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: THA_MOUSE
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence MMCERBA1_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 925.42 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=492 (x3=1476) and cDNA length=1233
THA_MOUSE 1 MEQKPSKVECGSDPEENSARSPDGKRKRKNGQCPLKSSMSGYIPSYLDK
MEQKPSKVECGSDPEENSARSPDGKRKRKNGQCPLKSSMSGYIPSYLDK
MEQKPSKVECGSDPEENSARSPDGKRKRKNGQCPLKSSMSGYIPSYLDK
MMCERBA1_2 1 agcacaaggtgtgcggaagatcggacaaaagctccaaaatgtacatcga
taaacgataggcacaaagcgccagagagaagagctaggtcgatcgataa
gaggacgggtgacaggctcgaatagaaagccatcgaccgagtcttcgca
THA_MOUSE 50 DEQCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPTYSCKYDSCCV
DEQCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPTYSCKYDSCCV
DEQCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPTYSCKYDSCCV
MMCERBA1_2 148 ggctggtggagagtctctaatggtagttccaacaacccatttatgattg
aaagttggaaccgaaaggtcgaggagttggctaaataccacgaaagggt
cggtcgtgcgccttccctcttgccgcctccacggtctcctccgtccctc
THA_MOUSE 99 IDKITRNQCQLCRFKKCIAVGMAMDLVLDDSKRVAKRKLIEQNRERRRK
IDKITRNQCQLCRFKKCIAVGMAMDLVLDDSKRVAKRKLIEQNRERRRK
IDKITRNQCQLCRFKKCIAVGMAMDLVLDDSKRVAKRKLIEQNRERRRK
MMCERBA1_2 295 agaaacactcctctaatagggagagtgcggtacggacacagcacgaaca
taatcgaagatggtaagtctgtctatttaacagtcagattaaagaggga
ccgccgtgcggcccggcttgcgcgcgtattggggcacggtggcggggag
THA_MOUSE 148 EEMIRSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDI
EEMIRSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDI
EEMIRSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDI
MMCERBA1_2 442 ggaactcccccgcacggtgcacggaggccaaagcgactacacatccgga
aattgctaagcacccaagattatccacaggcacaggagaaggattcaat
gggtcagggaagcttaggcgatttagctcctccgcctgaggaacggtct
THA_MOUSE 197 GQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCE
GQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCE
GQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCE
MMCERBA1_2 589 gctcagtacgggaggcggtagtaaaaacgaacgggtgaaccattgcctg
gaccttctcagaatatactgatcattccctcgttatcaatcttcatcga
cgattccggcacgacagcccgtcgcccgccgcggctcaagcgccggtca
THA_MOUSE 246 DQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGV
DQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGV
DQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGV
MMCERBA1_2 736 gcaaccagttagaatccgggctgcgagacacaggaggacgccaaggtgg
aattttagggtattctgcctgaacagactctggatctagaataaggtgt
cgcccggcccggcgcggatcccctgtccgcgtggggtggggcgttcgtg
THA_MOUSE 295 VSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLCVDKIEKSQE
VSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLCVDKIEKSQE
VSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLCVDKIEKSQE
MMCERBA1_2 883 gtggatgcgatctgtacggagggcccggccatagctgcctggaagaacg
tcacttatgactcctataacatcttacttttccagcgttgtaataagaa
ctccctagcgactctcgtcgagtgggtggagaaccccggcgcgcggtgg
THA_MOUSE 344 AYLLAFEHYVNHRKHNIPHFWPKLLMK
AYLLAFEHYVNHRKHNIPHFWPKLLMK
AYLLAFEHYVNHRKHNIPHFWPKLLMK
MMCERBA1_2 1030 gtccgtgctgaccacaaccttcaccaa
cattctaaataagaaatcatgcattta
ccgggtgccccccacctgccgcggggg
//
cmbi.kun.nl), 18-Feb-2005