AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_hpyl_reg_300.orf -o00252_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0031 108 H. pylori predicted coding region HP0031 #2 HP0032 30 conserved hypothetical protein #3 HP0252 300 outer membrane protein (omp7) #4 HP0255 99 adenylosuccinate synthetase (purA) #5 HP0616 77 chemotaxis protein (cheV) #6 HP0617 34 aspartyl-tRNA synthetase (aspS) #7 HP0640 62 poly(A) polymerase (papS) #8 HP0643 164 glutamyl-tRNA synthetase (gltX) #9 HP0649 57 aspartate ammonia-lyase (aspA) #10 HP0723 128 L-asparaginase II (ansB) #11 HP0942 40 D-alanine glycine permease (dagA) #12 HP0943 21 D-amino acid dehydrogenase (dadA) #13 HP0944 300 translation initiation inhibitor, putative #14 HP1084 66 aspartate transcarbamoylase (pyrB) #15 HP1108 259 pyruvate ferredoxin oxidoreductase, gamma subunit #16 HP1112 109 adenylosuccinate lyase (purB) #17 HP1241 119 alanyl-tRNA synthetase (alaS) Motif number 1 TTTGTGTCCTTTTTCTAAGCGAGA 1 1 1 TTTGTGTTTT 0.816275 -108 CATTAGGGTTTATTTGGTATAATACCAAAACTTC 1 68 1 TATTTGTATA 0.619797 -41 CGCTTAATTTTATTTGGGGTGTTAGCTCAGCTGG 3 134 0 TATTTGTGTA 0.476957 -167 AAATATCCTTTTTGCTTTGATAAGTGATTTTA 3 279 0 TTTTTGTGTA 0.852466 -22 GCTCTTTTTAGGGCTTATAAAGAGGCTTT 4 6 1 TTTTAGTTTA 0.959547 -94 TTTTACTTTTTTTTTGGTATTCTAACAAGCTTTT 4 38 1 TTTTTGTTTA 0.955431 -62 ATCTACTTTGTTTTAAGGATAATATTTT 4 82 1 TTTTAATATA 0.828427 -18 CCTAATTTAGTTTAAAAGGTTTTTACAAAC 5 7 0 TTTAAATTTT 0.788028 -71 ATTTAATTTTTGTTTTAATTTAAAGGGATA 6 7 1 TTTTTGTATT 0.888234 -28 TATTATATCTTTTTAGAATTTTTAAGGAATTTTG 7 11 0 TTTTAGTTTA 0.971085 -52 TTAAAATTTCTTTGTGTTATTATATCTTTTTAGA 7 28 0 TTTGTGTTTA 0.852466 -35 TTGAAAAATATTCTAGCTATTGTAACCAAATCTT 9 14 0 TTCTAGTTTA 0.682946 -44 TAACCCTTTTTAAATTTATTTTAACGATGT 10 7 1 TTTTTATTTT 0.830953 -122 ATTAAAAGATTTTATAGTATAGTAAAACATCGTT 10 33 0 TTTATATATA 0.59775 -96 AATGAGAATATTTTTGAAATTGTTGATTCTTTTA 10 84 1 TTTTTGTTTT 0.942803 -45 GAATTTCTTTTTTAAACCCTAGTTTATTAAGGAG 11 12 1 TTTAAATATT 0.641861 -29 AGAAAATGCTTTTGAGCATTTTTACAGACACTCA 13 44 0 TTTGAGTTTA 0.900633 -257 TTTGTTTGAGTTTTAGGCTTTGTTGTCATCAATT 13 124 0 TTTTAGTTTT 0.962763 -177 ACAAAACCCGTTTAAGAATTTCTAAATATGGGTA 13 153 1 TTTAAGTTTA 0.941831 -148 TTCATCTTATTATAAGGTATTGTATATTTTTTAC 13 184 0 TATAAGTTTA 0.717945 -117 AAAACCCCCTTTTAGTTATAATATAGATTTTAT 14 44 0 TTTTAGTATA 0.94169 -23 TTTGTTATTATTTAAGGTGTGATTTGATTTTAGT 15 26 0 TTTAAGTGTT 0.77065 -234 CTAATATTTATTTTAAACTTTGTTATTATTTAAG 15 44 0 TTTTAATTTT 0.885197 -216 TTAAAATAAATATTAGTGGTTTTTATTAAGAACG 15 62 1 TATTAGTTTT 0.803175 -198 AACAATATCTTTTTAGGAATTTTTATAGGAAAAT 15 154 0 TTTTAGTTTT 0.962766 -106 TTCAATTTATTTTATACGATATTAAGGAGACATA 15 231 1 TTTATATATA 0.597751 -29 CCCATTTTGATTTTAAGGATTGTCG 16 95 1 TTTTAATTTC 0.529366 -15 ATTTTGGATGTTTAAAGTATAATAAACTATCTTT 17 25 1 TTTAAATATA 0.699464 -95 TTATAGCTCTTTTAAGTTATTTTTTTAAAAAGAT 17 53 0 TTTAAGTTTT 0.925741 -67 TTATCGCGTATTTTAAGGCTATTTTATAGCTCTT 17 76 0 TTTTAATATT 0.788026 -44 GGGTATTCCTTTTTGTTGTTTTATCGCGTATTT 17 97 0 TTTTTGTTTA 0.955431 -23 ****** ** ** Masking position 10 Map Score: 35.8921 Number of sites scoring better than the average of aligned sites = 2285 Number in coding regions = 1880 Number in noncoding regions = 405 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 2 TACCAAAACTTCATTTAAGGTTGGTTCTT 1 90 1 TCATTTAAGT 0.65197 -19 CAAATTGACATCTTTTAAGCAAAATGTTATA 3 173 0 TCTTTTAAGA 0.945848 -128 TTAGAAAGTTTCTTTTATGGATTAAGTAAAA 3 253 1 TCTTTTATGA 0.858253 -48 AAATATCCTTTTTGCTTTGATAAGTG 3 285 0 TCCTTTTTGT 0.856076 -16 TTTGTAAAAACCTTTTAAACTAAATTAGGGT 5 12 1 CCTTTTAAAT 0.876884 -66 GTTTTATCCCTTTAAATTAAAACAAAAA 6 17 0 CCCTTTAAAT 0.905833 -18 TGTTATTATATCTTTTTAGAATTTTTAAGGA 7 17 0 TCTTTTTAGA 0.927418 -46 AAAAACCCTTTATTTAAAAATAGTTT 8 149 0 CCCTTTATTA 0.793407 -16 TAACCCTTTTTAAATTTATTTTAAC 10 5 1 CCTTTTTAAT 0.836909 -124 TACTATAAAATCTTTTAATTTCAAAAGGTGG 10 48 1 TCTTTTAATT 0.876571 -81 AATTGTTGATTCTTTTATTTTGTTTGAAGGG 10 101 1 TCTTTTATTT 0.709931 -28 GGAATTTCTTTTTTAAACCCTAGTTTA 11 7 1 TCTTTTTTAA 0.603506 -34 GCTGATAGTCCCTTTAATAAA 12 2 0 CCCTTTAATA 0.91765 -20 CGCTTGCAAGCCCTTTTATTATGGCTTATTA 13 79 0 CCCTTTTATA 0.889245 -222 CAAACAAAACCCGTTTAAGAATTTCTAAATA 13 150 1 CCGTTTAAGA 0.764726 -151 AAAACCCCCTTTTAGTTATAATATAGA 14 50 0 CCCTTTTAGT 0.952501 -17 AGAACGCTTGTCTTTTTAGAATAAATGGCCA 15 90 1 TCTTTTTAGA 0.927418 -170 TATAACAATATCTTTTTAGGAATTTTTATAG 15 160 0 TCTTTTTAGA 0.926183 -100 CCCTTTAATTAAATCAAGGGG 16 1 1 CCCTTTAATA 0.91765 -109 TTCTTTAAACCCCTTTAAAGTAACATAAATC 16 65 1 CCCTTTAAAT 0.905722 -45 GGTTTTCTCCTTTAATTTTGGATGTTTA 17 8 1 TCCTTTAATT 0.905583 -112 TAATAAACTATCTTTTTAAAAAAATAACTTA 17 44 1 TCTTTTTAAA 0.815382 -76 ATTTTATAGCTCTTTTAAGTTATTTTTTTAA 17 59 0 TCTTTTAAGT 0.946614 -61 GGGTATTCCTTTTTGTTGTTTTATCGC 17 103 0 TCCTTTTTGT 0.856076 -17 ********* * Masking position 6 Map Score: 30.6881 Number of sites scoring better than the average of aligned sites = 736 Number in coding regions = 595 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 3 CTTTATGGATCAAACCCGTTTTCTTGCTAG 3 27 0 CAAACCCGTT 0.816876 -274 TTAAAATTAGAAAGTTTCTTTTATGGATTA 3 247 1 AAAGTTTCTT 0.768499 -54 TGGATTAAGTAAAATCACTTATCAAAGCAA 3 270 1 AAAATCACTT 0.642733 -31 AAAAAAGTAAAAAGCCTCTTTATAAGCCCT 4 20 0 AAAGCCTCTT 0.959972 -80 GGATTATTTAAAAGCTTGTTAGAATACCAA 4 51 0 AAAGCTTGTT 0.699102 -49 GTTTGTAAAAACCTTTTAAACTAAATT 5 8 1 AAAACCTTTT 0.69325 -70 CAAAATTCCTTAAAAATTCTA 7 2 1 AAAATTCCTT 0.916171 -61 TTTTACTCTTAAAATTTCTTTGTGTTATTA 7 40 0 AAAATTTCTT 0.744845 -23 AAAAACCCTTTATTTAAAAA 8 155 0 AAAAACCCTT 0.849834 -10 AAAAGCTCCTTATGTAATAAT 9 47 0 AAAGCTCCTT 0.972782 -11 AAAAACTCCTTAATAAACTAG 11 30 0 AAAACTCCTT 0.969313 -11 GCTGATAGTCCCTTTAATAAA 12 8 0 ATAGTCCCTT 0.701668 -14 CACTCGCTTGCAAGCCCTTTTATTATGGCT 13 84 0 CAAGCCCTTT 0.692528 -217 AAACTCAAACAAAACCCGTTTAAGAATTTC 13 145 1 AAAACCCGTT 0.95027 -156 AAAACCCCCTTTTAGTTATAA 14 56 0 AAACCCCCTT 0.937038 -11 TTTTCCTATAAAAATTCCTAAAAAGATATT 15 155 1 AAAATTCCTA 0.452839 -105 AAGGCGCAAAAAAGCCCCTTGATTTAATTA 16 16 0 AAAGCCCCTT 0.988955 -94 CTTGATTCTTTAAACCCCTTTAAAGTAACA 16 60 1 TAAACCCCTT 0.871169 -50 ********** Masking position 9 Map Score: 17.9878 Number of sites scoring better than the average of aligned sites = 1891 Number in coding regions = 1625 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 4 TTTTACTTAATCCATAAAAGAAACTTTCTA 3 254 0 TCCATAAAAG 0.801024 -47 ATTCTAACAAGCTTTTAAATAATCCAATCT 4 56 1 GCTTTTAAAT 0.65403 -44 AAAATATTATCCTTAAAACAAAGTAGATT 4 81 0 TCCTTAAAAC 0.92058 -19 CAAAATTCCTTAAAAATTCTAAAAAG 7 7 1 TCCTTAAAAA 0.809541 -56 TAGTAAAACATCGTTAAAATAAATTTAAAA 10 18 0 TCGTTAAAAT 0.901973 -111 GTTTTACTATACTATAAAATCTTTTAATTT 10 39 1 ACTATAAAAT 0.595521 -90 GCGAGTGGTAGCTTTAAAATTGATGACAAC 13 107 1 GCTTTAAAAT 0.946427 -194 AGAATAAATGGCCATAAAATAGCCATAATT 15 107 1 GCCATAAAAT 0.968648 -153 GTAATATGTCTCCTTAATATCGTATAAAAT 15 239 0 TCCTTAATAT 0.762743 -21 CGACAATCCTTAAAATCAAAATGGGA 16 94 0 TCCTTAAAAT 0.967956 -16 ACTTAAAAGAGCTATAAAATAGCCTTAAAA 17 70 1 GCTATAAAAT 0.919031 -50 CTATAAAATAGCCTTAAAATACGCGATAAA 17 81 1 GCCTTAAAAT 0.97973 -39 CTTAAAATACGCGATAAAACAACAAAAAGG 17 93 1 GCGATAAAAC 0.783165 -27 ********** Masking position 7 Map Score: 11.5042 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 484 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 TAGCGCTTTATCTTTGAGCTTTCAGCGGGTCAT 1 38 1 TCTTGGCTTC 0.89618 -71 AACGCTGCCAGCGTTGCGCTCTCCCAGCTGAGC 3 111 1 GCTTGGCTTC 0.980367 -190 TTATAAAGAGGCTTTTTACTTTTTTTTTGGTAT 4 25 1 GCTTTACTTT 0.935121 -75 TCTTAAAATTTCTTTGTGTTATTATATCTTTTT 7 31 0 TCTTGGTTTT 0.676984 -32 GCTTTTTACTCTTAAAATTTCTT 7 50 0 GCTTTACTTT 0.935121 -13 AAACGCTGTTAGCTTTTTGATAACCAA 8 5 1 GCGTTGCTTT 0.901686 -160 CTAACGCCAAGCTTTTTATGGTTGGTTATCAAA 8 26 0 GCTTTATGTT 0.639515 -139 ACAGATTGCGGCTTTGCCCTCTTTTAGTGGCAA 13 11 1 GCTTGCCTTT 0.930951 -290 AAAATTCATGGCGTTTTGCGCTCATTTTTTATT 13 216 1 GCTTTGCGTC 0.957071 -85 GCTTTTTTGCGCCTTGTGCGATTTTTCCCCTTG 16 31 1 GCTTGGCGTT 0.980367 -79 ** *** *** ** Masking position 5 Map Score: 5.16281 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 394 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 TGGTATTATACCAAATAAACCCTAATGACC 1 65 0 CCAAATAAAC 0.638436 -44 AGCTAACACCCCAAATAAAATTAAGCGAGC 3 141 1 CCAAATAAAA 0.894369 -160 TGTTAGAATACCAAAAAAAAAGTAAAAAGC 4 35 0 CCAAAAAAAA 0.518263 -65 ATATTATCCTTAAAACAAAGTAGATTGGAT 4 77 0 TAAAACAAAG 0.641013 -23 CCCTTTAAATTAAAACAAAAATTAAAT 6 8 0 TAAAACAAAA 0.895421 -27 AAAACATCGTTAAAATAAATTTAAAAAGGG 10 14 0 TAAAATAAAT 0.85669 -115 ACCTGCCCCTTCAAACAAAATAAAAGAATC 10 108 0 TCAAACAAAA 0.902801 -21 AGCCTAAAACTCAAACAAAACCCGTTTAAG 13 139 1 TCAAACAAAA 0.902801 -162 TATTATGCAATCAAATTAATAAAGAAATAA 13 244 0 TCAAATTAAT 0.569796 -57 CATTTTTAGCTAAAATAAAATCTATATTAT 14 30 1 TAAAATAAAA 0.928124 -37 CCATACAGACTAAAATCAAATCACACCTTA 15 18 1 TAAAATCAAA 0.803131 -242 TAACAAAGTTTAAAATAAATATTAGTGGTT 15 53 1 TAAAATAAAT 0.85669 -207 TAATATCGTATAAAATAAATTGAATTCAGC 15 225 0 TAAAATAAAT 0.85669 -35 CGACAATCCTTAAAATCAAAATGGGATTTA 16 90 0 TAAAATCAAA 0.803131 -20 TTTAAACATCCAAAATTAAAGGAGAAAACC 17 11 0 CAAAATTAAA 0.614516 -109 ********** Masking position 5 Map Score: 12.4596 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 385 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 TTTCTTGCTAGTATTACCCATAATTAA 3 7 0 GTATTACCCT 0.949078 -294 AAGAAAACGGGTTTGATCCATAAAGAAAGAG 3 32 1 GTTTGATCCT 0.895016 -269 AAAATATTATCCTTAAAACAAAGT 4 86 0 ATATTATCCT 0.692464 -14 GTTTTATCCCTTTAAATTAAA 6 24 0 GTTTTATCCT 0.969786 -11 GCTTTTTACTCTTAAAATTTCTT 7 50 0 TTTTTACTCT 0.733523 -13 TATTGTATATTTTTTACCCATATTTAGAAAT 13 170 0 TTTTTACCCT 0.961014 -131 CCTTGTGCGATTTTTCCCCTTGATTCTTTAA 16 42 1 TTTTTCCCCT 0.933149 -68 GGTTTTCTCCTTTAATTTTGGA 17 2 1 GTTTTCTCCT 0.947851 -118 ********* * Masking position 4 Map Score: 2.73883 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 233 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 TTAATTATGGGTAATACTAGCAA 3 4 1 ATTATGGGTA 0.943539 -297 AAAGAAAGAGAATAAGCGTAATAATGGTGG 3 53 1 AATAAGCGTA 0.672109 -248 TTAATTTGCTATTAAGCGTTTCAAAAAAGC 3 206 0 ATTAAGCGTT 0.672109 -95 AATCTCTTAAATGATGCCTATTCATGTTTG 8 68 1 ATGATGCCTA 0.8191 -97 ATAGTTTTTGATTATACCTAAAGAATACTT 8 126 0 ATTATACCTA 0.787423 -39 ATTGAAAAATATTCTAGCTATTGTAACCAA 9 19 0 ATTCTAGCTA 0.62902 -39 AAGCCCTTTTATTATGGCTTATTATAGAAA 13 73 0 ATTATGGCTT 0.876775 -228 AGAATTTCTAAATATGGGTAAAAAATATAC 13 167 1 AATATGGGTA 0.80569 -134 ACCTACAAGAATTATGGCTATTTTATGGCC 15 116 0 ATTATGGCTA 0.966303 -144 AATAAATTGAATTCAGCCTAGAATTATACA 15 212 0 ATTCAGCCTA 0.84474 -48 TATCGCGTATTTTAAGGCTATTTTATAGCT 17 79 0 TTTAAGGCTA 0.68237 -41 ********** Masking position 9 Map Score: 3.27273 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 321 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 TTAATCCATAAAAGAAACTTTCTAATTTTAA 3 247 0 AAAGAAACTT 0.738759 -54 AAAATTCTAAAAAGATATAATAACACAAAGA 7 23 1 AAAGATATAT 0.851058 -40 ATAATAACACAAAGAAATTTTAAGAGTAAAA 7 39 1 AAAGAAATTT 0.902742 -24 CCCTTTATTTAAAAATAGTTTTTGATTATAC 8 139 0 AAAAATAGTT 0.868989 -26 GTAATAATTGAAAAATATTCTAGCTATTGTA 9 24 0 AAAAATATTT 0.921757 -34 TTTGAAATTAAAAGATTTTATAGTATAGTAA 10 42 0 AAAGATTTTT 0.845971 -87 CAACAATTTCAAAAATATTCTCATTATGGAC 10 78 0 AAAAATATTT 0.921757 -51 AAATTCCTAAAAAGATATTGTTATAAGACAC 15 166 1 AAAGATATTT 0.972957 -94 ATTTTTTTAAAAAGATAGTTTATTATACTTT 17 38 0 AAAGATAGTT 0.953005 -82 ********* * Masking position 5 Map Score: 6.42715 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 105 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 GGTTTATTTGGTATAATACCAAAACTTCATT 1 74 1 GTTAATACCA 0.719025 -35 CCAAGTAGCCAAATAGCATGGATAAGCG 2 8 1 GCAAATAGCA 0.779048 -23 AAGAGAATAAGCGTAATAATGGTGGAGTGTA 3 58 1 GCTAATAATG 0.583328 -243 AATTAAGCGAGCATTATAACATTTTGCTTAA 3 159 1 GCTTATAACA 0.972806 -142 TTTTTGAAACGCTTAATAGCAAATTAAGAAT 3 209 1 GCTAATAGCA 0.945244 -92 TTTTTTTTTGGTATTCTAACAAGCTTTTAAA 4 44 1 GTTTCTAACA 0.691558 -56 AATTAGGGTAGTATTATAGCATTTAATCTTT 5 34 1 GTTTATAGCA 0.888232 -44 TTCTAAAAAGATATAATAACACAAAGAAATT 7 27 1 ATTAATAACA 0.608234 -36 AATATACAATACCTTATAATAAGATGAAAAT 13 190 1 ACTTATAATA 0.56541 -111 TAATTTGATTGCATAATAATAGCTGACATAA 13 256 1 GCTAATAATA 0.898745 -45 CTATTAATGTGTCTTATAACAATATCTTTTT 15 174 0 GTTTATAACA 0.934277 -86 CTATAAAATAGCCTTAAAATACGCGATAAAA 17 81 1 GCTTAAAATA 0.677439 -39 CTTAAAATACGCGATAAAACAACAAAAAGGA 17 93 1 GCATAAAACA 0.598763 -27 ** ******** Masking position 8 Map Score: 2.92287 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 414 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 11 TTAATTATGGGTAATACTAGC 3 2 1 TAATTATGGG 0.95216 -299 TTATTCTCTTTCTTTATGGATCAAACCCGT 3 38 0 TCTTTATGGA 0.895839 -263 AAAAATATTCTCATTATGGACCACCTTTTG 10 69 0 TCATTATGGA 0.951497 -60 TAAGAATTTCTAAATATGGGTAAAAAATAT 13 165 1 TAAATATGGG 0.914274 -136 TTGATTTTAGTCTGTATGGGGCAAGT 15 7 0 TCTGTATGGG 0.889548 -253 ATCCTTAAAATCAAAATGGGATTTATGTTA 16 85 0 TCAAAATGGG 0.820476 -25 TTTTCTCCTTTAATTTTGGATGTTTAAAGT 17 13 1 TAATTTTGGA 0.666736 -107 ********** Masking position 7 Map Score: 0.698999 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 75 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 AGATGTCAATTTGATGCTTTTTTGAAACGC 3 191 1 TTGATGCTTT 0.968168 -110 AAATATCCTTTTTGCTTTGATAAGTGAT 3 283 0 TTTTTGCTTT 0.839458 -18 CAAAGTAGATTGGATTATTTAAAAGCTTGT 4 62 0 TGGATTATTT 0.280539 -38 TATTATAGCATTTAATCTTTGATAGGGCTT 5 45 1 TTTAATCTTT 0.528341 -33 TTTGAAATTGTTGATTCTTTTATTTTGTTT 10 96 1 TTGATTCTTT 0.95018 -33 ACAGATTGCGGCTTTGCCCTCTTTT 13 6 1 TTGCGGCTTT 0.820612 -295 TTGTTTGAGTTTTAGGCTTTGTTGTCATCA 13 127 0 TTTAGGCTTT 0.829713 -174 CGCTCATTTTTTATTTCTTTATTAATTTGA 13 234 1 TTATTTCTTT 0.564782 -67 ATTTTTCCCCTTGATTCTTTAAACCCCTTT 16 51 1 TTGATTCTTT 0.95018 -59 GTATTCCTTTTTGTTGTTTTATCGCGTATT 17 98 0 TTGTTGTTTT 0.609998 -22 ********** Masking position 8 Map Score: 0.245085 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 620 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 ********** No masking Map Score: 3.70436e-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: 3.70436e-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: 3.70436e-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