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 --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,74005,AF415210.1,1,sp|AF415210.1|AF415210 Uncultured Bartonella sp. clone BFl7541 16S-23S ribosomal RNA intergenic spacer; partial sequence.,0,6770,698,772,80.2,GGGGCCGUAGCUCAGCUGGGAGAGCACCUGCUUUGCAAGCAGGGGGUCGUCGGUUGAUCCCGUCCGGCUCCACCA,****    NEW  HIT  #35  ****,179-255,2,0,AF415210.1/698-772,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,150672,Y17360.1,1,sp|Y17360.1|LAM17360 Lactobacillus amylolyticus 23S rRNA gene,0,11944,232,308,79.35,GGGCCUAUAGCUCAGCUGGUUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGAUGGUUCCAAAGUCCAUUUAGGCCCA,****    NEW  HIT  #99  ****,365-437,2,0,Y17360.1/232-308,,,76.04
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135510,BX640428.1,1,sp|BX640428.1|BX640428 Bordetella parapertussis strain 12822; complete genome; segment 6/14,1,11116,236424,236349,77,CGCGGGGUGGAGCAGUCUGGCAGCUCGUCGGGCUCAUAACCCGAAGGUCGUAGGUUCAAACCUGCCCCCGCAACCA,****    NEW  HIT  #82  ****,98912-98988 99009-99084 232123-232198 347681-347757 231951-231876,2,0,BX640428.1/236424-236349,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,60368,AF302131.1,1,sp|AF302131.1|AF302131 Streptococcus agalactiae strain L48 23S ribosomal RNA gene; partial sequence; 5S ribosomal RNA gene; complete sequence; tRNA-Val; tRNA-Leu; tRNA-Lys; tRNA-Asp; tRNA-Glu; tRNA-Ser; tRNA-Met; tRNA-Phe; tRNA-Tyr; tRNA-Trp; tRNA-His; and tRNA-Gln genes; complete sequence; and tRNA-Leu gene; partial sequence.,0,5943,1381,1455,65.61,CGCGGGAUGGAGCAGCUAGGUAGCUCGUCGGGCUCAUAAACCCGAAGGUCGUAGGUUCAAAUCCUGCUCCCGCAA,****    NEW  HIT  #33  ****,681-753 756-830 833-905 915-995 1006-1078 1108-1185 1193-1264 1458-1530 1542-1622 1629-1700 1715-1786 1793-1864,2,0,AF302131.1/1381-1455,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,169458,M91385.1,1,sp|M91385.1|SCTRPSER Spiroplasma citri tryptophan codons.,0,13303,1291,1384,63.89,GGAAGUAUACCCAAGUCUCGGUUGAAGGGGGCGGUCUCGAAAACCGUUAGAUGGAGUAAUCCAUGCAAGAGUUCGAAUCUCUUUACUUCCGCCA,****    NEW  HIT  #110  ****,1046-1121 1205-1279,2,0,M91385.1/1291-1384,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95186,AP004593.1,1,sp|AP004593.1|AP004593 Oceanobacillus iheyensis HTE831 genomic DNA; section 1/13.,0,8757,16922,17017,61.71,GGAGGUAUACCCAAGUCUGGCUCGAAAGGGGAUCGGUCUUGAAAACCGACAGGCGGGUCAAACCGCGCGGGGGUUCGAAUCCCUCUACCUCCUCCA,****    NEW  HIT  #52  ****,21773-21845 96468-96543 96545-96620 96669-96744 96749-96833 96851-96925 96931-97019 97023-97099 97101-97177 97197-97272 102449-102524 102526-102601 102650-102725 102730-102814 102832-102906 102912-103000 103004-103080 103082-103158 103178-103253 216167-216243 216263-216335 219619-219693 219697-219770 244280-244354 244362-244437 244748-244823 244873-244956 244968-245042 245112-245187 70273-70197,2,0,AP004593.1/16922-17017,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,89453,AF514305.1,1,sp|AF514305.1|AF514305 Listeria monocytogenes strain 1340 16S-23S ribosomal RNA intergenic spacer and tRNA-Ile gene; partial sequence; and tRNA-Ala gene; complete sequence.,0,7525,1,68,58.96,AUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCA,****    NEW  HIT  #38  ****,115-190,2,0,AF514305.1/1-68,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95242,AP005075.1,1,sp|AP005075.1|AP005075 Vibrio parahaemolyticus DNA; chromosome 1; complete sequence; 3/11.,1,8995,175601,175519,57.18,GCGGAAGUGGCGGAAUUGGUAGACGCACCAGAUUUAGUUCUGGCGCCGCAAGGUGUGAGAGUUCAGUCUCUCCUUCCGCACCA,****    NEW  HIT  #59  ****,190715-190791 206193-206117 175718-175642 175487-175413 175335-175259 175181-175097 175066-174982 174933-174859 174823-174739 174709-174635 174580-174496 174466-174392 174339-174255 174230-174154 174100-174016 173986-173912 173859-173775 173750-173674 173626-173542 173512-173428 173380-173306 173252-173168,2,0,AP005075.1/175601-175519,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,98104,AY007502.1,1,sp|AY007502.1|AY007502 Streptococcus gordonii ComC (comC) gene; complete cds; and ComD (comD) gene; partial cds.,0,9425,1,69,54.76,CAUAGCUCAGCUGGAUAGAGCAUUCGCCUUCUAAGCGAACGGUCGCAAGUUCGAAUCUUGCUGGGAUCA,****    NEW  HIT  #64  ****,,2,0,AY007502.1/1-69,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,189600,AJ012073.1,1,sp|AJ012073.1|WSP012073 Wolbachia sp. Wri glnA and dnaA genes and 2 genes encoding hypothetical proteins,0,13660,4086,4172,53.61,GCGGCCGUGGUGGAAUUGGUAGACACGCAGCGUUGAGGUCGCUGUGGCUCAUAAGGCCUUGGAAGUUCAAGUUUCUCGGCCGCACCA,****    NEW  HIT  #115  ****,,2,0,AJ012073.1/4086-4172,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,98105,AY007503.1,1,sp|AY007503.1|AY007503 Streptococcus mitis strain SF100 ComC (comC) gene; complete cds; and ComD (comD) gene; partial cds.,0,9426,1,68,53.22,AUAGCUCAGCUGGAUAGAGCAUUCGCCUUCUAAGCGAACGGUCGCAGGUUCGAAUCCUGCUGGGAUCA,****    NEW  HIT  #65  ****,,2,0,AY007503.1/1-68,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,65725,AF345268.1,1,sp|AF345268.1|AF345268 Rhizobium giardinii strain H 152 16S ribosomal RNA gene; partial sequence; internal transcribed spacer; complete sequence; and 23S ribosomal RNA; partial sequence.,0,6245,346,416,53.01,GGCCCGUACUCAGUCGGUUAGAGCACACGCUUGAUAAGCGUGGGUCGGUAGUCGAGUCUACCGGGCCACCA,****    NEW  HIT  #34  ****,467-538,2,0,AF345268.1/346-416,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,137927,X86508.1,1,sp|X86508.1|CPPROTRNA C.perfringens Proline-tRNA,0,11296,4,76,50.66,CGGGGUGUGGCGCAGAUGGGAGCCGCGUGGUUUGGGACCAUGAGGUCGCAGGUCGACCCUGUCACCCCGACCA,****    NEW  HIT  #85  ****,,2,0,X86508.1/4-76,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,19339,AE006045.1,1,sp|AE006045.1|AE006045 Pasteurella multocida PM70 section 12 of 204 of the complete genome.,1,1364,10638,10571,49.13,GUUCAGCUGGUUAGAAUACCUGCCUGUCACGCAGGGGGUCGCGGGUUCGAGUCCCGUCCGUUCCGCCA,****    NEW  HIT  #8  ****,,2,0,AE006045.1/10638-10571,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95226,AP005037.1,1,sp|AP005037.1|AP005037 Streptomyces avermitilis genomic DNA; complete genome; section 17/30.,0,8914,280890,280961,48.61,GCGGGUGUAGUUCAGUAGUAGAACAUCCCCCUUCCAGGGGGAAGGCGCAGUGUGCAAUUCCUGUCACCCGCU,****    NEW  HIT  #57  ****,262337-262409 262457-262531 262556-262632 267373-267447 281041-281116 285029-285104 294474-294561 254811-254736 251293-251220 86156-86080,2,0,AP005037.1/280890-280961,,,
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,169376,AL939118.1,1,sp|AL939118.1|SCO939118 Streptomyces coelicolor A3(2) complete genome; segment 15/29,1,13275,243158,243087,48.61,GCGGGUGUAGUUCAGUAGUAGAACAUCCCCCUUCCAGGGGGAAGGCGCAGUGUGCAAUUCCUGUCACCCGCU,****    NEW  HIT (duplicate of new hit #57)   ****,155734-155818 180562-180652 180844-180916 271199-271271 278510-278583 264061-263989 263954-263880 263855-263782 259595-259521 243004-242932 239075-239000 230002-229915 206680-206596 32917-32841 16807-16732,2,0,AL939118.1/243158-243087
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,170874,X65556.1,1,sp|X65556.1|SLGLYUB S.lividans tRNA-GlyU beta gene,0,13333,197,268,48.61,GCGGGUGUAGUUCAGUAGUAGAACAUCCCCCUUCCAGGGGGAAGGCGCAGUGUGCAAUUCCUGUCACCCGCU,****    NEW  HIT (duplicate of new hit #57)   ****,351-423,2,0,X65556.1/197-268
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135460,BX294153.1,1,sp|BX294153.1|BX294153 Pirellula sp. strain 1 complete genome; segment 21/24,1,10861,134797,134726,48.58,GGGCUGGUAGCUGAGACGGUCUAGCGGCGGUCUGAAGAACCGCAGACGAGGAUUCGAGCGCCUCCCGGCCCA,****    NEW  HIT  #79  ****,193578-193650 193760-193832 170882-170809 134671-134599 134431-134359 134347-134275 134197-134125 134104-134033 133980-133910 133901-133830 133744-133673 133566-133492 133475-133402 133129-133055 132826-132756 132736-132665 132280-132207 132188-132118 132112-132041 132028-131955 131941-131858 131684-131609 131598-131526 131514-131444 131244-131173 130969-130897 130485-130415,2,0,BX294153.1/134797-134726
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,140133,Y15939.1,1,sp|Y15939.1|DNO15939 Dichelobacter nodosus askA gene (partial); glpA; tRNA-Ser; intC; vapG; and vapH genes and ORF242; ORF171; ORF374 and ORF108 DNA,0,11326,1266,1358,47.06,CGAGAGGUGGCCAGAGUGGCUGAAGGCACUCCCCUGCUAAGGAGCAUAGGGUUUAUAGCUCUAUCGAGAGUUCGAAUCUCUUCCUCUCCGCCA,****    NEW  HIT  #87  ****,,2,0,Y15939.1/1266-1358
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,18620,AE005323.1,1,sp|AE005323.1|AE005323 Escherichia coli O157:H7 EDL933 genome; contig 1 of 3; section 147 of 155.,0,1242,5995,6071,45.04,CCGCCAUUAGCUCAUCAGGAAAGAGCGCCAGCUUUCGAAGCUGGUUGCGCGGAGUUCGGGUCCCCGAAGGCGGUCCA,****    NEW  HIT  #5  ****,5912-5987 6085-6161,2,0,AE005323.1/5995-6071
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95081,AP002554.1,1,sp|AP002554.1|AP002554 Escherichia coli O157:H7 DNA; complete genome; section 5/20.,0,8298,42336,42412,45.04,CCGCCAUUAGCUCAUCAGGAAAGAGCGCCAGCUUUCGAAGCUGGUUGCGCGGAGUUCGGGUCCCCGAAGGCGGUCCA,****    NEW  HIT (duplicate of new hit #5)   ****,42253-42328 42426-42502 129458-129533 129543-129619 129633-129709 319627-319540 73668-73581,2,0,AP002554.1/42336-42412
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,150709,U61360.1,1,sp|U61360.1|LAU61360 Liberobacter africanum 16S/23S rDNA intergenic region; including tRNA-Ala gene.,0,11947,170,241,44.68,GGGCCCGUAGCUCAGGCGUUAGAGCGCUGCUUUGCAAGCAGAUGUCAGCGGUCGACUCGCUCGGCUCCACCA,****    NEW  HIT  #100  ****,,2,0,U61360.1/170-241
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,87085,AF500187.1,1,sp|AF500187.1|AF500187 Escherichia coli isolate EC152a serotype ONT:H29 variant Shiga toxin type 2 A subunit (stx2dA) and variant Shiga toxin type 2 B subunit (stx2dB) genes; complete cds.,0,7169,1,68,43.88,GCUCAGCCGGACAGAGCAAUUGCCUUCUAAGCAAUCGGUCACUGGUUCGAAUCCAGUACAACGCGCCA,****    NEW  HIT  #37  ****,,2,0,AF500187.1/1-68
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,167304,S63866.1,1,sp|S63866.1|S63866 (B4)=tRNA(Phe) [Escherichia coli; tRNA ttc Phe; 74 nt].,0,13070,1,74,41.56,GCCCGGAUAGCUCAGUAUGUAGAGCAAAGGUUUGAAAAUCCUUGUGUCCUCGCCCGUCCCGAGUCCGGGCACCA,****    NEW  HIT  #103  ****,,2,0,S63866.1/1-74
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,44932,AF176047.1,1,sp|AF176047.1|AF176047 Rhizobium leguminosarum strain CCT 6323 16S-23S ribosomal RNA gene intergenic spacer; partial sequence.,0,5341,260,318,40.1,UAGCUCAGUUGGUUAGAGCACACGCUUGAUAAGCGUGGGGUCGGAAGUUCAAGCUUCCA,****    NEW  HIT  #28  ****,,2,0,AF176047.1/260-318
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135524,BX640442.1,1,sp|BX640442.1|BX640442 Bordetella bronchiseptica strain RB50; complete genome; segment 6/16,0,11169,43017,43090,39.66,GCGGGCGUAGUUCAUGGUGAGCCGCCGGCCUUCCAAGCCGCGCUGAGAGGGUUCGAUCCCCUCCGCCCGCUCCA,****    NEW  HIT  #83  ****,11103-11178 43094-43168 89005-89097 103825-103901 119017-119093 235176-235252 235273-235348,2,0,BX640442.1/43017-43090
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135488,BX572097.1,1,sp|BX572097.1|BX572097 Prochlorococcus marinus MIT9313 complete genome; segment 3/7,0,11015,209656,209729,39.36,UGCAAGGGAAGUCAGCCAAGAACGUCGGGCUCAUAACCCGAAGGUCGGGAGUUCAAAUCUCCCCCCCGCCACCA,****    NEW  HIT  #81  ****,56621-56707 121344-121417 172810-172896 205864-205940 303936-304009,2,0,BX572097.1/209656-209729
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,167308,S63882.1,1,sp|S63882.1|S63882 (B8)=tRNA(Phe) [Escherichia coli; tRNA ttc Phe; 75 nt].,0,13074,1,75,36.09,GCCCGGAUAGCUCAGGUAGUAGAGCAGAGGAUUGAAAACCUUGUGUCCUUGGGGCGGUCCCGAGUCCGGGCACCA,****    NEW  HIT  #104  ****,,2,0,S63882.1/1-75
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,115856,AY204358.1,1,sp|AY204358.1|AY204358 Leptospirillum ferrooxidans 16S ribosomal RNA gene; partial sequence; 16S-23S intergenic spacer; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,9710,1,66,35.73,CUCAGUUGGGAGAGCGCCUGCUUUGCAAGCAGGAGGUCAGCGGUUCGAUCCCGCUCAUCUCCACCA,****    NEW  HIT  #70  ****,,2,0,AY204358.1/1-66
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,169245,D86328.1,1,sp|D86328.1|SCD328 Staphylococcus capitis DNA for ALE-1; complete cds.,1,13232,104,14,34.78,GGAGGGAUACCCAAGUCUGGUUUAAGGGAAAUUAAUACUAUGUAUUAAUUAGAAGCUUAUGCUUGCGUUGGUUCAAAUCCUUCUCCCUCCG,****    NEW  HIT  #107  ****,,2,0,D86328.1/104-14
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27107,AE016751.1,1,sp|AE016751.1|AE016751 Staphylococcus epidermidis ATCC 12228; section 8 of 9 of the complete genome.,0,3242,219213,219305,32.8,GGAGGGAUACUCAAGUCUGGUUUAAGAGGCUAAUCAUUCGUGAUUAGUAGGAGCUUUUUGCUCGCGUUGGUUCAAAUCCUUCUCCCUCCGCUA,****    NEW  HIT  #17  ****,281210-281118 230052-229977 229970-229895 229888-229816 229797-229723 229711-229623 229610-229534 229507-229434 229419-229344 227578-227502,2,0,AE016751.1/219213-219305
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,55547,AF269477.1,1,sp|AF269477.1|AF269477 Staphylococcus epidermidis strain SR1 clone step.1005d02 genomic sequence.,0,5722,2822,2914,32.8,GGAGGGAUACUCAAGUCUGGUUUAAGAGGCUAAUCAUUCGUGAUUAGUAGGAGCUUUUUGCUCGCGUUGGUUCAAAUCCUUCUCCCUCCGCUA,****    NEW  HIT (duplicate of new hit #17)   ****,,2,0,AF269477.1/2822-2914
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,175267,U66883.1,1,sp|U66883.1|SSU66883 Staphylococcus simulans lysostaphin (lss) and lysostaphin immunity factor (lif) genes; complete cds; insertion sequence IS1293; complete sequence; and IS257-1 transposase (tnp-1) gene; complete cds.,1,13511,2124,2030,32.4,GGAGGGAUACCCAAGUCUGGAUUAAGGGGAUUAAUAUAUUUUUAUUAAUUAGGAGCAUGUAUGUGCUUGCGUUGGUUCGAAUCCUUCUCCCUCCG,****    NEW  HIT  #113  ****,,2,0,U66883.1/2124-2030
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,105279,AY116644.1,1,sp|AY116644.1|AY116644 Streptomyces viridifaciens amino acid aminotransfease gene; partial cds; ketol-acid reductioisomerase; acetolactate synthetase small subunit; acetolactate synthetase large subunit; complete cds; azoxy antibiotic valanimycin gene cluster; complete sequence; and putative transferase; and putative secreted protein genes; complete cds.,0,9535,17603,17690,32.32,GGAGAGGUACCCGUAGCGGCCCAACGGGGACCGGGCGUCCAGCCCGGCCGGGCUCCGGCCCACGCAGGUUCGAAUCCUGCCCUCUCCG,****    NEW  HIT  #67  ****,17237-17324,2,0,AY116644.1/17603-17690
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,105279,AY116644.1,1,sp|AY116644.1|AY116644 Streptomyces viridifaciens amino acid aminotransfease gene; partial cds; ketol-acid reductioisomerase; acetolactate synthetase small subunit; acetolactate synthetase large subunit; complete cds; azoxy antibiotic valanimycin gene cluster; complete sequence; and putative transferase; and putative secreted protein genes; complete cds.,0,9536,17481,17568,32.32,GGAGAGGUACCCGUAGCGGCCCAACGGGGACCGGGCGUCCAGCCCGGCCGGGCUCCGGCCCACGCAGGUUCGAAUCCUGCCCUCUCCG,****    NEW  HIT (duplicate of new hit #67)   ****,17237-17324,2,0,AY116644.1/17481-17568
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,105279,AY116644.1,1,sp|AY116644.1|AY116644 Streptomyces viridifaciens amino acid aminotransfease gene; partial cds; ketol-acid reductioisomerase; acetolactate synthetase small subunit; acetolactate synthetase large subunit; complete cds; azoxy antibiotic valanimycin gene cluster; complete sequence; and putative transferase; and putative secreted protein genes; complete cds.,0,9537,17359,17446,32.32,GGAGAGGUACCCGUAGCGGCCCAACGGGGACCGGGCGUCCAGCCCGGCCGGGCUCCGGCCCACGCAGGUUCGAAUCCUGCCCUCUCCG,****    NEW  HIT (duplicate of new hit #67)   ****,17237-17324,2,0,AY116644.1/17359-17446
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,19687,AE006394.1,1,sp|AE006394.1|AE006394 Lactococcus lactis subsp. lactis IL1403 section 156 of 218 of the complete genome.,1,1459,10685,10622,32.13,UAGCCAAGCGGUAAGGCAAGGGACUUUGACUCCCUCAUGCGUUGGUUCGAAUCCAGCUACCCCA,****    NEW  HIT  #10  ****,,2,0,AE006394.1/10685-10622
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135441,BX294134.1,1,sp|BX294134.1|BX294134 Pirellula sp. strain 1 complete genome; segment 2/24,1,10802,115581,115507,31.3,GCCGGAGUAGCAGUUGUUGGUCGCUGCACCUCGCUCUGAACGAGGAGUCCAUUGGUUCAAUUCCUGUCCUCGGCC,****    NEW  HIT  #75  ****,157301-157382 263208-263291 116552-116480 116215-116143 116117-116045 115924-115854 115845-115774 115504-115431 115236-115162 114742-114672 114655-114584,2,0,BX294134.1/115581-115507
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,189851,L42976.1,1,sp|L42976.1|XATRNAF Xanthomonas albilineans transfer RNA-Ala; intergenic spacer; and transfer RNA-Ile gene.,0,13663,1,62,31.1,GCUGGUAGAGCACCUGCCUUGCAAGCAGGGGGUCGUCGGUUCGAUCCCGACUGGCUCCACCA,****    NEW  HIT  #117  ****,,2,0,L42976.1/1-62
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,170050,K00199.1,1,sp|K00199.1|SETRG1B S.epidermidis Gly-tRNA-1B.,0,13311,1,75,30.71,GCGGGAGUAUUUCAACUUUUAGAAUACGUUCCUUCCCGGAACGAGAUAUAGGUGCAAAUCCUAUCUUCCGCUCCA,****    NEW  HIT  #111  ****,,2,0,K00199.1/1-75
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,19662,AE006369.1,1,sp|AE006369.1|AE006369 Lactococcus lactis subsp. lactis IL1403 section 131 of 218 of the complete genome.,1,1457,9635,9575,30.44,GGUUCUUUAGCUCAGUUGGAAGCUAACCGUUCGGUCGCUGGUUCGAGUCCAGCAAGAACCA,****    NEW  HIT  #9  ****,6584-6495,2,0,AE006369.1/9635-9575
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95177,AP003604.1,1,sp|AP003604.1|AP003604 Nostoc sp. PCC 7120 plasmid pCC7120delta DNA; complete genome.,1,8725,52083,52006,30.32,AGCCUUGUGGACAAAUAAGAUAAGUCGCUGUGCCUCUCAAGCACGGAGGAGCGGGUGCAACUCCCGUCGAGGCUUCCA,****    NEW  HIT  #51  ****,52163-52087 51998-51928 51899-51823 51699-51615 51516-51440 51437-51364 51354-51280 51274-51198 51192-51118 51089-51012 51003-50927 50923-50850 50829-50752 50709-50634 50627-50554 50551-50474 50470-50399 50390-50320 50314-50239 50232-50161 50154-50081 50074-49998,2,0,AP003604.1/52083-52006
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135441,BX294134.1,1,sp|BX294134.1|BX294134 Pirellula sp. strain 1 complete genome; segment 2/24,1,10799,115333,115262,30.32,GCCGCAUUCGACUACUGGCUAGGUCGGCUGCUUCUCAGGCAGCAGGAAGGAGAUCGAAACUCCUAUGCGGUA,****    NEW  HIT  #73  ****,157301-157382 263208-263291 116552-116480 116215-116143 116117-116045 115924-115854 115845-115774 115504-115431 115236-115162 114742-114672 114655-114584,2,0,BX294134.1/115333-115262
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135460,BX294153.1,1,sp|BX294153.1|BX294153 Pirellula sp. strain 1 complete genome; segment 21/24,1,10849,133226,133155,30.32,GCCGCAUUCGACUACUGGCUAGGUCGGCUGCUUCUCAGGCAGCAGGAAGGAGAUCGAAACUCCUAUGCGGUA,****    NEW  HIT (duplicate of new hit #73)   ****,193578-193650 193760-193832 170882-170809 134671-134599 134431-134359 134347-134275 134197-134125 134104-134033 133980-133910 133901-133830 133744-133673 133566-133492 133475-133402 133129-133055 132826-132756 132736-132665 132280-132207 132188-132118 132112-132041 132028-131955 131941-131858 131684-131609 131598-131526 131514-131444 131244-131173 130969-130897 130485-130415,2,0,BX294153.1/133226-133155
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,89454,AF514306.1,1,sp|AF514306.1|AF514306 Listeria monocytogenes strain L285 16S-23S ribosomal RNA intergenic spacer and tRNA-Ile gene; partial sequence; and tRNA-Ala gene; complete sequence.,0,7527,1,61,30.13,AGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCA,****    NEW  HIT  #39  ****,108-183,2,0,AF514306.1/1-61
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,60367,AF302130.1,1,sp|AF302130.1|AF302130 Streptococcus agalactiae strain L41 23S ribosomal RNA gene; partial sequence; 5S ribosomal RNA gene; complete sequence; tRNA-Gly; tRNA-Asp; tRNA-Glu; tRNA-Ser; tRNA-Met; tRNA-Phe; tRNA-Trp; tRNA-His; and tRNA-Gln genes; complete sequence; and tRNA-Leu gene; partial sequence.,0,5933,1034,1126,30.1,GGAGGAUUACCCAAGUCCGGCUGAAGGGAACGGUCUUGAAAACCGUCAGGCGUGUAAAAGGCGUGCGUGGGGUUGGAAUCCCAAAAUCUUCCU,****    NEW  HIT  #32  ****,680-752 758-828 865-941 949-1020 1137-1210 1213-1285 1297-1377 1384-1454 1469-1541 1548-1619,2,0,AF302130.1/1034-1126
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95214,AP005025.1,1,sp|AP005025.1|AP005025 Streptomyces avermitilis genomic DNA; complete genome; section 5/30.,1,8890,16721,16649,30.04,GCGUUGGUGGUCCAAGGAAAGACGCCCCGCUUCCUGCGGGGAAAUGCAGGUGCAAGCCCUGCCCGGCGCUCCA,****    NEW  HIT  #55  ****,,2,0,AP005025.1/16721-16649
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,26873,AE015714.1,1,sp|AE015714.1|AE015714 Shewanella oneidensis MR-1 section 263 of 457 of the complete genome.,1,3095,1059,969,29.79,GGGUCGUUAGCUCAGUCGCUUUUUUUAUAAAGCUAGGGCAGUUGGCUUUUAACCAAUCAGUCGAAUGGUUUAAAUACUUCACGACCCACCA,****    NEW  HIT  #16  ****,1298-1223 1168-1093 935-860 826-751 717-642 480-405 371-296,2,0,AE015714.1/1059-969
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,189850,L42971.1,1,sp|L42971.1|XATRNA Xanthomonas albilineans transfer RNA-Ala; intergenic spacer; and transfer RNA-Ile gene.,0,13662,1,62,29.59,GCUGGUAGAGCGCCUGCUUUGCAAGCAGGGGGUCGUCGGUUCGAUCCCGACUGGCUCCACCA,****    NEW  HIT  #116  ****,,2,0,L42971.1/1-62
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,148199,M15314.1,1,sp|M15314.1|HIINT Haemohpilus influenzae integration region DNA.,1,11934,329,251,29.41,GUCGGAAUCGGUAGACACAAGGGAUUUAAAAUCCCUCGCCUUUCGAGGCGUGCCAGUUCAAGUCUGGCUUCGGGCACCA,****    NEW  HIT  #98  ****,200-125,2,0,M15314.1/329-251
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,16742,AE001911.1,1,sp|AE001911.1|AE001911 Deinococcus radiodurans R1 section 48 of 229 of the complete chromosome 1.,0,803,9233,9308,29.32,GCACCCCUCGCCCGUUUUCCCGCUCAUCCCCCUUCUAAGCGGUCGGUCGUAGGUUCAAGUCCUACAGGGUGCACCA,****    NEW  HIT  #3  ****,,2,0,AE001911.1/9233-9308
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95177,AP003604.1,1,sp|AP003604.1|AP003604 Nostoc sp. PCC 7120 plasmid pCC7120delta DNA; complete genome.,1,8721,51610,51520,29.22,GGAGAGAUUGCUAUUGGCAGGGCAAGCUGUUUGCUAAACAGUCGUGAGAUUCAUCAUCUCACUGUGGGUUCAACUCCCUCUCUCUCCGCCU,****    NEW  HIT  #50  ****,52163-52087 51998-51928 51899-51823 51699-51615 51516-51440 51437-51364 51354-51280 51274-51198 51192-51118 51089-51012 51003-50927 50923-50850 50829-50752 50709-50634 50627-50554 50551-50474 50470-50399 50390-50320 50314-50239 50232-50161 50154-50081 50074-49998,2,0,AP003604.1/51610-51520
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135460,BX294153.1,1,sp|BX294153.1|BX294153 Pirellula sp. strain 1 complete genome; segment 21/24,1,10863,131049,130978,28.21,GACUCGCGGGUGUGCUGGAUAGCAUGACAGUCUUCGAAACUGUCGGACCAGGUUCGAUUCCUGGGCGGGUUA,****    NEW  HIT  #80  ****,193578-193650 193760-193832 170882-170809 134671-134599 134431-134359 134347-134275 134197-134125 134104-134033 133980-133910 133901-133830 133744-133673 133566-133492 133475-133402 133129-133055 132826-132756 132736-132665 132280-132207 132188-132118 132112-132041 132028-131955 131941-131858 131684-131609 131598-131526 131514-131444 131244-131173 130969-130897 130485-130415,2,0,BX294153.1/131049-130978
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,189950,L42973.1,1,sp|L42973.1|XCTRNAB Xanthomonas campestris transfer RNA-Ala; intergenic spacer; and transfer RNA-Ile.,0,13685,1,62,27.83,GCUGGGAGAGCGCCUGCCUUGCAAGCAGGGGGUCGUCGGUUCGAUCCCGACAGGCUCCACCA,****    NEW  HIT  #119  ****,,2,0,L42973.1/1-62
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,54340,AF260010.1,1,sp|AF260010.1|AF260010 Chlamydia-associated clinical sample L2-comp1 16S ribosomal RNA gene; partial sequence; intergenic spacer region; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,5671,315,387,27.38,UCGGGCAUAGCUCAGCUGGAGAGCGCCUGCUUUGCACGCAGGAGGUCAGAGUCGAUCUCUNNNNCUCACAUCA,****    NEW  HIT  #30  ****,217-289,2,0,AF260010.1/315-387
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95214,AP005025.1,1,sp|AP005025.1|AP005025 Streptomyces avermitilis genomic DNA; complete genome; section 5/30.,1,8889,23198,23126,26.81,GCGUUGGUGGUCCAAGGAAAGACGCCCCGCUUCCUGCGGGGAGAUGCAGGUGCAAGGCCUGCCCGGCGCUCCA,****    NEW  HIT  #54  ****,,2,0,AP005025.1/23198-23126
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,169190,AB000222.1,1,sp|AB000222.1|SCAB222 Staphylococcus capitis epr gene ;complete cds.,0,13230,242,334,26.5,GGAGGGAUACCCAAGUCUGGUUUAAGGGAAAUUAAUACUAUGUAUUAAUUAGAAGCUUAUGCUUGCGCAUUGGUUCAAAUCCUUCUCCCUCCG,****    NEW  HIT  #106  ****,,2,0,AB000222.1/242-334
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,169372,AL939114.1,1,sp|AL939114.1|SCO939114 Streptomyces coelicolor A3(2) complete genome; segment 11/29,0,13255,156494,156594,26.17,GGCCGUGUGCCCGAGUGGCCCAGGGGCUCGCCUGCGCGGCGCCGGUCAGCGAGCUCCGCGCGCGGGGAGUCACGCGGGUUCGAAUCCCGCCCCGGCCUCCA,****    NEW  HIT  #108  ****,14947-15019 57377-57450 60689-60765 120737-120823 44748-44675,2,0,AL939114.1/156494-156594
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27128,AE016775.1,1,sp|AE016775.1|AE016775 Pseudomonas putida KT2440 section 2 of 21 of the complete genome.,0,3347,280896,280991,26.08,GGAAGGCAAUCGCGCCCGGUGGCGCGGCCGGGCUUCAAACCCGGUUGGGGACGGCAGCCGUUCCCGGGCAGGUUCGACUCCCGCUGCCUUCCGCCA,****    NEW  HIT  #19  ****,229203-229286 229311-229384 229414-229489 230816-230891 164029-163953 41007-40932 31880-31805,2,0,AE016775.1/280896-280991
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95128,AP003135.2,1,sp|AP003135.2|AP003135 Staphylococcus aureus subsp. aureus N315 genomic DNA; complete genome; section 7/10.,1,8458,115374,115300,25.75,GCGGGAGUAUUUCAACUCUUAGAAUACAUUCCUUCCUGGAAUGAGGUAUAGGUGUAAAUCCUAUCUUCCGCUCCA,****    NEW  HIT  #47  ****,121039-120963 120944-120869 117534-117459 117442-117367 117361-117286 117282-117201 117197-117123 117112-117024 117005-116932 116922-116849 116831-116756 116734-116658 116632-116559 116549-116460 116449-116374 116335-116243 116228-116155 116133-116058 116039-115967 115959-115884 115878-115798 115782-115709 115706-115634 115622-115551 115545-115472 115464-115390 115286-115212 115173-115090 81392-81319 81297-81222 81205-81133 81119-81044 81028-80955 80937-80863 80861-80790 80735-80647,2,0,AP003135.2/115374-115300
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95148,AP003363.2,1,sp|AP003363.2|AP003363 Staphylococcus aureus subsp. aureus Mu50 genomic DNA; complete sequence; section 6/9.,1,8614,258437,258363,25.75,GCGGGAGUAUUUCAACUCUUAGAAUACAUUCCUUCCUGGAAUGAGGUAUAGGUGUAAAUCCUAUCUUCCGCUCCA,****    NEW  HIT (duplicate of new hit #47)   ****,264102-264026 264007-263932 260597-260522 260505-260430 260424-260349 260345-260264 260260-260186 260175-260087 260068-259995 259985-259912 259894-259819 259797-259721 259695-259622 259612-259523 259512-259437 259398-259306 259291-259218 259196-259121 259102-259030 259022-258947 258941-258861 258845-258772 258769-258697 258685-258614 258608-258535 258527-258453 258349-258275 258236-258153 224454-224381 224359-224282 224265-224193 224179-224104 224088-224015 223997-223923 223921-223850 223795-223707,2,0,AP003363.2/258437-258363
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95205,AP004828.1,1,sp|AP004828.1|AP004828 Staphylococcus aureus subsp. aureus MW2 DNA; complete genome; strain:MW2; section 7/10.,1,8847,132387,132313,25.75,GCGGGAGUAUUUCAACUCUUAGAAUACAUUCCUUCCUGGAAUGAGGUAUAGGUGUAAAUCCUAUCUUCCGCUCCA,****    NEW  HIT (duplicate of new hit #47)   ****,138117-138041 138022-137947 134535-134460 134443-134368 134362-134287 134283-134202 134198-134124 134113-134025 134006-133933 133923-133850 133832-133757 133735-133659 133633-133560 133550-133461 133450-133375 133336-133244 133229-133156 133146-133071 133052-132980 132972-132897 132891-132811 132795-132722 132719-132647 132635-132564 132558-132485 132477-132403 132299-132225 132186-132103 99839-99766 99744-99669 99652-99580 99566-99491 99475-99402 99387-99313 99311-99240 99185-99097,2,0,AP004828.1/132387-132313
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,168352,L11530.1,1,sp|L11530.1|SATRNAA Staphylococcus aureus transfer RNA sequence with two rRNAs.,0,13198,2440,2514,25.75,GCGGGAGUAUUUCAACUCUUAGAAUACAUUCCUUCCUGGAAUGAGGUAUAGGUGUAAAUCCUAUCUUCCGCUCCA,****    NEW  HIT (duplicate of new hit #47)   ****,290-365 382-457 463-538 542-624 628-702 713-801 820-893 903-976 994-1069 1091-1167 1193-1266 1276-1365 1376-1451 1490-1582 1597-1670 1680-1755 1774-1846 1854-1929 1935-2016 2032-2105 2108-2180 2192-2263 2269-2342 2350-2424 2528-2602 2641-2724,2,0,L11530.1/2440-2514
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95323,AP005961.1,1,sp|AP005961.1|AP005961 Bradyrhizobium japonicum USDA 110 DNA; complete genome; section 27/31.,0,9348,138022,138097,25.17,GGCUGCGAGCGCUCAGCGGGAGAGCGUUCGCUUCACACGCGAGAGGUCCAUGACUAGAUCCCAAGUGCACCCACCA,****    NEW  HIT  #63  ****,271063-270989,2,0,AP005961.1/138022-138097
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95320,AP005958.1,1,sp|AP005958.1|AP005958 Bradyrhizobium japonicum USDA 110 DNA; complete genome; section 24/31.,1,9346,146884,146817,25.15,GAGUGUUUUCAGGCUAGAGCUGUCUCUUAAUCAGCGGGUCCUAGGUUCGAGCCCUGGUGCGCCCACCA,****    NEW  HIT  #62  ****,181399-181324,2,0,AP005958.1/146884-146817
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95177,AP003604.1,1,sp|AP003604.1|AP003604 Nostoc sp. PCC 7120 plasmid pCC7120delta DNA; complete genome.,1,8702,49994,49909,24.77,GGAAGAUGCCGCUAAAUGGUCGGCAACCGGUCUUGAAAACCGGGGUGGGGUAACACCCAGGGGUUCGAUUCCUCCAUCUUCCGCCU,****    NEW  HIT  #49  ****,52163-52087 51998-51928 51899-51823 51699-51615 51516-51440 51437-51364 51354-51280 51274-51198 51192-51118 51089-51012 51003-50927 50923-50850 50829-50752 50709-50634 50627-50554 50551-50474 50470-50399 50390-50320 50314-50239 50232-50161 50154-50081 50074-49998,2,0,AP003604.1/49994-49909
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,2966,AB020535.1,1,sp|AB020535.1|AB020535 Wolbachia sp. wTai DNA; insertion sequence ISW1 next to orfC; partial cds.,0,82,2,65,24.69,AGCUCGGUAGCUCGUCAGGCUCAUAACCUGAAGGUCGUAGGUUCAAAUCCUACUCCCGCAACCA,****    NEW  HIT  #0  ****,,2,0,AB020535.1/2-65
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,189949,L42972.1,1,sp|L42972.1|XCTRNAA Xanthomonas campestris transfer RNA-Ala; intergenic spacer; and transfer RNA-Ile gene.,0,13684,1,62,24.61,GUUGGUAGAGCGCCUGCCUUGCAAGCAGGGGGUCGUCGGUUCGAUCCCGACAGGCUCCACCA,****    NEW  HIT  #118  ****,,2,0,L42972.1/1-62
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,189952,L42975.1,1,sp|L42975.1|XCTRNAE Xanthomonas campestris transfer RNA-Ala; intergenic spacer; and transfer RNA-Ile gene.,0,13686,1,62,23.62,GUUGGUAGAGCGCCUGCUUUGCAAGCAGGGGGUCGUCGGUUCGAUCCCGACAGGCUCCACCA,****    NEW  HIT  #120  ****,,2,0,L42975.1/1-62
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,136270,X77657.1,1,sp|X77657.1|CDAMPC C.diversus recombinant plasmid ampC gene.,1,11225,1218,1141,23.43,CCGCCAUUAGCUCAUCUGGAAGAGCGAACCGACUUUUGUUGUAGGGAACCGGGGUUCCGAGGCCUCGAUGGCGGCCCA,****    NEW  HIT  #84  ****,,2,0,X77657.1/1218-1141
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135460,BX294153.1,1,sp|BX294153.1|BX294153 Pirellula sp. strain 1 complete genome; segment 21/24,1,10850,133309,133237,23.32,GGUGGCAAUUUCCUCUGGGAAGGAAGCUUGAUUGUCUAUCAAGUCGCUGCGGGUUCGACUCCCGUUGCCAUCG,****    NEW  HIT  #78  ****,193578-193650 193760-193832 170882-170809 134671-134599 134431-134359 134347-134275 134197-134125 134104-134033 133980-133910 133901-133830 133744-133673 133566-133492 133475-133402 133129-133055 132826-132756 132736-132665 132280-132207 132188-132118 132112-132041 132028-131955 131941-131858 131684-131609 131598-131526 131514-131444 131244-131173 130969-130897 130485-130415,2,0,BX294153.1/133309-133237
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,24823,AE013138.1,1,sp|AE013138.1|AE013138 Thermoanaerobacter tengcongensis strain MB4T; section 165 of 244 of the complete genome.,0,2462,4870,4964,22.75,GGGAGUAGAUAGGCGCUGGUGUGCCUCCUAGACUUCAAAUCUACGGUCUCGCUAUUUAAGCGAGAGGUGGGUUCGAUUCCCACAUACUCCCGCCA,****    NEW  HIT  #14  ****,,2,0,AE013138.1/4870-4964
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,94865,L36679.1,1,sp|L36679.1|AMUNA Amycolatopsis methanolica plasmid pMEA300 stf gene; complete cds.,0,8114,11820,11910,22.65,GGGCCGUUUGAGACCGCGGGACACGCCUGAGACGCGACCCGUUCUUCUGAUAACGAAGAGGUCGGAGGUUCAAGUCCUCCUGGGCCCACCA,****    NEW  HIT  #41  ****,,2,0,L36679.1/11820-11910
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,36559,AF091795.1,1,sp|AF091795.1|AF091795 Agrobacterium rhizogenes strain CCT 4832T 16S-23S ribosomal DNA intergenic spacer region; 5' end.,0,4854,534,605,22.1,GGGGCUGUANCUCAACUGGGAAAACACUGCUUUGCAANCANGGGGUCANCGGUUCNAUCCCUCACUCCACCA,****    NEW  HIT  #26  ****,332-408,2,0,AF091795.1/534-605
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135441,BX294134.1,1,sp|BX294134.1|BX294134 Pirellula sp. strain 1 complete genome; segment 2/24,1,10808,116686,116611,22.02,GCCGGCUUGCCCUAUUGGCUGACGCGGGCGGCGGUCUGAAGAACCGCAGACGAGGAUUCGAGCGCCUUCCGGCCCA,****    NEW  HIT  #76  ****,157301-157382 263208-263291 116552-116480 116215-116143 116117-116045 115924-115854 115845-115774 115504-115431 115236-115162 114742-114672 114655-114584,2,0,BX294134.1/116686-116611
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,7287,AB053119.1,1,sp|AB053119.1|AB053119 Streptomyces thermoviolaceus bxlA gene for beta-xylosidase; complete cds.,1,245,2765,2693,21.94,GCGUUGGUGGUCUAAGGCAAGACGCCCCGCUUCCUGCGGGGAGAUGCAGGUGCAAGGCCUGCCCGGCGCUCGA,****    NEW  HIT  #1  ****,,2,0,AB053119.1/2765-2693
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,36561,AF091797.1,1,sp|AF091797.1|AF091797 Agrobacterium rhizogenes strain CCT 4842 16S-23S ribosomal DNA intergenic spacer region; 5' end.,0,4856,532,603,21.87,GGGGCUGUNNCUCACUGGGAAANCACCUGCUUUGCAACAGGGGGUCACUGUUCGAUCCCGCUCACUCCACCA,****    NEW  HIT  #27  ****,330-406,2,0,AF091797.1/532-603
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95101,AP002998.2,1,sp|AP002998.2|AP002998 Mesorhizobium loti DNA; complete genome; section 5/21.,0,8398,112239,112317,21.57,GCCCGUCUGAACGGUUUGGAGAGAUCAAAGGCGCCCUUUGAAGGCGUGAAUCGUGGUUCGAGCCCAUGAGCGGGAACCA,****    NEW  HIT  #45  ****,110453-110526,2,0,AP002998.2/112239-112317
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135441,BX294134.1,1,sp|BX294134.1|BX294134 Pirellula sp. strain 1 complete genome; segment 2/24,1,10797,115064,114981,21.48,GGAAGUCACCCGGCCGGAUGAGGACACUGUCUUGAAAACAGCUGCGGUCAAAAACCGUUGUGGGUUCGAGUCCCACGGCUUCCG,****    NEW  HIT  #72  ****,157301-157382 263208-263291 116552-116480 116215-116143 116117-116045 115924-115854 115845-115774 115504-115431 115236-115162 114742-114672 114655-114584,2,0,BX294134.1/115064-114981
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,21434,AE008434.1,1,sp|AE008434.1|AE008434 Streptococcus pneumoniae R6 section 50 of 184 of the complete genome.,0,1781,7078,7143,21.36,GCCGAUUUAGCUCAGUUGGUAGAGCAAGGCACUCGUAAAGCCUAGGUUAUAGGUAGAUAAACGACU,****    NEW  HIT  #11  ****,,2,0,AE008434.1/7078-7143
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95233,AP005044.1,1,sp|AP005044.1|AP005044 Streptomyces avermitilis genomic DNA; complete genome; section 24/30.,0,8950,125086,125165,21.23,UGACCCGGGUAACGAAGCCGCCGACCACGUCCGCCCUCACAAGGCGGAUGCCGGCGGUUCGAAACCGUCCGCGUCCACCA,****    NEW  HIT  #58  ****,121734-121808,2,0,AP005044.1/125086-125165
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95117,AP003014.2,1,sp|AP003014.2|AP003014 Mesorhizobium loti DNA; complete genome; section 21/21.,0,8433,130537,130610,21.2,AUGCGAGGUUUCUGCGGUUCGAACGCUCGUUUACACCGAAGAUGUCGGCGGUUCGAGCCCGUCAUCGCCCACCA,****    NEW  HIT  #46  ****,85297-85372 85079-85003 34361-34285,2,0,AP003014.2/130537-130610
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95316,AP005954.1,1,sp|AP005954.1|AP005954 Bradyrhizobium japonicum USDA 110 DNA; complete genome; section 20/31.,1,9337,163506,163435,21.09,ACGCUCUUGGAUUUUUUAUUUUUGGGAUUUCGAUUCCGAGGGUCGGAGGUUCGAAUCCUUCCGAGCGCGCCA,****    NEW  HIT  #60  ****,278763-278688 167773-167697 100393-100309,2,0,AP005954.1/163506-163435
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95219,AP005030.1,1,sp|AP005030.1|AP005030 Streptomyces avermitilis genomic DNA; complete genome; section 10/30.,0,8895,103303,103400,20.69,GGAGAGGUGCCCGGAGUGGCUGAUCGGGGACCGAAGAGCACGUCUCGAGGUCGGGCUUCAACCAGCCCACGCAGGUUCGAAUCCUGCCCUCUCCGCCA,****    NEW  HIT  #56  ****,,2,0,AP005030.1/103303-103400
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,135441,BX294134.1,1,sp|BX294134.1|BX294134 Pirellula sp. strain 1 complete genome; segment 2/24,1,10800,115416,115344,20.52,GGUGGCGAUUUCCUCUGGGAAGGAAGCUUGAUUGUCUAUCAAGUCGCUGCGGGUUCGACUCCCGUUGCCAUCG,****    NEW  HIT  #74  ****,157301-157382 263208-263291 116552-116480 116215-116143 116117-116045 115924-115854 115845-115774 115504-115431 115236-115162 114742-114672 114655-114584,2,0,BX294134.1/115416-115344
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,19094,AE005800.1,1,sp|AE005800.1|AE005800 Caulobacter crescentus CB15 section 126 of 359 of the complete genome.,0,1328,117,202,71.84,GGGGGAAUGUCCCGAGUGGCAAAGGGGGGGGACUGUAAAUCCCCUGGCGUAAGCCUUCGUAGGUUCGAGUCCUACUUCCCCCACCA,****    NEW  HIT  #7  ****,119-202 313-386,1,83,AE005800.1/117-202
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27244,AE016960.1,1,sp|AE016960.1|AE016960 Coxiella burnetii strain RSA 493; section 1 of 7 of the complete genome.,0,3864,206092,206162,71.16,GCGGGUGUAGUUCAACGGUAGAACUUCAGCCUUCCAAGCUGAUAGCGUGGGUUCGACUCCCAUCACCCGCU,****    NEW  HIT  #21  ****,142604-142679 167224-167300 167305-167380 192923-192998 205880-205961 206092-206165 206165-206240 207635-207710 255593-255518 93392-93320 93275-93200,1,70,AE016960.1/206092-206162
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,23949,AE012045.1,1,sp|AE012045.1|AE012045 Xanthomonas axonopodis pv. citri str. 306;  section 423 of 469 of the complete genome.,0,2265,8353,8422,63.76,UGGAUAGCUCAAUUGGUAGAGCAGCAGAUUUGCAAUCUGUUAGUCGCGGGUUCGAAUCCCGCUCCAUGCA,****    NEW  HIT  #13  ****,8285-8351 8349-8422,1,69,AE012045.1/8353-8422
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,45683,AF182395.1,1,sp|AF182395.1|AF182395 Xanthomonas citri glnAB operon gene; complete sequence.,1,5379,699,630,63.76,UGGAUAGCUCAAUUGGUAGAGCAGCAGAUUUGCAAUCUGUUAGUCGCGGGUUCGAAUCCCGCUCCAUGCA,****    NEW  HIT (duplicate of new hit #13)   ****,767-701 703-630,1,69,AF182395.1/699-630
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95099,AP002996.2,1,sp|AP002996.2|AP002996 Mesorhizobium loti DNA; complete genome; section 3/21.,0,8392,291019,291087,63.67,CGGAUAGCUCAGUUUGGUUAGAGCAUCAGACUUAUAAUCUGACUGUCGAAGGUUCGAUUCCUUCUCCAA,****    NEW  HIT  #44  ****,63996-64070 190575-190659 192318-192402 237671-237745 290943-291018 291016-291093 236670-236597,1,68,AP002996.2/291019-291087
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,134698,M23210.1,1,sp|M23210.1|BSTRNAZ Bacillus subtilis precursor tRNA encoding Val-; Thr-; Leu-; Lys-; Gly-; and Arg-tRNAs.,0,10511,605,673,45.88,GCGCCCGUAGCUCAAUUGGAUAGAGCGUUUGACUACGGAUCAAAAGGUUAGGGGUUCGACUCCUCUCGG,****    NEW  HIT  #71  ****,22-97 130-205 243-318 329-415 421-495 510-595 609-673,1,64,M23210.1/605-673
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,99516,AY033402.1,1,sp|AY033402.1|AY033402 Myxococcus xanthus USC2-1p; USC2-2p; USC2-3p; USC2-4p; USC2-5p; and USC2-6p genes; complete cds.,1,9474,1141,1053,42.39,GCCCGGAUGGCGAAACUGGUAGACGCAUCGGAGUUGAAAAUCCGCCGGGGGGCAACCCCCAUGCCGGUUCGAUUCSGGCUCCGGCGGCA,****    NEW  HIT  #66  ****,1141-1053,1,88,AY033402.1/1141-1053
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95317,AP005955.1,1,sp|AP005955.1|AP005955 Bradyrhizobium japonicum USDA 110 DNA; complete genome; section 21/31.,1,9342,190740,190671,34.85,GCAGGACGUAGCUCAUGGAGAGCGUCGGGCUGAACGCCCGAAGGCAUCGGUUCGAUUCCGGUCUCUUGCA,****    NEW  HIT  #61  ****,62383-62457 148433-148521 190740-190668 190670-190597 59295-59210 46175-46102,1,69,AP005955.1/190740-190671
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,154404,U02104.1,1,sp|U02104.1|MG02104 Mycoplasma genitalium tRNA gene sequence.,1,12132,66,1,34.27,UGGGAUGUAGCCAAGCGGUAAGGCAAUAGACUUUGACUCUAUCAUGCGAUGGUUCGAUCCCAUCCA,****    NEW  HIT  #101  ****,156-71 61-1,1,65,U02104.1/66-1
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,139932,X75790.1,1,sp|X75790.1|DBTRNSE2 D.baculatus (DSM 1743) gene for transfer RNA-selenocysteine,0,11322,378,471,29.83,GGAAGCGUAUCGUCACCGGUGUGGCGCCCGGUCUUCAAAACCGGUGGAAGGUCGAGAGGUCUUCGGUAGGUUCGACUCCUAUACGCUUCCGCCA,****    NEW  HIT  #86  ****,378-467,1,93,X75790.1/378-471
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,75648,AF422520.1,1,sp|AF422520.1|AF422520 Uncultured bacterium clone t1029 16S-23S ribosomal RNA intergenic spacer; partial sequence; and 23S ribosomal RNA gene; partial sequence.,0,6823,10,90,25.06,GGGGAUUAAGCUCAAGUUGGAAAAGCACCUUGCUUUGCAAACCAGGGGGGUCGUCGGGUUCGAUCCCCGUCAUCCNUCCCA,****    NEW  HIT  #36  ****,Sep-93,1,80,AF422520.1/10-90
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,148010,U32753.1,1,sp|U32753.1|HI32753 Haemophilus influenzae Rd section 68 of 163 of the complete genome.,1,11912,7981,7887,24.62,GGAGGGGCGUCAUCUCCGGUGAGGUGGCAGGAUUUCAAAUCCUGUUGAGGACGCCAGCGUUCUUGGGUGGGUUCAACUCCCAUUCCCCUCCGCCA,****    NEW  HIT  #97  ****,7981-7891,1,90,U32753.1/7981-7887
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27322,AE017156.1,1,sp|AE017156.1|AE017156 Haemophilus ducreyi strain 35000HP section 6 of 6 of the complete genome.,0,4351,155150,155244,24.17,GGAAGUGAGUCGUCUCCGGUGAGACGGCAGGAUUUCAAAUCCUGUUAAGGACGCCAGCGUGCUUGGGUGGGUUCGACUCCCAUUCACUUCCGCCA,****    NEW  HIT  #23  ****,115967-116042 155150-155240 158958-158883 158877-158802 97358-97283 34637-34561 34533-34458 34431-34355 32538-32463,1,94,AE017156.1/155150-155244
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,15995,AE000720.1,1,sp|AE000720.1|AE000720 Aquifex aeolicus VF5 section 52 of 109 of the complete genome.,0,525,8712,8809,24.12,GGAGAGGUUGGCCGGCUGGUGCCGCCCCGGGACUUCAAAUCCCGUGGGAGGUCCCGCAAGGGAGCUCCGGAGGGUUCGAUUCCCUCCCUCUCCCGCCA,****    NEW  HIT  #2  ****,8711-8805 12016-11941,1,93,AE000720.1/8712-8809
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,18398,AE004893.1,1,sp|AE004893.1|AE004893 Pseudomonas aeruginosa PAO1; section 454 of 529 of the complete genome.,1,1208,5262,5167,24.11,GGAAGGCAAUCACGCCCGGUGGCGUGGCCGGACUUCAAAUCCGGUGGGGGACGGCAGCCGUUCCUGGGUGGGUUCGACUCCCACUGCCUUCCGCCA,****    NEW  HIT  #4  ****,5262-5171,1,91,AE004893.1/5262-5167
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,140511,AJ245960.1,1,sp|AJ245960.1|EAC245960 Eubacterium acidaminophilum selD1; selA; selB and ackA (partial) genes,0,11329,4674,4770,22.82,GGGAGUAGAUGGGUGCUGGUGUGCCCUCUGGUCUUCAAAACCAGUUCGGGGGGUUAAGAGCCUCCUGGGUGGGUUCGAUUCCCACAUAUUCCCGCCA,****    NEW  HIT  #88  ****,4675-4765,1,95,AJ245960.1/4674-4770
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,18890,AE005593.1,1,sp|AE005593.1|AE005593 Escherichia coli O157:H7 EDL933 genome; contig 3 of 3; section 212 of 290.,0,1291,7448,7542,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT  #6  ****,7448-7538,1,94,AE005593.1/7448-7542
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,21860,AE008874.1,1,sp|AE008874.1|AE008874 Salmonella typhimurium LT2; section 178 of 220 of the complete genome.,0,1931,15639,15733,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,15639-15729,1,94,AE008874.1/15639-15733
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,26538,AE015377.1,1,sp|AE015377.1|AE015377 Shigella flexneri 2a str. 301 section 340 of 412 of the complete genome.,0,3013,7453,7547,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,7453-7543,1,94,AE015377.1/7453-7547
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27123,AE016769.1,1,sp|AE016769.1|AE016769 Escherichia coli CFT073 section 15 of 18 of the complete genome.,0,3318,42024,42118,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,42024-42114 212184-212259 215625-215701 215710-215785 250255-250331 250390-250465 250486-250572 250615-250691,1,94,AE016769.1/42024-42118
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27181,AE016846.1,1,sp|AE016846.1|AE016846 Salmonella enterica subsp. enterica serovar Typhi Ty2; section 13 of 16 of the complete genome.,1,3595,279449,279355,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,279449-279359 126339-126264,1,90,AE016846.1/279449-279355
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27268,AE016991.1,1,sp|AE016991.1|AE016991 Shigella flexneri 2a str. 2457T section 14 of 16 of the complete genome.,1,4019,178697,178603,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,178697-178607 30220-30145 26782-26706 26697-26622,1,90,AE016991.1/178697-178603
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,30408,AF031371.1,1,sp|AF031371.1|AF031371 Escherichia coli enteropathogenic strain E2348/69 locus of enterocyte effacement (LEE) 3' flanking sequence.,1,4515,110,16,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUUAUCUUCCGCCA,****    NEW  HIT  #24  ****,110-20,1,90,AF031371.1/110-16
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,34725,AF071034.1,1,sp|AF071034.1|AF071034 Escherichia coli L0001 (yicJ) gene; partial cds; tRNA-Sec gene; complete sequence; CP4-like integrase (int); L0004; L0005; L0006; L0007; L0008; L0009; L0010; L0011; L0012; L0013; L0014; L0015; L0016; L0017; L0018 (escF); L0019; L0020 (espB); L0021 (espD); L0022 (espA); L0023 (sepL); L0024 (escD); L0025 (eaeA); L0026 (orfU); L0027 (tir); L0028; L0029; L0030; L0031 (sepQ); L0032; L0033; L0034 (escN); L0035 (escV); L0036; L0037 (sepZ); L0038; L0039 (escJ); L0040; L0041 (escC); L0042 (cesD); L0043; L0044; L0045; L0046 (escU); L0047 (escT); L0048 (escS); L0049 (escR); L0050; L0051; L0052; L0053; L0054; L0055; and L0056 genes; complete cds; and L0057 (yicL) gene; partial cds.,0,4659,793,887,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,793-883,1,94,AF071034.1/793-887
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,94610,AL627280.1,1,sp|AL627280.1|AL627280 Salmonella enterica serovar Typhi (Salmonella typhi) strain CT18; complete chromosome; segment 16/20,1,7940,172553,172459,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,172553-172463 19458-19382 19270-19195,1,90,AL627280.1/172553-172459
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95093,AP002566.1,1,sp|AP002566.1|AP002566 Escherichia coli O157:H7 DNA; complete genome; section 17/20.,0,8356,93720,93814,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,93720-93810 249830-249905 253268-253343 253352-253427,1,94,AP002566.1/93720-93814
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,141514,AE000443.1,1,sp|AE000443.1|ECAE443 Escherichia coli K12 MG1655 section 333 of 400 of the complete genome.,0,11412,7555,7649,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,7555-7645,1,94,AE000443.1/7555-7649
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,143903,AJ278144.1,1,sp|AJ278144.1|ECO278144 Escherichia coli partial genomic DNA for pathogenicity island; shiga toxin producing strain 4797/97,0,11566,2890,2984,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,2890-2980,1,94,AJ278144.1/2890-2984
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,144101,AJ488511.1,1,sp|AJ488511.1|ECO488511 Escherichia coli pathogenicity island I; strain 536,0,11571,1,95,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,Jan-91,1,94,AJ488511.1/1-95
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,145000,X15993.1,1,sp|X15993.1|ECSELC E.coli selC transfer RNA for transfer RNA-Ser(UCA),0,11602,1,95,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,Jan-91,1,94,X15993.1/1-95
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,145001,X17419.1,1,sp|X17419.1|ECSELC1 Escherichia coli selC gene for a novel tRNA species,0,11603,71,165,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,71-161,1,94,X17419.1/71-165
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,145002,Y00299.1,1,sp|Y00299.1|ECSELCY E.coli tRNA-Sec (selC; specific for selenocysteine),0,11604,1,95,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,Jan-91,1,94,Y00299.1/1-95
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,145318,X13994.1,1,sp|X13994.1|ECTRNSC Escherichia coli selC gene for tRNA-SeCys (selenocysteine),0,11740,39,133,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,39-129,1,94,X13994.1/39-133
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,145644,L10328.1,1,sp|L10328.1|ECUW82 E. coli; the region from 81.5 to 84.5 minutes.,0,11814,25614,25708,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,25614-25704 132819-132894,1,94,L10328.1/25614-25708
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,176108,Y13864.1,1,sp|Y13864.1|STSELC Salmonella typhimurium selC region,0,13534,420,514,21.65,GGAAGAUCGUCGUCUCCGGUGAGGCGGCUGGACUUCAAAUCCAGUUGGGGCCGCCAGCGGUCCCGGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT (duplicate of new hit #6)   ****,420-510,1,94,Y13864.1/420-514
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,164253,X14255.1,1,sp|X14255.1|PVSELC Proteus vulgaris selC gene for selenocysteyl-tRNA-Ser (UCA),0,12926,504,598,20.96,GGAAGAUCAUCGUCCCCGGUGGGGCGGCUGGACUUCAAAUCCAGAUGGGGCCGCCAGCGGUCCUUGGCAGGUUCGACUCCUGUGAUCUUCCGCCA,****    NEW  HIT  #102  ****,504-594,1,94,X14255.1/504-598
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,60683,AF305198.1,1,sp|AF305198.1|AF305198 Virginia creeper phytoplasma 16S ribosomal RNA gene; partial sequence; and tRNA-Ile gene; complete sequence.,0,5953,1599,1675,102.98,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCA,AF305198.1/1599-1675 AF305240.1/1598-1674 AY072722.1/1637-1713,1599-1675,0,76,AF305198.1/1599-1675
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,60684,AF305240.1,1,sp|AF305240.1|AF305240 Ziziphus jujube witches'-broom phytoplasma 16S ribosomal RNA gene; partial sequence; and tRNA-Ile gene; complete sequence.,0,5954,1598,1674,102.98,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCA,AF305198.1/1599-1675 AF305240.1/1598-1674 AY072722.1/1637-1713,1598-1674,0,76,AF305240.1/1598-1674
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,102535,AY072722.1,1,sp|AY072722.1|AY072722 Ziziphus jujube witches'-broom phytoplasma 16S ribosomal RNA gene; partial sequence; 16S-23S rRNA intergenic spacer region and tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,9501,1637,1713,102.98,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCA,AF305198.1/1599-1675 AF305240.1/1598-1674 AY072722.1/1637-1713,1637-1713,0,76,AY072722.1/1637-1713
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,84388,AF478110.1,1,sp|AF478110.1|AF478110 Bacillus lentus clone EK-3N_F 16S ribosomal RNA gene; partial sequence; 16S-23S internal transcribed spacer; complete sequence; tRNA-Ile and tRNA-Ala genes; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7116,278,354,102.92,GGGCCUGUAGCUCAGCUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AF478110.1/278-354,278-354 397-472,0,76,AF478110.1/278-354
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,53450,AF248958.1,1,sp|AF248958.1|AF248958 Apple proliferation phytoplasma 16S ribosomal RNA gene; complete sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,5656,1593,1669,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1593-1669,0,76,AF248958.1/1593-1669
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95353,U54985.1,1,sp|U54985.1|AP54985 Apple proliferation phytoplasma 16S/23S rDNA spacer region.,0,9355,88,164,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,88-164,0,76,U54985.1/88-164
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,99324,AY029540.1,1,sp|AY029540.1|AY029540 European stone fruit yellows phytoplasma 16S ribosomal RNA and 23S ribosomal RNA genes; partial sequence.,0,9429,1592,1668,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1592-1668,0,76,AY029540.1/1592-1668
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,137792,AJ542541.1,1,sp|AJ542541.1|CPH542541 Candidatus Phytoplasma mali 16S rRNA gene; tRNA-Ile gene and 23S rRNA gene (partial); strain AP15,0,11286,1592,1668,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1592-1668,0,76,AJ542541.1/1592-1668
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,137793,AJ542542.1,1,sp|AJ542542.1|CPH542542 Candidatus Phytoplasma mali 16S rRNA gene; tRNA-Ile gene and 23S rRNA gene (partial); strain AT1/93,0,11287,1592,1668,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1592-1668,0,76,AJ542542.1/1592-1668
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,137794,AJ542543.1,1,sp|AJ542543.1|CPH542543 Candidatus Phytoplasma pyri 16S rRNA gene; tRNA-Ile gene and 23S rRNA gene (partial); strain PD1,0,11288,1593,1669,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1593-1669,0,76,AJ542543.1/1593-1669
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,137795,AJ542544.1,1,sp|AJ542544.1|CPH542544 Candidatus Phytoplasma prunorum 16S rRNA gene; tRNA-Ile gene and 23S rRNA gene (partial); strain ESFY-G1,0,11289,1592,1668,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1592-1668,0,76,AJ542544.1/1592-1668
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,137796,AJ542545.1,1,sp|AJ542545.1|CPH542545 Candidatus Phytoplasma prunorum 16S rRNA gene; tRNA-Ile gene and 23S rRNA gene (partial); strain ESFY-G2,0,11290,1592,1668,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1592-1668,0,76,AJ542545.1/1592-1668
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,146307,U54988.1,1,sp|U54988.1|ES54988 European stone fruit yellows phytoplasma 16S/23S rDNA spacer region.,0,11862,88,164,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,88-164,0,76,U54988.1/88-164
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,155513,X68375.2,1,sp|X68375.2|MLOAT Candidatus Phytoplasma mali 16S rRNA gene (partial); IGS1; tRNA-Ile gene and 23S rRNA gene (partial); strain AT,0,12267,1592,1668,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1592-1668,0,76,X68375.2/1592-1668
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,160980,U54989.1,1,sp|U54989.1|PD54989 Pear decline phytoplasma 16S/23S rDNA spacer region.,0,12730,89,165,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,89-165,0,76,U54989.1/89-165
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,161084,Y16392.1,1,sp|Y16392.1|PDP16S Pear decline phytoplasma 16S rRNA gene,0,12764,1588,1664,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1588-1664,0,76,Y16392.1/1588-1664
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,163263,Y11933.1,1,sp|Y11933.1|PSP16IT23 Phytoplasma sp. 16S rRNA gene; internal transcribed spacer and 23S rRNA gene,0,12850,1592,1668,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1592-1668,0,76,Y11933.1/1592-1668
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,164283,U54990.1,1,sp|U54990.1|PY54990 Peach yellow leafroll phytoplasma 16S/23S rDNA spacer region.,0,12930,89,165,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,89-165,0,76,U54990.1/89-165
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,164284,Y16394.1,1,sp|Y16394.1|PYLRP16S Peach yellow leafroll phytoplasma 16S rRNA gene,0,12931,1588,1664,102.59,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUUAGGCCCACCA,AF248958.1/1593-1669 U54985.1/88-164 AY029540.1/1592-1668 AJ542541.1/1592-1668 AJ542542.1/1592-1668 AJ542543.1/1593-1669 AJ542544.1/1592-1668 AJ542545.1/1592-1668 U54988.1/88-164 X68375.2/1592-1668 U54989.1/89-165 Y16392.1/1588-1664 Y11933.1/1592-1668 U54990.1/89-165 Y16394.1/1588-1664,1588-1664,0,76,Y16394.1/1588-1664
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,4480,AB031214.1,1,sp|AB031214.1|AB031214 Bacillus halodurans yvgQ; rrnG-16S; trn-lle; trn-Ala; rrnG-23S; trn-5S; ykfC; nasA genes; partial and complete cds.,0,126,4204,4280,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,4204-4280 4292-4367,0,76,AB031214.1/4204-4280
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,84357,AF478079.1,1,sp|AF478079.1|AF478079 Bacillus amyloliquefaciens clone DH-11-1 16S ribosomal RNA gene; partial sequence; 16S-23S internal transcribed spacer; complete sequence; tRNA-Ile and tRNA-Ala genes; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7103,282,358,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,282-358 373-448,0,76,AF478079.1/282-358
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,84365,AF478087.1,1,sp|AF478087.1|AF478087 Bacillus licheniformis clone EI-3N_F 16S ribosomal RNA gene; partial sequence; 16S-23S internal transcribed spacer; complete sequence; tRNA-Ile and tRNA-Ala genes; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7107,283,359,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,283-359 371-446,0,76,AF478087.1/283-359
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95059,AP001509.1,1,sp|AP001509.1|AP001509 Bacillus halodurans genomic DNA; section 3/14.,0,8196,61205,61281,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,61205-61281 61293-61368,0,76,AP001509.1/61205-61281
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95186,AP004593.1,1,sp|AP004593.1|AP004593 Oceanobacillus iheyensis HTE831 genomic DNA; section 1/13.,0,8778,216167,216243,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,21773-21845 96468-96543 96545-96620 96669-96744 96749-96833 96851-96925 96931-97019 97023-97099 97101-97177 97197-97272 102449-102524 102526-102601 102650-102725 102730-102814 102832-102906 102912-103000 103004-103080 103082-103158 103178-103253 216167-216243 216263-216335 219619-219693 219697-219770 244280-244354 244362-244437 244748-244823 244873-244956 244968-245042 245112-245187 70273-70197,0,76,AP004593.1/216167-216243
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,95188,AP004595.1,1,sp|AP004595.1|AP004595 Oceanobacillus iheyensis HTE831 genomic DNA; section 3/13.,0,8796,70031,70107,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,62115-62189 62195-62285 62305-62376 62400-62476 62482-62556 62936-63011 63016-63099 69768-69844 69846-69922 69952-70025 70031-70107 79372-79448 79525-79601,0,76,AP004595.1/70031-70107
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,133788,D26185.1,1,sp|D26185.1|BSPURA1 B. subtilis DNA; 180 kilobase region of replication origin.,0,10380,75064,75140,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,75064-75140 75152-75227 85892-85984 95532-95608 95620-95695 133781-133857 133867-133938 158974-159049 159054-159129 159166-159241 159248-159330 159371-159445 159460-159545 159555-159631 159659-159735 159745-159820 3204-3129 3119-3048 2966-2890 2854-2782,0,76,D26185.1/75064-75140
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,133788,D26185.1,1,sp|D26185.1|BSPURA1 B. subtilis DNA; 180 kilobase region of replication origin.,0,10383,95532,95608,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,75064-75140 75152-75227 85892-85984 95532-95608 95620-95695 133781-133857 133867-133938 158974-159049 159054-159129 159166-159241 159248-159330 159371-159445 159460-159545 159555-159631 159659-159735 159745-159820 3204-3129 3119-3048 2966-2890 2854-2782,0,76,D26185.1/95532-95608
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,134657,J01551.1,1,sp|J01551.1|BSTGRG16 B.subtilis ile-tRNA and Ala-tRNA genes in 16s-23s rRNA spacer.,0,10430,265,341,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,265-341 353-428,0,76,J01551.1/265-341
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,134842,Z99104.2,1,sp|Z99104.2|BSUB0001 Bacillus subtilis complete genome (section 1 of 21): from 1 to 213080.,0,10525,11462,11538,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,11462-11538 11550-11625 22290-22382 31930-32006 32018-32093 70179-70255 70265-70336 95372-95447 95452-95527 95564-95639 95646-95728 95769-95843 95858-95943 95953-96029 96057-96133 96143-96218 165753-165824 165829-165901 165958-166032 166063-166139 166167-166243 166252-166327 194197-194268 194272-194347 194352-194424 194447-194531 194536-194610,0,76,Z99104.2/11462-11538
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,134842,Z99104.2,1,sp|Z99104.2|BSUB0001 Bacillus subtilis complete genome (section 1 of 21): from 1 to 213080.,0,10528,31930,32006,102.39,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUCAGGCCCACCA,AB031214.1/4204-4280 AF478079.1/282-358 AF478087.1/283-359 AP001509.1/61205-61281 AP004593.1/216167-216243 AP004595.1/70031-70107 D26185.1/75064-75140 D26185.1/95532-95608 J01551.1/265-341 Z99104.2/11462-11538 Z99104.2/31930-32006,11462-11538 11550-11625 22290-22382 31930-32006 32018-32093 70179-70255 70265-70336 95372-95447 95452-95527 95564-95639 95646-95728 95769-95843 95858-95943 95953-96029 96057-96133 96143-96218 165753-165824 165829-165901 165958-166032 166063-166139 166167-166243 166252-166327 194197-194268 194272-194347 194352-194424 194447-194531 194536-194610,0,76,Z99104.2/31930-32006
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,71440,AF390136.1,1,sp|AF390136.1|AF390136 Almond witches'- broom phytoplasma strain AlmWB1 16S ribosomal RNA gene; partial sequence; 16S-23S intergenic spacer; complete sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,6504,1607,1683,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1607-1683,0,76,AF390136.1/1607-1683
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,71441,AF390137.1,1,sp|AF390137.1|AF390137 Almond witches'- broom phytoplasma strain AlmWB2 16S ribosomal RNA gene; partial sequence; 16S-23S intergenic spacer; complete sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,6505,1607,1683,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1607-1683,0,76,AF390137.1/1607-1683
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,81957,AF455038.1,1,sp|AF455038.1|AF455038 Almond witches'-broom phytoplasma strain AlmWB3 16S ribosomal RNA gene; partial sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7019,1607,1683,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1607-1683,0,76,AF455038.1/1607-1683
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,81958,AF455039.1,1,sp|AF455039.1|AF455039 Almond witches'-broom phytoplasma strain AlmWB4 16S ribosomal RNA gene; partial sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7020,1607,1683,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1607-1683,0,76,AF455039.1/1607-1683
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,81959,AF455040.1,1,sp|AF455040.1|AF455040 Almond witches'-broom phytoplasma strain AlmWB-P1 16S ribosomal RNA gene; partial sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7021,1607,1683,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1607-1683,0,76,AF455040.1/1607-1683
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,81960,AF455041.1,1,sp|AF455041.1|AF455041 Almond witches'-broom phytoplasma strain AlmWB-N1 16S ribosomal RNA gene; partial sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7022,1607,1683,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1607-1683,0,76,AF455041.1/1607-1683
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,89686,AF515636.1,1,sp|AF515636.1|AF515636 Candidatus Phytoplasma phoenicium strain A4 16S ribosomal RNA gene; partial sequence; 16-23S ribosomal RNA intergenic spacer and tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7540,1582,1658,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1582-1658,0,76,AF515636.1/1582-1658
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,89687,AF515637.1,1,sp|AF515637.1|AF515637 Candidatus Phytoplasma phoenicium strain 21 16S ribosomal RNA gene; partial sequence; 16-23S ribosomal RNA intergenic spacer and tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7541,1584,1660,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,1584-1660,0,76,AF515637.1/1584-1660
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,172292,AJ274638.1,1,sp|AJ274638.1|SPH274638 Sugarcane phytoplasma type G (AY) 16S-23S intergenic spacer region; tRNA-Ile gene; variety Alu1,0,13439,114,190,102.04,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCAUUUAGGCCCACCA,AF390136.1/1607-1683 AF390137.1/1607-1683 AF455038.1/1607-1683 AF455039.1/1607-1683 AF455040.1/1607-1683 AF455041.1/1607-1683 AF515636.1/1582-1658 AF515637.1/1584-1660 AJ274638.1/114-190,114-190,0,76,AJ274638.1/114-190
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,28139,AF008220.1,1,sp|AF008220.1|AF008220 Bacillus subtilis rrnB-dnaB genomic region.,0,4462,6888,6964,101.99,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUCAGGCCCACCA,AF008220.1/6888-6964 K00637.1/6888-6964 K01390.1/1791-1867 Z99119.2/157821-157745,5322-5397 5430-5505 5543-5618 5629-5715 5721-5795 5810-5895 5905-5981 5997-6073 6079-6151 6172-6248 6251-6327 6334-6425 6443-6519 6531-6607 6620-6695 6713-6788 6799-6872 6888-6964 6975-7049 7053-7143 7169-7240,0,76,AF008220.1/6888-6964
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,134658,K00637.1,1,sp|K00637.1|BSTGRGC Bacillus subtilis 16S ribosomal RNA; 23S ribosomal RNA; and 5S ribosomal RNA genes; complete sequence; and tRNA-Val; tRNA-Thr; tRNA-Lys; tRNA-Leu; tRNA-Gly; tRNA-Leu; tRNA-Arg; tRNA-Pro; tRNA-Ala; tRNA-Met; tRNA-Ile; tRNA-Ser; tRNA-Met; tRNA-Asp; tRNA-Phe; tRNA-His; tRNA-Gly; tRNA-Ile; tRNA-Asn; tRNA-Ser; and tRNA-Glu genes; complete sequence.,0,10434,6888,6964,101.99,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUCAGGCCCACCA,AF008220.1/6888-6964 K00637.1/6888-6964 K01390.1/1791-1867 Z99119.2/157821-157745,5322-5397 5430-5505 5543-5618 5629-5715 5721-5795 5810-5895 5905-5981 5997-6073 6079-6151 6172-6248 6251-6327 6334-6425 6443-6519 6531-6607 6620-6695 6713-6788 6799-6872 6888-6964 6975-7049 7053-7143 7169-7240,0,76,K00637.1/6888-6964
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,134660,K01390.1,1,sp|K01390.1|BSTGTRNE B.subtilis 168 trrnE gene cluster coding for 23S and 5S rRNA's and 21 tRNA's.,0,10471,1791,1867,101.99,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUCAGGCCCACCA,AF008220.1/6888-6964 K00637.1/6888-6964 K01390.1/1791-1867 Z99119.2/157821-157745,221-296 329-404 442-517 528-614 620-694 709-794 804-880 897-973 979-1051 1071-1148 1151-1227 1234-1326 1344-1420 1434-1510 1523-1598 1616-1691 1702-1775 1791-1867 1878-1952 1956-2046 2072-2143,0,76,K01390.1/1791-1867
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,134857,Z99119.2,1,sp|Z99119.2|BSUB0016 Bacillus subtilis complete genome (section 16 of 21): from 3013458 to 3213379.,1,10587,157821,157745,101.99,GGGCCUGUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGAUGGUUCGAGUCCAUUCAGGCCCACCA,AF008220.1/6888-6964 K00637.1/6888-6964 K01390.1/1791-1867 Z99119.2/157821-157745,180109-180037 159387-159312 159279-159204 159166-159091 159080-158994 158988-158914 158899-158814 158804-158728 158712-158636 158630-158558 158537-158461 158458-158382 158375-158284 158266-158190 158178-158102 158089-158014 157996-157921 157910-157837 157821-157745 157734-157660 157656-157566 157540-157469,0,76,Z99119.2/157821-157745
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,39100,AF122910.1,1,sp|AF122910.1|AF122910 Elm yellows phytoplasma strain EY1 16S ribosomal RNA gene; partial sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,5013,1595,1671,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,1595-1671,0,76,AF122910.1/1595-1671
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,39101,AF122911.1,1,sp|AF122911.1|AF122911 Elm yellows phytoplasma strain WVEY 16S ribosomal RNA gene; partial sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,5014,1595,1671,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,1595-1671,0,76,AF122911.1/1595-1671
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,44981,AF176319.1,1,sp|AF176319.1|AF176319 Flavescence doree phytoplasma ribosomal RNA operon; partial sequence.,0,5343,1637,1713,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,1637-1713,0,76,AF176319.1/1637-1713
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,46143,AF189214.1,1,sp|AF189214.1|AF189214 Elm yellows phytoplasma ribosomal RNA operon; partial sequence.,0,5387,1637,1713,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,1637-1713,0,76,AF189214.1/1637-1713
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,82273,AF458378.1,1,sp|AF458378.1|AF458378 Flavescence doree phytoplasma isolate FD-C 16S ribosomal RNA gene; partial sequence; 16S-23S intergenic spacer; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7023,878,954,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,878-954,0,76,AF458378.1/878-954
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,82274,AF458379.1,1,sp|AF458379.1|AF458379 Flavescence doree phytoplasma isolate FD2000 16S ribosomal RNA gene; partial sequence; 16S-23S intergenic spacer; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,7024,861,937,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,861-937,0,76,AF458379.1/861-937
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,108633,AY139875.1,1,sp|AY139875.1|AY139875 Elm yellows phytoplasma 16S ribosomal RNA gene; partial sequence; tRNA-Ile gene; complete sequence; and 23S ribosomal RNA gene; partial sequence.,0,9558,173,249,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,173-249,0,76,AY139875.1/173-249
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,128283,Y16387.1,1,sp|Y16387.1|AYP16SR Alder yellows phytoplasma 16S rRNA gene,0,9925,1611,1687,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,1611-1687,0,76,Y16387.1/1611-1687
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,146677,U54991.1,1,sp|U54991.1|EY54991 Elm yellows phytoplasma 16S/23S rDNA spacer region.,0,11863,118,194,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,118-194,0,76,U54991.1/118-194
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,155515,X76560.1,1,sp|X76560.1|MLOFDNA Mycoplasma (MLO;FD) transmitted from V.vinifera to V.faba; 16S rRNA and tRNA(Ile) genes.,0,12268,1603,1679,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,1603-1679,0,76,X76560.1/1603-1679
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,166610,Y16395.1,1,sp|Y16395.1|RSP16S Rubus stunt phytoplasma 16S rRNA gene,0,13038,1578,1654,101.86,GGGCCUAUAGCUCAGUUGGUUAGAGCACACGCCUGAUAAGCGUGAGGUCGGUGGUUCAAGUCCACUUAGGCCCACCA,AF122910.1/1595-1671 AF122911.1/1595-1671 AF176319.1/1637-1713 AF189214.1/1637-1713 AF458378.1/878-954 AF458379.1/861-937 AY139875.1/173-249 Y16387.1/1611-1687 U54991.1/118-194 X76560.1/1603-1679 Y16395.1/1578-1654,1578-1654,0,76,Y16395.1/1578-1654
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,24478,AE012793.1,1,sp|AE012793.1|AE012793 Chlorobium tepidum TLS  section 14 of 194 of the complete genome.,0,2377,7212,7288,101.73,GGGCCUGUAGCUCAGUUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCAGUGGUUCAAAUCCACUCAGGCCCACCA,AE012793.1/7212-7288 AE012963.1/7013-6937,7212-7288 7332-7407,0,76,AE012793.1/7212-7288
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,24648,AE012963.1,1,sp|AE012963.1|AE012963 Chlorobium tepidum TLS  section 184 of 194 of the complete genome.,1,2421,7013,6937,101.73,GGGCCUGUAGCUCAGUUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCAGUGGUUCAAAUCCACUCAGGCCCACCA,AE012793.1/7212-7288 AE012963.1/7013-6937,7013-6937 6893-6818,0,76,AE012963.1/7013-6937
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,16038,AE000763.1,1,sp|AE000763.1|AE000763 Aquifex aeolicus VF5 section 95 of 109 of the complete genome.,0,544,10019,10094,101.68,GCGGGCGUAGCUCAGUUGGUAGAGCAGCGGCCUUCCAAGCCGCAGGUCGCGGGUUCGAGUCCCGUCGCCCGCUCCA,AE000763.1/10019-10094,9830-9902 9925-10009 10019-10094 10124-10199 11676-11751,0,75,AE000763.1/10019-10094
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27105,AE016749.1,1,sp|AE016749.1|AE016749 Staphylococcus epidermidis ATCC 12228; section 6 of 9 of the complete genome.,1,3201,93052,92976,101.59,GGGCCUAUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCA,AE016749.1/93052-92976 AE016751.1/227578-227502 AF142677.4/46418-46342 AF269622.1/2771-2847 AF269732.1/313-389 AF270316.1/2711-2787 AF270322.1/1825-1749 AF270413.1/645-721 AF478075.1/314-390 AP003130.2/209805-209881 AP003130.2/254236-254312 AP003135.2/121039-120963 AP003359.2/226537-226613 AP003363.2/264102-264026 AP004823.1/252413-252489 AP004828.1/138117-138041 U11773.1/201-277 U11776.1/202-278 U11780.1/202-278 U11781.1/202-278 U11782.1/202-278 U11784.1/199-275 U11786.1/199-275 U11787.1/201-277 U11789.1/202-278 L36472.1/4841-4917 U39769.1/92-168 U39814.1/100-176,219276-219190 219167-219094 93052-92976 92955-92880 89577-89502 89495-89420 89413-89338 89329-89247 89243-89169 89157-89069 89056-88983 88973-88900 88883-88808 88783-88707 88682-88609 88599-88510 88502-88427 88389-88297 88285-88212 88107-88035 88026-87951 87946-87863 87854-87781 87778-87706 87694-87623 87617-87544 87534-87460 87445-87371 87359-87285 87244-87161 53931-53858 53843-53768 53757-53685 53671-53596 53578-53505 53495-53421 53419-53348 53294-53206,0,76,AE016749.1/93052-92976
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,27107,AE016751.1,1,sp|AE016751.1|AE016751 Staphylococcus epidermidis ATCC 12228; section 8 of 9 of the complete genome.,1,3252,227578,227502,101.59,GGGCCUAUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCA,AE016749.1/93052-92976 AE016751.1/227578-227502 AF142677.4/46418-46342 AF269622.1/2771-2847 AF269732.1/313-389 AF270316.1/2711-2787 AF270322.1/1825-1749 AF270413.1/645-721 AF478075.1/314-390 AP003130.2/209805-209881 AP003130.2/254236-254312 AP003135.2/121039-120963 AP003359.2/226537-226613 AP003363.2/264102-264026 AP004823.1/252413-252489 AP004828.1/138117-138041 U11773.1/201-277 U11776.1/202-278 U11780.1/202-278 U11781.1/202-278 U11782.1/202-278 U11784.1/199-275 U11786.1/199-275 U11787.1/201-277 U11789.1/202-278 L36472.1/4841-4917 U39769.1/92-168 U39814.1/100-176,281210-281118 230052-229977 229970-229895 229888-229816 229797-229723 229711-229623 229610-229534 229507-229434 229419-229344 227578-227502,0,76,AE016751.1/227578-227502
./cmzasha --no-stderr --no-insert-hack --filter 250 20 data/tRNAscan/tRNAscan-TRNA2-bact.cm /projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz 1 specfile data/TRNA2-bact.filterspec ,data/tRNAscan/tRNAscan-TRNA2-bact.cm (global),/projects/bio/zasha/seqs/embl_release76/eubact.fasta.gz,41600,AF142677.4,1,sp|AF142677.4|AF142677 Bacillus megaterium plasmid pBM400; complete sequence.,1,5109,46418,46342,101.59,GGGCCUAUAGCUCAGCUGGUUAGAGCGCACGCCUGAUAAGCGUGAGGUCGGUGGUUCGAGUCCACUUAGGCCCACCA,AE016749.1/93052-92976 AE016751.1/227578-227502 AF142677.4/46418-46342 AF269622.1/2771-2847 AF269732.1/313-389 AF270316.1/2711-2787 AF270322.1/1825-1749 AF270413.1/645-721 AF478075.1/314-390 AP003130.2/209805-209881 AP003130.2/254236-254312 AP003135.2/121039-120963 AP003359.2/226537-226613 AP003363.2/264102-264026 AP004823.1/252413-252489 AP004828.1/138117-138041 U11773.1/201-277 U11776.1/202-278 U11780.1/202-278 U11781.1/202-278 U11782.1/202-278 U11784.1/199-275 U11786.1/199-275 U11787.1/201-277 U11789.1/202-278 L36472.1/4841-4917 U39769.1/92-168 U39814.1/100-176,47738-47663 47658-47583 47574-47491 47483-47409 47404-47329 47315-47234