AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_ecoli_reg_100.orf -o00330_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 Purged sequences: argI 161 ornithine carbamoyltransferase 1 Input sequences: #1 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #2 speE 105 spermidine synthase = putrescine aminopropyltransferase #3 proS 111 proline tRNA synthetase #4 pepD 260 aminoacyl-histidine dipeptidase (peptidase D) #5 argF 300 ornithine carbamoyltransferase 2, chain F #6 ylbE 266 orf, hypothetical protein #7 speF 300 ornithine decarboxylase isozyme, inducible #8 aspC 184 aspartate aminotransferase #9 putA 300 proline dehydrogenase, P5C dehydrogenase #10 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #11 tynA 247 copper amine oxidase (tyramine oxidase) #12 b1583 134 orf, hypothetical protein #13 speG 34 spermidine N1-acetyltransferase #14 eda 36 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase #15 edd 234 6-phosphogluconate dehydratase #16 argS 209 arginine tRNA synthetase #17 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #18 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #19 cvpA 165 membrane protein required for colicin V production #20 speB 137 agmatinase #21 yqgB 120 orf, hypothetical protein #22 speC 300 ornithine decarboxylase isozyme #23 ygjG 300 probable ornithine aminotransferase #24 agaZ 248 putative tagatose 6-phosphate kinase 2 #25 argG 300 argininosuccinate synthetase #26 argC 153 N-acetyl-gamma-glutamylphosphate reductase #27 argH 60 argininosuccinate lyase #28 adiA 195 biodegradative arginine decarboxylase Motif number 1 ATACATTCGGCGGGCCAGTTTAGCACAAAGAGCC 1 36 0 CGGCATTAGC 0.950698 -65 ATCAGTGGCGCAAGCCAATGCTGCGGTTATCGAA 6 28 1 CAGCATGTGC 0.649782 -239 CTCGTCCACACTGGCTGGATGTGCAACCGGCTTC 6 75 1 CGGCGATTGC 0.939678 -192 TGCTTCACGCCGGGCCGCCAATGCGCTGGCAGGA 6 144 1 CGGCGCATGC 0.981536 -123 TATTTATCAGCGGGGTAACTTTGCTTTTTTCCGG 7 214 1 CGGGACTTGC 0.972431 -87 GATGAAAACGCAGGCTGTTTTTGCAAGACGTGAG 8 83 0 CGGCGTTTGC 0.986848 -102 CGCAATGCGCCCGGCAATCTATACACAAAATCAT 10 37 1 CGGCACTTAC 0.957323 -238 CTTCATCCTTCAAGCCGCCTCTGCCTTGGCTGCG 10 143 0 CAGCGCTTGC 0.954999 -132 GGCATACGGCCCGGGGATCTCTGCGCCCTGACGT 10 208 1 CGGGACTTGC 0.972431 -67 TTAACTGGTGCGGGCAATTTTTGCTCGCTTCATC 16 170 1 CGGCATTTGC 0.983485 -40 GGGTGCCAGACCGGCACCCTCAGCGAAGGCA 17 8 0 CGGCCCTAGC 0.913762 -87 GTCAGACTTGCAGGCAGACTTTGCAGGATTTCGG 17 58 0 CGGCGCTTGC 0.994967 -37 TTCGCGCAATCATGGCACCTTTGCTAAAGCGTGC 22 63 0 CTGGACTTGC 0.791063 -238 TTACTGATGTCTGGCGGTCGGAGCTGGTGACCAG 22 262 1 CGGCGCGAGC 0.948935 -39 GCCCAAAAATCAGGCAATTATTGCCCTGAAAACG 23 186 1 CGGCATATGC 0.941218 -115 CACTATAATGCCTGCAGATTTTACGTCCCGTCTC 25 31 0 CTGCGTTTAC 0.535206 -270 AGCTGCGCCTCCGGCCAACAAAAC 27 1 0 CGGCACAAAC 0.661379 -60 * *** * ** *** Masking position 4 Map Score: 21.6033 Number of sites scoring better than the average of aligned sites = 1328 Number in coding regions = 1225 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 GAGCCTGTTCTACCTTCCAACTGGAACCGTAACAAC 3 86 1 TTTCACTACG 0.610561 -26 TGTGTTGACAACATTTTCTGCTAACCCTGTGACCTGCAA 4 197 1 ATTCGCTCCG 0.970862 -64 TTCGATCCAATGTCTTTCTGCTTCTGCAGAGAATCGGAG 5 131 1 TTTCGCTTCG 0.986692 -170 GGAGATTTACAAAATTCCAACTATTACTGATGAAAACGC 8 106 0 ATTCACTTCG 0.893196 -79 TATACACTTCATCCTTCAAGCCGCCTCTGCCTTGGCTGC 10 144 0 ATTAGCCCCG 0.839256 -131 GGCAACAGGGTAAATTAACGCTTTTACTGAAAGACGAAG 16 12 0 TTTAGCTTCG 0.950544 -198 AACCAACCGCTGATTTCACGCCGCTTCTGATGCAATAGT 16 58 1 TTTAGCCTCG 0.920746 -152 TCTGGCACCCTGACTTGCAACTCCCGCCGAAATCCTGCA 17 32 1 TTTCACTCCG 0.891087 -63 AACGCCATCGACTTTTTATGCCTTTGCGGCATCGGGCAA 19 16 0 ATTAGCCTCG 0.887311 -150 TTTCCCTTTCTATGTTACTGCTCATGCGGTGAAGTTAAC 22 178 1 TTTCGCTTCG 0.986692 -123 GTAAAATCAGAGCGTTTCTGCTTTTACTGATGTCTGGCG 22 239 1 ATTCGCTTCG 0.980488 -62 AATCTTTCGTTTTGTTTCAGTTGATACTGCGTCATGGTG 24 189 0 TTTCGTTTCG 0.807511 -60 ATGATGAGCCTGGATTTCCGCTCTCACTGAATTTTTATG 25 246 0 TTTCGCTCCG 0.980064 -55 CGGCTAAACTATTTTTTTGGCTGATACTGATATCGTCT 28 10 0 ATTTGCTTCG 0.798363 -186 TGCGGGCAAGTATCTTCCGGCCTTTTCGGGCTGTAAAGC 28 138 0 TTTCGCCTCG 0.978173 -58 * ** * *** * * * Masking position 6 Map Score: 17.4143 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 477 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 TGACCGCGGATGCACGGTCAATATTTCTACA 2 26 0 TGCCGGTCAA 0.899214 -80 ACATTTCTTTTGCACTGGTAAACTAAATCAC 3 31 1 TGCCTGGTAA 0.874917 -81 GGGCCGCCAATGCGCTGGCAGGAGATGACCG 6 155 1 TGCCTGGCAG 0.982127 -112 ATGAAGCGCAGGCGCTGGCAATACTGGAGCA 6 240 1 GGCCTGGCAA 0.964568 -27 GACGTGAGATTGCTCTGGAAGGTATAAAAAA 8 60 0 TGCCTGGAAG 0.971697 -125 TCTTTTTGTTCTGTAAGCCGGGTAAGC 10 7 1 TGTCTGTAAG 0.587399 -268 ATACAGTGGATGCCCTGAAAATAGATGTACA 11 90 0 TGCCTGAAAA 0.934971 -158 TGAATCATCCTGCTCTGACAACTCAATTTCA 15 205 1 TGCCTGACAA 0.958356 -30 TTCTTTAACTGGTGCGGGCAATTTTTGCTCG 16 166 1 GGTCGGGCAA 0.634877 -44 AAATAGTTGCCCTGTCAGACTTGCAGGC 17 77 0 TGCCTGTCAG 0.947395 -18 CAATAAAAATGGCGCTGAAAAAATATTCAAC 19 52 0 GGCCTGAAAA 0.878912 -114 TTTTTATTGATGCGCGGGAAGGAAATCCCTA 19 74 1 TGCCGGGAAG 0.94545 -92 AGGCAATTATTGCCCTGAAAACGTGCATTTG 23 197 1 TGCCTGAAAA 0.934971 -104 *** ******* Masking position 10 Map Score: 12.7418 Number of sites scoring better than the average of aligned sites = 1195 Number in coding regions = 1143 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 AATATTGACCGTGCATCCGCGGTCAATGTT 2 32 1 GTGCATCCGC 0.965973 -74 CTGGCTGGATGTGCAACCGGCTTCTTCACT 6 85 1 GTGCAACCGG 0.987991 -182 TCCGCTATCAGGGTAACGGGAGATTTACAA 8 133 0 GGGTAACGGG 0.849711 -52 ATGTGAGAGAGTGCAACCTGATGAAAAATA 9 64 0 GTGCAACCTG 0.833562 -237 TTTTTGAAAGGTGCAACCGCAAAAAATGTG 9 89 0 GTGCAACCGC 0.976692 -212 AGAAATAAACGGGCATACGGCCCGGGGATC 10 197 1 GGGCATACGG 0.86654 -78 TCTGATAGACGTGAAACAGGAGTCATA 10 258 1 GTGAAACAGG 0.71619 -17 GGTGAATGAAGGGCAACGGCGAATAGTTGC 11 13 1 GGGCAACGGC 0.953971 -235 TCTATTTTCAGGGCATCCACTGTATGAAAA 11 96 1 GGGCATCCAC 0.652157 -152 AGCCTCGTGGGTGAATCCGCACGAGGCCTG 15 87 0 GTGAATCCGC 0.84971 -148 ACTGAAACGCCTGTAACCGGAGCTCATAGG 15 148 0 CTGTAACCGG 0.654933 -87 GGTTGGCACAGGGCAACAGGGTAAATTAAC 16 32 0 GGGCAACAGG 0.932203 -178 TGATGCAATAGTGAAAACGGCAATACGCCA 16 85 1 GTGAAAACGG 0.637446 -125 TATGCCTTTGCGGCATCGGGCAATGCGT 19 9 0 CGGCATCGGG 0.820764 -157 AGGAGATGGCGTGCATCGGGCAAACTCCGT 22 112 0 GTGCATCGGG 0.962156 -189 ********** Masking position 5 Map Score: 14.0806 Number of sites scoring better than the average of aligned sites = 1157 Number in coding regions = 1091 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 TTTTTACGCACTGCCTCTCCCTGACGCGGGATA 4 128 1 CTGCTTCCTG 0.910585 -133 AAGGCCAATCATTCTCATTTCTGACTCGACCTG 5 89 1 ATTCCTTCTG 0.618147 -212 CAACCGGCTTCTTCACTTATCAGCGAACTAAAC 6 98 1 CTTCCTTCAG 0.939731 -169 ATCAGGTAGATTGCTTTTTTCAGAATGCAGAAA 7 180 0 TTGCTTTCAG 0.877721 -121 CGGGGTAACTTTGCTTTTTTCCGGCACGATCGA 7 224 1 TTGCTTTCCG 0.902356 -77 TAACGTTAAGTTGCACCTTTCTGAACAACAGGA 9 270 1 TTGCCTTCTG 0.939731 -31 GCCGGGCGCATTGCGCTTACCCGGCTTACAGAA 10 19 0 TTGCCTCCCG 0.877187 -256 CGTTCACAAACTGCATATATCTGATAGACGTGA 10 239 1 CTGCTTTCTG 0.960137 -36 AGGGGATTGCCTGCACCTGCCAGGTTGTTTGGC 11 138 0 CTGCCTCCAG 0.939991 -110 TATCTGCGCTTATCCTTTATGGTTAT 15 4 1 CTGCCTTCCT 0.729663 -231 TCTTCGTCTTTCAGTAAAAGCGTT 16 2 1 CTTCTTTCAG 0.895066 -208 CTCGGCGCTTCTCAGGATTCAAGAG 21 3 1 CGGCCTTCAG 0.834079 -118 TTGCGCGAATTTTCTCCTCTCTGTACGGAGTTT 22 88 1 TTTCCTTCTG 0.867755 -213 ACACTAAACTCTTCCTGTCTCCGATAAAAGATG 25 188 1 CTTCTTTCCG 0.916539 -113 GGCTATTCACCTTCTTATGTCTGGTTGCCAGGT 26 128 0 CTTCTTTCTG 0.910202 -26 **** * * **** Masking position 8 Map Score: 11.944 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 616 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 CGTATTATCTCGCCAAATTACCT 1 88 0 ATTATCTCGC 0.969137 -13 AATGTTAGCTATTATGTTGCGCCCTTTTTT 2 56 1 ATTATGTTGC 0.951502 -50 CCAGATCTCTATAATCTCGCGCAACCTATT 4 62 0 ATAATCTCGC 0.849111 -199 TGAAATATCCATGATGTTGCAACTTTGTGC 9 237 0 ATGATGTTGC 0.905571 -64 TATTGATGATATTATGTCGCCCTATAACTA 12 36 0 ATTATGTCGC 0.955068 -99 TACCGGTAACATGATCTTGCGCAGATTGTA 15 39 1 ATGATCTTGC 0.93407 -196 ATCTCCTTACATTCTCTCGCTTATCGCCGT 22 135 1 ATTCTCTCGC 0.867527 -166 GAAAACGTTAATTATCTTGCCCAAAAATCA 23 168 1 ATTATCTTGC 0.966649 -133 AGTGACTTTCATTATGTTTCTTTTGTGAAT 24 120 1 ATTATGTTTC 0.772292 -129 TCAGAAAACCATTATCTTTCGTTTTATTTT 24 154 1 ATTATCTTTC 0.833624 -95 ********** Masking position 5 Map Score: 8.56707 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 59 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 7 ATGACCGGACCCATGAAAGGGGCGTGCGTG 6 179 1 CCATGAAAGG 0.712891 -88 GCTTAAAAATGAATGAAATGTTAATAAAAG 9 178 0 GAATGAAATG 0.821347 -123 TCGGTGAATGAAGGGCAACGGCGAA 11 6 1 GAATGAAGGG 0.848405 -242 TTGATTTAAGGAATGTAAGGACACGTT 13 18 1 GAATGTAAGG 0.922101 -17 TTATTACACTGACTGAAACGTTTTTGCCCT 15 121 1 GACTGAAACG 0.949014 -114 GAGGATTTATGACTGAAACGCCTGTAACCG 15 159 0 GACTGAAACG 0.949014 -76 TAAATCCTCTGAATGAAACGCGTTGTGAAT 15 180 1 GAATGAAACG 0.967446 -55 CTCGCTTCATCAATGTAAGGTATTCCG 16 193 1 CAATGTAAGG 0.840046 -17 ATAAGCGAGAGAATGTAAGGAGATGGCGTG 22 129 0 GAATGTAAGG 0.922101 -172 AGGCAAAACGAAATGAAACGAAAGTTTTAC 24 24 0 AAATGAAACG 0.768443 -225 TAATGAAAGTCACTGAAACGAGAGTAGCTT 24 104 0 CACTGAAACG 0.891986 -145 ********** Masking position 7 Map Score: 7.98501 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 56 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 CCTTTGTTAACACCCGTAAAAAAAGGGCGCAACATAATA 2 65 0 CACGAAAAAG 0.968282 -41 TCAAGGCGAGCCTGGGACAAAAAAAAGTGATTTAGTTTA 3 49 0 CCGGAAAAAG 0.892092 -63 ACTTTTTAAGCCGTAGATAAACAGGCTGGGACACTTCAC 4 11 0 CCTGAAAAGG 0.915381 -250 CCTTGTCGATCACCCGCAAAACAGTATTGCAGGTCACAG 4 223 0 CACGAAAAGG 0.970689 -38 TTTGCCTCCACCTTTGTAAGAAAGAATTGTGAAATGGGG 5 201 1 CCTGAGAAGG 0.808798 -100 CAAAGTTACCCCGCTGATAAATAAATCAGGTAGATTGCT 7 198 0 CCCGAAAAAG 0.974662 -103 TTGAAAGGTGCAACCGCAAAAAATGTGAGAGAGTGCAAC 9 77 0 CACGAAAATG 0.811163 -224 ATGTTAACTGCCGCAGAGAAAAAGTCTGAGTTATTTTTT 9 118 1 CCCGAAAAGA 0.688054 -183 TTCAGGGCATCCACTGTATGAAAAGCTGGCACACCTGCC 11 102 1 CCCGTGAAAG 0.708291 -146 AAAGCTGGCACACCTGCCAAACAACCTGGCAGGTGCAGG 11 123 1 CACGAAAAAG 0.968282 -125 AATTTGTAATCAGGCGAGAGAAAACTCTG 14 18 1 CAGGAGAAAG 0.719543 -19 AAATTGCCCGCACCAGTTAAAGAAATTAGGGCGGGAGTA 16 151 0 CACGAAAAAG 0.968282 -59 CACTGCAGGACAACAGTAAAATCAGAGCGTTTCTGCTTT 22 224 1 CACGAAACAG 0.794725 -77 GGTGGGCTTGCATTTGCTTAATAGAAAGGCGTTAATAGG 24 51 0 CATGTAAAGG 0.580862 -198 CCAGGCTCATCATCAGTTAATTAAGCAGGGTGTTATTTT 25 272 1 CACGAATAAG 0.8313 -29 AATAGTTTAGCCGTCGATAATAAGCAGTGAAAATAATTT 28 36 1 CCTGAATAGG 0.635866 -160 ** * * *** ** * Masking position 6 Map Score: 9.67474 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 423 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 GGTTCCCATGTTTACATCAGTGGCGCAAGC 6 13 1 TTTACATCAG 0.912508 -254 ACAGCCTGCGTTTTCATCAGTAATAGTTGG 8 99 1 TTTTCATCAG 0.96344 -86 GCGACACTATTTTTCATCAGGTTGCACTCT 9 57 1 TTTTCATCAG 0.96344 -244 GGCAATCCCCTTTGCATCAGTACTGATAAT 11 160 1 TTTGCATCAG 0.976436 -88 CCTGGTACGTTTTGCGTCCGCAGTGGATGG 12 76 1 TTTGCGTCCG 0.895614 -59 CGTTTTCACTATTGCATCAGAAGCGGCGTG 16 74 0 ATTGCATCAG 0.895863 -136 CAAATGGCTGTTTTCGTCAGCAACGTGCGC 16 116 0 TTTTCGTCAG 0.946618 -94 ********** Masking position 7 Map Score: 4.72632 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 102 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 GGCAATACTGGAGCAGGGGAA 6 256 1 GAGCAGGGGA 0.942074 -11 TGAGTTGTCAGAGCAGGATGATTCACAACG 15 200 0 GAGCAGGATG 0.944094 -35 AATGCGCCCCGAACAGGATGACAGGGCGTA 19 130 1 GAACAGGATG 0.846968 -36 CAGGATTCAAGAGCTGGTTACAGTTACTGA 21 23 1 GAGCTGGTTA 0.945886 -98 CTGGCGGTCGGAGCTGGTGACCAGTTTGAC 22 272 1 GAGCTGGTGA 0.957455 -29 GTCCTGTGCAGGTTATATGGTTGTT 23 6 1 GTGCAGGTTA 0.772463 -295 GCAGTAATCTGAACTGGAGAGGAAA 24 234 1 GAACTGGAGA 0.92207 -15 AAATGAAAGTGAACTGGATATTCATTCACA 25 102 0 GAACTGGATA 0.901868 -199 GCTTAAGGGAGAGCAGGAGAAGGCAAAAGT 25 139 0 GAGCAGGAGA 0.978012 -162 ********** Masking position 4 Map Score: 4.78869 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 355 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 CACCCGTAAAAAAAGGGCGCAACATAATAGCTA 2 61 0 AAAAGGCGAC 0.805949 -45 ATGTCAAAAGAGAAGGGCGTGAAT 3 2 0 AGAAGGCGAA 0.942833 -110 GGCAGTGCGTAAAAAGACGCGGACTCATGTGAA 4 110 0 AAAAGACGGA 0.560165 -151 TTATGCTTCTAAAATGGCGGAGAACATGGCGAG 5 39 0 AAAAGGCGGA 0.950826 -262 GCGCATTGGCGGCCCGGCGTGAAGCAGTGTTTT 6 137 0 GGCCGGCGAA 0.741746 -130 TTCAAGTTGCATCAAGGCGGCAAGTGAGCGAAT 10 70 1 ATCAGGCGAA 0.843137 -205 GTTTGTGAACGTCAGGGCGCAGAGATCCCCGGG 10 217 0 GTCAGGCGGA 0.845032 -58 TATTGCATCAGAAGCGGCGTGAAATCAGCGGTT 16 62 0 GAAGGGCGAA 0.861968 -148 CGCATCAATAAAAATGGCGCTGAAAAAATATTC 19 55 0 AAAAGGCGGA 0.950826 -111 CGAACAGGATGACAGGGCGTAAAATCGTGGGAC 19 139 1 GACAGGCGAA 0.963918 -27 CGTTTCGCGCGAAACGGCGATAAGCGAGAGAAT 22 145 0 GAAAGGCGAA 0.973248 -156 TTTGCTTAATAGAAAGGCGTTAATAGGCAAAAC 24 45 0 AGAAGGCGAA 0.942833 -204 TTTACAGCCCGAAAAGGCCGGAAGATACTTGCC 28 140 1 GAAAGGCCAA 0.780295 -56 **** **** ** Masking position 8 Map Score: 7.04228 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 719 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 12 AAATCATAAAGAAGGCCAATCATTCTCATTTCTGAC 5 78 1 GAGGCAACTT 0.984068 -223 TTACAAAGGTGGAGGCAAACCCGTCCGTGTGTGAAA 5 184 0 GAGGCAACTC 0.992049 -117 CGAACTAAACGAAGGCAAAACACTGCTTCACGCCGG 6 121 1 GAGGCAACTC 0.992049 -146 CCTGGCAGGTGCAGGCAATCCCCTTTGCATCAGTAC 11 147 1 GAGGCATCTT 0.924384 -101 GAGAGCAGGAGAAGGCAAAAGTATTCAACAAATGAA 25 125 0 GAGGCAAGTC 0.960654 -176 TTTGTTGGCCGGAGGCGCAGCTTTCCGGCATTGAAT 27 13 1 GAGGCCACTC 0.975156 -48 GCTTATTATCGACGGCTAAACTATTTTTTTGGCTGA 28 25 0 GCGGCAACTT 0.950014 -171 * **** ** * * * Masking position 14 Map Score: 2.66556 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 52 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 TGGATATTTCACGATAACGTTAAGTTGCACC 9 256 1 ACGAAACGTT 0.963641 -45 AGCTCATAGGGCAAAAACGTTTCAGTCAGTG 15 127 0 GCAAAACGTT 0.797919 -108 GCAATACGCCACGCGCACGTTGCTGACGAAA 16 104 1 ACGCCACGTT 0.952415 -106 GGAAATCCCTACGCAAACGTTTTCTTTTTCT 19 94 1 ACGCAACGTT 0.982059 -72 CCGAACTTTCACACTTACGTTCGGTTAT 21 103 1 ACACTACGTT 0.867348 -18 CTGTTACTATACGAAAACGTTAATTATCTTG 23 156 1 ACGAAACGTT 0.963641 -145 GAATAAAAATACACTAACGTTGAGCGTAATA 26 61 1 ACACAACGTT 0.963641 -93 **** ****** Masking position 7 Map Score: 2.81398 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 92 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 AATCGTATCTGCCTCCGATTCTCTGCAGAA 5 152 0 GCCTCCGATT 0.802978 -149 GGACGGGTTTGCCTCCACCTTTGTAAGAAA 5 194 1 GCCTCCACCT 0.864477 -107 GCAGTGTTTTGCCTTCGTTTAGTTCGCTGA 6 117 0 GCCTTCGTTT 0.83168 -150 GTCATCTCCTGCCAGCGCATTGGCGGCCCG 6 154 0 GCCAGCGCAT 0.833738 -113 CTCCAGTATTGCCAGCGCCTGCGCTTCATC 6 239 0 GCCAGCGCCT 0.980825 -28 TGCAAAAACAGCCTGCGTTTTCATCAGTAA 8 92 1 GCCTGCGTTT 0.868952 -93 CCTTCAAGCCGCCTCTGCCTTGGCTGCGTT 10 141 0 GCCTCTGCCT 0.715942 -134 TGGCAGGTGTGCCAGCTTTTCATACAGTGG 11 112 0 GCCAGCTTTT 0.526397 -136 AAAGGGGATTGCCTGCACCTGCCAGGTTGT 11 143 0 GCCTGCACCT 0.912112 -105 TGCCTTCGCTGAGGGTGCCGG 17 2 1 GCCTTCGCTG 0.852725 -93 AATATTCAACGCCATCGACTTTTTATGCCT 19 32 0 GCCATCGACT 0.904229 -134 GAACAAACAAGCCATCGACGGCACCAAACG 22 18 0 GCCATCGACG 0.732661 -283 CCCGATGCACGCCATCTCCTTACATTCTCT 22 122 1 GCCATCTCCT 0.893778 -179 GAATACTTTTGCCTTCTCCTGCTCTCCCTT 25 135 1 GCCTTCTCCT 0.917227 -166 ********** Masking position 3 Map Score: 8.28921 Number of sites scoring better than the average of aligned sites = 2396 Number in coding regions = 2319 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 15 ATTCTCATTTCTGACTCGACCTGGTTGTAGAATTCG 5 99 1 CTGCTGTGTT 0.78439 -202 TATCAGCCACCTGACTGGTAAGGGTTTCTGCATTCT 7 156 1 CTGCTGGGTT 0.978801 -145 TTGCTTTTTTCCGGCACGATCGATTTCTCATTCGAG 7 234 1 CCGCAGGTTT 0.879206 -67 CAAGCCGCCTCTGCCTTGGCTGCGTTCGCTCCCCCG 10 131 0 CTGCTGGGTT 0.978801 -144 ATATAAACACCCTCCTGGTACGTTTTGCGTCCGCAG 12 63 1 CCTCTGGTTT 0.876743 -72 TTTTATTACACTGACTGAAACGTTTTTGCCCTATGA 15 119 1 CTGCTAGTTT 0.656682 -116 GTCGTTAGGCCCGACGAGGAAGGGTTGGATTTGTCA 20 68 0 CCGCGGGGTT 0.9742 -70 GTCGGGCCTAACGACGCGGAAGGGTTTTTTTATATC 20 89 1 ACGCGGGGTT 0.903412 -49 TCGCAAAGTCCTGGCTTGCACGCTTTAGCAAAGGTG 22 46 1 CTGCTGGTTT 0.960436 -255 ATGGTTGTTAACTTCTTGTCAGAGTTTATGTCGGCC 23 27 1 ACTCTGGGTT 0.770178 -274 CATTCACCTTACGGCTGGTGGGTTTTATTACGCTCA 26 81 0 ACGCTGGTTT 0.919594 -73 *** ** * * *** Masking position 15 Map Score: 5.10862 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 324 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789