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: GNAO_CAEEL
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence CEGOA1_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 860.67 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: mismatch(es) found
GNAO_CAEEL 1 GCTMSQEERAALERSRMIEKNLKEDGMQAAKDIKLLLLGAGESGKSTIV
GCTMSQEERAALERSRMIEKNLKEDGMQAAKDIKLLLLGAGESGKSTIV
GCTMSQEERAALERSRMIEKNLKEDGMQAAKDIKLLLLGAGESGKSTIV
CEGOA1_2 4 gtaatcggcggcgatcaagaacagggacggagaaccccggggtgataag
ggctcaaagcctagcgttaaataaagtaccaatattttgcgacgacctt
ttcgagagtcttaaaagtgattaaccgagaatcaggattaaaaaagtta
GNAO_CAEEL 50 KQMKIIHESGFTAEDYKQYKPVVYSNTVQSLVAILRAMSNLGVSFGSAD
KQMKIIHESGFTAEDYKQYKPVVYSNTVQSLVAILRAMSNLGVSFGSAD
KQMKIIHESGFTAEDYKQYKPVVYSNTVQSLVAILRAMSNLGVSFGSAD
CEGOA1_2 151 acaaaacgtgtagggtactacggtaaagcttggatcgaaatggttgtgg
aatattaacgtccaaaaaaacttagactacttcttgctgatgtctgcca
aggattcaaacaaaccagcggtcctcgtaagcttgccgccactattgtc
GNAO_CAEEL 99 REVDAKLVMDVVARMEDTEPFSEELLSSMKRLWGDAGVQDCFSRSNEYQ
REVDAKLVMDVVARMEDTEPFSEELLSSMKRLWGDAGVQDCFSRSNEYQ
REVDAKLVMDVVARMEDTEPFSEELLSSMKRLWGDAGVQDCFSRSNEYQ
CEGOA1_2 298 aggggatgaggggcaggagcttggtcataacttgggggcgtttaaagtc
gatacatttattcgtaacactcaattgctagtggacgtaagtcggaaaa
agataaaggtggaaggcagacaaagctagagggacatagttcagtcgta
GNAO_CAEEL 148 LNDSAKYFLDDLERLGEAIYQPTEQDILRTRVKTTGIVEVHFTFKNLNF
LNDSAKYFLDDLERLGEAIYQPTEQ-ILRTRVKTTGIVEVHFTFKNLNF
LNDSAKYFLDDLERLGEAIYQPTEQHILRTRVKTTGIVEVHFTFKNLNF
CEGOA1_2 445 tagtgattcggcgatgggatccagccaccacgaaagagggctataacat
taaccaattaatagtgactaaccaaattgcgtaccgttatatctaatat
gttacatctccgagaagaataatgattcattcaattttatccacatctc
*** !
GNAO_CAEEL 197 KLFDVGGQRSERKKWIHCFEDVTAIIFCVAMSEYDQVLHEDETTNRMHE
KLFDVGGQRSERKKWIHCFEDVTAIIFCVAMSEYDQ+LHEDETTNRMHE
KLFDVGGQRSERKKWIHCFEDVTAIIFCVAMSEYDQLLHEDETTNRMHE
CEGOA1_2 592 attggggcatgaaatacttgggagaattggatgtgcctcgggaaacacg
attatggagcagaagtagtaatcctttgtctcaaaattaaaaccagtaa
agctgataaaaggggtttcattttttcttcgagttaggcatgaacagca
*** !
GNAO_CAEEL 246 SLKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICFPEYSGRQ
SLKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICFPEYSGRQ
SLKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICFPEYSGRQ
CEGOA1_2 739 tcactgtataaattagataactcaaagctggaaaaactaattcgttgcc
ctattactgaaagtcacctttttaaaattaaataagctctgtcaacgga
ggggctgcttcagcatagttgcgcggtgtagacgacgagcccaataaaa
GNAO_CAEEL 295 DYHEASAYIQAQFEAKNKSANKEIYCHMTCATDTTNIQFVFDAVTDVII
DYHEASAYIQAQFEAKNKSANKEIYCHMTCATDTTNIQFVFDAVTDVII
DYHEASAYIQAQFEAKNKSANKEIYCHMTCATDTTNIQFVFDAVTDVII
CEGOA1_2 886 gtcggtgtacgctggaaatgaagattcaatgagaaaactgtgggaggaa
aaaacccatacatacaaaccaaatagatcgccaccatatttactcattt
cccgatgttaaatgtacaagtaactccgatcacatctatgtctcctgtt
GNAO_CAEEL 344 ANNLRGCGLY
ANNLRGCGLY
ANNLRGCGLY
CEGOA1_2 1033 gaaccgtgtt
caatggggta
cttttaccgt
//
cmbi.kun.nl), 24-May-2005