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:       CAI16439.1
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            local
Target Sequence      U30787
Strand:              forward
Start/End (protein)  local
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 404.57 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

CAI16439.1         1 MEANGL                          PQGFPELKNDTFLRAAW 
                     MEANGL                          PQGFPELKNDTFLRAAW 
                     MEANGL           G:G[gga]       PQGFPELKNDTFLRAAW 
U30787          1107 aggagtGGGTGAGTT  Intron 1   CAGAccgtcgcaagatccggt 
                     tacagt  <2-----[1127 : 1747]-2> cagtcataaacttgccg 
                     gagtgg                          tgttggggtcacgaacg 


CAI16439.1        25 GEETDYTPVWCMRQAGRYLP                          FRE 
                     GEETDYTPVWCMRQAGRYLP                          FRE 
                     GEETDYTPVWCMRQAGRYLP          E:E[gag]        FRE 
U30787          1800 gggagtacgttaccggcttcGGTAAGAG  Intron 2   CAGAGtag 
                     gaacaacctggtgacggatc <1-----[1861 : 1975]-1>  tga 
                     agaacctctgcgcgactcaa                          tga 


CAI16439.1        49 TRAAQDFFSTCRSPEACCELTLQ                       ALG 
                     TRAAQDFFSTCRSPEACCELTLQ                       ALG 
                     TRAAQDFFSTCRSPEACCELTLQ                       ALG 
U30787          1987 acggcgttaatctcggttgcaccGTGAGGG  Intron 3   CAGgcg 
                     cgccaattgcggccacggatcta<0-----[2056 : 2433]-0>ctg 
                     cgtcgctccgtcttgcctagtgg                       agc 


CAI16439.1        75 MEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQR 
                     MEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQR 
                     MEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQR 
U30787          2443 aggaagcgagcatcgctaggcgcgcccgcggggtgcgtgtcgaacaccc 
                     tatcttcgagcgtcactgaaaatagtgacattccatgattactctcgag 
                     gggcgatcaacccagaaaaggcaacagtaagactgactgcaccctcaaa 


CAI16439.1       124 LAGRVPLIGFAGAP                       WTLMTYMVEGGG 
                     LAGRVPLIGFAGAP                       WTLMTYMVEGGG 
                     LAGRVPLIGFAGAP                       WTLMTYMVEGGG 
U30787          2590 cggcgccagtgggcGTAATGT  Intron 4   TAGtacaataggggg 
                     tcggtcttgtcgcc<0-----[2632 : 2748]-0>gcttcattaggg 
                     gtatgggtctttca                       gcggacgtgttc 


CAI16439.1       150 SSTMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQ        
                     SSTMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQ        
                     SSTMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQ        
U30787          2785 taaagcgactctcaccgacccccacaggcgctcggcgggggc        
                     cgctcacaggtaagcacgaattgttcacttcattgattcgca        
                     accgtgcgcgctgatgttcggtccctttgcatgaaaggttcg        


//
Gene 1
Gene 1107 2910 
  Exon 1107 1126 phase 0
  Exon 1748 1860 phase 2
  Exon 1976 2055 phase 1
  Exon 2434 2631 phase 0
  Exon 2749 2910 phase 0
//