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: Q96PR1_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AY118169_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 1601.72 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.
Q96PR1_HUMAN 1 MGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTT
MGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTT
MGKIENNERVILNVGGTRHETYRSTLKTLPGTRLALLASSEPPGDCLTT
AY118169_2 1 agaagaagagacagggaccgatcaacaaccgaccgccgttgccggttaa
tgataaaagtttatggcgaacaggctactcgcgtcttcccaccgagtcc
gcgcgccgggcctcgccgcaccccccgcgtaacgcttcccgcacccgcg
Q96PR1_HUMAN 50 AGDKLQPSPPPLSPPPRAPPLSPGPGGCFEGGAGNCSSRGGRASDHPGG
AGDKLQPSPPPLSPPPRAPPLSPGPGGCFEGGAGNCSSRGGRASDHPGG
AGDKLQPSPPPLSPPPRAPPLSPGPGGCFEGGAGNCSSRGGRASDHPGG
AY118169_2 148 gggaccctcccctcccagccctcgcggttgggggatatcggagagccgg
cgaataccccctccccgccctccgcgggtaggcgaggcggggcgaacgg
gccggggggtagggggagcggccgaccccgccgccctccccgccctctc
Q96PR1_HUMAN 99 GREFFFDRHPGVFAYVLNYYRTGKLHCPADVCGPLFEEELAFWGIDETD
GREFFFDRHPGVFAYVLNYYRTGKLHCPADVCGPLFEEELAFWGIDETD
GREFFFDRHPGVFAYVLNYYRTGKLHCPADVCGPLFEEELAFWGIDETD
AY118169_2 295 gcgtttgcccggtgtgcattcagacctcgggtgcctgggcgttgaggag
ggatttagacgttcattaaagcgatagccatggcttaaatctggtaaca
ccgccccgcgcccctgctcccccggcccacgcggccggggccgcccgcc
Q96PR1_HUMAN 148 VEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGDDEDLAAKRLGIEDAA
VEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGDDEDLAAKRLGIEDAA
VEPCCWMTYRQHRDAEEALDIFETPDLIGGDPGDDEDLAAKRLGIEDAA
AY118169_2 442 ggctttaatccccgggggcgatgacgcagggcgggggcggaacgagggg
tacgggtcagaagacaactattaccattggacgaaaatccagtgtaacc
ggcccggccggccccggggcccgcccctcccccccgcggcgggccgcgg
Q96PR1_HUMAN 197 GLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILVSITT
GLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILVSITT
GLGGPDGKSGRWRRLQPRMWALFEDPYSSRAARFIAFASLFFILVSITT
AY118169_2 589 gcggcggatgctaaccccatgctggctttaggatagtgttttacgtaaa
gtggcagacgggggtacgtgcttaacaccgccgttctccttttttctcc
gcgccccatccgggggccggcccacccgcaccgttttttacccgtatat
Q96PR1_HUMAN 246 FCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFT
FCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFT
FCLETHEAFNIVKNKTEPVINGTSVVLQYEIETDPALTYVEGVCVVWFT
AY118169_2 736 ttcgacggtaagaaaagcgaagaaggcctgagagcgtatggggtggtta
tgtacaactattaaacacttagcgtttaaatacacctcatagtgttgtc
tcgaatatctttacgaaacctcatttagtatagttcggtaaagtgggtt
Q96PR1_HUMAN 295 FEFLVRIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDV
FEFLVRIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDV
FEFLVRIVFSPNKLEFIKNLLNIIDFVAILPFYLEVGLSGLSSKAAKDV
AY118169_2 883 tgttgcagttcaacgtaaactaaagtggacctttgggcagcttaggagg
tatttgtttccaatattaattattattcttctatatgtggtccaccaat
tatacttttactataccatcgtctctgccatccaggactggacattatg
Q96PR1_HUMAN 344 LGFLRVVRFVRILRIFKLTRHFVGLRVLGHTLRASTNEFLLLIIFLALG
LGFLRVVRFVRILRIFKLTRHFVGLRVLGHTLRASTNEFLLLIIFLALG
LGFLRVVRFVRILRIFKLTRHFVGLRVLGHTLRASTNEFLLLIIFLALG
AY118169_2 1030 cgtcaggatgaacaatacacctggcagcgcaccgaaagttccaatcgcg
tgttgttgttgttgttatcgattgtgttgactgcgcaattttttttctg
tcccggagtggcgatcgcccttatgggtatttattttatgggatcgtaa
Q96PR1_HUMAN 393 VLIFATMIYYAERVGAQPNDPSASEHTQFKNIPIGFWWAVVTMTTLGYG
VLIFATMIYYAERVGAQPNDPSASEHTQFKNIPIGFWWAVVTMTTLGYG
VLIFATMIYYAERVGAQPNDPSASEHTQFKNIPIGFWWAVVTMTTLGYG
AY118169_2 1177 gtatgaaattggagggccagctgagcactaaacagtttgggaaaacgtg
ttttccttaacagtgcacaacccgaacataatctgtggcttctcctgag
tgattcgcctcgagatatcctattgcagcactctgcggtagcgtcgttg
Q96PR1_HUMAN 442 DMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYSLAMAKQKLP
DMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYSLAMAKQKLP
DMYPQTWSGMLVGALCALAGVLTIAMPVPVIVNNFGMYYSLAMAKQKLP
AY118169_2 1324 gatccattgacgggctgcgggcaagacgcgagaatgattttgagacacc
atacacgcgtttgctgctcgttctctctctttaatgtaactctcaaatc
tgccaagacgggacgttgtaggaacgagtctctttagcccgagaggata
Q96PR1_HUMAN 491 RKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSV
RKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSV
RKRKKHIPPAPQASSPTFCKTELNMACNSTQSDTCLGKDNRLLEHNRSV
AY118169_2 1471 aaaaacaccgccgatcattaagtaagtaaacagatcgagacccgcaatg
gagaaatccccacgccctgacatatcgagcagacgtgaaagttaaagct
gaaggccttttgacatttcgaaatgccttagtcatgcactatgatcaag
Q96PR1_HUMAN 540 LSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASD
LSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASD
LSGDDSTGSEPPLSPPERLPIRRSSTRDKNRRGETCFLLTTGDYTCASD
AY118169_2 1618 ttgggaagagccctccgaccaactaaagaaaaggattccaaggtatgtg
tcgaagcggacctcccagtctggcgcgaaagggacgtttccgaacgcca
aatcctaatggaaacaagcccacttcacacaagaatcaggattcgtttt
Q96PR1_HUMAN 589 GGIRKGYEKSRSLNNIAGLAGNALRLSPVTSPYNSPCPLRRSRSPIPSI
GGIRKGYEKSRSLNNIAGLAGNALRLSPVTSPYNSPCPLRRSRSPIPSI
GGIRKGYEKSRSLNNIAGLAGNALRLSPVTSPYNSPCPLRRSRSPIPSI
AY118169_2 1765 ggaaagtgatcataaaggtggagcactcgatctatctccactctcacta
ggtgagaaacggtaatcgtcgactgtcctcccaaccgctggcgcctcct
agcgaataacacaccagcgacttggctaaaacccttttggctatccatc
Q96PR1_HUMAN 638 L
L
L
AY118169_2 1912 t
t
g
//
cmbi.kun.nl), 30-Jun-2005