params (warning: commas chnged to semicolons),CM file,fastaFile,sequence #,EMBL accession,is in RFAMSEQ,sequence description (warning: commas chnged to semicolons),is reversed?,hit #,start nuc,end nuc,score (bits),hit sequence,hit Id(s) in Rfam with same seq,hit ranges within the same EMBL id,new hitness (0=in Rfam; 1=overlaps hit in Rfam;2=entirely new),amount of overlap with Rfam,this hit in Rfam format
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,4974,AC002512.1,1,sp|AC002512.1|AC002512 Drosophila melanogaster (P1 DS00276 (D13)) DNA sequence; complete sequence.,0,0,78113,78409,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,78113-78409 76040-75744,0,296,AC002512.1/78113-78409
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,4974,AC002512.1,1,sp|AC002512.1|AC002512 Drosophila melanogaster (P1 DS00276 (D13)) DNA sequence; complete sequence.,1,1,76040,75744,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,78113-78409 76040-75744,0,296,AC002512.1/76040-75744
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6331,AC084446.1,1,sp|AC084446.1|AC084446 Caenorhabditis briggsae cosmid CB018G16; complete sequence.,1,2,16506,16211,133.97,ACCGGGUGUCGUGGCGGGCGCCUGUGAGUCAGCUUCUUGACGGUAGACAAGUGUGGAUGGAGUGAAGGGAGGAGUCCUGUGGGUGUUGUCGGCAACGGCGACCGAGCGUCCGUGCCAAGCGCUGCGUCGCCAGGGGUCUCCGGUCGGAAGGCUGGCGGUCCCGGGCGCAUAAGGAGUGGUGCACGGCUCAGGGCCGAAAGGCAGCAGGCAAAAGCCACCGCGCGGUGCAGUGGCCGGAUAGCGCUUGUGAGUUGUCGCUCGCCCACAGCCUCUCUGAUACCUUCAGACCACUUGUC,AC084446.1/16506-16211,16506-16211,0,295,AC084446.1/16506-16211
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6748,AC095014.1,1,sp|AC095014.1|AC095014 Drosophila melanogaster; chromosome 3R; region 83F-84A; BAC clone BACR19D23; complete sequence.,0,3,156446,156742,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,,0,0,AC095014.1/156446-156742
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6748,AC095014.1,1,sp|AC095014.1|AC095014 Drosophila melanogaster; chromosome 3R; region 83F-84A; BAC clone BACR19D23; complete sequence.,1,4,154373,154077,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,,0,0,AC095014.1/154373-154077
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7416,AE001572.2,1,sp|AE001572.2|AE001572 Drosophila melanogaster Antennapedia complex (ANT-C);complete sequence.,0,5,236401,236697,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,234328-234032 236401-236697,0,296,AE001572.2/236401-236697
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7416,AE001572.2,1,sp|AE001572.2|AE001572 Drosophila melanogaster Antennapedia complex (ANT-C);complete sequence.,1,6,234328,234032,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,234328-234032 236401-236697,0,296,AE001572.2/234328-234032
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7689,AE003673.3,1,sp|AE003673.3|AE003673 Drosophila melanogaster chromosome 3R; section 11 of 118 of the complete sequence.,0,7,44323,44619,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,42250-41954 44323-44619,0,296,AE003673.3/44323-44619
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7689,AE003673.3,1,sp|AE003673.3|AE003673 Drosophila melanogaster chromosome 3R; section 11 of 118 of the complete sequence.,1,8,42250,41954,108.54,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCUU,AC002512.1/78113-78409 AE001572.2/234328-234032 AE003673.3/42250-41954 AC002512.1/76040-75744 AE003673.3/44323-44619 AE001572.2/236401-236697,42250-41954 44323-44619,0,296,AE003673.3/42250-41954
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,43107,Z30973.1,1,sp|Z30973.1|CEB0284 Caenorhabditis elegans cosmid B0284,1,9,7231,6935,127.35,ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUAAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUUGUCAACGUCGACCGAGCGUCCGUGCCAAGCGCUGCGUCACCAGGGGAUGACUGUCGGAAGAUGGUCAGUCCCGGGUGCAUAAGGAGUGGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCCACCGCGCGGUGCAGUGGCCGGACUGCGCUUGUGAGUUGACACGUAUACACAGCCUUCUCAAUACCUUCAGACCACUUGUUU,Z30973.1/7231-6935,7231-6935,0,296,Z30973.1/7231-6935
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,43108,Z34533.1,1,sp|Z34533.1|CEB0285 Caenorhabditis elegans cosmid B0285,0,10,38786,39081,127.45,ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUGAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUUGUCAACGUCGACCGAGCGUCCGUGCCAAGCGCUGCGUCACCAGGGGAUGACUGUCGGAAGAUGGUCAGUCCCGGGUGCAUAAGGAGUGGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCCACCGCGCGGUGCAGUGGCCGGACAGCGCUUGUGAGUUGACACGUAUACACAGCCUUCUCAAUACCUUCAGACCACUUGUC,Z34533.1/38786-39081,38786-39081,0,295,Z34533.1/38786-39081
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,44091,U41993.1,1,sp|U41993.1|CEF44A2 Caenorhabditis elegans cosmid F44A2; complete sequence.,1,11,1858,1563,117.29,ACCGGGCGUCGUGGCGGGCGUCUGUAAGCCAGCUUCUUGGCGGUAGAUAAGUGUGGAUGGAGUGAAGGGAGGAGCCCUUUGGGUGUUGCUGGCAACGGCGACCGAGCGUCCGUGCCAAGCGCUGCGUCGCUAGGGGUCAUCUGGCGGAAGGCGGGCGGUCCCGGGCGCAUAAGGAGCGGUAUACGGCUCAGGGCCGAAAGGCAGCAGGCAAAAGCCUCCGCGCGGUGCAGUGGCCGGAUAGCGCUUGCGAGUUGUCGCUCACCCACUGCCUCUCUGAUACCUUUAGACCACUUAUC,U41993.1/1858-1563,1858-1563,0,295,U41993.1/1858-1563
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,44947,U23515.1,1,sp|U23515.1|CER144 Caenorhabditis elegans cosmid R144; complete sequence.,1,12,33862,33567,116.17,ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUAAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUCGUCUACGUCGACCGAGCGUCCGUGCCAAGCGCUACGUCACCAGGGGAUAACUGUCGGAAGGCGGUUAGUCCCGGGUGCAUAAGGAGUCGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCGACCGCGUGGUGCAGUGGCCGGACCGCGCUUGUAAGUUGACACACAUACACAGCCUUCUCGAUACCUUCAGACCACUUAUC,U23515.1/33862-33567,33862-33567,0,295,U23515.1/33862-33567
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,46068,U00064.1,1,sp|U00064.1|CEZC155 Caenorhabditis elegans cosmid ZC155; complete sequence.,0,13,12850,13145,121.37,ACCGAGCGUCGUGGCGGGCGCUUGUGAGUCAGCUUCUUGACGGUAGAUAAGUGUGGAUGGAGUGAGAGGAGGAGUCCUGUGUAUGUCGUUGUCUACGUCGACCGAGCGUCCGUGCCAAGCGCUACGUCACCAGGGGAUAACUGUCGGAAGGCGGUUAGUCCCGGGUGCAUAAGGAGUCGUGGAUGGUUCAGGACCGAAAGGUAGCAGACAAAAGCGACCGCGUGGUGCAGUGGCCGGACCGCGCUUGUGAGUUGACACACAUACGCAGCCUUCUCGAUACCUUCAGACCACUUAUC,U00064.1/12850-13145,12850-13145,0,295,U00064.1/12850-13145
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,213,X01056.1,1,sp|X01056.1|DM7SL Drosophila melanogaster 7SL RNA gene,0,14,2,295,99.85,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUCGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAACCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCU,X01056.1/2-295,2-295,0,293,X01056.1/2-295
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,3159,K01755.1,1,sp|K01755.1|DMKSG7SL D. melanogaster 7SL RNA gene.,0,15,2,295,101.58,ACUGGAAGGUUGGCAGCUUCUGUAAUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUCGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAACCAACAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCU,K01755.1/2-295,2-295,0,293,K01755.1/2-295
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,3956,X00952.1,1,sp|X00952.1|DMRN7S Drosophila 7SL RNA sequence of signal recognition particle,0,16,2,299,110.27,GACUGGAAGGUUGGCAGCUUCUGUAACUCACGCUUCUGUGAGGUCUGAUUGUGGGAUGGCCUGAGGCUGGGAUCUACUGCGUAGCGGACCAGCUCAUGUUGACGGAACGUCCGCACUAAGCUUGCCAUCAAUAUGGGUGCCAUGGAGGAGUCCGUGGCAUUCAGGUUGGCUAAGGAGGGAUGAACCGGGCCAGGGGUGAAAACCAGCAGCCAAGAGUUCCCGUGGUAGGCAGUAGUGGGAUAGCGUACCGGAGUGGACUGCCGUUAUCAGCCCAACCGAUAUGGUUGGACCACAAUCU,X00952.1/2-299,2-299,0,297,X00952.1/2-299
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,24707,X56981.1,1,sp|X56981.1|TT7SL T.thermophilus gene for 7SL RNA,0,17,102,389,76.41,GCCAGGGUAGCAAUACCUGUGUCUAUAUGUGGCAUAAACAAUGUAGGUUGUGAUAGAUAGGAUAUGAGAGUUUGAUGAGACAGUUUGCUAAGAGUGUGCCCGCUCCAAACAAUGAGUUGCUAUGGUGGUAACCUAGUAAUAGGACUCCACCAGGGCAUUAAAGAGCUAAGGAAACGCCUCAGGCUGGCAACAGAACAGGGAAAACUUGCCGCUUGUUGUGGUGGAAGGAUAACAUACUCAUUAACUGUCAAACUAAUCGUUCUACUAUCAAAGCCAGACAUUGCUUUU,X56981.1/102-389,102-389,0,287,X56981.1/102-389
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/mam.dat.fasta.gz,543,AB021174.1,1,sp|AB021174.1|AB021174 Oryctolagus cuniculus transforming scRNA.,0,18,1,298,126.12,GCCGGGCGCGGUGGCGCGCGCCUGUAGUCCCAGCUACUCGGGAGGCUGAGGCCGGAGGAUCGCUUGAGUCCAGGAGUUCUGGGCUGUCGUGCGCUAUGCCGAUCGGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGAUCGCGCCUGUGAAUAGCCACUGCACUCCAGCCUGGGCAACAUAGCGAGACCCUGUCUC,AB021174.1/1-298,1-298,0,297,AB021174.1/1-298
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,6983,AC126244.3,1,sp|AC126244.3|AC126244 Mus musculus chromosome 12 clone RP24-319A6; complete sequence.,0,19,141259,141557,130.23,GCCGGGCGCGGUGGCGCACGCCUGUAGUCCCAGCUACUCGGGAGGCUGAGACAGGAGGAUCGCUUGAGUCCAGGAGUUCUGGGCUGUAGUGCGCUAUGCCGAUCGGGUGUCCGCACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGGGAUCGCGCCUGUGAAUAGCCACUGCACUCCAGCCUGGGCAACAUAGCGAGACCCCGUCUCU,AC126244.3/141259-141557,141259-141557,0,298,AC126244.3/141259-141557
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,2031,AB020752.1,1,sp|AB020752.1|AB020752 Arabidopsis thaliana genomic DNA; chromosome 5; P1 clone:MTH16.,0,20,35792,36096,158.22,GUCGAGCUAUGUAACGAGAGCUUGUAACCCAAGUGGGGACUAUAAGAUGGUGGAACACUGGAUCGGCCCACGGGUCGGAUUUGUUGUUGGCAUAGGUCUGGACUGCCCAAUCCAAGCUGUGAGUGAACCGUAUGAACCAAGCGAAGGUUUGAUCCGUACGGUUGCUAAAGGUUGAGGGUAUUGCGUUAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCAGCAGUGGACGGACAACGGUUCGACGCCACACAAAUCCACUAUGGUCCGCUGGCUCGUAACCCGCUUGAACCACCAUUUU,AB020752.1/35792-36096 AL353994.1/33792-33488,35792-36096,0,304,AB020752.1/35792-36096
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,2649,AB026661.1,1,sp|AB026661.1|AB026661 Arabidopsis thaliana genomic DNA; chromosome 5; BAC clone:T30G6.,1,21,49999,49698,105.63,UUCCAAAUCAGUAACGAGGGCUUGUUAACCAAGUGGGGACAAUAAGUUGGUGGAACACUGACUCGGUCCACGGGUCAGAUCUGUUGUGGCAUUGUUCUGGGCUGCCCAGUCCAAGCUGUGAGUGAUCUGUGUGUGUUGAGCGAAGGCUUGGCUCAGGCGGUUCUUACAUUGGUGGGCAAUGCGUGAGGCUGGUUUCAUAGAGCAGCGAUCACCUCCCGCUCUCGGCAGUGGACGGAUCACAGCUCGACACCACUCAGAUUCACUAUGGCUUGCUCGCUCGUUCCCAGCUGGACCACCAAUUU,AB026661.1/49999-49698,49999-49698,0,301,AB026661.1/49999-49698
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8675,AC005275.1,1,sp|AC005275.1|AC005275 Arabidopsis thaliana BAC F4C21 from chromosome IV; top arm; near 17 cM; complete sequence.,0,22,105500,105804,164.81,GUCGAGCUAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUUAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUUCUAAAGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,AL161496.2/123872-124176 X72229.1/323-627 AC005275.1/105500-105804,109058-109362 105500-105804,0,304,AC005275.1/105500-105804
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8675,AC005275.1,1,sp|AC005275.1|AC005275 Arabidopsis thaliana BAC F4C21 from chromosome IV; top arm; near 17 cM; complete sequence.,0,23,109058,109362,164.56,GUCGAGCGAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGCUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUGCUAAAGUUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUGGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUCUGAACCACCAUUUU,AC005275.1/109058-109362 AL161496.2/127430-127734,109058-109362 105500-105804,0,304,AC005275.1/109058-109362
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8681,AC005311.3,1,sp|AC005311.3|AC005311 Arabidopsis thaliana chromosome 2 clone T16B12 map m283; complete sequence.,0,24,17031,17335,145.77,GUCGAGCUAAGUAACGAGAGCUUGUGACCCGAGUGGGGACAAUAAGGUGGUGGAACAGUGGUUCAAUUCCUCGGGUCGGACCUGAUGCUGACAUAUAUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUCUGUGUGGGUCAGGCGAAGGCUUGACUCAGGCGGAUUCUAAAGUCGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCUCUUACAGCAGUGGAUGGAUCAUAGUUCGAAGUCUCUCAGAUCCACUAUGGCCCGCUGGUUCGAUCUCUCCUGGACCACCACUUU,AC005311.3/17031-17335,17031-17335,0,304,AC005311.3/17031-17335
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8702,AC005662.3,1,sp|AC005662.3|AC005662 Arabidopsis thaliana chromosome 2 clone F13H10 map CIC11C08; complete sequence.,1,25,47366,47062,165.66,GUCGAACUCAGUAACGCGGGCUUGUGAUCCAAGUGGAGACAAUAAGGGGAUGGGACGUUGGGUCGAUCUCAUUGGGCCGGGUUCGGGUUGGGCUAUAUUCUGGCCCGCCCAUUCCAAGUUGGGAGUUGAGGCAUGGGCUUCGAGCGAAGGCUCGGGUCUCAUGUCUUCUAGAGUGGGGGAGACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACCUCCCGCUCUUGACGGUGGAAGGAUUACGGGCCAUUGCCUUCCGAGCCCACUAUGACCCAAUAAGCCGCUCCGAUUGGACCAUCACUUU,AC005662.3/47366-47062,47366-47062,0,304,AC005662.3/47366-47062
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,8921,AC007591.2,1,sp|AC007591.2|AC007591 Arabidopsis thaliana chromosome 1 BAC F9L1 sequence; complete sequence.,1,26,113708,113407,159.55,GUCGAGCUCAGUAACGUGGGCUUGUGACCCGUGUGGGGACAAUAAGUUGGUGGAACACUGGCUCGGCCCACGGGUCGGAUCUGUUGUGGCAUUGUUCCGGGCUGCCCAGUCCAAGCUGAGAGUGAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCUUGCAGUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUGGACGGAUCACAGCUCGACGCCACUCAGAUUCACCAUGGCCUGCUGGCUCGUUCCCAGCUGGACCACCAAUUU,AC013453.1/1552-1251 AC007591.2/113708-113407,113708-113407,0,301,AC007591.2/113708-113407
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9034,AC011807.4,1,sp|AC011807.4|AC011807 Arabidopsis thaliana chromosome I BAC F14J22 genomic sequence; complete sequence.,0,27,47784,48090,146.14,GUCGAACCUAGUAACGUGGGUUUAUGAUCCGAGUGGAGACAACAAGGUGAUGGUACAUUGGGUCGGAUCUCAAUGGGCCGGGUUCGGCUUGGGCUCUUUACUGGCCUGCCCAUUCCAAGUCGGGAGUUGAGAUAUCUUCUGAGCGAAGGUUCGGAGCCAAUAUCUCUUUAGAGCGGAGGAGACCGCGUGAGGCUGGUUUCACAGAGCAGCGUCCACCUUCCGUUCUCGACGGUGGAAGGAUAACGGGCCCGUUGUCUUCCGAGCCCACUAUGACCCAUUAGGCCGACUCCAACUGAGCCAUCACUUU,AC011807.4/47784-48090,47784-48090,0,306,AC011807.4/47784-48090
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9070,AC013453.1,1,sp|AC013453.1|AC013453 Arabidopsis thaliana chromosome I BAC T16N11 genomic sequence; complete sequence.,1,28,1552,1251,159.55,GUCGAGCUCAGUAACGUGGGCUUGUGACCCGUGUGGGGACAAUAAGUUGGUGGAACACUGGCUCGGCCCACGGGUCGGAUCUGUUGUGGCAUUGUUCCGGGCUGCCCAGUCCAAGCUGAGAGUGAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCUUGCAGUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUGGACGGAUCACAGCUCGACGCCACUCAGAUUCACCAUGGCCUGCUGGCUCGUUCCCAGCUGGACCACCAAUUU,AC013453.1/1552-1251 AC007591.2/113708-113407,1552-1251,0,301,AC013453.1/1552-1251
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9379,AC079888.9,1,sp|AC079888.9|AC079888 Oryza sativa chromosome 10 BAC OSJNBa0078O01 genomic sequence; complete sequence.,0,29,142244,142551,156.20,GCCGAGCCAAGUAGCGAUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGCGGAUGCCUGGUCGUUUGCGCUUUGGCCUGGGCCUGUGGUUCGCUCUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUAUGGGGCGCCCUGGCGAAAGCUAGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAUGUGCCUUCCAUGGCAGACCCCCAUCUU,AE017109.1/257283-257590 AC079888.9/142244-142551,27802-27493 142244-142551,0,307,AC079888.9/142244-142551
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9379,AC079888.9,1,sp|AC079888.9|AC079888 Oryza sativa chromosome 10 BAC OSJNBa0078O01 genomic sequence; complete sequence.,1,30,27802,27493,162.33,GCCGAGCCAGGUAGCGUUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGUUGGAUGCCUGGUCGUUUGCGCUUGGGGUCUGCGCCUGUGGUUUGCACUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUGUGGGGCGCCUGGGCGAAGGCUCGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAAGUGCCUUCCAUGGCAGACCACCACCUU,AE017109.1/142841-142532 AC079888.9/27802-27493,27802-27493 142244-142551,0,309,AC079888.9/27802-27493
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9694,AC121489.2,1,sp|AC121489.2|AC121489 Oryza sativa (japonica cultivar-group) chromosome 3 clone OJ1217B09; complete sequence.,0,31,123851,124137,100.98,GCCGAGCUCAGUAGCGAGAGCUUGUAACCCAUGUGGGGGCAUCAGGUGGUGUGGAUGAUCGGUGCUGAAUUUGGGCCUGGGUCCAUGUGUUGUUAACUAUGCUGGCUUGCGUAGUGGGUGGAGGGGCUUCGGCGAAAGCCUUGGUCUCUCCGGCCCUGAAGUUGGCAGACACGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCUUCCAACGGUGGAAGGAUAACAGGCCGCUGCACCAUGGGCCCGCUUCUGGCCCCACUAUUACAGACCACCAUCAU,AC121489.2/123851-124137,123851-124137,0,286,AC121489.2/123851-124137
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9721,AC123570.4,1,sp|AC123570.4|AC123570 Medicago truncatula clone mth2-33l22; complete sequence.,0,32,87824,88124,88.82,GCUGAGUUGGGUAGUGCCAACUUGGGACCCAAGUGAGAGCACUAAAAUAAUGGGACAUGGCUAUGGCUUGUCUUGGCUGAGCUGGUUUCUGCAAUAUGCUGGCUUGUCCGCUCCAAGUUGAGAGUUGUGCCAUGGGACUUUGGCAUACGCCUUCGUCUCAUGGCUCCUAGACUAGAGGGCACUGCGUGAGGCUCUGCUCACAGAGCAGCGAAGACCUCUCCCUCCUGACAGUGGAGGGAUUACAAGCUGCUGUACUUCUAGUCUACUAAGCCGGUGAGCCUAGCCUUUGAACCAUCAUUUU,AC123570.4/87824-88124,87824-88124,0,300,AC123570.4/87824-88124
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9905,AC137997.2,1,sp|AC137997.2|AC137997 Oryza sativa chromosome 3 BAC clone OJ1499_D04; complete sequence.,1,33,82646,82342,159.61,GCCGAGCUCAGCAGCGCGAGCUUGUAACCCGAGCGGGGGCAUUAAGGUGGUGUGGACGUUGCCGUAUGGCUGCGGGCCUGGGUUGGCAGUGCCAUAGAUGGCCCGCCCGUUCCAAGUUGCGUAGUUGGGCCGGCGGGGCUUGAGCGAAAGCUCUGGCCUCACGUUUCCCUAGAGUGGCAGGCAUUGCGUGAGGCUGGCUUCACAGAGCAGCGAAUACUGUCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCCGCACUGCUGGCCCGCUUGGGUCUCGCAGCCUACUCCAACGGACCACCACUUU,AC137997.2/82646-82342,82646-82342,0,304,AC137997.2/82646-82342
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,10389,AE017109.1,1,sp|AE017109.1|AE017109 Oryza sativa (japonica cultivar-group) chromosome 10; section 63 of 77 of the complete sequence.,0,34,257283,257590,156.20,GCCGAGCCAAGUAGCGAUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGCGGAUGCCUGGUCGUUUGCGCUUUGGCCUGGGCCUGUGGUUCGCUCUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUAUGGGGCGCCCUGGCGAAAGCUAGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAUGUGCCUUCCAUGGCAGACCCCCAUCUU,AE017109.1/257283-257590 AC079888.9/142244-142551,142841-142532 257283-257590,0,307,AE017109.1/257283-257590
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,10389,AE017109.1,1,sp|AE017109.1|AE017109 Oryza sativa (japonica cultivar-group) chromosome 10; section 63 of 77 of the complete sequence.,1,35,142841,142532,162.33,GCCGAGCCAGGUAGCGUUGGCUUGUCACCCGAGCGGGGGCAAUAAGGUGGUGUUGGAUGCCUGGUCGUUUGCGCUUGGGGUCUGCGCCUGUGGUUUGCACUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUGUGGGGCGCCUGGGCGAAGGCUCGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUAACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAAGUGCCUUCCAUGGCAGACCACCACCUU,AE017109.1/142841-142532 AC079888.9/27802-27493,142841-142532 257283-257590,0,309,AE017109.1/142841-142532
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,16313,AF069442.1,1,sp|AF069442.1|AF069442 Arabidopsis thaliana BAC T4I9; chromosome IV; near 17 cM; complete sequence.,0,36,64156,64461,142.97,GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,X72228.1/320-625 X55111.1/801-1106 AL161495.2/164946-164641 AF069442.1/64156-64461 X69901.1/3886-4191,64156-64461,0,305,AF069442.1/64156-64461
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,99211,AP003253.3,1,sp|AP003253.3|AP003253 Oryza sativa (japonica cultivar-group) genomic DNA; chromosome 1; PAC clone:P0451D05.,0,37,106424,106740,143.70,GCCGAGCUCAGUAGCGAGAGCCUGUAACCCAAGCGGGGGCACUAAAGGUGGCUGCGGAUGUUUGGUGUGGAUUCUGAUCCUGGGCCCCAUGUUGUUGUAAUCUUGCUGGCUUGCCCGUUCCAAGUUGCGUAGUGGGCCGGAGGGGCUUUGGCGAAGGCCUUUGCUUUGCUUCUCCGGCCCUAAAGUGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCUUCCAUCGGUGGAAGGAUAACAGGCUGCUGCACCUUGGGCCCGCUUCUGGCCCAGAGUCCCUCUACAACAGACCACCAUCUU,AP003333.4/45380-45696 AP003253.3/106424-106740,106424-106740,0,316,AP003253.3/106424-106740
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,99274,AP003333.4,1,sp|AP003333.4|AP003333 Oryza sativa (japonica cultivar-group) genomic DNA; chromosome 1; BAC clone:B1103C09.,0,38,45380,45696,143.70,GCCGAGCUCAGUAGCGAGAGCCUGUAACCCAAGCGGGGGCACUAAAGGUGGCUGCGGAUGUUUGGUGUGGAUUCUGAUCCUGGGCCCCAUGUUGUUGUAAUCUUGCUGGCUUGCCCGUUCCAAGUUGCGUAGUGGGCCGGAGGGGCUUUGGCGAAGGCCUUUGCUUUGCUUCUCCGGCCCUAAAGUGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUGCCCGCUUCCAUCGGUGGAAGGAUAACAGGCUGCUGCACCUUGGGCCCGCUUCUGGCCCAGAGUCCCUCUACAACAGACCACCAUCUU,AP003333.4/45380-45696 AP003253.3/106424-106740,45380-45696,0,316,AP003333.4/45380-45696
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,100168,AP006123.1,1,sp|AP006123.1|AP006123 Lotus corniculatus var. japonicus genomic DNA; chromosome 1; clone:LjT41E18; TM0207.,0,39,43412,43713,120.99,GCCGAGCUUGCACGAUAGCUUGUAACCCGAAUGGGGGCACCAAGAUGGUGGAACAUGGCUAUGACUUCACUGGGUUGGUCUGGUGGUUGCACCUUGUUGGCCUGCCCGCUCCAAGUCGAGAGGUGGGCCAUGUGUCUUUAGUGAAAGCUAAGGUCUUGUGGUUCCUAGACAGGAGGGCAAAGCGUGAGGCUGGUGUCACAGAGCAGCGAACACUUCUGGCUCCUGACAGUGGAGGGAUAACAGGCUGCUGCACCUUCAGCCCACAAAUGCCUAGUGAACCCAGCUACCUGAACUAUCAUUUU,AP006123.1/43412-43713,43412-43713,0,301,AP006123.1/43412-43713
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,100222,AP006364.1,1,sp|AP006364.1|AP006364 Lotus corniculatus var. japonicus genomic DNA; chromosome 4; clone:LjT28B04; TM0170.,1,40,60840,60537,129.92,GCCGAGUUGGGUUACUCCAGCUUGUGACCCAAGUGGGGGCACCAGGUUGAUGGAACAUGGUUCUGGCUUUCGUUAGGCUGGGCUGUUAGAUGCAAUAUUCUGGCCUGCCCACUCCAAGUUGAGAGUUGGACCGUGGGGCUUGGGCGAAGGCCCUUGUCUCUCGGCCCCUAAACUGGAGGGCAAAGCGUGAGGCUGGUUUCACAGAGCAGCGAAUACCUCUGGCUCCUGACAGUGGAGGGAUAACAGGCUGAUGCACUCUCAGCCCAUUGUGCCUAGUGGGCCUGGCCUCUUGAACCAUCAUCUU,AP006364.1/60840-60537,60840-60537,0,303,AP006364.1/60840-60537
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101245,X72228.1,1,sp|X72228.1|AT7SL1A A.thaliana gene At7SL-1 for 7SL RNA,0,41,320,625,142.97,GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,X72228.1/320-625 X55111.1/801-1106 AL161495.2/164946-164641 AF069442.1/64156-64461 X69901.1/3886-4191,320-625,0,305,X72228.1/320-625
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101246,X72229.1,1,sp|X72229.1|AT7SL2A A.thaliana gene At7SL-2 for 7SL RNA,0,42,323,627,164.81,GUCGAGCUAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUUAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUUCUAAAGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,AL161496.2/123872-124176 X72229.1/323-627 AC005275.1/105500-105804,323-627,0,304,X72229.1/323-627
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101247,X55111.1,1,sp|X55111.1|AT7SLRNA A. thaliana 7SL RNA gene,0,43,801,1106,142.97,GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,X72228.1/320-625 X55111.1/801-1106 AL161495.2/164946-164641 AF069442.1/64156-64461 X69901.1/3886-4191,801-1106,0,305,X55111.1/801-1106
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101759,X69901.1,1,sp|X69901.1|ATAUXIN A.thaliana gene for auxin-binding protein,0,44,3886,4191,142.97,GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,X72228.1/320-625 X55111.1/801-1106 AL161495.2/164946-164641 AF069442.1/64156-64461 X69901.1/3886-4191,3886-4191,0,305,X69901.1/3886-4191
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101926,AL161495.2,1,sp|AL161495.2|ATCHRIV7 Arabidopsis thaliana DNA chromosome 4; contig fragment No. 7,1,45,164946,164641,142.97,GUCGAGCUAAGUAACAAUAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGGACACUGGUUCGGUUCCUCGGAUCGGUUCUGAUGUGGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGAGUAAUUAGUGUUGAGUUGAGCGAAGGCUUGGCUCAUGCAGGUUCUAGAGUCGGAGGGUAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACGGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,X72228.1/320-625 X55111.1/801-1106 AL161495.2/164946-164641 AF069442.1/64156-64461 X69901.1/3886-4191,164946-164641,0,305,AL161495.2/164946-164641
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101937,AL161496.2,1,sp|AL161496.2|ATCHRIV8 Arabidopsis thaliana DNA chromosome 4; contig fragment No. 8,0,46,123872,124176,164.81,GUCGAGCUAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUUAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGUUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUUCUAAAGUUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUAGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUAUGAACCACCAUUUU,AL161496.2/123872-124176 X72229.1/323-627 AC005275.1/105500-105804,123872-124176 127430-127734,0,304,AL161496.2/123872-124176
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,101937,AL161496.2,1,sp|AL161496.2|ATCHRIV8 Arabidopsis thaliana DNA chromosome 4; contig fragment No. 8,0,47,127430,127734,164.56,GUCGAGCGAAGUAACAUGAGCUUGUAACCCAUGUGGGGACAUUAAGAUGGUGGAACACUGGUUCGGGUCCACGGGCCGGUUCUGUUGCUGGCAUGUUUCUGGGCUGCCCAGUCCAAGCUGUGAGUAAGACGUGUGUGUCAAGCGAAGGCUUGGCUCAAACGGCUGCUAAAGUUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUUACUUCCCGCUUACAGCAGUGGACGGAUCACAGUUUGGCGUCGCUCAGAACCACUAUGGCCUGCUGGUCCGAUCUCAUCUGAACCACCAUUUU,AC005275.1/109058-109362 AL161496.2/127430-127734,123872-124176 127430-127734,0,304,AL161496.2/127430-127734
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,102211,AL353994.1,1,sp|AL353994.1|ATF17I14 Arabidopsis thaliana DNA chromosome 5; BAC clone F17I14 (ESSA project),1,48,33792,33488,158.22,GUCGAGCUAUGUAACGAGAGCUUGUAACCCAAGUGGGGACUAUAAGAUGGUGGAACACUGGAUCGGCCCACGGGUCGGAUUUGUUGUUGGCAUAGGUCUGGACUGCCCAAUCCAAGCUGUGAGUGAACCGUAUGAACCAAGCGAAGGUUUGAUCCGUACGGUUGCUAAAGGUUGAGGGUAUUGCGUUAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCAGCAGUGGACGGACAACGGUUCGACGCCACACAAAUCCACUAUGGUCCGCUGGCUCGUAACCCGCUUGAACCACCAUUUU,AB020752.1/35792-36096 AL353994.1/33792-33488,33792-33488,0,304,AL353994.1/33792-33488
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,102940,AJ290403.1,1,sp|AJ290403.1|ATH290403 Arabidopsis thaliana 7SL-3 gene for signal recognition particle,0,49,66,369,153.59,GUCGAGCUAAGUAACAGUAGCUUGUAACCCAUGUGGGGACAAUAAGAUCGAGGGACACUGGUCGGUUCCUCGGGUCGGUUCUGGUGUUGGCAUGUUUCUGAGCUGCCCAGUCCAAGCUGUGGUAAUCCGUGUGAAUCAAGCGAAGGCUUGGCUCAGUCGGUUUCUAAAGGCGGAAGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACUUCCCGCUUACAGCAGUGGACGGGAUCACAGUUUGGCGUCGCUCAGAACCACUAUGGCCUGAUGGUCCGAUCUCAUAUGAACCACCAUUUU,AJ290403.1/66-369,66-369,0,303,AJ290403.1/66-369
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,103568,AJ505697.1,1,sp|AJ505697.1|ATH505697 Arabidopsis thaliana partial small cytoplasmic putative RNA 7SL (7SL RNA gene); clone Ath-29; 5' end incomplete,0,50,4,290,130.45,GUGGGCUUGUGACCCGUGUGGGGACAAUAAGUUGGUGGAACACUGGCUCGGCCCACGGGUCGGAUCUGUYGUGGCAUUGUUCCGGGCUGCCCAGUCCAAGCUGAGAGUGAUCCGUGUGUGUUAAGCGAAGGCUUGGCUCAGGCGGUUCUUGCAGUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGAUCACCUCCCGCUCUCAGCAGUGGACGGAUCACAGCUCGACGCCACUCAGAUUCACCAUGGCCUGCUGGCUCGUUCCCAGCUGGACCACCAAUUU,AJ505697.1/4-290,4-290,0,286,AJ505697.1/4-290
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,182773,X71484.1,1,sp|X71484.1|CRRNASC7 C.reinhardtii 7S(L) small cytoplasmic RNA,0,51,3,287,79.90,GCCGGCUGGAGUCACGUCCAGUUGUCACCCAUGUGGGGGCCAAGCGGAUGAAGGAACAUAUGGCUCUCCGGUCGUGAACGCUUCCGUCGAUAGCGUGUCCUCUUCGAGUCCACAGUCGGCAAGGUCGCUGCCCUGAUGGGUGGCUGACCUGGUUGAUGAUUAGUCCCGCACCGCGUGAGGCAGGAAACUGAGCAGCGAAAAGGGACAGCUGCGGACGGCGAAAGGAUCGCAUGCUUGAGGAGGUGCCACGACCACCCGGGGGGUCCUCUGUGGGACCAACUACCG,X71484.1/3-287,3-287,0,284,X71484.1/3-287
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188807,X65988.1,1,sp|X65988.1|HJ7SRPA Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene); clone_lib Z10o,0,52,1,301,123.35,GCCUAGCAACGUGGGCCUGUGACCCAAGUGGGGGGAUGUGGGAAAUGGGACUCUGGCGCAGCCGGUUGGCAUCGGGUCCAGUGUUAGCUGCUUCCUGGCCUGCCCAUUCCAAGCCGAGACUUGGGCUGUCUGAGCCGGACGAAGGUCUGGCUUGCUCAGCUCCUAAAGCGGAGGGCAAUGCCGUGAGGCUGGCUUCACAGAGCAGCGACCACCUCCCGGUCCCGGCAGUGGCAAGGAUAACGGGCCGUGCUACUUGGGUCCACCAUGUUCACUGGUGGACUCUAAAUAGGACCAUUUCUUU,X65988.1/1-301,1-301,0,300,X65988.1/1-301
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188808,X65989.1,1,sp|X65989.1|HJ7SRPB Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene); clone_lib Z11o,0,53,1,297,106.14,GCGUGGUAACGCGAGCCUGUAACCCGAGUGGGGGCAUUAAGGUGAUGGAACGUCAGUUCGGCCCAAUGGCCCGGAUUCGAUGUAGCUGUCUACUGGCUUGCCCGUUCCAAGCCGGGAGUUGAGCCGUGCGANAUUGAGCGGAGGCUCGGCUCGCACCUCUGCUGGAGUGGAGGGUACCGCGUGAGCUGGCUUCACAGAGCAGCGCUUACCUCCCGGUCCUGGCAGUGGAAGGAUAACGGCCCGGUGCUAGGUGGCUCCAAUAUGUUCUACUGGCUAAACAUGAUUGGGCAUACCUUU,X65989.1/1-297,1-297,0,296,X65989.1/1-297
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188809,X65990.1,1,sp|X65990.1|HJ7SRPC Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene); clone_lib Z13o,0,54,1,300,178.71,GGCCUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAGAUGGGACUUUGGGUCAGCCCAUUGGAUCGGGUCCAGUGUUAGCUGCUUGCUGGUCUGCCCAUUCCAAGCCGAGAGUUGGGCUGUGUGAUCUGGGCGAAGGCUGGGGUCGCACAGCUCCUAAAGAGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACCACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGUCGGUGCUACUUGGGCCACCAUGGUCACUGCAUGCACUCUUAAUCAGACCAUCUCUUU,X65990.1/1-300,1-300,0,299,X65990.1/1-300
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188810,X65991.1,1,sp|X65991.1|HJ7SRPD Humulus japonicus small cytoplasmic RNA 7S (7S RNA gene); clone_lib Z20p,0,55,1,302,178.01,GGCCUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAAAUGGGACUUUAGUUCGGCCCAUUGGAUCGGAUCCAGUGUUAGCUGCUUGCUGGGCUGCCCAUUCCAAGCCGAGAGUUGAGCUGUGUGAGCCGGACGAAGGUCUGGCUUGGUCAGCUCCUAAAGCGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACAACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGCCGGUGCUGCUUGGACCCACCAUGGUUCACUGAGCUGACUCUUAAUAGGACCAUUUCUUU,X65991.1/1-302,1-302,0,301,X65991.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188848,X65983.1,1,sp|X65983.1|HL7SRPA Humulus lupulus small cytoplasmic RNA 7S (7S RNA gene); clone_lib H10p,0,56,1,305,186.19,GACGGGCUUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAAAUGGGACUUUGGGUCAACCUAGUGGAUCGGGUCCAGUGUUAGCUGCUUACUGGUCUGCCCAUUCCAAGCCGGGAGUUGGGCUGAGUGACCUGGGCGAAGGCUGGGUUGCGCAGCUCCUAGAGUGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGCCGGUGCUACCUGGAUCCACCAUGCUUCACUGGGCUGACUCUUAAUAGGACCAUUUCUUU,X65983.1/1-305,1-305,0,304,X65983.1/1-305
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188849,X65984.1,1,sp|X65984.1|HL7SRPB Humulus lupulus small cytoplasmic RNA 7S (7S RNA gene); clone_lib H20o,0,57,1,306,179.66,GCCGGUCUUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAAAUGGGACUUUGGGUCAACCUAGUGGAUCGGGUCCAGUGUUAGCUGCUUACUGGUCUGCCCAUUCCAAGCCGGGAGUUGGGCUGAGUGACCUGGGCGAAGGGCUGGGUUGCGCACGUCCUAGAGUGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGCCGGUGCUACCUGGGUCCACCAUGCUUCACUAGGCUGACUCUUAAUAGGACCAUUUCUUU,X65984.1/1-306,1-306,0,305,X65984.1/1-306
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188850,X65985.1,1,sp|X65985.1|HL7SRPC Humulus lupulus small cytoplasmic RNA 7S (7S RNA gene); clone_lib H10o,0,58,1,302,177.99,GGCCUUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAAAUGGAACAUUGGGUCAGCCCAGUGGAUCGGGUCCAGUGUUAGCUGCUUACUGGUCUGCCCAUUCCAAGCCGGGAGUUGGGCUGAGUGACCUGGGCGAAGGCCUGGGUUGCGCAGCUCCUAGAGUGGAGGGCAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACCUCCCGCUCCCGGCAGUGGAAGGAUAACGGGCCGGUGCUACUUGGUCCACCAUGUUCACUGGUCCUGACUCUUAAUCGGACCAUUUCCUU,X65985.1/1-302,1-302,0,301,X65985.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188851,X65986.1,1,sp|X65986.1|HL7SRPD Humulus lupulus small cytoplasmic RNA 7S (7S RNA gene); clone_lib S11o,0,59,1,303,133.23,GGUCUUAGCAACUUGGUCCUGUAACCCAAGUGGGGGCAUGUGGGAAAUGGAACUUUGGGUCAACCCAGUGGUNCGGGNCCAGUGCUAGCUGCUUACCCGGCUGCCCAUUCCAAGCCGGGAGGUGGGCUGAGGGACCUGGGCGAAGGCUNNNGGNNGCGCACUCCUAGACUGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGCCGGUGCGCCUUGAGCCAACACUGUUCAACUGGGCUGACUCUUAAUAGGACCAUUUCUUU,X65986.1/1-303,1-303,0,302,X65986.1/1-303
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188852,X65987.1,1,sp|X65987.1|HL7SRPE Humulus lupulus small cytoplasmic RNA 7S (7S RNA gene); clone_lib S15o,0,60,1,299,114.27,GCCUUAGCAACGUGGGCUGUAACCCAAGUGGGGGCAUGUGGGACUUGGGACUUUGGGUCAACCCAGUGGAUCGGGUCCAGUGCUAGCUGCUUACUGGUCUGCCCAUUCCAAGCCGGGAGUUGGGCUGAGUGACCUGGGCGAAGGCUGGGUUGCGCAGCUCCUAGAGUGGGAGGCCAAUCGUGAGCUUGGCUUCACAGAGCAGCCACUACCUCCCGCUCCUCGGGGAUGAAGGAUAACGGGCCGGUGCUACUUGGUCCACCAUCUUCACUGGUCCUGACUCUUAAUAGGACCAUUUCCUU,X65987.1/1-299,1-299,0,298,X65987.1/1-299
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188880,AJ236703.1,1,sp|AJ236703.1|HLU236703 Humulus lupulus HL7SL-4 gene for signal recognition particle,0,61,148,452,159.10,GCCGGGCUCAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGAGGGAAAUGAGACUUUGGGCCGACCCGAGAGAUCGGAUUCAGUGUCGGCUGAUUACUGGUUCGCCCGUUCCAAGCAAAGAGCUGGGCUGGGUGAGUUGGACGAAGGUCUGGCUUACUCAGCUCCUAAAGCGGUGGGUAACGCGUGAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGUUCUUGGCAGUGGAAGGACAACGAGCCGGUGCUGCCUGGGCUCACCAUGGUUCACUUGGCUGAUCCUAAUUGGACCAUUUCUUU,AJ236703.1/148-452,148-452,0,304,AJ236703.1/148-452
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188881,AJ236704.1,1,sp|AJ236704.1|HLU236704 Humulus lupulus Hl7SL-2 gene and 7SL RNA pseudogene,0,62,1239,1544,184.20,GCUGGGCUUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAAAUGGAACUUUGGGUCAGCCCAGUGGAUCGGGUCCAGAGUUAGCUGUUUACUGGUCUGCCCAUUCCAAGCCGGGAGUUGGGCUGAGUGAUUUGGGCGAAGGCCUGGGUUGCGCAGCUCCUAGAGUGGAGGGUAAUGCGUGAGGCUGGUUUCACAGAGCAGCGACUACCUCUCGCUCUCGGCAGUGGAAGGAUAACGGGCCGGUGCUUCCUGGAUCCAACAUGGUUCACUGGGCUGACUCUUAAUAGGACCAUUUCUUU,AJ236704.1/1239-1544,1239-1544,0,305,AJ236704.1/1239-1544
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188882,AJ236705.1,1,sp|AJ236705.1|HLU236705 Humulus lupulus Hl7SL-3 gene for signal recognition particle,0,63,154,458,162.83,GCCGGGCUCAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGAGGGAAAUGAGACUUUGGGCCAGCCCAGAGAGUCGGAUUCAGUGUCGGCUGAUUACUGGUUCGCCCGUUCCAAGCAAAGAGCUGGGCUGGGUGAGUUGGACGAAGGUCUGGCUUACUCAGCUCCUAAAGCGGUGGGUAACGCGUGAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGUUCUUGGCAGUGGAAGGACAACGAGCCGGUGCUGCCUGGGCUCACCAUGGUUCACUUGGCUGAUCCUAAUUGGACCAUUUCUUU,AJ236705.1/154-458,154-458,0,304,AJ236705.1/154-458
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,188883,AJ236706.1,1,sp|AJ236706.1|HLU236706 Humulus lupulus Hl7SL-1 gene for signal recognition particle,0,64,153,458,195.88,GCCGGGCUUAGCAACGUGGGCCUGUAACCCAAGUGGGGGCAUGUGGGAAUUGGGACUUUGGGUCAACCCAGUGGAUCGGGUCCAGUGCUAGCUGCUUACUGGUCUGCCCAUUCCAAGCCGGGAGUUGGGCUGAGUGACCUGGGCGAAGGCCUGGGUUGCGCAGCUCCUAGAGUGGAGGGCAAUGCGUGAGGCUGGCUUCACAGAGCAGCGACUACCUCCCGCUCUCGGCAGUGGAAGGAUAACGGGCCGGUGCUACCUGGAUCCACCAUGCUUCACUGGGCUGACUCUUAAUAGGACCAUUUCUUU,AJ236706.1/153-458,153-458,0,305,AJ236706.1/153-458
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192099,X13958.1,1,sp|X13958.1|LE7SRNA Tomato 7S RNA for signal recognition particle,0,65,1,301,157.12,GGCGAGCUUAGUAACGUGGGCUUGUAAUCCAAGUGGAGACAUCAAAGUGGUUGAAUAUUGGGCUUUACCAGAAGGUUGGGCUUGGUGGGCUUAGUUCUGGCCUGCCCUGUCCAAGCACAGAGUUGGAUCACGAGGCCCAAAUGAAAAUAUGGGCUUCUUGAUUCCUAAAGUGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACGCUCCCGCUCUGUGCAGUGGAAGGAUAAUGGGUCGGUGUCUUAUCAAGUUCAGUAACGCCUAAUGGGUUGCUCCAAUAAACAACCACCUU,X13958.1/1-301,1-301,0,300,X13958.1/1-301
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192742,Z29112.1,1,sp|Z29112.1|LESRP7S0 L.esculentum 7S RNA for signal recognition particle 7S RNA(variant A),0,66,1,302,160.21,GUCGAGCUUAGUAAUGUGGGCUUGUAACCCAAAUGGGGGCAUUAAUGUGGUGGAAUGUUGGGCUGUACCAGAUGGUUGGGCUUGGUGGGCUAAUUUCUGACUUGCCCUAUCCAAGCUUAGAGUUGGAUCAUGUGGCCCAAUUGAAGAAAUGGACUACUUGAUUCGUAAAGUGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAACGAUAAGUUUCCGCUCUAAGCGGUGGAAGGAUAACGAGUCGGUGUUCUCUGAGUCCAGUAAUGCCUGAUGGGCUGCUCUAAUUAAACCACCACUUU,Z29112.1/1-302,1-302,0,301,Z29112.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192743,Z29099.1,1,sp|Z29099.1|LESRP7S1 L.esculentum mRNA for signal recognition particle 7S RNA (variant B),0,67,1,303,161.76,GCCGAGCUCAGUAGCGUGGGCUUGUAACUCAAGUGAGGGCAUCAGUGUGGUGGAAUGUUGAACAUGCCCAGAAGGUAGGGCUUGUGUGACAAUUCUCUGGCCUGCCCUGUCCAAGCAAAGAGUUGGGUCUUGUGGGCCAAGCGAAGGCUUGGGCUGCUGGGCUCCUAAAGUGGGGUGGACUGCGUGAGGCUGGUUUCACAGAGCAACGAAUAGCUCCCGCUCUGUGCAGUGGAAGGAUAACGAGCCAGUGUCAUAUAAGUUCAACGAAUGUCUGAUGGGCUGUUCUAGUUAAACUACCACAUU,Z29099.1/1-303,1-303,0,302,Z29099.1/1-303
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192745,Z29110.1,1,sp|Z29110.1|LESRP7S12 L.esculentum mRNA for signal recognition particle 7S RNA (variant M),0,68,3,273,94.04,AGUGGGGAUGUUAAGGUGGUGGAAUAUUGGGCUGUCCCAGAUGGCUGGGCUUGGUGGGCUAAUUUCUGGCCUGCCCUGUCCAAGCACAGAGUUGGAUCACGAGGCCCAAAUGAAAAUAUGGGCUUCUUGAUUCCUAAAGUGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGCUCCCGCUCUGUGCAGUGGAAGGAUAAUGGGUCGGUGUCUUAUCAAGUUCAGUAACGCCUAAUGGGUUGCUCCAAUAAACAACCACCUU,Z29110.1/3-273,3-273,0,270,Z29110.1/3-273
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192746,Z29111.1,1,sp|Z29111.1|LESRP7S13 L.esculentum mRNA for signal recognition particle 7S RNA (variant N),0,69,1,301,150.09,GUUGAGCUUAGUAACGUGGGCUUGUAACCCAAGUGGGGAUGUUAAUGUGGUGGAAUGUUGGGCUGUACCAGAUGGUUGGGCUUGGUGGGCUAAUUUCUGACUUGCCCUAUCCAAGCUUAGAGUUGGAUCAUGUGGCCCAAUUGAAGAAAUGGACUACUUGAUUCGUAAAGUGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAACGAUAAGUUUCGCUCUAAGCGGUGGAAGGAUAACGAGUCGGUGUUCUCUGAGUCCAGUAACGCCUGAUGGGUUGCUCCAAUUAAACCACCAUUUU,Z29111.1/1-301,1-301,0,300,Z29111.1/1-301
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192747,Z29261.1,1,sp|Z29261.1|LESRP7S14 L.esculentum mRNA for signal recognition particle 7S RNA (Variant K),0,70,1,303,172.50,GCCGAGCUUAGUAACGUGGGCUUGUAACCCAAGUGGGGAUGUUAAGGUGGUGGAAUAUUGGGCUGUCCCAGAUGGCUGGGCUUGGUGGGCUAAUUUCUGGCCUGCCCUAUCCAAGCACAGAGUUGGAUCAUGUGGUCCAAUUGAAAGAAUGGGCUACUAGAUUCCUAAAGUGGGGUGGACCGCGUGAGGCUGGUUUCACAGAGCAACGAAAAACUUCCGCUUUGUGCAGUGGAAGGAUAACGGACCGGUGCCUUCCAAGUUCCAUUAAUGCCUGAUGGGCUGCUCCAAUUAAACCACCACUUU,Z29261.1/1-303,1-303,0,302,Z29261.1/1-303
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192749,Z29101.1,1,sp|Z29101.1|LESRP7S3 L.esculentum mRNA for signal recognition particle 7S RNA (variant D),0,71,1,302,161.02,GUCGAGCUUAGUAACGUGGGCUUGUAACCCAAGUGGGGAUGUUAAGGUGGUGGAAUAUUGGGCUGUCCCAGAUGGCUGGGCUUGGUGGGCUAAUUUCUGGCCUGCCCUAUCCAAGUACAGAGUUGGAUCAUGUGGUCCAAUUGAAAGAAUGGGCUACUAGAUUCCUAAAGUGGGGUGGACCCGUGAGGCUGGUUUCACAGAGCAACGAAAAACUUCCGCUUUGUGCAGUGGAAGGAUAACGGACCGGUGCCUUCCAAGUUCCAUUAAUGCCUGAUGGGCUGUUCUAGUUAAACUACCACAUU,Z29101.1/1-302,1-302,0,301,Z29101.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192750,Z29103.1,1,sp|Z29103.1|LESRP7S4 L.esculentum mRNA for signal recognition particle 7S RNA (variant E),0,72,1,303,158.25,GCCGAGCUUUGUAACGUGGGCUUGUAACCCGAGUGGGGGCAACAAUGUGGUGGAAUGUUGGGUCCAUCUUGAUGGAUGGGCUUGAAGGGCUAAUGUUCUGGCCUGCCCUGUCCAAGCACAGAGUUGGGUCAAGUGGUCUAUACGAAAGUAUAGCCACUUGGCCUUUAGAGUGGGAUGGACUGCGUGAGGCUGGUUUCACAGAGCAACGACUAGUCCCCGCUCUGUGCAGUGGAAGGAUCACGGGCUAGUGCUCUUUGAGUCCUAACAAAAACCUGAUAGGUUGCCUAAUUAAACCAUCACUUU,Z29103.1/1-303,1-303,0,302,Z29103.1/1-303
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192751,Z29104.1,1,sp|Z29104.1|LESRP7S5 L.esculentum mRNA for signal recognition particle 7S RNA (variant G),0,73,1,303,172.65,GCCGAGCUUAGUAAUGUGGGCUUGUAACCCAAAUGGGGGCAUUAAUGUGGUGGAAUGUUGGGCUGUACCAGAUGGUUGGGCUUGGUGGGCUAAUUUCUGGCCUGCCCUAUCCAAGCACAGAGUUGGAUCAUGUGGUCCAAUUGAAAGAAUGGGCUACUAGAUUCCUAAAGUGGGGUGGACCGCGUGAGGCUGGUUUCACAGAGCAACGAAAAACUUCCGCUUUGUGCAGUGGAAGGAUAACGGACCGGUGCCUUCCAAGUUCCAUUAAUGCCUGAUGGGCUGCUCCAAUUAAACCACCACUUU,Z29104.1/1-303,1-303,0,302,Z29104.1/1-303
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192752,Z29105.1,1,sp|Z29105.1|LESRP7S6 L.esculentum mRNA for signal recognition particle 7S RNA (variant H),0,74,1,302,152.45,GUUGAGCUUAGUAACGUGGGCUUGUAAUCCAAGUGGAGACAUCAAAGUGGUUGAAUAUUGGGCUGUACCAGAUGGUUGGGCUUGGUGGGCUAAUUUCUGACUUGCCCUAUCCAAGCUUAGAGUUGGAUCAUGUGGCCCAAUUGAAGAAAUGGACUACUUGAUUCGUAAAGUGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAGUGAACAGCUCCCGCUCUGUGCAGUGGAAGGAUAAUGGGUCGGUGUCUUAUCAAGUUCAGUAACGCCUAAUGGGUUGCUCCAAUAAACAACCACCUU,Z29105.1/1-302,1-302,0,301,Z29105.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192753,Z29106.1,1,sp|Z29106.1|LESRP7S7 L.esculentum mRNA for signal recognition particle 7S RNA (variant F),0,75,1,301,153.37,GCCGAGCUUAGUAAUGUGGGCUUGUAACCCAAAUGGGGGCAUUAAUGUGGUGGAAUGUUGGGCUGUACCAGAUGGUUGGGCUUGGUGGGCUAAUUUCUGACUUGCCCUAUCCAAGCUUAGAGUUGGAUCAUGUGGCCCAAUUGAAGAAAUGGACUACUUGAUUCGUAAAGUGGGGCGGAAUGCGUGAGGCUGGUUUCACAGAGCAACGAUAAGUUUCGCUCUAAGCGGUGGAAGGAUAACGAGUCGGUGUUCUCUGAGUCCAGUAACGCCUGAUGGGUUGCUCCAAUUAAACCACCAUUUU,Z29106.1/1-301,1-301,0,300,Z29106.1/1-301
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192754,Z29107.1,1,sp|Z29107.1|LESRP7S8 L.esculentum mRNA for signal recognition particle 7S RNA (variant IR),0,76,1,302,162.61,GUCGAGCUUAGUAACGUGGGCUUGUAAUCCAAGUGGAGACAUCAAAGUGGUUGAAUAUUGGGCUUUACCAGAAGGUUGGGCUUGGUGGGCUUAGUUCUGGCCUGCCCUGUCCAAGCACAGAGUUGGAUCACGAGGCCCAAAUGAAAAUAUGGGCUUCUUGAUUCCUAAAGUGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGCUCCCGCUCUGUGCAGUGGAAGGAUAAUGGGUCGGUGUCUUAUCAAGUUCAGUAACGCCUAAUGGGUUGCUCCAAUAAACAACCACCUU,Z46745.1/134-435 Z29107.1/1-302,1-302,0,301,Z29107.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192755,Z29260.1,1,sp|Z29260.1|LESRP7S9 L.esculentum mRNA for signal recognition particle 7S RNA (variant IM),0,77,1,302,154.90,GUUGAGCUUAGUAACGUGGGCUUGUAAUCCAAGUGGAGACAUCAAAGUGGUUGAAUAUUGGGCUUUACCAGAAGGUUGGGCUUGGUGGGCUUAGUUCUGGCCUGCCCUGUCCAAGCACAGAGUAGGAUCACGAGGCCCAAAUGAAAAUAUGGGCUUCUUGAUUCCUAAAGCGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGCUCCCGCUCUGUGCAGUGGAAGGAUAAUGGGUCGGUGUCUUAUCAAGUUCAGUAACGCCUAAUGGGUUGCUCCAAUAAACAACCACCUU,Z29260.1/1-302 Z46744.1/231-532,1-302,0,301,Z29260.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192757,Z46740.1,1,sp|Z46740.1|LESRPA3 L.esculentum gene for 7S signal recognition particle RNA (713 bp),0,78,310,613,154.53,GCCGAGCUUAGUAACAUGGGCUUGUAACCCAAGUGGGGGCAUUAGUGUGGUGGAAUGUUGGGCCUGCUCCAGAUGGUUGGGCCUGGCGGGCUAAUUUAUGGCCUGCCCUGUCCAAGCAUAGAGUUGGGCCUUGCUAUCCAAUCGAAGGAAUGGGCUGAUGGGUUCCUAAAGUGGAACGGACUGCGUGAGGCUGGUUUCACAGAGCAACGAACAGUUCCCGCUCUAUACAGUGGAAGGAUAACGAGUCGGUACCCUCCUAAGUCCAAUAACGCCUGAUGGGCUGCUCCAAUUAAACCACCACUUU,Z46740.1/310-613,310-613,0,303,Z46740.1/310-613
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192760,Z46744.1,1,sp|Z46744.1|LESRPIMAS L.esculentum gene for 7S signal recognition particle RNA (785 bp),0,79,231,532,154.90,GUUGAGCUUAGUAACGUGGGCUUGUAAUCCAAGUGGAGACAUCAAAGUGGUUGAAUAUUGGGCUUUACCAGAAGGUUGGGCUUGGUGGGCUUAGUUCUGGCCUGCCCUGUCCAAGCACAGAGUAGGAUCACGAGGCCCAAAUGAAAAUAUGGGCUUCUUGAUUCCUAAAGCGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGCUCCCGCUCUGUGCAGUGGAAGGAUAAUGGGUCGGUGUCUUAUCAAGUUCAGUAACGCCUAAUGGGUUGCUCCAAUAAACAACCACCUU,Z29260.1/1-302 Z46744.1/231-532,231-532,0,301,Z46744.1/231-532
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192761,Z46745.1,1,sp|Z46745.1|LESRPIR L.esculentum gene for 7S signal recognition particle RNA (572 bp),0,80,134,435,162.61,GUCGAGCUUAGUAACGUGGGCUUGUAAUCCAAGUGGAGACAUCAAAGUGGUUGAAUAUUGGGCUUUACCAGAAGGUUGGGCUUGGUGGGCUUAGUUCUGGCCUGCCCUGUCCAAGCACAGAGUUGGAUCACGAGGCCCAAAUGAAAAUAUGGGCUUCUUGAUUCCUAAAGUGGGGCGGACCGCAUGAGGCUGGCUUCACAGAGCAGUGAACAGCUCCCGCUCUGUGCAGUGGAAGGAUAAUGGGUCGGUGUCUUAUCAAGUUCAGUAACGCCUAAUGGGUUGCUCCAAUAAACAACCACCUU,Z46745.1/134-435 Z29107.1/1-302,134-435,0,301,Z46745.1/134-435
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192762,Z46746.1,1,sp|Z46746.1|LESRPKM L.esculentum gene for 7S signal recognition particle RNA (1130 bp),0,81,392,694,175.91,GUCGAGCUUAGUAACGUGGGCUUGUAACCCAAGUGGGGAUGUUAAGGUGGUGGAAUAUUGGGCUGUCCCAGAUGGCUGGGCUUGGUGGGCUAAUUUCUGGCCUGCCCUAUCCAAGCACAGAGUUGGAUCAUGUGGUCCAAUUGAAAGAAUGGGCUACUAGAUUCCUAAAGUGGGGUGGACCGCGUGAGGCUGGUUUCACAGAGCAACGAAAAACUUCCGCUUUGUGCAGUGGAAGGAUAACGGACCGGUGCCUUCCAAGUUCCAUUAAUGCCUGAUGGGCUGCUCCAAUUAAACCACCACUUU,Z46746.1/392-694,392-694,0,302,Z46746.1/392-694
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192763,Z46747.1,1,sp|Z46747.1|LESRPM2 L.esculentum 7S signal recognition particle RNA pseudogene (1013 bp),0,82,387,681,116.70,GUCGAGCUUAGUAACGUGGGCUUGUAACCCGGCAUUAAGGUGGUAGAAUAUUGGGCUUAACCAAAUGGUUGGGCUUGAUGGGCUUAUUUCUGGCCUGCCCUAUCCAAGCACAGUGUUGGAUAAUGAGGCCCAAAUGUAAGUAUGGGCUUCUUGAUUCCUAAAGUGGGGCGGAUCGACGAGGCUGGCUUCAUAGAGCAGUAAACAGCUCCCGCUCUGUGUAGUGGAAGGAUAACGAGUCGGUGUCUAUCAAGUCCAGUAAAAGCUUGACGGAUUGCUCCAAAUAAACCUCCACCUU,Z46747.1/387-681,387-681,0,294,Z46747.1/387-681
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192764,Z46748.1,1,sp|Z46748.1|LESRPM3 L.esculentum gene for 7S signal recognition particle RNA (772 bp),0,83,214,515,142.25,GCCGAGCUUUGUAACAUGAGCUUGUAACUCAAGUGAGGGCAUUAAUGUGGUGGAAUGUUGGGCUGAUCCAGAAGGCUGGACUUUGUGGGCUAUUCUCUGGCCUGCCCUAUCCAAGCAUAGAGUUGGGCUAUGUAGCCAAGCGAAGGCAUAGGCUGCUUGGCUCCUAGAGUGGGGUGGAUCGCGUGAGGCUGGUUUCACAGAGCAACGAACAGCUCCCGUUCUAUCCAGUGGAAGGAUCACGGGUCAGUGUUCAUGAAGUCCAACUAAAACCUAAUGGGCUGCUUCAACUAAACCACCAUUUU,Z46748.1/214-515,214-515,0,301,Z46748.1/214-515
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,192765,Z46749.1,1,sp|Z46749.1|LESRPM4 L.esculentum gene for 7S signal recognition particle RNA (736 bp),0,84,198,500,156.53,GCCGAGCCUUGUAACGUGGGCUUGUAACCUAAGUUGGGGCAACAACGUAGUGGGAUGUUAGGCUGUUCCAGAUGGCUGGACUUUGGUUGGCAUUAGUCUGGCUUGCCCUAUCCAAGCACGGAGUUGAGUCACGUGGUCCAAACGAAAGUAUGGGCUGCUUGGCUCUUAGAGUGGGGUGGACUGCGUGAGGCUGGUUUCACAGAGCAACGAAUAACUCCCAGUCUGUGCAGUGGAAGGAUAACGAGUCAGUGCUUUCCAAGUUCAACAAAAACCUGAUGGACUACCUAAUUAAACCACCACUUU,Z46749.1/198-500,198-500,0,302,Z46749.1/198-500
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,209176,X13913.1,1,sp|X13913.1|TASRP7S1 Wheat signal recognition particle (SRP) 7S RNA variant 1,0,85,1,303,136.97,NCCGAGCUAGUUGCGAGAGCUUGUAACCCGAGUGGGGGCAUUAAAGUGAUGUGAACNCUGUUGUAGCGCUGCGGGCCUGGUCUGGGUGUGCUACUGCUGGCCCGCCCGUUCCAAGUUGCGUAGUGGACCGCCUGGGGCUUAUGCGAAAGCUGGGUCUCACGGUCCAUAAUGUGGCAGGCACAGCGUGAGGCUGGCUUCACAGAGCAGCGACAACUGCCCGCUUCCAACGGUGGAAGGAUAAUGGGCCGCUGCACUCCUAGGACCAAUUGGGCCUCGCAGCCUACUCCAGCAGACCACCAUCUU,X13913.1/1-303,1-303,0,302,X13913.1/1-303
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,209177,X13914.1,1,sp|X13914.1|TASRP7S2 Wheat signal recognition particle (SRP) 7S RNA variant 2,0,86,1,302,149.49,NCCGAGCUAGUUGCGGGAGCUUGUCACCCAUGUGGGGGCAUUGAGGCGGUGUGGAUGCUUGGUGCGGUUUGUUGGCCUGGGCUUGUGAUGUAACCUUGCUGGCCUGCCCGUUCCAAGUUGGUAGUGGGCUGGGUGGCUGGGGCGAAAGCUUCGCCUUCUCAGGCCUUAAGUGGCAGGCACCACGUUAGGCUGGUUUCACAGAGCAGCGACAACUGCCCGCUUCCAACGGUGGAAGGAUAACAGGCCGCUGCAGCAUGGGCCCGCUCUGGGCCUCCUACCCCGCCAUAGCAGACCACCAUCUU,****    NEW  HIT  #0  ****,,2,0,X13914.1/1-302
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,211344,U85037.1,1,sp|U85037.1|U85037 Oryza sativa signal recognition particle RNA sequence.,0,87,1,297,116.79,GCCGCGAAUUCGCGGCGCCGAGCGGGGGCAAUAAGGUGGUGCGGAUGCCUGGUCGUUUGCUCUUUGGCCUGGGCCUGUGGUUCGCUCUAUGCGGCCCGCCCGUUCCAAGUUGCGUAGCGUGUAUGGGGCGCCCUGGCGAAAGCUAGAGCGUCCCUGCACCUAGAGUGGCGGGUAUUGCGUGAGGCUGGUUUCACAGAGCAGCGAGUACCGCCCGCUUCCAACGGUGGAAGGAUUACGGGCCGCUGCAGCCCUGGCCCGCUUCCGGCCCAUGUGCCUUCCAUGGCAGACCCCCAUCUU,U85037.1/1-297,1-297,0,296,U85037.1/1-297
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,213145,X14661.1,1,sp|X14661.1|ZM7SL Maize 7SL RNA of signal recognition particle,0,88,1,308,153.70,NCCGAGCUCUGUAGCGAGAGCUUGUAACCCGAGCGGGGGCAUUAAGGUGGUGCGGAUUCUUUGCGAUGGCUUUCUGGGCCCGGGCUCGCUAUGUGCCUUUGGCCGGCCUGCCCGUCCCAAGUUGGUAGUGGCUGGCGGAGGCUUUAGCGGAAGCUUUGGUCUCUCCAGACCUGAAGUGGCAGGAAUGGCGUGAGGCUGGCUUCACAGAGCAGCGAUCACUCGCCCGCUUCCAACGGUGGGAGGAUAACGGGCCGCUGCACUUCGAGCCCAACUCAGGCCCAGAGCCUCACUAAGCAGACCACCAUCUU,X14661.1/1-308,1-308,0,307,X14661.1/1-308
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17154,AE000940.1,1,sp|AE000940.1|AE000940 Methanobacterium thermoautotrophicum from bases 1709212 to 1724499 (section 146 of 148) of the complete genome.,0,89,8761,9056,131.98,ACCGGAGGGUUAGGGGUCCUCUGUAAGCGCAAAUCCCCUAUAUGGCGCGGUUGAAGUUCGGGGGACGGCUGAUUGACUGUCCAUCGGCCCUGAUGGUCGGUGUCGAAGCCUCGUCCCGCAGGAUCAGUGGUGAUGGGGCCCUGACUGGAGGGUCAGGGUAAACCAUCUUAGUCAUGGGAACGGGUCAGGCCUGGAAAGGAGCAGCCCUACCAUGGACAGCUGAUGCUUGCGGAUUAACGGGGUGGAGCCGGUCAUCAGGAUCACCGGCGGAUGGAAGAUCUGUCAACCCCUGAACG,AE000940.1/8761-9056,8761-9056,0,295,AE000940.1/8761-9056
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,17256,AE001042.1,1,sp|AE001042.1|AE001042 Archaeoglobus fulgidus DSM 4304 section 65 of 172 of the complete genome.,0,90,6897,7188,154.43,GCCGGGGGGUUCGGCGUCCCCUGUAACCCGAAACCGCCGAUACGCGGGGGCCGAAGCCGAGGGGAGGCCUGUCAAGCGGGCGGCAGCGGUUCCAGGCACCGCAGAGUCCUCGUCCCGGAGGGCCGGCGGUUAUGGCCGGGCUGCCCGGAGGGGCUGUCCGCCAUAUUAGCCGGGGGGAACGGCCCAGGCCCGGAAGGGAGCAGGCUAACCCCGGACGACCGGCGCUUCCGGGGGUGCGGGGAGGAGGUGCCUGGGGCUUCAAGCCGCCCGUAAGGCAGGUCGACCCGAGGCG,AE001042.1/6897-7188 X17237.1/11-302,6897-7188,0,291,AE001042.1/6897-7188
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,19778,AE005009.1,1,sp|AE005009.1|AE005009 Halobacterium sp. NRC-1 section 40 of 170 of the complete genome.,1,91,4735,4442,126.04,GCCGGGCGGUUUGGCUCCGCCCGACACCCGUGAGACAGUCAUCAGCGGGGGCCGAACACCGGGCGCGUCCGACCGCCGCGGUCGGGCCCCGGAAGCCAACGUGGAAGCCUCGUCCGUCGGGGACGGCGGUCCGCGGCGUGCGCCCGCAGGGGCGUUCCGUCGUGGUUCGACGGUGGCAACCCGCCAGGCACGGAAGUGAGCAGCGGACCACCGAACGCCCGUCGCUCGACGGGUCGCGGGGUGGAGAAGGCGACCGGGACUACCCGGCCGGGAACGCCGGGCUACCCCGACUGU,AE005009.1/4735-4442,4735-4442,0,293,AE005009.1/4735-4442
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,21395,AE006647.1,1,sp|AE006647.1|AE006647 Sulfolobus solfataricus section 6 of 272 of the complete genome.,1,92,611,324,95.84,GUGGGGGAUCUCGCCAAUCCCUAUUACCCGCAAGGCGUAAUGCGGGCACCAGUAACUCCUACCCUAUGGUGUCUCCUAUCUGUAGGUCCCAGUGGAGCGAUGAAGGCUGCCCAGCGGGGCUUGGCGGUCAUGGGCUUUCUCUCCGGAGGGAGAGAAAGUACCAUGAUAGCUGGGGGAAUCGGCGAGGCCCGGAAGGGAGCAGCCGUGCCUGGACGCCAGCGUUCGCUGGUCAACAGCCAGAGUGAAACUGGGGUAAACCUAUAGAUAGGUAGGCCAUGGGGUAGGGGG,AE006647.1/611-324,611-324,0,287,AE006647.1/611-324
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,24837,AE010126.1,1,sp|AE010126.1|AE010126 Pyrococcus furiosus DSM 3638; section 1 of 173 of the complete genome.,0,93,9583,9877,152.65,GCCGGGGGGUUCGGCGUCCCCUGUAACCGGAAACCGCCGAUAUGCCGGGGCCGAAGCCCGGGGGGCGGUUCCCAAAGCCGCUCCCAGAAGCCGAGGUCGAACGAUGAGUCCUCGUCCCGCGGGGUGCCCGGUGGGGGAGGCACGGCUGAAGGGCCGUGCUAACCCCCUUUGGGCCCCGAACCCCGCAAGGCCCGGAAGGGAGCAGCGGUAGGGGCCACGGAGCACGCUCGCGGGGGUGCGGGGAUGAGAUAGGCCUCGGUGGAUGGGAGCGGUGGAGGGUUCCCACCCUCGGGCG,AE010126.1/9583-9877,9583-9877,0,294,AE010126.1/9583-9877
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25095,AE010387.1,1,sp|AE010387.1|AE010387 Methanopyrus kandleri AV19 section 86 of 157 of the complete genome.,1,94,4828,4528,138.02,GCCGGCGGGCUGGCGGUCCGCUGUAACCCGAAAUCCGCCUCAUGCGGGGGCCGAAGCCGAGGGGGCGGCCCGGUCCCCCGGAGUACCGGCCCCCCGGACCCGACCGAUGACCCUCCGGCCCCCCGGGGGCCCGGGGUGGCGGGGCCGCCGCCGGAGGGCGGCGCGCCACCGCCUUUGCCGGGGCACCGGGUCAGGCCCGAGAGGGAGCAGCCCACCCCGGACCCGCGGCCGCUCGGGGGUCGCCGGAGGCAGGUCGGCCGGGGGAGUACCGGGCUCCGGGGGCCGGGUCCACCCCUCGGCG,AE010387.1/4828-4528,4828-4528,0,300,AE010387.1/4828-4528
./cmzasha --no-stderr --filter 350 76 Rfam/cm/RF00017.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00017_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin hmm data/TryAllCm/RF00017_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-CU_-AG;33;l-AG-CU-_;193;r-CU_-AG;192;l-ACU-G_;235;r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/remember-nuc;13;l-ACU-G-_;12;r-AU-C-G-_;33;l-AG-CU-_;32;l-AGU-C-_;31;l-AGU-C-_;193;r-CU_-AG;192;l-ACU-G_;191;l-ACU-G_;190;r-AG-CU-_;235;l-AU_-C-G;234;r-CGU-A_;233;r-AGU-C_;229;r-AGU_-C 2struct-str data/TryAllCm_5.0/RF00017_manual_forwardinf_hmmtype1_Bordetella_0MM.bin 1/sub;176;75 ,Rfam/cm/RF00017.cm (global),/projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz,25817,AE011109.1,1,sp|AE011109.1|AE011109 Methanosarcina acetivorans str. C2A; section 454 of 534 of the complete genome.,0,95,7215,7509,114.27,UCCGGGUAGCCCGGCGUUACCUGUAACCCGAAAUCGCCGAUAUGCGGGGGACGAAGCCAAUGGAAGAUGC