AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i159_mjan_pyro_300.orf -o159_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: RMJ06212 36 M_jannaschii_chromosome RMJ10046 23 M_jannaschii_chromosome Input sequences: #1 RMJ14763 300 M_jannaschii_chromosome #2 RMJ07770 261 M_jannaschii_chromosome #3 RMJ04644 134 M_jannaschii_chromosome #4 RMJ15227 18 M_jannaschii_chromosome #5 RMJ03004 83 M_jannaschii_chromosome #6 RMJ05116 95 M_jannaschii_chromosome #7 RMJ02377 221 M_jannaschii_chromosome #8 RMJ03320 214 M_jannaschii_chromosome #9 RMJ13235 109 M_jannaschii_chromosome #10 RMJ03131 268 M_jannaschii_chromosome #11 RMJ13030 263 M_jannaschii_chromosome #12 RMJ05742 210 M_jannaschii_chromosome #13 RMJ05650 213 M_jannaschii_chromosome #14 RMJ11762 83 M_jannaschii_chromosome #15 RMJ12007 203 M_jannaschii_chromosome #16 RMJ14441 286 M_jannaschii_chromosome #17 RMJ05775 271 M_jannaschii_chromosome #18 RMJ14343 124 M_jannaschii_chromosome #19 RMJ14151 93 M_jannaschii_chromosome #20 RMJ14817 43 M_jannaschii_chromosome #21 RMJ11840 197 M_jannaschii_chromosome #22 RMJ12613 227 M_jannaschii_chromosome #23 RMJ07178 197 M_jannaschii_chromosome #24 RMJ06181 270 M_jannaschii_chromosome #25 RMJ05205 170 M_jannaschii_chromosome #26 RMJ01354 84 M_jannaschii_chromosome Motif number 1 CTCTGTGAGGAATTCAAAATTTTTTTAAAG 1 131 1 AATTCAAAAT 0.796787 -170 AAAATGATAAAATTAAAAAAATCTTTAAAA 1 162 0 AATTAAAAAA 0.913598 -139 AAAATAATAATATTAAAATGATAAAATTAA 1 176 0 TATTAAAATG 0.592723 -125 TCCTAAAAATTACTAAAAAATGTTAAAATA 1 200 0 TACTAAAAAA 0.66359 -101 GTAATATATTAACAAAAAGGTTGGTGTTGG 1 279 1 AACAAAAAGG 0.497434 -22 AAAATTTTAAAATTAAAAATAAAGTCCAAA 2 40 0 AATTAAAAAT 0.930639 -222 TATGCCCTCCAATTAAAATTTTAAAATTAA 2 54 0 AATTAAAATT 0.830908 -208 ATAAAAATTATATAAAAAATAGAAAAAAG 3 10 0 TATAAAAAAT 0.89184 -125 ATATATTAGATATTAAAAATTTTTGTTCAT 3 89 1 TATTAAAAAT 0.871139 -46 GACCTCATTATATAAAAAAGA 5 2 0 TATAAAAAAG 0.828838 -82 TTGCAGAATATATTCAAAAACAAACTTTAA 6 56 1 TATTCAAAAA 0.608895 -40 TATAGTTTCAAATAAAAACATAAAAATGAC 7 159 1 AATAAAAACA 0.75048 -63 TGATCAGGTGAATTAAAATG 7 212 1 AATTAAAATG 0.742827 -10 ATTTAATTAAAAATTTTTATTTAA 8 5 1 AATTAAAAAT 0.930639 -210 TTCAATACAGAATTAAAAAATAAAAATTAA 8 31 0 AATTAAAAAA 0.913598 -184 AAATAAAACAAATTAAAAAATTAGTAAATA 8 120 0 AATTAAAAAA 0.913598 -95 GTGATGAATTAATTCAAAAT 9 1 0 AATTCAAAAT 0.796787 -109 ATAATGTAATAATTAAAAAGTTAAAAAGGT 9 84 1 AATTAAAAAG 0.887384 -26 TTCTTAAAAAAATAAAAAAGTAAAAAAAGG 10 18 0 AATAAAAAAG 0.905758 -251 TTAATTTACATATACAAATATATTCTTAAA 10 40 0 TATACAAATA 0.410402 -229 TTTAATTAATAACTAAAATTTTTGCCAATA 10 133 0 AACTAAAATT 0.645524 -136 TTGTGAGCCTTATTAAAAATCTTAGTTCAA 10 226 1 TATTAAAAAT 0.871139 -43 TGAAAAATAAAATTAAAACAATTTATATAA 11 29 1 AATTAAAACA 0.711476 -235 TATAATTGTTAATAAAAAATAGAAGTTTTT 12 12 0 AATAAAAAAT 0.942414 -199 AGATAAATCTAATAAAAAATTTGTATAATT 12 35 0 AATAAAAAAT 0.942414 -176 GAATCCAAAATATAAAAAGATTTTTAGCCA 12 94 0 TATAAAAAGA 0.643798 -117 TTATGAATAAAATACAAATATTGAGGAAAA 12 171 1 AATACAAATA 0.5801 -40 ATACAAAATAAATAAAAAATAATGTTTGAG 13 123 0 AATAAAAAAT 0.942414 -91 ACTTGTCAAAAATACAAAATAAATAAAAAA 13 134 0 AATACAAAAT 0.827061 -80 AAAAAACATAAACAAAAACTTGTCAAAAAT 13 151 0 AACAAAAACT 0.585597 -63 GGAAAGGTTTAACAAAAAAGGATAAGCCAG 14 32 1 AACAAAAAAG 0.780631 -52 TCAAAGAAACTATAAAAAGGAGTTGATGGA 15 182 1 TATAAAAAGG 0.573906 -22 AACCATTTACAATAAAAAATAAAAAAATGA 16 21 0 AATAAAAAAT 0.942414 -266 GTGAAGATATTACTAAAAATACTACCAATA 16 107 0 TACTAAAAAT 0.714535 -180 ATGTTCAAACTACTCAAAATAATCAGCAAA 16 185 1 TACTCAAAAT 0.422454 -102 TAACAAAAAAATAAAATATTT 17 2 1 AACAAAAAAA 0.826844 -270 TGATTCCTCCAATTAAAAGAATTATCCAAA 17 120 0 AATTAAAAGA 0.746261 -152 CTTAAATGGTTATTAAAAAGTAATAACAAA 17 167 1 TATTAAAAAG 0.7988 -105 AAAAAGTAATAACAAAAATAACAGTAAAGC 17 181 1 AACAAAAATA 0.636417 -91 ATTCCTTTTAAACAAAAATAATATTTGAGG 17 215 1 AACAAAAATA 0.636417 -57 CAACCATGAAAATAAAAAAT 18 1 0 AATAAAAAAT 0.942414 -124 CAATTCTTTTTATAAAAATTGTAGGGGAGA 19 31 1 TATAAAAATT 0.751401 -63 TTTTGTGGTAAATAAAAACTGCCCTCATAA 19 63 0 AATAAAAACT 0.792383 -31 TACTAAAAACAATAAAAACAAAAGTTATCA 21 39 0 AATAAAAACA 0.75048 -159 ACAAGGATTGTATAAAAAAATTATAAATTA 21 161 0 TATAAAAAAA 0.866631 -37 TATTTTCACCAATTAAAAATAATT 22 5 0 AATTAAAAAT 0.930639 -223 TGCAAAGCTATATAAAAAATTTTGAGTCGT 22 35 1 TATAAAAAAT 0.89184 -193 TACTTACCAATATTAAAAGATATATCATTT 22 127 1 TATTAAAAGA 0.597072 -101 AAAATAAAACAATAAAAATGATATATCTTT 22 142 0 AATAAAAATG 0.77891 -86 AACAGCAGTATATTAAAATAAAACAATAAA 22 156 0 TATTAAAATA 0.66131 -72 CAACATTAAAAATACAAAAAACAGCAGTAT 22 175 0 AATACAAAAA 0.790304 -53 TAAAAGATAAAATTAAAAATTAAAGGTTAT 23 30 0 AATTAAAAAT 0.930639 -168 TAATATATAAAATAAAAAAAATGAAAAAAT 23 59 0 AATAAAAAAA 0.928041 -139 CAGTTGCATTTATAAAAAATATTCTTTAAA 23 154 1 TATAAAAAAT 0.89184 -44 CAAAAATAAAAATAAAAATTAAT 24 4 0 AATAAAAATT 0.857121 -267 TATTGTAGGTAATACAAAATCAGGATTTAT 24 80 1 AATACAAAAT 0.827061 -191 TGTTTGCAGATATTAAAAGTCTTAGGGTGA 24 247 1 TATTAAAAGT 0.652821 -24 TATAAATTATAATTAAAAATTTGTTGGTGA 25 26 1 AATTAAAAAT 0.930639 -145 AGTAGCATTAAACAAAAAAAGATACATTCA 25 128 1 AACAAAAAAA 0.826844 -43 TTTAAGTTAGAATAAAAATAGTTTTTTATG 26 58 1 AATAAAAATA 0.825405 -27 ********** Masking position 6 Map Score: 68.526 Number of sites scoring better than the average of aligned sites = 2672 Number in coding regions = 1882 Number in noncoding regions = 790 Number of orfs with sites within 600 bp upstream = 525 Fraction of orfs with sites within 600 bp upstream = 0.0843238 Motif number 2 TTTGAATCATAAAGAAAGCCTAAAAGTATCATCAA 1 64 0 AAAGAAAAAA 0.797063 -237 GATAAAATTAAAAAAATCTTTAAAATCTTTAAAAA 1 152 0 AAAAAAAAAA 0.884352 -149 AAAATGTTAAAATAATAATATTAAAATGATAAAAT 1 179 0 AATAATTAAA 0.595837 -122 ATTTTATCCTAAAAATTACTAAAAAATGTTAAAAT 1 201 0 AAAAATAAAA 0.884352 -100 AGCTGTAGTAATATATTAACAAAAAGGTTGGTGTT 1 272 1 ATATATAAAA 0.882934 -29 AAAGTCCAAAAAATAAAACTTAAAATAAGATAATA 2 15 0 AAATAAAAAA 0.950341 -247 TATGCCCTCCAATTAAAATTTTAAAATTAAAAATA 2 49 0 AATTAATAAA 0.786758 -213 CAATATTCATAAAAATTATATAAAAAATAGAAAAA 3 13 0 AAAAATAAAA 0.884352 -122 AGTTTATCAAAAATAATCGTTAAAAATACATCAAT 3 44 0 AAATAAAAAA 0.950341 -91 TTTATACTTCAAATATAATTTAAAATTTAAAAAAA 5 49 1 AAATATAAAA 0.950341 -35 ATTGAAAAAGAAATAATGAGAAAAAGATATTTCCT 7 35 0 AAATAAAAAA 0.950341 -187 TTTACATTTAAAATATTGTAATAAAGTATAATGGA 7 116 1 AAATATTAAA 0.92766 -106 ATATAGTTTCAAATAAAAACATAAAAATGACAAAA 7 158 1 AAATAATAAA 0.92766 -64 ATTAAAAAATAAAAATTAAATAAAAATTTTTAATT 8 15 0 AAAAATAAAA 0.884352 -200 AAATTAGTAAATATAAAGTGATAAAACATATAATA 8 98 0 ATATAATAAA 0.834816 -117 TGAACAATAAATAAAACAAATTAAAAAATTAGTAA 8 123 0 ATAAAATAAA 0.66881 -92 TTTTTATGGCAAATAACAGTTTAAACATTAATCAA 8 180 0 AAATAATAAA 0.92766 -35 GTTATTTGCCATAAAAAGGTGAAAAAT 8 198 1 ATAAAAAAAA 0.750854 -17 ATAATGTAATAATTAAAAAGTTAAAAAGGTGAAAG 9 84 1 AATTAATAAA 0.786758 -26 ATTCTTAAAAAAATAAAAAAGTAAAAAAAGGATTA 10 14 0 AAATAATAAA 0.92766 -255 TTACATATACAAATATATTCTTAAAAAAATAAAAA 10 30 0 AAATATTAAA 0.92766 -239 GATAAGTAATATATATATAAGAAAAATTAGAAGAT 10 79 1 ATATATAAAA 0.882934 -190 ACATATATTTAATTAATAACTAAAATTTTTGCCAA 10 135 0 AATTAAAAAA 0.846298 -134 TCTTAGTTCAAAATATTTACTTAAAATTTATTTT 10 245 1 AAATATTAAA 0.92766 -24 CACATATTTGAAAAATAAAATTAAAACAATTTATA 11 21 1 AAAAATTAAA 0.836709 -243 AAATTTACTTAAAGATTTATATAAATTGTTTTAAT 11 40 0 AAAGATTAAA 0.724656 -224 CTACAAATATAATTAAAGGTGAAAAAATATGAAAG 11 205 1 AATTAAAAAA 0.846298 -59 TAAAAATTAGATAAATCTAATAAAAAATTTGTATA 12 38 0 ATAAATAAAA 0.750853 -173 CCTATTTTTAAAATATCTGGCTAAAAATCTTTTTA 12 77 1 AAATATTAAA 0.92766 -134 AATAAAATACAAATATTGAGGAAAATATCTCAAAC 12 176 1 AAATATAAAA 0.950341 -35 GATAAAATCCAAATATTGAGGAAAATCTCTCAAAC 13 95 1 AAATATAAAA 0.950341 -119 TAAACTTCTCAATTATCCCAAAAAAACATAAACAA 13 166 0 AATTATAAAA 0.846298 -48 AGAAGTTAAGAAAGATTTTGTAAAACTTGAGGAA 14 60 1 AAAGATAAAA 0.797063 -24 GAAAAAACTCAAAGAAACTATAAAAAGGAGTTGAT 15 174 1 AAAGAAAAAA 0.797063 -30 ACCATTTACAATAAAAAATAAAAAAATGAGATGAA 16 15 0 ATAAAAAAAA 0.750854 -272 ATTAAAGGTGATAAATATGAAAAAAATAGCGATGA 16 72 1 ATAAATAAAA 0.750854 -215 AAACTACTCAAAATAATCAGCAAAATACCCAAGTT 16 191 1 AAATAAAAAA 0.950341 -96 AAGTAATAACAAAAATAACAGTAAAGCTTATATTC 17 184 1 AAAAATTAAA 0.836709 -88 ATAATTATATATTTAAATTTTGAAAGT 21 3 1 AATTATTAAA 0.786758 -195 CAGTATATTAAAATAAAACAATAAAAATGATATAT 22 146 0 AAATAATAAA 0.92766 -82 AATCCACAACATTAAAAATACAAAAAACAGCAGTA 22 176 0 ATTAAAAAAA 0.464405 -52 ATATAATATAAAATCCAAAATAACCTTTAA 23 6 1 ATATAAAAAA 0.882934 -192 AAAAATGAAAAAATAAAAGATAAAATTAAAAATTA 23 38 0 AAATAAAAAA 0.950341 -160 ATTAATTATAATATATAAAATAAAAAAAATGAAAA 23 62 0 ATATATAAAA 0.882934 -136 TATAGTGCAAAAATAAAAATAAAAATTAAT 24 6 0 AAATAAAAAA 0.950341 -265 ATACATCTGAATATAAACCTATAAAAGATAATAAT 24 46 1 ATATAATAAA 0.834816 -225 TAGTTGATATAATTATTATGATAAATCCTGATTTT 24 95 0 AATTATTAAA 0.786758 -176 ATAATTTATAATTTATGATAAAAAA 25 1 0 ATTTATAAAA 0.684541 -170 ATAAATTATAAATTATAATTAAAAATTTGTTGGTG 25 20 1 AATTATAAAA 0.846298 -151 TTGTAATTATATATAATTTCTTAAAAAGGGATGTG 26 16 0 ATATAATAAA 0.834816 -69 ****** **** Masking position 5 Map Score: 81.8154 Number of sites scoring better than the average of aligned sites = 1663 Number in coding regions = 1212 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 3 GAGGAATTCAAAATTTTTTTAAAGATTTTA 1 137 1 AAATTTTTTT 0.808676 -164 TATTTAGTATAAATCTTTTTCTAACAAGTG 2 197 0 AAATCTTTTT 0.759954 -65 TTAAAACCTAATATCTTATTTAGTATAAAT 2 213 0 ATATCTTATT 0.766976 -49 AGTCTGATTTAAATTTAATTAAAACCTAAT 2 231 0 AAATTTAATT 0.790991 -31 AATATCTAATATATATTTTTCGGTAGTTTA 3 73 0 ATATATTTTT 0.772706 -62 TTTATACTTCAAATATAATTTAAAATTTAA 5 49 1 AAATATAATT 0.766763 -35 CACTTAGAAATTTTTTTAAATTTTAAA 5 67 0 AAATTTTTTT 0.808676 -17 GCTTAAGTTTAAATATTATTGCAGAATATA 6 38 1 AAATATTATT 0.84506 -58 ACAAAATTTTCTTTCTATTTTCG 7 4 1 AAATTTTCTT 0.737406 -218 TTCGGAGGAAATATCTTTTTCTCATTATTT 7 30 1 ATATCTTTTT 0.71827 -192 ACATATACAAATATATTCTTAAAAAAATAA 10 33 0 ATATATTCTT 0.693054 -236 GCCAATATCGATATTTTATTACTCATATCT 10 110 0 ATATTTTATT 0.814681 -159 ATTTCGACATATATTTAATTAATAACTAAA 10 146 0 ATATTTAATT 0.752987 -123 CTATTACGGTATATATTATTAATTATACGA 10 176 0 ATATATTATT 0.814678 -93 GTAATAGCATAAATTTATTTGAATGGTTTG 10 199 1 AAATTTATTT 0.722918 -70 TTAGTTCAAAATATTTACTTAAAATTTATT 10 247 1 ATATTTACTT 0.610247 -22 TATTTACTTAAAATTTATTTT 10 258 1 AAATTTATTT 0.722918 -11 ATCTTTAAGTAAATTTTATTTATATTGTGA 11 59 1 AAATTTTATT 0.845376 -205 GAATTTCAACATATCTATTTAAATACCTCT 11 110 0 ATATCTATTT 0.63848 -154 TAATAACTACAAATATAATTAAAGGTGAAA 11 199 1 AAATATAATT 0.766763 -65 ATCTGGCTAAAAATCTTTTTATATTTTGGA 12 91 1 AAATCTTTTT 0.759954 -120 CACACCATAAATATTTTATTTTTTTGTTA 17 10 0 ATATTTTATT 0.814681 -262 TTCTCACCTCAAATATTATTTTTGTTTAAA 17 221 0 AAATATTATT 0.84506 -51 CAAAATTTAAATATATAATTAT 21 3 0 ATATATAATT 0.752706 -195 CATTTATAAAAAATATTCTTTAAATATGTG 23 160 1 AAATATTCTT 0.73713 -38 AGAAGGTCAAAAATATATTTATACAATGAA 24 172 1 AAATATATTT 0.467739 -99 TATTGTAATTATATATAATTTCTTAAAAAG 26 23 0 ATATATAATT 0.752706 -62 ********** Masking position 6 Map Score: 28.0274 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 652 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 4 ATAATATTAAAATGATAAAATTAAAAAAATC 1 169 0 AATGAAAAAT 0.848967 -132 ATTACTAAAAAATGTTAAAATAATAATATTA 1 191 0 AATGTAAAAT 0.818824 -110 TTTTAGGATAAAATAGAAAATTTTATATACC 1 222 1 AAATAAAAAT 0.837829 -79 CTCCAATTAAAATTTTAAAATTAAAAATAAA 2 47 0 AATTTAAAAT 0.776392 -215 ATTATATAAAAAATAGAAAAAAG 3 3 0 AAATAAAAAA 0.865327 -132 ATTATATTTGAAGTATAAAATAGCAATAACC 5 37 0 AAGTAAAAAT 0.780405 -47 TATAATTTAAAATTTAAAAAAATTTCTAAGT 5 62 1 AATTTAAAAA 0.812271 -22 AAAAAGAAATAATGAGAAAAAGATATTTCCT 7 35 0 AATGAAAAAA 0.874858 -187 AAAACATAAAAATGACAAAAATAGTCCCAAC 7 173 1 AATGAAAAAA 0.874858 -49 TTCAATACAGAATTAAAAAATAAAAATTAAA 8 30 0 AATTAAAAAT 0.812271 -185 TAAATAAAACAAATTAAAAAATTAGTAAATA 8 120 0 AAATTAAAAA 0.837829 -95 TTGCCATAAAAAGGTGAAAAAT 8 203 1 AAGGTAAAAA 0.821961 -12 TAATAATTAAAAAGTTAAAAAGGTGAAAGC 9 90 1 AAAGTAAAAA 0.870323 -20 AAAAAATAAAAAAGTAAAAAAAGGATTAAAT 10 11 0 AAAGTAAAAA 0.870323 -258 ACCTCTGCTAAATTTGAAAATACTATTTCAC 11 85 0 AATTTAAAAT 0.776392 -179 AATATAATTAAAGGTGAAAAAATATGAAAGC 11 210 1 AAGGTAAAAA 0.821961 -54 CTGGAATCCAAAATATAAAAAGATTTTTAGC 12 96 0 AAATAAAAAA 0.865327 -115 AATACAAAATAAATAAAAAATAATGTTTGAG 13 123 0 AAATAAAAAT 0.837829 -91 AACTTGTCAAAAATACAAAATAAATAAAAAA 13 134 0 AAATAAAAAT 0.837829 -80 GAGAAGTCATAAGGTGAAAAAACTCAAAGAA 15 159 1 AAGGTAAAAA 0.821961 -45 TTACAATAAAAAATAAAAAAATGAGATGAAA 16 14 0 AAATAAAAAA 0.865327 -273 ACAACCATGAAAATAAAAAAT 18 1 0 AAATAAAAAT 0.837829 -124 AAACCTCAATAATTTTAAAAACTTTTAATCG 21 69 1 AATTTAAAAA 0.812271 -129 ACAACATTAAAAATACAAAAAACAGCAGTAT 22 175 0 AAATAAAAAA 0.865327 -53 TGAAAAAATAAAAGATAAAATTAAAAATTAA 23 37 0 AAAGAAAAAT 0.870323 -161 AAATAAAAAAAATGAAAAAATAAAAGATAAA 23 49 0 AATGAAAAAT 0.848967 -149 CCAAAAGAAGAAGGTCAAAAATATATTTATA 24 164 1 AAGGTAAAAA 0.821961 -107 ***** ***** Masking position 7 Map Score: 38.4351 Number of sites scoring better than the average of aligned sites = 989 Number in coding regions = 771 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 5 TCTTTATGATTCAAAAAAATGCGTAAGTTC 1 84 1 TCAAAAAAAT 0.809033 -217 TTCTATTTTATCCTAAAAATTACTAAAAAA 1 210 0 TCCTAAAAAT 0.730212 -91 AAAAATAAAGTCCAAAAAATAAAACTTAAA 2 26 0 TCCAAAAAAT 0.958962 -236 CGGTAGTTTATCAAAAATAATCGTTAAAAA 3 53 0 TCAAAAATAA 0.604549 -82 AAAATCTTAGTTCAAAATATTTACTTAAAA 10 241 1 TTCAAAATAT 0.551138 -28 AACTCTGGAATCCAAAATATAAAAAGATTT 12 101 0 TCCAAAATAT 0.952766 -110 TTCTCAATTATCCCAAAAAAACATAAACAA 13 166 0 TCCCAAAAAA 0.755275 -48 CAAAATATCATCCAGAAAATCCAAATAAAA 17 94 0 TCCAGAAAAT 0.773178 -178 AAAAGAATTATCCAAAATATCATCCAGAAA 17 106 0 TCCAAAATAT 0.952766 -166 GATATCAATCCCAAAAATACCTCTACTA 20 26 0 TCCCAAAAAT 0.880705 -18 GGGTAAAGTATCCAAAAAAT 22 218 1 TCCAAAAAAT 0.958962 -10 TAATATAAAATCCAAAATAACCTTTAATTT 23 14 1 TCCAAAATAA 0.893982 -184 TACCCCTATCTCCAAAAGAAGAAGGTCAAA 24 153 1 TCCAAAAGAA 0.721807 -118 AAGAAGAAGGTCAAAAATATATTTATACAA 24 168 1 TCAAAAATAT 0.785267 -103 ********** Masking position 6 Map Score: 12.7881 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 208 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 TTAAAATAATAATATTAAAATGATAAAATTAAAAAAATCTT 1 167 0 ATAAAAATTA 0.447709 -134 CCAAAAAATAAAACTTAAAATAAGATAATAAAGA 2 4 0 ATAAAAATAA 0.91658 -258 CCTCCAATTAAAATTTTAAAATTAAAAATAAAGTCCAAAAA 2 38 0 ATATAAATAA 0.935874 -224 ATTTTATCAAAAGTTTTAGATAAAATAATATTAATGGAAGA 2 99 1 ATAAAAATAT 0.760387 -163 GTAGTTTATCAAAAATAATCGTTAAAAATACATCAATATTC 3 40 0 ATATAAATAC 0.532137 -95 TACTTCAAATATAATTTAAAATTTAAAAAAATTTCTAAGTG 5 53 1 ATATAAAAAA 0.372704 -31 ATCGCATTGTAGTATTTAAGTAAAATAATAAAATGGGAATT 7 67 0 ATAAAAATAA 0.91658 -155 ATCGAACTTTACATTTAAAATATTGTAATAAAGTATAATGG 7 109 1 ATATGAATAA 0.471168 -113 TATTCAATACAGAATTAAAAAATAAAAATTAAATAAAAATT 8 22 0 ATATAAATTA 0.522418 -193 AGTAAATATAAAGTGATAAAACATATAATAATATTATAATA 8 87 0 AAAAAAATAA 0.562297 -128 TAACAGTTTAAACATTAATCAAACATCATAAATATTAAGTA 8 161 0 ATAAACATAA 0.421244 -54 TTAACTTTTTAATTATTACATTATAAAATAAACAATCACGA 9 67 0 ATAAAAATAA 0.91658 -43 GAGCCTTATTAAAAATCTTAGTTCAAAATATTTACTTAAAA 10 230 1 ATTTAAATAT 0.240083 -39 CAATATACACATATTTGAAAAATAAAATTAAAACAATTTAT 11 14 1 ATATAATTAA 0.375396 -250 AAGTTCTTATACTACTTACACAATAAAATAAATAACTGATA 11 148 1 ATAAAAATAA 0.91658 -116 ATAAAACCCCAATTATCAAACTTTATAATATAAACTCTGGA 12 122 0 ATATAAATAT 0.810682 -89 GGAAGAGGAAAGGTTTAACAAAAAAGGATAAGCCAGAAGTT 14 26 1 ATAAAGATAA 0.572554 -58 CACATACATAACCATTTACAATAAAAAATAAAAAAATGAGA 16 19 0 ATAAAAATAA 0.91658 -268 AGCTTATATTCCTTTTAAACAAAAATAATATTTGAGGTGAG 17 208 1 CTAAAAATAT 0.272252 -64 TGTGAAAATTATTGCACAACCATGAAAATAAAAAAT 18 6 0 AAATAAATAA 0.634172 -119 AAAATTATTGAGGTTTTACTAAAAACAATAAAAACAAAAGT 21 44 0 ATAAAAATAA 0.91658 -154 ATCTATGAACAAGTATTAACACTCATAATATATAAACCTTT 21 100 0 ATATAAATAT 0.810685 -98 AATTATTTTTAATTGGTGAAAATATGCAAAGCTAT 22 5 1 ATATAAATAT 0.810675 -223 ATCTTTTAATATTGGTAAGTATTCAGAATAAAACAGACTCG 22 107 0 ATATAAATAA 0.936815 -121 AAAACAGCAGTATATTAAAATAAAACAATAAAAATGATATA 22 147 0 TTAAAAATAA 0.321979 -81 AATATATAAAATAAAAAAAATGAAAAAATAAAAGATAAAAT 23 47 0 AAAAAAATAA 0.562298 -151 TTTTTATTTTATATATTATAATTAATTATAAGATTGTAAAT 23 71 1 ATATATATAA 0.398537 -127 GTATAAGTATATAGTGCAAAAATAAAAATAAAAATTAAT 24 9 0 AGATAAATAA 0.651726 -262 CTGAATATAAACCTATAAAAGATAATAATATTGTAGGTAAT 24 52 1 ATATAAATAT 0.810685 -219 GGTAATACAAAATCAGGATTTATCATAATAATTATATCAAC 24 87 1 AGATAAATAA 0.651731 -184 ATTTTTAATTATAATTTATAATTTATGATAAAAAA 25 5 0 ATATAGATAA 0.643393 -166 GTTTTTGCCGCACTATCACATCTTAAAATAACTACCTTTGT 25 63 0 CTATAAATAA 0.636081 -108 TAATTACAATAAATGTTTTAAGTTAGAATAAAAATAGTTTT 26 42 1 ATTTAAATAA 0.522415 -43 * * * * * ***** Masking position 18 Map Score: 24.4237 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 238 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 7 TGGAAGAGACTTTGAGATAGAGAATCAAGC 2 133 1 TTTGAGATAG 0.788205 -129 AGGACGGTGGTTGTAAATGGATAAAATCCA 13 76 1 TTGTAAATGG 0.91107 -138 TTATTTTTTATTGTAAATGGTTATGTATGT 16 29 1 TTGTAAATGG 0.91107 -258 AATACCCAAGTTGGAAATGGGCTTGGAAAT 16 214 1 TTGGAAATGG 0.978162 -73 GGAAATGGGCTTGGAAATGGAGCGGGAAAA 16 226 1 TTGGAAATGG 0.978162 -61 ATAAAAGCAAATGGAAATGGTGAAAAGAAA 17 70 0 ATGGAAATGG 0.875945 -202 TGTTGTGGATTTTGAGATGGGTAAAGTATC 22 200 1 TTTGAGATGG 0.919062 -28 ATCACTCACTTTGAAGATAGTTGATATAAT 24 117 0 TTGAAGATAG 0.710265 -154 CCTTCTTCTTTTGGAGATAGGGGTAATTAA 24 148 0 TTGGAGATAG 0.949747 -123 ********** Masking position 5 Map Score: 6.77391 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 162 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 TTAAAATGATAAAATTAAAAAAATCTTTAAAA 1 162 0 AAATTAAAAA 0.390401 -139 ATAAAATAGAAAATTTTATATACCTATTACTA 1 229 1 AAATTTAATA 0.942213 -72 CCAAAAAATAAAACTTAAAATAAGATAATAAA 2 13 0 AAATTAAATA 0.598081 -249 CCTCCAATTAAAATTTTAAAATTAAAAATAAA 2 47 0 AAATTTAAAT 0.390401 -215 ATTTTATCAAAAGTTTTAGATAAAATAATATT 2 99 1 AAGTTTAATA 0.827049 -163 CAATATTCATAAAAATTATATAAAAAATAGAA 3 16 0 AAAATTAATA 0.750923 -119 ATATGAACAAAAATTTTTAATATCTAATATAT 3 89 0 AAATTTTATA 0.607746 -46 AATATAATTTAAAATTTAAAAAAATTTCTAAG 5 60 1 AAATTTAAAA 0.875264 -24 AAATTTTGCTTAAGTTTAAATATTATTGCAGA 6 31 1 TAATTTAATA 0.598088 -65 ATTCAAAAACAAACTTTAATTAATTTAGTAGG 6 67 1 AAATTTATTA 0.69831 -29 ATTAAAAAATAAAAATTAAATAAAAATTTTTA 8 18 0 AAAATTAATA 0.750923 -197 ATATTGGCAAAAATTTTAGTTATTAATTAAAT 10 132 1 AAATTTATTA 0.69831 -137 AAAATAAATTTTAAGTAAATATTTTGA 10 252 0 AAATTTAGTA 0.575934 -17 AATTTACTTAAAGATTTATATAAATTGTTTTA 11 42 0 AAGTTTAATA 0.827049 -222 CAATATAAATAAAATTTACTTAAAGATTTATA 11 54 0 AAATTTATTA 0.69831 -210 AATCTAATAAAAAATTTGTATAATTGTTAATA 12 28 0 AAATTTGATA 0.565644 -183 ATAGGAGGATAAAAATTAGATAAATCTAATAA 12 50 0 AAAATTAATA 0.750923 -161 CCCAATTATCAAACTTTATAATATAAACTCTG 12 124 0 AAATTTAAAT 0.390401 -87 AAAATTTTAGAAAGAGGAAGAGG 14 2 1 AAATTTAAAA 0.875264 -82 TTCCTCAAGTTTTACAAAATCTTTCTTA 14 66 0 AAGTTTAAAA 0.672979 -18 ACAACTTAGTAAAATTTATATATTTGTTTTCT 18 44 1 AAATTTAATA 0.942213 -81 TCATACTTTCAAAATTTAAATATATAATTAT 21 10 0 AAATTTAATA 0.942213 -188 AAAACCTCAATAATTTTAAAAACTTTTAATCG 21 68 1 TAATTTAAAA 0.390401 -130 TTTTAATCGAAAGGTTTATATATTATGAGTGT 21 91 1 AAGTTTAATA 0.827049 -107 GATTGTATAAAAAAATTATAAATTAATAATTC 21 154 0 AAAATTAAAA 0.564729 -44 TGACGACTCAAAATTTTTTATATAGCTTTGCA 22 35 0 AAATTTTATA 0.607746 -193 CCTTTTTAAGAAATTATATATAATTACAATAA 26 22 1 AAATATAATA 0.448073 -63 *** **** *** Masking position 2 Map Score: 24.8166 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 416 Number in noncoding regions = 311 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 9 TAATAATAGATTCAAACATTTTATCAAAAG 2 82 1 TTCAAACATT 0.960349 -180 CAAATAACAGTTTAAACATTAATCAAACAT 8 176 0 TTTAAACATT 0.758544 -39 AGGAAAATATCTCAAACATTATTTTTT 12 194 1 CTCAAACATT 0.97463 -17 AGGAAAATCTCTCAAACATTATTTTTTATT 13 113 1 CTCAAACATT 0.97463 -101 ATGTGATTGTCTCAACCATTAAAGGTGATA 16 55 1 CTCAACCATT 0.910743 -232 ATTTTCTCACCTCAAATATTATTTTTGTTT 17 224 0 CTCAAATATT 0.810961 -48 TTTTAATATCTGCAAACATTTACAATGTAT 24 235 0 TGCAAACATT 0.865463 -36 TTATTCTAACTTAAAACATTTATTGTAATT 26 43 0 TTAAAACATT 0.758544 -42 ********** Masking position 5 Map Score: 3.47876 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 33 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 TATTATTATGCCCTCCAATTAAAATTTTAA 2 60 0 CCCTCCAATT 0.840139 -202 TCTCAAAGTCTCTTCCATTAATATTATTTT 2 120 0 TCTTCCATTA 0.66398 -142 CAGTGTATGTTCCTCCACTTGTTAGAAAAA 2 182 1 TCCTCCACTT 0.96886 -80 CTAATTTTTATCCTCCTATTTTTAAAATAT 12 63 1 TCCTCCTATT 0.925004 -148 ACAACCACCGTCCTCCACTATGTAGGTGTT 13 60 0 TCCTCCACTA 0.91929 -154 AAACCTTTCCTCTTCCTCTTTCTAAAATTT 14 12 0 TCTTCCTCTT 0.883464 -72 AATCAACAAATCTTCCTTTTCCCGCTCCAT 16 242 0 TCTTCCTTTT 0.770887 -45 CTATAATGATTCCTCCAATTAAAAGAATTA 17 126 0 TCCTCCAATT 0.951892 -146 ********** Masking position 4 Map Score: 2.67698 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 189 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 TAGTAATAGGTATATAAAATTTTCTATTTTAT 1 229 0 TATATAATTT 0.48235 -72 TCATAAAAATTATATAAAAAATAGAAAAAAG 3 10 0 TATATAAAAT 0.482173 -125 TTATATAATTTTTATGAATATTGATGTATTTT 3 25 1 TTTATATATT 0.539004 -110 AAATAAAAATTAAATAAAAATTTTTAATTAAA 8 12 0 TAAATAAATT 0.605175 -203 AATATATTTGTATATGTAAATTAATAGTATTA 10 46 1 TATATAAATT 0.90063 -223 TAATTTTTCTTATATATATATTACTTATCCTA 10 76 0 TATATATATT 0.782463 -193 TGAGTAATAAAATATCGATATTGGCAAAAATT 10 115 1 AATATATATT 0.36352 -154 TAATTAAATATATGTCGAAATTCGTATAATTA 10 155 1 TATGTAAATT 0.864374 -114 AAATAAATTTTAAGTAAATATTTTGAACTAAG 10 246 0 TAAGTATATT 0.332893 -23 ATTTTTCAAATATGTGTATATTGGAA 11 5 0 TATGTATATT 0.752481 -259 TACTTAAAGATTTATATAAATTGTTTTAATTT 11 38 0 TTTATAAATT 0.710822 -226 TTAAGTAAATTTTATTTATATTGTGAAATAGT 11 63 1 TTTATATATT 0.539004 -201 TGTGAAATAGTATTTTCAAATTTAGCAGAGGT 11 84 1 TATTTAAATT 0.412886 -180 TTTAAATAGATATGTTGAAATTCGAATAGTTA 11 117 1 TATGTAAATT 0.864374 -147 TTTATTAACAATTATACAAATTTTTTATTAGA 12 26 1 ATTATAAATT 0.330131 -185 TAAGAAAACAAATATATAAATTTTACTAAGTT 18 46 0 AATATAAATT 0.617034 -79 ATCAATTCTTTTTATAAAAATTGTAGGGGAGA 19 29 1 TTTATAAATT 0.710822 -65 ATAATTATATATTTAAATTTTGAAAGTAT 21 8 1 TATATAAATT 0.90063 -190 CTATGTCAATATTATGCACAAGG 21 185 0 TATGTATATT 0.752481 -13 TATGCAAAGCTATATAAAAAATTTTGAGTCGT 22 33 1 TATATAAAAT 0.482173 -195 AAAACAGCAGTATATTAAAATAAAACAATAAA 22 156 0 TATATAAATA 0.330775 -72 ATTAGCAAATTAGGTTAAAATTCAGTTGCATT 23 132 1 TAGGTAAATT 0.528834 -66 TGCAAAAATAAAAATAAAAATTAAT 24 4 0 AAAATAAATT 0.235247 -267 TTATCTTTTATAGGTTTATATTCAGATGTATA 24 45 0 TAGGTATATT 0.350147 -226 TTATTGTAATTATATATAATTTCTTAAAAAGG 26 22 0 TATATAATTT 0.48235 -63 ***** ***** Masking position 5 Map Score: 13.0482 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 464 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 12 AAAAAATCTTTAAAATCTTTAAAAAAATTTTGA 1 144 0 TAAACTTAAA 0.698667 -157 TAAATTTAATTAAAACCTAATATCTTATTTAGT 2 219 0 TAAACTATAT 0.796776 -43 CAAAAATTTTTAATATCTAATATATATTTTTCG 3 81 0 TAAACTATAT 0.796776 -54 TTATTTTACTTAAATACTACAATGCGATTATCG 7 80 1 TAATCTAAAT 0.352812 -142 AATAATATTATAATACCCAGAATATCAATTTGT 8 69 0 TAAACCAAAT 0.632076 -146 TATATTTAATTAATAACTAAAATTTTTGCCAAT 10 134 0 TAAACTAAAT 0.902763 -135 ATATATACCGTAATAGCATAAATTTATTTGAAT 10 190 1 TAAACATAAT 0.651913 -79 TATTTTGAACTAAGATTTTTAATAAGGCTCACA 10 227 0 TAAATTTAAT 0.410764 -42 GTAAGTAGTATAAGAACTTAACTATTCGAATTT 11 134 0 TAAACTTACT 0.786217 -130 ATAAAATAACTAATAACTACAAATATAATTAAA 11 189 1 TAAACTAAAA 0.663321 -75 TAAAAACTTCTATTTTTTATTAA 12 1 1 TAAACTTTAT 0.821874 -210 AGATTTTAAGTAATCTCTTGTATTGGTTCTCCC 13 24 0 TAACCTTTAT 0.286501 -190 AGAGATTACTTAAAATCTATAAACACCTACATA 13 39 1 TAAACTAAAA 0.663321 -175 TTTTCATATTTATCACCTTTAATGGTTGAGACA 16 62 0 TATACTTAAT 0.698667 -225 GTATTTTTAGTAATATCTTCACTGGTCTTATTC 16 115 1 TAAACTTACT 0.786217 -172 TATTAAAAAGTAATAACAAAAATAACAGTAAAG 17 177 1 TAAACAAAAT 0.614112 -95 TTAAAAGGAATATAAGCTTTACTGTTATTTTTG 17 193 0 TATACTTACT 0.438339 -79 AATTGATGTTTAATACCAAAAATTT 19 3 0 TAAACAAAAT 0.614112 -91 TCAATAATTTTAAAAACTTTTAATCGAAAGGTT 21 74 1 TAAACTTTAA 0.494729 -124 ATATAATATAAAATCCAAAATAACCTTTAAT 23 9 1 TAAACCAAAT 0.632076 -189 CCTACAATATTATTATCTTTTATAGGTTTATAT 24 56 0 TATACTTTAT 0.494729 -215 CCTGATTTTGTATTACCTACAATATTATTATCT 24 71 0 TATACTAAAT 0.663321 -200 TGCTTTACATTAAAATCTTTTCTTTTTCATTGT 24 194 0 TAAACTTTCT 0.608313 -77 TATTTCACCCTAAGACTTTTAATATCTGCAAAC 24 248 0 TAAATTTAAT 0.410764 -23 *** * *** *** Masking position 1 Map Score: 12.2784 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 602 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 13 ATGGTTATGTATGTGATTGTCTCAACCATT 16 45 1 ATGTGATTGT 0.93865 -242 TTATTTTAAGATGTGATAGTGCGGCAAAAA 25 73 1 ATGTGATAGT 0.974785 -98 TTAAAAAGGGATGTGATAGA 26 1 0 ATGTGATAGA 0.93865 -84 ATAGTTTTTTATGTGATAGT 26 75 1 ATGTGATAGT 0.974785 -10 ********** Masking position 6 Map Score: 0.418944 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 3 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 GTTATGCCTATAACGTCATGTTGGACAGACCCCT 15 45 0 TAACCATTGG 0.9876 -159 GTTATAGGCATAACTCCATGTTGGACTTGGGAAT 15 65 1 TAACCATTGG 0.9876 -139 TCATCAACCTTAACTCCCTCTGGGTTCATTGGGA 15 98 1 TAACCCTTGG 0.972885 -106 AGCATGATGATAACAACATATTGGCATATGTCAC 17 37 0 TAACCATTGG 0.9876 -235 TGTATCTTTTTAACTACATATAGTAGTGTAAGAA 18 72 0 TAACCATTGT 0.938509 -53 **** *** * ** Masking position 9 Map Score: 0.485978 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 0 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 15 ATAGGAATCACTCCCACAATG 1 1 1 ATAGAATCAC 0.921174 -300 GTTCTATTGAATAGGGCTCACCTCTGTGAGG 1 110 1 ATAGGCTCAC 0.980604 -191 AAGATTTTTAATAAGGCTCACAAACCATTCA 10 218 0 ATAGGCTCAC 0.980595 -51 TATTTTATTCATAAGATTCACCATAAAACCC 12 154 0 ATAGATTCAC 0.921174 -57 AATGAGATATAAACGACTCACTA 16 274 1 AAAGACTCAC 0.937676 -13 GGGGTAATTAATATCACTCACTTTGAAGATA 24 128 0 ATACACTCAC 0.933258 -143 *** ******* Masking position 8 Map Score: 0.113556 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467