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: Q16976_APLCA
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence ACPOTCHAN_3
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 1424.51 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.
Q16976_APLCA 1 MSTPAVDCQSDRIPLTRPRTGAVPTLRARVKRQATSSYLGSAGCENTPT
MSTPAVDCQSDRIPLTRPRTGAVPTLRARVKRQATSSYLGSAGCENTPT
MSTPAVDCQSDRIPLTRPRTGAVPTLRARVKRQATSSYLGSAGCENTPT
ACPOTCHAN_3 1 aaacgggtctgcactacccagggcaccgagaccgaaattgtggtgaaca
tgccctagacagtctcgcgcgctcctgcgtagaccggatgccggaaccc
gcggcgccaaccccgacccgacgctgggaggtacgcccgcccccgcgct
Q16976_APLCA 50 RLEQADVFVEDGGDERILLNVGGVRHETHVSTLRTVPNSRLSRLAETHL
RLEQADVFVEDGGDERILLNVGGVRHETHVSTLRTVPNSRLSRLAETHL
RLEQADVFVEDGGDERILLNVGGVRHETHVSTLRTVPNSRLSRLAETHL
ACPOTCHAN_3 148 ccgcgggtgggggggaatcaggggacgacgtacaagcatactacggacc
gtaacatttaaggaagtttatggtgaacatcctgctcacgtcgtcacat
cggggtgcggcaccggcgccgcacgcggcgctggtgcccggcagcgtcg
Q16976_APLCA 99 ENGGGRQEYFFDRHPSVFNSIIDFYRTRELHVPLEVCGAVVKRELDFWQ
ENGGGRQEYFFDRHPSVFNSIIDFYRTRELHVPLEVCGAVVKRELDFWQ
ENGGGRQEYFFDRHPSVFNSIIDFYRTRELHVPLEVCGAVVKRELDFWQ
ACPOTCHAN_3 295 gagggacgtttgccctgtataagttaacgccgccggtggggacgcgttc
aaggggaaattagaccttacttatagcgatatctatggcttagatatga
gctcgagacttcccgcgccccctccagcgacctgacccggcgaggccgg
Q16976_APLCA 148 INELEIKACCWRHYRSYIENQHILDSFNHSLLSQAVDVDLNILTGWKKL
INELEIKACCWRHYRSYIENQHILDSFNHSLLSQAVDVDLNILTGWKKL
INELEIKACCWRHYRSYIENQHILDSFNHSLLSQAVDVDLNILTGWKKL
ACPOTCHAN_3 442 aagcgaagtttactcttagaccacgttacaccacgggggcaacagtaac
taatatacggggaagcataaaattactaagttgactatatattcggaat
ccgggcgtccgatcggccgcgccgcgccctgctgcgctcgccggcgggc
Q16976_APLCA 197 QWRVWLVLEYPRTSRLAMIYGVTSFLFVVTSIAGFCLETLPELRPKFLN
QWRVWLVLEYPRTSRLAMIYGVTSFLFVVTSIAGFCLETLPELRPKFLN
QWRVWLVLEYPRTSRLAMIYGVTSFLFVVTSIAGFCLETLPELRPKFLN
ACPOTCHAN_3 589 ctcgtcgtgtcaatacgaatggattttggataggttcgaccgcacatta
aggtgtttaacgccgtcttagtcctttttcctcgtgtactcatgcatta
gggcgcgggcggtcggtgacttggcgtcccaaactcggtcagaacgcgc
Q16976_APLCA 246 VTTECEGGHSRELGRVMTSHEALNTLDIICTVFFTLELILRFIFAPDKR
VTTECEGGHSRELGRVMTSHEALNTLDIICTVFFTLELILRFIFAPDKR
VTTECEGGHSRELGRVMTSHEALNTLDIICTVFFTLELILRFIFAPDKR
ACPOTCHAN_3 736 gaagtgggctagcgcgaatcggtaatgaatagttatgcacatatgcgac
tccagaggacgatggttccaactactattgctttctatttgtttccaag
gatgcaactcgagcggggccgcgtggccattgcctgaaacgtcctccgg
Q16976_APLCA 295 KFIFSLMNVIDLLALVPLYVQVIFTKSDNMQACYLNERFVIEIMFILRI
KFIFSLMNVIDLLALVPLYVQVIFTKSDNMQACYLNERFVIEIMFILRI
KFIFSLMNVIDLLALVPLYVQVIFTKSDNMQACYLNERFVIEIMFILRI
ACPOTCHAN_3 883 atatttaagagttgtgcctgcgataatgaacgttcagctgagaatacaa
atttcttattattcttctatatttcacaatacgataagtttatttttgt
attctggccccagtgggtctggcccggctgggccgcaccgtgcgccgac
Q16976_APLCA 344 IRMFRIFHLVKHYQALKVLVYAIKASIQELLMLFIFLLIGMLIFSTMIY
IRMFRIFHLVKHYQALKVLVYAIKASIQELLMLFIFLLIGMLIFSTMIY
IRMFRIFHLVKHYQALKVLVYAIKASIQELLMLFIFLLIGMLIFSTMIY
ACPOTCHAN_3 1030 acatcatccgactcgcagcgtgaagaacgtcactatccagacattaaat
tgttgttattaaaactatttactacgtaattttttttttgttttcctta
cggcctccgggtcaccgcgacccgctagggcgccctcccggcccccgcc
Q16976_APLCA 393 YAERKNTTEGGDMFSTIPMGFWWSIITMTTVGYGDVYPTTPVGYIVGTA
YAERKNTTEGGDMFSTIPMGFWWSIITMTTVGYGDVYPTTPVGYIVGTA
YAERKNTTEGGDMFSTIPMGFWWSIITMTTVGYGDVYPTTPVGYIVGTA
ACPOTCHAN_3 1177 tggcaaaaggggattaacagtttaaaaaaaggtgggtcaacggtaggag
acagaaccaggattcctctgtgggttctcctgagatacccctgattgcc
ccgggccagcctgcccctgccggccccgaggctgcgctcccgccagcgc
Q16976_APLCA 442 CSVSGVLLVALTIPVISNNFTLFYRHVQSRAAIPRSRGGDSSECDSNFN
CSVSGVLLVALTIPVISNNFTLFYRHVQSRAAIPRSRGGDSSECDSNFN
CSVSGVLLVALTIPVISNNFTLFYRHVQSRAAIPRSRGGDSSECDSNFN
ACPOTCHAN_3 1324 ttgaggccggcaacgataatacttacgctcggacaacgggatgtgtata
gctggttttctctcttcaatcttagatacgcctcgggggagcagacata
cagtcctggtcgcgcaccccacccactagctctgacagtctagctttcc
Q16976_APLCA 491 SEFERSVTRKTSNDSNVLTFVNGHVTGIHFSGSKSRSQQSGGRWSQTGE
SEFERSVTRKTSNDSNVLTFVNGHVTGIHFSGSKSRSQQSGGRWSQTGE
SEFERSVTRKTSNDSNVLTFVNGHVTGIHFSGSKSRSQQSGGRWSQTGE
ACPOTCHAN_3 1471 tgtgatgacaatagtagtatgagcgagacttgaatatcctggcttcagg
catagctcgaccaacattcttagatcgtatcggacgcaacggggcacga
gatggagctatcccactgatgtttgcgttccgcgcgcgggaccgaatta
Q16976_APLCA 540 SASSVSVKKSASDYMFQRNRSFRAYSDDGVMYKGETVV
SASSVSVKKSASDYMFQRNRSFRAYSDDGVMYKGETVV
SASSVSVKKSASDYMFQRNRSFRAYSDDGVMYKGETVV
ACPOTCHAN_3 1618 tgtagtgaatgtgtatcaaattagttggggataggagg
cccgtctaacccaattagagctgcacaagttaagactt
tagctcgaactgttgtgacaccgctacttggcaagtcg
//
cmbi.kun.nl), 30-Jun-2005