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 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,2252,AB033416.1,1,sp|AB033416.1|AB033416 Fusarium oxysporum sti35 gene for stress-responsive gene product; complete cds.,0,0,2117,2220,47.60,UCAGUUCAAACUGGUCGUGUUGAUGAUAGGGGGAUGUGGCUGAGAUUAUACGGCAAAACUUGAUCUGGAUAAUACCAGCGAAAGGAUCAUGUCAUCUCCCCUAU,AB033416.1/2117-2220,2117-2220,0,103,AB033416.1/2117-2220 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,17771,AF217503.1,1,sp|AF217503.1|AF217503 Aspergillus oryzae putative thiazole synthase (thiA) gene; complete cds.,0,1,595,688,26.28,ACAUGGCAUCGAUGGACUGGGUUCGUUCUGAGAUUAUACGGCUAAAACUUGAUCUGGAUAAUACCAGCGAAAAGGGUCAUGCCUUCUCUCGUUC,AF217503.1/595-688,595-688,0,93,AF217503.1/595-688 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,41166,AY007661.1,1,sp|AY007661.1|AY007661 Neurospora crassa thiamine biosynthesis protein NMT-1 (nmt-1) gene; complete cds.,0,2,633,726,41.37,GAUGGGCCAACUGCGGCGGUACCACGUUGGUCUGAGAAAUACCGGCGAACUUGAUCUGGAUAAUACCAGCGAAAGGAUUGGCUUCUUGGGACCC,AY007661.1/633-726,633-726,0,93,AY007661.1/633-726 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,61337,M33642.1,1,sp|M33642.1|FSSTI31X F.solani STI35 protein gene; complete cds.,0,3,428,524,46.70,GUGUACAUCAAUGUCAAGAAGAGGAGAGCGUGGCUGAGAUUAUACGGCGAAACUUGAUCUGGAUAAUACCAGCGAAAGGAUCAUGCUCUCCUCCCCC,M33642.1/428-524,428-524,0,96,M33642.1/428-524 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8695,AC005496.3,1,sp|AC005496.3|AC005496 Arabidopsis thaliana chromosome 2 clone T27A16 map mi54; complete sequence.,1,4,78594,78498,62.41,GCCUGCGAAAAGGCGGGCUAUCCGGGACCAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUGCAGUUUUUUUUUU,AC005496.3/78594-78498,78594-78498,0,96,AC005496.3/78594-78498 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9411,AC084406.7,1,sp|AC084406.7|AC084406 Oryza sativa chromosome 3 BAC OSJNBa0067E01 genomic sequence; complete sequence.,1,5,91393,91299,54.29,CCUCUUGGCCUGGAUUGUUGUGAAUUGGGCUGAGAAAGUCCCUUUGAACCUGAACAGGAUAAUGCCUGCGAAGGGAGUGUGCAUUUCUACUUUUA,AK068703.1/2124-2218 AC084406.7/91393-91299 AK065235.1/2130-2224,91393-91299,0,94,AC084406.7/91393-91299 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,35070,AF264021.1,1,sp|AF264021.1|AF264021 Poa secunda putative thiamine biosythesis protein ThiC mRNA; complete cds.,0,6,2254,2360,59.71,AACAAUCUGAAGGGCCCUUGGCCUGGAUUGUUGUGAUAUGGGCUGAGAAAGUCCCUUUGAACCUGAACAGGAUAAUGCCUGCGUAGGGAGUGUGCAUUUCUAUUUUG,AF264021.1/2254-2360,2254-2360,0,106,AF264021.1/2254-2360 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,74936,AK065235.1,1,sp|AK065235.1|AK065235 Oryza sativa (japonica cultivar-group) cDNA clone:J013002H20; full insert sequence.,0,7,2130,2224,54.29,CCUCUUGGCCUGGAUUGUUGUGAAUUGGGCUGAGAAAGUCCCUUUGAACCUGAACAGGAUAAUGCCUGCGAAGGGAGUGUGCAUUUCUACUUUUA,AK068703.1/2124-2218 AC084406.7/91393-91299 AK065235.1/2130-2224,2130-2224,0,94,AK065235.1/2130-2224 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,78403,AK068703.1,1,sp|AK068703.1|AK068703 Oryza sativa (japonica cultivar-group) cDNA clone:J013159A12; full insert sequence.,0,8,2124,2218,54.29,CCUCUUGGCCUGGAUUGUUGUGAAUUGGGCUGAGAAAGUCCCUUUGAACCUGAACAGGAUAAUGCCUGCGAAGGGAGUGUGCAUUUCUACUUUUA,AK068703.1/2124-2218 AC084406.7/91393-91299 AK065235.1/2130-2224,2124-2218,0,94,AK068703.1/2124-2218 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,178474,BT009095.1,1,sp|BT009095.1|BT009095 Triticum aestivum clone wkm2c.pk005.e4:fis; full insert mRNA sequence.,0,9,1820,1914,54.78,CCCCUUGGCCUGGAUUGUUGCGAUAUGGGCUGAGAAAGUCCCUUUGAACCUGAACAGGAUAAUGCCUGCGAAGGGAGUGUGCAUUUUUAUUUUCA,BT009095.1/1820-1914,1820-1914,0,94,BT009095.1/1820-1914 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,6576,AB042239.3,1,sp|AB042239.3|AB042239 Streptococcus criceti orf1; orf2; orf3; paaA; orf5; paaB; orf7 orf8; orf9; orf10 genes; complete cds.,1,10,9757,9659,51.26,AUUCCAUAACAUUGGAGUUUUGCGCAAAGUCUGGGUGUCUAAACUCUUUGAACCUGAACAAGGUAAUGCUUGCGUAAGGGAUGUGCAGAAAUAAGUGGA,AB042239.3/9757-9659,9757-9659,0,98,AB042239.3/9757-9659 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,12953,AB087258.1,1,sp|AB087258.1|AB087258 Haemophilus somnus ibpB; ibpA; tbpA genes for outer membrane transporter protein; high molecular weight-immunoglobulin binding proteins; hypothetical proteins; complete cds.,0,11,15478,15568,69.68,CCGACUUAGUCGGGGUGCUGAUAACAGCUGAGAUAAUACCCGUGAACCUGAUACAGUUAAUACUGACGUAGGAAACUAAUGGUCUUACUCC,AB087258.1/15478-15568,15478-15568,0,90,AB087258.1/15478-15568 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,16864,AE000633.1,1,sp|AE000633.1|AE000633 Helicobacter pylori 26695 section 111 of 134 of the complete genome.,0,12,3712,3819,64.68,AGCAUUUAAGGGGUGCUUUUUAAAACGCUCAAGUUUUUAAAAGGCUGAGAUCAAACCCGUAGAACUUGUCAAGGUAAUUCUUGCGUAAGGAAAUAGCAUGUUAAUAAC,AE000633.1/3712-3819,3712-3819,0,107,AE000633.1/3712-3819 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17682,AE001547.1,1,sp|AE001547.1|AE001547 Helicobacter pylori; strain J99 section 108 of 132 of the complete genome.,0,13,1336,1446,69.46,GGAGCAUUUAAGGGGUGCUUUUUAAAACGCUCAAGUUUUUAAAAGGCUGAGAUCAAACCCGUAGAACUUGUCAAGGUAAUUCUUGCGUAAGGAAUAACAUGUUAAUAACCA,AE001547.1/1336-1446,1336-1446,0,110,AE001547.1/1336-1446 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17878,AE001747.1,1,sp|AE001747.1|AE001747 Thermotoga maritima section 59 of 136 of the complete genome.,0,14,6884,6993,85.64,ACCUUCCCCAGGGGGAGCUCCUAUUCCGGGGCUGAGAGGAGGACGGAAGUCCUCGACCCCAAGAACCUGAUCCGGGUAAUGCCGGCGGAGGGAUCGGGGAAGGAGGAAAU,AE001747.1/6884-6993,6884-6993,0,109,AE001747.1/6884-6993 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17958,AE001862.1,1,sp|AE001862.1|AE001862 Deinococcus radiodurans R1 section 1 of 2 of the complete chromosome 2.,1,15,178389,178274,73.07,CAUCGUCAACAGGGGUGCCUCCGCAUAUGGGCCGGAGGCUGAGAGGGCAACUCGGGCCUAACCCUAUGAACCUGAACUGGUUAGCACCAGCGGAGGGAGUGUGACGGGCGCAGAGA,AE001862.1/178389-178274,178389-178274,0,115,AE001862.1/178389-178274 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17983,AE001887.1,1,sp|AE001887.1|AE001887 Deinococcus radiodurans R1 section 24 of 229 of the complete chromosome 1.,0,16,9104,9203,63.65,UCGCGUCACCGGGGGUGCCCUGCUUCGGCAGCGGCUGAGAACACACCCCAGGAACCUGAACCGGGUCAUUCCGGCGGAGGGAGUGUGAUGCUCUGCUCCG,AE001887.1/9104-9203,9104-9203,0,99,AE001887.1/9104-9203 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18623,AE002554.1,1,sp|AE002554.1|AE002554 Neisseria meningitidis serogroup B strain MC58 section 196 of 206 of the complete genome.,1,17,2672,2573,74.73,ACAUUGAAACAGGGGUGCUGCCUGAUGUUUAGGCGGCUGAGAAAUACCCUUUACACCCGAUCGGGAUAAUACCUGCGUGGGGAGUUUUCACGGAUUCUGC,AE002554.1/2672-2573,2672-2573,0,99,AE002554.1/2672-2573 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18625,AE002556.2,1,sp|AE002556.2|AE002556 Neisseria meningitidis serogroup B strain MC58 section 198 of 206 of the complete genome.,0,18,9004,9107,71.77,AGCUCCUUGUCGGAGUGCCGCCGCCGGGCGGCUGAGAUUGCGAAAGCAGAAUCCGUAGAACCUGUCGGGGUAAUGCCUGCGUAGGAAACAAACCGUCAAAUGCC,AE002556.2/9004-9107,9004-9107,0,103,AE002556.2/9004-9107 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18791,AE004009.1,1,sp|AE004009.1|AE004009 Xylella fastidiosa 9a5c; section 155 of 229 of the complete genome.,0,19,105,203,63.81,GCUUUGAAGCGGGGGUACCAUAGCCAAGCUGCGGUUGAGACACACCCUUCGAACCUGAUCCGGUUUACACCGGCGUAGGAAAGCUUCGUGGACCGCGCC,AE004009.1/105-203,105-203,0,98,AE004009.1/105-203 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18870,AE004097.1,1,sp|AE004097.1|AE004097 Vibrio cholerae chromosome I; section 5 of 251 of the complete chromosome.,0,20,4180,4278,82.58,UUCCACUUGUCGGAGUGCCAUUGGGCUGAGACCGUUUAUUCGGGAUCCGUUGAACCUGAUCAGGUUAAUACCUGCGAAGGGAACAAGAGAAGACUCUCU,AE004097.1/4180-4278,4180-4278,0,98,AE004097.1/4180-4278 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18982,AE004209.1,1,sp|AE004209.1|AE004209 Vibrio cholerae chromosome I; section 117 of 251 of the complete chromosome.,0,21,3590,3691,55.05,UUGGGUAUAACAACGUGCGAAUUAAAGGCUGAGAUCGCGUAGCGAGACCCGUUGAACCUGAUUCAGUUAGGACUGACGUAGGGAACUAUCCUCAACCGCUGG,AE004209.1/3590-3691,3590-3691,0,101,AE004209.1/3590-3691 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,19096,AE004323.1,1,sp|AE004323.1|AE004323 Vibrio cholerae chromosome I; section 231 of 251 of the complete chromosome.,1,22,4287,4150,38.06,AACCCACUCACGGGGGGCCACCCAUUCAUCCGAAUGGCGCUGAGAUCAAGCACUGCUUGGGACCCGCAAUGACUGCGAUGUUCGCGGUUGAACCUGAACCAGAUAAUGCUGGCGUAGGAAUUGAGCUAGGUUUGCAGA,AE004323.1/4287-4150,4287-4150,0,137,AE004323.1/4287-4150 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,19680,AE004910.1,1,sp|AE004910.1|AE004910 Pseudomonas aeruginosa PAO1; section 471 of 529 of the complete genome.,1,23,5287,5151,34.39,GGGUUCUUGUCGGGGUGCCCUAUACGAGGGGCUGAGAUCGGAUAGUUCCGGAUCCCGUUGAACCUGAUCGGGCUAGCGUCCGGUUCCGCCUCGCGCGGACCGCAGCAACCCGCGUAGGGAACAAGAUGUCCGCGCCA,AE004910.1/5287-5151,5287-5151,0,136,AE004910.1/5287-5151 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,19947,AE005183.1,1,sp|AE005183.1|AE005183 Escherichia coli O157:H7 EDL933 genome; contig 1 of 3; section 7 of 155.,1,24,12182,12083,74.38,CCGUUCUCAACGGGGUGCCACGCGGACGCGUGCGCUGAGAAAAUACCCGUCGAACCUGAUCCGGAUAACGCCGGCGAAGGGAUUUGAGGCUCCUUCUCAA,AE005183.1/12182-12083 AP002550.1/80429-80330,12182-12083,0,99,AE005183.1/12182-12083 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20200,AE005436.1,1,sp|AE005436.1|AE005436 Escherichia coli O157:H7 EDL933 genome; contig 3 of 3; section 55 of 290.,1,25,8098,8002,73.09,CCAAACGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCACGGACCACCAGG,AE005436.1/8098-8002 AE015232.1/7947-7851 AE016985.1/136499-136403 D90848.1/13353-13257 AE000299.1/8101-8005 AP002560.1/50173-50077,8098-8002,0,96,AE005436.1/8098-8002 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20395,AE005631.1,1,sp|AE005631.1|AE005631 Escherichia coli O157:H7 EDL933 genome; contig 3 of 3; section 250 of 290.,1,26,5793,5693,80.24,AAUUUCUUGUCGGAGUGCCUUAACUGGCUGAGACCGUUUAUUCGGGAUCCGCGGAACCUGAUCAGGCUAAUACCUGCGAAGGGAACAAGAGUUAAUCUGCU,M88701.1/79-179 AE016770.1/193697-193597 AP002567.1/237206-237106 AE015414.1/5697-5597 AE000473.1/6642-6542 U00006.1/61521-61421 AE016990.1/58866-58966 AE005631.1/5793-5693,5793-5693,0,100,AE005631.1/5793-5693 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20637,AE005876.1,1,sp|AE005876.1|AE005876 Caulobacter crescentus CB15 section 202 of 359 of the complete genome.,1,27,3727,3622,81.47,GUCUGUUCACCGGGGGGCCGCUCGCGCGGCUGAGAUUGGGCUCACGCCCUGACCCGUAGAACCUGAUCCGGGUCAUGCCGGCGAAGGGAGGGAACGCGGACGACAG,AE005876.1/3727-3622,3727-3622,0,105,AE005876.1/3727-3622 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20835,AE006074.1,1,sp|AE006074.1|AE006074 Pasteurella multocida PM70 section 41 of 204 of the complete genome.,0,28,48,140,71.36,GACUCUUAGUCGGGGUGCUAUUGCGUUAGCUGAGAUGAUACCCGUGAACCUGAUGCAGUUAAUACUGACGUAGGAAACUAGCAGUCAAUAUUG,AE006074.1/48-140,48-140,0,92,AE006074.1/48-140 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20926,AE006165.1,1,sp|AE006165.1|AE006165 Pasteurella multocida PM70 section 132 of 204 of the complete genome.,1,29,9171,9068,67.46,GCACUUUAGUCGGGGUGCUUUGUAACCAAAUUGUACAAAGCUGAGAUGAUACCCGUGAACCUGAUACAGCUAACACUGACGUAGGAAACUAAUUAUGCCAAUAA,AE006165.1/9171-9068,9171-9068,0,103,AE006165.1/9171-9068 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21028,AE006268.1,1,sp|AE006268.1|AE006268 Lactococcus lactis subsp. lactis IL1403 section 30 of 218 of the complete genome.,1,30,10610,10511,61.55,UAUUUGCACAAUGGGUCUAUUGACAAAACUGUCAGUAGCGAGAAAUACCAUCUGACCUGAUCUGGGUAAUGCCAGCGUAGGAAUGUGUUAAGACAAAUGU,AE006268.1/10610-10511,10610-10511,0,99,AE006268.1/10610-10511 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21118,AE006358.1,1,sp|AE006358.1|AE006358 Lactococcus lactis subsp. lactis IL1403 section 120 of 218 of the complete genome.,1,31,10289,10205,32.33,GGUAAAAACUAAAAUUACCGGUUGAGAAAGACCAUCAGACUUGAACAGGUUAAGACCUGCGUAAGAAUGUGUCCGAGUUUUAAUU,AE006358.1/10289-10205,10289-10205,0,84,AE006358.1/10289-10205 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21266,AE006515.1,1,sp|AE006515.1|AE006515 Streptococcus pyogenes M1 GAS strain SF370; section 44 of 167 of the complete genome.,1,32,5636,5540,69.07,UAUUUCACAAAGGAGUGCUUUGGCUGAGAUCGCAAUUGCGAAAUCCUGAGGACCUGAUCUUGUUAGUACAAGCGUAGGGAUUGUGACCAAUAAUCAA,AE010000.1/5636-5540 AP005145.1/186900-186996 AE006515.1/5636-5540 AE014145.1/5600-5504,5636-5540,0,96,AE006515.1/5636-5540 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21694,AE006947.1,1,sp|AE006947.1|AE006947 Mycobacterium tuberculosis CDC1551; section 33 of 280 of the complete genome.,0,33,1412,1522,66.66,CCCUGUAGACACGGGAGUCCCGGGAGCGGGGUCUGAGAGUGGGCGCGCCUGCCCUUACCGUCACACCUGAUCCGGAUCAUGCCGGCGAAGGGAGGUCAAGGAUGGCGUCCG,BX248335.1/159066-159176 AE006947.1/1412-1522 Z84724.1/10325-10435,10691-10581 1412-1522,0,110,AE006947.1/1412-1522 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21694,AE006947.1,1,sp|AE006947.1|AE006947 Mycobacterium tuberculosis CDC1551; section 33 of 280 of the complete genome.,1,34,10691,10581,69.28,GGGUACCCACGCGGGAGCGCACGCCGAGUGCGCUGAGAGGACGGCUCGGGGCCGUCGACCGUACGAACCUGACCGGGUAAUGCCGGCGUAGGGAGUUGCAAAUGACCAUCA,AE006947.1/10691-10581 Z84724.1/19604-19494 BX248335.1/168345-168235,10691-10581 1412-1522,0,110,AE006947.1/10691-10581 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22125,AE007380.1,1,sp|AE007380.1|AE007380 Streptococcus pneumoniae TIGR4 section 63 of 194 of the complete genome.,0,35,3446,3534,75.18,UAGAGACAUUUGGGGUGCUUUAGGCUGAGAUAAUACCCAUUGAACCUGAUACAGUUAAGACUGGCGAAGGGAAAUGUGAACAGUUUUUU,AE007380.1/3446-3534,3446-3534 6276-6364,0,88,AE007380.1/3446-3534 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22125,AE007380.1,1,sp|AE007380.1|AE007380 Streptococcus pneumoniae TIGR4 section 63 of 194 of the complete genome.,0,36,6276,6364,75.47,UAAAGACAUUUGGGGUGCUUUAGGCUGAGAUGAUACCCAUUGAACCUGAUACAGUUAAGACUGGCGAAGGGAAAUGUGAAAUGUUUUUU,AE007380.1/6276-6364 AE008441.1/6797-6885,3446-3534 6276-6364,0,88,AE007380.1/6276-6364 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22126,AE007381.1,1,sp|AE007381.1|AE007381 Streptococcus pneumoniae TIGR4 section 64 of 194 of the complete genome.,1,37,1109,1011,47.04,AACAACCACUAGGGGUGCGUAAAGCUGAGAUUAACGACUGUUAGAUCCCUCUGACUCAAUCUAGGUAAUGCUAGCUGAUGGAAGUGGAAAUGAUAAUGG,**** NEW HIT #0 ****,,2,0,AE007381.1/1109-1011 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22253,AE007508.1,1,sp|AE007508.1|AE007508 Streptococcus pneumoniae TIGR4 section 191 of 194 of the complete genome.,1,38,3048,2945,64.76,CAUAUAAUAUAUGGGAGUCUGUGUACAGUCUGAGAGGAAGUGUUAAACUUCGACCGCACCUGAUCUGGGUAAUGCCAGCGGAGGGAACGAUACUUAGUCUAAUU,AE007508.1/3048-2945,3048-2945,0,103,AE007508.1/3048-2945 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22395,AE007651.1,1,sp|AE007651.1|AE007651 Clostridium acetobutylicum ATCC824 section 139 of 356 of the complete genome.,0,39,7649,7751,74.90,UUUUAGUGCUAGGGGUGCCUUUUGGCUGAGAGAAGUUAAAAAACUUUAACCCUUUGAACCUGAUUCGGUUAAUUCUGACGAAGGAAAGCUUUUUAAAUGAUUA,AE007651.1/7649-7751,7649-7751,0,102,AE007651.1/7649-7751 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22533,AE007789.1,1,sp|AE007789.1|AE007789 Clostridium acetobutylicum ATCC824 section 277 of 356 of the complete genome.,0,40,11572,11662,62.73,UAUAUGUGCUAGGGGUGCCUUUAGGCUGAGAAACAGUUUGUCACGUUAACCCUUAACCUGAUCUGGAUAAUACCAGCGUAGGGAAGCAGUU,AE007789.1/11572-11662,9122-9015 11572-11662,0,90,AE007789.1/11572-11662 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22533,AE007789.1,1,sp|AE007789.1|AE007789 Clostridium acetobutylicum ATCC824 section 277 of 356 of the complete genome.,1,41,9122,9015,88.52,AUAUAGUUAACGGGGAGCCUGUAGACAGGCUGAGAGUGGAAUGUGAUUCCAGACCCUCAUAACCUGAUUUGGAUAAUGCCAACGUAGGGAGUUAAUGCAUCAUGUUUG,AE007789.1/9122-9015,9122-9015 11572-11662,0,107,AE007789.1/9122-9015 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22542,AE007798.1,1,sp|AE007798.1|AE007798 Clostridium acetobutylicum ATCC824 section 286 of 356 of the complete genome.,1,42,8173,8025,50.04,UAUUUUAGCUAGGGGUGCCUUUUAAGGCUUUUAUAGUUGAUAUCAUUAAAAAUAUUUAACUAAUAAAAGACUUUAGGCUGAGAGGAGAAAUCCAACCCUUUGAACUUGAUGUAGUUAAUACUACCGUAGGGAAGCAGUGCAUUGUAUAU,AE007798.1/8173-8025,8173-8025,0,148,AE007798.1/8173-8025 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22550,AE007806.1,1,sp|AE007806.1|AE007806 Clostridium acetobutylicum ATCC824 section 294 of 356 of the complete genome.,1,43,8808,8702,68.28,AAUAUUUUUCAGGGGAGCUUGUUUUCAGGCUGAGAGGAAGUAAUUGAACUUCGAUCCAUAUACCUGAUUUGGAUAAUGCCAACGUAGGAAAUAGGUUACUUGAUUUA,AE007806.1/8808-8702,8808-8702,0,106,AE007806.1/8808-8702 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22909,AE008169.1,1,sp|AE008169.1|AE008169 Agrobacterium tumefaciens str. C58 circular chromosome; section 227 of 254 of the complete sequence.,1,44,8240,8129,83.74,GCCAUUCACCAGGGGUGUCCCGUCAAGGGGCUGAGAUUCUGCUUUCAUGCGCAGUGACCCGUUGAACCUGAUCCAGUUCAUACUGGCGUAGGGACGGUGCAAAGACCUGAUG,AE009203.1/4053-3942 AE008169.1/8240-8129,8240-8129,0,111,AE008169.1/8240-8129 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22924,AE008184.1,1,sp|AE008184.1|AE008184 Agrobacterium tumefaciens str. C58 circular chromosome; section 242 of 254 of the complete sequence.,1,45,8540,8430,76.44,CUUGAUCUAACGGGGUGUCUUCUGUGCUUUUGUGCAGAAGGCUGAGAGGCUUGCCAACCCGAAGAACCUGAUCCGGUUCAUACCGGCGGAGGGAUUAGACGGCUUAAAGGC,AE009217.1/9644-9534 AE008184.1/8540-8430,8540-8430,0,110,AE008184.1/8540-8430 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23094,AE008354.1,1,sp|AE008354.1|AE008354 Agrobacterium tumefaciens str. C58 linear chromosome; section 158 of 187 of the complete sequence.,1,46,8291,8189,69.45,AGCUCUUCCGAGGGGAGCACCAGACGGUGCUGAGAUGGUGGUGAACCGGACCCUUGAACCUGAUCCGGGUCAUGCCGGCGUAGGAACGGAACUGUCGUGCGCU,AE008354.1/8291-8189 AE009258.1/7675-7777,8291-8189,0,102,AE008354.1/8291-8189 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23180,AE008441.1,1,sp|AE008441.1|AE008441 Streptococcus pneumoniae R6 section 57 of 184 of the complete genome.,0,47,3915,4003,72.18,UAGAGACAUUUGGGGUGCUUUAAGCUGAGAUGAUACCCAUUGAACCUGAUACAGUUAAGACUGGCGAAGGGAAAUGUGAAACGUUUUUU,AE008441.1/3915-4003,6797-6885 3915-4003,0,88,AE008441.1/3915-4003 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23180,AE008441.1,1,sp|AE008441.1|AE008441 Streptococcus pneumoniae R6 section 57 of 184 of the complete genome.,0,48,6797,6885,75.47,UAAAGACAUUUGGGGUGCUUUAGGCUGAGAUGAUACCCAUUGAACCUGAUACAGUUAAGACUGGCGAAGGGAAAUGUGAAAUGUUUUUU,AE007380.1/6276-6364 AE008441.1/6797-6885,6797-6885 3915-4003,0,88,AE008441.1/6797-6885 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23180,AE008441.1,1,sp|AE008441.1|AE008441 Streptococcus pneumoniae R6 section 57 of 184 of the complete genome.,1,49,13586,13488,47.04,AACAACCACUAGGGGUGCGUAAAGCUGAGAUUAACGACUGUUAGAUCCCUCUGACUCAAUCUAGGUAAUGCUAGCUGAUGGAAGUGGAAAUGAUAAUGG,**** NEW HIT (duplicate of new hit #0) ****,6797-6885 3915-4003,2,0,AE008441.1/13586-13488 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23303,AE008564.1,1,sp|AE008564.1|AE008564 Streptococcus pneumoniae R6 section 180 of 184 of the complete genome.,1,50,13544,13464,24.92,UACAGUCUGAGAGGAAGUGUUAAACUUCGACCGCACCUGAUCUGGGUAAUGCCAGCGGAGGGAACGAUACUUAGUCUAAUU,AE008564.1/13544-13464,13544-13464,0,80,AE008564.1/13544-13464 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23427,AE008698.1,1,sp|AE008698.1|AE008698 Salmonella typhimurium LT2; section 6 of 220 of the complete genome.,1,51,18540,18441,76.13,CCGAACUCAACGGGGUGCCGCGCUCAUGCGCGCGCUGAGAAAAUACCCGUCGAACCUGAUCCGGAUAAUGCCGGCGAAGGGAUUUGAGGCUACCUCUCAA,AE008698.1/18540-18441 AE016834.1/128207-128108 AL627265.1/128216-128117,18540-18441,0,99,AE008698.1/18540-18441 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23520,AE008795.1,1,sp|AE008795.1|AE008795 Salmonella typhimurium LT2; section 99 of 220 of the complete genome.,1,52,16610,16514,68.24,CUUGACGACUCGGGGUGCCCUUCUUUGUGAAGGCUGAGAAAUACCCGUACCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCUGACACUGCUCGU,AE016836.1/195900-195996 AE008795.1/16610-16514 U87940.1/125-221 AL627273.1/156556-156460,16610-16514,0,96,AE008795.1/16610-16514 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23619,AE008894.1,1,sp|AE008894.1|AE008894 Salmonella typhimurium LT2; section 198 of 220 of the complete genome.,1,53,19601,19483,61.11,ACGAAGCCAACGAAGAGGCAGCGCGAAGGAUGAAGUGGAAAAGGCUGAGACCGUUAAUUCGGGAUCCGCGGAACCUGAUCAGGUUAAUACCUGCGAAGGGAACAAGAGUAAUUCUGCUU,AE008894.1/19601-19483 AE016845.1/248940-249058 AF170176.1/27307-27189 AL627279.1/105944-106062,19601-19483,0,118,AE008894.1/19601-19483 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23924,AE009203.1,1,sp|AE009203.1|AE009203 Agrobacterium tumefaciens strain C58 circular chromosome; section 229 of 256 of the complete sequence.,1,54,4053,3942,83.74,GCCAUUCACCAGGGGUGUCCCGUCAAGGGGCUGAGAUUCUGCUUUCAUGCGCAGUGACCCGUUGAACCUGAUCCAGUUCAUACUGGCGUAGGGACGGUGCAAAGACCUGAUG,AE009203.1/4053-3942 AE008169.1/8240-8129,4053-3942,0,111,AE009203.1/4053-3942 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23938,AE009217.1,1,sp|AE009217.1|AE009217 Agrobacterium tumefaciens strain C58 circular chromosome; section 243 of 256 of the complete sequence.,1,55,9644,9534,76.44,CUUGAUCUAACGGGGUGUCUUCUGUGCUUUUGUGCAGAAGGCUGAGAGGCUUGCCAACCCGAAGAACCUGAUCCGGUUCAUACCGGCGGAGGGAUUAGACGGCUUAAAGGC,AE009217.1/9644-9534 AE008184.1/8540-8430,9644-9534,0,110,AE009217.1/9644-9534 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,23979,AE009258.1,1,sp|AE009258.1|AE009258 Agrobacterium tumefaciens str. C58 linear chromosome; section 28 of 187 of the complete sequence.,0,56,7675,7777,69.45,AGCUCUUCCGAGGGGAGCACCAGACGGUGCUGAGAUGGUGGUGAACCGGACCCUUGAACCUGAUCCGGGUCAUGCCGGCGUAGGAACGGAACUGUCGUGCGCU,AE008354.1/8291-8189 AE009258.1/7675-7777,7675-7777,0,102,AE009258.1/7675-7777 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,24188,AE009471.1,1,sp|AE009471.1|AE009471 Brucella melitensis 16M chromosome I; section 28 of 195 of the complete sequence.,1,57,6144,5974,24.77,GUCGCUCUAACGGGGUGCCAUCUGCUUUUGGGGAUGGCUGAGAGGCCAAACAAGGCAUUUCCAGCAAAAGCGUGAAACGGUUUUGCAUCAGGAAAUACUUGAAAACUGCCCGGCCAACCCGCUGAACCUGAUCCGGUUUGCACCGGCGGAGGGAUUAGACGCUCGAUGAAC,AE009471.1/6144-5974,6144-5974,0,170,AE009471.1/6144-5974 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,24324,AE009607.1,1,sp|AE009607.1|AE009607 Brucella melitensis 16M chromosome I; section 164 of 195 of the complete sequence.,0,58,63,169,76.26,CAAAAUUCGUUGGGGUGCCUUGAAAGAGGCUGAGAGACGCAUUCUCACGUCAACCCAUUGAACCUGAUCCGGGUAAUACCUGCGUAGGGAACGGAGUUUGGCGCGUC,AE009607.1/63-169,63-169,0,106,AE009607.1/63-169 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,24711,AE010000.1,1,sp|AE010000.1|AE010000 Streptococcus pyogenes strain MGAS8232; section 48 of 173 of the complete genome.,1,59,5636,5540,69.07,UAUUUCACAAAGGAGUGCUUUGGCUGAGAUCGCAAUUGCGAAAUCCUGAGGACCUGAUCUUGUUAGUACAAGCGUAGGGAUUGUGACCAAUAAUCAA,AE010000.1/5636-5540 AP005145.1/186900-186996 AE006515.1/5636-5540 AE014145.1/5600-5504,5636-5540,0,96,AE010000.1/5636-5540 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25187,AE010479.1,1,sp|AE010479.1|AE010479 Fusobacterium nucleatum subsp. nucleatum ATCC 25586; section 21 of 197 of the complete genome.,1,60,12991,12886,77.20,AACUAGUUACAAGGGAGUUAAUAAAUUGACUGAGAAAAGGAUGUGAGCCUUGACCUUUUGACCUGAUUUGGAUAAUGCCAACGUAGGAAGUAAAAGAGUUUAUUUU,AE010479.1/12991-12886,12991-12886,0,105,AE010479.1/12991-12886 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25244,AE010536.1,1,sp|AE010536.1|AE010536 Fusobacterium nucleatum subsp. nucleatum ATCC 25586; section 78 of 197 of the complete genome.,1,61,2776,2673,73.79,AUAUAUGUACUGGGGAGCUUUGUGCUGAGAUUAGAACCUUUUUUCUUAGACCCAUAGUACCUGAUUUGGAUAAUGCCAACGAAGGGAGUACCAUCUUAAUAAUA,AE010536.1/2776-2673,2776-2673,0,103,AE010536.1/2776-2673 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25990,AE011282.1,1,sp|AE011282.1|AE011282 Leptospira interrogans serovar lai str. 56601 chromosome I; section 91 of 397 of the complete sequence.,1,62,7576,7478,45.03,CUUGGACGUUGGGGGUGGGAUUCACUGCGUGAAUCUCUGAGAGAGUCCCCGGAACCUGAUCAGGAUAAGACCUGCGUAGGAAAACGGACCUGUAAAAUU,AE011282.1/7576-7478,7576-7478,0,98,AE011282.1/7576-7478 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,26699,AE011991.1,1,sp|AE011991.1|AE011991 Xanthomonas axonopodis pv. citri str. 306; section 369 of 469 of the complete genome.,1,63,4930,4833,66.87,CCGCCGAAGUGGGGGUACCGCAGCGUGCUGCGGUUGAGAUAGUCCCUUCGAACCUGAUCCGGCUGAUACCGGCGUAGGGAAGCUUCGUCAGAUGCGAU,AE011991.1/4930-4833,4930-4833,0,97,AE011991.1/4930-4833 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27156,AE012449.1,1,sp|AE012449.1|AE012449 Xanthomonas campestris pv. campestris str. ATCC 33913; section 357 of 460 of the complete genome.,1,64,4930,4832,69.45,CCGCCGAAGUGGGGGUACCACAGCACUGCUGCGGUUGAGAUAGUCCCUUCGAACCUGAUCCGGCUCAUACCGGCGUAGGGAAGCUUCGUUAGAUGCGCU,AE012449.1/4930-4832,4930-4832,0,98,AE012449.1/4930-4832 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27263,AE012556.1,1,sp|AE012556.1|AE012556 Xylella fastidiosa Temecula1; section 4 of 9 of the complete genome.,1,65,212138,212040,65.95,ACUUUGAAGCGGGGGUACCGUAGCCAAGCUGCGGUUGAGACACACCCUUCGAACCUGAUCCGGUUUACACCGGCGUAGGAAAGCUUCGUGGACCGCGCC,AE012556.1/212138-212040,212138-212040,0,98,AE012556.1/212138-212040 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27390,AE012901.1,1,sp|AE012901.1|AE012901 Chlorobium tepidum TLS section 122 of 194 of the complete genome.,0,66,6754,6860,63.94,AAAUCAUCUUGGGGGUGCUUCGCCAUGUUCCAUGAACCGAAGCUGAGAUCACACCCCUAUAACUUGAUGCAGGUAAUGCUGACGCAAGGAAAGAUGAAGCACGCAUC,AE012901.1/6754-6860,6754-6860,0,106,AE012901.1/6754-6860 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27601,AE013112.1,1,sp|AE013112.1|AE013112 Thermoanaerobacter tengcongensis strain MB4T; section 139 of 244 of the complete genome.,1,67,9358,9256,82.21,CUCAAGUGCUAGGGGAGCCAAAAAUGGCUGAGAGGGGAUUCGUUCCCGACCCUUAGAACCUGACCAGGGUAAUGCCUGCGAAGGGAAGCACGUUUUACGAAAU,AE013112.1/9358-9256,9358-9256,0,102,AE013112.1/9358-9256 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27616,AE013127.1,1,sp|AE013127.1|AE013127 Thermoanaerobacter tengcongensis strain MB4T; section 154 of 244 of the complete genome.,1,68,3291,3189,80.02,CUCAAGUGCUAGGGGAGCCAGAAAUGGCUGAGAGGGGAUUCGUUCCCGACCCUUAGAACCUGACCAGGGUAAUGCCUGCGAAGGGAAGCACGUUUUAUUGAGU,AE013127.1/3291-3189,3291-3189,0,102,AE013127.1/3291-3189 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27656,AE013167.1,1,sp|AE013167.1|AE013167 Thermoanaerobacter tengcongensis strain MB4T; section 194 of 244 of the complete genome.,1,69,14408,14306,81.34,UCAAAGUGCUAGGGGAGCCAGAAAUGGCUGAGAGGGGAUUCGUUCCCGACCCUUAGAACCUGACCAGGGUAAUGCCUGCGAAGGGAAGCACGUUUUACGGAAU,AE013167.1/14408-14306,14408-14306,0,102,AE013167.1/14408-14306 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27681,AE013192.1,1,sp|AE013192.1|AE013192 Thermoanaerobacter tengcongensis strain MB4T; section 219 of 244 of the complete genome.,1,70,4947,4844,75.11,UAUGUCCGCUGGGGGAGCCUGAAAAGGCUGAGACGGCAGAAAUGCCGAACCCUUGGAACCUGAUGAGGGUAAUGCCUCCGUAGGGAAUGCGGGCUCAAAAGGCA,AE013192.1/4947-4844,4947-4844,0,103,AE013192.1/4947-4844 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28135,AE013650.1,1,sp|AE013650.1|AE013650 Yersinia pestis KIM section 50 of 415 of the complete genome.,1,71,6078,5953,69.06,AGGCUCUUGUCGGAGUGCCUAGCACCUGCUUUUUUAGGAAAGCAAACGCAGGCUGAGACCGUUAAUUCGGGAUCCGCGGAACCUGAUCGGGUUAAUACCCGCGAAGGGAACAAGAGUAAUUUAUCG,AJ414158.1/174343-174468 AE013650.1/6078-5953,6078-5953,0,125,AE013650.1/6078-5953 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28224,AE013739.1,1,sp|AE013739.1|AE013739 Yersinia pestis KIM section 139 of 415 of the complete genome.,0,72,9688,9792,70.05,CAUUCUGACUCGGGGUGCCUGCCACAAUGCGGUGGUAAGGCUGAGAGAUGACCCGUAUUACCUGAUCUGGAUUAUGCCAGCGUAGGGAAGUCUCGGCACCGUAGG,AJ414154.1/26151-26047 AE013739.1/9688-9792,9688-9792,0,104,AE013739.1/9688-9792 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28453,AE013968.1,1,sp|AE013968.1|AE013968 Yersinia pestis KIM section 368 of 415 of the complete genome.,0,73,546,638,53.79,ACCACCUAACCGCCGCAAUUUUUUUCGCUGAGAGUAAACCCGUCGAACCUGAUCCGGUUAACCCCGGCGGAGGGAUUUGAGAAUGAUAACGAC,AE013968.1/546-638 AJ414143.1/65152-65060,546-638,0,92,AE013968.1/546-638 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28569,AE014145.1,1,sp|AE014145.1|AE014145 Streptococcus pyogenes MGAS315; section 10 of 37 of the complete genome.,1,74,5600,5504,69.07,UAUUUCACAAAGGAGUGCUUUGGCUGAGAUCGCAAUUGCGAAAUCCUGAGGACCUGAUCUUGUUAGUACAAGCGUAGGGAUUGUGACCAAUAAUCAA,AE010000.1/5636-5540 AP005145.1/186900-186996 AE006515.1/5636-5540 AE014145.1/5600-5504,5600-5504,0,96,AE014145.1/5600-5504 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28635,AE014229.1,1,sp|AE014229.1|AE014229 Streptococcus agalactiae 2603V/R section 39 of 100 of the complete genome.,1,75,2499,2401,62.84,AAAUACACAAGGGAGUGCCUUGAGCUGAGAUUGCAGAUAUGCAAAAUCCUCUAACCUGAUCUCGUUAGGACGAGCGUAGGAAUUGUGGUUUGAAUUGGU,AL766847.1/75304-75206 AE014229.1/2499-2401,2499-2401,0,98,AE014229.1/2499-2401 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28636,AE014230.1,1,sp|AE014230.1|AE014230 Streptococcus agalactiae 2603V/R section 40 of 100 of the complete genome.,0,76,102,191,59.05,AUAGGACAUUUGGGGUGCGUAACAGCUGAGAUUAUACCCAUUGAACUUGAUGCAGUUAGUACUGUCGAAGGGAAAUGUGUGCCAUUACAA,AE014230.1/102-191,102-191,0,89,AE014230.1/102-191 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28716,AE014334.1,1,sp|AE014334.1|AE014334 Brucella suis 1330 chromosome I section 20 of 190 of the complete genome.,1,77,9887,9781,77.10,CAAAAUUCGUUGGGGUGCCUUGAAAGAGGCUGAGAGACGCAUUCUCGCGUCAACCCAUUGAACCUGAUCCGGGUAAUACCUGCGUAGGGAACGGAGUUUGGCGCGUC,AE014334.1/9887-9781,9887-9781,0,106,AE014334.1/9887-9781 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,28849,AE014467.1,1,sp|AE014467.1|AE014467 Brucella suis 1330 chromosome I section 153 of 190 of the complete genome.,0,78,32,135,23.30,AAGCGUGAAACGGUUUUGCAUCAGGAAAUACUUGAAAACUGCCCGGCCAACCCGCUGAACCUGAUCCGGUUUGCACCGGCGGAGGGAUUAGACGCUCGAUGAAC,AE014467.1/32-135,32-135,0,103,AE014467.1/32-135 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29007,AE014626.1,1,sp|AE014626.1|AE014626 Bifidobacterium longum NCC2705 section 13 of 202 of the complete genome.,1,79,5916,5808,49.95,ACUGUAAUGCAGGGGAACUCGCAUGUGGUUCGCGAGUUGAGAAAGGCCUGAGCCUGACCCUUAGAACCUGUUGGUUAAGACCAUCGUAGGGAGCAGUAAAUGAGCAAUA,AE014626.1/5916-5808,5916-5808,0,108,AE014626.1/5916-5808 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29052,AE014671.1,1,sp|AE014671.1|AE014671 Bifidobacterium longum NCC2705 section 58 of 202 of the complete genome.,1,80,10278,10182,62.07,CCGAUUCGUAAGGGGUGCUUUAGGCUGAGACGGUAUGUGCCGAACCCUUCGAACCUGUGAGCUAACACUCGCGUAGGGAAUGCGACGGUUGAACUCC,AE014671.1/10278-10182,10278-10182,0,96,AE014671.1/10278-10182 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29110,AE014729.1,1,sp|AE014729.1|AE014729 Bifidobacterium longum NCC2705 section 116 of 202 of the complete genome.,1,81,1422,1319,56.56,ACCGUAACGAACGGGAGCCGUGAGGCUGAGAGGAAGUCGCCAGACUUCGACCGGGGAACUUGACGCGGGUCAUGCCGCCGUAAGGAAUCGUUGUCGCAGAUUUG,**** NEW HIT #2 ****,,2,0,AE014729.1/1422-1319 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29111,AE014730.1,1,sp|AE014730.1|AE014730 Bifidobacterium longum NCC2705 section 117 of 202 of the complete genome.,1,82,8718,8610,57.02,GGAGUUGACACGGGAGCUGCCGUUGGGCGGCUGAGAGGAGACUCAUAGUCUCGACCGAUGGAACGUGACCGGAUAAUGCCGGCGCACGGAAAUGUCGCUCUUACCUACC,AE014730.1/8718-8610,8718-8610,0,108,AE014730.1/8718-8610 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29257,AE014913.1,1,sp|AE014913.1|AE014913 Streptococcus mutans UA159 section 61 of 185 of the complete genome.,1,83,8949,8849,78.06,AAAUAUCACAAGGAGUGCUAACCUUAGCUGAGAUUGCAUUUGCAAAAUCCUAUGGACCUGAUCUAGUUAAUACUAGCGUGGGAAUGUGAUUCGUUUCAUGA,AE014913.1/8949-8849,8949-8849,0,100,AE014913.1/8949-8849 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29388,AE015044.1,1,sp|AE015044.1|AE015044 Shigella flexneri 2a str. 301 section 7 of 412 of the complete genome.,1,84,92,1,59.33,CCGUUCUCAACGGGGUGCCACGCAAACGCGUGCGCUGAGAAAAUACCCGUCGAACCUGAUCCGGAUAACGCCGGCGAAGGGAUUUGAGGCUC,AE015044.1/92-1,92-1,0,91,AE015044.1/92-1 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29576,AE015232.1,1,sp|AE015232.1|AE015232 Shigella flexneri 2a str. 301 section 195 of 412 of the complete genome.,1,85,7947,7851,73.09,CCAAACGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCACGGACCACCAGG,AE005436.1/8098-8002 AE015232.1/7947-7851 AE016985.1/136499-136403 D90848.1/13353-13257 AE000299.1/8101-8005 AP002560.1/50173-50077,7947-7851,0,96,AE015232.1/7947-7851 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29758,AE015414.1,1,sp|AE015414.1|AE015414 Shigella flexneri 2a str. 301 section 377 of 412 of the complete genome.,1,86,5697,5597,80.24,AAUUUCUUGUCGGAGUGCCUUAACUGGCUGAGACCGUUUAUUCGGGAUCCGCGGAACCUGAUCAGGCUAAUACCUGCGAAGGGAACAAGAGUUAAUCUGCU,M88701.1/79-179 AE016770.1/193697-193597 AP002567.1/237206-237106 AE015414.1/5697-5597 AE000473.1/6642-6542 U00006.1/61521-61421 AE016990.1/58866-58966 AE005631.1/5793-5693,5697-5597,0,100,AE015414.1/5697-5597 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30027,AE015685.1,1,sp|AE015685.1|AE015685 Shewanella oneidensis MR-1 section 234 of 457 of the complete genome.,1,87,10697,10614,35.83,UGCCUUUUGGCUGAGACCGUUUAUUCGGGAUCCGUUGAACCUGAUCAGGUUAAAACCUGCGAAGGAAACAAGCAUAAUAACUUC,AE015685.1/10697-10614,10697-10614,0,83,AE015685.1/10697-10614 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30052,AE015710.1,1,sp|AE015710.1|AE015710 Shewanella oneidensis MR-1 section 259 of 457 of the complete genome.,1,88,12073,11979,54.37,UGUUUGCCAAAAUUCGGCAGACUGAGAUGUCAUCAGACGAACCCUUAGAACCUGAUCCGGCUAAUACCGGCGUAGGAAUGGGCCAAUCAACAGCA,AE015710.1/12073-11979,12073-11979,0,94,AE015710.1/12073-11979 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30273,AE015936.1,1,sp|AE015936.1|AE015936 Clostridium tetani E88; section 1 of 10 of the complete genome.,1,89,222874,222760,61.69,AUGUAGUGCUAGGGGUGCUAUAUAAGAGCUGAGAAAUGAAUUAUUUAUGAUCAAUUCAUUAACCCUUGUACCUGAACUAGAUAAUUCUAGCGUAGGGAAGCCUUUUAUAGAUAUA,AE015936.1/222874-222760,222874-222760,0,114,AE015936.1/222874-222760 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30275,AE015938.1,1,sp|AE015938.1|AE015938 Clostridium tetani E88; section 3 of 10 of the complete genome.,0,90,273488,273596,78.03,AAAUAAAUUUAGGGGAGCUUAUAAAAAUAGGCUGAGAAAGAGAUGUUAUCUCUGACCCUCAUAACCUGAUUUGGCUAAUACCAACGUAGGGAACAUUGUGUAUUGUAGU,AE015938.1/273488-273596,273488-273596,0,108,AE015938.1/273488-273596 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30279,AE015942.1,1,sp|AE015942.1|AE015942 Clostridium tetani E88; section 7 of 10 of the complete genome.,1,91,58651,58542,69.93,AUAAAGUUUCAGGGGAGCUGGUUUAUGUCAGCUGAGAGUAAGAACUAAAUUCUUAGACCCUUUAACCUGAUCUGGAUAAUGCCAGCGUAGGGAGAUGGUUUACUAUAUAA,AE015942.1/58651-58542,58651-58542,0,109,AE015942.1/58651-58542 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30283,AE016744.1,1,sp|AE016744.1|AE016744 Staphylococcus epidermidis ATCC 12228; section 1 of 9 of the complete genome.,1,92,250277,250176,59.02,UAGUAUCACUAGGGGUGCAAUUCAAUUUGCUGAGAGAAAGUCUACUUUCAACCCUUGAACCUGUUGGUUAGCACCGGCGUAGGAAAGUGAGCAAUAUUGAUA,AE016744.1/250277-250176,250277-250176,0,101,AE016744.1/250277-250176 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.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.,1,93,27312,27213,72.33,UAUAUGCACUAGGGGUGUUUUUUAACUGAGAUGGAUAUCAUCCAAACCCUUUGAACCUGAACUAGCUUAUACUAGCGGAGGAAAGUGUUGAAUCUCAUCU,AE016745.1/27312-27213,27312-27213,0,99,AE016745.1/27312-27213 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30285,AE016746.1,1,sp|AE016746.1|AE016746 Staphylococcus epidermidis ATCC 12228; section 3 of 9 of the complete genome.,1,94,165122,165020,68.64,UGAACGCACUAGGGGUGUAUUCUUUACUGAGAUGAGGCCAACCUCAAACCCUUCGAACCUGAUCUAGCUAGUUACUAGCGUAGGAAAGUGUUGUUAUACAUCU,AE016746.1/165122-165020,165122-165020,0,102,AE016746.1/165122-165020 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30288,AE016749.1,1,sp|AE016749.1|AE016749 Staphylococcus epidermidis ATCC 12228; section 6 of 9 of the complete genome.,1,95,244290,244192,83.16,AUUUGCUACUAGGGGAGCCAAAAGGCUGAGAUGAAUGUAUUCAGACCCUUAUAACCUGAUUUGGUUAAUACCAACGUAGGAAAGUAGUUAUUAACUAUU,AF269819.1/1816-1718 AE016749.1/244290-244192,244290-244192,0,98,AE016749.1/244290-244192 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30289,AE016750.1,1,sp|AE016750.1|AE016750 Staphylococcus epidermidis ATCC 12228; section 7 of 9 of the complete genome.,0,96,293855,293964,73.32,UUUAACCACUGGAAGUGCCUUUGUUUAAGGCUGAGAGUAAAGAACUGACUUUAUAAUUCCUGGAACCUGAUCCAGUUCAUACUGGCGUAGGGAAGUGGCGACGCUCAAUU,AE016750.1/293855-293964,293855-293964,0,109,AE016750.1/293855-293964 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30292,AE016755.1,1,sp|AE016755.1|AE016755 Escherichia coli CFT073 section 1 of 18 of the complete genome.,1,97,79951,79852,72.38,CCGUUCUCAACGGGGUGCCACGCAGCCGCGUGCGCUGAGAAAAUACCCGUCGAACCUGAUCCGGAUAACGCCGGCGAAGGGAUUUGAGGCUCCUUCUCAA,AE016755.1/79951-79852,79951-79852,0,99,AE016755.1/79951-79852 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30300,AE016763.1,1,sp|AE016763.1|AE016763 Escherichia coli CFT073 section 9 of 18 of the complete genome.,1,98,55154,55058,72.37,CCAAACGACUCGGGGUGCCCUUCUUUGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCACGGACCACCAGG,AE016763.1/55154-55058,55154-55058,0,96,AE016763.1/55154-55058 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30307,AE016770.1,1,sp|AE016770.1|AE016770 Escherichia coli CFT073 section 16 of 18 of the complete genome.,1,99,193697,193597,80.24,AAUUUCUUGUCGGAGUGCCUUAACUGGCUGAGACCGUUUAUUCGGGAUCCGCGGAACCUGAUCAGGCUAAUACCUGCGAAGGGAACAAGAGUUAAUCUGCU,M88701.1/79-179 AE016770.1/193697-193597 AP002567.1/237206-237106 AE015414.1/5697-5597 AE000473.1/6642-6542 U00006.1/61521-61421 AE016990.1/58866-58966 AE005631.1/5793-5693,193697-193597,0,100,AE016770.1/193697-193597 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30321,AE016785.1,1,sp|AE016785.1|AE016785 Pseudomonas putida KT2440 section 12 of 21 of the complete genome.,0,100,288775,288889,67.30,AGCGCCACCAAGGGGAGCCCGGCAAUGGGCUGAGAAACCGCUGAACGCUACAGCGCGGUGACCCUUCGAACCUGAUCCGGAUCAUGCCGGCGAAGGGAUGGGGCUUGUAACCUGC,AE016785.1/288775-288889,288775-288889,0,114,AE016785.1/288775-288889 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30328,AE016792.1,1,sp|AE016792.1|AE016792 Pseudomonas putida KT2440 section 19 of 21 of the complete genome.,1,101,163969,163863,78.21,AUGUUCUUGUCGGGGUGCCUUGAAGCAAAGGCUGAGAUCGCAGAGGUGCGGAUCCCGUUGAACCUGAUCAGGUUAGCGCCUGCGUAGGGAACAAGAUUGCUCGCCUU,AE016792.1/163969-163863,163969-163863,0,106,AE016792.1/163969-163863 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30333,AE016799.1,1,sp|AE016799.1|AE016799 Vibrio vulnificus CMCP6 chromosome I section 3 of 11 of the complete sequence.,1,102,119184,119059,52.93,AACCACUCAUCGGGGCGCUUAACUGUGGUGUUUUAUUGCAUCGCAGUGGCUGAGACUAGGCAAAGGCCUAGGACCCGUAAACCUGAACCAGAUAAUGCUGGCGUAGGAAUUGAGUCGGGAUUAAUU,AE016799.1/119184-119059,119184-119059,0,125,AE016799.1/119184-119059 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30334,AE016800.1,1,sp|AE016800.1|AE016800 Vibrio vulnificus CMCP6 chromosome I section 4 of 11 of the complete sequence.,1,103,67341,67243,77.18,UUUCACUUGUCGGAGUGCCUUAGGGCUGAGACCGUUUAUUCGGGAUCCGUUGAACCUGAUCAGGUUAGAACCUGCGAAGGGAACAAGAGAAGAUACUUG,AE016800.1/67341-67243,67341-67243,0,98,AE016800.1/67341-67243 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30347,AE016813.1,1,sp|AE016813.1|AE016813 Vibrio vulnificus CMCP6 chromosome II section 6 of 6 of the complete sequence.,1,104,68647,68549,78.95,CCAACAUAGUCGGGGAGCCUUAUCGGCUGAGAUCGCCACGCGAGACCCGUUGAACCUGAUUCAGUUAAUACUGACGUAGGGAACUAUUACGCGCAUAUA,AE016813.1/68647-68549,68647-68549,0,98,AE016813.1/68647-68549 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30352,AE016834.1,1,sp|AE016834.1|AE016834 Salmonella enterica subsp. enterica serovar Typhi Ty2; section 1 of 16 of the complete genome.,1,105,128207,128108,76.13,CCGAACUCAACGGGGUGCCGCGCUCAUGCGCGCGCUGAGAAAAUACCCGUCGAACCUGAUCCGGAUAAUGCCGGCGAAGGGAUUUGAGGCUACCUCUCAA,AE008698.1/18540-18441 AE016834.1/128207-128108 AL627265.1/128216-128117,128207-128108,0,99,AE016834.1/128207-128108 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30354,AE016836.1,1,sp|AE016836.1|AE016836 Salmonella enterica subsp. enterica serovar Typhi Ty2; section 3 of 16 of the complete genome.,0,106,195900,195996,68.24,CUUGACGACUCGGGGUGCCCUUCUUUGUGAAGGCUGAGAAAUACCCGUACCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCUGACACUGCUCGU,AE016836.1/195900-195996 AE008795.1/16610-16514 U87940.1/125-221 AL627273.1/156556-156460,195900-195996,0,96,AE016836.1/195900-195996 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30363,AE016845.1,1,sp|AE016845.1|AE016845 Salmonella enterica subsp. enterica serovar Typhi Ty2; section 12 of 16 of the complete genome.,0,107,248940,249058,61.11,ACGAAGCCAACGAAGAGGCAGCGCGAAGGAUGAAGUGGAAAAGGCUGAGACCGUUAAUUCGGGAUCCGCGGAACCUGAUCAGGUUAAUACCUGCGAAGGGAACAAGAGUAAUUCUGCUU,AE008894.1/19601-19483 AE016845.1/248940-249058 AF170176.1/27307-27189 AL627279.1/105944-106062,248940-249058,0,118,AE016845.1/248940-249058 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30391,AE016874.1,1,sp|AE016874.1|AE016874 Pseudomonas syringae pv. tomato str. DC3000 section 19 of 21 of the complete genome.,1,108,27758,27654,75.15,GCGUUCUUGUCGGGGUGCCUUGCUAUGAGGCUGAGAUCGGUUAAACCGGAUCCCGUUGAACCUGAUCAGGUUAGCGCCUGCGUAGGGAACAAGAUUUCUCGUCUC,AE016874.1/27758-27654,27758-27654,0,104,AE016874.1/27758-27654 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30397,AE016928.1,1,sp|AE016928.1|AE016928 Bacteroides thetaiotaomicron VPI-5482; section 3 of 21 of the complete genome.,1,109,199416,199321,64.99,GUAAAGACAAAGGGGUGCCCCCAAAGAGGGGCUGAGAUUAUACCCUAGGAACCUGAGGCAGUUAGCACUGACGUAGGGAUUGUGUUUCUUUCUUAU,AE016928.1/199416-199321,199416-199321,0,95,AE016928.1/199416-199321 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30404,AE016935.1,1,sp|AE016935.1|AE016935 Bacteroides thetaiotaomicron VPI-5482; section 10 of 21 of the complete genome.,0,110,265475,265571,70.22,UUCACUAAGUAGGGGUGCCUUAACAUGACGGGCUGAGAACAUACCCAUAGAAUCUGAACCGGGUAAUGCCGGCGUAGAGAACUAAUUAAUAAGCAAG,AE016935.1/265475-265571,279858-279954 265475-265571,0,96,AE016935.1/265475-265571 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30404,AE016935.1,1,sp|AE016935.1|AE016935 Bacteroides thetaiotaomicron VPI-5482; section 10 of 21 of the complete genome.,0,111,279858,279954,63.64,UUCACGCAAUAGGGGUGCCCUAACAUGACAGGCUGAGAACAUACCCAUAGAAUCUGAUCCGGGUAAUGCCGGCGUAGAGAACGAAUAAAUAAGCAAA,AE016935.1/279858-279954,279858-279954 265475-265571,0,96,AE016935.1/279858-279954 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30424,AE016955.1,1,sp|AE016955.1|AE016955 Enterococcus faecalis V583; section 9 of 11 of the complete genome.,1,112,248631,248543,67.10,GAGAAACAUUUGGGGUGCUAUUAGCUGAGAUUAUACCCAUGGAACCUGAAACAGUUAGGACUGGCGCAGGGAAAUGUCUUGAAAUUUUG,AE016955.1/248631-248543,241328-241238 248631-248543,0,88,AE016955.1/248631-248543 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30424,AE016955.1,1,sp|AE016955.1|AE016955 Enterococcus faecalis V583; section 9 of 11 of the complete genome.,1,113,241328,241238,68.74,AAAAAACAUUUGGGGUGCUGUUAUGGCUGAGAUGAUACCCAUUGAACCUGAUGCAGUUAGUACUGUCGCAGGGAAAUGCCGAUUUACUUUG,AE016955.1/241328-241238,241328-241238 248631-248543,0,90,AE016955.1/241328-241238 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30427,AE016960.1,1,sp|AE016960.1|AE016960 Coxiella burnetii strain RSA 493; section 1 of 7 of the complete genome.,0,114,296476,296583,55.71,CUGCAUCUCUCGGGGAGCGAAAGCUGAGACGAUCCUAGAAAUUCGAAGAUCGGACCCGUUGAACCUGCACAAGAUAAUGCUUGCGAAGGGAAGGGACGAUGCGGCUGC,AE016960.1/296476-296583,296476-296583,0,107,AE016960.1/296476-296583 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.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.,0,115,6411,6516,65.41,AAUCAAUAACAGAGGUACCUCUUUUAUCUUGGAUAAAAGAAGUUGAGAAACACUCUUAUGAGCUGAUCUGGUUAACACCAGCGUAGCGAGUUAUAUCUCUCACAAG,AF242853.3/1001-1106 AE016968.1/6411-6516,6411-6516,0,105,AE016968.1/6411-6516 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30438,AE016978.1,1,sp|AE016978.1|AE016978 Shigella flexneri 2a str. 2457T section 1 of 16 of the complete genome.,1,116,72938,72839,73.35,CCGUUCUCAACGGGGUGCCACGCAAACGCGUGCGCUGAGAAAAUACCCGUCGAACCUGAUCCGGAUAACGCCGGCGAAGGGAUUUGAGGCUCCUUCUCAA,AE016978.1/72938-72839,72938-72839,0,99,AE016978.1/72938-72839 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30445,AE016985.1,1,sp|AE016985.1|AE016985 Shigella flexneri 2a str. 2457T section 8 of 16 of the complete genome.,1,117,136499,136403,73.09,CCAAACGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCACGGACCACCAGG,AE005436.1/8098-8002 AE015232.1/7947-7851 AE016985.1/136499-136403 D90848.1/13353-13257 AE000299.1/8101-8005 AP002560.1/50173-50077,136499-136403,0,96,AE016985.1/136499-136403 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30450,AE016990.1,1,sp|AE016990.1|AE016990 Shigella flexneri 2a str. 2457T section 13 of 16 of the complete genome.,0,118,58866,58966,80.24,AAUUUCUUGUCGGAGUGCCUUAACUGGCUGAGACCGUUUAUUCGGGAUCCGCGGAACCUGAUCAGGCUAAUACCUGCGAAGGGAACAAGAGUUAAUCUGCU,M88701.1/79-179 AE016770.1/193697-193597 AP002567.1/237206-237106 AE015414.1/5697-5597 AE000473.1/6642-6542 U00006.1/61521-61421 AE016990.1/58866-58966 AE005631.1/5793-5693,58866-58966,0,100,AE016990.1/58866-58966 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30454,AE016994.1,1,sp|AE016994.1|AE016994 Chlamydophila caviae GPIC section 1 of 4 of the complete genome.,0,119,214691,214787,22.18,ACCUUUAAACGUGUGAAUCUUUGCUGUUUAGACGAAAAAAAGUUUUUAGAACCUGCUCGAGUUAAUACUUGCGAAGGGAGUUGUGUUCAUUUCUGUU,**** NEW HIT #3 ****,214729-214788,1,58,AE016994.1/214691-214787 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30459,AE016999.1,1,sp|AE016999.1|AE016999 Bacillus cereus ATCC 14579 section 2 of 18 of the complete genome.,0,120,97492,97606,59.53,UAAGAAACACAUGGGAGUUUGUGGAUACAAACUGAGAGUAUGGCUACUAGUCCGUCAUUGACCAUUUGAACCUGUUGGAUAAUGCCAGCGUAGGGAGAGUGUAAAAGCACAUAUU,AE016999.1/97492-97606,106602-106704 97492-97606,0,114,AE016999.1/97492-97606 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30459,AE016999.1,1,sp|AE016999.1|AE016999 Bacillus cereus ATCC 14579 section 2 of 18 of the complete genome.,0,121,106602,106704,68.32,AAUUAAGGACCGGGGAGCCAAUUGGCUGAGAGGAUGUAAGUAAACAUCGACCCUCAACCUGAUCUGGAUAAUGCCAGCGUAGGGAGUUACUUAAAGUGAUGUA,AE016999.1/106602-106704,106602-106704 97492-97606,0,102,AE016999.1/106602-106704 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30460,AE017000.1,1,sp|AE017000.1|AE017000 Bacillus cereus ATCC 14579 section 3 of 18 of the complete genome.,0,122,121009,121112,71.17,UGAAACCACUAGGGGUGCUUGACUUGCUGAGAGAGGAAUAAUCCUUAACCCUUACAACACCUGAUCUAGGUAAUACUAGCGAAGGGAAGUGGAACAUCGAAUAA,AE017000.1/121009-121112,120837-120948 121009-121112,0,103,AE017000.1/121009-121112 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30460,AE017000.1,1,sp|AE017000.1|AE017000 Bacillus cereus ATCC 14579 section 3 of 18 of the complete genome.,0,123,120837,120948,62.52,AUAGUUUGCUAGGAGAGCUGGUGUUGCCAGCUGAGAGUAGGCCGUAAGCCUUUGAUCCUUUUUAUUACCUGAUCUAGAUUAUGCUAGCGUAGGGAAGCAAUUCGGACACUAA,AE017000.1/120837-120948,120837-120948 121009-121112,0,111,AE017000.1/120837-120948 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30466,AE017006.1,1,sp|AE017006.1|AE017006 Bacillus cereus ATCC 14579 section 9 of 18 of the complete genome.,0,124,104897,105002,83.45,UUCAUCCACUAGGGGGGCCUUUUAUAGGCUGAGAUCAAAUGUGAUUUUGAGACUCUUAGUACCUGAUCUGGUUAAUGCCAGCGUAGGGAAGUGGGAAAGACGUUGC,AE017006.1/104897-105002,104897-105002,0,105,AE017006.1/104897-105002 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30473,AE017013.1,1,sp|AE017013.1|AE017013 Bacillus cereus ATCC 14579 section 16 of 18 of the complete genome.,0,125,198598,198699,53.36,CGUUAUCACUGGGGGAGCCAUGCCGCUGAGAGGGAACACUUCGUUCCGACCCUUCGAACCUGUUAGUUAAUGCUAACGCAGGGAUUGUGCAAACGUCCGAAA,AE017013.1/198598-198699,198598-198699,0,101,AE017013.1/198598-198699 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.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.,1,126,297210,297095,78.12,GUGAUAAACUAGGGGUGCCUAACGUAUGCGUAGGCUGAGAGAGAAGCGCGUGAACUUCUUAACCCUUUGGACCUGAUCUGGCUCGUACCAGCGUAGGGAAGUUAACGGCUUUACAU,AE017014.1/297210-297095,297210-297095,0,115,AE017014.1/297210-297095 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30477,AE017025.1,1,sp|AE017025.1|AE017025 Bacillus anthracis str. Ames section 2 of 18 of the complete genome.,0,127,103945,104056,55.47,UAAUAAGCACAUGGGAGUUUGUGGAUGCAAACUGAGAGUAUGACUAUUCCGUCAUUGACCAUUUGAACCUGUUGGAUAAUGCCAGCGUAGGGAGAGUGUAAAAGCACAUGUU,AE017025.1/103945-104056,103945-104056 109350-109452,0,111,AE017025.1/103945-104056 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30477,AE017025.1,1,sp|AE017025.1|AE017025 Bacillus anthracis str. Ames section 2 of 18 of the complete genome.,0,128,109350,109452,69.36,AAUUAAGGACCGGGGAGCCAAUUGGCUGAGAGGAUGUGAGCAAACAUCGACCCUCAACCUGAUCUGGAUAAUGCCAGCGUAGGGAGUUACUUAAAGUAAUGUA,AE017025.1/109350-109452,103945-104056 109350-109452,0,102,AE017025.1/109350-109452 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30478,AE017026.1,1,sp|AE017026.1|AE017026 Bacillus anthracis str. Ames section 3 of 18 of the complete genome.,0,129,171648,171751,72.56,UGAAACCACUAGGGGUGCUUGUUGUGCUGAGAGAGGAAUAAUCCUUAACCCUUAUAACACCUGAUCUAGGUAAUACUAGCGAAGGGAAGUGGAACAACGAAUAA,AE017026.1/171648-171751,171475-171587 171648-171751,0,103,AE017026.1/171648-171751 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30478,AE017026.1,1,sp|AE017026.1|AE017026 Bacillus anthracis str. Ames section 3 of 18 of the complete genome.,0,130,171475,171587,61.55,AUAGUUUGCUAGGAGAGCUGGUGUUGCCAGCUGAGAGUAAGACCUUAAGUCUUUGAUCCUUUUUAUUACCUGAUCUAGAUUAUGCUAGCGUAGGGAAGCAAUUCGGACACUAA,AE017026.1/171475-171587,171475-171587 171648-171751,0,112,AE017026.1/171475-171587 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30484,AE017032.1,1,sp|AE017032.1|AE017032 Bacillus anthracis str. Ames section 9 of 18 of the complete genome.,0,131,107689,107794,83.75,UUUAUCCACUAGGGGGGCCUAUUAUAGGCUGAGAUCAAAUUGGAAUUUGAGACUCUUAGUACCUGAUCUGGUUAAUGCCAGCGUAGGGAAGUGGGAAAGACAUUGC,AE017032.1/107689-107794,107689-107794,0,105,AE017032.1/107689-107794 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30491,AE017039.1,1,sp|AE017039.1|AE017039 Bacillus anthracis str. Ames section 16 of 18 of the complete genome.,0,132,209525,209626,56.84,CGUUAUCACAGGGGGAGCCAUGCCGCUGAGAGGGAACACUUCGUUCCGACCCUUCGAACCUGUUAGUUAAUGCUAACGCAGGGAUUGUGCAAACGUCCGAAA,AE017039.1/209525-209626,209525-209626,0,101,AE017039.1/209525-209626 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.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.,1,133,281858,281743,80.21,GUGAUAAACUAGGGGUGCCUAACGUAUGCGUAGGCUGAGAGAGAAGCGCGUAAACUUCUUAACCCUUUGGACCUGAUCUGGCUCGUACCAGCGUAGGGAAGUUAACGGCUUUACAU,AE017040.1/281858-281743,281858-281743,0,115,AE017040.1/281858-281743 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30501,AE017152.1,1,sp|AE017152.1|AE017152 Haemophilus ducreyi strain 35000HP section 2 of 6 of the complete genome.,0,134,157588,157680,66.97,UUGUUCUCAUUGGGGUGCUGAAAAUAAGCUGAGAAAUACCCAUAGAACCUGAUCUGAUUCGUAUCAGCGUAGGGAUUUGAGGCCAUUUCUACU,AE017152.1/157588-157680,157588-157680,0,92,AE017152.1/157588-157680 ./cmzasha --no-stderr --filter 350 20 Rfam/cm/RF00059.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;113;40 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left;44;77;115;116;117 2struct-str data/TryAllCm_5.0/RF00059_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub;103;100 ,Rfam/cm/RF00059.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30515,AE017166.