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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 283.00 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         7 FPVLKNDNLLRAARGEVVDRVPVWVMRQAGRYLP                
                     FP LKND  LRAA GE  D  PVW MRQAGRYLP                
                     FPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLP                
HS307871        1758 tcgcaagatccggtgggagtacgttaccggcttc                
                     tcataaacttgccggaacaacctggtgacggatc                
                     tggggtcacgaacgagaacctctgcgcgactcaa                


drosophila        41                           FQELRKHHDFFTVCRTPELACEV 
                                               F+E R   DFF+ CR+PE  CE+ 
                               E:E[gag]        FRETRAAQDFFSTCRSPEACCEL 
HS307871        1860 GGTAAGAG  Intron 1   CAGAGtagacggcgttaatctcggttgc 
                      <1-----[1861 : 1975]-1>  tgacgccaattgcggccacggat 
                                               tgacgtcgctccgtcttgcctag 


drosophila        65 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        89                        ALGLTVEMHAGVGPVLPQPIVVPEDL 
                                            ALG+ V M  G GP  P+P+   +DL 
                                            ALGMEVTMVPGKGPSFPEPLREEQDL 
HS307871        2195 GTACCCA  Intron 3   CAGgcgaggaagcgagcatcgctaggcgc 
                     <0-----[2195 : 2433]-0>ctgtatcttcgagcgtcactgaaaat 
                                            agcgggcgatcaacccagaaaaggca 


drosophila       115 KRLT-PDGALSRLSYVGDAITMMRHKLEGRVPLIGFTGAP          
                     +RL  P+   S L YV  AIT+ R +L GRVPLIGF GAP          
                     ERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAP          
HS307871        2512 gcccgcggggtgcgtgtcgaacaccccggcgccagtgggc          
                     agtgacattccatgattactctcgagtcggtcttgtcgcc          
                     acagtaagactgactgcaccctcaaagtatgggtctttca          


drosophila       154                        WTLMGYMIEGGGSKTMSKAKAWLNEH 
                                            WTLM YM+EGGGS TM++AK WL +  
                                            WTLMTYMVEGGGSSTMAQAKRWLYQR 
HS307871        2632 GTAATGT  Intron 4   TAGtacaatagggggtaaagcgactctca 
                     <0-----[2632 : 2748]-0>gcttcattagggcgctcacaggtaag 
                                            gcggacgtgttcaccgtgcgcgctga 


drosophila       180 PEDSKLFLNLLTDAIVDYLEMQVKAGAQ                      
                     P+ S  +L +LTDA+V YL  QV AGAQ                      
                     PQASHQLLRILTDALVPYLVGQVVAGAQ                      
HS307871        2827 ccgacccccacaggcgctcggcgggggcGTGAGTC  Intron 5     
                     cacgaattgttcacttcattgattcgca<0-----[2911 : 3278]  
                     tgttcggtccctttgcatgaaaggttcg                      


drosophila       208    MLQVFESSAEHLSKEQFLQWCVPYLKRIRDELVDRLTKKAIPVVPM 
                         LQ+FES A HL  + F ++ +PY++ +  ++  RL +  +  VPM 
                        ALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVPM 
HS307871        3276 TAGgtcctgtcggccgccctaatgcctacgggacgagatcgggcgcgca 
                     -0>ctattacacgatgcattaatctcatgatcaatacgtgacgtcctct 
                        agggtgctagttcagcccgtagtccttgcgaggcggggacgaagcg 


drosophila       254                        TLFAKGAGHSLKEQSELGYDVIGLDW 
                                             +FAK    +L+E ++ GY+V+GLDW 
                                            IIFAKDGHFALEELAQAGYEVVGLDW 
HS307871        3417 GTGAGGA  Intron 6   TAGaatgaggctgcggcgcggtggggcgt 
                     <0-----[3417 : 3575]-0>tttcaagatctaatcacgaattgtag 
                                            ccttgtgttcggggcatctggtgtcg 


drosophila       280 TVDPLEA                          NLVGPNITLQGNLDPQ 
                     TV P +A                            VG  +TLQGNLDP  
                     TVAPKKA           R:R[cgg]       ECVGKTVTLQGNLDPC 
HS307871        3654 aggcaagCGGTAAGCC  Intron 7   CAGGgtggaagatcgacgct 
                     ctccaac  <2-----[3677 : 3779]-2> agtgactctagatacg 
                     agcagac                          gtgggggaggccgcct 


drosophila       304 DMYRDP                       DELRNLTTEMVHKFGKSRYI 
                      +Y                          +E+  L  +M+  FG  RYI 
                     ALYASE                       EEIGQLVKQMLDDFGPHRYI 
HS307871        3829 gttgtgGTAACAG  Intron 8   CAGggagctgacacggtgcccta 
                     ctacca<0-----[3847 : 4178]-0>aatgattaattaatgcagat 
                     cgtatg                       ggcggggggggtctaatcct 


drosophila       330 ANLGHGITPQTPITSMEVLVEAVHK                         
                     ANLGHG+ P      +   V+AVHK                         
                     ANLGHGLYPDMDPEHVGAFVDAVHK                         
HS307871        4239 gatgcgctcgagcgcgggtggggca                         
                     catgagtacatacaatgcttactaa                         
                     ccgctgtttcgcaatgcctgttgta                         


//
Gene 1
Gene 1758 4313 
  Exon 1758 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 4313 phase 0
//


 

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