NucleaRDB: Pairwise Alignments

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:       O16665_CAEEL
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            default
Target Sequence      AF016675_7
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 1018.58 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.

O16665_CAEEL       1 MNQVSTSTSPFCCRICDQRAHGNHFGVISCRACAAFFRRTASGKWDNQK 
                     MNQVSTSTSPFCCRICDQRAHGNHFGVISCRACAAFFRRTASGKWDNQK 
                     MNQVSTSTSPFCCRICDQRAHGNHFGVISCRACAAFFRRTASGKWDNQK 
AF016675_7         1 aacgtatatctttaatgcagcgactggaatcgtggttaaagtgatgaca 
                     taatcccccctgggtgaagcagaatgttgggcgccttggcccgagaaaa 
                     gcactgattatctatctgattccctattttggttttcaatttgagtcag 


O16665_CAEEL      50 CRGGSCDKKTYYCKPCRLQKCRDMGMDTTKFQFNRDNIPTAGQFQLPPQ 
                     CRGGSCDKKTYYCKPCRLQKCRDMGMDTTKFQFNRDNIPTAGQFQLPPQ 
                     CRGGSCDKKTYYCKPCRLQKCRDMGMDTTKFQFNRDNIPTAGQFQLPPQ 
AF016675_7       148 tcggttgaaatttactatcatcgagagaaatctacgaacaggctccccc 
                     ggggcgaaacaagacggtaaggatgtaccatatagaatcccgatatcca 
                     ttagtttgagcccagtaaaatacgagctcacaccacctccttacactga 


O16665_CAEEL      99 TFEAYVGRPEFLLFCDTDAPNSKVLIDVRYLLEEAGRLLNNGIITPIWA 
                     TFEAYVGRPEFLLFCDTDAPNSKVLIDVRYLLEEAGRLLNNGIITPIWA 
                     TFEAYVGRPEFLLFCDTDAPNSKVLIDVRYLLEEAGRLLNNGIITPIWA 
AF016675_7       295 atggtggccgtccttgaggcatagcaggatccggggcctaagaaacatg 
                     ctacatggcattttgacaccacatttatgattaacggttaagttcctgc 
                     tcattcagcacgccttcttaccacgaccacctaaccgagttgtcaatgt 


O16665_CAEEL     148 ENQLKKLTQGFKHIKLDTDNIKKVETADQKEFMEMWEYYFITVTKWLMY 
                     ENQLKKLTQGFKHIKLDTDNIKKVETADQKEFMEMWEYYFITVTKWLMY 
                     ENQLKKLTQGFKHIKLDTDNIKKVETADQKEFMEMWEYYFITVTKWLMY 
AF016675_7       442 gaccaatacgtacaacgagaaaaggaggcagtagatgtttaagaattat 
                     aaataatcagtaatatacaataataccaaaattatgaaattctcagtta 
                     atagggggactgctggtatcaggtatgtgagtgggggctttggaggggc 


O16665_CAEEL     197 FDEFQKLNRQIQMTMLQAIWHVFSKLHKYVATSAYQKATPRAKPTEVII 
                     FDEFQKLNRQIQMTMLQAIWHVFSKLHKYVATSAYQKATPRAKPTEVII 
                     FDEFQKLNRQIQMTMLQAIWHVFSKLHKYVATSAYQKATPRAKPTEVII 
AF016675_7       589 tggtcataacacaaaccgatcgtaatcatggatgtcagaccgacaggaa 
                     taataatagatatcttactgattgataaatccccaaacccgcaccattt 
                     ccgcgggcaatggagcaaagtgccagcacgagcctaaggattaaaacta 


O16665_CAEEL     246 KDVMMDIETVNFDCSWMSDYPTKDVFKFLSAQACKEMDIVGTLHELDPT 
                     KDVMMDIETVNFDCSWMSDYPTKDVFKFLSAQACKEMDIVGTLHELDPT 
                     KDVMMDIETVNFDCSWMSDYPTKDVFKFLSAQACKEMDIVGTLHELDPT 
AF016675_7       736 aggaagagagatgtttaagtcaaggtatctgcgtagagaggaccgcgca 
                     aatttatactatagcgtgaaccaattattccacgaatattgctaatacc 
                     actggcaatgtccttggctcaagtttataccgtcgagtttttccggttt 


O16665_CAEEL     295 DLEITYLFAQLCFEYVGKRYQGDILRVAEQFQEILANDLHHYYVEEMNR 
                     DLEITYLFAQLCFEYVGKRYQGDILRVAEQFQEILANDLHHYYVEEMNR 
                     DLEITYLFAQLCFEYVGKRYQGDILRVAEQFQEILANDLHHYYVEEMNR 
AF016675_7       883 gcgaatttgccttgtggactcggacagggctcgatgagcccttgggaaa 
                     atatcattcatgtaatgagaagattgtcaataattcaataaaataatag 
                     cgacttgttatccattcaatgtttcaacggtaatggttattttgaagca 


O16665_CAEEL     344 PRYFQRLARLLKVNNAIQRAIWESRPKMELGRVFNVLKIEFSHPEMFED 
                     PRYFQRLARLLKVNNAIQRAIWESRPKMELGRVFNVLKIEFSHPEMFED 
                     PRYFQRLARLLKVNNAIQRAIWESRPKMELGRVFNVLKIEFSHPEMFED 
AF016675_7      1030 cattcatgactagaagacagatgaccaagcgcgtagcaagttccgatgg 
                     cgatagtcgttataactagctgaggcatatggttattatatcacattaa 
                     caccaaggacgatctatgaacggccgaggttagttggatgcgtgagcgc 


O16665_CAEEL     393 SGYY                                              
                     SGYY                                              
                     SGYY                                              
AF016675_7      1177 tgtt                                              
                     cgaa                                              
                     tatt                                              


//

F.Horn (nucleardbcmbi.kun.nl), 18-Feb-2005