# STOCKHOLM 1.0
#=GF ID OTKONC
#=GF AC RF03053
#=GF DE OTKONC RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 141.4
#=GF NC 37.7
#=GF TC 145.8
#=GF SE Weinberg Z
#=GF SS Published; PMID:28977401;
#=GF TP Gene; sRNA;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 31.61 -Z 2958934 CM SEQDB
#=GF DR SO; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 28977401
#=GF RT Detection of 224 candidate structured RNAs by comparative analysis of
#=GF RT specific subsets of intergenic regions.
#=GF RA Weinberg Z, Lunse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins KR,
#=GF RA Sherlock ME, Breaker RR
#=GF RL Nucleic Acids Res. 2017;45:10811-10823.
#=GF CC Environmental. No recognized genes
#=GF WK OTKONC_RNA_motif
#=GF SQ 43

URS0000D65E42_12908/1-169 AUAUUAGACGAAAUGGGA---ACA-------UCCCAUAAUAAUUA-UAUAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGAUUCGUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-CUGUUAAG-AAGAGUUUGGAGCAUUUGUAAAAUGGGACAACAUUUUGUUAGUAUU
URS0000D67000_12908/1-161 AUAUUAGACGAAAUGGGA---GCA-------UCCCAUAAUAAUUA-UAUAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UCCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGACAACAUUUUGUUAGUAUU
URS0000D693EE_12908/1-161 AUAUUAGACGAAAUGGGA---GCA-------UCCCAUAAUAAUUA-UAUAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UUCGCAGAAAAUU-CCGUAAGG-AAGAGUUUGGAGCAUUUGUAAAAUGGGCCAACAUUUUGUUAGUAUU
URS0000D6BE22_12908/1-162 AUAGUAGACGAAAUGGGA---GCA-------UCCCAUAAUAAUUA-UAUAUUCUC-UUA--GAGAAUA-UAAUAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UUCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUGUAAAAUGGGCCAACAUUUUAUUAGUAUU
URS0000D664DC_12908/1-161 AUAUUAGACGAAAUUGGG---AACGGGC---CCCAAUAAUAGUUAUUAGAUU----UUU-----AAUAUAA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UUCGCAGAAAAUU-ACGCAAGU-AAGAGUUUGUAGCAUUUUUAAAAUGGGACAACAUUUUGUUAGUAUU
URS0000D6CC43_12908/1-165 AUAGUAGACGAAAUUGGU---UUGGCC----GCCAAUAAUAGUUAUUAGAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UUCGCAGAAAAUU-CCGUGAGG-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACAUUUUGUUAGUAUU
URS0000D6A838_12908/1-165 AUAUUAGACGAAAUUGGU---UUGGCC----GCCAAUAAUAGUUAUUAGAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UCCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACAUUUUGUUAGUAUU
URS0000D65FF7_12908/1-163 AUAGUAGACGAAAUUGG----UCGCCC-----CCAAUAAUAGUUAUUAUAUUCUC-UUA--GAGAAUA-UA-UAACGU-UAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UCUGCAGAAAAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACAUUUUAUUAGUAUU
URS0000D665C7_12908/1-163 AUAUUAGACGAAAUUGG----UCGCCC-----CCAAUAAUAGUUAUUAUAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUUGUCGUGUACGAUCCUUUUCGAGU--------UUCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACAUUUUAUUAGUAUU
URS0000D69465_12908/1-165 AUAUUAGACGAAAUGGGG---AACGGG----CCCAAUAAUAGUUAUUAGAUUCUC-UUA--GAAAAUA-UA-AAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UCCGCAGAAAAUU-CCGUAAGG-AAGAGUUUGGAGCAUUUAUAAAAUGGGACAACAUUUUGUUAGUAUU
URS0000D6637F_12908/1-165 AUAUUAGACGAAAUUGGG---AACGAGC---CCCAAUAAUAAUUA-UAUAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UCCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGUAGCAUUUGUAAAAUGGGACAACAUUUUAUUAGUAUU
URS0000D694C0_12908/1-163 AUAUUAGACGAAAUUGG----UUUGGCC----CCAAUAAUAAUUA-UAUAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UCCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGUAGCAUUUGUAAAAUGGGACAACAUUUUGUUAGUAUU
URS0000D6CA40_12908/1-166 AUAUUAGACGAAAUUGGG---AACGGG-C--CCCAAUAAUAGUUAUUAUAUUCUC-UUA--GAGAAUA-UA-AAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UUCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUGUAAAAUGGGCCAACAUUUUGUUAGUAUU
URS0000D6A834_12908/1-166 AUAACAGACGAAAUUGGG---AACGGGC---CCCAAUAAUAGUUAUUAGAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUUUUCGAGU--------UUCGCAGAAAAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUAUAAAAUGGGACAACAUUUUGUUAGUAUU
URS0000D673BB_12908/1-174 AUAUUAGACGAAAUUGGG---AACGGGC---CCCAAUAAUAGUUAUUAGAUUCUC-UUA--GAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUGUAAAAUGGGCCAACAUUUUGUUAGUAUU
URS0000D6BD97_12908/1-169 AUAGUAGACGAAAUUGGG---AACGGGC---CCCAAUAAUAGUUAUUAGAUU----UUU-----AAUAUAA-UAACGU-UAAUGGUUCGUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUAUAAAAUGGGACAACAUUUUGUUAGUAUU
URS0000D668B5_12908/1-168 AUAUUAGACGAAAUUGGG---AACGGGC---CCCAAUAAUAGUUAUUAGAUU----UUU-----AAUA-UA-AAACGU-UAAUGGUUCGUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUAUAAAAUGGGCCAACAUUUUGUUAGUAUU
URS0000D66221_12908/1-170 AUAUUAGACGAAAUUGGG---AACA------UCCCAUAAUAAUUA-UAUAUUCUCG-U--CGAGAAUA-UA-UAACGU-CAAUGGUUCGUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUGAGU-AAGAGUUUGGAGCAUUUGUAAAAUGGGCCAACAUUUUGUUAGUAUU
URS0000D6884C_12908/1-171 AUAUUAGAAUAAUAAUUAUA--UUAUA--UAUAAUUAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUGAGU-AAGGGUUUGGAGCAUUUAUAAAAUGGGCCAAUUUU-GUUUAUGCUU
URS0000D67B74_12908/1-171 AUAUUAGAAUAAUAAUUAUA--UUAUA--UAUAAUUAAGUAGUGCCGAGGGC----UAAG----GCAC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGGGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D662B0_12908/1-171 AUAUUAGAAUAAUAAUUAUA--UUAUA--UAUAAUUAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGGGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D65EE3_12908/1-171 AUAUUAGAAUAAUAAUUAUA--UUAUA--UAUAAUUAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUGAGU-AAGGGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D6BF6A_12908/1-171 AUAUUAGAAUAAUAAUUAUA--UUAUA--UAUAAUUAAGUAGUGCUGAGGGC----UAAG----GCCC-GA-AUACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUGAGU-AAGCGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D6643B_12908/1-171 AUAUUAGAAUAAUAAUUAU--AUUAUA--UAUAAUUAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGGUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUUAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D6CDA3_12908/1-171 AUAUUAGAAUAAUAAUUAUA--UUAUA--UAUAAUUAAGUAGUACCGAGGAC----UAAG----GCCC-GA-AUACGUUAAACGGUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUUAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D69CA7_12908/1-171 AUAUUAGAAUAAUAAUUAUAUUAU----AUAUAAUUAAGUAGUAUCGAGGGC----UAAG----GCCC-GA-AUACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D69C18_12908/1-169 AUAUUAGAAUAAUUAUAUA--UAUUA----UAUAUAAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGGGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D676D9_12908/1-169 AUAUUAGAAUAAUUAUAUA--UAUUA----UAUAUAAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUGAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D685D7_12908/1-171 AUAUUAGAAUAAUUAUAUA--UAUUA----UAUAUAAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGACGAACGAAUGUGAGGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D68FA8_12908/1-171 AUAUUAGAAUAAUUAUAUA--UAUUA----UAUAUAAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-ACACGUUAAACGUUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGACGAACGAAUGUGAGGAGUUUGGAGCAUUUGUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D6CD2E_12908/1-171 AUAUUAGAAUAAUAAUUAU--AUUAU----AUAAUUAAGUAGUACCGAGGGC----UAAG----GCCC-GA-AUACGUUAAACGGUUAUUCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGACGAGCGAAUGCGAGGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D65F0A_12908/1-164 AUAUUAGGACAAUUAU-----AUAU--------AUAAAGUAGUACCGAGGGC----UAAG----GCCC-GA-AUACGUUAAACGGUUGUCCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGACGAGCGAAUGCGAGGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D68932_12908/1-162 AUAUUAGGACAAUUAU-----AUAU--------AUAAAGUAGUGCCGAGGGC----UAAG----GCCC-GA-AUACGUUAAACGGUUGUCCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUGAGU-AAGAGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D69BB6_12908/1-162 AUAUUAGGACAAUUAU-----AUAU--------AUAAAGUAGUACCGAGGGC----UAAA----GCCC-GA-AUACGUUAAACGGUUGUCCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGCGUUUGGAGCAUUUUUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D66012_12908/1-162 AUAUUAGGACAAUUAU-----AUAU--------AUUAAGUAGUAUCGAGGGC----UAAG----GCCC-GA-AUACGUUAAACGGUUGUCCGUGUACGAUCCUCUGCGAGUUGUUUAUCUUCACAGCAGAUU-ACGUAAGU-AAGGGUUUGGAGCAUUUAUAAAAUGGGCCAACUUU-GUUUAUGCUU
URS0000D6BF60_12908/1-155 AUAUUAGAUUUAUAUUAU---AUUA------AUAAUAAGUAGAAUAAAGUCC----UAAG----GGAC-GA-CUUCGU--CACGUUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCUCAAGA-AAGA-UUAACAGCAUU-UUAAAAUGGGGUUACUUU-GUUUAUGAUU
URS0000D65EC8_12908/1-157 AUAUUAGAUUUAUAUUAU---AUUA------AUAAUAAAUAGAAUAAAGCUC----UAAG----GAGC-GA-CUUCGUAAAAUGUUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCUCAAGA-AAGA-UUAACAGCAUU-UUAAAAUGGGGUUACUUU-GUUUAUGAUU
URS0000D6B38A_12908/1-155 AUAUUAGAUUUAUUAUAU---AUUA------AUAUAAAGCAGGAUAAAGACG----UAAG----CGUC-GA-CUCCGU--AGCGCUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCUCAAGA-AAGA-UUAACAGCAUU-UUAAAAUGGGGUUACUUU-GUUUAUGAUU
URS0000D6BA79_12908/1-156 AUAUUAGAUUUAUUAUAU---AUUA------AUAUAAAGUAGAAUAAAGCCC----UAAG----GGGC-GA-CUUCGU-UAACGCUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCUCAAGA-AAGU-UUAACAGCAUU-CUAAAAUGGGGUUACUUU-GUUUAUGAUU
URS0000D668EA_12908/1-155 AUAUUAGAUUUAUUAUAU---AUUA------AUAUAAAGUAGAAUAAAGUCC----UAAG----GGAC-GA-CUUCGU--CACGCUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCGUAAGA-AAUA-UUAACAGCAUU-UUAAAAUGGGGUUACUUU-GUUUAUGAUU
URS0000D67E89_12908/1-155 AUAUUAGAUUUAUUAUAU---AUUA------AUAUAAAGCAGAAUAAAGUUC----UAAG----GAAC-GA-CUUCGU--AGCGCUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCUCAAGA-AAGA-UUAACAGCAUU-UUAAAAUGGGGUUACUUU-GUUUAUGAUU
URS0000D6D3D9_12908/1-155 AUAUUAGAUUUAUUAUAU---AUUA------AUAUAAAGCAGGAUAAAGUUC----UAAG----GAAC-GA-CUCCGU--AGCGCUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCGUAAGA-AAGA-UUAACAGCAUU-UUAAAAUGGGGUUACUUU-GUUUAUGAUU
URS0000D6CA8E_12908/1-155 AUAUUAGAUUUAUUAUA----UAUUAU-----UAUAAAGUAGAAUAAAGUCC----UAAA----GGAC-GA-CUUCGU--CACGCUAAAUCGUAUACGAUCCUUUUCGAGA-------CCUCGCAGAAAAUU-UCUCAAGA-AAGA-UUAACAGCAUU-UUAAAAUGGGGUUACUUU-GUUUAUGAUU
#=GC SS_cons              ::::::::((((<<<<<<..._____.....>>>>>>,,,,<<<<---<<<<....____....>>>>.--.>>>>,,.,,,,,,))))::::::::::::::<<<<____......._______>>>>:<<.<<____>>.>>::::<<<<_________________>>>>::::.::::::::::
#=GC RF                   AUAUUAGAcgaAuugggg...auuau.....ccccaaAgUAGugcuuAgggc....UaAG....gccc.gA.gcaCGU.aAAuGgUucgUCGUGUACGAUCCUcUgCGAGu.......CUUCaCAGcAgAuu.aCGuAAGu.aaGAGUUuGgAGCAUUUuUAAAAUGGGcCaACuUU.guUUAugaUU
//
