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:       slap_pknowlesi_prot
Comp Matrix:         blosum62.bla
Gap open:            12
Gap extension:       2
Start/End            global
Target Sequence      subseq(150000,5000)
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           syn
Algorithm            623

genewise output
Score 1199.81 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

slap_pknowlesi_    1 MHVRGIQKNNDLTLLCQTTINLPPYSILNYGRVPNEGLNEITIMSILHQ 
                     MHVRGIQKNNDLTLLCQTTINLPPYSILNYGRVPNEGLNEITIMSILHQ 
                     MHVRGIQKNNDLTLLCQTTINLPPYSILNYGRVPNEGLNEITIMSILHQ 
subseq(150000,5 2935 acgcgacaaagcacttcaaaaccctaacatgcgcaggtagaaaaaatcc 
                     tatggtaaaaatcttgacctatccagttaaggtcaagtaatcttgttaa 
                     gcgcaaaatttcatgtaaacctctcccatcctcatgaacaaccgctgtg 


slap_pknowlesi_   50 ISSQN                          ----KNVKIGERENRIYS 
                     ISSQN                              KNVKIGERENRIYS 
                     ISSQN           -:L[tta]       CNSEKNVKIGERENRIYS 
subseq(150000,5 3082 attcaTTGTACGTA  Intron 1   CAGAtaagaagaaggcgacata 
                     tccaa  <2-----[3099 : 3219]-2> gagaaatatgagaagtag 
                     attat                          cccggctaagaggtaatc 


slap_pknowlesi_   69 ALVRNKYIGFGHGIG                          SGNLDDVQ 
                     ALVRNKYIGFGHGIG                          SGNLDDVQ 
                     ALVRNKYIGFGHGIG           -:R[agg]       SGNLDDVQ 
subseq(150000,5 3275 gcgcaatagtgcgagAGGTAAGCA  Intron 2   CAGGtgatgggc 
                     cttgaaatgtgagtg  <2-----[3322 : 3429]-2> cgataata 
                     gcgtcgcaatgcctc                          agcaccgg 


slap_pknowlesi_   92 PKSAGNSILAKATTSFVKDLIRSFGIKGCEDVYILPYATGMCLSTCLLY 
                     PKSAGNSILAKATTSFVKDLIRSFGIKGCEDVYILPYATGMCLSTCLLY 
                     PKSAGNSILAKATTSFVKDLIRSFGIKGCEDVYILPYATGMCLSTCLLY 
subseq(150000,5 3455 caaggaaacgagaaatgagtaaatgaagtgggtacctgagattaatctt 
                     cagcgagttcacccgttaattggtgtaggaatattcaccgtgtgcgtta 
                     tgctactcgagccaccagtacactaaaccgtgcaaactaggtattcggc 


slap_pknowlesi_  141 TKKEREKSEYVIVSRIDHKTCYKCIDFCALKYLVVDMVYKDEELFTNLN 
                     TKKEREKSEYVIVSRIDHKTCYKCIDFCALKYLVVDMVYKDEELFTNLN 
                     TKKEREKSEYVIVSRIDHKTCYKCIDFCALKYLVVDMVYKDEELFTNLN 
subseq(150000,5 3602 aaagagaagtgagtaagcaattatagttgtattgggagtagggttaaca 
                     caaagaagaatttcgtaaacgaagtatgctaatttattaaaaattcata 
                     aagaaaatataagtaattgcccgtctttcggtaagtgtcgtaaatacgc 


slap_pknowlesi_  190 EIERLIQTYGEKICCVMSVTSSYAPRNSDDIVKIAHICKRYNVPHIINN 
                     EIERLIQTYGEKICCVMSVTSSYAPRNSDDIVKIAHICKRYNVPHIINN 
                     EIERLIQTYGEKICCVMSVTSSYAPRNSDDIVKIAHICKRYNVPHIINN 
subseq(150000,5 3749 gagacacatggaattgatgatatgcaatggagaagcataatagccaaaa 
                     atagttacagaatggttctccgaccgacaattatcatgagaatcattaa 
                     aagagaaattgaattcgagatttaagtatctaaattttggttaacattt 


slap_pknowlesi_  239 AFGLQCNYLCKEIQKCFESKGRVDFVVQSCDKNFLVPVNGGIVFSSDKK 
                     AFGLQCNYLCKEIQKCFESKGRVDFVVQSCDKNFLVPVNGGIVFSSDKK 
                     AFGLQCNYLCKEIQKCFESKGRVDFVVQSCDKNFLVPVNGGIVFSSDKK 
subseq(150000,5 3896 gtgtctatttagacattgtagcggtggcatgaatcgcgaggagtatgaa 
                     ctgtagaatgaataagtacaggtatttaggaaatttctaggtttgcaaa 
                     ctaagcttgtaaagattagatagttgtgtttgtctcagccgcactctga 


slap_pknowlesi_  288 KMKELKKHYPGRTPVHAYLDLFITLLELGKKKILNLRKEREENFSWLQE 
                     KMKELKKHYPGRTPVHAYLDLFITLLELGKKKILNLRKEREENFSWLQE 
                     KMKELKKHYPGRTPVHAYLDLFITLLELGKKKILNLRKEREENFSWLQE 
subseq(150000,5 4043 aaagtaactcgaacgcgttgctaatcgtgaaaacacaagaggattttcg 
                     ataataaaacggcctacatatttcttatgaaattatgaagaaatcgtaa 
                     ggaaaagccttaccgtatattctaaaaagaaatacaaagggattcggga 


slap_pknowlesi_  337 KVSTLCSKYNLTLIKASKNKISMAINLNELYNICHILNPKSITLLGSLL 
                     KVSTLCSKYNLTLIKASKNKISMAINLNELYNICHILNPKSITLLGSLL 
                     KVSTLCSKYNLTLIKASKNKISMAINLNELYNICHILNPKSITLLGSLL 
subseq(150000,5 4190 agtacttatatataagaaaaatagaatagctaatcacacaaaaccgtcc 
                     atcctgcaaatcttacgaaatctctataataatgattacagtcttgctt 
                     atttccagctatgcatcataacgcttatatcttcttacggttcacttat 


slap_pknowlesi_  386 FYRNVTGHRVICSPLLIRNGGVAQRRDQQIQTNVEPAFPIHHGAVDPNE 
                     FYRNVTGHRVICSPLLIRNGGVAQRRDQQIQTNVEPAFPIHHGAVDPNE 
                     FYRNVTGHRVICSPLLIRNGGVAQRRDQQIQTNVEPAFPIHHGAVDPNE 
subseq(150000,5 4337 ttaagagcagattcttacaggggcaagccacaaggcgtcaccggggcag 
                     tagatcgagttgcctttgaggtcaggaaatacatacctctaagctacaa 
                     ttattcgtgtaccgggactgagagaacgatgttaatatcttcgaatctg 


slap_pknowlesi_  435 VPTIEQGAHTDGEFFPNRGKKSEDAHQIRSSDNCNEECVGKEGSQINLV 
                     VPTIEQGAHTDGEFFPNRGKKSEDAHQIRSSDNCNEECVGKEGSQINLV 
                     VPTIEQGAHTDGEFFPNRGKKSEDAHQIRSSDNCNEECVGKEGSQINLV 
subseq(150000,5 4484 gcaagcggcagggttcacgaaagggccacttgataggtggaggtcaacg 
                     tcctaagcacagattcaggaagaacaatgccaagaaagtgaagcatatt 
                     tcatggtacctaatcattaggcatatactcactctgacaaaagcaatgg 


slap_pknowlesi_  484 KNENMNDARIHGKG                                    
                     KNENMNDARIHGKG                                    
                     KNENMNDARIHGKG                                    
subseq(150000,5 4631 aagaaaggaacgag                                    
                     aaaataacgtagag                                    
                     gcatgttaattaag                                    


//
Gene 1
Gene 2935 4672 
  Exon 2935 3098 phase 0
  Exon 3220 3321 phase 2
  Exon 3430 4672 phase 2
//
>subseq(150000,5000).[2935:4672].sp.tr
MHVRGIQKNNDLTLLCQTTINLPPYSILNYGRVPNEGLNEITIMSILHQISSQNLCNSEK
NVKIGERENRIYSALVRNKYIGFGHGIGRSGNLDDVQPKSAGNSILAKATTSFVKDLIRS
FGIKGCEDVYILPYATGMCLSTCLLYTKKEREKSEYVIVSRIDHKTCYKCIDFCALKYLV
VDMVYKDEELFTNLNEIERLIQTYGEKICCVMSVTSSYAPRNSDDIVKIAHICKRYNVPH
IINNAFGLQCNYLCKEIQKCFESKGRVDFVVQSCDKNFLVPVNGGIVFSSDKKKMKELKK
HYPGRTPVHAYLDLFITLLELGKKKILNLRKEREENFSWLQEKVSTLCSKYNLTLIKASK
NKISMAINLNELYNICHILNPKSITLLGSLLFYRNVTGHRVICSPLLIRNGGVAQRRDQQ
IQTNVEPAFPIHHGAVDPNEVPTIEQGAHTDGEFFPNRGKKSEDAHQIRSSDNCNEECVG
KEGSQINLVKNENMNDARIHGKG
//
>subseq(150000,5000).[2935:4672].sp
ATGCACGTGCGCGGAATACAAAAAAATAATGATCTCACACTTTTGTGTCAAACAACAATC
AACCTTCCCCCTTACAGCATCCTAAATTACGGCCGTGTCCCAAATGAGGGATTAAACGAA
ATAACCATCATGAGCATTTTGCATCAGATATCTTCTCAAAATTTATGCAACAGCGAGAAG
AACGTTAAAATAGGGGAACGGGAGAATCGAATATATAGCGCGCTCGTGCGTAACAAGTAC
ATAGGATTTGGGCACGGCATTGGCAGGTCAGGGAACTTAGACGACGTGCAGCCTAAGAGC
GCTGGAAACAGTATCCTGGCAAAGGCCACCACAAGCTTCGTAAAGGATTTAATCAGAAGC
TTTGGAATAAAAGGCTGCGAGGATGTGTACATACTACCATACGCTACAGGGATGTGTTTA
AGTACTTGCCTGTTGTACACAAAAAAGGAAAGAGAAAAAAGTGAATATGTAATAGTGTCT
AGAATAGATCATAAGACCTGCTACAAGTGTATCGATTTTTGTGCCTTGAAGTATTTAGTA
GTGGATATGGTTTACAAGGATGAAGAATTATTTACAAACCTGAACGAAATAGAGAGACTG
ATACAAACATATGGTGAGAAAATATGTTGTGTCATGTCAGTGACATCTAGTTATGCACCA
AGGAATTCAGATGACATTGTAAAAATAGCTCATATTTGTAAGAGGTATAATGTACCACAC
ATAATTAATAATGCCTTTGGATTACAGTGCAATTATTTGTGTAAAGAAATACAGAAATGT
TTTGAATCGAAAGGTCGAGTGGATTTTGTGGTTCAGAGTTGTGATAAGAATTTCCTTGTC
CCAGTGAACGGCGGGATCGTATTCAGTTCCGATAAGAAAAAGATGAAAGAATTAAAAAAG
CACTACCCTGGTAGAACCCCCGTGCATGCATATTTAGATCTTTTCATTACATTACTAGAA
TTAGGGAAAAAAAAAATTCTAAACCTAAGAAAAGAGAGGGAGGAAAATTTTTCCTGGTTG
CAGGAAAAAGTTTCTACTCTCTGCTCAAAGTACAATTTAACTTTGATCAAAGCTAGCAAA
AATAAAATATCCATGGCCATTAATTTAAATGAACTTTACAATATTTGCCATATTCTAAAC
CCGAAGAGTATTACCCTACTCGGTTCTCTACTTTTTTATAGAAATGTTACCGGGCATAGG
GTTATATGCTCCCCGTTGTTGATACGCAATGGGGGAGTGGCACAGAGAAGAGACCAGCAA
ATTCAGACTAATGTAGAACCTGCATTTCCCATTCATCACGGGGCAGTAGATCCCAATGAG
GTTCCCACAATTGAGCAGGGTGCACACACCGATGGAGAATTTTTCCCAAATCGTGGAAAG
AAGAGCGAAGATGCACATCAAATCCGTTCCTCAGACAATTGCAATGAGGAATGCGTAGGA
AAAGAAGGGTCCCAAATAAATCTGGTGAAGAACGAAAATATGAATGATGCAAGAATTCAT
GGAAAAGGG
//