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:       Secp43
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            global
Target Sequence      subseq(1858753,3500)
Strand:              forward
Start/End (protein)  global
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           flat
Algorithm            623

genewise output
Score 74.56 bits over entire alignment
Scores as bits over a flat simple random model

Warning: The bits scores is not probablistically correct for single seqs
See WWW help for more info

Secp43             1 masvhcqlwmgslesymtenfiiaafrkmgedpttvrlmrnkytgepag 
                          + ++++++++ +++  +   ++ ++     +++ ++  + +  + 
                     PSFSTASLYVGDLNEDVTEAVLYEIFNTVGH-VSSIRVCRDSVTRKSLG 
subseq(1858753,  979 cattagtctgggcagggagggctgataaggc gttaagtcgagaaatcg 
                     cgtcccctatgataaatcacttaattactga tcctgtggagtcgactg 
                     actccccgtagtgtgtgggattcatccatat gactaatatcaaaaagt 


Secp43            50 ycfvnfisddhaldamhklngkpipgtnpivrfrlnsasnsyklpgner 
                     ++++++ +   +  ++  ++   +++    +     + +  +   ++   
                     YAYVNYHNLADAERALDTLNYTNIKGQPARLMWSHRDPSLRKSGAGN-- 
subseq(1858753, 1123 tgtgatcatggggagcgatataaaagccgacatacagcttaaaggga   
                     acataaaatcacagctactaacatagaccgttggagacctgaggcga   
                     catgtctcaataaaagcgactataaagaaacggttacaggaattatt   


Secp43            99 efsvwvgdlssdvddyqlykvfsskftsiktakvildslgfskgygfvr 
                        +++ ++++ ++++ ++  ++  + ++   +++ ++++ ++ +++++ 
                     ---IFVKNLDKSIDNKALFDTFSM-FGNILSCKVATDEFGKSKSYGFVH 
subseq(1858753, 1264    atgaacgatagaagctgataa tgaatttaggaggtgaaaatgtgc 
                        tttaataactaaacttactgt tgattcgatccaatgagagagtta 
                        tcggctcgtattgtattgctg cattggtgtcgcatagcattattt 


Secp43           148 fgiedeqksalydmngyiglgtkpikicnavpkpkselggavgegntny 
                     +  ++  ++++ ++++ + ++ + + + + ++  +      +      + 
                     YEDEESAKEAIEKVNG-IQLGSKNVYVGHFIKRSERATNDTKFTNLYVK 
subseq(1858753, 1399 tggggagaggagagag actgtaagtggctaaatgagaagaataactga 
                     aaaaagcaactaatag tatgcaatatgattagcagccaacatcatata 
                     tatggtagaccagata tgaagatacgctttaggagtgctcgcccgtgg 


Secp43           197 gygsgmtaaggtd-ysqyydptstywqgyqa-----wqgyyeqagasit 
                      + + ++ +  ++ ++ + + ++   +  ++        + +   ++ + 
                     NFPDSVTEAHLKQLFSPYGEITSMIVKTDNKNRKFCFINYADSESAKNA 
subseq(1858753, 1543 atcgagaggctacctactggaataagaagaaaaatttaatggtgagaag 
                     atcagtcacataattgcagatcctttacaaaagatgttaacacagcaac 
                     ttactttgacgaagctataatacgtgagctgtagtttctttttataatt 


Secp43           240 daaayyqqamsqshsnpqtlaqhaeawsaqrsaqyeqqqqqqtasaang 
                           ++  +++  +    +++ ++ ++   ++   ++   +++ +++ 
                     MENLNGKKITDDGQIDHTYDAKKEEAENA--NANNGTNNGIATGADANG 
subseq(1858753, 1690 agacagaaaagggcagcatggaaggggag  agaagaaagagaggggag 
                     taatagaatcaagataacaacaaaacaac  acaagcaagtccgcacag 
                     gatgtagacccttaactgctgagaaggta  taccgcctttcatatttc 


Secp43           289 aede-------nglvehkf--vldvdklnreaidadrrlydalesskwl 
                      + +        ++ +++     +  + +++   + +      ++ +   
                     VEGEVGKGTTVDGKGDNKVSTAGDTGKSGEETEGGANTTGATSESVKGN 
subseq(1858753, 1831 ggggggagaagggaggaagtagggagaagggaggggaaaggatgtgaga 
                     tagatgagcctagagaaatcccgacgaggaacaggcaccgcccactaga 
                     aaaactaaaactagaccattttataaataaataaaccctgactaagagt 


Secp43           329 pieqlevf                                          
                       ++++                                            
                     EGNKVESD                                          
subseq(1858753, 1978 ggaaggtg                                          
                     agaataca                                          
                     atcgcatt                                          


//
Gene 1
Gene 979 2001 
  Exon 979 2001 phase 0
//
>subseq(1858753,3500).[979:2001].sp.tr
PSFSTASLYVGDLNEDVTEAVLYEIFNTVGHVSSIRVCRDSVTRKSLGYAYVNYHNLADA
ERALDTLNYTNIKGQPARLMWSHRDPSLRKSGAGNIFVKNLDKSIDNKALFDTFSMFGNI
LSCKVATDEFGKSKSYGFVHYEDEESAKEAIEKVNGIQLGSKNVYVGHFIKRSERATNDT
KFTNLYVKNFPDSVTEAHLKQLFSPYGEITSMIVKTDNKNRKFCFINYADSESAKNAMEN
LNGKKITDDGQIDHTYDAKKEEAENANANNGTNNGIATGADANGVEGEVGKGTTVDGKGD
NKVSTAGDTGKSGEETEGGANTTGATSESVKGNEGNKVESD
//
>subseq(1858753,3500).[979:2001].sp
CCAAGCTTTTCCACCGCCTCCCTGTATGTAGGGGATCTGAATGAGGATGTGACGGAGGCA
GTTCTTTACGAAATTTTCAACACAGTTGGACATGTGTCATCCATTAGAGTATGTCGAGAT
AGCGTAACAAGAAAATCACTGGGTTACGCATATGTGAATTACCATAACTTAGCAGATGCA
GAAAGAGCACTGGACACGTTAAACTATACAAATATAAAAGGACAGCCAGCAAGACTCATG
TGGAGTCATAGAGACCCATCGTTGAGAAAAAGTGGTGCAGGTAATATTTTCGTGAAGAAC
CTTGACAAGTCTATAGATAATAAGGCTCTATTTGATACGTTCAGTATGTTCGGAAATATT
TTGTCGTGTAAGGTTGCCACGGACGAATTTGGAAAGAGCAAAAGTTATGGATTTGTTCAT
TATGAAGATGAGGAGAGTGCAAAGGAAGCCATCGAAAAGGTAAATGGAATTCAGTTAGGA
TCGAAAAATGTATACGTGGGCCATTTTATTAAAAGGTCGGAAAGGGCTACGAACGATACC
AAGTTCACCAACCTGTATGTGAAGAATTTTCCAGACAGTGTTACTGAGGCACACTTGAAA
CAACTGTTCAGTCCATATGGAGAAATTACATCCATGATTGTGAAAACGGACAATAAGAAT
AGAAAGTTTTGTTTTATCAATTATGCTGATTCTGAAAGTGCAAAAAATGCTATGGAAAAT
CTGAATGGAAAGAAAATCACCGACGATGGTCAAATAGACCATACGTACGATGCGAAAAAG
GAAGAAGCGGAGAATGCAAATGCAAACAACGGGACCAACAATGGTATTGCCACAGGTGCA
GATGCTAATGGCGTAGAAGGAGAAGTCGGTAAAGGAACAACAGTCGATGGAAAGGGAGAC
AACAAAGTTTCTACTGCTGGAGATACAGGAAAAAGTGGAGAAGAAACTGAAGGAGGAGCC
AACACCACTGGGGCAACCTCTGAATCAGTGAAAGGGAATGAAGGTAACAAGGTCGAATCT
GAT
//