AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_hpyl_reg_100.orf -o00330_hpyl_100.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 Purged sequences: HP1157 22 H. pylori predicted coding region HP1157 Input sequences: #1 HP0056 300 delta-1-pyrroline-5-carboxylate dehydrogenase {Synechocystis sp.) #2 HP0090 300 malonyl coenzyme A-acyl carrier protein transacylase (fabD) #3 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #4 HP0320 71 conserved hypothetical secreted protein #5 HP0322 141 poly E-rich protein #6 HP0417 168 methionyl-tRNA synthetase (metS) #7 HP0830 58 amidase #8 HP0832 91 spermidine synthase (speE) #9 HP0833 76 H. pylori predicted coding region HP0833 #10 HP1054 63 H. pylori predicted coding region HP1054 #11 HP1057 148 H. pylori predicted coding region HP1057 #12 HP1100 65 6-phosphogluconate dehydratase #13 HP1156 107 H. pylori predicted coding region HP1156 #14 HP1399 201 arginase (rocF) #15 HP1483 26 gerC2 protein (gerC2) #16 HP1490 103 hemolysin Motif number 1 AATTTTTTGTAAATCCGTTTAAT 1 1 1 AATTTTTAAA 0.918693 -300 CGAATGTTATAATTTATTATTAAACGAAAAGTA 1 73 1 AATTATTTAA 0.808273 -228 AACGAAAAGTAAATGAAGCTAAAAACAATACAA 1 95 1 AAATAATAAA 0.708903 -206 GCTAGAACAAAATTTAAAATTAAAAAACATTAC 1 203 1 AATTAATTAA 0.708903 -98 CATTACCAATAAATGAGACTTAAAGCCACCCGC 1 230 1 AAATAGTTAA 0.653058 -71 AATCAAGTCAAATTCTTAAATAAAAGGTAAGCT 1 277 1 AATTTTATAA 0.823998 -24 TTCTAAACAAAAAGTTTTTAAAGGCAAAAAGGC 2 54 1 AAAGTTAAAG 0.502063 -247 CACAAAGTAGAATTATAGTAAAAATAAGTTAAA 2 184 1 AATTTAAAAA 0.791586 -117 AAATAAGTTAAAATAAACCTTAAACTTTAATGG 2 205 1 AAATAATTAA 0.634242 -96 CTTAAACTTTAATGGTTTCTAAACAAAACTAAG 2 223 1 AATGTTTAAA 0.839836 -78 CATAATTTAAAATTGTAATATAAAAGCCCTTAG 2 251 0 AATTTAATAA 0.730057 -50 TACAATTTTAAATTATGGATTAATAAAACTTAA 2 267 1 AATTTGTTAA 0.834575 -34 CTATAAAACAAAATTTTAAAAAGATTAAATAAT 3 45 1 AAATTTAAAG 0.684809 -161 TAAAAAGATTAAATAATATTAAATTGAATGGGG 3 61 1 AAATATTAAA 0.808273 -145 TATTTTTGTCAAATATTGATAAACCCCATTCAA 3 84 0 AAATTTTAAA 0.889448 -122 AGATCAAAAAAATTTTTTATTAACTCTTTTGGT 3 117 1 AATTTTTTAA 0.889448 -89 AGCCTAAAACAATTTTAAAAAAAGGACTTTTG 3 184 1 AATTTAAAAA 0.791586 -22 AACCTATCAATTATTTTTTAAAAAAGCTATA 4 9 1 AATTTTTTAA 0.889448 -63 AAAAAGCTATAATTCAAACAAAAACCAACCAAT 4 31 1 AATTAAAAAA 0.665571 -41 CATAGAGTGTAATTTAAAATAAGGATCATTTG 5 10 0 AATTAATAAG 0.613477 -132 GATTATAATAAAAGATTTAAAAAAAGCGATAAA 5 71 1 AAAGTTAAAA 0.684809 -71 CGTTAATTATAATGAATTTTAAGCTAAAAACAC 6 47 1 AATGATTAAG 0.560453 -122 AACACCCCACAAATAAGCATAAATGCAACCTCT 6 75 1 AAATAGTAAA 0.72554 -94 TCTATTCTCTAAATTTTTAAAAGCATGTTAAAA 6 105 1 AAATTTAAAG 0.684809 -64 GTGTTACCTTAAATTTGTTTAAATCTCTTAATT 6 136 0 AAATTGTAAA 0.834575 -33 CAAAAAATTTAATGGTAGTTTAACATGCTTAGA 7 23 0 AATGTATTAA 0.683227 -36 ACTACCATTAAATTTTTTGTAAGGCTAAAAAC 7 37 1 AATTTTTAAG 0.839836 -22 ATATTGTTAAAAAGTAAGCTAAGGAGTGTTT 8 71 1 AAAGAATAAG 0.344035 -21 ATTGTAATCTAATTTTGATTAAATTGAAGCGAT 9 18 0 AATTTGTAAA 0.876317 -59 ATAGTTATTTAAAGCTTAAATAAGGGTCTAGCG 9 54 1 AAAGTTATAA 0.607391 -23 AGTTTCTTTCAATTATACTAAAATAATTAAAAT 11 95 0 AATTTAAAAA 0.791586 -54 AAATCCCTTGAATTGTTTGTTAAAAGTTTCTTT 11 119 0 AATTTTTTAA 0.889448 -30 ATTATATATTAAATCTTAATTAAAGGGGTATTC 12 43 1 AAATTTTTAA 0.851386 -23 TTAGTCGCTTAATTGTTGATTAAAATGGGCTAT 13 12 0 AATTTTTTAA 0.889448 -96 CTTAAGCGATAAATAAGATAAAATTTAGGATAG 13 53 1 AAATAGAAAA 0.606033 -55 AGGATAGCTCAAATCTTTTAAAAAGAAAAGGAT 13 79 1 AAATTTAAAA 0.823998 -29 TTAATAAGCAAATGGATAATAAATAGAACAATT 14 118 0 AATGATTAAA 0.73316 -84 ATTAACAACCAATTATTAATAAGCAAATGGATA 14 133 0 AATTTTTAAG 0.839836 -69 ATTGGTTGTTAATTTTGGTTTAGAATAGAACAT 14 153 1 AATTTGTTAG 0.700712 -49 GAGGGGATTTAAAGGAGTTATAAA 14 188 1 AAAGAGATAA 0.33701 -14 AAAATCTCAGAATTTTAACATAAAAGATTAAGC 16 41 0 AATTTAATAA 0.730057 -63 **** ** **** Masking position 2 Map Score: 42.0736 Number of sites scoring better than the average of aligned sites = 1666 Number in coding regions = 1273 Number in noncoding regions = 393 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 2 AACGAAACGATTTTAAATTAAACGGATTTACAA 1 17 0 TTTTAAAAAC 0.721205 -284 CGTTCAATGGTTTTAAATTACACGATGCGAATG 1 46 1 TTTTAAACAC 0.906175 -255 TATAATTTATTATTAAACGAAAAGTAAATGAAG 1 80 1 TATTAAAAAA 0.8007 -221 TAGAACAAAATTTAAAATTAAAAAACATTACCA 1 205 1 TTTAAAAAAA 0.701854 -96 CGTTAATACATTCTAAACAAAAAGTTTTTAAAG 2 44 1 TTCTAAAAAA 0.932506 -257 ACAAAAAGTTTTTAAAGGCAAAAAGGCTGGCGG 2 60 1 TTTAAAAAAA 0.927759 -241 CTTTAATGGTTTCTAAACAAAACTAAGGGCTTT 2 229 1 TTCTAAAAAC 0.889841 -72 AACTAAGGGCTTTTATATTACAATTTTAAATTA 2 249 1 TTTTATACAA 0.593088 -52 TAAAATTTTGTTTTATAGTAAAACTCATTTTTA 3 30 0 TTTTATAAAA 0.657451 -176 TCAAGGTTTTTATGAAAATAAAAGCCTAAAACA 3 162 1 TATGAAAAAA 0.576597 -44 ATTATAGCTTTTTTAAAAAATAATTGATAGGTT 4 11 0 TTTTAAATAA 0.731579 -61 AAAGCTATAATTCAAACAAAAACCAACCAATAA 4 33 1 TTCAAAAAAC 0.736958 -39 ATGATCCTTATTTTAAATTACACTCTATGATAA 5 14 1 TTTTAAACAC 0.906175 -128 AAATCTTTTATTATAATCAAAAATCCACTTGGT 5 56 0 TTATAAAAAA 0.725822 -86 GGACTCCTTATTTGATAAGAAACGCTTCTTTAA 5 114 0 TTTGATAAAC 0.621439 -28 TTATAATGAATTTTAAGCTAAAAACACCCCACA 6 53 1 TTTTAAAAAA 0.711048 -116 TGAAAGAAACTTTTAACAAACAATTCAAGGGAT 11 117 1 TTTTAAACAA 0.945994 -32 AATAGCCCATTTTAATCAACAATTAAGCGACT 13 10 1 TTTTAAACAA 0.947627 -98 GCTCAAATCTTTTAAAAAGAAAAGGATAACCCC 13 85 1 TTTAAAAAAA 0.926502 -23 CATTCAAGTTTTTGATAGAAAAACACCCCAATA 14 63 0 TTTGATAAAA 0.737712 -139 TAATGTTCTATTCTAAACCAAAATTAACAACCA 14 155 0 TTCTAAAAAA 0.932506 -47 AATCTCAGAATTTTAACATAAAAGATTAAGCCT 16 39 0 TTTTAAAAAA 0.520372 -65 AACTTTAAACCTAAAACCTAACGATA 16 88 0 TTTAAAAAAA 0.920629 -16 ****** **** Masking position 1 Map Score: 33.2274 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 467 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 3 GTAAATCCGTTTAATTTAAAATCGTTTCGTT 1 19 1 TTAATTAAAA 0.787444 -282 TAATTTATTATTAAACGAAAAGTAAATGAAG 1 82 1 TTAACGAAAA 0.709405 -219 GAAAAGTAAATGAAGCTAAAAACAATACAAA 1 98 1 TGAACTAAAA 0.931511 -203 GAACAAAATTTAAAATTAAAAAACATTACCA 1 207 1 TAAATTAAAA 0.914394 -94 TACCAATAAATGAGACTTAAAGCCACCCGCT 1 233 1 TGAGCTTAAA 0.656808 -68 TAAGTTAAAATAAACCTTAAACTTTAATGGT 2 208 1 TAAACTTAAA 0.939314 -93 TATGGATTAATAAAACTTAAAGGATAACACC 2 280 1 TAAACTTAAA 0.939313 -21 AAAATGAGTTTTACTATAAAACAAAATTTTA 3 32 1 TTACATAAAA 0.756513 -174 AAGGTTTTTATGAAAATAAAAGCCTAAAACA 3 164 1 TGAAATAAAA 0.811855 -42 TCATTATAATTAACGCTCAAAAAATTGAAAA 6 31 0 TAACCTCAAA 0.770709 -138 ATAATGAATTTTAAGCTAAAAACACCCCACA 6 55 1 TTAACTAAAA 0.932778 -114 AAATTTTTTGTAAGGCTAAAAAC 7 46 1 TAAGCTAAAA 0.935697 -13 TATAGTTATTTAAAGCTTAAATAAGGGTCTA 9 53 1 TAAACTTAAA 0.939314 -24 ATCTTGGAGTTAAGGTTTAAAATTTTAGCGT 10 17 1 TAAGTTTAAA 0.600481 -47 TTAAAACGACTAACGCTAAAATTTTAAACCT 10 29 0 TAACCTAAAA 0.965796 -35 ATAACCCCCTAAAATTAAAACGACTAACGC 10 44 0 TAAATTAAAA 0.914394 -20 TATATAATAATAACTCAAAAACACTCTAAAA 12 20 0 TAACCAAAAA 0.645545 -46 ATTAAGCGACTAACCATTAAACTTAAGCGAT 13 32 1 TAACATTAAA 0.776073 -76 TCAAATCTTTTAAAAAGAAAAGGATAACCCC 13 87 1 TAAAAGAAAA 0.690697 -21 AGATTAAGCCTAACTTTAAAAATCAAGCCTT 16 19 0 TAACTTAAAA 0.882884 -85 TCTCAGAATTTTAACATAAAAGATTAAGCCT 16 39 0 TTAAATAAAA 0.814893 -65 AACCTAACGATAAATATAAAATATATAAAAT 16 69 0 TAAAATAAAA 0.92697 -35 AACTTTAAACCTAAAACCTAACGATA 16 88 0 TAAACTAAAA 0.975614 -16 **** ****** Masking position 1 Map Score: 27.2327 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 537 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 4 CGCATCGTGTAATTTAAAACCATTGAACGAAACGATT 1 38 0 AATAAAACGA 0.734402 -263 AAAGTAAATGAAGCTAAAAACAATACAAATTATCACT 1 100 1 AATAAAACAA 0.953226 -201 AAAATTTAAAATTAAAAAACATTACCAATAAATGAGA 1 211 1 ATAAAAAACA 0.72829 -90 TAGTAAAAATAAGTTAAAATAAACCTTAAACTTTAAT 2 199 1 AATAAAAACT 0.644785 -102 ATTAATCCATAATTTAAAATTGTAATATAAAAGCCCT 2 254 0 AATAAAATAA 0.739008 -47 ATAAAACAAAATTTTAAAAAGATTAAATAATATTAAA 3 47 1 ATTAAAAGAA 0.631633 -159 ATATTTGACAAAAATAAGATCAAAAAAATTTTTTATT 3 101 1 AATAAGACAA 0.757514 -105 GGTTTTTATGAAAATAAAAGCCTAAAACAATTTTAAA 3 166 1 AATAAAACAA 0.953226 -40 GCCTAAAACAATTTTAAAAAAAGGACTTTTG 3 185 1 ATTAAAAAAT 0.529554 -21 TATCAATTATTTTTTAAAAAAGCTATAATTCAAACAA 4 15 1 TTTAAAAAAA 0.518618 -57 GCTATAATTCAAACAAAAACCAACCAATAAGATTAAG 4 36 1 AAAAAAACCA 0.834014 -36 CATAGAGTGTAATTTAAAATAAGGATCATTTG 5 6 0 AATAAAAAAC 0.567695 -136 ATTACACTCTATGATAAAAACAACCAACCAAGTGGAT 5 30 1 ATTAAAACCA 0.944626 -112 ATTTTTGATTATAATAAAAGATTTAAAAAAAGCGATA 5 65 1 ATTAAAAAAA 0.915764 -77 CGCTCAAAAAATTGAAAAAGAGTTCAAGGAATAGACA 6 12 0 ATAAAAAACA 0.72829 -157 AATGAATTTTAAGCTAAAAACACCCCACAAATAAGCA 6 57 1 AATAAAACCA 0.959477 -112 AAGCATGTTAAAATTAAGAGATTTAAACAAATTTAAG 6 125 1 AATAAGAAAA 0.69816 -44 GCTAACATGCTAGCTAAAAAATCTAAATTATTGTAAC 8 17 0 TATAAAAAAA 0.599252 -75 TCTTTCAATTATACTAAAATAATTAAAATGACCGGTT 11 87 0 ATTAAAAAAA 0.915764 -62 ATATAATAATAACTCAAAAACACTCTAAAAGGGTTAT 12 13 0 AACAAAACCA 0.693581 -53 CAAGTTTTTGATAGAAAAACACCCCAATAGTCTTATT 14 55 0 ATAAAAAACA 0.72829 -147 ATTGTGTAAAAGAGTAAAACCATTCAAGTTTTTGATA 14 79 0 AGTAAAACCA 0.762615 -123 TTAATCTTTTATGTTAAAATTCTGAGATTTTATATAT 16 43 1 ATTAAAATAA 0.671059 -61 CCTAACGATAAATATAAAATATATAAAATCTCAGAAT 16 61 0 AATAAAAAAA 0.937844 -43 AACTTTAAACCTAAAACCTAACGATAAATATAAA 16 80 0 AATAAAACCA 0.959477 -24 ** ***** * * * Masking position 9 Map Score: 18.9215 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 613 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 5 ATTAAACGGATTTACAAAAAATT 1 4 0 TTTACAAAAA 0.744865 -297 ATCACGCATTTTTACACAATGATAAGAATT 1 139 0 TTTACACAAT 0.853045 -162 GTTAATACATTCTAAACAAAAAGTTTTTAA 2 45 1 TCTAAACAAA 0.918503 -256 TTTAATGGTTTCTAAACAAAACTAAGGGCT 2 230 1 TCTAAACAAA 0.918503 -71 CTAAAACAATTTTAAAAAAAGGACTTTTG 3 187 1 TTTAAAAAAA 0.872852 -19 TTATAGCTTTTTTAAAAAATAATTGATAGG 4 13 0 TTTAAAAAAT 0.780646 -59 AAAGCTATAATTCAAACAAAAACCAACCAA 4 33 1 TTCAAACAAA 0.783399 -39 TAATAAAAGATTTAAAAAAAGCGATAAAAT 5 76 1 TTTAAAAAAA 0.872852 -66 AATTAAGAGATTTAAACAAATTTAAGGTAA 6 136 1 TTTAAACAAA 0.963734 -33 TTAGCTTACTTTTTAACAATATCCATGCCT 8 63 0 TTTTAACAAT 0.704378 -29 ATCGCTTCAATTTAATCAAAATTAGATTAC 9 18 1 TTTAATCAAA 0.706185 -59 TGAAAGAAACTTTTAACAAACAATTCAAGG 11 117 1 TTTTAACAAA 0.821962 -32 GTTAATCCTTTAAATAATAGTGTCAGTT 14 9 1 TTTAAATAAT 0.519589 -193 GTTTTACTCTTTTACACAATGAAATTGTTC 14 96 1 TTTACACAAT 0.853045 -106 AATGTTCTATTCTAAACCAAAATTAACAAC 14 157 0 TCTAAACCAA 0.60462 -45 ********** Masking position 9 Map Score: 16.0595 Number of sites scoring better than the average of aligned sites = 643 Number in coding regions = 513 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 GAGCTTACCTTTTATTTAAGAATT 1 287 0 TTACCTTTTA 0.573684 -14 TAAGTTAAAATAAACCTTAAACTTTAATGG 2 208 1 TAAACCTTAA 0.652883 -93 TAAGTTTTATTAATCCATAATTTAAAATTG 2 269 0 TAATCCATAA 0.700788 -32 GGTGTTATCCTTTAAGTTTTATTA 2 287 0 TTATCCTTTA 0.91553 -14 TAATATTATTTAATCTTTTTAAAATTTTGT 3 52 0 TAATCTTTTT 0.820051 -154 ACTTTACTCCTTAATCTTATTGGT 4 58 0 TACTCCTTAA 0.873431 -14 CGCTTTTTTTAAATCTTTTATTATAATCAA 5 69 0 AAATCTTTTA 0.711774 -73 GCTAAAATTTTAAACCTTAACTCCAAGATC 10 16 0 TAAACCTTAA 0.652883 -48 GTAAAAATTTTACTCCATTTTAACCGGTCA 11 66 1 TACTCCATTT 0.664002 -83 CAATAACCCTTTTAGAGTGTTTT 12 4 1 TAACCCTTTT 0.848901 -62 GAATACCCCTTTAATTAAGATTT 12 53 0 TACCCCTTTA 0.899594 -13 AGGATAGCTCAAATCTTTTAAAAAGAAAAG 13 79 1 AAATCTTTTA 0.711774 -29 GGGGTTATCCTTTTCTTTTTAAAA 13 94 0 TTATCCTTTT 0.812279 -14 GTTAATCCTTTAAATAATAGTG 14 3 1 TAATCCTTTA 0.972769 -199 TGAATGGTTTTACTCTTTTACACAATGAAA 14 90 1 TACTCTTTTA 0.879066 -112 GTTCTATTTATTATCCATTTGCTTATTAAT 14 122 1 TTATCCATTT 0.483318 -80 TTTATAACTCCTTTAAATCCCCTCT 14 187 0 AACTCCTTTA 0.832033 -15 AAGTTAGGCTTAATCTTTTATGTTAAAATT 16 34 1 TAATCTTTTA 0.919321 -70 ********** Masking position 8 Map Score: 14.8612 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 437 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 7 GGTGTAGGATAGCGATCAAGGTTTTTATGA 3 147 1 AGCGATCAAG 0.900732 -59 ATTTAAAAAAAGCGATAAAATGGATAGGCT 5 85 1 AGCGATAAAA 0.983695 -57 CATTATAATTAACGCTCAAAAAATTGAAAA 6 31 0 AACGCTCAAA 0.925264 -138 TAACATGCTTAGAGATAAAACGAGC 7 6 0 AGAGATAAAA 0.87075 -53 AATTTTTTGTAAGGCTAAAAAC 7 47 1 AAGGCTAAAA 0.807395 -12 ATTAAATTGAAGCGATAAAAAAG 9 4 0 AGCGATAAAA 0.983695 -73 TAAAACGACTAACGCTAAAATTTTAAACCT 10 29 0 AACGCTAAAA 0.962018 -35 ATTAAACTTAAGCGATAAATAAGATAAAAT 13 47 1 AGCGATAAAT 0.956683 -61 CCTAAAACCTAACGATAAATATAAAATATA 16 75 0 AACGATAAAT 0.918308 -29 ********** Masking position 6 Map Score: 8.09721 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 759 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 CACCCGCTTAAAACATGCTACAATCAAGTC 1 256 1 AAACATGCTA 0.831948 -45 CTCTTAATTTTAACATGCTTTTAAAAATTT 6 115 0 TAACATGCTT 0.922032 -54 AATGGTAGTTTAACATGCTTAGAGATAAAA 7 16 0 TAACATGCTT 0.922032 -43 AATGAATTGCTAACATGCTAGCTAAAAAAT 8 32 0 TAACATGCTA 0.85471 -60 ********** Masking position 5 Map Score: 3.05999 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 GAGTTTATCACGCATTTTTACACAATGATA 1 145 0 CGCATTTTTA 0.592975 -156 GGTAATGTTTTTTAATTTTAAATTTTGTTC 1 207 0 TTTAATTTTA 0.742105 -94 TTTATTTTAACTTATTTTTACTATAATTCT 2 192 0 CTTATTTTTA 0.942929 -109 TATAAAAGCCCTTAGTTTTGTTTAGAAACC 2 236 0 CTTAGTTTTG 0.656193 -65 TATAGTAAAACTCATTTTTAAGGGGGATAG 3 20 0 CTCATTTTTA 0.902312 -186 TTTTTTTGATCTTATTTTTGTCAAATATTG 3 99 0 CTTATTTTTG 0.839223 -107 ACTTTACTCCTTAATCTTATTGGTTGGTT 4 53 0 CTTAATCTTA 0.782015 -19 CAAATGATCCTTATTTTAAATTACACTCT 5 10 1 CTTATTTTAA 0.637447 -132 GTTTAAATCTCTTAATTTTAACATGCTTTT 6 123 0 CTTAATTTTA 0.957879 -46 CGTTAGTCGTTTTAATTTTAGGGGGTTAT 10 45 1 TTTAATTTTA 0.742105 -19 AAAAATTTTACTCCATTTTAACCGGTCATT 11 68 1 CTCCATTTTA 0.667284 -81 TTATTTATCGCTTAAGTTTAATGGTTAGTC 13 39 0 CTTAAGTTTA 0.782015 -69 TTGAGCTATCCTAAATTTTATCTTATTTAT 13 61 0 CTAAATTTTA 0.76167 -47 ********** Masking position 8 Map Score: 6.85715 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 158 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 TTTTTGTAAATCCGTTTAATTTAAAATCGT 1 14 1 TCCGTTTAAT 0.834565 -287 TATTATTTAATCTTTTTAAAATTTTGTTTT 3 49 0 TCTTTTTAAA 0.681038 -157 TAAACCCCATTCAATTTAATATTATTTAAT 3 68 0 TCAATTTAAT 0.896888 -138 TTTAAGCCTATCCATTTTATCGCTTTTTTT 5 89 0 TCCATTTTAT 0.543734 -53 AGCTTAAAATTCATTATAATTAACGCTCAA 6 42 0 TCATTATAAT 0.640894 -127 TTTTATCGCTTCAATTTAATCAAAATTAGA 9 14 1 TCAATTTAAT 0.896888 -63 TTAGCGTTAGTCGTTTTAATTTTAGGGGGT 10 41 1 TCGTTTTAAT 0.859789 -23 TTTTAACCGGTCATTTTAATTATTTTAGTA 11 83 1 TCATTTTAAT 0.943728 -66 AATAGCCCATTTTAATCAACAATTAA 13 7 1 CCATTTTAAT 0.725662 -101 GTTATCCTTTTCTTTTTAAAAGATTTGAGC 13 85 0 TCTTTTTAAA 0.681038 -23 GTTAATCCTTTAAATAATAGTGTCA 14 6 1 TCCTTTAAAT 0.815153 -196 ATGAAATTGTTCTATTTATTATCCATTTGC 14 114 1 TCTATTTATT 0.365883 -88 TTTATAACTCCTTTAAATCCCCTCTAAT 14 184 0 TCCTTTAAAT 0.815153 -18 ********** Masking position 5 Map Score: 5.59944 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 155 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 11 ********** No masking Map Score: 6.53232e-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 12 ********** No masking Map Score: 6.53232e-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 13 ********** No masking Map Score: 6.53232e-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