AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ifruR_bsub_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #2 mtlD 52 mannitol-1-phosphate dehydrogenase #3 yjdD 147 similar to fructose phosphotransferase system enzyme II #4 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #5 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #6 fruR 279 transcriptional regulator (DeoR family) #7 pps 300 phosphoenolpyruvate synthase #8 kdgK 37 2-keto-3-deoxygluconate kinase #9 kdgR 221 transcriptional regulator (LacI family) #10 ypqE 137 similar to phosphotransferase system enzyme II #11 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #12 citC 163 isocitrate dehydrogenase #13 pykA 42 pyruvate kinase #14 pfk 183 6-phosphofructokinase #15 pckA 300 phosphoenolpyruvate carboxykinase #16 pgk 300 phosphoglycerate kinase #17 gap 46 glyceraldehyde-3-phosphate dehydrogenase #18 yvbQ 297 yvbQ #19 crh 23 catabolite repression HPr-like protein #20 yvcL 22 similar to hypothetical proteins #21 yvcJ 24 similar to hypothetical proteins #22 yvcI 300 similar to mutator MutT protein #23 yvkC 300 similar to pyruvate,water dikinase Motif number 1 TCCCTTTGACTCTATGTTAAAACGCTTACAGTCC 1 85 0 TTATAAAACG 0.710418 -88 CATTTTTCCCTATAACAAAAAAAGCAAGGAATAA 3 20 0 TTAAAAAAAG 0.951441 -128 TACCATAGGTTCCGGTAATAAAGGCATTTTTCCC 3 44 0 TCGATAAAGG 0.845553 -104 TACCGGAACCTATGGTAAAAAAAGCGATTTTAAT 3 61 1 TTGAAAAAAG 0.953102 -87 TTTGCCCTTTTACACAACAAAAAGGCATGAGCAA 4 120 0 TCACAAAAAG 0.832697 -119 GTAATAAAGCTTTAAGTTAAAAGGAGAATGATAA 5 72 1 TTATAAAAGG 0.824366 -26 TGATTTCTACTATGAATATAAAAGACTTTTTTCA 6 47 1 TTGATAAAAG 0.859571 -233 TTCTTCTTATTTTAATGAAAAAAGTCTTTTATAT 6 62 0 TTAAAAAAAG 0.951441 -218 TCTGTTTTTGTGCAATATAAAAAGAACCTGGGAA 7 153 0 TCATAAAAAG 0.931563 -148 AGACGCATAATCTGGTTAAAAAAGGCGGTGGCGA 10 13 0 TTGAAAAAAG 0.953102 -125 AAAGCCGGTCTTCATGGAAAAAGGGAAAGGGAGT 16 73 0 TCAAAAAAGG 0.946018 -228 TATGTCCCGCTATGACAAAAAACGTCCCGTCATA 18 239 0 TTGAAAAACG 0.855052 -59 ACATATAATGTCCAGCAAAAAAGGAAGGAACGTT 18 268 1 TCAAAAAAGG 0.946018 -30 AAAAAGTGTATTCATTATAAAAAGGGGGTCAATT 22 86 0 TCATAAAAAG 0.931563 -215 CCTTTTTTTGTCCATAAATAAAAGAGAATTCCAG 22 147 1 TCAATAAAAG 0.904802 -154 GACTTGATGATGTAATAAAAAAAGTGCCGCTGAT 23 38 0 TTAAAAAAAG 0.951441 -263 GCCGCCAGATTCCGAGAATAAAAGAAAATAGGCA 23 73 1 TCGATAAAAG 0.907904 -228 AAACACAGGCTCCGCAATAAAAAGACTAGAGAGA 23 241 1 TCGTAAAAAG 0.933857 -60 * ** ******* Masking position 1 Map Score: 17.5759 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 399 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 AGCAGGGATTATTCCTTGCTTTTTTTGTTATAGGGA 3 12 1 ATCTTTTTTT 0.706721 -136 CGCACCCAATTTTGCTCATGCCTTTTTGTTGTGTAA 4 109 1 TTCGCCTTTT 0.907321 -130 AAGAATTGACCTCCTCTTTTTACTAGTCTGA 4 218 0 TTCTCTTTTT 0.902939 -21 TTTTATCATTCTCCTTTTAACTTAAAGC 5 80 0 TTCTCCTTTT 0.964179 -18 CCTGGGAAATTTCACCAGGTTCTTTTCTTAATTTCC 7 125 0 TTCTTCTTTT 0.96789 -176 CCTGGTGAAATTTCCCAGGTTCTTTTTATATTGCAC 7 142 1 TTCTTCTTTT 0.96789 -159 TAGGAAGCTCTTGTCAATATTTTTTTTTGAAGGGGA 7 267 1 TTCTTTTTTT 0.912418 -34 CTCTTCCCAACCTCCTCTTAGTTGAGGGC 8 19 0 TTCTCCTCTT 0.932547 -19 TATCGCCACCGCCTTTTTTAACCAGAT 10 2 1 ATCGCCTTTT 0.693673 -136 TGTATTTTCTCCCTTCTCATTCACTTCAAC 10 118 0 TTCTTCTCAT 0.781713 -20 ATCGACAATATTCGCAGAGTTTTCATGCCGCGTCGT 18 125 0 TTCTTTTCAT 0.55311 -173 AATAAAGTAATTGACCCCCTTTTTATAATGAATACA 22 78 1 TTCTTTTTAT 0.706721 -223 GATTCTCCAGTTATCCGTGTCCTTTTTTTGTCCATA 22 127 1 TTCTCCTTTT 0.964179 -174 TGAAGAGACATTGACAATCTTTTCTTCTATTTTACA 22 218 0 TTCTTTTCTT 0.842541 -83 CTGGTACTGTATGCCTATTTTCTTTTATTCTCGGAA 23 82 0 ATCTTCTTTT 0.874565 -219 CATTTTGTTTTTCTCTCTAGTCTTTTTATTGCGGAG 23 250 0 TTCGTCTTTT 0.916412 -51 GAAACCCCTCTTTTCTTCATTCATTTTGTTTTTCTC 23 271 0 TTCTTCATTT 0.707692 -30 ** * ******* Masking position 2 Map Score: 15.5062 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 581 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 3 CAATTTTTTAAAAATAAAAAGGCTCCTGGTT 1 10 0 AAAAAAAAGG 0.909743 -163 TATACAATTGAAAGTAAAGAGGACTTTGGCAC 1 52 0 AAAGAAGAGG 0.840097 -121 AGCGACAAACAAAACAGGGAGGGTTTATAT 1 153 1 AAAAAGGAGG 0.910389 -20 TCTCCGCTAAAGCGAAGAAGATTTGATCGC 2 9 1 AAAGGAGAAG 0.528266 -44 CCCTATAACAAAAAAAGCAAGGAATAATCCCT 3 15 0 AAAAAGAAGG 0.910066 -133 GCCCTTTTACACAACAAAAAGGCATGAGCAAA 4 119 0 ACAAAAAAGG 0.839566 -120 TCAGACTAGTAAAAAGAGGAGGTCAATTCTT 4 218 1 AAAAGAGAGG 0.955787 -21 GCTTTAAGTTAAAAGGAGAATGATAAAA 5 80 1 AAAAGAAATG 0.83161 -18 TGTAAATTCGACAAAAATAAGGACAATTGTAC 6 102 0 ACAAAAAAGG 0.839566 -178 AATCTGGTTAAAAAAGGCGGTGGCGATA 10 7 0 AAAAGGGGTG 0.613669 -131 TGCCCTAAAAACAATGAAAAGGGATCTCCATC 14 115 0 ACAAGAAAGG 0.917894 -69 TTGAGGGAAAACAATGGAAATGCACACACAAA 15 190 1 ACAAGGAATG 0.720215 -111 CAAAACACAAAAAACGATAAAGGAAGGTTTCA 15 278 1 AAAAGAAAAG 0.682381 -23 ATGAAAGCGGACAAGGGAAGGGGACGGACTCC 16 46 1 ACAAGGAGGG 0.781736 -255 TCTTCATGGAAAAAGGGAAAGGGAGTCCGTCC 16 67 0 AAAAGGAAGG 0.955787 -234 ATTGCTGGATAAAACGACGCGGCATGAAAACT 18 112 1 AAAAGAGCGG 0.825662 -186 ATAATTAAAGAAAGCAGAAATGATTTTTTTTG 18 205 1 AAAGAGAATG 0.546479 -93 AATGTCCAGCAAAAAAGGAAGGAACGTTTGAG 18 274 1 AAAAAGAAGG 0.910066 -24 CCGTAAAGAAAAGGGGAGATCTT 19 5 1 AAAGAAGGGG 0.626385 -19 TATGGACAAAAAAAGGACACGGATAACTGGAG 22 131 0 AAAAGAACGG 0.825093 -170 GCGGTATAATAAAGAGACGATGACAGGACGAA 22 273 1 AAAGGAGATG 0.720215 -28 **** ** **** Masking position 3 Map Score: 16.9086 Number of sites scoring better than the average of aligned sites = 1518 Number in coding regions = 1141 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 371 Fraction of orfs with sites within 600 bp upstream = 0.0595888 Motif number 4 TTCACCTCGTTGAAATGGCGATCAAATCTTCTTCG 2 23 0 TGAAAGTCAA 0.980928 -30 CTTACGCCTGTGAATTCGTTGTCATGATTTTTAGC 4 176 1 TGAATGTCAT 0.801399 -63 GCGTTTACAATGAAATTGTATTCAAAATGAATACG 6 235 1 TGAAAGTCAA 0.980926 -45 CACCTCCTAATGAAAACGTATTCATTTTGAATACA 6 251 0 TGAAAGTCAT 0.906127 -29 TTTATGAATGGGGACTCTACGAACAAAGC 7 5 1 TGAATGTCTA 0.679121 -296 GCAAGTAAGTTCAAAAAGAACCCAACTTTAGGATT 7 38 1 TCAAAGCCAA 0.697964 -263 CAAGTGATGCTGAAATCCTAACCAAGGGGGAAATA 9 13 0 TGAAACCCAA 0.681088 -209 AAATTTTCTTTGAAACCGTTACCAAAATATTTTCA 9 50 0 TGAAAGCCAA 0.959468 -172 CTCATATATTTGAAACCGATTTCAAAACCGTTACA 9 181 0 TGAAAGTCAA 0.980926 -41 GAAGCAAAATTGAAAGTGTGGTTAAATAGTGGTGA 10 69 1 TGAAAGTTAA 0.866809 -69 ATATTGTCGATGAATTGGCTCTTAACAGTTGAATA 18 150 1 TGAATGTTAA 0.731231 -148 GTATTCATTATAAAAAGGGGGTCAATTACTTTATT 22 78 0 TAAAAGTCAA 0.77211 -223 AATTAAGGAATGAATATGCTGTAAAATAGAAGAAA 22 199 1 TGAATGTAAA 0.606753 -102 TAGGTTTTCAGGAAAATGCTGTCAAACGCAGAAAG 23 174 0 GGAAAGTCAA 0.882403 -127 ***** * **** Masking position 4 Map Score: 9.99894 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 379 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 GTCGCTGTAAGATACAAAAATATGTTCAGAGAATGA 1 123 0 GAAAAAAATT 0.657131 -50 CTTTAAAGTGTGAATAATAAGATCTTGTCTCAACTG 3 112 0 TAAATAAATT 0.884731 -36 CAAGTACGGTTGTATGATATAATATTGTGAAGTAAT 5 41 1 TAGATATATT 0.746446 -57 TCTTCTTATTTTAATGAAAAAAGTCTTTTATATTCA 6 59 0 TAGAAAAAGT 0.698163 -221 TTCCTAGCAGGATATAATAAAATTATAAGATGGATA 7 237 0 GAAATAAATT 0.657129 -64 ACATCTCCCCTTCAAAAAAAAATATTGACAAGAGCT 7 272 0 TAAAAAAATT 0.884734 -29 CAGCATCACTTGAATGAAAATATTTTGGTAACGGTT 9 36 1 TAGAAAAATT 0.948023 -186 GTGAAAAGAGTCAACGAAAAAATAATGAATTGACAT 9 96 1 TAGAAAAATT 0.948023 -126 TGATATTCTGTGCAAGAAAACATAAGATGCATCATA 11 62 1 TAGAAAAATG 0.712205 -144 TTTTCTTATATAGAAAATAAAATGATTTTTCCTAAC 12 92 0 TAAATAAATT 0.884734 -72 ACATATATGATTAAACATAACATGATCATTGCCCTA 14 140 0 TACATAAATT 0.702537 -44 TGCAAACCCTTTTACGATAAGATATTTCATTGAGCG 15 119 0 TAGATAAATT 0.948023 -182 GATAAAGATATATAGGATAAAATATTGCTGGATAAA 18 89 1 TAGATAAATT 0.948023 -209 TGCTGTAAAATAGAAGAAAAGATTGTCAATGTCTCT 22 215 1 TAGAAAAATT 0.948023 -86 GGCCGCATTTTTCAGGATAATATAACCAACTTAACT 23 121 1 TAGATAAATC 0.712203 -180 GGAGCCTGTGTTTAAAAAATGATAGTAAACACTATC 23 218 0 TAAAAATATT 0.553379 -83 * * ***** ** * Masking position 9 Map Score: 8.73136 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 214 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 ATATAAACCCTCCCTGTTTTGTTTGT 1 157 0 AACCTCCCTG 0.840972 -16 AGGAAACCTCCTTTAAAGTGTGAA 3 134 0 AAACTCCTTT 0.873531 -14 GAACGAGAATGAACTTCCCGTTTTTTTCCCT 4 73 0 GAACTCCCGT 0.924538 -166 AATAAAAACCTCCCAGTATGTAATTC 12 148 0 AAACTCCCAG 0.834225 -16 ATGAAACCTTCCTTTATCGTTTTT 15 287 0 AAACTTCCTT 0.917395 -14 GCTTTTAGACGAACTGCCCTGTGCCGAAAAA 16 185 1 GAACGCCCTG 0.909739 -116 GAAAAACGTGAAACCGTCTGTTCAAGCGATA 16 240 0 AAACGTCTGT 0.532549 -61 CGCTTTAATGAAACAGCCCTTTCTACGGGAA 18 14 1 AAACGCCCTT 0.976705 -284 ATCCCAATATAAACAGCCCTTCCCGTAGAAA 18 33 0 AAACGCCCTT 0.976705 -265 CTATGACAAAAAACGTCCCGTCATAGCCAAA 18 233 0 AAACTCCCGT 0.969625 -65 GACTCAAACGTTCCTTCCTTTTTTGC 18 282 0 AAACTTCCTT 0.917392 -16 **** ****** Masking position 2 Map Score: 7.217 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 172 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 ATATAAACCCTCCCTGTTTTGTTTGTC 1 156 0 CCCTCCCTGT 0.926586 -17 AACGAGAATGAACTTCCCGTTTTTTTCCCT 4 73 0 AACTTCCCGT 0.748365 -166 AAGAATTGACCTCCTCTTTTTACTAGTC 4 221 0 ACCTCCTCTT 0.901978 -18 TCTACATCTCCCCTTCAAAAAAAAA 7 286 0 ATCTCCCCTT 0.910739 -15 CTCTTCCCAACCTCCTCTTAGTTGAGGGC 8 19 0 ACCTCCTCTT 0.901978 -19 AATAAAAACCTCCCAGTATGTAATTCA 12 147 0 ACCTCCCAGT 0.842303 -17 ATGAAACCTTCCTTTATCGTTTTTT 15 286 0 ACCTTCCTTT 0.911109 -15 GGAGTCCGTCCCCTTCCCTTGTCCGCTTTC 16 48 0 CCCTTCCCTT 0.974809 -253 GGACGGACTCCCTTTCCCTTTTTCCATGAA 16 67 1 CCTTTCCCTT 0.735211 -234 ATATAAACAGCCCTTCCCGTAGAAAGGGCT 18 28 0 CCCTTCCCGT 0.969544 -270 ACTCAAACGTTCCTTCCTTTTTTGCTGGAC 18 277 0 TCCTTCCTTT 0.647491 -21 AAGATCTCCCCTTTTCTTTACGG 19 11 0 ATCTCCCCTT 0.910739 -13 ********** Masking position 4 Map Score: 9.52797 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 195 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 8 AGAATGAACTTCCCGTTTTTTTCCCTCAAT 4 69 0 TCCCGTTTTT 0.938796 -170 TCAAAATCTTTCACGTTTCTCCATATTAAC 6 157 0 TCACGTTTCT 0.966238 -123 GCCAAAGGCTTCACGTTTAT 14 1 0 TCACGTTTAT 0.971469 -183 AGCCTTTGGCTCACGTTTATTTTTTGTGAC 14 21 1 TCACGTTTAT 0.971469 -163 ACAGACGGTTTCACGTTTTTCGTGCTGTAT 16 250 1 TCACGTTTTT 0.971469 -51 ********** Masking position 6 Map Score: 3.25465 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 50 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 CTGTTTTGTTTGTCGCTGTAAGATACAAAAA 1 139 0 TGTGCTGTAA 0.951332 -34 TGTCATGATTTTTAGCTGTAAGGTCAGACTA 4 195 1 TTTGCTGTAA 0.959511 -44 TATGGTATTCTTTTGTTGTAACGGTTTTGAA 9 165 1 TTTGTTGTAA 0.69909 -57 ATCTTCAGCCTTCAGCTGTACA 13 2 0 TTCGCTGTAC 0.975174 -41 TTCCTTCCTTTTTTGCTGGACATTATATGTC 18 267 0 TTTGCTGGAC 0.876976 -31 TGGGTTTTAATTCCGCTGTAACACATGTGTA 22 28 1 TTCGCTGTAA 0.968229 -273 ATTCAGATGATTTTGCTGTAACTGGAATTCT 22 171 0 TTTGCTGTAA 0.959511 -130 TATTCCATGGTGCCGCTGTTCTAATCAGCGG 23 15 1 TGCGCTGTTC 0.836268 -286 TCCTGAAAAATGCGGCCGTACTGGTACTGTA 23 107 0 TGCGCCGTAC 0.883314 -194 *** ******* Masking position 1 Map Score: 4.72691 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 134 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GTCAGTTCACCTCGTTGAAATGGCGATCAA 2 33 0 CCTCGTTAAA 0.911151 -20 ACCGAAATCAGCTCATTAAAATCGCTTTTTT 3 78 0 GCTCATTAAA 0.899112 -70 AGGAAACCTCCTTTAAAGTGTGAATAA 3 131 0 CCTCCTTAAA 0.964901 -17 AAGAGTATCCGCTCAATGAAATATCTTATCG 15 110 1 GCTCAATAAA 0.85889 -191 CCTAGGAGATCCTCCTTCAAAATGGTTTGCA 16 279 0 CCTCCTTAAA 0.964901 -22 TCCCTCAATATAAATATCTCTCA 17 3 1 CCTCAATTAA 0.782071 -44 GATTGTTTCCTCCTTTAAATAAGTGAGAG 17 28 0 CCTCCTTAAA 0.964901 -19 ATAGCCACCTCATTTCAAGGCT 20 5 0 CCTCATTCAA 0.886195 -18 CGCAGAAAGTCCTAAATAAAATGAATAGTTA 23 152 0 CCTAAATAAA 0.665426 -149 AACACAGGCTCCGCAATAAAAAGACTAGAGA 23 242 1 CCGCAATAAA 0.826012 -59 ******* *** Masking position 7 Map Score: 5.04153 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 128 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 11 AGGGACTGTAAGCGTTTTAACATAGAGTCA 1 83 1 AGCGTTTTAA 0.949243 -90 GAATCAGTAACACGTTATAAGGATAAACTG 4 24 0 CACGTTATAA 0.817192 -215 ATCATAAATTAGCGTTATAATCGTTGATTT 11 92 1 AGCGTTATAA 0.960555 -114 TTCGAATAGAAGCGCTATAATGAAAGCGGA 16 27 1 AGCGCTATAA 0.952805 -274 GAGAAACGACCGCGTTTTAAGCAGCTTTGC 16 126 1 CGCGTTTTAA 0.926388 -175 AAACGCTTTAATGAAACAGCC 18 2 1 AACGCTTTAA 0.80878 -296 GGCATCTTGAAGCGGTATAATAAAGAGACG 22 262 1 AGCGGTATAA 0.916459 -39 ********** Masking position 9 Map Score: 2.3734 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 52 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 TGCTCCTGTATCTCATATATTTGAAACCGATT 9 195 0 TCTCAATATT 0.856464 -27 TTTTCTCCCTTCTCATTCACTTCAACCGTTAT 10 112 0 TCTCATCATT 0.950837 -26 ACCTTGGTTGTCTCACTCAGTTGAACATAATA 15 19 1 TCTCATCATT 0.950837 -282 GCAACCGGTTTCTCTGTTATTTATTATGTTCA 15 40 0 TCTCTTTATT 0.925944 -261 TATAAATATCTCTCACTTATTTAAAGGAGGAA 17 19 1 TCTCATTATT 0.966377 -28 TAACTGGAATTCTCTTTTATTTATGGACAAAA 22 152 0 TCTCTTTATT 0.925944 -149 TAGTAAACACTATCATTTAATTGTAGGTTTTC 23 200 0 TATCATTATT 0.788494 -101 ***** *** ** Masking position 9 Map Score: 2.10256 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 55 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 GGAAGTTCATTCTCGTTCTTTTGCGCACCCA 4 86 1 TCCGTTCTTT 0.901118 -153 AATCCTAAAGTTGGGTTCTTTTTGAACTTAC 7 42 0 TTGGTTCTTT 0.961943 -259 GGAAATTTCACCAGGTTCTTTTCTTAATTTC 7 126 0 CCGGTTCTTT 0.984251 -175 GTGAAATTTCCCAGGTTCTTTTTATATTGCA 7 146 1 CCGGTTCTTT 0.984251 -155 CTGGCTGCTTTTTGGTTCTTACGCCTGATAT 11 37 1 TTGGTTCTTA 0.861798 -169 GACCTGACTTGGTTCTTTCGAATAGAAG 16 8 1 CTGGTTCTTT 0.975457 -293 ** ******** Masking position 6 Map Score: 1.90291 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 36 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 GGCATCAGTGATTGAGGGAAAAAAACGGGA 4 59 1 ATTGAGGGAA 0.914471 -180 TTTGATAGTTATTGAATGAATTTGAATGAT 6 182 1 ATTGAATGAA 0.910994 -98 TTCAGCATCACTTGAATGAAAATATTTTGG 9 34 1 CTTGAATGAA 0.797088 -188 GTTGTTATAAATTGAAGCAAAATTGAAAGT 10 56 1 ATTGAAGCAA 0.76489 -82 AATAGTGGTGAATGAAGGGATAACGGTTGA 10 93 1 AATGAAGGGA 0.755694 -45 TTTAAATAAAATTTAAGGAATGTCACAAAA 14 42 0 ATTTAAGGAA 0.873428 -142 AGGCACCTATATTGAGGGAAAACAATGGAA 15 179 1 ATTGAGGGAA 0.914471 -122 AAACGCTTTAATGAAACAGCCCTTT 18 6 1 CTTTAATGAA 0.49317 -292 TCCAGCAAAAAAGGAAGGAACGTTTGAGTC 18 278 1 AAGGAAGGAA 0.755694 -20 AAATCATCTGAATTAAGGAATGAATATGCT 22 189 1 AATTAAGGAA 0.802709 -112 AGAAAAACAAAATGAATGAAGAAAAGAGGG 23 272 1 AATGAATGAA 0.857847 -29 ********** Masking position 5 Map Score: 2.89308 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 739 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 15 ATCACACTACGTGCGCTTTCTAGTTAAAAAG 7 199 1 GGCGCTTTCT 0.964097 -102 AGTCAGTGCGGAGCGCTGGCTGCTTTTTGGT 11 22 1 GGCGCTGGCT 0.971336 -184 TACTCTTATCCCGAGCTGGCGGAGGGACAGG 15 86 0 CGAGCTGGCG 0.816786 -215 CTCTATCACAGAGCGTTTTCTGAAAGCCGGT 16 98 0 GGCGTTTTCT 0.72471 -203 GCAGCTTTGCCGGCGCTTTCGCCTAAGGCCG 16 146 1 CGCGCTTTCG 0.972999 -155 CCTAAGGCCGCTGCCCTGGCTTTTAGACGAA 16 167 1 CGCCCTGGCT 0.966 -134 AGACTGCGATCTGCCCTAGCGGAGTTATCGC 16 215 1 CGCCCTAGCG 0.855042 -86 TTTAATGAAACAGCCCTTTCTACGGGAAGGG 18 17 1 CGCCCTTTCT 0.957474 -281 ATGCACCATTTGGCGCTTTCTGTATAAGATA 18 62 1 TGCGCTTTCT 0.871113 -236 * ********* Masking position 7 Map Score: 2.38407 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 460 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344