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_HUMAN
Comp Matrix: blosum62.bla
Gap open: 12
Gap extension: 2
Start/End default
Target Sequence BC000066
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 1414.71 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_HUMAN 204 ARALRIVRFTKILSLLRLLRLSRLIRYIHQWEEIFHMTYDLASAVVRIF
AR LRIVRFTKILSLLRLLRLSRLIRYIHQWEEIFHMTYDLASAVVRIF
ARGLRIVRFTKILSLLRLLRLSRLIRYIHQWEEIFHMTYDLASAVVRIF
BC000066 2 gcgccagctaaacaccacccctccactacctggatcaatgcgagggcat
cggtgttgtcattgttgttgtcgttgataagaattatcaatcgcttgtt
aacacctcccgcacggggcccccccccacggggctcgctcgcttgtccc
HCN3_HUMAN 253 NLIGMMLLLCHWDGCLQFLVPMLQDFPPDCWVSINHMVNHSWGRQYSHA
NLIGMMLLLCHWDGCLQFLVPMLQDFPPDCWVSINHMVNHSWGRQYSHA
NLIGMMLLLCHWDGCLQFLVPMLQDFPPDCWVSINHMVNHSWGRQYSHA
BC000066 149 acagaaccctctggtcctcgcaccgtccgttgtaacagacttgccttcg
attgtttttgagaggtatttcttaatccaggtctaattaacgggaacac
cctgggggatcgtctggcggcgggcctcccgcccccggccggccgtctc
HCN3_HUMAN 302 LFKAMSHMLCIGYGQQAPVGMPDVWLTMLSMIVGATCYAMFIGHATALI
LFKAMSHMLCIGYGQQAPVGMPDVWLTMLSMIVGATCYAMFIGHATALI
LFKAMSHMLCIGYGQQAPVGMPDVWLTMLSMIVGATCYAMFIGHATALI
BC000066 296 ctagaacactagtgccgcggacggtcaacaaagggattgatagcgagca
ttactgattgtgagaacctgtcatgtcttgtttgccgactttgaccctt
gcgcgccggctctgggatacgcccgccgccgcatcacccgccctcgacc
HCN3_HUMAN 351 QSLDSSRRQYQEKYKQVEQYMSFHKLPADTRQRIHEYYEHRYQGKMFDE
QSLDSSRRQYQEKYKQVEQYMSFHKLPADTRQRIHEYYEHRYQGKMFDE
QSLDSSRRQYQEKYKQVEQYMSFHKLPADTRQRIHEYYEHRYQGKMFDE
BC000066 443 ctcgttccctcgatacggctattcaccggacccacgttgcctcgaatgg
actaccggaaaaaaaataaatctaatccacgagtaaaaaagaagattaa
gcgctcgtgcgggcgggggcgcccggaacgggcccgctgcccgcggctg
HCN3_HUMAN 400 ESILGELSEPLREEIINFTCRGLVAHMPLFAHADPSFVTAVLTKLRFEV
ESILGELSEPLREEIINFTCRGLVAHMPLFAHADPSFVTAVLTKLRFEV
ESILGELSEPLREEIINFTCRGLVAHMPLFAHADPSFVTAVLTKLRFEV
BC000066 590 gaacggcagcccggaaatatcgcggcacctgcggcatgaggcaacctgg
agttgatgactgaattatcgggttcatcttcacacgttccttcatgtat
accgcggcggtcggctccctgcggccgggtctcccccctatccgtctgc
HCN3_HUMAN 449 FQPGDLVVREGSVGRKMYFIQHGLLSVLARGARDTRLTDGSYFGEICLL
FQPGDLVVREGSVGRKMYFIQHGLLSVLARGARDTRLTDGSYFGEICLL
FQPGDLVVREGSVGRKMYFIQHGLLSVLARGARDTRLTDGSYFGEICLL
BC000066 737 tccggcggcggtggaaattaccgccagcgcggcgaccaggtttggatcc
tacgatttgagctggatattaagttgttcggcgacgtcagcatgatgtt
cgggtcggtgccgggggcccgtggctggccccgcaccctacctggccga
HCN3_HUMAN 498 TRGRRTASVRADTYCRLYSLSVDHFNAVLEEFPMMRRAFETVAMDRLLR
TRGRRTASVRADTYCRLYSLSVDHFNAVLEEFPMMRRAFETVAMDRLLR
TRGRRTASVRADTYCRLYSLSVDHFNAVLEEFPMMRRAFETVAMDRLLR
BC000066 884 aagccagagcggattccttcaggctaggcggtcaaccgtgaggagcccc
cggggccgtgcacaggtactgtaatacttaatcttggctactctagttg
tgcgcacttgtccccctcaccgctcttgtggccggcgctgtgcgtggcc
HCN3_HUMAN 547 IGKKNSILQRKRSEPSPGSSGGIMEQHLVQHDRDMARGVRGRAPSTGAQ
IGKKNSILQRKRSEPSPGSSGGIMEQHLVQHDRDMARGVRGRAPSTGAQ
IGKKNSILQRKRSEPSPGSSGGIMEQHLVQHDRDMARGVRGRAPSTGAQ
BC000066 1031 agaaatacccactgcacgaaggaagcctgccgagagcggcgcgcaaggc
tgaaacttagagcacgcgggggttaaattaaagatcggtgggccgcgca
ccggtcaggggccgataccttccgggcggatcacgtgttgtgcgcaatg
HCN3_HUMAN 596 LSGKPVLWEPLVHAPLQAAAVTSNVAIALTHQRGPLPLSPDSPATLLAR
LSGKPVLWEPLVHAPLQAAAVTSNVAIALTHQRGPLPLSPDSPATLLAR
LSGKPVLWEPLVHAPLQAAAVTSNVAIALTHQRGPLPLSPDSPATLLAR
BC000066 1178 cagacgctgccgcgcccggggataggagcacccgcccctcgtcgaccgc
tggacttgacttacctaccctccatctctcaaggctctccaccccttcg
ttagaagggagatgctgattgcctgctcgttggctgccctctacccttc
HCN3_HUMAN 645 SAWRSAGSPASPLVPVRAGPWASTSRLPAPPARTLHASLSRAGRSQVSL
SAWRSAGSPASPLVPVRAGPWASTSRLPAPPARTLHASLSRAGRSQVSL
SAWRSAGSPASPLVPVRAGPWASTSRLPAPPARTLHASLSRAGRSQVSL
BC000066 1325 tgtctggtcgtccgcgcggctgtatcccgccgcaccgactcggctcgtc
ccggccgcccccttctgcgcgccccgtcccccgctacgtcgcggcatct
ttgcaactatcgggccatcagaccccgccatcacgcccacgagccgccg
HCN3_HUMAN 694 LGPPPGGGGRRLGPRGRPLSASQPSLPQRATGDGSPGRKGSGSERLPPS
LGPPPGGGGRRLGPRGRPLSASQPSLPQRATGDGSPGRKGSGSERLPPS
LGPPPGGGGRRLGPRGRPLSASQPSLPQRATGDGSPGRKGSGSERLPPS
BC000066 1472 cgcccggggcccgccgccctgtcctccccgagggtcgcagtgagcccct
tgcccggggggtgcgggctcccacctcagccgagccggagcggagtccc
gtctaaataggaatgccacaccactgtggaactcttgtgaaatgggtca
HCN3_HUMAN 743 GLLAKPPRTAQPPRPPVPEPATPRGLQLSANM
GLLAKPPRTAQPPRPPVPEPATPRGLQLSANM
GLLAKPPRTAQPPRPPVPEPATPRGLQLSANM
BC000066 1619 gccgaccaagcccaccgcgcgaccgccctgaa
gttcaccgccaccgcctcaccccggtatccat
gcgcatagacgccgaagtgacacgtcgttccg
//
cmbi.ru.nl), 24-Jul-2003