AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_bsub_reg_100.orf -o00620_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pabB 166 para-aminobenzoate synthase (subunit A) #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 lctE 176 L-lactate dehydrogenase #5 yclB 89 similar to phenylacrylic acid decarboxylase #6 ydaO 300 similar to hypothetical proteins #7 mutT 58 mutator protein #8 ydaP 66 similar to pyruvate oxidase #9 yflL 66 similar to hypothetical proteins #10 yjmC 104 similar to malate dehydrogenase #11 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #12 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #13 ylaO 205 similar to cell-division protein #14 pycA 74 pyruvate carboxylase #15 pps 300 phosphoenolpyruvate synthase #16 ypjD 300 alternate gene name: jojD #17 yqkI 140 similar to Na+/H+ antiporter #18 yqiS 124 similar to phosphate butyryltransferase #19 mmgA 137 acetyl-CoA acetyltransferase #20 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #21 yraG 248 similar to spore coat protein #22 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #23 citH 43 malate dehydrogenase #24 citC 163 isocitrate dehydrogenase #25 pykA 42 pyruvate kinase #26 pfk 183 6-phosphofructokinase #27 yttI 300 similar to acetyl-CoA carboxylase #28 ackA 300 acetate kinase #29 ytcI 172 similar to acetate-CoA ligase #30 acsA 160 acetyl-CoA synthetase #31 malS 81 malate dehydrogenase (decarboxylating) #32 ytnP 145 ytnP #33 pckA 300 phosphoenolpyruvate carboxykinase #34 ywkA 238 similar to malate dehydrogenase #35 pta 269 phosphotransacetylase #36 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #37 aldX 142 aldehyde dehydrogenase Motif number 1 TATCATTCCTCTATTTTCTTTTTTACTTGTTT 1 142 0 CTATTTTTTT 0.826853 -25 GCTCCTTCCCATATATCCTTTTGTTTAATTGT 2 132 0 ATATTCTTTT 0.73891 -95 CTGATGGATGTTTTATTGTTTTAATTGAAAAA 6 253 1 TTTTTTTTTT 0.684085 -48 TCCCCTTTTAATTTCTCATTTTTCAATTAAAA 6 271 0 ATTTTCTTTT 0.929029 -30 ACGTATCCTCCTTTTTCCTTTTTTCAATACCA 8 44 0 CTTTTCTTTT 0.954647 -23 ATGTATTTATCTTTTTTATTTTACTACAATTT 13 140 0 CTTTTTTTTT 0.956688 -66 GCTCTTGTCAATATTTTTTTTTGAAGGGGAGA 15 273 1 ATATTTTTTT 0.748096 -28 TAAAAAACATATTTTTTATTTTAATCGGAGCG 16 121 0 ATTTTTTTTT 0.93214 -180 AGCACGTTTGCTGTTTTCTTTTTCATCCACTA 16 215 0 CTGTTTTTTT 0.736924 -86 TATGTATGAAATTTCTTTTTTTATAGGTTACT 20 121 0 ATTTTTTTTT 0.93214 -35 ACTCGGTATCATTTTTTGTTTTAAGAATCGCT 21 161 0 ATTTTTTTTT 0.93214 -88 CGGAAGCATACTTTTTCTTTTTCGTGAATATA 27 238 0 CTTTTCTTTT 0.954647 -63 TATCCCCACTCTTTTTCATTTTTTACATATAA 29 45 1 CTTTTCTTTT 0.954647 -128 AGTCTATACTATTTATTGTTTTTTGTGTGTGC 33 211 0 ATTTTTTTTT 0.93214 -90 TGAAACCTTCCTTTATCGTTTTTTGTGTTTTG 33 278 0 CTTTTCTTTT 0.954647 -23 GGAAGACAACATTTATTTTTTTGGAGGGTGCT 36 13 0 ATTTTTTTTT 0.93214 -155 GCAGATATGAGTTTGTTATTTTTTCTGACAAA 36 73 1 GTTTTTTTTT 0.855206 -95 TCCGTTTCTCCTTTTTGTAAGGTAT 36 153 0 GTTTTCTTTT 0.849138 -15 CCCTCATTTGCTTTCTTCTTTTCTCGGACCTA 37 111 0 CTTTTTTTTT 0.956688 -32 **** ** **** Masking position 6 Map Score: 24.4537 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 463 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 2 TCCCGGCGAACCGGGAGTTTTGGCTTTTT 1 8 0 CGGAGTTTTG 0.6323 -159 TCCCGGTTCGCCGGGAGTTTTTTTATATTTCG 1 24 1 CGGAGTTTTT 0.539127 -143 AGCCTGGTCAGCCGGCTGTTTGGT 2 3 0 GGGCTGTTTG 0.982717 -224 AGCCGGCTGACCAGGCTGTTTTTTTGCTGCGC 2 18 1 CGGCTGTTTT 0.96132 -209 GTTTCTCTTTGATGTCTTTTTGTTTGTGAAGT 4 135 0 GGTCTTTTTG 0.842528 -42 AATAGAACGGCTTTTTGCCGTTGGGGT 6 6 1 AGGCTTTTTG 0.828338 -295 GCAAGACACTGATGGATGTTTTATTGTTTTAA 6 245 1 GGGATGTTTT 0.907817 -56 CTCATAAAAGACGGTCTTTTTTTACACATTCC 13 72 1 AGTCTTTTTT 0.39754 -134 ATTATATCACCGTGTCTGTTTTTGTGCAATAT 15 169 0 CGTCTGTTTT 0.833223 -132 CAATCTGGCTGAGGGCGGTTTTACAGGTATTA 16 48 0 GGGCGGTTTT 0.93856 -253 GTTTAAGCACGTTTGCTGTTTTCTTTTTCATC 16 220 0 GTGCTGTTTT 0.60602 -81 GTTGTTAGAAGGAGGCTGTTTGACGCAGCCTT 19 21 1 GGGCTGTTTG 0.982717 -117 CGCTTGTTTAGCGGGCTTTTTTCCCTCATTC 20 10 0 GGGCTTTTTT 0.947661 -146 CGCTAAACAAGCGGGCTTTTTGCGTTGCTGTC 20 29 1 GGGCTTTTTG 0.963789 -127 GCAGTTACTGCGCGGCTGATTGTGGGCGGAAG 22 197 1 CGGCTGATTG 0.70207 -104 TTGTGGGCGGAAGGGCTTTTTTTATTGAATAA 22 216 1 AGGCTTTTTT 0.766495 -85 GAATTACATACTGGGAGGTTTTTATT 24 148 1 CGGAGGTTTT 0.714207 -16 TTAAAGAAGGCATGTATTTTTGATAAGAATTG 30 27 0 CGTATTTTTG 0.466745 -134 CTTCAGCAAAGGGGGATGTTTGGGC 30 146 1 GGGATGTTTG 0.935387 -15 GACTCTGACAGGAGTCTGTTTTTTTTATGGGC 32 16 1 GGTCTGTTTT 0.886046 -130 TATAATGAAAGTTGGCTGTTTGAATTTGATTG 35 190 1 GGGCTGTTTG 0.982717 -80 * ********* Masking position 10 Map Score: 21.1562 Number of sites scoring better than the average of aligned sites = 1250 Number in coding regions = 1028 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 ATACACAAATAACAGGAGGTTATGTTG 2 210 1 AACAGGAGGT 0.755546 -17 AAAAGGTATGATAAGGAGGCGCTTTCTT 5 9 0 ATAAGGAGGC 0.848223 -81 TTTTAGCGGGAAAAGGAGGTATGGGG 7 43 1 AAAAGGAGGT 0.96498 -16 GAAAAAAGGAAAAAGGAGGATACGTT 8 51 1 AAAAGGAGGA 0.96038 -16 TCATAAAAAGAAAAGGTGGTTTTTAC 9 51 1 AAAAGGTGGT 0.872654 -16 AAAAAACTGAAAAGGAAGGAGGCACTTGC 10 86 1 AAAGGAAGGA 0.740747 -19 CTCATCTCATAAAAGACGGTCTTTTTTTAC 13 67 1 AAAAGACGGT 0.646049 -139 TAATAAAATTATAAGATGGATATCTATAAC 15 229 0 ATAAGATGGA 0.325068 -72 CTTGCATAATAAAAGGCGGAGTCGAAACAA 18 90 1 AAAAGGCGGA 0.866795 -35 AATAGTTGTTAGAAGGAGGCTGTTTGACGC 19 17 1 AGAAGGAGGC 0.715713 -121 AATGAATGAAAAAAGAAGGCTGCGTCAAAC 19 38 0 AAAAGAAGGC 0.809828 -100 TAACGTTGATAAAAGGAGGTTACATCAAT 21 230 1 AAAAGGAGGT 0.96498 -19 ATGAAAATCCAAAAGGAGGAACTAAA 22 285 1 AAAAGGAGGA 0.96038 -16 GTAAGGTTTCATAGGGAGGATGGAGATCCC 26 97 1 ATAGGGAGGA 0.789464 -87 ACCCTTCACAAAAGGGAGGTAATCATTTGT 27 201 1 AAAGGGAGGT 0.929399 -100 AAAAAACGATAAAGGAAGGTTTCAT 33 286 1 AAAGGAAGGT 0.764601 -15 ATACCTTACAAAAAGGAGAAACGGA 36 153 1 AAAAGGAGAA 0.530993 -15 CGGACCTATTATAAGGTGGTACCTTTTCTG 37 89 0 ATAAGGTGGT 0.689344 -54 ********** Masking position 1 Map Score: 19.2821 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 276 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 278 Fraction of orfs with sites within 600 bp upstream = 0.0446515 Motif number 4 GGCCTCTATCTGTAAGCGCTTTTATTAATT 2 178 0 TGTAAGCGCT 0.976993 -49 AAGAAAGCGCCTCCTTATCAT 5 2 1 AGAAAGCGCC 0.818232 -88 CAGCTAACCTCGTAAGCGTTCGTGAGAGGA 6 82 1 CGTAAGCGTT 0.790635 -219 CTTTTTAACTAGAAAGCGCACGTAGTGTGA 15 200 0 AGAAAGCGCA 0.884716 -101 CACTATATATTGAAAGCGTTTTAGCTTTTA 17 103 1 TGAAAGCGTT 0.972344 -38 AACTAGAAATTGTAAGCGCTGTCTATCTTC 19 102 1 TGTAAGCGCT 0.976993 -36 ACGACAAGGTTGACAGCGCATTCAAAAATA 27 16 0 TGACAGCGCA 0.87403 -285 GAATTGAGGATGACAGCGTTTGACAAAAAA 27 108 1 TGACAGCGTT 0.910757 -193 AACCGCAAATTGTAAGCGTTCATCAATACA 28 86 1 TGTAAGCGTT 0.952501 -215 GACTTCTTATTGTAAGCGTTATCAATACGC 28 146 1 TGTAAGCGTT 0.952501 -155 TAAACCATGTTGAAAACGCTTTATAATTTG 30 65 0 TGAAAACGCT 0.896347 -96 GATTTTTTTATGAAAGCGCTATAATGAAAG 35 171 1 TGAAAGCGCT 0.986747 -99 TGCTAGTAAAAGAAAGCGTTTTTGTAACTT 35 233 1 AGAAAGCGTT 0.918617 -37 AAATTCCTGCTGAAAACGCAGATATGAGTT 36 56 1 TGAAAACGCA 0.735189 -112 ********** Masking position 5 Map Score: 17.4001 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 191 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 CAACATAACCTCCTGTTATTTGTGTA 2 211 0 AACCTCCTGT 0.810816 -16 CCCCATACCTCCTTTTCCCGCTAAA 7 44 0 TACCTCCTTT 0.967084 -15 AACGTATCCTCCTTTTTCCTTTTTT 8 52 0 ATCCTCCTTT 0.879371 -15 GTAAAAACCACCTTTTCTTTTTATG 9 52 0 AACCACCTTT 0.879612 -15 GCAAGTGCCTCCTTCCTTTTCAGTT 10 90 0 TGCCTCCTTC 0.869667 -15 TGAACGAAACCTCCTATCATCCTCTTA 16 284 0 AACCTCCTAT 0.836041 -17 CTGTTACCACCTTTCTTGTTTCGA 18 111 0 TACCACCTTT 0.879612 -14 TGCGTCAAACAGCCTCCTTCTAACAACTAT 19 18 0 AGCCTCCTTC 0.869667 -120 TGTTTGACGCAGCCTTCTTTTTTCATTCAT 19 37 1 AGCCTTCTTT 0.804312 -101 ATCGAGTGCCTCCTATAAAACCATAC 21 7 1 TGCCTCCTAT 0.822628 -242 ATTGATGTAACCTCCTTTTATCAACGTT 21 231 0 AACCTCCTTT 0.967084 -18 CTTTCCGCGGTACCACCCTTGTTTACGGCC 22 139 0 TACCACCCTT 0.74074 -162 TTTAGTTCCTCCTTTTGGATTTTCA 22 286 0 TTCCTCCTTT 0.879371 -15 AACAAATGATTACCTCCCTTTTGTGAAGGG 27 202 0 TACCTCCCTT 0.919929 -99 CAAAAATACATGCCTTCTTTAAGAATACCA 30 37 1 TGCCTTCTTT 0.804312 -124 ATGAAACCTTCCTTTATCGTTTTT 33 287 0 AACCTTCCTT 0.638608 -14 ********** Masking position 4 Map Score: 15.9361 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 148 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 6 TAATCATCCTTGCAGGGTATG 4 166 0 AATCATCCTT 0.381394 -11 AGGTTTCATTCATCTCCTCTCACGAACGCT 6 96 0 CATCTCCTCT 0.65535 -205 AACGTATCCTCCTTTTTCCTTTTT 8 53 0 TATCCTCCTT 0.757929 -14 ACAAACACATCCCCTTTACAGGTTGTA 9 8 1 CATCCCCTTT 0.651593 -59 GCAAGTGCCTCCTTCCTTTTCAGTTTT 10 88 0 CCTCCTTCCT 0.702598 -17 ACTAAGTCACCTCTTCCTTTCTTTTAAAC 11 282 0 CCTCTTCCTT 0.959202 -19 GGAAAACGTTCATCTTCCCTCTCGATTATG 12 19 0 CATCTTCCCT 0.967381 -96 AACATCCTCTTCCCTGCTTCTAACT 13 191 0 CCTCTTCCCT 0.971219 -15 ACTTTTCTCCCCCTTACCCGAATGG 14 60 0 TCTCCCCCTT 0.710199 -15 TCTACATCTCCCCTTCAAAAAAAA 15 287 0 CATCTCCCCT 0.953273 -14 ACACAAAACCCCTTTTCCTTCCATTAGATA 16 173 1 CCTTTTCCTT 0.538311 -128 TACTATACTTCCTCATCCCTATGTTGTAAA 17 64 0 CCTCATCCCT 0.903665 -77 CTGCGTCAAACAGCCTCCTTCTAACAACTA 19 19 0 CAGCCTCCTT 0.776405 -119 AAGGGATCTCCATCCTCCCTATGAAACCTT 26 99 0 CATCCTCCCT 0.976672 -85 GCCCAAACATCCCCCTTTGCTGAAGTT 30 144 0 CATCCCCCTT 0.952528 -17 CCTGCCTCTTCCTTTCTGAGCATA 31 68 0 CCTCTTCCTT 0.959202 -14 TAAGTGACTCAATCTTCCCTTATAGGTTCT 35 123 0 AATCTTCCCT 0.76096 -147 ********** Masking position 10 Map Score: 12.6468 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 431 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 7 AGGCCGTATACACAAATAACAGGAGGTTAT 2 203 1 CACAAATAAC 0.770347 -24 CCAGAAAAAACACGAAAGGGG 3 2 1 CAGAAAAAAC 0.950611 -28 GTTCATAAATCAGACAAAACTTTTCTCTTG 4 66 1 CAGACAAAAC 0.848182 -111 AAAAATGAACAACAAAAAACACAGAGGCAA 6 157 0 AACAAAAAAC 0.798322 -144 TTGGAGAGTGCCCAAAAAACTGAAAAGGAA 10 73 1 CCCAAAAAAC 0.832541 -32 CTCCAAGCATCACACAAAACCCCTTTTCCT 16 162 1 CACACAAAAC 0.908195 -139 TTTGCAGAATAAACGCAAACATCT 18 5 1 CAGAATAAAC 0.654502 -120 CGATTCTTAAAACAAAAAATGATACCGAGT 21 163 1 AACAAAAAAT 0.417808 -86 TTGAAGCATACAGAAAATACACTCGGTATC 21 183 0 CAGAAAATAC 0.783166 -66 TAAGGAATGTCACAAAAAATAAACGTGAGC 26 29 0 CACAAAAAAT 0.860703 -155 AGCTTTGAAACACAAAATACAGAGGGAAAA 28 57 1 CACAAAATAC 0.864783 -244 GAAATGCACACACAAAAAACAATAAATAGT 33 206 1 CACAAAAAAC 0.971495 -95 ATTAGCAAAACACAAAAAACGATAAAGGAA 33 273 1 CACAAAAAAC 0.971495 -28 CAAGGTTTGTCAGAAAAAATAACAAACTCA 36 80 0 CAGAAAAAAT 0.777258 -88 ********** Masking position 4 Map Score: 13.3959 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 296 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 8 TTTATGAACAAAAAAGAAACCATCATTGAT 4 45 0 AAAAAGAAAC 0.858101 -132 AAAAGACATCAAAGAGAAACATACCCTGCA 4 147 1 AAAGAGAAAC 0.84616 -30 TTTTCCCGCTAAAAAGGACCAAGGTGATTC 7 27 0 AAAAAGGACC 0.914784 -32 ACACCAAATAAAGAAGAACCGTCAATCGTT 11 58 0 AAGAAGAACC 0.939275 -243 AAGTAAGTTCAAAAAGAACCCAACTTTAGG 15 40 1 AAAAAGAACC 0.958894 -261 TGGAAATTAAGAAAAGAACCTGGTGAAATT 15 124 1 GAAAAGAACC 0.94484 -177 TGTGCAATATAAAAAGAACCTGGGAAATTT 15 149 0 AAAAAGAACC 0.958894 -152 TCTGCATATTGAAATGAACCAAGCCAAATG 16 81 1 GAAATGAACC 0.762714 -220 GAAAATCCAAAAGGAGGAACTAAA 22 287 1 AAGGAGGAAC 0.626636 -14 ATTTCAGAAGGAAGTGAACCAA 25 31 1 GAAGTGAACC 0.745131 -12 GACATGCGGTGAAGAGAACCCTTCACAAAA 27 184 1 GAAGAGAACC 0.939686 -117 TTTACATATAAAAAAGGACCAGCGGCCTAT 29 66 1 AAAAAGGACC 0.914784 -107 TCCATCAAAATAGAAGAACCTATAAGGGAA 35 109 1 TAGAAGAACC 0.685183 -161 ACCTTACAAAAAGGAGAAACGGA 36 155 1 AAGGAGAAAC 0.784812 -13 ********** Masking position 8 Map Score: 12.9755 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 154 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 AAAGCAATGTTGTTAGTGAAAAAAGTGAATTTC 1 101 0 TGAGTAAAAA 0.417807 -66 CAACATTGCTTTACAATTAAAAACAAGTAAAAA 1 122 1 TTAATAAAAA 0.7422 -45 TTTATTTGTCTTACAATTAAACAAAAGGATATA 2 120 1 TTAATAAACA 0.424554 -107 TGTATGCGATTTGCATTCAAAAATGAACAACAA 6 172 0 TTATTAAAAA 0.920399 -129 GTTTTATTGTTTTAATTGAAAAATGAGAAATTA 6 262 1 TTATTAAAAA 0.920399 -39 CTTTCTCCTGTGGTATTGAAAAAAGGAAAAAGG 8 34 1 TGATTAAAAA 0.776618 -33 TACAAACACATTTTATTTACAAATTATTTTAAA 10 30 0 TTATTACAAA 0.501311 -75 ATAAATTGTAGTAAAATAAAAAAGATAAATACA 13 138 1 GTAATAAAAA 0.424554 -68 CCATAGCTAGTCGCATTAAAAAACTTGGTTTGA 15 94 0 TCATTAAAAA 0.776618 -207 TCTGTTTTTGTGCAATATAAAAAGAACCTGGGA 15 154 0 TGATAAAAAA 0.436933 -147 TACGTGCGCTTTCTAGTTAAAAAGTTATAGATA 15 206 1 TTAGTAAAAA 0.70473 -95 GCCGCTCCGATTAAAATAAAAAATATGTTTTTT 16 119 1 TTAATAAAAA 0.7422 -182 CTTGGAGAAATTAGATTAAAAAACATATTTTTT 16 136 0 TTATTAAAAA 0.920397 -165 TAGCTGATTATTCAATAAAAAAAGCCCTTCCGC 22 222 0 TTATAAAAAA 0.720731 -79 ATTCCTTAAATTTTATTTAAAAACAATTTATTT 26 51 1 TTATTAAAAA 0.919938 -133 AAGGTTGACAGCGCATTCAAAAATAATGTT 27 8 0 GCATTAAAAA 0.471163 -293 TATCTGACTTTTCCATTTAAACATTGTCATGTC 28 194 0 TTATTAAACA 0.747673 -107 TTTTCATTTTTTACATATAAAAAAGGACCAGCG 29 57 1 TTATAAAAAA 0.720732 -116 TCAACATGGTTTATATTTTAAAAATTGAGAAGA 30 82 1 TTATTTAAAA 0.404183 -79 TCTGATAATATTCAATTAAAAAATTTAAATAAG 34 72 1 TTATTAAAAA 0.920399 -167 ATTTAAATAAGTATATTAAAAAATTAAGTAATT 34 94 1 GTATTAAAAA 0.747672 -145 ATTATAGCGCTTTCATAAAAAAATCTTATTTTT 35 163 0 TTATAAAAAA 0.720642 -107 CTTCTTCCAATCAAATTCAAACAGCCAACTTTC 35 196 0 TCATTAAACA 0.471163 -74 ** *** ***** Masking position 5 Map Score: 15.3717 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 335 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 10 AGCCAAAACTCCCGGTTCGCCGGGAGTTTTTTT 1 15 1 CCGGTTGCGG 0.989384 -152 AAAAAAACAGCCTGGTCAGCCGGCTGTTTGGT 2 10 0 CCGGTCGCGG 0.991744 -217 TGCGCAGAATCCCGGCCGGACAGTGATTTACCG 2 45 1 CCGGCCGCAG 0.977731 -182 GGGCAAGGCTAGACGGGACTTACCGA 4 4 1 CAGGCTGCGG 0.959678 -173 TTTCGGTATACCTGGTATGACAGCACCCTTAAG 18 44 1 CCGGTAGCAG 0.867288 -81 TCGTGCTTCGCTTGATCAGACGGTACGGAAGCA 27 262 0 CTGATCGCGG 0.792028 -39 CTTTTGAAGACCGGACTTGACGAATTGAATCCA 28 25 1 CCGACTGCGA 0.748715 -276 ATCACGTTGACCTGGCTTGACGGAGGCGTGACG 32 105 1 CCGGCTGCGG 0.991794 -41 ATACTCTTATCCCGAGCTGGCGGAGGGACAGGC 33 85 0 CCGAGCGCGG 0.92576 -216 GTCAATCGCGCAAGGTTTGTCAGAAAAAATAAC 36 87 0 CAGGTTGCAG 0.839129 -81 ** **** * *** Masking position 11 Map Score: 6.6318 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 144 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 ACAGGTTTCATTCATCTCCTCTCACGAACGC 6 97 0 TTCATCCCTC 0.832029 -204 AGGGAAAACGTTCATCTTCCCTCTCGATTAT 12 20 0 TTCATCTCCC 0.983938 -95 AACATCCTCTTCCCTGCTTCTAAC 13 192 0 ATCCTCTCCC 0.825181 -14 TCTACATCTCCCCTTCAAAAAAA 15 288 0 TACATCCCCC 0.912966 -13 TATACTATACTTCCTCATCCCTATGTTGTAA 17 65 0 TTCCTCTCCC 0.967682 -76 AAAAGGGATCTCCATCCTCCCTATGAAACCT 26 100 0 TCCATCTCCC 0.971979 -84 TAATTCACCGTCCCATCAATTCTT 30 4 1 TTCACCTCCC 0.967682 -157 TGTTTCCATTTTCACCCCCCCCTATCATCAT 32 59 0 TTCACCCCCC 0.961086 -87 TTTAAGTGACTCAATCTTCCCTTATAGGTTC 35 124 0 TCAATCTCCC 0.772759 -146 ****** **** Masking position 6 Map Score: 3.85989 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 110 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 TTTTTTACACATTCCTTCCGAATCGTATAG 13 89 1 ATTCCTTCCG 0.920645 -117 CGGAAAGAAAAGCCTTTTCGCCCCTTTTAG 22 162 1 AGCCTTTTCG 0.832679 -139 CAATAAAAAAAGCCCTTCCGCCCACAATCA 22 213 0 AGCCCTTCCG 0.989605 -88 ATTTCATACAAGCCTTTCCGAGCACGTCAT 27 62 1 AGCCTTTCCG 0.969851 -239 AATGCCTTCCGGAACATCGTG 27 290 0 ATGCCTTCCG 0.94504 -11 AACCTTGAACATCCCTTCCGTATAACTCCA 35 83 1 ATCCCTTCCG 0.983751 -187 ********** Masking position 6 Map Score: 2.74449 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 42 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 13 ATGCAAGTTCCATGCCAGCTCTTAAGGGTG 18 67 0 CATGCCAGCT 0.945199 -58 TTCATTCATTCATGCCCGTTTCAAAGCATA 19 58 1 CATGCCCGTT 0.851265 -80 ATGAGGGAAAAAAGCCCGCTAAACAAGCGG 20 13 1 AAAGCCCGCT 0.943064 -143 AGCAACGCAAAAAGCCCGCTTGTTTAGCGG 20 28 0 AAAGCCCGCT 0.943064 -128 GTTGAATTCACAAGTCCGCTCCTGTAAGAT 20 69 1 CAAGTCCGCT 0.964996 -87 CTCATTGACGCAAGCCAGCCTCCAATGGTT 24 13 0 CAAGCCAGCC 0.884822 -151 TTCAATTCGTCAAGTCCGGTCTTCAAAAGC 28 24 0 CAAGTCCGGT 0.907007 -277 TAAACATTGTCATGTCGGCTTTTCAAGTCA 28 180 0 CATGTCGGCT 0.768293 -121 ACGCCTCCGTCAAGCCAGGTCAACGTGATG 32 104 0 CAAGCCAGGT 0.920841 -42 ********** Masking position 2 Map Score: 3.64163 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 250 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 CCGTCAATCGTTTTCATCGCTGATTTTCAAT 11 39 0 TTTTCATGCT 0.902906 -262 TATATATCTGTTTTCAATGCTTACGATGTAA 12 55 1 TTTTCAAGCT 0.518563 -60 CTTTTCTTAATTTCCATAGCTAGTCGCATTA 15 109 0 TTTCCATGCT 0.838678 -192 CAGCCTTCTTTTTTCATTCATTCATGCCCGT 19 46 1 TTTTCATCAT 0.613054 -92 CTATGTCAAGTTTCCATACTTCACCCTTATT 21 83 1 TTTCCATCTT 0.84891 -166 TCCTTTTGGATTTTCATCCTTTAAAGATCAT 22 271 0 TTTTCATCTT 0.909505 -30 TGGAGATCCCTTTTCATTGTTTTTAGGGCAA 26 117 1 TTTTCATGTT 0.936899 -67 ACAACTTCGTTTTTCGTACTTTTTTCCCGGT 28 252 0 TTTTCGTCTT 0.633071 -49 TCCCCACTCTTTTTCATTTTTTACATATAAA 29 47 1 TTTTCATTTT 0.658222 -126 ATGTTTCCAATTTTCATTGTTTCCATTTTCA 32 76 0 TTTTCATGTT 0.936899 -70 TGTGTGTGCATTTCCATTGTTTTCCCTCAAT 33 189 0 TTTCCATGTT 0.892479 -112 TCCCATTATCTTTTCATGATTGCCTTCACTA 35 21 1 TTTTCATATT 0.658222 -249 ******* *** Masking position 3 Map Score: 4.03643 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 154 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 15 TAGATTTAATAGATATTTTTCATATGGATAT 5 51 1 AGATATTTTC 0.865538 -39 CGAATCGTATAGAGATTCTTCGTCTCGTTTG 13 107 1 AGAGATTTTC 0.959343 -99 CCGCCCTCAGCCAGATTGTTCTGCATATTGA 16 62 1 CCAGATTTTC 0.793909 -239 TGTATAAAATACAGCTTATTCATCTCCGAAT 17 15 1 ACAGCTTTTC 0.891457 -126 TATGTTGTAAACAGCTTATTCATCCGACTAT 17 44 0 ACAGCTTTTC 0.891457 -97 TGGAAAAGTCAGATATTTTTCGGAGAAGATG 28 212 1 AGATATTTTC 0.865538 -89 AATAGTTTTGAGACATTGTTCGAATAATTGT 34 179 1 AGACATTTTC 0.844003 -60 GACAAGCAGAAGAGATTTTTCACATAATAAA 36 117 1 AGAGATTTTC 0.959344 -51 ******* *** Masking position 3 Map Score: 0.92894 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 51 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493