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: Q28656_RABIT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence OC38240_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 1277.97 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.
Q28656_RABIT 1 MTVVPGDHLLEPEAADGGGGPPQGGGAGCDRYEPLPAGEQECCGERVVI
MTVVPGDHLLEPEAADGGGGPPQGGGAGCDRYEPLPAGEQECCGERVVI
MTVVPGDHLLEPEAADGGGGPPQGGGAGCDRYEPLPAGEQECCGERVVI
OC38240_2 1 aaggcggcccgcggggggggcccgggggtgctgcccgggcgttggcgga
tcttcgaattacaccaggggccagggcggagaactccgaaagggagttt
ggggcgccgggcggcccagcgtgcccgctcccggggcggggccggcgcc
Q28656_RABIT 50 NISGVRFETQLKTLCQFPETLLGDPKRRMRYFDPVRNEYFFDRNRPSFD
NISGVRFETQLKTLCQFPETLLGDPKRRMRYFDPVRNEYFFDRNRPSFD
NISGVRFETQLKTLCQFPETLLGDPKRRMRYFDPVRNEYFFDRNRPSFD
OC38240_2 148 aatggctgaccaactctcgaccggcaccacttgcgcagtttgcaccatg
atcgtgtacatactgatcacttgacaggtgatactgaaattagagcgta
ccgcgccgggcgcccgcaggtgcccggcggcccccccgccccccgcccc
Q28656_RABIT 99 AILYYYQSGGRIRRPVNVPIDIFSEEIRFYQLGEEAMEKFREDEGFLRE
AILYYYQSGGRIRRPVNVPIDIFSEEIRFYQLGEEAMEKFREDEGFLRE
AILYYYQSGGRIRRPVNVPIDIFSEEIRFYQLGEEAMEKFREDEGFLRE
OC38240_2 295 gactttctggcacccgagcagattggacttccggggagatcggggtccg
cttaaaacgggtggctatctattcaatgtaatgaactaatgaaagttga
ccccctgcgccccggccgccccccggccccggcggcgggccgcgccggg
Q28656_RABIT 148 EERPLPRRDFQRQVWLLFEYPESSGPARGIAIVSVLVILISIVIFCLET
EERPLPRRDFQRQVWLLFEYPESSGPARGIAIVSVLVILISIVIFCLET
EERPLPRRDFQRQVWLLFEYPESSGPARGIAIVSVLVILISIVIFCLET
OC38240_2 442 ggccccccgtcccgtcctgtcgatgcgcgagagtgcgacatagattcga
aagctcggatagatgtttaacagcgccggtcttcttttttcttttgtac
gggggcccccgcggggccgctgccggcgccccgcgcccccccccccggg
Q28656_RABIT 197 LPEFRDEKDYPAAPSQDVVEAAGNGTSGAPAGASSFSDPFFVVETLCII
LPEFRDEKDYPAAPSQDVVEAAGNGTSGAPAGASSFSDPFFVVETLCII
LPEFRDEKDYPAAPSQDVVEAAGNGTSGAPAGASSFSDPFFVVETLCII
OC38240_2 589 ccgtcggagtcggctcgggggggagatggcgggtattgcttgggactaa
tcatgaaaaacccccaattaccgagccgcccgccgtcacttttactgtt
gcgtctggccgcggggtggggccccgggcccacccccccccgggcgccc
Q28656_RABIT 246 WFSFELLVRFFACPSKATFSRNIMNLIDIVAIIPYFITLGTELAERQGN
WFSFELLVRFFACPSKATFSRNIMNLIDIVAIIPYFITLGTELAERQGN
WFSFELLVRFFACPSKATFSRNIMNLIDIVAIIPYFITLGTELAERQGN
OC38240_2 736 ttttgccgcttgtcaagattcaaaacagaggaacttaacgagcggccga
gtctatttgttcgcgacctcgattattattcttcattctgcatcagaga
gcccggcgcccttccacccgaccgcgcccgcctcccccgccggcgagcc
Q28656_RABIT 295 GQQAMSLAILRVIRLVRVFRIFKLSRHSKGLQILGQTLKASMRDVGLLI
GQQAMSLAILRVIRLVRVFRIFKLSRHSKGLQILGQTLKASMRDVGLLI
GQQAMSLAILRVIRLVRVFRIFKLSRHSKGLQILGQTLKASMRDVGLLI
OC38240_2 883 gccgatcgacagaccgagtcatactcctagccacgcacagtacgggcca
gaactctcttgttgttgttgttatcgacagtattgactacctgatgttt
aggcgcgccggcccgggcccccggctccggggcggggggtcggcgggcc
Q28656_RABIT 344 FFLFIGVILFSSAVYFAEADDPTSGFSSIPDAFWWAVVTMTTVGYGDMH
FFLFIGVILFSSAVYFAEADDPTSGFSSIPDAFWWAVVTMTTVGYGDMH
FFLFIGVILFSSAVYFAEADDPTSGFSSIPDAFWWAVVTMTTVGYGDMH
OC38240_2 1030 ttctaggacttaggttgggggcatgtaaacggtttgggaaaaggtggac
tttttgttttcgctatcacaacccgtggtcactggcttctcctgagata
cccctgccccccccctcggccctgctctcgtccggaggcgaacccctgc
Q28656_RABIT 393 PVTIGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQYM
PVTIGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQYM
PVTIGGKIVGSLCAIAGVLTIALPVPVIVSNFNYFYHRETEGEEQAQYM
OC38240_2 1177 cgaaggaaggtctgagggtaagtcgcgagtatatttccgaggggcgcta
ctctggattgctgctcgttctctctctttcataataagacagaaacaat
tgcagcgtgctgtcccgtgctagcttgttccctccccggcagagacgcg
Q28656_RABIT 442 HVGSCQHLSSSAEELRKARSNSTLSKSEYMVIEEGGMNHSAFPQTPFKT
HVGSCQHLSSSAEELRKARSNSTLSKSEYMVIEEGGMNHSAFPQTPFKT
HVGSCQHLSSSAEELRKARSNSTLSKSEYMVIEEGGMNHSAFPQTPFKT
OC38240_2 1324 cggatccctttgggccagaaatacaatgtagaggggaacagtccactaa
atgggaatccccaatgacggacctgacaatttaaggtaagctcacctac
cgatcgccctacggcaaagtcgtgtgggcggcaggtgctttccgctcag
Q28656_RABIT 491 GNSTATCTTNNNPNSCVNIKKIFTDV
GNSTATCTTNNNPNSCVNIKKIFTDV
GNSTATCTTNNNPNSCVNIKKIFTDV
OC38240_2 1471 gatagataaaaacattgaaaaatagg
gaccccgccaaacacgtataattcat
ccctctccgctcccctcccagacctt
//
cmbi.kun.nl), 30-Jun-2005