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_MOUSE
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence S71213_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 819.68 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.
Warning: protein length=354 (x3=1062) and cDNA length=1002
Warning: mismatch(es) found
GNAI2_MOUSE 22 LREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECRQYRA
LREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECRQYRA
LREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEDGYSEEECRQYRA
S71213_3 1 ccggggaggcggatcctggggtgaaaagacaaaacgggttgggtcctcg
tgaagaaccgatattttgcgacgagcttaatattaaagacaaaggaagc
gggccgggggggggtgattagaggccccggggcctatccaaggcggctc
GNAI2_MOUSE 71 VVYSNTIQSILAIVKAMGNLQIDFADPQRADDARQLFALSCAAEEQGML
VVYSNTIQSI+AIVKAMGNLQIDFADPQRADDARQLFALSCAAEEQGML
VVYSNTIQSIIAIVKAMGNLQIDFADPQRADDARQLFALSCAAEEQGML
S71213_3 148 ggtaaaactaagagagagaccagtggcccggggacctgcttggggcgac
ttagactacttcttactgatatatcacagcaacgattctcgccaaagtt
gccccccgtccccggcgccggcctttcgtgttcgggccgcttagaaggt
*** !
GNAI2_MOUSE 120 PEDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYI
PEDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYI
PEDLSGVIRRLWADHGVQACFGRSREYQLNDSAAYYLNDLERIAQSDYI
S71213_3 295 cggctggacactggcggcgttgctcgtccagtggttcagcgcagcagta
caatcgttggtgcaagtacgtggcgaaataacccaataatagtcagaat
tacgctccggcgtcctgacctccaaacgctcactccgttggctagtccc
GNAI2_MOUSE 169 PTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEG
PTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEG
PTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEG
S71213_3 442 caccggccacgaaagaggactatagtctaatggggcctgcaatacttgg
ccaaattgcgtaccgttacatctaatatattatggagcagaagtagtag
taggtgggctggcgccgaaccccgcaccggttgttggtgcgggccctgc
GNAI2_MOUSE 218 VTAIIFCVALSAYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIIL
VTAIIFCVALSAYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIIL
VTAIIFCVALSAYDLVLAEDEEMNRMHESMKLFDSICNNKWFTDTSIIL
S71213_3 589 gagaattggtagtgtgcgggggaacacgaaactgaataaattagataac
tcctttgtctgcaatttcaaaatagtaagtattagtgaaagtcaccttt
cgcccctccgcttcgggtgtgggccgtgcgggtccccccggcacccccc
GNAI2_MOUSE 267 FLNKKDLFEEKITQSSLTICFPEYTGANKYDEAASYIQSKFEDLNKRKD
FLNKKDLFEEKITQSSLTICFPEYTGANKYDEAASYIQSKFEDLNKRKD
FLNKKDLFEEKITQSSLTICFPEYTGANKYDEAASYIQSKFEDLNKRKD
S71213_3 736 tcaaagctggaaacatcaattcgtaggaatggggatacaatggcaacag
ttaaaattaaatcagctctgtcaacgcaaaaaccgatagataataagaa
cccggcgtaagcagccgcctctgcggccgccgaccccgcgtgtatgcac
GNAI2_MOUSE 316 TKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
TKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
TKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
S71213_3 883 aagatactatgagaaagctgtgggaggaaaaacagtgct
caatacatcgccacaatatttactcatttaaataaggtt
cggccgccgcccccgcggtgctcctccccgccggctccc
//
cmbi.kun.nl), 24-May-2005