AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ityrR_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 aroP 300 aromatic amino acid transport protein #2 aroL 182 shikimate kinase II #3 yaiA 49 orf, hypothetical protein #4 aroM 257 protein of aro operon, regulated by aroR #5 aroG 300 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, phenylalanine repressible) #6 tyrR 147 transcriptional regulation of aroF, aroG, tyrA and aromatic amino acid transport #7 tyrP 190 tyrosine-specific transport system #8 aroF 170 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tyrosine repressible) #9 mtr 153 tryptophan-specific transport protein #10 tyrB 252 tyrosine aminotransferase, tyrosine repressible #11 ydgF 171 similar to amino acid ABC transporter (permease) #12 gabP 300 gamma-aminobutyrate (GABA) permease #13 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #14 aapA 300 amino acid permease #15 ytnA 135 similar to proline permease #16 gerAA 300 gerAA #17 yvbW 300 similar to amino acid permease #18 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 AGAAACCGTTTGTAAAGCTCAGCCTCAACCCCTCTCAA 1 77 0 TGTAAATCAA 0.695939 -224 ACTTCTTTGATGTAAACAAATTAATACAACAAACGGAA 1 213 1 TGTAAATACA 0.961326 -88 AAGAATGAAGTGTAAATAATAAATTACAT 2 2 0 TGTAAATACA 0.680307 -181 CAATTTCGATTGTAAAGAAAAAATTCCACTTAAAGTGA 2 78 0 TGTAAATCCA 0.941338 -105 CGTCAGAATGTGTAAACGGGGTTTTACACTATGAACGG 5 213 0 TGTAAATACA 0.499721 -88 TTACATATGGTGTAAATATAAATGTACAATAAAAAGCA 7 82 0 TGTAAATACA 0.535588 -109 ACGGCTGCTTCGTCAAACCGACGTTACATATGGTGTAA 7 105 0 CGTCAATACA 0.81113 -86 AGGGAGTGTAAATTTATCTATACAGAGGTAAGGG 8 7 1 TGTAAATACA 0.673126 -164 ATCCATATTTCGTACATTTTTATTTACACAGGCAATTT 8 59 0 CGTACATACA 0.579984 -112 TAACACATAAAGTAAAGTTTTCAATCCATATTTCGTAC 8 82 0 AGTAAATCCA 0.744554 -89 GATCAACTATCGCAAACGAGCATAAACAGGATCGCCAT 8 142 1 CGCAAAAACA 0.767397 -29 GAACACAATCTGTAAAATAATATATACAGCCCCGATTT 9 26 1 TGTAAATACA 0.673126 -128 ACCACCTGCCCGTAAACCTGGAGAACCATCGC 10 231 1 CGTAAAACCA 0.824116 -22 TCTATCGAATTGTAAATATTACGCAAAATCACACAGCG 12 98 1 TGTAAAAAAA 0.506159 -203 TCGCTGAAAGCGCAAACAAAACACTACAAATTTGAAAT 12 166 1 CGCAAATACA 0.929901 -135 TAAATAGGTGTGCAAATTTTTTCATACAAAGGGGTATC 13 122 1 TGCAAATACA 0.941324 -31 ****** **** Masking position 6 Map Score: 16.6287 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 55 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 TTGATCTGACGGAAGTCTTTTTGTAACAATTCAA 1 179 1 GAGCTTTTTT 0.978359 -122 CACGTCTGCTGCTACGCTTTTTGTCATTTGTAGC 4 159 1 GACCTTTTTT 0.970267 -99 CAATCGCTACGCTAGGCTTTTTTTGAGGAGGGAC 7 12 0 GAGCTTTTTT 0.978359 -179 TTTTACCATCGGGGCTTTTTTTCTGTCTTTTGTA 9 62 1 GGCTTTTTTT 0.855623 -92 TAACAACGCAGTCGCACTATTTTTCACTGGAGAG 9 122 1 GGCCTATTTT 0.905165 -32 GTGACGAAGGAACACTTTTTCTCTCATCCAAT 12 9 1 GACCTTTTTT 0.970267 -292 TGGACAATCTGACAGGCTAGTTTTAATCGGTAAC 14 97 0 GAGCTAGTTT 0.899856 -204 TACATGTCTTGTGGCTCTATTTTTCACTCGTGAT 14 167 0 GGCCTATTTT 0.905165 -134 TCGACTACTCGAAAGCCTTGTTGTCTG 15 4 0 GAGCTTGTTT 0.961939 -132 TCGAGTAGTCGAAAGCCTTGTTGTTATCCTTTTA 15 26 1 GAGCTTGTTT 0.961939 -110 ATTTCATGGAGTAAGTTTTTTTATGAAAGCGGAG 16 202 0 GAGTTTTTTT 0.908924 -99 GTAGGAGACGGCGGGCTTTTTTGTTTTTGAAAAC 17 256 1 GGGTTTTTTT 0.891423 -45 * ** ****** * Masking position 8 Map Score: 12.0961 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 62 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 CGTTCTTCCTTATTTCACGGGATGAACGTTAAGTA 3 25 0 TATTTGGGAA 0.564965 -25 ACGCTAGGCTTTTTTTGAGGAGGGACG 7 3 0 TTTTTGGAGA 0.984357 -188 GTCGCACTATTTTTCACTGGAGAGAAGCCCTC 9 132 1 TTTTCGGAGA 0.968418 -22 ATGGAGCCGCTTTTTTCGGGAAATAGTCCAAATCA 11 27 1 TTTTTGGAAA 0.869624 -145 CAATAAACAATTTTCAATGGAGGAACACATAAA 11 149 1 TTTTCGGAGA 0.968511 -23 TTTGATGGGATTTTTGGCGGAGCAAATAAATTGGA 12 37 0 TTTTTGGAGA 0.984353 -264 AATGATTGCATTTTAAAAGGAGGTAACTT 12 282 1 TTTTAGGAGA 0.918546 -19 ACTCATCTTTTTATTACTGGAGGAAAATAAAA 14 279 1 TTATTGGAGA 0.89834 -22 TAATGATATTTTTTTCTAGGGGAGAAGAAGC 15 115 1 TTTTTGGGGA 0.964252 -21 TGTGTTAGAGTATTTCATGGAGTAAGTTTTTTTAT 16 212 0 TATTTGGAGA 0.945113 -89 ***** **** * Masking position 4 Map Score: 7.78933 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 40 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 4 TACACATTCTGACGGAAGATATAGATTGGAAGT 5 237 1 GCGGAAAATA 0.966916 -64 AATTTTCAATGGAGGAACACATAAA 11 157 1 GAGGAAAATA 0.966308 -15 TGGGATTTTTGGCGGAGCAAATAAATTGGATGA 12 34 0 GCGGAGAATA 0.821734 -267 GAAAATTCGTGTAAGAAAATATACCAGCTTATT 12 201 0 GAAGAAAATA 0.87661 -100 ACAATAAAGGAAATGAAAAGATAAAGGGGTTTT 13 17 0 AATGAAAATA 0.78207 -136 TTTATTGTCCAGCGGAAAAAATATTTTGTCAAG 13 42 1 ACGGAAAATA 0.954861 -111 AAATTATTGCAACGGAATAAATAGGTGTGCAAA 13 105 1 ACGGAAAATA 0.954861 -48 ATACCCCTTTGTATGAAAAAATTTGCACACCTA 13 126 0 GATGAAAATT 0.614163 -27 TATAACATTTAAAAGAATAGATACTTTTATTTT 14 229 0 AAAGAAAATA 0.837191 -72 TTTTATTACTGGAGGAAAATAAAA 14 287 1 GAGGAAAAAA 0.753217 -14 TAGCTGGAAAACAAGAAGAAATTGAACAGCTCA 16 145 0 AAAGAAAATT 0.622766 -156 CATTTTTTTAACAGGAAAAGATAACCTCTACTA 16 253 1 AAGGAAAATA 0.954042 -48 GGTAAGACGGAACGGAATAGATTGAATATTCCC 17 107 1 ACGGAAAATT 0.871652 -194 * ***** * *** Masking position 6 Map Score: 7.85006 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 100 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TAATTGAATTAAAAATCACAAAATTGGTAAGT 1 19 0 AAAAATCAAA 0.83591 -282 TATACCAATAAATATTCAAGAATGAAGTGTAA 2 25 0 AATATTCAAA 0.943371 -158 TAATAATTAGAATATTAAACAATAACAATCCA 4 90 1 AATATTAAAA 0.742255 -168 AGAATCTTGAAATAATTAACAAACAAAGGAGT 5 106 1 AATAATTAAA 0.598976 -195 TAAAATCCTAAAAATTCAATAAGTTGATGTTC 10 70 1 AAAATTCAAA 0.907596 -183 TTAGTGTTATAATAATCATTAAAAATAGATTG 11 111 1 AATAATCAAA 0.896267 -61 CAATTATCATAATATTCAGTAATGATTGCATT 12 262 1 AATATTCAAA 0.943371 -39 AAATAGTTTTAAAATTTAAAAATAAAAGTATC 14 211 1 AAAATTTAAA 0.629347 -90 ATCCGTACGGAATATTCAGAAAAATGATATAA 15 86 1 AATATTCAAA 0.943371 -50 ATTCTTCATGAAGAATCAACAAGAGTGGTACC 17 181 1 AAGAATCAAA 0.696497 -120 TTTCGAGCGAAAATTTCAGCAAGTGCAAAATT 18 146 1 AAATTTCAAA 0.532198 -95 AAATAGAAGCAATATTAAGAAAATAATTGAGG 18 207 1 AATATTAAAA 0.742255 -34 ******** ** Masking position 8 Map Score: 6.32592 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 122 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 GAATAATGGTATGCGGCAGCGAATGCACCC 1 149 0 ATGCGGCAGC 0.861477 -152 TATGAAAAATGTGACGCAGATCCCTTGTAG 4 47 0 GTGACGCAGA 0.817303 -211 ATGACAAAAAGCGTAGCAGCAGACGTGCAC 4 156 0 GCGTAGCAGC 0.914701 -102 AGGTTATGAAACGCAGCAGAGAATCTTGAA 5 87 1 ACGCAGCAGA 0.94637 -214 CGTCGGTTTGACGAAGCAGCCGTTATGCCT 7 120 1 ACGAAGCAGC 0.954641 -71 GCCTTAACCTGCGCCGCAGATATCACTCAT 7 146 1 GCGCCGCAGA 0.983081 -45 TAAGGCATTCACGCCGCATCCGGCACAGAC 10 31 0 ACGCCGCATC 0.931051 -222 GCGTCGCACCACCCCGCAGCTCTCTGTTCT 17 45 0 ACCCCGCAGC 0.952409 -256 GCGGGGTGGTGCGACGCAGCCTGATTCTTC 17 58 1 GCGACGCAGC 0.985677 -243 ********** Masking position 8 Map Score: 6.49398 Number of sites scoring better than the average of aligned sites = 1351 Number in coding regions = 1290 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 TCCACCTTACTTTTCTTTCGTCGTTAATTACC 4 230 0 TTTTCTCGTC 0.963295 -28 AAGTGCCCGTTTTTCCGTCTTTGTGTCAATGA 6 47 1 TTTTCTCTTT 0.849392 -101 TCGGGGCTTTTTTTCTGTCTTTTGTACTCGTG 9 70 1 TTTTCTCTTT 0.849392 -84 AATAAGTTGATGTTCTTTCATGCTCTTATAAA 10 87 1 TGTTCTCATG 0.861328 -166 AGAGAAAAAGTGTTCCTTCGTCAC 12 3 0 TGTTCTCGTC 0.927685 -298 AAGGAACACTTTTTCTCTCATCCAATTTATTT 12 17 1 TTTTCTCATC 0.943472 -284 GTGGCTCTATTTTTCACTCGTGATTCTACCTG 14 159 0 TTTTCTCGTG 0.952338 -142 ATCCTTTTATTTCTCCATCATCATTGATTTAC 15 51 1 TTCTCTCATC 0.795903 -85 TTTTTCGATCTTGGCAGATTTTA 16 2 1 TTTTCTCTTG 0.927045 -299 ***** ***** Masking position 8 Map Score: 3.18731 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 92 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GCAGCGAATGCACCCGCTTTATGCATGGTT 1 134 0 CACCCGCTTT 0.980751 -167 ATTCTCATGACACCGGCTTTCGCCGCATTG 2 140 1 CACCGGCTTT 0.939464 -43 ATCCGGTCAGCACCCGATATTGCA 6 5 0 CACCCGATAT 0.912643 -143 ATCGGGTGCTGACCGGATATCTTTACGCCG 6 17 1 GACCGGATAT 0.719809 -131 TTTGACGAAGCAGCCGTTATGCCTTAACCT 7 126 1 CAGCCGTTAT 0.717624 -65 AATATATACAGCCCCGATTTTTACCATCGG 9 44 1 GCCCCGATTT 0.887124 -110 TCCATTTAGGGAGCCGCTTTT 11 2 0 GAGCCGCTTT 0.961952 -170 TCCCTAAATGGAGCCGCTTTTTTCGGGAAA 11 20 1 GAGCCGCTTT 0.961952 -152 CACTTCGTATCCTCCGCTTTCATAAAAAAA 16 191 1 CCTCCGCTTT 0.793935 -110 ********** Masking position 8 Map Score: 2.90605 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 519 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 GTGAATGCAATACTTCCAATCTATATCTTCCGTCAG 5 245 0 TCTCTCTATT 0.968644 -56 CTTTCTTCTGTCCTGACGATCTTTATGAGTGATATC 7 164 0 TCTCTCTTTT 0.962958 -27 CATCGGGGCTTTTTTTCTGTCTTTTGTACTCGTGTA 9 68 1 TTTCTCTTTG 0.714969 -86 GATCTTCGCCTTCTTCCGGTTTATTGTGTTTTAACC 10 198 1 TCTCTTTATG 0.910496 -55 ACACTAAAATTTCTATCTTTTTTACTAAAAAAGGAT 11 82 0 TCTCTTTTAT 0.634592 -90 ACACCAGTGCTTCTCGCATTCTATCGAATTGTAAAT 12 79 1 TCTCTCTATG 0.950856 -222 AAAGCCTTGTTGTTATCCTTTTATTTCTCCATCATC 15 37 1 TTTCTTTATT 0.714468 -99 TTTCTTTTACTGCTCCCAATCTATGTGT 17 3 0 TCTCTCTATT 0.968644 -298 CCTCTTCTACCTCTCCTTCTCGTTTTCAAA 17 281 0 TCTCTCCTTT 0.830382 -20 CATGTTATCCTGCTTTCCCTTTATATAAATGCAAGT 18 41 1 TCTCTTTATT 0.942002 -200 CTTTTGCATATCCTCTCCGTTTTTTTATAAAATAGA 18 178 1 TCTCTTTTTT 0.931824 -63 * ** * ***** * Masking position 10 Map Score: 3.76914 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 83 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 AACAATTCAAACTTCTTTGATGTAAACAAA 1 203 1 ACTTCTTTGA 0.927605 -98 TCTAACTGTAACTCCTTTGTTTGTTAATTA 5 118 0 ACTCCTTTGT 0.973025 -183 CTTCAGAAAACCCCTTTATCTTTTCATTT 13 10 1 ACCCCTTTAT 0.758947 -143 CCCGATACCCCTTTGTATGAAAAAAT 13 137 0 ACCCCTTTGT 0.960432 -16 TATACGCGGGAATCCTTTGAATATTTGTAT 16 48 1 AATCCTTTGA 0.859004 -253 GTCCTGCCGTACTCCTTTGATGTATAAGAG 16 87 1 ACTCCTTTGA 0.979153 -214 GCAGCCTGATTCTTCTTTGAACTCGCCCGG 17 73 1 TCTTCTTTGA 0.726782 -228 ********** Masking position 6 Map Score: 1.61514 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 63 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TTTCATAATTCATGTTTTTCTAATAATTAG 4 70 1 CATGTTTTTC 0.802092 -188 TAGGAGAGATCTCGTTTTTCGCGACAATCT 5 153 1 CTCGTTTTTC 0.852597 -148 CGCCGAAGTGCCCGTTTTTCCGTCTTTGTG 6 42 1 CCCGTTTTTC 0.850062 -106 ACCATCGGGGCTTTTTTTCTGTCTTTTGTA 9 66 1 CTTTTTTTCT 0.620476 -88 GACGAAGGAACACTTTTTCTCTCATCCAAT 12 13 1 CACTTTTTCT 0.605863 -288 AAAAACGAAACATTTTTTCCACACATTCGC 12 140 1 CATTTTTTCC 0.783167 -161 CCTATGTTACCACGTTTTCTTCTCTTGACA 13 68 0 CACGTTTTCT 0.874426 -85 AAATGACTTTCCTGTTTTACTCTGCTATTC 14 130 1 CCTGTTTTAC 0.659514 -171 TCAATTTCTTCTTGTTTTCCAGCTAGCCTT 16 153 1 CTTGTTTTCC 0.952736 -148 ACCTCTCCTTCTCGTTTTCAAAAACAAAAA 17 273 0 CTCGTTTTCA 0.722804 -28 TGAATTCCCCCTTGTTTTCTGTTTCAACAT 18 14 1 CTTGTTTTCT 0.881037 -227 AACATGTTATCCTGCTTTCCCTTTATATAA 18 39 1 CCTGCTTTCC 0.772306 -202 ********** Masking position 6 Map Score: 3.40655 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 548 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 12 ACTTACACACGCATCACTGCGTAGATCAAA 1 257 1 GCATCACTGC 0.880727 -44 GGGATTCTGAGTGCCACTACAAGGGATCTG 4 31 1 GTGCCACTAC 0.89938 -227 ATTATGCCGTGCACGTCTGCTGCTACGCTT 4 148 1 GCACGTCTGC 0.760367 -110 CAAGTGTGAAGCACCACTGCTGACACTTAC 4 197 0 GCACCACTGC 0.987719 -61 TGAAGACTTTGCGCCAGCGCAGGACTGAAT 7 53 1 GCGCCAGCGC 0.933447 -138 GCATTGCACTGTACCAGTACACGAGTACAA 9 91 0 GTACCAGTAC 0.78326 -63 GTGAAAAATAGTGCGACTGCGTTGTTATGC 9 119 0 GTGCGACTGC 0.912628 -35 AAACCCAAGGACACCAGTGCTTCTCGCATT 12 69 1 ACACCAGTGC 0.765783 -232 AGCCTTACCTGTGCCACTTCGTATCCTCCG 16 177 1 GTGCCACTTC 0.835259 -124 AGGCTGCGTCGCACCACCCCGCAGCTCTCT 17 50 0 GCACCACCCC 0.874804 -251 ********** Masking position 10 Map Score: 2.0066 Number of sites scoring better than the average of aligned sites = 1587 Number in coding regions = 1525 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 13 TAAGTTTGCAATTCCGTTTGTTGTATTAATTTGT 1 228 0 ATTCTTTTGT 0.93212 -73 TCAAACCGACGTTACATATGGTGTAAATATAAAT 7 97 0 GTTCTTGTGT 0.846457 -94 TTCAATCCATATTTCGTACATTTTTATTTACACA 8 67 0 ATTCTCTTTT 0.715963 -104 CCTTCTTCCGGTTTATTGTGTTTTAACCACCTGC 10 206 1 GTTATTTTTT 0.549638 -47 TGGAAAAAATGTTTCGTTTTTTATTCGCTGTGTG 12 127 0 GTTCTTTTAT 0.752973 -174 TTATCTTTTCATTTCCTTTATTGTCCAGCGGAAA 13 26 1 ATTCTTTTGT 0.93212 -127 TTTAAGTGCTGTTACATGTCTTGTGGCTCTATTT 14 179 0 GTTCTTTTGT 0.940853 -122 TAAAAGAATAGATACTTTTATTTTTAAATTTTAA 14 219 0 GATCTTTTTT 0.792141 -82 GAGCTGTTCAATTTCTTCTTGTTTTCCAGCTAGC 16 146 1 ATTCTTGTTT 0.835764 -155 TAGATTGAATATTCCCTATGTTTTAACGGCTAAC 17 124 1 ATTCTTTTTT 0.936234 -177 CCAAATCAAGAATTCGTGTGTTTTCTACAATTTT 18 83 1 AATCTTTTTT 0.766892 -158 TTTTCTTAATATTGCTTCTATTTTATAAAAAAAC 18 196 0 ATTCTTTTTT 0.936238 -45 *** * * * **** Masking position 7 Map Score: 4.35902 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 52 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 CATAAAGCGGGTGCATTCGCTGCCGCATAC 1 141 1 GTGCATTCGC 0.883549 -160 GTGTGTAAGTTTGCAATTCCGTTTGTTGTA 1 237 0 TTGCAATTCC 0.690433 -64 AATTGCAAACTTACACACGCATCACTGCGT 1 249 1 TTACACACGC 0.756757 -52 TCTTCCAACAGTGCATTTGCAGGTGAATAT 5 32 1 GTGCATTTGC 0.710127 -269 ATTGGAAGTATTGCATTCACTAAGATAAGT 5 261 1 TTGCATTCAC 0.788041 -40 ATAGATAAATTTACACTCCCT 8 2 0 TTACACTCCC 0.870885 -169 TTGCAATAATTTGCACAACCCTATGTTACC 13 87 0 TTGCACAACC 0.769559 -66 ATGAAAAAATTTGCACACCTATTTATTCCG 13 117 0 TTGCACACCT 0.691709 -36 ATTTGTATAATTGCATACCCACTATGATTG 14 66 0 TTGCATACCC 0.955123 -235 TGATTCTTCTTTGAACTCGCCCGGGAGTGG 17 79 1 TTGAACTCGC 0.829606 -222 ATTTGAATTCCCCCTTGTTTTC 18 3 1 TTGAATTCCC 0.808172 -238 CAAAAGAATTTTGCACTTGCTGAAATTTTC 18 154 0 TTGCACTTGC 0.925438 -87 CAAAATTCTTTTGCATATCCTCTCCGTTTT 18 171 1 TTGCATATCC 0.872849 -70 ********** Masking position 5 Map Score: 3.75909 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 580 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 15 TGGAATCTTTACATTATGCCGTGCACGTCTG 4 136 1 ACATTATGCG 0.813064 -122 GTTTTTCGCGACAATCTGGCGTTTTTCTTGC 5 166 1 ACAATCTGCG 0.97761 -135 CCCCGTTTACACATTCTGACGGAAGATATAG 5 230 1 ACATTCTGCG 0.971041 -71 AACAGCGAACACAATCTGTAAAATAATATAT 9 20 1 ACAATCTGAA 0.848335 -134 AGTCATTTGGACAATCTGACAGGCTAGTTTT 14 107 0 ACAATCTGCA 0.973087 -194 AATTAAAATTAAAATCTGCCAAGATCGAAAA 16 12 0 AAAATCTGCA 0.824249 -289 AGGTGCAAAAACATTCTGATATTTCGAGCGA 18 125 1 ACATTCTGTA 0.811168 -116 ******** ** Masking position 3 Map Score: 0.836423 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 111 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911