AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_hpyl_reg_300.orf -o294_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: RHP01150 25 AE000511 RHP01470 22 AE000511 Input sequences: #1 RHP01047 300 AE000511 #2 RHP01145 214 AE000511 #3 RHP01148 64 AE000511 #4 RHP01149 66 AE000511 #5 RHP01151 74 AE000511 #6 RHP01152 24 AE000511 #7 RHP01163 95 AE000511 #8 RHP01200 300 AE000511 #9 RHP01202 99 AE000511 #10 RHP01432 290 AE000511 #11 RHP01433 60 AE000511 #12 RHP01471 300 AE000511 #13 RHP01472 230 AE000511 #14 RHP01473 41 AE000511 #15 RHP01627 100 AE000511 #16 RHP01474 247 AE000511 #17 RHP00088 297 AE000511 #18 RHP00089 82 AE000511 #19 RHP00203 107 AE000511 #20 RHP00204 127 AE000511 #21 RHP00363 77 AE000511 #22 RHP00458 63 AE000511 #23 RHP00461 148 AE000511 #24 RHP00559 54 AE000511 #25 RHP00560 89 AE000511 #26 RHP00561 93 AE000511 #27 RHP00617 40 AE000511 #28 RHP00618 65 AE000511 #29 RHP00650 116 AE000511 #30 RHP00768 171 AE000511 #31 RHP00769 300 AE000511 #32 RHP00932 248 AE000511 #33 RHP00960 126 AE000511 Motif number 1 TTAAAAACTTTTTGTTTAGAATGTATTAACGA 1 43 0 TTTGTTAAAT 0.777436 -258 TTTAACTTATTTTTACTATAATTCTACTTTGT 1 185 0 TTTTATAAAT 0.88095 -116 CTAAGGGCTTTTATATTACAATTTTAAATTAT 1 251 1 TTATATAAAT 0.88095 -50 TTTTAAAAAATTTTTGTATAATCAACAATTCA 4 32 1 TTTTTTAAAT 0.923609 -35 TTTGATATGATTTTTCTAAAATCTTAGTTTTG 7 23 1 TTTTTTAAAT 0.923545 -73 TGAAAAAGTTTTATTGTAGCATGGAGGTTAGT 7 53 1 TTATTTACAT 0.777436 -43 TTAAGAATGATTATCTTAAAATTAGAAAGTTT 8 232 1 TTATCTAAAT 0.807333 -69 CCACCAATTTTTATAATATCATCCCATAATTG 10 259 0 TTATATACAT 0.681313 -32 GTAGCAAAAATCATGCTAACATTATGAGGTTA 13 50 1 TCATGTACAT 0.668717 -181 GGCGTTTATTTCATGTTAGAATAGCCGTCATG 16 121 0 TCATGTAAAT 0.874795 -127 TCATCATTATTTTTGATAAAAAAGCTTATCTT 16 212 0 TTTTGTAAAA 0.683653 -36 TCATTATCATTTATGCTATAATTATGGGACAA 17 36 0 TTATGTAAAT 0.968728 -262 AAATAGATTTTTATGATAAAATCTAAGCTTTA 17 139 0 TTATGTAAAT 0.968727 -159 AAAGGGGATATTTTTATATAATATGTAAAAAG 17 217 1 TTTTTTAAAT 0.923534 -81 TTAAGCAAGATTAGGTTACAATCACAAGTTTT 19 54 1 TTAGGTAAAT 0.899494 -54 CAATCACAAGTTTTATTAAAATTTTATTAATT 19 72 1 TTTTATAAAT 0.880949 -36 GTAAAAAGAGTTTTGTTATCATGGGGCAAACG 20 50 0 TTTTGTACAT 0.899494 -78 GTATCCAAGTTTTGCTTATAATAAACAAAATT 21 23 0 TTTGCTAAAT 0.547636 -55 CCTAATAAAGTCATGCTACAATGCCACTATAT 23 30 0 TCATGTAAAT 0.874795 -119 ATTTTAATTATTTTAGTATAATTGAAAGAAAC 23 95 1 TTTTATAAAT 0.88095 -54 AAACGCTATCTTTTAGTATAATAATCAGTTCA 26 39 0 TTTTATAAAT 0.88095 -55 TAACATAACCTTATTTTAAAAACTAAGGATAA 28 13 0 TTATTTAAAA 0.463603 -53 TAAAATAAGGTTATGTTACAATGATTTGATAA 28 27 1 TTATGTAAAT 0.968728 -39 AGCGGTTTTCTTATGGTATAATAGCGGTTATT 30 87 1 TTATGTAAAT 0.968728 -85 ATAGCGGTTATTTTTTTAGAATAACCAACGCT 30 107 1 TTTTTTAAAT 0.923609 -65 TTTAACCGAATCATTATAAAATATAATAAGGA 31 152 0 TCATTTAAAT 0.731688 -149 TTTCGCTAGTTTTGGATATAATCCCAATAACT 31 199 0 TTTGGTAAAT 0.899493 -102 TATCAAACAATTTTGGTAAAATCAATTTTCGC 31 225 0 TTTTGTAAAT 0.968727 -76 AAAAAGGCTTTTAGGTTATAATAAAGACAAAA 32 34 0 TTAGGTAAAT 0.899494 -215 AACCTTAATCTTTTGCTATAATCGTAGGGTTT 32 80 1 TTTTGTAAAT 0.968728 -169 GGTTTTGTCGTTTTTCTATCATTTTAATAGGA 32 107 1 TTTTTTACAT 0.777436 -142 TCAAGCTATCTTTTGCTATAATAGTGAAAATA 33 27 0 TTTTGTAAAT 0.968728 -100 GAGGCGGGTTTTATGTTACAATTCCAAAAATC 33 81 1 TTATGTAAAT 0.968728 -46 CCAAAAATCATTATTATAAAATAAAGGATAGT 33 104 1 TTATTTAAAT 0.923534 -23 ***** ** *** Masking position 7 Map Score: 53.2381 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 155 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 2 AATACATTCTAAACAAAAAGTTTTTAAAGGCAAA 1 48 1 AAAAAAAGTT 0.423983 -253 AAAGTTTTTAAAGGCAAAAAGGCTGGCGGACAGG 1 64 1 AAGAAAAAGT 0.705867 -237 TACCACCTATAAAATAAGGATCGTTCA 2 198 1 AAAAAGGATT 0.900941 -17 GTTTGATCCATAAAGAAAGAGAATAAGCGTAATA 8 42 1 TAAAAAGAGT 0.619403 -259 GCTTAATAGCAAATTAAGAATGATTATCTTAAAA 8 219 1 AAAAAGAATT 0.825011 -82 GATTATCTTAAAATTAGAAAGTTTCTTTTATGGA 8 240 1 AAAAGAAAGT 0.705867 -61 ATCACTTATCAAAGCAAAAAGGATATTT 8 283 1 AAAAAAAAGT 0.93996 -18 TACCAAAAAAAAAGTAAAAAGCCTCTTTATAAGC 9 23 0 AAAAAAAAGT 0.93996 -77 ATTATCCTTAAAACAAAGTAGATTGGATTATTTA 9 71 0 AAAAAGTAGT 0.882498 -29 TTTATGGGGCAAAAAAAGTAGAATCTGTATCAAG 10 65 1 AAAAAGTAGT 0.882499 -226 AAAATCCGCTAAATCAAGGAGTGTTATTATGGAA 10 120 1 AAAAAGGAGT 0.978322 -171 CAACTTATTCAAAATAAAGAGTATAATTACAAAT 11 16 1 AAAAAAGAGT 0.967949 -45 CCCCTTGCTTAAAGCAAGGAGCTTCCTAACTAAA 12 237 0 AAAAAGGAGT 0.978322 -64 TCCTAAACAAAGGGTTCTTTTAGCGATA 13 5 1 AAAAAGGGTT 0.67967 -226 AGGTTATTCTAAAACAAAGAGGTTATTATCAAAT 13 76 1 AAAAAAGAGT 0.96795 -155 AATTTTTACAAAACAAGGGAGTTTTAATT 13 212 1 AAAAGGGAGT 0.873701 -19 AAAAATTTAAAAATTAAGGATTATTGAATA 14 22 1 AAAAAGGATT 0.900941 -20 CAATGGCTACAAATGAAATAGTATTATATAAGAC 15 35 0 AAAAAATAGT 0.834057 -66 AGAATTAGGTAAAAAAAAGGGGTTGGCATCAATA 17 175 1 AAAAAAGGGT 0.875709 -123 AACTTAACTAAAAGTAAAAAGAGTTTTGTTATCA 20 61 0 AAAAAAAAGT 0.93996 -67 CTACCATGCGATACAAAAAAGGATTTTAA 20 109 1 ATAAAAAAGT 0.608066 -19 TAAAGATATAAGAAGAAGTTTAAAAAAGCCC 24 34 0 ATAAAGAAGT 0.698642 -21 AATTGAATCCAAAACAAGGAGTTTATTTT 30 153 1 AAAAAGGAGT 0.978321 -19 TTTTTAGCTTAAGTAAAAAAGGCTTTTAGGTTAT 32 47 0 AAGAAAAAGT 0.705867 -202 CATTATTATAAAATAAAGGATAGTC 33 112 1 AAAAAGGATT 0.900941 -15 *** ****** * Masking position 14 Map Score: 30.4864 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 327 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 AATATAAAAGCCCTTAGTTTTGTTTAGAAAC 1 237 0 CCCTTATTTT 0.921318 -64 TGAACGATCCTTATTTTATAGGTGGTAA 2 197 0 TCCTTATTTA 0.841354 -18 TACGCTTATTCTCTTTCTTTATGGATCAAAC 8 42 0 CTCTTTTTTA 0.631211 -259 AAGATAATCATTCTTAATTTGCTATTAAGCG 8 218 0 TTCTTATTTG 0.682867 -83 AGAGGCTTTTTACTTTTTTTTTGGTATTCTA 9 31 1 TACTTTTTTT 0.747045 -69 TAATCCAATCTACTTTGTTTTAAGGATAATA 9 75 1 TACTTTTTTT 0.747045 -25 ATACAGATTCTACTTTTTTTGCCCCATAAAT 10 64 0 TACTTTTTTG 0.636044 -227 ATAATAACACTCCTTGATTTAGCGGATTTTA 10 119 0 TCCTTGTTTA 0.87991 -172 TGTAATTATACTCTTTATTTTGAATAAGTTG 11 16 0 CTCTTTTTTT 0.821828 -45 GTTAGGAAGCTCCTTGCTTTAAGCAAGGGGT 12 241 1 TCCTTGTTTA 0.87991 -60 GCTAAAAGAACCCTTTGTTTAGGA 13 4 0 CCCTTTTTTA 0.870509 -227 TGATAATAACCTCTTTGTTTTAGAATAACCT 13 76 0 CTCTTTTTTT 0.821828 -155 AATTAAAACTCCCTTGTTTTGTAAAAATTAA 13 210 0 CCCTTGTTTG 0.90542 -21 TATTCAATAATCCTTAATTTTTAAATTTTTC 14 21 0 TCCTTATTTT 0.934607 -21 AGTATCTCCTTTGTGTTGGTTTAAGTT 17 7 1 TCCTTTTGTT 0.648116 -291 TGATGCCAACCCCTTTTTTTTACCTAATTCT 17 175 0 CCCTTTTTTT 0.94769 -123 GGTTAAATTGCCCTTTCGTTTTAAAGATAAA 17 277 0 CCCTTTGTTT 0.743692 -21 GTTTTTCCTTAATTTTGCAGTTTTGT 21 62 0 TCCTTATTTT 0.934607 -16 ATCCAATCCTTGTGTTTAAAGATATTA 25 73 0 TCCTTGGTTT 0.759759 -17 GTTTATCCTTAGTTTTTAAAATAAGG 28 6 1 TCCTTATTTT 0.934607 -60 AAAATAAACTCCTTGTTTTGGATTCAATTA 30 152 0 TCCTTGTTTG 0.921164 -20 GGGATTATTTTTCTTGATTTGTGGTTTTATT 31 105 1 TTCTTGTTTG 0.748423 -196 GCTCATTTGATTCTTAATTTTCTTAAGAACA 32 188 0 TTCTTATTTT 0.784427 -61 GACTATCCTTTATTTTATAATAATGA 33 111 0 TCCTTTTTTT 0.956734 -16 ****** **** Masking position 5 Map Score: 25.7493 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 358 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 ATTATAGTAAAAATAAGTTAAAATAAACCTTAAA 1 195 1 AAATTAAAAT 0.943849 -106 AAAAACTCAAAATTAACCTAAAATCGCTTGACGC 2 24 1 AATTTAAAAT 0.837553 -191 TTTATAAGAAAAATTATTTCAAATGTAGTAGAAT 2 73 0 AAATTCAAAT 0.747288 -142 ACAAAACCTAAATTGAGAAAAAATTCAATTCAAA 2 106 1 AATTAAAAAT 0.749515 -109 TAAAAAATGTAAATTTTAAACAATAGCCCCTTTG 2 136 0 AAATAACAAT 0.784691 -79 GATTATACAAAAATTTTTTAAAATATTACCCTTA 4 21 0 AAATTAAAAT 0.943841 -46 AAGCGTTTCAAAAAAGCATCAAATTGACATCTTT 8 189 0 AAAATCAAAT 0.64867 -112 TTTTTTGAAGAAAATCAAAACAATCAATTTGTCA 10 178 1 AAAAAACAAT 0.694695 -113 ATTCAAGCTAAAAGAGGTTAAAATAGTCTTTTTG 12 138 1 AAAGTAAAAT 0.710313 -163 CCTATACAACAAATAAATTACAATGAGAAACAAT 13 128 0 AAATTACAAT 0.86256 -103 TTTTTGCTCCAAAACATCTAAAATCCTATACAAC 13 152 0 AAAATAAAAT 0.913003 -79 AGACTTTAAGAAAAATTTAAAAATTAAGGATTAT 14 12 1 AAAAAAAAAT 0.859043 -30 TTTATTTCCTAATTCCATTAAAATTTCCTTTTTT 16 68 1 AATTTAAAAT 0.837565 -180 TCATTTTTGTAAATTTTTAAAAATTTTCATACTC 17 80 0 AAATAAAAAT 0.907066 -218 TCTTAAATCTAAAAATGCTACAATGTTTATCTTT 17 252 1 AAAATACAAT 0.796678 -46 ATCATTCTTAAAAACGCTAAAAATTA 18 3 0 AAAAAAAAAT 0.859043 -80 TGACCGGTTAAAATGGAGTAAAATTTTTACCCAC 23 62 0 AAATTAAAAT 0.943849 -87 CAATTATACTAAAATAATTAAAATGACCGGTTAA 23 85 0 AAAATAAAAT 0.913002 -64 AGAAGTTTAAAAAAGCCCTAAAATTTAGGGCTTA 24 18 0 AAAATAAAAT 0.913003 -37 AAATGCCTAAAATTTAGAAAAAATCACGCTTGAT 29 84 0 AATTAAAAAT 0.748901 -33 ATAAAACCACAAATCAAGAAAAATAATCCCAGTA 31 101 0 AAATAAAAAT 0.907074 -200 TATATCAAACAATTTTGGTAAAATCAATTTTCGC 31 225 0 AATTTAAAAT 0.837082 -76 **** ****** Masking position 14 Map Score: 24.4622 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 265 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 TTTTGTTTAGAAACCATTAAAGTTTAAGGTT 1 220 0 AACCATTAAA 0.58779 -81 TTATATCTAATAGCGTTTAAAAAATGTAAAT 2 156 0 TACGTTTAAA 0.862523 -59 TTTAAAATATTACCCTTAAAATATTTTT 4 8 0 TACCTTAAAA 0.937397 -59 AATCCGTTGCAATCCTTTAAAATACTTTCTA 5 32 0 AACCTTTAAA 0.851786 -43 TTTATTTTACCCTTTAAAATTACTAACC 7 78 0 TACCTTTAAA 0.898906 -18 GATTTTACTTAATCCATAAAAGAAACTTTCT 8 255 0 AACCATAAAA 0.705994 -46 GCCTCTTTATAAGCCCTAAAAAGAGC 9 6 0 AACCCTAAAA 0.932844 -94 GTATTCTAACAAGCTTTTAAATAATCCAATC 9 54 1 AACTTTTAAA 0.443979 -46 AAAATATTATCCTTAAAACAAAGTAGAT 9 82 0 TACCTTAAAA 0.937397 -18 GGATATTTCCTACCCCAAAAAGACTATTTTA 12 156 0 TACCCAAAAA 0.605932 -145 TACAAACTTTTATCGCTAAAAGAACCCTTTG 13 18 0 TACGCTAAAA 0.938136 -213 CTACAATGTTTATCTTTAAAACGAAAGGGCA 17 269 1 TACTTTAAAA 0.675372 -29 TCATTCTTAAAAACGCTAAAAATTA 18 5 0 AACGCTAAAA 0.907418 -78 TTAAAACGACTAACGCTAAAATTTTAAACCT 22 29 0 TACGCTAAAA 0.938136 -35 AAGTTTAAAAAAGCCCTAAAATTTAGGGCTT 24 19 0 AACCCTAAAA 0.932844 -36 TACTAAAAGATAGCGTTTAAATCACCAATAG 26 53 1 TACGTTTAAA 0.862523 -41 TGCCTTTACCCTTTAAAGAAATTCTTT 27 24 0 TACCTTTAAA 0.898906 -17 TTAGAATAACCAACGCTAAAAATAGCGCTTT 30 122 1 CACGCTAAAA 0.722473 -50 AGACGCCACCTACCGCTAAAATGAGATTTAC 31 73 1 TACGCTAAAA 0.938136 -228 ** ******** Masking position 9 Map Score: 20.7333 Number of sites scoring better than the average of aligned sites = 1051 Number in coding regions = 881 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 6 TAAAAATAAGTTAAAATAAACCTTAAACTTTAATGGT 1 202 1 TTAACTTAAA 0.645054 -99 TCCTAAAAACTCAAAATTAACCTAAAATCGCTTGACG 2 20 1 TCAACTAAAA 0.889561 -195 GGTAACTATCCCTTATTATATCTAATAGCGTTTAAAA 2 165 0 CCAACTAATA 0.586175 -50 TAAAAAGCCTCTTTATAAGCCCTAAAAAGAGC 9 6 0 CTACCTAAAA 0.880582 -94 TGGGATAAAACTAGATTTTAGCTAAAGCCAAATTTTT 12 42 0 CTAACTAAAG 0.917973 -259 AGCTGTTAGGCTATATTCAAGCTAAAAGAGGTTAAAA 12 124 1 CTAACTAAAA 0.975219 -177 TTTATTTTTGCTCCAAAACATCTAAAATCCTATACAA 13 153 0 CTAACTAAAA 0.975229 -78 AAGCGTGTCGCTGTAGATGAGCTGAAACGCAATTTTT 16 13 0 CTAACTGAAA 0.727593 -235 CATGATATTACTACACACTAACTAAAAAAGGAAATTT 16 88 0 CTAACTAAAA 0.975234 -160 AAACGCCGTTTTATATTAAATCTAAAGAAAAATATTT 16 146 1 TTAACTAAAG 0.8836 -102 CAAATGGGTATTCTAGCACATCTAAAAATATTTTTCT 16 171 0 TTAACTAAAA 0.938581 -77 ACGCTACTAACAACACTCAAGCTAAAATCTATTAAGG 18 48 1 CAAACTAAAA 0.748762 -35 CTAAAGTTTCTTACAACTTAACTAAAAGTAAAAAGAG 20 72 0 TTAACTAAAA 0.963677 -56 CTTTTTTGTATCGCATGGTAGCTAAAGTTTCTTACAA 20 93 0 TCAACTAAAG 0.696019 -35 TAAAAGTTTCTTTCAATTATACTAAAATAATTAAAAT 23 95 0 TTATCTAAAA 0.642183 -54 AAGAAGAAGTTTAAAAAAGCCCTAAAATTTAGGGCTT 24 19 0 TTACCTAAAA 0.839419 -36 AAAAATCACGCTTGATCTTATCTAAAATTTGCTAAGA 29 63 0 CTAACTAAAA 0.974169 -54 AAAATAGCGCTTTAATTGAATCCAAAACAAGGAGTTT 30 140 1 TTAACCAAAA 0.719146 -32 TAATTTTGTCTTTATTATAACCTAAAAGCCTTTTTTA 32 31 1 TTTACTAAAA 0.633265 -218 TAAAAGCCTTTTTTACTTAAGCTAAAAAACCTTAATC 32 53 1 TTAACTAAAA 0.808538 -196 TCTTAATTTTCTTAAGAACACCTAATACAAGGATTAG 32 171 0 CTAACTAATA 0.822607 -78 ** * * ****** Masking position 15 Map Score: 22.8152 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 63 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 AAAAACTGCTCCTAAAAACTC 2 2 1 AAAACTGCTC 0.591947 -213 TTTACATTTTTTAAACGCTATTAGATATAA 2 157 1 TTAAACGCTA 0.715087 -58 AAGCCTCTTTATAAGCCCTAAAAAGAGC 9 9 0 ATAAGCCCTA 0.809607 -91 TTTTTGCCCCATAAATGCTATAATCACCCC 10 50 0 ATAAATGCTA 0.763379 -241 GCATGCGGTAAAATCCGCTAAATCAAGGAG 10 111 1 AAATCCGCTA 0.641826 -180 ATTTTCTTCAAAAAATCCTAATAGTGTGGT 10 163 0 AAAAATCCTA 0.762023 -128 AACAGCACGAAAAACTCCTATCCTTTAGGT 12 78 1 AAAACTCCTA 0.724515 -223 CCAAAACATCTAAAATCCTATACAACAAAT 13 148 0 TAAAATCCTA 0.458337 -83 TGGAGCAAAAATAAACGCTCCAACGAATGG 13 175 1 ATAAACGCTC 0.740649 -56 TCTTAAATCTAAAAATGCTACAATGTTTAT 17 252 1 AAAAATGCTA 0.854528 -46 AATCATTCTTAAAAACGCTAAAAATTA 18 8 0 AAAAACGCTA 0.945336 -75 GATTAGTTATAATAACGCTACTAACAACAC 18 34 1 AATAACGCTA 0.539849 -49 TAAAAATCCTAAGTGTTAAAT 23 2 1 AAAAATCCTA 0.762023 -147 TTTTTTATAAGCCCTAAATTTTAGGG 24 7 1 ATAAGCCCTA 0.809607 -48 AGAAGTTTAAAAAAGCCCTAAAATTTAGGG 24 22 0 AAAAGCCCTA 0.885617 -33 ATGTTTAATTAAATGCGCTAGACTACGCCC 25 16 1 AAATGCGCTA 0.641826 -74 TATTGGTGATTTAAACGCTATCTTTTAGTA 26 53 0 TTAAACGCTA 0.715087 -41 ATACCATAAGAAAACCGCTCGCTTGTATTT 30 76 0 AAAACCGCTC 0.810273 -96 TTCTAAAAAAATAACCGCTATTATACCATA 30 98 0 ATAACCGCTA 0.886374 -74 TGGATTCAATTAAAGCGCTATTTTTAGCGT 30 134 0 TAAAGCGCTA 0.789624 -38 ********** Masking position 9 Map Score: 16.0392 Number of sites scoring better than the average of aligned sites = 1550 Number in coding regions = 1386 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 8 TTAATGGTTTCTAAACAAAACTAAGGGCTTTT 1 231 1 CAAAAAAACT 0.844196 -70 TAAATTATGGATTAATAAAACTTAAAGGATAA 1 275 1 ATAAAAAACT 0.786595 -26 AATCGCTTGACGCAAAAACACTGCCTTAATTC 2 45 1 CCAAAACACT 0.865725 -170 AATTTTTCTTATAAACAAAACCTAAATTGAGA 2 92 1 AAAAAAAACC 0.615123 -123 CCGCATGCATCTTAATAAAACTTGATACAGAT 10 87 0 CTAAAAAACT 0.93429 -204 CGTCTGCTTCCATAATAACACTCCTTGATTTA 10 129 0 CTAAAACACT 0.953288 -162 TACAAAAATGAGAAAGAACACCGGCTAATGGC 17 103 1 AAAAAACACC 0.696412 -195 ACTAATCATTCTTAAAAACGCTAAAAATTA 18 9 0 CTAAAACGCT 0.708402 -74 TAATAACGCTACTAACAACACTCAAGCTAAAA 18 43 1 ATAAAACACT 0.841028 -40 CCTAATCTTGCTTAAAAACACCCTTTCTGAAT 19 37 0 CTAAAACACC 0.958713 -71 TTAATAAAATTTTAATAAAACTTGTGATTGTA 19 70 0 TTAAAAAACT 0.663924 -38 TTTGCCCCATGATAACAAAACTCTTTTTACTT 20 52 1 GTAAAAAACT 0.624123 -76 TGGATACAATCCTAACAAAACTGCAAAATTAA 21 48 1 CTAAAAAACT 0.93429 -30 CGCTTGTATTTGCAAAAACACCGATGCATTGC 30 55 0 TCAAAACACC 0.504773 -117 GCTATTATACCATAAGAAAACCGCTCGCTTGT 30 80 0 CTAAAAAACC 0.941787 -92 GAGGAATGAGCAAAATAAAACCACAAATCAAG 31 117 0 CAAAAAAACC 0.860436 -184 TCTTAATTTTCTTAAGAACACCTAATACAAGG 32 176 0 CTAAAACACC 0.958713 -73 * *** ****** Masking position 7 Map Score: 16.3426 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 157 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 AGGGATAGTTACCACCTATAAAATAAGGATC 2 189 1 ACCACCTAAA 0.862154 -26 TCAATCCCCTTAACATAGTCATCT 6 11 0 ATCCCCTTAC 0.851583 -14 AGGGGTTCGAACCCCCTACACTCCACCATTA 8 74 0 ACCCCCTAAC 0.931775 -227 TAACCACCTTTAATTGTTATGAA 10 3 1 ACCACCTTAA 0.913852 -288 ATCCCCTTTAAGTTGTAAGTA 11 50 0 ATCCCCTTAA 0.930285 -11 TCCCCTTTTAACCCCCTATTGATGCCAACCC 17 194 0 ACCCCCTATG 0.747216 -104 ATATAAAAATATCCCCTTTTAACCCCCTATT 17 205 0 ATCCCCTTTA 0.841652 -93 ATAACCCCCTAAAATTAAAACGAC 22 50 0 ACCCCCTAAA 0.969477 -14 ATATTAACGCACCCGCTTTTAGCGAATGCTT 25 48 0 ACCCGCTTTA 0.714763 -42 ACCACCGCCTTTAACGCACCACGC 29 4 1 ACCGCCTTAA 0.942557 -113 AAAAGACCGCCTTAAAACCAGCGCTC 31 285 0 ACCGCCTTAA 0.942557 -16 ******** ** Masking position 1 Map Score: 7.44802 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 298 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 10 TTAAGGTTTATTTTAACTTATTTTTACTATAATT 1 194 0 TTTTAATTTT 0.932991 -107 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 2 23 0 TTTTAAATTT 0.579794 -192 TTCTACTACATTTGAAATAATTTTTCTTATAAAC 2 74 1 TTTGAATTTT 0.764606 -141 TGAATTGAATTTTTTCTCAATTTAGGTTTTGTTT 2 104 0 TTTTTATTTA 0.483982 -111 AAGGGTAATATTTTAAAAAATTTTTGTATAATCA 4 22 1 TTTTAATTTT 0.932991 -45 TTTTTCCTATTTTGATATGATTTTTCTAAAATCT 7 13 1 TTTGAATTTT 0.764606 -83 TTTTTACTTTTTTTTTGGTATTCTAACAAGCTTT 9 37 1 TTTTTATTCT 0.698918 -63 ACACTCCTTGATTTAGCGGATTTTACCGCATGCA 10 110 0 ATTTAATTTT 0.579794 -181 AAAAAGACTATTTTAACCTCTTTTAGCTTGAATA 12 137 0 TTTTACTTTT 0.547861 -164 AATTTATTTGTTGTATAGGATTTTAGATGTTTTG 13 143 1 TTGTAATTTT 0.52652 -88 TTTTTGTAAATTTTTAAAAATTTTCATACTCTCA 17 77 0 TTTTTATTTT 0.900581 -221 AACCCCTTTTTTTTACCTAATTCTCATTAAATAG 17 165 0 TTTTAATTCT 0.781088 -133 TTAAGAATGCTTTTTACATATTATATAAAAATAT 17 224 0 TTTTTATTAT 0.507457 -74 TAATTTTTAGCGTTTTTAAGAATGATT 18 4 1 TTTTTTTTTT 0.483982 -79 CAATCACAAGTTTTATTAAAATTTTATTAATTAA 19 72 1 TTTTAAATTT 0.579794 -36 GTTTTTCCTTAATTTTGCAGTTTTGT 21 62 0 TTTTCATTTT 0.776616 -16 TGGGTAAAAATTTTACTCCATTTTAACCGGTCAT 23 63 1 TTTTAATTTT 0.932991 -86 TTAACCGGTCATTTTAATTATTTTAGTATAATTG 23 85 1 ATTTTATTTT 0.473041 -64 AAGCCCTAAATTTTAGGGCTTTTTTAAACTTCTT 24 19 1 TTTTATTTTT 0.590438 -36 TAAAACTAAATTTTAGTGTATTCTTAGCAAATTT 29 42 1 TTTTAATTCT 0.781088 -75 CAAGCGTGATTTTTTCTAAATTTTAGGCATTTAA 29 86 1 TTTTTATTTT 0.900581 -31 ACTGGGATTATTTTTCTTGATTTGTGGTTTTATT 31 102 1 TTTTTATTTG 0.440819 -199 AAATTCTAATTTTGTCTTTATTATAACCTAAAAG 32 25 1 TTTGTATTAT 0.193779 -224 GTTTTGTCGTTTTTCTATCATTTTAATAGGAACA 32 108 1 TTTTCATTTT 0.776616 -141 TTTTTATTGGATTTAGTATTTTCAC 33 2 1 TTTTAATTTA 0.590438 -125 ***** ***** Masking position 12 Map Score: 14.1371 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 517 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 11 ATTTGAAATAATTTTTCTTATAAACAAAACC 2 83 1 ATTTTCTTAT 0.667931 -132 TTGAATTGAATTTTTTCTCAATTTAGGTTTT 2 108 0 TTTTTCTCAA 0.648936 -107 TTTTGATATGATTTTTCTAAAATCTTAGTTT 7 22 1 ATTTTCTAAA 0.860096 -74 GCATTATAACATTTTGCTTAAAAGATGTCAA 8 169 1 ATTTTCTTAA 0.96374 -132 TTGATAAGTGATTTTACTTAATCCATAAAAG 8 264 0 ATTTTCTTAA 0.96374 -37 AAAATATTATCCTTAAAACAAAGTAG 9 84 0 ATTATCTTAA 0.680995 -16 AAATGGGGATTATTTACTTAATATTGTTTCT 13 106 1 TATTTCTTAA 0.658652 -125 TAATTTTTAAATTTTTCTTAAAGTCTA 14 7 0 ATTTTCTTAA 0.96374 -35 ATCTAAAAATATTTTTCTTTAGATTTAATAT 16 158 0 ATTTTCTTTA 0.680995 -90 CAACCCCTTTTTTTTACCTAATTCTCATTAA 17 169 0 TTTTTCCTAA 0.749039 -129 TTGTAACCTAATCTTGCTTAAAAACACCCTT 19 44 0 ATCTTCTTAA 0.748818 -64 GTTTTTCCTTAATTTTGCAGTT 21 66 0 TTTTTCTTAA 0.931619 -12 TCAAGCGTGATTTTTTCTAAATTTTAGGCAT 29 85 1 TTTTTCTAAA 0.75911 -32 TACTGGGATTATTTTTCTTGATTTGTGGTTT 31 101 1 ATTTTCTTGA 0.759844 -200 GCGAAAATTGATTTTACCAAAATTGTTTGAT 31 225 1 ATTTTCCAAA 0.573895 -76 CTAAAAGCCTTTTTTACTTAAGCTAAAAAAC 32 52 1 TTTTTCTTAA 0.931619 -197 TTTGATTCTTAATTTTCTTAAGAACACCTAA 32 183 0 AATTTCTTAA 0.790107 -66 GAGAATTCTCCTTAAAGTTATTTTG 32 234 0 ATTCTCTTAA 0.759844 -15 ***** ***** Masking position 5 Map Score: 15.0231 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 170 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 CAATTTTAAATTATGGATTAATAAAACTTAA 1 269 1 TTATGGTTAA 0.835678 -32 TTCTCTTTCTTTATGGATCAAACCCGTTTTC 8 34 0 TTATGGTCAA 0.95357 -267 AAAGTTTCTTTTATGGATTAAGTAAAATCAC 8 257 1 TTATGGTTAA 0.835678 -44 ATTATAGCATTTATGGGGCAAAAAAAGTAGA 10 56 1 TTATGGGCAA 0.976967 -235 ATTTTAGATGTTTTGGAGCAAAAATAAACGC 13 162 1 TTTTGGGCAA 0.843504 -69 TATGCTATAATTATGGGACAACTTAAACCAA 17 26 0 TTATGGACAA 0.963889 -272 AGTTTTGTTATCATGGGGCAAACGATTAGGG 20 43 0 TCATGGGCAA 0.888747 -85 TAAAATAAGGTTATGTTACAATGATTTGATA 28 27 1 TTATGTACAA 0.804637 -39 TTCTTGAAGCTTATGGCGCAATGCATCGGTG 30 38 1 TTATGGGCAA 0.976859 -134 AGCGGTTTTCTTATGGTATAATAGCGGTTAT 30 87 1 TTATGGATAA 0.866836 -85 GAGGCGGGTTTTATGTTACAATTCCAAAAAT 33 81 1 TTATGTACAA 0.804637 -46 ****** **** Masking position 10 Map Score: 12.1696 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 41 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 13 CATAGTTTCTAAGCATTCCTTTTACGA 1 7 0 AACATTCCTT 0.956074 -294 TTATTAAAATAATCATTCGTATTCAAAATGG 3 35 0 AACATTCGTA 0.945088 -30 ATTTTAAGATAATCATTCTTAATTTGCTATT 8 223 0 AACATTCTTA 0.916287 -78 TTCCTAACTAAAGCATTCCATTGAATGCTAA 12 218 0 AACATTCCAT 0.780847 -83 AAATTAAATCAACCATTCGTTGGAGCGTTTA 13 186 0 AACATTCGTT 0.943912 -45 CATAGCTTAAAATCATTGCTTAACAATGGCT 15 61 0 AACATTGCTT 0.742429 -40 AATATGTAAAAAGCATTCTTAAATCTAAAAA 17 236 1 AACATTCTTA 0.916244 -62 TATTATAACTAATCATTCTTAAAAACGCTAA 18 17 0 AACATTCTTA 0.916287 -66 CTACGCCCACAAGCATTCGCTAAAAGCGGGT 25 38 1 AACATTCGCT 0.800813 -52 TCCTTAAACATTCCTATTTATCAAAT 28 50 0 AACATTCCTA 0.957617 -16 ** ******** Masking position 6 Map Score: 7.38999 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 67 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 TGGTAACTATCCCTTATTATATCTAATAGCGT 2 171 0 CCCTTATTAT 0.765118 -44 TGAACGATCCTTATTTTATAGGTGGTAAC 2 196 0 TCCTTATTAT 0.936984 -19 TGATTGTCCTTATTAAAATAATCATTCG 3 47 0 TCCTTATTAA 0.884013 -18 TCTTTTTCCTATTTTGATATGATTTTTC 7 7 1 TCCTATTTAT 0.705902 -89 GTCAATTTGATGCTTTTTTGAAACGCTTAATA 8 195 1 TGCTTTTTAA 0.615474 -106 AAATATCCTTTTTGCTTTGATAAGTGA 8 284 0 TCCTTTTTTT 0.828025 -17 TTCGCATTATTCCTTTTTCCAACTATACAACC 10 227 0 TCCTTTTTAA 0.884013 -64 CAATAGCTCCTCATTTCAAAACTTTAATT 12 282 0 TCCTCATTAA 0.655542 -19 TATTCAATAATCCTTAATTTTTAAATTTTTCT 14 20 0 TCCTTAATTT 0.405443 -22 TATTTTTATTTCCTAATTCCATTAAAATTTCC 16 64 1 TCCTAATTAT 0.705902 -184 CATTAAAATTTCCTTTTTTAGTTAGTGTGTAG 16 83 1 TCCTTTTTGT 0.684442 -165 TGATGCCAACCCCTTTTTTTTACCTAATTCTC 17 174 0 CCCTTTTTTA 0.35094 -124 GATTTAAGAATGCTTTTTACATATTATATAAA 17 229 0 TGCTTTTTAT 0.757433 -69 ACTGATTTCCTTAATAGATTTTAGCTTGA 18 64 0 TCCTTAATAT 0.678032 -19 TTCTCCTTTTTAAATCGCATTATTG 20 4 1 TCCTTTTTAT 0.936984 -124 TTAAAATCCTTTTTTGTATCGCATGGTA 20 110 0 TCCTTTTTTA 0.711652 -18 ATTCCTCAACTCCTTATTATATTTTATAATGA 31 142 1 TCCTTATTAT 0.936984 -159 TCTTCCTCCATGCTCATTTGATTCTTAATTTT 32 198 0 TGCTCATTAT 0.438106 -51 ******** ** Masking position 8 Map Score: 9.72164 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 232 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 15 ATTACAAATTACTTACAACTTAAAGGGGAT 11 41 1 ACTTAACTAA 0.886563 -20 ACAGCTATGCACTTATATCTCTACCTAAAGGAT 12 97 0 ACTTAACTTA 0.821684 -204 TATTTTAACCTCTTTTAGCTTGAATATAGCCTA 12 130 0 TCTTTACTGA 0.674885 -171 CGCCGTTTTATATTAAATCTAAAGAAAAATATT 16 149 1 TATTAACTAA 0.791671 -99 TAAAAAGCATTCTTAAATCTAAAAATGCTACAA 17 242 1 TCTTAACTAA 0.956489 -56 AGCTAAAGTTTCTTACAACTTAACTAAAAGTAA 20 78 0 TCTTAACTAA 0.956489 -50 AACGCTAAAATTTTAAACCTTAACTCCAAGATC 22 16 0 TTTTAACTAA 0.791671 -48 TTAAACTTCTTCTTATATCTTTA 24 42 1 TCTTAACTTA 0.928372 -13 CTCTTTAATCTTTATGATTAGGAT 26 2 1 TCTTTACTTA 0.821684 -92 CCACGCTTGAAATTAAAACTAAATTTTAGTGTA 29 29 1 AATTAACTAA 0.57466 -88 AAGATTAAGGTTTTTTAGCTTAAGTAAAAAAGG 32 59 0 TTTTTACTAA 0.57466 -190 AAAACCCGCCTCTTACACCTATAAGATTTTATC 33 60 0 TCTTAACTTA 0.928372 -67 ***** * ** ** Masking position 7 Map Score: 5.71383 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 39 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925