AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i148_mjan_pyro_300.orf -o148_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: RMJ02153 57 M_jannaschii_chromosome Input sequences: #1 RMJ07936 89 M_jannaschii_chromosome #2 RMJ13354 75 M_jannaschii_chromosome #3 RMJ01522 39 M_jannaschii_chromosome #4 RMJ14619 28 M_jannaschii_chromosome #5 RMJ10200 71 M_jannaschii_chromosome #6 RMJ08904 180 M_jannaschii_chromosome #7 RMJ10274 104 M_jannaschii_chromosome #8 RMJ15352 128 M_jannaschii_chromosome #9 RMJ02377 221 M_jannaschii_chromosome #10 RMJ03320 214 M_jannaschii_chromosome #11 RMJ13235 109 M_jannaschii_chromosome #12 RMJ03131 268 M_jannaschii_chromosome #13 RMJ13030 263 M_jannaschii_chromosome #14 RMJ05742 210 M_jannaschii_chromosome #15 RMJ05650 213 M_jannaschii_chromosome #16 RMJ11762 83 M_jannaschii_chromosome #17 RMJ12007 203 M_jannaschii_chromosome #18 RMJ14441 286 M_jannaschii_chromosome #19 RMJ05775 271 M_jannaschii_chromosome #20 RMJ14343 124 M_jannaschii_chromosome #21 RMJ14151 93 M_jannaschii_chromosome #22 RMJ14817 43 M_jannaschii_chromosome #23 RMJ11840 197 M_jannaschii_chromosome #24 RMJ12613 227 M_jannaschii_chromosome #25 RMJ07178 197 M_jannaschii_chromosome #26 RMJ06181 270 M_jannaschii_chromosome #27 RMJ05205 170 M_jannaschii_chromosome #28 RMJ01354 84 M_jannaschii_chromosome Motif number 1 GATTTAGAAATTTATAATATGTGTTAAATA 1 33 0 TTTATAATAT 0.429769 -57 TTTCTAAATCTTTTTAATTAATTGTAATTG 1 53 1 TTTTTAATTA 0.909243 -37 GTTTTATTGGTTTTTATTTTATATTTGCTT 2 16 0 TTTTTATTTT 0.969778 -60 TTTATTTTATCTTTTGTTTATTTAAGTTTT 2 41 0 CTTTTGTTTA 0.682188 -35 TCTCCCCTCCTTTTTATTTTATCTTTTGTT 2 53 0 TTTTTATTTT 0.969778 -23 AATTAAAATAATTTTATTATT 3 2 0 ATTTTATTAT 0.636969 -38 TAATAAAATTATTTTAATTAAACTTTTTGG 3 13 1 ATTTTAATTA 0.639356 -27 TTCACATCGCGTTTTATTTAA 5 2 0 GTTTTATTTA 0.744687 -70 TATAGATAATCTTTTATTTATTAATTTAAT 7 14 1 CTTTTATTTA 0.893649 -91 AATTTCTATTTAAAAAATTTAG 8 3 1 TTTCTATTTA 0.636161 -126 ATATATTATATTTTTGATTTTAGATAGTAT 8 43 0 TTTTTGATTT 0.780092 -86 CAAAATTTTCTTTCTATTTTCGGAGGAAAT 9 12 1 TTTCTATTTT 0.707905 -210 TTCAATTCCCATTTTATTATTTTACTTAAA 9 64 1 ATTTTATTAT 0.636969 -158 CATTTTTATGTTTTTATTTGAAACTATATA 9 157 0 TTTTTATTTG 0.893729 -65 TAAATAAAAATTTTTAATTAAAT 10 4 0 TTTTTAATTA 0.909243 -211 TAATTAAAAATTTTTATTTAATTTTTATTT 10 14 1 TTTTTATTTA 0.958593 -201 TTTTATTTAATTTTTATTTTTTAATTCTGT 10 25 1 TTTTTATTTT 0.969778 -190 GTTTTATCACTTTATATTTACTAATTTTTT 10 106 1 TTTATATTTA 0.802619 -109 ATTTACTAATTTTTTAATTTGTTTTATTTA 10 121 1 TTTTTAATTT 0.932826 -94 TTTTTAATTTGTTTTATTTATTGTTCAACA 10 131 1 GTTTTATTTA 0.744687 -84 CCTTTTTAACTTTTTAATTATTACATTATA 11 83 0 TTTTTAATTA 0.909243 -27 TTTTTTTACTTTTTTATTTTTTTAAGAATA 12 20 1 TTTTTATTTT 0.969778 -249 TGAACTAAGATTTTTAATAAGGCTCACAAA 12 225 0 TTTTTAATAA 0.755783 -44 AATTGTTTTAATTTTATTTTTCAAATATGT 13 22 0 ATTTTATTTT 0.85026 -242 CTTTAAGTAAATTTTATTTATATTGTGAAA 13 61 1 ATTTTATTTA 0.803789 -203 GTTATTAGTTATTTTATTATCAGTTATTTA 13 176 0 ATTTTATTAT 0.636969 -88 AAACTTCTATTTTTTATTAACAATTATACA 14 14 1 TTTTTATTAA 0.877342 -197 TTATACAAATTTTTTATTAGATTTATCTAA 14 37 1 TTTTTATTAG 0.722118 -174 TAAAAATCTTTTTATATTTTGGATTCCAGA 14 98 1 TTTATATTTT 0.849315 -113 GATTCCAGAGTTTATATTATAAAGTTTGAT 14 119 1 TTTATATTAT 0.635255 -92 TTCCTCAATATTTGTATTTTATTCATAAGA 14 169 0 TTTGTATTTT 0.779259 -42 CAAACATTATTTTTTATTTATTTTGTATTT 15 125 1 TTTTTATTTA 0.958593 -89 TTTTATTTATTTTGTATTTTTGACAAGTTT 15 136 1 TTTGTATTTT 0.779259 -78 TTTTGACAAGTTTTTGTTTATGTTTTTTTG 15 153 1 TTTTTGTTTA 0.855361 -61 GGCTTATCCTTTTTTGTTAAACCTTTCCTC 16 30 0 TTTTTGTTAA 0.646316 -54 TCATCTCATTTTTTTATTTTTTATTGTAAA 18 16 1 TTTTTATTTT 0.969778 -271 CACCATAAATATTTTATTTTTTTGTTA 19 8 0 ATTTTATTTT 0.85026 -264 TTTCCATTTGCTTTTATTTGGATTTTCTGG 19 83 1 CTTTTATTTG 0.75324 -189 TTGGATAATTCTTTTAATTGGAGGAATCAT 19 121 1 CTTTTAATTG 0.569152 -151 TTGTTATTACTTTTTAATAACCATTTAAGT 19 166 0 TTTTTAATAA 0.755783 -106 TTTACTGTTATTTTTGTTATTACTTTTTAA 19 179 0 TTTTTGTTAT 0.716949 -93 TCAAATATTATTTTTGTTTAAAAGGAATAT 19 213 0 TTTTTGTTTA 0.855361 -59 ATTTTTTATTTTCATGGTTGTG 20 3 1 TTTTTATTTT 0.969778 -122 ATGAGGGCAGTTTTTATTTACCACAAAAAT 21 65 1 TTTTTATTTA 0.958593 -29 AGTATGATAACTTTTGTTTTTATTGTTTTT 23 35 1 CTTTTGTTTT 0.748445 -163 GAATTATTAATTTATAATTTTTTTATACAA 23 154 1 TTTATAATTT 0.709234 -44 AATTATTTTTAATTGGTGAAAATAT 24 6 1 TTTTTAATTG 0.784457 -222 AATGATATATCTTTTAATATTGGTAAGTAT 24 126 0 CTTTTAATAT 0.608992 -102 CATTTTTATTGTTTTATTTTAATATACTGC 24 152 1 GTTTTATTTT 0.801702 -76 ACTGCTGTTTTTTGTATTTTTAATGTTGTG 24 177 1 TTTGTATTTT 0.779259 -51 TATTTTGGATTTTATATTATAT 25 3 0 TTTATATTAT 0.635255 -195 TAACCTTTAATTTTTAATTTTATCTTTTAT 25 31 1 TTTTTAATTT 0.932826 -167 TTAATTTTATCTTTTATTTTTTCATTTTTT 25 44 1 CTTTTATTTT 0.920931 -154 TTTTTCATTTTTTTTATTTTATATATTATA 25 61 1 TTTTTATTTT 0.969778 -137 GATTTACAATCTTATAATTAATTATAATAT 25 83 0 CTTATAATTA 0.389772 -115 ATTAATTTTTATTTTTATTTTTGCA 26 6 1 TTTTTATTTT 0.969778 -265 CACCCTAAGACTTTTAATATCTGCAAACAT 26 246 0 CTTTTAATAT 0.608992 -25 TTAATTATAATTTATAATTTATGATAAAAA 27 12 0 TTTATAATTT 0.709234 -159 CACCAACAAATTTTTAATTATAATTTATAA 27 25 0 TTTTTAATTA 0.909243 -146 AATGTATCTTTTTTTGTTTAATGCTACTGC 27 126 0 TTTTTGTTTA 0.855361 -45 ********** Masking position 5 Map Score: 77.0439 Number of sites scoring better than the average of aligned sites = 2332 Number in coding regions = 1575 Number in noncoding regions = 757 Number of orfs with sites within 600 bp upstream = 478 Fraction of orfs with sites within 600 bp upstream = 0.0767748 Motif number 2 TTTTTATTTTATATTTGCTTTTCTT 2 1 0 ATATTTTTTT 0.887457 -75 TATCTTTTGTTTATTTAAGTTTTATTGGTTTTTAT 2 29 0 TTATTTTTAT 0.6305 -47 CCTTTGTGCTATTTTTGTCATTATTTATCTTAGTC 6 148 0 ATTTTTTTTT 0.937233 -33 TCCCATTTTATTATTTTACTTAAATACTACAATGC 9 70 1 TTATTTTAAT 0.590375 -152 AGTTGGGACTATTTTTGTCATTTTTATGTTTTTAT 9 170 0 ATTTTTTTTT 0.937233 -52 TTAAAAATTTTTATTTAATTTTTATTTTTTAATTC 10 17 1 TTATTTTTAT 0.6305 -198 ATATTTACTAATTTTTTAATTTGTTTTATTTATTG 10 119 1 ATTTTTTTTT 0.937233 -96 ATTTTTCACCTTTTTATGGCAAATA 10 200 0 ATTTTTTTTT 0.937233 -15 ATTTAATCCTTTTTTTACTTTTTTATTTTTTTAA 12 10 1 TTTTTTTTTT 0.819609 -259 ATATCTTCTAATTTTTCTTATATATATATTACTTA 12 81 0 ATTTTTTAAT 0.899361 -188 TTTTAATTTTATTTTTCAAATATGTGTATATTGGA 13 12 0 ATTTTTTAGT 0.585856 -252 ACCTTTAATTATATTTGTAGTTATTAGTTATTTTA 13 190 0 ATATTTTTTT 0.887457 -74 TTATCCTCCTATTTTTAAAATATCTGGCTAAAAAT 14 70 1 ATTTTTTACT 0.860521 -141 ATTTTCCTCAATATTTGTATTTTATTCATAAGATT 14 167 0 ATATTTTTAT 0.848663 -44 ATTTTCCTCAATATTTGGATTTTATCCATTTACAA 15 86 0 ATATTTTTAT 0.848663 -128 CTCAAACATTATTTTTTATTTATTTTGTATTTTTG 15 123 1 ATTTTTTATT 0.926536 -91 TTGTTTATGTTTTTTTGGGATAATTGAGAAGTTTA 15 166 1 TTTTTTTATT 0.793288 -48 ATTTCATCTCATTTTTTTATTTTTTATTGTAAATG 18 13 1 ATTTTTTTTT 0.937233 -274 TATCATCGCTATTTTTTTCATATTTATCACCTTTA 18 74 0 ATTTTTTATT 0.926533 -213 ATTTTGCTGATTATTTTGAGTAGTTTGAACATTTT 18 182 0 TTATTTTATT 0.669603 -105 CACACCATAAATATTTTATTTTTTTGTTA 19 5 0 ATATTTTTTT 0.887457 -267 CCATTTGCTTTTATTTGGATTTTCTGGATGATATT 19 86 1 TTATTTTTCT 0.539972 -186 TTTCTGGATGATATTTTGGATAATTCTTTTAATTG 19 106 1 ATATTTTATT 0.869453 -166 CTTTACTGTTATTTTTGTTATTACTTTTTAATAAC 19 175 0 ATTTTTTTCT 0.879584 -97 ATTTTTTATTTTCATGGTTGTGCAA 20 1 1 ATTTTTTTAT 0.913932 -124 TCTTTGATTATTTTTGTGGTAAATAAAAACTGCC 21 70 0 ATTTTTTAAT 0.899684 -24 TAGTAGAGGTATTTTTGGGATTGATATC 22 26 1 ATTTTTTTAT 0.913932 -18 ACGACTCAAAATTTTTTATATAGCTTTGCATATTT 24 30 0 ATTTTTTACT 0.860524 -198 ATTTTTTGGATACTTTACCCATCTC 24 213 0 ATTTTTTATT 0.926536 -15 TTTATCTTTTATTTTTTCATTTTTTTTATTTTATA 25 49 1 ATTTTTTTTT 0.937233 -149 TATTTAAAGAATATTTTTTATAAATGCAACTGAAT 25 151 0 ATATTTTAAT 0.825109 -47 TTTTATTTTTATTTTTGCACTATATACTTATACAT 26 17 1 ATTTTTTAAT 0.899687 -254 GTATAAATATATTTTTGACCTTCTTCTTTTGGAGA 26 161 0 ATTTTTTTTT 0.937233 -110 TTTTTTATCATAAATTATAAATTAT 27 1 1 TTTTTTTAAT 0.731837 -170 ATAAAAAACTATTTTTATTCTAACTTAAAACATTT 28 52 0 ATTTTTTACT 0.860524 -33 ****** ** ** Masking position 6 Map Score: 56.6081 Number of sites scoring better than the average of aligned sites = 1256 Number in coding regions = 925 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 3 CTATATATTTAACACATATTATAAATTTCTAAATCTTTTTA 1 28 1 AAAATAATTA 0.771501 -62 GCAAATATAAAATAAAAACCAATAAAACTTAAATAAACAAA 2 18 1 AAAAAAAATA 0.960832 -58 TATAAAGTAAAAAATAATAAACTAAAAACTAATAACTTGCA 6 22 1 AAAACAAATA 0.733441 -159 AAGGGTATGAAATAAATTAAATTAATAAATAAAAGATTATC 7 18 0 AAAATAATTA 0.771522 -87 TGAATTAGGTAGTAAAACCACTCAAAAAATAACTTATAAAG 8 72 1 AGAATAAATA 0.876347 -57 CTTTACATTTAAAATATTGTAATAAAGTATAATGGAAAACG 9 115 1 AAAAAAAATA 0.960829 -107 TATATAGTTTCAAATAAAAACATAAAAATGACAAAAATAGT 9 157 1 CAAAAAAAGA 0.471256 -65 TGCAATATTCAATACAGAATTAAAAAATAAAAATTAAATAA 10 27 0 AAAAAAAAAA 0.514617 -188 AAAATTAGTAAATATAAAGTGATAAAACATATAATAATATT 10 93 0 AAAAAAAATA 0.960832 -122 TGAACAATAAATAAAACAAATTAAAAAATTAGTAAATATAA 10 117 0 ATAATAAATA 0.522992 -98 CTTTTTATGGCAAATAACAGTTTAAACATTAATCAAACATC 10 175 0 CAAATAAATA 0.798046 -40 TTTATTTTATAATGTAATAATTAAAAAGTTAAAAAGGTGAA 11 76 1 AAGATAAATA 0.581272 -34 TTCTTAAAAAAATAAAAAAGTAAAAAAAGGATTAAAT 12 7 0 AAAAAAAAGA 0.846928 -262 TATAATTAATAATATATACCGTAATAGCATAAATTTATTTG 12 179 1 AAAATATATA 0.63687 -90 ATCTTAGTTCAAAATATTTACTTAAAATTTATTTT 12 244 1 AAAATAAATA 0.960829 -25 GCTAAATTTGAAAATACTATTTCACAATATAAATAAAATTT 13 69 0 AAAATACATA 0.595815 -195 GAGGTATTTAAATAGATATGTTGAAATTCGAATAGTTAAGT 13 111 1 AAAATAAAGA 0.846928 -153 TAAATCTAATAAAAAATTTGTATAATTGTTAATAAAAAATA 14 21 0 AAAAAAATTA 0.771523 -190 AGATATTTTAAAAATAGGAGGATAAAAATTAGATAAATCTA 14 54 0 AAAAAAAATA 0.960832 -157 ACAAATATTGAGGAAAATATCTCAAACATTATTTTTT 14 184 1 AGAATAAATA 0.876347 -27 CCAAATATTGAGGAAAATCTCTCAAACATTATTTTTTATTT 15 103 1 AGAATAAATA 0.876347 -111 TCATAAGGTGAAAAAACTCAAAGAAACTATAAAAAGGAGTT 17 165 1 AAAAAAAATA 0.960832 -39 AAGACCAGTGAAGATATTACTAAAAATACTACCAATATCAT 18 103 0 AAAAAAAATA 0.960832 -184 TAACAAAAAAATAAAATATTTATGGTGTGACA 19 2 1 AAAAAAATTA 0.771522 -270 ATTTGAGGTGAGAAAATGTGGAAAAAACTGATGTTGCTACT 19 237 1 AGAAAAAAGA 0.615161 -35 GTAGTGTAAGAAAACAAATATATAAATTTTACTAAGTTGTG 20 43 0 AAAAAAAATA 0.960832 -82 TATTGTTTTTAGTAAAACCTCAATAATTTTAAAAACTTTTA 23 55 1 AGAAATAATA 0.420641 -143 AGTATATTAAAATAAAACAATAAAAATGATATATCTTTTAA 24 139 0 AAAAAAAATA 0.960832 -89 ATGAAAAAATAAAAGATAAAATTAAAAATTAAAGGTTATTT 25 28 0 AAAATAAATA 0.960832 -170 TCACCCATATAAAACACATATTTAAAGAATATTTTTTATAA 25 163 0 AAAATAAATA 0.960832 -35 GTATATAGTGCAAAAATAAAAATAAAAATTAAT 26 3 0 CAAAAAAATA 0.798046 -268 TATACATCTGAATATAAACCTATAAAAGATAATAATATTGT 26 45 1 AAAAAAAATA 0.960832 -226 TATACAATGAAAAAGAAAAGATTTTAATGTAAAGCATCTGT 26 191 1 AAAATTTATA 0.152307 -80 ATTAAACAAAAAAAGATACATTCAAAGACTATGAGAATGTT 27 134 1 AAAATAAATA 0.960832 -37 ATTCTAACTTAAAACATTTATTGTAATTATATATAATTTCT 28 30 0 AAAATTAATA 0.715347 -55 ** * * * *** ** Masking position 6 Map Score: 45.8233 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 388 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 4 TCAGTTTATTAAAGGTGATTATTG 4 15 1 AAAGGTGATT 0.854191 -14 AAAATAGCACAAAGGTGATAGAA 6 168 1 AAAGGTGATA 0.95242 -13 TAAACGATAAAAAGGTGAAAAA 8 117 1 AAAGGTGAAA 0.98559 -12 GACTAATTGATCAGGTGAATTAAAATG 9 205 1 TCAGGTGAAT 0.782937 -17 TTTGCCATAAAAAGGTGAAAAAT 10 202 1 AAAGGTGAAA 0.98559 -13 AAAAAGTTAAAAAGGTGAAAGC 11 98 1 AAAGGTGAAA 0.98559 -12 AAATATAATTAAAGGTGAAAAAATATGAAA 13 209 1 AAAGGTGAAA 0.98559 -55 ATTGGGGTTTTATGGTGAATCTTATGAATA 14 150 1 TATGGTGAAT 0.785656 -61 TGAGAAGTCATAAGGTGAAAAAACTCAAAG 17 158 1 TAAGGTGAAA 0.975007 -46 CTCAACCATTAAAGGTGATAAATATGAAAA 18 65 1 AAAGGTGATA 0.95242 -222 AGCAAATGGAAATGGTGAAAAGAAAGCATG 19 65 0 AATGGTGAAA 0.956444 -207 TAACTACCCTTCAGGTGAAAAA 20 113 1 TCAGGTGAAA 0.924951 -12 ATTATTTTTAATTGGTGAAAATATGCAAAG 24 12 1 ATTGGTGAAA 0.717787 -216 TTAAAAGTCTTAGGGTGAAATA 26 259 1 TAGGGTGAAA 0.88019 -12 ********** Masking position 8 Map Score: 22.5365 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 43 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 TTTCGCATAATATAATGAAATTAAAGACGATT 6 85 0 TATAAAAATT 0.791469 -96 AATTTCTATTTAAAAAATTTAGAAAGTTAT 8 9 1 TTTAAAATTT 0.645094 -120 TTTTAGATAGTATATATAACTTTCTAAATTTT 8 24 0 TATATAACTT 0.760433 -105 AAAAATAACTTATAAAGAACTTAAACGATAAA 8 96 1 TATAAAACTT 0.628911 -33 ATTAAAAATTTTTATTTAATTTTTATTTTTTA 10 16 1 TTTATAATTT 0.772951 -199 TGATAAAACATATAATAATATTATAATACCCA 10 83 0 TATAAATATT 0.755934 -132 AATATATTTGTATATGTAAATTAATAGTATTA 12 46 1 TATATAAATT 0.876667 -223 TAATTTTTCTTATATATATATTACTTATCCTA 12 76 0 TATATATATT 0.852413 -193 TAATTAAATATATGTCGAAATTCGTATAATTA 12 155 1 TATGTAAATT 0.788935 -114 ATTTTTCAAATATGTGTATATTGGAA 13 5 0 TATGTATATT 0.753096 -259 TACTTAAAGATTTATATAAATTGTTTTAATTT 13 38 0 TTTATAAATT 0.834856 -226 TTAAGTAAATTTTATTTATATTGTGAAATAGT 13 63 1 TTTATATATT 0.80489 -201 TTTAAATAGATATGTTGAAATTCGAATAGTTA 13 117 1 TATGTAAATT 0.788935 -147 TTTTTTCACCTTTAATTATATTTGTAGTTATT 13 200 0 TTTAAATATT 0.687761 -64 TTTTATTAGATTTATCTAATTTTTATCCTCCT 14 48 1 TTTATAATTT 0.772951 -163 TATGTAGGTGTTTATAGATTTTAAGTAATCTC 15 40 0 TTTATATTTT 0.735321 -174 AACATTATTTTTTATTTATTTTGTATTTTTGA 15 127 1 TTTATATTTT 0.735321 -87 TAAGAAAGATTTTGTAAAACTTGAGGAA 16 66 1 TTTGTAACTT 0.542743 -18 TTTTGAGTAGTTTGAACATTTTGAGCTGTTTC 18 172 0 TTTGAATTTT 0.438189 -115 AGAAAACAAATATATAAATTTTACTAAGTTGT 20 44 0 TATATATTTT 0.796186 -81 GTAGTTATAGTATATGTATCTTTTTAACTACA 20 88 0 TATATATCTT 0.721471 -37 ATCAATTCTTTTTATAAAAATTGTAGGGGAGA 21 29 1 TTTATAAATT 0.834856 -65 TCTTTGATTATTTTTGTGGTAAAT 21 80 0 TTTGAATTTT 0.438189 -14 ATAATTATATATTTAAATTTTGAAAGTAT 23 8 1 TATATAAATT 0.876667 -190 ACAAGGATTGTATAAAAAAATTATAAATTAAT 23 159 0 TATAAAAATT 0.791469 -39 CTATGTCAATATTATGCACAAGG 23 185 0 TATGTATATT 0.753096 -13 TGCAAAGCTATATAAAAAATTTTGAGTCGTCA 24 35 1 TATAAAATTT 0.718779 -193 TTTTTCATTGTATAAATATATTTTTGACCTTC 26 173 0 TATAAATATT 0.755934 -98 TTATTGTAATTATATATAATTTCTTAAAAAGG 28 22 0 TATATAATTT 0.827201 -63 ***** ***** Masking position 8 Map Score: 27.3799 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 513 Number in noncoding regions = 307 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 6 AAGAAAAGCAAATATAAAATAAAAACCAATAAAA 2 11 1 AAATAATAAA 0.520921 -65 AAATAAACAAAAGATAAAATAAAAAGGAGGGGAG 2 48 1 AAATAATAAA 0.520921 -28 TAATAACTTGCATATAAAAAATCACAAATACGAT 6 51 1 CAATAAAATA 0.509925 -130 CTAACTGACTAAGATAAATAATGACAAAAATAGC 6 142 1 AAATAAAATA 0.840249 -39 TAATAAATAAAAGATTATCTATAAGT 7 3 0 AAATTATATA 0.372981 -102 TAAAATCAAAAATATAATATATGAATTAGGTAGT 8 51 1 AAATAATATA 0.927824 -78 AACCACTCAAAAAATAACTTATAAAGAACTTAAA 8 87 1 AAATAATATA 0.927824 -42 TGGGAATTGAAAAAGAAATAATGAGAAAAAGATA 9 41 0 AAAGAAAATA 0.606697 -181 ACAGAATTAAAAAATAAAAATTAAATAAAAATTT 10 21 0 AAATAAATTA 0.764646 -194 TTAATCAAACATCATAAATATTAAGTATGTTGAA 10 154 0 ATATAAATTA 0.467938 -61 ATTACATTATAAAATAAACAATCACGATTATATA 11 60 0 AAATAAAATA 0.840249 -50 TATAAGAAAAATTAGAAGATATGAGTAATAAAAT 12 94 1 ATAGAATATA 0.505089 -175 AAAATAAATTTTAAGTAAATATTT 12 255 0 AAATAATTTA 0.888149 -14 AACTGATAATAAAATAACTAATAACTACAAATAT 13 181 1 AAATAAAATA 0.840249 -83 GTTAATAAAAAATAGAAGTTTTTA 14 1 0 AAAGAATTTA 0.69959 -210 CAGAGTTTATATTATAAAGTTTGATAATTGGGGT 14 124 1 ATATAATTTA 0.682489 -87 AAAAAATAATGTTTGAGATATTTTCC 14 195 0 AAATAATTTA 0.88815 -16 AAATAAATAAAAAATAATGTTTGAGAGATTTTCC 15 114 0 AAATAATTTA 0.88815 -100 TGAAAAAACTCAAAGAAACTATAAAAAGGAGTTG 17 173 1 CAAGAATATA 0.427202 -31 TAACAAAAAAATAAAATATTTATGGTGTGAC 19 8 1 AAATAATATT 0.372981 -264 CTTTTAAACAAAAATAATATTTGAGGTGAGAAAA 19 219 1 AAATAATTTA 0.88815 -53 AAACAATAAAAACAAAAGTTATCATACTTTCAAA 23 29 0 AAAAAATATA 0.560232 -169 AGTATTAACACTCATAATATATAAACCTTTCGAT 23 96 0 CTATAATATA 0.407723 -102 TATAAAATCCAAAATAACCTTTAATTTTTAATTT 25 17 1 AAATAATTTA 0.88815 -181 AAAAAATGAAAAAATAAAAGATAAAATTAAAAAT 25 40 0 AAATAAGATA 0.55135 -158 CTTATAATTAATTATAATATATAAAATAAAAAAA 25 69 0 ATATAATATA 0.776779 -129 TGCAAAAATAAAAATAAAAATTAAT 26 2 0 AAATAAATTA 0.764646 -269 TACAATGAAAAAGAAAAGATTTTAATGTAAAGCA 26 193 1 AAAAAATTTA 0.440371 -78 CAAATTTTTAATTATAATTTATAATTTATGATAA 27 15 0 ATATAATATA 0.776779 -156 ** **** *** * Masking position 7 Map Score: 26.626 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 469 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 7 GTTTTATTGGTTTTTATTTTATATTTGCTT 2 16 0 TTTTTATTTT 0.857751 -60 TCTCCCCTCCTTTTTATTTTATCTTTTGTT 2 53 0 TTTTTATTTT 0.857751 -23 AATCCCATTTTTATAAAGTAAAAAATAAT 6 10 1 TTTATAAAGT 0.171942 -171 TTTTTCACCTTTTTATCGTTTAAGTTCTT 8 110 0 TTTTTATCGT 0.599441 -19 TATTACAATATTTTAAATGTAAAGTTCGAT 9 109 0 TTTTAAATGT 0.350271 -113 TATTTTTGTCATTTTTATGTTTTTATTTGA 9 166 0 ATTTTTATGT 0.238949 -56 TTTTATTTAATTTTTATTTTTTAATTCTGT 10 25 1 TTTTTATTTT 0.857751 -190 ATTTACTAATTTTTTAATTTGTTTTATTTA 10 121 1 TTTTTAATTT 0.763005 -94 TAATTTGTTTTATTTATTGTTCAACATACT 10 135 1 TATTTATTGT 0.484104 -80 GATTGTTTATTTTATAATGTAATAATTAAA 11 71 1 TTTATAATGT 0.702823 -39 TTTTTTTACTTTTTTATTTTTTTAAGAATA 12 20 1 TTTTTATTTT 0.857751 -249 GTAAATTTTATTTATATTGTGAAATAGTAT 13 67 1 TTTATATTGT 0.815821 -197 TCAGTTATTTATTTTATTGTGTAAGTAGTA 13 157 0 ATTTTATTGT 0.775446 -107 TTATTTTTTATTTATTTTGTATTTTTGACA 15 131 1 TTTATTTTGT 0.42997 -83 CATCAACTCCTTTTTATAGTTTCTTTGAGT 17 180 0 TTTTTATAGT 0.64035 -24 ATTTTTTTATTTTTTATTGTAAATGGTTAT 18 23 1 TTTTTATTGT 0.953005 -264 TAAATATTTTATTTTTTTGTTA 19 3 0 ATTTTTTTGT 0.370298 -269 ATTTTTTATTTTCATGGTTGTG 20 3 1 TTTTTATTTT 0.857751 -122 ATAACTTTTGTTTTTATTGTTTTTAGTAAA 23 41 1 TTTTTATTGT 0.953005 -157 AGATATATCATTTTTATTGTTTTATTTTAA 24 144 1 TTTTTATTGT 0.953005 -84 GTTTTTTGTATTTTTAATGTTGTGGATTTT 24 183 1 TTTTTAATGT 0.91545 -45 TAACCTTTAATTTTTAATTTTATCTTTTAT 25 31 1 TTTTTAATTT 0.763005 -167 TTTTTCATTTTTTTTATTTTATATATTATA 25 61 1 TTTTTATTTT 0.857751 -137 TTAATTTTTATTTTTATTTTTGCACTATAT 26 12 1 TTTTTATTTT 0.857751 -259 AATCTTTTCTTTTTCATTGTATAAATATAT 26 184 0 TTTTCATTGT 0.733623 -87 AAAAGAAAAGATTTTAATGTAAAGCATCTG 26 201 1 ATTTTAATGT 0.648354 -70 TCTGCAAACATTTACAATGTATTTGACAGA 26 227 0 TTTACAATGT 0.243107 -44 TAAAAAACTATTTTTATTCTAACTTAAAAC 28 56 0 TTTTTATTCT 0.557038 -29 ATAAAAATAGTTTTTTATGTGATAGT 28 69 1 TTTTTTATGT 0.648354 -16 ********** Masking position 3 Map Score: 33.258 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 601 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 8 ATTTCCACCTCAAAAAACAATTACA 1 75 0 CACCTCAAAA 0.94314 -15 CAATAATCACCTTTAATAAACTGACTT 4 12 0 CACCTTTAAT 0.87513 -17 ATTAATCAAACATCATAAATATTAAGTATG 10 159 0 CATCATAAAT 0.78975 -56 TGAATTAATTCATCACAAATGTATCGAATT 11 15 1 CATCACAAAT 0.813127 -95 CATATTTTTTCACCTTTAATTATATTTGTA 13 206 0 CACCTTTAAT 0.87513 -58 TCATAAGATTCACCATAAAACCCCAATTAT 14 147 0 CACCATAAAA 0.881328 -64 TCATATTTATCACCTTTAATGGTTGAGACA 18 62 0 CACCTTTAAT 0.87513 -225 AATACAGAAACAGCTCAAAATGTTCAAACT 18 166 1 CAGCTCAAAA 0.732999 -121 GCATATGTCACACCATAAATATTTTATTTT 19 18 0 CACCATAAAT 0.910904 -254 CACATTTTCTCACCTCAAATATTATTTTTG 19 227 0 CACCTCAAAT 0.958044 -45 ATACTTTACCCATCTCAAAATCCACAACAT 24 199 0 CATCTCAAAA 0.859039 -29 CGCACTATCACATCTTAAAATAACTACCTT 27 66 0 CATCTTAAAA 0.840277 -105 ********** Masking position 8 Map Score: 10.4271 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 52 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 ATATGTAAGTATGTAAATAGTTCATGTAAA 5 42 1 ATGTAAATAG 0.650626 -30 TTTCTAAATTTTTTAAATAGAAATT 8 6 0 TTTTAAATAG 0.53624 -123 AGGACGGTGGTTGTAAATGGATAAAATCCA 15 76 1 TTGTAAATGG 0.953333 -138 TTATTTTTTATTGTAAATGGTTATGTATGT 18 29 1 TTGTAAATGG 0.953333 -258 AATACCCAAGTTGGAAATGGGCTTGGAAAT 18 214 1 TTGGAAATGG 0.970218 -73 GGAAATGGGCTTGGAAATGGAGCGGGAAAA 18 226 1 TTGGAAATGG 0.970218 -61 ATAAAAGCAAATGGAAATGGTGAAAAGAAA 19 70 0 ATGGAAATGG 0.889906 -202 TGTTGTGGATTTTGAGATGGGTAAAGTATC 24 200 1 TTTGAGATGG 0.758655 -28 ATCACTCACTTTGAAGATAGTTGATATAAT 26 117 0 TTGAAGATAG 0.536977 -154 CCTTCTTCTTTTGGAGATAGGGGTAATTAA 26 148 0 TTGGAGATAG 0.882304 -123 GTCAAATACATTGTAAATGTTTGCAGATAT 26 230 1 TTGTAAATGT 0.616804 -41 ********** Masking position 5 Map Score: 7.45676 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 247 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ACAATTACAATTAATTAAAAAGATTTAGAA 1 54 0 TTAATTAAAA 0.873652 -36 ACCAAAAAGTTTAATTAAAATAATTTTATT 3 14 0 TTAATTAAAA 0.873652 -26 TTTTATTATTTTACTTAAATACTACAATGC 9 75 1 TTACTTAAAT 0.695254 -147 ATTTAATTAAAAATTTTTATTT 10 3 1 TTAATTAAAA 0.873652 -212 TTTGTGAGCCTTATTAAAAATCTTAGTTCA 12 225 1 TTATTAAAAA 0.67582 -44 TTCAAAATATTTACTTAAAATTTATTTT 12 251 1 TTACTTAAAA 0.955431 -18 TAAATAAAATTTACTTAAAGATTTATATAA 13 51 0 TTACTTAAAG 0.771759 -213 TGTATAATTGTTAATAAAAAATAGAAGTTT 14 14 0 TTAATAAAAA 0.797651 -197 ATACAAGAGATTACTTAAAATCTATAAACA 15 34 1 TTACTTAAAA 0.955431 -180 AGTGAAGATATTACTAAAAATACTACCAAT 18 108 0 TTACTAAAAA 0.92431 -179 ACTTAAATGGTTATTAAAAAGTAATAACAA 19 166 1 TTATTAAAAA 0.67582 -106 TATTGAGGTTTTACTAAAAACAATAAAAAC 23 50 0 TTACTAAAAA 0.92431 -148 TTATATATAATTTCTTAAAAAGGGATGTGA 28 15 0 TTTCTTAAAA 0.678392 -70 ATTTTTATTCTAACTTAAAACATTTATTGT 28 47 0 TAACTTAAAA 0.678458 -38 ********** Masking position 7 Map Score: 14.1619 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 44 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TCAATGAAATTACTATATATTTAACACATA 1 16 1 TACTATATAT 0.723633 -74 TTTAGAAATTTATAATATGTGTTAAATATA 1 31 0 TATAATATGT 0.335553 -59 ACGCGATGTGAAGTATATGTCTATATGTAA 5 20 1 AAGTATATGT 0.833686 -52 TGATTTTAGATAGTATATATAACTTTCTAA 8 29 0 TAGTATATAT 0.774731 -100 CTAATTCATATATTATATTTTTGATTTTAG 8 50 0 TATTATATTT 0.624654 -79 TTTTATTTGAAACTATATATCGTTTTCCAT 9 146 0 AACTATATAT 0.672032 -76 ATTATAATATTATTATATGTTTTATCACTT 10 88 1 TATTATATGT 0.855112 -127 AAGAATATATTTGTATATGTAAATTAATAG 12 43 1 TTGTATATGT 0.35364 -226 TTAGGATAAGTAATATATATATAAGAAAAA 12 75 1 TAATATATAT 0.624114 -194 GTTATTAATTAAATATATGTCGAAATTCGT 12 150 1 AAATATATGT 0.699011 -119 TTTCACCTTTAATTATATTTGTAGTTATTA 13 199 0 AATTATATTT 0.559512 -65 TTTCTTACACTACTATATGTAGTTAAAAAG 20 71 1 TACTATATGT 0.829588 -54 AGGGTAGTTATAGTATATGTATCTTTTTAA 20 93 0 TAGTATATGT 0.864757 -32 ATAATTATATATTTAAATTTTG 23 3 1 AATTATATAT 0.712892 -195 AGAAGGTCAAAAATATATTTATACAATGAA 26 172 1 AAATATATTT 0.324084 -99 CATTTATTGTAATTATATATAATTTCTTAA 28 27 0 AATTATATAT 0.712892 -58 ********** Masking position 5 Map Score: 5.85675 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 100 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 AATTTCTAAATCTTTTTAATTAATTGTAATT 1 51 1 TTTTTTAATT 0.670537 -39 TTTATATGCAAGTTATTAGTTTTTAGTTTAT 6 38 0 ATTATTAGTT 0.762014 -143 ATAATCTTTTATTTATTAATTTAATTTATTT 7 19 1 ATTATTAATT 0.93505 -86 AATAGTCCCAACTGACTAATTGATCAGGTGA 9 192 1 ATGACTAATT 0.505425 -30 ATTAAATAAAAATTTTTAATTAAAT 10 5 0 ATTTTTAATT 0.890955 -210 TTTAATTTTTATTTTTTAATTCTGTATTGAA 10 30 1 ATTTTTAATT 0.909021 -185 ATCACTTTATATTTACTAATTTTTTAATTTG 10 111 1 ATTACTAATT 0.828078 -104 CACCTTTTTAACTTTTTAATTATTACATTAT 11 84 0 ATTTTTAATT 0.909021 -26 CAAAAATTTTAGTTATTAATTAAATATATGT 12 139 1 ATTATTAATT 0.93505 -130 TTACGGTATATATTATTAATTATACGAATTT 12 172 0 TTTATTAATT 0.755422 -97 TTTTATTATCAGTTATTTATTTTATTGTGTA 13 164 0 ATTATTTATT 0.526053 -100 TTATATTTGTAGTTATTAGTTATTTTATTAT 13 186 0 ATTATTAGTT 0.762014 -78 CACAACCGTGAATTATTAATTTATAATTTTT 23 145 1 ATTATTAATT 0.767242 -53 AATTATTTTTAATTGGTGAAAATA 24 4 1 TTTTTTAATT 0.670314 -224 AATAACCTTTAATTTTTAATTTTATCTTTTA 25 29 1 ATTTTTAATT 0.890955 -169 AATCAGCAAAATTGATTAATTGAATTAGCAA 25 109 1 ATGATTAATT 0.762011 -89 TTTTAACCTAATTTGCTAATTCAATTAATCA 25 121 0 ATTGCTAATT 0.45943 -77 TTTTATCATAAATTATAAATTATAATTAAAA 27 13 1 ATTATAAATT 0.461522 -158 ATCACCAACAAATTTTTAATTATAATTTATA 27 26 0 ATTTTTAATT 0.890955 -145 * ********* Masking position 3 Map Score: 20.5889 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 198 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 13 CAATAATCACCTTTAATAAACTGA 4 15 0 TAACACCTTT 0.809661 -14 TGATTAATGATATATACCTCTAACTGACTAA 6 123 1 TATTACCTCT 0.880131 -58 CATATCTATTTAAATACCTCTGCTAAATTTG 13 100 0 TAATACCTCT 0.976175 -164 TCATCAACCTTAACTCCCTCTGGGTTCATTG 17 98 1 TAATCCCTCT 0.915842 -106 ACATATACTATAACTACCCTTCAGGTGAAAA 20 103 1 TAATACCCTT 0.900686 -22 ATCAATCCCAAAAATACCTCTACTACATACC 22 20 0 AAATACCTCT 0.880131 -24 TGAGTGATATTAATTACCCCTATCTCCAAAA 26 139 1 TAATACCCCT 0.95868 -132 CATCTTAAAATAACTACCTTTGTCACAATAT 27 55 0 TAATACCTTT 0.94123 -116 *** ******* Masking position 2 Map Score: 2.5141 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 59 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 TACTATCTAAAATCAAAAATATAATATATG 8 44 1 AATCAAAAAT 0.835138 -85 ATTTAATTAAAAATTTTTATTTAA 10 5 1 AATTAAAAAT 0.758764 -210 TTTTATTTATTGTTCAACATACTTAATATT 10 142 1 TGTTCAACAT 0.687872 -73 TTTAAACATTAATCAAACATCATAAATATT 10 166 0 AATCAAACAT 0.806053 -49 GTGATGAATTAATTCAAAAT 11 1 0 AATTCAAAAT 0.835138 -109 TTGTGAGCCTTATTAAAAATCTTAGTTCAA 12 226 1 TATTAAAAAT 0.670285 -43 TAAAAATCTTAGTTCAAAATATTTACTTAA 12 239 1 AGTTCAAAAT 0.806052 -30 TAAACTCTGGAATCCAAAATATAAAAAGAT 14 103 0 AATCCAAAAT 0.890812 -108 AACAAAAACTTGTCAAAAATACAAAATAAA 15 141 0 TGTCAAAAAT 0.728716 -73 CTGTCCAACACTTCCCTTTAA 15 203 0 TGTCCAACAC 0.284751 -11 TACAGGGGTCTGTCCAACATGACGTTATAG 17 42 1 TGTCCAACAT 0.780188 -162 ATGATTCCCAAGTCCAACATGGAGTTATGC 17 72 0 AGTCCAACAT 0.845953 -132 TTAAAAGAATTATCCAAAATATCATCCAGA 19 108 0 TATCCAAAAT 0.84059 -164 AAATTTTTGGTATTAAACATCAATTCTTTT 21 11 1 TATTAAACAT 0.625168 -83 TATTTTCACCAATTAAAAATAATT 24 5 0 AATTAAAAAT 0.758764 -223 TATAATATAAAATCCAAAATAACCTTTAAT 25 12 1 AATCCAAAAT 0.890812 -186 TAAAAGATAAAATTAAAAATTAAAGGTTAT 25 30 0 AATTAAAAAT 0.758764 -168 TATAAATTATAATTAAAAATTTGTTGGTGA 27 26 1 AATTAAAAAT 0.758764 -145 ********** Masking position 3 Map Score: 16.4776 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 230 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 15 TTCTATCACCTTTGTGCTATT 6 170 0 TCTATCACCT 0.901339 -11 AATGGTTGAGACAATCACATACATAACCAT 18 45 0 ACAATCACAT 0.898294 -242 TTTTTGCCGCACTATCACATCTTAAAATAA 27 73 0 ACTATCACAT 0.966732 -98 TCTATCACATCCCTTTTTAA 28 1 1 TCTATCACAT 0.953007 -84 ACTATCACATAAAAAACTAT 28 75 0 ACTATCACAT 0.966732 -10 ********** Masking position 5 Map Score: 1.95639 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