AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_ecoli_reg_300.orf -o00400_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/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 ycaP 120 orf, hypothetical protein #6 serC 198 3-phosphoserine aminotransferase #7 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #8 aspC 184 aspartate aminotransferase #9 ompF 300 outer membrane protein 1a (Ia;b;F) #10 trpE 91 anthranilate synthase component I #11 trpL 137 trp operon leader peptide #12 tyrS 128 tyrosine tRNA synthetase #13 pdxH 58 pyridoxinephosphate oxidase #14 ydhA 178 orf, hypothetical protein #15 b1640 273 orf, hypothetical protein #16 b1689 300 orf, hypothetical protein #17 b1690 99 putative transport system permease protein #18 b1691 220 putative amino acid/amine transport protein #19 aroD 30 3-dehydroquinate dehydratase #20 ydiA 300 orf, hypothetical protein #21 aroH 156 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tryptophan repressible) #22 pheS 283 phenylalanine tRNA synthetase, alpha-subunit #23 pheM 122 phenylalanyl-tRNA synthetase (pheST) operon leader peptide #24 rplT 52 50S ribosomal subunit protein L20, and regulator #25 rpmI 96 50S ribosomal subunit protein A #26 thrS 300 threonine tRNA synthetase #27 pabB 73 p-aminobenzoate synthetase, component I #28 hisL 255 his operon leader peptide #29 hisG 145 ATP phosphoribosyltransferase #30 aroC 34 chorismate synthase #31 b2595 134 orf, hypothetical protein #32 b2596 29 orf, hypothetical protein #33 yfiA 34 putative yhbH sigma 54 modulator #34 pheL 103 leader peptide of chorismate mutase-P-prephenate dehydratase #35 pheA 98 chorismate mutase-P and prephenate dehydratase #36 aroF 170 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase (DAHP synthetase, tyrosine repressible) #37 eno 87 enolase #38 pyrG 227 CTP synthetase #39 mazG 70 orf, hypothetical protein #40 chpR 77 suppressor of inhibitory function of ChpA, PemI-like, autoregulated #41 relA 47 (p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor #42 ygcA 56 putative enzyme #43 yrdD 62 putative DNA topoisomerase #44 smf_2 53 orf, fragment 2 #45 smf_1 129 orf, fragment 1 #46 pabA 31 p-aminobenzoate synthetase, component II #47 yhfG 104 orf, hypothetical protein #48 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #49 aroB 56 3-dehydroquinate synthase #50 aroK 199 shikimate kinase I #51 yrfD 68 orf, hypothetical protein #52 dnaB 82 replicative DNA helicase; part of primosome #53 alr 52 alanine racemase 1 #54 BIME213 26 BIME #55 tyrB 192 tyrosine aminotransferase, tyrosine repressible Motif number 1 CGCCTTTAGGGCGCTTTTTTACATTGGTGG 3 29 0 GCGCTTTTTT 0.96372 -272 CGCCCTAAAGGCGCTTTTTTGCTATTCAGG 3 46 1 GCGCTTTTTT 0.96372 -255 CGCGACAATCTGGCGTTTTTCTTGCTAATT 4 172 1 TGGCGTTTTT 0.831784 -129 ATGAAAACGCAGGCTGTTTTTGCAAGACGT 8 86 0 AGGCTGTTTT 0.582107 -99 CCTAATGAGCGGGCTTTTTTTTGAACAAAA 10 59 1 GGGCTTTTTT 0.973185 -33 CTCCCACGATGGGCTTTTTTTTAACATTTT 16 179 1 GGGCTTTTTT 0.973185 -122 TTGTTTTTGATCGCGATTTTCCTTAGTTAG 18 66 0 TCGCGATTTT 0.590804 -155 CTACGCTTCTGTGCGTTTTTAATTTATGCT 20 245 1 GTGCGTTTTT 0.712778 -56 AGGCTTTCAGGCGCTGTTTTCCGTTTCTCT 22 34 0 GCGCTGTTTT 0.877015 -250 CTCCCAGTGGAGGCTTTTTTTGTATGCGCG 22 62 1 AGGCTTTTTT 0.838417 -222 TTTTTTGTATGCGCGTTTTGAAAAATAAAA 22 77 1 GCGCGTTTTG 0.717933 -207 CTATCCCATCAGGCTATTTTACTTGCCATT 22 215 0 AGGCTATTTT 0.674272 -69 AATCCAGGCTTCGCTATTTTTGGTGCCATC 28 82 1 TCGCTATTTT 0.602397 -174 TAGAAAGCAAGGGCTTTTTTATATATTTTA 28 178 0 GGGCTTTTTT 0.973185 -78 CACCTTCCGGGGGCTTTTTTATTGCGCGGT 29 88 1 GGGCTTTTTT 0.973185 -58 GCGCCTTCGGGCGCGTTTTTTGTTGACAGC 34 37 1 GCGCGTTTTT 0.961997 -67 CCAAATCGGGGGGCCTTTTTTATTGATAAC 35 65 1 GGGCCTTTTT 0.851286 -34 TACCCCAAAGGGGCTATTTTCTCACTCCTG 38 83 1 GGGCTATTTT 0.935397 -145 TGCCGCGAGCGGGCGATTTTAGGTGATTTT 48 51 1 GGGCGATTTT 0.932424 -220 TTATACTACCGCGCGTTTGTTTATAAACTG 51 16 0 GCGCGTTTGT 0.717933 -53 ********** Masking position 7 Map Score: 28.5179 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 302 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 ATCGATTGACCGCGGGTTAATAGCAACGCAACGTGGTGAGG 6 164 1 CGCGAAACGA 0.987207 -35 AAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAAT 14 129 0 AGCGAAACGA 0.98447 -50 TGAAACGCCACGCAAGCATCCCTCATGGTCAAAGTATATGG 15 32 1 CGCGTCAGGA 0.881493 -242 AGGAGGCTAGCGCGTGAGAAGAGAAACGGAAAACAGCGCCT 22 15 1 CGCGAAACGA 0.987207 -269 TTTCGAGCACAGCCCGGGACCAAAATGGCAAGTAAAATAGC 22 192 1 AGCGAAAGGA 0.972869 -92 AACCTTTCAGACGCACCGTGATGTTATCAGT 26 1 1 AACTACACGA 0.548752 -300 TGTGCCGGGTAGCATGAAATAATTAGCGCCAACAATTTAGC 27 22 0 AGCGAAACGA 0.984495 -52 TAAACGGCAAAGCCGTAAAACCCCAACGATAAACGAAGAAG 31 19 0 AGCTACACGA 0.870259 -116 CAGAAACCTGAAACACAAAACGGCAGCCC 32 5 1 AACGACACGA 0.912819 -25 TTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAA 34 54 1 AGCGAAAGGA 0.972869 -50 GTTGATCCTCAGCGAGGATGACGTAACGATAACACATAAAG 36 108 0 AGCGTCACGA 0.915522 -63 TTCAATAGTGCGCTGGCGAAGAGGAGGGATAATGAAAGTTT 38 115 1 CGCGAAAGGA 0.977569 -113 GGCGATAAATCACCGGGTAAGATTAGCGTAAAAAAGACAGC 50 163 0 CACGAAACGA 0.933291 -37 TATAAACAAACGCGCGGTAGTATAAAGGCAAGCCAGACGCA 51 21 1 CGCGAAAGGA 0.977569 -48 *** * * * * ** * Masking position 15 Map Score: 14.7834 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 359 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 CTCAAAGGCGCTATCACCGCCGCCATGCCGATGAA 5 50 1 CTTCCGCGCA 0.907923 -71 AAATTTTGCTTAATCCCCACAGCCAGCCTGTGGGG 7 16 1 TATCCACGCA 0.818647 -55 TTAAGGAACTTTGTGAACACCGTCATATTTCCATA 9 64 0 TTTGCACGCA 0.950117 -237 CTGGATAATGTTTTTTGCGCCGACATCATAACGGT 11 25 1 TTTTCGCGCA 0.969093 -113 TGGGTGACGCTATTGTGCGCCGCCCCTGGAAAAAT 13 12 0 TATGCGCGCC 0.907047 -47 TTTTTACCCTTTCTGCACGCGGTCAGCCTG 19 6 0 TTTGCGCGCA 0.980463 -25 TCATCAGGTGTAATTGTCGCAGCCAGACTGGACAC 22 115 1 TATTCGCGCA 0.916515 -169 ACGCTCCGGTTTCTCCGCGCTGGCCGTGTCCAGTC 22 140 0 TTTCCGCGCC 0.949662 -144 TACGTGAGAATTTCGAGCACAGCCCGGGACCAAAA 22 182 1 TTCGCACGCC 0.75432 -102 CAACGAACCAGTGTCACCACTGACACAATGAGGAA 22 255 1 GTTCCACGCA 0.789135 -29 AGCCTGGATTTTCGTCTCACTGACAATACCTTGAT 28 57 0 TTGTCACGCA 0.775495 -199 TACCCGTACTGTTTTCACGCTGTCAACAAAAAACG 34 50 0 GTTTCGCGCA 0.901003 -54 TCGTACATTTTTATTTACACAGGCAATTTAGTCGC 36 53 0 TTTTCACGCA 0.922483 -118 TGATTTCTCGCGCGGGCAATCTTGCCCG 47 4 1 TTCTCGCGCA 0.901003 -101 GCCATTTTATTTTTGAACGCAGGCCAATC 48 5 0 TTTGCGCGCC 0.965363 -266 AAATCATCATCATGGAACGCAGGCAGCGAAGAGCA 50 109 0 CAGGCGCGCA 0.596845 -91 ** ** *** * ** Masking position 8 Map Score: 11.4057 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 578 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 ATTCGAGTGACTTTTCCCCACCATTCGACTAT 3 187 1 CTTTTCCCCC 0.889735 -114 TTCAAACTAACGTTTCGCTACCGTGAAAGTGC 9 154 0 CGTTTCCTCC 0.889735 -147 AACATTTTTCCGCTTCGCTACCTCGCCCCTCA 16 201 1 CGCTTCCTCC 0.981265 -100 TATCGTGATGCGCATCACTTCCCGGCAGTCCT 21 103 1 CGCATCCTCC 0.869366 -54 TTTTCCGTTTCTCTTCTCACGCGCTAGCCTCC 22 16 0 CTCTTCCAGC 0.836992 -268 GAGGACAGTCCTCTTAGCCCCCTCCTTTCCCC 28 118 1 CTCTTACCCC 0.820658 -138 AAATTTTACCTCTTGTCTTCCCGTCTTGGTG 33 14 0 CTCTTGCTCC 0.904992 -21 ATTATCCCTCCTCTTCGCCAGCGCACTATTGA 38 116 0 CTCTTCCCGC 0.953272 -112 ACCAGTGAGGCCCTTCGCTTCCCGGATTCC 44 9 0 CCCTTCCTCC 0.951311 -45 TATTTAGAATCTCTTCACTTGCTTTTTTTCTG 48 227 1 CTCTTCCTGC 0.966276 -44 AGAGTTGGTGCTCTTCGCTGCCTGCGTTCCAT 50 101 1 CTCTTCCTCC 0.986588 -99 ****** ** ** Masking position 5 Map Score: 8.88913 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 170 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 ATAGCAAAAAAGCGCCTTTAGGGCGCTTTTTT 3 39 0 AGCGCCTTAG 0.947078 -262 CGGCGGTGATAGCGCCTTTGAGATAAAACCCG 5 40 0 AGCGCCTTGG 0.966265 -81 CTCCGGCTGTAGCGCCTTTAATCAGCTGGTTG 14 152 1 AGCGCCTTAT 0.541016 -27 AAGCATGGAAATCCCCTGAGTGAAACAACGAA 16 123 1 ATCCCCTGGG 0.928873 -178 AACGGAAAACAGCGCCTGAAAGCCTCCCAGTG 22 39 1 AGCGCCTGAG 0.978277 -245 TCCAGCACACATCGCCTGAAAGA 29 2 0 ATCGCCTGAG 0.947078 -144 CGCATGAGAAAGCCCCCGGAAGATCACCTTCC 29 64 1 AGCCCCCGAG 0.944103 -82 GCAATAAAAAAGCCCCCGGAAGGTGATCTTCC 29 81 0 AGCCCCCGAG 0.944103 -65 GTATCGCCAACGCGCCTTCGGGCGCGTTTTTT 34 26 1 CGCGCCTTGG 0.818764 -78 GTGAGAAAATAGCCCCTTTGGGGTAAATGTTT 38 76 0 AGCCCCTTGG 0.928873 -152 CGCGGGCAAGATTGCCCGCGCGAGAAATCA 47 9 0 ATTGCCCGGG 0.608004 -96 ATCACCTAAAATCGCCCGCTCGCGGCATATCC 48 46 0 ATCGCCCGTG 0.753474 -225 CCGGTGATTTATCGCCAGAGCG 50 188 1 ATCGCCAGGG 0.818681 -12 ******** * * Masking position 6 Map Score: 8.39119 Number of sites scoring better than the average of aligned sites = 1022 Number in coding regions = 965 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 AACAGTTCATCGGCATGGCGGCGGTGATAGC 5 59 0 CGGCATGGCG 0.86412 -62 TTATCCAGAACGGGAGTGCGCC 11 2 0 CGGGAGTGCC 0.766149 -136 AGTCGTGTACCGGCAAAGGTGCAGTCGTTAT 12 92 1 CGGCAAAGGG 0.894864 -37 CCAAGTGTAACGGCAGACGCGGTAAGAAAAA 14 28 0 CGGCAGACGG 0.851331 -151 GGAAAGTCTTCGGGATATGACTATGAAAAAA 14 92 1 CGGGATATGC 0.460528 -87 CATCACTTCCCGGCAGTCCTGCCGTAGAAGC 21 115 1 CGGCAGTCCG 0.816313 -42 AGAAAGCCCCCGGAAGATCACCTTCCGGGGG 29 70 1 CGGAAGATCC 0.636474 -76 CTATATTAAACGGCAAAGCCGTAAAACCCCA 31 35 0 CGGCAAAGCG 0.893745 -100 ATAACCAAGACGGGAAAGCAGTATACCCGAA 38 171 0 CGGGAAAGCG 0.931178 -57 CTGCCGAAATCGGCAAATCGCAA 41 3 0 CGGCAAATCC 0.913317 -45 TTGCCGATTTCGGCAGGTCTGGTCCCTAAAG 41 18 1 CGGCAGGTCG 0.924792 -30 CGGGTTACGCCGGGAGAGCAGAAGCGCGGGC 47 34 0 CGGGAGAGCG 0.96278 -71 CAAGTATAAGCGGCAAATCCGGGTTACGCCG 47 53 0 CGGCAAATCG 0.941755 -52 CGCCCGCTCGCGGCATATCCCGCTATGCCAT 48 35 0 CGGCATATCC 0.867716 -236 ********* * Masking position 5 Map Score: 8.08848 Number of sites scoring better than the average of aligned sites = 999 Number in coding regions = 960 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 GAAAAACGCCAGATTGTCGCGAAAAACGAGATCT 4 159 0 AGAGTGCGAA 0.912904 -142 GTTCACGTAAAAAGGGTATCGACA 11 124 1 AAAGTTCGCA 0.916447 -14 AGTTTATGTTTGAGTGGTGCGCAAACGTCAGATT 15 235 1 TGAGGGCGAA 0.759423 -39 AACAAATGCTAAATTGGTTCGCAATCAGGTACAC 26 185 0 AAAGGTCGAA 0.881682 -116 TTTGTTGGCTAGATGGTTTCGCAATGAACTGTTA 26 213 1 AGAGTTCGAA 0.960594 -88 TCCTTTATATTGAGTGTATCGCCAACGCGCCTTC 34 11 1 TGAGTTCGCA 0.915298 -93 AAACGAGCATAAACAGGATCGCCATC 36 155 1 AAAGGTCGCA 0.922381 -16 TGTTAAATTGAGAAAGTCTCGCCA 42 43 1 AGAGTTCGCA 0.974921 -14 GTGTCCTCCAGAACGTATCGTCAGGGTCTGCTT 52 10 1 AGAGTTCGCA 0.974921 -73 ACCGAGATAAAGAATGGGTCGAAACTTTATCATA 52 46 0 AGAGGTCGAA 0.963517 -37 *** ** *** ** Masking position 3 Map Score: 5.12148 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 92 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 CATTCAGTGACACACATCGCAATGAGTAAA 6 90 0 CACACATCGC 0.984347 -109 TAGCACACCTCTTTGTTAAATGC 8 4 1 CACACCTCTT 0.837902 -181 CGAGGTGTGTCACACCTCGCCGGGTGGTTA 21 48 0 CACACCTCGC 0.989988 -109 CGAGGTGTGACACACCTCGCACTTGAAATC 21 59 1 CACACCTCGC 0.989988 -98 TGTCTTCCAGCACACATCGCCTGAAAGA 29 9 0 CACACATCGC 0.984347 -137 CTAACTCCTGAACACATCTCTGGAGATTT 45 10 0 AACACATCTC 0.766755 -120 ********** Masking position 4 Map Score: 4.94265 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 7 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TTTCACTTTGTAAACCTGATGACATCGTCAGA 3 85 1 TAAACCGTGA 0.967312 -216 TCGCAATGAGTAAAACCGTTGAGGGCAAAAAT 6 72 0 TAAAACGTGA 0.722949 -127 GCGCTCAACCAGCTGATTAAAGGCGC 14 163 0 TCAACCGTGA 0.82567 -16 AATAACATTATCAGCCTGCTGACGGCTTGAAG 16 270 0 TCAGCCGTGA 0.786062 -31 CTTTGCATATTTAACCGGATGAAAAAAACGGT 20 36 1 TTAACCGTGA 0.846956 -265 CTGCGACAATTACACCTGATGAGACAGGCTTT 22 105 0 TACACCGTGA 0.927785 -179 TTAACATCGCTCAACCGGGTGGAAGGTGAGAG 26 136 1 TCAACCGTGG 0.815331 -165 AAATCCGGGTTACGCCGGGAGAGCAGAAGCGC 47 38 0 TACGCCGAGA 0.714418 -67 TAAAACACAATAAACCGGAAGAAGGCGAAGAT 55 139 0 TAAACCGAGA 0.930591 -54 CACCTGCCCGTAAACCTGGAGAACCATCGC 55 173 1 TAAACCGAGA 0.931175 -20 ****** * *** Masking position 1 Map Score: 4.58683 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 195 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 AGCAAGAAAAACGCCAGATTGTCGCGAAAA 4 168 0 ACGCCAGATT 0.852177 -133 TTTTTGCAAGACGTGAGATTGCTCTGGAAG 8 70 0 ACGTGAGATT 0.965252 -115 TATCAGGGTAACGGGAGATTTACAAAATTC 8 128 0 ACGGGAGATT 0.982869 -57 TTCATGGTGAACAGGAGATTTTTCA 15 6 0 ACAGGAGATT 0.864987 -268 TGGTGCGCAAACGTCAGATTGAAAAAGGAT 15 249 1 ACGTCAGATT 0.907646 -25 GTATTTAAGTACGTGAGAATTTCGAGCACA 22 173 1 ACGTGAGAAT 0.832722 -111 ACACTAAAAAAAGGGAGATTGTACCTTTCC 26 107 0 AAGGGAGATT 0.864987 -194 AAAATGTAATACGGGAGATTCTCTGTTCCT 31 97 0 ACGGGAGATT 0.982869 -38 ********** Masking position 6 Map Score: 5.04061 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 44 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 GTCTGTTCCAGTGTTGCCATACTTATCT 4 283 0 CCAGTGTGCC 0.924291 -18 GATTTTTCCAGGGGCGGCGCACAATAGC 13 8 1 CCAGGGGGGC 0.890097 -51 TTTGTTCTTCCCGTGATGCAGACATAATTC 20 281 0 CCCGTGAGCA 0.765387 -20 TGAAAGCCTCCCAGTGGAGGCTTTTTTTGTA 22 55 1 CCAGTGGGGC 0.954755 -229 CCTCATTGTGTCAGTGGTGACACTGGTTCGT 22 257 0 TCAGTGGGAC 0.739746 -27 AGTAGCACTGTCTGTGGAGCCTTCGGGCTTC 25 19 1 TCTGTGGGCC 0.889621 -78 GCGAACAAAGCCTGTGAAGCCCGAAGGCTCC 25 34 0 CCTGTGAGCC 0.932231 -63 TTCAGATCTTCCAGTGGTGCATGAACGCATG 29 39 1 CCAGTGGGCA 0.95702 -107 GTTTTATTAACCAGTGAGGCCCTTCGCTTCC 44 19 0 CCAGTGAGCC 0.980193 -35 TTGCGATTGGTCAGTGATGCTGTCAATCAGA 45 74 0 TCAGTGAGCT 0.669999 -56 ATGGACACGTTCAGGGAGGCATCAA 47 90 1 TCAGGGAGCA 0.663172 -15 ******* *** Masking position 2 Map Score: 4.39658 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 386 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 CTTTGGTCCTGTTTTTTTTATACCTTCCAGA 8 47 1 GTTTTTTTAT 0.802137 -138 TACCCTCATGGTTTTTTTTATGACACCTGCC 9 273 0 GTTTTTTTAT 0.802137 -28 CATCATGAATGTTTTGTTTATAATTGGTTGA 15 134 0 GTTTGTTTAT 0.959102 -140 CATTTTTATGGTTTCGTTTATACCGATGGTT 20 154 0 GTTTGTTTAT 0.959102 -147 AGAACGTTATGTCTGGTTTATAAAATGAACC 20 216 0 GTCTGTTTAT 0.909777 -85 AATCAGCAGCGATTGGTTTATCGTGATGCGC 21 85 1 GATTGTTTAT 0.867002 -72 GTTCGCCTTTGTTTCGTTTATTAACAATGCG 25 59 1 GTTTGTTTAT 0.959102 -38 TATGGCAATGGATTTGTTTAATGAATGAGCG 28 149 0 GATTGTTTAA 0.644396 -107 CGTGAAAGTGGTTTAGGTTAAAAGACATCAG 28 209 1 GTTTGGTTAA 0.737051 -47 CTGCTTTCCCGTCTTGGTTATTCCATCGTCT 38 181 1 GTCTGGTTAT 0.812586 -47 **** ****** Masking position 4 Map Score: 3.47392 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 52 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 13 CAGTAAAAACATCGGCTTTTTGCTAA 6 5 1 AAAAACATCC 0.927452 -194 TGTCGGCGCAAAAAACATTATCCAGAACGGGA 11 18 0 AAAAACATTC 0.958099 -120 CCGTTGGTAGTAAAACATTATCTTCAAATCAA 15 169 0 TAAAACATTC 0.743953 -105 TAAAATATAAATAACATTATCAGCCTGCTGA 16 280 0 AATAACATTC 0.743953 -21 GTACCCAGGGAAAATCATCTTCAGTATAGTAA 18 139 1 AAAATCATCC 0.596894 -82 TCAACGCCATCAAAACATTGACTTTTATCGCC 23 49 1 CAAAACATTC 0.811549 -74 TTAAAAAGTTAAAAACGTTAACGGC 24 4 0 AAAAACGTTC 0.79696 -49 TACACAAATGAAAGACATTAACCTCTCACCTT 26 158 0 AAAGACATTC 0.796981 -143 CATCAGTTGAATAAACATTCACAGAGACTTTT 28 234 1 ATAAACATTC 0.725927 -22 GATTTGCGTCAAAAACATTTACCCCAAAGGGG 38 64 1 AAAAACATTC 0.958099 -164 CGTTCAGCGTAAAAACATTACCGCTTTTACGG 50 15 0 AAAAACATTC 0.958102 -185 AAGAGCATGAAAGAACATCAACTTATTGAATT 55 22 0 AAGAACATCC 0.706529 -171 ********* * Masking position 8 Map Score: 4.58639 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 62 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 GATCGCTATTCTCATGACACCGGCTTTCGCCG 2 133 1 CTCATGAACG 0.878436 -50 CTTTGTAAACCTGATGACATCGTCAGAGCTTA 3 90 1 CTGATGAACG 0.968075 -211 TGCAAATGCACTGTTGGAAGAGGTTATCCGAC 4 21 0 CTGTTGGAAG 0.77769 -280 CACATTCTGACGGAAGATATAGATTGGAAGTA 4 239 1 CGGAAGAAAG 0.728635 -62 CCAACTATTACTGATGAAAACGCAGGCTGTTT 8 97 0 CTGATGAACG 0.968074 -88 CATATTTAACCGGATGAAAAAAACGGTGAATC 20 41 1 CGGATGAAAA 0.765016 -260 ACAATTACACCTGATGAGACAGGCTTTTTATT 22 100 0 CTGATGAAAG 0.957618 -184 GTAAAATAGCCTGATGGGATAGGCTCTAAGTC 22 223 1 CTGATGGAAG 0.934005 -61 GTCCTCTTAGCTGATGGCACCAAAAATAGCGA 28 92 0 CTGATGGACA 0.745287 -164 GGTGCATGAACGCATGAGAAAGCCCCCGGAAG 29 54 1 CGCATGAAAG 0.834323 -92 TTTTATTGCGCGGTTGATAACGGTTCAGACAG 29 104 1 CGGTTGAACG 0.875557 -42 ******* * ** Masking position 9 Map Score: 3.24337 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 334 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 15 CGGTGTAATTTGTTTTATATGCTAAACAAGATAGT 3 214 0 TTTTTATGAA 0.919906 -87 TAACTGTAACTCCTTTGTTTGTTAATTATTTCAAG 4 111 0 TTTTTTTGAA 0.740243 -190 AGCGAAACGTTAGTTTGAATGGAAAGATGCCTGCA 9 167 1 TTTTAATGAA 0.755398 -134 ACCCTCATGGTTTTTTTTATGACACCTGCCACTGC 9 268 0 TTTTTATGAC 0.663491 -33 CAACGACAATTCCTTTCTGTGGAAAAA 17 3 0 TTTTTGTGAA 0.893997 -97 TTTATACCGATGGTTTATGTGGAAATTGTCGAAGA 20 134 0 TTTTTGTGAA 0.893997 -167 CCTTCAATTTTATTTTTTATGAAAACAGCATTTCA 20 183 0 TTTTTATGAA 0.919906 -118 GTGCATTAGCTTATTTTTTTGTTATCATGCTAACC 21 18 1 TTTTTTTGAT 0.454748 -139 ACAATCTCCCTTTTTTTAGTGTTAACATCGCTCAA 26 115 1 TTTTAGTGAA 0.693975 -186 AAACAAATTTTTCTTTGTATGTGATCTTTCGTGTG 26 249 1 TTTTTATGAT 0.770712 -52 GGCTTTTTTATATATTTTATGGCAATGGATTTGTT 28 162 0 TATTTATGAA 0.512533 -94 TTGAAAACTTTACTTTATGTGTTATCGTTACGTCA 36 96 1 TTTTTGTGAT 0.711667 -75 ATTTGTGTCATTTTTTAAATGACAAGCGCTTGATT 38 33 1 TTTTAATGAA 0.755398 -195 CATTTTGCTGTCTTTTTTACGCTAATCTTACCCGG 50 157 1 TTTTTACGAA 0.609121 -43 CGTCAGGGTCTGCTTCATATGATAAAGTTTCGACC 52 29 1 TTTCTATGAA 0.609121 -54 * *** **** ** Masking position 14 Map Score: 2.99092 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 41 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097