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: GNAI2_CANFA
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AY563036_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 873.03 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.
GNAI2_CANFA 1 GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
AY563036_2 4 gtagagggaggggctaaagaaccggggaggcggatcctggggtgaaaag
ggctgcaaacccagcattaaatgaagaaccgatattttgcgacgagctt
cccgtcgcgggcaccggccgcggacgggggggggggtgttggaggcctc
GNAI2_CANFA 50 KQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFDDPS
KQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFDDPS
KQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFDDPS
AY563036_2 151 acaaaacgggttgggtcctcgggtaaaactaagagagagaccagtggct
aatattaaagacaaaggaagcttagactacttcttactgatatataacc
ggggcccgtccaggacggcggcccccccgtcgttcacgctggtcttccc
GNAI2_CANFA 99 RADDARQLFALSCTAEEQGVLPEDLSCVIRRLWADNGVQACFGRSREYQ
RADDARQLFALSCTAEEQGVLPEDLSCVIRRLWADNGVQACFGRSREYQ
RADDARQLFALSCTAEEQGVLPEDLSCVIRRLWADNGVQACFGRSREYQ
AY563036_2 298 cggggacttgcttagggcggccggcttgacactggaggcgttgctcgtc
gcaacgattctcgccaaagttcaatcgttggtgcaagtacgtggcgaaa
agtttgggtagtcttgggtgctgtgttccggcgtcctggcctcccggcg
GNAI2_CANFA 148 LNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
LNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
LNDSAAYYLNDLERIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
AY563036_2 445 cagtggttcagcgcagcagtacaccggccacgaaagaggactatagcct
taacccaataatagtcagaatccaaattgcgtaccgttacatctaatat
cccctcccgtcggctagtccccaggcgagctggcgccgggccccgtgcc
GNAI2_CANFA 197 KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
AY563036_2 592 aatggggcctgcaatacttgggagaattggtagtgcgcgggggaacacg
attatggagcagaagtagtagtcctttgtctgcaatttcaaaatagtaa
ggttgttggtgggggccctgtcgcccctacgcctcggatgtgggccgtg
GNAI2_CANFA 246 SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGAN
SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGAN
SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGAN
AY563036_2 739 aaactgaataaattagataactcaaagctggaaacaccaattcgtagga
gtattagtgaaagtcacctttttaaaattaaatcagctctgtcaacgca
cgggtctccccggcacgcccccccggcgtgggcacccgcccctgcagcc
GNAI2_CANFA 295 KYEEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
KYEEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
KYEEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
AY563036_2 886 atggggatacaatggcaacagaagatactatgagaaagctgtgggagga
aaaaccgatagataataagaacaatacatcgccacaatatttactcatt
gtggaccccgtgtgcgcgcgtcggccgccgcctccgcggtgttcctccc
GNAI2_CANFA 344 IKNNLKDCGLF
IKNNLKDCGLF
IKNNLKDCGLF
AY563036_2 1033 aaaacagtgct
taaataaggtt
cgccggccccc
//
cmbi.kun.nl), 24-May-2005