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 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,13824,AB090330.1,1,sp|AB090330.1|AB090330 Clostridium sporogenes genes for 5; 10-methylene tetrahydrofolate reductase; collagenase; hypothetical protein; partial and complete cds.,1,0,380,279,116.82,UACUUAUCAAGAGCGGUGGAGGGACUGGCCCUAUGAAGCCCAGCAACCUAUAUGAAAAUAUAUAAGGUGCUAAAUCCUGCAGCAUAAGCUGAGAGAUGAGGA,AB090330.1/380-279,380-279,0,101,AB090330.1/380-279
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18078,AE001982.1,1,sp|AE001982.1|AE001982 Deinococcus radiodurans R1 section 119 of 229 of the complete chromosome 1.,0,1,1022,1133,26.80,CCUUUAUCCAGAGUCGGCGCAGGGACCUGGCCCCAUGACCGCCGCAGCAACCGGCCCUCAUCACGGCAGCGGUGCUUUCCAGACCCGCGCGAGCAGCGCCCGACGAUGGGCG,****    NEW  HIT  #0  ****,,2,0,AE001982.1/1022-1133
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22298,AE007554.1,1,sp|AE007554.1|AE007554 Clostridium acetobutylicum ATCC824 section 42 of 356 of the complete genome.,0,2,96,198,108.56,UUCUUAUCAAGAGUGACGGAGGGAUAGGCCCUAUGAAGUCCGGCAACAUCCAAUUAUUUUGGAGAUGUGCUAAUUCCUACAGGUUUAUCCUGAGAGAUGAGAA,AE007554.1/96-198,96-198,0,102,AE007554.1/96-198
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22317,AE007573.1,1,sp|AE007573.1|AE007573 Clostridium acetobutylicum ATCC824 section 61 of 356 of the complete genome.,1,3,4052,3947,110.94,AUCUUAUCAAGAGUGGUGGAGGGACUGGCCCUUUGAAACCCGGCAACCAGUAUAUUUUUUAAUAUAUGUGGUGCUAAAUCCUGCAGCAAACGCUGAUAGAUGAGAA,AE007573.1/4052-3947,4052-3947,0,105,AE007573.1/4052-3947
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22352,AE007608.1,1,sp|AE007608.1|AE007608 Clostridium acetobutylicum ATCC824 section 96 of 356 of the complete genome.,1,4,12720,12617,111.54,UCCUUAUCAAGAGAAACGGAGGGACUGGCCCAAUGAUGUUUCAGCAACCAAGGUUUUAUACUUAUGGUGCUAAUUCCAGCAGGAUAUUUUCUGAAAGAUGAGGA,AE007608.1/12720-12617,12720-12617,0,103,AE007608.1/12720-12617
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22358,AE007614.1,1,sp|AE007614.1|AE007614 Clostridium acetobutylicum ATCC824 section 102 of 356 of the complete genome.,0,5,6196,6300,109.97,CACUUAUCAAGAGAGGUGGAGGGACCGGCCCUGUGAAGCCCAGCAACCUGUAUAUGUUAAUUAUACAAGGUGCUAAUUCCUGCAGCGCUAGCUGAGAGAUGAGAA,AE007614.1/6196-6300,6196-6300,0,104,AE007614.1/6196-6300
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22435,AE007691.1,1,sp|AE007691.1|AE007691 Clostridium acetobutylicum ATCC824 section 179 of 356 of the complete genome.,0,6,7901,8001,105.16,UUCUUAUCAAGAAGGUGGAGGGACUGGCCCUAUGAAGCCUGACAACCGGCAAAUGUACGGUGUUAAUUCCUGCAAAACUUAUUUGUUUUGAAAGAUAAGAA,AE007691.1/7901-8001,7901-8001,0,100,AE007691.1/7901-8001
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22520,AE007776.1,1,sp|AE007776.1|AE007776 Clostridium acetobutylicum ATCC824 section 264 of 356 of the complete genome.,1,7,3380,3272,117.71,GUCUUAUCAAGAGAGGUGGAGGGACUGGCCCUAUGAAACCCAACAACCAGCAUUUUUUAAUUAGAUGUAUGGUGUUAAUUCCUGCAAAGUUAAUUUUGAGAGAUAAGAG,AE007776.1/3380-3272,3380-3272,0,108,AE007776.1/3380-3272
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22527,AE007783.1,1,sp|AE007783.1|AE007783 Clostridium acetobutylicum ATCC824 section 271 of 356 of the complete genome.,1,8,7014,6904,115.52,CUCUUAUCAAGAGAGGUGGAGGGAAAGGGCCCGUUGAAACCCGGCAACCGAUGUAUUAAUUUAAGUACAUAAUGGUGCCAAUUCCUGCAGAAUUAUUCUGCAAGAUAAGAG,AE007783.1/7014-6904,7014-6904,0,110,AE007783.1/7014-6904
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25255,AE010547.1,1,sp|AE010547.1|AE010547 Fusobacterium nucleatum subsp. nucleatum ATCC 25586; section 89 of 197 of the complete genome.,1,9,5644,5538,71.14,AAACCAUCAAGAGAGAUUGAGGGACAGGCCCGUUGAGAUCUCAGCAACCUACGUAAAAUGUGUGGUGCUAAUUCCUGAUAGAUGGAAAAGAUUAUAAUACAUCUCUC,AE010547.1/5644-5538,5644-5538,0,106,AE010547.1/5644-5538
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25285,AE010577.1,1,sp|AE010577.1|AE010577 Fusobacterium nucleatum subsp. nucleatum ATCC 25586; section 119 of 197 of the complete genome.,1,10,3358,3260,74.35,UAACCAUCCAGAGAAACGGAGGGACUGGCCCAAUGAUGUUUCAGCAACCUACUUAAAUGUGUGGUGCUAAUUCCAGAGAGAUGGAGAGGAAAAUUGAAA,AE010577.1/3358-3260,3358-3260,0,98,AE010577.1/3358-3260
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,26654,AE011946.1,1,sp|AE011946.1|AE011946 Xanthomonas axonopodis pv. citri str. 306;  section 324 of 469 of the complete genome.,1,11,7029,6909,43.36,UCACCAUCGAGACCGGCGGAGGGACAGGCCCUUUGAUGCCGGGGCAGCCAGCGGAGCGCGCAAGCGUCCGCGUUUGGUGCCAAAUCCUGCGGGGACCUCCGCGUCCGCCGAAAGAUGGUUC,AE011946.1/7029-6909,7029-6909,0,120,AE011946.1/7029-6909
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27105,AE012398.1,1,sp|AE012398.1|AE012398 Xanthomonas campestris pv. campestris str. ATCC 33913;  section 306 of 460 of the complete genome.,1,12,12711,12591,43.36,UCACCAUCGAGACCGGCGGAGGGACAGGCCCUUUGAUGCCGGGGCAGCCAGCGGAGCGCGCAAGCGCCCGCGUUUGGUGCCAAAUCCUGCGGGGACCUCCGCGUCCGCCGAAAGAUGGUUC,AE012398.1/12711-12591,12711-12591,0,120,AE012398.1/12711-12591
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27323,AE012834.1,1,sp|AE012834.1|AE012834 Chlorobium tepidum TLS  section 55 of 194 of the complete genome.,0,13,3852,3958,83.46,CUAUCAUCCAGAAAGGCGGAGGGACUGGCCCUGCGAAGCCUUGGCAACCUUCAUUCCACAUGAGCGGUGCCAAAUCCAUCCCGGAGGAAAUCCGGGAAAGAUGAUGU,AE012834.1/3852-3958,3852-3958,0,106,AE012834.1/3852-3958
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27509,AE013020.1,1,sp|AE013020.1|AE013020 Thermoanaerobacter tengcongensis strain MB4T; section 47 of 244 of the complete genome.,0,14,702,811,102.46,CUCUUAUCAAGAGAGGUGGAGGGAAAGAGCCCGAUGAAACCCGGCAACCUGUCCUUUUAAGGAUAAGGUGCCAAUUCUCUCAGAAGAUUUUUUCUUCUGAAAGAUGAGGG,AE013020.1/702-811,702-811,0,109,AE013020.1/702-811
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27621,AE013132.1,1,sp|AE013132.1|AE013132 Thermoanaerobacter tengcongensis strain MB4T; section 159 of 244 of the complete genome.,1,15,12640,12541,118.84,CUCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCAGCCUUAGGGCAUGGUGCCAAUUCCUGCAGCGGUUUCGCUGAAAGAUGAGAG,AE013132.1/12640-12541,12640-12541,0,99,AE013132.1/12640-12541
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27651,AE013162.1,1,sp|AE013162.1|AE013162 Thermoanaerobacter tengcongensis strain MB4T; section 189 of 244 of the complete genome.,1,16,3974,3865,112.84,CUCUUAUCAAGAGUGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCGGCACGUAAGUGCUUGGUGCCAAUUCCUGCAGGUUGGGGUUACCCAGCCUGAGAGAUGAGAG,AE013162.1/3974-3865,3974-3865,0,109,AE013162.1/3974-3865
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30274,AE015937.1,1,sp|AE015937.1|AE015937 Clostridium tetani E88; section 2 of 10 of the complete genome.,0,17,3369,3474,117.67,CUCUUAUCGAGAGAGGUGGAGGGAAAGGGCCCUAUGAAACCCGGCAACCAAUAUUUUUAGAAGUAUUAAGGUGCCAAUUCCUGCAGAAAGUUCUGCAAGAUAAGAG,AE015937.1/3369-3474,3369-3474,0,105,AE015937.1/3369-3474
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30277,AE015940.1,1,sp|AE015940.1|AE015940 Clostridium tetani E88; section 5 of 10 of the complete genome.,1,18,248618,248510,103.56,AGCUUAUUAAGAGCGGUGGAGGGACUGGCCCUAUGAAGCCCGGCAACCUGUAUAUGUGUUUGCAUAUUAUAAGGUGCUAAAUCCUGCGGUGUAAACCGAGAGAUGAGGA,AE015940.1/248618-248510,248618-248510 18048-17945,0,108,AE015940.1/248618-248510
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30277,AE015940.1,1,sp|AE015940.1|AE015940 Clostridium tetani E88; section 5 of 10 of the complete genome.,1,19,18048,17945,119.16,AUCUUAUCAAGAGCGGUUGAGGGACUGGCCCUAUGAAACCCAGCAACCUAUACACAAAGUAUAAAGGUGCUAACUCCAGCAGGAAAUUUCCUGAAAGAUAAGAA,AE015940.1/18048-17945,248618-248510 18048-17945,0,103,AE015940.1/18048-17945
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30281,AE015944.1,1,sp|AE015944.1|AE015944 Clostridium tetani E88; section 9 of 10 of the complete genome.,1,20,267219,267117,116.97,UUCUUAUCAAGAGAGGCGGAGGGACUGGCCCUAUGAAACCCGGCAACCAAAAAUAAUAAUUUUAAGGUGCCAAUUCCAGCAGGUGAAACCUGACAGAUAAGAC,AE015944.1/267219-267117,267219-267117,0,102,AE015944.1/267219-267117
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,0,21,15971,16071,80.42,ACCUUAUUUUGAGAAGCAGAGGGAUUUGGCCCGUAGAAGCUUCAGCAACCGACUUUAAAUAGCACGGUGCUAAUACCAACGAGCAACUCGAAUGAUAAGUA,AE016744.1/15971-16071,15971-16071,0,100,AE016744.1/15971-16071
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30284,AE016745.1,1,sp|AE016745.1|AE016745 Staphylococcus epidermidis ATCC 12228; section 2 of 9 of the complete genome.,0,22,287368,287470,101.58,CUCUUAUCGAGAGAGGUGGAGGGAUGUGCCCUAAGAAGCCCGGCAACCGUCUAAAAUAGAAAUGGUGCCAAUUCACAUAAAGUAUAACUUUAGAAGAUGAGAG,AE016745.1/287368-287470,287368-287470,0,102,AE016745.1/287368-287470
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,23,3761,3652,98.68,CUCUUAUCCUGAGUGGUGGAGGGACAUGGACCCAAUGAAACCCAGCAACCUCUUUAUUUAAAGAAAGGUGCCAAACCGUUUGCAGACAAAUAUGGUCUGAACGAUAAGAG,AE016749.1/3761-3652 AF270301.1/145-36,3761-3652,0,109,AE016749.1/3761-3652
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,24,132874,132778,90.86,AACUUAUCAAGAGAAGUGGAGGGACUGGCCCAAAGAAGCUUCGGCAACAUUGUAUCAUGUGCCAAUUCCAGUAACCGAGAAGGUUAGAAGAUAAGGU,AE016750.1/132874-132778,132874-132778,0,96,AE016750.1/132874-132778
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30458,AE016998.1,1,sp|AE016998.1|AE016998 Bacillus cereus ATCC 14579 section 1 of 18 of the complete genome.,0,25,183064,183169,96.44,UACUUAUCCAGAGAGGUAGAGGGACUGGCCCUAUGACACCUCAGCAGCGGGUUCUGUAAUAGGAACACCGUGCUAAUUCCAGCAAGCAAGUCUUGAAAGAUAAGUG,AE016998.1/183064-183169 AE017024.1/185584-185689,183064-183169 194622-194518 174290-174176,0,105,AE016998.1/183064-183169
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30458,AE016998.1,1,sp|AE016998.1|AE016998 Bacillus cereus ATCC 14579 section 1 of 18 of the complete genome.,1,26,194622,194518,102.16,AUUGUAUCAAGAGAGGUGGAGGGACUGGCCCUUUGAAACCUCGGCAACAGGUUCAUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUGCUUGAAAGAUAGAAU,AE016998.1/194622-194518,183064-183169 194622-194518 174290-174176,0,104,AE016998.1/194622-194518
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30458,AE016998.1,1,sp|AE016998.1|AE016998 Bacillus cereus ATCC 14579 section 1 of 18 of the complete genome.,1,27,174290,174176,116.04,CUCUUAUCAAGAGUGGCGGAGGGACUGGCCCGAUGAUGCCCGGCAACCGAGCUUAUGACGUAUAAGCUAAGGUGCUAAUUCCUGCAAAACGAGUUUUCGUUUUGGAAGAUAAGAG,AE016998.1/174290-174176,183064-183169 194622-194518 174290-174176,0,114,AE016998.1/174290-174176
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,0,28,16775,16881,106.67,UUCUUAUCCAGAGAGGUGGAGGGACUGGCCCUACGAUACCUCAGCAACGGGUUUUUUUAAUACCGUGCUAACUCCAGCAAGCCAUAUAAAGGCUUGGAAGAUGAGAA,AE016999.1/16775-16881 AE017025.1/30636-30742,16775-16881 67707-67595,0,106,AE016999.1/16775-16881
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,29,67707,67595,96.99,UCUUUAUCAAGAGAGGCAGAGGGACCGGCCCUUUGAAGCCCAGCAACCUCAGUUUAUACAAACUGAAUAGGUGCUAAUUCCUGCAAAAUGCAAUGCAUUUUGGAAGAUAAAAC,AE016999.1/67707-67595,16775-16881 67707-67595,0,112,AE016999.1/67707-67595
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,30,146968,146863,102.50,GUCUUAUCAAGAGCAGGUGGAGGGAUGAGCCCUACGAAGCCCGGCAACCGACCCAUUUAUGGGCACGGUGCUAAUUCUUACAACACAUUGUGUUGAAAGAUAAGAG,AE017000.1/146968-146863,146968-146863,0,105,AE017000.1/146968-146863
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30462,AE017002.1,1,sp|AE017002.1|AE017002 Bacillus cereus ATCC 14579 section 5 of 18 of the complete genome.,0,31,167884,167992,112.33,AGCUUAUCAAGAGAAGCGGAGGGAACUGGCCCGAAGAAGCUCGGCAACCUGCUUAUAGAAAGCAAGGUGCUAAAUCCAGCAAAAUGGGAUCCAUUUUGAAAGAUAAGGU,AE017002.1/167884-167992,180645-180750 167884-167992,0,108,AE017002.1/167884-167992
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30462,AE017002.1,1,sp|AE017002.1|AE017002 Bacillus cereus ATCC 14579 section 5 of 18 of the complete genome.,0,32,180645,180750,93.39,UUCUUAUAAAGAGAGGCGGAGGGACUGGCCCUACGAUGCCUCGGCAGCGGACUCGAUUUCAGAGUGCUGUGCCAAAUCCAGCAAGCGUGUGCUUGAAAGAUGAGAA,AE017002.1/180645-180750,180645-180750 167884-167992,0,105,AE017002.1/180645-180750
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,0,33,167098,167213,84.37,UACUUAUCCAGAGAGGUGGAGGGAACGGCCCUAAAAAACCUCAGCAACCCCUAUGCAAUUUUAUAGGAAGGUGCUAAUUCCGCAGAGGACACGAUGUGUUUUUUGAAAGAUAAGAG,AE017006.1/167098-167213,167098-167213,0,115,AE017006.1/167098-167213
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30468,AE017008.1,1,sp|AE017008.1|AE017008 Bacillus cereus ATCC 14579 section 11 of 18 of the complete genome.,1,34,120824,120723,104.16,UUCUUAUCACGAGAGGUGGAGGGACUGGCCCUAUGAUACCUCGGCAGCGGAUUCGUUAUGAAUACUGUGCCAAUUCCAGCAAGGUAACUUGAAAGAUAAGAA,AE017008.1/120824-120723,120824-120723,0,101,AE017008.1/120824-120723
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30471,AE017011.1,1,sp|AE017011.1|AE017011 Bacillus cereus ATCC 14579 section 14 of 18 of the complete genome.,0,35,79744,79849,93.09,UUCUUAUCAAGAGCAGGUGGAGGGACGAGCCCGACGAAACCCGGCAACCGAUCUACAAUUGUAGACACGGUGCUAAUUCUCGCAGCAUUACGCUGACAGAUAAGGA,AE017011.1/79744-79849,269078-268969 79744-79849 269282-269392 77551-77411,0,105,AE017011.1/79744-79849
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30471,AE017011.1,1,sp|AE017011.1|AE017011 Bacillus cereus ATCC 14579 section 14 of 18 of the complete genome.,0,36,269282,269392,107.55,UUCUUAUCUAGAGAGGUAGAGGGACUGGCCCUGUGACGCCUCAGCAACCAUUAACAUUUUGUUAAUAAGGUGCUAAUUCCAGCAAAUUGUGAAAGAUUUGACAGAUGAGAA,AE017011.1/269282-269392,269078-268969 79744-79849 269282-269392 77551-77411,0,110,AE017011.1/269282-269392
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30471,AE017011.1,1,sp|AE017011.1|AE017011 Bacillus cereus ATCC 14579 section 14 of 18 of the complete genome.,1,37,269078,268969,100.57,CUCUUAUUGAGAGCGGUGGAGGGAAAGGCCCUGUGAAACCCGGCAACCUUCAAACGAAAUGUUUGAAACGGUGCUAAUACCUGCAAAACGAAUGUUUUGCAUAAUAAGAG,AE017011.1/269078-268969 AE017037.1/274295-274186,269078-268969 79744-79849 269282-269392 77551-77411,0,109,AE017011.1/269078-268969
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30471,AE017011.1,1,sp|AE017011.1|AE017011 Bacillus cereus ATCC 14579 section 14 of 18 of the complete genome.,1,38,77551,77411,99.88,CUCUUAUCAAGAGCAGGUGGAGGGAUUUGGCCCGAUGAAGCCCACAACCGACCGUAAUACCAUUGUGAAAUGGGGCGUUUAUUACGCCAAAAGGCACGGUGCUAAUUCCAGCAGAAAGUAAAACUUUCUGGCAGAUAAGAG,AE017011.1/77551-77411,269078-268969 79744-79849 269282-269392 77551-77411,0,140,AE017011.1/77551-77411
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,39,161744,161623,79.87,CUCUUAUCCCGAGCUGGCGGAGGGACAGGCCCGAUGAAGCCCAGCAACCUCACUUGUAGUGGUAAAUACAGGUGAAUAGGUGCUAAAACCUGUGCGAGGCUACAGGUCUCGAACGAUAAGAG,AE017013.1/161744-161623 AE017039.1/173784-173663,161744-161623,0,121,AE017013.1/161744-161623
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,40,59727,59620,112.83,CUCUUAUCAAGAGAGGUGGAGGGACUGUGCCCUGUGAAGCCCGGCAACCGUCAACUUAUGUUGAAAUGGUGCCAAUUCCUGCAAAGCAAAUGCUUUGAGAGAUGAGAG,AE017040.1/68333-68226 AE017014.1/59727-59620,59727-59620,0,107,AE017014.1/59727-59620
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30475,AE017015.1,1,sp|AE017015.1|AE017015 Bacillus cereus ATCC 14579 section 18 of 18 of the complete genome.,1,41,186161,186057,107.15,GUCUUAUCAAGAAAAGGUGGAGGGACAGGCCCGAUGAAACCUUGGCAACAGCCGUAUAACGGAAUUGUGCCAAAUCCUGCAGGUAGUAAUCCUGAGAGAUAAGAA,AE017015.1/186161-186057,186161-186057,0,104,AE017015.1/186161-186057
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30476,AE017024.1,1,sp|AE017024.1|AE017024 Bacillus anthracis str. Ames section 1 of 18 of the complete genome.,0,42,185584,185689,96.44,UACUUAUCCAGAGAGGUAGAGGGACUGGCCCUAUGACACCUCAGCAGCGGGUUCUGUAAUAGGAACACCGUGCUAAUUCCAGCAAGCAAGUCUUGAAAGAUAAGUG,AE016998.1/183064-183169 AE017024.1/185584-185689,177274-177160 197187-197081 185584-185689,0,105,AE017024.1/185584-185689
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30476,AE017024.1,1,sp|AE017024.1|AE017024 Bacillus anthracis str. Ames section 1 of 18 of the complete genome.,1,43,197187,197081,97.44,AUUGUAUCAAGAGAGGUGGAGGGACUGGCCCUUUGAAACCUCGGCAGCAGGUUCAUUUUUGAAUACUGUGCCACUUCCUGCAAGCUUUAUAGCUUGAAAGAUAGAAU,AE017024.1/197187-197081,177274-177160 197187-197081 185584-185689,0,106,AE017024.1/197187-197081
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30476,AE017024.1,1,sp|AE017024.1|AE017024 Bacillus anthracis str. Ames section 1 of 18 of the complete genome.,1,44,177274,177160,116.81,CUCUUAUCAAGAGUGGCGGAGGGACUGGCCCGAUGAUGCCCGGCAACCGAGCUUAUGACGUAUAAGCUAAGGUGCUAAUUCCUGCAAAAUGAGUUUUCGUUUUGGAAGAUAAGAG,AE017024.1/177274-177160,177274-177160 197187-197081 185584-185689,0,114,AE017024.1/177274-177160
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,0,45,30636,30742,106.67,UUCUUAUCCAGAGAGGUGGAGGGACUGGCCCUACGAUACCUCAGCAACGGGUUUUUUUAAUACCGUGCUAACUCCAGCAAGCCAUAUAAAGGCUUGGAAGAUGAGAA,AE016999.1/16775-16881 AE017025.1/30636-30742,30636-30742 81160-81048,0,106,AE017025.1/30636-30742
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,46,81160,81048,97.27,UCUUUAUCAAGAGAGGCAGAGGGACCGGCCCUUUGAAGCCCAGCAACCUCAGUUUAUACAAACUGAAUAGGUGCUAAUUCCUGCAAAAUGCAUUGCAUUUUGAAAGAUAAAAC,AE017025.1/81160-81048,30636-30742 81160-81048,0,112,AE017025.1/81160-81048
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30480,AE017028.1,1,sp|AE017028.1|AE017028 Bacillus anthracis str. Ames section 5 of 18 of the complete genome.,0,47,201911,202019,111.88,AGCUUAUCAAGAGAAGCGGAGGGAACUGGCCCGGCGAAGCUCGGCAACCUGCUUAUAGAAAGCAAGGUGCUAAAUCCAGCAAAAUGGAAUCCAUUUUGAAAGAUAAGGU,AE017028.1/201911-202019,201911-202019 214605-214710,0,108,AE017028.1/201911-202019
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30480,AE017028.1,1,sp|AE017028.1|AE017028 Bacillus anthracis str. Ames section 5 of 18 of the complete genome.,0,48,214605,214710,92.76,UUCUUAUAAAGAGAGGCGGAGGGACUGGCCCUACGAUGCCUCGGCAGCGGACUCGAUUUUAGAGUGCUGUGCCAAAUCCAGCAAGCAUGUGCUUGAAAGAUGAGAA,AE017028.1/214605-214710,201911-202019 214605-214710,0,105,AE017028.1/214605-214710
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,0,49,133458,133573,96.22,UACUUAUCCAGAGAGGUGGAGGGAACGGCCCUAUGAAACCUCAGCAACCCCUAUGUAAAUGCAUAGGAAGGUGCUAAUUCCGCAGAGAACACGUUGUGUUUUUUGGAAGAUGAGAG,AE017032.1/133458-133573,133458-133573,0,115,AE017032.1/133458-133573
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30486,AE017034.1,1,sp|AE017034.1|AE017034 Bacillus anthracis str. Ames section 11 of 18 of the complete genome.,1,50,185225,185127,106.94,UUCUUAUCCAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCAGCAACCGCGAUGCAGGUGCUAAUUCCAGCAGAACAAAUUUGUUCUGGGAGAUAAGAC,AE017034.1/185225-185127,46775-46674 185225-185127,0,98,AE017034.1/185225-185127
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30486,AE017034.1,1,sp|AE017034.1|AE017034 Bacillus anthracis str. Ames section 11 of 18 of the complete genome.,1,51,46775,46674,107.01,UUCUUAUCACGAGAGGUGGAGGGACUGGCCCUAUGAAACCUCGGCAGCGGAUUCGUUAUGAAUACUGUGCCAAUUCCAGCAAGGUAACUUGAAAGAUAAGAA,AE017034.1/46775-46674,46775-46674 185225-185127,0,101,AE017034.1/46775-46674
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30489,AE017037.1,1,sp|AE017037.1|AE017037 Bacillus anthracis str. Ames section 14 of 18 of the complete genome.,0,52,93146,93253,92.79,UUCUUAUCAAGAGCAGGUGGAGGGACGAGCCCGACGAAACCCGGCAACCGAUCUACAUAAUUGUAGACACGGUGCUAAUUCUCGCAGCAUUACGCUGACAGAUAAGGA,AE017037.1/93146-93253,274498-274607 93146-93253 90953-90812 274295-274186,0,107,AE017037.1/93146-93253
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30489,AE017037.1,1,sp|AE017037.1|AE017037 Bacillus anthracis str. Ames section 14 of 18 of the complete genome.,0,53,274498,274607,109.39,UUCUUAUCUAGAGAGGUAGAGGGACUGGCCCUAUGACGCCUCAGCAACCAUUAACAUUUGUUAAUAAGGUGCUAAUUCCAGCAAAUUGCGAAAAAUUUGACAGAUGAGAA,AE017037.1/274498-274607,274498-274607 93146-93253 90953-90812 274295-274186,0,109,AE017037.1/274498-274607
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30489,AE017037.1,1,sp|AE017037.1|AE017037 Bacillus anthracis str. Ames section 14 of 18 of the complete genome.,1,54,274295,274186,100.57,CUCUUAUUGAGAGCGGUGGAGGGAAAGGCCCUGUGAAACCCGGCAACCUUCAAACGAAAUGUUUGAAACGGUGCUAAUACCUGCAAAACGAAUGUUUUGCAUAAUAAGAG,AE017011.1/269078-268969 AE017037.1/274295-274186,274498-274607 93146-93253 90953-90812 274295-274186,0,109,AE017037.1/274295-274186
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30489,AE017037.1,1,sp|AE017037.1|AE017037 Bacillus anthracis str. Ames section 14 of 18 of the complete genome.,1,55,90953,90812,112.22,CUCUUAUCAAGAGCAGGUGGAGGGAUUUGGCCCGAUGAAGCCCAGCAACCGACCGUAAUACCAUUGUGAAAUGGGGCGUUUAUGACGCCAAAAGGCACGGUGCUAAUUCCAGCAGAAAGUAAAACUUUCUGGCAGAUAAGAG,AE017037.1/90953-90812,274498-274607 93146-93253 90953-90812 274295-274186,0,141,AE017037.1/90953-90812
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,56,173784,173663,79.87,CUCUUAUCCCGAGCUGGCGGAGGGACAGGCCCGAUGAAGCCCAGCAACCUCACUUGUAGUGGUAAAUACAGGUGAAUAGGUGCUAAAACCUGUGCGAGGCUACAGGUCUCGAACGAUAAGAG,AE017013.1/161744-161623 AE017039.1/173784-173663,173784-173663,0,121,AE017039.1/173784-173663
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.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.,1,57,68333,68226,112.83,CUCUUAUCAAGAGAGGUGGAGGGACUGUGCCCUGUGAAGCCCGGCAACCGUCAACUUAUGUUGAAAUGGUGCCAAUUCCUGCAAAGCAAAUGCUUUGAGAGAUGAGAG,AE017040.1/68333-68226 AE017014.1/59727-59620,68333-68226,0,107,AE017040.1/68333-68226
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30493,AE017041.1,1,sp|AE017041.1|AE017041 Bacillus anthracis str. Ames section 18 of 18 of the complete genome.,1,58,177535,177430,107.70,GUCUUAUCAAGAAAAGGUGGAGGGACAGGCCCGAUGAAACCUUGGCAACAGCCGUAUAACGGAAUUGUGCCAAAUCCUGCAGGUAAUAAAUCCUGAGAGAUAAGAA,AE017041.1/177535-177430,177535-177430,0,105,AE017041.1/177535-177430
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,31346,AF008220.1,1,sp|AF008220.1|AF008220 Bacillus subtilis rrnB-dnaB genomic region.,0,59,49783,49921,89.17,CUCUUAUCCCGAGCUGGCGGAGGGACAGGCCCUAUGAAGCCCAGCAACCGGUUUCUCUGUUAUUUAUUAUGUUCAACUGAGUGAGACAACCAAGGUGCUAACCUGUUGCAAGGUUGUAUGAUUCCUUGAGCGAUAAGAG,Z99119.2/114925-114787 AF008220.1/49783-49921,49783-49921,0,138,AF008220.1/49783-49921
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,33353,AF027868.1,1,sp|AF027868.1|AF027868 Bacillus subtilis chromosome region between terC and odhAB.,1,60,5245,5154,94.03,UUUCUAUCCAGAGAGGUGGAGGGACUGGCCCUAUGAAACCUCGGCAACAUUAUUGUGCCAAUUCCAGCAAGCGCUAGCUUGAAAGAUAGGAA,AF027868.1/5245-5154 Z99114.2/9567-9476,5245-5154,0,91,AF027868.1/5245-5154
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,10272,AF269983.1,1,sp|AF269983.1|AF269983 Staphylococcus epidermidis strain SR1 clone step.1038e03 genomic sequence.,0,61,571,671,79.05,ACCUUAUUUUGAGAAGCUGAGGGAUUUGGCCCAUAGAAGCUUCAGCAACCGACUUUAAAUAGCACGGUGCUAAUACCAACGAGCAACUCGAAUGAUAAGUA,AF269983.1/571-671,571-671,0,100,AF269983.1/571-671
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,10590,AF270301.1,1,sp|AF270301.1|AF270301 Staphylococcus epidermidis strain SR1 clone step.3049f07b genomic sequence.,1,62,145,36,98.68,CUCUUAUCCUGAGUGGUGGAGGGACAUGGACCCAAUGAAACCCAGCAACCUCUUUAUUUAAAGAAAGGUGCCAAACCGUUUGCAGACAAAUAUGGUCUGAACGAUAAGAG,AE016749.1/3761-3652 AF270301.1/145-36,145-36,0,109,AF270301.1/145-36
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,407,AL591973.1,1,sp|AL591973.1|AL591973 Listeria monocytogenes strain EGD; complete genome; segment 1/12,0,63,137133,137235,78.93,UUCUUAUCAAGAGUGGUGGAGGGAAUCGGCCCAGUGAAACCCAGCAGCGGAGCGCAAGUUCUAUGCUAAUUCCGAUCAGAAGUAAUAUUCUGGCAGAUAAGUA,AL591973.1/137133-137235,137133-137235,0,102,AL591973.1/137133-137235
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,408,AL591974.1,1,sp|AL591974.1|AL591974 Listeria monocytogenes strain EGD; complete genome; segment 2/12,1,64,109385,109266,112.78,CUCUUAUCGAGAGCGGCAGAGGGACUGGCCCGAUGAAGCCCGGCAACCUAACUUUAUUUAAGCAUAAAGUGAAGGUGCUAAUUCCAGCAAAAUGGUGUAUUCCGUUUUGGUAGAUAAGAG,AL591974.1/109385-109266,109385-109266,0,119,AL591974.1/109385-109266
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,409,AL591975.1,1,sp|AL591975.1|AL591975 Listeria monocytogenes strain EGD; complete genome; segment 3/12,1,65,277926,277826,107.92,UUCUUAUCACGAAAGGUGGAGGGACUGGCCCUUUGAAGCCUUAGCAACCGGAAUUUAUUUUCACGGUGCUAAUUCCAGCAGUAUAUUCUGAAAGAUAAGUC,AL596165.1/180914-180814 AL591975.1/277926-277826,277926-277826,0,100,AL591975.1/277926-277826
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,410,AL591976.1,1,sp|AL591976.1|AL591976 Listeria monocytogenes strain EGD; complete genome; segment 4/12,0,66,242770,242867,86.52,AACUUAUCAAGAAAGGUGGAGGGUUCUGGCCCCGUGAAGCCUUGGCAACCGGAUUUUUCACGGUGCCAAAUCCAGCAGGUAACACUGACAGAUAAGGC,AL591976.1/242770-242867,242770-242867,0,97,AL591976.1/242770-242867
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,414,AL591980.1,1,sp|AL591980.1|AL591980 Listeria monocytogenes strain EGD; complete genome; segment 8/12,1,67,89597,89491,107.92,CUCUUAUAAUGAGUGGUAGAGGGACUGGCCCGUUGAAACCCGGCAACCUUUCAAUACGUUGAAAAGGUGCUAAAUCCUGCGAAGUGUGAUGCUUCGAGAGAUAAGAG,AL591980.1/89597-89491,89597-89491 66651-66543,0,106,AL591980.1/89597-89491
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,414,AL591980.1,1,sp|AL591980.1|AL591980 Listeria monocytogenes strain EGD; complete genome; segment 8/12,1,68,66651,66543,98.71,CUCUUAUCCAGAGCGGUAGAGGGACUGACCCUUUGAAGCCCAGCAACCUACACAUAUAAGUGAAAGGUGCUAAUCUGUUGCAGGAGUAUUAUCUUCUGAACGAUGAGAG,AL591980.1/66651-66543,89597-89491 66651-66543,0,108,AL591980.1/66651-66543
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,417,AL591983.1,1,sp|AL591983.1|AL591983 Listeria monocytogenes strain EGD; complete genome segment 11/12,1,69,96176,96058,103.40,AUCUUAUCCAGAGUGGUGGAGGGAAAUGCCCUAUGAAGCCCAGCAACCUAAACAAUAAUUCAUUAUGUGUUUAAGGUGCUAAGUCAUGCAGAACAACUAAUUGUUCUGAAAGAUGAGAA,AL591983.1/96176-96058,96176-96058,0,118,AL591983.1/96176-96058
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,419,AL596163.1,1,sp|AL596163.1|AL596163 Listeria innocua Clip11262 complete genome; segment 1/12,0,70,172398,172500,77.19,UUCUUAUCCAGAGUGGUGGAGGGAAUCGGCCCAGUGAAACCCGGCAGCGGAGCGCAAGUUCUAUGCUAAUUCCGAUCAGAAGUAAUAUUCUGGCAGAUAAGUA,AL596163.1/172398-172500,172398-172500,0,102,AL596163.1/172398-172500
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,420,AL596164.1,1,sp|AL596164.1|AL596164 Listeria innocua Clip11262 complete genome; segment 2/12,1,71,95936,95817,112.78,CUCUUAUCGAGAGCGGCAGAGGGACUGGCCCGAUGAAGCCCGGCAACCUAACUUUAUUUAAGCGUAAAGUGAAGGUGCUAAUUCCAGCAAAAUGGUGUAUUCCGUUUUGGUAGAUAAGAG,AL596164.1/95936-95817,95936-95817,0,119,AL596164.1/95936-95817
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,421,AL596165.1,1,sp|AL596165.1|AL596165 Listeria innocua Clip11262 complete genome; segment 3/12,1,72,180914,180814,107.92,UUCUUAUCACGAAAGGUGGAGGGACUGGCCCUUUGAAGCCUUAGCAACCGGAAUUUAUUUUCACGGUGCUAAUUCCAGCAGUAUAUUCUGAAAGAUAAGUC,AL596165.1/180914-180814 AL591975.1/277926-277826,180914-180814,0,100,AL596165.1/180914-180814
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,422,AL596166.1,1,sp|AL596166.1|AL596166 Listeria innocua Clip11262 complete genome; segment 4/12,0,73,166748,166844,87.02,AACUUAUCAAGAAAGGUGGAGGGUUCUGGCCCAGUGAAGCCUUGGCAACCGGACUUUUCACGGUGCCAAAUCCAGCAGUAUCACUGACAGAUAAGGC,AL596166.1/166748-166844,166748-166844,0,96,AL596166.1/166748-166844
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,425,AL596169.1,1,sp|AL596169.1|AL596169 Listeria innocua Clip11262 complete genome; segment 7/12,1,74,221462,221354,99.98,CUCUUAUCCAGAGCGGUAGAGGGACUGACCCUUUGAAGCCCAGCAACCUACACAUAUAAGUGAAAGGUGCUAAUCUGUUGCAGGAGUAAUAUCUCCUGAACGAUGAGAG,AL596169.1/221462-221354,221462-221354,0,108,AL596169.1/221462-221354
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,426,AL596170.1,1,sp|AL596170.1|AL596170 Listeria innocua Clip11262 complete genome; segment 8/12,1,75,192,86,110.35,CUCUUAUUAUGAGUGGUAGAGGGACUGGCCCGUUGAAACCCAGCAACCUUUCAAUUCGUUGAAAAGGUGCUAAAUCCUGCGAAGUGUGAUGCUUCGAGAGAUAAGAG,AL596170.1/192-86,192-86,0,106,AL596170.1/192-86
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,428,AL596172.1,1,sp|AL596172.1|AL596172 Listeria innocua Clip11262 complete genome; segment 10/12,1,76,176254,176136,100.15,AUCUUAUCCAGAGUGGUGGAGGGAAAUGCCCUGUGAAACCCAGCAACCUAAACAAUAAUUCAUUAUGUGUUUAAGGUGCUAAGUCAUGCAGAACAACGAUUUGUUCUGAAAGAUGAGAA,AL596172.1/176254-176136,176254-176136,0,118,AL596172.1/176254-176136
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,929,AP001510.1,1,sp|AP001510.1|AP001510 Bacillus halodurans genomic DNA; section 4/14.,1,77,12492,12388,127.16,UUCUUAUCCAGAGUGGUGGAGGGACUGGCCCUGUGAAGCCCGGCAACCUCUUUUUUUAAAGAAGGUGCCAAUUCCAGCAGAACAUGAUGUUCUGAAAGAUAAGAA,AP001510.1/12492-12388,12492-12388,0,104,AP001510.1/12492-12388
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,930,AP001511.1,1,sp|AP001511.1|AP001511 Bacillus halodurans genomic DNA; section 5/14.,0,78,149016,149129,102.41,GACUUAUCGAGAGAGGCAGAGGGACUGACCCGAUGAUGCCCGGCAACCCGUUUGUUAGCCAAGCAAACGAAGGUGCUAAUUUCAGCAGAAUGAUUUCAUUCUGGAAGAUAAGCG,AP001511.1/149016-149129,149016-149129,0,113,AP001511.1/149016-149129
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,931,AP001512.1,1,sp|AP001512.1|AP001512 Bacillus halodurans genomic DNA; section 6/14.,0,79,200657,200766,109.08,UUCUUAUCCAGAGAGGUGGAGGGAACGGCCCGAAGAAACCUCAGCAACCAGCCACGAUCCUGUGGUCAGGUGCUAAUUCCUGCAAGCAUUAUUUGCUUGAGAGAUAAGAG,AP001512.1/200657-200766,200657-200766,0,109,AP001512.1/200657-200766
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,937,AP001518.1,1,sp|AP001518.1|AP001518 Bacillus halodurans genomic DNA; section 12/14.,1,80,300422,300310,114.98,CUCUUAUCAUGAGAGGUGGAGGGACUGGCCCGAUGAAGCCCAGCAACCGCCAAGCAGCAAAUCGCUUGGAAAAGGUGCUAAUUCCUGCAAAGCGAUGCUUUGAGAGAUGAGAG,AP001518.1/300422-300310,300422-300310 137068-136956,0,112,AP001518.1/300422-300310
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,937,AP001518.1,1,sp|AP001518.1|AP001518 Bacillus halodurans genomic DNA; section 12/14.,1,81,137068,136956,94.65,CUCUUAUCCAGAGUUGGUGGAGGGACAGGCCCGAAGAAACCCCAGCAACCAACACCUGUUAAACAAAGGUGAAAAGGUGCUAACCUGCAAGGCGUUGCCUUGAAAGAUAAGAG,AP001518.1/137068-136956,300422-300310 137068-136956,0,112,AP001518.1/137068-136956
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,991,AP003129.2,1,sp|AP003129.2|AP003129 Staphylococcus aureus subsp. aureus N315 genomic DNA; complete genome; section 1/10.,0,82,15956,16054,80.12,UUCUUAUUGUGAGAAGUUGAGGGACUUGGCCCUGUGAUACUUCAGCAACCGACUUUAUAGCACGGUGCUAAAACCAACGAGUUACUCGAAUGAUAAGUA,AP003129.2/15956-16054 AP003358.2/15956-16054 AP004822.1/15949-16047,15956-16054,0,98,AP003129.2/15956-16054
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,993,AP003131.2,1,sp|AP003131.2|AP003131 Staphylococcus aureus subsp. aureus N315 genomic DNA; complete genome; section 3/10.,0,83,276406,276509,103.24,CUCUUAUCGAGAGUGGUGGAGGGAUGUGCCCUACGAAGCCCGGCAACCGUCUUAUAUAGAAAUGGUGCCAAUUCACAUAAAGUUUUAACUUUUGAAGAUGAGAG,AP003131.2/276406-276509 AP003360.2/213745-213848 AP004824.1/261550-261653,276406-276509,0,103,AP003131.2/276406-276509
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,997,AP003135.2,1,sp|AP003135.2|AP003135 Staphylococcus aureus subsp. aureus N315 genomic DNA; complete genome; section 7/10.,1,84,43428,43317,97.80,CUCUUAUCCUGAGUGGUGGAGGGACAUGGACCCAAUGAAACCCAGCAACCUCUUUUUUUAUAAAAGAAAGGUGCCAAACCGUUUGCAGACAAAUAGGUCUGAACGAUAAGAG,AP003363.2/186489-186378 AP003135.2/43428-43317 AP004828.1/56121-56010,43428-43317,0,111,AP003135.2/43428-43317
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,998,AP003136.2,1,sp|AP003136.2|AP003136 Staphylococcus aureus subsp. aureus N315 genomic DNA; complete genome; section 8/10.,1,85,289345,289250,95.11,CACUUAUCUAGAGAGGUGGAGGGACUGGCCCUAUGAAGCCUCGGCAACAUCUCGAAUGUGCCAAUUCCAGUAACCGUAAUGGUUUGAAGAUAAGCA,AP003136.2/289345-289250 AP003365.2/23502-23407 AP004829.1/296359-296264,289345-289250,0,95,AP003136.2/289345-289250
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1010,AP003193.2,1,sp|AP003193.2|AP003193 Clostridium perfringens str. 13 DNA; complete genome; section 9/10.,1,86,260931,260768,99.88,AUCUUAUCAAGAGAGGUGGAGGGACUGGCCCUGUGAAACCCAGCAACCGGUAAUUCUUUGCGGUUAAAACAAUGCUGAUUUUAAAAUAAAAAAAUCAGUAGUAAUUUCCUAUGCAAAGAUUUAUAGCGGUGCUAAAUCCUGCGGUAGAAACUGAGAGAUAAGAA,AP003193.2/260931-260768,95783-95678 260931-260768,0,163,AP003193.2/260931-260768
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1010,AP003193.2,1,sp|AP003193.2|AP003193 Clostridium perfringens str. 13 DNA; complete genome; section 9/10.,1,87,95783,95678,104.26,CUCUUAUCCAGAGAGGUGGAGGGAAAAAGGCCCUAUGAAACCCGGCAACCAGUGAGAAAUCACUACGGUGCCAAUUCCGGUAAAGAAAUUCUUUACAAGAUGAGAG,AP003193.2/95783-95678,95783-95678 260931-260768,0,105,AP003193.2/95783-95678
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1012,AP003358.2,1,sp|AP003358.2|AP003358 Staphylococcus aureus subsp. aureus Mu50 genomic DNA; complete sequence; section 1/9.,0,88,15956,16054,80.12,UUCUUAUUGUGAGAAGUUGAGGGACUUGGCCCUGUGAUACUUCAGCAACCGACUUUAUAGCACGGUGCUAAAACCAACGAGUUACUCGAAUGAUAAGUA,AP003129.2/15956-16054 AP003358.2/15956-16054 AP004822.1/15949-16047,15956-16054,0,98,AP003358.2/15956-16054
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1014,AP003360.2,1,sp|AP003360.2|AP003360 Staphylococcus aureus subsp. aureus Mu50 genomic DNA; complete sequence; section 3/9.,0,89,213745,213848,103.24,CUCUUAUCGAGAGUGGUGGAGGGAUGUGCCCUACGAAGCCCGGCAACCGUCUUAUAUAGAAAUGGUGCCAAUUCACAUAAAGUUUUAACUUUUGAAGAUGAGAG,AP003131.2/276406-276509 AP003360.2/213745-213848 AP004824.1/261550-261653,213745-213848,0,103,AP003360.2/213745-213848
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1017,AP003363.2,1,sp|AP003363.2|AP003363 Staphylococcus aureus subsp. aureus Mu50 genomic DNA; complete sequence; section 6/9.,1,90,186489,186378,97.80,CUCUUAUCCUGAGUGGUGGAGGGACAUGGACCCAAUGAAACCCAGCAACCUCUUUUUUUAUAAAAGAAAGGUGCCAAACCGUUUGCAGACAAAUAGGUCUGAACGAUAAGAG,AP003363.2/186489-186378 AP003135.2/43428-43317 AP004828.1/56121-56010,186489-186378,0,111,AP003363.2/186489-186378
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1019,AP003365.2,1,sp|AP003365.2|AP003365 Staphylococcus aureus subsp. aureus Mu50 genomic DNA; complete sequence; section 8/9.,1,91,23502,23407,95.11,CACUUAUCUAGAGAGGUGGAGGGACUGGCCCUAUGAAGCCUCGGCAACAUCUCGAAUGUGCCAAUUCCAGUAACCGUAAUGGUUUGAAGAUAAGCA,AP003136.2/289345-289250 AP003365.2/23502-23407 AP004829.1/296359-296264,23502-23407,0,95,AP003365.2/23502-23407
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1057,AP004595.1,1,sp|AP004595.1|AP004595 Oceanobacillus iheyensis HTE831 genomic DNA; section 3/13.,0,92,126926,127031,108.62,GACUUAUCAAGAGAGAUGGAGGGAUUGGCCCGAUGAAGUCUCAGCAACCAGCCUAGAUAAGGUAUGGUGCUAAUUCCAAUAGGCUUACAAGCCUUAAAGAUAAGAA,AP004595.1/126926-127031,126926-127031,0,105,AP004595.1/126926-127031
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1058,AP004596.1,1,sp|AP004596.1|AP004596 Oceanobacillus iheyensis HTE831 genomic DNA; section 4/13.,1,93,197999,197893,110.38,UUCUUAUCCAGAGAGGUGGAGGGACUGGCCCAAGGAAGCCUCGGCAACAGACUUAUUUGAUUAAGUACUGUGCCAAUUCCAGUAGCGUAAUUGCUAGAAGAUGAGAA,AP004596.1/197999-197893,197999-197893,0,106,AP004596.1/197999-197893
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1059,AP004597.1,1,sp|AP004597.1|AP004597 Oceanobacillus iheyensis HTE831 genomic DNA; section 5/13.,0,94,118941,119041,102.67,UACUUAUCAAGAGAGGUGGAGGGACUGGCCCGCUGAAACCUCAGCAACAGAACGCAUCUGUCUGUGCUAAAUCCUGCAAGCAAUAGCUUGAAAGAUAAGUU,AP004597.1/118941-119041,118941-119041,0,100,AP004597.1/118941-119041
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1062,AP004600.1,1,sp|AP004600.1|AP004600 Oceanobacillus iheyensis HTE831 genomic DNA; section 8/13.,1,95,266413,266303,90.51,CUCUUAUUCAGAGUUGGUGGAGGGACAGACCCGAUGAAGCCCAGCAACCAUCACUACUGGUGAAAAGGUGCUAAUCUGAUGCAAGGAUAAUAGUUCCUUGAACAAUAAGAG,AP004600.1/266413-266303,266413-266303 35266-35164,0,110,AP004600.1/266413-266303
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1062,AP004600.1,1,sp|AP004600.1|AP004600 Oceanobacillus iheyensis HTE831 genomic DNA; section 8/13.,1,96,35266,35164,85.61,AACUUAUCCAGAGUGACGGAGGGAACAGGACCUACGAUGUCACAGCAACCUACCUUUACGGAGUGGUGCUUCUUCCUGCAGAAUUUUUUCUGAAAGAUAAGGU,AP004600.1/35266-35164,266413-266303 35266-35164,0,102,AP004600.1/35266-35164
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1063,AP004601.1,1,sp|AP004601.1|AP004601 Oceanobacillus iheyensis HTE831 genomic DNA; section 9/13.,1,97,38307,38208,105.50,CUCUUAUCUAGAGCGGUGGAGGGACUGGCCCUUUGAAACCGCGGCAACCUUCAUAAUUAAAUGAAAGGUGCCAAUUCCUGCAGAAAAUGAAAGAUGAGAG,AP004601.1/38307-38208,38307-38208,0,99,AP004601.1/38307-38208
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1064,AP004602.1,1,sp|AP004602.1|AP004602 Oceanobacillus iheyensis HTE831 genomic DNA; section 10/13.,1,98,158065,157957,76.52,UCCUUAUCAAGAGUCGGGGGAGGAAUCUGGUCCAUUGAUCCCGCAGCAACCAGUUACAAUGAAGUAACAUGGUGCUCAUUCCAGCAAGCGUAGGCUUGAUAGAUGAGAA,****    NEW  HIT  #1  ****,9845-9739,2,0,AP004602.1/158065-157957
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1064,AP004602.1,1,sp|AP004602.1|AP004602 Oceanobacillus iheyensis HTE831 genomic DNA; section 10/13.,1,99,9845,9739,105.20,UUCUUAUCAUGAGAGGCGGAGGGAAAUGGCCCAACGAAACCUCGGCAACAGGUUCUUAUUAGAAUACUGUGCCAAUUCCAUCAAGCAAAUUGCUUGAAAGAUAAGAG,AP004602.1/9845-9739,9845-9739,0,106,AP004602.1/9845-9739
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1065,AP004603.1,1,sp|AP004603.1|AP004603 Oceanobacillus iheyensis HTE831 genomic DNA; section 11/13.,0,100,162173,162282,107.00,CUCUUAUCAAGAGUGGUGGAGGGAAUAGGCCCUGCGAAGCCCGGCAACCUGUAGCAAUUGCUAUUGAAAGGUGCUAAAUCCUACAGACUUCAUCGUCUGGAAGAUAAGAG,AP004603.1/162173-162282,294572-294688 162173-162282 200738-200630,0,109,AP004603.1/162173-162282
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1065,AP004603.1,1,sp|AP004603.1|AP004603 Oceanobacillus iheyensis HTE831 genomic DNA; section 11/13.,0,101,200864,200971,95.20,UUCUUAUCGAGAGAAGCUAAGGGACCUGGCCUGUUGACGCUUCAGCAACCUCUAUCUCCAUUAGAAAGGUGCUACCUCCAGCAAGAUGUAUGUCUUGAAAGAUAAGAG,****    NEW  HIT  #2  ****,294572-294688 162173-162282 200738-200630,2,0,AP004603.1/200864-200971
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1065,AP004603.1,1,sp|AP004603.1|AP004603 Oceanobacillus iheyensis HTE831 genomic DNA; section 11/13.,0,102,294572,294688,90.42,UUCUUAUCUAGAGAGAUUGAGGGAUCAGGCCCUAUGACAUCUCGGCAGCGGAUUCUUUAUAUUAAAGAAUACUGUGCCAAUUCCUGCAAAUGCAAACGAGCAUUUGAAAGAUGAGAA,AP004603.1/294572-294688,294572-294688 162173-162282 200738-200630,0,116,AP004603.1/294572-294688
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1065,AP004603.1,1,sp|AP004603.1|AP004603 Oceanobacillus iheyensis HTE831 genomic DNA; section 11/13.,1,103,200738,200630,95.48,AUCUUAUCCUGAGAGGUGGAGGGAAAUGGCCCAAAGAAGCCUCGGCAACAGGUUCUAGCUUGAAUACUGUGCCAAAUCCAUCAAGUAUUCUAUGCUUGGUAGAUAAGAG,AP004603.1/200738-200630,294572-294688 162173-162282 200738-200630,0,108,AP004603.1/200738-200630
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1066,AP004604.1,1,sp|AP004604.1|AP004604 Oceanobacillus iheyensis HTE831 genomic DNA; section 12/13.,1,104,167020,166901,97.80,CUCUUAUUGAGAGUGGCUGAGGGACUGGCCCUGUGACGCCCGGCAACCGUUCAUCGUAAUUCCAGUGAUGAAUAGGUGCUAAAUCCUGCAAAAUACGGACAGUAUUUUGAGAAAUAAGAG,AP004604.1/167020-166901,167020-166901,0,119,AP004604.1/167020-166901
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1068,AP004822.1,1,sp|AP004822.1|AP004822 Staphylococcus aureus subsp. aureus MW2 DNA; complete genome; strain:MW2; section 1/10.,0,105,15949,16047,80.12,UUCUUAUUGUGAGAAGUUGAGGGACUUGGCCCUGUGAUACUUCAGCAACCGACUUUAUAGCACGGUGCUAAAACCAACGAGUUACUCGAAUGAUAAGUA,AP003129.2/15956-16054 AP003358.2/15956-16054 AP004822.1/15949-16047,15949-16047,0,98,AP004822.1/15949-16047
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1070,AP004824.1,1,sp|AP004824.1|AP004824 Staphylococcus aureus subsp. aureus MW2 DNA; complete genome; strain:MW2; section 3/10.,0,106,261550,261653,103.24,CUCUUAUCGAGAGUGGUGGAGGGAUGUGCCCUACGAAGCCCGGCAACCGUCUUAUAUAGAAAUGGUGCCAAUUCACAUAAAGUUUUAACUUUUGAAGAUGAGAG,AP003131.2/276406-276509 AP003360.2/213745-213848 AP004824.1/261550-261653,261550-261653,0,103,AP004824.1/261550-261653
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1074,AP004828.1,1,sp|AP004828.1|AP004828 Staphylococcus aureus subsp. aureus MW2 DNA; complete genome; strain:MW2; section 7/10.,1,107,56121,56010,97.80,CUCUUAUCCUGAGUGGUGGAGGGACAUGGACCCAAUGAAACCCAGCAACCUCUUUUUUUAUAAAAGAAAGGUGCCAAACCGUUUGCAGACAAAUAGGUCUGAACGAUAAGAG,AP003363.2/186489-186378 AP003135.2/43428-43317 AP004828.1/56121-56010,56121-56010,0,111,AP004828.1/56121-56010
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1075,AP004829.1,1,sp|AP004829.1|AP004829 Staphylococcus aureus subsp. aureus MW2 DNA; complete genome; strain:MW2; section 8/10.,1,108,296359,296264,95.11,CACUUAUCUAGAGAGGUGGAGGGACUGGCCCUAUGAAGCCUCGGCAACAUCUCGAAUGUGCCAAUUCCAGUAACCGUAAUGGUUUGAAGAUAAGCA,AP003136.2/289345-289250 AP003365.2/23502-23407 AP004829.1/296359-296264,296359-296264,0,95,AP004829.1/296359-296264
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1095,AP005037.1,1,sp|AP005037.1|AP005037 Streptomyces avermitilis genomic DNA; complete genome; section 17/30.,1,109,57876,57730,64.31,CGCUCAUCCAGAGGGGCAGAGGGAUACGGCCCGAUGAAGCCCCGGCAACCCUCCAGCCGGUCUUGUCACGUUGAUGUGGCGAGGCUCCCGGCUCGGGAAGGUGCCAAAUCCGUCUCACGGCGAAGUGCGUCGUGAGGAAGAUGAGGA,AP005037.1/57876-57730,57876-57730,0,146,AP005037.1/57876-57730
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,39796,U52812.1,1,sp|U52812.1|BS52812 Bacillus subtilis S-adenosylmethionine synthetase (metE) gene; complete cds; and phosphoenolpyruvate carboxykinase (ppc) and asparagine synthetase (asn) genes; partial cds.,0,110,691,829,89.17,CUCUUAUCCCGAGCUGGCGGAGGGACAGGCCCUAUGAAGCCCAGCAACCGGUUUCUCUGUUAUUUAUUAUGUUCAAUUGAGUGAGACAACCAAGGUGCUAACCUGUUGCAAGGUUGUAUGAUUCCUUGAGCGAUAAGAG,U52812.1/691-829,691-829,0,138,U52812.1/691-829
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,39862,AJ002571.1,1,sp|AJ002571.1|BSAJ2571 Bacillus subtilis 168 56 kb DNA fragment between xlyA and ykoR,1,111,38016,37861,83.94,CUCUUAUCGAGAGUUGGGCGAGGGAUUGGCCUUUUGACCCCAACAGCAACCGACCGUAAUACCAUUGUGAAAUGGGGCGCACUGCUUUUCGCGCCGAGACUGAUGUCUCAUAAGGCACGGUGCUAAUUCCAUCAGAUUGUGUCUGAGAGAUGAGAG,AJ002571.1/38016-37861 Z99110.2/175456-175301,38016-37861,0,155,AJ002571.1/38016-37861
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,40073,D83026.1,1,sp|D83026.1|BSD026 Bacillus subtilis genome sequence covering lic-cel region.,1,112,26298,26192,103.62,ACCUUAUCAAGAGAGGUGGAGGGACUGGCCCUAUGAUACCCGGCAACCGCUGUUUCAAACAGAAUGGUGCUAAAUCCUUAAGAACAUUGCGUUCUUGCAGAUGAGGC,D83026.1/26298-26192 Z99123.2/187154-187260,24908-24802 26298-26192,0,106,D83026.1/26298-26192
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,40073,D83026.1,1,sp|D83026.1|BSD026 Bacillus subtilis genome sequence covering lic-cel region.,1,113,24908,24802,104.96,UCCUUAUCAAGAGAGGUGGAGGGACUGGCCCUGCGAUACCCGGCAACCGCUGUUUAACAGAAUGGUGCUAAAUCCUUUAGAGCAAUGAUUGCUCUUGAAGAUAAGGU,D83026.1/24908-24802 Z99123.2/188544-188650,24908-24802 26298-26192,0,106,D83026.1/24908-24802
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,41459,AJ000974.1,1,sp|AJ000974.1|BSPYREYLO Bacillus subtilis pyrE to yloA gene region,0,114,281,386,104.73,AACUUAUCAAGAGCGGCUGAGGGACUGGACCUAUGAAGCCCGGCAACCUGCAUAGUUUGUAAGGUGCUACUUCCAGCAAAAUGAAUUCCAUUUUGAAAGAUAAGGG,M59757.2/12498-12603 Z99112.2/26533-26638 AJ000974.1/281-386,281-386,0,105,AJ000974.1/281-386
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,41460,M59757.2,1,sp|M59757.2|BSPYROP Bacillus subtilis ORF1A (pyrR); putative membrane-bound uracil permease (pyrP); aspartate transcarbamylase (pyrB); dihydroorotase (pyrC); glutaminase of carbamyl phosphate synthetase (pyrAA); carbamyl phosphate synthetase (pyrAB); dihydroorotase dehydrogenase (pyrD); OMP decarboxylase (pyrF); and OMP-PRPP transferase (pyrE) genes; complete cds; and unknown gene.,0,115,12498,12603,104.73,AACUUAUCAAGAGCGGCUGAGGGACUGGACCUAUGAAGCCCGGCAACCUGCAUAGUUUGUAAGGUGCUACUUCCAGCAAAAUGAAUUCCAUUUUGAAAGAUAAGGG,M59757.2/12498-12603 Z99112.2/26533-26638 AJ000974.1/281-386,12498-12603,0,105,M59757.2/12498-12603
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42386,Z99109.2,1,sp|Z99109.2|BSUB0006 Bacillus subtilis complete genome (section 6 of 21): from 1011039 to 1209781.,1,116,169069,168952,116.40,UUCUUAUCAAGAGAAGCAGAGGGACUGGCCCGACGAAGCUUCAGCAACCGGUGUAAUGGCGAUCAGCCAUGACCAAGGUGCUAAAUCCAGCAAGCUCGAACAGCUUGGAAGAUAAGAA,Y09476.1/38002-37885 Z99109.2/169069-168952,169069-168952,0,117,Z99109.2/169069-168952
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42387,Z99110.2,1,sp|Z99110.2|BSUB0007 Bacillus subtilis complete genome (section 7 of 21): from 1209742 to 1410982.,0,117,47875,47995,114.57,UUCUUAUCGUGAGAGGUGGAGGGACUGGCCCUUAGAAACCUCAGCAACCGGCUUGUUUUGCAUUUGCAAAGCGCCAAGGUGCUAAAUCCAGCAAGCGUUUUUUAUGCUUGGAAGAUAAGAA,Z99110.2/47875-47995,175456-175301 47875-47995,0,120,Z99110.2/47875-47995
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42387,Z99110.2,1,sp|Z99110.2|BSUB0007 Bacillus subtilis complete genome (section 7 of 21): from 1209742 to 1410982.,1,118,175456,175301,83.94,CUCUUAUCGAGAGUUGGGCGAGGGAUUGGCCUUUUGACCCCAACAGCAACCGACCGUAAUACCAUUGUGAAAUGGGGCGCACUGCUUUUCGCGCCGAGACUGAUGUCUCAUAAGGCACGGUGCUAAUUCCAUCAGAUUGUGUCUGAGAGAUGAGAG,AJ002571.1/38016-37861 Z99110.2/175456-175301,175456-175301 47875-47995,0,155,Z99110.2/175456-175301
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42388,Z99111.2,1,sp|Z99111.2|BSUB0008 Bacillus subtilis complete genome (section 8 of 21): from 1410943 to 1602922.,0,119,15242,15342,100.44,UUCUUAUCAAGAGCAGGCAGAGGGACGAGCCCGAUGAAGCCCGGCAACCGACUUAUAAAGCACGGUGCUAAUUCUUGCAGCUAGCGGCUGAGAGAUAAGAU,Z99111.2/15242-15342,13049-12893 15242-15342,0,100,Z99111.2/15242-15342
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42388,Z99111.2,1,sp|Z99111.2|BSUB0008 Bacillus subtilis complete genome (section 8 of 21): from 1410943 to 1602922.,1,120,13049,12893,70.49,CUCUUAUCGAGAGUUGGGCGAGGGAUUUGGCCUUUUGACCCCAAAAGCAACCGACCGUAAUUCCAUUGUGAAAUGGGGCGCAUUUUUUUCGCGCCGAGACGCUGGUCUCUUAAGGCACGGUGCUAAUUCCAUUCAGAUCUGAUCUGAGAGAUAAGAG,Z99111.2/13049-12893,13049-12893 15242-15342,0,156,Z99111.2/13049-12893
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42389,Z99112.2,1,sp|Z99112.2|BSUB0009 Bacillus subtilis complete genome (section 9 of 21): from 1602883 to 1807145.,0,121,26533,26638,104.73,AACUUAUCAAGAGCGGCUGAGGGACUGGACCUAUGAAGCCCGGCAACCUGCAUAGUUUGUAAGGUGCUACUUCCAGCAAAAUGAAUUCCAUUUUGAAAGAUAAGGG,M59757.2/12498-12603 Z99112.2/26533-26638 AJ000974.1/281-386,26533-26638,0,105,Z99112.2/26533-26638
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42391,Z99114.2,1,sp|Z99114.2|BSUB0011 Bacillus subtilis complete genome (section 11 of 21): from 2014895 to 2207855.,1,122,9567,9476,94.03,UUUCUAUCCAGAGAGGUGGAGGGACUGGCCCUAUGAAACCUCGGCAACAUUAUUGUGCCAAUUCCAGCAAGCGCUAGCUUGAAAGAUAGGAA,AF027868.1/5245-5154 Z99114.2/9567-9476,9567-9476,0,91,Z99114.2/9567-9476
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42396,Z99119.2,1,sp|Z99119.2|BSUB0016 Bacillus subtilis complete genome (section 16 of 21): from 3013458 to 3213379.,1,123,114925,114787,89.17,CUCUUAUCCCGAGCUGGCGGAGGGACAGGCCCUAUGAAGCCCAGCAACCGGUUUCUCUGUUAUUUAUUAUGUUCAACUGAGUGAGACAACCAAGGUGCUAACCUGUUGCAAGGUUGUAUGAUUCCUUGAGCGAUAAGAG,Z99119.2/114925-114787 AF008220.1/49783-49921,114925-114787,0,138,Z99119.2/114925-114787
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42397,Z99120.2,1,sp|Z99120.2|BSUB0017 Bacillus subtilis complete genome (section 17 of 21): from 3213330 to 3414388.,1,124,150201,150095,97.20,CUCUUAUCAAGAGAGGUGGAGGGAAGUGCCCUAUGAAGCCCGGCAACCAUCAACACUGUUGAAAUGGUGCCAAUUCACACGAAGCGUUCAGCUUUGAAAGAUGAGAG,Z99120.2/150201-150095,150201-150095,0,106,Z99120.2/150201-150095
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42400,Z99123.2,1,sp|Z99123.2|BSUB0020 Bacillus subtilis complete genome (section 20 of 21): from 3809641 to 4010779.,0,125,187154,187260,103.62,ACCUUAUCAAGAGAGGUGGAGGGACUGGCCCUAUGAUACCCGGCAACCGCUGUUUCAAACAGAAUGGUGCUAAAUCCUUAAGAACAUUGCGUUCUUGCAGAUGAGGC,D83026.1/26298-26192 Z99123.2/187154-187260,188544-188650 187154-187260,0,106,Z99123.2/187154-187260
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42400,Z99123.2,1,sp|Z99123.2|BSUB0020 Bacillus subtilis complete genome (section 20 of 21): from 3809641 to 4010779.,0,126,188544,188650,104.96,UCCUUAUCAAGAGAGGUGGAGGGACUGGCCCUGCGAUACCCGGCAACCGCUGUUUAACAGAAUGGUGCUAAAUCCUUUAGAGCAAUGAUUGCUCUUGAAGAUAAGGU,D83026.1/24908-24802 Z99123.2/188544-188650,188544-188650 187154-187260,0,106,Z99123.2/188544-188650
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42450,Y09476.1,1,sp|Y09476.1|BSY09476 B.subtilis 54kb genomic DNA fragment,1,127,38002,37885,116.40,UUCUUAUCAAGAGAAGCAGAGGGACUGGCCCGACGAAGCUUCAGCAACCGGUGUAAUGGCGAUCAGCCAUGACCAAGGUGCUAAAUCCAGCAAGCUCGAACAGCUUGGAAGAUAAGAA,Y09476.1/38002-37885 Z99109.2/169069-168952,38002-37885,0,117,Y09476.1/38002-37885
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,26737,U36379.1,1,sp|U36379.1|SA36379 Staphylococcus aureus S-adenosylmethionine synthetase gene; complete cds.,0,128,1,106,66.18,AUCCUGAGUGGUGGAGGGACAUGGACCCAAUGAAACCCAGCAACCUCUUUUUUAUAAAAGAAAGGUGCCAAACCGUUUGCAGACAAAUAGGUCUGAACGAUAAGAG,U36379.1/1-106,1-106,0,105,U36379.1/1-106
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,27117,L42943.1,1,sp|L42943.1|SAPEPCK Staphylococcus aureus (clone KIN50) phosphoenolpyruvate carboxykinase (pckA) gene; complete cds.,1,129,254,144,97.95,CUCUUAUCCUGAGUGGUGGAGGGACAUGGACCCAAUGAAACCCAGCAACCUCUUUUUUAUAAAAGAAAGGUGCCAAACCGUUUGCAGACAAAUAGGUCUGAACGAUAAGAG,L42943.1/254-144,254-144,0,110,L42943.1/254-144
./cmzasha --no-stderr --filter 200 25 Rfam/cm/RF00162.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00162_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00162_fwdinf_hmmtype1_Saureus_advance_copy.bin ,Rfam/cm/RF00162.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,28286,AL939119.1,1,sp|AL939119.1|SCO939119 Streptomyces coelicolor A3(2) complete genome; segment 16/29,0,130,177986,178133,69.12,CGCUCAUCCAGAGGGGCAGAGGGAUACGGCCCGAUGAAGCCCCGGCAACCCUCCAGUCGGUUCUUGUCACACGGACGUGGCGAGGCUCCCGGCUAGGGAAGGUGCCAAAUCCGUCUCACGGCGAGAUGCGUCGUGAGGAAGAUGAGGA,AL939119.1/177986-178133,177986-178133,0,147,AL939119.1/177986-178133



THINGS IN Rfam THAT WEREN'T FOUND:


# hits found that weren't in Rfam: 3 (totally new = 3, overlaps hit in Rfam = 0, overlap hits with more than 10 nucs = 0,  total # hits with 0 overlap with Rfam (ignoring sequence matching) = 3)
# Rfam hits not found: 0 (no overlap of >= 10 nucs: 0)
# Rfam seqs not found: 0 (no overlap of >= 10 nucs: too tricky to calculate)