AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_hinf_reg_100.orf -o00260_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0086 300 cystathionine gamma-synthase (metB) #2 HI0087 42 threonine synthase (thrC) #3 HI0089 300 aspartokinase I / homoserine dehydrogenase I (thrA) #4 HI0110 166 seryl-tRNA synthetase (serS) #5 HI0160 156 phosphatidylserine decarboxylase proenzyme (psd) #6 HI0288 34 L-serine deaminase (sdaA) #7 HI0289 222 serine transporter (sdaC) #8 HI0425 146 phosphatidylserine synthase (pssA) #9 HI0464 132 ribose 5-phosphate isomerase A (rpiA) #10 HI0465 29 D-3-phosphoglycerate dehydrogenase (serA) #11 HI0646 158 aspartate-semialdehyde dehydrogenase (asd) #12 HI0737 247 acetohydroxy acid synthase II, putative #13 HI0738 71 dihydroxyacid dehydratase (ilvD) #14 HI0738.1 79 threonine deaminase (ilvA) #15 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #16 HI0924 300 glycyl-tRNA synthetase, beta chain (glyS) #17 HI0927 265 glycyl-tRNA synthetase, alpha chain (glyQ) #18 HI1033 149 phosphoserine phosphatase (serB) #19 HI1167 190 phosphoserine aminotransferase (serC) #20 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #21 HI1367 284 threonyl-tRNA synthetase (thrS) Motif number 1 GATTACGGATAAAGTGCGGTTATTTTTCAT 3 132 0 AAAGTGCGGT 0.997336 -169 ATTCTAATACAAAGTGCGGTCAATTTTTCT 4 52 1 AAAGTGCGGT 0.997336 -115 CTTGTTAAAAAAAGAGGCGTGATTATAGCA 5 129 0 AAAGAGGCGT 0.922191 -28 TTTTTTATAAAAAGTGCGGTAATTTTCAGC 7 64 0 AAAGTGCGGT 0.997336 -159 ATTAAATAAAAAAGTGTGGTTAATTTAAAA 11 37 0 AAAGTGTGGT 0.967212 -122 AAATAAGCCAAAAGAGCGGTAAAAATTCAC 12 74 1 AAAGAGCGGT 0.996247 -174 AAAACGAAAAAAAGTGCGGTGAAAATTGGC 12 142 0 AAAGTGCGGT 0.997336 -106 CCCTCTTATGAAAGAGGGGAACCGTTAAA 14 10 0 AAAGAGGGGA 0.973889 -70 TTTTGATGATAAAGTGCGGTTAGTTTTTCC 14 52 0 AAAGTGCGGT 0.997336 -28 CCTCTTTAGCAAAGAGGGGTAGGGGAGATT 16 60 0 AAAGAGGGGT 0.993837 -241 CCTCTTTGCTAAAGAGGGGAATTCTTGAAT 16 73 1 AAAGAGGGGA 0.973889 -228 CCTCTTTGCTAAAGAGGGGATTGGATCTTT 16 203 0 AAAGAGGGGA 0.973889 -98 CCTCTTTAGCAAAGAGGGGTAGGGGCGATT 16 216 1 AAAGAGGGGT 0.993837 -85 ATAAAGGCGAAAAATGCGGTTGAAAATCAG 17 189 0 AAAATGCGGT 0.948893 -77 AAAGACCGTAAAAGTGCGGTCAATATTTTT 20 74 1 AAAGTGCGGT 0.997336 -40 TGGGTATTTAAAAGTGCGGTTATTCTAGCC 21 25 1 AAAGTGCGGT 0.997336 -260 AAGTAGGGCAAAAGTGCGGTTAATTTTTAT 21 206 1 AAAGTGCGGT 0.997336 -79 ********** Masking position 3 Map Score: 61.639 Number of sites scoring better than the average of aligned sites = 1187 Number in coding regions = 751 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 2 TACGGATAAAGTGCGGTTATTTTTCATTGTGTT 3 126 0 GTGCGGTATT 0.998144 -175 CTAATACAAAGTGCGGTCAATTTTTCTTTATTT 4 55 1 GTGCGGTATT 0.998144 -112 TTTATAAAAAGTGCGGTAATTTTCAGCGACAAA 7 58 0 GTGCGGTATT 0.998144 -165 AAATAAAAAAGTGTGGTTAATTTAAAAGAAAAT 11 31 0 GTGTGGTATT 0.979163 -128 TAAGCCAAAAGAGCGGTAAAAATTCACTAAATT 12 77 1 GAGCGGTAAT 0.954623 -171 ACGAAAAAAAGTGCGGTGAAAATTGGCTTATTT 12 136 0 GTGCGGTAAT 0.993356 -112 TGATGATAAAGTGCGGTTAGTTTTTCCTTTGTT 14 46 0 GTGCGGTATT 0.998144 -34 GACCGTAAAAGTGCGGTCAATATTTTTAACGTT 20 77 1 GTGCGGTATT 0.998144 -37 GTATTTAAAAGTGCGGTTATTCTAGCCTTTATT 21 28 1 GTGCGGTATT 0.998144 -257 TAGGGCAAAAGTGCGGTTAATTTTTATAGAATT 21 209 1 GTGCGGTATT 0.998144 -76 ******* * * * Masking position 7 Map Score: 34.3897 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 216 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TAAATCACAGAAAATGATGGAAAAATGAAATTTTAT 1 203 1 AAATAAAAAT 0.794354 -98 TAGAAATTAGAAAATTACATAAAATTTCATTTTTCC 1 221 0 AAATAAAATT 0.955738 -80 GGCACAAAGGAAAAAGTGATAAAAGTAGAAATTAGA 1 246 0 AAAAAAAAGT 0.823466 -55 CTTAGTCAATAAATTTCGTGTAAACTAACCG 3 6 0 AAATTAAACT 0.523264 -295 TTGACTAAGAAAATTTCTGAAAAATTTGTCACTTTC 3 33 1 AAATAAAATT 0.9187 -268 TGAATGCGTAAAGAAATACCGAAATTTCCCGAGCTT 3 77 0 AAGAGAAATT 0.550002 -224 TTTCAAGATAAAACACAATGAAAAATAACCGCACTT 3 115 1 AAAAAAAAAT 0.794354 -186 CCAACGTATAAAAATAAAGAAAAATTGACCGCACTT 4 63 0 AAATAAAATT 0.955986 -104 ATTTCAACGAAAAAAGTAAGGAAATTCT 4 149 1 AAAAGAAATT 0.896454 -18 AAAAGGTTGGAACTATAACAAAAATTGCTATAATCA 5 104 1 AACAAAAATT 0.625409 -53 AAATTTCTCAAAATTCGTTAAAAATTAAAGGCGA 6 9 0 AAATAAAATT 0.940494 -26 TTTTTTAGCCAAAAAATGCTAAAATTTGTGAGCATT 8 37 1 AAAAAAAATT 0.956115 -110 AAAAAGAGTGATTAAATTAAATTTTCTT 11 3 1 AAAATAAATT 0.881988 -156 AAGTGTGGTTAATTTAAAAGAAAATTTAATTTAATC 11 20 0 AATTAAAATT 0.533262 -139 TCGCGAAAGAAATTAAATAAAAAAGTGTGGTTAATT 11 42 0 AATAAAAAGT 0.494533 -117 GCGAAAGATCAATTTTCATTAAAAATACTTGATTTT 11 74 1 AATTAAAAAT 0.430895 -85 AAAGAGCGGTAAAAATTCACTAAATTTTTTAGGGGA 12 84 1 AAAATAAATT 0.881985 -164 TTGGAGAGAAAAAAACGAAAAAAAGTGCGGTGAAAA 12 147 0 AAAAAAAAGT 0.823466 -101 ATATTTTATCAATTAACGAAGAAATTAATCATACAA 13 13 1 AATAGAAATT 0.635856 -59 TTAATCATACAAACGAACCCTAAATTTTACTCGGAG 13 37 1 AAAGTAAATT 0.470811 -35 GAGGGGGATAAAACAAAGGAAAAACTAACCGCACTT 14 35 1 AAAAAAAACT 0.762038 -45 TTATGGATAAAAATTTAATTAAAATTTCATTCCTAA 15 55 0 AAATAAAATT 0.9187 -69 CAGATAATTTAATCTCTATTGAAATTAAAATGTAAA 16 124 0 AATTGAAATT 0.634478 -177 TAATCAAAAAAAACTATACTAAAATAAAACTTAAAA 17 106 1 AAATAAAATA 0.762118 -160 AATAAAACTTAAAATCTACCTAAATATTCAAAATTA 17 128 1 AAATTAAATA 0.523582 -138 AATAACAGATAAAATATTCTAAAATTAATTGCACTT 18 25 1 AAATAAAATT 0.955986 -125 AAAATCCTGTAAGTTGCTAAAAAATTGAATTACTCT 18 123 0 AAGTAAAATT 0.754185 -27 ACGATTGATTAAAAAAAAGCTAAATTACGGCACAGT 19 39 0 AAAATAAATT 0.881987 -152 ATCATTCATAAAATAGAGGGTAAATTTTGACGATTG 19 68 0 AAAATAAATT 0.881983 -123 TTATTTTCATAAAAAGCAAGGAAATACA 19 173 1 AAAAGAAATA 0.560068 -18 TTTACCTCGTAAAAACGTTAAAAATATTGACCGCAC 20 87 0 AAAAAAAATA 0.762119 -27 TGAACGAGCGAAATTAGGCAAAAAATGCGTGGCGAA 21 153 0 AAATAAAAAT 0.794246 -132 TGTTCATTTAAAATTCTATAAAAATTAACCGCACTT 21 217 0 AAATAAAATT 0.940494 -68 *** * ****** Masking position 12 Map Score: 33.3482 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 518 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 4 CAGAAAATGATGGAAAAATGAAATTTTATGTAA 1 210 1 TGAAATGAAA 0.499084 -91 GCACAAAGGAAAAAGTGATAAAAGTAGAAATTA 1 248 0 AAAGATAAAA 0.512069 -53 GTTAATTTAAATAGATGAAATCAGATTAAA 2 8 1 TAAGATGAAA 0.714428 -35 ACGAAATTTATTGACTAAGAAAATTTCTGAAAA 3 23 1 TTAAAGAAAA 0.795086 -278 CGCATTCATTTTTCAAGATAAAACACAATGAAA 3 105 1 TTCGATAAAA 0.692102 -196 CGTGCTAATGATTACGGATAAAGTGCGGTTATT 3 138 0 ATAGATAAAG 0.397193 -163 TTGTTTTCATTTCAACGAAAAAAGTAAGGAAAT 4 141 1 TTAGAAAAAA 0.933766 -26 CGCCTCTTTTTTTAACAAGGAAAGATA 5 140 1 TTAAAGGAAA 0.642652 -17 TGCGGTAATTTTCAGCGACAAAAAAATCGGTGC 7 47 0 TTAGACAAAA 0.707618 -176 ATGGCTGTTTTTTAGCCAAAAAATGCTAAAATT 8 30 1 TTACAAAAAA 0.809755 -117 TTGTGAGCATTATAACGAAAAAAAGCCTTTTTT 8 62 1 TAAGAAAAAA 0.799493 -85 CACGTGCTTATTAATAGAAAAAAGGCTTTTTTT 8 79 0 TTAGAAAAAA 0.933766 -68 TGAAATAACATTGCTTGAGAAAAACGCCTGTTA 9 35 1 TTCGAGAAAA 0.554325 -98 GCGAAAGAAATTAAATAAAAAAGTGTGGTTAAT 11 43 0 TTAAAAAAAG 0.479238 -116 TTATCCTATGTAAAAAAATGAAAAGAGTTTCAA 12 14 1 TAAAATGAAA 0.479068 -234 TGGTAGGGCTTGGAGAGAAAAAAACGAAAAAAA 12 159 0 TGAGAAAAAA 0.812028 -89 AATTTCTTCGTTAATTGATAAAATATTC 13 6 0 TTAGATAAAA 0.950204 -66 TTAATTTCATTTAAGTGATGAAAATTTAGGAAT 15 30 1 TTAGATGAAA 0.89842 -94 GTGATGAAAATTTAGGAATGAAATTTTAATTAA 15 44 1 TTAAATGAAA 0.76479 -80 AGTTTAACTGTTTATGGATAAAAATTTAATTAA 15 69 0 TTAGATAAAA 0.950204 -55 ATCTATTAAATTAATCAAAAAAAACTATACTAA 17 95 1 TTAAAAAAAA 0.83825 -171 ATATCATATAATAACAGATAAAATATTCTAAAA 18 16 1 ATAGATAAAA 0.787711 -134 ATTTTGACGATTGATTAAAAAAAAGCTAAATTA 19 48 0 TTAAAAAAAA 0.83825 -143 AATTCTTTCTATCATTCATAAAATAGAGGGTAA 19 81 0 ATACATAAAA 0.528367 -110 TGCTTTTTACTGAAATCAAAAAAATTCTTTCTA 19 103 0 TGACAAAAAA 0.566024 -88 TATCGATTTTTGTAGTGATAAAAAAGACATCAT 19 141 1 TGAGATAAAA 0.853966 -50 AAATACCCAGTTAAGGAATAAAA 21 1 0 TTAAATAAAA 0.875238 -284 GCCTTTATTTTTAAGAGATAAAGCCTTTAGTCA 21 52 1 TTAGATAAAG 0.772149 -233 AGATAAAGCCTTTAGTCAGAAAAACATTATTTC 21 67 1 TTACAGAAAA 0.760925 -218 GCCCATATTTTACAAAAAGGAAATAATGTTTTT 21 86 0 TAAAAGGAAA 0.337155 -199 AACGAGCGAAATTAGGCAAAAAATGCGTGGCGA 21 154 0 ATACAAAAAA 0.452834 -131 GTGACCACTGTATAAGGAAAAAACA 21 270 1 TAAGAAAAAA 0.799493 -15 ** * ******* Masking position 8 Map Score: 22.5488 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 707 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 5 CAATTACAGATTTAAAAAAATTGTCTAACC 1 146 1 TTTAAAAAAA 0.923023 -155 TGTCTAACCGTTTAAAAAAAGTTCATTTTG 1 167 1 TTTAAAAAAA 0.923023 -134 GTTCATTTTGTTCAAATAAATCACAGAAAA 1 187 1 TTCAAATAAA 0.853222 -114 ATTTCATCTATTTAAATTAAC 2 2 0 TTTAAATTAA 0.646727 -41 TGTTTTTAAATTTATAAAAAAACCCGCTAT 3 260 0 TTTATAAAAA 0.780766 -41 GCGTGCTTTCTTCAAATAAACCAGTTTAAA 4 101 0 TTCAAATAAA 0.853222 -66 TTAAAATTTTTTTATAAAAAGTGCGGTAAT 7 71 0 TTTATAAAAA 0.780766 -152 TTCATAATAAAAATCATAAG 10 1 1 TTCATAATAA 0.762619 -29 TAAATTTTCTTTTAAATTAACCACACTTTT 11 28 1 TTTAAATTAA 0.646727 -131 AACAGGAATATTCAAAATAAGCCAATTTTC 12 122 1 TTCAAAATAA 0.908481 -126 ATTATCTGCTTTCAAAAAACGTTAAAGTAG 16 152 1 TTCAAAAAAC 0.684764 -149 TATTAAATTAATCAAAAAAAACTATACTAA 17 98 1 ATCAAAAAAA 0.732825 -168 AACAACTCCCTTTAAAATAAATAAAATGAC 19 11 1 TTTAAAATAA 0.860516 -180 TGACGATTGATTAAAAAAAAGCTAAATTAC 19 47 0 TTAAAAAAAA 0.769869 -144 TTTTACTGAAATCAAAAAAATTCTTTCTAT 19 102 0 ATCAAAAAAA 0.732825 -89 CATCATTATTTTCATAAAAAGCAAGGAAAT 19 168 1 TTCATAAAAA 0.862038 -23 GCTTTATCTCTTAAAAATAAAGGCTAGAAT 21 46 0 TTAAAAATAA 0.631792 -239 ATGCCCATATTTTACAAAAAGGAAATAATG 21 91 0 TTTACAAAAA 0.637052 -194 ********** Masking position 2 Map Score: 14.2367 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 219 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 TTTTAAACGGTTAGACAATTTTTTTAAATCTG 1 152 0 TTAACATTTT 0.422152 -149 ATTTCTACTTTTATCACTTTTTCCTTTGTGCC 1 250 1 TTACATTTTT 0.708291 -51 GCCAAAATGCTAAACGTTTTTTAACACGTAAA 1 279 1 TAACGTTTTT 0.925541 -22 ATTTAATCCGTTTTTAATCTGATTT 2 28 0 TAACCTTTTT 0.785899 -15 CAATGAAAAATAACCGCACTTTATCCGTAATC 3 130 1 TAACGACTTT 0.882012 -171 CCTTTAATTTTTAACGAATTTTGAGAAATTT 6 14 1 TTACGATTTT 0.956866 -21 TCGCTGAAAATTACCGCACTTTTTATAAAAAA 7 62 1 TTACGACTTT 0.936036 -161 CTCACAAATTTTAGCATTTTTTGGCTAAAAAA 8 37 0 TTACATTTTT 0.708291 -110 TAGTGAATTTTTACCGCTCTTTTGGCTTATTT 12 74 0 TTACGTCTTT 0.94136 -174 ATATTCAAAATAAGCCAATTTTCACCGCACTT 12 129 1 TAACCATTTT 0.769911 -119 ACCGCACTTTTTTTCGTTTTTTTCTCTCCAAG 12 152 1 TTTCGTTTTT 0.610841 -96 AAGGAAAAACTAACCGCACTTTATCATCAAAA 14 50 1 TAACGACTTT 0.882012 -30 ATGTTCTACTTTAACGTTTTTTGAAAGCAGAT 16 155 0 TTACGTTTTT 0.96053 -146 TTTTTCGCCTTTATCCCTTTTACGGATTCAAG 17 205 1 TTACCTTTTA 0.462252 -61 TTTTAGCAACTTACAGGATTTTT 18 137 1 TTAAGATTTT 0.712158 -13 GTGCCGTAATTTAGCTTTTTTTTAATCAATCG 19 42 1 TTACTTTTTT 0.579294 -149 AAAGCATTGATTATCGATTTTTGTAGTGATAA 19 130 1 TTACGTTTTT 0.96053 -61 GTCAATATTTTTAACGTTTTTACGAGGTAAAA 20 92 1 TTACGTTTTA 0.744318 -22 AAGGCTAGAATAACCGCACTTTTAAATACCCA 21 25 0 TAACGACTTT 0.882012 -260 CTATAAAAATTAACCGCACTTTTGCCCTACTT 21 206 0 TAACGACTTT 0.882012 -79 CGGTTAATTTTTATAGAATTTTAAATGAACAC 21 222 1 TTAAGATTTT 0.712158 -63 *** ** ***** Masking position 10 Map Score: 23.5872 Number of sites scoring better than the average of aligned sites = 786 Number in coding regions = 521 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 7 ATAAATCACAGAAAATGATGGAAAAATGAAA 1 202 1 GAAAATATGG 0.881325 -99 TTTTATCTTGAAAAATGAATGCGTAAAGAAA 3 97 0 AAAAATAATG 0.768682 -204 GCCAACGTATAAAAATAAAGAAAAATTGACC 4 69 0 AAAAATAAGA 0.768682 -98 ATTTCAACGAAAAAAGTAAGGAAATTCT 4 149 1 AAAAAGAAGG 0.942528 -18 TCCGCTAACTAAAAAGGTTGGAACTATAACA 5 93 1 AAAAAGTTGG 0.857768 -64 AAATTCGTTAAAAATTAAAGGCGA 6 4 0 AAAATTAAGG 0.646381 -31 GATTGCGTATAAAAATAAATGAAA 7 4 0 AAAAATAATG 0.768682 -219 AAATTAAATAAAAAAGTGTGGTTAATTTAAA 11 38 0 AAAAAGGTGG 0.730948 -121 TTTAAGTGATGAAAATTTAGGAATGAAATTT 15 39 1 GAAAATTAGG 0.779212 -85 TAATGTGATTAAAAATGTTGGTATTATACTT 17 234 0 AAAAATTTGG 0.880135 -32 TGATTTCAGTAAAAAGCATTGATTATCGATT 19 118 1 AAAAAGATTG 0.705958 -73 TGCTTTTTATGAAAATAATGATGTCTTTTTT 19 160 0 GAAAATATGA 0.552759 -31 TTATTTTCATAAAAAGCAAGGAAATACA 19 173 1 AAAAAGAAGG 0.942528 -18 TAAAAACGTTAAAAATATTGACCGCACTTTT 20 83 0 AAAAATTTGA 0.549955 -31 TTTATCTCTTAAAAATAAAGGCTAGAATAAC 21 43 0 AAAAATAAGG 0.952307 -242 ****** **** Masking position 4 Map Score: 8.3435 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 330 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 AATGATGGAAAAATGAAATTTTATGTAATTT 1 215 1 AAATAAATTT 0.738683 -86 ATTTATTGACTAAGAAAATTTCTGAAAAATT 3 28 1 TAAGAAATTT 0.73745 -273 CGTAAAGAAATACCGAAATTTCCCGAGCTTG 3 76 0 TACCAAATTT 0.732519 -225 GTTGGAACTATAACAAAAATTGCTATAATCA 5 109 1 TAACAAAATT 0.53185 -48 GCACTTTTTATAAAAAAATTTTAACTTGATC 7 77 1 TAAAAAATTT 0.654592 -146 CATAACATAATACTCAAATTTAGTTGGAGCG 7 149 1 TACTAAATTT 0.866258 -74 AAGCATAAATTACTTAAATTTGTCAATTTGT 7 191 0 TACTAAATTT 0.866182 -32 AAGAGTGATTAAATTAAATTTTCTTTTAAAT 11 14 1 AAATAAATTT 0.626233 -145 CAAGTATTTTTAATGAAAATTGATCTTTCGC 11 74 0 TAATAAAATT 0.728773 -85 AGTTTCAATATAATGAAATCTAATCATCAGT 12 39 1 TAATAAATCT 0.901446 -209 GAAAATTTAGGAATGAAATTTTAATTAAATT 15 49 1 GAATAAATTT 0.707225 -75 AATGAAATTTTAATTAAATTTTTATCCATAA 15 60 1 TAATAAATTT 0.942699 -64 TGAAAGCAGATAATTTAATCTCTATTGAAAT 16 135 0 TAATTAATCT 0.438633 -166 CATTTCAACCTAACTAAATTTATTAACTTTA 17 24 0 TAACAAATTT 0.88269 -242 TAATCATACATAATAAAATCTTCTTAATTAT 18 77 1 TAATAAATCT 0.901446 -73 TTAGTTAGAGTAATTCAATTTTTTAGCAACT 18 117 1 TAATCAATTT 0.692383 -33 GCCCACCGATTAATGAAATCTTTGGTGGGCA 20 29 1 TAATAAATCT 0.901446 -85 **** ****** Masking position 7 Map Score: 12.2168 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 100 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 TTAAATTTATAAAAAAACCCGCTATTCAGT 3 255 0 AAAAAAACCC 0.732217 -46 TGCTTTCTTCAAATAAACCAGTTTAAAAGC 4 98 0 AAATAAACCA 0.908725 -69 CGTTGAAATGAAAACAACCTTATTCTAGCG 4 128 0 AAAACAACCT 0.772383 -39 TTTTGGCTAAAAAACAGCCATTTTTACTCA 8 21 0 AAAACAGCCA 0.921649 -126 ATTATAACGAAAAAAAGCCTTTTTTCTATT 8 70 1 AAAAAAGCCT 0.906898 -77 ATTTTCTTTTAAATTAACCACACTTTTTTA 11 31 1 AAATTAACCA 0.583486 -128 ATCAGTCAATAAATAAGCCAAAAGAGCGGT 12 64 1 AAATAAGCCA 0.941097 -184 GGAATATTCAAAATAAGCCAATTTTCACCG 12 126 1 AAATAAGCCA 0.941097 -122 CTTTATCATCAAAACAAACACT 14 68 1 AAAACAAACA 0.655194 -12 ATTAAAATGTAAATGAGCCAGTTACTATCA 16 107 0 AAATGAGCCA 0.769159 -194 TAAATTAATCAAAAAAAACTATACTAAAAT 17 101 1 AAAAAAAACT 0.611428 -165 AACTATACTAAAATAAAACTTAAAATCTAC 17 117 1 AAATAAAACT 0.544381 -149 GATTGATTAAAAAAAAGCTAAATTACGGCA 19 43 0 AAAAAAGCTA 0.561561 -148 TTGTAGTGATAAAAAAGACATCATTATTTT 19 150 1 AAAAAAGACA 0.845072 -41 ********** Masking position 6 Map Score: 6.79591 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 351 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 10 TTTCCGTAAAATGCGCACCAATAACAGCGAA 1 102 0 ATGCCACCAA 0.898211 -199 ACGGCATCAGCATCACCACTAACTAAATGGG 4 15 1 CATCCCACTA 0.73139 -152 CTTTGACTATCTTCGCAACAACAGGTAATAT 5 20 0 CTTCCAACAA 0.603686 -137 TCGGTGTCGTCATCGCACCGATTTTTTTGTC 7 33 1 CATCCACCGA 0.949093 -190 AATGCTATTCAAGCACAACAAACTAAGGAAA 11 133 1 AAGCCAACAA 0.845861 -26 AAATAATCTCTCCGAGTAAAATTTA 13 57 0 AATCCTCCGA 0.781304 -15 GAAGCGAGTAAATCTCCCCTACCCCTCTTTG 16 50 1 AATCCCCCTA 0.921593 -251 ATTTCTGCCAAATCGCCCCTACCCCTCTTTG 16 225 0 AATCCCCCTA 0.921593 -76 GGTGGGCTTAAAGCCCACCTACAGA 20 5 0 AAGCCACCTA 0.956811 -109 GGTGGGCTTTAAGCCCACCGATTAATGAAAT 20 17 1 AAGCCACCGA 0.963968 -97 GGATGGGTTTCTGCCCACCAAAGATTTCATT 20 40 0 CTGCCACCAA 0.89192 -74 **** ****** Masking position 11 Map Score: 4.60334 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 112 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 GTTAGTTTACACGAAATTTATTGACTAAGAA 3 13 1 ACGAAATTAT 0.896867 -288 TGACAAATTTAAGTAATTTATGCTTTGGAGC 7 197 1 AAGTAATTAT 0.839017 -26 TCTTTCGCGAAAGAAATTAAATAAAAAAGTG 11 51 0 AAGAAATTAA 0.636714 -108 TCAATTAACGAAGAAATTAATCATACAAACG 13 21 1 AAGAAATTAT 0.945793 -51 CATCACTTAAATGAAATTAATTCATCATAAT 15 19 0 ATGAAATTAT 0.885586 -105 TTCTCCTGTTATGTAATTTATGGCAGATAGT 15 99 0 ATGTAATTAT 0.790973 -25 GGAATTCTTGAATAAATTGATAGTAACTGGC 16 90 1 AATAAATTAT 0.763439 -211 TTTCAACCTAACTAAATTTATTAACTTTACA 17 22 0 ACTAAATTAT 0.612066 -244 TATGATACGCAAGAAATTCATTTCAACCTAA 17 42 0 AAGAAATTAT 0.941156 -224 ATCGAAATCTATTAAATTAATCAAAAAAAAC 17 89 1 ATTAAATTAT 0.669363 -177 AAGATATATCAAGTAAGTAATTTTGAATATT 17 150 0 AAGTAAGTAT 0.622155 -116 CTGTTATTATATGATATTTATG 18 2 0 ATGATATTAT 0.559786 -148 CTTGCTTTTTATGAAAATAATGATGTCTTTT 19 162 0 ATGAAAATAT 0.596778 -29 ACAATACTTCAAGAAAGTGATAGAATTCGCC 21 128 1 AAGAAAGTAT 0.849084 -157 ******** ** Masking position 6 Map Score: 9.2435 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 149 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 ATGGCGGTAATCGTGCTAATGATTACGGATA 3 151 0 TCGTCTAATG 0.824807 -150 ATAATAATGGTCATCATAATGGCGGTAATCG 3 169 0 TCATATAATG 0.96475 -132 GCACCATTAATCATAATAATGGTCATCATAA 3 181 0 TCATATAATG 0.96475 -120 AGGCTTTTTTTCGTTATAATGCTCACAAATT 8 59 0 TCGTATAATG 0.957582 -88 TTAAATACTCTCGTAATAAAGTAACACAATC 9 85 1 TCGTATAAAG 0.939098 -48 TTCATAATAAAAATCATAAGGA 10 2 1 TCATATAAAA 0.620242 -28 TGATTAGATTTCATTATATTGAAACTCTTTT 12 34 0 TCATATATTG 0.793861 -214 GTGTTTGTTTTGATGATAAAGTGCGGTTAGT 14 58 0 TGATATAAAG 0.707662 -22 TGAAATTAATTCATCATAATGATATGGA 15 8 0 TCATATAATG 0.96475 -116 ACTTGATATATCTTTATAAAGCCTGATTTTC 17 167 1 TCTTATAAAG 0.795127 -99 **** ****** Masking position 7 Map Score: 7.1905 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 54 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 TTGTATTAGAATCCACGCCCCATTTAGTTA 4 34 0 ATCCACGCCC 0.98408 -133 AACAGGTAATATTCACGCCCT 5 2 0 ATTCACGCCC 0.975193 -155 TAATAATGCTATTCAAGCACAACAAACTAA 11 129 1 ATTCAAGCAC 0.880034 -30 GTTTTTTTCTCTCCAAGCCCTACCAATGAC 12 167 1 CTCCAAGCCC 0.98408 -81 CTCTCCAAAGATCCAATCCCCTCTTTAGCA 16 197 1 ATCCAATCCC 0.920223 -104 AATCGGTGGGCTTAAAGCCCACCTACAGA 20 10 0 CTTAAAGCCC 0.858789 -104 ********** Masking position 5 Map Score: 1.61554 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 58 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 AAATTTTCTTAGTCAATAAATTTCGTGTAA 3 19 0 AGTCAATAAA 0.949527 -282 TTATTGAGTTATCCAATAAAAAATGTGATT 5 54 0 ATCCAATAAA 0.920208 -103 TTATTGGATAACTCAATAAAGGAAATTATC 5 65 1 ACTCAATAAA 0.8118 -92 TATTATGTTATGCCAATAAATAGAGAATCT 7 131 0 TGCCAATAAA 0.641909 -92 GCTGTTTTTTAGCCAAAAAATGCTAAAATT 8 33 1 AGCCAAAAAA 0.641909 -114 TTACGAGAGTATTTAATAAACAAGTGTAAT 9 71 0 ATTTAATAAA 0.683512 -62 CGCGAAAGAAATTAAATAAAAAAGTGTGGT 11 47 0 ATTAAATAAA 0.550502 -112 TCTAATCATCAGTCAATAAATAAGCCAAAA 12 57 1 AGTCAATAAA 0.949527 -191 AGCGGTAAAAATTCACTAAATTTTTTAGGG 12 88 1 ATTCACTAAA 0.706449 -160 CTCCTTGTAAAGTTAATAAATTTAGTTAGG 17 17 1 AGTTAATAAA 0.743476 -249 GCAGAAACCCATCCTATAAAGACCGTAAAA 20 57 1 ATCCTATAAA 0.720975 -57 TTCATTTAAAATTCTATAAAAATTAACCGC 21 221 0 ATTCTATAAA 0.758491 -64 ********** Masking position 8 Map Score: 3.56079 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 177 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 15 GTTTCCCGCTCCAATTCGTGGCGTGTT 1 8 0 CCAATTCGTG 0.901031 -293 ACGACCTTGCCAAGGTCGGGGTCGCGAGTT 1 46 0 CAAGGTCGGG 0.956043 -255 CCGACCTTGGCAAGGTCGTGCTCTACCAAC 1 57 1 CAAGGTCGTG 0.957141 -244 TTCTGTTTGACAAGCTCGGGAAATTTCGGT 3 66 1 CAAGCTCGGG 0.919507 -235 AATCCATCTCGTGATTAAAGACT 8 134 0 CCATCTCGTG 0.882998 -13 CCTAATCGTGAAATAACCTA 9 1 1 CCTAATCGTG 0.76912 -132 CGTGAAATAACCTAGTCGTGAAATAACATT 9 17 1 CCTAGTCGTG 0.94563 -116 AGGAATGAAGCCAAGTAGGGCAAAAGTGCG 21 194 1 CCAAGTAGGG 0.838723 -91 ********** Masking position 6 Map Score: 0.855678 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 53 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701