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_CAVPO
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence CCGI2PAS2_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 872.45 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_CAVPO 1 GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
GCTVSAEDKAAAERSKMIDKNLREDGEKAAREVKLLLLGAGESGKSTIV
CCGI2PAS2_2 4 gtagagggaggggctaaagaaccggggaggcggatcctggggtgaaaag
ggctgcaaacccagcattaaatgaagaaccgatattttgcgacgagctt
gccgtcgcgggcgccggccgcgggccgggggggggtgatttggggcccc
GNAI2_CAVPO 50 KQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPL
KQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPL
KQMKIIHEDGYSEEECRQYRAVVYSNTIQSIMAIVKAMGNLQIDFADPL
CCGI2PAS2_2 151 acaaaacgggttgggtcctcgggtaaaactaagagagagaccagtggcc
aatattaaagacaaaggaagcttagactacttcttactgatatatcact
agggcctatctagggtggcggcccctccgccgcccgcgccggtctcccc
GNAI2_CAVPO 99 RADDARQLFALSCTAEEQGMLPEDLSGVIRRLWADHGVQACFSRSREYQ
RADDARQLFALSCTAEEQGMLPEDLSGVIRRLWADHGVQACFSRSREYQ
RADDARQLFALSCTAEEQGMLPEDLSGVIRRLWADHGVQACFSRSREYQ
CCGI2PAS2_2 298 cggggacctgcttagggcgaccggctggacactggcggcgttactagtc
gcaacgattctcgccaaagttcaatcgttggtgcaagtacgtggcgaaa
tgcccgggtagtcttggacgctgcgccccggcgtcttggcccccaaacg
GNAI2_CAVPO 148 LNDSAAYYLNDLDRIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
LNDSAAYYLNDLDRIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
LNDSAAYYLNDLDRIAQSDYIPTQQDVLRTRVKTTGIVETHFTFKDLHF
CCGI2PAS2_2 445 cagtggttcagcgcagcagtacaccggccacgaaagaggactatagcct
taacccaataatagtcagaatccaaattgcgtaccgttacatctaatat
cctatcccgtcgtatagtccccaggtgggctggcgttgaaccccgtacc
GNAI2_CAVPO 197 KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSAYDLVLAEDEEMNRMHE
CCGI2PAS2_2 592 aatggggcctgaaatacttgggagaattggtagtgtgcgggggaacacg
attatggagcagaagtagtagtcctttgtctgcaatttcaaaatagtaa
ggttattggtgggggccccgtcacccctacgtgtcggatgtgggccgtg
GNAI2_CAVPO 246 SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGAN
SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGAN
SMKLFDSICNNKWFTDTSIILFLNKKDLFEEKITHSPLTICFPEYTGAN
CCGI2PAS2_2 739 aaactgaataaattagataactcaaagctggaaacaccaattcgtagga
gtattagtgaaagtcacctttttaaaattaaatcagctctgtcaacgca
cgggtccctccagcgcacccccccggcgtgggcaccggccccagcaacc
GNAI2_CAVPO 295 KYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
KYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
KYDEAASYIQSKFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVI
CCGI2PAS2_2 886 atggggatacaatggcaacagaagatactatgagaaagctgtgggagga
aaaaccgatagataataagaacaatacatcgccacaatatttactcatt
gttgaccccgtgtacgtacaccggccactgtccccgcggtgtttcctcc
GNAI2_CAVPO 344 IKNNLKDCGLF
IKNNLKDCGLF
IKNNLKDCGLF
CCGI2PAS2_2 1033 aaaacagtgct
taaataaggtt
cgccggccccc
//
cmbi.kun.nl), 24-May-2005