AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipurR_ecoli_opreg_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 codB 300 cytosine permease/transport #3 purE 117 phosphoribosylaminoimidazole carboxylase = AIR carboxylase, catalytic subunit #4 pyrD 110 dihydro-orotate dehydrogenase #5 pyrC 105 dihydro-orotase #6 ycfC 35 orf, hypothetical protein #7 ymfC 201 orf, hypothetical protein #8 prsA 150 phosphoribosylpyrophosphate synthetase #9 purR 300 transcriptional repressor for pur regulon, glyA, glnB, prsA, speA #10 purT 133 phosphoribosylglycinamide formyltransferase 2 #11 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #12 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #13 cvpA 258 membrane protein required for colicin V production #14 purC 212 phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase #15 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #16 guaA 68 GMP synthetase (glutamine-hydrolyzing) #17 guaB 161 IMP dehydrogenase #18 glyA 300 serine hydroxymethyltransferase #19 glnB 60 regulatory protein P-II for glutamine synthetase #20 yfhG 164 putative alpha helix protein #21 purL 300 phosphoribosylformyl-glycineamide synthetase = FGAM synthetase #22 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #23 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #24 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #25 yqgB 120 orf, hypothetical protein #26 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #27 purA 103 adenylosuccinate synthetase Motif number 1 CTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGT 1 66 1 CGCAACGTTC 0.998662 -235 TATTTCCCCACGAAAACGATTGCTTTTTATCTT 2 220 1 CGAAACGTTC 0.978462 -81 TTCACAGCCACGCAACCGTTTTCCTTGCTCTCT 3 32 1 CGCAACGTTC 0.998662 -86 GCAAAAAAAACGCAAACGTTTTCCGAACCTGTT 4 11 0 CGCAACGTTC 0.998662 -100 AAAGGATAAGCGGAAACGTTTTCCTTTGCACGA 5 41 0 CGGAACGTTC 0.985365 -65 GGTGTGTAAAGGCAAACGTTTACCTTGCGATTT 9 242 1 GGCAACGTTC 0.985365 -59 TAAAGACACACGCAAACGTTTTCGTTTATACTG 10 82 1 CGCAACGTTC 0.998662 -52 GAAATCCCTACGCAAACGTTTTCTTTTTCTGTT 13 188 1 CGCAACGTTC 0.998662 -71 TGATATGATACGCAAACGTGTGCGTCTGCAGGA 14 45 1 CGCAACGGTC 0.990221 -168 AAAGCAGTCTCGCAAACGTTTGCTTTCCCTGTT 15 220 1 CGCAACGTTC 0.998662 -78 AAGGGGTAGATGCAATCGGTTACGCTCTGTATA 17 94 1 TGCAACGTTC 0.978462 -68 AAGGAATTTACGCAAACGATTACCTTCAGGCTA 18 169 0 CGCAACGTTC 0.998662 -132 TTTATTTCCACGCAAACGGTTTCGTCAGCGCAT 21 210 1 CGCAACGTTC 0.998662 -91 CGGTCCCCAACGCAATCGTTCTCTTTTGCCTGA 24 197 0 CGCAACGTCC 0.990221 -104 GCGAGCGTTGCGCAAACGTTTTCGTTACAATGC 26 179 1 CGCAACGTTC 0.998662 -122 ***** ** ** * Masking position 5 Map Score: 63.3914 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 8 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GTGTGCCGATGCCTGATGCGACGCTGACGCGTT 2 19 1 GCTGATGGCG 0.997529 -282 TGAACCGTAGGTCGGATAAGGCGCTCGCGTCGC 2 70 1 GCGGATAGCG 0.996593 -231 TGAGCATGGTGTCGGATGCGACGCGAGCGCCTT 2 87 0 GCGGATGGCG 0.998455 -214 ATGCTCAGATGCCTGATGCGACGCTGACGCGTC 2 113 1 GCTGATGGCG 0.997529 -188 CAGTGGGTAGGCCTGATAAGACGCGTCAGCGTC 2 132 0 GCTGATAGCG 0.994557 -169 TACGGTCTTGCCTGATGCGACGCTGGCGCGTC 13 10 1 GCTGATGGCG 0.997529 -249 CCCTGCGTAGGCCTGATAAGACGCGCCAGCGTC 13 29 0 GCTGATAGCG 0.994557 -230 AGAACCGTAGGTCGGATAAGGCGTTTACGCCGC 13 64 1 GCGGATAGCG 0.996593 -195 GGCAATGCGTGTCGGATGCGGCGTAAACGCCTT 13 81 0 GCGGATGGCG 0.998455 -178 TCGGACGTAGTTCGGATAAGGCGTTCACGCCGC 14 117 1 TCGGATAGCG 0.954516 -96 CGGATGTTTTGTCGGATGCGGCGTGAACGCCTT 14 134 0 GCGGATGGCG 0.998455 -79 ATCTTTTGCTGTCTGGTGTGCCGGATGTTTTGT 14 155 0 GCTGGTGGCG 0.985776 -58 * ****** * ** Masking position 7 Map Score: 43.9791 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 84 Number in noncoding regions = 563 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 CAATCTTCTTGCTGCGCAAGCGTTTTCCAGAAC 1 62 1 GCTGCGCCGT 0.886342 -239 GATGCCTGATGCGACGCTGACGCGTTTTATCAT 2 26 1 GCGACGCCGC 0.993158 -275 GGTGTCGGATGCGACGCGAGCGCCTTATCCGAC 2 80 0 GCGACGCCGC 0.99815 -221 GATGCCTGATGCGACGCTGACGCGTCTTATCAG 2 120 1 GCGACGCCGC 0.993158 -181 TGATTTCACAGCCACGCAACCGTTTTCCTTGCT 3 28 1 GCCACGCCGT 0.918976 -90 TCACGAGGGCGCATTCGCGCCCTTTATT 5 6 1 AGGGCGCCGC 0.970606 -100 TCCGTATCGCAGGACGCAAACGCATATGCAACG 7 54 0 AGGACGCCGC 0.970069 -148 CTTGCCTGATGCGACGCTGGCGCGTCTTATCAG 13 17 1 GCGACGCCGC 0.993158 -242 CGTGTCGGATGCGGCGTAAACGCCTTATCCGAC 13 74 0 GCGGCGTCGC 0.98631 -185 CATCCTGTTCGGGGCGCATTCTAACAGAAAAAG 13 210 0 GGGGCGCCTA 0.809842 -49 TTTGTCGGATGCGGCGTGAACGCCTTATCCGAA 14 127 0 GCGGCGTCGC 0.98631 -86 TTTTCAAGCTGGGACGCGCACGACACAGAGAAT 21 61 0 GGGACGCCGA 0.984485 -240 AAACGTTTGCGCAACGCTCGCGAATTTTTCTCT 26 167 0 GCAACGCCGA 0.916429 -134 ******* *** Masking position 5 Map Score: 27.3555 Number of sites scoring better than the average of aligned sites = 1008 Number in coding regions = 710 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 CCCCACGAAAACGATTGCTTTTTATCTTCAG 2 225 1 ACGATTCTTT 0.893669 -76 AGCCACGCAACCGTTTTCCTTGCTCTCTTTC 3 37 1 CCGTTTCCTT 0.967708 -81 GGTTCGGAAAACGTTTGCGTTTTTTTTGCCG 4 15 1 ACGTTTCGTT 0.988382 -96 ATAAGCGGAAACGTTTTCCTTTGCACGAAAA 5 38 0 ACGTTTCCTT 0.980229 -68 GTAAAGGCAAACGTTTACCTTGCGATTTTGC 9 247 1 ACGTTTCCTT 0.980228 -54 ACACACGCAAACGTTTTCGTTTATACTGCGC 10 87 1 ACGTTTCGTT 0.988382 -47 CCCTACGCAAACGTTTTCTTTTTCTGTTAGA 13 193 1 ACGTTTCTTT 0.968999 -66 GCAGACGCACACGTTTGCGTATCATATCAGA 14 43 0 ACGTTTCGTA 0.941054 -170 AGTCTCGCAAACGTTTGCTTTCCCTGTTAGA 15 225 1 ACGTTTCTTT 0.968999 -73 GAAAAGAAATCCGTTTCCGGTTGCAAGCTCT 18 118 1 CCGTTTCGGT 0.874643 -183 ATTTACGCAAACGATTACCTTCAGGCTACGC 18 166 0 ACGATTCCTT 0.93022 -135 GCTGACGAAACCGTTTGCGTGGAAATAAAAT 21 208 0 CCGTTTCGTG 0.89024 -93 GCAAAAGAGAACGATTGCGTTGGGGACCGGG 24 201 1 ACGATTCGTT 0.958117 -100 CGTTGCGCAAACGTTTTCGTTACAATGCGGG 26 184 1 ACGTTTCGTT 0.988382 -117 TTCAAAATCACCGTTTGCTTAAAAATGGATT 27 81 0 CCGTTTCTTA 0.779995 -23 ****** **** Masking position 6 Map Score: 29.4897 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 62 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GACGAATTTCTGGCAAACGGCGGCATTCTGGAGATATGG 1 190 0 TCAGGCGTTT 0.978218 -111 TTCAGATGAATAGAATGCGGCGGATTTTTTGGGTTTCAA 2 251 1 TAAGGCGTTT 0.984909 -50 ATGCAACGTCTGGAACAAGGTGACGTTGTCACCGAAACT 8 24 0 TAAGGTGTTT 0.928954 -127 TGCCTTCGCTGAGGGTGCCGGTCTGGCACCCTGA 11 6 1 TCTGGTGGTT 0.485479 -89 AGAAAGGAGGTATAATCCGTCGATTTTTTTT 15 3 0 TAAGTCGTTT 0.928949 -295 ACCTCCTTTCTTCAAGGCGGCAATATTCTTTTCGTTGAC 15 31 1 TAAGGCATTT 0.903231 -267 AAAACTAACCTTTACCCTGGCACAAGTCTTCTTTCGCCG 15 146 1 TACGGCAGTT 0.743447 -152 GGTAGAAAAATAAAATTCGGCGCAATTCTAACAGGGAAA 15 243 0 TAAGGCGTTT 0.98485 -55 GCTATTCCTTGAAAAGGTCGCCTGTCTTTTGATCTGC 19 34 0 TAAGTCGGTT 0.870397 -27 TTAAAGCCTATCCCAGTGGGCGTAATTGTTGCAGACAGT 20 125 0 TCAGGCGTTT 0.978219 -40 TGTAATAAGTTGCCATCTGGCGCAGGTTTACGCAAAATG 21 133 0 TCAGGCGGTT 0.958449 -168 GCGTTGCTAATTCACGATGGTGATTTTATTTCCACGCAA 21 186 1 TACGGTGTTT 0.887684 -115 ACCCAAGGGGGGGAAACGGGCGTCATTATAAAGAATCTG 21 243 0 GAAGGCGTTT 0.886001 -58 CATCTTTGTATAGAAACTGGTGTATTTTTTGGTTTTTTA 24 70 1 TAAGGTGTTT 0.928954 -231 TTTTTGGTTTTTTATTCTGTCGCGATTTTTGCATTTTTT 24 95 1 TATGTCGTTT 0.727564 -206 TACTGAGGACTGAACAAGGGCGCTCTTGTAAAAACAAGA 25 47 1 TACGGCGTTT 0.975286 -74 TTGCCCACGGTAACCACAGTCAAAATTGTGATCACCATT 26 125 1 TCCGTCATTT 0.437339 -176 * ** **** ** * Masking position 17 Map Score: 17.0364 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 614 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 AAAACGAGCAGAAAAAAGTGGACCAAATGG 1 23 0 GAAAAAAGTG 0.840465 -278 ATGAATGAGTGCAAAAAGGTGGGGGAAAAA 2 180 0 GCAAAAAGGT 0.959024 -121 GTTTCAAACAGCAAAAAGGGGGAATTTC 2 283 1 GCAAAAAGGG 0.990656 -18 GCGAGTTCGGACCAAAAGGGAATTGACCTG 4 46 0 ACCAAAAGGG 0.815071 -65 TTATTACCACACAAAAAGTGATATTACGCA 9 29 1 ACAAAAAGTG 0.883025 -272 GCCGATCTTGACGAAAAGGGGAAGTGGTAA 9 112 0 ACGAAAAGGG 0.815072 -189 TGGCCAGTACGCAAATAGTGTAAGCGTGGA 9 148 0 GCAAATAGTG 0.79842 -153 TATCATATCAGAAAAAAGGGCCGGATGATT 14 25 0 GAAAAAAGGG 0.942308 -188 GAAAAGACGTGCAAAAAGGTTGTGTAAAGC 15 195 1 GCAAAAAGGT 0.959024 -103 AGCATTTTTTGCAAAAAGGGGTAGATGCAA 17 79 1 GCAAAAAGGG 0.990656 -83 AACTCTGTGCGTAAAAAGGTATAAAGCGGG 26 65 0 GTAAAAAGGT 0.671567 -236 ATTTTTGAGTGCAAAAAGTGCTGTAACTCT 27 35 1 GCAAAAAGTG 0.971588 -69 ********** Masking position 5 Map Score: 15.7098 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 338 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 GCTGCGCAAGCGTTTTCCAGAACAGGTTAGA 1 72 1 CGTTTCCAGA 0.743972 -229 AGAATGCCGCCGTTTGCCAGAAATTCGTCGG 1 200 1 CGTTGCCAGA 0.956914 -101 GGTTCAGGTCCGTAGGCATGATAAAACGCGT 2 45 0 CGTGGCATGA 0.680455 -256 GGACCTGAACCGTAGGTCGGATAAGGCGCTC 2 65 1 CGTGGTCGGA 0.956797 -236 AAAAACAGTGGGTAGGCCTGATAAGACGCGT 2 139 0 GGTGGCCTGA 0.907933 -162 TGAAGGGATGTTTTTGCCGGACACAAAGGAT 5 67 0 TTTTGCCGGA 0.878707 -39 AAAAACATCCCTTCAGCCGGAGCATAGAGAT 5 83 1 CTTAGCCGGA 0.780915 -23 ACAACGTCACCTTGTTCCAGACGTTGCATCG 8 34 1 CTTTTCCAGA 0.521891 -117 CACCAATGGACGCATGCCTGAGGTTCTTCTC 8 130 1 CGCTGCCTGA 0.901962 -21 AAAGTGTTGCGGTACGCCGGAAAAACGACAC 9 199 0 GGTCGCCGGA 0.827737 -102 CTTTGCAGGATTTCGGCGGGAGTTGCAAGTC 11 43 0 TTTGGCGGGA 0.479912 -52 TACGGTCTTGCCTGATGCGACGCTG 13 5 1 GTCTGCCTGA 0.541458 -254 TCTACCCCTGCGTAGGCCTGATAAGACGCGC 13 36 0 CGTGGCCTGA 0.966514 -223 GGGGTAGAACCGTAGGTCGGATAAGGCGTTT 13 59 1 CGTGGTCGGA 0.956797 -200 CATCGGGCAATGCGTGTCGGATGCGGCGTAA 13 88 0 TGCTGTCGGA 0.551095 -171 TCATCCGGCCCTTTTTTCTGATATGATACGC 14 27 1 CTTTTTCTGA 0.325479 -186 CAAACGTGTGCGTCTGCAGGAAAACGCGATT 14 57 1 CGTTGCAGGA 0.891087 -156 GCACGAAATTTGTTTGTCGGACGTAGTTCGG 14 101 1 TGTTGTCGGA 0.834063 -112 GTTTGTCGGACGTAGTTCGGATAAGGCGTTC 14 112 1 CGTGTTCGGA 0.743433 -101 TGTGCCGGATGTTTTGTCGGATGCGGCGTGA 14 141 0 GTTTGTCGGA 0.787672 -72 TTTGCTGTCTGGTGTGCCGGATGTTTTGTCG 14 153 0 GGTTGCCGGA 0.974286 -60 GGAAAGCAAACGTTTGCGAGACTGCTTTACA 15 217 0 CGTTGCGAGA 0.786868 -81 CTTTATTCCTCTTCTGCGGGAGAGGATCAGG 22 14 1 CTTTGCGGGA 0.873815 -105 CAATCGTTCTCTTTTGCCTGAACTTACCACC 24 187 0 CTTTGCCTGA 0.933994 -114 *** ******* Masking position 11 Map Score: 22.7715 Number of sites scoring better than the average of aligned sites = 2794 Number in coding regions = 2227 Number in noncoding regions = 567 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 8 CGACGAATTTCTGGCAAACGGCGGCATTCTGGA 1 197 0 CGGCAACGCG 0.949772 -104 AGCGTCGCATCAGGCATCGGCACACAGTGCCGG 2 11 0 CGGCACGCAC 0.770477 -290 CGCGTTTTATCATGCCTACGGACCTGAACCGTA 2 46 1 CTGCCACGAC 0.866193 -255 CGCGTCTTATCAGGCCTACCCACTGTTTTTACA 2 140 1 CGGCCACCAC 0.963266 -161 GCCGGGCAAGCTGAGTTTCGGTGAC 8 3 1 CGGCAGCGAG 0.981981 -148 AGGATCATGCCTGGCCCGCACAGTTTTCGGCAG 8 89 1 CGGCCGCCAG 0.967237 -62 AGAAGAACCTCAGGCATGCGTCCATTGGTGGAA 8 127 0 CGGCAGCTCC 0.796984 -24 TGTCGTTTTTCCGGCGTACCGCAACACTTTTGT 9 200 1 CGGCGACGCA 0.59983 -101 GGGTGCCAGACCGGCACCCTCAGCGAAGGCA 11 9 0 CGGCACCCAG 0.970046 -86 GGGTGCCGGTCTGGCACCCTGACTTGCAACTCC 11 23 1 CGGCACCGAC 0.979923 -72 CCCTGTCAGACTTGCAGGCAGACTTTGCAGGAT 11 63 0 CTGCAGCGAC 0.939852 -32 CGCGTCTTATCAGGCCTACGCAGGGGTAGAACC 13 37 1 CGGCCACCAG 0.951969 -222 ATCGCGTTTTCCTGCAGACGCACACGTTTGCGT 14 54 0 CTGCAACCAC 0.895515 -159 GTCTTTTCCCCAGGCGCGCGGCGAAAGAAGACT 15 170 0 CGGCGGCGCG 0.912961 -128 GAATAAAGAGCTTGCAACCGGAAACGGATTTCT 18 122 0 CTGCACCGAA 0.64645 -179 TTTTTTCAAGCTGGGACGCGCACGACACAGAGA 21 63 0 CGGGAGCCAC 0.832183 -238 * **** ** *** Masking position 4 Map Score: 13.6753 Number of sites scoring better than the average of aligned sites = 1739 Number in coding regions = 1641 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 9 CAACTTAATGGCGGGATTTTTTATATTATT 1 149 0 GCGGGATTTT 0.91331 -152 TTGACTTTTAGCGCCCATATCTCCAGAATG 1 176 1 GCGCCCATAT 0.811643 -125 CTGGCAAACGGCGGCATTCTGGAGATATGG 1 190 0 GCGGCATTCT 0.970766 -111 CAAAAAATCCGCCGCATTCTATTCATCTGA 2 252 0 GCCGCATTCT 0.856443 -49 GGGCGCATTCGCGCCCTTTATTTTTCGTGC 5 17 1 GCGCCCTTTA 0.728682 -89 ATTATGAATTGCCGCATTATAGCCTAATAA 7 169 0 GCCGCATTAT 0.898639 -33 TATTTTTTCAGCGCCATTTTTATTGATGCG 13 151 1 GCGCCATTTT 0.967743 -108 TTTCTTCAAGGCGGCAATATTCTTTTCGTT 15 37 1 GCGGCAATAT 0.902538 -261 AAATATTGCCGCGGCATTATACAGAGCGTA 17 114 0 GCGGCATTAT 0.980138 -48 CAAAAGACAGGCGACCTTTTCAAGGAATAG 19 40 1 GCGACCTTTT 0.839459 -21 TCATAAATGAGCGGCATTTTGCGTAAACCT 21 119 1 GCGGCATTTT 0.983233 -182 GGGGAAACGGGCGTCATTATAAAGAATCTG 21 243 0 GCGTCATTAT 0.828704 -58 TTTTACAAGAGCGCCCTTGTTCAGTCCTCA 25 50 0 GCGCCCTTGT 0.893576 -71 AAGGTATAAAGCGGGCTTTTGCTGGGGAAT 26 50 0 GCGGGCTTTT 0.905504 -251 ********** Masking position 8 Map Score: 14.084 Number of sites scoring better than the average of aligned sites = 697 Number in coding regions = 596 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 10 TACACCGATAATTTTTCCCCCACCTTTTTGCAC 2 169 1 ATTTTTCCCC 0.970103 -132 ATGACGGGAGATTTTTTCATCACAGTGTGTAAA 9 61 0 ATTTTTTACC 0.945948 -240 GGCGTTGAATATTTTTTCAGCGCCATTTTTATT 13 142 1 ATTTTTTACC 0.945948 -117 GCCGAATTTTATTTTTCTACCGCAAGTAACGCG 15 261 1 ATTTTTCACC 0.96553 -37 CCGCGGCAATATTTATTAACCACTCTGGTCGAG 17 130 1 ATTTATTACC 0.669647 -32 TGAGGCATAAATTTTCCTCACCCTGATCCTCTC 22 33 0 ATTTTCCCCC 0.8478 -86 TTTTTGACATTTTTTTAGCTCTTAATATTGT 24 9 1 ATTTTTTACC 0.945948 -292 CGATTTTTGCATTTTTTAACCATAAGCTAATGT 24 117 1 ATTTTTTACT 0.556682 -184 TTTTTCTGCAATTTTTCTATTGCGG 26 3 0 ATTTTTCATC 0.795579 -298 ACGCTCGCGAATTTTTCTCTTTCAATGGTGATC 26 154 0 ATTTTTCCTC 0.818457 -147 GGGCATCCTTATTTTTCGCCCGCATTGTAACGA 26 200 0 ATTTTTCCCC 0.970103 -101 GAGTTACAGCACTTTTTGCACTCAAAAATGACC 27 31 0 ACTTTTTCCC 0.776798 -73 ******* * * * Masking position 1 Map Score: 8.98382 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 111 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 11 CAGGCATTAAGCGACAAAAAGATCATCTAACC 1 96 0 GCGCAAAAGA 0.839114 -205 ACATGCATGAGCCACAAAATAATATAAAAAAT 1 132 1 GCCCAAAAAA 0.6963 -169 GTGCAAAAAGGTGGGGGAAAAATTATCGGTGT 2 170 0 GTGGGGAAAA 0.819869 -131 GAATTGACCTGCGGCAAAAAAAACGCAAACGT 4 25 0 GCGCAAAAAA 0.916089 -86 CAAACCAGTAGCGCTCGAAGGAGAGGTGA 7 8 0 GCGTCGAAGA 0.718984 -194 TTAATACACCGCCTGGAAAGGATCATGCCTGG 8 71 1 GCCGGAAAGA 0.764273 -80 TTTACACACTGTGATGAAAAAATCTCCCGTCA 9 61 1 GTGTGAAAAA 0.597725 -240 GTGTTGCGGTACGCCGGAAAAACGACACGGAG 9 195 0 ACGCGGAAAA 0.738476 -106 TTTATACTGCGCGCGGAATTAATCAGGGGATA 10 106 1 GCGGGAATAA 0.709781 -28 AATAAAAATGGCGCTGAAAAAATATTCAACGC 13 143 0 GCGTGAAAAA 0.944417 -116 TTTTATTGATGCGCGGGAAGGAAATCCCTACG 13 168 1 GCGGGGAAGA 0.961337 -91 CCCCAGGCGCGCGGCGAAAGAAGACTTGTGCC 15 164 0 GCGCGAAAAA 0.974051 -134 CGCGTTACTTGCGGTAGAAAAATAAAATTCGG 15 262 0 GCGTAGAAAA 0.888379 -36 TGTTTCACTTGCCTCGGAATAAGCGTCA 16 51 1 GCCCGGAAAA 0.926986 -18 GAAACCGTTTGCGTGGAAATAAAATCACCATC 21 201 0 GCGGGAAAAA 0.969985 -100 TGCAAAAATCGCGACAGAATAAAAAACCAAAA 24 96 0 GCGCAGAAAA 0.946187 -205 TCGTTACAATGCGGGCGAAAAATAAGGATGCC 26 200 1 GCGGCGAAAA 0.910604 -101 CTCTGAAAAAGCGATGGTAGAATCCATTTTTA 27 61 1 GCGTGGTAAA 0.674367 -43 *** ***** ** Masking position 12 Map Score: 15.8205 Number of sites scoring better than the average of aligned sites = 1321 Number in coding regions = 1218 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 12 CTGGAGATATGGGCGCTAAAAGTCAACTTA 1 172 0 GGGCGCTAAA 0.695522 -129 GTGCAAAAAGGTGGGGGAAAAATTATCGGT 2 172 0 GTGGGGGAAA 0.924356 -129 AATCGTTTTCGTGGGGAAATATATTTTTTA 2 211 0 GTGGGGAAAT 0.546678 -90 TGTGCAAACCGGGGGCGTATTATGTGCGAG 4 71 0 GGGGGCGTAT 0.661467 -40 GAAAAATAAAGGGCGCGAATGCGCCCTCGT 5 13 0 GGGCGCGAAT 0.930113 -93 CAAACCAGTAGCGCTCGAAGGAGAGGTGA 7 10 0 GCGCTCGAAG 0.740374 -192 CGTTTATACTGCGCGCGGAATTAATCAGGG 10 104 1 GCGCGCGGAA 0.916815 -30 AATAAAAATGGCGCTGAAAAAATATTCAAC 13 145 0 GCGCTGAAAA 0.60313 -114 TTTTATTGATGCGCGGGAAGGAAATCCCTA 13 168 1 GCGCGGGAAG 0.91147 -91 AAATACAGGGCTGGAATCATCCGGCCC 14 8 1 GGGCTGGAAT 0.692914 -205 GCCCCGGGCAGTGCTCGAAATCTTCACGTA 20 54 1 GTGCTCGAAA 0.812248 -111 GACATGGACAGCGCGGAGAAACCGGAGCGT 20 92 0 GCGCGGAGAA 0.670575 -73 GCCTATCCCAGTGGGCGTAATTGTTGCAGA 20 129 0 GTGGGCGTAA 0.745608 -36 GTGTACCCAAGGGGGGGAAACGGGCGTCAT 21 256 0 GGGGGGGAAA 0.951189 -45 TGTGGTTACCGTGGGCAAAATACAGAAATT 26 113 0 GTGGGCAAAA 0.786651 -188 TCGTTACAATGCGGGCGAAAAATAAGGATG 26 200 1 GCGGGCGAAA 0.967434 -101 ********** Masking position 9 Map Score: 9.62436 Number of sites scoring better than the average of aligned sites = 1753 Number in coding regions = 1614 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 13 ATATAAAAAATCCCGCCATTAAGTTGACTT 1 153 1 TCCCGCCATT 0.944541 -148 ATCTCCAGAATGCCGCCGTTTGCCAGAAAT 1 194 1 TGCCGCCGTT 0.742817 -107 ACCCAAAAAATCCGCCGCATTCTATTCATC 2 255 0 TCCGCCGCAT 0.851049 -46 GAGGGCGCATTCGCGCCCTTTATTTTTCGT 5 15 1 TCGCGCCCTT 0.948256 -91 AGACGTTGCATCGCGCTCTTTAATACACCG 8 52 1 TCGCGCTCTT 0.783046 -99 GGGATTTCCTTCCCGCGCATCAATAAAAAT 13 166 0 TCCCGCGCAT 0.970267 -93 ATGTGTCCCACGATTTTACGCCCTG 13 244 0 TCCCACGATT 0.573006 -15 GCTGGAATCATCCGGCCCTTTTTTCTGATA 14 20 1 TCCGGCCCTT 0.948264 -193 CTGTTAGAATTGCGCCGAATTTTATTTTTC 15 248 1 TGCGCCGAAT 0.458396 -50 CGACTTCATGTCGGGCGATTTATATTATCT 16 22 1 TCGGGCGATT 0.668015 -47 GTCGATAGTAACCCGCCCTTCGGGGATAGC 17 48 1 ACCCGCCCTT 0.895867 -114 TTACGCAAAATGCCGCTCATTTATGAGTAA 21 115 0 TGCCGCTCAT 0.748788 -186 TAGCAACGCGTGCCGCCAATGGCTGTAATA 21 165 0 TGCCGCCAAT 0.828607 -136 GACGCCCGTTTCCCCCCCTTGGGTACACCG 21 258 1 TCCCCCCCTT 0.964489 -43 AAAAGTTGTCAGCCCCGCTTATTCAATGAG 24 275 1 AGCCCCGCTT 0.670344 -26 TCCTTATTTTTCGCCCGCATTGTAACGAAA 26 198 0 TCGCCCGCAT 0.851048 -103 ********** Masking position 10 Map Score: 10.229 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1293 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 14 CAGAGAATAGCACGGAAAGAGAGCAAGGAA 3 52 0 CACGGAAAGA 0.834274 -66 GTGACGTTGTCACCGAAACTCAGCTTGCCC 8 14 0 CACCGAAACT 0.680169 -137 CCGGCACCCTCAGCGAAGGCA 11 2 0 CAGCGAAGGC 0.881147 -93 TTGCAACTCCCGCCGAAATCCTGCAAAGTC 11 46 1 CGCCGAAATC 0.774016 -49 GCACACCAGACAGCAAAAGATTTTAAAACG 14 167 1 CAGCAAAAGA 0.629181 -46 CCCAGGCGCGCGGCGAAAGAAGACTTGTGC 15 165 0 CGGCGAAAGA 0.930008 -133 GCAATTCTAACAGGGAAAGCAAACGTTTGC 15 231 0 CAGGGAAAGC 0.958629 -67 ACCCGCCCTTCGGGGATAGCAAGCATTTTT 17 58 1 CGGGGATAGC 0.674725 -104 ATGGACAGCGCGGAGAAACCGGAGCGTACA 20 89 0 CGGAGAAACC 0.719044 -76 CCCTTGGGTACACCGAAAGCTTAGAAGACG 21 273 1 CACCGAAAGC 0.974627 -28 CTGAACTTACCACCGAAACAGACTGTTAAC 24 171 0 CACCGAAACA 0.874951 -130 TGTGAAAGTTCGGCGAAACCACGAGAAAAC 25 86 0 CGGCGAAACC 0.966989 -35 CTGCATTCCCCAGCAAAAGCCCGCTTTATA 26 46 1 CAGCAAAAGC 0.855132 -255 GTATTTTGCCCACGGTAACCACAGTCAAAA 26 120 1 CACGGTAACC 0.522057 -181 ********** Masking position 1 Map Score: 6.61654 Number of sites scoring better than the average of aligned sites = 1607 Number in coding regions = 1533 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 15 GTTAGATGATCTTTTTGTCGCTTAATGCCT 1 97 1 CTTTTTGTCG 0.869972 -204 CCGGCACTGTGTGCCGATGCCTGATG 2 7 1 CTGTGTGCCG 0.959038 -294 TTTCCCCCACCTTTTTGCACTCATTCATAT 2 182 1 CTTTTTGCAC 0.739743 -119 GAAATTCCCCCTTTTTGCTGTTTGAAACCC 2 281 0 CTTTTTGCTG 0.670356 -20 CCGTGCTATTCTCTGTGCCCTCTAAAGCCG 3 67 1 CTCTGTGCCC 0.912723 -51 CGTTTGCGTTTTTTTTGCCGCAGGTCAATT 4 26 1 TTTTTTGCCG 0.906684 -85 CTGAAGGGATGTTTTTGCCGGACACAAAGG 5 69 0 GTTTTTGCCG 0.78035 -37 TACTACCCTATTGTTTGCCGTCATGAAAGA 7 133 1 TTGTTTGCCG 0.908264 -69 CTTCCTGACGCTCCGTGTCGTTTTTCCGGC 9 185 1 CTCCGTGTCG 0.310687 -116 CGCACGAAATTTGTTTGTCGGACGTAGTTC 14 100 1 TTGTTTGTCG 0.664754 -113 TTTTGCTGTCTGGTGTGCCGGATGTTTTGT 14 155 0 TGGTGTGCCG 0.447745 -58 TTTACACAACCTTTTTGCACGTCTTTTCCC 15 193 0 CTTTTTGCAC 0.739743 -105 TTCTCTTCGCCCGACTTCATGT 16 3 1 CTCTTCGCCC 0.846848 -66 TTCGGTTATACTGTTCGCCGTTGTCCAACA 18 228 1 CTGTTCGCCG 0.925259 -73 TTAGTTAATTCTCTGTGTCGTGCGCGTCCC 21 54 1 CTCTGTGTCG 0.791067 -247 GGCATCCTTATTTTTCGCCCGCATTGTAAC 26 202 0 TTTTTCGCCC 0.661576 -99 AGTTACAGCACTTTTTGCACTCAAAAATGA 27 33 0 CTTTTTGCAC 0.739743 -71 ********** Masking position 7 Map Score: 7.21094 Number of sites scoring better than the average of aligned sites = 2475 Number in coding regions = 2288 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809