2005, NucleaRDB.
The pairwise alignment has been generated with the "genewise" program of the Wise2 package. The output shows the protein sequence on the first line, followed by a line indicating the similarity level of the match, followed by 4 lines representing the DNA sequence; The DNA sequence descending in triplets, each triplet being a codon. The translation of each codon is shown above it.
Between the two protein sequences a line indicating the similarity of the match is printed. "+" indicates a conservative mismatch while "- "indicates a dramatic one. Mismatches are indicated by "***" in the left column in addition to "!" at the relevant position(s).
genewise $Name: wise2-2-0 $ (unreleased release)
This program is freely distributed under a GPL. See source directory
Copyright (c) GRL limited: portions of the code are from separate copyright
Query protein: NHR8_CAEEL
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF083226_2
Strand: forward
Start/End (protein) default
Gene Paras: human.gf
Codon Table: codon.table
Subs error: 1e-05
Indel error: 1e-05
Model splice? model
Model codon bias? flat
Model intron bias? tied
Null model syn
Algorithm 623
genewise output
Score 1388.97 bits over entire alignment
Scores as bits over a synchronous coding model
Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info.
NHR8_CAEEL 1 MPSSSPSMDESRRSAVPPKEPAGRICTVCSDRANGYNFGVLTCESCKAF
MPSSSPSMDESRRSAVPPKEPAGRICTVCSDRANGYNFGVLTCESCKAF
MPSSSPSMDESRRSAVPPKEPAGRICTVCSDRANGYNFGVLTCESCKAF
AF083226_2 1 actttctaggtcatggccagcggaatagttgcgagtatggcatgttagt
tcccccctaacggcctccaaccggtgctgcagcagaatgttcgacgact
gtgttaggcgtagtttaaagttcatcatccctatactttactcattggt
NHR8_CAEEL 50 FRRNASKHKEIKCPFSDSCQITSASRKFCQACRLNKCFAVGMNSEWLND
FRRNASKHKEIKCPFSDSCQITSASRKFCQACRLNKCFAVGMNSEWLND
FRRNASKHKEIKCPFSDSCQITSASRKFCQACRLNKCFAVGMNSEWLND
AF083226_2 148 tacagtacagaatcttgttcaatgtcattcgtctaattgggaaagttag
tggaccaaaatagctcacgatccccgatgacggtaagtctgtagagtaa
cgattagtgatattcttttacaaatcgtcattagtattttagctagatt
NHR8_CAEEL 99 LKPKSSIVSGKFKRKKPDMKNNLKVEVDDTEEDLENDDEEQISVPKALL
LKPKSSIVSGKFKRKKPDMKNNLKVEVDDTEEDLENDDEEQISVPKALL
LKPKSSIVSGKFKRKKPDMKNNLKVEVDDTEEDLENDDEEQISVPKALL
AF083226_2 295 tacaatagtgataaaacgaaaatagggggagggtgaggggcaagcagtc
tacagcttcgatagaacataaatatataacaaataaaaaaatgtcactt
gaggtatttaacaaggttggtcgagaatttaatgatttaaattccaaat
NHR8_CAEEL 148 EKLINKANEKSKDRCTCKCQCGFYPITQRLTAYEPKDTTAVNSPQDISF
EKLINKANEKSKDRCTCKCQCGFYPITQRLTAYEPKDTTAVNSPQDISF
EKLINKANEKSKDRCTCKCQCGFYPITQRLTAYEPKDTTAVNSPQDISF
AF083226_2 442 gacaaagagatagatatatctgttcaacacagtgcagaaggaaccgatt
aattaacaaacaaggcgagaggtactcagtccaacaaccctagcaatct
agtctattaaaacatacacgtactattaaccacaagtaatgctaataac
NHR8_CAEEL 197 SHHLHHSDSFYSSSTSTLSPMSVISCAPSSHDSSGYNTSQLVTQSPTNY
SHHLHHSDSFYSSSTSTLSPMSVISCAPSSHDSSGYNTSQLVTQSPTNY
SHHLHHSDSFYSSSTSTLSPMSVISCAPSSHDSSGYNTSQLVTQSPTNY
AF083226_2 589 tccccctgttttttatactcatgaatgcttcgtagtaatccgactcaat
caataacactacccccctcctcttggccccaacggaaccattcacccaa
ctttttgtgtttattatttaggtctttatattcttctttatttataccc
NHR8_CAEEL 246 TVSPASIPSSITELSPQMPSQYPPMLSPFQFGVMAQMAAPANFLNFPPM
TVSPASIPSSITELSPQMPSQYPPMLSPFQFGVMAQMAAPANFLNFPPM
TVSPASIPSSITELSPQMPSQYPPMLSPFQFGVMAQMAAPANFLNFPPM
AF083226_2 736 agtcgtacataagctccactctccattctctggagcaggcgattatcca
ctcccctcgctcatccatccaaccttcctatgttcatccccattatcct
attggtagcaatagtaagagattagaaatatttgcagtgacctgtttag
NHR8_CAEEL 295 PERTWTPIQAVSTVPVTETLPPNLLEQIHSKIDKYIGVLNEDEITLLEE
PERTWTPIQAVSTVPVTETLPPNLLEQIHSKIDKYIGVLNEDEITLLEE
PERTWTPIQAVSTVPVTETLPPNLLEQIHSKIDKYIGVLNEDEITLLEE
AF083226_2 883 cgaatacacggtagcgagacccatcgcactaagataggtagggaactgg
cagcgcctactcctctcactccattaatacataaatgttaaaatcttaa
taaagtataagcataatatatatgaaattagtcactatgtacgattaaa
NHR8_CAEEL 344 LHVQNEPLNAPLIQWHNPKSIDGVFRIIEEALRRIVNMACQLSLFRELH
LHVQNEPLNAPLIQWHNPKSIDGVFRIIEEALRRIVNMACQLSLFRELH
LHVQNEPLNAPLIQWHNPKSIDGVFRIIEEALRRIVNMACQLSLFRELH
AF083226_2 1030 ccgcagctagccactcacaaagggtaaagggccaagaagtctactcgcc
tataaactaccttagaacagtagttgttaactggttatcgatgttgata
ttaatgaattaatagctgacttattaaaaataagttcgacaatacagtc
NHR8_CAEEL 393 VDDRKNLLKSGFGELLIVRGLMAYDKSDNSWNHSFGVRGKMEVKVEVLK
VDDRKNLLKSGFGELLIVRGLMAYDKSDNSWNHSFGVRGKMEVKVEVLK
VDDRKNLLKSGFGELLIVRGLMAYDKSDNSWNHSFGVRGKMEVKVEVLK
AF083226_2 1177 gggaaactaagtggttagcgcagtgaagaatacttggcgaaggagggca
taagaattaggtgattttggttcaaagaaggaactgtggatatatatta
gctgatcgatatggggtggttgctcgttccgttataaaaaggaggattg
NHR8_CAEEL 442 NPKLEEHYKAHMNLLSTFGEDVRNNEHLMLIFNAAVIFHPHVSNLRDSK
NPKLEEHYKAHMNLLSTFGEDVRNNEHLMLIFNAAVIFHPHVSNLRDSK
NPKLEEHYKAHMNLLSTFGEDVRNNEHLMLIFNAAVIFHPHVSNLRDSK
AF083226_2 1324 acacggctagcaatctatggggaaagctacatagggatcccgtatcgaa
acataaaaacatattcctgaatgaaaatttttacctttacatcatgaga
taataatcaacgcgtagtaatggttatggctctattattttcccattta
NHR8_CAEEL 491 RVHSTQAKYFQMLLKLLTFEYGKSRADIAYSNLLNQVVELHRVNRTLLR
RVHSTQAKYFQMLLKLLTFEYGKSRADIAYSNLLNQVVELHRVNRTLLR
RVHSTQAKYFQMLLKLLTFEYGKSRADIAYSNLLNQVVELHRVNRTLLR
AF083226_2 1471 cgctacgattcactaccatgtgatcggagtaaccacgggcccgaaatcc
gtaccacaatatttattctaagacgcatcagattaattatagtagcttg
agcaaaaatcggcgattatattaattctactttgtaccgtttgtgcatt
NHR8_CAEEL 540 VFYGLDIAQLDPLIRELCSFE
VFYGLDIAQLDPLIRELCSFE
VFYGLDIAQLDPLIRELCSFE
AF083226_2 1618 gttgcgagctgccacgttttg
ttagtatcatacttgatgcta
gttaatttagttgaaaattta
//
cmbi.kun.nl), 18-Feb-2005