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 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,17581,AF029248.1,1,sp|AF029248.1|AF029248 Mouse hepatitis virus strain MHV-A59 C12 mutant; complete genome.,0,0,31093,31154,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,22238,AF058942.1,1,sp|AF058942.1|AF058942 Bovine coronavirus strain LY-138 32 kDa putative non-structural protein; hemagglutinin esterase (HE); spike glycoprotein (S); 4,0,1,9316,9377,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,22239,AF058943.1,1,sp|AF058943.1|AF058943 Bovine coronavirus strain LSU-94LSS-051-2 32 kDa putative non-structural protein; hemagglutinin esterase (HE); spike glycoprote,0,2,9309,9370,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,22240,AF058944.1,1,sp|AF058944.1|AF058944 Bovine coronavirus strain OK-0514-3 32 kDa putative non-structural protein; hemagglutinin esterase (HE); spike glycoprotein (S),0,3,9309,9370,44.84,GCACUCUCUAUCAGAUUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF058944.1/9309-9370,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,22674,AF061835.1,1,sp|AF061835.1|AF061835 Murine hepatitis virus strain 2 nucleocapsid protein (N) gene; complete cds; and unknown gene.,0,4,1416,1477,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,29950,AF104420.1,1,sp|AF104420.1|AF104420 Porcine transmissible gastroenteritis virus RNA dependent RNA polymerase gene; partial cds; virus envelope protein spike (S); e,0,5,7745,7807,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,45238,AF201929.1,1,sp|AF201929.1|AF201929 Murine hepatitis virus strain 2; complete genome.,0,6,31021,31082,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,46949,AF207551.1,1,sp|AF207551.1|AF207551 Sialodacryoadenitis virus 28 kD nonstructural protein (NS2); hemagglutinin-esterase glycoprotein (HE); spike protein (S); 15 kD,0,7,9581,9642,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,46978,AF207902.1,1,sp|AF207902.1|AF207902 Murine hepatitis virus strain ML-11 RNA-directed RNA polymerase (orf1A); RNA-directed RNA polymerase (orf1B); non-structural pr,0,8,31022,31083,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,46994,AF208066.1,1,sp|AF208066.1|AF208066 Murine hepatitis virus strain Penn 97-1; complete genome.,0,9,30858,30919,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,46995,AF208067.1,1,sp|AF208067.1|AF208067 Murine hepatitis virus strain ML-10; complete genome.,0,10,31031,31092,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,48769,AF220295.1,1,sp|AF220295.1|AF220295 Bovine coronavirus strain Quebec; complete genome.,0,11,30814,30875,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,60793,AF304460.1,1,sp|AF304460.1|AF304460 Human coronavirus 229E; complete genome.,0,12,27063,27125,47.96,CUAGUCUUAUACACAAUGGUAAGCCAGUGGUAGUAAAGGUAUAAGAAAUUUGCUACUAUGUUA,AF304460.1/27063-27125 X51325.1/1443-1505 J04419.1/1482-1544,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,66905,AF353511.1,1,sp|AF353511.1|AF353511 Porcine epidemic diarrhea virus strain CV777; complete genome.,0,13,27820,27882,47.50,UUGGUCUUGCACACAACGGUAAGCCAGUGGUAAUGUCAGUGCAAGAAGGAUAUUACCAUAGCA,AF353511.1/27820-27882 Z14976.1/1482-1544,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,73430,AF391541.1,1,sp|AF391541.1|AF391541 Bovine coronavirus isolate BCoV-ENT; complete genome.,0,14,30798,30859,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,73431,AF391542.1,1,sp|AF391542.1|AF391542 Bovine coronavirus isolate BCoV-LUN; complete genome.,0,15,30798,30859,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,93265,AF523847.1,1,sp|AF523847.1|AF523847 Human coronavirus OC43 3'UTR; partial sequence.,0,16,62,123,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,93266,AF523848.1,1,sp|AF523848.1|AF523848 Human enteric coronavirus 4408 3'UTR; partial sequence.,0,17,62,123,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,93267,AF523849.1,1,sp|AF523849.1|AF523849 Porcine hemagglutinating encephalomyelitis virus 3'UTR; partial sequence.,0,18,62,123,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,93268,AF523850.1,1,sp|AF523850.1|AF523850 Equine Coronavirus NC99 3'UTR; partial sequence.,0,19,62,123,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,134724,AY342160.1,0,sp|AY342160.1|AY342160 Canine coronavirus strain BGF10 complete genome.,0,20,8980,9042,53.96,CUACUCUUGUACAGAAUGGUAAGCACGUGUGAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,AY342160.1/8980-9042,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,135558,M36656.1,1,sp|M36656.1|BECNA Bovine coronavirus nucleocapsid gene; complete cds; and unknown gene.,0,21,1479,1540,45.50,GCAUUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,M36656.1/1479-1540,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,137439,D13096.1,1,sp|D13096.1|CCOINSAVC Canine coronavirus (CCV) genome.,0,22,9359,9422,54.74,CUACUCUUGUACAGAAUGGUAAGCCAAGUGUCAAUAGGAGGUACAAGCAACCUAUUGCAUAUUA,D13096.1/9359-9422,,0,64 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,137443,X66717.1,1,sp|X66717.1|CCVNUPR Canine corona virus mRNA of orfs 6a;6b and for nucleocapsid protein,0,23,2272,2334,53.13,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCCACCCUAUUGCAUAUUA,X66717.1/2272-2334,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138100,X51325.1,1,sp|X51325.1|COHVNP Human coronavirus 229E mRNA for nucleocapsid protein,0,24,1443,1505,47.96,CUAGUCUUAUACACAAUGGUAAGCCAGUGGUAGUAAAGGUAUAAGAAAUUUGCUACUAUGUUA,AF304460.1/27063-27125 X51325.1/1443-1505 J04419.1/1482-1544,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138121,X00509.1,1,sp|X00509.1|COMHVA Coronavirus MHV-A59 mRNA6 for E1 glycoprotein,0,25,2201,2262,40.40,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCUGCCCU,X00509.1/2201-2262,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138124,X00990.1,1,sp|X00990.1|COMHVJM7 Mouse Hepatitis Virus JHM mRNA7 for nucleocapsid protein,0,26,1511,1572,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138174,M14878.1,1,sp|M14878.1|CORTGEVM Porcine transmissible gastroenteritis virus matrix glycoprotein gene; partial cds; and nucleocapsid protein and hydrophobic pro,0,27,1781,1843,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138175,U00735.2,0,sp|U00735.2|CORU00735 Bovine coronavirus strain Mebus; complete genome.,0,28,30802,30863,47.51,GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA,AF523850.1/62-123 AF391541.1/30798-30859 AF058942.1/9316-9377 U00735.2/30802-30863 AF523849.1/62-123 AF523848.1/62-123 AF058943.1/9309-9370 AF523847.1/62-123 AF391542.1/30798-30859 AF220295.1/30814-30875,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138178,X06371.1,1,sp|X06371.1|COTGEV3 Enteric coronavirus TGEV RNA genome 3'-region,0,29,3701,3763,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,138182,Y00542.1,1,sp|Y00542.1|COTGEVNP Transmissible gastroenteritis virus (TGEV) mRNA for nucleoprotein (virulent TGEV strain FS772/70),0,30,1484,1546,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140893,X90572.1,1,sp|X90572.1|FC7A7BFD Feline coronavirus mRNA for 7a and 7b protein (strain FIPV Dahlberg),0,31,1000,1062,53.39,CUACUCUUGUACAGAAUGGUAAGCACGUGUAGUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,X90572.1/1000-1062,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140894,X90574.1,1,sp|X90574.1|FC7A7BFEU Feline coronavirus mRNA for 7a and 7b protein (strain FECV UCD),0,32,1000,1062,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140895,X90573.1,1,sp|X90573.1|FC7A7BFN Feline coronavirus mRNA for 7a and 7b protein (strain FIPV NOR15),0,33,1000,1062,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140896,X90575.1,1,sp|X90575.1|FC7A7BFU1 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD1),0,34,1000,1062,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140897,X90576.1,1,sp|X90576.1|FC7A7BFU2 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD2),0,35,809,871,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140898,X90577.1,1,sp|X90577.1|FC7A7BFU3 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD3),0,36,1000,1062,53.71,CUACUCUUGUACAGAAUGGUAAACACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,X90577.1/1000-1062,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140899,X90578.1,1,sp|X90578.1|FC7A7BFU4 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD4),0,37,1000,1062,51.70,CUACUCUUGUACAGAAUGGUAAGCACGUGUGAUGGGAGGUACAAGCAACCCCAUUACAUAUUA,X90578.1/1000-1062,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,140900,X90571.1,1,sp|X90571.1|FC7A7BFW Feline coronavirus mRNA for 7a and 7b protein (strain FIPV Wellcome),0,38,1000,1062,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,141185,X66718.1,1,sp|X66718.1|FECV6A6B Feline enteric corona virus mRNA of orf 6a and orf 6b,0,39,795,857,54.18,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUGGGAGGUACAAGCAACCCCAUUGCAUAUUA,X66718.1/795-857,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,141331,M23694.1,1,sp|M23694.1|FIPORFS Feline infectious peritonitis virus ORF1 and ORF2 mRNAs; complete cds.,0,40,1056,1118,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,141333,X90570.1,1,sp|X90570.1|FIPVGP7AB Feline infectious peritonitis virus mRNA for 7a and 7b proteins (strain TN406),0,41,1000,1062,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,174825,J04419.1,1,sp|J04419.1|HOBNC229 Human coronavirus 229E nucleocapsid protein mRNA; complete cds.,0,42,1482,1544,47.96,CUAGUCUUAUACACAAUGGUAAGCCAGUGGUAGUAAAGGUAUAAGAAAUUUGCUACUAUGUUA,AF304460.1/27063-27125 X51325.1/1443-1505 J04419.1/1482-1544,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181485,M35253.1,1,sp|M35253.1|MHV1NP Murine hepatitis virus hepatitis virus nucleocapsid (N-MHV1) ORF 1 and hepatitis virus nucleocapsid (N-MHV1) ORF 2 genes; compl,0,43,1428,1489,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181488,M35254.1,1,sp|M35254.1|MHV3NP Murine hepatitis virus hepatitis virus nucleocapsid (N-MHV3) ORF 1 and hepatitis virus nucleocapsid (N-MHV3) ORF 2 genes; compl,0,44,1425,1486,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181489,M35256.1,1,sp|M35256.1|MHVA59NP Murine hepatitis virus hepatitis virus nucleocapsid (N-MHVA59) ORF 1 and hepatitis virus nucleocapsid (N-MHVA59) ORF 2 genes; c,0,45,1425,1486,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181492,M61144.1,1,sp|M61144.1|MHVDIAA Murine hepatitis virus defective-interfering protein (DIssF) gene; complete cds.,0,46,3317,3378,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181508,X63538.1,1,sp|X63538.1|MHVNCP Murine Hepatitis Virus gene N for nucleocapsid protein,0,47,1434,1495,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181509,M80644.1,1,sp|M80644.1|MHVNCP1 Murine hepatitis virus deletion mutant nucleopcapsid protein mRNA; complete cds.,0,48,1338,1399,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181518,M35255.1,1,sp|M35255.1|MHVSHV Mouse hepatitis virus nucleocapsid (N-MHVS) RNA; complete cds.,0,49,1425,1486,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,181793,M23258.1,1,sp|M23258.1|MUCDIPORF Murine coronavirus proviral defective interfering particle (DlssE) obtained after serial passage 17; with 2 recombination sites,0,50,1974,2035,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,184426,Z14976.1,1,sp|Z14976.1|PEDVNGENE Porcine epidemic diarrhea virus (PEDV)for nucleocapsid protein,0,51,1482,1544,47.50,UUGGUCUUGCACACAACGGUAAGCCAGUGGUAAUGUCAGUGCAAGAAGGAUAUUACCAUAGCA,AF353511.1/27820-27882 Z14976.1/1482-1544,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,185116,X60056.1,1,sp|X60056.1|PRCVORFS Porcine respiratory coronavirus (PRCV) 3'end of ORF-3; ORF-4 and ORF-7 and genes for membrane protein and nucleoprotein,0,52,2565,2627,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,185155,Z24675.1,1,sp|Z24675.1|PRPROTSA Porcine respiratory coronavirus spike protein; ORF3b; small membrane protein; membrane glycoprotein; nucleocapsid protein; and ,0,53,7290,7352,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,185792,AJ544718.1,1,sp|AJ544718.1|PVI544718 Puffinosis virus N gene for nucleocapsid protein; genomic RNA,0,54,1487,1548,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,188897,S59673.1,1,sp|S59673.1|S59673 DIssE RNA gene 1 homolog {DI-2 RNA; defective-interfering 2 RNA} [mouse hepatitis virus MHV; Genomic RNA Recombinant; 2868 nt].,0,55,2627,2688,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,189615,D10760.1,1,sp|D10760.1|SDVNP Sialodacaryoadenitis virus (SDAV) gene for nucleocapsid protein; complete cds.,0,56,1454,1515,45.30,ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC,M23258.1/1974-2035 AF061835.1/1416-1477 AF029248.1/31093-31154 X63538.1/1434-1495 AF207902.1/31022-31083 M61144.1/3317-3378 M80644.1/1338-1399 AF207551.1/9581-9642 M35253.1/1428-1489 AJ544718.1/1487-1548 AF201929.1/31021-31082 AF208066.1/30858-30919 AF208067.1/31031-31092 M35254.1/1425-1486 M35255.1/1425-1486 M35256.1/1425-1486 S59673.1/2627-2688 D10760.1/1454-1515 X00990.1/1511-1572,,0,62 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,192733,AJ011482.1,1,sp|AJ011482.1|TGA011482 Porcine transmissible gastroenteritis virus minigenome,0,57,9491,9553,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,192734,AJ271965.2,1,sp|AJ271965.2|TGA271965 Transmissible gastroenteritis virus complete genome; genomic RNA,0,58,28363,28425,56.55,CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA,Z24675.1/7290-7352 X90576.1/809-871 M23694.1/1056-1118 AJ011482.1/9491-9553 X90570.1/1000-1062 X90571.1/1000-1062 X90573.1/1000-1062 X90574.1/1000-1062 X90575.1/1000-1062 X60056.1/2565-2627 AF104420.1/7745-7807 AJ271965.2/28363-28425 X06371.1/3701-3763 Y00542.1/1484-1546 M14878.1/1781-1843,,0,63 ./cmzasha --no-stderr --filter 100 40 Rfam/cm/RF00165.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00165_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00165.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,192747,Z35758.1,1,sp|Z35758.1|TGVTFIVIR Transmissible gastroenteritis virus TFI virion protein genes,0,59,8161,8224,51.26,CUACUCUUAUACAGAAUGGUAAGCACGUGUAAUAGGAGGUAAUAAGCAACCCUAUUGCAUAUUA,Z35758.1/8161-8224,,0,64 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)