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 AF019044_3
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 988.50 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: protein length=471 (x3=1413) and cDNA length=1171
DAX1_PIG 1 MAGEDHQWQGSILYNMLMSAKQTHATREAPEARLRGSCWGCSCGSEPPV
MAGEDHQWQGSILYNMLMSAKQTHATREAPEARLRGSCWGCSCGSEPPV
MAGEDHQWQGSILYNMLMSAKQTHATREAPEARLRGSCWGCSCGSEPPV
AF019044_3 1 aggggcctcgaactaacaagacacgacggcggccagtttgtttgtgccg
tcgaaaagaggttaatttgcaacaccgaccacgtggcggggcggcacct
ggcgctgggccccccgcgcaaagtgagggcgagggtgcgccctcggcgg
DAX1_PIG 50 GREGQPGGPAVALLYRCCFCGEDHPRQGSILYNMLTSAKQTQETPEAPE
GREGQPGGPAVALLYRCCFCGEDHPRQGSILYNMLTSAKQTQETPEAPE
GREGQPGGPAVALLYRCCFCGEDHPRQGSILYNMLTSAKQTQETPEAPE
AF019044_3 148 gaggccggcgggcctcttttgggccacgaactaacaagacacgacggcg
ggagacggcctcttagggtggaaacgaggttaattcgcaacaaccacca
caggggtagaggcgctcctctaccgggccccccgcgcagaggatggccg
DAX1_PIG 99 ARLGGACWGCSCGSEPRVGREELPGGRATVLLYRCCFCGEEHPRQGSIL
ARLGGACWGCSCGSEPRVGREELPG ATVLLYRCCFCGEEHPRQGSIL
ARLGGACWGCSCGSEPRVGREELPGAGATVLLYRCCFCGEEHPRQGSIL
AF019044_3 295 gccgggttgtttgtgccggaggccggggagcctcttttgggccccgaac
cgtggcggggcggcacgtggaatcgcgcctttagggtggaaacgaggtt
agcgaacgccatctgcggtagagctggcagcgcccctctggcaggcccg
DAX1_PIG 148 YSLLTSAKQTHVALEAPEARPGGAWWDRSYCAQRLGAREELPGGRPVTL
YSLLTSAKQTHVALEAPEARPGGAWWDRSYCAQRLGAREELPGGRPVTL
YSLLTSAKQTHVALEAPEARPGGAWWDRSYCAQRLGAREELPGGRPVTL
AF019044_3 442 tatcaagacacggcggcggccgggttgctttgcacggaggccggccgac
agttcgcaacatctaccacgcggcggagcagcagtgcgaatcgggctct
ccgcccagagcgtgatggggggcaggcccccagggacagggtcgggggc
DAX1_PIG 197 PYRCCFCGEDHPRQSGILCNMPMSAKQTHVAPEAQPGAPWWDPSCAAQR
PYRCCFCGEDHPRQSGILCNMPMSAKQTHVAPEAQPGAPWWDPSCA +R
PYRCCFCGEDHPRQSGILCNMPMSAKQTHVAPEAQPGAPWWDPSCAQRR
AF019044_3 589 ctcttttgggccccagactaacaagacacggcggccggcttgcttgccc
cagggtggaaacgaggttgatctgcaacatccacacgccggaccgcagg
acccctctaccaggtcccccgtgcagagcgtagggggccggccgtgggg
DAX1_PIG 246 VALKSPQVVCEAASAGLLKTLRFVKYLPCFQVLPLDQQLVLVRSCWAPL
VALKSPQVVCEAASAGLLKT+RFVKYLPCFQVLPLDQQLVLVR+CWAPL
VALKSPQVVCEAASAGLLKTVRFVKYLPCFQVLPLDQQLVLVRTCWAPL
AF019044_3 736 ggcaaccggtgggtggctaagctgattcttcgcctgcctgcgcattgcc
tctagcattgaccccgttactgttaatcgtattctaaattttgcggcct
gccgcaggtcgacggcgggggcccgcgcccgggcgcggggtgcgtgggc
DAX1_PIG 295 LMLELAQDRLNFETVETLEPSLLQMILTTRRQETEGDEPPSPQPPVQPH
LMLELAQDRLNFETVETLEPSLLQMILTTRRQETEGDEPPSPQPPVQPH
LMLELAQDRLNFETVETLEPSLLQMILTTRRQETEGDEPPSPQPPVQPH
AF019044_3 883 cacgcgcgctatgaggatgcacccaacaaaccgaggggcctccccgccc
tttatcaagtatactactacgttatttccggaacagaaccccacctaca
cgaggcgccgctggggcggccgaggccccggggagatggtgcgcaggac
DAX1_PIG 344 LVLPSEAEHLPSVAEVQAIKGFLAKCWSLDISTKEYAYLKGTVLFNP
LVLPSEAEHLPSVAEVQAIKGFLAKCWSLDISTKEYAYLKGTVLFNP
LVLPSEAEHLPSVAEVQAIKGFLAKCWSLDISTKEYAYLKGTVLFNP
AF019044_3 1030 tgcctgggccctggggcgaagtcgattacgaaaagtgtcagagctac
tttccacaatcctcatactagttcagggtatgcaaacatagctttac
gaggggcgtgagccgcaccgcctcgcgcacctcggtcccggcgcttg
//
cmbi.kun.nl), 18-Feb-2005