AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_hpyl_reg_100.orf -o199_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: RHP00051 16 AE000511 RHP00601 17 AE000511 Input sequences: #1 RHP01302 205 AE000511 #2 RHP01432 290 AE000511 #3 RHP01433 60 AE000511 #4 RHP00049 77 AE000511 #5 RHP00050 34 AE000511 #6 RHP00596 88 AE000511 #7 RHP00597 223 AE000511 #8 RHP00598 45 AE000511 #9 RHP00599 108 AE000511 #10 RHP00600 44 AE000511 #11 RHP00602 300 AE000511 #12 RHP01697 35 AE000511 #13 RHP00603 300 AE000511 #14 RHP00639 22 AE000511 #15 RHP00641 153 AE000511 #16 RHP00648 31 AE000511 #17 RHP00649 116 AE000511 #18 RHP00688 22 AE000511 #19 RHP00690 78 AE000511 #20 RHP00693 42 AE000511 #21 RHP00708 16 AE000511 #22 RHP00710 34 AE000511 #23 RHP00711 36 AE000511 #24 RHP00712 164 AE000511 #25 RHP00757 83 AE000511 #26 RHP00760 300 AE000511 Motif number 1 AGAAGCAGTATTTTAGCTTTTTAATCCTTTA 1 56 1 TTTAGCTTTT 0.923829 -150 AACTTCAATTTTTCAGTATTTTTAAAGGATT 1 78 0 TTTAGTATTT 0.788619 -128 TACTGAAAAATTGAAGTTTTTTAAAATTTGG 1 91 1 TTGAGTTTTT 0.923829 -115 TTTTTAAAATTTGGAGTTTTTTCTGGCTTTT 1 108 1 TTGAGTTTTT 0.923829 -98 ATCCCCTTTAAGTTGTAAGTAATTTGT 3 44 0 TTTAGTTGTA 0.789209 -17 TACTACCCTAATTTAGTTTAAAAGGTTTTTA 4 16 0 ATTAGTTTAA 0.803028 -62 ATTTAATTTTTGTTTTAATTTAAAGGG 5 7 1 TTTTGTTTTA 0.90128 -28 ATGGGGGAACTTTTAGTTTTAAATTTTTAGA 6 55 1 TTTAGTTTTA 0.977284 -34 CGCAAAGGCCTTTCTGTTTTTAAGTC 7 6 0 TTTTGTTTTT 0.884345 -218 GATCAAAAATTTTGAGTTATTTAATGCATTA 7 190 0 TTTAGTTATT 0.679048 -34 AAAAAGAAATTTTAAGCTTTTTAGCTCTTAC 9 43 0 TTTAGCTTTT 0.923829 -66 AATTTTTTAATTTTAGTTTAAGCTATTTTGG 11 11 1 TTTAGTTTAA 0.922052 -290 GTATAAATGTATTAAGTTTAAGTGAGGGCGA 11 65 1 ATTAGTTTAA 0.802977 -236 AACGCACTTATTTCTGTTTTGGTGGTGGTGA 11 186 1 TTTTGTTTTG 0.726029 -115 ATCACGCTGTTTTTAGCTTTGTTGGATTTTT 11 222 1 TTTAGCTTTG 0.807816 -79 TAGGATAACATTTTAGTTTTTGAGACGCCTA 13 84 1 TTTAGTTTTT 0.972996 -217 CGTTTTTCGTTTTGAGCTTTAATATTACTAA 15 24 1 TTTAGCTTTA 0.935405 -130 TTTGGATTAAATTGAGTTTTATTAGTAATAT 15 45 0 ATTAGTTTTA 0.936813 -109 ATACACTAAAATTTAGTTTTAATTTCAAGCG 17 75 1 ATTAGTTTTA 0.936813 -42 TTGAGTAGTATTTCAGTTTTTATTTTATTGT 24 94 1 TTTAGTTTTT 0.972996 -71 TTATTGTTTTATTCTGTTTTTTAGTAACGGA 24 118 1 ATTTGTTTTT 0.724904 -47 TTATAACCGCTTTTAGTATAAAGGCAATTAG 25 48 1 TTTAGTATAA 0.550544 -36 GCGCAATTTTATGAAGTTTTAGAAAACCTTT 26 17 0 ATGAGTTTTA 0.833068 -284 GCAAAACCCATTGAAGTTTAATAAAAGGTAA 26 272 1 TTGAGTTTAA 0.799266 -29 *** ******* Masking position 2 Map Score: 28.0912 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 496 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 2 GCAGTATTTTAGCTTTTTAATCCTTTAAAA 1 60 1 AGCTTTTTAA 0.882437 -146 GAAAAATTGAAGTTTTTTAAAATTTGGAGT 1 95 1 AGTTTTTTAA 0.965336 -111 GGGGTTTTAAATTCTTTTAAGGTATTCTAA 1 141 1 ATTCTTTTAA 0.775651 -65 CACTATTAGGATTTTTTGAAGAAAATCAAA 2 167 1 ATTTTTTGAA 0.909802 -124 ATTCCCACCAATTTTTATAATATCATCCCA 2 265 0 ATTTTTATAA 0.821499 -26 AAATCGGTTAAGATTTTTAAAAGAAAAATT 6 17 1 AGATTTTTAA 0.653888 -72 TTAGTTTTAAATTTTTAGAATAAGGAAAAA 6 67 1 ATTTTTAGAA 0.692437 -22 AAAAATTTTGAGTTATTTAATGCATTAATT 7 187 0 AGTTATTTAA 0.620521 -37 AATCCTTCACATTTTTTTAAATTAAAGCCA 8 21 0 ATTTTTTTAA 0.953745 -25 AGAAATTTTAAGCTTTTTAGCTCTTACGAT 9 40 0 AGCTTTTTAG 0.737016 -69 CTGCAAGATTATCTTTTTAAAAAAGAAATT 9 63 0 ATCTTTTTAA 0.847506 -46 AATTTTTTAATTTTAGTTTA 11 1 1 AATTTTTTAA 0.686937 -300 AGAATTAAAAATTCTTTTAATGTATAAATG 11 44 1 ATTCTTTTAA 0.775651 -257 ATAACATTTTAGTTTTTGAGACGCCTATAT 13 88 1 AGTTTTTGAG 0.835699 -213 TTTCTCCTTAATTTTTTGAAATGGATTTTA 13 276 0 ATTTTTTGAA 0.909802 -25 TATAATCAAAAGTTTTTTAGACCTTGCTCT 15 93 1 AGTTTTTTAG 0.912262 -61 GTAGTGCCTAATTTTTTCAAAGGAGAAAAA 19 57 1 ATTTTTTCAA 0.698137 -22 TGTTTTATTCTGTTTTTTAGTAACGGATAA 24 122 1 TGTTTTTTAG 0.628878 -43 AAGGGAGTGTTTTTTTATAACCGCTTTTAG 25 34 1 TTTTTTATAA 0.428585 -50 AATTTTATGAAGTTTTAGAAAACCTTTTCA 26 14 0 AGTTTTAGAA 0.752517 -287 ATACTTCCTATGTTTTTTAAGGAGCGTTAT 26 64 0 TGTTTTTTAA 0.819447 -237 GCAAAAAAAGATTTTTTTATTAGAAGACGA 26 134 1 ATTTTTTTAT 0.595995 -167 TGACTGACTCATTTTTTTAAAATACCCCCA 26 220 1 ATTTTTTTAA 0.953745 -81 ********** Masking position 6 Map Score: 20.844 Number of sites scoring better than the average of aligned sites = 1064 Number in coding regions = 878 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 3 AAATACTGCTTCTTTATTTTCTACTTCTTA 1 39 0 TCTTTATTTT 0.851351 -167 AATTGAAGTTTTTTAAAATTTGGAGTTTTT 1 99 1 TTTTAAAATT 0.5139 -107 CTTTTAGGGGGTTTTAAATTCTTTTAAGGT 1 134 1 GTTTTAAATT 0.673383 -72 TCCTTAATTTCCTTAAAACTATCTCAATGA 1 181 0 CCTTAAAACT 0.626191 -25 TTTGTTCCTTAATTTCCTTAAAACT 1 191 0 TCCTTAATTT 0.639116 -15 GTAATTATACTCTTTATTTTGAATAAGTTG 3 16 0 TCTTTATTTT 0.851351 -45 TTGTAAAAACCTTTTAAACTAAATTAGGGT 4 13 1 CTTTTAAACT 0.569962 -65 GTTTTATCCCTTTAAATTAAAACAAAAA 5 17 0 CCTTTAAATT 0.84598 -18 CCCCATTTTACCCTAATTTTTCTTTTAAAA 6 31 0 CCCTAATTTT 0.626624 -58 GGAACTTTTAGTTTTAAATTTTTAGAATAA 6 60 1 GTTTTAAATT 0.673383 -29 TATTTTTCCTTATTCTAAAAATTTAA 6 73 0 TCCTTATTCT 0.527904 -16 TGCAAAAGGATCTTTAAACTTTAGAACCAT 7 146 0 TCTTTAAACT 0.678878 -78 GCCTGTGATGGCTTTAATTTAAAAAAATGT 8 13 1 GCTTTAATTT 0.843625 -33 CGTTAGGAGTTTTTAATCTTAGGCTGAAG 9 10 1 TTTTTAATCT 0.536083 -99 GAGCTAAAAAGCTTAAAATTTCTTTTTTAA 9 47 1 GCTTAAAATT 0.72267 -62 AATTTTTTAATTTTAGTTTAAGC 11 4 1 TTTTTAATTT 0.686395 -297 TTAAAAGAATTTTTAATTCTATCCAAAATA 11 34 0 TTTTAATTCT 0.443927 -267 GACAAAAATGTCTTAAATTTTGTGGTAGCA 13 211 1 TCTTAAATTT 0.734492 -90 TTGTATTTCTCCTTAATTTTTTGAAATGGA 13 281 0 CCTTAATTTT 0.819436 -20 AATGTCTCCTTAATTTTAACCC 14 6 0 CCTTAATTTT 0.819436 -17 TCGTTTTGAGCTTTAATATTACTAATAAAA 15 30 1 CTTTAATATT 0.634277 -124 CTAATTTTAATATTTTAATTTATC 16 18 0 TTTTAATATT 0.558372 -14 TTCCTTAAATGCCTAAAATTTAGAAAAAAT 17 14 1 GCCTAAAATT 0.490744 -103 CTAAAATTTAGTTTTAATTTCAAGCGTGGT 17 80 1 GTTTTAATTT 0.711457 -37 CTACTAAAAACTTTTATATTAACATATTTT 19 31 0 CTTTTATATT 0.750143 -48 TTTTAGTAGTGCCTAATTTTTTCAAAGGAG 19 52 1 GCCTAATTTT 0.579533 -27 ATCAAACCCTTTATATTATATTCAATG 22 18 0 CCTTTATATT 0.867881 -17 ATCTAACCCTTATTTTATTATCTCAA 23 21 0 CCCTTATTTT 0.743935 -16 TTTTTATATTTCCTTATAAA 24 1 1 TTTTTATATT 0.686395 -164 AGTATTTCAGTTTTTATTTTATTGTTTTAT 24 100 1 TTTTTATTTT 0.723574 -65 TTATTTTATTGTTTTATTCTGTTTTTTAGT 24 113 1 GTTTTATTCT 0.608896 -52 AAAAGACACCGCTTTATTTTA 25 2 0 GCTTTATTTT 0.865808 -82 GCGCTAATTGCCTTTATACTAAAAGCGGTT 25 52 0 CCTTTATACT 0.776193 -32 ********** Masking position 6 Map Score: 29.2177 Number of sites scoring better than the average of aligned sites = 1584 Number in coding regions = 1243 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 4 TTTTTAAAATTTGGAGTTTTTTCTGGCTTTT 1 108 1 TTGGAGTTTT 0.630591 -98 TTCTGGCTTTTAGGGGGTTTTAAATTCTTTT 1 128 1 TAGGGGTTTT 0.983697 -78 GTTTGATTGATAGGGGTGATTATAGCATTTA 2 38 1 TAGGGGGATT 0.72336 -253 CTCCTTGATTTAGCGGATTTTACCGCATGCA 2 110 0 TAGCGGTTTT 0.9655 -181 TTAAAAATCTTAACCGATTTTTCATA 6 6 0 TAACCGTTTT 0.738581 -83 CGTTAGGAGTTTTTAATCTTAGGC 9 4 1 TAGGAGTTTT 0.945486 -105 GATTTTTCTCTAGGGGCTTTTGTCTCTAGTG 11 246 1 TAGGGGTTTT 0.983697 -55 CCACAAAATTTAAGACATTTTTGTCTTATCG 13 205 0 TAAGACTTTT 0.700562 -96 AAAATGCCTAAGGCGTTTTTCGTTTTGAG 15 9 1 TAAGGCTTTT 0.890582 -145 TGTGGTTGTATAGCCCTTTTTTTACTAAAAA 15 123 0 TAGCCCTTTT 0.818363 -31 ATTTAAGGGTTATTTCAATGAAAA 19 4 1 TAAGGGTATT 0.739097 -75 TTGCTATTTTTAGGGCTTTTTAGAGATTTTT 24 39 0 TAGGGCTTTT 0.9655 -126 ATTGACTAAATGGCGCATTTTGAGTAGTATT 24 75 1 TGGCGCTTTT 0.77701 -90 CGAGTTCTTTTAGGAGAGTTT 24 154 1 TAGGAGGTTT 0.823199 -11 TGTTTTTTTATAACCGCTTTTAGTATAAAGG 25 41 1 TAACCGTTTT 0.738571 -43 TACAATGAAATGGGGGTATTTTAAAAAAATG 26 229 0 TGGGGGATTT 0.614534 -72 ****** **** Masking position 10 Map Score: 14.0119 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1253 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 TGCTTCTTTATTTTCTACTTCTTATGTGCG 1 33 0 TTTTCTACTT 0.810505 -173 TTTGTTCCTTAATTTCCTTA 1 196 0 TTTGTTCCTT 0.821214 -10 TATTTTTCCTTATTCTAAAAA 6 78 0 ATTTTTCCTT 0.765954 -11 CAGAAAGGCCTTTGCGCCTTTCTCTGATCT 7 21 1 TTTGCGCCTT 0.919798 -203 GGCAGATGATTTTGCTCCATGATTTTGTTT 7 56 1 TTTGCTCCAT 0.807874 -168 CTTTTCCTCCTTTCTAGACTAG 9 97 0 TTTCCTCCTT 0.931237 -12 CCATAGTTCCTTTTCGCCCTCACTTAAACT 11 79 0 TTTTCGCCCT 0.778856 -222 TATTCTCCTTATTTAAAGCC 11 291 0 TATTCTCCTT 0.92989 -10 TTGTATTTCTCCTTAATTTTTTGA 13 287 0 ATTTCTCCTT 0.962778 -14 AATGTCTCCTTAATTTTAACC 14 12 0 ATGTCTCCTT 0.803121 -11 CCATTCTCCTTGTGGTTGTAT 15 143 0 CATTCTCCTT 0.850812 -11 GATTTTTCTCCTTTGAAAAAATT 19 66 0 TTTTCTCCTT 0.984834 -13 AACGCTTTCTCCTTTC 21 3 0 CTTTCTCCTT 0.965425 -14 ********** Masking position 10 Map Score: 11.4656 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 112 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 TTAAAATTTGGAGTTTTTTCTGGCTTTTAG 1 111 1 GAGTTTTTTC 0.757012 -95 GTTATGAATTGAGTTTGATTGATAGGGGTG 2 26 1 GAGTTTGATT 0.937224 -265 AATCTGTATCAAGTTTTATTAAGATGCATG 2 86 1 AAGTTTTATT 0.565622 -205 CTAAATCAAGGAGTGTTATTATGGAAGCAG 2 128 1 GAGTGTTATT 0.862817 -163 TTTGCTCCATGATTTTGTTTGTGAGCGTGT 7 66 1 GATTTTGTTT 0.828042 -158 GAATACTTAGGATTTTGTTTAGTATAATTC 13 246 1 GATTTTGTTT 0.828042 -55 GGATTAAATTGAGTTTTATTAGTAATATTA 15 43 0 GAGTTTTATT 0.947775 -111 GATCAAGCGTGATTTTTTCTAAATTTTAGG 17 25 0 GATTTTTTCT 0.765937 -92 GCTTTTTAGAGATTTTTACTTCCTTTTTAT 24 26 0 GATTTTTACT 0.765937 -139 CGGATAAAACGAGTTCTTTTAGGAGAGTTT 24 145 1 GAGTTCTTTT 0.757012 -20 TTTTTTAAGGGAGTGTTTTTTTATAACCGC 25 28 1 GAGTGTTTTT 0.862817 -56 GAGCGTTAAGGAGTTTGACTCATTGAAAAT 26 179 1 GAGTTTGACT 0.893006 -122 ********** Masking position 2 Map Score: 6.62623 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 218 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TGCTATAATCACCCCTATCAATCAAACTCA 2 35 0 ACCCCTATCA 0.752185 -256 TTTCCCCTAAAGCCCTATCAAAGATTAAAT 4 54 0 AGCCCTATCA 0.959084 -24 GAAGATCGTAAGAGCTAAAAAGCTTAAAAT 9 36 1 AGAGCTAAAA 0.747567 -73 GGTGGTGGTGAGCGCTATCACGCTGTTTTT 11 206 1 AGCGCTATCA 0.971933 -95 TAGCAAAAAGAGAGTTACCATAAAGGGTCA 12 14 1 AGAGTTACCA 0.728199 -22 CTAGAGCATCAGCCTTCCAAGCTGAGGGTC 13 22 1 AGCCTTCCAA 0.668804 -279 ATCTCTAAAAAGCCCTAAAAATAGCAAAAG 24 43 1 AGCCCTAAAA 0.92061 -122 AAAGGCAATTAGCGCTACAATACCCCC 25 67 1 AGCGCTACAA 0.980657 -17 TTTTTTAAGGAGCGTTATAATGAAAACGAA 26 52 0 AGCGTTATAA 0.900186 -249 CCGCTCATTAAGCGCTACAATACCCCCATG 26 105 1 AGCGCTACAA 0.980657 -196 ********** Masking position 6 Map Score: 5.36887 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 468 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 AGAATACCTTAAAAGAATTTAAAACCCCCT 1 139 0 AAAAGAATTT 0.84604 -67 TATAGTTGGAAAAAGGAATAATGCGAACAA 2 232 1 AAAAGGAATA 0.676807 -59 AATTTAGTTTAAAAGGTTTTTACAAAC 4 8 0 AAAAGGTTTT 0.941979 -70 TAAGCATTGCAAAAGGATCTTTAAACTTTA 7 153 0 AAAAGGATCT 0.830862 -71 ATCTTTTTAAAAAAGAAATTTTAAGCTTTT 9 53 0 AAAAGAAATT 0.830938 -56 TTCTTTTTTAAAAAGATAATCTTGCAGAGG 9 66 1 AAAAGATAAT 0.617089 -43 TTTATACATTAAAAGAATTTTTAATTCTAT 11 42 0 AAAAGAATTT 0.84604 -259 AGTGAGGGCGAAAAGGAACTATGGATAAAT 11 85 1 AAAAGGAACT 0.814294 -216 TAATTTTTTGAAATGGATTTTAGAATTATA 13 268 0 AAATGGATTT 0.555182 -33 AGGTATAATCAAAAGTTTTTTAGACCTTGC 15 90 1 AAAAGTTTTT 0.790497 -64 ATGTTAATATAAAAGTTTTTAGTAGTGCCT 19 36 1 AAAAGTTTTT 0.790497 -43 TTTCCTTATAAAAAGGAAGTAAAAATCTCT 24 19 1 AAAAGGAAGT 0.704373 -146 TAAAAATAGCAAAAGTTATTGACTAAATGG 24 58 1 AAAAGTTATT 0.774342 -107 CTATGAAAAGGTTTTCTAAAACTTC 26 6 1 AAAAGGTTTT 0.941979 -295 CCCATGCAAAAAAAGATTTTTTTATTAGAA 26 129 1 AAAAGATTTT 0.857119 -172 GCTCTCGCTTAAAAGGTAATCGTCTTCTAA 26 153 0 AAAAGGTAAT 0.819842 -148 GAAGTTTAATAAAAGGTAAAAATAAGA 26 284 1 AAAAGGTAAA 0.407098 -17 ********** Masking position 3 Map Score: 14.3308 Number of sites scoring better than the average of aligned sites = 951 Number in coding regions = 794 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 9 GATTCTACTTTTTTTGCCCCATAAATGCTAT 2 59 0 TTTTTCCCCA 0.718926 -232 GATTTAGCGGATTTTACCGCATGCATCTTAA 2 104 0 ATTTTCCGCA 0.720582 -187 GTAATTTGTAATTATACTCTTTATTTTGAAT 3 22 0 ATTATCTCTT 0.59031 -39 CTATTTTCCCCTAAAGCCCTATC 4 65 0 ATTTTCCCTA 0.955891 -13 TTTTACCCTAATTTTTCTTTTAAAAATCTTA 6 25 0 ATTTTCTTTT 0.652926 -64 AAGTTCCCCCATTTTACCCTAATTTTTCTTT 6 36 0 ATTTTCCCTA 0.955891 -53 TATTTTTCCTTATTCTAAAAAT 6 77 0 ATTTTCCTTA 0.750686 -12 GCGGCAGATGATTTTGCTCCATGATTTTGTT 7 54 1 ATTTTCTCCA 0.94112 -170 CTTTTCCTCCTTTCTAGACTA 9 98 0 CTTTTCTCCT 0.703135 -11 GCTTTGTTGGATTTTTCTCTAGGGGCTTTTG 11 237 1 ATTTTCTCTA 0.940068 -64 AATTTAAGACATTTTTGTCTTATCGCCATTC 13 199 0 ATTTTGTCTT 0.590145 -102 GATTTTTCTCCTTTGAAAAAAT 19 67 0 ATTTTCTCCT 0.932419 -12 TCTTATTTTTACCTTTTATTAAACT 26 286 0 ATTTTACCTT 0.573056 -15 ***** ***** Masking position 5 Map Score: 5.41568 Number of sites scoring better than the average of aligned sites = 406 Number in coding regions = 356 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 TTTTCAGTATTTTTAAAGGATTAAAAAGCTAA 1 68 0 TTTTAGGATT 0.571215 -138 CATTGAGATAGTTTTAAGGAAATTAAGGAACA 1 182 1 GTTTAGGAAA 0.555755 -24 TATTAGGATTTTTTGAAGAAAATCAAAACAAT 2 170 1 TTTTAGAAAA 0.62869 -121 AATTATACTCTTTATTTTGAATAAGTTGGGTT 3 12 0 TTTATTGAAT 0.398499 -49 TTAATTTTTGTTTTAATTTAAAGGGATAAAAC 5 13 1 TTTTTTTAAA 0.470135 -22 GGTTAAGATTTTTAAAAGAAAAATTAGGGTAA 6 22 1 TTTAAGAAAA 0.399356 -67 TGGGGGAACTTTTAGTTTTAAATTTTTAGAAT 6 56 1 TTTATTTAAA 0.424571 -33 CTTCACATTTTTTTAAATTAAAGCCATCACAG 8 15 0 TTTTATTAAA 0.648066 -31 TTGGGTTTTGTTGGAATTGAAAGAAAT 10 6 1 TTTTTGGAAT 0.686466 -39 TTGAAAGAAATTTTTAAGGATTAGAATC 10 27 1 TTTTAGGATT 0.571215 -18 TTAAAAATTCTTTTAATGTATAAATGTATTAA 11 48 1 TTTTTGTATA 0.388285 -253 GTATCTGCTCTTTAATAGGAAATATCACTTTA 11 152 0 TTTAAGGAAA 0.850064 -149 TGAAATGGATTTTAGAATTATACTAAACAAAA 13 258 0 TTTAATTATA 0.332653 -43 TAAATTGAGTTTTATTAGTAATATTAAAGCTC 15 37 0 TTTAAGTAAT 0.668038 -117 TTTCGCTTGTTTTTGGATTAAATTGAGTTTTA 15 55 0 TTTTATTAAA 0.751561 -99 GACCTTGCTCTTTTTTAGTAAAAAAAGGGCTA 15 112 1 TTTTAGTAAA 0.860269 -42 TATTAACATATTTTCATTGAAATAACCCTTAA 19 13 0 TTTTTTGAAA 0.686297 -66 ATCAGCTTGATTTAAGAGGAATAAGTTATT 20 23 1 TTTAAGGAAT 0.798315 -20 TTACTTCCTTTTTATAAGGAAATATAAAAA 24 9 0 TTTAAGGAAA 0.904882 -156 TTTTATTCTGTTTTTTAGTAACGGATAAAACG 24 124 1 TTTTAGTAAC 0.46959 -41 ATGAAAGAATTTTACAATGAAATGGGGGTATT 26 240 0 TTTAATGAAA 0.761463 -61 CTTCAATGGGTTTTGCATGAAAGAATTTTACA 26 256 0 TTTTATGAAA 0.855906 -45 **** ****** Masking position 3 Map Score: 12.1642 Number of sites scoring better than the average of aligned sites = 786 Number in coding regions = 629 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 11 CCTTTTTCCAACTATACAACCTCTGATAGAT 2 217 0 ACTATACACC 0.954403 -74 ATTAAATGCTATAATACTACCCTAATTTAGT 4 30 0 ATAATACACC 0.93975 -48 AAACCCACCTGCAATACTAACCACTTTAGGC 7 97 0 GCAATACAAC 0.78334 -127 TAAAAAAAGGGCTATACAACCACAAGGAGAA 15 130 1 GCTATACACC 0.922196 -24 AATTAGCGCTACAATACCCCC 25 73 1 ACAATACCCC 0.985724 -11 GGGCTTTGTTATAATACTTCCTATGTTTTTT 26 76 0 ATAATACTCC 0.825806 -225 ATTAAGCGCTACAATACCCCCATGCAAAAAA 26 111 1 ACAATACCCC 0.985724 -190 TCATTTTTTTAAAATACCCCCATTTCATTGT 26 228 1 AAAATACCCC 0.914395 -73 ******* *** Masking position 6 Map Score: 4.23573 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 GTTTTTTCTGGCTTTTAGGGGGTTTTAAAT 1 123 1 GCTTTTAGGG 0.94555 -83 GGTGATTATAGCATTTATGGGGCAAAAAAA 2 52 1 GCATTTATGG 0.950763 -239 TCTTTGATAGGGCTTTAGGGGAAAATAG 4 60 1 GGCTTTAGGG 0.919536 -18 AATGACCCTTTATGGTAACTCTCTT 12 21 0 CCCTTTATGG 0.784424 -15 TTTTGTGGTAGCATTTAGGAATACTTAGGA 13 228 1 GCATTTAGGA 0.864787 -73 TAAATTTTAGGCATTTAAGGAATCA 17 6 0 GCATTTAAGG 0.950841 -111 ACCACCGCCTTTAACGCACCACGCTT 17 101 0 GCCTTTAACG 0.892107 -16 TAGTATAAAGGCAATTAGCGCTACAATACC 25 61 1 GCAATTAGCG 0.784106 -23 ********** Masking position 7 Map Score: 1.21781 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 411 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 AGTATTTTTAAAGGATTAAAAAGCTAAAAT 1 65 0 AAGGATTAAA 0.884081 -141 AAAAAATGTGAAGGATTGGATT 8 34 1 AAGGATTGGA 0.958926 -12 AGAAATTTTTAAGGATTAGAATC 10 32 1 AAGGATTAGA 0.97549 -13 ATATAATATAAAGGGTTTGAT 22 24 1 AAGGGTTTGA 0.944457 -11 ATAATAAAATAAGGGTTAGAT 23 26 1 AAGGGTTAGA 0.977254 -11 ********** Masking position 6 Map Score: 1.79711 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 27 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 14 ATCCCATAATTGTTCGCATTATTCCTTTTT 2 241 0 TGTTCGCATT 0.769317 -50 TTATAAAAATTGGTGGGAATGATAAG 2 275 1 TGGTGGGAAT 0.793212 -16 ATTTTGAATAAGTTGGGTTT 3 1 0 AGTTGGGTTT 0.856581 -60 TTAGTATTGCAGGTGGGTTTTTGGTATTTT 7 108 1 AGGTGGGTTT 0.90452 -116 GAGCCTGTGATGGCTTTAATTTAAAAA 8 8 1 TGATGGCTTT 0.882978 -38 TTGGGTTTTGTTGGAATTGAAAGAAATT 10 9 1 TGTTGGAATT 0.871937 -36 TTTTTAGCTTTGTTGGATTTTTCTCTAGGG 11 231 1 TGTTGGATTT 0.893485 -70 TTCTATAGGTTGGTGGCTTTAAATAAGGAG 11 277 1 TGGTGGCTTT 0.975233 -24 TTAAATTTTGTGGTAGCATTTAGGAATACT 13 223 1 TGGTAGCATT 0.781135 -78 ********** Masking position 4 Map Score: 1.02392 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 341 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 ********** No masking Map Score: -6.49903e-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