Params: ./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 Build: release Host: bicycle.cs.washington.edu pid: 24519 ----cmFile: Rfam/cm/RF00165.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/phg.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #17581,sp|AF029248.1|AF029248 Mouse hepatitis virus strain MHV-A59 C12 mutant, complete genome. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 0 : 31093 31154 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 31093 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 31151 ::: 60 uUA 62 ++ 31152 CCC 31154 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #22238,sp|AF058942.1|AF058942 Bovine coronavirus strain LY-138 32 kDa putative non-structural protein, hemagglutinin esterase (HE), spike glycoprotein (S), 4 ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 1 : 9316 9377 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 9316 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 9374 ::: 60 uUA 62 +UA 9375 CUA 9377 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #22239,sp|AF058943.1|AF058943 Bovine coronavirus strain LSU-94LSS-051-2 32 kDa putative non-structural protein, hemagglutinin esterase (HE), spike glycoprote ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 2 : 9309 9370 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 9309 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 9367 ::: 60 uUA 62 +UA 9368 CUA 9370 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #22240,sp|AF058944.1|AF058944 Bovine coronavirus strain OK-0514-3 32 kDa putative non-structural protein, hemagglutinin esterase (HE), spike glycoprotein (S) ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAUUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 3 : 9309 9370 (fwd) 44.84 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGA UGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 9309 GCACUCUCUAUCAGAUUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 9367 ::: 60 uUA 62 +UA 9368 CUA 9370 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #22674,sp|AF061835.1|AF061835 Murine hepatitis virus strain 2 nucleocapsid protein (N) gene, complete cds; and unknown gene. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 4 : 1416 1477 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1416 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1474 ::: 60 uUA 62 ++ 1475 CCC 1477 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #29950,sp|AF104420.1|AF104420 Porcine transmissible gastroenteritis virus RNA dependent RNA polymerase gene, partial cds; virus envelope protein spike (S), e ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 5 : 7745 7807 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 7745 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 7804 ::: 60 uUA 62 UUA 7805 UUA 7807 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #45238,sp|AF201929.1|AF201929 Murine hepatitis virus strain 2, complete genome. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 6 : 31021 31082 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 31021 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 31079 ::: 60 uUA 62 ++ 31080 CCC 31082 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #46949,sp|AF207551.1|AF207551 Sialodacryoadenitis virus 28 kD nonstructural protein (NS2), hemagglutinin-esterase glycoprotein (HE), spike protein (S), 15 kD ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 7 : 9581 9642 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 9581 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 9639 ::: 60 uUA 62 ++ 9640 CCC 9642 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #46978,sp|AF207902.1|AF207902 Murine hepatitis virus strain ML-11 RNA-directed RNA polymerase (orf1A), RNA-directed RNA polymerase (orf1B), non-structural pr ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 8 : 31022 31083 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 31022 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 31080 ::: 60 uUA 62 ++ 31081 CCC 31083 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #46994,sp|AF208066.1|AF208066 Murine hepatitis virus strain Penn 97-1, complete genome. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 9 : 30858 30919 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 30858 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 30916 ::: 60 uUA 62 ++ 30917 CCC 30919 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #46995,sp|AF208067.1|AF208067 Murine hepatitis virus strain ML-10, complete genome. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 10 : 31031 31092 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 31031 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 31089 ::: 60 uUA 62 ++ 31090 CCC 31092 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #48769,sp|AF220295.1|AF220295 Bovine coronavirus strain Quebec, complete genome. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 11 : 30814 30875 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 30814 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 30872 ::: 60 uUA 62 +UA 30873 CUA 30875 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #60793,sp|AF304460.1|AF304460 Human coronavirus 229E, complete genome. ----isReversed: 0 ----hitSequence: CUAGUCUUAUACACAAUGGUAAGCCAGUGGUAGUAAAGGUAUAAGAAAUUUGCUACUAUGUUA hit 12 : 27063 27125 (fwd) 47.96 bits ::::::::::::::::::::::::::<<<.<<<<<<<____________>>>>>>>.>>> 1 cUAcUCUUguACAGAAUGGUAAGCcagug.uaauaacAGGUacAAGAAgguuauua.cau 58 CUA+UCUU UACA+AAUGGUAAGCCAGU: UA::AA: GUA AAGAA+:UU::UA :AU 27063 CUAGUCUUAUACACAAUGGUAAGCCAGUGgUAGUAAAG-GUAUAAGAAAUUUGCUAcUAU 27121 :::: 59 AuUA 62 UUA 27122 GUUA 27125 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #66905,sp|AF353511.1|AF353511 Porcine epidemic diarrhea virus strain CV777, complete genome. ----isReversed: 0 ----hitSequence: UUGGUCUUGCACACAACGGUAAGCCAGUGGUAAUGUCAGUGCAAGAAGGAUAUUACCAUAGCA hit 13 : 27820 27882 (fwd) 47.50 bits ::::::::::::::::::::::::::<<<.<<<<<<<____________>>>>>>>.>>> 1 cUAcUCUUguACAGAAUGGUAAGCcagug.uaauaacAGGUacAAGAAgguuauua.cau 58 U +UCUUG ACA+AA GGUAAGCCAGUG UAAU::CA GU CAAGAAGG::AUUA CAU 27820 UUGGUCUUGCACACAACGGUAAGCCAGUGgUAAUGUCA-GUGCAAGAAGGAUAUUAcCAU 27878 :::: 59 AuUA 62 A +A 27879 AGCA 27882 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #73430,sp|AF391541.1|AF391541 Bovine coronavirus isolate BCoV-ENT, complete genome. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 14 : 30798 30859 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 30798 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 30856 ::: 60 uUA 62 +UA 30857 CUA 30859 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #73431,sp|AF391542.1|AF391542 Bovine coronavirus isolate BCoV-LUN, complete genome. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 15 : 30798 30859 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 30798 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 30856 ::: 60 uUA 62 +UA 30857 CUA 30859 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #93265,sp|AF523847.1|AF523847 Human coronavirus OC43 3'UTR, partial sequence. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 16 : 62 123 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 62 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 120 ::: 60 uUA 62 +UA 121 CUA 123 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #93266,sp|AF523848.1|AF523848 Human enteric coronavirus 4408 3'UTR, partial sequence. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 17 : 62 123 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 62 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 120 ::: 60 uUA 62 +UA 121 CUA 123 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #93267,sp|AF523849.1|AF523849 Porcine hemagglutinating encephalomyelitis virus 3'UTR, partial sequence. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 18 : 62 123 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 62 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 120 ::: 60 uUA 62 +UA 121 CUA 123 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #93268,sp|AF523850.1|AF523850 Equine Coronavirus NC99 3'UTR, partial sequence. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 19 : 62 123 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 62 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 120 ::: 60 uUA 62 +UA 121 CUA 123 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #134724,sp|AY342160.1|AY342160 Canine coronavirus strain BGF10 complete genome. ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUGAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 20 : 8980 9042 (fwd) 53.96 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG::AUA::AGGUACAAG+A+ ::UAU::CAUA 8980 CUACUCUUGUACAGAAUGGUAAGCACGUGUGAUAGGAGGUACAAGCAAcCCUAUUGCAUA 9039 ::: 60 uUA 62 UUA 9040 UUA 9042 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #135558,sp|M36656.1|BECNA Bovine coronavirus nucleocapsid gene, complete cds; and unknown gene. ----isReversed: 0 ----hitSequence: GCAUUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 21 : 1479 1540 (fwd) 45.50 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +A UCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 1479 GCAUUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 1537 ::: 60 uUA 62 +UA 1538 CUA 1540 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #137439,sp|D13096.1|CCOINSAVC Canine coronavirus (CCV) genome. ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCCAAGUGUCAAUAGGAGGUACAAGCAACCUAUUGCAUAUUA hit 22 : 9359 9422 (fwd) 54.74 bits ::::::::::::::::::::::::.::<<<.<<<<<<<____________>>>>>>>>>> 1 cUAcUCUUguACAGAAUGGUAAGC.cagug.uaauaacAGGUacAAGAAgguuauuacau 58 CUACUCUUGUACAGAAUGGUAAGC +AGUG :AAUA::AGGUACAAG+A+::UAUU:CAU 9359 CUACUCUUGUACAGAAUGGUAAGCcAAGUGuCAAUAGGAGGUACAAGCAACCUAUUGCAU 9418 :::: 59 AuUA 62 AUUA 9419 AUUA 9422 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #137443,sp|X66717.1|CCVNUPR Canine corona virus mRNA of orfs 6a,6b and for nucleocapsid protein ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCCACCCUAUUGCAUAUUA hit 23 : 2272 2334 (fwd) 53.13 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+ + ::UAUU:CAUA 2272 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCCAcCCUAUUGCAUA 2331 ::: 60 uUA 62 UUA 2332 UUA 2334 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #138100,sp|X51325.1|COHVNP Human coronavirus 229E mRNA for nucleocapsid protein ----isReversed: 0 ----hitSequence: CUAGUCUUAUACACAAUGGUAAGCCAGUGGUAGUAAAGGUAUAAGAAAUUUGCUACUAUGUUA hit 24 : 1443 1505 (fwd) 47.96 bits ::::::::::::::::::::::::::<<<.<<<<<<<____________>>>>>>>.>>> 1 cUAcUCUUguACAGAAUGGUAAGCcagug.uaauaacAGGUacAAGAAgguuauua.cau 58 CUA+UCUU UACA+AAUGGUAAGCCAGU: UA::AA: GUA AAGAA+:UU::UA :AU 1443 CUAGUCUUAUACACAAUGGUAAGCCAGUGgUAGUAAAG-GUAUAAGAAAUUUGCUAcUAU 1501 :::: 59 AuUA 62 UUA 1502 GUUA 1505 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #138121,sp|X00509.1|COMHVA Coronavirus MHV-A59 mRNA6 for E1 glycoprotein ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCUGCCCU hit 25 : 2201 2262 (fwd) 40.40 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:+G::A:AACA G++++AGAAGGUU:U::C+: 2201 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCUGC 2259 ::: 60 uUA 62 ++ 2260 CCU 2262 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #138124,sp|X00990.1|COMHVJM7 Mouse Hepatitis Virus JHM mRNA7 for nucleocapsid protein ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 26 : 1511 1572 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1511 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1569 ::: 60 uUA 62 ++ 1570 CCC 1572 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #138174,sp|M14878.1|CORTGEVM Porcine transmissible gastroenteritis virus matrix glycoprotein gene, partial cds; and nucleocapsid protein and hydrophobic pro ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 27 : 1781 1843 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1781 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1840 ::: 60 uUA 62 UUA 1841 UUA 1843 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #138175,sp|U00735.2|CORU00735 Bovine coronavirus strain Mebus, complete genome. ----isReversed: 0 ----hitSequence: GCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUA hit 28 : 30802 30863 (fwd) 47.51 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::AUAA:A G++++AGAAG:UUAU::CA:A 30802 GCACUCUCUAUCAGAAUGGAUGUCuUGCUGCUAUAAUA-GAUAGAGAAGGUUAUAGCAGA 30860 ::: 60 uUA 62 +UA 30861 CUA 30863 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #138178,sp|X06371.1|COTGEV3 Enteric coronavirus TGEV RNA genome 3'-region ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 29 : 3701 3763 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 3701 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 3760 ::: 60 uUA 62 UUA 3761 UUA 3763 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #138182,sp|Y00542.1|COTGEVNP Transmissible gastroenteritis virus (TGEV) mRNA for nucleoprotein (virulent TGEV strain FS772/70) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 30 : 1484 1546 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1484 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1543 ::: 60 uUA 62 UUA 1544 UUA 1546 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140893,sp|X90572.1|FC7A7BFD Feline coronavirus mRNA for 7a and 7b protein (strain FIPV Dahlberg) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAGUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 31 : 1000 1062 (fwd) 53.39 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:A:UA::AGGUACAAG+A+ ::UA:U:CAUA 1000 CUACUCUUGUACAGAAUGGUAAGCACGUGUAGUAGGAGGUACAAGCAAcCCUAUUGCAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140894,sp|X90574.1|FC7A7BFEU Feline coronavirus mRNA for 7a and 7b protein (strain FECV UCD) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 32 : 1000 1062 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1000 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140895,sp|X90573.1|FC7A7BFN Feline coronavirus mRNA for 7a and 7b protein (strain FIPV NOR15) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 33 : 1000 1062 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1000 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140896,sp|X90575.1|FC7A7BFU1 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD1) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 34 : 1000 1062 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1000 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140897,sp|X90576.1|FC7A7BFU2 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD2) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 35 : 809 871 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 809 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 868 ::: 60 uUA 62 UUA 869 UUA 871 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140898,sp|X90577.1|FC7A7BFU3 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD3) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAACACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 36 : 1000 1062 (fwd) 53.71 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAA C+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1000 CUACUCUUGUACAGAAUGGUAAACACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140899,sp|X90578.1|FC7A7BFU4 Feline coronavirus mRNA for 7a and 7b protein (strain FIPV UCD4) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUGAUGGGAGGUACAAGCAACCCCAUUACAUAUUA hit 37 : 1000 1062 (fwd) 51.70 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUGU:AU:::AGGUACAAG+A+ :::AU:ACAUA 1000 CUACUCUUGUACAGAAUGGUAAGCACGUGUGAUGGGAGGUACAAGCAAcCCCAUUACAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #140900,sp|X90571.1|FC7A7BFW Feline coronavirus mRNA for 7a and 7b protein (strain FIPV Wellcome) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 38 : 1000 1062 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1000 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #141185,sp|X66718.1|FECV6A6B Feline enteric corona virus mRNA of orf 6a and orf 6b ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUGGGAGGUACAAGCAACCCCAUUGCAUAUUA hit 39 : 795 857 (fwd) 54.18 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAU:::AGGUACAAG+A+ :::AUU:CAUA 795 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUGGGAGGUACAAGCAAcCCCAUUGCAUA 854 ::: 60 uUA 62 UUA 855 UUA 857 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #141331,sp|M23694.1|FIPORFS Feline infectious peritonitis virus ORF1 and ORF2 mRNAs, complete cds. ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 40 : 1056 1118 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1056 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1115 ::: 60 uUA 62 UUA 1116 UUA 1118 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #141333,sp|X90570.1|FIPVGP7AB Feline infectious peritonitis virus mRNA for 7a and 7b proteins (strain TN406) ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 41 : 1000 1062 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 1000 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 1059 ::: 60 uUA 62 UUA 1060 UUA 1062 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #174825,sp|J04419.1|HOBNC229 Human coronavirus 229E nucleocapsid protein mRNA, complete cds. ----isReversed: 0 ----hitSequence: CUAGUCUUAUACACAAUGGUAAGCCAGUGGUAGUAAAGGUAUAAGAAAUUUGCUACUAUGUUA hit 42 : 1482 1544 (fwd) 47.96 bits ::::::::::::::::::::::::::<<<.<<<<<<<____________>>>>>>>.>>> 1 cUAcUCUUguACAGAAUGGUAAGCcagug.uaauaacAGGUacAAGAAgguuauua.cau 58 CUA+UCUU UACA+AAUGGUAAGCCAGU: UA::AA: GUA AAGAA+:UU::UA :AU 1482 CUAGUCUUAUACACAAUGGUAAGCCAGUGgUAGUAAAG-GUAUAAGAAAUUUGCUAcUAU 1540 :::: 59 AuUA 62 UUA 1541 GUUA 1544 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181485,sp|M35253.1|MHV1NP Murine hepatitis virus hepatitis virus nucleocapsid (N-MHV1) ORF 1 and hepatitis virus nucleocapsid (N-MHV1) ORF 2 genes, compl ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 43 : 1428 1489 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1428 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1486 ::: 60 uUA 62 ++ 1487 CCC 1489 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181488,sp|M35254.1|MHV3NP Murine hepatitis virus hepatitis virus nucleocapsid (N-MHV3) ORF 1 and hepatitis virus nucleocapsid (N-MHV3) ORF 2 genes, compl ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 44 : 1425 1486 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1425 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1483 ::: 60 uUA 62 ++ 1484 CCC 1486 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181489,sp|M35256.1|MHVA59NP Murine hepatitis virus hepatitis virus nucleocapsid (N-MHVA59) ORF 1 and hepatitis virus nucleocapsid (N-MHVA59) ORF 2 genes, c ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 45 : 1425 1486 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1425 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1483 ::: 60 uUA 62 ++ 1484 CCC 1486 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181492,sp|M61144.1|MHVDIAA Murine hepatitis virus defective-interfering protein (DIssF) gene, complete cds. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 46 : 3317 3378 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 3317 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 3375 ::: 60 uUA 62 ++ 3376 CCC 3378 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181508,sp|X63538.1|MHVNCP Murine Hepatitis Virus gene N for nucleocapsid protein ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 47 : 1434 1495 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1434 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1492 ::: 60 uUA 62 ++ 1493 CCC 1495 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181509,sp|M80644.1|MHVNCP1 Murine hepatitis virus deletion mutant nucleopcapsid protein mRNA, complete cds. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 48 : 1338 1399 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1338 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1396 ::: 60 uUA 62 ++ 1397 CCC 1399 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181518,sp|M35255.1|MHVSHV Mouse hepatitis virus nucleocapsid (N-MHVS) RNA, complete cds. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 49 : 1425 1486 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1425 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1483 ::: 60 uUA 62 ++ 1484 CCC 1486 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #181793,sp|M23258.1|MUCDIPORF Murine coronavirus proviral defective interfering particle (DlssE) obtained after serial passage 17, with 2 recombination sites ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 50 : 1974 2035 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1974 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 2032 ::: 60 uUA 62 ++ 2033 CCC 2035 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #184426,sp|Z14976.1|PEDVNGENE Porcine epidemic diarrhea virus (PEDV)for nucleocapsid protein ----isReversed: 0 ----hitSequence: UUGGUCUUGCACACAACGGUAAGCCAGUGGUAAUGUCAGUGCAAGAAGGAUAUUACCAUAGCA hit 51 : 1482 1544 (fwd) 47.50 bits ::::::::::::::::::::::::::<<<.<<<<<<<____________>>>>>>>.>>> 1 cUAcUCUUguACAGAAUGGUAAGCcagug.uaauaacAGGUacAAGAAgguuauua.cau 58 U +UCUUG ACA+AA GGUAAGCCAGUG UAAU::CA GU CAAGAAGG::AUUA CAU 1482 UUGGUCUUGCACACAACGGUAAGCCAGUGgUAAUGUCA-GUGCAAGAAGGAUAUUAcCAU 1540 :::: 59 AuUA 62 A +A 1541 AGCA 1544 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #185116,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 ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 52 : 2565 2627 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 2565 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 2624 ::: 60 uUA 62 UUA 2625 UUA 2627 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #185155,sp|Z24675.1|PRPROTSA Porcine respiratory coronavirus spike protein, ORF3b, small membrane protein, membrane glycoprotein, nucleocapsid protein, and ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 53 : 7290 7352 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 7290 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 7349 ::: 60 uUA 62 UUA 7350 UUA 7352 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #185792,sp|AJ544718.1|PVI544718 Puffinosis virus N gene for nucleocapsid protein, genomic RNA ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 54 : 1487 1548 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1487 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1545 ::: 60 uUA 62 ++ 1546 CCC 1548 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #188897,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]. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 55 : 2627 2688 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 2627 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 2685 ::: 60 uUA 62 ++ 2686 CCC 2688 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #189615,sp|D10760.1|SDVNP Sialodacaryoadenitis virus (SDAV) gene for nucleocapsid protein, complete cds. ----isReversed: 0 ----hitSequence: ACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCC hit 56 : 1454 1515 (fwd) 45.30 bits ::::::::::::::::::::::::.::<<<<<<<<<<____________>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGC.caguguaauaacAGGUacAAGAAgguuauuacauA 59 +ACUCU++++CAGAAUGG++++C ++:UG::A:AACA G++++AGAAGGUU:U::CA:A 1454 ACACUCUCUAUCAGAAUGGAUGUCuUGCUGUCAUAACA-GAUAGAGAAGGUUGUGGCAGA 1512 ::: 60 uUA 62 ++ 1513 CCC 1515 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #192733,sp|AJ011482.1|TGA011482 Porcine transmissible gastroenteritis virus minigenome ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 57 : 9491 9553 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 9491 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 9550 ::: 60 uUA 62 UUA 9551 UUA 9553 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #192734,sp|AJ271965.2|TGA271965 Transmissible gastroenteritis virus complete genome, genomic RNA ----isReversed: 0 ----hitSequence: CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAACCCUAUUGCAUAUUA hit 58 : 28363 28425 (fwd) 56.55 bits ::::::::::::::::::::::::::<<<<<<<<<<____________.>>>>>>>>>>: 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUacAAGAAg.guuauuacauA 59 CUACUCUUGUACAGAAUGGUAAGC+ GUG:AAUA::AGGUACAAG+A+ ::UAUU:CAUA 28363 CUACUCUUGUACAGAAUGGUAAGCACGUGUAAUAGGAGGUACAAGCAAcCCUAUUGCAUA 28422 ::: 60 uUA 62 UUA 28423 UUA 28425 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----sequence: #192747,sp|Z35758.1|TGVTFIVIR Transmissible gastroenteritis virus TFI virion protein genes ----isReversed: 0 ----hitSequence: CUACUCUUAUACAGAAUGGUAAGCACGUGUAAUAGGAGGUAAUAAGCAACCCUAUUGCAUAUUA hit 59 : 8161 8224 (fwd) 51.26 bits ::::::::::::::::::::::::::<<<<<<<<<<______.______.>>>>>>>>>> 1 cUAcUCUUguACAGAAUGGUAAGCcaguguaauaacAGGUac.AAGAAg.guuauuacau 58 CUACUCUU UACAGAAUGGUAAGC+ GUG:AAUA::AGGUA+ AAG+A+ ::UAUU:CAU 8161 CUACUCUUAUACAGAAUGGUAAGCACGUGUAAUAGGAGGUAAuAAGCAAcCCUAUUGCAU 8220 :::: 59 AuUA 62 AUUA 8221 AUUA 8224 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum08.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum09.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum11.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum12.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum13.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum17.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum18.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum19.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum25.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum26.dat.fasta.gz done 1.65905e+10 nucs (frac lets thru so far=3.97335e-07, 2d-fracLetsThru=2.20266e-07). Filter report: done 1.65905e+10 nucs (frac lets thru so far=3.97335e-07, 2d-fracLetsThru=2.20266e-07). done 1.65905e+10 nucs (frac lets thru so far=3.97335e-07, 2d-fracLetsThru=2.20266e-07). CPU time: 251242.22u 252.72s 69:51:34.94 Elapsed: 78:27:12