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SEQUENCE ANALYSIS
 
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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:       drosophila
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            local
Target Sequence      HS307871
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 244.02 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

drosophila        16 QAFPPLKNDNLLRAARGEVVDRVPVWVMRQAGRYLP              
                     Q FP LKND  LRAA GE  D  PVW MRQAGRYLP              
                     QGFPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLP              
HS307871        1752 cgtcgcaagatccggtgggagtacgttaccggcttc              
                     agtcataaacttgccggaacaacctggtgacggatc              
                     gttggggtcacgaacgagaacctctgcgcgactcaa              


drosophila        52                           FQELRKQHDFFTVCRTPELACEV 
                                               F+E R   DFF+ CR+PE  CE+ 
                               E:E[gag]        FRETRAAQDFFSTCRSPEACCEL 
HS307871        1860 GGTAAGAG  Intron 1   CAGAGtagacggcgttaatctcggttgc 
                      <1-----[1861 : 1975]-1>  tgacgccaattgcggccacggat 
                                               tgacgtcgctccgtcttgcctag 


drosophila        76 TMQ                       PLRRFDLDASIIFSDILVIPQ   
                     T+Q                       PLRRF LDA+IIFSDILV+PQ   
                     TLQ                       PLRRFLLDAAIIFSDILVVPQ   
HS307871        2047 accGTGAGGG  Intron 2   CAGcccctccgggaattgacggcc   
                     cta<0-----[2056 : 2131]-0>ctggtttacctttcattttca   
                     tgg                       agtcctgttcctccccttacg   


drosophila       100                        ALGLTVEMHAGVGPVLPQPICTPEDL 
                                            ALG+ V M  G GP  P+P+   +DL 
                                            ALGMEVTMVPGKGPSFPEPLREEQDL 
HS307871        2195 GTACCCA  Intron 3   CAGgcgaggaagcgagcatcgctaggcgc 
                     <0-----[2195 : 2433]-0>ctgtatcttcgagcgtcactgaaaat 
                                            agcgggcgatcaacccagaaaaggca 


drosophila       126 KRLT-PDGALSRLTYVGDAITMMRHKLDGRVPLIGFTGAP          
                     +RL  P+   S L YV  AIT+ R +L GRVPLIGF GAP          
                     ERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAP          
HS307871        2512 gcccgcggggtgcgtgtcgaacaccccggcgccagtgggc          
                     agtgacattccatgattactctcgagtcggtcttgtcgcc          
                     acagtaagactgactgcaccctcaaagtatgggtctttca          


drosophila       165                        WTLMGYMIEGGGSKTMSKAKAWLTNY 
                                            WTLM YM+EGGGS TM++AK WL    
                                            WTLMTYMVEGGGSSTMAQAKRWLYQR 
HS307871        2632 GTAATGT  Intron 4   TAGtacaatagggggtaaagcgactctca 
                     <0-----[2632 : 2748]-0>gcttcattagggcgctcacaggtaag 
                                            gcggacgtgttcaccgtgcgcgctga 


drosophila       191 PEDTKLFLILLTDVIVDYLEMQVIAGAQ                      
                     P+ +  +L +LTD +V YL  QV+AGAQ                      
                     PQASHQLLRILTDALVPYLVGQVVAGAQ                      
HS307871        2827 ccgacccccacaggcgctcggcgggggcGTGAGTC  Intron 5     
                     cacgaattgttcacttcattgattcgca<0-----[2911 : 3278]  
                     tgttcggtccctttgcatgaaaggttcg                      


drosophila       219    MLQVFESSAEHLSKEEFLLGSEPYLRRIRDDLVDRLTKKVIPAVPL 
                         LQ+FES A HL  + F   + PY+R +   +  RL +  +  VP  
                        ALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVP- 
HS307871        3276 TAGgtcctgtcggccgccctaatgcctacgggacgagatcgggcgcgc  
                     -0>ctattacacgatgcattaatctcatgatcaatacgtgacgtcctc  
                        agggtgctagttcagcccgtagtccttgcgaggcggggacgaagc  


drosophila       265 VSSYPNNIFTLLTYLISLL                       IIFAKGA 
                                       +                       IIFAK   
                     ------------------M                       IIFAKDG 
HS307871        3414                   aGTGAGGA  Intron 6   TAGaatgagg 
                                       t<0-----[3417 : 3575]-0>tttcaag 
                                       g                       ccttgtg 


drosophila       291 GHSLKEQSELGYDVIGLDWTVDPVEA                        
                       +L+E ++ GY+V+GLDWTV P +A                        
                     HFALEELAQAGYEVVGLDWTVAPKKA           R:R[cgg]     
HS307871        3597 ctgcggcgcggtggggcgtaggcaagCGGTAAGCC  Intron 7     
                     atctaatcacgaattgtagctccaac  <2-----[3677 : 3779]  
                     ttcggggcatctggtgtcgagcagac                        


drosophila       317     AVVGPNITLQGNLDPQSMYCEP                        
                           VG  +TLQGNLDP ++Y                           
                         ECVGKTVTLQGNLDPCALYASE                        
HS307871        3777 CAGGgtggaagatcgacgctgttgtgGTAACAG  Intron 8   CAG 
                     -2> agtgactctagatacgctacca<0-----[3847 : 4178]-0> 
                         gtgggggaggccgcctcgtatg                        


drosophila       340 NELRSLATEMVHKCGKSRYIANVGHGITPQTPITSMEVLVEAAH      
                      E+  L  +M+   G  RYIAN+GHG+ P      +   V+A H      
                     EEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVH      
HS307871        4179 ggagctgacacggtgccctagatgcgctcgagcgcgggtggggc      
                     aatgattaattaatgcagatcatgagtacatacaatgcttacta      
                     ggcggggggggtctaatcctccgctgtttcgcaatgcctgttgt      


//
Gene 1
Gene 1752 4310 
  Exon 1752 1860 phase 0
  Exon 1976 2055 phase 1
  Exon 2132 2194 phase 0
  Exon 2434 2631 phase 0
  Exon 2749 2910 phase 0
  Exon 3279 3416 phase 0
  Exon 3576 3676 phase 0
  Exon 3780 3846 phase 2
  Exon 4179 4310 phase 0
//


 

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