AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_ecoli_reg_100.orf -o00400_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #2 aroL 182 shikimate kinase II #3 nadA 300 quinolinate synthetase, A protein #4 aroG 300 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, phenylalanine repressible) #5 serC 198 3-phosphoserine aminotransferase #6 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #7 aspC 184 aspartate aminotransferase #8 trpE 91 anthranilate synthase component I #9 trpL 137 trp operon leader peptide #10 tyrS 128 tyrosine tRNA synthetase #11 b1691 220 putative amino acid/amine transport protein #12 aroD 30 3-dehydroquinate dehydratase #13 aroH 156 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tryptophan repressible) #14 pheS 283 phenylalanine tRNA synthetase, alpha-subunit #15 pabB 73 p-aminobenzoate synthetase, component I #16 hisG 145 ATP phosphoribosyltransferase #17 aroC 34 chorismate synthase #18 pheL 103 leader peptide of chorismate mutase-P-prephenate dehydratase #19 pheA 98 chorismate mutase-P and prephenate dehydratase #20 aroF 170 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tyrosine repressible) #21 eno 87 enolase #22 pyrG 227 CTP synthetase #23 yrdD 62 putative DNA topoisomerase #24 smf_2 53 orf, fragment 2 #25 smf_1 129 orf, fragment 1 #26 pabA 31 p-aminobenzoate synthetase, component II #27 yhfG 104 orf, hypothetical protein #28 aroB 56 3-dehydroquinate synthase #29 aroK 199 shikimate kinase I #30 tyrB 192 tyrosine aminotransferase, tyrosine repressible Motif number 1 AGCGCCTTTAGGGCGCTTTTTTACATTGGTG 3 30 0 GGGCGCTTTT 0.979281 -271 AGCGCCCTAAAGGCGCTTTTTTGCTATTCAG 3 44 1 AGGCGCTTTT 0.926571 -257 TGATGAAAACGCAGGCTGTTTTTGCAAGACG 7 87 0 GCAGGCGTTT 0.874664 -98 CGCCTAATGAGCGGGCTTTTTTTTGAACAAA 8 57 1 GCGGGCTTTT 0.984459 -35 GGAGGCTTTCAGGCGCTGTTTTCCGTTTCTC 14 35 0 AGGCGCGTTT 0.785534 -249 GCCTCCCAGTGGAGGCTTTTTTTGTATGCGC 14 60 1 GGAGGCTTTT 0.982599 -224 ACCTGATGAGACAGGCTTTTTATTTTTCAAA 14 93 0 ACAGGCTTTT 0.865207 -191 GTGATCTTCCGGGGGCTTTCTCATGCGTTCA 16 60 0 GGGGGCTTCT 0.973788 -86 ATCACCTTCCGGGGGCTTTTTTATTGCGCGG 16 86 1 GGGGGCTTTT 0.993324 -60 ACGCGCCTTCGGGCGCGTTTTTTGTTGACAG 18 35 1 GGGCGCTTTT 0.979281 -69 ATGGGAGGCGTTTCGTCGTGTGAA 19 4 1 GGAGGCTTTC 0.870502 -95 CCCCGATTTGGGAGGCCTTATTGTTCGTCTT 19 45 0 GGAGGCTTAT 0.837909 -54 TCCCAAATCGGGGGGCCTTTTTTATTGATAA 19 63 1 GGGGGCTTTT 0.993324 -36 TTTTATTTACACAGGCAATTTAGTCGCGCTT 20 49 0 ACAGGCATTT 0.633153 -122 TTTACCCCAAAGGGGCTATTTTCTCACTCCT 22 81 1 AGGGGCATTT 0.914391 -147 GATTTCTCGCGCGGGCAATCTTGCCCGCGCT 27 12 1 GCGGGCATCT 0.809636 -93 TTATCATTCAGGCGGCATTTTGCTGTCTTTT 29 142 1 GGCGGCTTTT 0.945579 -58 ****** **** Masking position 9 Map Score: 28.9754 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 354 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 TCGCAATCGATTGACCGCGGGTTAATAGCAA 5 159 1 TGACCGCGGG 0.855486 -40 TTAATCCCCACAGCCAGCCTGTGGGGTTTTT 6 25 1 CGCCAGCCTG 0.964194 -46 CTTGCAAAAACAGCCTGCGTTTTCATCAGTA 7 90 1 CGCCTGCGTT 0.884391 -95 ATCAGATACCCAGCCCGCCTAATGAGCGGGC 8 42 1 CGCCCGCCTA 0.897274 -50 CAGGCTGACCGCGTGCAGAAAGGGT 12 5 1 CGACCGCGTG 0.972802 -26 GTAATTGTCGCAGCCAGACTGGACACGGCCA 14 124 1 CGCCAGACTG 0.753261 -160 AGACTGGACACGGCCAGCGCGGAGAAACCGG 14 139 1 CGCCAGCGCG 0.992519 -145 ATTGAGTGTATCGCCAACGCGCCTTCGGGCG 18 19 1 TGCCAACGCG 0.842322 -85 GCGTTTTTTGTTGACAGCGTGAAAACAGTAC 18 49 1 TGACAGCGTG 0.94829 -55 CAAATGGCGCTTGACCGCGTAATTCCC 22 7 0 TGACCGCGTA 0.848326 -221 TCCCTCCTCTTCGCCAGCGCACTATTGAAAT 22 113 0 TGCCAGCGCA 0.954215 -115 GCGGGCAAGATTGCCCGCGCGAGAAATCA 27 9 0 TGCCCGCGCG 0.992392 -96 GCGGGCAATCTTGCCCGCGCTTCTGCTCTCC 27 22 1 TGCCCGCGCT 0.966437 -83 GTGCTCTTCGCTGCCTGCGTTCCATGATGAT 29 108 1 CGCCTGCGTT 0.884393 -92 CGGTGATTTATCGCCAGAGCG 29 189 1 TGCCAGAGCG 0.910184 -11 * ********* Masking position 5 Map Score: 17.9896 Number of sites scoring better than the average of aligned sites = 2722 Number in coding regions = 2643 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 AAAAAAGCGCCTTTAGGGCGCTTTTTTACA 3 36 0 CTTTAGGGCG 0.832182 -265 ATCATGCTAACCACCCGGCGAGGTGTGACA 13 41 1 CCACCCGGCG 0.954834 -116 ATGCGCATCACTTCCCGGCAGTCCTGCCGT 13 110 1 CTTCCCGGCA 0.948562 -47 CACTGGGAGGCTTTCAGGCGCTGTTTTCCG 14 41 0 CTTTCAGGCG 0.968225 -243 TTATTTCATGCTACCCGGCACATAGCCAGT 15 41 1 CTACCCGGCA 0.820646 -33 TCTTTCAGGCGATGTGTGCTG 16 2 1 CTTTCAGGCG 0.968225 -144 GGAAGGTGATCTTCCGGGGGCTTTCTCATG 16 66 0 CTTCCGGGGG 0.96517 -80 GGAAGATCACCTTCCGGGGGCTTTTTTATT 16 81 1 CTTCCGGGGG 0.96517 -65 CGCCAACGCGCCTTCGGGCGCGTTTTTTGT 18 30 1 CCTTCGGGCG 0.978159 -74 GCGCTTCTGCTCTCCCGGCGTAACCCGGAT 27 38 1 TCTCCCGGCG 0.870385 -67 GATGATTTATCATTCAGGCGGCATTTTGCT 29 136 1 CATTCAGGCG 0.845218 -64 ********** Masking position 7 Map Score: 11.761 Number of sites scoring better than the average of aligned sites = 1072 Number in coding regions = 1006 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 TGCGACCTATTGGGGAAAACCCACG 2 168 1 TGGGGAAAAC 0.985795 -15 AGTCGAATGGTGGGGAAAAGTCACTCGAAT 3 187 0 TGGGGAAAAG 0.964323 -114 CACATCGCAATGAGTAAAACCGTTGAGGGC 5 78 0 TGAGTAAAAC 0.797074 -121 CAACTATTACTGATGAAAACGCAGGCTGTT 7 98 0 TGATGAAAAC 0.90881 -87 GCTTTACGCATGGTGAATACACTGCCCGTT 8 11 0 TGGTGAATAC 0.792396 -81 CTTTCGCATCTGGCGAAAAGTCGTGTACCG 10 74 1 TGGCGAAAAG 0.943226 -55 ACTGACACAATGAGGAAAACC 14 273 1 TGAGGAAAAC 0.962259 -11 ACTAGTGACTTGAGGAAAACCTA 21 75 1 TGAGGAAAAC 0.962259 -13 AATAGTGCGCTGGCGAAGAGGAGGGATAAT 22 118 1 TGGCGAAGAG 0.776022 -110 TAAGTTGTTATGGCGAAATCAGCACTGTTC 23 30 1 TGGCGAAATC 0.844228 -33 TACGGGCAGGTGGTTAAAACACAATAAACC 30 155 0 TGGTTAAAAC 0.806913 -38 ********** Masking position 6 Map Score: 9.91213 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 387 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 AAATGTCGTTGCGCGCACAGTACAGCGCAACTTATTT 1 27 0 GCGACAAACG 0.959722 -50 TCGATTGACCGCGGGTTAATAGCAACGCAACGTGGTG 5 165 1 GCGTAAGACG 0.970152 -34 GAAGGGAAGTCCGCTATCAGGGTAACGGGAGATTTAC 7 135 0 CCGTCAGACG 0.836854 -50 AATGTTTTTTGCGCCGACATCATAACGGTTCTGGCAA 9 31 1 GCGACAAACG 0.959722 -107 ACGCAAGTTCACGTAAAAAGGGTATCGACA 9 118 1 ACGAAAGACG 0.911675 -20 GGAGGCTAGCGCGTGAGAAGAGAAACGGAAAACAGCG 14 16 1 GCGGAAGACG 0.964689 -268 CACGGCCAGCGCGGAGAAACCGGAGCGTATTTAAGTA 14 147 1 GCGAAAGACG 0.992424 -137 GAAATAATTAGCGCCAACAATTTAGCAGGAGTTAACA 15 11 0 GCGACATACA 0.677829 -63 TTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACT 18 55 1 GCGAAAGAGG 0.927473 -49 TATCGCAAACGAGCATAAACAGGATCGCCATC 20 149 1 GAGAAAGACG 0.89614 -22 GGCGGCTCCGGTACAAAAGAACCGCGCTATT 26 8 0 CCGCAAGACG 0.854469 -24 AACACGTTCAGCGTAAAAACATTACCGCTTTTACGGC 29 14 0 GCGAAATACG 0.957709 -186 GGTAAGATTAGCGTAAAAAAGACAGCAAAATGCCGCC 29 152 0 GCGAAAAACA 0.804137 -48 *** *** * * ** Masking position 9 Map Score: 10.2877 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 470 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 CATTTTGTCCGAGTCGTGAGGTACTGAA 1 59 1 GAGTCGTGAG 0.856404 -18 TTTACTCATTGCGATGTGTGTCACTGAATG 5 90 1 GCGATGTGTG 0.977509 -109 TAGCAACGCAACGTGGTGAGGGGAA 5 184 1 ACGTGGTGAG 0.900981 -15 GCATTTAACAAAGAGGTGTGCTA 7 4 0 AAGAGGTGTG 0.892484 -181 CTGTTTTTGCAAGACGTGAGATTGCTCTGG 7 73 0 AAGACGTGAG 0.741043 -112 TAACCACCCGGCGAGGTGTGACACACCTCG 13 48 1 GCGAGGTGTG 0.988983 -109 GATTTCAAGTGCGAGGTGTGTCACACCTCG 13 59 0 GCGAGGTGTG 0.988983 -98 TCTTTCAGGCGATGTGTGCTGGAAGACA 16 9 1 GCGATGTGTG 0.977509 -137 GGGAGGCGTTTCGTCGTGTGAAACAGAATG 19 13 1 TCGTCGTGTG 0.858254 -86 CCCTGGGTACGCGTTGTTTGTCTGGAGTTT 21 38 1 GCGTTGTTTG 0.721731 -50 ********** Masking position 7 Map Score: 8.66071 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 247 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TAAGCTCTGACGATGTCATCAGGTTTACAAAGTG 3 88 0 CTCATCAGGT 0.947016 -213 AACTCTATGTCGGTGGAATTAGGCGTAAAATGAC 3 132 1 CTAATTAGGC 0.872884 -169 AATGACGCATCCTGCACATTAGGCGTAATTCGAG 3 160 1 CGCATTAGGC 0.984459 -141 TCTCGTTTTTCGCGACAATCTGGCGTTTTTCTTG 4 162 1 CGAATCTGGC 0.887733 -139 CAAAAAAAAGCCCGCTCATTAGGCGGGCTGGGTA 8 48 0 CGCATTAGGC 0.984459 -44 TTCTATGTCTCTTTCGCATCTGGCGAAAAGTCGT 10 64 1 CTCATCTGGC 0.966311 -65 AGAACTAGTGCATTAGCTTATTTTTTTG 13 5 1 CGCATTAGCT 0.826971 -152 AATAAAAAGCCTGTCTCATCAGGTGTAATTGTCG 14 100 1 CTCATCAGGT 0.947016 -184 GACTTAGAGCCTATCCCATCAGGCTATTTTACTT 14 221 0 CTCATCAGGC 0.984459 -63 CCTCCCTGAACGTGTCCATTTGCCACAAGTATAA 27 75 0 CGCATTTGCC 0.884658 -30 * * ******** Masking position 8 Map Score: 7.19753 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 480 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 AGCAAAAAAGCGCCTTTAGGGCGCTTTTTTAC 3 37 0 CGCCTTTGGC 0.851715 -264 GGCGCTTTTTTGCTATTCAGGCATCCTCAATT 3 55 1 TGCTATTGGC 0.791802 -246 CGGTGTAATTTGTTTTATATGCTAAACAAGAT 3 217 0 TGTTTTATGC 0.720306 -84 CTTACCATCTCGTTTTACAGGCTTAACGTTAA 3 279 0 CGTTTTAGGC 0.91983 -22 GGAGAGATCTCGTTTTTCGCGACAATCTGGCG 4 155 1 CGTTTTTCGA 0.663709 -146 GACAATCTGGCGTTTTTCTTGCTAATTCCAGG 4 175 1 CGTTTTTTGC 0.890997 -126 ACCAAAGTCCTGTTTTTTCGGCATTTAACAAA 7 22 0 TGTTTTTGGC 0.972277 -163 TTCTGGATAATGTTTTTTGCGCCGACATCATA 9 23 1 TGTTTTTCGC 0.967111 -115 GCAAAAATCTTGCTTTAATCGCTGGTACTCCT 10 17 1 TGCTTTACGC 0.905837 -112 AGAAATTTGTTGCTTCTACGGCAGGACTGCCG 13 125 0 TGCTTCTGGC 0.849322 -32 TTGGGGTAAATGTTTTTGACGCAAATCAAGCG 22 59 0 TGTTTTTCGC 0.967111 -169 AAAACATTACCGCTTTTACGGCTGT 29 4 0 CGCTTTTGGC 0.973274 -196 CATTTTGCTGTCTTTTTTACGCTAATCTTACC 29 157 1 TCTTTTTCGC 0.741642 -43 ******* *** Masking position 11 Map Score: 7.33828 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 681 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 9 TTGGTGGGTCGTGCAGGATGACTCG 3 6 0 GTGCAGGATG 0.937569 -295 TACGCCTAATGTGCAGGATGCGTCATTTTA 3 157 0 GTGCAGGATG 0.937569 -144 ACGTGAGATTGCTCTGGAAGGTATAAAAAA 7 60 0 GCTCTGGAAG 0.880653 -125 TCCTTAGTTAGCGCAGAAAGAGTTATTTAT 11 47 0 GCGCAGAAAG 0.948882 -174 AGCTCCTTGCTGAAAGATAATTTCGT 11 205 0 TTGCTGAAAG 0.50555 -16 GGCTGACCGCGTGCAGAAAGGGTAAAAA 12 13 1 GTGCAGAAAG 0.952036 -18 CGGTTTCTCCGCGCTGGCCGTGTCCAGTCT 14 139 0 GCGCTGGCCG 0.83209 -145 CAGGCGATGTGTGCTGGAAGACATTCAGAT 16 16 1 GTGCTGGAAG 0.969559 -130 GTTGATAACGGTTCAGACAGGTTTAAAGAG 16 116 1 GTTCAGACAG 0.777811 -30 AAATGGACACGTTCAGGGAGGCATCAA 27 88 1 GTTCAGGGAG 0.780432 -17 TCATCATGGAACGCAGGCAGCGAAGAGCAC 29 108 0 ACGCAGGCAG 0.758622 -92 ********** Masking position 4 Map Score: 5.33164 Number of sites scoring better than the average of aligned sites = 2184 Number in coding regions = 2116 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 10 ACAGGACCAAAGTCCTGTTTTTTCGGCATT 7 29 0 AGTCCTGTTT 0.92562 -156 ACAGGACTTTGGTCCTGTTTTTTTTATACC 7 41 1 GGTCCTGTTT 0.943533 -144 AATCGCTGGTACTCCTGATTCTGGCACTTT 10 33 1 ACTCCTGATT 0.968492 -96 TAAACCAATCGCTGCTGATTTCAAGTGCGA 13 75 0 GCTGCTGATT 0.908946 -82 ACTTAAATACGCTCCGGTTTCTCCGCGCTG 14 153 0 GCTCCGGTTT 0.822806 -131 CAGTCCTGACTCTACTGGCTA 15 63 0 AGTCCTGACT 0.818876 -11 GATGGCGATCCTGTTTATGCTCGTTT 20 155 0 GATCCTGTTT 0.762013 -16 CTATTTTCTCACTCCTGATTTCAATAGTGC 22 96 1 ACTCCTGATT 0.968492 -132 CACCGTGAACAGTGCTGATTTCGCCATAAC 23 36 0 AGTGCTGATT 0.834267 -27 AATCTTTCTAACTCCTGAACACATCTCTGG 25 17 0 ACTCCTGAAC 0.768955 -113 ATTGCCGTTCGCTCCTGAACATCCACTCGA 30 110 1 GCTCCTGAAC 0.817113 -83 ********** Masking position 3 Map Score: 4.55408 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 236 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 GATAAGTATGGCAACACTGGAACAGAC 4 284 1 GCCACTGGAG 0.975996 -17 ATTGCGATGTGTGTCACTGAATGATAAAACCGATA 5 97 1 GTCACTGAAT 0.945809 -102 TGTGTCAGTGGTGACACTGGTTCGTTGGACTTAGA 14 247 0 GTCACTGGGT 0.951659 -37 ATGCGTTCATGCACCACTGGAAGATCTGAATGTCT 16 34 0 GCCACTGGAT 0.992489 -112 GAAGCGAAGGGCCTCACTGGTTAATAAAACAAGGT 24 20 1 GCCACTGGAT 0.992489 -34 CTGATTGACAGCATCACTGACCAATCGCAAAGATT 25 75 1 GCCACTGAAT 0.973008 -55 TATAAAGGTCGTGCCTCTGGCGGATGTACGTTTGT 30 53 1 GTCTCTGGAT 0.929985 -140 ** ****** ** Masking position 8 Map Score: 3.44985 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 72 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CAGCGCCTGAAAGCCTCCCAGTGGAGGCTT 14 48 1 AAGCCTCCCA 0.977842 -236 ACGCATGAGAAAGCCCCCGGAAGATCACCT 16 63 1 AAGCCCCCGG 0.972497 -83 CGCAATAAAAAAGCCCCCGGAAGGTGATCT 16 84 0 AAGCCCCCGG 0.972497 -62 ACACGACGAAACGCCTCCCAT 19 2 0 ACGCCTCCCA 0.962806 -97 ACGAACAATAAGGCCTCCCAAATCGGGGGG 19 48 1 AGGCCTCCCA 0.97944 -51 TCAATAAAAAAGGCCCCCCGATTTGGGAGG 19 61 0 AGGCCCCCCG 0.989065 -38 TTGATGCCTCCCTGAACGTGTCC 27 92 0 ATGCCTCCCT 0.873616 -13 ********** Masking position 1 Map Score: 6.39771 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 52 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 TGTACCCAGGGAAAATCATCTTCAGTATAGT 11 138 1 GAAAATCACT 0.923613 -83 AAAGCCCCCGGAAGATCACCTTCCGGGGGCT 16 72 1 GAAGATCACT 0.970571 -74 CATCCTCGCTGAGGATCAACTATCGCAAACG 20 129 1 GAGGATCACT 0.956883 -42 CAGTATACCCGAACATGACCTGTGCCACAAA 22 153 0 GAACATGACT 0.923841 -75 AGGCAGCGAAGAGCACCAACTCTCAAATCGG 29 93 0 GAGCACCACT 0.9289 -107 GAGCATGAAAGAACATCAACTTATTGAATTT 30 21 0 GAACATCACT 0.984399 -172 GTTCGCTCCTGAACATCCACTCGATCTTCGC 30 116 1 GAACATCCCT 0.951017 -77 ******** ** Masking position 5 Map Score: 2.07255 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 70 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 CATGTTTTTAACAAAATAAGTTGCGCTGTACTGT 1 14 1 AAAAAAGTTC 0.924338 -63 AATGAAGTGTAAATAATAAATTACAT 2 3 0 AAAAAAATTC 0.947795 -180 TTTCGATTGTAAAGAAAAAATTCCACTTAAAGTG 2 79 0 AAAAAAATTC 0.947795 -104 TGTTTAGCATATAAAACAAATTACACCGATAACA 3 221 1 AAAAAAATTC 0.947795 -80 CGAAAGAGACATAGAATAAAGTGCCAGAATCAGG 10 46 0 AAAAAAAGTC 0.946795 -83 CCTGCCGTAGAAGCAACAAATTTCTGAGACTTGT 13 132 1 AGAAAAATTC 0.828241 -25 TTGCCTGTGTAAATAAAAATGTACGAAATATGGA 20 62 1 AAAAAATGTC 0.814476 -109 TCACTGGTTAATAAAACAAGGTGCGATTCTT 24 33 1 AAAAAAGGTC 0.922926 -21 * * ** ***** * Masking position 8 Map Score: 1.99728 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 22 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 CTGGATAATGTTTTTTGCGCCGACATCATAA 9 25 1 TTTTTGCGCC 0.871693 -113 TCGCTGCTGATTTCAAGTGCGAGGTGTGTCA 13 66 0 TTTAAGTGCG 0.806407 -91 GAGGCTTTTTTTGTATGCGCGTTTTGAAAAA 14 71 1 TTGATGCGCG 0.968715 -213 CGGGGGCTTTTTTATTGCGCGGTTGATAACG 16 95 1 TTTTTGCGCG 0.972482 -51 GAGGTAAGGGTTGAAAGCGCGACTAAATTGC 20 35 1 TTGAAGCGCG 0.955771 -136 TGATTTCTCGCGCGGGCAATCTTG 27 4 1 TTTTCGCGCG 0.974457 -101 GTTTCATCTATTTGACGCGCGCAGGTATTTA 29 48 1 TTTACGCGCG 0.980266 -152 *** ******* Masking position 2 Map Score: 2.73102 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 179 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727