AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ipurR_mjan_opreg_300.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0059 215 nitrogen regulatory protein P-II (glnB) #2 MJ0102 300 Phenylacrylic acid decarboxylase #3 MJ0202 56 conserved hypothetical protein #4 MJ0203 120 phosphoribosylformylglycinamidine cyclo-ligase (purM) #5 MJ0204 99 amidophosphoribosyltransferase (purF) #6 MJ0561 281 adenylosuccinate synthetase (purA) #7 MJ0616 108 phosphoribosylaminoimidazole carboxylase, (purE) #8 MJ0929 300 adenylosuccinate lyase (purB) #9 MJ0934 300 polyferredoxin (mvhB) #10 MJ0936 94 conserved hypothetical protein #11 MJ0937 63 phosphoribosylamine--glycine ligase (purD) #12 MJ1019 132 carbamoyl-phosphate synthase, small (or glutamine) subunit (carA) #13 MJ1132 188 conserved hypothetical protein #14 MJ1264 76 phosphoribosylformylglycinamidine synthase II (purL) #15 MJ1265 189 nucleoside diphosphate kinase, (ndk) #16 MJ1344 300 nitrogen regulatory protein P-II (glnB) #17 MJ1368 122 sulfate transport system permease protein (cysT) #18 MJ1378 184 carbamoyl-phosphate synthase, medium subunit (carB1) #19 MJ1379 196 conserved hypothetical protein #20 MJ1381 124 carbamoyl-phosphate synthase, large subunit (carB2) #21 MJ1486 109 phosphoribosylglycinamide formyltransferase 2 (purT) #22 MJ1592 300 phosphoribosylaminoimidazolesuccinocarboxamide synthase (purC) #23 MJ1597 226 serine hydroxymethyltransferase (glyA) #24 MJ1616 228 inosine-5'-monophosphate dehydrogenase, (guaB) Motif number 1 GTAGTAATCATTTTTATTTTTATCTAAAAG 1 135 0 TTTTTATTTT 0.931487 -81 AATTTGGTGGTTTTTAGATTAATTTGAATT 1 167 0 TTTTTAGATT 0.804627 -49 CTCAACCTCATTTTTATAATTTTACAAATT 1 193 0 TTTTTATAAT 0.865951 -23 TAGGTTGTTATATTTATTTTTTTAGATTTA 2 213 1 TATTTATTTT 0.881449 -88 GGATTAACTATTTTTAAATAGTATTTATTT 2 244 1 TTTTTAAATA 0.573884 -57 TTTTAAATAGTATTTATTTTTTAAATCTTA 2 255 1 TATTTATTTT 0.881449 -46 CATTATGGAATATTTAAACTACAGAAAGTC 4 27 0 TATTTAAACT 0.719654 -94 GAATAAAAATTTTTTAAACATCCAATTTGC 4 56 0 TTTTTAAACA 0.595001 -65 ATAAATTATCTTTTTAATTTTACTAATTCT 5 13 1 TTTTTAATTT 0.901068 -87 TTCTTCTTTCTTTTTATTTATTTGCTAAAA 5 51 1 TTTTTATTTA 0.814126 -49 TAAAAACCCTTTTTTAGTTTTTTAGACTTT 5 78 0 TTTTTAGTTT 0.754089 -22 TATGTTATACTATTTATATTCCAAAATATA 6 156 1 TATTTATATT 0.908919 -126 TATTATAAGTTTTTTATAGTTCTATATATT 6 180 0 TTTTTATAGT 0.937255 -102 GTAATTGTAATATTTAAAGTTAATTAATAT 6 239 0 TATTTAAAGT 0.845364 -43 AACCATAATTTATTTATAATTAGTTTTAAA 7 51 1 TATTTATAAT 0.779342 -58 AATTATTTAATTTTTATTTTCAAAAATCTG 8 17 1 TTTTTATTTT 0.931487 -284 CTGGTTTGATTATTTAGAATATTTAAGTTT 8 58 0 TATTTAGAAT 0.443483 -243 AAAGGATTTTTATTTAATTTCTAAGGGTTT 8 89 0 TATTTAATTT 0.832777 -212 GGTTTTAGGATTTTTAATTTTGTTGTTTGG 8 189 0 TTTTTAATTT 0.901068 -112 TGAAAATGCTTTTTTAAATAAACATCAAAC 8 259 1 TTTTTAAATA 0.573884 -42 TTGCTAATGATTTTTATAGTTTGATGTTTA 8 277 0 TTTTTATAGT 0.937255 -24 CGCCGGCCACTTTTTATTATTTTAAATTCT 9 108 1 TTTTTATTAT 0.827913 -193 GCCGGGCTTCTTTTTATTTTAGAACAATTA 9 243 1 TTTTTATTTT 0.931487 -58 ATTTTAAAAATATTTAAATTTATCGATTAA 9 270 0 TATTTAAATT 0.859564 -31 AATTTAAATATTTTTAAAATATCTTAAGTA 9 280 1 TTTTTAAAAT 0.806031 -21 ATATAACAATTTTTTAATGAGAGAAATA 10 9 0 TTTTTAATGA 0.705917 -86 CTTTTTTACTTTTTTATTATTACATTAATC 11 24 1 TTTTTATTAT 0.827913 -40 ACCACCAAAGTTTTTATAGTTTTTTGCAAA 13 14 1 TTTTTATAGT 0.937255 -175 CTTTGCTTAATATTTAAAGTGATAAC 13 173 1 TATTTAAAGT 0.845364 -16 GCAATTTCATTTTTTATATATGAGCAATAT 15 46 1 TTTTTATATA 0.851048 -144 ATATGAGCAATATTTAAATTTTTCGAGATA 15 63 1 TATTTAAATT 0.859564 -127 ATTATCATTATTTTTAATAACTTCCGTATC 15 108 1 TTTTTAATAA 0.505524 -82 CACATTAGTTTATTTAAAGTTAATAAGATT 16 32 1 TATTTAAAGT 0.845364 -269 TATAATTAAATTTTTATATTTATAATTATA 16 98 0 TTTTTATATT 0.948061 -203 ATTTCCTACATTTTTATACTTGGCTCTATA 16 173 1 TTTTTATACT 0.875158 -128 TACCGAAAAGTTTTTATACTATTTTTAGAG 16 206 1 TTTTTATACT 0.875158 -95 TTTTATACTATTTTTAGAGTAGTTAGGAAT 16 217 1 TTTTTAGAGT 0.771121 -84 TTTAATAAATTTTTAATGAAAATATTATA 17 10 1 TTTTTAATGA 0.705917 -113 TCAGTTAAGGTTTTTAAAGTTAATGGTAGG 18 25 0 TTTTTAAAGT 0.909104 -160 TATTTTACAATATTTATATATTTAACTATT 18 147 0 TATTTATATA 0.753779 -38 AAAATTAATATATTTATTTTGGTTTCTTTT 19 25 0 TATTTATTTT 0.881449 -172 AATCACCTATTTTTTATTTTCAATATCTTT 20 103 0 TTTTTATTTT 0.931487 -22 CTTTGATATATTTTTATTTTTTATTTCACT 22 70 1 TTTTTATTTT 0.931487 -231 ACTATAGTTCTTTTTAAAATATTTTGTAAT 22 106 1 TTTTTAAAAT 0.806031 -195 AACTATAAATTTTTTATATTACATTGTAAG 22 214 1 TTTTTATATT 0.948061 -87 TCTCATTTAATTTTTAATCTTTATACTTAC 22 239 0 TTTTTAATCT 0.777635 -62 ACCAAAAACTTTTTTATATAGTGTCTTTCA 23 18 1 TTTTTATATA 0.851048 -209 GGCATTTAAATATTTATTGTCAAATATTTA 23 95 1 TATTTATTGT 0.858791 -132 TATTGTCAAATATTTATTAATAAACTTTAA 23 109 1 TATTTATTAA 0.458729 -118 TAATACGGTATATTTATTGTTTCTATTTCT 23 181 1 TATTTATTGT 0.858791 -46 TGTCAATCAATTTTTATATTATTGATGCCC 24 65 1 TTTTTATATT 0.948061 -164 TTTATTTTATTTTTTATTGAATTAATGTTA 24 107 1 TTTTTATTGA 0.781808 -122 GTTCATAAACTATTTAAATAATCATATACT 24 138 1 TATTTAAATA 0.449806 -91 AGAAGAGGGGTATTTATACTTTTTATATGA 24 176 0 TATTTATACT 0.793115 -53 ********** Masking position 5 Map Score: 71.7492 Number of sites scoring better than the average of aligned sites = 2079 Number in coding regions = 1360 Number in noncoding regions = 719 Number of orfs with sites within 600 bp upstream = 507 Fraction of orfs with sites within 600 bp upstream = 0.0814327 Motif number 2 TGAGTAAATTTGAACTCCTTCCTAATGGAAGG 6 116 1 TAACCCTTCC 0.997201 -166 ATAACATAGATAAACTCCTTCCATTAGGAAGG 6 132 0 TAACCCTTCC 0.997208 -150 AAGGAAAGTTTAAACGCCTTCCAAAAGGAAGG 13 59 1 TAACCCTTCC 0.997195 -130 AAGGTATTTATGAACGCCTTCCTTTTGGAAGG 13 75 0 TAACCCTTCC 0.997123 -114 ATCATTATTTTTAATAACTTCCGTATCAAAAA 15 111 1 TAATACTTCC 0.858299 -79 TAAAACTATCTCAACTTCTTTCTTTATTTTAG 20 71 0 TAACTCTTTC 0.858299 -54 AAGGCACTGATGAACTCCTTCCATTAGGAAGG 22 140 1 TAACCCTTCC 0.997201 -161 TAATTAAGTTTGAACTCCCTTCCTAATGGAAG 22 157 0 TAACCCCTTC 0.927981 -144 CAGTAGCTTATGAACACCTTCCAAAGGAAGGC 23 66 1 TAACCCTTCC 0.997201 -161 AATAAATATTTAAATGCCTTCCTTTGGAAGGT 23 81 0 TAATCCTTCC 0.984058 -146 * *** ****** Masking position 4 Map Score: 22.5885 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 19 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 CCCTAATGGAAAAGCTTAAATATATAACTTACT 1 53 1 AAATAAATAT 0.897608 -163 TCCTTTTAGATAAAAATAAAAATGATTACTACC 1 133 1 TAATAAAAAT 0.810335 -83 CAAATTTGTAAAATTATAAAAATGAGGTTGAGA 1 191 1 AAATAAAAAT 0.897608 -25 ATAACAACCTAAAATAAAATAATAAAATGGTGC 2 191 0 AAAAAATAAT 0.784172 -110 CATAAATCTAAAAAAATAAATATAACAACCTAA 2 212 0 AAATAAATAT 0.897607 -89 AACTATTTTTAAATAGTATTTATTTTTTAAATC 2 249 1 AAATATTTAT 0.897607 -52 GTAAAATTAAAAAGATAATTTATTT 5 3 0 AAAAATTTAT 0.748858 -97 CAAAACTAATAAAATCTATTTATGAGTAAATTT 6 94 1 AAATATTTAT 0.897606 -188 TGTAATATTTAAAGTTAATTAATATTAAGAATT 6 231 0 AAAAATTAAT 0.748864 -51 TAAGAGATTTTAAAACTAATTATAAATAAATTA 7 56 0 TAATAATTAT 0.838861 -53 TTTGAAAATAAAAATTAAATAATTATCTAA 8 8 0 AAAAAATAAT 0.784169 -293 AATAATTCAATAAACTTAAATATTCTAAATAAT 8 47 1 TAATAAATAT 0.810335 -254 AAAAATCCTAAAACCCAAATAATAAATTATAAA 8 204 1 AAAAAATAAT 0.784172 -97 AATAAACATCAAACTATAAAAATCATTAGCAAT 8 275 1 AAATAAAAAT 0.897608 -26 AATTAATCGATAAATTTAAATATTTTTAAAATA 9 268 1 TAATAAATAT 0.810333 -33 TTTTGCAAAGTAATAAAATTTATTAAGGAAAGT 13 35 1 TAAAATTTAT 0.592383 -154 TTTTAGGATAAAAAGGTATTTATGAACGCCTTC 13 86 0 AAATATTTAT 0.897608 -103 ATGTTTTGCAAAAAACTATATATATTTCTTAGC 13 118 1 AAATATATAT 0.877968 -71 GTATATCCACAAATAATATTAATTAACTAATAA 14 45 1 AAATATTAAT 0.897608 -32 TCTATCTCGAAAAATTTAAATATTGCTCATATA 15 62 0 AAATAAATAT 0.897415 -128 TTAGTAATAATAATAGTAATTATATAATATCAA 15 154 1 TAATAATTAT 0.838861 -36 TATAATGTCATAAAACAATTAATACCCCAATCT 16 57 0 TAAAATTAAT 0.592383 -244 CGCTATAATATAATTATAAATATAAAAATTTAA 16 90 1 TAATAAATAT 0.810335 -211 TATAAATATAAAAATTTAATTATAAAAGTCCAT 16 104 1 AAATAATTAT 0.914198 -197 TAAAATTGCATAACTATATTTATGTTACTTAAC 18 78 0 TAATATTTAT 0.810335 -107 TAATAATAGTTAAATATATAAATATTGTAAAAT 18 143 1 TAATATAAAT 0.778095 -42 GAAACCAAAATAAATATATTAATTTTGATGAAT 19 29 1 TAATATTAAT 0.810335 -168 ATTGCTCCCTAAACAATATTTATCTCAAATGAG 21 11 1 AAATATTTAT 0.897608 -99 AATTAACAAAAAACTATATTAATGATTCCTTTA 21 46 1 AAATATTAAT 0.897608 -64 AATAAAATTTTAATGCTAAAAATTTT 21 94 1 TAATAAAAAT 0.810335 -16 ACAGTGAAATAAAAAATAAAAATATATCAAAGA 22 69 0 AAATAAAAAT 0.897608 -232 AAATGTTAATAAAGTTTATTAATTAAGTTTGAA 22 175 0 AAATATTAAT 0.897608 -126 ACTTACAATGTAATATAAAAAATTTATAGTTCT 22 212 0 TAAAAAAAAT 0.592383 -89 TTGTAAGTATAAAGATTAAAAATTAAATGAGAG 22 237 1 AAATAAAAAT 0.897608 -64 CTATAACTTTAAATTTTAATTATTAAAACTCTC 22 265 0 AAATAATTAT 0.914233 -36 AAAATTAATTAAAGTTTATTAATAAATATTTGA 23 114 0 AAATATTAAT 0.897608 -113 ATAGAAATAGAAACAATAAATATACCGTATTAA 23 180 0 AAATAAATAT 0.897608 -47 TGATTGACAAAAAATAAAATAATTATCTAGTTC 24 41 0 AAAAAATAAT 0.784172 -188 AAAATAAAATAAAGTTAATATATGGGGGCATCA 24 87 0 AAAAATATAT 0.709909 -142 GGCATCATATAAAAAGTATAAATACCCCTCTTC 24 172 1 AAATATAAAT 0.877969 -57 *** ******* Masking position 8 Map Score: 60.3743 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 526 Number in noncoding regions = 419 Number of orfs with sites within 600 bp upstream = 346 Fraction of orfs with sites within 600 bp upstream = 0.0555734 Motif number 4 TTGTTTAACTTTTTCTAAAAGTTTCGTTTGTATC 2 148 1 TTCTAAATTT 0.498239 -153 GGATTAACTATTTTTAAATAGTATTTATTTTTTA 2 244 1 TTTAAAATAT 0.655693 -57 TTTTAAATCTTAACTTAACAGTTTTTAATGGTGA 2 273 1 TATTAAATTT 0.728014 -28 TATCGCCGTATTGTTTAAGAGTTTGAAGATTTAT 3 14 1 TTTTAAATTT 0.840582 -43 AAAGATAATAGTATAAGACTTTCTGTAGTTTA 4 9 1 TAATAAATTT 0.846918 -112 GCAAATTGGATGTTTAAAAAATTTTTATTCCTAC 4 56 1 TGTAAAATTT 0.42029 -65 TTAGTAAAATTAAAAAGATAATTTATTT 5 5 0 TAAAGAATTT 0.624027 -95 AATATTACAATTACAAAAAAATATAAGGTTTTGA 6 255 1 TTAAAAATAT 0.797416 -27 TTAAAATCTCTTACATAAAAATTTAGACCTTTTT 7 76 1 TTATAAATTT 0.915956 -33 TGCCAAGGATTACCTTGAGAATTTAAAATAATAA 9 121 0 TATTGAATTT 0.506775 -180 TTACTTAAGATATTTTAAAAATATTTAAATTTAT 9 277 0 TATTAAATAT 0.552963 -24 TCATTATCTCTTATATAACAATTTTTTAATGAGA 10 17 0 TTATAAATTT 0.915956 -78 ATGGAGAATATTTTATAACACTATCTATGTCATT 10 46 0 TTATAAATAT 0.834341 -49 TTTTATTACTTTGCAAAAAACTATAAAAACTTTG 13 19 0 TTAAAAATAT 0.797416 -170 ATATAGTTTTTTGCAAAACATTTTAGGATAAAAA 13 105 0 TTAAAAATTT 0.894932 -84 ACCTTATTAGTTAATTAATATTATTTGTGGATAT 14 47 0 TTTTAAATAT 0.709024 -30 AAAATGAAATTGCCATAACATTTTGAGGTGATAC 15 25 0 TGATAAATTT 0.657228 -165 GTATTAATTGTTTTATGACATTATACGCTATAAT 16 65 1 TTATGAATAT 0.65909 -236 TGACATTTGATAGTATAATATTTTCATTAAAAAT 17 19 0 TAATAAATTT 0.846918 -104 AATTACCTAATTATATAAAATTTGTGTTAAACAA 17 59 0 TTATAAATTG 0.659321 -64 TATATAAATATTGTAAAATATTATTGTGGTGGAT 18 157 1 TTAAAAATAT 0.797416 -28 TTCATAAATATTTTGGGATTGATT 20 1 1 TTTAAAATTT 0.804723 -124 ATGAGATAATTAACAAAAAACTATATTAATGATT 21 39 1 TAAAAAATAT 0.666461 -71 AGCTAAAGTATAGAATAAAATTTTAATGCTAAAA 21 81 1 TAATAAATTT 0.846918 -29 GCCTTAGTTATTACAAAATATTTTAAAAAGAACT 22 111 0 TTAAAAATTT 0.894932 -190 ATTAATAAACTTTATTAACATTTGAAAAGAACTA 22 185 1 TTTTAAATTG 0.483558 -116 AGATTAAAAATTAAATGAGAGTTTTAATAATTAA 22 249 1 TTATGAATTT 0.807083 -52 TATAGTGTCTTTCAAAAACATTTTGAAGTAACCA 23 34 1 TTAAAAATTT 0.894932 -193 TTTAATTAATTTTGAAGACAGTATAGTTTAAAGA 23 134 1 TTAAGAATAT 0.601748 -93 GACAGTATAGTTTAAAGATATTTTTAAGTATTAA 23 150 1 TTAAGAATTT 0.765787 -77 GGGGCATCAATAATATAAAAATTGATTGACAAAA 24 62 0 TAATAAATTG 0.495568 -167 AGTATATGATTATTTAAATAGTTTATGAACTTAA 24 134 0 TATAAAATTT 0.676576 -95 ** **** * *** Masking position 8 Map Score: 27.6966 Number of sites scoring better than the average of aligned sites = 1195 Number in coding regions = 847 Number in noncoding regions = 348 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 5 GGAAGGAAAATTCTTTCCTTAGTAAGTTAT 1 76 0 TTCTTTCCTT 0.736721 -140 GGAAAGAATTTTCCTTCCTATTATTTAGGA 1 88 1 TTCCTTCCTA 0.956288 -128 TAAATTTGAACTCCTTCCTAATGGAAGGAG 6 120 1 CTCCTTCCTA 0.972135 -162 CATAGATAAACTCCTTCCATTAGGAAGGAG 6 130 0 CTCCTTCCAT 0.958554 -152 AAAGTTTAAACGCCTTCCAAAAGGAAGGCG 13 63 1 CGCCTTCCAA 0.953135 -126 TATTTATGAACGCCTTCCTTTTGGAAGGCG 13 73 0 CGCCTTCCTT 0.98502 -116 GATTTCGATGTGCCTCCCTTAAAGGGTTCG 22 41 0 TGCCTCCCTT 0.895828 -260 CACTGATGAACTCCTTCCATTAGGAAGGGA 22 144 1 CTCCTTCCAT 0.958554 -157 AAGTTTGAACTCCCTTCCTAATGGAAGGAG 22 154 0 TCCCTTCCTA 0.888879 -147 AATATTTAAATGCCTTCCTTTGGAAGGTGT 23 79 0 TGCCTTCCTT 0.976323 -148 ********** Masking position 5 Map Score: 10.7721 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 76 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TACGCTTTCCAGCTATGAAAACTCTTTTAG 2 69 1 AGCTATGAAA 0.703397 -232 TTAACTTAACAGTTTTTAATGGTGAATTT 2 282 1 AGTTTTTAAT 0.812954 -19 TTTTAAGATAAGTTATAAATAAATCTTCAA 3 36 0 AGTTATAAAT 0.6132 -21 AGATTTTATTAGTTTTGAAAAGAACCATAT 6 81 0 AGTTTTGAAA 0.866882 -201 ATGGCAAGTAAGTTATTATAAGTTTTTTAT 6 193 0 AGTTATTATA 0.851781 -89 TTATAGAGTAAGCTATAAAATATCAGGAGG 7 17 0 AGCTATAAAA 0.778969 -92 ATTTATAATTAGTTTTAAAATCTCTTACAT 7 62 1 AGTTTTAAAA 0.906345 -47 AGCATTTAGAAGTTATTAATTAGTTCAAAG 8 115 0 AGTTATTAAT 0.754992 -186 ATACCACCAAAGTTTTTATAGTTTTTTGCA 13 12 1 AGTTTTTATA 0.890173 -177 TTGATACGGAAGTTATTAAAAATAATGATA 15 110 0 AGTTATTAAA 0.93018 -80 ATTACCGAAAAGTTTTTATACTATTTTTAG 16 204 1 AGTTTTTATA 0.890173 -97 ATTGAGGATGAGCTTTTAAAATTGCATAAC 18 97 0 AGCTTTTAAA 0.906112 -88 ATATTCTTCCAGTTATTAAAGCCAATAATG 19 81 0 AGTTATTAAA 0.93018 -116 AAGTTGAGATAGTTTTAAAAGATATTGAAA 20 86 1 AGTTTTAAAA 0.906345 -39 TCTATACTTTAGCTTTTAAAGGAATCATTA 21 65 0 AGCTTTTAAA 0.906112 -45 GGCAGTTTTTATAACGTTCTTAC 22 4 1 AGTTTTTATA 0.890173 -297 ATTAAATGAGAGTTTTAATAATTAAAATTT 22 258 1 AGTTTTAATA 0.806743 -43 ********** Masking position 6 Map Score: 18.1781 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 398 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 7 CCAAATTTGTAAAATTATAAAAATGAGGTTGA 1 190 1 AAAATTATAA 0.752879 -26 ACTTTTAGAAAAAGTTAAACAAAATCTTTCAG 2 138 0 AAAGTTAAAA 0.930621 -163 ATAACAACCTAAAATAAAATAATAAAATGGTG 2 192 0 AAAATAAAAA 0.852233 -109 CAAAAATCGTATAGTTATTGAAACAAATAATG 4 89 1 ATAGTTATAA 0.557958 -32 AAGAATTAGTAAAATTAAAAAGATAATTTATT 5 12 0 AAAATTAAAG 0.829306 -88 AAGAAAGAAGAAAATTAAGAAGAATTAGTAAA 5 31 0 AAAATTAAAG 0.829306 -69 TGTAATATTTAAAGTTAATTAATATTAAGAAT 6 232 0 AAAGTTAAAA 0.930611 -50 TTTGAAAATAAAAATTAAATAATTATCTAA 8 9 0 AAAATTAAAA 0.908522 -292 TTGAGAATTTAAAATAATAAAAAGTGGCCGGC 9 109 0 AAAATAATAA 0.638885 -192 TAATAATAAAAAAGTAAAAAAGTGGTTTAAAT 11 14 0 AAAGTAAAAG 0.792122 -50 AGTTTTTTGCAAAGTAATAAAATTTATTAAGG 13 31 1 AAAGTAATAA 0.704969 -158 TAGTTTATTTAAAGTTAATAAGATTGGGGTAT 16 37 1 AAAGTTAAAG 0.867756 -264 TAGGAAATGCAAAATAAACAAATATTGGGATA 16 149 0 AAAATAAAAA 0.852233 -152 AAGGATACTTAAAGTTAAGTAACATAAATATA 18 65 1 AAAGTTAAAA 0.930621 -120 TAACATAAATATAGTTATGCAATTTTAAAAGC 18 84 1 ATAGTTATAA 0.557958 -101 TCTTTGGAAGATAGTTAAAGAAGACGTTCCTA 20 42 1 ATAGTTAAAA 0.804486 -83 AGACGTTCCTAAAATAAAGAAAGAAGTTGAGA 20 63 1 AAAATAAAAA 0.852233 -62 CTCAAATGAGATAATTAACAAAAAACTATATT 21 34 1 ATAATTAAAA 0.752869 -76 TACTGTCTTCAAAATTAATTAAAGTTTATTAA 23 125 0 AAAATTAAAA 0.908513 -102 TGATTGACAAAAAATAAAATAATTATCTAGTT 24 42 0 AAAATAAAAA 0.852233 -187 AATTCAATAAAAAATAAAATAAAGTTAATATA 24 98 0 AAAATAAAAA 0.852233 -131 TCTTCTAAATATAGTTAAAAAGGTTATAAAGG 24 200 1 ATAGTTAAAG 0.668092 -29 ******** ** Masking position 5 Map Score: 28.6576 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 547 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 8 GGGAATTAGGAAGATGGGTAGTAGGTAAGA 1 25 0 AAGATGGGTA 0.847563 -191 ATGGTGCCGAGGGAGGGATACAAACGAAAC 2 168 0 GGGAGGGATA 0.905491 -133 ATAAAATATCAGGAGGGATATT 7 3 0 AGGAGGGATA 0.973026 -106 ATAATATCAAAAGCGGGATAGTT 15 177 1 AAGCGGGATA 0.944195 -13 ATTGGCATTAAAGAGGGTTAAAGAAGAATA 19 151 1 AAGAGGGTTA 0.940175 -46 CTATCTTCCAAAGAAGGATATAATCAATCC 20 26 0 AAGAAGGATA 0.89204 -99 AAACGTTAATAAGAGGGATAAAA 23 214 1 AAGAGGGATA 0.984544 -13 CTATATTTAGAAGAGGGGTATTTATACTTT 24 184 0 AAGAGGGGTA 0.977203 -45 ********** Masking position 10 Map Score: 7.03048 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 51 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AGGTAAGATAATTCCTATAAAA 1 2 0 ATTCCTTAAA 0.798342 -214 ATTAATCTAAAAACCACCAAATTTGTAAAAT 1 174 1 AAACCACAAA 0.888115 -42 GTAGCTTTCCATTTCATCAAAATAGGATGCA 2 41 0 ATTTCACAAA 0.814439 -260 AGTTATAAATAAATCTTCAAACTCTTAAACA 3 25 0 AAATCTCAAA 0.660455 -32 AAAAATTTTTATTCCTACAAAAATCGTATAG 4 72 1 ATTCCTCAAA 0.900041 -49 TAAATAATTTAAACCTTCAAATAATAAACCA 6 35 0 AAACCTCAAA 0.849125 -247 AAATCTGAATAATTCAATAAACTTAAATATT 8 40 1 AATTCATAAA 0.518454 -261 CTAAATAATCAAACCAGCAAACCCTTAGAAA 8 71 1 AAACCACAAA 0.888115 -230 TTTCACCAAAATACCTATAAACTATCACATA 12 109 0 ATACCTTAAA 0.816017 -24 ATATTTCACCAAAATACCTATAA 12 120 0 ATTTCACAAA 0.814439 -13 GATACCACCAAAGTTTTTATAG 13 2 1 ATACCACAAA 0.934329 -187 TTTTGAGGTGATACCATTAAAAGAATAA 15 8 0 ATACCATAAA 0.862174 -182 TGAAAATATTATACTATCAAATGTCATCAAT 17 27 1 ATACTACAAA 0.413688 -96 TACACATATAATTCCAACTAAAGTTACCAAT 19 109 0 ATTCCACTAA 0.504949 -88 TATATTAATGATTCCTTTAAAAGCTAAAGTA 21 60 1 ATTCCTTAAA 0.798342 -50 ATACTTAAAAATATCTTTAAACTATACTGTC 23 150 0 ATATCTTAAA 0.605195 -77 ACTTAACATTAATTCAATAAAAAATAAAATA 24 109 0 AATTCATAAA 0.518454 -120 ****** **** Masking position 10 Map Score: 12.6068 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 402 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 10 TTTATTCCTAAATAATAGGAAGGAAAATTC 1 93 0 AATAATAGGA 0.686147 -123 CCTAAAATAAAATAATAAAATGGTGCCGAG 2 187 0 AATAATAAAA 0.850048 -114 AAGAAAGAAGAAAATTAAGAAGAATTAGTA 5 33 0 AAAATTAAGA 0.57276 -67 TTAGCAAATAAATAAAAAGAAAGAAGAAAA 5 49 0 AATAAAAAGA 0.73408 -51 AAAGTTAATTAATATTAAGAATTTCCAATG 6 224 0 AATATTAAGA 0.926458 -58 GAGAATTTAAAATAATAAAAAGTGGCCGGC 9 109 0 AATAATAAAA 0.850048 -192 ATTGTTCTAAAATAAAAAGAAGCCCGGCAA 9 241 0 AATAAAAAGA 0.73408 -60 GGATTAATGTAATAATAAAAAAGTAAAAAA 11 25 0 AATAATAAAA 0.850048 -39 GAATAAGATTAATATTAAAATTGGCTAAGA 13 144 0 AATATTAAAA 0.785588 -45 ATATTAAGCAAAGAATAAGATTAATATTAA 13 156 0 AAGAATAAGA 0.930592 -33 TATCACTTTAAATATTAAGCAAAGAATAAG 13 167 0 AATATTAAGC 0.58558 -22 AAGTATTAGTAATAATAATAGTAATTATAT 15 149 1 AATAATAATA 0.71149 -41 CCTTTTCCCTAAGAATAAGATTTCCGTTTC 16 254 1 AAGAATAAGA 0.930592 -47 TACCTTAAAAATGATTAAGATTGATTAGGG 17 97 1 ATGATTAAGA 0.396067 -26 GCTCATCCTCAATATTAAGATAATCTGAAT 18 114 1 AATATTAAGA 0.926458 -71 AGATAATCTGAATAATAATAGTTAAATATA 18 131 1 AATAATAATA 0.71149 -54 AGGGTTAAAGAAGAATAAGAAATATAGTAT 19 164 1 AAGAATAAGA 0.930592 -33 TGTAAGTATAAAGATTAAAAATTAAATGAG 22 238 1 AAGATTAAAA 0.715938 -63 ********** Masking position 4 Map Score: 15.0134 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 161 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 AATCTAAAAAAATAAATATAACAACCTAAA 2 211 0 AATAAATATA 0.780956 -90 TATTTGTTTCAATAACTATACGATTTTTGT 4 88 0 AATAACTATA 0.879706 -33 TAGTTTTGAAAAGAACCATATAATTTCACA 6 72 0 AAGAACCATA 0.886154 -210 CCAAAATATATAGAACTATAAAAAACTTAT 6 176 1 TAGAACTATA 0.630066 -106 TACAATTACAAAAAAATATAAGGTTTTGAA 6 260 1 AAAAAATATA 0.78096 -22 ATCAATTATTAACAACCATAAATTATAAAA 12 27 1 AACAACCATA 0.562991 -106 TTACTTTGCAAAAAACTATAAAAACTTTGG 13 18 0 AAAAACTATA 0.87971 -171 ATGTTTTGCAAAAAACTATATATATTTCTT 13 118 1 AAAAACTATA 0.87971 -71 AAAATTGGCTAAGAAATATATATAGTTTTT 13 128 0 AAGAAATATA 0.90658 -61 ACTTAAAGTTAAGTAACATAAATATAGTTA 18 71 1 AAGTAACATA 0.245112 -114 AAGAAACCAAAATAAATATATTAATTTTGA 19 27 1 AATAAATATA 0.780956 -170 AAAGAAGAATAAGAAATATAGTATATAGTG 19 170 1 AAGAAATATA 0.90658 -27 ATAATTAACAAAAAACTATATTAATGATTC 21 44 1 AAAAACTATA 0.87971 -66 ATATTTTAAAAAGAACTATAGTCAAAACAG 22 98 0 AAGAACTATA 0.952165 -203 AACATTTGAAAAGAACTATAAATTTTTTAT 22 201 1 AAGAACTATA 0.952165 -100 AAATAGAAACAATAAATATACCGTATTAAT 23 179 0 AATAAATATA 0.780956 -48 ********** Masking position 5 Map Score: 19.9188 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 159 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 TTCTTAATATTAATTAACTTTAAATATTAC 6 233 1 TAATTAACTT 0.737918 -49 AAAAATTAAATAATTATCTAA 8 2 0 TAATTATCTA 0.931596 -299 ATGATTGGGATAATCATCTATCTACTGCTT 12 74 0 TAATCATCTA 0.873129 -59 CAAATAATATTAATTAACTAATAAGGTGTA 14 54 1 TAATTAACTA 0.84202 -23 ATAATAATAGTAATTATATAATATCAAAAG 15 160 1 TAATTATATA 0.844114 -30 TTTATATTTATAATTATATTATAGCGTATA 16 86 0 TAATTATATT 0.737511 -215 TGGACTTTTATAATTAAATTTTTATATTTA 16 106 0 TAATTAAATT 0.528076 -195 TTAAATTACCTAATTATATAAAATTTGTGT 17 66 0 TAATTATATA 0.844114 -57 TTAGGTAATTTAATTACCTTAAAAATGATT 17 83 1 TAATTACCTT 0.752489 -40 ATAATCACCTATTTTTTATTT 20 114 0 TAATCACCTA 0.747422 -11 AGTTTTTTGTTAATTATCTCATTTGAGATA 21 31 0 TAATTATCTC 0.761061 -79 AAAAATAAAATAATTATCTAGTTCTGCAAT 24 35 0 TAATTATCTA 0.931596 -194 ACTATTTAAATAATCATATACTCAAGGGCA 24 146 1 TAATCATATA 0.732246 -83 ********** Masking position 6 Map Score: 8.35207 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 110 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 GATGGGTTCGGGTGTGGCCCCCCCGCTAT 9 9 0 GGTGTGCCCC 0.989873 -292 CGAACTCGGAAGTTAAGCCCCCCAGCGATGC 9 41 1 AGTTAGCCCC 0.911423 -260 TAAGCCCCCCAGCGATGCCCCGAGTACTGCC 9 54 1 AGCGAGCCCC 0.982164 -247 AGTGGCCGGCGGCGTCGCCCCTTTCCCGCCA 9 88 0 GGCGTGCCCC 0.987943 -213 ATGCCCTGGTGGTGTAGCCCGGCCTATCATA 9 160 1 GGTGTGCCCG 0.959931 -141 TTTTTATATTATTGATGCCCCCATATATTAA 24 75 1 ATTGAGCCCC 0.911423 -154 ***** ***** Masking position 7 Map Score: 1.85532 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 5 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 GTATTTATTTTTTAAATCTTAACTTAACAG 2 264 1 TTTAAATCTT 0.941793 -37 CTTTCTGTAGTTTAAATATTCCATAATGCA 4 29 1 TTTAAATATT 0.879862 -92 TTTTTAGTTTTTTAGACTTTTAGCAAATAA 5 68 0 TTTAGACTTT 0.561355 -32 TGATAAATAATTTAAACCTTCAAATAATAA 6 39 0 TTTAAACCTT 0.923746 -243 ATTAATTAACTTTAAATATTACAATTACAA 6 241 1 TTTAAATATT 0.879862 -41 TACATAAAAATTTAGACCTTTTTGGTGAAA 7 87 1 TTTAGACCTT 0.738717 -22 AATCGATAAATTTAAATATTTTTAAAATAT 9 272 1 TTTAAATATT 0.879862 -29 AAAAAAGTGGTTTAAATCTT 11 1 0 TTTAAATCTT 0.941793 -63 TTGGAAGGCGTTTAAACTTTCCTTAATAAA 13 53 0 TTTAAACTTT 0.845759 -136 GTTATCACTTTAAATATTAAGCAAAGAA 13 171 0 TTTAAATATT 0.879862 -18 AGGATGTGTTATTAAACCTTTATGC 14 6 0 ATTAAACCTT 0.646367 -71 ATGAGCAATATTTAAATTTTTCGAGATAGA 15 65 1 TTTAAATTTT 0.879862 -125 TTACTAATACTTTAAAGCTTTTTGATACGG 15 131 0 TTTAAAGCTT 0.735281 -59 GACTTTTATAATTAAATTTTTATATTTATA 16 104 0 ATTAAATTTT 0.524946 -197 CTCATTTAATTTTTAATCTTTATACTTACA 22 238 0 TTTTAATCTT 0.565133 -63 TAGCTATAACTTTAAATTTTAATTATTAAA 22 271 0 TTTAAATTTT 0.879862 -30 AAGGAAGGCATTTAAATATTTATTGTCAAA 23 89 1 TTTAAATATT 0.879862 -138 ********** Masking position 6 Map Score: 20.4227 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 332 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 15 TTTAAGCTTTTCCATTAGGGGAATTAGGAA 1 43 0 TCCATTAGGG 0.848562 -173 TTTATTTTTATCTAAAAGGAAAAAAGATTC 1 123 0 TCTAAAAGGA 0.894582 -93 ATAAACTCCTTCCATTAGGAAGGAGTTCAA 6 125 0 TCCATTAGGA 0.900758 -157 ATTACATTAATCCAAAAGCAAAAGGTGAGA 11 42 1 TCCAAAAGCA 0.928943 -22 CATAATGTCCTCTAAAAGCAGTAGATAGAT 12 59 1 TCTAAAAGCA 0.783104 -74 TTAAACGCCTTCCAAAAGGAAGGCGTTCAT 13 68 1 TCCAAAAGGA 0.938903 -121 ATGAACTCCTTCCATTAGGAAGGGAGTTCA 22 149 1 TCCATTAGGA 0.900758 -152 ********** Masking position 4 Map Score: 1.96687 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 84 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678