AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iaraC_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 araD 284 L-ribulose-5-phosphate 4-epimerase #2 araB_araC 338 araB: L-ribulokinase, araC: transcriptional regulator for ara operon #3 araJ 125 involved in either transport or processing of arabinose polymers #4 araH_2 23 high-affinity L-arabinose transport system; membrane protein, fragment 2 #5 araG 69 ATP-binding component of high-affinity L-arabinose transport system #6 araF 300 L-arabinose-binding periplasmic protein #7 araE 300 low-affinity L-arabinose transport system proton symport protein #8 ydjK 300 similar to sugar transporter #9 yfiG 174 similar to metabolite transport protein #10 yfhI 142 similar to antibiotic resistance protein #11 yncC 300 similar to metabolite transport protein #12 araA 207 L-arabinose isomerase #13 ytbD 183 similar to antibiotic resistance protein #14 yufN 300 similar to ABC transporter (lipoprotein) #15 yufO 75 similar to ABC transporter (ATP-binding protein) #16 araE 137 permease #17 ywtG 300 similar to metabolite transport protein #18 rbsR 300 transcriptional regulator (LacI family) #19 yxcC 238 similar to metabolite transport protein Motif number 1 GGCGTTACATACCGGATGCGGCTAC 1 6 0 ACCGGATGCG 0.961038 -279 GGTATGTAACGCCTGATGCGACGCTGACGC 1 23 1 GCCTGATGCG 0.993828 -262 CAGCGTGTAGGCCAGATAAGACGCGTCAGC 1 45 0 GCCAGATAAG 0.930141 -240 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 76 1 GCCGGATAAG 0.992691 -209 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 91 0 GCCGGATGCG 0.997538 -194 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 108 1 GCCTGATGCG 0.993828 -177 CAGCGCGTAGGCCTGATAAGACGCGCCAGC 1 130 0 GCCTGATAAG 0.981808 -155 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 161 1 GCCGGATAAG 0.992691 -124 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 1 176 0 GCCGGATGCG 0.997538 -109 GGCATTCAACGCCTGATGCGACGCTGGCGC 1 193 1 GCCTGATGCG 0.993828 -92 CAGCGTGTAGGCCTGATAAGACGCGCCAGC 1 215 0 GCCTGATAAG 0.981808 -70 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 1 246 1 GCCGGATAAG 0.992691 -39 ACTCCTTCGTGCCGGATGCGCTTTGCTTAT 1 261 0 GCCGGATGCG 0.997538 -24 CACATGACTGGCCGGATCAGCTTTGAACCA 14 232 1 GCCGGATCAG 0.97663 -69 ********** Masking position 6 Map Score: 48.8279 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 140 Number in noncoding regions = 584 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 2 CGCGTCTTATCTGGCCTACACGCTGCGATT 1 50 1 CTGGCCTACA 0.981986 -235 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 71 0 CCGGCCTACA 0.99717 -214 CAAAGCGCATCCGGCATTCAACGCCTGATG 1 96 1 CCGGCATTCA 0.967219 -189 CGCGTCTTATCAGGCCTACGCGCTGCGATT 1 135 1 CAGGCCTACG 0.962309 -150 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 156 0 CCGGCCTACA 0.99717 -129 CAAAGCGCATCCGGCATTCAACGCCTGATG 1 181 1 CCGGCATTCA 0.967219 -104 CGCGTCTTATCAGGCCTACACGCTGCGATT 1 220 1 CAGGCCTACA 0.989704 -65 CTTTGCTTATCCGGCCTACAAAATCGCAGC 1 241 0 CCGGCCTACA 0.99717 -44 ********** Masking position 7 Map Score: 19.2361 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 37 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 CTGGCCTACACGCTGCGATTTTGTAGGCCG 1 60 1 CGCTGCGATT 0.981228 -225 CAGGCCTACGCGCTGCGATTTTGTAGGCCG 1 145 1 CGCTGCGATT 0.981228 -140 CAGGCCTACACGCTGCGATTTTGTAGGCCG 1 230 1 CGCTGCGATT 0.981228 -55 GTATAAAAAACCCTGCCATGCGGCAGGGTC 7 17 0 CCCTGCCATG 0.939018 -284 GTGTCGGGTGCTCTGCCATTCTTGAAAGAA 9 142 1 CTCTGCCATT 0.909227 -33 TTCCCCTGCCTTTAAGAATACTT 11 288 0 CCCTGCCTTT 0.984884 -13 GGGGGCAGAGCCCGGCTTTTTATTCAATAG 12 33 0 CCCGGCTTTT 0.917577 -175 GGGCTCTGCCCCCGGCTTTTTTTAAAAGAA 12 50 1 CCCGGCTTTT 0.917577 -158 TCCTTCTCTTCCCCGCCTTTCGAAGGAAAT 14 96 1 CCCCGCCTTT 0.938361 -205 ACCTCCTTATCCCTGCGATTC 15 2 0 CCCTGCGATT 0.988974 -74 AGCCTCTTTTTCCGGCCATTAAACCTTTTT 17 215 0 TCCGGCCATT 0.801232 -86 ATCACAGATCCGCTGAGTTTAGGAAAAACG 19 83 0 CGCTGAGTTT 0.731503 -156 ********** Masking position 9 Map Score: 13.7714 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 415 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 AAGCGGGACCAAAGCCATGACAAAAACGCGTA 2 146 1 AAAGCTGACA 0.883146 -193 ATTTCTCGCTAAAACTATGTCAACACAGTCAC 6 179 1 AAAACTGTCA 0.952932 -122 ACAGGTATAAAAAACCCTGCCATGCGGCAGGG 7 19 0 AAAACTGCCA 0.776565 -282 AATCCCTATGGAAGCGATTTCATTTCTCGTTA 8 129 0 GAAGCTTTCA 0.729873 -172 CTGAAATGACAAAACAATGTCTTCATATGATA 9 17 1 AAAACTGTCT 0.765708 -158 ATCTTTTTAGAAAGCGGTTACAACAAGGGGTA 9 77 1 AAAGCTTACA 0.857101 -98 CATAATTCTAAAAGCATTTTCAGTCAATATTA 11 85 0 AAAGCTTTCA 0.940261 -216 GTTAAAAATGTAAACGGTTACAAATCCAGAGG 11 194 1 TAAACTTACA 0.7 -107 GAATACTTAATAAGCTCTTTCAGTGTGGTTAT 11 264 0 TAAGCTTTCA 0.857101 -37 CTCATAAAATAAAACGCTTTCAAATACAAAAG 12 171 0 AAAACTTTCA 0.941409 -37 TTGATCCCGAAAAACTAAGTCATAAGTCTTAC 14 19 1 AAAACAGTCA 0.634012 -282 CTTACTTCAGAAAACGATGTCACGGTTTTCCG 14 46 1 AAAACTGTCA 0.952932 -255 AATGTTGAGTAAAGCGTTTTCATTTAAACCTT 16 101 0 AAAGCTTTCA 0.940261 -37 CTAACATAATTAAACATTTTCTGGGATGATAG 18 27 1 TAAACTTTCT 0.497083 -274 CATATTTGTGAAGACTTTGTCAAAAAAAGAGT 18 149 1 AAGACTGTCA 0.719693 -152 TCTATCTATGTAAACGGTTACATAAACAAGGA 18 270 1 TAAACTTACA 0.7 -31 ***** ***** Masking position 2 Map Score: 14.0237 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 93 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 GATCCGCTAATCTTATGGATAAAAATGCTATGGCA 2 245 0 TCTTATTAAA 0.787094 -94 TTCCCTTATGTCTTTTCCCGCTAAATTTATGCACG 6 96 1 TCTTTTGAAA 0.946062 -205 CAGTCACTTATCTTTTAGTTAAAAGGTAATGCTTT 6 204 1 TCTTTTTAAG 0.835209 -97 TGACCATTGTTCTTTTAACGAGAAATGAAATCGCT 8 114 1 TCTTTTGAAA 0.946061 -187 ACTTGAAAAATCTTTTAAGATGAAACTCGTTGTTT 10 93 1 TCTTTTAAAA 0.815314 -50 CGTCATCGCCTCCTTTGATTTTAAAAAACAACGAG 10 118 0 TCCTTTTAAA 0.835209 -25 TTAGGTTTATTCTATTGGTTAAAAATGTAAACGGT 11 177 1 TCTATTTAAA 0.773713 -124 ATACTGTCAATCTTTTCTTTTAAAAAAAGCCGGGG 12 59 0 TCTTTTTAAA 0.972021 -149 TTAGTACGTATCTTTTGTATTTGAAAGCGTTTTAT 12 160 1 TCTTTTTGAA 0.835209 -48 TTGAATCTGCTCTTTTTTATTTATATAGCTTACTC 13 114 1 TCTTTTTATA 0.773736 -70 CCCTTGTTTTTCTTTTATTTTGAAATAAAGGAGCG 15 43 1 TCTTTTTAAA 0.972024 -33 ATTTATAAGTTCTTGTTTTTGAAAATTGATAACGA 17 75 1 TCTTGTTAAA 0.845679 -226 AGGTTTTCACTCTTTTTTTGACAAAGTCTTCACAA 18 154 0 TCTTTTGAAA 0.946061 -147 TGTGATCATCTCTTTTGGCTATAAAGTTTCCGTTT 19 107 1 TCTTTTTAAA 0.972021 -132 ****** * *** Masking position 6 Map Score: 13.1218 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 17 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TGATGCGACGCTGACGCGTCTTATCTGGCCTA 1 36 1 CTGCGCTCTT 0.982344 -249 TGATGCGACGCTGGCGCGTCTTATCAGGCCTA 1 121 1 CTGCGCTCTT 0.982509 -164 TGATGCGACGCTGGCGCGTCTTATCAGGCCTA 1 206 1 CTGCGCTCTT 0.982509 -79 AGACACTTTTGTTACGCGTTTTTGTCATGGCT 2 158 0 GTTCGCTTTT 0.681402 -181 CGGATCCTACCTGACGCTTTTTATCGCAACTC 2 274 1 CTGCGCTTTT 0.968019 -65 ACTGTTTCTCCATACCCGTTTTTTTGGATGGA 2 309 1 CATCCCTTTT 0.849001 -30 AACCTCATAACCTTCCCTTCTTCTTAGCATGT 8 162 0 CCTCCCTCTT 0.859778 -139 AAGTTTTTGACATACGCATTTTGAAAAAGACT 8 267 1 CATCGCTTTT 0.886225 -34 GGCTTTCTTCCCCTTCTTTCAAGAATGG 9 157 0 CTTCCCTCTT 0.967106 -18 GGCTGATGATCAGCCTCTTTTTGTTTGCAGCA 10 23 1 CAGCTCTTTT 0.545814 -120 GTAAACTGCCCCTTTCTCATAAAATAA 12 191 0 CTGCCCTTCT 0.873463 -17 CCCGGAACGCCTTCCGCATCCTTCTCTTCCCC 14 78 1 CTTCGCTCCT 0.927892 -223 GCATCCTTCTCTTCCCCGCCTTTCGAAGGAAA 14 93 1 CTTCCCCCTT 0.822609 -208 *** *** **** Masking position 12 Map Score: 12.4908 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 307 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 CCAGATAAGACGCGTCAGCGTCGCATCAGGC 1 33 0 CGCGCAGCGT 0.981044 -252 CCTGATAAGACGCGCCAGCGTCGCATCAGGC 1 118 0 CGCGCAGCGT 0.981044 -167 CCTGATAAGACGCGCCAGCGTCGCATCAGGC 1 203 0 CGCGCAGCGT 0.981044 -82 CAGACATTGCCGTCACTGCGTCTTTTACTGG 2 62 1 CGTCCTGCGT 0.929662 -277 AGATAATTCGCCCCTCTGTATTCATTATCCT 3 20 0 CCCCCTGTAT 0.824037 -106 CGGAAAAATTCCCCTCTGCATGATGCAGAGG 5 16 1 CCCCCTGCAT 0.979494 -54 TCGTTCACACCCCCTCTGCATCATGCAGAGG 5 28 0 CCCCCTGCAT 0.979494 -42 TTTTTCCTGCCAGCAGAGAGTAAGAC 7 285 0 CCTGCAGCAG 0.706185 -16 CTTAGATTTTCGCCTCTGGATTTGTAACCGT 11 207 0 CGCCCTGGAT 0.91114 -94 TTATATTGGACGCCGCAGCAGGTAAAATGTT 17 127 1 CGCCCAGCAG 0.968096 -174 **** ****** Masking position 6 Map Score: 9.17211 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 887 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 TCACTGCGTCTTTTACTGGCTCTTCTCGCT 2 74 1 TTTTACTGGC 0.922087 -265 CCGGAATTATTCTGGCTTCACGT 4 7 1 TTATTCTGGC 0.835965 -17 CAGAGGGGAATTTTTCCGGCAAA 5 4 0 TTTTTCCGGC 0.9845 -66 TTTTTCCTGCCAGCAGAGAG 7 291 0 TTTTTCCTGC 0.925964 -10 TCATAATCACATTTGCCGGCTGATTTGAAT 13 90 1 ATTTGCCGGC 0.860644 -94 TTGAACCAAATTTTTCTGGGGGGTTATATC 14 254 1 TTTTTCTGGG 0.907807 -47 CGCCGAAACATTTTACCTGCTGCGGCGTCC 17 134 0 TTTTACCTGC 0.820745 -167 TTTTAGCCTCTTTTTCCGGCCATTAAACCT 17 219 0 TTTTTCCGGC 0.9845 -82 ATAATTAAACATTTTCTGGGATGATAGTCT 18 32 1 ATTTTCTGGG 0.756789 -269 ********** Masking position 4 Map Score: 6.55324 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 668 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 TATCTGGCCTACACGCTGCGATTTTGTAGG 1 57 1 ACACGCTGCG 0.912696 -228 AATGCCGGATGCGCTTTGCTTATCCGGCCT 1 84 0 GCGCTTTGCT 0.959275 -201 TATCAGGCCTACGCGCTGCGATTTTGTAGG 1 142 1 ACGCGCTGCG 0.963957 -143 AATGCCGGATGCGCTTTGCTTATCCGGCCT 1 169 0 GCGCTTTGCT 0.959275 -116 TATCAGGCCTACACGCTGCGATTTTGTAGG 1 227 1 ACACGCTGCG 0.912696 -58 CGTGCCGGATGCGCTTTGCTTATCCGGCCT 1 254 0 GCGCTTTGCT 0.959275 -31 GCACGGCGTCACACTTTGCTATGCCATAGC 2 224 1 ACACTTTGCT 0.92822 -115 TTTTATCGCAACTCTCTACTGTTTCTCCAT 2 292 1 ACTCTCTACT 0.713295 -47 ACTATGTCTTACTCTCTGCTGGCAGGAAAA 7 280 1 ACTCTCTGCT 0.93503 -21 TTAAATGAAAACGCTTTACTCAACATTCGG 16 106 1 ACGCTTTACT 0.851167 -32 ********** Masking position 7 Map Score: 8.54392 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 514 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 10 CACCTGCGTGAGTTGTTCACGTATTTTTTCACTATGTC 7 250 1 ATTTTCAGTT 0.902831 -51 TTCAGAAAATAGTTGTTCATGTTTTTATCCAATAACCT 8 189 0 ATTTTCAGTT 0.902831 -112 CATTTACACGAATTCTTAAAGAAAAAATCATTGAATTC 10 55 1 ATTTTAAGAT 0.851874 -88 CATCTTAAAAGATTTTTCAAGTGAATTCAATGATTTTT 10 77 0 GTTTTCAGAC 0.962644 -66 ACGTACTTTTATTTCTTAACGATATGTTTCATAATCAC 13 62 1 ATTTTAAGAT 0.852469 -122 CTCACACCACGCTTATTCAGGGAAGAATAGAACTGTCT 14 127 1 GTTTTCAGAT 0.972953 -174 GATTCTAAGAAATTGTTCAGGACAGCCCATCACATGAC 14 202 1 ATTTTCAGAC 0.959674 -99 CCGATTTTTCGTTTATTCAAGATATAACCCCCCAGAAA 14 266 0 GTTTTCAGAC 0.962477 -35 AAAACTTAATATTTGTTCAAGAAATCTTCATCCATATT 18 117 1 ATTTTCAGAT 0.970919 -184 GCTAACTTCGGATTGTTCATGATAATCTATCTATGTAA 18 245 1 GTTTTCAGAT 0.972348 -56 * ** **** * * * Masking position 9 Map Score: 5.97948 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 40 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 GAAGAAACCAATTGTCCATATTGCATCAGA 2 36 1 ATTGTCCATA 0.785918 -303 CCATAGCATTTTTATCCATAAGATTAGCGG 2 247 1 TTTATCCATA 0.94585 -92 CTCTCTACTGTTTCTCCATACCCGTTTTTT 2 303 1 TTTCTCCATA 0.935097 -36 GCACAGCAGATTAATCCATAAGATTAGCCT 6 38 0 TTAATCCATA 0.934114 -263 CGAGAAATTAATTCTCCATAGGAGAGCAAT 6 157 0 ATTCTCCATA 0.907758 -144 GTAGATCATCATAATCCATATCATGGTTAT 7 49 1 ATAATCCATA 0.906402 -252 TGGTTATGAAATAATCCATATTAATTATCA 7 72 1 ATAATCCATA 0.906402 -229 TCGCAGCAATTTAATCCATATTTATGCTGT 7 209 1 TTAATCCATA 0.934114 -92 GATGACTCCCTTTCTCCATCAGCTGCAATG 17 278 0 TTTCTCCATC 0.750292 -23 TCAAGAAATCTTCATCCATATTTGTGAAGA 18 133 1 TTCATCCATA 0.864624 -168 ********** Masking position 5 Map Score: 8.91157 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 53 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 GCTGTAAAATTAGGTGGTTAATAATAATCTCAATAATTCAA 7 128 1 TGGTATTTTC 0.640231 -173 AGTGATGTTATAGTGACATTTTTGTTATATCTGATATTATC 8 14 0 TGTTTTTTTC 0.973328 -287 AGTCACTTAATAGTTCAATTGTAGTGATGTTATAGTGACAT 8 36 0 TGTTTTTTTT 0.848987 -265 GCGAGAAATCTCGTTGTCTTATAATCTTTTTAGAAAGCGGT 9 54 1 TGTTTTTTTT 0.848987 -121 CGCTATGTGATGGTGATGTTTTGATCATCTCGTTGTGAAGT 11 24 0 TGTTTTTTTC 0.973328 -277 AGTAATGTCTTTGTCACATTATTGTCATTTCTCATATTATC 11 116 0 TGTTTTTTTC 0.973328 -185 AAGCTATTAGTTGTTATGTTGTAGTAATGTCTTTGTCACAT 11 138 0 TGTTTTTTTC 0.973328 -163 AAATATTTATTTATAGGTTTATTTTCCTATCATTAGTACGT 12 128 1 TATTTTTTTC 0.93059 -80 AGTTTTCCAATCATTTACTTGTATTTTTTTCAATGTCGCCG 17 159 0 TATTTTTTTC 0.93059 -142 TTTTCTGGGATGATAGTCTTTTCTGTTTCTCCCCATTTACA 18 43 1 TATTTTGTTC 0.7163 -258 TCCGCGCGGGTAAGGTTTTTTTAATGGTTTCTCTGAGCATA 19 33 1 TAGTTTTTTC 0.837284 -206 * ** ** * * * ** Masking position 12 Map Score: 5.31377 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 30 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 TCCCTATGGAAGCGATTTCATTTCTCGTTA 8 129 0 AGCGATTTCA 0.909021 -172 CTTTTTAGAAAGCGGTTACAACAAGGGGTA 9 79 1 AGCGGTTACA 0.961158 -96 TAATTCTAAAAGCATTTTCAGTCAATATTA 11 85 0 AGCATTTTCA 0.695615 -216 TAAAAATGTAAACGGTTACAAATCCAGAGG 11 196 1 AACGGTTACA 0.906303 -105 ATACTTAATAAGCTCTTTCAGTGTGGTTAT 11 264 0 AGCTCTTTCA 0.779491 -37 CATAAAATAAAACGCTTTCAAATACAAAAG 12 171 0 AACGCTTTCA 0.914184 -37 TGTTGAGTAAAGCGTTTTCATTTAAACCTT 16 101 0 AGCGTTTTCA 0.94629 -37 TATCTATGTAAACGGTTACATAAACAAGGA 18 272 1 AACGGTTACA 0.906303 -29 ********** Masking position 1 Map Score: 2.76127 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 203 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 TAATGCTTTGTTTTCCGATTAATTTAACGAA 6 230 1 TTTTCCGATA 0.966009 -71 GATATTCCAATTTTCAAATTAAGTTGAATTA 7 161 0 TTTTCAAATA 0.61818 -140 GTTCATGTTTTTATCCAATAACCTCATAACC 8 182 0 TTATCCAATA 0.652498 -119 TATAGGTTTATTTTCCTATCATTAGTACGTA 12 139 1 TTTTCCTATA 0.815123 -69 ATCGATAAAATTTTCTGATAATAACAAATGG 14 174 0 TTTTCTGATA 0.837659 -127 GCCAATCCGATTTTTCGTTTATTCAAGATAT 14 279 0 TTTTTCGTTA 0.53085 -22 TCGAAAGACATTTTTCGATAAATATTCCTAT 17 44 1 TTTTTCGATA 0.887962 -257 TGATCATAAGTTTTCCAATCATTTACTTGTA 17 177 0 TTTTCCAATA 0.935484 -124 ACCTTTTTATTTTTCTGATCATAAGTTTTCC 17 192 0 TTTTCTGATA 0.848418 -109 AAACCTTAAATTTTTCAATTATATATACAAT 18 183 1 TTTTTCAATA 0.803641 -118 ********* * Masking position 4 Map Score: 3.07559 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 160 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 TATCCATCACATAACGACATGTCGCAGCAATTT 7 188 1 ATAAGAATGC 0.841958 -113 GAGGTTATGCACAAAGAAATGACCATTGTTCTT 8 95 1 ACAAGAATGC 0.968566 -206 AGATTATAAGACAACGAGATTTCTCGCGTCTTT 9 48 0 ACAAGAATTC 0.966037 -127 AGTTAACTTCACAACGAGATGATCAAAACATCA 11 19 1 ACAAGAATGT 0.896846 -282 CAATAATGTGACAAAGACATTACTACAACATAA 11 133 1 ACAAGAATTC 0.965491 -168 TTTTGTACGAACAATTTTATTATAGTAATTGAC 12 98 0 ACAATTATTT 0.489539 -110 TGAAAAAAATACAAGTAAATGATTGGAAAACTT 17 168 1 ACAATAATGT 0.710324 -133 AATCCCACAGACAATGTCATTGCAGCTGATGGA 17 261 1 ACAAGTATTC 0.7788 -40 TATACAATTTACAATTAGATTTCTTTTGATATT 18 206 1 ACAATAATTC 0.88915 -95 TTCTCTGAGCATAAAGTTATTTCGTTTTTCCTA 19 61 1 ATAAGTATTC 0.690072 -178 **** ** *** * Masking position 9 Map Score: 2.95956 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 99 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863