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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:       mus
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 669.55 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

mus                1 MEANGF                          LQNFPELKNDTFLRAAW 
                     MEANG+                           Q FPELKNDTFLRAAW 
                     MEANGL           G:G[gga]       PQGFPELKNDTFLRAAW 
HS307871        1107 aggagtGGGTGAGTT  Intron 1   CAGAccgtcgcaagatccggt 
                     tacagt  <2-----[1127 : 1747]-2> cagtcataaacttgccg 
                     gagtgg                          tgttggggtcacgaacg 


mus               25 GEETDYTPVWCMRQAGRYLP                          FRE 
                     GEETDYTPVWCMRQAGRYLP                          FRE 
                     GEETDYTPVWCMRQAGRYLP          E:E[gag]        FRE 
HS307871        1800 gggagtacgttaccggcttcGGTAAGAG  Intron 2   CAGAGtag 
                     gaacaacctggtgacggatc <1-----[1861 : 1975]-1>  tga 
                     agaacctctgcgcgactcaa                          tga 


mus               49 TRAAQDFFSTCRSPEACCELTLQ                       PLR 
                     TRAAQDFFSTCRSPEACCELTLQ                       PLR 
                     TRAAQDFFSTCRSPEACCELTLQ                       PLR 
HS307871        1987 acggcgttaatctcggttgcaccGTGAGGG  Intron 3   CAGccc 
                     cgccaattgcggccacggatcta<0-----[2056 : 2131]-0>ctg 
                     cgtcgctccgtcttgcctagtgg                       agt 


mus               75 RFPLDAAIIFSDILVVPQ                       ALGMEVTM 
                     RF LDAAIIFSDILVVPQ                       ALGMEVTM 
                     RFLLDAAIIFSDILVVPQ                       ALGMEVTM 
HS307871        2141 ctccgggaattgacggccGTACCCA  Intron 4   CAGgcgaggaa 
                     gtttacctttcattttca<0-----[2195 : 2433]-0>ctgtatct 
                     cctgttcctccccttacg                       agcgggcg 


mus              101 VPGKGPSFPEPLREERDLERLRDPAAAASELGYVFQAITLTRQRLAGRV 
                     VPGKGPSFPEPLREE+DLERLRDP   ASELGYVFQAITLTRQRLAGRV 
                     VPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRV 
HS307871        2458 gcgagcatcgctaggcgcgcccgcggggtgcgtgtcgaacaccccggcg 
                     tcgagcgtcactgaaaatagtgacattccatgattactctcgagtcggt 
                     atcaacccagaaaaggcaacagtaagactgactgcaccctcaaagtatg 


mus              150 PLIGFAGAP                       WTLMTYMVEGGSSSTMA 
                     PLIGFAGAP                       WTLMTYMVEGG SSTMA 
                     PLIGFAGAP                       WTLMTYMVEGGGSSTMA 
HS307871        2605 ccagtgggcGTAATGT  Intron 5   TAGtacaatagggggtaaag 
                     cttgtcgcc<0-----[2632 : 2748]-0>gcttcattagggcgctc 
                     ggtctttca                       gcggacgtgttcaccgt 


mus              176 QAKRWLYQRPQASHKLLGILTDVLVPYLIGQVAAGAQ             
                     QAKRWLYQRPQASH+LL ILTD LVPYL+GQV AGAQ             
                     QAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQ             
HS307871        2800 cgactctcaccgacccccacaggcgctcggcgggggc             
                     acaggtaagcacgaattgttcacttcattgattcgca             
                     gcgcgctgatgttcggtccctttgcatgaaaggttcg             


mus              213                        ALQLFESHAGHLGTELFSKFALPYIR 
                                            ALQLFESHAGHLG +LF+KFALPYIR 
                                            ALQLFESHAGHLGPQLFNKFALPYIR 
HS307871        2911 GTGAGTC  Intron 6   TAGgtcctgtcggccgccctaatgcctac 
                     <0-----[2911 : 3278]-0>ctattacacgatgcattaatctcatg 
                                            agggtgctagttcagcccgtagtcct 


mus              239 DVAKRVKAGLQKAGLAPVPM                       IIFAKD 
                     DVAK+VKA L++AGLAPVPM                       IIFAKD 
                     DVAKQVKARLREAGLAPVPM                       IIFAKD 
HS307871        3357 gggacgagatcgggcgcgcaGTGAGGA  Intron 7   TAGaatgag 
                     atcaatacgtgacgtcctct<0-----[3417 : 3575]-0>tttcaa 
                     tgcgaggcggggacgaagcg                       ccttgt 


mus              265 GHFALEELAQAGYEVVGLDWTVAPKKA                       
                     GHFALEELAQAGYEVVGLDWTVAPKKA                       
                     GHFALEELAQAGYEVVGLDWTVAPKKA           R:R[cgg]    
HS307871        3594 gctgcggcgcggtggggcgtaggcaagCGGTAAGCC  Intron 8    
                     gatctaatcacgaattgtagctccaac  <2-----[3677 : 3779] 
                     gttcggggcatctggtgtcgagcagac                       


mus              292     ERVGKAVTLQGNLDPCALYASE                        
                         E VGK VTLQGNLDPCALYASE                        
                         ECVGKTVTLQGNLDPCALYASE                        
HS307871        3777 CAGGgtggaagatcgacgctgttgtgGTAACAG  Intron 9   CAG 
                     -2> agtgactctagatacgctacca<0-----[3847 : 4178]-0> 
                         gtgggggaggccgcctcgtatg                        


mus              315 EEIGRLVQQMLDDFGPQRYIANLGHGLYPDMDPERVGAFVDAVHKHSRL 
                     EEIG+LV+QMLDDFGP RYIANLGHGLYPDMDPE VGAFVDAVHKHSRL 
                     EEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSRL 
HS307871        4179 ggagctgacacggtgccctagatgcgctcgagcgcgggtggggcactcc 
                     aatgattaattaatgcagatcatgagtacatacaatgcttactaaacgt 
                     ggcggggggggtctaatcctccgctgtttcgcaatgcctgttgtacatg 


mus              364 LRQN                                              
                     LRQN                                              
                     LRQN                                              
HS307871        4326 ccca                                              
                     tgaa                                              
                     tagc                                              


//
Gene 1
Gene 1107 4337 
  Exon 1107 1126 phase 0
  Exon 1748 1860 phase 2
  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 4337 phase 0
//


 

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