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: DAX1_PIG
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF035816_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 1173.95 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.
DAX1_PIG 1 MAGEDHQWQGSILYNMLMSAKQTHATREAPEARLRGSCWGCSCGSEPPV
MAGEDHQWQGSILYNMLMSAKQTHATREAPEARLRGSCWGCSCGSEPPV
MAGEDHQWQGSILYNMLMSAKQTHATREAPEARLRGSCWGCSCGSEPPV
AF035816_2 1 aggggcctcgaactaacaagacacgacggcggccagtttgtttgtgccg
tcgaaaagaggttaatttgcaacaccgaccacgtggcggggcggcacct
ggcgctgggccccccgcgcaaagtgagggcgagggtgcgccctcggcgg
DAX1_PIG 50 GREGQPGGPAVALLYRCCFCGEDHPRQGSILYNMLTSAKQTQETPEAPE
GREGQPGGPAVALLYRCCFCGEDHPRQGSILYNMLTSAKQTQETPEAPE
GREGQPGGPAVALLYRCCFCGEDHPRQGSILYNMLTSAKQTQETPEAPE
AF035816_2 148 gaggccggcgggcctcttttgggccacgaactaacaagacacgacggcg
ggagacggcctcttagggtggaaacgaggttaattcgcaacaaccacca
caggggtagaggcgctcctctaccgggccccccgcgcagaggatggccg
DAX1_PIG 99 ARLGGACWGCSCGSEPRVGREELPGGRATVLLYRCCFCGEEHPRQGSIL
ARLGGACWGCSCGSEPRVGREELPGGRATVLLYRCCFCGEEHPRQGSIL
ARLGGACWGCSCGSEPRVGREELPGGRATVLLYRCCFCGEEHPRQGSIL
AF035816_2 295 gccgggttgtttgtgccggaggccggcgagcctcttttgggccccgaac
cgtggcggggcggcacgtggaatcgggcctttagggtggaaacgaggtt
agcgaacgccatctgcggtagagctggcagcgcccctctggcaggcccg
DAX1_PIG 148 YSLLTSAKQTHVALEAPEARPGGAWWDRSYCAQRLGAREELPGGRPVTL
YSLLTSAKQTHVALEAPEARPGGAWWDRSYCAQRLGAREELPGGRPVTL
YSLLTSAKQTHVALEAPEARPGGAWWDRSYCAQRLGAREELPGGRPVTL
AF035816_2 442 tatcaagacacggcggcggccgggttgctttgcacggaggccggccgac
agttcgcaacatctaccacgcggcggagcagcagtgcgaatcgggctct
ccgcccagagcgtgatggggggcaggcccccagggacagggtcgggggc
DAX1_PIG 197 PYRCCFCGEDHPRQSGILCNMPMSAKQTHVAPEAQPGAPWWDPSCAAQR
PYRCCFCGEDHPRQSGILCNMPMSAKQTHVAPEAQPGAPWWDPSCAAQR
PYRCCFCGEDHPRQSGILCNMPMSAKQTHVAPEAQPGAPWWDPSCAAQR
AF035816_2 589 ctcttttgggccccagactaacaagacacggcggccggcttgcttggcc
cagggtggaaacgaggttgatctgcaacatccacacgccggaccgccag
acccctctaccaggtcccccgtgcagagcgtagggggccggccgtcggg
DAX1_PIG 246 VALKSPQVVCEAASAGLLKTLRFVKYLPCFQVLPLDQQLVLVRSCWAPL
VALKSPQVVCEAASAGLLKTLRFVKYLPCFQVLPLDQQLVLVRSCWAPL
VALKSPQVVCEAASAGLLKTLRFVKYLPCFQVLPLDQQLVLVRSCWAPL
AF035816_2 736 ggcaaccggtgggtggctaacctgattcttcgcctgcctgcgcattgcc
tctagcattgaccccgttactgttaatcgtattctaaattttggggcct
gccgcaggtcgacggcgggggcccgcgcccgggcgcggggtgcctgggc
DAX1_PIG 295 LMLELAQDRLNFETVETLEPSLLQMILTTRRQETEGDEPPSPQPPVQPH
LMLELAQDRLNFETVETLEPSLLQMILTTRRQETEGDEPPSPQPPVQPH
LMLELAQDRLNFETVETLEPSLLQMILTTRRQETEGDEPPSPQPPVQPH
AF035816_2 883 cacgcgcgctatgaggatgcacccaacaaaccgaggggcctccccgccc
tttatcaagtatactactacgttatttccggaacagaaccccacctaca
cgaggcgccgctggggcggccgaggccccggggagatggtgcgcaggac
DAX1_PIG 344 LVLPSEAEHLPSVAEVQAIKGFLAKCWSLDISTKEYAYLKGTVLFNPDL
LVLPSEAE VQAIKGFLAKCWSLDISTKEYAYLKGTVLFNPDL
LVLPSEAE-------VQAIKGFLAKCWSLDISTKEYAYLKGTVLFNPDL
AF035816_2 1030 tgcctggg gcgaagtcgattacgaaaagtgtcagagctacgc
tttccaca tactagttcagggtatgcaaacatagctttacat
gaggggcg caccgcctcgcgcacctcggtcccggcgcttgcg
DAX1_PIG 393 PGLQCVKYIQGLQWGTQQILSEHIRMTHRGYQARFAELNSALFLLRFIN
PGLQCVKYIQGLQWGTQQILSEHIRMTHRGYQARFAELNSALFLLRFIN
PGLQCVKYIQGLQWGTQQILSEHIRMTHRGYQARFAELNSALFLLRFIN
AF035816_2 1156 cgcctgatacgcctgaccacagcaaaacagtcgatggcaagctccataa
cgtagtaatagtaggcaattgaatgtcaggaacgtcatagcttttgtta
agtgcggccgatggatggctcaccggacggcgcattggccctcggacct
DAX1_PIG 442 ANVLAELFFRPIIGTVSMDDMMLEMLCAKL
ANVLAELFFRPIIGTVSMDDMMLEMLCAKL
ANVLAELFFRPIIGTVSMDDMMLEMLCAKL
AF035816_2 1303 gagcggcttacaagagaaggaacgactgat
cattcatttgcttgctgtaatttattgcat
ctctcagccgcctctccgtcgggagctaga
//
cmbi.kun.nl), 18-Feb-2005