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: KCND3_RABIT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF493549_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 1344.74 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
KCND3_RABIT 73 FFFNEDTKEYFFDRDPEVFRCVLNFYRTGKLHYPRYECISAYDDELAFY
FFFNEDTKEYFFDRDPEVFRCVLNFYRTGKLHYPRYECISAYDDELAFY
FFFNEDTKEYFFDRDPEVFRCVLNFYRTGKLHYPRYECISAYDDELAFY
AF493549_2 3 tttaggaagtttgcgcggtctgcattcagacctcctgtatgtgggcgtt
tttaaacaaattagacattggttatagcgataacgaagtccaaaatcta
ccccgccggcccccccgccccgcccccccggccgccgccgccccggccc
KCND3_RABIT 122 GILPEIIGDCCYEEYKDRKRENAERLMDDNDSENNQESMPSLSFRQTMW
GILPEIIGDCCYEEYKDRKRENAERLMDDNDSENNQESMPSLSFRQTMW
GILPEIIGDCCYEEYKDRKRENAERLMDDNDSENNQESMPSLSFRQTMW
AF493549_2 150 gaccgaaggtttggtagcaagaggccaggagtgaacgtactcatccaat
gttcattgaggaaaaaagagaacagttaaaacaaaaactcctgtgactg
ccgcgctcccccggcgccgggccgccgccccggccggcgggccccgcgg
KCND3_RABIT 171 RAFENPHTSTLALVFYYVTGFFIAVSVITNVVETVPCGTVPGSKELPCG
RAFENPHTSTLALVFYYVTGFFIAVSVITNVVETVPCGTVPGSKELPCG
RAFENPHTSTLALVFYYVTGFFIAVSVITNVVETVPCGTVPGSKELPCG
AF493549_2 297 cgtgaccaaacgcgtttgagttaggtgaaagggagctgagcgaagcctg
gctaacacgctctttaatcgtttctcttcattactcggctcggaatcgg
cccgccccccgcgcccccgccccccgccccggggggccggcgcggggcc
KCND3_RABIT 220 ERYSVAFFCLDTACVMIFTVEYLLRLFAAPSRYRFIRSVMSIIDVVAIM
ERYSVAFFCLDTACVMIFTVEYLLRLFAAPSRYRFIRSVMSIIDVVAIM
ERYSVAFFCLDTACVMIFTVEYLLRLFAAPSRYRFIRSVMSIIDVVAIM
AF493549_2 444 gcttggtttcgagtgaataggtcccctggcactctacagaaaaggggaa
agactcttgtaccgttttctaattgttcccggagttggttgttattctt
gccggccccgcgcccgcccgacgggcccgccccccccccgccacggccg
KCND3_RABIT 269 PYYIGLVMTNNEDVSGAFVTLRVFRVFRIFKFSRHSQGLRILGYTLKSC
PYYIGLVMTNNEDVSGAFVTLRVFRVFRIFKFSRHSQGLRILGYTLKSC
PYYIGLVMTNNEDVSGAFVTLRVFRVFRIFKFSRHSQGLRILGYTLKSC
AF493549_2 591 cttagcgaaaagggtggtgaccgtcgtcatattcctcgccacgtacaat
caatgtttcaaaatcgcttctgttgttgttatcgacagtgttgactagg
ctcatgcgcccgcgcggccggcccccccccgccccggcgccgccgcgcc
KCND3_RABIT 318 ASELGFLLFSLTMAIIIFATVMFYAEKGSSASKFTSIPASFWYTIVTMT
ASELGFLLFSLTMAIIIFATVMFYAEKGSSASKFTSIPASFWYTIVTMT
ASELGFLLFSLTMAIIIFATVMFYAEKGSSASKFTSIPASFWYTIVTMT
AF493549_2 738 gtgcgtccttcaagaaatgagattggagttgaataaacgttttaagaaa
ccatgttttctctcttttcctttacaagcccgatcgtccctgacttctc
cggcccccccccgcccccctggtccggcccccgcgccgcctgcccccgc
KCND3_RABIT 367 TLGYGDMVPKTIAGKIFGSICSLSGVLVIALPVPVIVSNFSRIYHQNQR
TLGYGDMVPKTIAGKIFGSICSLSGVLVIALPVPVIVSNFSRIYHQNQR
TLGYGDMVPKTIAGKIFGSICSLSGVLVIALPVPVIVSNFSRIYHQNQR
AF493549_2 885 acgtggagcaaaggaatgtattcaggcgagccgcgagtatacatccaca
ctgagattcactcgattgctgctggttttctctctttcatggtaaaaag
cgatacggcgataggcccccccgtccggtcgaccgttccccgtccgcga
KCND3_RABIT 416 ADKRRAQKKARLARIRVAKTGSSNAYLHSKRNGLLNEALELTGTPEEEH
ADKRRAQKKARLARIRVAKTGSSNAYLHSKRNGLLNEALELTGTPEEEH
ADKRRAQKKARLARIRVAKTGSSNAYLHSKRNGLLNEALELTGTPEEEH
AF493549_2 1032 ggacagcaagccgaacggaagatagtccaacagccaggcgcagacgggc
caaggcaaacgtcgtgtcacggcacatagagagttaactatcgccaaaa
ttacgaagacctcgccgcagccccccgccgccgcccggggggtctgggc
KCND3_RABIT 465 MGKTASLIESQHHHLLHCLEKTTGLSYLVDDPLLSVRTSTIKNHEFIDE
MGKTASLIESQHHHLLHCLEKTT-------------------NHEFIDE
MGKTASLIESQHHHLLHCLEKTT-------------------NHEFIDE
AF493549_2 1179 agaagtcagaccccccctcgaaa acgtagg
tgacccttagaaaattagtaacc aaattaa
gcgccaccgcgctcggccggact ccgcttg
*** !!!!!!!!!!!!!!!!!!!
KCND3_RABIT 514 QMFEQNCMESSMQNYPSTRSPSLSSHAGLTTTCCSRRSKKTTHLPNSNL
QMFEQNCMESSMQNYPSTRSPSLSSHAGLTTTCCSRRSKKTTHLPNSNL
QMFEQNCMESSMQNYPSTRSPSLSSHAGLTTTCCSRRSKKTTHLPNSNL
AF493549_2 1269 catgcatagatacatctaaactctacggcaaatttccaaaaacccatac
attaaagtagctaaacccggcctcgacgtcccggcgggaaccatcacat
ggcggccggcgggccgccgtcggcccgcccccccccctggcacgccccg
KCND3_RABIT 563 PATRLRSMQELSTIHIQGSEQPSLTTSRSSLNLKADDGLRPNCKTSQIT
PATRLRSMQELSTIHIQGSEQPSLTTSRSSLNLKADDGLRPNCKTSQIT
PATRLRSMQELSTIHIQGSEQPSLTTSRSSLNLKADDGLRPNCKTSQIT
AF493549_2 1416 cgacccaacgcaaacacgagcctcaaactacacaggggcacataatcaa
cccgtggtaatgctataggaacctccggcgtatacaagtgcagaccatc
actggccgggccccccgccggccccctcccttgaaccagaaccaacgcc
KCND3_RABIT 612 TAIISIPAPPALTPEGETRPPPASPGPNTNIPSI
TAIISIPAPPALTPEGETRPPPASPGPNTNIPSI
TAIISIPAPPALTPEGETRPPPASPGPNTNIPSI
AF493549_2 1563 agaaaacgccgcacgggaccccgacgcaaaacta
ccttgtccccctccagacgccccgcgcacatcct
ccccccttcagacagcgtgactccacccgcttca
//
cmbi.kun.nl), 28-Jun-2005