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
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,1777,AB013618.2,1,sp|AB013618.2|AB013618 Human astrovirus gene for capsid protein precursor; complete cds.,0,0,2444,2486,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,3943,AB031030.1,1,sp|AB031030.1|AB031030 Human astrovirus gene for capsid protein; complete cds; strain:katano24.,0,1,2444,2486,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,3944,AB031031.1,1,sp|AB031031.1|AB031031 Human astrovirus gene for capsid protein; complete cds; strain:Katano23-6.,0,2,2314,2356,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,4388,AB033998.1,1,sp|AB033998.1|AB033998 Avian nephritis virus gene for structural polyprotein; non-structural polyprotein; complete cds.,0,3,6702,6744,53.24,CUUUCCCGAGGCCACGGCGAGUAGCAUCGAGGGUACAGGAAAG,AB033998.1/6702-6744,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,5169,AB037272.1,1,sp|AB037272.1|AB037272 Porcine astrovirus gene for capsid protein precursor; complete cds.,0,4,2612,2654,57.67,GAAAGCCGAGGCCACGCCGAGUAGGAACGAGGGUACAGCUUUC,AB037272.1/2612-2654 Y15938.2/2354-2396,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,5170,AB037273.1,1,sp|AB037273.1|AB037273 Human astrovirus type 5 gene for capsid protein precursor; complete cds; strain:CHN146.,0,5,2393,2435,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,5171,AB037274.1,1,sp|AB037274.1|AB037274 Human astrovirus type 5 gene for capsid protein precursor; complete cds; strain:CHN198.,0,6,2632,2674,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,6181,AB046864.1,1,sp|AB046864.1|AB046864 Avian nephritis virus ORF 2 gene for virus capsid polyprotein; complete cds.,0,7,2311,2353,53.24,CUUUCCCGAGGCCACGGCGAGUAGCAUCGAGGGUACAGGAAUG,AB046864.1/2311-2353,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,21789,AF056197.1,1,sp|AF056197.1|AF056197 Feline astrovirus capsid precursor protein mRNA; complete cds.,0,8,2428,2470,60.14,GAGAGCCGAGGCCACGCCGAGUAGGAUCGAGGGUACAGCUCUC,AF056197.1/2428-2470,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,31409,AF111995.1,1,sp|AF111995.1|AF111995 Turkey coronavirus strain Indiana nucleocapsid protein gene; complete cds.,0,9,1596,1638,50.83,CAGUGCCGGGGCCACGCGGCGUACGAUCGUGGGUACAGCACUA,AF111995.1/1596-1638,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,31410,AF111996.1,1,sp|AF111996.1|AF111996 Turkey coronavirus strain Minnesota nucleocapsid protein gene; complete cds.,0,10,1596,1638,59.11,CAGUGCCGAGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,U52598.1/1583-1625 L06251.1/371-413 AJ278334.1/373-415 AF203002.1/370-412 AF111996.1/1596-1638,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,31411,AF111997.1,1,sp|AF111997.1|AF111997 Turkey coronavirus strain NC95 nucleocapsid protein gene; complete cds.,0,11,1443,1485,54.97,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACAA,AF111997.1/1443-1485 AJ310642.1/102-144,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,31998,AF117209.1,1,sp|AF117209.1|AF117209 Human astrovirus type 3 capsid protein precursor; gene; complete cds.,0,12,2373,2415,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,36072,AF141381.1,1,sp|AF141381.1|AF141381 Human astrovirus putative serine protease gene; complete cds; putative RNA-dependent RNA polymerase gene; partial cds; and caps,0,13,6710,6752,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,45311,AF203002.1,1,sp|AF203002.1|AF203002 Avian infectious bronchitis virus strain DE072 3' noncoding region.,0,14,370,412,59.11,CAGUGCCGAGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,U52598.1/1583-1625 L06251.1/371-413 AJ278334.1/373-415 AF203002.1/370-412 AF111996.1/1596-1638,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,45316,AF203007.1,1,sp|AF203007.1|AF203007 Avian infectious bronchitis virus strain D1466 3' noncoding region.,0,15,392,434,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,52651,AF248738.2,1,sp|AF248738.2|AF248738 Human astrovirus type 7 ORF1b gene; partial cds; and capsid protein precursor; gene; complete cds.,0,16,2981,3023,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,54168,AF257226.1,1,sp|AF257226.1|AF257226 Human astrovirus type 2 M358 capsid precursor protein gene; partial cds.,0,17,425,467,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,54541,AF260508.1,1,sp|AF260508.1|AF260508 Human astrovirus type 8; complete genome.,0,18,6651,6693,54.95,GGAAGCCGCGACCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,Z66541.1/2326-2368 AF260508.1/6651-6693,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,62856,AF322368.2,1,sp|AF322368.2|AF322368 Avian infectious bronchitis virus strain D41 3' noncoding region.,0,19,392,434,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,68160,AF361253.1,1,sp|AF361253.1|AF361253 Equine rhinovirus 3 strain P313/75; complete genome.,0,20,8721,8763,54.56,ACUCGCCGAGGCCACGCCGAGUAGGACCGAGGGUACAGCGAGU,AF361253.1/8721-8763 X96871.1/8728-8770,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,74088,AF395733.1,1,sp|AF395733.1|AF395733 Human astrovirus type 1 strain HUN-1b capsid protein precursor; gene; partial cds.,0,21,1118,1160,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,74089,AF395734.1,1,sp|AF395734.1|AF395734 Human astrovirus type 1 strain HUN-1a capsid protein precursor; gene; partial cds.,0,22,1118,1160,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,74090,AF395735.1,1,sp|AF395735.1|AF395735 Human astrovirus type 3 strain HUN-3 capsid protein precursor; gene; partial cds.,0,23,1133,1175,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,74092,AF395737.1,1,sp|AF395737.1|AF395737 Human astrovirus type 5 strain HUN-5 capsid protein precursor; gene; partial cds.,0,24,1109,1151,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,74093,AF395738.1,1,sp|AF395738.1|AF395738 Human astrovirus type 8 strain HUN-8 capsid protein precursor; gene; partial cds.,0,25,1103,1145,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98350,U04804.1,1,sp|U04804.1|AI04804 Avian infectious bronchitis virus 3' noncoding region.,0,26,368,410,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98381,Z30541.1,1,sp|Z30541.1|AIBVCG Avian infectious bronchitis virus mRNA for chimeric gene,0,27,8944,8986,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98384,AJ278334.1,1,sp|AJ278334.1|AIN278334 Avian infectious bronchitis virus; strain UK/918/68; 3'UTR,0,28,373,415,59.11,CAGUGCCGAGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,U52598.1/1583-1625 L06251.1/371-413 AJ278334.1/373-415 AF203002.1/370-412 AF111996.1/1596-1638,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98385,AJ278335.1,1,sp|AJ278335.1|AIN278335 Avian infectious bronchitis virus; strain D207; 3' UTR,0,29,370,412,54.34,CAGUGCCAGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,AJ278335.1/370-412,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98386,AJ278336.1,1,sp|AJ278336.1|AIN278336 Avian infectious bronchitis virus; strain H120; 3' UTR,0,30,395,437,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98387,AJ278337.1,1,sp|AJ278337.1|AIN278337 Avian infectious bronchitis virus; strain HV10; 3' UTR,0,31,374,416,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98388,AJ278338.1,1,sp|AJ278338.1|AIN278338 Avian infectious bronchitis virus; strain HVI-140; 3' UTR,0,32,374,416,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98435,U49858.1,1,sp|U49858.1|AIU49858 Avian infectious bronchitis virus strain CU-T2 spike protein (gene 2); gene 3; membrane protein (gene 4); gene 5; nucleocapsid ,0,33,7267,7309,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98436,U52594.1,1,sp|U52594.1|AIU52594 Avian infectious bronchitis virus Vic S nucleocapsid protein mRNA; complete cds.,0,34,1540,1582,55.80,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUU,U52595.1/1520-1562 U52594.1/1540-1582,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98437,U52595.1,1,sp|U52595.1|AIU52595 Avian infectious bronchitis virus V5/90 nucleocapsid protein mRNA; partial cds.,0,35,1520,1562,55.80,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUU,U52595.1/1520-1562 U52594.1/1540-1582,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98438,U52596.1,1,sp|U52596.1|AIU52596 Avian infectious bronchitis virus N1/62 nucleocapsid protein mRNA; partial cds.,0,36,1581,1623,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98439,U52597.1,1,sp|U52597.1|AIU52597 Avian infectious bronchitis virus N9/74 nucleocapsid protein mRNA; partial cds.,0,37,1581,1623,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98440,U52598.1,1,sp|U52598.1|AIU52598 Avian infectious bronchitis virus N2/75 nucleocapsid protein mRNA; partial cds.,0,38,1583,1625,59.11,CAGUGCCGAGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,U52598.1/1583-1625 L06251.1/371-413 AJ278334.1/373-415 AF203002.1/370-412 AF111996.1/1596-1638,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98441,U52599.1,1,sp|U52599.1|AIU52599 Avian infectious bronchitis virus N1/88 nucleocapsid protein mRNA; complete cds.,0,39,1405,1447,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98442,U52600.1,1,sp|U52600.1|AIU52600 Avian infectious bronchitis virus Q3/88 nucleocapsid protein mRNA; complete cds.,0,40,1419,1461,55.17,CAGUGCCGAGGCCACUCGGAGUACGAUCGAGGGUACAGCACUA,U52600.1/1419-1461,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98443,U52601.1,1,sp|U52601.1|AIU52601 Avian infectious bronchitis virus V18/91 nucleocapsid protein mRNA; complete cds.,0,41,1396,1438,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98684,AP006557.1,0,sp|AP006557.1|AP006557 SARS coronavirus TWH genomic RNA; complete genome.,0,42,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98685,AP006558.1,0,sp|AP006558.1|AP006558 SARS coronavirus TWJ genomic RNA; complete genome.,0,43,29582,29624,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98686,AP006559.1,0,sp|AP006559.1|AP006559 SARS coronavirus TWK genomic RNA; complete genome.,0,44,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98687,AP006560.1,0,sp|AP006560.1|AP006560 SARS coronavirus TWS genomic RNA; complete genome.,0,45,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,98688,AP006561.1,0,sp|AP006561.1|AP006561 SARS coronavirus TWY genomic RNA; complete genome.,0,46,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,108696,AY044186.1,1,sp|AY044186.1|AY044186 Avian infectious bronchitis virus mRNA; 3'UTR.,0,47,184,226,53.97,CAGUGCCGGGGCCACGCUGAGUACGACCGAGGGUACAGCACUA,AY044186.1/184-226,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,120517,AY179509.1,0,sp|AY179509.1|AY179509 Mink astrovirus; complete genome.,0,48,6505,6548,49.18,ACUACCCGAGGCCACGCCGAGUUAGGAUCGAGGGUACAGGUAGU,AY179509.1/6505-6548,,0,44
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130501,AY274119.3,0,sp|AY274119.3|AY274119 SARS coronavirus TOR2; complete genome.,0,49,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130717,AY278487.3,0,sp|AY278487.3|AY278487 SARS coronavirus BJ02; complete genome.,0,50,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130718,AY278488.2,0,sp|AY278488.2|AY278488 SARS coronavirus BJ01; complete genome.,0,51,29565,29607,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130719,AY278489.2,0,sp|AY278489.2|AY278489 SARS coronavirus GD01; complete genome.,0,52,29597,29639,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130720,AY278490.3,0,sp|AY278490.3|AY278490 SARS coronavirus BJ03; complete genome.,0,53,29580,29622,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130721,AY278491.2,0,sp|AY278491.2|AY278491 SARS coronavirus HKU-39849; complete genome.,0,54,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130727,AY278554.2,0,sp|AY278554.2|AY278554 SARS coronavirus CUHK-W1; complete genome.,0,55,29569,29611,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130730,AY278741.1,0,sp|AY278741.1|AY278741 SARS coronavirus Urbani; complete genome.,0,56,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,130736,AY279354.2,0,sp|AY279354.2|AY279354 SARS coronavirus BJ04; complete genome.,0,57,29568,29610,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131145,AY282752.1,0,sp|AY282752.1|AY282752 SARS coronavirus CUHK-Su10; complete genome.,0,58,29569,29611,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131194,AY283794.1,0,sp|AY283794.1|AY283794 SARS coronavirus Sin2500; complete genome.,0,59,29568,29610,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131195,AY283795.1,0,sp|AY283795.1|AY283795 SARS coronavirus Sin2677; complete genome.,0,60,29562,29604,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131196,AY283796.1,0,sp|AY283796.1|AY283796 SARS coronavirus Sin2679; complete genome.,0,61,29568,29610,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131197,AY283797.1,0,sp|AY283797.1|AY283797 SARS coronavirus Sin2748; complete genome.,0,62,29563,29605,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131198,AY283798.1,0,sp|AY283798.1|AY283798 SARS coronavirus Sin2774; complete genome.,0,63,29568,29610,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131610,AY290752.1,0,sp|AY290752.1|AY290752 SARS coronavirus ZJ-HZ01 nucleocapsid protein; uncharacterized protein 9b; and uncharacterized protein 9c genes; complete cds.,0,64,1539,1581,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131613,AY291315.1,0,sp|AY291315.1|AY291315 SARS coronavirus Frankfurt 1; complete genome.,0,65,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131617,AY291451.1,0,sp|AY291451.1|AY291451 SARS coronavirus TW1; complete genome.,0,66,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,131812,AY297028.1,0,sp|AY297028.1|AY297028 SARS coronavirus ZJ01; complete genome.,0,67,29575,29617,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,133007,AY310120.1,0,sp|AY310120.1|AY310120 SARS coronavirus strain FRA; complete genome.,0,68,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,133291,AY319651.1,0,sp|AY319651.1|AY319651 Avian infectious bronchitis virus isolate BJ; complete genome.,0,69,27580,27622,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,133312,AY321118.1,0,sp|AY321118.1|AY321118 SARS coronavirus TWC; complete genome.,0,70,29582,29624,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,133385,AY322208.1,0,sp|AY322208.1|AY322208 SARS coronavirus Shanhgai LY Orf7a gene; partial cds; and Orf7b; Orf8A; Orf8b; and nucleocapsid protein genes; complete cds.,0,71,2219,2261,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,133420,AY323977.2,0,sp|AY323977.2|AY323977 SARS coronavirus HSR 1; complete genome.,0,72,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,134652,AY338174.1,0,sp|AY338174.1|AY338174 SARS coronavirus Taiwan TC1; complete genome.,0,73,29515,29557,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,134653,AY338175.1,0,sp|AY338175.1|AY338175 SARS coronavirus Taiwan TC2; complete genome.,0,74,29515,29557,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,134732,AY348314.1,0,sp|AY348314.1|AY348314 SARS coronavirus Taiwan TC3; complete genome.,0,75,29515,29557,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,134954,AY351680.1,0,sp|AY351680.1|AY351680 SARS coronavirus ZMY 1; complete genome.,0,76,29604,29646,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,135140,AY362698.1,0,sp|AY362698.1|AY362698 SARS coronavirus TWC2; complete genome.,0,77,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,135141,AY362699.1,0,sp|AY362699.1|AY362699 SARS coronavirus TWC3; complete genome.,0,78,29584,29626,44.63,UUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAU,AY362698.1/29584-29626 AY283798.1/29568-29610 AP006559.1/29584-29626 AY338175.1/29515-29557 AY282752.1/29569-29611 AY283797.1/29563-29605 AY351680.1/29604-29646 AY279354.2/29568-29610 AY348314.1/29515-29557 AY291451.1/29584-29626 AY274119.3/29584-29626 AY321118.1/29582-29624 AP006558.1/29582-29624 AY278489.2/29597-29639 AY283794.1/29568-29610 AY338174.1/29515-29557 AP006561.1/29584-29626 AY290752.1/1539-1581 AY362699.1/29584-29626 AY283795.1/29562-29604 AY283796.1/29568-29610 AP006557.1/29584-29626 AY278554.2/29569-29611 AY323977.2/29584-29626 AY297028.1/29575-29617 AY278491.2/29584-29626 AY278741.1/29584-29626 AY310120.1/29584-29626 AY322208.1/2219-2261 AY278488.2/29565-29607 AP006560.1/29584-29626 AY278490.3/29580-29622 AY291315.1/29584-29626 AY278487.3/29584-29626,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138149,M21515.1,1,sp|M21515.1|CORIBASP Avian infectious bronchitis virus spike; membrane; and nucleocapsid protein genes; complete cds; and fusion (F2) polypeptide; 3,0,79,8676,8718,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140483,X96871.1,1,sp|X96871.1|ERPROTYP2 Equine Rhinovirus type 2 genomic sequence,0,80,8728,8770,54.56,ACUCGCCGAGGCCACGCCGAGUAGGACCGAGGGUACAGCGAGU,AF361253.1/8721-8763 X96871.1/8728-8770,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143086,Z11682.1,1,sp|Z11682.1|HA13TERM Human astrovirus type 1; 3' terminal sequence RNA,0,81,931,973,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143092,U15136.1,1,sp|U15136.1|HA15136 Human astrovirus type 5 major capsid protein precursor mRNA; complete cds.,0,82,2344,2382,43.05,GAAGCCGCGCCCACGCCGAGUAGGAUCGAGGGUACAGUC,U15136.1/2344-2382,,0,39
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143094,Z25771.1,1,sp|Z25771.1|HA1CAPNS Human astrovirus type 1 genes for capsid protein and nonstructural protein,0,83,6710,6752,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143119,Z33883.1,1,sp|Z33883.1|HA4VP13 Human astrovirus type 4 gene encoding structural polyprotein vp1-3,0,84,2293,2335,58.54,GGGAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUCCC,Y08630.1/191-233 Z33883.1/2293-2335,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143163,AB005257.1,1,sp|AB005257.1|HAAB5257 Human astrovirus type 6 RNA for capsid protein; partial cds.,0,85,253,295,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143240,Y08627.1,1,sp|Y08627.1|HAS1CAP Human astrovirus type 1 gene encoding capsid protein precursor (partial),0,86,197,239,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143241,Y08628.1,1,sp|Y08628.1|HAS2CAP Human astrovirus type 2 gene encoding capsid protein precursor (partial),0,87,197,239,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143242,Y08629.1,1,sp|Y08629.1|HAS3CAP Human astrovirus type 3 gene encoding capsid protein precursor (partial),0,88,197,239,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143243,Y08630.1,1,sp|Y08630.1|HAS4CAP Human astrovirus type 4 gene encoding capsid protein precursor (partial),0,89,191,233,58.54,GGGAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUCCC,Y08630.1/191-233 Z33883.1/2293-2335,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143244,Y08631.1,1,sp|Y08631.1|HAS5CAP Human astrovirus type 5 gene encoding capsid protein precursor (partial),0,90,197,239,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143245,Y08632.2,1,sp|Y08632.2|HAS7CAP Human astrovirus type 7 gene for capsid protein precursor,0,91,2379,2421,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143246,Y08633.1,1,sp|Y08633.1|HASCAPU1 Human astrovirus gene encoding capsid protein precursor (partial); isolate GII33,0,92,291,333,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143247,Y08634.1,1,sp|Y08634.1|HASCAPU2 Human astrovirus gene encoding capsid protein precursor (partial); isolate B55,0,93,188,230,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143248,M87668.1,1,sp|M87668.1|HAT3TERMS Human astrovirus type 1 RNA; 3' terminal sequence.,0,94,931,973,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143309,Z46658.1,1,sp|Z46658.1|HAV6ORF2 Human astrovirus type 6 gene for capsid polyprotein precursor.,0,95,2314,2356,58.71,GGAAGCCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,AB037273.1/2393-2435 AF395738.1/1103-1145 AF395733.1/1118-1160 AB031031.1/2314-2356 AB031030.1/2444-2486 AB037274.1/2632-2674 Y08631.1/197-239 AB013618.2/2444-2486 AB005257.1/253-295 Z46658.1/2314-2356 Y08633.1/291-333 AF395737.1/1109-1151,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,143310,Z66541.1,1,sp|Z66541.1|HAVCAPSP Human astrovirus type 8 orf2 gene for capsid protein,0,96,2326,2368,54.95,GGAAGCCGCGACCACGCCGAGUAGGAUCGAGGGUACAGCUUCC,Z66541.1/2326-2368 AF260508.1/6651-6693,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178318,L06802.1,1,sp|L06802.1|HUACAPSID Human astrovirus capsid protein mRNA; complete cds.,0,97,2379,2421,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178319,L13745.1,1,sp|L13745.1|HUANSSPS Human astrovirus serotype 2; complete sequence of genomic RNA.,0,98,6692,6734,54.69,GGAGACCGCGGCCACGCCGAGUAGGAUCGAGGGUACAGUCUCC,L06802.1/2379-2421 AF248738.2/2981-3023 AF395735.1/1133-1175 AF257226.1/425-467 L13745.1/6692-6734 Y08632.2/2379-2421 Y08629.1/197-239 AF117209.1/2373-2415 AF141381.1/6710-6752 Y08628.1/197-239,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178325,L23513.1,1,sp|L23513.1|HUAPOLY6A Human astrovirus type 1 strain Oxford; complete genome.,0,99,6668,6710,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178941,M28565.1,1,sp|M28565.1|IBABEAU Avian infectious bronchitis virus (Beaudette) nucleocapsid protein genomic RNA; complete cds.,0,100,1700,1742,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178942,M95169.1,1,sp|M95169.1|IBACGB Avian infectious bronchitis virus pol protein; spike protein; small virion-associated protein; membrane protein; and nucleocaps,0,101,27471,27513,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178945,L06251.1,1,sp|L06251.1|IBAHYPVA1 Avian infectious bronchitis virus hypervariable region - related RNA sequence.,0,102,371,413,59.11,CAGUGCCGAGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,U52598.1/1583-1625 L06251.1/371-413 AJ278334.1/373-415 AF203002.1/370-412 AF111996.1/1596-1638,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178946,L06253.1,1,sp|L06253.1|IBAHYPVA2 Avian infectious bronchitis virus hypervariable region - related RNA sequence.,0,103,392,434,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178947,L06252.1,1,sp|L06252.1|IBAHYPVAR Avian infectious bronchitis virus hypervariable region - related RNA sequence.,0,104,368,410,51.49,CAGUGCCAGGGCCACGCGGAGUACGAUCGAGGGUACAGCACCA,L06252.1/368-410,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,178957,M28566.1,1,sp|M28566.1|IBAMPUP Avian infectious bronchitis virus (M41) nucleocapsid protein genomic RNA; complete cds.,0,105,1515,1557,55.98,CAGUGCCGGGGCCACGCGGAGUACGACCGAGGGUACAGCACUA,M28566.1/1515-1557,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,179081,AJ311317.1,1,sp|AJ311317.1|IBR311317 Avian infectious bronchitis virus (strain Beaudette CK) complete genomic RNA,0,106,27471,27513,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,179082,AJ311362.1,1,sp|AJ311362.1|IBR311362 Avian infectious bronchitis virus (strain Beaudette US) s gene; 3a gene; 3b gene; 3c gene; m gene; 5a gene; 5b gene and n gene;,0,107,7164,7206,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,179128,Z69629.1,1,sp|Z69629.1|IBVCD61 Infectious bronchitis virus RNA (defective RNA CD-61),0,108,5991,6033,57.82,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACUA,M95169.1/27471-27513 AF322368.2/392-434 M21515.1/8676-8718 U52601.1/1396-1438 AJ278338.1/374-416 U52599.1/1405-1447 M28565.1/1700-1742 U52596.1/1581-1623 AJ278336.1/395-437 U52597.1/1581-1623 Z30541.1/8944-8986 AF203007.1/392-434 Z69629.1/5991-6033 AY319651.1/27580-27622 L06253.1/392-434 AJ278337.1/374-416 AJ311317.1/27471-27513 U04804.1/368-410 AJ311362.1/7164-7206 U49858.1/7267-7309,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,183639,Y15938.2,1,sp|Y15938.2|PACAPSID Porcine astrovirus gene for capsid protein precursor; genomic RNA,0,109,2354,2396,57.67,GAAAGCCGAGGCCACGCCGAGUAGGAACGAGGGUACAGCUUUC,AB037272.1/2612-2654 Y15938.2/2354-2396,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,188771,S47249.1,1,sp|S47249.1|S47249 {astrovirus genome 3' end} [human astrovirus type 1; Genomic RNA; 118 nt].,0,110,15,57,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,189089,S68561.1,1,sp|S68561.1|S68561 non-structural protein; capsid protein [human astrovirus serotype 1; isolate A88/2; Newcastle; Genomic RNA; 2739 nt].,0,111,2636,2678,56.07,GGAAGCCGCGGCCACGCCGAGUAGGAACGAGGGUACAGCUUCC,S47249.1/15-57 S68561.1/2636-2678 AF395734.1/1118-1160 Y08634.1/188-230 Y08627.1/197-239 Z11682.1/931-973 Z25771.1/6710-6752 L23513.1/6668-6710 M87668.1/931-973,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,189562,Y15937.2,1,sp|Y15937.2|SACAPSID Sheep astrovirus; complete genome; genomic RNA,0,112,6358,6400,58.92,CAAUCCCGAGGCCACGCCGAGUAGGAUCGAGGGUACAGGAUUG,Y15937.2/6358-6400,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,192586,Y15936.2,1,sp|Y15936.2|TACAPSID Turkey astrovirus; complete genome; genomic RNA,0,113,6871,6913,56.60,UGAUGCCGAGGCCACGCCGGGUAGGAUCGAGGGUACAGCAUCG,Y15936.2/6871-6913,,0,43
./cmzasha --no-stderr --filter 70 40 Rfam/cm/RF00164.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00164_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00164.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,192676,AJ310642.1,1,sp|AJ310642.1|TCO310642 Turkey coronavirus genomic RNA; partial 3' UTR; strain turkey/UK/412/00,0,114,102,144,54.97,CAGUGCCGGGGCCACGCGGAGUACGAUCGAGGGUACAGCACAA,AF111997.1/1443-1485 AJ310642.1/102-144,,0,43



THINGS IN Rfam THAT WEREN'T FOUND:


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