$ GenomeThreader 0.9.32 (2005-04-20 15:14:06) $ Date run: 2005-04-20 16:53:15 $ Splice Site Model: Bayesian $ $ genomicfile = "OSchr10" $ referencefile = "long_intron.fna" $ species = "rice" $ proteinsmap = "protein" $ scorematrix = "BLOSUM62" $ bssmfile = "rice" $ searchmode = (forward=True,reverse=True) $ frompos = 0 (default) $ topos = 0 (default) $ width = 0 (default) $ verbose = True (non-df.) $ gs2out = False (default) $ showintronmaxlen = 120 (default) maximum length of a fully shown intron $ minorflen = 64 (default) minimum length of an ORF to be shown $ minmatchlen = 20 (default) minimum match length $ seedlength = 18 (default) the seed length $ exdrop = 2 (default) the xdrop value for edit distance $ online = False (default) run the similarity filter online $ inverse = False (default) invert query and index in vmatch call $ exact = False (default) use exact matches $ noautoindex = False (default) do not create indices automatically $ maskpolyatails = False (default) mask poly(A) tails in cDNA/EST files $ maxnumofmatches = 0 (default) maximum number of matches $ matchnumdistri = False (default) show the distribution of matches $ chainlocal = 1 (default) local chains (according to L1-model). $ uselocalchaining = False (default) enable local chaining $ chainwf = 0.500000 (default) weight factor > 0.0 for local chaining $ gcmaxgapwidth = 1000000 (default) maximum gap width for global chains $ gcfilterthreshold= 50 (default) threshold for filter of global chains $ introncutout = False (default) enable the intron cutout technique $ autointroncutout = 0 (default) automatic intron cutout matrix size $ icinitialdelta = 50 (default) initial delta used for intron cutouts $ iciterations = 2 (default) number of intron cutout iterations $ icdeltaincrease = 50 (default) delta increase during every iteration $ icminremintronlen= 10 (default) minimum remaining intron length $ probies = 0.500000 (default) initial exon state probability $ probdelgen = 0.030000 (default) genomic sequence deletion probability $ identityweight = 2.000000 (default) pairs of identical characters weight $ mismatchweight = -2.000000 (default) weight for mismatching characters $ undetcharweight = 0.000000 (default) weight for undetermined characters $ deletionweight = -4.000000 (default) weight for deletions $ dpminexonlen = 5 (default) minimum exon length for the DP $ dpminintronlen = 50 (default) minimum intron length for the DP $ shortexonpenal = 100 (default) short exon penalty $ shortintronpenal = 100 (default) short intron penalty $ wzerotransition = 80 (default) zero transition weights window size $ wdecreasedoutput = 80 (default) decreased output weights window size $ leadcutoffsmode = RELAXED (default) cutoffs mode for leading bases $ termcutoffsmode = STRICT (default) cutoffs mode for terminal bases $ cutoffsminexonlen= 5 (default) cutoffs minimum exon length $ scoreminexonlen = 50 (default) score minimum exon length $ minaveragessp = 0.500000 (default) minimum average splice site prob. $ intermediate = False (default) stop after calc. of spliced alignments $ sortags = False (default) sort alternative gene structures $ sortagswf = 1.000000 (default) weight factor for the sorting of AGSs $ first = 0 (default) maximum number of spliced alignments $ $ special output characters for starting lines: $ GTHINFOCHAR = $ (info line) $ VMATCHCHAR = # (mkvtree and vmatch output) $ ******************************************************************************** EST Sequence: file=long_intron.fna, strand=+, description=gi|37988995|dbj|AK119372.1| Oryza sativa (japonica cultivar-group) cDNA clone:001-132-A02, full insert sequence 1 ACACAAACAG GTCAACCCCT TCTCAGTTCT CACCCTGCTA GGCTGCTAGA CCCTCTCTTC 61 CTCATCATTC CTACCAGATA AACAGAGAAA GAAAAGGTCT CATAGCATAG GAACCAACGA 121 GGCAGGACGG CAGGAGGCCT GTTCCTTGAG GTGTCTAGCC TGGAGTGCTT GCCACTAGGA 181 GTGAGGCAGC GAAGGGGACA TGGTTGCTGG CGGCGGAGTC AATTTGATGG TGACGACTGT 241 ATGCGGTGGG TCTCGACCAG TAGCGACGGG AAAGAAGGCG TGTTCCCCGG CCGACGGCGA 301 GGAGGCGCCG TCCCCTCGGC GGCGGGGTGA AGGCCTGCAG ATGAAGGTAG TAGCAGCCCA 361 GGCGGCGGTG AAAATCAAGA GACGAGGCGG AGGAGGCTAG CGTGACGTTA GGGAAAAAGG 421 CGGGTCCAGA TCGGCGCAGG CCCAGTGGAC ATGGAAGAGA GGGCCGACGA GATGAGGCTC 481 CATGCTAGTA GTGGAGACCT GGACGGAGGG CGCTCGATCT GACCAGATCG AGTCAGCGGC 541 GGTGGTTGGA GACGCCTTGA TGTAGCCACG CGAAAAAGAT GATTTTTCGC TCCTCGTAGG 601 CTGAGAAGAC GCGGGAGCGT AGGATTGGGA ATGGGAGAGG AGCCCTCACT CAGCCTCAGT 661 ATTGAGAGCG AATATTACGG GATAGAAACT CCACAAGTTT AGCATCCGAG GGAGAAGATC 721 TGCATGGGTT GCATCGGAGC TTCAAAGGTT CTTAATTACT TTTAGTCAGA CATGCAAGAG 781 CTGCTGGAAA TACTTGGCAG CTCTGGTTGT TTATTCGCTC AAGATAGTGT TGGTTCTCTT 841 TCCTTGCTGC GAAGCTTGCT GTTTCAGTCT ATTGTTTAAT TAGGGGTTGA TATTGCTCTG 901 GTTTCCCTGC CTTTTCCCCT TCCTGTCAGT TCGGTCTGCC TTTGTGCTGA AGATTCCATA 961 TGGCGCATGT ACTGATTTCA CAGCTATCGT TTGGAGATTC AAACAAAAGA ATCCTTGCAA 1021 GGGTCTCCAG GCTATGGAAC TTTACTGATC TCAACAATCA TACAAAAATT TTCCACACTG 1081 ATCTTGTCTT ACTCGATGAA ATGGGGACTA GCATACATGC CCAAATTTAC CCCCCTATAA 1141 CAGAAAAGAT GAAACCTCTC CTTAAGGAAG AAAAGGTTTA CTACATTGAC TCATTCACTG 1201 TTAGGGCTGC AAACAGAACA TACAGGCCAG TTGCAAACAA CCTAATGATC CTCTTCAGTA 1261 AATGGACAAC ACTTGAAGAA CACATTAATG TCCCTCCTCA TTTCCCTGGT ATTACATTTT 1321 CACTGACACC ATTCGAAGAT GTTCCTTCCC TTGTCGAGAA AAATTCATTC TACGTTGGTA 1381 ATAACATACT TTTATTGTGT TACAATTATT GTTATATACA TCTTCTGCAA TGCCATATCA 1441 TTTTATTAAA CTTATATGCC ATATCACTGA AGTTGGTGCA GTCACTACTA TACGTCCTAA 1501 GTCCAGAAAC GCTGAGAGCT TAAAAAGGAC ATTACAGATC CGCGATGCAA GCAATTCAAC 1561 TCTTCCTGTC ACACTCTGGG GAGAAAGAGC AACCTCTTTT GATGCTAATG ACATATACAA 1621 TGCTGGTCAA ACTCAAGCTC AAGTTGTTGT GTTTGTTGGA ACACTTGTGA AAGATTACAG 1681 AGGATTAGGC CTTACACTAA CTGGAAGCTC ACCATGCAAA TGGTATATTA ATCTAAATAT 1741 TCCTGAAGTA GCAGAACTAA ATGAGAGCTT TAGCACAAAC TTTCAGCCAA TCAAGTGGGT 1801 TGATGAGCCT GCTACAGGAT ACAACCAGGA TGTACCAGAA GAAAAGAGTA TTGCAGAAAT 1861 CCTTAATATC AACCCTCACA AACACAAGGG AACATGTTTT ATAGTAAATG TGACTGTCAG 1921 AAGGATATGT AATGAATATT CTTGGTGGTA CAATTCATGT TGAATGTGCT ACAAAACTTC 1981 AAAACCATAT GGCTCTAGCT ACAGATGCTC CAGCTATTCT AACATCGGAA TACCAGATCC 2041 AAGGTACAAA GTAGTATTAA TTTCCGGCGA TGATGATGCT AATGCTACAT TTATCCTTTT 2101 CGGAAGGATC GCACAACGGC TACTACGCAG GCCCATAGAA TCTCTCATTG AAGAAAATCC 2161 ACCAAACAGT GAATACATTC CAAGTGAAAT CACGTCACTT ATTGGCAGCA ATTTTCCATG 2221 GAATGTTAGC TTTACACGGG ATACTGTTAT GAGAAGTCAA GAGTGCCTAC AAGTTAATAG 2281 CATTATATCC GCTGGTGCTT CAAACCAACC ACTACTCCTT ATGTCCCCAG ATGCTTCACA 2341 AGTGACATCA GCTATTGTCT CAGCAACCTC AAGCAGCTCT GTCCAAACAG CACCAACACC 2401 AAATGAAACA AGCAATGAAT CACAGCAGCC CATTCAACCA AGACAAACCA TCTCAACACC 2461 AACCAAGTTC ACTATCGCTC AGGGAACACA GGACACCCCA ACTAGCAAAT CAAGTTCTTC 2521 AACACCTACC AAGAAAAGCA TTGTCTCAGT GTCTCACATG CAGTCTAGCA GGACCAAACC 2581 TAAAACTGAT GATAAGCCCA AAACTGACAC AAAAGCTGAA GAAAACATCT CACATGATAA 2641 ATCTTCAATT GTTGTCCTGC CTGATACTGC TGAAAATATG GGAAAGGGAC TACCAGAAAC 2701 TGCTGAAGAA GCCAAACAAG CAACCCCATC CTTCCCTACA CATACCCCAG CCAAAAAAAG 2761 AGGAAGGCCT ACACCTACAG CAACACCTCC GGTTGCTAAG AAATTGTTCA AGGATGGTGC 2821 CAAGCAAAAA GGCAATGACA GCTCTTAATT CATCTACACA ATGAATGAGT TGTCGACGTG 2881 CAATCCATCT CAAGACTTTT GCTTATATAT ATGTACAAAG CTATGTCCCA GCTAGAAGAC 2941 AGATGGCAGT TGTGAAATTA CCCAGGACTA AAGAACCAAG ATCTTTTGTT CATGGCTTTT 3001 TGTCATGATT ATCATTGTAT ATAAGTGTTG CCTTATCT Genomic Template: file=OSchr10, strand=-, from=495380, to=478168, description=OSchr10-v3 TIGR Release 3.0 chr10|11676 osa1 22698374 bp Predicted gene structure: Exon 1 495080 494371 ( 710 n); cDNA 1 709 ( 709 n); score: 0.977 Intron 1 494370 494240 ( 131 n); Pd: 0.000 (s: 0.96), Pa: 0.988 (s: 1.00) Exon 2 494239 494156 ( 84 n); cDNA 710 793 ( 84 n); score: 0.964 Intron 2 494155 491176 (2980 n); Pd: 0.001 (s: 0.94), Pa: 0.000 (s: 0) Exon 3 491175 491169 ( 7 n); cDNA 794 800 ( 7 n); score: 1.000 Intron 3 491168 491056 ( 113 n); Pd: 0.932 (s: 0), Pa: 0.545 (s: 0.96) Exon 4 491055 490904 ( 152 n); cDNA 801 952 ( 152 n); score: 0.980 Intron 4 490903 481471 (9433 n); Pd: 0.999 (s: 1.00), Pa: 0.996 (s: 1.00) Exon 5 481470 481320 ( 151 n); cDNA 953 1103 ( 151 n); score: 0.987 Intron 5 481319 481229 ( 91 n); Pd: 0.998 (s: 0.96), Pa: 0.996 (s: 1.00) Exon 6 481228 480759 ( 470 n); cDNA 1104 1551 ( 448 n); score: 0.940 Intron 6 480758 480606 ( 153 n); Pd: 0.968 (s: 0.98), Pa: 0.001 (s: 1.00) Exon 7 480605 480440 ( 166 n); cDNA 1552 1710 ( 159 n); score: 0.892 Intron 7 480439 480385 ( 55 n); Pd: 0.001 (s: 0.68), Pa: 0.581 (s: 0.78) Exon 8 480384 480323 ( 62 n); cDNA 1711 1767 ( 57 n); score: 0.823 Intron 8 480322 480219 ( 104 n); Pd: 0.966 (s: 0.88), Pa: 0.851 (s: 0.98) Exon 9 480218 480098 ( 121 n); cDNA 1768 1888 ( 121 n); score: 0.992 Intron 9 480097 480004 ( 94 n); Pd: 0.984 (s: 1.00), Pa: 0.985 (s: 0.98) Exon 10 480003 479849 ( 155 n); cDNA 1889 2043 ( 155 n); score: 0.955 Intron 10 479848 479763 ( 86 n); Pd: 0.952 (s: 0.92), Pa: 0.998 (s: 0.96) Exon 11 479762 479207 ( 556 n); cDNA 2044 2596 ( 553 n); score: 0.969 Intron 11 479206 479124 ( 83 n); Pd: 0.996 (s: 0.98), Pa: 0.790 (s: 0.96) Exon 12 479123 479040 ( 84 n); cDNA 2597 2680 ( 84 n); score: 0.952 Intron 12 479039 478976 ( 64 n); Pd: 0.995 (s: 0.96), Pa: 0.802 (s: 1.00) Exon 13 478975 478896 ( 80 n); cDNA 2681 2760 ( 80 n); score: 0.975 Intron 13 478895 478818 ( 78 n); Pd: 0.917 (s: 0.96), Pa: 0.945 (s: 1.00) Exon 14 478817 478737 ( 81 n); cDNA 2761 2841 ( 81 n); score: 0.975 Intron 14 478736 478665 ( 72 n); Pd: 0.996 (s: 0.96), Pa: 0.001 (s: 0.98) Exon 15 478664 478468 ( 197 n); cDNA 2842 3038 ( 197 n); score: 0.985 MATCH OSchr10-v3- 37988995+ 0.962 3069 1.010 C PGS_OSchr10-v3-_37988995+ (495080 494371,494239 494156,491175 491169,491055 490904,481470 481320,481228 480759,480605 480440,480384 480323,480218 480098,480003 479849,479762 479207,479123 479040,478975 478896,478817 478737,478664 478468) Alignment (genomic DNA sequence = upper lines): ACACAAACAG GTCAACCCCT TCTCAGTTCT CACCCTGCTA GGCTGCTAGA CCCTCTCTTC 495021 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ACACAAACAG GTCAACCCCT TCTCAGTTCT CACCCTGCTA GGCTGCTAGA CCCTCTCTTC 60 CTCCTCATTC CTACCAGATA AACAGAGAAA GAAAAGGTCT CATAGCATAG GAACCAACGA 494961 ||| |||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| CTCATCATTC CTACCAGATA AACAGAGAAA GAAAAGGTCT CATAGCATAG GAACCAACGA 120 GGCAGGACGG CAGGAGGCCT GTTCGCTTGA GGTGTCTAGC CTGGAGTGCT TGCCACTAGG 494901 |||||||||| |||||||||| |||| ||||| |||||||||| |||||||||| |||||||||| GGCAGGACGG CAGGAGGCCT GTTC-CTTGA GGTGTCTAGC CTGGAGTGCT TGCCACTAGG 179 AGTGAGGCAG CGAAGGGGAC ATGGTTGCTG GCGGCGGAGT CAATTTGATG GTGACGACTG 494841 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| AGTGAGGCAG CGAAGGGGAC ATGGTTGCTG GCGGCGGAGT CAATTTGATG GTGACGACTG 239 TATGCGGTGG GTCTCGACCA GTAGTGACGA GGAAGAAGGC GTGTTCCCCG GCCGACGGCG 494781 |||||||||| |||||||||| |||| |||| | |||||||| |||||||||| |||||||||| TATGCGGTGG GTCTCGACCA GTAGCGACGG GAAAGAAGGC GTGTTCCCCG GCCGACGGCG 299 AGGAGGCGCC GTCCCCTCGG CGGCGGGGTG AAGGCCTGCA GACGAAGGTA GTAGCAGCCC 494721 |||||||||| |||||||||| |||||||||| |||||||||| || ||||||| |||||||||| AGGAGGCGCC GTCCCCTCGG CGGCGGGGTG AAGGCCTGCA GATGAAGGTA GTAGCAGCCC 359 AGGCGGCGGT GAAAATCAAG AGACGAGGCG GAGGAGGCTA GCGTGACGTT AGGGAAAAAG 494661 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| AGGCGGCGGT GAAAATCAAG AGACGAGGCG GAGGAGGCTA GCGTGACGTT AGGGAAAAAG 419 GTGGGTCCAG ATCGGCGCAG GCCCAGTGGA CATGGATGAG AGGGCCGACG AGATGAGGCT 494601 | |||||||| |||||||||| |||||||||| |||||| ||| |||||||||| |||||||||| GCGGGTCCAG ATCGGCGCAG GCCCAGTGGA CATGGAAGAG AGGGCCGACG AGATGAGGCT 479 CCATGCTAGC AGTGGAGACC TGGACGGAGG GCGCTCGATC TGACCAGATC GAGTCAGCGG 494541 ||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| CCATGCTAGT AGTGGAGACC TGGACGGAGG GCGCTCGATC TGACCAGATC GAGTCAGCGG 539 CGGTGGTTGG AGACGCCTTG ACATAGCCAC GCGAAAAAGA TGATTTTTCA CTCCTCGCAG 494481 |||||||||| |||||||||| | ||||||| |||||||||| ||||||||| ||||||| || CGGTGGTTGG AGACGCCTTG ATGTAGCCAC GCGAAAAAGA TGATTTTTCG CTCCTCGTAG 599 GCTGAGAAGA CGCGGGAGCG TAGGATTGGG AATAGGAGAG GAGCCCTCAC TCAGCCTCAG 494421 |||||||||| |||||||||| |||||||||| ||| |||||| |||||||||| |||||||||| GCTGAGAAGA CGCGGGAGCG TAGGATTGGG AATGGGAGAG GAGCCCTCAC TCAGCCTCAG 659 TATTGAGAGC GAATATTACA GGATAGAAAC TCCACAAGTT TAGCATCTGA ATAGGAAATC 494361 |||||||||| ||||||||| |||||||||| |||||||||| ||||||| || TATTGAGAGC GAATATTACG GGATAGAAAC TCCACAAGTT TAGCATCCGA .......... 709 TATTGGAGCA TATTTTTTTA AAGTAAAATC CTCAAAAATT AAGATTCATT GCTGCTCTTC 494301 ........... .......... .......... .......... .......... .......... 709 CTTTCGATGG TGTTCAATCT TGATTGCTTA TTGATTTGCT TTGATCTTTC CATTTTGTTA 494241 ........... .......... .......... .......... .......... .......... 709 GGGGAGAAGA TCTGCATGGG TTGCATCGGA GCTTCAAAGG TTCTTAATTA CTTTTAGTTA 494181 ||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||| | ..GGGAGAAGA TCTGCATGGG TTGCATCGGA GCTTCAAAGG TTCTTAATTA CTTTTAGTCA 768 GACGTGCAAG AGCTGCTGGA AATATGTCAC GCCCGAAAAT TCACTAGTAA TTTTCGAACT 494121 ||| |||||| |||||||||| |||| GACATGCAAG AGCTGCTGGA AATAC..... .......... .......... .......... 793 TATTTGTGCA TAAAACTCTC ATCCAGGAAT TAGCCGAAGT ACACAAACTG ACAATTCAAT 494061 ........... .......... .......... .......... .......... .......... 793 // intron part 494060 491241 (2820 n) not shown // //........ .......... .......... .......... .......... ........// TTCTAATAAT GATTTATTAA ATAATTTATA AATCCTAAGA CGAAAATCAG GATGTGACAA 491181 ........... .......... .......... .......... .......... .......... 793 AATACTTGGC AGGTAATTTC AGTTCATCCT TCTGTTCAGT CTGGCATTTC TCTGAGGAGT 491121 ||||| || ......TTGGC AG........ .......... .......... .......... .......... 800 TCTTCTACTG TTACGCGTTA GATTTAAACT TGCTAGTGTC TAACCATGAT GTTTGTACCA 491061 ........... .......... .......... .......... .......... .......... 800 TGCAGCTCTG GTTGTTTATT CGCTCAAGAT AGTGTTGGTT AACTTTCCTT GCTGCGAAGC 491001 ||||| |||||||||| |||||||||| |||||||||| |||||||| |||||||||| ......CTCTG GTTGTTTATT CGCTCAAGAT AGTGTTGGTT CTCTTTCCTT GCTGCGAAGC 855 TTGCTGTTTC AGTCTATTGT TTAATTAGGG GTTGATATTG CTCTTGTTTC CCTGCCTTTT 490941 |||||||||| |||||||||| |||||||||| |||||||||| |||| ||||| |||||||||| TTGCTGTTTC AGTCTATTGT TTAATTAGGG GTTGATATTG CTCTGGTTTC CCTGCCTTTT 915 CCCCTTCCTG TCAGTTCGGT CTGCCTTTGT GCTGAAGGTA TTTTCTTCTT CTTTATTGTT 490881 |||||||||| |||||||||| |||||||||| ||||||| CCCCTTCCTG TCAGTTCGGT CTGCCTTTGT GCTGAAG... .......... .......... 952 ATACATTACT ATATTTCTCT GGTTGTTTAA TTCTTTGCAT GATATTATAT GGTATATGTG 490821 ........... .......... .......... .......... .......... .......... 952 // intron part 490820 481581 (9240 n) not shown // //........ .......... .......... .......... .......... ........// TATGATTTGT CCGCTGCAGT TATATGTACT GTTCTTCTTA GTAACATTTC CTTGTACATA 481521 ........... .......... .......... .......... .......... .......... 952 TATAGTAGTG TTGTTTTGTC TATACTAAAA GTATTTTGTG CTTATTGCAG ATTCCATATG 481461 |||||||||| ........... .......... .......... .......... .......... ATTCCATATG 962 GCGCATGTAC TGATTTCACA GCTATCGTTT GGAGATTCAA ACAAAAGAAT CCTTGCAAGG 481401 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| GCGCATGTAC TGATTTCACA GCTATCGTTT GGAGATTCAA ACAAAAGAAT CCTTGCAAGG 1022 GTCTCCAGGC TATGGAACTT TACTGATCTC AACGATGATA CAAAAATTTT CCACACTGAT 481341 |||||||||| |||||||||| |||||||||| ||| || ||| |||||||||| |||||||||| GTCTCCAGGC TATGGAACTT TACTGATCTC AACAATCATA CAAAAATTTT CCACACTGAT 1082 CTTGTCTTAC TCGATGAAAT GGTAATAATT TACGTGCCAA ATCCATTTTC TATATTTTCC 481281 |||||||||| |||||||||| | CTTGTCTTAC TCGATGAAAT G......... .......... .......... .......... 1103 TTTCTATACC GATAATTCTC TTGATAACAT GATTTGTATT TATAATCTGC AGGGGACTAG 481221 |||||||| ........... .......... .......... .......... .......... ..GGGACTAG 1111 CATACATGCC CAAATTTACC CCCCTATAAC AGAAAAGATG AAACCTCTCC TTAAGGAAGA 481161 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| CATACATGCC CAAATTTACC CCCCTATAAC AGAAAAGATG AAACCTCTCC TTAAGGAAGA 1171 AAAGGTTTAC TACATTGACT CATTCACTGT TAGGGCTGCA AACAGAACAT ACAGGCTAGT 481101 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||| ||| AAAGGTTTAC TACATTGACT CATTCACTGT TAGGGCTGCA AACAGAACAT ACAGGCCAGT 1231 TGCAAACAAC CTAATGATCC TCTTCAGTAA ATGGACAACA CTTGAAGAAC ACATTAATGT 481041 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| TGCAAACAAC CTAATGATCC TCTTCAGTAA ATGGACAACA CTTGAAGAAC ACATTAATGT 1291 CCCTCCTCAT TTCCCTGGTA TTACATTTTC ACTGACACCA TTCGAAGATG TTCCTTCCCT 480981 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| CCCTCCTCAT TTCCCTGGTA TTACATTTTC ACTGACACCA TTCGAAGATG TTCCTTCCCT 1351 TGTCGAGAAA AAATCATTCT ACGTTGGTAA TAACATACTT TTATTGTGTT GCAATTATTG 480921 |||||||||| || ||||||| |||||||||| |||||||||| |||||||||| ||||||||| TGTCGAGAAA AATTCATTCT ACGTTGGTAA TAACATACTT TTATTGTGTT ACAATTATTG 1411 TTATATACAT CTTTTGCAAT GCCATATCAT TTTATTAAAT TTATATGCAA TGCAAACAGA 480861 |||||||||| ||| |||||| |||||||||| ||||||||| | ||| | || | TTATATACAT CTTCTGCAAT GCCATATCAT TTTATTAAA- CT-TAT---A TG----C--- 1459 CATTATGGGT GTGATCACTG AAGTTGGTGC AGTCACTACT ATACGTCCTA AGTCCAGAAA 480801 | | | ||||||| |||||||||| |||||||||| |||||||||| |||||||||| C---A----- -T-ATCACTG AAGTTGGTGC AGTCACTACT ATACGTCCTA AGTCCAGAAA 1509 CGCTAAGAGC TTAAAAAGGA CATTACAGAT CCGCGATGCA AGGCTAGTTT AGTACAACTA 480741 |||| ||||| |||||||||| |||||||||| |||||||||| || CGCTGAGAGC TTAAAAAGGA CATTACAGAT CCGCGATGCA AG........ .......... 1551 AATATTTACA TATTTATTAT TTACTTAATC TTTTTCGCTA GCATTCACAC AAACTATCTC 480681 ........... .......... .......... .......... .......... .......... 1551 ACATATTCTT AACACTAAGT CATCTCTTCC AATTAAAATT AAATCACTTT TTCCCCTCCA 480621 ........... .......... .......... .......... .......... .......... 1551 AATCTACAAA ACTAGCAATT CAACTCTTCC TGTCACACTC TGGGGAGAAA GAGCAACCTC 480561 ||||| |||||||||| |||||||||| |||||||||| |||||||||| ........... .....CAATT CAACTCTTCC TGTCACACTC TGGGGAGAAA GAGCAACCTC 1596 TTTTGATGCT GATGACATAT ACAATGCTGG TCAAACTCAA GCTCAAGTTG CTGTGTTTGT 480501 |||||||||| ||||||||| |||||||||| |||||||||| |||||||||| ||||||||| TTTTGATGCT AATGACATAT ACAATGCTGG TCAAACTCAA GCTCAAGTTG TTGTGTTTGT 1656 TGGAACACTT GTGAAAGATT ATAGAGGATT AGGTACATTT CTTTCTAAAC TTTCAATTAC 480441 |||||||||| |||||||||| | |||||||| ||| | || | || ||| | || | TGGAACACTT GTGAAAGATT ACAGAGGATT AGG--CCTTA C--ACT-AAC -TGGAAGCTC 1710 TGTAGTATTG ACTACATGCA ACTAACAATA TCTAATAATT TCCTCCACAT ATATAGGCCT 480381 || -......... .......... .......... .......... .......... ......ACCA 1714 TACACTAACT GGAAGCTTAC CATCTAAATA TTCCTGAAGT AGCAGAACTA AATGAGAGGT 480321 | || || | || | ||| ||||||||| |||||||||| |||||||||| |||||||| TGCA--AA-T GGTATATTA- -ATCTAAATA TTCCTGAAGT AGCAGAACTA AATGAGAG.. 1767 AATTTAATTT ATTTAACGTT ATTCTTACAA TCTATGTGCA TCACTGTATT CTTCAAGGTT 480261 ........... .......... .......... .......... .......... .......... 1767 TTCACAGTAT CCATTAATCT AAGATACAAT TCTTCTATGT AGCTTTAGCA CAAACTTTCA 480201 |||||||| |||||||||| ........... .......... .......... .......... ..CTTTAGCA CAAACTTTCA 1785 ACCAATCAAG TGGGTTGATG AGCCTGCTAC AGGATACAAC CAGGATGTAC CAGAAGAAAA 480141 ||||||||| |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| GCCAATCAAG TGGGTTGATG AGCCTGCTAC AGGATACAAC CAGGATGTAC CAGAAGAAAA 1845 GAGTATTGCA GAAATCCTTA ATATCAACCC TCACAAACAC AAGGTTGACA CTATCTCTAG 480081 |||||||||| |||||||||| |||||||||| |||||||||| ||| GAGTATTGCA GAAATCCTTA ATATCAACCC TCACAAACAC AAG....... .......... 1888 AACACATCTT AACTACATCT ATCCACTTTT TGATGATATA ATTACCAATA TGATATTTTC 480021 ........... .......... .......... .......... .......... .......... 1888 ATTGTCTTCT TATGCAGGGA ACACGTTTTA TAGTAAATGT GACTGTCAGA AGGATATGTA 479961 ||| ||| |||||| |||||||||| |||||||||| |||||||||| ........... .......GGA ACATGTTTTA TAGTAAATGT GACTGTCAGA AGGATATGTA 1931 ATGAATATTC TTGGTGGTAC AATTCATGTC GAATATGCTA CAAAACTTCA AAACCATATG 479901 |||||||||| |||||||||| ||||||||| |||| ||||| |||||||||| |||||||||| ATGAATATTC TTGGTGGTAC AATTCATGTT GAATGTGCTA CAAAACTTCA AAACCATATG 1991 GCTCTAGCTA CAGATACTCC AGCTGTTCTA GCATCGGAAT AACAGATCCA AGGTTCATAA 479841 |||||||||| ||||| |||| |||| ||||| ||||||||| | |||||||| || GCTCTAGCTA CAGATGCTCC AGCTATTCTA ACATCGGAAT ACCAGATCCA AG........ 2043 CAGAACACGC TCTGTCCTCT TACATCTTTA GCAATTATCA TCCACACATT GCTATAGCCA 479781 ........... .......... .......... .......... .......... .......... 2043 TATCCATTTT TCATGCAGGT ACAAAGTAGT ATTAATTGCC AGCGATGATG ATGCTAATGC 479721 || |||||||||| ||||||| || ||||||||| |||||||||| ........... ........GT ACAAAGTAGT ATTAATTTCC GGCGATGATG ATGCTAATGC 2085 TACATTTATC CTTTTCGGAA GGATCGCACA ACGGCTACTA CGCAGGCCCG TAGAATCTCT 479661 |||||||||| |||||||||| |||||||||| |||||||||| ||||||||| |||||||||| TACATTTATC CTTTTCGGAA GGATCGCACA ACGGCTACTA CGCAGGCCCA TAGAATCTCT 2145 CATTGAAGAA AAACCACCAA ACAGTGAATA CATTCCAAGT GAAATCACGT CACTTATTGG 479601 |||||||||| || ||||||| |||||||||| |||||||||| |||||||||| |||||||||| CATTGAAGAA AATCCACCAA ACAGTGAATA CATTCCAAGT GAAATCACGT CACTTATTGG 2205 TAGCAATTTT GCATGGAATG TTAGCTTTAC GCGGGATACT GTTATGAGAA GTCAAGAGTG 479541 ||||||||| ||||||||| |||||||||| ||||||||| |||||||||| |||||||||| CAGCAATTTT CCATGGAATG TTAGCTTTAC ACGGGATACT GTTATGAGAA GTCAAGAGTG 2265 CCTACAAGTT AATAGCATTA TATCCGCTGG TGCTTCAAAC CAGCCACTAC TCCTTATGTC 479481 |||||||||| |||||||||| |||||||||| |||||||||| || ||||||| |||||||||| CCTACAAGTT AATAGCATTA TATCCGCTGG TGCTTCAAAC CAACCACTAC TCCTTATGTC 2325 CCCAGATGCT TCACAAGTGA CATCAGCTAT TGTCTCAGCA AGCTCAAGCA GCTCTGTCCA 479421 |||||||||| |||||||||| |||||||||| |||||||||| | |||||||| |||||||||| CCCAGATGCT TCACAAGTGA CATCAGCTAT TGTCTCAGCA ACCTCAAGCA GCTCTGTCCA 2385 AACAGCACCA ACACCAAATG AAACAAGCAA TGAATCACAG CAGCCCATTT AACCAAGACA 479361 |||||||||| |||||||||| |||||||||| |||||||||| ||||||||| |||||||||| AACAGCACCA ACACCAAATG AAACAAGCAA TGAATCACAG CAGCCCATTC AACCAAGACA 2445 AACCATCTCA ACACCAACCA AGTTCATCAT CGCTCAGGGA ACACAGGACA CCCCAACTAG 479301 |||||||||| |||||||||| |||||| || |||||||||| |||||||||| |||||||||| AACCATCTCA ACACCAACCA AGTTCACTAT CGCTCAGGGA ACACAGGACA CCCCAACTAG 2505 CAAATCAAGT TCTTCAGCAC CTACCAAGAA AAGCATTGTT GTCTCAGTGT CTCACATGCA 479241 |||||||||| |||||| ||| |||||||||| ||||| || |||||||||| |||||||||| CAAATCAAGT TCTTCAACAC CTACCAAGAA AAGCA---TT GTCTCAGTGT CTCACATGCA 2562 GTCTAGCAAG ACCAAACCTA AAACTGATGA TAAGGTAACC ACTTTATAGC CACCCTTAAA 479181 |||||||| | |||||||||| |||||||||| |||| GTCTAGCAGG ACCAAACCTA AAACTGATGA TAAG...... .......... .......... 2596 CTTGTTGTCA CTCATACTGA ATTACATCCA CTCTCACTTC TTTCCTAATT TTGCAAGCCC 479121 ||| ........... .......... .......... .......... .......... .......CCC 2599 AAAACTGACA CAAAAGCTAA AGAAAACACC TCACATGATA AATCTTCAAT TGTTGTACTG 479061 |||||||||| |||||||| | |||||||| | |||||||||| |||||||||| |||||| ||| AAAACTGACA CAAAAGCTGA AGAAAACATC TCACATGATA AATCTTCAAT TGTTGTCCTG 2659 CCTGATACTG CTGAAAATAA GGTACTACTA CATCTCTTTC CTTTCATCTC ATTCATTAAG 479001 |||||||||| ||||||||| | CCTGATACTG CTGAAAATAT G......... .......... .......... .......... 2680 ACCTAACCGC CACTTCTTTT ACAAGGGAAA GGGACTACCA GAAACTGCTG AAGAAGCCAA 478941 ||||| |||||||||| |||||||||| |||||||||| ........... .......... .....GGAAA GGGACTACCA GAAACTGCTG AAGAAGCCAA 2715 ACAAGCAACC CCATCCTTCC CTACAGATAC CCTAGCCAAA AAAAGGTGCT TTGATCACTC 478881 |||||||||| |||||||||| ||||| |||| || ||||||| ||||| ACAAGCAACC CCATCCTTCC CTACACATAC CCCAGCCAAA AAAAG..... .......... 2760 CTAGGTGCAT TCCAATAATA AAGATTTCTT CCATTGTAAC TAACACATCA TTTCAATAAA 478821 ........... .......... .......... .......... .......... .......... 2760 CAGAGGAAGG CCTACACCTA CAGCAACACC TCCGGTTGCT AAGAAATTGT TCAAGGATGA 478761 ||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||||||||| ....AGGAAGG CCTACACCTA CAGCAACACC TCCGGTTGCT AAGAAATTGT TCAAGGATGG 2817 TGCCCAGCAA AAAGGCAATG ACAGGTTACT CCTCAAACAC AAACTCACCT ATCTACACAT 478701 |||| ||||| |||||||||| |||| TGCCAAGCAA AAAGGCAATG ACAG...... .......... .......... .......... 2841 AACAAATTAG CAATTTAAAG GCATTCCTAA TCTCAGCTCT TAATTCATCT ACACAGTGAA 478641 |||| |||||||||| ||||| |||| ........... .......... .......... ......CTCT TAATTCATCT ACACAATGAA 2865 TGAGTTGTCG ACGTGCAATC CATCTCAAGA CTTTTTCTTA TATATATGTA CAAAGCTATG 478581 |||||||||| |||||||||| |||||||||| ||||| |||| |||||||||| |||||||||| TGAGTTGTCG ACGTGCAATC CATCTCAAGA CTTTTGCTTA TATATATGTA CAAAGCTATG 2925 TCCCAGCTAG AAGACAGATG GCAGTTGTGA AATTACCCAG GACTAAGGAA CCAAGATCTT 478521 |||||||||| |||||||||| |||||||||| |||||||||| |||||| ||| |||||||||| TCCCAGCTAG AAGACAGATG GCAGTTGTGA AATTACCCAG GACTAAAGAA CCAAGATCTT 2985 TTGTTCATGG CTTTTTGTCA TGATTATCAT TGTATATAAG TGTTGCCTTA TCT 478468 |||||||||| |||||||||| |||||||||| |||||||||| |||||||||| ||| TTGTTCATGG CTTTTTGTCA TGATTATCAT TGTATATAAG TGTTGCCTTA TCT 3038 -------------------------------------------------------------------------------- Predicted gene locations (1): PGL 1 (- strand): 495080 478468 AGS-1 (495080 494371,494239 494156,491175 491169,491055 490904,481470 481320,481228 480759,480605 480440,480384 480323,480218 480098,480003 479849,479762 479207,479123 479040,478975 478896,478817 478737,478664 478468) SCR (e 0.977 d 0.000 a 0.988,e 0.964 d 0.001 a 0.000,e 1.000 d 0.932 a 0.545,e 0.980 d 0.999 a 0.996,e 0.987 d 0.998 a 0.996,e 0.940 d 0.968 a 0.001,e 0.892 d 0.001 a 0.581,e 0.823 d 0.966 a 0.851,e 0.992 d 0.984 a 0.985,e 0.955 d 0.952 a 0.998,e 0.969 d 0.996 a 0.790,e 0.952 d 0.995 a 0.802,e 0.975 d 0.917 a 0.945,e 0.975 d 0.996 a 0.001,e 0.985) Exon 1 495080 494371 ( 710 n); score: 0.977 Intron 1 494370 494240 ( 131 n); Pd: 0.000 Pa: 0.988 Exon 2 494239 494156 ( 84 n); score: 0.964 Intron 2 494155 491176 (2980 n); Pd: 0.001 Pa: 0.000 Exon 3 491175 491169 ( 7 n); score: 1.000 Intron 3 491168 491056 ( 113 n); Pd: 0.932 Pa: 0.545 Exon 4 491055 490904 ( 152 n); score: 0.980 Intron 4 490903 481471 (9433 n); Pd: 0.999 Pa: 0.996 Exon 5 481470 481320 ( 151 n); score: 0.987 Intron 5 481319 481229 ( 91 n); Pd: 0.998 Pa: 0.996 Exon 6 481228 480759 ( 470 n); score: 0.940 Intron 6 480758 480606 ( 153 n); Pd: 0.968 Pa: 0.001 Exon 7 480605 480440 ( 166 n); score: 0.892 Intron 7 480439 480385 ( 55 n); Pd: 0.001 Pa: 0.581 Exon 8 480384 480323 ( 62 n); score: 0.823 Intron 8 480322 480219 ( 104 n); Pd: 0.966 Pa: 0.851 Exon 9 480218 480098 ( 121 n); score: 0.992 Intron 9 480097 480004 ( 94 n); Pd: 0.984 Pa: 0.985 Exon 10 480003 479849 ( 155 n); score: 0.955 Intron 10 479848 479763 ( 86 n); Pd: 0.952 Pa: 0.998 Exon 11 479762 479207 ( 556 n); score: 0.969 Intron 11 479206 479124 ( 83 n); Pd: 0.996 Pa: 0.790 Exon 12 479123 479040 ( 84 n); score: 0.952 Intron 12 479039 478976 ( 64 n); Pd: 0.995 Pa: 0.802 Exon 13 478975 478896 ( 80 n); score: 0.975 Intron 13 478895 478818 ( 78 n); Pd: 0.917 Pa: 0.945 Exon 14 478817 478737 ( 81 n); score: 0.975 Intron 14 478736 478665 ( 72 n); Pd: 0.996 Pa: 0.001 Exon 15 478664 478468 ( 197 n); score: 0.985 PGS (495080 494371,494239 494156,491175 491169,491055 490904,481470 481320,481228 480759,480605 480440,480384 480323,480218 480098,480003 479849,479762 479207,479123 479040,478975 478896,478817 478737,478664 478468) 37988995+ 3-phase translation of AGS-1 (-strand): . . . . . . 495080 ACACAAACAGGTCAACCCCTTCTCAGTTCTCACCCTGCTAGGCTGCTAGACCCTCTCTTC T Q T G Q P L L S S H P A R L L D P L F H K Q V N P F S V L T L L G C * T L S S T N R S T P S Q F S P C * A A R P S L . . . . . . 495020 CTCCTCATTCCTACCAGATAAACAGAGAAAGAAAAGGTCTCATAGCATAGGAACCAACGA L L I P T R * T E K E K V S * H R N Q R S S F L P D K Q R K K R S H S I G T N E P P H S Y Q I N R E R K G L I A * E P T . . . . . . 494960 GGCAGGACGGCAGGAGGCCTGTTCGCTTGAGGTGTCTAGCCTGGAGTGCTTGCCACTAGG G R T A G G L F A * G V * P G V L A T R A G R Q E A C S L E V S S L E C L P L G R Q D G R R P V R L R C L A W S A C H * . . . . . . 494900 AGTGAGGCAGCGAAGGGGACATGGTTGCTGGCGGCGGAGTCAATTTGATGGTGACGACTG S E A A K G T W L L A A E S I * W * R L V R Q R R G H G C W R R S Q F D G D D C E * G S E G D M V A G G G V N L M V T T . . . . . . 494840 TATGCGGTGGGTCTCGACCAGTAGTGACGAGGAAGAAGGCGTGTTCCCCGGCCGACGGCG Y A V G L D Q * * R G R R R V P R P T A M R W V S T S S D E E E G V F P G R R R V C G G S R P V V T R K K A C S P A D G . . . . . . 494780 AGGAGGCGCCGTCCCCTCGGCGGCGGGGTGAAGGCCTGCAGACGAAGGTAGTAGCAGCCC R R R R P L G G G V K A C R R R * * Q P G G A V P S A A G * R P A D E G S S S P E E A P S P R R R G E G L Q T K V V A A . . . . . . 494720 AGGCGGCGGTGAAAATCAAGAGACGAGGCGGAGGAGGCTAGCGTGACGTTAGGGAAAAAG R R R * K S R D E A E E A S V T L G K K G G G E N Q E T R R R R L A * R * G K R Q A A V K I K R R G G G G * R D V R E K . . . . . . 494660 GTGGGTCCAGATCGGCGCAGGCCCAGTGGACATGGATGAGAGGGCCGACGAGATGAGGCT V G P D R R R P S G H G * E G R R D E A W V Q I G A G P V D M D E R A D E M R L G G S R S A Q A Q W T W M R G P T R * G . . . . . . 494600 CCATGCTAGCAGTGGAGACCTGGACGGAGGGCGCTCGATCTGACCAGATCGAGTCAGCGG P C * Q W R P G R R A L D L T R S S Q R H A S S G D L D G G R S I * P D R V S G S M L A V E T W T E G A R S D Q I E S A . . . . . . 494540 CGGTGGTTGGAGACGCCTTGACATAGCCACGCGAAAAAGATGATTTTTCACTCCTCGCAG R W L E T P * H S H A K K M I F H S S Q G G W R R L D I A T R K R * F F T P R R A V V G D A L T * P R E K D D F S L L A . . . . . . 494480 GCTGAGAAGACGCGGGAGCGTAGGATTGGGAATAGGAGAGGAGCCCTCACTCAGCCTCAG A E K T R E R R I G N R R G A L T Q P Q L R R R G S V G L G I G E E P S L S L S G * E D A G A * D W E * E R S P H S A S . . . . . : . 494420 TATTGAGAGCGAATATTACAGGATAGAAACTCCACAAGTTTAGCATCTGA : GGGAGAAGAT Y * E R I L Q D R N S T S L A S E : G E D I E S E Y Y R I E T P Q V * H L : R E K I V L R A N I T G * K L H K F S I * : G R R . . . . . . 494229 CTGCATGGGTTGCATCGGAGCTTCAAAGGTTCTTAATTACTTTTAGTTAGACGTGCAAGA L H G L H R S F K G S * L L L V R R A R C M G C I G A S K V L N Y F * L D V Q E S A W V A S E L Q R F L I T F S * T C K . . : . : . . . 494169 GCTGCTGGAAATAT : TTGGCAG : CTCTGGTTGTTTATTCGCTCAAGATAGTGTTGGTTAACT A A G N I : W Q : L W L F I R S R * C W L T L L E I : F G S : S G C L F A Q D S V G * L S C W K Y : L A : A L V V Y S L K I V L V N . . . . . . 491016 TTCCTTGCTGCGAAGCTTGCTGTTTCAGTCTATTGTTTAATTAGGGGTTGATATTGCTCT F L A A K L A V S V Y C L I R G * Y C S S L L R S L L F Q S I V * L G V D I A L F P C C E A C C F S L L F N * G L I L L . . . . . . : 490956 TGTTTCCCTGCCTTTTCCCCTTCCTGTCAGTTCGGTCTGCCTTTGTGCTGAAG : ATTCCAT C F P A F S P S C Q F G L P L C * R : F H V S L P F P L P V S S V C L C A E : D S I L F P C L F P F L S V R S A F V L K : I P . . . . . . 481463 ATGGCGCATGTACTGATTTCACAGCTATCGTTTGGAGATTCAAACAAAAGAATCCTTGCA M A H V L I S Q L S F G D S N K R I L A W R M Y * F H S Y R L E I Q T K E S L Q Y G A C T D F T A I V W R F K Q K N P C . . . . . . 481403 AGGGTCTCCAGGCTATGGAACTTTACTGATCTCAACGATGATACAAAAATTTTCCACACT R V S R L W N F T D L N D D T K I F H T G S P G Y G T L L I S T M I Q K F S T L K G L Q A M E L Y * S Q R * Y K N F P H . . . : . . . 481343 GATCTTGTCTTACTCGATGAAATG : GGGACTAGCATACATGCCCAAATTTACCCCCCTATA D L V L L D E M : G T S I H A Q I Y P P I I L S Y S M K W : G L A Y M P K F T P L * * S C L T R * N : G D * H T C P N L P P Y . . . . . . 481192 ACAGAAAAGATGAAACCTCTCCTTAAGGAAGAAAAGGTTTACTACATTGACTCATTCACT T E K M K P L L K E E K V Y Y I D S F T Q K R * N L S L R K K R F T T L T H S L N R K D E T S P * G R K G L L H * L I H . . . . . . 481132 GTTAGGGCTGCAAACAGAACATACAGGCTAGTTGCAAACAACCTAATGATCCTCTTCAGT V R A A N R T Y R L V A N N L M I L F S L G L Q T E H T G * L Q T T * * S S S V C * G C K Q N I Q A S C K Q P N D P L Q . . . . . . 481072 AAATGGACAACACTTGAAGAACACATTAATGTCCCTCCTCATTTCCCTGGTATTACATTT K W T T L E E H I N V P P H F P G I T F N G Q H L K N T L M S L L I S L V L H F * M D N T * R T H * C P S S F P W Y Y I . . . . . . 481012 TCACTGACACCATTCGAAGATGTTCCTTCCCTTGTCGAGAAAAAATCATTCTACGTTGGT S L T P F E D V P S L V E K K S F Y V G H * H H S K M F L P L S R K N H S T L V F T D T I R R C S F P C R E K I I L R W . . . . . . 480952 AATAACATACTTTTATTGTGTTGCAATTATTGTTATATACATCTTTTGCAATGCCATATC N N I L L L C C N Y C Y I H L L Q C H I I T Y F Y C V A I I V I Y I F C N A I S * * H T F I V L Q L L L Y T S F A M P Y . . . . . . 480892 ATTTTATTAAATTTATATGCAATGCAAACAGACATTATGGGTGTGATCACTGAAGTTGGT I L L N L Y A M Q T D I M G V I T E V G F Y * I Y M Q C K Q T L W V * S L K L V H F I K F I C N A N R H Y G C D H * S W . . . . . . 480832 GCAGTCACTACTATACGTCCTAAGTCCAGAAACGCTAAGAGCTTAAAAAGGACATTACAG A V T T I R P K S R N A K S L K R T L Q Q S L L Y V L S P E T L R A * K G H Y R C S H Y Y T S * V Q K R * E L K K D I T . . : . . . . 480772 ATCCGCGATGCAAG : CAATTCAACTCTTCCTGTCACACTCTGGGGAGAAAGAGCAACCTCT I R D A S : N S T L P V T L W G E R A T S S A M Q : A I Q L F L S H S G E K E Q P L D P R C K : Q F N S S C H T L G R K S N L . . . . . . 480559 TTTGATGCTGATGACATATACAATGCTGGTCAAACTCAAGCTCAAGTTGCTGTGTTTGTT F D A D D I Y N A G Q T Q A Q V A V F V L M L M T Y T M L V K L K L K L L C L L F * C * * H I Q C W S N S S S S C C V C . . . . . . : 480499 GGAACACTTGTGAAAGATTATAGAGGATTAGGTACATTTCTTTCTAAACTTTCAATTACT : G T L V K D Y R G L G T F L S K L S I T : E H L * K I I E D * V H F F L N F Q L L : W N T C E R L * R I R Y I S F * T F N Y : . . . . . . 480384 GCCTTACACTAACTGGAAGCTTACCATCTAAATATTCCTGAAGTAGCAGAACTAAATGAG A L H * L E A Y H L N I P E V A E L N E P Y T N W K L T I * I F L K * Q N * M R C L T L T G S L P S K Y S * S S R T K * . : . . . . . 480324 AG : CTTTAGCACAAACTTTCAACCAATCAAGTGGGTTGATGAGCCTGCTACAGGATACAAC S : F S T N F Q P I K W V D E P A T G Y N : A L A Q T F N Q S S G L M S L L Q D T T E : L * H K L S T N Q V G * * A C Y R I Q . . . . . . 480160 CAGGATGTACCAGAAGAAAAGAGTATTGCAGAAATCCTTAATATCAACCCTCACAAACAC Q D V P E E K S I A E I L N I N P H K H R M Y Q K K R V L Q K S L I S T L T N T P G C T R R K E Y C R N P * Y Q P S Q T . : . . . . . 480100 AAG : GGAACACGTTTTATAGTAAATGTGACTGTCAGAAGGATATGTAATGAATATTCTTGG K : G T R F I V N V T V R R I C N E Y S W R : E H V L * * M * L S E G Y V M N I L G Q : G N T F Y S K C D C Q K D M * * I F L . . . . . . 479946 TGGTACAATTCATGTCGAATATGCTACAAAACTTCAAAACCATATGGCTCTAGCTACAGA W Y N S C R I C Y K T S K P Y G S S Y R G T I H V E Y A T K L Q N H M A L A T D V V Q F M S N M L Q N F K T I W L * L Q . . . . : . . 479886 TACTCCAGCTGTTCTAGCATCGGAATAACAGATCCAAG : GTACAAAGTAGTATTAATTGCC Y S S C S S I G I T D P R : Y K V V L I A T P A V L A S E * Q I Q : G T K * Y * L P I L Q L F * H R N N R S K : V Q S S I N C . . . . . . 479740 AGCGATGATGATGCTAATGCTACATTTATCCTTTTCGGAAGGATCGCACAACGGCTACTA S D D D A N A T F I L F G R I A Q R L L A M M M L M L H L S F S E G S H N G Y Y Q R * * C * C Y I Y P F R K D R T T A T . . . . . . 479680 CGCAGGCCCGTAGAATCTCTCATTGAAGAAAAACCACCAAACAGTGAATACATTCCAAGT R R P V E S L I E E K P P N S E Y I P S A G P * N L S L K K N H Q T V N T F Q V T Q A R R I S H * R K T T K Q * I H S K . . . . . . 479620 GAAATCACGTCACTTATTGGTAGCAATTTTGCATGGAATGTTAGCTTTACGCGGGATACT E I T S L I G S N F A W N V S F T R D T K S R H L L V A I L H G M L A L R G I L * N H V T Y W * Q F C M E C * L Y A G Y . . . . . . 479560 GTTATGAGAAGTCAAGAGTGCCTACAAGTTAATAGCATTATATCCGCTGGTGCTTCAAAC V M R S Q E C L Q V N S I I S A G A S N L * E V K S A Y K L I A L Y P L V L Q T C Y E K S R V P T S * * H Y I R W C F K . . . . . . 479500 CAGCCACTACTCCTTATGTCCCCAGATGCTTCACAAGTGACATCAGCTATTGTCTCAGCA Q P L L L M S P D A S Q V T S A I V S A S H Y S L C P Q M L H K * H Q L L S Q Q P A T T P Y V P R C F T S D I S Y C L S . . . . . . 479440 AGCTCAAGCAGCTCTGTCCAAACAGCACCAACACCAAATGAAACAAGCAATGAATCACAG S S S S S V Q T A P T P N E T S N E S Q A Q A A L S K Q H Q H Q M K Q A M N H S K L K Q L C P N S T N T K * N K Q * I T . . . . . . 479380 CAGCCCATTTAACCAAGACAAACCATCTCAACACCAACCAAGTTCATCATCGCTCAGGGA Q P I * P R Q T I S T P T K F I I A Q G S P F N Q D K P S Q H Q P S S S S L R E A A H L T K T N H L N T N Q V H H R S G . . . . . . 479320 ACACAGGACACCCCAACTAGCAAATCAAGTTCTTCAGCACCTACCAAGAAAAGCATTGTT T Q D T P T S K S S S S A P T K K S I V H R T P Q L A N Q V L Q H L P R K A L L N T G H P N * Q I K F F S T Y Q E K H C . . . . . . : 479260 GTCTCAGTGTCTCACATGCAGTCTAGCAAGACCAAACCTAAAACTGATGATAAG : CCCAAA V S V S H M Q S S K T K P K T D D K : P K S Q C L T C S L A R P N L K L M I S : P K C L S V S H A V * Q D Q T * N * * * : A Q . . . . . . 479117 ACTGACACAAAAGCTAAAGAAAACACCTCACATGATAAATCTTCAATTGTTGTACTGCCT T D T K A K E N T S H D K S S I V V L P L T Q K L K K T P H M I N L Q L L Y C L N * H K S * R K H L T * * I F N C C T A . . : . . . . 479057 GATACTGCTGAAAATAAG : GGAAAGGGACTACCAGAAACTGCTGAAGAAGCCAAACAAGCA D T A E N K : G K G L P E T A E E A K Q A I L L K I R : E R D Y Q K L L K K P N K Q * Y C * K * : G K G T T R N C * R S Q T S . . . . : . . 478933 ACCCCATCCTTCCCTACAGATACCCTAGCCAAAAAAAG : AGGAAGGCCTACACCTACAGCA T P S F P T D T L A K K R : G R P T P T A P H P S L Q I P * P K K : E E G L H L Q Q N P I L P Y R Y P S Q K K : R K A Y T Y S . . . . . . : 478795 ACACCTCCGGTTGCTAAGAAATTGTTCAAGGATGATGCCCAGCAAAAAGGCAATGACAG : C T P P V A K K L F K D D A Q Q K G N D S : H L R L L R N C S R M M P S K K A M T : A N T S G C * E I V Q G * C P A K R Q * Q : . . . . . . 478663 TCTTAATTCATCTACACAGTGAATGAGTTGTCGACGTGCAATCCATCTCAAGACTTTTTC S * F I Y T V N E L S T C N P S Q D F F L N S S T Q * M S C R R A I H L K T F S L L I H L H S E * V V D V Q S I S R L F . . . . . . 478603 TTATATATATGTACAAAGCTATGTCCCAGCTAGAAGACAGATGGCAGTTGTGAAATTACC L Y I C T K L C P S * K T D G S C E I T Y I Y V Q S Y V P A R R Q M A V V K L P L I Y M Y K A M S Q L E D R W Q L * N Y . . . . . . 478543 CAGGACTAAGGAACCAAGATCTTTTGTTCATGGCTTTTTGTCATGATTATCATTGTATAT Q D * G T K I F C S W L F V M I I I V Y R T K E P R S F V H G F L S * L S L Y I P G L R N Q D L L F M A F C H D Y H C I . . 478483 AAGTGTTGCCTTATCT K C C L I S V A L S * V L P Y Maximal non-overlapping open reading frames (>= 64 codons) >OSchr10-v3-_PGL-1_AGS-1_PPS_1 (490905 490904,481470 481320,481228 480759,480605 480440,480384 480373) (frame '0'; 798 bp, 266 residues) 1 RFHMAHVLIS QLSFGDSNKR ILARVSRLWN FTDLNDDTKI FHTDLVLLDE MGTSIHAQIY 61 PPITEKMKPL LKEEKVYYID SFTVRAANRT YRLVANNLMI LFSKWTTLEE HINVPPHFPG 121 ITFSLTPFED VPSLVEKKSF YVGNNILLLC CNYCYIHLLQ CHIILLNLYA MQTDIMGVIT 181 EVGAVTTIRP KSRNAKSLKR TLQIRDASNS TLPVTLWGER ATSFDADDIY NAGQTQAQVA 241 VFVGTLVKDY RGLGTFLSKL SITALH* >OSchr10-v3-_PGL-1_AGS-1_PPS_2 (480372 480323,480218 480098,480003 479849,479762 479369) (frame '0'; 717 bp, 239 residues) 1 LEAYHLNIPE VAELNESFST NFQPIKWVDE PATGYNQDVP EEKSIAEILN INPHKHKGTR 61 FIVNVTVRRI CNEYSWWYNS CRICYKTSKP YGSSYRYSSC SSIGITDPRY KVVLIASDDD 121 ANATFILFGR IAQRLLRRPV ESLIEEKPPN SEYIPSEITS LIGSNFAWNV SFTRDTVMRS 181 QECLQVNSII SAGASNQPLL LMSPDASQVT SAIVSASSSS SVQTAPTPNE TSNESQQPI* >OSchr10-v3-_PGL-1_AGS-1_PPS_3 (479368 479207,479123 479040,478975 478896,478817 478737,478664 478658) (frame '0'; 411 bp, 137 residues) 1 PRQTISTPTK FIIAQGTQDT PTSKSSSSAP TKKSIVVSVS HMQSSKTKPK TDDKPKTDTK 61 AKENTSHDKS SIVVLPDTAE NKGKGLPETA EEAKQATPSF PTDTLAKKRG RPTPTATPPV 121 AKKLFKDDAQ QKGNDSS* >OSchr10-v3-_PGL-1_AGS-1_PPS_4 (495031 494750) (frame '1'; 279 bp, 93 residues) 1 TLSSSSFLPD KQRKKRSHSI GTNEAGRQEA CSLEVSSLEC LPLGVRQRRG HGCWRRSQFD 61 GDDCMRWVST SSDEEEGVFP GRRRGGAVPS AAG* $ memory statistics: $ 2948 bytes spliced alignments in total $ 1 spliced alignments have been stored $ 2948 bytes was the average size of a spliced alignment $ 2720 bytes predicted gene locations in total $ 1 predicted gene locations have been stored $ 2720 bytes was the average size of a predicted gene location $ 99 megabytes was the average size of the backtrace matrix $ 1 backtrace matrix has been allocated