AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_aful_mthe_300.orf -o199_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RTH00618 16 M.thermo RAG28489 22 Archaeoglobus_fulgidus RTH00964 38 M.thermo RAG28495 21 Archaeoglobus_fulgidus RTH01019 18 M.thermo RTH00961 18 M.thermo RTH01010 21 M.thermo RTH00858 16 M.thermo RTH01561 41 M.thermo Input sequences: #1 RAG45971 128 Archaeoglobus_fulgidus #2 RAG45930 32 Archaeoglobus_fulgidus #3 RAG50433 95 Archaeoglobus_fulgidus #4 RAG33159 72 Archaeoglobus_fulgidus #5 RAG49679 165 Archaeoglobus_fulgidus #6 RAG48732 101 Archaeoglobus_fulgidus #7 RAG50374 41 Archaeoglobus_fulgidus #8 RAG50371 57 Archaeoglobus_fulgidus #9 RAG32612 62 Archaeoglobus_fulgidus #10 RAG48823 189 Archaeoglobus_fulgidus #11 RAG47824 166 Archaeoglobus_fulgidus #12 RAG10300 21 Archaeoglobus_fulgidus #13 RAG10399 117 Archaeoglobus_fulgidus #14 RAG50247 109 Archaeoglobus_fulgidus #15 RAG11044 30 Archaeoglobus_fulgidus #16 RAG45849 97 Archaeoglobus_fulgidus #17 RAG45848 94 Archaeoglobus_fulgidus #18 RAG11879 223 Archaeoglobus_fulgidus #19 RAG45739 71 Archaeoglobus_fulgidus #20 RAG24795 202 Archaeoglobus_fulgidus #21 RAG49671 32 Archaeoglobus_fulgidus #22 RAG50227 57 Archaeoglobus_fulgidus #23 RAG47407 166 Archaeoglobus_fulgidus #24 RAG24310 104 Archaeoglobus_fulgidus #25 RAG46792 83 Archaeoglobus_fulgidus #26 RAG31578 216 Archaeoglobus_fulgidus #27 RTH01790 170 M.thermo #28 RTH00571 19 M.thermo #29 RTH02039 22 M.thermo #30 RTH00851 46 M.thermo #31 RTH00189 109 M.thermo #32 RTH01001 16 M.thermo #33 RTH01648 30 M.thermo #34 RTH00952 236 M.thermo #35 RTH01420 17 M.thermo #36 RTH00723 62 M.thermo #37 RTH01329 300 M.thermo #38 RTH01081 40 M.thermo #39 RTH00257 22 M.thermo #40 RTH00179 113 M.thermo #41 RTH00330 34 M.thermo #42 RTH01858 70 M.thermo #43 RTH00707 98 M.thermo #44 RTH01259 73 M.thermo #45 RTH01854 151 M.thermo #46 RTH01592 235 M.thermo #47 RTH00422 120 M.thermo #48 RTH00483 26 M.thermo #49 RTH01562 52 M.thermo #50 RTH00987 33 M.thermo #51 RTH00617 300 M.thermo Motif number 1 CAGAGTTTGTTGGACGGGAGTAAAAATTA 6 8 1 TGGGACGGGA 0.951424 -94 GCTTTGAAAATCAATGCCGGGGAAAAAGTAAT 6 36 0 TCTGCCGGGG 0.782465 -66 CGCAGCCTTTGCTGGGTCGGGAAGCAATATAA 9 30 0 GCGGTCGGGA 0.890177 -33 TAGGAGGCTACGGCCGCTGGGACTACGGGGTG 11 140 1 CGCGCTGGGA 0.954256 -27 AGGTCTTTTTGGCAGGCCGGGAGGAGCCGCTG 13 96 1 GGGGCCGGGA 0.991382 -22 TTTGAACCCGCGACCGACGGGTTAAAAGCCCG 20 144 0 CGCGACGGGT 0.914013 -59 TTTAAATACGGGCTCGACGGGATTTGAACCCG 20 166 0 GGCGACGGGA 0.976658 -37 GACCCCGCAGCGGAGGCTGGGAGGATGGAGGC 26 101 0 CGGGCTGGGA 0.966552 -116 AAAGTTTTTTCGCTGGACTGGAAAATATGCCC 31 24 0 CGGGACTGGA 0.877932 -86 TATGATACATCCTGTGCCGGGATAGCCTAGCC 34 57 1 CCTGCCGGGA 0.980801 -180 GTTGCTTTAACCGACGCCGGGACTGGGATTTG 34 139 0 CCCGCCGGGA 0.992289 -98 AGAGTGAATTCGCGGGACGGGGGTTTGCGAAT 34 199 0 CGGGACGGGG 0.983023 -38 TCAGGAAACGCCCTGGCCGGGAATTGAACCCG 37 163 0 CCGGCCGGGA 0.867249 -138 TTAGATAGCGGGCCCGACGGGAATTGAACCCG 37 245 0 GGCGACGGGA 0.976657 -56 GGAGGGATGACCATTGCCGGGGGTCTCAGGGT 51 152 0 CCTGCCGGGG 0.959069 -149 ** ******** Masking position 6 Map Score: 23.4147 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 141 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 CATCAGAAGCACAGGAAGAGGGCGGAGCGA 1 52 1 ACAGGAAGAG 0.906251 -77 GTTAAATCCATTAGGAGGATATATAAACCT 8 12 0 TTAGGAGGAT 0.677035 -46 GAAAAACCAGAAAGGAGGAGATAGGT 8 42 1 AAAGGAGGAG 0.926398 -16 ACTGCTGATACTCGGAGGAGCGTCGGCATC 10 27 0 CTCGGAGGAG 0.901444 -163 GTTCTCTGAAATGGGCAGATAAAATTTCAA 11 68 0 ATGGGCAGAT 0.518145 -99 TTTTGGCAGGCCGGGAGGAGCCGCTG 13 102 1 CCGGGAGGAG 0.988822 -16 CTTACAGGGAGGAGGAAATCCTGA 18 5 1 CAGGGAGGAG 0.961478 -219 CGTAGCTCAGCCAGGCAGAGCGACGGGCTT 20 121 1 CCAGGCAGAG 0.873577 -82 GTATTTAAAAATAGGAGGATCAAC 20 189 1 ATAGGAGGAT 0.921246 -14 GCAGCGGAGGCTGGGAGGATGGAGGCTATT 26 97 0 CTGGGAGGAT 0.958672 -120 AAATAACCAGGAGGATATTCGG 29 7 1 CCAGGAGGAT 0.975463 -16 GGATTTGAACCCAGGAGGAGCAAAGCTCCA 34 116 0 CCAGGAGGAG 0.987885 -121 TTTTCCACCGGGAGGCTGTTAA 39 8 1 CCGGGAGGCT 0.845418 -15 TCCTGTAAAAAAGGGAAGAGGTGGGT 41 7 0 AAGGGAAGAG 0.7474 -28 TCCCTTTTTTACAGGAGGATTTAA 41 21 1 ACAGGAGGAT 0.956039 -14 GATGTGCCAGATAGGCGGAGGATTATTACC 51 115 1 ATAGGCGGAG 0.903683 -186 ********** Masking position 5 Map Score: 17.808 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 602 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 TCAGAAAAGTTAAAAATGTTGCCCAAAGCTCA 3 24 1 TAAAAATTGC 0.78721 -72 CAGTTACACCTTTAAACTTTTTGATTTTTACC 4 39 0 TTTAAATTTT 0.898965 -34 AGTTGTTAGTTAAAAATGTTTTGTCTAATACT 5 24 1 TAAAAATTTT 0.898885 -142 AAATCTATTTTAAAAAACTTGCGAAAGCGTGC 5 108 0 TAAAAATTGC 0.787213 -58 ATCAGCTGATTTAAAACGTTTTTCCGTT 7 7 0 TTAAAATTTT 0.874783 -35 ACTTCAATAATTTAAATTTTTTGCTCAGATAA 10 102 1 TTTAAATTTT 0.898963 -88 ATAAGAGGAATTAAAACGTTTCCCCTTCTGTC 11 22 1 TTAAAATTTC 0.839501 -145 ATGAGATGAATATAAAGTTTTTGAAGTTCTTT 14 60 0 TATAAATTTT 0.918908 -50 ATGGTGAGGATTTAAATCTTTTTCGTGCTCTA 20 71 0 TTTAAATTTT 0.898965 -132 GTAGTGTTTATTAAAAGTTTTTTTTATATATC 23 97 1 TTAAAATTTT 0.874781 -70 CAACAAAGCATTTAAACTTTGCCAAAAGCGCG 23 132 0 TTTAAATTGC 0.787213 -35 CGGATTTATTTATAAATATTTCCACAATGCAG 27 134 0 TATAAATTTC 0.894561 -37 GGTATCCCCTTAAAAAGTTTTTTCGCTGGACT 31 37 0 TAAAAATTTT 0.898885 -73 TTACTACCTTTATAAAAATTTTTCCTATACCT 45 71 1 TATAAATTTT 0.918909 -81 CTTCAAGATTTATAAAGGTTTTCCTTGAGTGG 47 28 0 TATAAATTTT 0.918909 -93 GGAATCTATATATAAACTTTGTGCATTGTCGC 51 43 1 TATAAATTGT 0.862884 -258 ****** **** Masking position 6 Map Score: 15.5432 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 72 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 4 GTATTTAAATGTTGAGGGATTTCGCCTCATGAGCTT 3 49 0 GTGAGGGTTC 0.967639 -47 CTCTGATAGAGTCGAGGGGGCTATGCCGAAAAACTC 18 97 0 GCGAGGGGCC 0.97649 -127 CATTAGCGATGGTGAGGATTTAAATCTTTTTCGTGC 20 75 0 GTGAGGATTC 0.631364 -128 ATCGCTAATGGATGAGGGCTCGTAGCTCAGCCAGGC 20 101 1 GTGAGGGTCC 0.98303 -102 TAACCCGTCGGTCGCGGGTTCAAATCCCGTCGAGCC 20 152 1 GCGCGGGTCC 0.991925 -51 CTCTCGTTCACACGAGGGAGCACTAC 26 1 0 CCGAGGGGCC 0.873367 -216 TTATGGAGGAGCTGAGGGATTACGAGGTCGTTGAGC 26 63 0 GTGAGGGTTG 0.925628 -154 CCCAGCCTCCGCTGCGGGGTCGGAGGTGTAGACGGT 26 112 1 GTGCGGGTCG 0.9651 -105 GAATTCGCGGGACGGGGGTTTGCGAATTCTTCATAA 34 190 0 GCGGGGGTTA 0.803026 -47 TTGAACCCGAGTCGCGGGCTCGACAGGCCCGCATGA 37 136 0 GCGCGGGTCG 0.980583 -165 CAGGGCGTTTCCTGAGGGCCCGTAGCTCAGTCTGGC 37 180 1 CTGAGGGCCC 0.721232 -121 TAACCAAGTGGTCGCGGGTTCAATTCCCGTCGGGCC 37 231 1 GCGCGGGTCC 0.991933 -70 AACATGTCATGATGGGGGGTCCCGCCCAGATTCATG 46 20 1 GTGGGGGTCC 0.979024 -216 GTGCCAGATAGGCGGAGGATTATTACCATTATACAC 51 118 1 GCGGAGGTTC 0.745414 -183 GATGACCATTGCCGGGGGTCTCAGGGTGTATAATGG 51 143 0 GCGGGGGCTG 0.870278 -158 * ****** ** * Masking position 7 Map Score: 16.4889 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 193 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 CACCAACATCGAAAAAAATTATAAGAATTTC 1 16 1 GAAAAAAATA 0.899352 -113 CGGAGCAAGAGAAAAAAAGGAATAAATTT 4 9 0 GAAAAAAAGA 0.925068 -64 CTCTTGCTCCGGTAAAAATCAAAAAGTTTAA 4 29 1 GGTAAAAATA 0.86775 -44 ATCAATGCCGGGGAAAAAGTAATTTTTACTC 6 28 0 GGGAAAAAGA 0.898842 -74 TTTTTGCTCAGATAAAAATGCTCACTCTAAT 10 119 1 GATAAAAATC 0.738427 -71 GATACTACAAGATAAAAAGAACTTCAAAAAC 14 45 1 GATAAAAAGA 0.925068 -65 TGAAAAATCTGAAAAAAAGTAATACGAGGTG 16 72 1 GAAAAAAAGA 0.925068 -26 GAAAGCTTAAGGGAAAAATTATAAGATGTGC 18 177 1 GGGAAAAATA 0.865435 -47 TGTGTGGGGTGATAAAAAGTATTAGCCCAAA 22 27 0 GATAAAAAGA 0.925068 -31 TTTGGGCGAGGAGAAAAATAATAGTCTTTCG 23 67 1 GAGAAAAATA 0.897525 -100 CAGTCCTCCAGATAAAAAGTCACCGTAAAAT 37 276 0 GATAAAAAGC 0.79593 -25 CATGGCTGAAGGAAAAAATCATTAATTAATG 43 38 1 GGAAAAAATA 0.86775 -61 GACTTCACCAGAAAAAAATTAATTGGGAGGA 50 11 0 GAAAAAAATA 0.899352 -23 ********* * Masking position 6 Map Score: 12.9367 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 131 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 GAACATCCCCCATTTCTTTTTCAATTATC 1 110 0 ATCCCCATTT 0.794449 -19 AACGTTTTAAATCAGCTGATTAACTCGCCGAGT 7 19 1 ATCAGCGAAT 0.685166 -23 AAAATCATCACCGCAGCCTTTGCTGGGTCGG 9 42 0 ATCACCCATT 0.983703 -21 TATATCACCTGTGAATTTTAGGGCCAGC 18 206 0 ATCACCGTTT 0.922695 -18 AATACTTTTTATCACCCCACACAATTAAGCATC 22 35 1 ATCACCCAAT 0.928829 -23 CCTATCACCAAAAGTTTTTGAGGAAGTC 23 4 1 ATCACCAATT 0.945508 -163 AGGAAGATTGACCACCTGAAAATCTGCCTCGAAGA 25 22 1 ACCACCGATT 0.920567 -62 AAGATCGTTTTTCACCCGAAGTTCTACACCGTCTA 26 140 0 TTCACCGATT 0.720663 -77 CCTCACCAGCGGAAAGTTTAAATATGGAT 27 5 1 ACCAGCGATT 0.77386 -166 TCTGCGGTGGATCCGCTCACATTGTATGCTCTGAT 27 68 1 ATCCGCCATT 0.918961 -103 TAAATCACCTCAGTAACTTTTAGTATGA 33 13 0 ATCACCCAAT 0.928829 -18 CCTTCAGTTCATCAGCACACCTTATAAATAATAAT 42 45 0 ATCAGCCATT 0.946869 -26 TTAATTAATGATCCCCCATAAATGTAAACAAGAAG 43 59 1 ATCCCCATTT 0.794449 -40 GAAAACACCACCTACTTATATATACCTGATC 45 131 0 ACCACCACTT 0.631292 -21 GGTTTATCCCCGCTATTTATATAGTTAAAA 47 101 0 ATCCCCCTTT 0.930776 -20 ATGATCACCTCAAATTTTATTTTTTATG 49 35 0 ATCACCCATT 0.983704 -18 TATCTGGCACATCCCCACCATTTATTAAAAAGGTC 51 93 0 ATCCCCCCTT 0.917676 -208 ATTAGTAATAATCACTTCAACCTTTATATTATATG 51 225 1 ATCACTCATT 0.738182 -76 ****** ** * * Masking position 15 Map Score: 12.7453 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 190 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GATATTATCTGGAATTTTAACGTTTGGGGGA 13 20 1 GGAATTTAAC 0.809141 -98 GCAGAGCGACGGGCTTTTAACCCGTCGGTCG 20 135 1 GGGCTTTAAC 0.955552 -68 CGGGCTCGACGGGATTTGAACCCGCGACCGA 20 159 0 GGGATTGAAC 0.989809 -44 CAGGATACACGGGACTTGAAGACGTG 25 68 1 GGGATTGAAG 0.941434 -16 CGCCGGGACTGGGATTTGAACCCAGGAGGAG 34 126 0 GGGATTGAAC 0.989809 -111 CGCCCTGGCCGGGAATTGAACCCGAGTCGCG 37 156 0 GGGATTGAAC 0.989808 -145 GCAGAGCGCTTGGCTTTTAACCAAGTGGTCG 37 214 1 TGGCTTTAAC 0.705941 -87 CGGGCCCGACGGGAATTGAACCCGCGACCAC 37 238 0 GGGATTGAAC 0.989808 -63 **** ****** Masking position 9 Map Score: 9.77094 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 17 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 CAGGTATGATTTATCTCAGCACGCTTTCGCA 5 90 1 TTATCTCACA 0.843329 -76 TTCATCACCTCTAATAGATATA 5 154 0 TCATCACCCT 0.932777 -12 AAAATCATCACCGCAGCCTTTGCTG 9 48 0 TCATCACCCA 0.967714 -15 GTGAGCATTTTTATCTGAGCAAAAAATTTAA 10 113 0 TTATCTGACA 0.65126 -77 ACTCTAATAATCATCAACTCAACTTAAAGCT 10 142 1 TCATCAACCA 0.723653 -48 TTTTGAAATTTTATCTGCCCATTTCAGAGAA 11 66 1 TTATCTGCCA 0.86667 -101 AACTTTATATTCATCTCATCTCCATCGAACA 14 73 1 TCATCTCACT 0.799538 -37 GTCATCTCACCTTTCTCTTTTT 21 21 0 TCATCTCACT 0.799541 -12 CTAATACTTTTTATCACCCCACACAATTAAG 22 33 1 TTATCACCCA 0.949307 -25 CAGGTTTCTCTTATCTCCACACCAGGTGATC 36 40 1 TTATCTCCCA 0.949307 -23 ACCTTCAGTTCATCAGCACACCTTATAAAT 42 51 0 TCATCAGCCA 0.912309 -20 GGTTTATCCCCGCTATTTATATAG 47 107 0 TTATCCCCCT 0.72734 -14 ATGATCACCTCAAATTTTATTT 49 41 0 TGATCACCCA 0.851955 -12 ******** ** Masking position 3 Map Score: 10.0131 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 422 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 TTCGCCTCATGAGCTTTGGGCAACATTTTT 3 35 0 GAGCTTTGGG 0.827505 -61 ATACTCGGAGGAGCGTCGGCATCTGCAGTG 10 20 0 GAGCGTCGGC 0.900865 -170 AGTCCGTAGGAGGCTACGGCCGCTGGGACT 11 134 1 AGGCTACGGC 0.729675 -33 ACGGCCGCTGGGACTACGGGGTGGTAAG 11 149 1 GGACTACGGG 0.969113 -18 TGCTGGAGAAGTACTTCGGGAAAGCTTAAG 18 158 1 GTACTTCGGG 0.823205 -66 CTGCCTGGCTGAGCTACGAGCCCTCATCCA 20 109 0 GAGCTACGAG 0.890548 -94 CAGCCAGGCAGAGCGACGGGCTTTTAACCC 20 128 1 GAGCGACGGG 0.984774 -75 TTGAACCCGCGACCGACGGGTTAAAAGCCC 20 145 0 GACCGACGGG 0.92556 -58 AGACGGTGTAGAACTTCGGGTGAAAAACGA 26 141 1 GAACTTCGGG 0.962939 -76 CGATTAGACTACGGGAAAAACTTAA 26 202 0 AGACTACGGG 0.828587 -15 CTGCCAGACTGAGCTACGGGCCCTCAGGAA 37 188 0 GAGCTACGGG 0.990409 -113 ********** Masking position 4 Map Score: 9.02784 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 167 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 CCTTTCACCAACATCGAAAAAAA 1 2 1 CTTTCCCACA 0.90719 -127 ACATTTAAATACATTCCCCTAAGGATTGATTT 3 73 1 ACATTCCCAA 0.603747 -23 ATACCTCTCCACTACTCCCTAAGGAGTCCGTA 11 110 1 ACTACCCCAA 0.784521 -57 GTTTTATCTTATTTCCCCCAAACGTTAAAATT 13 32 0 ATTTCCCCAA 0.907022 -86 AAGATAAAACCTTGCACCAACACTTCATCATG 13 54 1 CTTGCCCACA 0.553494 -64 TTATTCATAATTTTCTCCAAAATACTAAAATC 16 20 1 TTTTCCCAAA 0.627752 -78 TTCCCGAAGTACTTCTCCAGCACCTTTTTCTG 18 148 0 ACTTCCCACA 0.940459 -76 GCGTTTTCTCCCTTTACCCTCAGCAGCCCCT 19 10 0 CCTTTCCCCA 0.826936 -62 GCCTTTTCCCCGCAAATCTCGAAT 20 3 1 CTTTTCCCCA 0.782805 -200 CCTATCACCAAAAGTTTTTGAGG 23 2 1 CTATCCCAAA 0.71888 -165 AAGCATTTAAACTTTGCCAAAAGCGCGCTGGA 23 127 0 ACTTTCCAAA 0.801861 -40 TGAAGATCGTTTTTCACCCGAAGTTCTACACC 26 145 0 TTTTCCCCAA 0.646717 -72 TTATTTATAAATATTTCCACAATGCAGACTGG 27 129 0 ATATTCCAAA 0.514265 -42 CATGATAGCCCCTACACCACCAGGGCAAGTCT 37 109 0 CCTACCCACA 0.784859 -192 CAATAATTTTATTTTGCCCCAACCTTGAGCCG 46 79 1 ATTTTCCCAA 0.768176 -157 TTACTACCCCCACACTTATCTATG 46 222 0 ACTACCCCCA 0.82838 -14 TGAAGGATAGATTACTCCATCACTCATCCCAA 47 55 1 ATTACCCACA 0.770328 -66 TCGACTTCACCAGAAAAAAATTAAT 50 19 0 ACTTCCCAAA 0.922566 -15 CCTATCTGGCACATCCCCACCATTTATTAAAA 51 98 0 ACATCCCACA 0.845638 -203 TCAGGGTGCGATATTACCACAATATAAGGGAA 51 186 1 ATATTCCAAA 0.514265 -115 ***** *** ** Masking position 12 Map Score: 12.0558 Number of sites scoring better than the average of aligned sites = 1000 Number in coding regions = 941 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 AGCTTTAAAAACAGGTTGTGGAT 2 1 1 ACTTAAAAAA 0.761774 -32 AACTGTCAGAAAAGTTAAAAATGTTGCCCAAAG 3 19 1 AATTAAAAAG 0.687349 -77 AAATCCCTCAACATTTAAATACATTCCCCTAAG 3 63 1 AATTAAATAA 0.817644 -33 GATTTTAACAATAAATAAATATATCTATTAGAG 5 135 1 AAATAAATAA 0.419886 -31 ATAAAATTTCAAAATTAAAAAGCACAGACAGAA 11 47 0 AATTAAAAAC 0.885594 -120 CGTCGAGCCCGTATTTAAAAATAGGAGGATCAA 20 179 1 GATTAAAAAA 0.761774 -24 AGCGCGCTGGATATATAAAAAAAACTTTTAATA 23 105 0 AAATAAAAAA 0.673978 -62 GGGGCACATAACCTTTAAATATCCTTACAGGCT 24 58 1 ACTTAAATAC 0.4036 -47 CATTGTGGAAATATTTATAAATAAATCCGGACA 27 137 1 AATTATAAAA 0.52285 -34 GACGGCAGCAATACTTAAATAGATGTCATAATA 34 16 1 AATTAAATAA 0.817644 -221 TTAAACTTATATAATTAAAAAGAATATAGGAAA 40 16 1 AATTAAAAAA 0.92757 -98 GCTCACATTCAAAATTAAAAATCAATTTCTGTG 46 125 0 AATTAAAAAC 0.885594 -111 GTGATAAGACATATTTAAAAGCAACGGTTAATC 46 177 0 AATTAAAAGA 0.618913 -59 CGCTATTTATATAGTTAAAAAACAAGGGCTAGG 47 88 0 AATTAAAAAC 0.885594 -33 TAGATTCCATAAAATTAAAAACATCATTATAAA 51 18 0 AATTAAAAAA 0.92757 -283 TATAGTGATTGGAATTAAAAAAAGATTAAGGAG 51 269 1 GATTAAAAAA 0.761774 -32 * * ******* * Masking position 7 Map Score: 6.90925 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 28 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 GAAATAACTTCACACCCCAACAAGATTGCC 14 13 0 CACACCCCAA 0.968753 -97 TTATATTCATCTCATCTCCATCGAACATAT 14 77 1 CTCATCTCCA 0.829806 -33 ATTTCTCTAACACCTCCCAAGCGTTTTCTC 19 32 0 CACCTCCCAA 0.931852 -40 TATTCTTCCACACACCCCCACTCAAGGAAA 47 11 1 CACACCCCCA 0.9799 -110 TACTCCATCACTCATCCCAATCCTAGCCCT 47 67 1 CTCATCCCAA 0.952479 -54 GCCTATCTGGCACATCCCCACCATTTATTA 51 101 0 CACATCCCCA 0.983279 -200 ********** Masking position 10 Map Score: 2.9455 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 43 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 TTTTTTTCTCTTGCTCCGGTAAAAATCAAAA 4 22 1 TTGCTCCGGA 0.868268 -51 TATAAAGCTGTTGCTCCGGAAGGCTTTGAAA 6 59 0 TTGCTCCGGA 0.868266 -43 TGATGATTATTAGAGTGAGCATTTTTATCTG 10 127 0 TAGAGTGAGA 0.565377 -63 CTGTGAATTTTAGGGCCAGCACATCTTATAA 18 195 0 TAGGGCCAGA 0.907092 -29 CGTTCTCTTTTTGGGCGAGGAGAAAAATAAT 23 58 1 TTGGGCGAGA 0.852194 -109 GAAGAGGAGGTTGAGTCAGGATACACGGGAC 25 52 1 TTGAGTCAGA 0.914848 -32 TACGAGGTCGTTGAGCCGGAACCGGCAAAGA 26 48 0 TTGAGCCGGA 0.976324 -169 CCTGATTTTTTAGATCCAGCAAATGGGCATG 40 66 0 TAGATCCAGA 0.829491 -48 CACCTTCTGTTTGAGTCAGAAATAACGGGAT 45 16 1 TTGAGTCAGA 0.914847 -136 TGCCCCAACCTTGAGCCGGTATTTTCAGAGG 46 93 1 TTGAGCCGGA 0.976329 -143 ********* * Masking position 1 Map Score: 3.50693 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 99 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 GTTCGCTCCGCCCTCTTCCTGTGCTTCTGA 1 54 0 CCCTCTTCCT 0.707935 -75 ACCTATCTCCTCCTTTCTGGTTTTTCGT 8 40 0 CCTCCTTTCT 0.567697 -18 TTCAGGATTTCCTCCTCCCTGTAAG 18 6 0 CCTCCTCCCT 0.7344 -218 CCTTTTTCTGCCCCCTTCTTAGTATCTCTG 18 128 0 CCCCCTTCTT 0.866607 -96 GAGCTACGAGCCCTCATCCATTAGCGATGG 20 99 0 CCCTCATCCA 0.614492 -104 GGTTATGTGCCCCCCTTCAATTGAGGATTA 24 41 0 CCCCCTTCAA 0.940789 -64 TCCCTCAGCTCCTCCATAATAGCCTCCATC 26 80 1 CCTCCATAAT 0.706885 -137 TCCATAATAGCCTCCATCCTCCCAGCCTCC 26 92 1 CCTCCATCCT 0.888323 -125 TTAACTTTACCTCCTTACA 28 1 0 CCTCCTTACA 0.902201 -19 TGGAAAATATGCCCCTTCCAGTCCTCC 31 8 0 GCCCCTTCCA 0.692888 -102 ATTTCAGGTATCCCCTTAAAAAGTTTTTTC 31 45 0 TCCCCTTAAA 0.315778 -65 TCAAGAAACCTCCTTGTATTCAGCATTT 31 92 0 CCTCCTTGTA 0.466847 -18 CCCCATTAAACTTATATAAT 40 1 1 CCCCATTAAA 0.30369 -113 AATATACCTCCATATATGATGGTTTA 40 98 0 CCTCCATATA 0.547366 -16 AATTAATGATCCCCCATAAATGTAAACAAG 43 61 1 CCCCCATAAA 0.854388 -38 ATACTGCCCCCTTGCATAGTATTATC 44 7 1 CCCCCTTGCA 0.897064 -67 TGGGCGGGACCCCCCATCATGACATGTTAT 46 18 0 CCCCCATCAT 0.894958 -218 TTACTACCCCCACACTTATCTATGAA 46 220 0 CCCCCACACT 0.691683 -16 GCTATTCGCCTCCTTAATCTTTTTTTAA 51 283 0 CCTCCTTAAT 0.802417 -18 ********** Masking position 2 Map Score: 10.2857 Number of sites scoring better than the average of aligned sites = 1055 Number in coding regions = 998 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 15 GTCGCGGGTTCAAATCCCGTCGAGCCCGTA 20 162 1 CAAATCCCGT 0.94446 -41 CACGTCTTCAAGTCCCGTGTATCCTGAC 25 66 0 CAAGTCCCGT 0.978895 -18 GGTTCAAATCCCAGTCCCGGCGTCGGTTAA 34 135 1 CCAGTCCCGG 0.983569 -102 GACTCGGGTTCAATTCCCGGCCAGGGCGTT 37 159 1 CAATTCCCGG 0.985415 -142 GTCGCGGGTTCAATTCCCGTCGGGCCCGCT 37 241 1 CAATTCCCGT 0.977256 -60 GGAGGGATGACCATTGCCGGGGGTCTCAGG 51 154 0 CCATTGCCGG 0.927755 -147 ********** Masking position 5 Map Score: 3.81162 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 54 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701