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: HCN4_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence HSA238850_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 2962.83 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.
HCN4_HUMAN 1 MDKLPPSMRKRLYSLPQQVGAKAWIMDEEEDAEEEGAGGRQDPSRRSIR
MDKLPPSMRKRLYSLPQQVGAKAWIMDEEEDAEEEGAGGRQDPSRRSIR
MDKLPPSMRKRLYSLPQQVGAKAWIMDEEEDAEEEGAGGRQDPSRRSIR
HSA238850_2 1 agaccctacacctaccccgggagtaagggggggggggggccgcacaaac
taatccctgagtagtcaatgcacgttaaaaacaaagcgggaacggggtg
gcggggcgcggccccgggggcgggcgcgagccggggcgccaccccgccg
HCN4_HUMAN 50 LRPLPSPSPSAAAGGTESRSSALGAADSEGPARGAGKSSTNGDCRRFRG
LRPLPSPSPSAAAGGTESRSSALGAADSEGPARGAGKSSTNGDCRRFRG
LRPLPSPSPSAAAGGTESRSSALGAADSEGPARGAGKSSTNGDCRRFRG
HSA238850_2 148 ccccctctctgggggagtcatgcggggaggcgcgggataaaggtactcg
tgctcccccccccggcacggcctgccagagccggcgacgcagagggtgg
ggagcgcccggcgtcggcgcgccgagccaggcccgcgccgccccgcccg
HCN4_HUMAN 99 SLASLGSRGGGSGGTGSGSSHGHLHDSAEERRLIAEGDASPGEDRTPPG
SLASLGSRGGG+GGTGSGSSHGHLHDSAEERRLIAEGDASPGEDRTPPG
SLASLGSRGGGTGGTGSGSSHGHLHDSAEERRLIAEGDASPGEDRTPPG
HSA238850_2 295 acgtcgacgggaggagagaacgcccgtgggcccagggggtcgggaaccg
gtcctggggggcggcgggggagataaccaaggttcagacccgaagcccg
cgcggccgcccgccggccctcacgtccgggggcccgccgcccgcggcac
HCN4_HUMAN 148 LAAEPERPGASAQPAASPPPPQQPPQPASASCEQPSVDTAIKVEGGAAA
LAAEPERPGASAQPAASPPPPQQPPQPASASCEQPSVDTAIKVEGGAAA
LAAEPERPGASAQPAASPPPPQQPPQPASASCEQPSVDTAIKVEGGAAA
HSA238850_2 442 cgggcgccggtgccggtccccccccccgtgttgcctggagaaggggggg
tccacagcgcccaccccccccaaccacccccgaacctacctataggccc
ggcgcgccccgggcacggggcggagggcccccggcggcctcaggacgtc
HCN4_HUMAN 197 GDQILPEAEVRLGQAGFMQRQFGAMLQPGVNKFSLRMFGSQKAVEREQE
GDQILPEAEVRLGQAGFMQRQFGAMLQPGVNKFSLRMFGSQKAVEREQE
GDQILPEAEVRLGQAGFMQRQFGAMLQPGVNKFSLRMFGSQKAVEREQE
HSA238850_2 589 ggcaccggggccgcggtaccctggacccggaattcaatgacagggcgcg
gaattcacatgtgacgttagatgcttacgtaatctgttggaactagaaa
ccgccggcggcgcgcccggcgcgcgcacgccaccaggcccgacggcagg
HCN4_HUMAN 246 RVKSAGFWIIHPYSDFRFYWDLTMLLLMVGNLIIIPVGITFFKDENTTP
RVKSAGFWIIHPYSDFRFYWDLTMLLLMVGNLIIIPVGITFFKDENTTP
RVKSAGFWIIHPYSDFRFYWDLTMLLLMVGNLIIIPVGITFFKDENTTP
HSA238850_2 736 agatggttaacctagtatttgcaacccaggacaaacggaattaggaaac
gtaccgtgttacagatgtagatcttttttgattttctgtcttaaaaccc
gcggcatgtcccctccatcgcgcggggggacgtcttgcccccgtgccac
HCN4_HUMAN 295 WIVFNVVSDTFFLIDLVLNFRTGIVVEDNTEIILDPQRIKMKYLKSWFM
WIVFNVVSDTFFLIDLVLNFRTGIVVEDNTEIILDPQRIKMKYLKSWFM
WIVFNVVSDTFFLIDLVLNFRTGIVVEDNTEIILDPQRIKMKYLKSWFM
HSA238850_2 883 tagtaggtgattcagtgcatcagaggggaagaacgcccaaaatcaatta
gtttattcacttttatttatgcgtttaaacatttacagtataataggtt
gtcctggacacccccgcccccagcgggccagccgcgggtaggcgacgcg
HCN4_HUMAN 344 VDFISSIPVDYIFLIVETRIDSEVYKTARALRIVRFTKILSLLRLLRLS
VDFISSIPVDYIFLIVETRIDSEVYKTARALRIVRFTKILSLLRLLRLS
VDFISSIPVDYIFLIVETRIDSEVYKTARALRIVRFTKILSLLRLLRLS
HSA238850_2 1030 ggtattacggtatcaggacagtggtaagcgccagctaaacactcctcct
tattcctctaatttttacgtacataaccgctgttgtcattgttgttgtc
atctccccgccccctggacccggccgtcgcgctcccggccccacgaccc
HCN4_HUMAN 393 RLIRYIHQWEEIFHMTYDLASAVVRIVNLIGMMLLLCHWDGCLQFLVPM
RLIRYIHQWEEIFHMTYDLASAVVRIVNLIGMMLLLCHWDGCLQFLVPM
RLIRYIHQWEEIFHMTYDLASAVVRIVNLIGMMLLLCHWDGCLQFLVPM
HSA238850_2 1177 ccactacctggatcaatgcgagggcagacagaaccctctggtcctcgca
gttgataagaattatcaatcgcttgttattgtttttgagaggtatttct
cctattcggagcccgcccgcccggccgccccggcgcccgcccggcgacg
HCN4_HUMAN 442 LQDFPDDCWVSINNMVNNSWGKQYSYALFKAMSHMLCIGYGRQAPVGMS
LQDFPDDCWVSINNMVNNSWGKQYSYALFKAMSHMLCIGYGRQAPVGMS
LQDFPDDCWVSINNMVNNSWGKQYSYALFKAMSHMLCIGYGRQAPVGMS
HSA238850_2 1324 ccgtcggttgtaaaagaattgactttgctagaacactagtgccgcggat
taatcaaggtctaattaacggaaacacttactgattgtgaggacctgtc
agcctcccggccccggcccggggcccgccgcgccggccccggggcgcgc
HCN4_HUMAN 491 DVWLTMLSMIVGATCYAMFIGHATALIQSLDSSRRQYQEKYKQVEQYMS
DVWLTMLSMIVGATCYAMFIGHATALIQSLDSSRRQYQEKYKQVEQYMS
DVWLTMLSMIVGATCYAMFIGHATALIQSLDSSRRQYQEKYKQVEQYMS
HSA238850_2 1471 ggtcaacaaagggattgatagcgagcactcgttccctcgatacggctat
atgtcttgtttgccgactttgacccttactaccggaaaaaaaataaatc
ccgccgccgcgtcccccgctccctcccgcgcccgcgcgagcgggggcgc
HCN4_HUMAN 540 FHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRK
FHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRK
FHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRK
HSA238850_2 1618 tcacccgacccacgttgcctcgaatgggaacggcagcccggaaatatca
taatccacgagtaaaaaagaagattaaagttgatgactgaattatagga
tcgcgcccggccccccgcccgcggccggccgcgacgcggggccctctgg
HCN4_HUMAN 589 LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQH
LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQH
LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQH
HSA238850_2 1765 cggtacctgaggcatgatacaacctggtccggtaacggaagaaattacc
ttcctcttcacacattccttcatgtattacgaattgagctgaatattaa
ggccgagtctgccccggcggcggtcgccgtgccccgacctcgggcccgt
HCN4_HUMAN 638 GVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSV
GVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSV
GVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSV
HSA238850_2 1912 gggagcaagaagaacgggtttggatccacgccagagaggattccttcag
gttgttcagaaacatcagcatgatgttcggggccgtgcacaggtactgt
cgccgccgccggcggccccctagccggcgcgcaccggccccccccggcg
HCN4_HUMAN 687 DNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILLHKVQHDLNSGVFN
DNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILLHKVQHDLNSGVFN
DNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILLHKVQHDLNSGVFN
HSA238850_2 2059 gataggcggtcaacagtgaggcgccgcagaaatacccagccgcatggta
aataattaaacttggctactctagtagtgaaactttaataaatacgtta
ccctgggggccggagccgcgggccgcctcggccccccacgccccccccc
HCN4_HUMAN 736 YQENEIIQQIVQHDREMAHCAHRVQAAASATPTPTPVIWTPLIQAPLQA
YQENEIIQQIVQHDREMAHCAHRVQAAASATPTPTPVIWTPLIQAPLQA
YQENEIIQQIVQHDREMAHCAHRVQAAASATPTPTPVIWTPLIQAPLQA
HSA238850_2 2206 tcgagaaccagccgcgagctgccgcgggtgacacacgataccacgcccg
aaaaattaattaaagatcagcagtacccccccccccttgccttacctac
cggtgccggtggtcgggcccgcccgttctccaccgcccgcggcgaaggt
HCN4_HUMAN 785 AAATTSVAIALTHHPRLPAAIFRPPPGSGLGNLGAGQTPRHLKRLQSLI
AAATTSVAIALTHHPRLPAAIFRPPPGSGLGNLGAGQTPRHLKRLQSLI
AAATTSVAIALTHHPRLPAAIFRPPPGSGLGNLGAGQTPRHLKRLQSLI
HSA238850_2 2353 gggaatggagcaccccccggatccccgtgcgacgggcacaccaccctca
cccccctctctcaacgtcccttgcccgcgtgatgcgaccgatagtactt
ctccttgcaccccctcgttcccctcaatggccctcgggagcgagggcgc
HCN4_HUMAN 834 PSALGSASPASSPSQVDTPSSSSFHIQQLAGFSAPAGLSPLLPSSSSSP
PSALGSASPASSPSQVDTPSSSSFHIQQLAGFSAPAGLSPLLPSSSSSP
PSALGSASPASSPSQVDTPSSSSFHIQQLAGFSAPAGLSPLLPSSSSSP
HSA238850_2 2500 ctgcgtgtcgaactcggactttttcacccggttgcggcaccccttattc
ccctgcccccggccatacccccctataatcgtccccgtgcttcccgccc
ttggcccgccccgcggcagtacccccaggtactcctagcacgcacccca
HCN4_HUMAN 883 PPGACGSPSAPTPSAGVAATTIAGFGHFHKALGGSLSSSDSPLLTPLQP
PPGACGSPSAPTPSAGVAATTIAGFGHFHKALGGSLSSSDSPLLTPLQP
PPGACGSPSAPTPSAGVAATTIAGFGHFHKALGGSLSSSDSPLLTPLQP
HSA238850_2 2647 ccggtgtctgcactgggggaaaggtgctcagcggtctttgtcccacccc
ccgcggcccccccccgtcccctcgtgataactggctcccaccttcctac
ccgctcccgtcaaatcaccccacgtccccgggtccgcccctcgccggga
HCN4_HUMAN 932 GARSPQAAQPSPAPPGARGGLGLPEHFLPPPPSSRSPSSSPGQLGQPPG
GARSPQAAQPSPAPPGARGGLGLPEHFLPPPPSSRSPSSSPGQLGQPPG
GARSPQAAQPSPAPPGARGGLGLPEHFLPPPPSSRSPSSSPGQLGQPPG
HSA238850_2 2794 ggctccggcctcgccggcggcgccgctcccccttatcttacgccgcccg
gcgccaccaccccccgcgggtgtcaattccccccgccccgcgatgaccg
ccccggtcgatcgacgcgacgacggccgacacacacgatccgggcgtcg
HCN4_HUMAN 981 ELSLGLATGPLSTPETPPRQPEPPSLVAGASGGASPVGFTPRGGLSPPG
ELSLGLATGPLSTPETPPRQPEPPSLVAGASGGASPVGFTPRGGLSPPG
ELSLGLATGPLSTPETPPRQPEPPSLVAGASGGASPVGFTPRGGLSPPG
HSA238850_2 2941 gttcgcgagccaacgacccccgcctcggggtgggtcggtaccggcaccg
atctgtccgctgccacccgacacccttcgccggccctgtccgggtgccg
ggcatgctcagcgagacaggtgggctgagctggtctacttcaatccctc
HCN4_HUMAN 1030 HSPGPPRTFPSAPPRASGSHGSLLLPPASSPPPPQVPQRRGTPPLTPGR
HSPGPPRTFPSAPPRASGSHGSLLLPPASSPPPPQVPQRRGTPPLTPGR
HSPGPPRTFPSAPPRASGSHGSLLLPPASSPPPPQVPQRRGTPPLTPGR
HSA238850_2 3088 cacgccaatcagcccgtgtcgttccccgtacccccgccccgacccacgc
agcgccgctcgcccgccgcagctttccccgccccatcagggccctccgg
ccaccaaccgtcgcgctcccacgcgatacccaacgccgcgcacgccccc
HCN4_HUMAN 1079 LTQDLKLISASQPALPQDGAQTLRRASPHSSGESMAAFPLFPRAGGGSG
LTQDLKLISASQPALPQDGAQTLRRASPHSSGESMAAFPLFPRAGGGSG
LTQDLKLISASQPALPQDGAQTLRRASPHSSGESMAAFPLFPRAGGGSG
HSA238850_2 3235 cacgcacatgtccgcccgggcaccagtccttggtaggtcctcaggggag
tcaatattcccacctcaagcactggcccaccgactcctcttcgcggggg
ccgccgcccgtgacgtgcgggtccaccgccaggcgtccgcccgtgtccg
HCN4_HUMAN 1128 GSGSSGGLGPPGRPYGAIPGQHVTLPRKTSSGSLPPPLSLFGARATSSG
GSGSSGGLGPPGRPYGAIPGQHVTLPRKTSSGSLPPPLSLFGARATSSG
GSGSSGGLGPPGRPYGAIPGQHVTLPRKTSSGSLPPPLSLFGARATSSG
HSA238850_2 3382 gagaaggcgccgactggacgccgacccaattgttcccctttggagattg
gggggggtgccggcagctcgaatctcgacccgctccctcttgcgccccg
ctgccgcctctggcttccccgcctgtggacattgactgtgtgaaccttg
HCN4_HUMAN 1177 GPPLTAGPQREPGARPEPVRSKLPSNL
GPPLTAGPQREPGARPEPVRSKLPSNL
GPPLTAGPQREPGARPEPVRSKLPSNL
HSA238850_2 3529 gcccaggccagcggacgcgctacctac
gcctccgcagacgcgcactgcatccat
gctgttacggatgcgtgagccaggcta
//
cmbi.ru.nl), 24-Jul-2003