# STOCKHOLM 1.0
#=GF ID rne-II
#=GF AC RF01756
#=GF DE rne-II RNA
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 50.0
#=GF NC 35.8
#=GF TC 52.7
#=GF SE Published; PMID:20230605;
#=GF SS Published; PMID:20230605;
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 20.58 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory_region;
#=GF RN [1]
#=GF RM 20230605
#=GF RT Comparative genomics reveals 104 candidate structured RNAs from bacteria,
#=GF RT archaea and their metagenomes.
#=GF RA Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR
#=GF RL Genome Biol. 2010;11:R31.
#=GF WK Rne-II_RNA_motif
#=GF SQ 16

CP000712.1/4270107-4270479 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCAGCCCACUGA-CGGUUGG-UGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCCUCCG---GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACAAGGCCCGCUUGGUUGAUUCGGAUAC
AE004091.2/3332603-3332870 ACAUGUGUAGGGUGGAGAUGUACGGCUGUUGGACUGCGU-------------------------------------------------------AGCUUCUAGCUUGAUCCA-GACG--CAUU-UUU--CGUCCGCCUCCGA-CAGC-CGAUUCCUCCUCCUGACUCAAGUGCUUCUGAA--------------------
CT573326.1/1679634-1679264 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUGGCACUGCGUCC-CCCACCGCCCCAGUGAUCGGGCGACGGAC-GGACAAGGUCCU-------------GAACA-GACGCCCUUGC---GGCGUCCACGGACGAUCGGU-UGAUUCCUCCUCCUGACUGAGUGCACCAGGCCCGUUCGAUUGAUUCGGAUGA
CP000926.1/1667321-1666950 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCAGCCCACUCA-CGGCUGG-CGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCUCCG----GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACAAGGCCCGCUUGGUUGAUUCGGAUAC
CP000438.1/2236725-2236458 ACAUGUGUAGGGUGGAGAUGUACGGCUGUUGGACUGCGU-------------------------------------------------------AGCUUCUAGCUUGAUCCA-GACG--CAUU-UUU--CGUCCGCCUCCGA-CAGC-CGAUUCCUCCUCCUGACUCAAGUGCUUCUGAA--------------------
CP000076.1/1992152-1991866 AUACGUGUAGGGUGGAGAUGCACAACCGUCGGACUGUGU-------------------------------------------------------AGCAUUAGGCUUUAUCAA-GACG--CUUCAUCU--CGUCCACAGUCGC-CGGU-UGAUUCCUCCUCCUGACAGACUUUUGCUUAAGCGGUGCCUUAGUC-------
AE015451.1/2150898-2150526 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCAGCCCACUGA-CGGCUGG-UGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCCUCCG---GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACAAGGCCCGCUUGGUUGAUUCGGAUAC
CP000058.1/1897287-1896999 AUACGUGUAGGGUGGAGACGCACAACCAUCGGACUGUGU-------------------------------------------------------AGCACAAGGCUUGUUCUA-GACG--CUUCAUCU--CGUCCGCUACCGA-UGGU-CGAUUCCUCCUCCUGACAAAGCUUUUGCUGAAAAGGGUGUCUUAUGCC----
CP000949.1/1675457-1675072 AUACGUGCAGGGUGGAGAUGCACAGCCCUCGGACCGUGUAGCACCGCGUCCGGCCACCGGCCCAGUGAAUGGCCGG-CGAGCGGAUAAGGUCCU-------------GAACA-GAUGCCCCAUG---GGCGUCCACGGCUGA-CGGU-UGAUUCCUCCUCCUGACUGAGUGCACGAGGCCUGCUGGGUUGAUUCGGAUAU
CP001157.1/1465433-1465164 AUACGUGCAGGGUGGAGAUGCACAACCAUCGGAUUGCGU-------------------------------------------------------AGCUGCAAGCUUUCAUCCAGACGC-ACAAG----GCGUCCGCUGCCGA-UGCU-UGAUUCCUCCUCCUGAUUGAUUGCUUUCUGCC--------------------
CP000744.1/2242576-2242309 ACAUGUGUAGGGUGGAGAUGUACGGCUGUUGGACUGCGU-------------------------------------------------------AGCUUCUAGCUUGAUCCA-GACG--CAUU-UUU--CGUCCGCCUCCGA-CAGU-CGAUUCCUCCUCCUGACUCAAGUGCUUCUGA---------------------
CP000680.1/1785155-1784883 AUACGUGUAGGGUGGAGAUGUACAACUGUCGGACUGCGU-------------------------------------------------------AGCAUAUCGCUUGAUCAAAGACG--CCUCAUCU--CGUCCGCUACCGC-CAGU-UGAUUCCUCCUCCUGACUGAGUGCUUUCUGUC--------------------
AE016853.1/4346971-4347259 AUACGUGUAGGGUGGAGACGCACAACCAUCGGACUGUGU-------------------------------------------------------AGCACAAGGCUUGUUUUA-GACG--CUUCAUCU--CGUCCGCUACCGA-UGGU-CGAUUCCUCCUCCUGACAAAGCUUUUGCUGAAAAGGGUGUCUUAUGCC----
CP000304.1/2848416-2848682 AUGCGUGUUGGGUGGAGAUGCACAGCAU-CGGAUUGCGU-------------------------------------------------------AGCAAAG-GCUU-UCACA-GACG--CUCCAUUC--CGUCCGCUACCG--AUGCCUGAUUCCUCCUCCCGAACCAUUGCUUCUGUU---------------------
CP000075.1/1845898-1845610 AUACGUGUAGGGUGGAGACGCACAACCAUCGGACUGUGU-------------------------------------------------------AGCACAAGGCUUGUUCUA-GACG--CUUCAUCU--CGUCCGCUACCGA-UGGU-CGAUUCCUCCUCCUGACAAAGCUUUUGCUGAAAGGGGUGUCUUAUGCC----
CP000094.2/4701518-4701785 AUACGUGUAGGGUGGAGAUGCACAACCGCUGGACUGUGU-------------------------------------------------------AGCAACAGGCUUUAUCAA-GACG--CUUCAUCU--CGUCCACAGCCAC-CGGU-UGAUUCCUCCUCCUGACUGAGUGCUUAAGUA---------------------
#=GC SS_cons               :::::::::::::((((-----((((((((((---(((,.......................................................<<<_____>>>,,,,,,,.<<<<..________..>>>>)))--)))).)))).))----))))<<<<<______________________________.......
#=GC RF                    AUAcGUGuAGGGUGGAGAUGcACggCcgucGGACuGcGU.......................................................aGCauaaaGCuUgauacA.GAcG..cuucaUuU..CgUCCgCuaCCga.cgGc.cGAUUCCUCCUCCuGAcugAgugcuuuaugaaaguuuugUuuauu.......

CP000712.1/4270107-4270479 CUAUUCGAAGCCACCGGGGCCUUGUUGGC------------ACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGACGUCGUGUGUGCCGAACGCCGUU
AE004091.2/3332603-3332870 -----------------------------------------AC-ACAGGAAGCAGGAGACGUA-GUCGCGGAC-CG---GCA---CCCAG--------UGC-----CGAGCGCCGCUGGACACGGGAAUGGCCCG-----CCAUUCCUGAAUACGCGCCCGAGCACCGACCGUGAGA-GUCGUGUGUGCCGAUCGCCGUU
CT573326.1/1679634-1679264 CAUUCGAAAAGCUCGACAGGUCUUUUGGC------------ACCGC--AAAACAGGACGCGUC-GUCGCGACCACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCCAGACACGGGGGUGGCCCG-----CCACCCUU---UGCGCACCUUGGCACCGAUCAUGAAAAAUCGCGUGUGCCGAACGCCGUU
CP000926.1/1667321-1666950 CUAUUCGAAGCCACCGGGGCCUUGUUGGC------------ACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGACGUCGUGUGUGCCGAACGCCGUU
CP000438.1/2236725-2236458 -----------------------------------------AC-ACAGGAAGCAGGAGACGUA-GUCGCGGAC-CG---GCA---CCCAG--------UGC-----CGAGCGCCGCUGGACACGGGAAUGGCCCG-----CCAUUCCUGAAUACGCGCCCGAGCACCGACCGUGAGA-GUCGUGUGUGCCGAUCGCCGUU
CP000076.1/1992152-1991866 -----------------------------------------ACCACAGCAAGCAGGACGCGUAAGUCGCGACUUCGUUC------UUAGUUACCC--------GGACGAACCUCGCUAGACACUCGAGUGGUCAA-----CCACUCCU---GACGCACCU-GACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUU
AE015451.1/2150898-2150526 CUAUUCGAAGCCACCGGGGCCUUGUUGGC------------ACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGCAA------CCGGCUGGUGCCGAACGUCGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGACGUCGUGUGUGCCGAACGCCGUU
CP000058.1/1897287-1896999 -----------------------------------------ACCACAGCAAGCAGGAAACGUC-GUCGCGAC--CCUA-CGCCC-CCUCU------GGGCG----AGGA-CCUCGCUAGACACUGGAGUG-UCCAAC----CACUCCU---GACGUGCCCUGACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUU
CP000949.1/1675457-1675072 CGAUUCGGAUAUCUCUGCAGAUACCGCAGGGGCCUCUUGGCACCGCAGCAAACAGGACGCGUC-GUCGCGACAACGGCAGGCUGGGAAA------CCGGCUGGUGCCGAACGUUGCUCGACACGGGGGUGGCCCGG----CCACCCUU---UGCGCACCUUGGCACCGACCAUGAGAAGUCGUGUGUGCCGAACGCCGUU
CP001157.1/1465433-1465164 -----------------------------------------ACAACAGUAAGCAGGAGACGUA-GUCGCGACUCUGGC-------CACCA--------------GCCAAAUGUUGCUUGACACGGGAACGGACGACAA--CCUUUCCUG--AACGGCCCCUGUCACCGACCGCGAGA-GUCGUGUGUGCCGAACGCCGUU
CP000744.1/2242576-2242309 -----------------------------------------AACACAGGAAGCAGGAGACGUA-GUCGCGGAC-CGGCA------UCCGA-------------UGCCGAGCGCCGCUGGACACGGGAAUGGCCCG-----CCAUUCCUGAAUACGCGCCCGAACACCGACCGUGAGA-GUCGUGUGUGCCGAUCGCCGUU
CP000680.1/1785155-1784883 -----------------------------------------ACCACAGCAAGCAGGAGACGUCCGUCGCGACC-GC-A-GCC---UCUGAU-------GGCAG---GC--CGUCGCUCGACAGUGGAACG-AUUUACGAC-CGUUUCU---GACGCGCCU-GACACCGACCCUGAGA-GUCGUGUGUGCCUAACGUGGCU
AE016853.1/4346971-4347259 -----------------------------------------ACCACAGCAAGCAGGAAACGUC-GUCGCGAC--CCUC-CGCCC-CCUCU------GGGCG----AGGA-CCUCGCUAGACACUGGAGUGGCCAA-----CCACUCCU---GACGCGCCCUGACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUU
CP000304.1/2848416-2848682 -----------------------------------------CCGACAGCAAGCAGGAGACGUC-GUCGCGACGCCG---GCC---CAUUU--------GGC-----CGCACAUCGCUGGACACUGGAGUG-CCUUACAAC-CAUUCCU---GACUCACCU-GACACCGACCGCGAGA-GUCGUGUGUGCCGAACGCCGUU
CP000075.1/1845898-1845610 -----------------------------------------ACCACAGCAAGCAGGAAACGUC-GUCGCGAC--CCUC-CGCCC-CCUCU------GGGCG----AGGA-CCUCGCUAGACACUGGAGUG-UCCAAC----CACUCCU---GACGUGCCCUGACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUU
CP000094.2/4701518-4701785 -----------------------------------------GCCACAGCAAGCAGGACGCGUACGUCGCGAUAACGGCC------CAAUU-------------GGCCGGACAUCGCUGGACACGGGAAUGGCCAA-----CCACUCCC---GACGCACCU-GACACCGACCGUGAGAAGUCGUGUGUGCCGAACGCCGUU
#=GC SS_cons               .........................................___________>>>>>::((((.<<<<<<<---<<<<.<<<..._____........>>>...>>>>---->>>>-->>>,,,<<<<<<<_____....>>>>>>>,...)))):::::::<<<<<<<<________>>>>->>>>::::::::::<<<
#=GC RF                    .........................................ACcACAGcAAgCaGGAaaCGuc.GUCGCGacaacggc.ggc...ucuau........gcc...gccgAaCguCGCUaGACACggGgguGGcCcaa....CCaccCcU...gaCGcaCCuuGaCACCGACCgUGAGAaGUCGUGUGuGCCGAACGCCGuU

CP000712.1/4270107-4270479 UCCGGCAGCC-CGGAAACCGA
AE004091.2/3332603-3332870 UCCGGUAGCCCCGGAAACC-A
CT573326.1/1679634-1679264 UCCGGCAGCC-CGGAAACCGA
CP000926.1/1667321-1666950 UCCGGCAGCC-CGGAAACCGA
CP000438.1/2236725-2236458 UCCGGUAGCCCCGGAAACC-A
CP000076.1/1992152-1991866 UCCGGCAGCC-CGGAAACCGA
AE015451.1/2150898-2150526 UCCGGCAGCC-CGGAAACCGA
CP000058.1/1897287-1896999 UCCGGCAGCC-CGGAAACCGA
CP000949.1/1675457-1675072 UCCGGCAGCC-CGGAAACCGA
CP001157.1/1465433-1465164 UCCGGCAGCC-CGGAAACCGA
CP000744.1/2242576-2242309 UCCGGUAGCCCCGGAAACC-A
CP000680.1/1785155-1784883 UCCGCUAGCCCCGGAACCC-A
AE016853.1/4346971-4347259 UCCGGCAGCC-CGGAAACCGA
CP000304.1/2848416-2848682 UCCGGAUGCCACGGAAACCGA
CP000075.1/1845898-1845610 UCCGGCAGCC-CGGAAACCGA
CP000094.2/4701518-4701785 UCCGGCAGCC-CGGAAACCGA
#=GC SS_cons               <<<<______.>>>>>>>:::
#=GC RF                    UCCGGcAGCC.CGGAAaCCGA
//
