2005, NucleaRDB.
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: Q866S0_CAPHI
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AY178574_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 1173.63 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.
Q866S0_CAPHI 1 MVDTEMPFWPTNFGISSVDLSMMDDHSHAFDIKPFTTVDFSSISAPHYE
MVDTEMPFWPTNFGISSVDLSMMDDHSHAFDIKPFTTVDFSSISAPHYE
MVDTEMPFWPTNFGISSVDLSMMDDHSHAFDIKPFTTVDFSSISAPHYE
AY178574_2 1 aggagacttcaatgaatggctaaggctcgtgaactaaggttaatgcctg
ttacatctgccatgtgctatcttaaacactatactcctatcgtcccaaa
gtcagggtgccctgcccgcttggtccctcttcgcccctcccctctgccg
Q866S0_CAPHI 50 DIPFPRADPMVADYKYDLKLQEYQSAIKVEPVSPPYYSEKTQLYSKPHE
DIPFPRADPMVADYKYDLKLQEYQSAIKVEPVSPPYYSEKTQLYSKPHE
DIPFPRADPMVADYKYDLKLQEYQSAIKVEPVSPPYYSEKTQLYSKPHE
AY178574_2 148 gactcaggcagggtatgcaccgtcagaaggcgtcctttgaacctaaccg
atctcgcacttcaaaaatataaaagctatactcccaacaacatagacaa
ctgcaatcggtattgtcggcagcatacaggtacattttagtggctgtta
Q866S0_CAPHI 99 EPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD
EPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD
EPSNSLMAIECRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLIYDRCD
AY178574_2 295 gctatcagagtcgtggagtgtctggcgtggtagttcaaaatacatgatg
accacttctaggtggaaccgtaagtacgaggagttggctgtattaagga
gtccccgctgcgctgtagagcctattttaacgtccgggcagattttgtt
Q866S0_CAPHI 148 LYCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEIS
LYCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEIS
LYCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEIS
AY178574_2 442 cttcacaaaaaatcttctcatcgggatcagaatgcaccggagactggat
taggtaaaggaagaaggtaagtctgtcaactgtggtcacaaaattcatc
tctgccgatatacgccacggcttgggttcccgcgcgagcggagaaggcc
Q866S0_CAPHI 197 SDIDQLNPESADLRALAKHLYDSYIKSFPLTRAKARAILTGKTTDKSPF
SDIDQLNPESADLRALAKHLYDSYIKSFPLTRAKARAILTGKTTDKSPF
SDIDQLNPESADLRALAKHLYDSYIKSFPLTRAKARAILTGKTTDKSPF
AY178574_2 589 agagccacgtggccgcgacttgttaattccaagagagatagaaagatct
gataatacaccatgctcaataacatactctcgcacgcttcgaccaacct
ccccagcagttccgcgagtgtcgcagccggcagggggcggaggacaagt
Q866S0_CAPHI 246 VIYDMNSLMMGEDKIKFKHISPLQEPSKEVAIRIFQGCQFRSVEAVQEI
VIYDMNSLMMGEDKIKFKHISPLQEPSKEVAIRIFQGCQFRSVEAVQEI
VIYDMNSLMMGEDKIKFKHISPLQEPSKEVAIRIFQGCQFRSVEAVQEI
AY178574_2 736 gatgaattaagggaaatacaacccgcaagggacatcgtctctggggcga
ttaatactttgaaatataatgctaacgaatctgttaggatgctactaat
tctcgccaggaatacgcgccccgggccaggcccccggtgtccgacgggc
Q866S0_CAPHI 295 TEYAKNIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQ
TEYAKNIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQ
TEYAKNIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQ
AY178574_2 883 agtgaaacgtgacgtagcgaccatggcgaataacgttaaagggcatggc
caacaatcgttatataaatcttaagtaattacttccttaaagtttcaga
agccgtccttgctcgccaatcaaccgcgctcgggccggcgtgccacgca
Q866S0_CAPHI 344 GFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILS
GFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILS
GFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILS
AY178574_2 1030 gtaaagtcaaccactggtagcatgtggatagcgtggagtgataggaaca
gttcgattagtgactgattacatatctatactataagatctttcttttg
acgaggtagcgagcttctggcgcgttggccagaatcccaaatatcttct
Q866S0_CAPHI 393 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLR
GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLR
GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLR
AY178574_2 1177 ggccgtcagacaggacgatccgtgcccacaccgttcctgatccaaagca
gagcgttatactaataaattactatatataacaccattcattaatcatg
accatggtggctgcaaccgggcggggcggcccgccgctcggcgaggccg
Q866S0_CAPHI 442 QIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
QIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
QIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
AY178574_2 1324 cagagcgccccgaaaagagaaccccccgatagtt
attcaatattattaacacatgtacttaataaata
gtgagcggggaaagaaggcgtccatagaccgcgt
//
cmbi.kun.nl), 18-Feb-2005