AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_fla_operon_hpyl_reg_300.orf -o259_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: RHP00445 140 AE000511 RHP00808 16 AE000511 Input sequences: #1 RHP01127 300 AE000511 #2 RHP01289 259 AE000511 #3 RHP01290 43 AE000511 #4 RHP01291 17 AE000511 #5 RHP00195 87 AE000511 #6 RHP00290 207 AE000511 #7 RHP00291 300 AE000511 #8 RHP00443 128 AE000511 #9 RHP00444 30 AE000511 #10 RHP00446 140 AE000511 #11 RHP00809 24 AE000511 #12 RHP00810 101 AE000511 #13 RHP00937 207 AE000511 #14 RHP00960 126 AE000511 #15 RHP00962 64 AE000511 #16 RHP00963 179 AE000511 Motif number 1 AAAAAAAATGTTAAAGAAGATTCAAAAATTCTCGATGC 1 97 1 TTAAAATAAA 0.968355 -204 TAATATGGGATAACATGCAATGCTAAAAAACCAAATAT 1 208 0 TAACAATAAA 0.684133 -93 TTTTTGCTTCTTAAATTGTAGTCTAAAAAGGGTTAAAA 2 31 1 TTAAAAGAAA 0.930634 -229 AGGGCAAAAATTAAAGCGATTTCAAAAAAAAAAAAAAA 2 80 1 TTAAATTAAA 0.956611 -180 AAAATTGCTCTTAAAAGTTTTAAGACAATGAAGTTTAA 2 172 0 TTAAATTAAA 0.95661 -88 CACTAAAAGCTTAAATAAAAGGGCATAAGGGATAAAGG 5 13 0 TTAAAAGAAA 0.929956 -75 ATAACGCTTTTTAAAGGTTATCGCTCAAGCTTAAGAAT 6 21 0 TTAAAATTAA 0.854034 -187 AAAGTTGTTCCTAAATAGCTTTTTAGAATGATTGGTTG 6 134 0 CTAAATTAAA 0.881251 -74 TTTTAAAAAATTAAATAGCTTGCACTAAGCAGGCGATA 7 68 0 TTAAATTCAA 0.896984 -233 TTAAAAAAGCTAAAAGAATTTTTTAAAAAATTAAATAG 7 88 0 TAAAATTAAA 0.949315 -213 AACCTATTTTTAAAAAGAGATTTTTGAATACTAACTAG 7 147 0 TAAAAATTAA 0.832542 -154 ACTAATAAGTTAAAATTCATTAAAATAATCATAATGAT 7 195 1 TAAAATTAAA 0.949323 -106 ATTAAAGATTTTAACCACTATTGTAGAAAAATAACAAG 7 231 1 TTAACATAAA 0.71791 -70 AAAACTCTCATTAAAAACAAGGAGCAAAAAAG 7 279 1 TTAAAAGCAA 0.841242 -22 AGGGGTAAGATAAAAACTTATGCTATAATGTGGTCTCA 8 73 1 TAAAAATAAA 0.962952 -56 TATCATACGCTTAAACTTTATATTATAATAAGCCTAAA 10 72 1 TTAAAATAAA 0.967149 -69 AATCTAAAATCAATGCCTTAATCTGGTAGGT 10 120 0 CTAAAATTAA 0.663049 -21 GGATAAAAACTTAAAGAATAGGGTAAAATAAACGC 12 77 1 TTAAAAGAAA 0.929727 -25 AAAATACCCATAAAATACCTTAAGAGAACGCCTATTCA 13 35 0 TAAAATTAAA 0.949327 -173 TCATAACATGCAAAAAGCATTCCAATAATCGGCTCGTT 13 149 0 CAAAATTAAA 0.863126 -59 AATAAAACCCCTTTTTCAAACCCTTGCAAA 13 188 0 TAAAATTCAA 0.880937 -20 GTTACAATTCCAAAAATCATTATTATAAAATAAAGGAT 14 95 1 CAAAATTAAA 0.863123 -32 AGATTTTAAAATACAAGCCAACAAGGTATAATTC 15 7 1 TAAAAAGAAA 0.919374 -58 CCCTTTAAACTAAAACTTAATAACCTAAAATTGTAACC 16 146 0 TAAAAATCAA 0.911265 -34 ***** ** * ** Masking position 3 Map Score: 31.2186 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 503 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 ATTCAAAGCGGGTAAAAGTGTTCGCCT 1 6 1 AAGGGTAAAA 0.792444 -295 GAATAAAACTAACACCAAAAAAGACAATAAAT 1 54 0 AACCAAAAAA 0.854037 -247 TTTCTTTCCAAAAAGAATAAAACTAACACCAA 1 68 0 AAGAATAAAA 0.788883 -233 TTCTTTTTGGAAAGAAAAAAAATGTTAAAGAA 1 83 1 AAAAAAAAAA 0.541207 -218 ACTACAATTTAAGAAGCAAAAATTAAAGGAAC 2 21 0 AAAGCAAAAA 0.860307 -239 TGTAGTCTAAAAAGGGTTAAAAAGCTTTAAAA 2 47 1 AAGGTTAAAA 0.886504 -213 CGATTTCAAAAAAAAAAAAAAACAATTTCAGT 2 96 1 AAAAAAAAAA 0.541207 -164 AATGAAGTTTAAACACATAAAAGCTTTTCATT 2 152 0 AAACATAAAA 0.907688 -108 GTTTTGAATGAACTACTAAAAAAAGGGTTTTA 2 234 1 AAACTAAAAA 0.779689 -26 ACGAACGGCTTAAAAGAATGAAAAT 3 4 1 AAGCTTAAAA 0.918104 -40 GACAAGTATCAACCCCCTAAGATCGCATGGTG 7 30 1 AACCCTAAGA 0.865966 -271 GATAACATTAAAAAAGCTAAAAGAATTTTTTA 7 101 0 AAAGCTAAAA 0.937701 -200 TTTGAATACTAACTAGAAAAAAATTAAATTGA 7 131 0 AAAGAAAAAA 0.737058 -170 AATAAGTTAAAATTCATTAAAATAATCATAAT 7 198 1 AACATTAAAA 0.786707 -103 CATTAAAAACAAGGAGCAAAAAAG 7 287 1 AAAGCAAAAA 0.860307 -14 TACCCCTTAAATCCCCCTAAGAACGAATCACA 8 48 0 ATCCCTAAGA 0.457976 -81 CCACACCCTAAAACCGATAAAAA 9 2 0 AACGATAAAA 0.908789 -29 TTATATTATAATAAGCCTAAAAAGACAAACCA 10 89 1 ATGCCTAAAA 0.785487 -52 ACAAATTCCTTAAAAAGAGTGGTGG 12 4 1 AACCTTAAAA 0.926359 -98 GCTGAATGCTAACATGCTAAAACTAAAACCCT 12 35 1 AATGCTAAAA 0.656651 -67 AAACTTAAAGAATAGGGTAAAATAAACGC 12 83 1 AAGGGTAAAA 0.792444 -19 ACGCCTATTCAAAAACCAAAAATAAGGAAATC 13 14 0 AAACCAAAAA 0.898365 -194 ATACCCATAAAATACCTTAAGAGAACGCCTAT 13 38 0 AACCTTAAGA 0.721202 -170 GAAAATACTAAATCCAATAAAAA 14 2 0 AACAATAAAA 0.807431 -125 CGCATGATAAAACGCCCTAAAATTTATCAATA 16 29 1 AACCCTAAAA 0.969153 -151 ATTTTGAGGCAAGAGCTTAAAAAAGAGGGTGT 16 77 1 AAGCTTAAAA 0.918104 -103 ATAAGATTAAATTTGACTAAAACGCGCTTTTT 16 111 0 ATGACTAAAA 0.517757 -69 ACTAAAACTTAATAACCTAAAATTGTAACCAA 16 144 0 AAACCTAAAA 0.955758 -36 ** ******** Masking position 9 Map Score: 26.401 Number of sites scoring better than the average of aligned sites = 2347 Number in coding regions = 1989 Number in noncoding regions = 358 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 3 TTAACCCTTTTTAGACTACAATTTAAGAAGCA 2 35 0 TTAGCTAAAT 0.946741 -225 ATTAGCTAGGTTTGATTAAAATGAAAAGCTTT 2 133 1 TTTGTTAAAT 0.702866 -127 GTTTATTATGTTACACTAAAAGCTTAAATAAA 5 32 0 TTACCTAAAG 0.803304 -56 GGTTATCCTTTAATTTAAAGAAAT 6 194 0 TTATCTTAAT 0.894111 -14 CCTCTTGTTATTTTTCTACAATAGTGGTTAAA 7 240 0 TTTTCTAAAT 0.950343 -61 AGATAAAAACTTATGCTATAATGTGGTCTCAT 8 80 1 TTATCTAAAT 0.976383 -49 AAAGCTTATTTTACGCTATAATGCGAACTTTA 10 36 0 TTACCTAAAT 0.962816 -105 CGCTTAAACTTTATATTATAATAAGCCTAAAA 10 79 1 TTATTTAAAT 0.922381 -62 TATGGGTATTTTACACTATAATGGCTCTGAAT 13 61 1 TTACCTAAAT 0.962816 -147 TCAAGCTATCTTTTGCTATAATAGTGAAAATA 14 27 0 TTTTCTAAAT 0.950345 -100 GAGGCGGGTTTTATGTTACAATTCCAAAAATC 14 81 1 TTATTTAAAT 0.922381 -46 GACTATCCTTTATTTTATAATAATGATTTTT 14 106 0 TTATTTAAAT 0.922381 -21 TGGGTGGTGTTTTTGCTTGAATTATACCTTGT 15 31 0 TTTTCTTAAT 0.796293 -34 **** *** *** Masking position 10 Map Score: 15.8911 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 95 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 CTACTAAAAAAAGGGTTTTAAATA 2 246 1 AAGGGTTTTA 0.97636 -14 TAAGAAAATAGGGGGTTTTGCAACACCACC 6 61 0 GGGGGTTTTG 0.946316 -147 ATGATTGGTTGCGGATTTTAAAGTTTTGTT 6 115 0 GCGGATTTTA 0.778939 -93 TGTCAAAATAAAGCGTTTTATAA 7 4 0 AAGCGTTTTA 0.915313 -297 ATGCGATCTTAGGGGGTTGATACTTGTCAA 7 28 0 AGGGGGTTGA 0.85356 -273 AAAATAACAAGAGGGTTTGCAAAAACTCTC 7 258 1 GAGGGTTTGC 0.8694 -43 CATCAAGGGGTTTGACATTAGTCAA 8 6 1 AGGGGTTTGA 0.975584 -123 TTCGTTCTTAGGGGGATTTAAGGGGTAAGA 8 53 1 GGGGGATTTA 0.922441 -76 CATAACTTATAAGGGTTTTAGTTTTAGCAT 12 48 0 AAGGGTTTTA 0.97636 -54 ATGAATTTGCAAGGGTTTGAAAAAGGGGTT 13 183 1 AAGGGTTTGA 0.961486 -25 GGTTTGAAAAAGGGGTTTTATT 13 196 1 AGGGGTTTTA 0.985098 -12 GGTGTAAGAGGCGGGTTTTATGTTACAATT 14 74 1 GCGGGTTTTA 0.984196 -53 ATAAATTTTAGGGCGTTTTATCATGCGCTT 16 26 0 GGGCGTTTTA 0.969346 -154 GCTTAAAAAAGAGGGTGTTAAAAAAGCGCG 16 91 1 GAGGGTGTTA 0.911061 -89 TGTTAAAAAAGCGCGTTTTAGTCAAATTTA 16 106 1 GCGCGTTTTA 0.942185 -74 ********** Masking position 8 Map Score: 24.3164 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 569 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 ATTCAAAGCGGGTAAAAGTGTTCG 1 5 1 AAAGCGGGTA 0.470632 -296 ATTGTAGTCTAAAAAGGGTTAAAAAGCTTT 2 45 1 AAAAAGGGTT 0.963266 -215 AAAAAGGGTTAAAAAGCTTTAAAAGAGGGC 2 55 1 AAAAAGCTTT 0.46353 -205 GAACTACTAAAAAAAGGGTTTTAAATA 2 243 1 AAAAAGGGTT 0.963266 -17 AAGATAGAAGGTTAAAA 4 4 1 ATAGAAGGTT 0.384475 -14 GATAACCTTTAAAAAGCGTTATGGGGTGGT 6 37 1 AAAAAGCGTT 0.948722 -171 TCATAAGAAAATAGGGGGTTTTGCAACACC 6 64 0 ATAGGGGGTT 0.906842 -144 ACTTGTCAAAATAAAGCGTTTTATAA 7 7 0 ATAAAGCGTT 0.872865 -294 CCATGCGATCTTAGGGGGTTGATACTTGTC 7 30 0 TTAGGGGGTT 0.677894 -271 AGAAAAATAACAAGAGGGTTTGCAAAAACT 7 255 1 CAAGAGGGTT 0.82866 -46 CCTTGTTTTTAATGAGAGTTTTTGCAAACC 7 271 0 AATGAGAGTT 0.518148 -30 CAAATTCCTTAAAAAGAGTGGTGGCTGAAT 12 12 1 AAAAAGAGTG 0.443882 -90 ATCCATAACTTATAAGGGTTTTAGTTTTAG 12 51 0 TATAAGGGTT 0.534999 -51 TTGGTTTTTGAATAGGCGTTCTCTTAAGGT 13 27 1 AATAGGCGTT 0.7209 -181 CATAACATGCAAAAAGCATTCCAATAATCG 13 156 0 AAAAAGCATT 0.463568 -52 AAGGGTTTGAAAAAGGGGTTTTATT 13 193 1 AAAAGGGGTT 0.947474 -15 TTGATAAATTTTAGGGCGTTTTATCATGCG 16 29 0 TTAGGGCGTT 0.59758 -151 AGAGCTTAAAAAAGAGGGTGTTAAAAAAGC 16 88 1 AAAGAGGGTG 0.893103 -92 GGGTGTTAAAAAAGCGCGTTTTAGTCAAAT 16 103 1 AAAGCGCGTT 0.880443 -77 ********** Masking position 9 Map Score: 13.3832 Number of sites scoring better than the average of aligned sites = 1982 Number in coding regions = 1679 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 6 GCATCGAGAATTTTTGAATCTTCTTTAACA 1 105 0 TTTTTGAATC 0.892135 -196 TTCGTAATTATTGTTGTATGCATTCTCTTT 1 151 1 TTGTTGTATG 0.728588 -150 GTTCCTTTAATTTTTGCTTCTTAAATTGTA 2 21 1 TTTTTGCTTC 0.718486 -239 ATTGTTTTTTTTTTTTTTTGAAATCGCTTT 2 92 0 TTTTTTTTTG 0.551353 -168 TATAATATCCGTTTTGAATGAACTACTAAA 2 224 1 GTTTTGAATG 0.788227 -36 TGTTAAGTCGTTGTTTATTATGTTACACTA 5 46 0 TTGTTTATTA 0.246502 -42 TTGGTCGATCTTTTTGATTAACAAAACTTT 6 96 1 TTTTTGATTA 0.784716 -112 CTAAATAGCTTTTTAGAATGATTGGTTGCG 6 132 0 TTTTAGAATG 0.867526 -76 TTCTTTTAGCTTTTTTAATGTTATCAATTT 7 108 1 TTTTTTAATG 0.863963 -193 TAAAAAGAGATTTTTGAATACTAACTAGAA 7 145 0 TTTTTGAATA 0.898414 -156 TTTGCTCCTTGTTTTTAATGAGAGTTTTTG 7 277 0 GTTTTTAATG 0.54027 -24 TTATTTCTCCTTGTTTAATATGGAATGAGA 8 106 0 TTGTTTAATA 0.442509 -23 AAAATAAGCTTTTTTGTATCATACGCTTAA 10 56 1 TTTTTGTATC 0.795214 -85 AGGGTTTTAGTTTTAGCATGTTAGCATTCA 12 37 0 TTTTAGCATG 0.830596 -65 TTATTTTTGGTTTTTGAATAGGCGTTCTCT 13 21 1 TTTTTGAATA 0.898414 -187 ATTGGAATGCTTTTTGCATGTTATGAATTT 13 161 1 TTTTTGCATG 0.937733 -47 CTATCCTTTATTTTATAATAATGATTTTTG 14 105 0 TTTTATAATA 0.476103 -22 TTGGGTGGTGTTTTTGCTTGAATTATACCT 15 34 0 TTTTTGCTTG 0.861245 -31 ATGCGCTTTCTTTTTGTATCCAT 16 4 0 TTTTTGTATC 0.795214 -176 TTTTAGGGCGTTTTATCATGCGCTTTCTTT 16 21 0 TTTTATCATG 0.607547 -159 GGTTATTAAGTTTTAGTTTAAAGGGAAAAT 16 159 1 TTTTAGTTTA 0.357802 -21 ********** Masking position 4 Map Score: 17.3173 Number of sites scoring better than the average of aligned sites = 1566 Number in coding regions = 1382 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 7 CTCGATGCAATTATGAATATAATATTCGTA 1 127 1 TTATGAATAT 0.964551 -174 ACAACAATAATTACGAATATTATATTCATA 1 138 0 TTACGAATAT 0.864194 -163 CATAGTAAGCTTATCAATATGAGATTGATT 1 266 0 TTATCAATAT 0.933461 -35 CCCTATTTTCTTATGAATTTGGTCGATCTT 6 78 1 TTATGAATTT 0.956718 -130 TTTTTTAATGTTATCAATTTAATTTTTTTC 7 118 1 TTATCAATTT 0.919302 -183 ATGATTATTTTAATGAATTTTAACTTATTA 7 197 0 TAATGAATTT 0.777029 -104 TCTTTAATCATTATGATTATTTTAATGAAT 7 209 0 TTATGATTAT 0.811089 -92 TTTTTGCATGTTATGAATTTGCAAGGGTTT 13 171 1 TTATGAATTT 0.956718 -37 GCCCTAAAATTTATCAATAGCGTCAAGTAT 16 42 1 TTATCAATAG 0.766297 -138 ********** Masking position 6 Map Score: 7.78698 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 62 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TTCTTTCCAAAAAGAATAAAACTAACACCAA 1 68 0 AAAGAAAAAA 0.653792 -233 TTCTTTTTGGAAAGAAAAAAAATGTTAAAGA 1 83 1 AAAGAAAAAA 0.653792 -218 CCTGGTAACCAAGGAAAGAGAATGCATACAA 1 164 0 AAGGAAGAGA 0.936708 -137 GCAAAAATTAAAGGAACGCAATAACTT 2 7 0 AAGGAAGCAA 0.919544 -253 AAAAGCTTTAAAAGAGGGCAAAAATTAAAGC 2 66 1 AAAGAGGCAA 0.771153 -194 AGAGGGCAAAAATTAAAGCGATTTCAAAAAA 2 78 1 AATTAAGCGA 0.601836 -182 GAACGGCTTAAAAGAATGAAAATTTTATCAA 3 13 1 AAAGAAGAAA 0.946217 -31 AATCTATGCAAAATAAAGCAAAAGTTGTTCC 6 161 0 AAATAAGCAA 0.877134 -47 ATACTTGTCAAAATAAAGCGTTTTATAA 7 8 0 AAATAAGCGT 0.581369 -293 CTCTCATTAAAAACAAGGAGCAAAAAAG 7 283 1 AAACAAGAGC 0.689878 -18 CTTGTTTAATATGGAATGAGACCACATTATA 8 96 0 ATGGAAGAGA 0.575341 -33 ATTCCATATTAAACAAGGAGAAATAAATA 8 110 1 AAACAAGAGA 0.884578 -19 CAAAAACCAAAAATAAGGAAATCCTA 13 6 0 AAATAAGAAA 0.834903 -202 TTTTCTCATCAAAGAATGCGATCAATTCAAA 13 120 0 AAAGAAGCGA 0.978448 -88 ATGGATACAAAAAGAAAGCGCATGATAAAAC 16 11 1 AAAGAAGCGC 0.929468 -169 ****** **** Masking position 5 Map Score: 8.84043 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 728 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 AAAATTCGTTGGCGTATAATATCCGTTTTGA 2 210 1 GGCGTATATA 0.971566 -50 TTAAGCTTTTAGTGTAACATAATAAACAACG 5 37 1 AGTGTAAATA 0.916502 -51 GTCAAAATAAAGCGTTTTATAA 7 2 0 AGCGTTTATA 0.871011 -299 GGGGATTTAAGGGGTAAGATAAAAACTTATG 8 64 1 GGGGTAAATA 0.923599 -65 TTCGCATTATAGCGTAAAATAAGCTTTTTTG 10 41 1 AGCGTAAATA 0.979588 -100 ATAAAGTTTAAGCGTATGATACAAAAAAGCT 10 62 0 AGCGTATATA 0.979588 -79 TGTCTTTTTAGGCTTATTATAATATAAAGTT 10 85 0 GGCTTATATA 0.749074 -56 CTTAAAGAATAGGGTAAAATAAACGC 12 86 1 AGGGTAAATA 0.944379 -16 GAGCCATTATAGTGTAAAATACCCATAAAAT 13 57 0 AGTGTAAATA 0.916503 -151 ACAAAAAGAAAGCGCATGATAAAACGCCCTA 16 17 1 AGCGCATATA 0.909159 -163 ******* *** Masking position 9 Map Score: 11.2513 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 8 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 AGTCCCTTAATCTTACATAGTAAGC 1 286 0 CTTAATCTTA 0.947263 -15 TGCCCTTTTATTTAAGCTTTTAGTGTAACA 5 26 1 TTTAAGCTTT 0.883436 -62 GAGTTAGATTCTTAAGCTTGAGCGATAACC 6 14 1 CTTAAGCTTG 0.965429 -194 TAGCATAAGTTTTTATCTTACCCCTTAAAT 8 68 0 TTTTATCTTA 0.518904 -61 GTATCATACGCTTAAACTTTATATTATAAT 10 71 1 CTTAAACTTT 0.77289 -70 GGTTTGTCTTTTTAGGCTTATTATAATATA 10 90 0 TTTAGGCTTA 0.809283 -51 AAATCAATGCCTTAATCTGGTAGGTGGTTT 10 115 0 CTTAATCTGG 0.818958 -26 TGATTAATCCTTAGTCTTTTGTCT 11 6 0 CTTAGTCTTT 0.855729 -19 TCAAAGCATGCTTAAGCTTGAGCGATAAGC 13 95 0 CTTAAGCTTG 0.965429 -113 TTTAGTCAAATTTAATCTTATCTTGGTTAC 16 122 1 TTTAATCTTA 0.884598 -58 ********** Masking position 3 Map Score: 4.44337 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 133 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 TTAATTTTTGCCCTCTTTTAAAGCTTTTTA 2 64 0 CCCTCTTTTA 0.917981 -196 TATTTAAAACCCTTTTTTTAGTAGTTCAT 2 241 0 CCCTTTTTTT 0.971732 -19 ATCCCTTATGCCCTTTTATTTAAGCTTTTA 5 18 1 CCCTTTTATT 0.844214 -70 TTGCAAAACCCCCTATTTTCTTATGAATTT 6 68 1 CCCTATTTTC 0.950609 -140 ACTTTTAGTAACCTATTTTTAAAAAGAGAT 7 164 0 ACCTATTTTT 0.779098 -137 TTTTTGCAAACCCTCTTGTTATTTTTCTAC 7 253 0 CCCTCTTGTT 0.943144 -48 ATTCAGCCACCACTCTTTTTAAGGAATTTG 12 12 0 CACTCTTTTT 0.848351 -90 GTTTATTTTACCCTATTCTTTAAGTTTTTA 12 80 0 CCCTATTCTT 0.912726 -22 TAGGATTTCCTTATTTTTGGTTTTTGAA 13 9 1 CCTTATTTTT 0.779098 -199 AATAAAACCCCTTTTTCAAACCCTTGC 13 191 0 CCCCTTTTTC 0.735699 -17 TTTTTTAACACCCTCTTTTTTAAGCTCTTG 16 86 0 CCCTCTTTTT 0.986111 -94 ********** Masking position 6 Map Score: 10.2373 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 402 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 12 CTAAGATCGCATGGTGAAAAATTATCGCCT 7 46 1 ATGGTGAAAA 0.864809 -255 AGTTCGCATTATAGCGTAAAATAAGCTTTT 10 39 1 ATAGCGTAAA 0.972403 -102 AACTTAAAGAATAGGGTAAAATAAACGC 12 84 1 ATAGGGTAAA 0.950365 -18 CAGAGCCATTATAGTGTAAAATACCCATAA 13 60 0 ATAGTGTAAA 0.970275 -148 TTTTGCTATAATAGTGAAAATACTAAATCC 14 19 0 ATAGTGAAAA 0.945931 -108 AAATTTATCAATAGCGTCAAGTATCGGTTA 16 48 1 ATAGCGTCAA 0.927973 -132 ********** Masking position 2 Map Score: 2.87 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 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 Motif number 13 ********** No masking Map Score: 2.70249e-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: 2.70249e-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 GCATTGCATGTTATCCCATATTAAATAACT 1 223 1 TTATCCCATA 0.885897 -78 TCCCTTTATCCCTTATGCCCTTTTA 5 6 1 TTATCCCTTA 0.965434 -82 TTTTTAAAGGTTATCGCTCAAGCTTAAGAA 6 22 0 TTATCGCTCA 0.906355 -186 GGTTATCCTTTAATTTAAAGAA 6 196 0 TTATCCTTTA 0.795108 -12 TGGTGAAAAATTATCGCCTGCTTAGTGCAA 7 57 1 TTATCGCCTG 0.784862 -244 TCACAAGAAACTACCGCTTGACTAATGTCA 8 23 0 CTACCGCTTG 0.652229 -106 AGTTTTTATCTTACCCCTTAAATCCCCCTA 8 61 0 TTACCCCTTA 0.906365 -68 TGAGACCACATTATAGCATAAGTTTTTATC 8 81 0 TTATAGCATA 0.631528 -48 AAAGTTCGCATTATAGCGTAAAATAAGCTT 10 37 1 TTATAGCGTA 0.590258 -104 CTGAATTGGCTTATCGCTCAAGCTTAAGCA 13 87 1 TTATCGCTCA 0.906355 -121 GACTATCCTTTATTTTATAATA 14 115 0 CTATCCTTTA 0.573546 -12 TTTGCTTGAATTATACCTTGTTGGCTTGTA 15 22 0 TTATACCTTG 0.775123 -43 ********** Masking position 3 Map Score: 3.99052 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 528 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312