AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_hpyl_reg_300.orf -o293_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RHP00877 54 AE000511 RHP00163 146 AE000511 Input sequences: #1 RHP01034 89 AE000511 #2 RHP00006 47 AE000511 #3 RHP00008 57 AE000511 #4 RHP00009 51 AE000511 #5 RHP00010 20 AE000511 #6 RHP00013 73 AE000511 #7 RHP00020 81 AE000511 #8 RHP00021 228 AE000511 #9 RHP00114 300 AE000511 #10 RHP00156 41 AE000511 #11 RHP00158 91 AE000511 #12 RHP00160 119 AE000511 #13 RHP00164 146 AE000511 #14 RHP00165 77 AE000511 #15 RHP00169 64 AE000511 #16 RHP00443 128 AE000511 #17 RHP00444 30 AE000511 #18 RHP00445 140 AE000511 #19 RHP00623 73 AE000511 #20 RHP00624 150 AE000511 #21 RHP00873 138 AE000511 Motif number 1 ACCTTTTAAACTATTTTTAATCAATTTTTA 1 59 0 CTATTTTTAA 0.765786 -31 CTACAATAATAGGATTTTAATTATATAAAG 6 49 1 AGGATTTTAA 0.70078 -25 TTCATAAACTTTGTCTTTAATGGCTTCATT 8 21 0 TTGTCTTTAA 0.698566 -208 AGAGAGAAAGCGTTTTTTAAGGGCTTCATC 8 72 0 CGTTTTTTAA 0.796272 -157 TTGAATGCGGTTGATTTTAACCGAAAGCGT 8 159 0 TTGATTTTAA 0.932837 -70 AGCCCCGTCATTGATTTTAGTGATGACGAG 9 30 0 TTGATTTTAG 0.897007 -271 TAGCGTCAATCTCTCTTTAAACGCTCCTAA 9 120 0 CTCTCTTTAA 0.851674 -181 GCGTTTTTTCATTTTTTTAATCCTCATTTG 9 192 0 ATTTTTTTAA 0.553757 -109 CTCATTTTAGGGAATTTTAACATGCCTTAT 9 268 0 GGAATTTTAA 0.577135 -33 AATCCTTAAACTCATTTTAGGGAATTTTAA 9 278 0 CTCATTTTAG 0.95571 -23 TGGCGCATTCGGTATTTTAACACAAAT 11 8 0 GGTATTTTAA 0.722362 -84 AATTTTCTGACGCATTTTAACAAAAAAAAA 12 84 0 CGCATTTTAA 0.955714 -36 ACAATAAGGCTTAATTTTAAGCACGTTTTA 13 56 0 TTAATTTTAA 0.796313 -91 TTAAGAAAATCGCTTTTTAATGCAAATAAA 13 86 1 CGCTTTTTAA 0.930217 -61 TTTAAATCATGGCATTTTAGCATTTTATTT 13 109 0 GGCATTTTAG 0.84766 -38 TTGCCTTAAATTCTTTTTAAATCATGGCAT 13 124 0 TTCTTTTTAA 0.940262 -23 ATTCAAAAGCCTTTTTTTAGGTAAATATAG 14 21 1 CTTTTTTTAG 0.796272 -57 TGCGCTACAATTGATTTTAATTCATTTTAG 15 33 1 TTGATTTTAA 0.932837 -32 TTGATTTTAATTCATTTTAGGGAGTGTAAG 15 43 1 TTCATTTTAG 0.941095 -22 GATTAAGGCATTGATTTTAGATT 18 4 0 TTGATTTTAG 0.897007 -137 TAGGTGGTTTGTCTTTTTAGGCTTATTATA 18 37 1 GTCTTTTTAG 0.845707 -104 TTCATTTTAAGCAAAACTTA 19 1 1 TTCATTTTAA 0.962233 -73 TTGTAATTGTATCATTTTAAGATCATTTTG 19 34 1 ATCATTTTAA 0.872639 -40 GGGCTTGAAACTCATTTTAATAGCGCCCAA 20 36 0 CTCATTTTAA 0.97176 -115 TTCTTAATTTTTGATTTTAATGGCATTCTT 20 70 1 TTGATTTTAA 0.932837 -81 AGGTCTTTATTTTAGCTCTTTCTTG 20 136 0 TTTATTTTAG 0.824094 -15 TATCAAACAACGCTTTTTAAGAGTGGCTCA 21 64 0 CGCTTTTTAA 0.930217 -75 TCTTTAAAATTTTACTTTAAGATACCATAT 21 107 0 TTTACTTTAA 0.668658 -32 TTTTTAAAACTCTCTTTAAAATTTTACTT 21 120 0 CTCTCTTTAA 0.851674 -19 ********** Masking position 6 Map Score: 34.1187 Number of sites scoring better than the average of aligned sites = 1341 Number in coding regions = 1051 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 2 CAAAGGGATTAAAACAAGGCT 1 1 0 AAAACAGGCT 0.984213 -89 ATGAAGCCCTTAAAAAACGCTTTCTCTCTTT 8 73 1 TAAAAACGCT 0.913662 -156 ATTTTAACCGAAAGCGTGGCTTTTTTCATGG 8 145 0 AAAGCGGGCT 0.963369 -84 TAAAAGATTTAAAACACCGCTTACTAGCCAA 11 60 0 AAAACACGCT 0.982319 -32 CATAAGGCTAAAAGCACGGCTAAAGCGTGGC 12 19 1 AAAGCAGGCT 0.980844 -101 AAGCACGGCTAAAGCGTGGCTAAAGCGTGGC 12 30 1 AAAGCGGGCT 0.963369 -90 AAGCGTGGCTAAAGCGTGGCTGGAGCGTGGG 12 41 1 AAAGCGGGCT 0.963369 -79 TAACAAAAAAAAAAAAACGCAAACCCCCACG 12 66 0 AAAAAACGCA 0.759675 -54 TTATTGTTTAAGAAAATCGCTTTTTAATGCA 13 79 1 AGAAAACGCT 0.8241 -68 ATATTTACCTAAAAAAAGGCTTTTGAATTTT 14 18 0 AAAAAAGGCT 0.977857 -60 AAACAAACGCTTTTAGTTTGG 15 1 1 AAACAACGCT 0.931693 -64 GAATCACAAGAAACTACCGCTTGACTAATGT 16 25 0 AAACTACGCT 0.791299 -104 TAATAGCGCCCAAATAACGCTATTAAAACGG 20 18 0 CAAATACGCT 0.76051 -133 AAAAATTAAGAAAAAAGGGCTTGAAACTCAT 20 51 0 AAAAAAGGCT 0.977857 -100 CAACGCTTTTTAAGAGTGGCTCAAGGGCTAA 21 56 0 TAAGAGGGCT 0.833591 -83 CCATTTTTATCAAACAACGCTTTTTAAGAGT 21 70 0 CAAACACGCT 0.941611 -69 CGTTGTTTGATAAAAATGGCTCATTATATGG 21 82 1 TAAAAAGGCT 0.922327 -57 ****** **** Masking position 3 Map Score: 27.1868 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 623 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TTTTGATTTATTATAGCGTTT 3 1 0 TTTAGCGTTT 0.786769 -57 TGTAGCAAAAATCATGCGTTTAATGGAATAA 6 23 0 ATATGCGTTT 0.913672 -51 ATGACGCTCAATGAAGCCATTAAAGACAAAG 8 12 1 ATAAGCCATT 0.778078 -217 GCTTCATCGCAGTTAGCGATTTCTACGATTT 8 49 0 AGTAGCGATT 0.913361 -180 GCTAACTGCGATGAAGCCCTTAAAAAACGCT 8 63 1 ATAAGCCCTT 0.891489 -166 ACCAAAAGAGAGAAAGCGTTTTTTAAGGGCT 8 77 0 AGAAGCGTTT 0.971614 -152 TAAAGCCACTTGAATGCGGTTGATTTTAACC 8 167 0 TGATGCGGTT 0.717089 -62 TAATGAGCGCTGATAGCGCTTTGCCTAGCGT 9 144 0 TGTAGCGCTT 0.914206 -157 TTTGCCCTTTAATATGCCCTTTAATGAGCGC 9 165 0 AAATGCCCTT 0.804808 -136 TAAGGCTAGAATTTTGCGTTTTTTCATTTTT 9 206 0 ATTTGCGTTT 0.86273 -95 CATGCTGAATGGGTTGCGCTT 10 1 0 GGTTGCGCTT 0.840471 -41 CAACCCATTCAGCATGCGTTTAACACAGATT 10 16 1 AGATGCGTTT 0.961759 -26 GCCAAAAACTAGCAAGCGTTTTAGCGTTGGC 11 34 0 AGAAGCGTTT 0.971614 -58 GGAGCGTGGGGGTTTGCGTTTTTTTTTTTTT 12 62 1 GGTTGCGTTT 0.812558 -58 TATTTGCATTAAAAAGCGATTTTCTTAAACA 13 83 0 AAAAGCGATT 0.836146 -64 GCACCCAAACTAAAAGCGTTTGTTT 15 5 0 TAAAGCGTTT 0.809309 -60 TAAAATGAGTTTCAAGCCCTTTTTTCTTAAT 20 47 1 TTAAGCCCTT 0.779924 -104 ACTAGCTTTAAGAATGCCATTAAAATCAAAA 20 78 0 AGATGCCATT 0.859579 -73 TATTCTATCCAATTAGCCCTTGAGCCACTCT 21 44 1 AATAGCCCTT 0.769178 -95 ** ******** Masking position 10 Map Score: 19.2977 Number of sites scoring better than the average of aligned sites = 1364 Number in coding regions = 1207 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 TAGAATTTTGATTTATTATAGCGTTT 3 4 0 ATTTTTAGCG 0.900006 -54 CTGTTAAAATATCCTTTTTAGCGAAACGATGTA 4 28 0 ATCTTTAGCG 0.986137 -24 TAAGGGCTTCATCGCAGTTAGCGATTTCTACGA 8 52 0 ATCAGTAGCG 0.958801 -177 CTCTTTTGGTATCCATGAAGGGGTTCAATGCAT 8 98 1 ATCTGAGGGG 0.91092 -131 TGGCTTTAAGATCCCATGAAGCACAATACCTTG 8 190 1 ATCATAAGCA 0.599793 -39 ATACCTTGTCATCAAAGAAAGCGT 8 215 1 ATCAGAAGCG 0.92349 -14 CATCACTAAAATCAATGACGGGGCTAAAACTAA 9 35 1 ATCTGCGGGG 0.821638 -266 CCCTTTAATGAGCGCTGATAGCGCTTTGCCTAG 9 147 0 AGCTGTAGCG 0.91957 -154 GGTGTTTTAAATCTTTTAAAGGAAAGGCG 11 73 1 ATCTTAAGGA 0.800754 -19 CTTTATTGCAATCGTTTTTAGGGAGTTTGATC 14 56 1 ATCTTTAGGG 0.983934 -22 ATGAATTAAAATCAATTGTAGCGCACCCAAACT 15 25 0 ATCTTTAGCG 0.986138 -40 ATTGATTTTAATTCATTTTAGGGAGTGTAAGCG 15 42 1 ATTTTTAGGG 0.885698 -23 TTTTTATCGGTTTTAGGGTGTGGCGAGT 17 6 1 ATCTTTAGGG 0.983934 -25 *** ** ***** Masking position 1 Map Score: 12.7275 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 300 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 ATGTAAAATTTGGCATAATTCTATCTAAAAATTGATTA 1 34 1 TGCTATTTAA 0.960876 -56 TCTCCTTTTTTAATTTCATATCTTTCAAGAATTGTATT 2 16 0 TATTATATAA 0.647661 -32 ACCTAATGTAGTATAATTACATCGTTTCGCTAAAAA 4 9 1 TGTTATTTTT 0.47265 -43 TGGCTTTATTTGTTATAAAATTTATAGT 7 1 1 TGCTATTTAA 0.960877 -81 ATGCATTCTTTTGCATTATTCCATGAAAAAAGCCACGC 8 125 1 TGCTATTTAA 0.960605 -104 AAGCACGTTTTAGTATGATAACTTTTAAATTCTCTCAA 13 30 0 TGTTATATAA 0.965324 -117 TTTTAAATCATGGCATTTTAGCATTTTATTTGCATTAA 13 102 0 TGCTTTATTA 0.65101 -45 TGCTATAATGTGGTCTCATTCCATATTAAACAAGGAGA 16 93 1 TGTTATTTTA 0.885558 -36 ATAAGCTTTTTTGTATCATACGCTTAAACTTTATATTA 18 65 0 TGTTATATAA 0.965415 -76 TTAATAAAGTTCGCATTATAGCGTAAAATAAGCTTTTT 18 92 0 TGCTATATAA 0.966039 -49 TTGATTAAGATGGTATTATAGTGTATACTAGCTTTAAG 20 97 0 TGTTATATAC 0.827389 -54 GTTCTAATAGTGGTCTTATTCTATCCAATTAGCCCTTG 21 28 1 TGTTATTTAA 0.960163 -111 GCTCATTATATGGTATCTTAAAGTAAAATTTTAAAGAG 21 100 1 TGTTTTATAA 0.85076 -39 * ** * *** * ** Masking position 9 Map Score: 10.2389 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 76 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TGTTAAAATATCCTTTTTAGCGAAACGATGTA 4 28 0 TCCTTTAGCG 0.964555 -24 AAGGGCTTCATCGCAGTTAGCGATTTCTACGA 8 52 0 TCGATTAGCG 0.926316 -177 CTGTTTAGGATCATTAGGAGCGTTTAAAGAGA 9 107 1 TCATGGAGCG 0.743807 -194 GCTAGGCAAAGCGCTATCAGCGCTCATTAAAG 9 146 1 GCGTTCAGCG 0.889032 -155 GTCAGAAAATTCGGCATGAGGGCAAAA 12 103 1 TCGCTGAGGG 0.90526 -17 TTTATTGCAATCGTTTTTAGGGAGTTTGATC 14 57 1 TCGTTTAGGG 0.990703 -21 TGAATTAAAATCAATTGTAGCGCACCCAAACT 15 25 0 TCATGTAGCG 0.871003 -40 TTGATTTTAATTCATTTTAGGGAGTGTAAGCG 15 43 1 TTCTTTAGGG 0.718892 -22 TTCTTGTGATTCGTTCTTAGGGGGATTTAAGG 16 44 1 TCGTTTAGGG 0.990702 -85 TTTTTATCGGTTTTAGGGTGTGGCGAGT 17 7 1 TCGTTTAGGG 0.990703 -24 CGTTTTAATAGCGTTATTTGGGCGCTATTAAA 20 19 1 GCGTTTTGGG 0.838614 -132 *** * ****** Masking position 10 Map Score: 8.33442 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 368 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 ATCCCTTTGTAATGTAAAATTTGGCATAATTCT 1 23 1 AATAAATTTG 0.625924 -67 CAAACTAGGTTTTTATTCCATTAA 6 2 1 AATAGGTTTT 0.949432 -72 TTTTGCTACAATAATAGGATTTTAATTATATAA 6 44 1 ATTAGGTTTT 0.795826 -30 ATTTATAGTAAAATTAAGATTTTATAATCAAAG 7 30 1 AATAAGTTTT 0.948488 -52 CATTCTTGAAAGAGTAGAGTTTT 7 69 1 AGTAGATTTT 0.896244 -13 CAAAGATTTAAGGCTAGAATTTTGCGTTTTTTC 9 212 0 AGTAGATTTT 0.896244 -89 CCCTAAAATGAGTTTAAGGATTTTA 9 286 1 AGTAAGATTT 0.758357 -15 TATTTACCTAAAAAAAGGCTTTTGAATTTTCTT 14 15 0 AAAAGGTTTT 0.685004 -63 ACCACATTATAGCATAAGTTTTTATCTTACCCC 16 74 0 AGTAAGTTTT 0.967203 -55 ATTATAGCGTAAAATAAGCTTTTTTGTATCATA 18 83 0 AATAAGTTTT 0.948513 -58 TACAATTACAAGTTTAAGTTTTGCTTAAAATGA 19 12 0 AGTAAGTTTG 0.903073 -62 GACCACTATTAGAACAAGGTTTTTATGACGAT 21 10 0 AGCAAGTTTT 0.835055 -129 ATGGTATCTTAAAGTAAAATTTTAAAGAGAGTT 21 109 1 AATAAATTTT 0.841169 -30 ** **** **** Masking position 6 Map Score: 10.9722 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 205 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 TATAAAATACCTTTTAAACTATTTTTAATC 1 67 0 CTTTTAAACT 0.775438 -23 AAAGTCTCCTTTTTTAATTTCATATCTTTC 2 28 0 TTTTTAATTT 0.714291 -20 TTTGATTTCCTTTAATATAACGGATTGG 3 40 0 CCTTTAATAT 0.835376 -18 CGCTTTCTCTCTTTTGGTATCCATGAAGGG 8 90 1 CTTTTGGTAT 0.618423 -139 CCTGCTCACGCTTTTAGTTTTAGCCCCGTC 9 51 0 CTTTTAGTTT 0.908305 -250 CCTCATTTGCCCTTTAATATGCCCTTTAAT 9 171 0 CCTTTAATAT 0.835376 -130 AAAATTCTAGCCTTAAATCTTTGATGAAAC 9 222 1 CCTTAAATCT 0.506891 -79 CATGCCTTATCTTATAATTTGACTTCGTTT 9 248 0 CTTATAATTT 0.679342 -53 TAAAATTAACCTTTAATTTTTGAGAGAAT 13 10 1 CCTTTAATTT 0.934525 -137 AGTATGATAACTTTTAAATTCTCTCAAAAA 13 27 0 CTTTTAAATT 0.899956 -120 TAAAAAAAGGCTTTTGAATTTTCTTAAAA 14 10 0 CTTTTGAATT 0.805485 -68 AAACAAACGCTTTTAGTTTGGGTGCGCTA 15 10 1 CTTTTAGTTT 0.908305 -55 TTTTTCTTAATTTTTGATTTTAATGGCATT 20 67 1 TTTTTGATTT 0.534993 -84 TTAAAACTCTCTTTAAAATTTTACTTTAAG 21 116 0 CTTTAAAATT 0.628058 -23 ********** Masking position 3 Map Score: 7.17116 Number of sites scoring better than the average of aligned sites = 1058 Number in coding regions = 885 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 9 AAAACTCTACTCTTTCAAGAATGATTTGA 7 63 0 CTCTTTCAAG 0.874119 -19 CCTTAAAAAACGCTTTCTCTCTTTTGGTAT 8 80 1 CGCTTTCTCT 0.936813 -149 TAAAATCAACCGCATTCAAGTGGCTTTAAG 8 170 1 CGCATTCAAG 0.917653 -59 ACGCTTTCTTTGATGACAAGG 8 218 0 CGCTTTCTTT 0.905526 -11 AACGCTAAAACGCTTGCTAGTTTTTGGCTA 11 37 1 CGCTTGCTAG 0.953886 -55 TTTAAAACACCGCTTACTAGCCAAAAACTA 11 54 0 CGCTTACTAG 0.96094 -38 CGCTTACACTCCCTAAAATG 15 55 0 CGCTTACACT 0.740065 -10 TAATAAAGTTCGCATTATAGCGTAAAATAA 18 99 0 CGCATTATAG 0.675601 -42 TTTATTTTAGCTCTTTCTTGTTTGATTAAG 20 126 0 CTCTTTCTTG 0.852045 -25 ********** Masking position 5 Map Score: 3.83592 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 436 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 AAAGCGTTTTTTAAGGGCTTCATCGCAGTT 8 66 0 TTAAGGGCTT 0.892523 -163 TTGGTATCCATGAAGGGGTTCAATGCATTC 8 103 1 TGAAGGGGTT 0.976789 -126 TCAACCGCATTCAAGTGGCTTTAAGATCCC 8 175 1 TCAAGTGGCT 0.818716 -54 CTAAAATCAATGACGGGGCTAAAACTAAAA 9 40 1 TGACGGGGCT 0.881113 -261 TCAGCGCTCATTAAAGGGCATATTAAAGGG 9 162 1 TTAAAGGGCA 0.825813 -139 AAAGGGCATATTAAAGGGCAAATGAGGATT 9 174 1 TTAAAGGGCA 0.825813 -127 AAACGCATGCTGAATGGGTTGCGCTT 10 7 0 TGAATGGGTT 0.804897 -35 CATCAAGGGGTTTGACATTAGT 16 3 1 TCAAGGGGTT 0.98223 -126 TTGACATTAGTCAAGCGGTAGTTTCTTGTG 16 22 1 TCAAGCGGTA 0.857612 -107 TTAGGGGGATTTAAGGGGTAAGATAAAAAC 16 60 1 TTAAGGGGTA 0.967024 -69 TAAGAGTGGCTCAAGGGCTAATTGGATAGA 21 47 0 TCAAGGGCTA 0.917249 -92 ********** Masking position 3 Map Score: 8.53344 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 367 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 11 CGTTATAAAATACCTTTTAA 1 80 0 CGTTATAAAA 0.954302 -10 AAACGCTATAATAAATCAAAATT 3 4 1 CGCTATAATA 0.859978 -54 ACAACCAATCCGTTATATTAAAGGAAATCA 3 36 1 CGTTATATTA 0.850701 -22 AAACTCTCCTTGATAAAAGA 5 3 0 CTTGATAAAA 0.643156 -18 TTGTCCTTTATATAATTAAAATCCT 6 59 0 CTTTATATAA 0.832095 -15 TGGCTTTATTTGTTATAAAATTTATAGTAA 7 11 1 TGTTATAAAA 0.588661 -71 TACGCTTAAACTTTATATTATAATAAGCCT 18 55 0 CTTTATATTA 0.720581 -86 ATAATGCGAACTTTATTAAATTACCAATTA 18 111 1 CTTTATTAAA 0.832142 -30 GCCCAAATAACGCTATTAAAACGGAGAGGG 20 12 0 CGCTATTAAA 0.859979 -139 GTTATTTGGGCGCTATTAAAATGAGTTTCA 20 31 1 CGCTATTAAA 0.859979 -120 AGGTCTTTATTTTAGCTCTTTCTT 20 137 0 CTTTATTTTA 0.572227 -14 ATCGTCATAAAAACCTTGTTCT 21 3 1 CGTCATAAAA 0.799541 -136 ********** Masking position 5 Map Score: 6.19902 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 253 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 TTAACCGAAAGCGTGGCTTTTTTCATGGAA 8 143 0 GCGTGGCTTT 0.968475 -86 CACGGCTAAAGCGTGGCTAAAGCGTGGCTG 12 33 1 GCGTGGCTAA 0.968475 -87 CGTGGCTAAAGCGTGGCTGGAGCGTGGGGG 12 44 1 GCGTGGCTGG 0.992344 -76 CGTGGCTGGAGCGTGGGGGTTTGCGTTTTT 12 55 1 GCGTGGGGGT 0.962534 -65 CGGTTTTAGGGTGTGGCGAGTTT 17 18 1 GTGTGGCGAG 0.945455 -13 ********** Masking position 4 Map Score: 0.157441 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 132 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 ********** No masking Map Score: 4.05963e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 4.05963e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 4.05963e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0