laptm4a.32414563-2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GGAAGGUGGAAGCAAGAGAAUCAGAAGUUCAUGGUAAUUCUCCACUAAAUAGAGUGCUGAGCAGGUAUGUACAAGGAUCUGACUUUACCUGUGGCACCAAAAAAAAAAAAACAAAA-ACAAAAACAAAAAACAAAAAACCCUUAUGUGUAG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Opcml.28141848-1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AUUUUUCUCUAUCCUGAAAGAGAAGACUCCUCACUAUAAAGCAUUCUGAAAUAUGGUAGACCUUGGCCAUCCAAAUGUAUGUGUACUUUGGAGAGUAUCUGA-----------UGAUCUCAGUGAUG--ACCAAAAAGAAAGAAACAAAACAGAACAAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ App.24539484-5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UUCAGAUGUUCAGAAAGCACUUUAAAAAAAAAACGCAGGAAAUCACAAAAAAAAAAAAAAAAAAAC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Boll.54127808-9 GUAUUGAAAGUGGUGACCUACACUUGCAAUCCCUGCACUUGAGAGGGAUCAGAAGUUCAAAAUC-UUUCUUGAUUAUAAAGAUAAUGGAGGCCAGUCUGAGAA-----------------AUUUGAGGUCCUAUCUAAAAAAAAAGAAAGAAAGAAAAAUAGUUGUUA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Shank1.94837356-1 ~~~CUGUUCUCUGUCCCCAUCCCUUCCAUCUCUCUCCCCC--------UUGAAAACCCACCCUCUUUUUGUUGUUGUUACGUUUGUUUCUGUCUCCCUGUCUUCCACUCUGCUAUAACUGACCAUAACCAAAACAAAAAACAAACAAAAAAAAAAAAAACC~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Atp5j.24319157-7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~AAAG-UUCAUGUUAGG----CUUUGAA--GGUAGUGCGUGGGU-----------------CAUU-CUGCCCUUUUGAGAGUCUCUUGAGCAGCUAUAA-AUCAUCUCCCCAGUGUUAAAAAAAAAAAAAAAA~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Canx.35855359-6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UAUACUUUGGGGUUGGGGAUUUA---AGGCCCUGGGUCCAGUCCCCAGCUCCGAAAAAAUGAAAAGGAAAAAAAAAUUAUUUAUACUUUGUCAGAUUCAAAGGUUUCUUUCUAGCCUU-ACCCUCAUCAUUCACUGUUGGAGUAUAUGUAUCUG //