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: wise2-1-20c $ (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: HCN3_MOUSE
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AK032225_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 1917.05 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.
HCN3_MOUSE 1 MEEEARPAAGAGEAATPARETPPAAPAQARAASGGVPESAPEPKRRQLG
MEEEARPAAGAGEAATPARETPPAAPAQARAASGGVPESAPEPKRRQLG
MEEEARPAAGAGEAATPARETPPAAPAQARAASGGVPESAPEPKRRQLG
AK032225_2 1 aggggccggggggggacgcgaccggcgcgcggtgggcgtgcgcaacccg
taaacgcccgcgacccccgacccccccacgcccggtcacccacaggatg
ggggggggggccaggctacggttgtgcgccgcatggggtgcggggggcg
HCN3_MOUSE 50 TLLQPTVNKFSLRVFGSHKAVEIEQERVKSAGAWIIHPYSDFRFYWDLI
TLLQPTVNKFSLRVFGSHKAVEIEQERVKSAGAWIIHPYSDFRFYWDLI
TLLQPTVNKFSLRVFGSHKAVEIEQERVKSAGAWIIHPYSDFRFYWDLI
AK032225_2 148 accccagaattccgtgacagggagcgagatgggtaacctagtctttgca
cttacctaatctgttggaactataaagtaccgcgttacagatgtagatt
ggggggccgctcgcccccaaaacggggggccgcgccccccccgtcgtcc
HCN3_MOUSE 99 MLLLMVGNLIVLPVGITFFKEENSPPWIVFNVLSDTFFLLDLVLNFRTG
MLLLMVGNLIVLPVGITFFKEENSPPWIVFNVLSDTFFLLDLVLNFRTG
MLLLMVGNLIVLPVGITFFKEENSPPWIVFNVLSDTFFLLDLVLNFRTG
AK032225_2 295 acccaggacagccggaattaggatcctagtagctgattccgcgcatcag
ttttttgattttctgtcttaaaacccgtttattcacttttatttatgcg
gggggggccatgtgtctccgggctacgccctcctctccggtggcccatc
HCN3_MOUSE 148 IVVEEGAEILLAPRAIRTRYLRTWFLVDLISSIPVDYIFLVVELEPRLD
IVVEEGAEILLAPRAIRTRYLRTWFLVDLISSIPVDYIFLVVELEPRLD
IVVEEGAEILLAPRAIRTRYLRTWFLVDLISSIPVDYIFLVVELEPRLD
AK032225_2 442 agggggggaccgcagacactccattcggcattacggtatcgggcgcccg
tttaagcatttccgctgcgatgcgtttattcctctaatttttatacgta
cgggatcgcgggagccagtcgccgcgttgcccctgttccagggggaaat
HCN3_MOUSE 197 AEVYKTARALRIVRFTKILSLLRLLRLSRLIRYIHQWEEIFHMTYDLAS
AEVYKTARALRIVRFTKILSLLRLLRLSRLIRYIHQWEEIFHMTYDLAS
AEVYKTARALRIVRFTKILSLLRLLRLSRLIRYIHQWEEIFHMTYDLAS
AK032225_2 589 gggtaagcgccagataaacaccccccctccactacctggatcaatgcga
cataaccgctgttgtcattgttgttgtcgttgataagaattatcaatcg
tgccagagcgcctaccgctcggggcccccccccacggggctcgcccgct
HCN3_MOUSE 246 AVVRIFNLIGMMLLLCHWDGCLQFLVPMLQDFPSDCWVSMNRMVNHSWG
AVVRIFNLIGMMLLLCHWDGCLQFLVPMLQDFPSDCWVSMNRMVNHSWG
AVVRIFNLIGMMLLLCHWDGCLQFLVPMLQDFPSDCWVSMNRMVNHSWG
AK032225_2 736 gggcatacagaatcctctggtcctcgcaccgtctgttgtaacagacttg
cttgttattgtttttgagaggtatttcttaatccaggtctagttaacgg
agtccccctagggggtcgcctggtgctgggccgcccgccgccggccggc
HCN3_MOUSE 295 RQYSHALFKAMSHMLCIGYGQQAPVGMPDVWLTMLSMIVGATCYAMFIG
RQYSHALFKAMSHMLCIGYGQQAPVGMPDVWLTMLSMIVGATCYAMFIG
RQYSHALFKAMSHMLCIGYGQQAPVGMPDVWLTMLSMIVGATCYAMFIG
AK032225_2 883 ccttcgctagaacactagtgccgcggacggtcaacaaagggattgatag
gaacacttactgattgtgagaacctgtcatgtcttgtttgccgactttg
cgtcccgcgcgtcgactctgggagacgtccgccgctgtgccgttcgcct
HCN3_MOUSE 344 HATALIQSLDSSRRQYQEKYKQVEQYMSFHKLPADTRQRIHEYYEHRYQ
HATALIQSLDSSRRQYQEKYKQVEQYMSFHKLPADTRQRIHEYYEHRYQ
HATALIQSLDSSRRQYQEKYKQVEQYMSFHKLPADTRQRIHEYYEHRYQ
AK032225_2 1030 cgagcactcgttccctcgatacggctattcaccggacccacgttgcctc
acccttactaccggaaaaaaaataaatctaatccacgagtaaaaaagaa
ccccccgcgctcgagcgggcgggggcgcccggctccggcccgccgtccg
HCN3_MOUSE 393 GKMFDEESILGELSEPLREEIINFTCRGLVAHMPLFAHADPSFVTAVLT
GKMFDEESILGELSEPLREEIINFTCRGLVAHMPLFAHADPSFVTAVLT
GKMFDEESILGELSEPLREEIINFTCRGLVAHMPLFAHADPSFVTAVLT
AK032225_2 1177 gaatgggaacggcagcccggaaatatcgcggcacctgcggcatgaggca
gattaaagttgatgactgaattatcgggttcatcttcacacgttccttc
cggttagccggggcgatgggttccccgcggccgggttttccccccagcc
HCN3_MOUSE 442 KLRFEVFQPGDLVVREGSVGRKMYFIQHGLLSVLARGARDTRLTDGSYF
KLRFEVFQPGDLVVREGSVGRKMYFIQHGLLSVLARGARDTRLTDGSYF
KLRFEVFQPGDLVVREGSVGRKMYFIQHGLLSVLARGARDTRLTDGSYF
AK032225_2 1324 acctggtccggcggcggtggaaattaccgccagcgcggcgaccaggttt
atgtattacgatttgagctggatattaagttgttcggcgacgtcagcat
gcttgccaagcgggtgccgcgggcccgcgggtggatcccccccttacct
HCN3_MOUSE 491 GEICLLTRGRRTASVRADTYCRLYSLSVDHFNAVLEEFPMMRRAFETVA
GEICLLTRGRRTASVRADTYCRLYSLSVDHFNAVLEEFPMMRRAFETVA
GEICLLTRGRRTASVRADTYCRLYSLSVDHFNAVLEEFPMMRRAFETVA
AK032225_2 1471 ggatccacgcaagagaggattccttcaggctaggcggtcaacagtgagg
gatgttcggggccgtgcacaggtactgtaatacttaatcttggctactc
ggccggtatgaactagtccttcccgccgccctggtggcaggcgttgggc
HCN3_MOUSE 540 MDRLRRIGKKNSILQRKRSEPSPGSSGGVMEQHLVQHDRDMARGVRGLA
MDRLRRIGKKNSILQRKRSEPSPGSSGGVMEQHLVQHDRDMARGVRGLA
MDRLRRIGKKNSILQRKRSEPSPGSSGGVMEQHLVQHDRDMARGVRGLA
AK032225_2 1618 agccccagaaatacccactgcacgaagggagcctgccgagagcggcgcg
tagtggtgaaacttagagcacgcgggggttaaattaaagatcggtggtc
gcgtgcccagtgagggactggtaccctccgggtgaaccacgttttgcgt
HCN3_MOUSE 589 PGTGARLSGKPVLWEPLVHAPLQAAAVTSNVAIALTHQRGPLPLSPDSP
PGTGARLSGKPVLWEPLVHAPLQAAAVTSNVAIALTHQRGPLPLSPDSP
PGTGARLSGKPVLWEPLVHAPLQAAAVTSNVAIALTHQRGPLPLSPDSP
AK032225_2 1765 cgaggccagacgctgccgcgcccggggataggagtacccgcccctcgtc
cgcgcgtggacttgacttacctaccctccatctctcaaggctctccacc
ttaatactagagggaaggcctggattgcccgcacgtcgactgcccttta
HCN3_MOUSE 638 ATLLARSARRSAGSPASPLVPVRAGPLLARGPWASTSRLPAPPARTLHA
ATLLARSARRSAGSPASPLVPVRAGPLLARGPWASTSRLPAPPARTLHA
ATLLARSARRSAGSPASPLVPVRAGPLLARGPWASTSRLPAPPARTLHA
AK032225_2 1912 gaccgctgactggtcgtccgcgcggcccgcgctgtatcccgccgcaccg
ccttcgccggccgcccccttctgcgcttcggcgccccgtcccccgctac
cccatattacaaccaccaggtcaattggcgacggcttcgttatcacctc
HCN3_MOUSE 687 SLSRTGRSQVSLLGPPPGGGARRLGPRGRPLSASQPSLPQRATGDGSPR
SLSRTGRSQVSLLGPPPGGGARRLGPRGRPLSASQPSLPQRATGDGSPR
SLSRTGRSQVSLLGPPPGGGARRLGPRGRPLSASQPSLPQRATGDGSPR
AK032225_2 2059 actcagctcgtctgcccggggcacgccgccctgtcctccccgagggtca
gtcgcggcatcttgcccgggcggtgcgggctcccacctcagccgagccg
cacgagtcgatggctcaaattggaatgccattcgactgtgaaagtcttg
HCN3_MOUSE 736 RKGSGSERLPPSGLLAKPPGTVQPPRSSVPEPVTPRGPQISANM
RKGSGSERLPPSGLLAKPPGTVQPPRSSVPEPVTPRGPQISANM
RKGSGSERLPPSGLLAKPPGTVQPPRSSVPEPVTPRGPQISANM
AK032225_2 2206 cagtgagcccctgctgaccgagcccattgcgcgacagccatgaa
gagcggagtcccgttcaccgctaccgcctcactccggcatccat
tactatgcgcctgcgcatagacgacgaagtgatccatcattccg
//
cmbi.ru.nl), 24-Jul-2003