params (warning: commas chnged to semicolons),CM file,fastaFile,sequence #,EMBL accession,is in RFAMSEQ,sequence description (warning: commas chnged to semicolons),is reversed?,hit #,start nuc,end nuc,score (bits),hit sequence,hit Id(s) in Rfam with same seq,hit ranges within the same EMBL id,new hitness (0=in Rfam; 1=overlaps hit in Rfam;2=entirely new),amount of overlap with Rfam,this hit in Rfam format
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/org.dat.fasta.gz,18951,AF022186.2,1,sp|AF022186.2|AF022186 Cyanidium caldarium strain RK1 chloroplast; complete genome.,1,0,109751,109498,43.06,GGGGCUGAAAGGAUAUUCGACAUAUUAAUUUCGUGCGCUAUGAUGCAAGCCGAGAAUGCUUAUCUCGUAAAAAAGCAGACAAAGAAAUAAAUGCAAACAAUAUUAUUGAAAUUAGCAAUAUUAGAAAACCAGCUCUAGUAGUCUAGCCUGAUUCAGUUAUUUCUAAAUUAUUUAUGUUAUGUUAUUUAAGCUUGUAGUAACUAUCUAGUGUACAAUUUCUAUGGACGUGGGUUCAAUUCCCACCAGCUCCACAA,AF022186/109751-109498,,0,0,AF022186.2/109751-109498
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/org.dat.fasta.gz,21972,AF041468.1,1,sp|AF041468.1|AF041468 Guillardia theta complete plastid genome.,1,1,50514,50188,59.40,GGGGCUGAUUUGGAUUCGACAUAUAAAUUUGCGUGUUUCAUUAUGAAGCAAGUCAAGUUUAAUGAUCUUGUAAAAAACAUUAAAGUACAAAUAAAUGCAAGCAAUAUAGUUUCAUUUAGUUCAAAACGUUUAGUCUCUUUUGCAUAAGCAAAAUGUGUUAAUAACUUUCUUAGUAGAAAUUGGAGAAGUUUACUAAGAUUUAUAUUUACUCCAUAAUUAUUUUAAAGAUGGUAAAAAGGUGAUUCAUCAUUUGUAUGUUUCUAAACUUUGUGAAAGAAUAGUGGGCUCCAUUUAUAAUGAACGUGGGUUCAAAUCCCACCAGCUCCA,AF041468/50514-50188,,0,0,AF041468.1/50514-50188
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/org.dat.fasta.gz,22742,AF049491.1,1,sp|AF049491.1|AF049491 Thalassiosira weissflogii cytochrome c-550 (psbV) gene; partial cds; tRNA-Arg; tmRNA and tRNA-Met genes; complete sequence; and ribosomal protein L19 (rpL19) and 2 Fe-2 S ferredoxin (petF) genes; complete cds; chloroplast genes for chloroplast products.,0,2,488,832,66.91,GGGGCUGAUUUGGUUUCGACAUUUAAAACUUCUUUCUAUGUGUCAGGUCAAAGUUUGUAUUCUUUGUAAAAAAAUACUAAAAUACUAAUAAAUGCUAAUAAUAUAAUACCGUUUAUUUUUAAAGCAGUAAAAACAAAAAAAGAAGCAAUGGCUUUAAAUUUUGCUGUAUAGUUCAUUAACUUAGGUUAUUAAAUAUUUUUUCAUUAUAACUGGACUUUUCUCUAGUUUAUAGUUUAGAAUAAAUUUAAAUUUUGCAAAACUCGUUCGAAAAUUUUCGGGCUAAACCUGUAAACGCAAAUACUAAGAAAUUUUAGAUGGACAUGGGUUCAAUUCCCAUCAGUUCCA,AF049491/488-832,,0,0,AF049491.1/488-832
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/org.dat.fasta.gz,43523,AF166114.1,1,sp|AF166114.1|AF166114 Mesostigma viride chloroplast DNA; complete genome.,0,3,20729,21084,81.00,GGGGUUGAAAUGGUUUCGACGUUUUAGUAUAUAUCUUCUUACAAGCAAGUCGAGAAUGAACCAAUCUCGUAAACUUGAGUUCAAUUGCAAAUAAAUGCUAACAAUAUUUUACCUUUUAAUCGUAAGACAGCCGUAGCUGUUUAAAAGUUUUUUGAUAACUUCGAGCAUUUUUGAUUUGUUAAAUACAAUUGUUAUAAAACAAAUUAAAUAAUAGUUUUUGUUUCUUUACAAAUAAUGUAGAAAUAAUUUUUUUUAGCUUUUCAAGCUCCAGCUUUGUGGAUUAGCAAAGCUAAACUUGUGAAUACAAAGAAGAGAUCAAACUAAAGCGGACGCGGGUUCAAAACCCGCCAGCUCCA,AF166114/20729-21084,,0,0,AF166114.1/20729-21084
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/org.dat.fasta.gz,175040,U30821.1,1,sp|U30821.1|CC30821 Cyanophora paradoxa cyanelle; complete genome.,1,4,84810,84520,71.05,GGGGCUGUUUAGGUUUCGACGUUUUUUUCUAAUUAUGUUUGUUAAGCAAGUCGAGGAUUUGUUCUAUCUCGAAAAUCAAGAACUCUCAAAAUUUAAACGCAACUAAUAUUGUACGUUUUAACCGUAAAGCAGCUUUCGCUGUUUAAUAAUUACUUUUAAUUUAAAAACCUAAUUUUUUUAGGAAUUUAUUUAUUUAUUGUUUAUCCUGCUUAAUGAAUUAAAAAAAGCUAUACUUGUGAAUAAACGCAUAAUUUAAAAAAACGGACGUGGGUUCAAAUCCCACCAGCUCCA,U30821/84810-84520,,0,0,U30821.1/84810-84520
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/org.dat.fasta.gz,207907,Z67753.1,1,sp|Z67753.1|OSCHLPLXX Odontella sinensis complete chloroplast genome,0,5,95843,96210,83.00,GGGGCUGACUUGGUUUCGACAUUUAAAAAUUGUUACAGUAUGAUGCAGGUCGAAGUUUCUAAUCUUCGUAAAAAAAGAGAAAUUUAUAAUAAAUGCUAAUAAUUUAAUUUCUUCUGUGUUUAAAAGUUUAUCAACUAAGCAAAAUAGUUUAAAUUUAAGUUUUGCUGUUUAAGUUUUAUGCACAUUUAAUGAUCUAGUAAAUAACUUUGUUCGCUAUAAUUUAUAUUUAUAACUAGACUUUUGUCUUUUUUAUAGUUUAGAAUAACUUUAUCAUUUCAAACCUCGUUCCAUCUAGUUGAACUAAACCUGUGAACGAAUACUAUAAUAAAAUUUUUAGAUGGACGUGGGUUCGACUCCCAUCAGCUCCA,Z67753/95843-96210,,0,0,Z67753.1/95843-96210
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,355,AB003477.1,1,sp|AB003477.1|AB003477 Synechococcus sp. gene for hypothetical protein; partial cds.,0,6,1390,1780,91.95,GGGGCUGUAAUGGUUUCGACGUGUUGGUGAAUCCUUCACCGUGAUUCAGGCCGAGAGGGAGUCCACUCUCGUAAAUCCAGGCUCAACCAAAAGUAACUGCGAACAACAUCGUUCCUUUCGCUCGUAAGGCUGCUCCUGUAGCUGCUUAAACGCCACAAACUUUCUGGCUCGAGCGUCUAGUCGUAGACUCCGUUAAUACGCCUAGACUUAAACCCCCAACGGAUGCUCGAGUGGCGGCCUCAGGUCCGUCCUCUCGCUAAGCAAAAACCUGAGCAUCCCGCCAACGGGGAUAAUCGUUGGCUCCCGCACAGUGGGUCAACCGUGCUAAGCCUGUGAACGAGCGGAAAGUUACUAGUCAAUGCGGACAGCGGUUCGAUUCCGCUCAGCUCCA,AB003477/1390-1780,,0,0,AB003477.1/1390-1780
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,9272,AB063521.2,1,sp|AB063521.2|AB063521 Wigglesworthia brevipalpis DNA; complete genome; section 1/2.,0,7,122211,122572,110.79,GGGGCUGAUUAUGGAUUCGACGAAAUAAACAAAACUAAAGAUGCAUGUCGAGCAGAGGUGGACUCGUAAAACCUCAAAUUGAUAAUUGCAAAACAUAAGUACAACGAGCCUGCUCUAUUAGCAGCUUAAUUAGAAUAAAAUCUUAGGCUCCUUCUUAGAUAUAUUAUCUCUAGAUGUAUCAAUAGAAGUCAAAAUUAGAGAUCGCGAUAUGAACGGGCUUGUACGUUCCUACGCUAAAAUAAUACAAGAUAAUUUUUAGUUCACACUUCUUUCUGUAGAACUAAAAAUAUUUAAGAAAGAAUAAACAUGUAGUAUCAAUAGAAUUGAAGUUUCGGACGCGGGUUCAAAUCCCGCCAGCUCCA,AB063521/122211-122572,,0,0,AB063521.2/122211-122572
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,16410,AC074317.5,1,sp|AC074317.5|AC074317 Staphylococcus aureus clone sabac-103; complete sequence.,1,8,11254,10896,146.69,GGGGACGUUCAUGGAUUCGACAGGGGUCCCCCGAGCUCAUUAAGCGUGUCGGAGGGUUGUCUUCGUCAUCAACACACACAGUUUAUAAUAACUGGCAAAUCAAACAAUAAUUUCGCAGUAGCUGCCUAAUCGCACUCUGCAUCGCCUAACAGCAUUUCCUAUGUGCUGUUAACGCGAUUCAACCUUAAUAGGAUAUGCUAAACACUGCCGUUUGAAGUCUGUUUAGAAGAAACUUAAUCAAACUAGCAUCAUGUUGGUUGUUUAUCACUUUUCAUGAUGCGAAACCUAUCGAUAAACUACACACGUAGAAAGAUGUGUAUCAGGACCUUUGGACGCGGGUUCAAAUCCCGCCGUCUCCA,AC074317/11254-10896,,0,0,AC074317.5/11254-10896
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,16821,AE000590.1,1,sp|AE000590.1|AE000590 Helicobacter pylori 26695 section 68 of 134 of the complete genome.,1,9,7784,7399,98.32,GGGGCUGACUUGGAUUUCGACAGAUUUCUUGUCGCACAGAUAGCAUGCCAAGCGCUGCUUGUAAAACAGCAACAAAAAUAACUGUAAACAACACAGAUUACGCUCCAGCUUACGCUAAAGCUGCGUGAGUUAAUCUCCUUUUGGAGCUGGACUGAUUAGAAUUUCUAGCGUUUUAAUCGCUCCAUAACCUUAAGCUAGACGCUUUUAAAAGGUGGUUCGCCUUUUAAACUAAGAAACAAGAACUCUUGAAACUAUCUCAAGGUUUUAGAAAGUUGGACCAGAGCUAGUUUUAAGGCUAAAAAACCAACCAAUUUUCUAAGCAUUGUAGAAGUUUGUGUUUAGGGCAAGAUUUUUGGACUGGGGUUCGAUUCCCCACAGCUCCACCA,AE000590/7784-7399,,0,0,AE000590.1/7784-7399
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,16969,AE000749.1,1,sp|AE000749.1|AE000749 Aquifex aeolicus VF5 section 81 of 109 of the complete genome.,1,10,2436,2090,111.21,GGGGGCGGAAAGGAUUCGACGGGGACAGGCGGUCCCCGAGGAGCAGGCCGGGUGGCUCCCGUAACAGCCGCUAAAACAGCUCCCGAAGCUGAACUCGCUCUCGCUGCCUAAUUAAACGGCAGCGCGUCCCCGGUAGGUUUGCGGGUGGCCUACCGGAGGGCGUCAGAGACACCCGCUCGGGCUACUCGGUCGCACGGGGCUGAGUAGCUGACACCUAACCCGUGCUACCCUCGGGGAGCUUGCCCGUGGGCGACCCGAGGGGAAAUCCUGAACACGGGCUAAGCCUGUAGAGCCUCGGAUGUGGCCGCCGUCCUCGGACGCGGGUUCGAUUCCCGCCGCCUCCACCA,AE000749/2436-2090,,0,0,AE000749.1/2436-2090
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17332,AE001118.1,1,sp|AE001118.1|AE001118 Borrelia burgdorferi B31 (section 4 of 70) of the complete genome.,1,11,7347,6989,113.52,GGGGAUGUUUUGGAUUUGACUGAAAAUGUUAAUAUUGUAAGUUGCAGGCAGAGGGAAUCUCUUAAAACUUCUAAAAUAAAUGCAAAAAAUAAUAACUUUACAAGCUCAAAUCUUGUAAUGGCUGCUUAAGUUAGCAGAGGGUUUUGUUGAAUUUGGCUUUGAGGUUCACUUAUACUCUUUUCGACAUCAAAGCUUGCUUAAAAAUGUUUUCAAGUUGAUUUUUAGGGACUUUUAUACUUGAGAGCAAUUUGGUGGUUUGCUAGUAUUUCCAAACCAUAUUGCUUAAUAAAAUACUAGAUAAGCUUGUAGAAGCUUAUAGUAUUAUUUUUAGGACGCGGGUUCAAUUCCCGCCAUCUCCA,AE001118/7347-6989,,0,0,AE001118.1/7347-6989
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17488,AE001276.1,1,sp|AE001276.1|AE001276 Chlamydia trachomatis section 3 of 87 of the complete genome.,1,12,9890,9474,118.97,GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUUCGCUGAUCUCGAAGAUCUAAGAGUAGCUGCUUAAUUAGCAAAGUUGUUACCUAAAUACGGGUGACCCGGUGUUCGCGAGCUCCACCAGAGGUUUUCGAAACACCGUCAUGUAUCUGGUUAGAACUUAGGUCCUUUAAUUCUCGAGGAAAUGAGUUUGAAAUUUAAUGAGAGUCGUUAGUCUCUAUAGGGGUUUCUAGCUGAGGAGACAUAACGUAUAGUACCUAGGAACUAAGCAUGUAGAGGUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGACUCUCUCCACCUCCA,AE001276/9890-9474,,0,0,AE001276.1/9890-9474
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17638,AE001503.1,1,sp|AE001503.1|AE001503 Helicobacter pylori; strain J99 section 64 of 132 of the complete genome.,1,13,7009,6624,98.10,GGGGCUGACUUGGAUUUCGACAGAUUUCUUGUCGCACAGAUAGCAUGCCAAGCGCUGCUUGUAAAACAGCAACAAAAAUAACUGUAAACAACGCAGAUUACGCUCCAGCUUACGCUAAAGCUGCGUGAGUUAAUCUCCUUUUGGAGCUGGACUGAUUAGAAUUUCUAGCGUUUUAAUCGCUCCAUAACCUUAAGCUAGACGCUUUUAAAAGGUGGUUCGCCUUUUAAACUAAGAAACAAGAACUCUUGAAACUAUCUCAAGGUUUUAGAAAGUUGGACCAGAACUAGUUUUAAGGCUAAAAAGCUAAUCAAUUUUCUAAGCAUUGUAGAAGUUUGUGUUUAGGACAAGAUUUUUGGACUGGGGUUCGAUUCCCCACAGCUCCACCA,AE001503/7009-6624,,0,0,AE001503.1/7009-6624
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17729,AE001597.1,1,sp|AE001597.1|AE001597 Chlamydia pneumoniae section 13 of 103 of the complete genome.,1,14,3555,3133,98.79,GGGGGUGUAUAGGUUUCGACUUGAAAAUGAAGUGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCAACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUAGCUUGUUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAUUAGCAAAAGUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAUCUGCGAGCUCCACCAGAGGCUUGCAAAAUACCGUCAUUUAUCUGGUUGGAACUUACUUUCUCUAAUUCUCAAGGAAGUUCGUUCGAGAUUUUUGAGAGUCAUUGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGUCCAAUGUAAACAAUUCUAGAAGAUAAGCAUGUAGAGGUUAGCAGGGAGUUUGUCAAGGACGAGAGUUCGAGUCUCUCCACCUCCA,AE001597/3555-3133 AE002224/6757-7179 AP002545/138204-137782,,0,0,AE001597.1/3555-3133
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17858,AE001727.1,1,sp|AE001727.1|AE001727 Thermotoga maritima section 39 of 136 of the complete genome.,0,15,1,335,64.69,GGAUGGAGUCCCCUGGGAAGCGAGCCGAGGUCCCCACCUCCUCGUAAAAAAGGUGGGACAAAGAAUAAGUGCCAACGAACCUGUUGCUGUUGCCGCUUAAUAGAUAAGCGGCCGUCCUCUCCGAAGUUGGCUGGGCUUCGGAAGAGGGCGUGAGAGAUCCAGCCUACCGAUUCAGCUUCGCCUUCCGGCCUGAAUCGGGAAAACUCAGGAAGGCUGUGGGAGAGGACACCCUGCCCGUGGGAGGUCCCUCCCGAGAGCGAAAACACGGGCUGCGCUCGGAGAAGCCCAGGGGCCUCCAUCUUCGGACGGGGGUUCGAAUCCCCCCGCCUCCACCA,AE001727/1-335,,0,0,AE001727.1/1-335
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18035,AE001939.1,1,sp|AE001939.1|AE001939 Deinococcus radiodurans R1 section 76 of 229 of the complete chromosome 1.,0,16,5041,5389,135.42,GGGGGUGACCCGGUUUCGACAGGGGAACUGAAGGUGAUGUUGCGUGUCGAGGUGCCGUUGGCCUCGUAAACAAACGGCAAAGCCAUUUAACUGGCAACCAGAACUACGCUCUCGCUGCUUAAGUGAGAUGACGACCGUGCAGCCCGGCCUUUGGCGUCGCGGAAGUCACUAAAAAAGAAGGCUAGCCCAGGCGAUUCUCCAUAGCCGACGGCGAAACUUUAUGGAGCUACGGCCUGCGAGAACCUGCCCACUGGUGAGCGCCGGCCCGACAAUCAAACAGUGGGAUACACACGUAGACGCACGCUGGACGGACCUUUGGACGGCGGUUCGACUCCGCCCACCUCCACCA,AE001939/5041-5389,,0,0,AE001939.1/5041-5389
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18243,AE002154.1,1,sp|AE002154.1|AE002154 Ureaplasma urealyticum section 55 of 59 of the complete genome.,1,17,2543,2131,115.98,GGGGAUGUCACGGUUUCGACGUGACACAUUAAUUUUUAAUUGCAGUGGGGUUAGCCCCUUAUCGCUUUCGAGGCAUUUUAAAUGCAGAAAAUAAAAAAUCUUCUGAAGUAGAAUUAAACCCAGCGUUUAUGGCUUCAGCUACUAAUGCAAACUACGCUUUUGCGUACUAAUUAGUUAUUAGUAGAAACGUUCAUUAACAUAAUUACUAUUGGUUGGUUUUUGGGCUUAUUUUACAAUAGUUUUAAAUUUAAAAUUCUUAUUUGUUGUUUAAAUUUAAAUAGAUUUAACAAAUAGUUAGUUAAUUUUAAAUUUGUUUUAUUAGUUAUUAACUACACUAUUUUUAAUAAAACUAAACUGUAGAUAUUAUUAAUUAUGUGUUGCGGAAAGGGGUUCGACUCCCCUCAUCUCCACCA,AE002154/2543-2131,,0,0,AE002154.1/2543-2131
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18300,AE002224.2,1,sp|AE002224.2|AE002224 Chlamydophila pneumoniae AR39; section 52 of 94 of the complete genome.,0,18,6757,7179,98.79,GGGGGUGUAUAGGUUUCGACUUGAAAAUGAAGUGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCAACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUAGCUUGUUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAUUAGCAAAAGUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAUCUGCGAGCUCCACCAGAGGCUUGCAAAAUACCGUCAUUUAUCUGGUUGGAACUUACUUUCUCUAAUUCUCAAGGAAGUUCGUUCGAGAUUUUUGAGAGUCAUUGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGUCCAAUGUAAACAAUUCUAGAAGAUAAGCAUGUAGAGGUUAGCAGGGAGUUUGUCAAGGACGAGAGUUCGAGUCUCUCCACCUCCA,AE001597/3555-3133 AE002224/6757-7179 AP002545/138204-137782,,0,0,AE002224.2/6757-7179
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18370,AE002296.1,1,sp|AE002296.1|AE002296 Chlamydia muridarum section 28 of 85 of the complete genome.,1,19,3595,3178,125.34,GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUUCGCUGAUCUUAAUGAUCUAAGAGUUGCUGCUUAAUUAGCAAAGUUGUUACCUAAGUACUGGUAACCCGGUGUUCGCGAGCUCCACCAGAGGUUUUCGAAACGCCGUCAUUUAUCUGGUUAGAAUUAGGGCCUUUUAACUCUCAAGGGAACUAAUUUGAAUUUUAAUGAGAGUCGUUGGUCUCUAUAGAGGUUUCUAGCUGAGGAGAUAUAACGUAAAAUAUUCUAGAAACUAAGCAUGUAGAGGUUAGCGGGGAGUUUACUAAGGACGAGAGUUCGAAUCUCUCCACCUCCA,AE002296/3595-3178,,0,0,AE002296.1/3595-3178
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18521,AE002452.1,1,sp|AE002452.1|AE002452 Neisseria meningitidis serogroup B strain MC58 section 94 of 206 of the complete genome.,1,20,5751,5389,155.68,GGGGGCGACCUUGGUUUCGACGAGGGUUGCGAAGCAGAUGCGGGCAUACCGGGGUCUCAGAUUCCCGUAAAACACUGAAUUCAAAUAGUCGCAAACGACGAAACUUACGCUUUAGCCGCUUAAGGCUAGCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGCGAAAGCCACCGCAACGUCAUCUUACAUUGACUGGUUUCCUACCGGGUUACUUGGCAGGAAAUAAGACUUAAGGUAACUGGUUUCCAAAAGGCCUGUUGGUCGGCAUGAUGGAAAUAAGAUUUUCAAAUAGACACAACUAAGUAUGUAGAACGCUUUGUAGAGGACUUUCGGACGGGGGUUCGAUUCCCCCCGCCUCCACCA,AE002452/5751-5389,,0,0,AE002452.1/5751-5389
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18860,AE004078.1,1,sp|AE004078.1|AE004078 Xylella fastidiosa 9a5c; section 224 of 229 of the complete genome.,0,21,5137,5491,152.44,GGGGGUGCACUGGCUUCGACGGGGGUCACAAAAUCACUUGGUGCAUGCCGAGGGGGCCGCUUUCCUCGUAAAUCCAGCAGCAAACUUAUAGUUGCCAACGAAGACAACUUCGCUGUAGCCGCUUAAGGCUUAAGCCUCGAAACUGCUUGUGUCCGUGCUCGCAGCGUAGAGUCAUCAUCACGGAACCGCUGAGACGUGGCCGUCUGCCCAUCCUCGGUUAAAUCUAGCAGACUGGUUUCCGGGUGCGCUUUGCCUGUCGUGCUGCCCGGCGACGAGACCUAACGGCGAGGAUAAGCAUGUAGGGCCGGGGAUGGAGUACUUUCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA,AE004078/5137-5491,,0,0,AE004078.1/5137-5491
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18943,AE004170.1,1,sp|AE004170.1|AE004170 Vibrio cholerae chromosome I; section 78 of 251 of the complete chromosome.,1,22,3459,3093,210.38,GGGGCUGAUUCAGGAUUCGACGGGAAUUUUGCAGUCUGAGGUGCAUGCCGAGGUGCGGUAGGCCUCGUUAACAAACCGCAAAAAAAUAGUCGCAAACGACGAAAACUACGCACUAGCAGCUUAAUACCCUGCUCAGAGCCCUUCCUCCCUAGCUUCCGCUUGUAAGACGGGGAAAUCAGGAAGGUCAAACCAAAUCAAGCUGGCGUGGAUUCCCCCACCUGAGGGAUGAAGCGCGAGAUCUAAUUCAGGUUAGCCAUUCGUUAGCGUGUCGGUUCGCAGGCGGUGGUGAAAUUAAAGAUCGACUAAGCAUGUAGUACCAAAGAUGAAUGGUUUUCGGACGGGGGUUCAACUCCCCCCAGCUCCACCA,AE004170/3459-3093 U39068/12723-12357,,0,0,AE004170.1/3459-3093
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,19287,AE004517.1,1,sp|AE004517.1|AE004517 Pseudomonas aeruginosa PAO1; section 78 of 529 of the complete genome.,1,23,7001,6649,155.32,GGGGCCGAUUAGGAUUCGACGCCGGUAACAAAACUUGAGGGGCAUGCCGAGCUGGUAGCAGAACUCGUAAAUUCGCUGCUGCAAACUUAUAGUUGCCAACGACGACAACUACGCUCUAGCUGCUUAAUGCGGCUAGCAGUCGCUAGGGGAUGCCUGUAAACCCGAAACGACUGUCAGAUAGAACAGGAUCGCCGCCAAGUUCGCUGUAGACGUAACGGCUAAAACUCAUACAGCUCGCUCCAAGCACCCUGCCACUCGGGCGGCGCGGAGUUAACUCAGUAGAGCUGGCUAAGCAUGUAGAACCGAUAGCGGAGAGCUGGCGGACGGGGGUUCAAAUCCCCCCGGCUCCACCA,AE004517/7001-6649,,0,0,AE004517.1/7001-6649
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20255,AE005491.1,1,sp|AE005491.1|AE005491 Escherichia coli O157:H7 EDL933 genome; contig 3 of 3; section 110 of 290.,0,24,9259,9621,224.09,GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGACGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA,AP002562/101226-101588 AE005491/9259-9621,,0,0,AE005491.1/9259-9621
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20876,AE006115.1,1,sp|AE006115.1|AE006115 Pasteurella multocida PM70 section 82 of 204 of the complete genome.,1,25,421,55,218.50,GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGCCCAAGGUGCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAAAAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUAAUAACCUGCUCAUAGCCUUCUCUCCCCAGCUUCCGCUCGUAAGACGGGGAUCAAGAGGAGUCAAAUUCAAACGAGAUCGCGUGGACGCCUCCGCUUGAGGAUCGAAGCGUUAAAUUGAAUCAAGCUAGUUUAUCUAUCGCGUGUCUGUCCGCAGUGGGUAAAUGAAAUUAAAGACGAGACUAAACGUGUAGUACUGAAGGUAGAGUAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA,AE006115/421-55,,0,0,AE006115.1/421-55
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21133,AE006373.1,1,sp|AE006373.1|AE006373 Lactococcus lactis subsp. lactis IL1403 section 135 of 218 of the complete genome.,1,26,6190,5835,112.26,GGGGGCGUUACGGAUUCGACAGGCAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCUCUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAGGGGUUCGACUCCCCUCGCCUCCA,AE006373/6190-5835,,0,0,AE006373.1/6190-5835
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21319,AE006568.1,1,sp|AE006568.1|AE006568 Streptococcus pyogenes M1 GAS strain SF370; section 97 of 167 of the complete genome.,0,27,801,1148,139.25,GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUUGCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACUGCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACCAGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGAAGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUUUCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGAGUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAUGGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCAGCUCCAUCA,AE006568/801-1148,,0,0,AE006568.1/801-1148
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21882,AE007135.1,1,sp|AE007135.1|AE007135 Mycobacterium tuberculosis CDC1551;  section 221 of 280 of the complete genome.,1,28,3867,3500,65.17,GGGGCUGAACGGUUUCGACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGAUUCACAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGGCUAGUCUGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGGCAUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUCGCGGGACUCCUCGGGACAACCACAGCGACUGGGAUCGUCAUCUCGGCUAGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCGAACUGCGCACGGAGAAGCCUUGAGGGAAUGCCGUAGGACCCGGGUUCGAUUCCCGGCAGCUCCACCG,AE007135/3867-3500 Z95150/11031-10664,,0,0,AE007135.1/3867-3500
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22138,AE007393.1,1,sp|AE007393.1|AE007393 Streptococcus pneumoniae TIGR4  section 76 of 194 of the complete genome.,0,29,1725,2069,133.81,GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUUGCGACUCGUGUGGCGACGUAAACGCUCAGUUAAAUAUAACUGCAAAAAAUAACACUUCUUACGCUCUAGCUGCCUAAAAACCAGCAGGCGUGACCCGAUUUGGAUUGCUCGUGUUCAAUGACAGGUCUUAUUAUUAGCGAGAUACGAUUAAGCCUUGUCUAGCGGUUUGAUAAGAGAUUGAUAGACUCGCAGUUUCUAGACUUGAGUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUGGUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCA,AE007393/1725-2069,,0,0,AE007393.1/1725-2069
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22331,AE007587.1,1,sp|AE007587.1|AE007587 Clostridium acetobutylicum ATCC824 section 75 of 356 of the complete genome.,0,30,2639,2997,137.34,GGGGGCGCUUUUGGUUUCGACGGGGAUGAUGUUACGUUUGAGAAGCGAGUCGAGGGAACCUGUGGACCCGCGUUAAAAAACUAUAGGCCUUAAAAAUAAAGGAUAACGAAAAUAAUUUAGCUUUAGCUGCGUAGUCAGCUAACGUCAGCCUGAGAGUCCCGCGACUCAGAGUCUGGCGUCGACAGCGGGGAACCGAGCCUUACAAAGCUUUGAGUAAGGAACGGAAUUUAUGAAGCUACUGAAGUGAAAAGCUUGUUUGUAGGCGUUUCAUGGAGGGAAUGUUAAAAUACAAACUGCACUCGGAGAUGCUUAAAUGAAACCAUUUUCGGACAGGGGUUCGAUUCCCCUCGCCUCCACUA,AE007587/2639-2997,,0,0,AE007587.1/2639-2997
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23192,AE008453.1,1,sp|AE008453.1|AE008453 Streptococcus pneumoniae R6 section 69 of 184 of the complete genome.,0,31,8604,8948,134.03,GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUAUUUUGCGACUCGUGUGGCGACGUAAACGCUCAGUUAAAUAUAACUGCAAAAAAUAACACUUCUUACGCUCUAGCUGCCUAAAAACCAGCAGGCGUGACCCGAUUUGGAUUGCUCGUGUUCAAUGACAGGUCUUAUUAUUAGCGAGAUACGAUUAAGCCUUGUCUAGCGGCUUGAUAAGAGAUUGAUAGACUCGCAGUUUCUAGACUUGAGUUAUGUGUCGAGGGGCUGUUAAAAUAAUACAUAACCUAUGGUUGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCA,AE008453/8604-8948,,0,0,AE008453.1/8604-8948
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23548,AE008823.1,1,sp|AE008823.1|AE008823 Salmonella typhimurium LT2; section 127 of 220 of the complete genome.,0,32,1,285,38.37,UAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAACCUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGCGGAUGCCCUGCCUGGGGUUGAAGCGUUAAAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUCCGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGC,AE008823/1-285,,0,0,AE008823.1/1-285
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,24759,AE010048.1,1,sp|AE010048.1|AE010048 Streptococcus pyogenes strain MGAS8232; section 96 of 173 of the complete genome.,0,33,800,1147,134.14,GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUUGCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACUGCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACCAGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGAAGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUUUCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGAGUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAUGGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCAUCA,AE010048/800-1147 AE014155/8794-9141,,0,0,AE010048.1/800-1147
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25275,AE010567.1,1,sp|AE010567.1|AE010567 Fusobacterium nucleatum subsp. nucleatum ATCC 25586; section 109 of 197 of the complete genome.,1,34,1932,1589,119.43,GGGGAUGCAAAGGUUUCGACGGGGUUGUGAGGUUAUAGGUAGCAAGUCAGGCUUGUCGCUGUGAGAGACUAAACACAUCUUUUAGAUGGAAACAAAGAUUACGCUUUAGCUGCUUAGUUCAGCUACACCUUGGAUAACUUAUUCUAUACGGGUUUUUCAAAGGUGUUGACUAGUAUAGAUCACCAUAAAUGAUUUCUCUAAGUUUAUGGGACAUUUUAGAGGAUAGUUUUAGUUAGCCCUGUUUACGGGAGUAAUUAUUACGAAAUUUAAUAGUAAACUAAACUUGUAGAAGCUUAUGGUCAUUAUGAUUUCGGACACGAGUUCGACUCUCGUCAUCUCCACCA,AE010567/1932-1589,,0,0,AE010567.1/1932-1589
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25915,AE011207.1,1,sp|AE011207.1|AE011207 Leptospira interrogans serovar lai str. 56601 chromosome I; section 16 of 397 of the complete sequence.,0,35,9134,9480,102.71,GGGGACGAAAUUGGUUUCGACUGUUGUUGCCAGGGGUUAUGUGGCGUGUAGAGGUUGUAGGCUCCUCUAAAAACCUUCAAACAAUAACCGCUAAUAACGAAUUAGCUUUAGCAGCUUAAUCUCUGCUACGGAACUUUAGUUUUUUCUCUCGAAUUCUAAAUGUUCUGACAAUGAUCGGGAGGCGAUUCUUUUGGUUUUUGGUUCCUAAAAGAGUUUGUAUUUGAGCCGAAUAGGAAAGAGAGUCCUGUCUGAGGGUGAACCUCUUUCCGAAAUUUUAUACACAGACUACACACGUAGAGGCUGAUCUGGGGCGCAAUAGGACGCGGGUUCGAACCCCGCCGUCUCCA,AE011207/9134-9480,,0,0,AE011207.1/9134-9480
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,26491,AE011783.1,1,sp|AE011783.1|AE011783 Xanthomonas axonopodis pv. citri str. 306;  section 161 of 469 of the complete genome.,1,36,5129,4733,144.70,GGGGGUGCACUGGUUUCGACGGGGGUCGCGAAGUCGCUUGGCGCAUGCCGAGGGGGCAGCUUUCCUCGUUAAUCCAGCAGCAAACUUUUAGUUGCCAACGAUGACAACUACGGUUCGGACUUCGCUAUCGCCGCUUAAUUGGCUUUAGUUGUAGUUCUACAGCCGCCUAAGGCGAACCCCCGAACCUACUUGUGCCCGUGCUCGUAGGUGUAGGGUCAUUAUCACGGAACCAUCGGUAGUGGCUGCCUGUCAGCUACCGGUCAGAUAAAGCAGGCUGGUUUCCAGGUGCGCUUUGCCAACCGUGCUGCCUGGGAACGAGAUCUAACGGAGGGCUAAGCAUGUAGUGCUGGGGAUGGAGUGCUUCCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA,AE011783/5129-4733,,0,0,AE011783.1/5129-4733
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,26954,AE012247.1,1,sp|AE012247.1|AE012247 Xanthomonas campestris pv. campestris str. ATCC 33913;  section 155 of 460 of the complete genome.,1,37,3390,2994,143.03,GGGGGUGCACUGGUUUCGACGGGGGUCGCGAAGUCGCUUGGCGCAUGCCGAGGGGGCAGCUUUCCUCGUUAAUCCAGCAGCAAACUUUUAGUUGCCAACGACGACAACUACGGUUCGGACUUCGCUAUCGCCGCUUAAUUGGCUUUAGUUGUAGUUCUACAGCCGCCUAAGGCGAACCCCCGAAACUACUUGUGCCCGUGCUCGUAGAUGUAGGGUCAUUAUCACGGAACCGCCGGUAGUGGCUGCCUGUCAGCUAUCGGUUAGAUCAAGCAGGCUGGUUUUCAGGUGCGCUUUGCCCGCCGUGCUGCCUGGGAACGAGAUCUAACGGAGGGAUAAGCAUGUAGUGCUGGGGAUGGAGUGCUUCCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA,AE012247/3390-2994,,0,0,AE012247.1/3390-2994
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27268,AE012561.1,1,sp|AE012561.1|AE012561 Xylella fastidiosa Temecula1;  section 9 of 9 of the complete genome.,0,38,39892,40246,151.19,GGGGGUGCACUGGCUUCGACGGGGGUCACAAAAUCACUUGGUGCAUGCCGAGGGGGCCGCUUUCCUCGUAAAUCCAGCAGCACACUUAUAGUUGCCAACGAAGACAACUUCGCUCUAGCCGCUUAAGGCUUAAGCCUCGAAACUGCUUGUGUCCGUGCUCGCAGCGUAGAGUCAUCAUCACGGAACCGCUGAGACGUGGCCGUCUGCCCACCCUUGGUUAAAUCUAGCAGACUGGUUUCCGGGUGCGCUUUGCCUGUCGUGCUGCCCGGCGACGAGACCUAACGGCCAGGAUAAGCAUGUAGGGCCGGGGACGGAGUACUUUCGGACGGCGGUUCGAUUCCGCCCACCUCCACCA,AE012561/39892-40246,,0,0,AE012561.1/39892-40246
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27328,AE012839.1,1,sp|AE012839.1|AE012839 Chlorobium tepidum TLS  section 60 of 194 of the complete genome.,0,39,3209,3612,42.50,GGGGAUGACAGGCUAUCGACAGGAUAGGUGUGAGAUGUCGUUGCACUCCGAGUUUCAGCAUGGACGGACUCGUUAAACAAGUCUAUGUACCAAUAGAUGCAGACGAUUAUUCGUAUGCAAUGGCUGCCUGAUUAGCACAAGUUAAUUCAGAAGCCAUCGUCCUGCGGUGAAUGCGCUUACUCUGAAGCCGCCGGAUGGCAUAACCCGCGCUUGAGCCUACGGGUUCGCGCAAGUAAGCUCCGUACAUUCAUGCCCGAGGGGGUGUGCGGGUAACCAAUCGGGAUAAGGGGACGAACGCUGCUGGCGGUGUAAUCGGACCACGAAAAACCAACCACCAGAGAUGAGUGUGGUAACUGCAUCGAGCAGUGUCCUGGACGCGGGUUCAAGUCCCGCCAUCUCCACCA,AE012839/3209-3612,,0,0,AE012839.1/3209-3612
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27552,AE013063.1,1,sp|AE013063.1|AE013063 Thermoanaerobacter tengcongensis strain MB4T; section 90 of 244 of the complete genome.,0,40,8484,8834,136.95,GGGGGUGUGUUGGUUUCGACGGGGGCGGUCGAGGUAAAAGUAGCGAGCCGAGUUCUCCACCAGCUCGUAAAAAAGGUGGAAAAAAAUAAACGCAGACAGAGAACUCGCUUACGCUGCCUAAUUAAAGGCGGCCGUCCAGCCUGAAAUGCCCACGUUUCAGGACUGGGCGUCAAAAGAGUGGGGAACUGGUUUUGCCUGCGCCUCGGGGCAAAACCGGAAUAAUGAGGCUACCGAAGCGGUUAUCCUGUCGCUGGGAGAACCGCUGAGGGAAAGCUAAAACAGCGACUGCGCUCGGAGAAGCUUUUACCGGGACGCCUUCGGACCGGGGUUCGAAUCCCCGCACCUCCACCA,AE013063/8484-8834,,0,0,AE013063.1/8484-8834
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28393,AE013908.1,1,sp|AE013908.1|AE013908 Yersinia pestis KIM section 308 of 415 of the complete genome.,0,41,10909,11272,212.10,GGGGCUGAUUCUGGAUUCGACGGGAUUCGCGAAACCCAAGGUGCAUGCCGAGGUGCGGUGGCCUCGUAAAAAACCGCAAAAAAAAUAGUUGCAAACGACGAAAACUACGCACUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCUAAAAGAGCUCGUGUGGAAACCUUGCCUGGGGUGGAAGCAUUAAAACUAAUCAGGAUAGUUUGUCAGUAGCGUGUCCAUCCGCAGCUGGCCGGCGAAUGUAAUGAUUGGACUAAGCAUGUAGUGCCGACGGUGUAGUAAUUUCGGACGGGGGUUCAAAUCCCCCCAGCUCCACCA,AE013908/10909-11272 AJ414146/126951-126588,,0,0,AE013908.1/10909-11272
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28501,AE014016.1,1,sp|AE014016.1|AE014016 Buchnera aphidicola str. Bp (Baizongia pistaciae); section 1 of 2 of the complete genome.,1,42,200304,199941,135.33,GGGGCUGAUAUUGGAUUUGACAAAAUUAUUGAAAACUGAUGUGCAUGCCGAGGAUGGUUUGCCUCGUUAAAAAACCAUAAAAAAUAGUAGCAAAACAAAAUCAAUACGCUUUAGCAGCUUAAUAAUCUGAAUAAAGCCCUUCUUUUAAACAUAUUCUCUUAAUGUUUAAUUUAUAUAGAAGGUUAAUCUAAAGAGAUCGCAACUCAAAUCUAUUUUGAAAGAUUUUUUGUUGCUAAAUAAAAACUUCAAAAUAUAUAUCUAUAAUGAGUCUAUACAUCGAUAGAUAAGAAAAGAUAAUAGACUAAGCAUGUAGUAUCUGAAGUCGUAAAAAUUUUGGACGCGGGUUCGAAUCCCGCCAGCUCCA,AE014016/200304-199941,,0,0,AE014016.1/200304-199941
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28521,AE014094.1,1,sp|AE014094.1|AE014094 Buchnera aphidicola str. Sg (Schizaphis graminum) section 19 of 57 of the complete genome.,1,43,4741,4369,159.48,GGGGCUGUUUUUGGAUUCGACAAAGUUAUCAAAAAAGUAAAGUGCAUGCCGAGGAACGGUUUGCCUCGAUAAAAAACCGUAAAAAAAUAGCUGCAAAUAAUAAACAAAACUACGCUUUAGCAGCUUAAAAAACUGUAUAAAGCCCUUUCAUCUCUGACUUCUCUCUUGAGAACGAGAAAUUUUUAAGAAAGGCCGACAUUUAAAGAGAAAAAUGUGAGCACUAUGCUUGAUAGUGACACAAAAUUAAUUUUUCAAGCUAUAAGCUUAAAAUGAGUUUUUCCAAAUUAAGCAAUGAAAAAAUAAAGAAAAACUAAGCAUGUAGUAUCUUUAUUUAUAGAAAUUUUGGACGCGGGUUCAAAUCCCGCCAGCUCCA,AE014094/4741-4369,,0,0,AE014094.1/4741-4369
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28579,AE014155.1,1,sp|AE014155.1|AE014155 Streptococcus pyogenes MGAS315; section 20 of 37 of the complete genome.,0,44,8794,9141,134.14,GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUUUUGCGUCCCAUCGGCAGAUGUAAAUUGCCAGUUAAAUAUAACUGCAAAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACCAGCUAGCGUGACUUCUACAAGAUUGCUUGUGUCCUGUUAGAAGUCUCAAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUUUCGUGACAAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGAGUUAUGUGUCUUUAGUUUGUUAAAUGAAGACAUAACCUAUGGACGUAGACAAAUAUGUUGGCAGGUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCAUCA,AE010048/800-1147 AE014155/8794-9141,,0,0,AE014155.1/8794-9141
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28639,AE014233.1,1,sp|AE014233.1|AE014233 Streptococcus agalactiae 2603V/R section 43 of 100 of the complete genome.,1,45,14673,14327,125.82,GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGUAUAUUUCGCGACUCAUCGGCAGAUGUAAAAUGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCUUACGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCUUCACAAGAUUGUUUGCGUUUUGCUAGAAGGUCUUAUUUAUCAGCAAACUACGUUUGGCUACUGUCUAGUUAGUUAAAAAGAGAUUUAUAGACUCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACCUAGUUAAAUCAAUACAUAACCUAUAGUUGUAGACAAAUAUAUUAGCAGAUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCA,AE014233/14673-14327,,0,0,AE014233.1/14673-14327
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29142,AE014761.1,1,sp|AE014761.1|AE014761 Bifidobacterium longum NCC2705 section 148 of 202 of the complete genome.,0,46,658,1054,83.08,GGGGGCGAUCGGUUUCGACGGUGACCUGUUCGCUGCAGGGAAGCGUGCCGAGAACGCCGGGUCCGCUCGUGGAUGACCCCGGCAAAAGAAUAAGUGCUAAAUCUAACCGCACUGAGUUCGCUCUCGCUGCCUGAUUUUUAGUCAGGAUUAACCAGUGAGCAGCCGCUCCGUUCACUCCUCCUCGUCUUUGGGAGGAUGCUGAGCGUCGUUUAGAAGACUUGCUGAUGCAGUUGAGCCUCAGGGCUGCAUCGGGACUUUAACUGCGGAUAUGCUCGCCAUCAGUUGUCUGCGACAUCGAUGGGGGCAGAAAAAUCGCCAACUUGGCCAGCAGACUACGCACGUAGAAGACUGUGGGCUCGGUCAUCGGACCGGGGUUCAAUUCCCCGCGCCUCCACCA,AE014761/658-1054,,0,0,AE014761.1/658-1054
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29300,AE014956.1,1,sp|AE014956.1|AE014956 Streptococcus mutans UA159 section 104 of 185 of the complete genome.,1,47,7415,7070,119.25,GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGACCUAUUUUGCGACUCAUCUAGCGGAUGUAAAACGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCUUACGCAGUAGCUGCCUAAAAACCAGCCUGUGUGAUCAAUAACAAAUUGCUUGUGUUUGUUGAUUGGUCUUAUUGUUAACAAGCUACGUUAGAACUGAGUCAGGCUGUUCUAAAAGAGUUCUACUGACUCGCAUCGUUAGAGUUUGAGUUAUGUAUUGUAACGGUGUUAAAUAAACACAUAACCUAUAGUUGUAGACAAAUGGGUUAGCAGAUGUUUGGACGUGGGUUCGACUCCCACCGGCUCCA,AE014956/7415-7070,,0,0,AE014956.1/7415-7070
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29627,AE015283.1,1,sp|AE015283.1|AE015283 Shigella flexneri 2a str. 301 section 246 of 412 of the complete genome.,0,48,3872,4234,225.20,GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA,D12501/1355-1717 U68074/1-363 AE015283/3872-4234 D90888/18478-18840 U36840/4547-4909 AE000347/9315-9677,,0,0,AE015283.1/3872-4234
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29934,AE015592.1,1,sp|AE015592.1|AE015592 Shewanella oneidensis MR-1 section 141 of 457 of the complete genome.,1,49,7308,6954,169.01,GGGGGCGAUUCUGGAUUCGACAGGAUUCACGAAACCCUGGGAGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAGUUAUAGUUGCAAACGACGAUAACUACGCUCUAGCCGCUUAAUGCCGCUAGCCAUCUACCACACGCUUUGCACAUGGGCAGUGGAUUUGAUGGUCAUCUCACAUCGUGCUAGCGAGGGAACCCUGUCUGGGGGUGAACCGCGAAACAGUACCGGACUCACCGUGUGGGAUCCUGUCUUUCGGAGUUCAAACGGUUAAACAAUAGAAAGACUAAGCAUGUAGCGCCUUGGAUGUAGGUUUUCUGGACGCGGGUUCAAGUCCCGCCGCCUCCACCA,AE015592/7308-6954,,0,0,AE015592.1/7308-6954
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30274,AE015937.1,1,sp|AE015937.1|AE015937 Clostridium tetani E88; section 2 of 10 of the complete genome.,0,50,79621,79952,102.91,AAAUGGUUUCGACGGGGGCAAGUUGCUCCUGAGAAGCGAGUCGAGGGGUCCUGGGCCCGCGUUAAAAAACUGGGAAAAAUUAUAAACGCAGACGAUAAUUUCGUUUUAGCUGCCUAAUUAGUGCAGCUCGUCCUACUUGGGAGUCCCACGACCUAAGAUAGGGCGUCAAUUAGUGGGGAACCGAGCUCUACAAAGCUUUGAGUAGAGAACGGAACUUAUGAAGCUACUGAAUCUAGAAACCUGUUUAUCGGUGUCUAGAGGAGGGAAUGUUAAAAGGUAAACUGCACUCGGAGAUGCUCAGGGGUUACUGCUUUCGGACAGGGGUUCGAUUC,AE015937/79621-79952,,0,0,AE015937.1/79621-79952
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30284,AE016745.1,1,sp|AE016745.1|AE016745 Staphylococcus epidermidis ATCC 12228; section 2 of 9 of the complete genome.,0,51,263858,264215,143.38,GGGGACGUUCUUGGAUUCGACAGGGGUCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGGCUCCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAUCAAACAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAUCGCCUAACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAACCCUAGUAGGAUAUGCUAAACACUGCCGCUUGAAGUCUGUUUAGAUGAAAUAUAAUCAAGCUAGUAUCAUGUUGGUUGUUUAUUGCUUAGCAUGAUGCGAAAAUUAUCAAUAAACUACACACGUAGAAAGAUUUGUAUCAGGACCUCUGGACGCGGGUUCGAAUCCCGCCGUCUCCA,AE016745/263858-264215,,0,0,AE016745.1/263858-264215
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30301,AE016764.1,1,sp|AE016764.1|AE016764 Escherichia coli CFT073 section 10 of 18 of the complete genome.,0,52,296159,296521,219.01,GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCACAGCUGGCAAGCGAAUGUAAAGACURACUAAGCAUGUAGUACCGAGGAUGUAGAAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA,AE016764/296159-296521,,0,0,AE016764.1/296159-296521
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30327,AE016791.1,1,sp|AE016791.1|AE016791 Pseudomonas putida KT2440 section 18 of 21 of the complete genome.,0,53,258517,258915,128.12,GGGGCCGAUUAGGAUUCGACGCCGGUAGCGAAACUCUAGGUGCAUGCCGAGUUGGUAACAGAACUCGUAAAUCCACUGUUGCAACUUUUAUAGUUGCCAAUGACGAAAACUACGGCGCGGAGUACAAGCUGGCUGCGUAAGCAGUCCUCUUGACCCGUUGCUUCUGGUAGCUUCGGCUCCAGCAAUCACUAGGGGAUGCCUGUAAACCCGAACUGAUUGUCAUACAGAACAGGAUCGUCGCGUAGCACGUUGUGGGCGAAGUGACUAAAACUUACACAACUCAUCCAAAGCACCCUGCCCGUCGGGCGGCUGCGGAUUAAAUCAGUAGACACGGCUAAGCAUGUAGUACCGACAGCGGAGUACUGGCGGACGGGGGUUCAAAUCCCCCCGGCUCCACCA,AE016791/258517-258915,,0,0,AE016791.1/258517-258915
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30332,AE016798.1,1,sp|AE016798.1|AE016798 Vibrio vulnificus CMCP6 chromosome I section 2 of 11 of the complete sequence.,0,54,53813,54179,207.91,GGGGCUGAUUUAGGAUUCGACGGGAAUUUUGCAGUCUGAGGUGCAUGCCGAGGUGCGGUAGGCCUCGUUAACAAACCGCAAAAAAAUAGUCGCAAACGACGAAAACUACGCACUAGCAGCUUAAUAAACUGCUCAGAGCCCUCUCGCCCUAGCUUCCGCUUGUAAGACGGGGAAUCACGAGGGGUCAAACCAAAUCAAGCUGGCGUGGAUUCCCCCACCUGAGGGAUGAAGCGUAAGAUAUAAUUCAGGUUAGCUAUUCAUUCGCGUGUCGGUUCGCAGGUGGUAGUGAAAUUAAAGAUCGACUAAGCAUGUAGUACCAAUGAUGAAUGGUUUUCGGACGGGGGUUCAAAUCCCCCCAGCUCCACCA,AE016798/53813-54179,,0,0,AE016798.1/53813-54179
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30361,AE016843.1,1,sp|AE016843.1|AE016843 Salmonella enterica subsp. enterica serovar Typhi Ty2; section 10 of 16 of the complete genome.,0,55,30589,30951,218.92,GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAACCUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGCGGAUGCCCUGCCUGGGGUUGAAGCGUUAAAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUCCGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA,AL627276/57262-57624,,0,0,AE016843.1/30589-30951
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30368,AE016850.1,1,sp|AE016850.1|AE016850 Tropheryma whipplei str. Twist; section 1 of 3 of the complete genome.,0,56,278117,278482,74.94,GGGGAUGACUGGUUUCGACGCUGUUUGUGUACUCGUGGGAAGCGGGUCGAGGAUGCGAGGUUGUCUCGUUAACGAUCCUCGCAAAAUAUAAGUGCCAACUUAAAGCGCACUGAUCUAAGUCUUGCUGCUUAAGCGCUUAGAUCUGUCGGUAUAGGGCUUGUCUUCGGCCCUGUAUCCGGCAUGGUUUUAGAGGACUUGCCGCGUGUUUGCCGCUUGCGUGAACACCGGGACUUUAUUGCAAGCUGGGCCUGUUGAUUUAGAUUCCGCUGCAAAGAAUCAGGGCUGAGUAUAACGGUUUUAGCGGAUACACCCGUAGAAGUCACGGGCUCCAUGCCGCGGACGGGGGUUCGAUUCCCCCCAUCUCCA,BX251411/292510-292145 AE016850/278117-278482,,0,0,AE016850.1/278117-278482
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30389,AE016872.1,1,sp|AE016872.1|AE016872 Pseudomonas syringae pv. tomato str. DC3000 section 17 of 21 of the complete genome.,0,57,87728,88115,130.56,GGGGCCGAUUUGGAUUCGACGCCGGUGAUGAAACUUUAGGUGCAUGCCGAGUUGGUAACAGAACUCGUAAAUCCACUGUUGCAACUUUCUAUAGUUGCCAAUGACGAAAACUACGGUGCUCAACUAGCUGCGUAAGCAGCCUAGCCGCACUUCUGGUAGCUUCGGCUCCAGCAAUCAUCAGGGGAUGCCUGUAAACCCAAAAUGAUUGUCAUAUAGAACAGGAUCGUCGCCUAGUACGUUGUGGACGAAGCGACUAAAACUUACGCAACUCGCCCAAUGCACCCUGCCCGUCGGGUCGCUGAGGGUUAACUUAAUAGACACGGCUACGCAUGUAGUACCGACAGCGGAGUACUGGCGGACGGGGGUUCAAAUCCCCCCGGCUCCACCA,****    NEW  HIT  #0  ****,,2,0,AE016872.1/87728-88115
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30414,AE016945.1,1,sp|AE016945.1|AE016945 Bacteroides thetaiotaomicron VPI-5482; section 20 of 21 of the complete genome.,0,58,56887,57283,67.41,GGGGUUGACUGGAUUUGACAGCGGGCAGAAAUGGUAGGUAAGCAUGCAGUGGGUCGGUAAUUUCCACUUAAAUCUCAGUUAUCAAAACUUUAUCUGGCGAAACUAAUUACGCUCUUGCUGCUUAAUCGAAUCACAGUAGAUUAGCUUAAUCCAGGCACUAGGUGCCAGGACGAGACAUCACUCGGAAGCUGUUGCUCCGAAGCAUUCCGGUUCAGUGGUGCAGUAACAUCGGGGAUAGUCAGAAGCGGCCUCGCGUUUUUGAUGAAACUUUAGAGGAUAAGGCAGGAAUUGAUGGCUUUGGUUCUGCUCCUGCACGAAAAUUUAGGCAAAGAUAAGCAUGUAGAAAGCUUAUGAUUUCCUCGUUUGGACGAGGGUUCGAUUCCCUCCAGCUCCACCU,****    NEW  HIT  #1  ****,,2,0,AE016945.1/56887-57283
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30419,AE016950.1,1,sp|AE016950.1|AE016950 Enterococcus faecalis V583; section 4 of 11 of the complete genome.,1,59,138415,138052,162.92,GGGGGCGUUACGGAUUCGACAGGCAUAGUUGAGCUUGAAUUGCGUUUCGUAGGUUACGGCUACGUUAAAACGUUACAGUUAAAUAUAACUGCUAAAAACGAAAACAAUUCUUUCGCUUUAGCUGCCUAAAAACCAGCUAGCGAAGAUCCUCCCGGCAUCGCCCAUGUGCUCGGGUCAGGGUCCUAAUCGAAGUGGGAUACGCUAAAUUUUUCCGUCUGUAAAAUUUAGAGGAGCUUACCAGACUAGCAAUACAGAAUGCCUGUCACUCGGCACGCUGUAAAGCGAACCUUUAAAUGAGUGUCUAUGAACGUAGAGAUUUAAGUGGCAAUAUGUUUGGACGCGGGUUCGACUCCCGCCGUCUCCA,****    NEW  HIT  #2  ****,,2,0,AE016950.1/138415-138052
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30431,AE016964.1,1,sp|AE016964.1|AE016964 Coxiella burnetii strain RSA 493; section 5 of 7 of the complete genome.,0,60,55099,55458,100.26,GGGGGCGACCAGGCUUCGACGUGGAUCCUGAAACCCGAGACGCAUGUCGAGCCGGCAACGAAGGCUCGUAAAUCCAUCAGUUGCAAACAGAUAGUUGCAAACGAUAGUAAUUAUCUCCAAGAAGCUUACGCAUAAAGCUUCUUCCGUUGCUGGGAUUCGCUUAUAGAUCCCUACCAACGGCCAUAGCAUAUAAGCUCGCCCUCAAGCAUGGCUCAUGACUUGAAGGUUAAACAGAAGAGCUCGCAGUCAAUUUCCCCUGCACGUCGGGCGAUUGACUGUUAAAUCAUAGACGAUGCUAAGCAUGUAGUGUCAACGGCGGAUGAUUUACGGACGCGGGUUCAAUUCCCGCCGCCUCCAUCA,****    NEW  HIT  #3  ****,,2,0,AE016964.1/55099-55458
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30435,AE016968.1,1,sp|AE016968.1|AE016968 Mycoplasma gallisepticum strain R section 2 of 4 of the complete genome.,1,61,206794,206387,58.28,GGGGAUGUCAAGGCUUCGACAUGAUUGAUAAACUUAUUAGUUCAGUAGGGUCUGCCCUUUAUAGCUCAAGGUAAUAAUAACCGACAAAACUUCUAAAGAACUAGCUGACGAAAACUUUGUUUUAAAUCAGUUAGCAUCAAACAACUACGCUUUAAACUUCUAAAUAAAUAAUAAAUAGCGUACUAGGUUUUUUAAAAACCUAGAUUUAUAGGAUAAAACUAGAUUUUGUAACUCGUUUUUAGUUUUACUAUUAAUACUGAUUAAUUAGUUUUUUGACCCAACGAUUACUACGAACCAAGAUGUUGAUACUUAUCACUUGGUUUGAGCUUCAUAAGUAUCUAAACUGUAAAUAAAACUAAUUUGCUGAGUCGAUUGUGGAAACGGGUUCGAUUCCCGUCAUCUCCACCA,****    NEW  HIT  #4  ****,,2,0,AE016968.1/206794-206387
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30447,AE016987.1,1,sp|AE016987.1|AE016987 Shigella flexneri 2a str. 2457T section 10 of 16 of the complete genome.,0,62,125129,125491,225.20,GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA,D12501/1355-1717 U68074/1-363 AE015283/3872-4234 D90888/18478-18840 U36840/4547-4909 AE000347/9315-9677,,0,0,AE016987.1/125129-125491
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30456,AE016996.1,1,sp|AE016996.1|AE016996 Chlamydophila caviae GPIC section 3 of 4 of the complete genome.,0,63,154850,155271,106.05,GGGGGUGUAUAGGUUUCGACUUGGAAAUGAAGUGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGUUUCUCUGACCUCACCGAGGAAAGAUUAGCUGCUUAAUUAGCAAAAGUUGUUGUCUAGAUAACCUCUAGAUAACCCGGUGCUCAUAGACUCCACCAGAGGUUUGUGAAACACCGUCAUCUAUCUGGUUGGAAUCUACCUUCUCUAAUUCUCAAGGAGGUUUAUUCGAGAUUAUUGAGAGUCGUUGGCUUCCAUAGAUGUUCUUAGCUGAGGAAGUUCAAUGUAUGAUUACUAGGGACUAAGCAUGUAGAGGUUAGCAGGGAGUUUACUAAGGACGAGAGUUCGAGUCUCUCCACCUCCA,****    NEW  HIT  #5  ****,,2,0,AE016996.1/154850-155271
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30474,AE017014.1,1,sp|AE017014.1|AE017014 Bacillus cereus ATCC 14579 section 17 of 18 of the complete genome.,1,64,195676,195322,166.23,GGGGACGUUACGGAUUCGACAGGGAUAGUUCGAGCUUAGGUUGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCCUAUAAUUGGCAAACAAAACAAUCUUUCUUUAGCUGCUUAAUUGCACUAAAGGUUCCUCCCUCCAUCGUCCAUGUGGUAGGGUAAGGGACUCAAACUAAGUGGACUACGCCGGAGUUCGCCGUCUGAGGACAAAGGAAGAGAACAACCAGACUAGCAACUUGGAAGCCUGUCGAUAGGCCGAAGAGUUCGCGAAAUGCUAAUAUAUCGACUACACUCGUAGAAGCUUAAGUGCCGAUAUUUUUGGACGUGGGUUCGACUCCCACCGUCUCCACCA,****    NEW  HIT  #6  ****,,2,0,AE017014.1/195676-195322
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30492,AE017040.1,1,sp|AE017040.1|AE017040 Bacillus anthracis str. Ames section 17 of 18 of the complete genome.,1,65,163093,162739,166.23,GGGGACGUUACGGAUUCGACAGGGAUAGUUCGAGCUUAGGUUGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCCUAUAAUUGGCAAACAAAACAAUCUUUCUUUAGCUGCUUAAUUGCACUAAAGGUUCCUCCCUCCAUCGUCCAUGUGGUAGGGUAAGGGACUCAAACUAAGUGGACUACGCCGGAGUUCGCCGUCUGAGGACAAAGGAAGAGAACAACCAGACUAGCAACUUGGAAGCCUGUCGAUAGGCCGAAGAGUUCGCGAAAUGCUAAUAUAUCGACUACACUCGUAGAAGCUUAAGUGCCGAUAUUUUUGGACGUGGGUUCGACUCCCACCGUCUCCACCA,****    NEW  HIT (duplicate of new hit #6)   ****,,2,0,AE017040.1/163093-162739
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30499,AE017149.1,1,sp|AE017149.1|AE017149 Helicobacter hepaticus ATCC 51449 section 6 of 6 of the complete genome.,0,66,235442,235810,95.22,GGGGCUGAUUGGCUUUCGACAGGAGCAAAGAGACUUAAGUGCAUGUGAGCUGGUAAGCUCUAAAACUACCACAAAUAAAUAAACGCAAACAACGCAAAUUACGCUCCAGCUUACGCAAAAGUCGCGUAAGUUUAUCACACUUUUGGAGUCGGCUUAAGAACUUCUAAUCUAGCUAGAAUCUUUCAAGCUGUAAUCUUUGCUAGAUGCUCUUUUUGUCAUACCUUAGCAAAAAGAAAAGAAUAAGGUUGCUUGUGGGAUUUAUCUUGGGGUGUUGGAUAACCACGAAAAGAAAACAAUACCUACUAAACAUGUAGAUUCUUAAGAAGCUCAAGCUUUUGGACUGGGGUUCAACUCCCCACAGCUCCACCA,****    NEW  HIT  #8  ****,,2,0,AE017149.1/235442-235810
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30500,AE017151.1,1,sp|AE017151.1|AE017151 Haemophilus ducreyi strain 35000HP section 1 of 6 of the complete genome.,1,67,71003,70637,207.53,GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGUCCAAGGUGCACGUCGAGGUGCGGUAGGCCUCGUAAACAAACCGCAAAAAAAUAGUCGCAAACGACGAACAAUACGCUUUAGCAGCUUAAUAACCUGCAUUUAGCCUUCGCGCCCUAGCUUUCGCUCGUAAGACGGGGAGCACGCGGAGUCAAACCAAAACGAGAUCGUGUGGACGCUUCGGCUUGUAGAUCGAAACACCAAAUUGAAUCAAGCUAGUUUAUUUCUUGCGUGUCUGUCCGCUGGAGAUAAGCGAAAUUAAAGACCAGACUAAACGUGUAGUACUGAAGAUAGAGUAAUUUCGGACGGGGGUUCAAAUCCCCCCAGCUCCACCA,****    NEW  HIT  #9  ****,,2,0,AE017151.1/71003-70637
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30506,AE017157.1,1,sp|AE017157.1|AE017157 Chlamydophila pneumoniae TW-183; section 1 of 4 of the complete genome.,1,68,135988,135566,98.79,GGGGGUGUAUAGGUUUCGACUUGAAAAUGAAGUGUUAAUUGCAUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCAACAAAACAAUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUUAGCUUGUUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAUUAGCAAAAGUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAUCUGCGAGCUCCACCAGAGGCUUGCAAAAUACCGUCAUUUAUCUGGUUGGAACUUACUUUCUCUAAUUCUCAAGGAAGUUCGUUCGAGAUUUUUGAGAGUCAUUGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGUCCAAUGUAAACAAUUCUAGAAGAUAAGCAUGUAGAGGUUAGCAGGGAGUUUGUCAAGGACGAGAGUUCGAGUCUCUCCACCUCCA,AE001597/3555-3133 AE002224/6757-7179 AP002545/138204-137782,,0,0,AE017157.1/135988-135566
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30519,X51902.1,1,sp|X51902.1|AE10SARN Alcaligenes eutrophus gene for 10Sa RNA,1,69,376,28,109.05,UGGGCCGACCUGGUUUCGACGUGGUUACAAAGCAGUGAGGCAUACCGAGGACCCGUCACCUCGUUAAUCAAUGGAAUGCAAUAACUGCUAACGACGAACGUUACGCACUCGCUUAAUUGCGGCCGUCCUCGCACUGGCUCGCUGACGGGCUAGGGUCGCAAGACCACGCGAGGUAUUUACGUCAGAUAAGCUCCGGAAGGGUCACGAAGCCGGGGACGAAAACCUAGUGACUCGCCGUCGUAGAGCGUGUUCGUCCGAUGCGCCGGUUAAAUCAAAUGACAGAACUAAGUAUGUAGAACUCUCUGUGGAGGGCUUACGGACGCGGGUUCGAUUCCCGCCGGCUCCACCA,X51902/376-28,,0,0,X51902.1/376-28
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,48782,AF176556.1,1,sp|AF176556.1|AF176556 Lactococcus lactis TcsBorf1 (tcsBorf1); LlrrB (rrB); KinB (kinB); TcsBorf2 (tcsBorf2); TcsBorf3 (tcsBorf3); and TcsBorf4 (tcsBorf4) genes; complete cds.,1,70,601,246,110.59,GGGGGCGUUACGGAUUCGACAGGCAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGACUUGACGCAGCAAAAGAGAUUUAAAGUCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAGGGGUUCGACUCCCCUCGCCUCCA,AF176556/601-246,,0,0,AF176556.1/601-246
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,6729,AF242564.1,1,sp|AF242564.1|AF242564 Anabaena PCC7120 atp1 operon; complete sequence.,0,71,6545,6929,69.79,GGGUCCGUCGGUUUCGACAGGUUGGCGAACGCUACUCUGUGAUUCAGGUCGAGAGUGAGUCUCCUCUGCAAAUCAAGGCUCAAAACAAAAGUAAAUGCGAAUAACAUCGUUAAAUUUGCUCGUAAGGACGCUCUAGUAGCUGCCUAAAUAGCCUCUUUCAGGUUCGAGCGUCUUCGGUUUGACUCCGUUAAGGACUGAAGACCAACCCCCAACGGAUGCUCUAGCAAUGUUCUCUGGUUGGCUUGCUAGCUAAGAUUUAAUCAGAGCAUCCUACGUUCGGGAUAAUGAACGAUUCCCGCCUUGAGGGUCAGAAAGGCUAAACCUGUGAAUGAGCGGGGGGUCAAUACCCAAUUUGGACAGCAGUUCGACUCUGCUGGAUCCACUA,AF242564/6545-6929,,0,0,AF242564.1/6545-6929
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,9747,AF269456.1,1,sp|AF269456.1|AF269456 Staphylococcus epidermidis strain SR1 clone step.1004b11 genomic sequence.,1,72,1525,1167,142.91,GGGGACGUUCUUGGAUUCGACAGGGGUCCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGGCUCCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAUCAAACAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAUCGCCUAACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAACCCUAGUAGGAUAUGCUAAACACUGCCGCUUGAAGUCUGUUUAGAUGAAAUAUAAUCAAGCUAGUAUCAUGUUGGUUGUUUAUUGCUUAGCAUGAUGCGAAAAUUAUCAAUAAACUACACACGUAGAAAGAUUUGUAUCAGGACCUCUGGACGCGGGUUCGAAUCCCGCCGUCUCCA,AF269873/1626-1984 AF269456/1525-1167,,0,0,AF269456.1/1525-1167
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,10162,AF269873.1,1,sp|AF269873.1|AF269873 Staphylococcus epidermidis strain SR1 clone step.1027h08 genomic sequence.,0,73,1626,1984,142.91,GGGGACGUUCUUGGAUUCGACAGGGGUCCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGGCUCCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAUCAAACAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAUCGCCUAACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAACCCUAGUAGGAUAUGCUAAACACUGCCGCUUGAAGUCUGUUUAGAUGAAAUAUAAUCAAGCUAGUAUCAUGUUGGUUGUUUAUUGCUUAGCAUGAUGCGAAAAUUAUCAAUAAACUACACACGUAGAAAGAUUUGUAUCAGGACCUCUGGACGCGGGUUCGAAUCCCGCCGUCUCCA,AF269873/1626-1984 AF269456/1525-1167,,0,0,AF269873.1/1626-1984
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24603,AF375552.1,1,sp|AF375552.1|AF375552 Lactococcus lactis subsp. lactis strain NCDO2118 tmRNA gene; partial sequence.,0,74,1,310,34.36,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375561/1-310 AF375552/1-310 AF375555/1-310 AF375557/1-310 AF375558/1-310,,0,0,AF375552.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24604,AF375553.1,1,sp|AF375553.1|AF375553 Lactococcus lactis subsp. lactis bv. diacetylactis strain IL1403 tmRNA gene; partial sequence.,0,75,1,310,35.17,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCUCUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375562/1-310 AF375553/1-310 AF375565/1-310 AF375566/1-310,,0,0,AF375553.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24605,AF375554.1,1,sp|AF375554.1|AF375554 Lactococcus lactis subsp. lactis strain IL2961 tmRNA gene; partial sequence.,0,76,1,310,34.19,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAACUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGUCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375554/1-310,,0,0,AF375554.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24606,AF375555.1,1,sp|AF375555.1|AF375555 Lactococcus lactis subsp. lactis strain IL2962 tmRNA gene; partial sequence.,0,77,1,310,34.36,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375561/1-310 AF375552/1-310 AF375555/1-310 AF375557/1-310 AF375558/1-310,,0,0,AF375555.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24607,AF375556.1,1,sp|AF375556.1|AF375556 Lactococcus lactis subsp. cremoris strain IL582 tmRNA gene; partial sequence.,0,78,1,310,33.50,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGACUUGACGCAGCAAAAGAGAUUUAAAGUCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375559/1-310 AF375560/1-310 AF375563/1-310 AF375564/1-310 AF375556/1-310,,0,0,AF375556.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24608,AF375557.1,1,sp|AF375557.1|AF375557 Lactococcus lactis subsp. lactis strain IL638 tmRNA gene; partial sequence.,0,79,1,310,34.36,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375561/1-310 AF375552/1-310 AF375555/1-310 AF375557/1-310 AF375558/1-310,,0,0,AF375557.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24609,AF375558.1,1,sp|AF375558.1|AF375558 Lactococcus lactis subsp. lactis bv. diacetylactis strain IL890 tmRNA gene; partial sequence.,0,80,1,310,34.36,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375561/1-310 AF375552/1-310 AF375555/1-310 AF375557/1-310 AF375558/1-310,,0,0,AF375558.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24610,AF375559.1,1,sp|AF375559.1|AF375559 Lactococcus lactis subsp. cremoris strain CNRZ355 tmRNA gene; partial sequence.,0,81,1,310,33.50,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGACUUGACGCAGCAAAAGAGAUUUAAAGUCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375559/1-310 AF375560/1-310 AF375563/1-310 AF375564/1-310 AF375556/1-310,,0,0,AF375559.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24611,AF375560.1,1,sp|AF375560.1|AF375560 Lactococcus lactis subsp. lactis bv. diacetylactis strain IL960 tmRNA gene; partial sequence.,0,82,1,310,33.50,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGACUUGACGCAGCAAAAGAGAUUUAAAGUCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375559/1-310 AF375560/1-310 AF375563/1-310 AF375564/1-310 AF375556/1-310,,0,0,AF375560.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24612,AF375561.1,1,sp|AF375561.1|AF375561 Lactococcus lactis subsp. lactis strain CNRZ337 tmRNA gene; partial sequence.,0,83,1,310,34.36,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375561/1-310 AF375552/1-310 AF375555/1-310 AF375557/1-310 AF375558/1-310,,0,0,AF375561.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24613,AF375562.1,1,sp|AF375562.1|AF375562 Lactococcus lactis subsp. lactis bv. diacetylactis strain IL986 tmRNA gene; partial sequence.,0,84,1,310,35.17,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCUCUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375562/1-310 AF375553/1-310 AF375565/1-310 AF375566/1-310,,0,0,AF375562.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24614,AF375563.1,1,sp|AF375563.1|AF375563 Lactococcus lactis subsp. cremoris strain CNRZ112 tmRNA gene; partial sequence.,0,85,1,310,33.50,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGACUUGACGCAGCAAAAGAGAUUUAAAGUCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375559/1-310 AF375560/1-310 AF375563/1-310 AF375564/1-310 AF375556/1-310,,0,0,AF375563.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24615,AF375564.1,1,sp|AF375564.1|AF375564 Lactococcus lactis subsp. lactis strain CNRZ119 tmRNA gene; partial sequence.,0,86,1,310,33.50,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCACUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGACUUGACGCAGCAAAAGAGAUUUAAAGUCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375559/1-310 AF375560/1-310 AF375563/1-310 AF375564/1-310 AF375556/1-310,,0,0,AF375564.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24616,AF375565.1,1,sp|AF375565.1|AF375565 Lactococcus lactis subsp. lactis strain CNRZ188 tmRNA gene; partial sequence.,0,87,1,310,35.17,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCUCUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375562/1-310 AF375553/1-310 AF375565/1-310 AF375566/1-310,,0,0,AF375565.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24617,AF375566.1,1,sp|AF375566.1|AF375566 Lactococcus lactis subsp. lactis bv. diacetylactis strain CNRZ124 tmRNA gene; partial sequence.,0,88,1,310,35.17,CAUUGUCGCGCAUGAACUGCAACUGCUGAGGGAUCAGGAUAAUCAUCCGCAGAUAAAUAUAACUGCUAAAAAUAAUACACAAACUUACGCAAUGGCAGCCUAAACAGCACCAUGCGUGCCUGAUUUUUGCUCUCUGAUGGCAAUUUGACGGCCUAAACUUUUAGUCAGAUACGUUGUUGUGGAGGCUUGACGCAGCAAAAGAGAUUUAAAGCCCCGCAAAAUGUCGCUGUUUGAGACUGGCUUUGGCAUUUUGUUAAAUUUGAGAAAGUCCUAUGGUUGUAGACGUUGAUGUAGCAAGGUGUUUGGACAG,AF375562/1-310 AF375553/1-310 AF375565/1-310 AF375566/1-310,,0,0,AF375566.1/1-310
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24618,AF375567.2,1,sp|AF375567.2|AF375567 Lactococcus plantarum strain CNRZ1322 tmRNA gene; partial sequence.,0,89,1,304,51.23,UGUUGUCGCGUAUGAGCUGCGAUUAGUGAGACGUCACUCUAAACCGUCGCAGAUAAAUAUAACUGCUAAAAAUACACAAACUUACGCUUUAGCUGCCUAAACCACAGCCGGCGUGCCAGACUUUCGUUCGCCUAUGACGAUUUGAUGGCCUAAUUUAGUAGGAUACGCUUUUGUGGUGUCUUGACAUGAAAGAAGAGAUUAAGAGACUCGCCAGCUGACUUUGUUCGAGGAUUGUCUUGUCAGUUGGGUAAAUUUAGACAGUCCCUAUGAUUGUAGACGCUGAUAUAGCAAGGCAUUUGGACAG,AF375567/1-304,,0,0,AF375567.2/1-304
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24619,AF375568.1,1,sp|AF375568.1|AF375568 Streptococcus thermophilus strain CNRZ1358 tmRNA gene; partial sequence.,0,90,1,301,63.63,CAUUAUGAGGCAUAUUCUGCGACUCGUGUGGCGACGUUAACGCUCAGUUAAAUAUAACUGCAAAAAAUACUAAUUCUUACGCUGUAGCAGCCUAAACACCUGCUCGCGUGACUUCUAGCAGAUUGCUUAUGUUUGUUUAGAAGUUUUAUUGAUUUAUAAGCUACGUUCGAUCAUUGCCUAGCUGGUCGAAAAGAGAUUUAUAGGCUCGCAUAUAGAAGGCUUGAGUUAUGUGUCGCCUAUCUGUUAAAUGAAAGACAUAACCUAUGGUCGUAGACGAAUAUGUUGGCAGAUGCUUGGACGU,AF375568/1-301,,0,0,AF375568.1/1-301
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24620,AF375569.1,1,sp|AF375569.1|AF375569 Leuconostoc lactis strain CIP102422 tmRNA gene; partial sequence.,0,91,1,308,63.98,CUGUUUAGGGCAUGGACUGCGUUUCGCCAUCCGGGCGUUAAAACGGGCAGAAAUUUUAACUGCAAAAAACGAAAACUCUUUCGCAAUCGCUGCCUAAAAAACAGUGAUGCGUCACUUAAUCUUGGUAGCUGGCGUCUAAGGUUAGGUCAUAAAAAGUCAGAUCGCGUCGUUGCUUAGAUUCGGAACAGCGGCGUUAAAUGAAUCGAGUUAGUGAUUGAUGUUAGCCUCGUGUUGUGGCGGAAUCAAUCAUGAAACUUAAAUGACAACACUAUAAGCGUAGAGGUUCAUGUACCGGGCAGUUUGGACAG,AF375569/1-308,,0,0,AF375569.1/1-308
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24621,AF375570.1,1,sp|AF375570.1|AF375570 Leuconostoc pseudomesenteroides strain CIP103316 tmRNA gene; partial sequence.,0,92,1,307,64.08,UCGUUUAGAGCAUUGCCUGCGUUUCGCCGUCCGGGCGUUAAACGGGCAGACAUUUUAACUGCAAAAAACGAAAACUCUUACGCAAUCGCUGCUUAAAAACCAGCAAUACGUAGCUUAAUCUUGGUUUCUGACGUCUGAGAUUAGGCCAUAAAAGGUCAGAUCGCAUUGUUGUUUACAUCUGGAAUGGCAAUGUUAAAUUUAUCAGAUUAGUUAAUUUGAUUAGCCGUGUGUUAUGGCGUACAAAUUGAUGAAAUUCAAAUGAUAGCACUAUAAGCGUAGGCGCCAAUGUAUCGGACGGUUUGGACAG,AF375570/1-307,,0,0,AF375570.1/1-307
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24622,AF375571.1,1,sp|AF375571.1|AF375571 Leuconostoc mesenteroides subsp. cremoris strain CNRZ361 tmRNA gene; partial sequence.,0,93,1,307,61.66,UCGUUUAGAGCAUUGAUUGCGUUUCGCCAUCCGGGCGCAAAACGGGCAGAAAUUUUAACUGCAAAAAACGAAAACUCUUUCGCUAUCGCUGCCUAAAAACCAGUGAUGCGUAGCUUAAUCUUGGUUGCUGGCGUCUGAGGUUAGGCCAUAAAAGGCCAGAUCGUACUGCUUCUUACAUCUGGAAAAGCAGUAUUAAAUCAAUCAGGUUAGUUAUAUUGAAGAGCCUUGAGCUAUGGCAGACAAUAUAAUGAACUACAAAUAAUAGCCCUAUAAACGUAGAUAUUGGUGUAUCGGGCGAUUUGGACAG,AF375571/1-307 AF375572/1-307 AF375573/1-307 AF375574/1-307,,0,0,AF375571.1/1-307
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24623,AF375572.1,1,sp|AF375572.1|AF375572 Leuconostoc mesenteroides subsp. mesenteroides strain CNRZ1022 tmRNA gene; partial sequence.,0,94,1,307,61.66,UCGUUUAGAGCAUUGAUUGCGUUUCGCCAUCCGGGCGCAAAACGGGCAGAAAUUUUAACUGCAAAAAACGAAAACUCUUUCGCUAUCGCUGCCUAAAAACCAGUGAUGCGUAGCUUAAUCUUGGUUGCUGGCGUCUGAGGUUAGGCCAUAAAAGGCCAGAUCGUACUGCUUCUUACAUCUGGAAAAGCAGUAUUAAAUCAAUCAGGUUAGUUAUAUUGAAGAGCCUUGAGCUAUGGCAGACAAUAUAAUGAACUACAAAUAAUAGCCCUAUAAACGUAGAUAUUGGUGUAUCGGGCGAUUUGGACAG,AF375571/1-307 AF375572/1-307 AF375573/1-307 AF375574/1-307,,0,0,AF375572.1/1-307
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24624,AF375573.1,1,sp|AF375573.1|AF375573 Leuconostoc mesenteroides subsp. mesenteroides strain CNRZ749 tmRNA gene; partial sequence.,0,95,1,307,61.66,UCGUUUAGAGCAUUGAUUGCGUUUCGCCAUCCGGGCGCAAAACGGGCAGAAAUUUUAACUGCAAAAAACGAAAACUCUUUCGCUAUCGCUGCCUAAAAACCAGUGAUGCGUAGCUUAAUCUUGGUUGCUGGCGUCUGAGGUUAGGCCAUAAAAGGCCAGAUCGUACUGCUUCUUACAUCUGGAAAAGCAGUAUUAAAUCAAUCAGGUUAGUUAUAUUGAAGAGCCUUGAGCUAUGGCAGACAAUAUAAUGAACUACAAAUAAUAGCCCUAUAAACGUAGAUAUUGGUGUAUCGGGCGAUUUGGACAG,AF375571/1-307 AF375572/1-307 AF375573/1-307 AF375574/1-307,,0,0,AF375573.1/1-307
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100/sub;270;100 ,Rfam/cm/RF00023.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,24625,AF375574.1,1,sp|AF375574.1|AF375574 Leuconostoc mesenteroides subsp. dextranicum strain CNRZ77 tmRNA gene; partial sequence.,0,96,1,307,61.66,UCGUUUAGAGCAUUGAUUGCGUUUCGCCAUCCGGGCGCAAAACGGGCAGAAAUUUUAACUGCAAAAAACGAAAACUCUUUCGCUAUCGCUGCCUAAAAACCAGUGAUGCGUAGCUUAAUCUUGGUUGCUGGCGUCUGAGGUUAGGCCAUAAAAGGCCAGAUCGUACUGCUUCUUACAUCUGGAAAAGCAGUAUUAAAUCAAUCAGGUUAGUUAUAUUGAAGAGCCUUGAGCUAUGGCAGACAAUAUAAUGAACUACAAAUAAUAGCCCUAUAAACGUAGAUAUUGGUGUAUCGGGCGAUUUGGACAG,AF375571/1-307 AF375572/1-307 AF375573/1-307 AF375574/1-307,,0,0,AF375574.1/1-307
./cmzasha --no-stderr --filter 450 28.9 Rfam/cm/RF00023.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype0_Saureus_0MM.bin hmm data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;104;r-ACGU-_;103;l-ACGU-_;160;l-ACGU-_;159;l-ACGU-_;199;r-ACGU-_;198;l-ACGU-_;239;r-ACGU-_;238;l-ACGU-_;284;l-ACGU-_;283;r-ACGU-_;302;l-ACGU-_;299;r-AU-CG-_ 2struct-str data/TryAllCm_5.0/RF00023_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;189;100/sub;227;100 2struc