AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 gltJ 169 glutamate/aspartate transport system permease #2 ybeJ 249 putative periplasmic binding transport protein #3 trs5_3 300 IS5 transposase #4 artP 217 ATP-binding component of 3rd arginine transport system #5 ybjP 125 putative enzyme #6 fliY 87 putative periplasmic binding transport protein #7 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #8 BIME89 108 BIME #9 fliC 265 flagellar biosynthesis; flagellin, filament structural protein #10 hisQ 89 histidine transport system permease protein #11 hisJ 220 histidine-binding periplasmic protein of high-affinity histidine transport system #12 argT 265 lysine-, arginine-, ornithine-binding periplasmic protein #13 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #14 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #15 cvpA 165 membrane protein required for colicin V production #16 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #17 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #18 dedA 82 orf, hypothetical protein #19 usg 65 putative PTS system enzyme II A component #20 pdxB 98 erythronate-4-phosphate dehyrogenase #21 yhdW 300 putative periplasmic binding transport protein #22 yhdX 49 putative transport system permease protein #23 yhdY 98 putative transport system permease protein #24 livH 47 high-affinity branched-chain amino acid transport system; membrane component #25 livK 300 high-affinity leucine-specific transport system; periplasmic binding protein #26 HI1079 67 amino acid ABC transporter, permease protein #27 HI1080 300 amino acid ABC transporter, periplasmic-binding protein Motif number 1 ACTCGTATACTGGCAGTCTGATAGCTATTG 4 194 0 TGGCAGTCTG 0.864167 -24 AATAATAGCGTATCAGTCTGATAATGCTTT 5 46 0 TATCAGTCTG 0.928623 -80 AATGTTGTTATGTCTGTTTGCAGTGTAGAG 6 58 0 TGTCTGTTTG 0.619234 -30 GCGGGGTTTTTTTCTGCCTGGAATTTACCT 7 54 1 TTTCTGCCTG 0.908577 -125 CAATTCAACTTGTAGGCCTGATAAGCGCAG 8 64 0 TGTAGGCCTG 0.711803 -45 ATACCGGGGTTATCGGTCTGAATTGCGCAA 9 45 1 TATCGGTCTG 0.937776 -221 TCGCTGAGGGTGCCGGTCTGGCACCCTGAC 13 16 1 TGCCGGTCTG 0.969827 -79 AAAGTCTGCCTGCAAGTCTGACAGGGCAAC 13 70 1 TGCAAGTCTG 0.708153 -25 TTTTACGCCCTGTCATCCTGTTCGGGGCGC 15 133 0 TGTCATCCTG 0.532446 -33 TTATCCAAAGTTTCGGGCTGTTATGTTTTA 17 39 1 TTTCGGGCTG 0.910344 -117 TAGGGACCTTTCTGTCTGAACCTGGTTC 17 138 0 TTTCTGTCTG 0.942666 -18 GCTCGGAACATTTCAGGCTGTAGCCAACGT 18 21 1 TTTCAGGCTG 0.897597 -62 ACTCGTCATCTTTCAGGCTGTAACTACGTT 18 46 0 TTTCAGGCTG 0.897597 -37 TTTTTATTATTTCCTGTCTACACTCAGCTT 21 50 1 TTCCTGTCTA 0.497249 -251 AAACGTCTTTTACCTGTCTGTGGCCATCCT 21 130 0 TACCTGTCTG 0.88539 -171 CCATGACCATGTCGGTCTATCTGATTATC 23 10 1 TGTCGGTCTA 0.803387 -89 TCTATCTGATTATCAGCCTGACTATCTCGC 23 26 1 TATCAGCCTG 0.887184 -73 GCACTGTTTTTGCCTGTCTGATTAAGGGGT 25 203 0 TGCCTGTCTG 0.959922 -98 ********** Masking position 9 Map Score: 16.0651 Number of sites scoring better than the average of aligned sites = 1696 Number in coding regions = 1574 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 CCCTAACAGGCACAACACTGCACAATAAAGT 2 155 1 CACAACCTGC 0.893806 -95 TGTTTTTGCGAGATGCGCCGCACCATTCCGA 3 197 0 AGATGCCCGC 0.677319 -104 TAAACACAAAAACAACTCCGCTACATCTTAT 6 17 0 AACAACCCGC 0.929106 -71 CCAGGCAGAAAAAAACCCCGCCGGTGGCGGG 7 44 0 AAAAACCCGC 0.964829 -135 TCGTCCGATTAAAAACCCTGCAGAAACGGAT 7 119 1 AAAAACCTGC 0.95871 -60 GATAAACAGCCCTGCGTTATATGAG 7 164 0 AACAGCCTGC 0.779722 -15 CATCGGTGAAAGAAAGCCCGCTCCCTTCGGG 10 15 1 AGAAAGCCGC 0.77512 -75 CATCAAGGCAAAATATCCCGCCCCGTTAGAC 11 126 0 AAATATCCGC 0.690314 -95 GCCATTCAATCGAAACGCTGCGATTCAACCG 12 76 1 CGAAACCTGC 0.954162 -190 CAACTCCCGCCGAAATCCTGCAAAGTCTGCC 13 49 1 CGAAATCTGC 0.892869 -46 GCGCATCAATAAAAATGGCGCTGAAAAAATA 15 58 0 AAAAATGCGC 0.83752 -108 AAAGTAACTCCGCGGTTCGACCA 17 3 1 AGTAACCCGC 0.747927 -153 AACAGCGCCCCGCAATGGTGCGAAAATGAAA 21 21 0 CGCAATGTGC 0.651389 -280 AGGAAATAATAAAAACAGCGCCCCGCAATGG 21 34 0 AAAAACGCGC 0.927923 -267 TATTGCGACGCGAAATCGTGCGCAAAAGCTG 21 79 1 CGAAATGTGC 0.796386 -222 TCTTATAAGCAAAAGTAGTGCCAGCTTTTGC 21 100 0 AAAAGTGTGC 0.58198 -201 GCTATTATCACAAAATACTGCGCTAACCCCT 25 178 1 CAAAATCTGC 0.87584 -123 TCAGACAGGCAAAAACAGTGCAGTATAAAAA 25 212 1 AAAAACGTGC 0.915942 -89 TTAGATACGCTGCTTTTCTATTA 27 3 1 AGATACCTGC 0.847731 -298 ****** **** Masking position 10 Map Score: 16.2213 Number of sites scoring better than the average of aligned sites = 1558 Number in coding regions = 1413 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 CTGCTACCCTCTTTTTTCTGGAGTAGATTT 1 150 1 CTTTTTTCTG 0.980442 -20 ACCGGCGGGGTTTTTTTCTGCCTGGAATTT 7 50 1 TTTTTTTCTG 0.962286 -129 CCGAAATACTCTTTTCTCTGCCCCTTATTC 9 107 0 CTTTTCTCTG 0.921339 -159 TCCTCGACATTTTGTTTCTGCCATTCAATC 12 57 1 TTTGTTTCTG 0.856354 -209 GTGAAAATGGCTTTTTTATGTTGTGTATTG 12 233 0 CTTTTTTATG 0.830925 -33 GCAAACGTTTTCTTTTTCTGTTAGAATGCG 15 106 1 TCTTTTTCTG 0.856354 -60 AAAACCTTTTTTCTGAACGGCATCA 21 286 0 CTTTTTTCTG 0.980442 -15 GACAAAGGCACTTTTTTCTGTTTATCTATC 25 93 1 CTTTTTTCTG 0.980442 -208 AGAAAGGCATTTTTTTACTGAAATTTTATA 27 84 1 TTTTTTACTG 0.800888 -217 ********** Masking position 5 Map Score: 10.145 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 53 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 GCCGGTGGCGGGGAAGCACGTTGCTGACAAATTGC 7 21 0 GGAGCGTGCT 0.918071 -158 CCTGATAAGCGCAGCGCATCAGGCAATTTGGCGTT 8 43 0 GCGGCCGGCA 0.785369 -66 CATGGTGCACGCCAGGTTTGTTGCACTATCGTGGT 11 48 1 GCAGTGTGCA 0.867259 -173 GGCGGGAGTTGCAAGTCAGGGTGCCAGACCGGCAC 13 25 0 GCATCGTGCC 0.976623 -70 ACGCATTGCCCGATGCCGCAAAGGCAT 15 3 1 GCTGCGTGCC 0.986948 -163 TAGCAAAAGGGCAGAGCCAGTGGCCCTGCCCTTAT 16 17 0 GCGGCGGGCC 0.987525 -53 TTTATCTTTGGGGACGCATAATGCCATTTTTGCCC 17 94 0 GGAGCATGCC 0.917223 -62 TCCAGAAATAGCAAAGCTCCCTGCCAATGTTACAG 19 31 0 GCAGCCTGCC 0.992085 -35 GATGATGATAGCCACACTGGCTGCCGCCAGCGTGC 21 212 1 GCAACGTGCC 0.975787 -89 CGCTGCTGGCGCGACGCTTGATGCCGTTCAGAAAA 21 268 1 GCAGCGTGCC 0.997916 -33 CGCCGCCGTAGCGACGCTCGTTACCTCACACCGAC 22 11 0 GCAGCGTACC 0.97422 -39 ** * ** * **** Masking position 14 Map Score: 9.26378 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 612 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 ATAGGCTGATTCAAGGCATTTACGGGAGAA 2 52 1 TCAAGGCATT 0.854684 -198 GGATGCGGCATCAGTGCATTATCCGGATAA 3 30 1 TCAGTGCATT 0.540821 -271 GCCTTGTATAACAAAGCAATAGATGTGCCA 3 81 0 ACAAAGCAAT 0.797445 -220 GCTTTGTTATACAAGGCAAACCCTGAAACA 3 94 1 ACAAGGCAAA 0.922758 -207 AAATTGACCATCAAGGCAAAATATCCCGCC 11 135 0 TCAAGGCAAA 0.896672 -86 TTGCCCTGAAACAGGGCAACAGCGGAG 12 8 0 ACAGGGCAAC 0.956064 -258 TTGCCCTGTTTCAGGGCAATTTTGCAACCG 12 19 1 TCAGGGCAAT 0.950405 -247 ATCTTCAACTTCAGGACAATAATGCAACGT 12 118 1 TCAGGACAAT 0.57895 -148 TGCAAGTCTGACAGGGCAACTATTT 13 80 1 ACAGGGCAAC 0.956064 -15 GATGACGAGTACAAGGCATAGGCAAAT 18 66 1 ACAAGGCATA 0.809427 -17 ACACATAAAAACAAAGCAACACAACATCAC 25 263 1 ACAAAGCAAC 0.764559 -38 ACGTTTCTAAACAATGCAATCAATCTACTC 27 115 0 ACAATGCAAT 0.797445 -186 ********** Masking position 3 Map Score: 8.59761 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 391 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GGAATTTCCGCCCCTGGTTCTTGTAA 1 7 0 CCCCTGGTTC 0.947829 -163 CGGTCTAAATAGGCTGATTCAAGGCATTTA 2 44 1 AGGCTGATTC 0.644924 -206 AAATTCTTCTCGGCTGACTCAGTCATTTCA 2 106 0 CGGCTGACTC 0.887957 -144 AAGAATTTCCCCGCTTATTCGCACCTTCCC 2 128 1 CCGCTTATTC 0.927185 -122 TTTAGTGCTACCGCTGGATTACTGTGGTGC 3 143 0 CCGCTGGATT 0.757409 -158 CGCCTTGATCAACCAATAAA 4 1 1 CGCCTTGATC 0.79266 -217 CCCCAAATAACCCCTCATTTCACCCACTAA 7 89 1 CCCCTCATTT 0.677595 -90 CTTTTCTCTGCCCCTTATTCCCGCTATTAA 9 97 0 CCCCTTATTC 0.927185 -169 TTCCACCCGTCGGCTCAATCGCCGTCAACC 9 203 0 CGGCTCAATC 0.873212 -63 GCAGGTATAGCGGTTGAATCGCAGCGTTTC 12 87 0 CGGTTGAATC 0.610566 -179 GGTATCCGCTGATTCGTTACGGTGA 16 55 0 CCGCTGATTC 0.975296 -15 GCGCCAGCAGCGCCTGATTTGCAACGGCAA 21 250 0 CGCCTGATTT 0.855916 -51 CCAGCATAATCCCCTGAATGATAGTGAATT 25 33 1 CCCCTGAATG 0.799184 -268 ACTGCGCTAACCCCTTAATCAGACAGGCAA 25 194 1 CCCCTTAATC 0.916608 -107 ********** Masking position 5 Map Score: 7.29167 Number of sites scoring better than the average of aligned sites = 1110 Number in coding regions = 1005 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 AATAAACATAGCACAAAATAACGGGGGCGGT 4 86 0 GCACAAAAAA 0.869891 -132 TTGTTTGTAAACACAAAAACAACTCCGCTAC 6 24 0 ACACAAAACA 0.946264 -64 CTGCAAACAGACATAACAACATTCGGGGTGA 6 65 1 ACATAACACA 0.918956 -23 GCCTGCAAACACACAACACAATACACAACAT 12 215 1 ACACAACAAA 0.964123 -51 ACAACACAATACACAACATAAAAAAGCCATT 12 227 1 ACACAACAAA 0.964123 -39 GCCTTTGTCAGCATAAAATAACGGCACAAAG 25 71 0 GCATAAAAAA 0.68664 -230 ATTTGTTAACACATAAAAACAAAGCAACACA 25 255 1 ACATAAAACA 0.852319 -46 AAACAAAGCAACACAACATCACGAATGGGGA 25 271 1 ACACAACACA 0.971908 -30 GCTTAGACAAACACAACACAAGGAAGAAAAA 27 280 1 ACACAACAAA 0.964123 -21 ******** ** Masking position 6 Map Score: 7.67918 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 50 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 AACAATCTTCGAGGGTAGCAGTTAACGCTGC 1 123 1 GAGGTAGCAG 0.968602 -47 CCAGAAAAAAGAGGGTAGCAGCGTTAACTGC 1 140 0 GAGGTAGCAG 0.968602 -30 TAAAGTTGCAGACGATAACAACACAAACACT 2 180 1 GAGATAACAA 0.913253 -70 TTTTACGACAGACGATAACAGGGTTGACGGC 9 182 1 GAGATAACAG 0.953883 -84 TCCTGAAGTTGAAGATAGCAGGTATAGCGGT 12 103 0 GAGATAGCAG 0.984402 -163 ATGCCATCTTGACGACAACAGTAACATTCAA 12 167 0 GAGACAACAG 0.828552 -99 TCGTTACGGTGAGAATAGCAAAAGGGCAGAG 16 36 0 GAAATAGCAA 0.758983 -34 TTGCTTATAAGAGGATGGCCACAGACAGGTA 21 119 1 GAGATGGCCA 0.785801 -182 TGAAAAAGATGATGATAGCCACACTGGCTGC 21 205 1 GAGATAGCCA 0.940125 -96 ** ******** Masking position 2 Map Score: 5.18425 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 198 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 ACAAGAACCAGGGGCGGAAATTCCAGCCCTCT 1 13 1 GGGCGGAATT 0.909581 -157 AAACCCTGCAGAAACGGATAATCATGCCGATA 7 131 1 GAACGGTAAT 0.526256 -48 GAGACTGACGGCAACGCCAAATTGCCTGATGC 8 31 1 GAACGCAAAT 0.748942 -78 TTCGTTTTACGTGTCGAAAGATAAAAGGAAAT 9 14 0 GGTCGAAGAT 0.534777 -252 AGGGAGACAAGAGGCGGTAATTCACCACACAC 10 53 1 GGGCGGAATT 0.909581 -37 TACGTCTAACGGGGCGGGATATTTTGCCTTGA 11 123 1 GGGCGGATAT 0.703628 -98 TTTATCTTTGGGGACGCATAATGCCATTTTTG 17 97 0 GGACGCTAAT 0.913151 -59 TTACCTGTATGAGACGAGAGTTAACCGGACAA 20 70 0 GGACGAAGTT 0.829661 -29 GTGGCGCATGTTTCATTTTCGC 21 1 1 GGGCGCTGTT 0.938422 -300 TCAGCTTATTGCGACGCGAAATCGTGCGCAAA 21 73 1 GGACGCAAAT 0.942708 -228 TGCTTCCTGTGAGGCGAAAATTATCGTTATAG 21 170 0 GGGCGAAATT 0.829661 -131 CGTCGCGCCAGCAGCGCCTGATTTGCAACGGC 21 252 0 GAGCGCTGAT 0.784416 -49 CGCTGCTGGCGCGACGCTTGATGCCGTTCAGA 21 268 1 GGACGCTGAT 0.935594 -33 CGCCGCCGTAGCGACGCTCGTTACCTCACACC 22 14 0 GGACGCCGTT 0.801319 -36 * ***** **** Masking position 12 Map Score: 6.08393 Number of sites scoring better than the average of aligned sites = 1184 Number in coding regions = 1110 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 10 AAATGTCGGCATTCCTCACGAAATGCCGGAC 4 42 0 ATTCTCACGA 0.854321 -176 GCCGACATTTATGCTCGCCGACCACCGCCCC 4 63 1 ATGCCGCCGA 0.984603 -155 ATTCACCCCGAATGTTGTTAT 6 77 0 ATTCCCCCGA 0.984983 -11 AGAAACGGATAATCATGCCGATAACTCATAT 7 140 1 AATCTGCCGA 0.765903 -39 ATGCATTTCAATGCACCACGATAGTGCAACA 11 66 0 ATGCCCACGA 0.959672 -155 CTGACTTGCAACTCCCGCCGAAATCCTGCAA 13 41 1 ACTCCGCCGA 0.925403 -54 TTCTGTTAGAATGCGCCCCGAACAGGATGAC 15 121 1 ATGCCCCCGA 0.99048 -45 AAATGGCATTATGCGTCCCCAAAGATAAAAC 17 100 1 ATGCTCCCCA 0.870649 -56 **** ****** Masking position 1 Map Score: 3.28152 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 168 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 TTACAAGAACCAGGGGCGGAAATTCCAGC 1 10 1 CCAGGGGCGG 0.918194 -160 GTTTTCAGGCCCGATGGGGAACGACCATCA 1 78 0 CCGATGGGGA 0.866882 -92 GGCACGCTCACCGGATGCGGCATCAGTGCA 3 18 1 CCGGATGCGG 0.737377 -283 GCACAAAATAACGGGGGCGGTGGTCGGCGA 4 77 0 ACGGGGGCGG 0.981198 -141 AAAAACCCCGCCGGTGGCGGGGAAGCACGT 7 35 0 CCGGTGGCGG 0.987726 -144 CTTTCTTTCACCGATGGCGA 10 1 0 CCGATGGCGA 0.88592 -89 CTCCGGTTACCCGAAGGGAGCGGGCTTTCT 10 25 0 CCGAAGGGAG 0.866881 -65 CTTCGGGTAACCGGAGGGAGACAAGAGGCG 10 39 1 CCGGAGGGAG 0.938489 -51 AATACGTCTAACGGGGCGGGATATTTTGCC 11 121 1 ACGGGGCGGG 0.836916 -100 GGCAAGCAGCACGCTGGCGGCAGCCAGTGT 21 225 0 ACGCTGGCGG 0.892357 -76 ACACAACATCACGAATGGGGATTTTTGACT 25 281 1 ACGAATGGGG 0.70522 -20 ********** Masking position 2 Map Score: 6.0004 Number of sites scoring better than the average of aligned sites = 2048 Number in coding regions = 1761 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 12 CCCCGCTTATTCGCACCTTCCCTAACAGGC 2 136 1 TCGCACCTTC 0.941478 -114 ATATTTCGGCACGCTCACCGGATGCG 3 7 1 CGGCACGCTC 0.951195 -294 GCGAGATGCGCCGCACCATTCCGAAGCAAA 3 191 0 CCGCACCATT 0.816291 -110 AGGGACTTGTTCGCACCTTCCTTAGGTAAC 3 270 0 TCGCACCTTC 0.941478 -31 GAAAGAAAGCCCGCTCCCTTCGGGTAACCG 10 22 1 CCGCTCCCTT 0.837325 -68 GGTGCCAGACCGGCACCCTCAGCGAAGGCA 13 11 0 CGGCACCCTC 0.990232 -84 GGTGCCGGTCTGGCACCCTGACTTGCAACT 13 24 1 TGGCACCCTG 0.864638 -71 GTCGCTACGGCGGCGCTCTCTTCAGCGTT 22 31 1 CGGCGCTCTC 0.860313 -19 AAATAATCTACCGCACTTTCTTGTAGAAAA 27 147 0 CCGCACTTTC 0.918215 -154 ********** Masking position 9 Map Score: 2.99092 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 356 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 ATAAGAATAAGATGTAGCGGAGTTG 6 6 1 AATAAGATGT 0.780162 -82 TTTAATGAAAAATAATACGTCTAACGGGGC 11 108 1 AATAATACGT 0.881846 -113 TAAATATGTTAATAAGACGTTGCATTATTG 12 134 0 AATAAGACGT 0.964739 -132 CTTAACGAGGAAAAAGACGT 14 27 1 AAAAAGACGT 0.954569 -10 CACAGACAGGTAAAAGACGTTTCCCAAACG 21 138 1 TAAAAGACGT 0.901387 -163 AAATTATCGTTATAGGACGTTTGGGAAACG 21 155 0 TATAGGACGT 0.785513 -146 TTTCTTGTAGAAAAATACGTTTCTAAACAA 27 131 0 AAAAATACGT 0.851453 -170 ********** Masking position 4 Map Score: 1.62679 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 ATTATTCTGTCAAAGGTACTATCTTCGACC 4 163 1 CAAAGGTACT 0.853612 -55 CCTTCGATCTCAAAAGCATTATCAGACTGA 5 34 1 CAAAAGCATT 0.875524 -92 CCCGATGCCGCAAAGGCATAAAAAGTCGAT 15 19 1 CAAAGGCATA 0.918144 -147 TTTATGCTGACAAAGGCACTTTTTTCTGTT 25 85 1 CAAAGGCACT 0.974155 -216 CCTTTCTAAAGAAAGGCATTAATAGAAATT 27 61 0 GAAAGGCATT 0.959618 -240 CCTTTCTTTAGAAAGGCATTTTTTTACTGA 27 75 1 GAAAGGCATT 0.959618 -226 ********** Masking position 4 Map Score: 1.44909 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 105 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 TTTAATTGTTTTTTTTAATAGCGGGAATAA 9 83 1 TTTTTTAATA 0.527652 -183 CTTTAGAATTTTTTTCAAAAACAGCCATTT 9 148 0 TTTTTCAAAA 0.815936 -118 AGACGTATTATTTTTCATTAAAAATGCTTA 11 100 0 TTTTTCATTA 0.886488 -121 TATCATCATCTTTTTCATAATGCTTCCTGT 21 192 0 TTTTTCATAA 0.925871 -109 ATGCTGGACATTTTTCATTCTCTAATGTT 25 10 0 TTTTTCATTC 0.81559 -291 AGACTGTTCTTTTTTTATACTGCACTGTTT 25 224 0 TTTTTTATAC 0.734978 -77 CTTATATTAATTTTTTATAACTAAAATTCA 27 197 1 TTTTTTATAA 0.830246 -104 ATAATCTTTTTTTTTCATAAGTTTGGTTTT 27 241 1 TTTTTCATAA 0.925871 -60 ********** Masking position 7 Map Score: 1.19397 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 107 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529