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: O76457_APLCA
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF069526_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 1280.41 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.
O76457_APLCA 1 MNLNLADADNRVIINVGGIRHETYKATLKKIPATRLSRLTEALANYDPV
MNLNLADADNRVIINVGGIRHETYKATLKKIPATRLSRLTEALANYDPV
MNLNLADADNRVIINVGGIRHETYKATLKKIPATRLSRLTEALANYDPV
AF069526_2 1 aacacggggacgaaagggaccgatagacaaacgacctccaggtgatgcg
tatatcacaagtttatggtgaacaacctaatcccgtcgtcactcaaact
gtgcggcgcccccccgccatcgccgcgcgacccgccttgggcgcctccc
O76457_APLCA 50 LNEYFFDRHPGVFAQILNYYRSGKLHYPTDVCGPLFEEELEFWGLDSNQ
LNEYFFDRHPGVFAQILNYYRSGKLHYPTDVCGPLFEEELEFWGLDSNQ
LNEYFFDRHPGVFAQILNYYRSGKLHYPTDVCGPLFEEELEFWGLDSNQ
AF069526_2 148 cagtttgcccggtgcacattctgacctcaggtgcctgggcgttgcgtac
taaattagacgttcattaaagcgataaccatggcttaaatatggtacaa
ccaccccccgcgcggccccccgaggccggccccggcgagggcgggcccg
O76457_APLCA 99 VEPCCWMTYTQHRDTQDVLAILDRLDLDTDKPTEEDIMKKFGLEEEYKS
VEPCCWMTYTQHRDTQDVLAILDRLDLDTDKPTEEDIMKKFGLEEEYKS
VEPCCWMTYTQHRDTQDVLAILDRLDLDTDKPTEEDIMKKFGLEEEYKS
AF069526_2 295 ggctttaatacccgacggtgacgccgcgagacagggaaaatgcgggtat
tacgggtcacaagacaattcttagtatacaaccaaattaatgtaaaaac
ggaccggcccgcgccgcggactcggtgcacgcgggccgggccggggcac
O76457_APLCA 148 GELNCWQRIQPKIWALFDEPYSSTAAKIIAVISVFFIVISILSFCLKTH
GELNCWQRIQPKIWALFDEPYSSTAAKIIAVISVFFIVISILSFCLKTH
GELNCWQRIQPKIWALFDEPYSSTAAKIIAVISVFFIVISILSFCLKTH
AF069526_2 442 ggcattccaccaatgttggctttaggaaaggatgttagatactttcaac
gataggagtacatgcttaacacccccattcttcttttttcttctgtaca
gacccgagagaacgggtcgccagttcgccagtcgtcccccccgccggtc
O76457_APLCA 197 PEMRVPVLKNATSRTVNGTYTWRLEKKETEPHEAFFYIECASNAWFTFE
PEMRVPVLKNATSRTVNGTYTWRLEKKETEPHEAFFYIECASNAWFTFE
PEMRVPVLKNATSRTVNGTYTWRLEKKETEPHEAFFYIECASNAWFTFE
AF069526_2 589 cgacgcgtaagatcagagatatctgaagagccggtttagtgtagttatg
catgtcttaacccgctagcacggtaaaacacaacttatagccacgtcta
aggagtgggcccggtccaccagcgggagcgtcggtcccgctgccgctcg
O76457_APLCA 246 IIIRFVVAPNKLDFLKAPVNIIDIVATLSFYLDFMLTELKQESDMLEFF
IIIRFVVAPNKLDFLKAPVNIIDIVATLSFYLDFMLTELKQESDMLEFF
IIIRFVVAPNKLDFLKAPVNIIDIVATLSFYLDFMLTELKQESDMLEFF
AF069526_2 736 aaactgggcaacgtcagcgaaagaggacattcgtacagcacgagacgtt
tttgtttccaatattacctattattcctgtatatttcataaagattatt
ctactgggccacccgagcgccaccgctgccctccgctgagggctgcact
O76457_APLCA 295 SIIRIMRLCKLTRHSAGLKILIHTFKASAKELILLIFFLVLGIVIFAAL
SIIRIMRLCKLTRHSAGLKILIHTFKASAKELILLIFFLVLGIVIFAAL
SIIRIMRLCKLTRHSAGLKILIHTFKASAKELILLIFFLVLGIVIFAAL
AF069526_2 883 taacaaactacacctggcaacacatagagagcaccattcgcgagatggc
cttgttgtgatcgaccgtatttactacgcaattttttttttgttttcct
tccacgggcgccccgtccgtcccccactgggcccgtccctgttcccctc
O76457_APLCA 344 IYYAERIQYNPENDFESIPVGLWWAIVTMTTVGYGDMAPKTYVGMFVGA
IYYAERIQYNPENDFESIPVGLWWAIVTMTTVGYGDMAPKTYVGMFVGA
IYYAERIQYNPENDFESIPVGLWWAIVTMTTVGYGDMAPKTYVGMFVGA
AF069526_2 1030 attggaactacgagtgaacggcttgagaaaaggtggagcaatggatggg
taacagtaaacaaatagtctgtggcttctcctgagatccacatgtttgc
cccgggagccggcctgttcgtcggccccgacgccccggaggcgcgtgct
O76457_APLCA 393 LCALAGVLCIALPVPVIVSNFALFYSHTQARSKLPKKRRRVLPVEAPRP
LCALAGVLCIALPVPVIVSNFALFYSHTQARSKLPKKRRRVLPVEAPRP
LCALAGVLCIALPVPVIVSNFALFYSHTQARSKLPKKRRRVLPVEAPRP
AF069526_2 1177 ctgcgggttagccgcgagtatgctttcacgataccaacccgccgggccc
tgctcgttgtctctctttcatcttacacacgcatcaagggttctaccgc
gttagcggcctgcgcccgcccgctcgcagcgcggcgggaaggtgggtgt
O76457_APLCA 442 KGSKAPGMPGGGGGVGGPQNRRMNAIKHNHPGALDVKMNRIAHGGALQE
KGSKAPGMPGGGGGVGGPQNRRMNAIKHNHPGALDVKMNRIAHGGALQE
KGSKAPGMPGGGGGVGGPQNRRMNAIKHNHPGALDVKMNRIAHGGALQE
AF069526_2 1324 agtagcgacggggggggccacaaagaacaccggcggaaaaagcgggccg
agcaccgtcgggggtggcaaggtactaaaacgctatatagtcaggctaa
atcatgcgaagctcgcacgcgggcccaccccgggccggcgattttagag
O76457_APLCA 491 LMPFRNNQSSSGALSGLLVAPSRR
LMPFRNNQSSSGALSGLLVAPSRR
LMPFRNNQSSSGALSGLLVAPSRR
AF069526_2 1471 tactcaactttggctgccggcaca
ttctgaaacccgctcgtttccggg
ggccttcaatcgtcgtggggcccg
//
cmbi.kun.nl), 30-Jun-2005