AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifur_ecoli_hinf_300.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 fldA 139 flavodoxin 1 #8 ybfE 70 orf, hypothetical protein #9 ybfF 184 orf, hypothetical protein #10 tonB 127 energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins #11 cirA 293 outer membrane receptor for iron-regulated colicin I receptor; porin; requires tonB gene product #12 lysP 204 lysine-specific permease #13 yeiE 98 putative transcriptional regulator LYSR-type #14 sodA 284 superoxide dismutase, manganese #15 HI0190 28 ferric uptake regulation protein (fur) #16 HI0191 96 flavodoxin (fldA) #17 HI0253 168 biopolymer transport protein (exbB) #18 HI0254 100 bacterioferritin comigratory protein (bcp) #19 HI0262 300 heme-hemopexin utilization protein C #20 HI0866 300 H. influenzae predicted coding region HI0866 #21 HI1088 248 superoxide dismutase (sodA) Motif number 1 CGCCGTCACACCATAACCCCATGTTTACTG 2 80 1 CCATAACCCC 0.882126 -241 CCGTTCTGCCCCCTCTCCCTTCCAGGGTGA 5 209 1 CCCTCTCCCT 0.993611 -166 CTCACCCCAGCCCTCACCCTGGAAGGGAGA 5 222 0 CCCTCACCCT 0.995627 -153 CGAACATTAACCCTCACCCCAGCCCTCACC 5 234 0 CCCTCACCCC 0.995963 -141 CTGGCTGTTCCCCTCACCCTAACCCTCTCC 5 272 1 CCCTCACCCT 0.995627 -103 CTCACCCTAACCCTCTCCCCAAAGGGGCGA 5 284 1 CCCTCTCCCC 0.9941 -91 ACAATCCGTCCCCTCGCCCCTTTGGGGAGA 5 297 0 CCCTCGCCCC 0.986997 -78 TGTCATTACGCCCTTAACCTTATTAATAAC 5 342 1 CCCTTAACCT 0.779387 -33 CAACATAATACCCTAACCCGACAACGCGAA 9 150 1 CCCTAACCCG 0.932415 -35 TTTTTCAATTCCATTTCCCTGACAAATCAT 11 52 1 CCATTTCCCT 0.825117 -242 AACCCTCTCCTTTAACCGGGCA 13 3 1 CCCTCTCCTT 0.924554 -96 ********** Masking position 4 Map Score: 19.9282 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 70 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 AGGCGTTCACGCCGCATCCGGCATGAACGACG 1 40 0 GCCGATCCGC 0.502694 -126 CGGCGTGAACGCCTTATCCGGCCTACAAAAAT 1 58 1 GCCTATCCGC 0.667482 -108 TTTCGCGGTAGCGGGATGCGTCGTGTTGATGA 2 249 1 GCGGATGCGC 0.98363 -72 TTTACATATTGCGCAATGCGCAGGGGCAATTC 3 53 1 GCGCATGCGA 0.762537 -165 ACGCATTGTTGCGGCCACAGACTGAATTGCCC 3 76 0 GCGGCACAGC 0.966807 -142 TGTGTCAGCCGCAGTCACAGGCGTCCTGCCAG 3 131 1 GCAGCACAGC 0.786606 -87 AAGCCCACTGGCGTACTCTGACACCGACGAAT 3 173 1 GCGTCTCTGC 0.632178 -45 TCGACAAAGCGCACAATCCGTCCCCTCGCCCC 5 307 0 GCACATCCGC 0.870186 -68 GCGGAATCTGTCCTGTTACTAA 6 277 0 GCGGATCTGC 0.969812 -12 AGGCAGTCTTGCGGAATCAGCAAACGAGCAGG 7 42 0 GCGGATCAGA 0.897503 -98 ACGCCCACGCGCGGAAAGCGACGCGGACGCTG 8 29 0 GCGGAAGCGC 0.98878 -42 CAGCGCGATGAGTCACGCCAACGC 8 57 0 GCGCATGAGC 0.938242 -14 AATCCCGGCAGCGGATAGCGTCAAGCCTGGCT 9 65 1 GCGGTAGCGC 0.904142 -120 ATCCCAGAAAGCCGGAACAGCCTCTGATTTGT 11 159 0 GCCGAACAGC 0.943222 -135 ATCTTTATAAGTGGTAAGCGACT 13 86 1 GTGGAAGCGC 0.82406 -13 ATCGACAACGGCGGCAACAGGCGAAAGGTTAA 14 80 0 GCGGAACAGC 0.980734 -205 **** ***** * Masking position 10 Map Score: 16.4601 Number of sites scoring better than the average of aligned sites = 2061 Number in coding regions = 1539 Number in noncoding regions = 522 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 ATGCAAATAGTTATCAATAATATTATCAATATATTT 2 132 0 TTTCATATTT 0.978334 -189 TTAATAATGATTATCATTTATATTTTCGGTCGCTAA 5 38 1 TTTCATATTT 0.978334 -337 TCAATAATGCTTCTCATTTTCATTGTAACCACAACC 5 140 0 TTTCATATTT 0.978334 -235 GTAGCAATTATTTTGATTGGCATTATCTATTAATAC 6 41 0 TTTGATATTT 0.815093 -248 CTGTGCCACGTTTTTATTAACAATATTTGCCAGGGA 6 150 1 TTTTATAATT 0.760113 -139 CGAGAGGGCTTTTTCAATTCCATTTCCCTGACAAAT 11 43 1 TTTCATATTC 0.843147 -251 ACGATAACAATTATCAATCCAAATGTTAAATTTTAT 11 88 0 TTTCATAATT 0.935988 -206 TTGATAATTGTTATCGTTTGCATTATCGTTACGCCG 11 107 1 TTTCGTATTT 0.851335 -187 TATAAATATATAATCAATTTTATTTTTAAACCAGTT 13 46 0 TATCATATTT 0.912624 -53 ACGGCATTGATAATCATTTTCAATATCATTTAATTA 14 194 1 TATCATAATT 0.771804 -91 AATTTTCCTTCCTATTATGCACAAAATG 15 11 0 TTTCCTATTT 0.851335 -18 TTGAAATTCATTCTCAATTATATTCTCAAAGAAATT 17 121 1 TTTCATATTT 0.978334 -48 CCTCCGTCGGTTTTTAATTTTATTATTTGGTTTCAC 18 15 1 TTTTATATTT 0.907282 -86 ATCTCTCGCTTATTTAGTCCAATTTTTGCAGGTACA 19 138 1 TATTATATTT 0.693573 -163 ATTATTATTATTATTATTATTATTATTATCGCCATT 19 241 1 TTTTATATTT 0.907264 -60 TTCTGTAGCGTTATCAGGTTCATTGTATGGTCAATT 20 101 1 TTTCAGATTT 0.843147 -200 AGAGACTACATTTTCAATATAAATATGTCTTTATTC 20 224 0 TTTCATAATT 0.935988 -77 ** *** * *** * Masking position 12 Map Score: 16.7627 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 35 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 AAGGCTTTAATAATGATTATCATTTATATTTT 5 32 1 TATGATTATA 0.934329 -343 CGCAACTGATTAAAAACCCAGCGTC 8 4 1 AATGATTAAA 0.874662 -67 CGTCTTGCCTTATTGAATATGATTGCTATTTG 10 58 1 TATGAATATA 0.622847 -70 TTTTCTACTGAAATGATTATGACTTCA 10 111 1 AATGATTATA 0.951507 -17 TTAAAAATAAAATTGATTATATATTTATAATT 13 53 1 AATGATTATT 0.694508 -46 ATGATATTGAAAATGATTATCAATGCCGTACT 14 191 0 AATGATTATA 0.951507 -94 AAATTTAATCTATTGATTATAAGGCTTATCCA 16 54 0 TATGATTATA 0.934413 -43 GACAGCAAGTTATTGATTTTTAACTTAAAAAA 19 69 0 TATGATTTTA 0.83519 -232 AATTAAATTCAAATGATTATAAATAAACCAAT 19 207 1 AATGATTATA 0.951507 -94 TAAATAAACCAATTGATTATTATTATTATTAT 19 226 1 AATGATTATA 0.951303 -75 TCGATAGGTTTATTGATTTAAAACAAAATTTA 21 97 1 TATGATTTAA 0.643142 -152 ATAGCAAAAAAATTGATTTAGATCATTAAATG 21 157 0 AATGATTTAA 0.71273 -92 ** ******* * Masking position 6 Map Score: 11.1472 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 21 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 GTGCGCGTCGTTCATGCCGGATGCGGCGTG 1 35 1 TTCATGCCGG 0.81729 -131 GGATAAGGCGTTCACGCCGCATCCGGCATG 1 47 0 TTCACGCCGC 0.977903 -119 CTTCCTACTTTTAACGCCGTCACACCATAA 2 66 1 TTAACGCCGT 0.950661 -255 TTGCAATAGCGTAATGGCGCGCCGTGGGAA 2 168 1 GTAATGGCGC 0.684654 -153 GGGGGAAATCTCCACGGCGCTCACTTTACC 4 168 0 TCCACGGCGC 0.907941 -48 TAGACATGAGTCTACGCCGCATCACA 6 7 0 TCTACGCCGC 0.963397 -282 TAGACTCATGTCTACGCCGTATTAATAGAT 6 23 1 TCTACGCCGT 0.91825 -266 TTGCATTATCGTTACGCCGCAATCAAAAAA 11 124 1 GTTACGCCGC 0.915266 -170 AATCACCCACTTAATGCCGTGATTGCCAGT 14 114 0 TTAATGCCGT 0.910157 -171 AAAATGATTATCAATGCCGTACTTTTCGTA 14 184 0 TCAATGCCGT 0.904526 -101 CGGCCGATTGTTAATGCCGCGTAAGCAGTT 14 243 0 TTAATGCCGC 0.959577 -42 ********** Masking position 4 Map Score: 9.87456 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 926 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 TGAACGACGCGCACTTTGTCAACAATCTGA 1 19 0 GCACTTTGTC 0.902059 -147 TTAACCAACTGCACTGCGTGTCTTTCAGGA 2 211 1 GCACTGCGTG 0.883059 -110 TTTACATATTGCGCAATGCGCAGGGGCAAT 3 53 1 GCGCAATGCG 0.751149 -165 AAGCAAACGCGCACTATGTCAACTCTTGAG 5 79 1 GCACTATGTC 0.945008 -296 ATTCGCATAAGCGCAATGTGATGTCCTGCG 5 179 1 GCGCAATGTG 0.941275 -196 GACGGATTGTGCGCTTTGTCGAATTTGTCA 5 317 1 GCGCTTTGTC 0.945997 -58 TGTTGTACCTGTACAATGTCCCGGTGTTCA 6 94 1 GTACAATGTC 0.781759 -195 CTTTCATGTAGCACAGTGTGCAGTCCTGCT 7 18 1 GCACAGTGTG 0.943043 -122 CTTAATCCAGTGCAGTGTCTTAGCTGAAT 9 10 1 GTGCAGTGTC 0.930486 -175 GAACATGCTGGTGCTGTGTCGATTTCGTGA 12 23 1 GTGCTGTGTC 0.940851 -182 CATGCTGAAGGCGCTGCGTCACGAAATCGA 12 41 0 GCGCTGCGTC 0.961007 -164 ********** Masking position 4 Map Score: 8.59767 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 694 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 GATGACAAACGCAAAACTGCCTGATGCGCT 1 136 0 GCAAAACTGC 0.93923 -30 GGTGGCAGTCGAAACATGGCCCGGAATGGC 2 28 0 GAAACATGGC 0.70997 -293 TGCAATCAATGAAAAATTGCACAGTAAACA 2 101 0 GAAAAATTGC 0.859874 -220 GCAATTCGTGGCAAAAATGCAGGAATAAAA 2 299 1 GCAAAAATGC 0.887921 -22 GTCTGTGGCCGCAACAATGCGTCTTACCGG 3 86 1 GCAACAATGC 0.849647 -132 GGGAGAGGGGGCAGAACGGCGCAGGACATC 5 198 0 GCAGAACGGC 0.930293 -177 CAGCAAACGAGCAGGACTGCACACTGTGCT 7 27 0 GCAGGACTGC 0.923443 -113 TGCTGATTCCGCAAGACTGCCTGTTCTGCT 7 52 1 GCAAGACTGC 0.924052 -88 AAATGGGGGTGGAAAATTGCCCACGGATAA 7 92 0 GGAAAATTGC 0.906003 -48 CTTGCGTACGGCAGCATCGCGGTGGACTTA 11 209 0 GCAGCATCGC 0.766916 -85 ATTTCTGCCGGAAGGATTGCCAATCGTCTG 12 144 1 GAAGGATTGC 0.816644 -61 CACTTTATGTGGAAAAGTGCGGTTATTTTT 17 18 0 GGAAAAGTGC 0.748456 -151 ATTAAAAAGAGGAGAATGGCGATAATAATA 19 261 0 GGAGAATGGC 0.846359 -40 ********** Masking position 6 Map Score: 6.81253 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 784 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 TGTTTCGACTGCCACCAGCTCTCACTTCCTACT 2 42 1 GCACCAGCTC 0.868891 -279 TCAACACGACGCATCCCGCTACCGCGAAAACCT 2 245 0 GCTCCCGCCC 0.985655 -76 ATATGGCATTCAGTAATCCCTTCGATGA 3 6 1 GCTTCAGTTC 0.618055 -212 GCAGTCACAGGCGTCCTGCCAGCAGTGGCTGGA 3 141 1 GCTCCTGCGC 0.972533 -77 ACGCCAGTGGGCTTCCAGCCACTGCTGGCAGGA 3 154 0 GCTCCAGCCT 0.96264 -64 TGTGCCTCCTGCAACTGGGTAAAATT 3 202 0 GCTCCTGCCT 0.969457 -16 TTGAGGTAACGCAATCTGCAACTCGGGGTTGCA 5 104 1 GCATCTGCCT 0.875797 -271 ATGTCCTGCGCCGTTCTGCCCCCTCTCCCTTCC 5 199 1 CCTTCTGCCC 0.823316 -176 AAATCAGCTTCCTGTTATTAATAAGGTTA 5 356 0 GCTCCTGTTT 0.591096 -19 CGTCCGCGTCGCTTTCCGCGCGTGGGCGTTGGC 8 32 1 GCTTCCGCGT 0.909245 -39 CAGGCTTGACGCTATCCGCTGCCGGGATTTATT 9 61 0 GCATCCGCCC 0.93853 -124 GTGACGCAGCGCCTTCAGCATGCATTCGCCAGA 12 49 1 GCTTCAGCGC 0.929448 -156 ** ****** ** Masking position 6 Map Score: 7.19401 Number of sites scoring better than the average of aligned sites = 1569 Number in coding regions = 1441 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 TTCATTGATTGCAGAAATATATTGATAATA 2 118 1 GCAGAAATAT 0.902855 -203 TGGCAAAAATGCAGGAATAAAACA 2 307 1 GCAGGAATAA 0.736773 -14 AGCCTGGCTTGCAGAAAAACTCGGAATAAA 9 88 1 GCAGAAAAAC 0.951014 -97 AATCATTTCAGTAGAAAAACCAGGTCTCGA 10 99 0 GTAGAAAAAC 0.715763 -29 AATCCTTCCGGCAGAAATACACGGTTATAA 12 132 0 GCAGAAATAC 0.909659 -73 GATGTGACGCGACGAAAAATGATGAGGATA 14 16 0 GACGAAAAAT 0.617938 -269 GTATGGTTTTGCAGGAAAATGCCCGAGATG 14 151 0 GCAGGAAAAT 0.936474 -134 TGCATAATAGGAAGGAAAATT 15 18 1 GAAGGAAAAT 0.885723 -11 CTCCTTTAATGAAAAAAAATTTGCAAATTA 18 75 0 GAAAAAAAAT 0.566917 -26 AAATTGATCCGAAGAAAAAAGATTTAACTG 20 279 1 GAAGAAAAAA 0.775234 -22 GCAAATAATAGCAAAAAAATTGATTTAGAT 21 166 0 GCAAAAAAAT 0.713445 -83 TTTAACAATAGAAGGAATACATT 21 236 1 GAAGGAATAC 0.813266 -13 ********** Masking position 6 Map Score: 4.08366 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 707 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 10 TAACTATTTGCATTTGCAATAGCGTAATGG 2 155 1 CATTTGCAAT 0.935186 -166 CCATGCCCGACAGTTGCAATTCGTGGCAAA 2 284 1 CAGTTGCAAT 0.750567 -37 TAATGCTTCTCATTTTCATTGTAACCACAA 5 142 0 CATTTTCATT 0.85742 -233 CCAAAAATGACATTTTCACTGATCCTGATC 10 29 1 CATTTTCACT 0.942538 -99 AAATAGCAATCATATTCAATAAGGCAAGAC 10 59 0 CATATTCAAT 0.825228 -69 ACCGAGAGGGCTTTTTCAATTCCATTTCCC 11 41 1 CTTTTTCAAT 0.825228 -253 CATTGATAATCATTTTCAATATCATTTAAT 14 198 1 CATTTTCAAT 0.971062 -87 ATCATAAAAGCATTCTCACTTAAACTAC 16 9 0 CATTCTCACT 0.875821 -88 GATTGAAATTCATTCTCAATTATATTCTCA 17 119 1 CATTCTCAAT 0.935186 -50 TTAGAGACTACATTTTCAATATAAATATGT 20 232 0 CATTTTCAAT 0.971062 -69 ********** Masking position 8 Map Score: 9.63313 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 56 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 11 TGGGTTTTTTATTTGTTTGATTTATAGGTT 4 52 1 ATTTGTTTGA 0.917964 -164 ATTTGTAGCAATTATTTTGATTGGCATTAT 6 51 0 ATTATTTTGA 0.886334 -238 GGGTTAGGGTATTATGTTGACCATTGTGCC 9 139 0 ATTATGTTGA 0.770267 -46 TATTTGAGAAATTTCTTTGAGAATATAATT 17 136 0 ATTTCTTTGA 0.88482 -33 ACTAAATATAATTATTTTGACAGCAAGTTA 19 89 0 ATTATTTTGA 0.886334 -212 TAAGGTATAGATTTTTATGACTAAATATAA 19 108 0 ATTTTTATGA 0.616321 -193 GAAATCCAAAATTAGTTTGAATTTTACGCA 19 178 1 ATTAGTTTGA 0.884301 -123 CTAAAGAGTTATGTGTTTGAGTTGCGAAAA 21 60 0 ATGTGTTTGA 0.700025 -189 ATCTAAATCAATTTTTTTGCTATTATTTGC 21 166 1 ATTTTTTTGC 0.704212 -83 TTAAAAACAGATTTCGTTGAGGTTTTGGTC 21 211 0 ATTTCGTTGA 0.767612 -38 ********** Masking position 8 Map Score: 1.76248 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 84 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 TTGTAGGCCGGATAAGGCGTTCACGCCGCA 1 56 0 GATAAGGCGT 0.956804 -110 CTGTGGCCGCAACAATGCGTCTTACCGGCA 3 88 1 AACAATGCGT 0.685072 -130 CGAATCCATCAATAATGCTTCTCATTTTCA 5 154 0 AATAATGCTT 0.815916 -221 ATTATCTATTAATACGGCGTAGACATGAGT 6 26 0 AATACGGCGT 0.749654 -263 TTGCTCTTGAGATAATGCGTATCATTATAG 6 215 0 GATAATGCGT 0.93284 -74 CCTCTCGGTTGAGAGGGCTTAGCAAGGAAG 11 20 0 GAGAGGGCTT 0.848489 -274 CCTCTCAACCGAGAGGGCTTTTTCAATTCC 11 34 1 GAGAGGGCTT 0.848489 -260 TAGTTTAAGTGAGAATGCTTTTATGATATA 16 12 1 GAGAATGCTT 0.877762 -85 ATCTATTGATTATAAGGCTTATCCAAATTT 16 49 0 TATAAGGCTT 0.682418 -48 GCAAAGGCTAAATAATGCGTAAACCTTGAA 17 74 0 AATAATGCGT 0.876079 -95 ********** Masking position 4 Map Score: 1.79915 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 190 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 13 ACGGCGTTAAAAGTAGGAAGTGAGAGCTGG 2 56 0 AAGTAGGAAG 0.784718 -265 GAGAGGGCTTAGCAAGGAAGGGAGGAAAC 11 10 0 AGCAAGGAAG 0.887733 -284 TGTGCATAATAGGAAGGAAAATT 15 16 1 AGGAAGGAAA 0.921574 -13 ATTTAATATAAAAAAGGAAATAAAA 16 82 1 AAAAAGGAAA 0.902057 -15 TTTCTCAAATAACAAGGAAAAAAA 17 155 1 AACAAGGAAA 0.93441 -14 TAATTATTACAATAAGGAAAACAG 19 287 1 AATAAGGAAA 0.839306 -14 AATCTCTAGAAAGAAGGAAGTGCCTAAATT 20 133 0 AAGAAGGAAG 0.95314 -168 TCACTTTTTAAAAAAGGAAAAACATTTAAT 21 135 1 AAAAAGGAAA 0.902057 -114 ********** Masking position 5 Map Score: 3.66445 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 68 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 ATCAATAATATTATCAATATATTTCTGCAA 2 126 0 TTATCAATAT 0.75792 -195 ATGCAAATAGTTATCAATAATATTATCAAT 2 138 0 TTATCAATAA 0.811661 -183 AATTATGGGTTTATAAATAATATTAAT 4 8 0 TTATAAATAA 0.839637 -208 GCCCTTAACCTTATTAATAACAGGAAGCTG 5 351 1 TTATTAATAA 0.471567 -24 CGCCCAGGGATTATAAGTAAAGCAGCCAAT 12 88 0 TTATAAGTAA 0.770813 -117 ACTAACTGGTTTAAAAATAAAATTGATTAT 13 43 1 TTAAAAATAA 0.695286 -56 TAAAGATTAATTATAAATATATAATCAATT 13 63 0 TTATAAATAT 0.822115 -36 ATTCAAATGATTATAAATAAACCAATTGAT 19 213 1 TTATAAATAA 0.839637 -88 ********** Masking position 6 Map Score: 1.26784 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 47 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 TGCCACCAGCTCTCACTTCCTACTTTTAAC 2 51 1 TCTCACTTCC 0.806658 -270 CCCCTATTGGACTCATTTTCAGGTTATACC 4 194 1 ACTCATTTTC 0.695842 -22 CAATAATGCTTCTCATTTTCATTGTAACCA 5 145 0 TCTCATTTTC 0.891658 -230 GCAAATTCTGTCACTTCTTCTAATGAAGTG 6 241 1 TCACTTCTTC 0.64872 -48 ACGCCAAAAATGACATTTTCACTGATCCTG 10 26 1 TGACATTTTC 0.847813 -102 GGGTTATCGCTCACATCTTCTTCACGTCCC 11 239 0 TCACATCTTC 0.929201 -55 CACGGTTATAAGACACCTTCATGATCGCCC 12 113 0 AGACACCTTC 0.63746 -92 TTTCGTCGCGTCACATCTCCGACGAGATGA 14 29 1 TCACATCTCC 0.903332 -256 TTTATTCTTCTGTCATCTCCTTAGTATAAT 20 201 0 TGTCATCTCC 0.863488 -100 ATTAGAATACTGTCACTTTCTATTTTCCCT 21 19 0 TGTCACTTTC 0.79865 -230 ********** Masking position 8 Map Score: 1.45128 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 216 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775