AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i035_mjan_pyro_300.orf -o035_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMJ06829 19 M_jannaschii_chromosome RMJ14114 60 M_jannaschii_chromosome Input sequences: #1 RMJ00808 300 M_jannaschii_chromosome #2 RMJ00407 205 M_jannaschii_chromosome #3 RMJ01820 25 M_jannaschii_chromosome #4 RMJ02054 97 M_jannaschii_chromosome #5 RMJ04312 88 M_jannaschii_chromosome #6 RMJ00776 21 M_jannaschii_chromosome #7 RMJ00835 128 M_jannaschii_chromosome #8 RMJ09510 85 M_jannaschii_chromosome #9 RMJ09945 140 M_jannaschii_chromosome #10 RMJ06351 220 M_jannaschii_chromosome #11 RMJ07785 131 M_jannaschii_chromosome #12 RMJ15852 162 M_jannaschii_chromosome #13 RMJ09311 240 M_jannaschii_chromosome #14 RMJ09076 45 M_jannaschii_chromosome #15 RMJ08813 224 M_jannaschii_chromosome #16 RMJ02718 147 M_jannaschii_chromosome #17 RMJ10497 83 M_jannaschii_chromosome #18 RMJ00477 121 M_jannaschii_chromosome #19 RPH01786 71 Pyrococcus_OT3 Motif number 1 CTAATTATCATTTTAAAGTTTTTAAGGTTTT 1 66 1 TTTTAAATTT 0.953164 -235 TAAGATTTCTTTATATTTATTCTTTCTGCAA 1 96 0 TTATATTATT 0.781671 -205 ATCACATCAGTTATTAAAATTAACTTAATAA 1 132 0 TTATTAAATT 0.90489 -169 TCTAAATACCTTTTTAATATAAAAACTGCGA 2 80 1 TTTTTAAATA 0.567633 -126 AAACCATATGTTATTTATTTTATTATCCACA 2 152 1 TTATTTATTT 0.785629 -54 CCACAATAAATTTTAAGATTTTATAAATAAT 2 178 1 TTTTAAGTTT 0.861803 -28 GCTTCAAACTTTTTATTTTTTGTTGTAAAT 4 10 1 TTTTTATTTT 0.902182 -88 GTTCTATAAATTATAAATATTTACAACAAAA 4 28 0 TTATAAAATT 0.938828 -70 GTTGTTATTGTTATTATCTTTAAAACCTTAA 4 64 1 TTATTATTTT 0.893574 -34 CAAATAGCTATTATTAACATATACCTTTTAT 7 20 0 TTATTAAATA 0.544452 -109 TCAATACATTTTTTAATCTTTGGAAAAGTTG 7 79 1 TTTTAATTTT 0.937019 -50 ATATATACTTTTTTAAAGATAGCAAAAAA 8 9 0 TTTTAAAATA 0.67926 -77 ATATCAACCCTTATAATTTTCAATCACATAT 8 38 0 TTATAATTTC 0.729634 -48 TTTTGACATCTTATAAATATCAACCCTTATA 8 54 0 TTATAAAATC 0.753574 -32 TTTTTTTCTCTTTTATTTATTATGTATAAAT 9 29 1 TTTTATTATT 0.797276 -112 TTATATTTATTTTTATAAATTTATACATAAT 9 47 0 TTTTATAATT 0.843249 -94 TGGGAGGTTATTATATTATTTTTTGCAAGTA 9 102 1 TTATATTTTT 0.812096 -39 TTTTATCTGATTATTTTAATTGGATATGTGT 10 126 1 TTATTTTATT 0.689388 -95 TTAGGTTATATTTTTAGTTTTTTGCTCCCCA 10 177 1 TTTTTAGTTT 0.794485 -44 TTTTAATTTTTTATTTTTTAT 12 1 1 TTTTAATTTT 0.937019 -162 TTATTATAAGTTATTAATATTACGGTGGTGT 12 123 1 TTATTAAATT 0.90489 -40 ATTGGACTATTTTTATTTTTGTAAAATTTT 13 10 1 TTTTTATTTT 0.902182 -231 TAATTTAATTTTTTAAAGTTATATAAAAGGT 13 42 0 TTTTAAATTA 0.718823 -199 AATTACTTATTTATAATATTTTAGCTGGATA 13 68 1 TTATAATTTT 0.931244 -173 ATCTTTACAATTTTTAATTTTGGCTATGGAA 13 131 0 TTTTTAATTT 0.926557 -110 CTTGTCATGCTTATATAAATTTTCTATCTTT 13 156 0 TTATATAATT 0.830431 -85 CCGTAGAACTTTATAAAAATTCTTATGCTTG 13 183 0 TTATAAAATT 0.938828 -58 ATGAGGAAATTTTTAATATTTTTAATATTT 13 221 1 TTTTAATTTT 0.937019 -20 TTCATCCTTTTTATAAAAATTTACGTATATA 14 13 1 TTATAAAATT 0.938828 -33 TTTTTAACTTTTGTCTATTTT 15 1 1 TTTTTAATTT 0.926557 -224 TTTTGTCTATTTTTATGGATTTCTATAGAAA 15 19 1 TTTTATGATT 0.622418 -206 ACGGTTTAATTTTTTAAATTTCTATAGAAAT 15 37 0 TTTTTAATTT 0.926557 -188 AAACCGTTTTTTATAAATATCTTTTATGCAG 15 61 1 TTATAAAATC 0.753574 -164 TCAATAAATTTTATTAATTTTGAAAAACACT 15 169 1 TTATTAATTT 0.919904 -56 TTTATATAATTTTGTGGGATGT 16 2 1 TTATATATTT 0.855319 -146 TTGCAGTATTTTATAATATTTGCATGGTTAA 16 69 0 TTATAATTTT 0.931244 -79 TTTATTAGAGTTTTATTCATCTCCTCAACAT 16 114 0 TTTTATTATC 0.439342 -34 AAGTTTTTAGTTTTTATTATTTTATTTTTAG 17 28 1 TTTTTATATT 0.884264 -56 TATTATTTTATTTTTAGTTTTTAATAGAAAA 17 42 1 TTTTTAGTTT 0.794485 -42 ATCACCTGAATTATAAAATTTTCTATTAAAA 17 60 0 TTATAAATTT 0.948788 -24 GTCATCAGAGTTTTAATAATTAGTTAAAGTT 19 12 1 TTTTAATATT 0.924952 -60 AGGGGCATTCTTTTAAACTTTAACTAATTAT 19 27 0 TTTTAAATTT 0.953164 -45 ******* *** Masking position 4 Map Score: 55.9574 Number of sites scoring better than the average of aligned sites = 2725 Number in coding regions = 1829 Number in noncoding regions = 896 Number of orfs with sites within 600 bp upstream = 535 Fraction of orfs with sites within 600 bp upstream = 0.08593 Motif number 2 TCATTTGTAGAAACTTTTCTTAGATATTTCCTAATT 1 36 1 AAATTTTATA 0.968353 -265 AAAACCTTAAAAACTTTAAAATGATAATTAGGAAAT 1 61 0 AAATTTAATA 0.92942 -240 ATCAGTTATTAAAATTAACTTAATAATTATTTAAGA 1 122 0 AAATTATTAA 0.631592 -179 AGTATTTGTAAAAATTTAATGCCATAGTTATCACAT 1 156 0 AAATTTGATA 0.915493 -145 ATGGTTTTTGAAAGTTTATGTATTTATTTTCAGCAT 1 249 0 AAATTTTTTA 0.944568 -52 TAAAATCTTAAAATTTATTGTGGATAATAAAATAAA 2 165 0 AAATTATATA 0.951237 -41 CAAAGTTATTATTTATAAAATCTTAAA 2 189 0 AAATTATATA 0.951237 -17 AATTAAAAATTTTTGGAGGGATATA 3 8 1 AATTTTGATA 0.794327 -18 TTTGTTGTAAATATTTATAATTTATAGAACATCTGG 4 29 1 ATATTATATA 0.605901 -69 CTATTTGTTTAATTTTTTTATCTATATTGGTTTATT 7 44 1 AATTTTTATA 0.916029 -85 TAATCTTTGGAAAAGTTGATTACATATTAAGCTATT 7 92 1 AAAGTTTATA 0.66218 -37 TTATTTTTATAAATTTATACATAATAAATAAAAGAG 9 36 0 AAATTAAATA 0.89356 -105 CCCAAAATTTAAACTTAACTAAAATAGTTTATATTT 9 70 0 AAATTAAATA 0.893414 -71 AGTTAAGTTTAAATTTTGGGAGGTTATTATATTATT 9 86 1 AAATTTATTA 0.879999 -55 AATATAAAATTTTTTGGGGATAACAATGTTTA 10 7 1 AAATTTGATA 0.915493 -214 ATGTGTTTGGAATTTTTAGTTTGATATTAGGTTATA 10 151 1 AATTTTTATA 0.91603 -70 TTTTAATTTTTTATTTTTTATGAAATTTAT 12 5 1 AATTTTTTTA 0.858654 -158 ACATTATTACAATTTTAGTATTTATAATTTGTCATT 12 51 0 AATTTATATA 0.874283 -112 TAAAAGGTAAAAATTTTACAAAAATAAAAATAGTCC 13 14 0 AAATTTAATA 0.929184 -227 ATAACTTTAAAAAATTAAATTACTTATTTATAATAT 13 51 1 AAATTATTTA 0.915701 -190 CTTATTTATAATATTTTAGCTGGATAATATTTTCAC 13 73 1 ATATTTTATA 0.70689 -168 ATGCTTATATAAATTTTCTATCTTTACAATTTTTAA 13 145 0 AAATTTTTTA 0.944568 -96 AAATATTAAAAATATTAAAAATTTCCT 13 224 0 AATTTAATTA 0.624982 -17 CCTTTTTATAAAAATTTACGTATATATAGGTGATAT 14 18 1 AAATTTTATA 0.968355 -28 ATTTCTATAGAAATTTAAAAAATTAAACCGTTTTTT 15 37 1 AAATTAATAA 0.424529 -188 CAAAATTAATAAAATTTATTGATAAAGATTTGAACG 15 155 0 AAATTTGAAA 0.630955 -70 AGTATTTTATAATATTTGCATGGTTAAAATGCGTAT 16 60 0 AATTTTTTTA 0.858654 -88 TAAAAACTAAAAACTTAAATTTATTAAATACTT 17 8 0 AAATTATTTA 0.915705 -76 CTGAATTATAAAATTTTCTATTAAAAACTAAAAATA 17 50 0 AAATTTTAAA 0.828451 -34 AAAATTGTTAAATTTTAAATAAAATAGCTACAAGGG 18 90 1 AATTTAAATA 0.749329 -32 GCATTCTTTTAAACTTTAACTAATTATTAAAACTCT 19 18 0 AAATTTTTTA 0.944568 -54 *** *** * *** Masking position 6 Map Score: 42.9681 Number of sites scoring better than the average of aligned sites = 863 Number in coding regions = 608 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 3 ATCATTTTAAAGTTTTTAAGGTTTTTGCAGAAAGAA 1 72 1 ATTTTTATTT 0.954176 -229 TAACTTAATAATTATTTAAGATTTCTTTATATTTAT 1 107 0 ATATTTATTT 0.9286 -194 CAATTATTGAATTATTTAGAATATTGAAGTGTAAGG 1 213 0 ATATTTAATG 0.554114 -88 AAACAATAACATTTTTTAATGGTTTTTGAAAGTTTA 1 267 0 ATTTTTATTT 0.954176 -34 CAAAGTTATTATTTATAAAATCTTAAAATTTAT 2 183 0 ATATTTAATT 0.900705 -23 GCTTCAAACTTTTTATTTTTTGTTGTAAATATT 4 8 1 ATTTTTATTT 0.954176 -90 TTTTGTTGTAAATATTTATAATTTATAGAACATCTG 4 28 1 ATATTTATTT 0.928485 -70 AATTAATATCCATATTTAGGTGATTTC 5 72 1 CTATTTAATT 0.716675 -17 TATTTGTTTAATTTTTTTATCTATATTGGTTTATTC 7 45 1 ATTTTTTATT 0.82727 -84 TATTCAATACATTTTTTAATCTTTGGAAAAGTTGAT 7 76 1 ATTTTTATTG 0.690752 -53 TCTTTAAAAAAGTATATATATGTGATTGAAAATTAT 8 21 1 ATATATATGT 0.381529 -65 TAACTAAAATAGTTTATATTTATTTTTATAAATTTA 9 55 0 ATTTATATTT 0.741348 -86 TGGGGATAACAATGTTTAAGGAATTTAAAGCACTGT 10 25 1 ATGTTTAATT 0.628246 -196 AACATTGCCAACTATTTTTATCTGATTATTTTAATT 10 111 1 ATATTTTTGT 0.536426 -110 TTGCTCCCCAATTTTTTATCTGCTGTTTTAATT 10 198 1 ATTTTTACTT 0.688282 -23 TTAATTTTTTATTTTTTATGAAATTTATCATGATTT 12 13 1 ATTTTTAATT 0.948677 -150 TTACAATTTTAGTATTTATAATTTGTCATTAAAAAT 12 45 0 ATATTTATTT 0.928485 -118 CTTTAGTGCTAATTTTTTGTAGATTTTATTACTACA 12 84 0 ATTTTTTATT 0.82727 -79 ATTTTTGTAAAATTTTTACCTTTTATATAACTTTAA 13 25 1 ATTTTTATTT 0.954176 -216 TAAGTAATTTAATTTTTTAAAGTTATATAAAAGGTA 13 41 0 ATTTTTTTTT 0.843155 -200 AATTAAATTACTTATTTATAATATTTTAGCTGGATA 13 63 1 CTATTTAATT 0.716659 -178 TTAGCTGGATAATATTTTCACAATTTGTATTATTAT 13 88 1 ATATTTTATT 0.74946 -153 CCACCGTAGAACTTTATAAAAATTCTTATGCTTGTC 13 181 0 ATTTATATTT 0.738974 -60 ACTATGAGGAAATTTTTAATATTTTTAATATTT 13 218 1 ATTTTTATTT 0.954176 -23 AAAACGGTTTAATTTTTTAAATTTCTATAGAAATCC 15 35 0 ATTTTTTTTT 0.843155 -190 AAAATTAAACCGTTTTTTATAAATATCTTTTATGCA 15 55 1 CTTTTTTATT 0.511174 -170 CTTTATCAATAAATTTTATTAATTTTGAAAAACACT 15 164 1 AATTTTATTT 0.67392 -61 AAAACACTATAATTTTTAGTTAAGATTAAATGTAGG 15 192 1 ATTTTTAAGT 0.864705 -33 GTCTATGAGAAAAATTTACCTCATCTCTGATACGCA 16 31 1 AAATTTAATT 0.542717 -117 ATTATTCCAATTTTTTATTAGAGTTTTATTCATCT 16 123 0 ATTTTTAAGT 0.864705 -25 AAGTATTTAATAAATTTAAGTTTTTAG 17 2 1 ATATTTAATT 0.920494 -82 AATAAATTTAAGTTTTTAGTTTTTATTATTTTATTT 17 19 1 ATTTTTATTT 0.954176 -65 TTAATAGAAAATTTTATAATTCAGGTGATATT 17 62 1 ATTTATAAGT 0.468026 -22 CCCCGAACAACCTTTTTAGAAAAGGTTGATCAAAAC 18 33 0 CTTTTTAAGT 0.582547 -89 TATTTTATTTAAAATTTAACAATTTTCCACTCGCAT 18 80 0 AAATTTATTT 0.569539 -42 * ****** ** * Masking position 7 Map Score: 50.004 Number of sites scoring better than the average of aligned sites = 1336 Number in coding regions = 961 Number in noncoding regions = 375 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 4 TTCTTTCTGCAAAAACCTTAAAAACTTTAA 1 78 0 AAAAACCTTA 0.568664 -223 ATAAACTTTCAAAAACCATTAAAAAATGTT 1 266 1 AAAAACCATT 0.587708 -35 CCTCAATATTATAGAACTTTCGCAGGAATA 2 18 1 ATAGAACTTT 0.615394 -188 TTAGGCATCTAAATACCTTTTTAATATAAA 2 73 1 AAATACCTTT 0.874148 -133 TATTATTAACATATACCTTTTATCATTCAT 7 13 0 ATATACCTTT 0.943243 -116 TTAATATGTAATCAACTTTTCCAAAGATTA 7 92 0 ATCAACTTTT 0.753794 -37 AATCACATATATATACTTTTTTAAAGATAG 8 18 0 ATATACTTTT 0.658729 -68 TCTTATAAATATCAACCCTTATAATTTTCA 8 47 0 ATCAACCCTT 0.806114 -39 ATGCATTATCATGAACCTTTAATAAAGGTT 11 37 1 ATGAACCTTT 0.932331 -95 ACTCATTTTGATGAACCTTTATTAAAGGTT 11 50 0 ATGAACCTTT 0.932331 -82 TTTACCTTTTATATAACTTTAAAAAATTAA 13 39 1 ATATAACTTT 0.65873 -202 AAATACTGCAATAGACCTTTTTCAAATGTT 16 89 1 ATAGACCTTT 0.932292 -59 TTTAGTTTTGATCAACCTTTTCTAAAAAGG 18 29 1 ATCAACCTTT 0.963451 -93 ATACTCCCCGAACAACCTTTTTAGAAAAGG 18 44 0 AACAACCTTT 0.916799 -78 ********** Masking position 5 Map Score: 9.86613 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 354 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 TAATATAGAACTTCGCAGTTTTTATATTAAAAA 2 90 0 CTTCCATTTT 0.932986 -116 ATATTAATTCATTCATTAATTTTGTTAAATAAC 2 117 1 ATTCTTTTTT 0.346731 -89 TATATCCCTCCAAAAATTTTTAATT 3 6 0 CTCCAATTTT 0.890084 -20 GCTTCAAACTTTTTATTTTTTGTT 4 2 1 CTTCAATTTT 0.754503 -96 CCTCTCACCTTTTATAATAAA 6 9 0 CCTCCATTTT 0.946071 -13 ATAAATATCAACCCTTATAATTTTCAATCACAT 8 40 0 ACCCTAATTT 0.637962 -46 CTACTCCCACCTTTTGACATCTTAT 8 71 0 ACTCCATTTT 0.791735 -15 ATACTAACTTCCCCATTCTTTTTTTCTCTTTTA 9 11 1 CCCCTTTTTT 0.89049 -130 AATATAATAACCTCCCAAAATTTAAACTTAACT 9 86 0 CCTCCAATTT 0.914797 -55 ACATTGTTATCCCCAAAAAATTTTATATT 10 7 0 CCCCAAATTT 0.861972 -214 TAGTTTTTTGCTCCCCAATTTTTTATCTGCTGT 10 191 1 CTCCCATTTT 0.973463 -30 CGAAGTGAAGCCCCACTCATTTTGATGAACCTT 11 61 0 CCCCCTTTTT 0.965858 -71 CTTCGTTCAGCTCCACTTTATTTATAGCTACAA 11 89 1 CTCCCTATTT 0.93216 -43 AAAAAATCACTCCATTACTTTTGTAGCTATAA 11 110 0 CTCCTTTTTT 0.865833 -22 GTTATCCCCTACATTTAATCTTAACT 15 209 0 ATCCCTATTT 0.748594 -16 TTTTATTCATCTCCTCAACATTTGAAAAAGGTC 16 102 0 CTCCCAATTT 0.957358 -46 **** ** **** Masking position 11 Map Score: 16.9719 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 416 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 AGTTATTAAAATTAACTTAATAATTATTTAAGATT 1 120 0 ATAATAAATT 0.728516 -181 ATAGTCGGCAAATAAAGTATGCCTTACACTTCAAT 1 192 1 ATAAGATCTT 0.897779 -109 CAATATTCTAAATAATTCAATAATTGATGCTGAAA 1 223 1 ATAATAAATT 0.700059 -78 CTTTCGCAGGAATAAATGATTTATTGAATAATGAT 2 34 1 ATAATATATT 0.493027 -172 TGATTTATTGAATAATGATGCCTTTAGGCATCTAA 2 50 1 ATAAGTGTTT 0.365212 -156 ATTTAACAAAATTAATGAATGAATTAATATAGAAC 2 112 0 ATAAGATATT 0.940529 -94 TTAAAACCTTAATAATGGTGAGATT 4 83 1 ATAAGTGATT 0.843896 -15 CCACCCGTCTATTAAGTTAGGACTTTCAGTCCTAA 5 39 1 ATAATAGCTT 0.897779 -50 AATAGCTATTATTAACATATACCTTTTATCATTCA 7 14 0 ATAAAATCTT 0.685093 -115 TTTTCCAAAGATTAAAAAATGTATTGAATAAACCA 7 71 0 ATAAAATATT 0.796335 -58 ATGTAATAAAAAATAGCTTAATATGTAAT 7 110 0 ATAAAATCTT 0.685089 -19 TTGCAAGTAGATTAAGGGGGATATTAT 9 124 1 ATAAGGGATT 0.819627 -17 TAGCTACAAAAGTAATGGAGTGATTTTTT 11 113 1 ATAAGAGATT 0.970989 -19 CTAAAATTGTAATAATGTAGTAATAAAATCTACAA 12 69 1 ATAAGAGATA 0.728981 -94 AAAAATTAGCACTAAAGTAGTTATTATAAGTTATT 12 103 1 ATAAGAGATT 0.96821 -60 ACTTTAAAAAATTAAATTACTTATTTATAATATTT 13 54 1 ATAATACATT 0.626482 -187 AAACTTCTTAAATAACTAAGGTATTAATGAACTCC 15 108 1 ATAATAGATT 0.772397 -117 * *** * ** *** Masking position 5 Map Score: 10.4742 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 397 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 7 AAATGACGATAATCTATTAAAACTTCTAAAA 1 11 0 AATCTATTAA 0.468373 -290 TTATCATTTTAAAGTTTTTAAGGTTTTTGCA 1 70 1 AAAGTTTTAA 0.285975 -231 TTTGAAAGTTTATGTATTTATTTTCAGCATC 1 248 0 TATGTATTAT 0.444781 -53 TTATATTAAAAAGGTATTTAGATGCCTAAAG 2 71 0 AAGGTATTAG 0.808381 -135 AAAATTAATGAATGAATTAATATAGAACTTC 2 109 0 AATGAATTAT 0.707667 -97 CACCATTATTAAGGTTTTAAAGATAATAACA 4 72 0 AAGGTTTTAA 0.835609 -26 AAGATTAAAAAATGTATTGAATAAACCAATA 7 68 0 AATGTATTAA 0.900248 -61 AACAATGTTTAAGGAATTTAAAGCACTGTTG 10 32 1 AAGGAATTAA 0.796072 -189 ATCTATGTAGAAGATTTTGATTTTGAAAACA 10 84 1 AAGATTTTAT 0.422786 -137 AATAGTTGGCAATGTTTTCAAAATCAAAATC 10 96 0 AATGTTTTAA 0.717566 -125 AAATTGTAATAATGTAGTAATAAAATCTACA 12 72 1 AATGTAGTAT 0.542819 -91 TAGTTATTATAAGTTATTAATATTACGGTGG 12 120 1 AAGTTATTAT 0.829192 -43 TATTATAAATAAGTAATTTAATTTTTTAAAG 13 55 0 AAGTAATTAA 0.458272 -186 AACTGCATAAAAGATATTTATAAAAAACGGT 15 63 0 AAGATATTAT 0.722364 -162 TTAAATAACTAAGGTATTAATGAACTCCTTC 15 115 1 AAGGTATTAT 0.957268 -110 AAATTAATAAAATTTATTGATAAAGATTTGA 15 158 0 AATTTATTAT 0.70815 -67 TAAAAACTTAAATTTATTAAATACTT 17 6 0 AATTTATTAA 0.661673 -78 CATTATAAGGTATTGATATTTAGTTTT 18 7 1 AAGGTATTAT 0.957268 -115 AAATAGCTACAAGGGATTAAT 18 111 1 AAGGGATTAT 0.739646 -11 ******** ** Masking position 8 Map Score: 9.86637 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 707 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 8 GATTATCGTCATTTGTAGAAACTTTTCTTA 1 28 1 ATTTGTAGAA 0.568694 -273 ATGGCATTAAATTTTTACAAATACTATAGT 1 167 1 ATTTTTACAA 0.902507 -134 AATTATTGAATTATTTAGAATATTGAAGTG 1 218 0 TTATTTAGAA 0.413505 -83 GGAATAAATGATTTATTGAATAATGATGCC 2 42 1 ATTTATTGAA 0.242591 -164 CAAAGTTATTATTTATAAAATCTTAAAATT 2 186 0 ATTTATAAAA 0.494596 -20 AATTAAAAATTTTTGGAGGGATATA 3 9 1 ATTTTTGGAG 0.324985 -17 TAAATTATAAATATTTACAACAAAAAATAA 4 23 0 ATATTTACAA 0.525484 -75 AATATTTATAATTTATAGAACATCTGGTTG 4 38 1 ATTTATAGAA 0.830113 -60 TATTGTTATTATCTTTAAAACCTTAATAAT 4 69 1 ATCTTTAAAA 0.577187 -29 ACATTTTTTAATCTTTGGAAAAGTTGATTA 7 84 1 ATCTTTGGAA 0.773353 -45 TTTTTTGCTATCTTTAAAAAAGTATATAT 8 10 1 ATCTTTAAAA 0.577187 -76 GTTTATATTTATTTTTATAAATTTATACAT 9 50 0 ATTTTTATAA 0.85225 -91 TATTATATTATTTTTTGCAAGTAGATTAAG 9 110 1 TTTTTTGCAA 0.676292 -31 ACTGTTGTCATTTTTTACAAGGATTCCAAT 10 56 1 TTTTTTACAA 0.807676 -165 GGGGAGTTTTATGGAAGGGAGAACTT 11 7 1 TTTTATGGAA 0.52705 -125 TTATTACTACATTATTACAATTTTAGTATT 12 65 0 ATTATTACAA 0.315503 -98 GACTATTTTTATTTTTGTAAAATTTTTACC 13 15 1 ATTTTTGTAA 0.7415 -226 AATTTTTACCTTTTATATAACTTTAAAAAA 13 35 1 TTTTATATAA 0.474755 -206 GCTGGATAATATTTTCACAATTTGTATTAT 13 91 1 ATTTTCACAA 0.405875 -150 TAAATTTTCTATCTTTACAATTTTTAATTT 13 142 0 ATCTTTACAA 0.828813 -99 AAGATAGAAAATTTATATAAGCATGACAAG 13 157 1 ATTTATATAA 0.685469 -84 AAGCATAAGAATTTTTATAAAGTTCTACGG 13 184 1 ATTTTTATAA 0.85225 -57 ATATACGTAAATTTTTATAAAAAGGATGAA 14 13 0 ATTTTTATAA 0.85225 -33 TTTTTTAAATTTCTATAGAAATCCATAAAA 15 29 0 TTCTATAGAA 0.394687 -196 AATTAAACCGTTTTTTATAAATATCTTTTA 15 57 1 TTTTTTATAA 0.723149 -168 AATGAACTCCTTCTTTGGAAGGCGTTCAAA 15 133 1 TTCTTTGGAA 0.607531 -92 CCCGAACAACCTTTTTAGAAAAGGTTGATC 18 38 0 CTTTTTAGAA 0.581683 -84 ********** Masking position 2 Map Score: 16.3928 Number of sites scoring better than the average of aligned sites = 1150 Number in coding regions = 881 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 9 TTAATAACTGATGTGATAACTATGGCATTA 1 146 1 ATGTGATAAC 0.746185 -155 ATCCATATTTAGGTGATTTC 5 79 1 AGGTGATTTC 0.918526 -10 AAATTTTGGGAGGTTATTATATTATTTTTT 9 96 1 AGGTTATTAT 0.551308 -45 AGTAGATTAAGGGGGATATTAT 9 129 1 GGGGGATATT 0.79266 -12 TAAAATTTTTTGGGGATAACAATGTTTAAG 10 15 1 TGGGGATAAC 0.656216 -206 GTTTGATATTAGGTTATATTTTTAGTTTTT 10 169 1 AGGTTATATT 0.798903 -52 ATAAAATGTGATTTTCATAACACCA 12 148 0 ATGTGATTTT 0.642712 -15 ACGTATATATAGGTGATATTT 14 35 1 AGGTGATATT 0.9583 -11 GATTAAATGTAGGGGATAAC 15 215 1 AGGGGATAAC 0.923714 -10 TTTATAATTCAGGTGATATT 17 74 1 AGGTGATATT 0.9583 -10 ********** Masking position 6 Map Score: 3.15169 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 186 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 10 ATTTGCCGACTATAGTATTTGTAAAAATTT 1 175 0 TATAGTATTT 0.865316 -126 GTGTAAGGCATACTTTATTTGCCGACTATA 1 191 0 TACTTTATTT 0.521512 -110 TGCGAAGTTCTATATTAATTCATTCATTAA 2 106 1 TATATTAATT 0.655735 -100 ACATATGGTTTATGTTATTTAACAAAATTA 2 133 0 TATGTTATTT 0.82335 -73 ACATAAACCATATGTTATTTATTTTATTAT 2 148 1 TATGTTATTT 0.82335 -58 TTTTTTTATCTATATTGGTTTATTCAATAC 7 56 1 TATATTGGTT 0.55256 -73 TCTTTTTTTCTCTTTTATTTATTATGTATA 9 27 1 TCTTTTATTT 0.548705 -114 AAATATAAACTATTTTAGTTAAGTTTAAAT 9 70 1 TATTTTAGTT 0.703682 -71 GGGAGGTTATTATATTATTTTTTGCAAGTA 9 103 1 TATATTATTT 0.930789 -38 TTTATCTGATTATTTTAATTGGATATGTGT 10 127 1 TATTTTAATT 0.605557 -94 TTTTAATTTTTTATTTTTTATGAAAT 12 7 1 TTTTTTATTT 0.591262 -156 TTATTACAATTTTAGTATTTATAATTTGTC 12 54 0 TTTAGTATTT 0.461608 -109 ATTACTTATTTATAATATTTTAGCTGGATA 13 69 1 TATAATATTT 0.684637 -172 TATGCAGTTATATAGTGTTTTTCAAACTTC 15 85 1 TATAGTGTTT 0.729214 -140 AACTAAAAATTATAGTGTTTTTCAAAATTA 15 183 0 TATAGTGTTT 0.729214 -42 TTTATATAATTTTGTGGGATGT 16 3 1 TATATAATTT 0.629175 -145 TGCAGTATTTTATAATATTTGCATGGTTAA 16 69 0 TATAATATTT 0.684637 -79 TAGTTTTTATTATTTTATTTTTAGTTTTTA 17 35 1 TATTTTATTT 0.915539 -49 AAGGTATTGATATTTAGTTTTGATCAACCT 18 17 1 TATTTAGTTT 0.364356 -105 CCCTTGTAGCTATTTTATTTAAAATTTAAC 18 96 0 TATTTTATTT 0.915539 -26 ********** Masking position 9 Map Score: 15.0864 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 342 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 11 AATTATTTAGAATATTGAAGTGTAAGGCATAC 1 208 0 AATATTAGTG 0.896163 -93 AAAGTTCTATAATATTGAGGTGAATCT 2 6 0 AATATTGGTG 0.980363 -200 GTCCTAACTTAATAGACGGGTGGTATACCAAT 5 30 0 AATAGAGGTG 0.825005 -59 AATTAATATCCATATTTAGGTGATTTC 5 72 1 CATATTGGTG 0.921021 -17 CAGCAGATAAAAAATTGGGGAGCAAAAAACTA 10 191 0 AAAATTGGAG 0.760816 -30 ATAAGTTATTAATATTACGGTGGTGTTATGAA 12 128 1 AATATTGGTG 0.980363 -35 AAAATTTACGTATATATAGGTGATATTT 14 28 1 TATATAGGTG 0.780877 -18 ATCTTAACTAAAAATTATAGTGTTTTTCAAAA 15 186 0 AAAATTAGTG 0.796248 -39 AGAAAATTTTATAATTCAGGTGATATT 17 67 1 ATAATTGGTG 0.760816 -17 CCCTCTCACAAATCTATGGGTGTAAGAA 19 54 1 AATCTAGGTG 0.825005 -18 ****** **** Masking position 10 Map Score: 4.08184 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 104 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 ********** No masking Map Score: 2.59591e-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: 2.59591e-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: 2.59591e-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