AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifur_ecoli_bsub_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 entD 165 enterochelin synthetase, component D #2 fepA_fes 320 fepA: outer membrane receptor for ferric enterobactin (enterochelin) and colicins B and D, fes: enterochelin esterase #3 entF 217 ATP-dependent serine activating enzyme (may be part of enterobactin synthase as component F) #4 fepE 215 ferric enterobactin (enterochelin) transport #5 fepB_entC 374 fepB: ferric enterobactin (enterochelin) binding protein; periplasmic component, entC: isochorismate hydroxymutase 2, enterochelin biosynthesis #6 fur 288 negative regulator #7 tonB 127 energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins #8 cirA 293 outer membrane receptor for iron-regulated colicin I receptor; porin; requires tonB gene product #9 sodA 284 superoxide dismutase, manganese #10 feuA 90 iron-binding protein #11 ybbB 190 alternate gene name: yzbC; similar to transcriptional regulator (AraC/XylS family) #12 yqkL 112 similar to transcriptional regulator (Fur family) #13 sodA 178 superoxide dismutase #14 menF 288 menaquinone-specific isochorismate synthase #15 yukL 87 similar to antibiotic synthetase #16 yukM 300 similar to antibiotic synthetase #17 dhbB 27 isochorismatase #18 dhbE 28 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E) #19 dhbC 25 isochorismate synthase #20 dhbA 193 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase Motif number 1 TCCTGCAATATATTGAATTGGCAAGATTTTTGTAGGCCGGA 1 74 0 TTAGAATTTT 0.64687 -92 CCATTACGCTATTGCAAATGCAAATAGTTATCAATAATATT 2 144 0 ATAGAATTAT 0.981682 -177 TTATAAACCCATAATTACAGAAAATAATTATGGGTTTTTTA 4 22 1 AAAGAATTAT 0.850542 -194 AGCGACCGAAAATATAAATGATAATCATTATTAAAGCCTTT 5 31 0 ATAGAATTAT 0.981674 -344 TTGTGGTTACAATGAAAATGAGAAGCATTATTGATGGATTC 5 142 1 ATAGAATTAT 0.981691 -233 AAAATTTAACATTTGGATTGATAATTGTTATCGTTTGCATT 8 90 1 ATAGAATTAT 0.981639 -204 TAGTTAATTAAATGATATTGAAAATGATTATCAATGCCGTA 9 193 0 ATAGAATTAT 0.981567 -92 ATTCTCTATAATTCCAATTGATAATAGTTATCAATTGAACA 10 47 1 ATAGAATTAT 0.981639 -44 ATTTGGTACAATTTTTATTGAAAATGATTATCAATTGAAAG 11 138 1 ATAGAATTAT 0.981306 -53 ATTATTATAAACTGATAAATAAAATGGTTTTCTTTTAATAA 12 16 0 ATATAATTTT 0.68533 -97 ATACGCGCAGAGTTCCAACTATAATTATTATAAACTGATAA 12 39 0 ATATAATTAT 0.871529 -74 AGTCAAATATAATTTCAGTGACAAATATTTTTTTAAAGGCA 20 25 0 ATAGAATTTT 0.945095 -169 TATTTTTATAATTGATAATGATAATCATTATCAATAGATTG 20 89 1 ATAGAATTAT 0.981689 -105 * * * * ** **** Masking position 13 Map Score: 19.8044 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 12 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 AAGGCGTTCACGCCGCATCCGGCATGAACG 1 43 0 CGCCGCATCC 0.995842 -123 GCGGCGTGAACGCCTTATCCGGCCTACAAA 1 57 1 CGCCTTATCC 0.791749 -109 GTCATCAACACGACGCATCCCGCTACCGCG 2 252 0 CGACGCATCC 0.981217 -69 TTCAGTCTGTGGCCGCAACAATGCGTCTTA 3 82 1 GGCCGCAACA 0.948736 -136 CATGAGTCTACGCCGCATCACA 6 3 0 CGCCGCATCA 0.993375 -286 CTCATGTCTACGCCGTATTAATAGATAATG 6 27 1 CGCCGTATTA 0.914368 -262 ATTATCGTTACGCCGCAATCAAAAAAGGCT 8 128 1 CGCCGCAATC 0.964943 -166 AATCGACAACGGCGGCAACAGGCGAAAGGT 9 83 0 GGCGGCAACA 0.799097 -202 CAACTGCTTACGCGGCATTAACAATCGGCC 9 242 1 CGCGGCATTA 0.912247 -43 TTCCCTCCTACGCCGCATTCCATGACTCAT 12 89 0 CGCCGCATTC 0.987248 -24 TTGGGTCACCGGACGTATCAGTTCTGAGCA 16 147 0 GGACGTATCA 0.717249 -154 CGTTCGCGTGCGACGCATCCTTTATTCCAA 16 278 1 CGACGCATCC 0.981217 -23 ********** Masking position 7 Map Score: 17.9559 Number of sites scoring better than the average of aligned sites = 1383 Number in coding regions = 1059 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 CGCCGTCACACCATAACCCCATGTTTACTG 2 80 1 CCATAACCCC 0.867058 -241 CCGTTCTGCCCCCTCTCCCTTCCAGGGTGA 5 209 1 CCCTCTCCCT 0.991977 -166 CTCACCCCAGCCCTCACCCTGGAAGGGAGA 5 222 0 CCCTCACCCT 0.994983 -153 CGAACATTAACCCTCACCCCAGCCCTCACC 5 234 0 CCCTCACCCC 0.996099 -141 CTGGCTGTTCCCCTCACCCTAACCCTCTCC 5 272 1 CCCTCACCCT 0.994983 -103 CTCACCCTAACCCTCTCCCCAAAGGGGCGA 5 284 1 CCCTCTCCCC 0.993757 -91 ACAATCCGTCCCCTCGCCCCTTTGGGGAGA 5 297 0 CCCTCGCCCC 0.989403 -78 TGTCATTACGCCCTTAACCTTATTAATAAC 5 342 1 CCCTTAACCT 0.816425 -33 TTTTTCAATTCCATTTCCCTGACAAATCAT 8 52 1 CCATTTCCCT 0.847756 -242 ********** Masking position 4 Map Score: 17.5262 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 44 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 AGTTATCAATAATATTATCAATATATTTCTG 2 129 0 AAATTATCAA 0.854677 -192 GCAAATGCAAATAGTTATCAATAATATTATC 2 141 0 ATGTTATCAA 0.941318 -180 TCAGCTTCGGATAATTATCACCAACTGGTAA 4 142 1 ATATTATCAC 0.888109 -74 ATAAATGATAATCATTATTAAAGCCTTTATC 5 28 0 ATATTATTAA 0.876999 -347 GCAAACGATAACAATTATCAATCCAAATGTT 8 97 0 ACATTATCAA 0.897083 -197 GATATTGAAAATGATTATCAATGCCGTACTT 9 190 0 ATATTATCAA 0.978066 -95 CCAATTGATAATAGTTATCAATTGAACAGGA 10 60 1 ATGTTATCAA 0.941318 -31 TTTATTGAAAATGATTATCAATTGAAAGCTT 11 151 1 ATATTATCAA 0.978066 -40 AATCATTATTAAAAGAAAACCA 12 2 1 ATATTATTAA 0.876999 -111 TCCAACTATAATTATTATAAACTGATAAATA 12 36 0 ATATTATAAA 0.801688 -77 GATAATGATTATCATTATCAATTATAAAAAT 20 90 0 ATATTATCAA 0.978836 -104 GATAATGATAATCATTATCAATAGATTGCGT 20 102 1 ATATTATCAA 0.978836 -92 ** ******** Masking position 7 Map Score: 17.3255 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TCAGATTGTTGACAAAGTGCGCGTCGTTCATG 1 19 1 GACAAGTCGC 0.989295 -147 TGCAATCAATGAAAAATTGCACAGTAAACATG 2 99 0 GAAAATTCAC 0.707454 -222 TCATCAACACGACGCATCCCGCTACCGCGAAA 2 249 0 GACGATCCGC 0.881527 -72 GGGAGCGTTTTACATATTGCGCAATGCGCAGG 3 45 1 TACAATTCGC 0.740963 -173 ATTCGTCGGTGTCAGAGTACGCCAGTGGGCTT 3 173 0 GTCAAGTCGC 0.89429 -45 CTCAAGAGTTGACATAGTGCGCGTTTGCTTTT 5 77 0 GACAAGTCGC 0.989295 -298 TGACAAATTCGACAAAGCGCACAATCCGTCCC 5 315 0 GACAAGCCAC 0.966461 -60 TTAGTAACAGGACAGATTCCGC 6 277 1 GACAATTCGC 0.980598 -12 AAATGGAATTGAAAAAGCCCTCTCGGTTGAGA 8 36 0 GAAAAGCCTC 0.719896 -258 CCATTTCCCTGACAAATCATGCGGATATAAAA 8 62 1 GACAATCTGC 0.756271 -232 TAACACCATGGACAAATTCCTGATTTA 10 6 0 GACAATTCTG 0.670847 -85 CATTTCAGCGGACATATTTCACTTTAACCGAT 13 44 0 GACAATTCAC 0.93561 -135 TGTAATCAATGAAAAAGCTCACGATTTGGCTC 13 75 0 GAAAAGCCAC 0.827446 -104 GCCGCTTATTGACAAGGCTCGGGGCGGGCACC 16 33 1 GACAGGCCGG 0.780674 -268 TGAGCTTCTAGACAGAGTACGGGAAGTGAATC 16 184 1 GACAAGTCGG 0.960291 -117 **** *** *** Masking position 2 Map Score: 14.7526 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 451 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 GGATAAGGCGTTCACGCCGCATCCGGCATG 1 47 0 TTCACGCCGC 0.979046 -119 CTTCCTACTTTTAACGCCGTCACACCATAA 2 66 1 TTAACGCCGT 0.614738 -255 GTCCGCGCTTCCCACGGCGCGCCATTACGC 2 176 0 CCCACGGCGC 0.972507 -145 GGGGGAAATCTCCACGGCGCTCACTTTACC 4 168 0 TCCACGGCGC 0.956864 -48 AATGTGATGTCCTGCGCCGTTCTGCCCCCT 5 193 1 CCTGCGCCGT 0.849543 -182 ACAATCCGTCCCCTCGCCCCTTTGGGGAGA 5 297 0 CCCTCGCCCC 0.812855 -78 TAGACATGAGTCTACGCCGCATCACA 6 7 0 TCTACGCCGC 0.987163 -282 TAGACTCATGTCTACGCCGTATTAATAGAT 6 23 1 TCTACGCCGT 0.944382 -266 TTGCATTATCGTTACGCCGCAATCAAAAAA 8 124 1 GTTACGCCGC 0.959062 -170 GAACCAACTGCTTACGCGGCATTAACAATC 9 238 1 CTTACGCGGC 0.855166 -47 GTCTTTCCCTCCTACGCCGCATTCCATGAC 12 93 0 CCTACGCCGC 0.99191 -20 CTTCAATCCGGTCTCGCCGCTTATTGACAA 16 18 1 GTCTCGCCGC 0.886361 -283 ********** Masking position 5 Map Score: 12.9291 Number of sites scoring better than the average of aligned sites = 2055 Number in coding regions = 1802 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 7 TATATTGCAGGACCATGTAGGCCTGATAAGCGTA 1 103 1 GACCATGGCT 0.898014 -63 GAAAACCTTTGATCCTGAAAGACACGCAGTGCAG 2 219 0 GATCCTGGCA 0.977279 -102 TGTTGATGACGACCATGCCCGACAGTTGCAATTC 2 272 1 GACCATGGCA 0.970368 -49 GGCAGGCTGGGACATTGTGTGTCAGCCGCAGTCA 3 114 1 GACATTGGCA 0.816341 -104 TGGTTACAATGAAAATGAGAAGCATTATTGATGG 5 145 1 GAAAATGACA 0.87653 -230 CGTATTAATAGATAATGCCAATCAAAATAATTGC 6 40 1 GATAATGACA 0.952308 -249 TTGCTCTTGAGATAATGCGTATCATTATAGAATT 6 211 0 GATAATGACA 0.952308 -78 CATTTTCACTGATCCTGATCGTCTTGCCTTATTG 7 39 1 GATCCTGGCT 0.920417 -89 AAATGATATTGAAAATGATTATCAATGCCGTACT 9 191 0 GAAAATGACA 0.87653 -94 AATTTTTATTGAAAATGATTATCAATTGAAAGCT 11 147 1 GAAAATGACA 0.87653 -44 GTCAAACACAGATCATGCAGTCCAAATGGCCTGC 14 205 0 GATCATGTCA 0.867395 -84 TGCCGAGTCTGATCCTGACGAGCAAATCGGAAAT 15 31 1 GATCCTGACA 0.964032 -57 TGCGCTGGGCGATCTTGTAGGGCTGTTCATTAAT 16 106 1 GATCTTGGCT 0.796251 -195 TCAAACGGCAGATCCTGATTGTCATAGGCGGCCA 16 216 0 GATCCTGGCA 0.977279 -85 GCAATCTATTGATAATGATTATCATTATCAATTA 20 97 0 GATAATGACA 0.952308 -97 ******* * ** Masking position 2 Map Score: 16.6605 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 282 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 GGAAGTGAGAGCTGGTGGCAGTCGAAACATGGCCC 2 36 0 GCGGTGGTGA 0.950697 -285 GACACGCAGTGCAGTTGGTTAATTAATGTCCGCGC 2 198 0 GCGTTGGATA 0.981144 -123 GGTAAAATTCGTCGGTGTCAGAGTACGCCAGTGGG 3 176 0 GTGGTGTATA 0.769722 -42 TGTAACTTTTGCTGTTGTACCTGTACAATGTCCCG 6 82 1 GCGTTGTTTA 0.970263 -207 AAGTGGCCTTGCCGTTGTAAATGTAAGCTGTGCCA 6 123 1 GCGTTGTTTA 0.970263 -166 GCCTGTTGCCGCCGTTGTCGATTTACTGGCAATCA 9 90 1 GCGTTGTTTA 0.970263 -195 TGCCGCGTAAGCAGTTGGTTCATTATAGTTAATTA 9 224 0 GCGTTGGATA 0.981144 -61 CCTATATAAAGCGGGTGGGTTTTTAGCATGAAAAA 11 90 0 GCGGTGGTTA 0.988028 -101 TTCATAAATGGCGGGTGGAGGAATATAGGAGGTTT 14 71 1 GCGGTGGATA 0.985292 -218 ** ***** * ** Masking position 6 Map Score: 9.46599 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 84 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 AATGCGTCTTACCGGCAGGCTGGGACATTGTG 3 101 1 ACCGGCGGCG 0.975307 -117 AGCCGCAGTCACAGGCGTCCTGCCAGCAGTGG 3 137 1 ACAGGCTCCG 0.975422 -81 AAATCAGCTTCCTGTTATTAATAA 5 361 0 ATCAGCTCCG 0.814415 -14 CAGAGGCTGTTCCGGCTTTCTGGGATGATCAC 8 165 1 TCCGGCTTCG 0.77926 -129 CGAAAGGTTAATCGACAGCACGATTTTTACAC 9 59 0 ATCGACGCAG 0.740096 -226 GGCATTAACAATCGGCCGCCCGACAATACTGG 9 255 1 ATCGGCGCCG 0.991938 -30 GCCCCATTAAACCTGCCGCCAGCATTTC 13 7 0 ACCTGCGCCG 0.955394 -172 TTTAGTATGAACAGATCGCCTGAGAACTTTCA 14 43 1 ACAGATGCCG 0.669868 -246 CGGGGCGGGCACCGACATTCCGATCGGCAGTC 16 52 1 ACCGACTTCG 0.907669 -249 CGACATTCCGATCGGCAGTCCGATCGCGGGAC 16 64 1 ATCGGCGTCG 0.968232 -237 CCTGATTGTCATAGGCGGCCAGATTCACTTCC 16 205 0 ATAGGCGCCG 0.975422 -96 TAAATGCCAAACAGACATCCAGCGAAAAAGAC 20 149 0 ACAGACTCCG 0.927539 -45 ****** *** * Masking position 12 Map Score: 9.14858 Number of sites scoring better than the average of aligned sites = 1893 Number in coding regions = 1817 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 GCATGAACGACGCGCACTTTGTCAACAATC 1 22 0 CGCGCACTTT 0.963488 -144 GAAGCCCACTGGCGTACTCTGACACCGACG 3 172 1 GGCGTACTCT 0.820738 -46 ATCTCCACGGCGCTCACTTTACCAGTTGGT 4 161 0 CGCTCACTTT 0.942815 -55 TAAAAGCAAACGCGCACTATGTCAACTCTT 5 76 1 CGCGCACTAT 0.825448 -299 CTCACCCCAGCCCTCACCCTGGAAGGGAGA 5 222 0 CCCTCACCCT 0.880994 -153 CTGGCTGTTCCCCTCACCCTAACCCTCTCC 5 272 1 CCCTCACCCT 0.880994 -103 GGCGTAATTACCCTTACTTT 7 1 0 CCCTTACTTT 0.951731 -127 GATTATCAATGCCGTACTTTTCGTAAGGGT 9 179 0 GCCGTACTTT 0.871505 -106 GAACGAAAGACCCTTACTTTTACACATAAG 11 52 1 CCCTTACTTT 0.951731 -139 ATGAAAAAAACCCTTACTTATGTGTAAAAG 11 68 0 CCCTTACTTA 0.695473 -123 TGGAACTCTGCGCGTATTTTGTTATAATGA 12 63 1 CGCGTATTTT 0.620423 -50 AGATTCACTTCCCGTACTCTGTCTAGAAGC 16 187 0 CCCGTACTCT 0.967227 -114 ********** Masking position 6 Map Score: 9.72302 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 204 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 GCAAATTCTGTCACTTCTTCTAATGAAGTGA 6 241 1 TCACTCTTCT 0.960404 -48 CACATCTTCTTCACGTCCCCTTGCGTACGGC 8 227 0 TCACTCCCCT 0.983738 -67 GGGTTATCGCTCACATCTTCTTCACGTCCCC 8 238 0 TCACTCTTCT 0.960404 -56 TTTCGTCGCGTCACATCTCCGACGAGATGAG 9 29 1 TCACTCTCCG 0.971189 -256 GTGATTTGCTTCACATCTCGGGCATTTTCCT 9 138 1 TCACTCTCGG 0.934315 -147 GCGGCCAGATTCACTTCCCGTACTCTGTCTA 16 192 0 TCACTCCCGT 0.962302 -109 ATGAACACTTCCTCTCAAATTGTTG 17 13 0 ACACTCCTCT 0.858773 -15 **** ****** Masking position 3 Map Score: 4.11237 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 46 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CAGACGCTGCCATTCCGGGCCATGTTTCGAC 2 20 1 CATCCGGGCC 0.971702 -301 TAACCAACTGCACTGCGTGTCTTTCAGGATC 2 212 1 CATGCGTGTC 0.972793 -109 CCGACAGTTGCAATTCGTGGCAAAAATGCAG 2 290 1 CATTCGTGGC 0.881808 -31 AGGGGCAATTCAGTCTGTGGCCGCAACAATG 3 74 1 CATCTGTGGC 0.904731 -144 GTGGCCGCAACAATGCGTCTTACCGGCAGGC 3 90 1 CATGCGTCTT 0.738894 -128 CAGGCTGGGACATTGTGTGTCAGCCGCAGTC 3 116 1 CATGTGTGTC 0.875632 -102 ACAAAGCGCACAATCCGTCCCCTCGCCCCTT 5 305 0 CATCCGTCCC 0.982673 -70 AGCGCATCATCATTCCGTCCCGCGATCGGAC 16 81 0 CATCCGTCCC 0.982673 -220 TAGAGGTGCTCAATCCGGCTCGTTCGCGTGC 16 258 1 CATCCGGCTC 0.958257 -43 ** ******** Masking position 4 Map Score: 4.81378 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 164 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 GCATCAGGCAGTTTTGCGTTTGTCATCAGTC 1 139 1 GTTTTGCTTT 0.912521 -27 ATAATTATGGGTTTTTTATTTGTTTGATTTA 4 45 1 GTTTTTTTTT 0.411115 -171 TTATTAAAGCCTTTATCATTTTGTGGAGGAT 5 14 0 CTTTATCTTT 0.637364 -361 ACATAGTGCGCGTTTGCTTTTAGGTTAGCGA 5 67 0 CGTTTGCTTT 0.943737 -308 AAATTTGTAACTTTTGCTGTTGTACCTGTAC 6 77 1 CTTTTGCGTT 0.703205 -212 AGGGACTTGTGGTTTTCATTTAGGCGTGGCA 6 181 1 GGTTTTCTTT 0.933058 -108 ACCGAGAGGGCTTTTTCAATTCCATTTCCCT 8 41 1 CTTTTTCATT 0.756053 -253 TAATTGTTATCGTTTGCATTATCGTTACGCC 8 111 1 CGTTTGCTTA 0.640937 -183 CTGTTGCCGCCGTTGTCGATTTACTGGCAAT 9 92 1 CGTTGTCATT 0.543377 -193 TAAATAAAATGGTTTTCTTTTAATAATGATT 12 11 0 GGTTTTCTTT 0.933058 -102 AAATCGTGAGCTTTTTCATTGATTACAAAGC 13 80 1 CTTTTTCTTG 0.705305 -99 GAATATAGGAGGTTTTCCTTTTATGGTAAGC 14 91 1 GGTTTTCTTT 0.933058 -198 AAGCTTGTTTCTTTTTCATTTCTGAAATTAG 14 158 1 CTTTTTCTTT 0.938173 -131 CTGGATGTCTGTTTGGCATTTAGAGCGAAGA 20 159 1 GTTTGGCTTT 0.767202 -35 ******* *** Masking position 4 Map Score: 4.90499 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 247 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 14 TATAAACCCATAATTACAGAAAATAATTAT 4 23 1 TAATTACAGA 0.830062 -193 ATAATGCGTATCATTATAGAATTGCCACGC 6 204 0 TCATTATAGA 0.758749 -85 GAAGTCATAATCATTTCAGTAGAAAAACCA 7 107 0 TCATTTCAGT 0.949918 -21 AGCAGTTGGTTCATTATAGTTAATTAAATG 9 220 0 TCATTATAGT 0.834591 -65 CAGTTTATAATAATTATAGTTGGAACTCTG 12 43 1 TAATTATAGT 0.719741 -70 ACGATTTGGCTCATTTCAGCGGACATATTT 13 57 0 TCATTTCAGC 0.873981 -122 CTGTGAAGCGTCATTTCAGTACATATATAC 13 144 1 TCATTTCAGT 0.949918 -35 ATTATAAACCTAATTTCAGAAATGAAAAAG 14 168 0 TAATTTCAGA 0.857506 -121 CAGTCAAATATAATTTCAGTGACAAATATT 20 37 0 TAATTTCAGT 0.906138 -157 ********** Masking position 5 Map Score: 5.08685 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 109 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 CAATGTCCCAGCCTGCCGGTAAGACGCATT 3 101 0 GCCTGCCGGT 0.953229 -117 AGTATTGTCGGGCGGCCGATTGTTAATGCC 9 255 0 GGCGGCCGAT 0.990364 -30 GAAATGCTGGCGGCAGGTTTAATGGGGC 13 9 1 GGCGGCAGGT 0.930416 -170 GCCTGTTGGAGGCTGCCGAGTCTGATCCTG 15 18 1 GGCTGCCGAG 0.973793 -70 CCCGCGATCGGACTGCCGATCGGAATGTCG 16 64 0 GACTGCCGAT 0.951237 -237 AAGTGAATCTGGCCGCCTATGACAATCAGG 16 207 1 GGCCGCCTAT 0.902503 -94 ********** Masking position 5 Map Score: 0.768045 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 290 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678