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: KCNA1_MOUSE
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence MMPCP1_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 1218.96 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.
KCNA1_MOUSE 1 MTVMSGENADEASTAPGHPQDGSYPRQADHDDHECCERVVINISGLRFE
MTVMSGENADEASTAPGHPQDGSYPRQADHDDHECCERVVINISGLRFE
MTVMSGENADEASTAPGHPQDGSYPRQADHDDHECCERVVINISGLRFE
MMPCP1_2 1 aagatggaggggtagcgcccggatcacggcggcgttgcggaaatgcctg
tcttcgaacaacccccgacaaggacgacaaaaaaggagtttatcgtgta
gggggggtgcgtgctatccgtcccggggcccccaccgcaaccccggcca
KCNA1_MOUSE 50 TQLKTLAQFPNTLLGNPKKRMRYFDPLRNEYFFDRNRPSFDAILYYYQS
TQLKTLAQFPNTLLGNPKKRMRYFDPLRNEYFFDRNRPSFDAILYYYQS
TQLKTLAQFPNTLLGNPKKRMRYFDPLRNEYFFDRNRPSFDAILYYYQS
MMPCP1_2 148 accaacgctcaaccgacaacacttgccaagtttgcaccatggactttct
catactcatcacttgacaagtgatactgaaattagagcgtacttaaaac
ggcgtgagcccgggccggacgcctccggcgcctcccgccctccttccgc
KCNA1_MOUSE 99 GGRLRRPVNVPLDMFSEEIKFYELGEEAMEKFREDEGFIKEEERPLPEK
GGRLRRPVNVPLDMFSEEIKFYELGEEAMEKFREDEGFIKEEERPLPEK
GGRLRRPVNVPLDMFSEEIKFYELGEEAMEKFREDEGFIKEEERPLPEK
MMPCP1_2 295 ggcccacgagccgattggaattgtggggagatcggggtaagggccccga
gggtggctatctattcaatataatgaactaatgaaagttaaaagctcaa
gccgcggccgcgcgccggtatcggcgacgggcgatgcccgaggccacgg
KCNA1_MOUSE 148 EYQRQVWLLFEYPESSGPARVIAIVSVMVILISIVIFCLETLPELKDDK
EYQRQVWLLFEYPESSGPARVIAIVSVMVILISIVIFCLETLPELKDDK
EYQRQVWLLFEYPESSGPARVIAIVSVMVILISIVIFCLETLPELKDDK
MMPCP1_2 442 gtcccgtcctgtcgatgcgcgagagtgagacatagattcgaccgcagga
aaagatgtttaacagcgccgttcttcttttttcttttgtactcataaaa
gcgcggggctgtggcaatcgttctggcgcccccacctcggtctgggccg
KCNA1_MOUSE 197 DFTGTIHRIDNTTVIYTSNIFTDPFFIVETLCIIWFSFELVVRFFACPS
DFTGTIHRIDNTTVIYTSNIFTDPFFIVETLCIIWFSFELVVRFFACPS
DFTGTIHRIDNTTVIYTSNIFTDPFFIVETLCIIWFSFELVVRFFACPS
MMPCP1_2 589 gtagaaccagaaagatataatagcttaggattaattttgcggcttgtca
atcgctagtaaccttaccattcacttttactgttgtctatttgttcgcg
ccgcccccccccaccttccccactcctgacgtccgcttggggccccccc
KCNA1_MOUSE 246 KTDFFKNIMNFIDIVAIIPYFITLGTEIAEQEGNQKGEQATSLAILRVI
KTDFFKNIMNFIDIVAIIPYFITLGTEIAEQEGNQKGEQATSLAILRVI
KTDFFKNIMNFIDIVAIIPYFITLGTEIAEQEGNQKGEQATSLAILRVI
MMPCP1_2 736 aagttaaaaatagaggaacttaacgagaggcggacaggcgatcgacaga
acattaattattattcttcattctgcatcaaagaaagaaccctcttgtt
gacctgccgcccctgcccttctcgcggatgggatggcggctcgcccgcc
KCNA1_MOUSE 295 RLVRVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSA
RLVRVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSA
RLVRVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSA
MMPCP1_2 883 ctgagtaatactcctagccacgcacagaaagtgccattctaggacttag
gttgttgttatcgacagtattgactacgtgatgttttttttgttttcgc
cgaggcaccacccccgctgcgcgccattgggaggcctccctgcagttca
KCNA1_MOUSE 344 VYFAEAEEAESHFSSIPDAFWWAVVSMTTVGYGDMYPVTIGGKIVGSLC
VYFAEAEEAESHFSSIPDAFWWAVVSMTTVGYGDMYPVTIGGKIVGSLC
VYFAEAEEAESHFSSIPDAFWWAVVSMTTVGYGDMYPVTIGGKIVGSLC
MMPCP1_2 1030 gttgggggggtcttaacggtttgggtaaaggtggatcgaaggaaggttt
tatcacaacacatcgtcactggcttctcctgagatactctggattgctg
gctgggaatggccctccttcgggggcgctgactcgctgatacgcgccgt
KCNA1_MOUSE 393 AIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQLLHVSSPNLASDSDL
AIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQLLHVSSPNLASDSDL
AIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQLLHVSSPNLASDSDL
MMPCP1_2 1177 gagggcaagccgcgagtatatttccgaggggcgctccgatcatgtgagc
ctcgttctctctctttcataataagacagaaacattatgccatccagat
ccttggatcgcatctgctcctcccaatggaggtggctttttcactctcc
KCNA1_MOUSE 442 SRRSSSTISKSEYMEIEEDMNNSIAHYRQANIRTGNCTTADQNCVNKSK
SRRSSSTISKSEYMEIEEDMNNSIAHYRQANIRTGNCTTADQNCVNKSK
SRRSSSTISKSEYMEIEEDMNNSIAHYRQANIRTGNCTTADQNCVNKSK
MMPCP1_2 1324 accattaaaatgtagagggaaaaagctacgaaaagataaggcatgaaaa
ggggccctgacaatataaataagtcaagacatgcgagcccaaagtaaga
cccccttccgtgcggcagtgctcactcagttcattcccattaccttgcg
KCNA1_MOUSE 491 LLTDV
LLTDV
LLTDV
MMPCP1_2 1471 ccagg
ttcat
cgctt
//
cmbi.kun.nl), 28-Jun-2005