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 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,16415,AC078832.7,1,sp|AC078832.7|AC078832 Staphylococcus aureus clone sabac-135; complete sequence.,1,0,19455,19280,110.81,AAUUGAGUUAGAGGUUGCAUGUUUAAUUAGUAACUUGUCAGAAGUAUUUAUGGUACAUAAGUUGAACAAGUGAAAGGUAAAGAUGCCGAAAUAGAUAUAAACCAUAAAUUAUAUCUAUUGGGACAGUUUUCGAAUAGGAACUGUACUGUCACAGAAUGUGAUGUGCUACCUUAUAU,AP003363.2/54377-54202 AP003134.2/214217-214042 AP004827.1/261938-261763 AC078832.7/19455-19280,19455-19280,0,175,AC078832.7/19455-19280 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17930,AE001799.1,1,sp|AE001799.1|AE001799 Thermotoga maritima section 111 of 136 of the complete genome.,1,1,20444,20268,102.70,GACCCGACGGAGGCGCGCCCGAGAUGAGUAGGCUGUCCCAUCAGGGGAGGAAUCGGGGACGGCUGAAAGGCGAGGGCGCCGAAGGGUGCAGAGUUCCUCCCGCUCUGCAUGCCUGGGGGUAUGGGGAAUACCCAUACCACUGUCACGGAGGUCUCUCCGUGGAGAGCCGAUCGGGUC,AE001799.1/20444-20268,20444-20268,0,176,AE001799.1/20444-20268 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18900,AE004127.1,1,sp|AE004127.1|AE004127 Vibrio cholerae chromosome I; section 35 of 251 of the complete chromosome.,1,2,7715,7538,90.34,UCUAGCAGAAGAGGAGCACUGCCCAGGCAGAUGUUUUGUGGAGCCUCAACUCCAAUACAGAACAUUCAGGGGGAGUAGUGCCGAGGUGAAUCAAAGUUGUGGCUUUGGUUUAUCGGUUGAACGGGCUGAAUCCCUUCAACUGUCAUCAGCUCGAAUCUGAUGAAGAGCUUCUGAGGGA,AE004127.1/7715-7538,7715-7538,0,177,AE004127.1/7715-7538 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,18966,AE004193.1,1,sp|AE004193.1|AE004193 Vibrio cholerae chromosome I; section 101 of 251 of the complete chromosome.,0,3,5679,5861,124.58,UUUCGCCGUAGAGGAGCGGUUACGAAAAGUAUCCACAGUUGGGGUGAUGCCAAUGAAUUGUGGAAAAAGGCGUUGCCGCCGAAGUCAACUUGCCCAUCAACGCAGUUGGCUGGGGUUACAUUCAAUAGGUGUAACACUGCCAUAGUCUAUAUUGUUGUUAAACUAUGGAGCGCUACUGUAGGG,AE004193.1/5679-5861,5679-5861,0,182,AE004193.1/5679-5861 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,19134,AE004361.1,1,sp|AE004361.1|AE004361 Vibrio cholerae chromosome II; section 18 of 93 of the complete chromosome.,1,4,7554,7382,134.63,CCUUUAAGUAGAGGCGCGCUGUUCAUGAGUCGCCAGUCGUAGGUUGACCCCGAUGAUGACUGGUUAAAGGGUACAGCGCCGAAGUGAUCGUUGCGUCAUCAACGUUCGCUGGGCCAGCAUUGAACAAAUGCCGGACUGCCAUAGUGUGUUGUCUAUGGAGCGCUACCUUGAAG,AE004361.1/7554-7382,7554-7382,0,172,AE004361.1/7554-7382 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20399,AE005635.1,1,sp|AE005635.1|AE005635 Escherichia coli O157:H7 EDL933 genome; contig 3 of 3; section 254 of 290.,1,5,3229,3033,63.19,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,AE016989.1/208694-208498 U00006.1/98763-98567 AE005635.1/3229-3033 AE015427.1/2664-2860 AE000476.1/232-36 AP002568.1/229-33,3229-3033,0,196,AE005635.1/3229-3033 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,20887,AE006126.1,1,sp|AE006126.1|AE006126 Pasteurella multocida PM70 section 93 of 204 of the complete genome.,1,6,222,48,132.49,UACUUGUGUAGAGGAGCGAUCACUAUAAGUAUUUUUUCUGAGUGGAUAACGAAGAGGAAAAAGGAAAGGAGUGACCGCCGAAAUCAAUUGAAAGUCAUUUUGAUUGGUUGGUGGCGUAUUCGAAAGGAACGUCAUUGUCAUAGUCUUUUUUAAACUAUGGAGCGCUACUGGUUGG,AE006126.1/222-48,222-48,0,174,AE006126.1/222-48 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21208,AE006448.1,1,sp|AE006448.1|AE006448 Lactococcus lactis subsp. lactis IL1403 section 210 of 218 of the complete genome.,0,7,6071,6253,49.70,CACAUCGAUAGAGGUCGCAACUGAUAUGAAUCUACGCCGAGUUGGAGCACAACAAAGACGCGUAUUUAGAGGAGGAGAGGUUGCCGAAAGAAUUUUGUUGCUCAGCAAGGUUCUUGGGCUAGUGAGAAAAACUCACUAGACUGUCGCAAAUGGUUAAUAACCAUGCGGAGGGCUAUUCGUUCA,**** NEW HIT #0 ****,,2,0,AE006448.1/6071-6253 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22320,AE007576.1,1,sp|AE007576.1|AE007576 Clostridium acetobutylicum ATCC824 section 64 of 356 of the complete genome.,0,8,1562,1747,115.71,ACCUUUUGUAGAGGUGCUUUAAGUCAAGAGUAACCGUUUGGAGUUGGCAAACUUAGAUGAACGGUAAAAGGGGCUUUUAGCCGAAGCAUUUAGAUUGGCAGAUUUAUUUGCUGGCUUUUCAUACAACAUAUGAAUGGCUGUCACUUUAUUAGUUAGUUAUUAGGUAAGUGGAGCGCUACAAGGUAC,AE007576.1/1562-1747,1562-1747,0,185,AE007576.1/1562-1747 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22587,AE007843.1,1,sp|AE007843.1|AE007843 Clostridium acetobutylicum ATCC824 section 331 of 356 of the complete genome.,1,9,1920,1745,130.62,AACUGAGGUAGAGGCGCAAAAUUUAAGAGUAGAACUGUGGAGACAAGCACUAUGAAGCAGUUUAAAAGGAAAUUUUGCCGAAGCGUAUAGCUAAUGCUUUAAUGCUGUACUGCUGGGUUUGUAUAAAAUAUGUGCAAAACUGUCACAAAGUAUAAUUGUGGAGAACUAUCAUUGGU,AE007843.1/1920-1745,1920-1745,0,175,AE007843.1/1920-1745 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,22600,AE007856.1,1,sp|AE007856.1|AE007856 Clostridium acetobutylicum ATCC824 section 344 of 356 of the complete genome.,0,10,5090,5262,115.74,ACCUAGGGUAAAGGUGCUGUAGUUAUUAUUAUUUAUUCUUAGCUGGCAAGCUUUGAGGGAUAAAGAAAGGAAUUGCAGCCGAAGAAGGAUUUCCGGCAGGAACUUUUUCUGGUUUUGUAUAAAAUAUAUGCAGAACUGUCACUAUUCUUUUAUAGUGGAGAGCUACAAGGUGC,AE007856.1/5090-5262,5090-5262,0,172,AE007856.1/5090-5262 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25197,AE010489.1,1,sp|AE010489.1|AE010489 Fusobacterium nucleatum subsp. nucleatum ATCC 25586; section 31 of 197 of the complete genome.,1,11,2647,2468,83.21,AUAAAAAAUAGAGGUGCAUAUAUGUAGGUAGUGUGAAAAUGUUAAGGUAUAAGCCACCAAUGUUUCACAUGAAGGGCAUAGUUGCCGAAAGAAAGUUAAUUGCUUAUGAUUAAUUUUCUUGGUCAAUGUCAACAAGCAUUGACUGUCAUAUUCUUUUGAAUAUGGAGAGCUAUUUAUAGU,**** NEW HIT #1 ****,,2,0,AE010489.1/2647-2468 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27528,AE013039.1,1,sp|AE013039.1|AE013039 Thermoanaerobacter tengcongensis strain MB4T; section 66 of 244 of the complete genome.,0,12,9145,9323,74.65,CGCAUAAAUAGAGGAGCUGCCAAGCAUGUAUUUGGCGAGGUGUUAAGGAGAAGAACCUCCAAUACUCGCUGAAGAAGGUUUGGCUGCCGAAAGGGUGAGCUUGUUCUUGAGCUCAUCCUUGGUGGUAAACACAAAGUUUACCACUGUCAUGGGACCUCCCAUGAAGCGCUAUUUAUGCA,AE013039.1/9145-9323,9145-9323,0,178,AE013039.1/9145-9323 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,27638,AE013149.1,1,sp|AE013149.1|AE013149 Thermoanaerobacter tengcongensis strain MB4T; section 176 of 244 of the complete genome.,0,13,9167,9356,113.52,AGGUGAGGUAGAGGCGCGGGUCAUCAAGAGUAACAUGCCAGAGGUGUUAAGGGCCGAUGAAGGUGUGUGAAAGGGGUGCCCGCCGAAGCGCGUAAACUUCCUUAAGGUUUACGCAGCUGGGCCUAUGCCGAACAGGUAUAGGACUGUCACUGAAGGCUCCCCAGGCCUUCAGUGGAGAGCUAUCUCGCUA,AE013149.1/9167-9356,9167-9356,0,189,AE013149.1/9167-9356 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29771,AE015427.1,1,sp|AE015427.1|AE015427 Shigella flexneri 2a str. 301 section 390 of 412 of the complete genome.,0,14,2664,2860,63.19,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,AE016989.1/208694-208498 U00006.1/98763-98567 AE005635.1/3229-3033 AE015427.1/2664-2860 AE000476.1/232-36 AP002568.1/229-33,2664-2860,0,196,AE015427.1/2664-2860 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,29887,AE015545.1,1,sp|AE015545.1|AE015545 Shewanella oneidensis MR-1 section 94 of 457 of the complete genome.,0,15,1265,1436,127.31,CCUUUAAGUAGAGGCGCGCUGCCUAUGACUACUUGUGCGGAGGGUGAUGCCGCAGAUGUACAAGGAAAGGAGUCAGCGCCGAAGUAGCCAGGUCAUCAAACCGAGCUGCUGGUUUUGCAUCAAAUAGGUGCAAGACUGCCAUAGUCAUCCACUAUGGAGCGCUACCUGAAGG,AE015545.1/1265-1436,1265-1436,0,171,AE015545.1/1265-1436 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30171,AE015829.1,1,sp|AE015829.1|AE015829 Shewanella oneidensis MR-1 section 378 of 457 of the complete genome.,1,16,4454,4280,88.23,AGGAACAGAAGAGGAGCGUUAACUAGGUAGUCAAUCAGAGGAGCACAAACUCCAGCGAUGAUUGAUGAGGGAGAUUAGCGCCGAGGCAUAGAUGUGGUUGCUGCAUGUUUAUGUCGGUCGCUUAGGCUGAAUCCUAACGAUUGUCACCUGUAAUUGGUGGAGAGCUUCUGGUGAC,AE015829.1/4454-4280,4454-4280,0,174,AE015829.1/4454-4280 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,0,17,285886,286061,129.00,UAGAAAGGUAGAGGCGCGGUAUUUAAUAGUAUCUGUACAGAUAAAAGCAAGAUGAUGUACAGUGAAAGGAAAUAUCGCCGAAGCAUGCAGUUAAAGCUUUGAUACUGUAUGACUGGUCUUAUUUAAAAUAUGAAUAAGAUUGUCACAAAAUGAAUUUGUGGAGAGCUAUCAUUCAA,AE015937.1/285886-286061,285886-286061,0,175,AE015937.1/285886-286061 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,1,18,195870,195703,98.23,ACCCAGGGUAGAGGAGCUAUAAUUAAGAGUACUUAUCUUAAACUGCCAAGUAAUGAUAGAUAGGAAAAGGAAUUAUAGCCGAAGAAAAUAGGGUGGUAAUCUAUUUUCUGGCUUUGCAUAAAAUAUGUGUAAAGCUGUCACUUUAAAAAGUGUUGAGCUACAGAGGUC,AE015944.1/195870-195703,195870-195703,0,167,AE015944.1/195870-195703 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30286,AE016747.1,1,sp|AE016747.1|AE016747 Staphylococcus epidermidis ATCC 12228; section 4 of 9 of the complete genome.,0,19,182196,182375,109.58,AGAUUUUGAUGAGGCGCAUCAAUCAUGAGUAAACUUUAGAUAAUUUGUCUGCUAACAAUUAUAGAGUUAAAAGGGUGAGAUGCCGAAAUGAUUCAUAAUAGCAGUUAUGAAUCGUUGGACUUAAUGGUUAAGAGCUAUAAGUUUGUCAUUAUUAUUAAAUAAUGGAGUGCAUCACUUGUA,AE016747.1/182196-182375,182196-182375,0,179,AE016747.1/182196-182375 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30287,AE016748.1,1,sp|AE016748.1|AE016748 Staphylococcus epidermidis ATCC 12228; section 5 of 9 of the complete genome.,1,20,182015,181840,106.77,AAUAGAGUUAGAGGUUGCAUUAUUAAUGACUAACUUAUCAGAAGUCGUAUGGGACAUGUGUUGAAUAAGUGAAAGGUAAUAAUGCCGAAAUGAUGUUAUUUCCAUAAAUUAGCAUUGUUGGGACAACUUUCGAAUAGAAGUUGUACUGUCACUUUAUGUGAUGUGCUACCUUAUAU,AF270308.1/2156-2331 AE016748.1/182015-181840 AF269374.1/1074-899,182015-181840,0,175,AE016748.1/182015-181840 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,1,21,235405,235209,62.61,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUAAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,AE016770.1/235405-235209,235405-235209,0,196,AE016770.1/235405-235209 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30335,AE016801.1,1,sp|AE016801.1|AE016801 Vibrio vulnificus CMCP6 chromosome I section 5 of 11 of the complete sequence.,1,22,201083,200905,86.57,UUUUGCAGAAGAGGAGCACUGCCCAGGCAGAUGUUUUGUGGAGCCGCAACUCCAACACAGAACAUUCAGGGGGAGUAGUGCCGAGGUAGAUCAAAAUUGCAGGAUUUGAUCUGUCGGUUGACUUGGGUUGAGUCCCAUCAACUGUCAUCAGCUCAGCCUGAUGAAGAGCUUCUGAGAUG,AE016801.1/201083-200905,201083-200905,0,178,AE016801.1/201083-200905 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30340,AE016806.1,1,sp|AE016806.1|AE016806 Vibrio vulnificus CMCP6 chromosome I section 10 of 11 of the complete sequence.,1,23,278821,278642,131.84,UAUCGACGUAGAGGCGCAAUGGUAAAGAGUAACUAUUAUUGGGGUGAUGCCAAUGAAUAAUAGUGAAAGGUAUCCAUUGCCGAAGUGAAUUGCAUAUCAAAGCAGUUUGCUGGGGUUGCAUCCGAAAGGAACAACACUGCCAUAGUAUUUAAUGUAUAACUAUGGAGCGCUACUGUAGGU,AE016806.1/278821-278642,278821-278642,0,179,AE016806.1/278821-278642 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30416,AE016947.1,1,sp|AE016947.1|AE016947 Enterococcus faecalis V583; section 1 of 11 of the complete genome.,1,24,224792,224618,55.13,AAAAGAGGUAGAGGUCGCGGUUUUUAUUACGCUUGUGGAGUGAGAGGACACUGGGAAGCAAGUUUAGGAUCAAUCGCCGAAAUGCAUAACGGAGCCUCUUCUGUUGUGUGUUGGGACGUAAGUUAAGAGCUUGCGGACUGUCUUAGUAGUGAUGCUAAGUUGUGCUAUGUUUCGU,**** NEW HIT #2 ****,,2,0,AE016947.1/224792-224618 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30449,AE016989.1,1,sp|AE016989.1|AE016989 Shigella flexneri 2a str. 2457T section 12 of 16 of the complete genome.,1,25,208694,208498,63.19,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,AE016989.1/208694-208498 U00006.1/98763-98567 AE005635.1/3229-3033 AE015427.1/2664-2860 AE000476.1/232-36 AP002568.1/229-33,208694-208498,0,196,AE016989.1/208694-208498 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,1,26,234265,234084,119.14,CGGUGAGGUAGAGGUUGCAAUCAUUAAGAGUAUCAUUUCAGGAGAUGUAGUGGCAUUGAUGAAGGAAUGAGAAAGGAAUGGUUGCCGAAGUAAGUCGUGUCCACCAUGCACGCUUGCUGGGUCUGCAUUUAAUAAGUGCAGAACUGUCACAAACGUUUCGUUUGUGGAGAGCUAUCGAGAGG,AE017000.1/234265-234084,234265-234084,0,181,AE017000.1/234265-234084 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,0,27,166090,166271,100.04,CUCAAAGGUAGAGGCCGCGAUAGGAAAGAGUAAGCUAUGGGAGAUUUAAUGGAAUCUGUGAUCAUAGGUUGAAAGGGACUAUUGCCGAAAUAUAAGAAUAACCAUCUUAUUCAUAUAUUGGGACUGCAUUGAAUAAAUGUAGUACUGUCAUAAGAUUUAUUUUAUGGAGAGCUAUUUGGAGA,AE017002.1/166090-166271 AE017028.1/200117-200298,166090-166271,0,181,AE017002.1/166090-166271 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30463,AE017003.1,1,sp|AE017003.1|AE017003 Bacillus cereus ATCC 14579 section 6 of 18 of the complete genome.,1,28,180245,180059,112.27,ACGUGAGAUAGAGGUUGCGAUACUUAUGAGUAUUCUAAUGGAGACACAGAGAUGUCUAUGAACUUAGAUGAAAGGAAGUAUUGCCGAAAUUGAUAAAUUUCUCUGCAUUUAUCAAUUGGGGCUGUUUUCGAAUAGAAACAGAACUGUCAUAUGUACAGACGUGUACGUAUGAAGAGCUAUCUACAAA,AE017003.1/180245-180059,180245-180059,0,186,AE017003.1/180245-180059 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30467,AE017007.1,1,sp|AE017007.1|AE017007 Bacillus cereus ATCC 14579 section 10 of 18 of the complete genome.,0,29,287994,288186,83.86,CGAUGAGGUAGAGGUUGCGACUUUUAAGAGUACGACGGACGAGACACAGAGAAUGUCACCGACUCCGUUUGAAAGGAAAAGUUGCCGAAGUUUAUAUUUCUUCUCUGGAAAUAUGAGCUGGGGCUGUCUCCGAAAGGAACAGAACUGUCACGUUUACAAAAUUACCGUGUAAACGUGGGGUGCUAUCUUAACG,**** NEW HIT #3 ****,,2,0,AE017007.1/287994-288186 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,1,30,274819,274638,120.67,CGGUGAGGUAGAGGUUGCAGUCAUUAAGAGUAUCAUUUCUGGAGAUGUAGUGGCAUUGAUGAAGGAAUGAGAAAGGAAUGAUUGCCGAAGUAAGUUGUGUCCACCAUGCACACUUGCUGGGUCUGCAUUUAAUAAGUGCAGAACUGUCACAAACGUUUCGUUUGUGGAGAGCUAUCGAGAGG,AE017026.1/274819-274638,274819-274638,0,181,AE017026.1/274819-274638 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,0,31,200117,200298,100.04,CUCAAAGGUAGAGGCCGCGAUAGGAAAGAGUAAGCUAUGGGAGAUUUAAUGGAAUCUGUGAUCAUAGGUUGAAAGGGACUAUUGCCGAAAUAUAAGAAUAACCAUCUUAUUCAUAUAUUGGGACUGCAUUGAAUAAAUGUAGUACUGUCAUAAGAUUUAUUUUAUGGAGAGCUAUUUGGAGA,AE017002.1/166090-166271 AE017028.1/200117-200298,200117-200298,0,181,AE017028.1/200117-200298 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30481,AE017029.1,1,sp|AE017029.1|AE017029 Bacillus anthracis str. Ames section 6 of 18 of the complete genome.,1,32,246029,245843,111.94,ACGUGAGAUAGAGGUUGCGAUACUUAUGAGUAUUCUAAUGGAGACACAGAGAGGUCCAUGAAAUUAGAUGAAAGGAAGUAUUGCCGAAAUCGAUAUAUUUCUCUGUAUGUAUCGAUUGGGGCUGUUUUCGAAUAGAAACAGAACUGUCAUAUGUACAGACAUGUACGUAUGAAGAGCUAUCUACAAA,AE017029.1/246029-245843,246029-245843,0,186,AE017029.1/246029-245843 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30485,AE017033.1,1,sp|AE017033.1|AE017033 Bacillus anthracis str. Ames section 10 of 18 of the complete genome.,0,33,217118,217310,91.60,CGAUGAGGUAGAGGUUGCGACUUUUAAGAGUAAAACGGACGAGAUACAGAGAAUGUCUAAGACUCCGUUUGAAAGGAAAAGUUGCCGAAGUUUAUAUUUCUUCUCUGGAAAUAUGAGCUGGGGCUGUGUCUGAAAGGAACAGAACUGUCACGUUUACAAAAUUACCGUGUAAACGUGGGGUGCUAUCUUAACG,**** NEW HIT #4 ****,,2,0,AE017033.1/217118-217310 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,30503,AE017154.1,1,sp|AE017154.1|AE017154 Haemophilus ducreyi strain 35000HP section 4 of 6 of the complete genome.,0,34,86844,87014,104.81,ACAAAUUGUAGAGGUGCAAAUCCGAUAAGUAUUUCUUCUGAGUGGAAAGCGAUGAAGGGGAAGGAAAGGCGUAUUUGCCGAAAUCAAUUAAGCGUCAUCUUAGUUGGUUGGGGUCGUUGCCGAAAGGGACGACACUGUCGUAAUUCAAUAUUACGGAGUGCUACUAUUAGG,AE017154.1/86844-87014,86844-87014,0,170,AE017154.1/86844-87014 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,9665,AF269374.1,1,sp|AF269374.1|AF269374 Staphylococcus epidermidis strain SR1 clone step.1002g10 genomic sequence.,1,35,1074,899,106.77,AAUAGAGUUAGAGGUUGCAUUAUUAAUGACUAACUUAUCAGAAGUCGUAUGGGACAUGUGUUGAAUAAGUGAAAGGUAAUAAUGCCGAAAUGAUGUUAUUUCCAUAAAUUAGCAUUGUUGGGACAACUUUCGAAUAGAAGUUGUACUGUCACUUUAUGUGAUGUGCUACCUUAUAU,AF270308.1/2156-2331 AE016748.1/182015-181840 AF269374.1/1074-899,1074-899,0,175,AF269374.1/1074-899 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,9827,AF269536.1,1,sp|AF269536.1|AF269536 Staphylococcus epidermidis strain SR1 clone step.1008f05 genomic sequence.,1,36,680,500,41.17,AAUAGAGUUAGAGGUUGCAUUAUUAAUGACUAACUUAUCAGAAGUCGUAUGGGACAUGUGUUGAAUAAGUGAAAGGUAAUAAUGCCGAAAUGAUGUUAUUUCCAUAAAUUAGCAUUGUGAAGUUGGUUGAACAAUAAAAACAUCACAACCACGAAUGCUUUCUUCAAUAUUUAUUUGAAUU,AF269536.1/680-500,680-500,0,180,AF269536.1/680-500 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,10597,AF270308.1,1,sp|AF270308.1|AF270308 Staphylococcus epidermidis strain SR1 clone step.4001a10a genomic sequence.,0,37,2156,2331,106.77,AAUAGAGUUAGAGGUUGCAUUAUUAAUGACUAACUUAUCAGAAGUCGUAUGGGACAUGUGUUGAAUAAGUGAAAGGUAAUAAUGCCGAAAUGAUGUUAUUUCCAUAAAUUAGCAUUGUUGGGACAACUUUCGAAUAGAAGUUGUACUGUCACUUUAUGUGAUGUGCUACCUUAUAU,AF270308.1/2156-2331 AE016748.1/182015-181840 AF269374.1/1074-899,2156-2331,0,175,AF270308.1/2156-2331 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz,15278,AF306669.1,1,sp|AF306669.1|AF306669 Staphylococcus aureus strain 8325-4 dap operon; complete sequence.,0,38,1019,1194,102.11,AUAUUUUGAUGAGGCGCAUCAAUCAUGAGUAAAGUUUAGAUUACUGUCUGCUAACAGCUAAAUUUGAAAGGGUGCGAUGCCGAAGCAAUUAUAAUAGCAGUUAUAAUUUGUUGGACUUUUUGGUUAAGAGCUGAGAGUUUGUCAUUAUUUAAAAAUAAUGGAGUGCAUCACUUGUA,AF306669.1/1019-1194,1019-1194,0,175,AF306669.1/1019-1194 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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 4/12,1,39,186683,186486,60.46,UGGUGAGGUAGAGGUUGCGAGAUGCACUAGUAAUUUUUUCGAGGCGAAACAAAGACGCCGACGACAAAGAAUGAACAGGUUGAUCGCCGAAGUGACUAUUUUCUCUUUGUUUAGAAAUAGUUGUUGGGACAGUUUCCUAAAGGGGCUGGACUGCUAUAAGAAUUUGUCGAAAUUUCUUAUAGGUGUGCUAUCUGACAA,**** NEW HIT #5 ****,,2,0,AL591976.1/186683-186486 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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 4/12,1,40,112469,112272,65.23,UGGUGAGGUAGAGGUUGCGAGAUGCACUAGUAAUUUUUUCGAGGCGAAACAAAGACGCCAAUGACAAAAAACGAACAGGUUAAUCGCCGAAGUGACUAUUUUUUCUUUGUAUCGAAAUAGUUGUUGGGACAGUUUCCUAAAGGAGCUGGACUGCUAUAAGAAUUUGUCGAAAUUUCUUAUAGGUGUGCUAUCUGACAA,**** NEW HIT #6 ****,,2,0,AL596166.1/112469-112272 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,483,AL935254.1,1,sp|AL935254.1|AL935254 Lactobacillus plantarum strain WCFS1 complete genome; segment 3/11,0,41,261916,262097,67.20,AUCGAAAGAAGAGGAUGCGGUUAACAAUAGUAGCCGGCUGGAAGUGGGUCACCACUUAUGAAGGUCAGUGAACGGGGCAACCGCCGAAAUCGAUGGAUCAGUGACCGAUUCAUCCGUUGGGCCUUGGUUGAAUAAAUCAUGGACUGUCGCAGCUAGAAUAGUUGCGGGGCGCUAUCGACGAU,**** NEW HIT #7 ****,,2,0,AL935254.1/261916-262097 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,0,42,119931,120105,98.26,GGAUGAGGUAGAGGUGCAAUGCGAAUCAGUACCCACUUGGAGUUUGAUGGAACUAGGAAGAGUGGGGAAAGGUCAAUUUGCCGAAGUGAAUGUAUGUCCAUCCCAUACGUUUGCUGGGUCGUUUUUGAAUAAAAAACGAACUGCCGCUGACUGUUAGCGGAGAGCUAUCUGCCAA,**** NEW HIT #8 ****,,2,0,AP001512.1/119931-120105 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,932,AP001513.1,1,sp|AP001513.1|AP001513 Bacillus halodurans genomic DNA; section 7/14.,1,43,19957,19775,124.39,AGUGAGGAUAGAGGUGCAAAAACCAAGAGUACACAAUUGGAGGAGAAUGAGAUCCGUUGAGAAUUGUGGAAAGGGGAAUUUGCCGAAGCUGGAAGAAUCUCAUGUUCUGAAGGCUGGUUCUGUAUUAAAUAAAUACAGAACUGUCAUAUAGCGGAUGUUGCUAUAUGGAGGGCUAUCUCACGC,AP001513.1/19957-19775,19957-19775,0,182,AP001513.1/19957-19775 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,936,AP001517.1,1,sp|AP001517.1|AP001517 Bacillus halodurans genomic DNA; section 11/14.,1,44,215539,215348,121.13,AGUGAUGGUAGAGGUGCGAAAACCAAGAGUACACAGUCUGAGAGAAAUGAGAAUCGUUGACGACUGUUGGAAAGGGGGAUUCGCCGAAGUGCAGAUCGGGGCUCAUUCCCAUUUGCGCUGGACCUAUGUUGAAUAAGCAUAGGGCUGUCACAACACUAGCCCCAACUAGUGCUGUGGAGAACUAUCUCACGU,AP001517.1/215539-215348,215539-215348,0,191,AP001517.1/215539-215348 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,1,45,272531,272358,137.02,AGAUGGGGUAGAGGAGCGGGUUUUAAGAGUAAGCGCUUGGAGGAUGACAACGAGGAUAAGCGCCGAAAGGAAAACUCGCCGAAGCGGAAGAUGAGUCAAGCGUCUUCUUGCUGGGGUUGCAUUGAAUAAAUGUAACACUGUCACAGCAGAUUGCUGUGGAGAACUACUAACGUU,AP001518.1/272531-272358,272531-272358,0,173,AP001518.1/272531-272358 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,964,AP002568.1,1,sp|AP002568.1|AP002568 Escherichia coli O157:H7 DNA; complete genome; section 19/20.,1,46,229,33,63.19,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,AE016989.1/208694-208498 U00006.1/98763-98567 AE005635.1/3229-3033 AE015427.1/2664-2860 AE000476.1/232-36 AP002568.1/229-33,229-33,0,196,AP002568.1/229-33 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,995,AP003133.2,1,sp|AP003133.2|AP003133 Staphylococcus aureus subsp. aureus N315 genomic DNA; complete genome; section 5/10.,0,47,203486,203661,98.71,AUAUUUUGAUGAGGCGCAUCAAUCAUGAGUAAAGUUUAGAUUACUGUCUGCUAACAGCUGAAUUUGAAAGGGUGCGAUGCCGAAGCGAUUAUAAUAGCAGUUAUAAUUUGUUGGACUUUUUGGUUAAGAGCUGAGAGUUUGUCAUUAUUUAAAAAUAAUGGAGUGCAUCACUUGUA,AP003133.2/203486-203661 AP003362.2/86735-86910,203486-203661,0,175,AP003133.2/203486-203661 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,996,AP003134.2,1,sp|AP003134.2|AP003134 Staphylococcus aureus subsp. aureus N315 genomic DNA; complete genome; section 6/10.,1,48,214217,214042,110.81,AAUUGAGUUAGAGGUUGCAUGUUUAAUUAGUAACUUGUCAGAAGUAUUUAUGGUACAUAAGUUGAACAAGUGAAAGGUAAAGAUGCCGAAAUAGAUAUAAACCAUAAAUUAUAUCUAUUGGGACAGUUUUCGAAUAGGAACUGUACUGUCACAGAAUGUGAUGUGCUACCUUAUAU,AP003363.2/54377-54202 AP003134.2/214217-214042 AP004827.1/261938-261763 AC078832.7/19455-19280,214217-214042,0,175,AP003134.2/214217-214042 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1004,AP003187.2,1,sp|AP003187.2|AP003187 Clostridium perfringens str. 13 DNA; complete genome; section 3/10.,0,49,139222,139393,123.64,GACCAAAGUAGAGGUGCCGUAAUUAAGAGUAGUCAUAAGUAGCUGACAAGUGUUUUAUGUAUGAUGAAAGGGAUUAUGGCCGAAGAGAUAUUAAUGGUGAUUAAUAUUUCUGGGUAUAUGUAUAAUAUGCAUAUAACUGUCACUUUGAAAAAAGUGGAGUGCUACAAGGUAC,AP003187.2/139222-139393,139222-139393,0,171,AP003187.2/139222-139393 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1006,AP003189.2,1,sp|AP003189.2|AP003189 Clostridium perfringens str. 13 DNA; complete genome; section 5/10.,1,50,159236,159062,138.99,AACUGAGAUAGAGGCGCGAUGAUUAAUAGUAUCUUUGCAGAGGUAAGCACAUUGAAGCAAAGUGAAAGGAUGAAUCGCCGAAACCAUUAGAAGAGGCUUUAAUUCUAUUAGGUUGGGGUUGCAUAGAAUAUAUGUAACACUGUCACAAAUUAUUUUGUGGUGUGCUAUCAUGAAA,AP003189.2/159236-159062,159236-159062,0,174,AP003189.2/159236-159062 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1011,AP003194.2,1,sp|AP003194.2|AP003194 Clostridium perfringens str. 13 DNA; complete genome; section 10/10.,1,51,187997,187828,128.08,AAAAGAGGUAGAGGCGCGAGAAUCAAGAUUACUAAAAUGGAGUUAAGUAGCGUAGAAGUUUUAGGAAAGGGAUUAUCGCCGAAGUUUUUGGCUAAUACUUUAAGGCUAAAUGCUGGGGUUGUAUAGAAUAUAUACAACACUGUCACAAAAUGUGGAGAGCUAUCAUCUUA,AP003194.2/187997-187828,187997-187828,0,169,AP003194.2/187997-187828 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1016,AP003362.2,1,sp|AP003362.2|AP003362 Staphylococcus aureus subsp. aureus Mu50 genomic DNA; complete sequence; section 5/9.,0,52,86735,86910,98.71,AUAUUUUGAUGAGGCGCAUCAAUCAUGAGUAAAGUUUAGAUUACUGUCUGCUAACAGCUGAAUUUGAAAGGGUGCGAUGCCGAAGCGAUUAUAAUAGCAGUUAUAAUUUGUUGGACUUUUUGGUUAAGAGCUGAGAGUUUGUCAUUAUUUAAAAAUAAUGGAGUGCAUCACUUGUA,AP003133.2/203486-203661 AP003362.2/86735-86910,86735-86910,0,175,AP003362.2/86735-86910 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,1,53,54377,54202,110.81,AAUUGAGUUAGAGGUUGCAUGUUUAAUUAGUAACUUGUCAGAAGUAUUUAUGGUACAUAAGUUGAACAAGUGAAAGGUAAAGAUGCCGAAAUAGAUAUAAACCAUAAAUUAUAUCUAUUGGGACAGUUUUCGAAUAGGAACUGUACUGUCACAGAAUGUGAUGUGCUACCUUAUAU,AP003363.2/54377-54202 AP003134.2/214217-214042 AP004827.1/261938-261763 AC078832.7/19455-19280,54377-54202,0,175,AP003363.2/54377-54202 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1060,AP004598.1,1,sp|AP004598.1|AP004598 Oceanobacillus iheyensis HTE831 genomic DNA; section 6/13.,0,54,253855,254037,102.28,GUUUUGGAUAGAGGUGCGGAGACCAUCAGUAUAUACGCGGAAGGGAAAUGAGCCCUAGUGAAGCGUAUGGAAAGGGGAAUCUGCCGAAGCGAGUGAAAUACUCAUUCAUUAACUCGUUGGUGCUGCUAUUGAACAAAUAACAGUGCUGUCAUAUAGGAGACUAUAUGGAGGGCUAUCGAGCUG,AP004598.1/253855-254037,253855-254037,0,182,AP004598.1/253855-254037 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.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.,1,55,22341,22165,132.61,CGGUGAGGUAGAGGAGCAUACAACAUUAGUAAUCGACAAGAGGAUGACAACGAUGAUAGUUGGUGGAAGGGUUGUUUGCCGAAGCAUAAUAAGGGUCAGACUUAUUAUUGCUGGUACAUCUUUGAAUAAAAGAUGCACUGUCAUGCAAAAUUAAGUGCAUGGAGAACUACUGAUCGA,AP004601.1/22341-22165,22341-22165,0,176,AP004601.1/22341-22165 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1072,AP004826.1,1,sp|AP004826.1|AP004826 Staphylococcus aureus subsp. aureus MW2 DNA; complete genome; strain:MW2; section 5/10.,0,56,205532,205707,101.92,AUAUUUUGAUGAGGCGCAUCAAUCAUGAGUAAAGUUUAGAUUACUGUCUGCUAACAGCUAAAUUUGAAAGGGUGCGAUGCCGAAGCGAUUAUAAUAGCAGUUAUAAUUUGUUGGACUUUUUGGUUAAGAGCUGAGAGUUUGUCAUUAUUUAAAAAUAAUGGAGUGCAUCACUUGUA,AP004826.1/205532-205707,205532-205707,0,175,AP004826.1/205532-205707 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1073,AP004827.1,1,sp|AP004827.1|AP004827 Staphylococcus aureus subsp. aureus MW2 DNA; complete genome; strain:MW2; section 6/10.,1,57,261938,261763,110.81,AAUUGAGUUAGAGGUUGCAUGUUUAAUUAGUAACUUGUCAGAAGUAUUUAUGGUACAUAAGUUGAACAAGUGAAAGGUAAAGAUGCCGAAAUAGAUAUAAACCAUAAAUUAUAUCUAUUGGGACAGUUUUCGAAUAGGAACUGUACUGUCACAGAAUGUGAUGUGCUACCUUAUAU,AP003363.2/54377-54202 AP003134.2/214217-214042 AP004827.1/261938-261763 AC078832.7/19455-19280,261938-261763,0,175,AP004827.1/261938-261763 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1112,AP005076.1,1,sp|AP005076.1|AP005076 Vibrio parahaemolyticus DNA; chromosome 1; complete sequence; 4/11.,0,58,290738,290918,129.43,UGUUGCCGUAGAGGCGCAGUCUCGAAGAGUAGCUAUUAUUGGGGUGAUGCCAAUGAAUAAUAGUGGAAGGCGAAGAUUGCCGAAGUAAGUCGUAUAUCAAAACGCCUUGCUGGGGUUGUAUCUGAAAGGAACAACACUGCCAUAGUAUAUUUACAUUAAACUAUGGAGCGCUACUGUAGGG,AP005076.1/290738-290918,290738-290918,0,180,AP005076.1/290738-290918 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,1118,AP005082.1,1,sp|AP005082.1|AP005082 Vibrio parahaemolyticus DNA; chromosome 1; complete sequence; 10/11.,0,59,169934,170112,73.28,UUAUGUAGAAGAGGAGCACUGCCCAGGCAGAUGAUUUGUGGAACCGCAAUUCCAAUACCAAUCAUUCAGGGGGAGUAGUGCCGAGGUAAGUCAAAAUUGCAGGGUUUGGCUUGUCGGUUGACUUGGGUUGAGUCCCAUCAACUGUCAUCAGCACCGUCUGAUGAAGAGCUUCUGAGGGU,AP005082.1/169934-170112,169934-170112,0,178,AP005082.1/169934-170112 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,39774,AJ223978.1,1,sp|AJ223978.1|BS43KBDNA Bacillus subtilis 42.7kB DNA fragment from yvsA to yvqA.,0,60,6877,7056,85.27,CAGUGAGGUAGAGGUUGCGCGGAUGAUGAGUCACACAUGCUAGGCUGACAGGGGCUGUUAAACAUGUGUAAAAGGCAUCAGCGCCGAAGUGUGGAGAAAGCCGAUCCUUCUCUAUGCUGGGACUGUAUCUGAAUAAGUGCAGGACUGCCGCGUGCUUUUUCGCGGAGGGCUAUCCGGAGA,**** NEW HIT #9 ****,,2,0,AJ223978.1/6877-7056 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,39914,J03294.1,1,sp|J03294.1|BSAPKII Bacillus subtilis thioredoxin (trx); uvrB and aspartokinase II genes; complete cds.,0,61,2297,2476,118.71,GGUGAAGAUAGAGGUGCGAACUUCAAGAGUAUGCCUUUGGAGAAAGAUGGAUUCUGUGAAAAAGGCUGAAAGGGGAGCGUCGCCGAAGCAAAUAAAACCCCAUCGGUAUUAUUUGCUGGCCGUGCAUUGAAUAAAUGUAAGGCUGUCAAGAAAUCAUUUUCUUGGAGGGCUAUCUCGUUG,Z75208.1/54883-55062 J03294.1/2297-2476 Z99118.2/97320-97141,2297-2476,0,179,J03294.1/2297-2476 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,39939,M93419.1,1,sp|M93419.1|BSASPKIN Bacillus sp. aspartokinase II (alpha and beta subunits) gene; complete cds.,0,62,332,511,126.04,AGUGAAGAUAGAGGUGCGAACUUCAUCAGUAAAAGCUUGGAGAAGAAUGAGCUUCAAUGAAAAGCUUUGAAAGGGAACGUUCGCCGAAGUGAAGAAAAACUCAUUUUUUUCUUUGCUGGUCCUGCAUUUAAGAGAUGCCGGAUUGUCAAGGCGGUGCCGCCUUGGAGAGCUAUCUCACUG,M93419.1/332-511,332-511,0,179,M93419.1/332-511 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42395,Z99118.2,1,sp|Z99118.2|BSUB0015 Bacillus subtilis complete genome (section 15 of 21): from 2812801 to 3013507.,1,63,97320,97141,118.71,GGUGAAGAUAGAGGUGCGAACUUCAAGAGUAUGCCUUUGGAGAAAGAUGGAUUCUGUGAAAAAGGCUGAAAGGGGAGCGUCGCCGAAGCAAAUAAAACCCCAUCGGUAUUAUUUGCUGGCCGUGCAUUGAAUAAAUGUAAGGCUGUCAAGAAAUCAUUUUCUUGGAGGGCUAUCUCGUUG,Z75208.1/54883-55062 J03294.1/2297-2476 Z99118.2/97320-97141,97320-97141,0,179,Z99118.2/97320-97141 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42398,Z99121.2,1,sp|Z99121.2|BSUB0018 Bacillus subtilis complete genome (section 18 of 21): from 3414339 to 3609030.,1,64,6040,5861,85.27,CAGUGAGGUAGAGGUUGCGCGGAUGAUGAGUCACACAUGCUAGGCUGACAGGGGCUGUUAAACAUGUGUAAAAGGCAUCAGCGCCGAAGUGUGGAGAAAGCCGAUCCUUCUCUAUGCUGGGACUGUAUCUGAAUAAGUGCAGGACUGCCGCGUGCUUUUUCGCGGAGGGCUAUCCGGAGA,**** NEW HIT (duplicate of new hit #9) ****,,2,0,Z99121.2/6040-5861 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,42502,Z75208.1,1,sp|Z75208.1|BSZ75208 B.subtilis genomic sequence 89009bp,0,65,54883,55062,118.71,GGUGAAGAUAGAGGUGCGAACUUCAAGAGUAUGCCUUUGGAGAAAGAUGGAUUCUGUGAAAAAGGCUGAAAGGGGAGCGUCGCCGAAGCAAAUAAAACCCCAUCGGUAUUAUUUGCUGGCCGUGCAUUGAAUAAAUGUAAGGCUGUCAAGAAAUCAUUUUCUUGGAGGGCUAUCUCGUUG,Z75208.1/54883-55062 J03294.1/2297-2476 Z99118.2/97320-97141,54883-55062,0,179,Z75208.1/54883-55062 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz,49193,AE000476.1,1,sp|AE000476.1|ECAE476 Escherichia coli K12 MG1655 section 366 of 400 of the complete genome.,1,66,232,36,63.19,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,AE016989.1/208694-208498 U00006.1/98763-98567 AE005635.1/3229-3033 AE015427.1/2664-2860 AE000476.1/232-36 AP002568.1/229-33,232-36,0,196,AE000476.1/232-36 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,1177,X00008.1,1,sp|X00008.1|ECLYSC E.coli lysC gene promoter region,0,67,296,492,62.93,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUAAGGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,X00008.1/296-492,296-492,0,196,X00008.1/296-492 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,1998,X15196.1,1,sp|X15196.1|ECPGI E. coli pgi gene for phosphoglucose isomerase (EC 5.3.1.9),1,68,270,75,54.69,GCAGCCAGAAGAGGCGCGUUGCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,X15196.1/270-75,270-75,0,195,X15196.1/270-75 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,3293,U00006.1,1,sp|U00006.1|ECUW89 E. coli chromosomal region from 89.2 to 92.8 minutes.,1,69,98763,98567,63.19,CAGGCCAGAAGAGGCGCGUUGCCCAAGUAACGGUGUUGGAGGAGCCAGUCCUGUGAUAACACCUGAGGGGGUGCAUCGCCGAGGUGAUUGAACGGCUGGCCACGUUCAUCAUCGGCUACAGGGGCUGAAUCCCCUGGGUUGUCACCAGAAGCGUUCGCAGUCGGGCGUUUCGCAAGUGGUGGAGCACUUCUGGGUGA,AE016989.1/208694-208498 U00006.1/98763-98567 AE005635.1/3229-3033 AE015427.1/2664-2860 AE000476.1/232-36 AP002568.1/229-33,98763-98567,0,196,U00006.1/98763-98567 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00168.cm @RF00168_nonhuman_full_embl.list 1 hmm data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/remember-nuc;56;l-ACGU-_;54;l-AG_-CU;93;l-ACU-G_;92;l-CGU-A-_;110;r-AG-CU-_;109;l-ACU-G_;125;l-ACG-U-_;124;r-AC-GU-_ 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;86;40 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;100;65 2struct-str data/TryAllCm_5.0/RF00168_forwardinf_hmmtype1_Saureus_0MM.bin 1/sub;118;70/sub;100;65 ,Rfam/cm/RF00168.cm (global),/projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz,5859,U32832.1,1,sp|U32832.1|HI32832 Haemophilus influenzae Rd section 147 of 163 of the complete genome.,1,70,9495,9319,132.41,UACAAAAGUAGAGGCGCAAUUAUUAUAAGUAUUUUUUCAGAGUGGAUAACGAAGAAGAAAAAAGAAAGGAAUAGUUGCCGAAAUCAAAUAAAAGUCGUUUUGUUUGGUUGGUGGCGUGCUCGAAAGGGGCGACACUGUCAUAGUUUUUCUGAUUAACUAUGGAGUGCUACGGUUGUU,U32832.1/9495-9319,9495-9319,0,176,U32832.1/9495-9319 THINGS IN Rfam THAT WEREN'T FOUND: # hits found that weren't in Rfam: 11 (totally new = 11, overlaps hit in Rfam = 0, overlap hits with more than 10 nucs = 0, total # hits with 0 overlap with Rfam (ignoring sequence matching) = 11) # 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)