AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_hpyl_reg_100.orf -o294_hpyl_100.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 RHP00088 297 AE000511 #17 RHP00089 82 AE000511 #18 RHP00203 107 AE000511 #19 RHP00363 77 AE000511 #20 RHP00458 63 AE000511 #21 RHP00461 148 AE000511 #22 RHP00559 54 AE000511 #23 RHP00560 89 AE000511 #24 RHP00561 93 AE000511 #25 RHP00617 40 AE000511 #26 RHP00618 65 AE000511 #27 RHP00650 116 AE000511 #28 RHP00768 171 AE000511 #29 RHP00932 248 AE000511 #30 RHP00960 126 AE000511 Motif number 1 TTAAAAACTTTTTGTTTAGAATGTATTAACGA 1 43 0 TTTGTTAAAT 0.933477 -258 TTTAACTTATTTTTACTATAATTCTACTTTGT 1 185 0 TTTTCTAAAT 0.92369 -116 TATAGTAAAAATAAGTTAAAATAAACCTTAAA 1 197 1 ATAATTAAAT 0.627167 -104 CTAAGGGCTTTTATATTACAATTTTAAATTAT 1 251 1 TTATTTAAAT 0.939226 -50 AAACTCAAAATTAACCTAAAATCGCTTGACGC 2 26 1 TTAACTAAAT 0.80663 -189 CAATTTAGGTTTTGTTTATAAGAAAAATTATT 2 89 0 TTTGTTAAAG 0.699942 -126 CAAAGGGGCTATTGTTTAAAATTTACATTTTT 2 136 1 ATTGTTAAAT 0.806563 -79 AGAATGAAATAAGCTATAATAAGCCCATTT 3 9 1 ATAACTAAAT 0.568509 -56 TTATACAAAAATTTTTTAAAATATTACCCTTA 4 21 0 ATTTTTAAAT 0.820453 -46 TTTGATATGATTTTTCTAAAATCTTAGTTTTG 7 23 1 TTTTCTAAAT 0.923684 -73 ATTATAACATTTTGCTTAAAAGATGTCAATTT 8 171 1 TTTGTTAAAG 0.699943 -130 TTAAGAATGATTATCTTAAAATTAGAAAGTTT 8 232 1 TTATTTAAAT 0.939226 -69 TCTCCAGGTTTTAGTCAAAAATTTGGCTTTAG 12 26 1 TTAGCAAAAT 0.665684 -275 AAAATTTGGCTTTAGCTAAAATCTAGTTTTAT 12 43 1 TTTACTAAAT 0.80663 -258 TATACAACAAATAAATTACAATGAGAAACAAT 13 128 0 ATAATTAAAT 0.627167 -103 AACTCCCTTGTTTTGTAAAAATTAAATCAACC 13 203 0 TTTTTAAAAT 0.73677 -28 CCTCTTTTCCATAGCTTAAAATCATTGCTTAA 15 69 0 ATAGTTAAAT 0.815913 -32 TCATTATCATTTATGCTATAATTATGGGACAA 16 36 0 TTATCTAAAT 0.92369 -262 GAGTATGAAAATTTTTAAAAATTTACAAAAAT 16 80 1 ATTTTAAAAT 0.359181 -218 TTTTTACATATTATATAAAAATATCCCCTTTT 16 216 0 TTATTAAAAT 0.736828 -82 TTTAAGAATGATTAGTTATAATAACGCTACTA 17 25 1 ATTATTAAAT 0.627145 -58 TTAAGCAAGATTAGGTTACAATCACAAGTTTT 18 54 1 TTAGTTAAAT 0.933479 -54 CAATCACAAGTTTTATTAAAATTTTATTAATT 18 72 1 TTTTTTAAAT 0.939225 -36 GTATCCAAGTTTTGCTTATAATAAACAAAATT 19 23 0 TTTGTTAAAT 0.933478 -55 TTTCTTTCAATTATACTAAAATAATTAAAATG 21 94 0 TTATCTAAAT 0.92369 -55 GAACTGATTATTATACTAAAAGATAGCGTTTA 24 40 1 TTATCTAAAG 0.668011 -54 TAAAATAAGGTTATGTTACAATGATTTGATAA 26 27 1 TTATTTAAAT 0.939226 -39 TTATCTAAAATTTGCTAAGAATACACTAAAAT 27 51 0 TTTGTAAAAT 0.717694 -66 ATAGCGGTTATTTTTTTAGAATAACCAACGCT 28 107 1 TTTTTTAAAT 0.939224 -65 AAAAAGGCTTTTAGGTTATAATAAAGACAAAA 29 34 0 TTAGTTAAAT 0.933479 -215 AACCTTAATCTTTTGCTATAATCGTAGGGTTT 29 80 1 TTTTCTAAAT 0.92369 -169 TCAAGCTATCTTTTGCTATAATAGTGAAAATA 30 27 0 TTTTCTAAAT 0.92369 -100 GAGGCGGGTTTTATGTTACAATTCCAAAAATC 30 81 1 TTATTTAAAT 0.939226 -46 GACTATCCTTTATTTTATAATAATGATTTTT 30 106 0 TTATTTAAAT 0.939225 -21 **** *** *** Masking position 8 Map Score: 46.3442 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 217 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 AATACATTCTAAACAAAAAGTTTTTAAAGGCAAA 1 48 1 AAAAAAAGTT 0.479601 -253 AAAGTTTTTAAAGGCAAAAAGGCTGGCGGACAGG 1 64 1 AAGAAAAAGT 0.662015 -237 GTTTCTAAACAAAACTAAGGGCTTTTATATTACA 1 237 1 AAATAAGGGT 0.741242 -64 AAATTATTTCAAATGTAGTAGAATTAAGGCAGTG 2 63 0 AAATAGTAGT 0.777035 -152 TACCACCTATAAAATAAGGATCGTTCA 2 198 1 AAAAAGGATT 0.9316 -17 AAACTTTTTCAAAACTAAGATTTTAGAAAAATCA 7 30 0 AAATAAGATT 0.667012 -66 GCTTAATAGCAAATTAAGAATGATTATCTTAAAA 8 219 1 AAAAAGAATT 0.83018 -82 GATTATCTTAAAATTAGAAAGTTTCTTTTATGGA 8 240 1 AAAAGAAAGT 0.563614 -61 ATCACTTATCAAAGCAAAAAGGATATTT 8 283 1 AAAAAAAAGT 0.901465 -18 TACCAAAAAAAAAGTAAAAAGCCTCTTTATAAGC 9 23 0 AAAAAAAAGT 0.901465 -77 ATTATCCTTAAAACAAAGTAGATTGGATTATTTA 9 71 0 AAAAAGTAGT 0.921688 -29 TTTATGGGGCAAAAAAAGTAGAATCTGTATCAAG 10 65 1 AAAAAGTAGT 0.921688 -226 AAAATCCGCTAAATCAAGGAGTGTTATTATGGAA 10 120 1 AAAAAGGAGT 0.980885 -171 CAACTTATTCAAAATAAAGAGTATAATTACAAAT 11 16 1 AAAAAAGAGT 0.962248 -45 TCTCTACCTAAAGGATAGGAGTTTTTCGTGCTGT 12 79 0 AAGTAGGAGT 0.764884 -222 CCCCTTGCTTAAAGCAAGGAGCTTCCTAACTAAA 12 237 0 AAAAAGGAGT 0.980885 -64 TCCTAAACAAAGGGTTCTTTTAGCGATA 13 5 1 AAAAAGGGTT 0.837912 -226 AGGTTATTCTAAAACAAAGAGGTTATTATCAAAT 13 76 1 AAAAAAGAGT 0.962248 -155 AATTTTTACAAAACAAGGGAGTTTTAATT 13 212 1 AAAAGGGAGT 0.878708 -19 AAAAATTTAAAAATTAAGGATTATTGAATA 14 22 1 AAAAAGGATT 0.9316 -20 CAATGGCTACAAATGAAATAGTATTATATAAGAC 15 35 0 AAAAAATAGT 0.853927 -66 AGAATTAGGTAAAAAAAAGGGGTTGGCATCAATA 16 175 1 AAAAAAGGGT 0.906318 -123 CCTAAGTGTTAAATATAGTGGCATTGTAGCATGA 21 18 1 AAATAGTGGT 0.569477 -131 AATTGAATCCAAAACAAGGAGTTTATTTT 28 153 1 AAAAAGGAGT 0.980883 -19 TAATAAAGACAAAATTAGAATTTTAGGATAGATC 29 14 0 AAATAGAATT 0.591294 -235 TTTTTAGCTTAAGTAAAAAAGGCTTTTAGGTTAT 29 47 0 AAGAAAAAGT 0.662015 -202 CATTATTATAAAATAAAGGATAGTC 30 112 1 AAAAAGGATT 0.9316 -15 *** ****** * Masking position 2 Map Score: 33.2405 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 505 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 AATAAGTTAAAATAAACCTTAAACTTTAATGG 1 206 1 AAAACCTTAA 0.934662 -95 ATTATGGATTAATAAAACTTAAAGGATAACAC 1 278 1 AAAAACTTAA 0.779903 -23 TTTTCTTATAAACAAAACCTAAATTGAGAAAA 2 95 1 AAAAACCTAA 0.894524 -120 ATTTTAAGATAATCATTCTTAATTTGCTATTA 8 222 0 AACATCTTAA 0.897796 -79 AAAGCCTCTTTATAAGCCCTAAAAAGAGC 9 8 0 TAAACCCTAA 0.900472 -92 TAAATGCTATAATCACCCCTATCAATCAAACT 10 37 0 AACACCCTAT 0.852294 -254 GATTTTCTTCAAAAAATCCTAATAGTGTGGTT 10 162 0 AAAATCCTAA 0.959765 -129 CAACAGCACGAAAAACTCCTATCCTTTAGGTA 12 77 1 AAAATCCTAT 0.820186 -224 TATTCAATAATCCTTAATTTTTAAATT 14 25 0 AAAACCTTAA 0.934662 -17 AATATGTAAAAAGCATTCTTAAATCTAAAAAT 16 236 1 AACATCTTAA 0.897796 -62 TATTATAACTAATCATTCTTAAAAACGCTAAA 17 16 0 AACATCTTAA 0.897796 -67 CAAAACTTGGATACAATCCTAACAAAACTGCA 19 41 1 ATCATCCTAA 0.800805 -37 ACGCTAAAATTTTAAACCTTAACTCCAAGATC 20 16 0 TTAACCTTAA 0.419564 -48 TAAAAATCCTAAGTGTTAAATA 21 1 1 TAAATCCTAA 0.86308 -148 TTTTTTATAAGCCCTAAATTTTAGGGC 22 6 1 TAAACCCTAA 0.900472 -49 AAGAAGTTTAAAAAAGCCCTAAAATTTAGGGC 22 21 0 AAAACCCTAA 0.971621 -34 TAATCAGTTCATGCAATCCTAATCATAAAGAT 24 18 0 ATCATCCTAA 0.800805 -76 TCCTTAAACATTCCTATTTATCAAATC 26 49 0 AACATCCTAT 0.800805 -17 TACTTAAGCTAAAAAACCTTAATCTTTTGCTA 29 66 1 AAAACCTTAA 0.934662 -183 TAATTTTCTTAAGAACACCTAATACAAGGATT 29 173 0 AAAAACCTAA 0.894524 -76 ** ** ****** Masking position 10 Map Score: 24.1433 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 525 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 4 AGAATGAAATAAGCTATAATAAGCCCATT 3 7 1 ATAGCTATAA 0.832878 -58 AATTACTAACCTCCATGCTACAATAAAACTTTT 7 56 0 CCAGCTACAA 0.835209 -40 AAAATCACTTATCAAAGCAAAAAGGATATTT 8 280 1 AAAGCAAAAA 0.746794 -21 TTTTTGCCCCATAAATGCTATAATCACCCCTAT 10 47 0 AAAGCTATAA 0.939479 -244 AAACCTGGAGACAAACGCTCCAAGTT 12 4 0 AAAGCTCCAA 0.923388 -297 GTTAGGCTATATTCAAGCTAAAAGAGGTTAAAA 12 128 1 ACAGCTAAAA 0.969705 -173 AAGTAGCAAAAATCATGCTAACATTATGAGGTT 13 48 1 ACAGCTAACA 0.792117 -183 TGGAGCAAAAATAAACGCTCCAACGAATGGTTG 13 175 1 AAAGCTCCAA 0.923388 -56 TCATTGCTTAACAATGGCTACAAATGAAATAGT 15 47 0 AATGCTACAA 0.806334 -54 TTTCATTATCATTTATGCTATAATTATGGGACA 16 37 0 ATAGCTATAA 0.832878 -261 TCTTAAATCTAAAAATGCTACAATGTTTATCTT 16 252 1 AAAGCTACAA 0.982148 -46 AATCATTCTTAAAAACGCTAAAAATTA 17 5 0 AAAGCTAAAA 0.974982 -78 GATTAGTTATAATAACGCTACTAACAACACTCA 17 34 1 AAAGCTACTA 0.815457 -49 TACTAACAACACTCAAGCTAAAATCTATTAAGG 17 52 1 ACAGCTAAAA 0.969705 -31 AATTAAAACGACTAACGCTAAAATTTTAAACCT 20 29 0 AAAGCTAAAA 0.974982 -35 ACCCTAATAAAGTCATGCTACAATGCCACTATA 21 31 0 ACAGCTACAA 0.978348 -118 TTTTAGAATAACCAACGCTAAAAATAGCGCTTT 28 120 1 AAAGCTAAAA 0.974982 -52 AGCCTTTTTTACTTAAGCTAAAAAACCTTAATC 29 57 1 ATAGCTAAAA 0.925991 -192 * ** ******* Masking position 13 Map Score: 24.7381 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 211 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CTTTTTGCCTTTAAAAACTTTTTGTTTAGAATGT 1 51 0 TTAAATTTTG 0.599027 -250 AAAAATAAGTTAAAATAAACCTTAAACTTTAATG 1 203 1 TAAAACCTTA 0.657931 -98 TCTACTACATTTGAAATAATTTTTCTTATAAACA 2 75 1 TTGAATTTTT 0.468855 -140 ATTGTCCTTATTAAAATAATCATTCGTATTCAAA 3 39 0 TTAAATCATT 0.791549 -26 GGGTAATATTTTAAAAAATTTTTGTATAATCAAC 4 24 1 TTAAATTTTG 0.599027 -43 TATAAAAGCTATCTTTAGTGATAGAA 5 3 1 TAAAATCTTT 0.93676 -72 CTTTCTAATTTTAAGATAATCATTCTTAATTTGC 8 227 0 TTAAGTCATT 0.400502 -74 ATCTTAAAATTAGAAAGTTTCTTTTATGGATTAA 8 244 1 TAGAATCTTT 0.775875 -57 AAAAAAAAAGTAAAAAGCCTCTTTATAAGCCCTA 9 19 0 TAAAATCTTT 0.93676 -81 CTAAAAGAGGTTAAAATAGTCTTTTTGGGGTAGG 12 145 1 TTAAATCTTT 0.94943 -156 CTTTTATCGCTAAAAGAACCCTTTGTTTAGGA 13 9 0 TAAAACCTTT 0.885841 -222 TTTGTAAAAATTAAATCAACCATTCGTTGGAGCG 13 190 0 TTAAACCATT 0.66511 -41 AATTAAAACTCCCTTGTTTTGTAAAA 13 215 0 TTAAACCTTG 0.795003 -16 TCCTTAATTTTTAAATTTTTCTTAAAGTCTA 14 8 0 TTAAATCTTA 0.82369 -34 TGTAAATTTTTAAAAATTTTCATACTCTCATTTA 16 73 0 TAAAATCATA 0.427625 -225 CTAATTCTCATTAAATAGATTTTTATGATAAAAT 16 149 0 TTAAATTTTT 0.790873 -149 GGTTAAATTGCCCTTTCGTTTTAAAG 16 282 0 TTAAACCTTT 0.907576 -16 TAATCTTGCTTAAAAACACCCTTTCTGAATTTTA 18 33 0 TAAAACCTTT 0.885841 -75 GAATTGTTTGTTAAAAGTTTCTTTCAATTATACT 21 109 0 TTAAATCTTT 0.94943 -40 AGGGCTTTTTTAAACTTCTTCTTATATCTTTA 22 33 1 TAAACTCTTA 0.486274 -22 ATTGGTGATTTAAACGCTATCTTTTAGTATAATA 24 48 0 TAAACTCTTT 0.791783 -46 CTTTACCCTTTAAAGAAATTCTTTAATTATACAC 25 14 0 TAAAGTCTTT 0.722998 -27 TATTATAACCTAAAAGCCTTTTTTACTTAAGCTA 29 43 1 TAAAATTTTT 0.742716 -206 ATGTGTGAATTTGACGCTGTCTTTGCCTTGTTCC 29 136 0 TTGACTCTTT 0.528848 -113 AGAATTCTCCTTAAAGTTATTTTGGTTCTCTTCC 29 224 0 TTAAATTTTG 0.599027 -25 ***** ***** Masking position 13 Map Score: 15.6702 Number of sites scoring better than the average of aligned sites = 1241 Number in coding regions = 1022 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 6 GAGTTTTTAGGAGCAGTTTTT 2 2 0 GAGCAGTTTT 0.639617 -213 TTATATCTAATAGCGTTTAAAAAATGTAAA 2 157 0 TAGCGTTTAA 0.866929 -58 TCACTAAAGATAGCTTTTATA 5 2 0 TAGCTTTTAT 0.732297 -73 GGGGTGATTATAGCATTTATGGGGCAAAAA 10 50 1 TAGCATTTAT 0.873606 -241 AACTTGGAGCGTTTGTCTCCAGGTTT 12 7 1 GAGCGTTTGT 0.94997 -294 CCATTCGTTGGAGCGTTTATTTTTGCTCCA 13 175 0 GAGCGTTTAT 0.958368 -56 ATAAACATTGTAGCATTTTTAGATTTAAGA 16 252 0 TAGCATTTTT 0.853295 -46 TAATTTTTAGCGTTTTTAAGAATGATT 17 8 1 TAGCGTTTTT 0.966904 -75 GTGTTGTTAGTAGCGTTATTATAACTAATC 17 34 0 TAGCGTTATT 0.856467 -49 TTTAAAATTTTAGCGTTAGTCGTTTTAATT 20 32 1 TAGCGTTAGT 0.853988 -32 TACTAAAAGATAGCGTTTAAATCACCAATA 24 53 1 TAGCGTTTAA 0.866929 -41 AAATACAAGCGAGCGGTTTTCTTATGGTAT 28 76 1 GAGCGGTTTT 0.89914 -96 TATGGTATAATAGCGGTTATTTTTTTAGAA 28 98 1 TAGCGGTTAT 0.941095 -74 GCGCTATTTTTAGCGTTGGTTATTCTAAAA 28 120 0 TAGCGTTGGT 0.830965 -52 ********** Masking position 2 Map Score: 11.5873 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 488 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 GGTGGTAACTATCCCTTATTATATCTAATA 2 175 0 ATCCCTTATT 0.603433 -40 AGGGATAGTTACCACCTATAAAATAAGGAT 2 189 1 ACCACCTATA 0.822158 -26 TCAATCCCCTTAACATAGTCATC 6 12 0 ATCCCCTTAA 0.879446 -13 AGGGGTTCGAACCCCCTACACTCCACCATT 8 75 0 ACCCCCTACA 0.873111 -226 TAACCACCTTTAATTGTTATGA 10 3 1 ACCACCTTTA 0.858922 -288 ATGCGGTAAAATCCGCTAAATCAAGGAGTG 10 113 1 ATCCGCTAAA 0.498788 -178 ATCCCCTTTAAGTTGTAAGT 11 51 0 ATCCCCTTTA 0.957846 -10 TAAGTAAATAATCCCCATTTGATAATAACC 13 96 0 ATCCCCATTT 0.629377 -135 ATTGATGCCAACCCCTTTTTTTTACCTAAT 16 178 0 ACCCCTTTTT 0.809296 -120 TCCCCTTTTAACCCCCTATTGATGCCAACC 16 195 0 ACCCCCTATT 0.965211 -103 ATATAAAAATATCCCCTTTTAACCCCCTAT 16 206 0 ATCCCCTTTT 0.945217 -92 ATAACCCCCTAAAATTAAAACGA 20 51 0 ACCCCCTAAA 0.921449 -13 ATATTAACGCACCCGCTTTTAGCGAATGCT 23 49 0 ACCCGCTTTT 0.8678 -41 ACCACCGCCTTTAACGCACCACG 27 4 1 ACCGCCTTTA 0.836528 -113 ********** Masking position 1 Map Score: 9.00518 Number of sites scoring better than the average of aligned sites = 742 Number in coding regions = 613 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 8 TAATAAAACTTAAAGGATAACACC 1 287 1 TAAAGGATAA 0.942786 -14 AAAAATATTTTAAGGGTAATATTTTAAAA 4 10 1 TTAAGGGTAA 0.953088 -57 GATGACTATGTTAAGGGGATTGA 6 12 1 TTAAGGGGAT 0.508094 -13 TTAGTAATTTTAAAGGGTAAAATAAA 7 80 1 TAAAGGGTAA 0.918932 -16 TTAATTATGGGTAATACTAGCAAG 8 5 1 TTATGGGTAA 0.619986 -296 CTACTTTGTTTTAAGGATAATATTTT 9 84 1 TTAAGGATAA 0.967242 -16 TATCTCTACCTAAAGGATAGGAGTTTTTCG 12 85 0 TAAAGGATAG 0.804482 -216 AATTTAAAAATTAAGGATTATTGAATA 14 25 1 TTAAGGATTA 0.703462 -17 AATTATAGCATAAATGATAATGAAAAAGTA 16 45 1 TAAATGATAA 0.717074 -253 AAAAATCTATTTAATGAGAATTAGGTAAAA 16 159 1 TTAATGAGAA 0.716138 -139 CCCTTTCGTTTTAAAGATAAACATTGTAGC 16 268 0 TTAAAGATAA 0.642584 -30 ATTTTATTAATTAATGAGAAGGGATC 18 92 1 TTAATGAGAA 0.716138 -16 AACTGCAAAATTAAGGAAAAAC 19 66 1 TTAAGGAAAA 0.758637 -12 AGAATTTCTTTAAAGGGTAAAGGCA 25 26 1 TAAAGGGTAA 0.918932 -15 ATTTTAAAAACTAAGGATAAAC 26 3 0 CTAAGGATAA 0.778564 -63 CAAAATAACTTTAAGGAGAATTCTC 29 234 1 TTAAGGAGAA 0.942537 -15 TATTATAAAATAAAGGATAGTC 30 115 1 TAAAGGATAG 0.804482 -12 ********** Masking position 3 Map Score: 14.1536 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 195 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 TAACCTAAAATCGCTTGACGCAAAAACACTGCC 2 37 1 TCGCTTGAAA 0.867499 -178 GTTATAATGCTCGCTTAATTTTATTTGGGGTGT 8 146 0 TCGCTTAATA 0.920722 -155 AATTTGGCTTTAGCTAAAATCTAGTTTTATCCC 12 45 1 TAGCTAAATA 0.627109 -256 TAACCTCTTTTAGCTTGAATATAGCCTAACAGC 12 125 0 TAGCTTGATA 0.975305 -176 CTCATAATGTTAGCATGATTTTTGCTACTTACA 13 45 0 TAGCATGATT 0.624107 -186 CTCTTTTCCATAGCTTAAAATCATTGCTTAACA 15 67 0 TAGCTTAACA 0.748647 -34 TAATAGATTTTAGCTTGAGTGTTGTTAGTAGCG 17 49 0 TAGCTTGATT 0.890462 -34 TAAACAAAATTAGCTTAAGAGTA 19 1 0 TAGCTTAATA 0.940529 -77 AGTGGCATTGTAGCATGACTTTATTAGGGTGGG 21 34 1 TAGCATGATA 0.890458 -115 TTAACGCACCACGCTTGAAATTAAAACTAAATT 27 21 1 ACGCTTGATA 0.856514 -96 AGAAAAAATCACGCTTGATCTTATCTAAAATTT 27 70 0 ACGCTTGATA 0.856515 -47 TAAGGTTTTTTAGCTTAAGTAAAAAAGGCTTTT 29 54 0 TAGCTTAAAA 0.779917 -195 TAGCAAAAGATAGCTTGATGATAAAATCTTATA 30 41 1 TAGCTTGATA 0.972856 -86 ******** ** Masking position 8 Map Score: 8.47244 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 99 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 TTAAAATTTACATTTTTTAAACGCTATTAGATAT 2 151 1 CTTTTAAAGC 0.95261 -64 CAATTTGATGCTTTTTTGAAACGCTTAATAGCAA 8 197 1 CTTTGAAAGC 0.896307 -104 AAGTAGATTGGATTATTTAAAAGCTTGTTAGAAT 9 56 0 GTTTTAAAGC 0.978115 -44 GCAAGATGTTTAATTAAATGCGCTAGACTAC 23 8 1 GTTTTAAAGC 0.978406 -82 CGCCCACAAGCATTCGCTAAAAGCGGGTGCGTTA 23 41 1 CTTCTAAAGC 0.842261 -49 TCAACCTATTGGTGATTTAAACGCTATCTTTTAG 24 55 0 GTGTTAAAGC 0.95118 -39 TTTCAAGCGTGGTGCGTTAAAGGCGGTGGT 27 7 0 GTGTTAAAGC 0.95118 -110 TGATTCCTTAAATGCCTAAAATTTA 27 102 0 GTTTTAAAGC 0.978407 -15 TGCGCCATAAGCTTCAAGAAACGCTTTGCATAGA 28 24 0 GTTAGAAAGC 0.858961 -148 CCTTGTTTTGGATTCAATTAAAGCGCTATTTTTA 28 138 0 GTTATTAAGC 0.667549 -34 * ** ***** ** Masking position 10 Map Score: 7.95777 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 124 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 CAATTTTAAATTATGGATTAATAAAACTTAA 1 269 1 TTATGGTTAA 0.882133 -32 CGTCAAGCGATTTTAGGTTAATTTTGAGTTT 2 26 0 TTTTAGTTAA 0.691363 -189 AAGGCAGTGTTTTTGCGTCAAGCGATTTTAG 2 41 0 TTTTGCTCAA 0.488365 -174 TTTTAAAAAATTTTTGTATAATCAACAATTC 4 32 1 TTTTTGATAA 0.379208 -35 TTCTCTTTCTTTATGGATCAAACCCGTTTTC 8 34 0 TTATGGTCAA 0.842164 -267 AAAGTTTCTTTTATGGATTAAGTAAAATCAC 8 257 1 TTATGGTTAA 0.882133 -44 ATTATAGCATTTATGGGGCAAAAAAAGTAGA 10 56 1 TTATGGGCAA 0.796752 -235 ATGCGAACAATTATGGGATGATATTATAAAA 10 252 1 TTATGGATGA 0.476248 -39 TTTTTCGTGCTGTTGGGATAAAACTAGATTT 12 61 0 TGTTGGATAA 0.675528 -240 AAAATAGTCTTTTTGGGGTAGGAAATATCCA 12 157 1 TTTTGGGTAG 0.342078 -144 AACCTCTTTGTTTTAGAATAACCTCATAATG 13 69 0 TTTTAGATAA 0.774054 -162 ATTTTAGATGTTTTGGAGCAAAAATAAACGC 13 162 1 TTTTGGGCAA 0.829804 -69 ATCTCCTTTGTGTTGGTTTAAGTTGTCCCAT 16 14 1 TGTTGGTTAA 0.575281 -284 TATGCTATAATTATGGGACAACTTAAACCAA 16 26 0 TTATGGACAA 0.890995 -272 TGTCCCATAATTATAGCATAAATGATAATGA 16 37 1 TTATAGATAA 0.485428 -261 GATCTTGGAGTTAAGGTTTAAAATTTTAGCG 20 16 1 TTAAGGTTAA 0.274146 -48 ATTTTAATTATTTTAGTATAATTGAAAGAAA 21 95 1 TTTTAGATAA 0.770059 -54 AAACGCTATCTTTTAGTATAATAATCAGTTC 24 40 0 TTTTAGATAA 0.770059 -54 TAAAATAAGGTTATGTTACAATGATTTGATA 26 27 1 TTATGTACAA 0.343441 -39 TTCTTGAAGCTTATGGCGCAATGCATCGGTG 28 38 1 TTATGGGCAA 0.796354 -134 AGCGGTTTTCTTATGGTATAATAGCGGTTAT 28 87 1 TTATGGATAA 0.721608 -85 GCGGTTATTTTTTTAGAATAACCAACGCTAA 28 110 1 TTTTAGATAA 0.774054 -62 AAACTCCTTGTTTTGGATTCAATTAAAGCGC 28 146 0 TTTTGGTTCA 0.423976 -26 GATTAAGGTTTTTTAGCTTAAGTAAAAAAGG 29 59 0 TTTTAGTTAA 0.690434 -190 AACCTTAATCTTTTGCTATAATCGTAGGGTT 29 80 1 TTTTGCATAA 0.652291 -169 TCAAGCTATCTTTTGCTATAATAGTGAAAAT 30 28 0 TTTTGCATAA 0.652291 -99 GAGGCGGGTTTTATGTTACAATTCCAAAAAT 30 81 1 TTATGTACAA 0.343441 -46 ****** **** Masking position 1 Map Score: 20.4643 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 511 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 12 ACATTCTAAACAAAAAGTTTTTAAAGGCAA 1 51 1 CAAAAAGTTT 0.701063 -250 CAACAATTCACAAGGAGTTTAAA 4 54 1 CAAGGAGTTT 0.979166 -13 TTTATTGTAGCATGGAGGTTAGTAATTTTA 7 62 1 CATGGAGGTT 0.878967 -34 TCCGCTAAATCAAGGAGTGTTATTATGGAA 10 124 1 CAAGGAGTGT 0.916536 -167 TATTCAAGCTAAAAGAGGTTAAAATAGTCT 12 137 1 AAAAGAGGTT 0.696849 -164 TTGCTTAAAGCAAGGAGCTTCCTAACTAAA 12 237 0 CAAGGAGCTT 0.94501 -64 TATTCTAAAACAAAGAGGTTATTATCAAAT 13 80 1 CAAAGAGGTT 0.959096 -151 GGTTTCTATGCAAAGCGTTTCTTGAAGCTT 28 20 1 CAAAGCGTTT 0.848214 -152 GAATCCAAAACAAGGAGTTTATTTT 28 157 1 CAAGGAGTTT 0.979166 -15 ********** Masking position 2 Map Score: 5.72139 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 101 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 TCTTTTTCCTATTTTGATATGAT 7 3 1 TTTTTCCTAT 0.940311 -93 CAAACCCGTTTTCTTGCTAGTATTACCCATA 8 16 0 TTCTTGCTAT 0.79668 -285 TTTTACTTTTTTTTTGGTATTCTAACAAGCT 9 38 1 TTTTTGGTAT 0.851254 -62 GCATTATTCCTTTTTCCAACTATACAACCTC 10 225 0 TTTTTCCAAT 0.929858 -66 GTTAGCATGATTTTTGCTACTTACAAACTTT 13 39 0 TTTTTGCTAT 0.949466 -192 TTCTTTCTCATTTTTGTAAATTTTTAAAAAT 16 90 0 TTTTTGTAAT 0.756868 -208 AACCCCTTTTTTTTACCTAATTCTCATTAAA 16 168 0 TTTTACCTAT 0.666848 -130 CAAGCGTGATTTTTTCTAAATTTTAGGCATT 27 86 1 TTTTTCTAAT 0.722997 -31 TGCATCGGTGTTTTTGCAAATACAAGCGAGC 28 59 1 TTTTTGCAAT 0.940508 -113 TGTCTTTGCCTTGTTCCTATTAAAATGATAG 29 122 0 TTGTTCCTAT 0.766646 -127 ATAATAATGATTTTTGGAATTGTAACATAAA 30 90 0 TTTTTGGAAT 0.828058 -37 ********* * Masking position 9 Map Score: 3.37645 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 161 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 ATTGTAATATAAAAGCCCTTAGTTTTGTTT 1 243 0 AAAAGCCCTT 0.948026 -58 AATTTTAAACAATAGCCCCTTTGAATTGAA 2 129 0 AATAGCCCCT 0.834925 -86 TATTATATCTAATAGCGTTTAAAAAATGTA 2 159 0 AATAGCGTTT 0.603538 -56 ATAGGTGGTAACTATCCCTTATTATATCTA 2 178 0 ACTATCCCTT 0.787782 -37 ACGGATTGCAACAAGCCTTTTAAGGACGC 5 56 1 ACAAGCCTTT 0.885089 -19 AAATATCCTTTTTGCTTTGAT 8 290 0 AATATCCTTT 0.803075 -11 AAAAAAAGTAAAAAGCCTCTTTATAAGCCC 9 21 0 AAAAGCCTCT 0.830919 -79 TGGTATTCTAACAAGCTTTTAAATAATCCA 9 52 1 ACAAGCTTTT 0.251585 -48 TGCATGCGGTAAAATCCGCTAAATCAAGGA 10 110 1 AAAATCCGCT 0.283298 -181 ACGAAAAACTCCTATCCTTTAGGTAGAGAT 12 84 1 CCTATCCTTT 0.552638 -217 CTTTAAAGAACAAAGCCTTTCGTGTTAGCA 12 194 1 CAAAGCCTTT 0.85891 -107 CAAAACATCTAAAATCCTATACAACAAATA 13 147 0 AAAATCCTAT 0.306146 -84 AATTAAAACTCCCTTGTTTTGTAAA 13 216 0 AAACTCCCTT 0.45034 -15 CCTATTGATGCCAACCCCTTTTTTTTACCT 16 181 0 CCAACCCCTT 0.351248 -117 ATTATATAAAAATATCCCCTTTTAACCCCC 16 209 0 AATATCCCCT 0.70305 -89 GGTTAAATTGCCCTTTCGTTTTAAA 16 283 0 AATTGCCCTT 0.452367 -15 AATCGCCAAATCCCTTGAATTGTTTG 21 133 0 CAAATCCCTT 0.807419 -16 AGAAGTTTAAAAAAGCCCTAAAATTTAGGG 22 22 0 AAAAGCCCTA 0.529527 -33 GGTTTCTATGCAAAGCGTTTCTTGAAGCTT 28 20 1 CAAAGCGTTT 0.51617 -152 CAACGCTAAAAATAGCGCTTTAATTGAATC 28 132 1 AATAGCGCTT 0.6919 -40 ATTATAACCTAAAAGCCTTTTTTACTTAAG 29 44 1 AAAAGCCTTT 0.918045 -205 GACTATCCTTTATTTTATAAT 30 116 0 ACTATCCTTT 0.716332 -11 ********** Masking position 6 Map Score: 8.61396 Number of sites scoring better than the average of aligned sites = 2192 Number in coding regions = 1955 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 15 ATTTTTACTATAATTCTACTTTGTGAATGAGGAC 1 175 0 TAATTTACTT 0.949946 -126 AACACTGCCTTAATTCTACTACATTTGAAATAAT 2 61 1 TAATTTACTT 0.949946 -154 TGATTGTCCTTATTAAAATAATCA 3 51 0 TGATTTCCTT 0.831674 -14 CTTTGATAAGTGATTTTACTTAATCCATAAAAGA 8 263 0 TGATTTACTT 0.948985 -38 AACTTGATACAGATTCTACTTTTTTTGCCCCATA 10 67 0 AGATTTACTT 0.871924 -224 AAGTAATTTGTAATTATACTCTTTATTTTGAATA 11 21 0 TAATTTACTT 0.949945 -40 GGGTGGGTAAAAATTTTACTCCATTTTAACCGGT 21 60 1 AAATTTACTT 0.874178 -89 AGAAATTCTTTAATTATACACCAT 25 1 0 TAATTTACAT 0.772782 -40 ***** **** * Masking position 3 Map Score: 1.46912 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 7 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555