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_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence RNERBAA_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 1204.08 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.
THA_RAT 1 MEQKPSKVECGSDPEENSARSPDGKRKRKNGQCPLKSSMSGYIPSYLDK
MEQKPSKVECGSDPEENSARSPDGKRKRKNGQCPLKSSMSGYIPSYLDK
MEQKPSKVECGSDPEENSARSPDGKRKRKNGQCPLKSSMSGYIPSYLDK
RNERBAA_2 1 agcacaaggtgtgcggaagatcggacaaaagctccaaaatgtacatcga
taaacgataggcacaaagcgccagagagaagagctaggtcgatcgataa
gaggacgggtgacaggctcgaatagaaggccatcgaccgagtcttcgca
THA_RAT 50 DEQCVVCGDKATGYHYRCITCEGCKGFFRRTIQKNLHPTYSCKYDSCCV
DEQCVVCGDKATGYHYRCITCE CKGFFRRTIQKNLHPTYSCKYDSCCV
DEQCVVCGDKATGYHYRCITCECCKGFFRRTIQKNLHPTYSCKYDSCCV
RNERBAA_2 148 ggctggtggagagtctctaatgttagttccaacaacccatttatgattg
aaagttggaaccgaaaggtcgaggagttggctaaataccacgaaagggt
cggtcgtgcgccttccctcttgccgcctctacggcctcctccatccccc
THA_RAT 99 IDKITRNQCQLCRFKKCIAVGMAMDLVLDDSKRVAKRKLIEQNRERRRK
IDKITRNQCQLCRFKKCIAVGMAMDLVLDDSKRVAKRKLIEQNRERRRK
IDKITRNQCQLCRFKKCIAVGMAMDLVLDDSKRVAKRKLIEQNRERRRK
RNERBAA_2 295 agaaacactcttctaatagggagagcgcggtacggacacagcacgaaca
taatcgaagatggtaagtctgtctatttaacagtcagattaaagaggga
ccgccgtgcggcccggcctgcgcgcgtactagggcacggtggcggggag
THA_RAT 148 EEMIRSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDI
EEMIRSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDI
EEMIRSLQQRPEPTPEEWDLIHVATEAHRSTNAQGSHWKQRRKFLPDDI
RNERBAA_2 442 ggaactcccccgcacggtgcacggaggccaaagcgactacacatccgga
aattgctaagcacccaagattatccacaggcacaggagaaggattcaat
gggccgggaaagcttaggtgccttagctccctcgcctgaggaacggtct
THA_RAT 197 GQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCE
GQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCE
GQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELPCE
RNERBAA_2 589 gctcagtacgggaggcggtagtaaaaacgaacgggtgaaccattgcctg
gaccttctcagaatatactgatcattccctcgttatcaatcttcatcga
cgattccggcacgacagcccgtcgcccgccccggctcaagcgccggtta
THA_RAT 246 DQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGV
DQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGV
DQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKNGGLGV
RNERBAA_2 736 gcaaccagttagaatccgggctgcgagacacaggaggacgccaaggtgg
aattttagggtattctgcctgaacagactctggatctagaataaggtgt
cgcccggcccggcgcggatcctctgcccgcgtggggtggggcgttcgta
THA_RAT 295 VSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLCVDKIEKSQE
VSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLCVDKIEKSQE
VSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLCVDKIEKSQE
RNERBAA_2 883 gtggatgcgatctgtacggagggcccggctatagctgcctggaagaacg
tcacttatgactcctataacatcttacttttccagcgttgtaataagaa
ccccctagcgactctcgttgagtgggtggagaacctcggtgcgcggtgg
THA_RAT 344 AYLLAFEHYVNHRKHNIPHFWPKLLMKEREVQSSILYKGAAAEGRPGGS
AYLLAFEHYVNHRKHNIPHFWPKLLMKEREVQSSILYKGAAAEGRPGGS
AYLLAFEHYVNHRKHNIPHFWPKLLMKEREVQSSILYKGAAAEGRPGGS
RNERBAA_2 1030 gtccgtgctgaccacaaccttcaccaagaggcatactaggggggccggt
cattctaaataagaaatcatgcatttaagatagcttaagcccaggcggc
ccgggtgccccccacctgccgcggggggaaggtgtgcggagaacggcga
THA_RAT 393 LGVHPEGQQLLGMHVVQGPQVRQLEQQFGEAGSLRGPVLQHQSPKSPQQ
LGVHPEGQQLLGMHVVQGPQVRQLEQQFGEAGSLRGPVLQHQSPKSPQQ
LGVHPEGQQLLGMHVVQGPQVRQLEQQFGEAGSLRGPVLQHQSPKSPQQ
RNERBAA_2 1177 cggccggccccgacggcgccgcccgcctggggaccgcgccccacaaccc
tgtacagaattgtattagcatgataaatgacggtggcttaaagcagcaa
gcccgaaggtcagtttgtggcggtgggttagatcaggttgcgcggcggg
THA_RAT 442 RLLELLHRSGILHSRAVCGEDDSSEASSLSSSSSDEDTEVFEDLAGKAA
RLLELLHRSGILHSRAVCGEDDSSEASSLSSSSSDEDTEV EDLAGKAA
RLLELLHRSGILHSRAVCGEDDSSEASSLSSSSSDEDTEVCEDLAGKAA
RNERBAA_2 1324 cccgccccagacctcggtggggaaggatcattttgggaggtggcggagg
gttattagggttacgctggaaaggacgctgccccaaacatgaatcgacc
tcgggccacatctcagctgaccctgaccgcctctcgcggccgcgacgac
THA_RAT 491 SP
SP
SP
RNERBAA_2 1471 tc
cc
tc
//
cmbi.kun.nl), 18-Feb-2005