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: Q90WV1_CARAU
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AY055725_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 1410.32 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.
Q90WV1_CARAU 1 MYPKEEHSTGGISSSLNYLDGAYDFSNLSETFGTSSPTEPASFGYYPAP
MYPKEEHSTGGISSSLNYLDGAYDFSNLSETFGTSSPTEPASFGYYPAP
MYPKEEHSTGGISSSLNYLDGAYDFSNLSETFGTSSPTEPASFGYYPAP
AY055725_2 1 atcaggcaaggaattcatcgggtgttactgatgattcagcgttgttcgc
tacaaaagcggtgcctaatagcaatcatcactgcccccaccctgaaccc
gctgggccgggctctcctttacttcaccagccccgaccgtcgcaccatc
Q90WV1_CARAU 50 PDPHAPPAEEHLQNLGTGPGSPLMFAPSSPQLSPYLNHHGGHHSTHQVS
PDPHAPPAEEHLQNLGTGPGSPLMFAPSSPQLSPYLNHHGGHHSTHQVS
PDPHAPPAEEHLQNLGTGPGSPLMFAPSSPQLSPYLNHHGGHHSTHQVS
AY055725_2 148 cgccgccgggcccatgagcgaccatgctaccttctcaccggcctaccgt
cacaccccaaataatgcgcggctttcccgcatccataaaggaaccaatc
gcccacttaatggcaccaccctcgtaccctggcgcgcttgaccgccggc
Q90WV1_CARAU 99 YYLDSPSSTVYRSSVVCSQQAGVGLCEELCSAADRQELFSGSRAAGGFD
YYLDSPSSTVYRSSVVCSQQAGVGLCEELCSAADRQELFSGSRAAGGFD
YYLDSPSSTVYRSSVVCSQQAGVGLCEELCSAADRQELFSGSRAAGGFD
AY055725_2 295 ttcgactaagtataggttccggggttggctagggacgcttgtaggggtg
aatagccgctagcgttgcaacgtgtgaatggccagaattcgcgccggta
tcgccttccccgcttgttggatttgtgggctctcagggccaaataagtt
Q90WV1_CARAU 148 SEKETRFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYVCPATNQ
SEKETRFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYVCPATNQ
SEKETRFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYVCPATNQ
AY055725_2 442 tgagacttggtagtgtgtctggtttggtagttaaaacgcagtgtcgaac
caaacgtgctggaaccgaaagtgcgaggacttaggtagaaaatgcccaa
tggggcctggctctgcctttaggctgacatccgactatctctttaaccg
Q90WV1_CARAU 197 CTIDRNRRKSCQACRLRKCYEVGMMKGGIRKERGGRAIRRDRRRSGNED
CTIDRNRRKSCQACRLRKCYEVGMMKGGIRKERGGRAIRRDRRRSGNED
CTIDRNRRKSCQACRLRKCYEVGMMKGGIRKERGGRAIRRDRRRSGNED
AY055725_2 589 taagaacaaatcgtaccattgggaaaggacagcggcgaacgaaaagagg
gctagaggaggacggtgagaatgttaggtgaaggggctggagggggaaa
cttcaccggccgacaacgttaacggaatttggcacttcgtcgggcttat
Q90WV1_CARAU 246 RVKSYSEQSNRTGLRTAPPQDRRKSSSTGVVSTLCMPPDQVLVLLLGAE
RVKSYSEQSNRTGLRTAPPQDRRKSSSTGVVSTLCMPPDQVLVLLLGAE
RVKSYSEQSNRTGLRTAPPQDRRKSSSTGVVSTLCMPPDQVLVLLLGAE
AY055725_2 736 cgaatagctacagcaagcccgaaaaaaagggaattaccgcgcgtccggg
gtagagaacagcgtgccccaaggagggcgttgctgtccaattttttgca
tcgcttagaccctgaattggcgggtccttgcctacgttcgggggtggag
Q90WV1_CARAU 295 PPAVCSRQKHSRPYTEITMMSLLTNMADKELVHMIAWAKKVPGFQDLSL
PPAVCSRQKHSRPYTEITMMSLLTNMADKELVHMIAWAKKVPGFQDLSL
PPAVCSRQKHSRPYTEITMMSLLTNMADKELVHMIAWAKKVPGFQDLSL
AY055725_2 883 ccggttccacacctagaaaatccaaaggagcgcaagtgaagcgtcgctc
ccctgcgaaaggcacatcttcttcatcaaattattcgcaatcgtaatct
gatccaagacccaccgccggcgcacgtcgacccgtcgtgaaaccgtctg
Q90WV1_CARAU 344 HDKVQLLESTWLEVLMIGLIWRSIHSPGKLIFAQDLILDRNEGECVEGM
HDKVQLLESTWLEVLMIGLIWRSIHSPGKLIFAQDLILDRNEGECVEGM
HDKVQLLESTWLEVLMIGLIWRSIHSPGKLIFAQDLILDRNEGECVEGM
AY055725_2 1030 cgagcttgaatcggtaagcatatactcgacatgcgcacgaagggtggga
aaatattagcgtattttgttggctaccgatttcaatttagaagagtagt
ctgtggggctggggggcacaggtttataaccttgtccttgtaaatcggg
Q90WV1_CARAU 393 AEIFDMLLATVTRFRSLKLKLEEFVCLKALILLNSGAFSFCSSPVEPLM
AEIFDMLLATVTRFRSLKLKLEEFVCLKALILLNSGAFSFCSSPVEPLM
AEIFDMLLATVTRFRSLKLKLEEFVCLKALILLNSGAFSFCSSPVEPLM
AY055725_2 1177 ggatgactgagactcacacacggtgtcagcaccatggtttttacggcta
cattatttcctcgtggtatataattgtacttttacgctctgcgctactt
tgtccgcggtgtccttcacgggacatcatcatctttataccctgggcgg
Q90WV1_CARAU 442 DSFMVQCMLDNITDAFIYGISKSGASLQLQSRRQAQLLLLLSHIRHMSN
DSFMVQCMLDNITDAFIYGISKSGASLQLQSRRQAQLLLLLSHIRHMSN
DSFMVQCMLDNITDAFIYGISKSGASLQLQSRRQAQLLLLLSHIRHMSN
AY055725_2 1324 gatagctacgaaaggtatgaaatggtcccctcccgcccccctcaacaaa
agtttagttaatcacttagtgacgcctatacggacatttttcatgatga
cccgggcggccctccctccctagtcgggagcctgcgcgggcaccacgcc
Q90WV1_CARAU 491 KGMEHLYRMKCKNRVPLYDLLLEMLDAQRFHSSGKVQRLWAQSEKDPPS
KGMEHLYRMKCKNRVPLYDLLLEMLDAQRFHSSGKVQRLWAQSEKDPPS
KGMEHLYRMKCKNRVPLYDLLLEMLDAQRFHSSGKVQRLWAQSEKDPPS
AY055725_2 1471 agagcttcaataacgcctgcttgacggcctcttgagccctgcagagcct
agtaatagtagaagtctaatttattacagtaccgatagtgcagaaaccc
aaggcacagatgcacgctctggggatcgacttaagggaggagtgaccat
Q90WV1_CARAU 540 TPTTSSRGPGTMLPNIACHEQSPDP
TPTTSSRGPGTMLPNIACHEQSPDP
TPTTSSRGPGTMLPNIACHEQSPDP
AY055725_2 1618 acaaaaagcgaaccaagtcgcacgc
ccccggggcgcttcatcgaaagcac
acacccattacggcccctcggtacc
//
cmbi.kun.nl), 18-Feb-2005