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_RAT
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence AF247453
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 2956.13 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_RAT 1 MDKLPPSMRKRLYSLPQQVGAKAWIMDEEEDGEEEGAGGLQDPSRRSIR
MDKLPPSMRKRLYSLPQQVGAKAWIMDEEEDGEEEGAGGLQDPSRRSIR
MDKLPPSMRKRLYSLPQQVGAKAWIMDEEEDGEEEGAGGLQDPSRRSIR
AF247453 228 agaccctacacctaccccgggagtaagggggggggggggccgcacaaac
taatccctgagtagtcaatgcacgttaaaaagaaagcggtaacggggtg
gcggggcgcggccctgggggcgggcgcgagttgaggcgccgcacagctg
HCN4_RAT 50 LRPLPSPSPSVAAGCSESRGAALGAADSEGPGRSAGKSSTNGDCRRFRG
LRPLPSPSPSVAAGCSESRGAALGAADSEGPGRSAGKSSTNGDCRRFRG
LRPLPSPSPSVAAGCSESRGAALGAADSEGPGRSAGKSSTNGDCRRFRG
AF247453 375 ccccctctctggggttgtcgggcggggaggcgcaggataaaggtactcg
tgctcccccctccggcacggcctgccagagcgggcgacgcagagggtgg
ggggcgcgcggcccccgcgtgccggaccgggcccccgcccctccgcccg
HCN4_RAT 99 SLASLGSRGGGSGGAGGGSSLGHLHDSAEERRLIAAEGDASPGEDRTPP
SLASLGSRGGGSGGAGGGSSLGHLHDSAEERRLIAAEGDASPGEDRTPP
SLASLGSRGGGSGGAGGGSSLGHLHDSAEERRLIAAEGDASPGEDRTPP
AF247453 522 acgtcgacgggaggggggaacgcccgtgggcccaggggggtcgggaacc
gtcctgggggggggcgggggtgataaccaaggttccagacccgaagccc
tgcggccgcccttaagccctcgcgtccgggggccctgctgcccgcggcg
HCN4_RAT 148 GLATEPERPGAAAQPAASPPPQQPPQPASASCEQPSADTAIKVEGGAAA
GLATEPERPGAAAQPAASPPPQQPPQPASASCEQPSADTAIKVEGGAAA
GLATEPERPGAAAQPAASPPPQQPPQPASASCEQPSADTAIKVEGGAAA
AF247453 669 gcgagcgccggggccggtcccccccccgtgttgcctggagaaggggggg
gtccacagcgcccacccccccaaccacccccgaacccacctataggccc
cggcgcgcgccgaacacgggcagggggcccccggcggcatcagaacgcc
HCN4_RAT 197 SDQILPEAEVRLGQSGFMQRQFGAMLQPGVNKFSLRMFGSQKAVEREQE
SDQILPEAEVRLGQSGFMQRQFGAMLQPGVNKFSLRMFGSQKAVEREQE
SDQILPEAEVRLGQSGFMQRQFGAMLQPGVNKFSLRMFGSQKAVEREQE
AF247453 816 agcaccggggccgcagtaccctggacccggaattcaatgacagggcgcg
gaattcacatgtgaggttagatgcttacgtaatctgttggaactagaaa
ccgcctgcggcgcgcccggcgctcggatgccacgaggcccgaaggtggg
HCN4_RAT 246 RVKSAGFWIIHPYSDFRFYWDLTMLLLMVGNLIIIPVGITFFKDENTTP
RVKSAGFWIIHPYSDFRFYWDLTMLLLMVGNLIIIPVGITFFKDENTTP
RVKSAGFWIIHPYSDFRFYWDLTMLLLMVGNLIIIPVGITFFKDENTTP
AF247453 963 agatggttaacctagtatttgcaactcaggacaaacggaattaggaaac
gtaccgtgttacagatgtagatcttttttgattttctgtcttaaaaccc
gtgatgtgtcccccccatcgcgggggggggtgccctgcccccgtgcccc
HCN4_RAT 295 WIVFNVVSDTFFLIDLVLNFRTGIVVEDNTEIILDPQRIKMKYLKSWFV
WIVFNVVSDTFFLIDLVLNFRTGIVVEDNTEIILDPQRIKMKYLKSWFV
WIVFNVVSDTFFLIDLVLNFRTGIVVEDNTEIILDPQRIKMKYLKSWFV
AF247453 1110 tagtaggtgattcagtgcatcagaggggaagaacgcccaaaatcaattg
gtttattcacttttatttatgcgtttaaacatttacagtataataggtt
gccccggacaccctcgcccccggcgggccaacctcaggcgggcgacgtg
HCN4_RAT 344 VDFISSIPVDYIFLIVETRIDSEVYKTARALRIVRFTKILSLLRLLRLS
VDFISSIPVDYIFLIVETRIDSEVYKTARALRIVRFTKILSLLRLLRLS
VDFISSIPVDYIFLIVETRIDSEVYKTARALRIVRFTKILSLLRLLRLS
AF247453 1257 ggtattacggtatcaggacagtggtaagagccagctaaacaccccccct
tattcctctaatttttacgtacataaccgctgttgtcattgttgttgtc
gcccccccgcccctaggtctcggccaccgtgctcccggccccgccggtc
HCN4_RAT 393 RLIRYIHQWEEIFHMTYDLASAVVRIVNLIGMMLLLCHWDGCLQFLVPM
RLIRYIHQWEEIFHMTYDLASAVVRIVNLIGMMLLLCHWDGCLQFLVPM
RLIRYIHQWEEIFHMTYDLASAVVRIVNLIGMMLLLCHWDGCLQFLVPM
AF247453 1404 ccactacctggatcaatgcgagggcagacagaaccctctggtcctcgca
gttgataagaattatcaatcgcttgttattgtttttgagaggtatttct
cctgctcggagcccgcccgctcgaccgcctcggtgtccgtccggcggcg
HCN4_RAT 442 LQDFPHDCWVSINGMVNNSWGKQYSYALFKAMSHMLCIGYGRQAPVGMS
LQDFPHDCWVSINGMVNNSWGKQYSYALFKAMSHMLCIGYGRQAPVGMS
LQDFPHDCWVSINGMVNNSWGKQYSYALFKAMSHMLCIGYGRQAPVGMS
AF247453 1551 ccgtccgttgtaagagaattgactttgctagaacactagtgccgcggat
taatcaaggtctagttaacggaaacacttactgattgtgaggacctgtc
ggccctccggccccggtccggggcctcccgcgccggttgcaggacacgt
HCN4_RAT 491 DVWLTMLSMIVGATCYAMFIGHATALIQSLDSSRRQYQEKYKQVEQYMS
DVWLTMLSMIVGATCYAMFIGHATALIQSLDSSRRQYQEKYKQVEQYMS
DVWLTMLSMIVGATCYAMFIGHATALIQSLDSSRRQYQEKYKQVEQYMS
AF247453 1698 ggtcaacaaagggattgatagcgagcactcgttccctcgatacggctat
atgtcttgtttgccgactttgacccttactaccggaaaaaaaataaatc
ccgccgccgcgcccctcgccgcctcccgggcccgcgcgggcgggggcgc
HCN4_RAT 540 FHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRK
FHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRK
FHKLPPDTRQRIHDYYEHRYQGKMFDEESILGELSEPLREEIINFNCRK
AF247453 1845 tcacccgaaccacgttgcctcgaatgggaacggcagcccggaaatatca
taatccacgagtaaaaaagaagattaaagttgatgactgaattatagga
ccgcgtccggccccccacccgcggtcgaccgtggtggtaggccctccgg
HCN4_RAT 589 LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQH
LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQH
LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQH
AF247453 1992 cggtacctgaggcatgatacaatctggtccggtaacggaagaaattacc
ttcctcttcacacattccttcatgtattacgaattgagctgaatattaa
ggacgagcctaccctggtggcggttgctgtgcccctaccccgggctcgc
HCN4_RAT 638 GVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSV
GVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSV
GVVSVLTKGNKETKLADGSYFGEICLLTRGRRTASVRADTYCRLYSLSV
AF247453 2139 gggagcaagaagaacgggtttggattcacgccagagaggattccttcag
gttgttcagaaacatcagcatgatgttcggggccgtgcacaggtactgt
cgctgctgccggcggttccttagccggcactcagcgggttcccccagcg
HCN4_RAT 687 DNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILLHKVQHDLNSGVFN
DNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILLHKVQHDLNSGVFN
DNFNEVLEEYPMMRRAFETVALDRLDRIGKKNSILLHKVQHDLNSGVFN
AF247453 2286 gataggcggtcaacagtgaggcgccgcagaaatacccagccgcatggta
aataattaaacttggctactctagtagtgaaactttaataaatacgtta
ccccgggggtcggcgtcggtggctgccacggccccccgggccccacccc
HCN4_RAT 736 YQENEIIQQIVRHDREMAHCAHRVQAAASATPTPTPVIWTPLIQAPLQA
YQENEIIQQIVRHDREMAHCAHRVQAAASATPTPTPVIWTPLIQAPLQA
YQENEIIQQIVRHDREMAHCAHRVQAAASATPTPTPVIWTPLIQAPLQA
AF247453 2433 tcgagaaccagccgcgagctgccgcgggtgacacacgataccacgcccg
aaaaattaattgaagatcagcagtacccccccccccttgccttacctac
cagcgccggcggtctggccttcccgttcaccacagtcagcagcgaaggt
HCN4_RAT 785 AAATTSVAIALTHHPRLPAAIFRPPPGPGLGNLGAGQTPRHPRRLQSLI
AAATTSVAIALTHHPRLPAAIFRPPPGPGLGNLGAGQTPRHPRRLQSLI
AAATTSVAIALTHHPRLPAAIFRPPPGPGLGNLGAGQTPRHPRRLQSLI
AF247453 2580 gggaatggagcaccccccggatccccgcgcgacgggcacaccaatctta
cccccctctctcaacgtcccttgcccgcgtgatgcgaccgacggtactt
tttttggcaccaccccgactccgctcatggtcggtagaggcaggggcgc
HCN4_RAT 834 PSALGSASPASSPSQVDTPSSSSFHIQQLAGFSAPPGLSPLLPSSSSSP
PSALGSASPASSPSQVDTPSSSSFHIQQLAGFSAPPGLSPLLPSSSSSP
PSALGSASPASSPSQVDTPSSSSFHIQQLAGFSAPPGLSPLLPSSSSSP
AF247453 2727 ctgcgtgtcgaactcggactttttcacccggttgccgtacctcttattc
ccctgcccccggccatacccccctataatcgtccccgtgcttcccgccc
tagacttaaccccaggcagtatccccaggtactattagttcgcctctca
HCN4_RAT 883 PPGACSSPPAPTPSTSTAATTTGFGHFHKALGGSLSSSDSPLLTPLQPG
PPGACSSPPAPTPSTSTAATTTGFGHFHKALGGSLSSSDSPLLTPLQPG
PPGACSSPPAPTPSTSTAATTTGFGHFHKALGGSLSSSDSPLLTPLQPG
AF247453 2874 ccggtatccgcactataggaaagtgctcagcggtctttgtcccaccccg
ccgcggccccccccccccccccgtgataactggctcccaccttcctacg
taaccttcacctacccttccccgcccttggatccgtcttcggccagagc
HCN4_RAT 932 ARSPQAAQPPPPLPGARGGLGLLEHFLPPPPSSRSPSSSPGQLGQPPGE
ARSPQAAQPPPPLPGARGGLGLLEHFLPPPPSSRSPSSSPGQLGQPPGE
ARSPQAAQPPPPLPGARGGLGLLEHFLPPPPSSRSPSSSPGQLGQPPGE
AF247453 3021 gctccggcccccccggcggcgccgcttccccttctcttacgccgcccgg
cgccaccacccctcgcgggtgttaattccccccgccccgcgatgaccga
tctagtcggacagtgcaacgacggccggcatgcgaaatctgggcgttag
HCN4_RAT 981 LSPGLAAGPPSTPETPPRPERPSFMAGASGGASPVAFTPRGGLSPPGHS
LSPGLAAGPPSTPETPPRPERPSFMAGASGGASPVAFTPRGGLSPPGHS
LSPGLAAGPPSTPETPPRPERPSFMAGASGGASPVAFTPRGGLSPPGHS
AF247453 3168 ttcgcgggccaacgaccccgccttagggtgggtcggtaccggcaccgca
tccgtccgccgccacccgcagccttcgccggccctctccgggtgccgag
gcatgattaataagacggcagactgagctggtttactccaaccctgccc
HCN4_RAT 1030 PGPPRTFPSAPPRASGSHGSLLLPPASSPPPPQVPQRRGTPPLTPGRLT
PGPPRTFPSAPPRASGSHGSLLLPPASSPPPPQVPQRRGTPPLTPGRLT
PGPPRTFPSAPPRASGSHGSLLLPPASSPPPPQVPQRRGTPPLTPGRLT
AF247453 3315 cgccaatcagcccgtgtcgtcccccgtacccccgcccagacccacgcca
cgccgctcgcccgccgcagctttccccgccccatcagggccctccggtc
aacaatcgtcacgctccttcgcgatacctgtcgcagcgcaaccccccca
HCN4_RAT 1079 QDLKLISASQPALPQDGAQTLRRASPHSSGESMAAFSLYPRAGGGSGSS
QDLKLISASQPALPQDGAQTLRRASPHSSGESMAAFSLYPRAGGGSGSS
QDLKLISASQPALPQDGAQTLRRASPHSSGESMAAFSLYPRAGGGSGSS
AF247453 3462 cgcacatgtccgcccgggcaccagtccttggtaggttctcaggggagaa
aatattcccacctcaagcactggcccaccgactcctctacgcggggggg
gcggccactgacccgtgagtacgcttccaggggtccacccatgtctgct
HCN4_RAT 1128 GGLGPPGRPYGAIPGQHVTLPRKTSSGSLPPPLSLFGARAASSGGPPLT
GGLGPPGRPYGAIPGQHVTLPRKTSSGSLPPPLSLFGARAASSGGPPLT
GGLGPPGRPYGAIPGQHVTLPRKTSSGSLPPPLSLFGARAASSGGPPLT
AF247453 3609 ggcgccgactggacgccgatccaattgttcccctttggaggttggccca
ggtgccggcagctcgaatctcgacccgctccctcttgcgccccggcctc
gctgttagattccacgtctgtggacattgacattgtgaaccttagctgt
HCN4_RAT 1177 AAPQREPGARSEPVRSKLPSNL
AAPQREPGARSEPVRSKLPSNL
AAPQREPGARSEPVRSKLPSNL
AF247453 3756 ggccagcggatgcgctacctat
cccagacgcgcactgcatccat
tacggatctgcgaaccaggtta
//
cmbi.ru.nl), 24-Jul-2003