AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_ecoli_reg_100.orf -o00130_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: caiA 30 probable carnitine operon oxidoreductase Input sequences: #1 caiC 58 probable crotonobetaine/carnitine-CoA ligase #2 caiB 35 l-carnitine dehydratase #3 caiT 300 probable carnitine transporter #4 surA 52 survival protein #5 imp 254 organic solvent tolerance #6 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #7 entC 300 isochorismate hydroxymutase 2, enterochelin biosynthesis #8 lipB 166 protein of lipoate biosynthesis #9 potF 300 periplasmic putrescine-binding protein; permease protein #10 ybjO 59 orf, hypothetical protein #11 ybjF 40 putative enzyme #12 trpE 91 anthranilate synthase component I #13 trpL 137 trp operon leader peptide #14 pabB 73 p-aminobenzoate synthetase, component I #15 ubiG 146 3-demethylubiquinone-9 3-methyltransferase and 2-octaprenyl-6-hydroxy phenol methylase #16 menD 88 2-oxoglutarate decarboxylase; SHCHC synthase #17 menF 300 isochorismate hydroxymutase 2, menaquinone biosynthesis #18 nuoN 186 NADH dehydrogenase I chain N #19 nuoM 89 NADH dehydrogenase I chain M #20 BIME110 38 BIME #21 nuoG 46 NADH dehydrogenase I chain G #22 nuoC 93 NADH dehydrogenase I chain C, D #23 nuoA 300 NADH dehydrogenase I chain A #24 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #25 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #26 cvpA 165 membrane protein required for colicin V production #27 ygcA 56 putative enzyme #28 pepP 25 proline aminopeptidase P II #29 ygfB 161 orf, hypothetical protein #30 dnaG 110 DNA biosynthesis; DNA primase #31 ispB 258 octaprenyl diphosphate synthase #32 yhdT 108 orf, hypothetical protein #33 pabA 31 p-aminobenzoate synthetase, component II #34 yhfG 104 orf, hypothetical protein #35 yigN 140 putative alpha helix chain #36 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone #37 ubiC 111 chorismate lyase #38 yjfG 175 putative ligase #39 lplA 27 lipoate-protein ligase A #40 smp 105 orf, hypothetical protein Motif number 1 AGGGGAACAGCCAGCACTGGTGCGAACATT 7 36 1 CCAGCACTGG 0.686982 -265 GGGAGAGGGGGCAGAACGGCGCAGGACATC 7 94 1 GCAGAACGGC 0.813879 -207 GTTACCCGACCAGGAGCCGGGTAACGGAGA 8 17 0 CAGGAGCCGG 0.559599 -150 TTTCTCCCGGCCAGCACTGCTCGCTATATA 9 173 0 CCAGCACTGC 0.80728 -128 AATGCCGCGACATGCGCGGCATTATGTAGC 10 34 0 CATGCGCGGC 0.970722 -26 CAGCCCGCCTAATGAGCGGGCTTTTTTTTG 12 52 1 AATGAGCGGG 0.774811 -40 AAAACATTATCCAGAACGGGAGTGCGCC 13 9 0 CCAGAACGGG 0.859885 -129 TTTACCTCAAACTGCGCGGCTGTGTTATAA 15 56 0 ACTGCGCGGC 0.969563 -91 ATCACTTACTACGGCGCTGGAAAATCTACT 17 91 1 ACGGCGCTGG 0.555771 -210 CAGAGCGAAACCAGCGCCGCGTTAAGCCCA 18 145 0 CCAGCGCCGC 0.592758 -42 AGTCAGGGTGCCAGACCGGCACCCTCAGCG 24 17 0 CCAGACCGGC 0.838674 -78 CATTTTTATTGATGCGCGGGAAGGAAATCC 26 72 1 GATGCGCGGG 0.887221 -94 CTGCTGATTGACTGCGCTGCCTTCGTCTTT 29 20 1 ACTGCGCTGC 0.850983 -142 ATTCCTTTCGGAAGCACGGCCTTACAACTA 30 48 0 GAAGCACGGC 0.863306 -63 TTCCGAAAGGAATGCGCGGCTTATTTTCGT 30 65 1 AATGCGCGGC 0.943209 -46 ATCGGGGCGAAAAGCCCGGCTTTTGCG 31 242 1 AAAGCCCGGC 0.789613 -17 CTCCGGTACAAAAGAACCGCGCTATT 33 7 0 AAAGAACCGC 0.448664 -25 TTCTTTTGTACCGGAGCCGCC 33 21 1 CCGGAGCCGC 0.779619 -11 CGGGAGAGCAGAAGCGCGGGCAAGATTGCC 34 25 0 GAAGCGCGGG 0.911311 -80 AAAGGCATTTCCTGCGAGGCGCTACGCAAA 35 56 0 CCTGCGAGGC 0.708312 -85 GTTGCCCTCGCCAGCACGGGCATCGGTAAA 37 62 1 CCAGCACGGG 0.941536 -50 ATATGCGTAAAATGAGCGGCAGATTAAAAA 38 143 1 AATGAGCGGC 0.85635 -33 ********** Masking position 4 Map Score: 22.7061 Number of sites scoring better than the average of aligned sites = 5121 Number in coding regions = 4927 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 TGCCTGACTAGCGCCCGCCCAATAACAAAC 1 31 1 GCGCCCGCCC 0.977194 -28 CCTCACCCTAACCCTCTCCCCAAAGGGG 7 9 0 ACCCTCTCCC 0.953872 -292 GCTGGCTGTTCCCCTCACCCTAACCCTCTC 7 21 0 CCCCTCACCC 0.973823 -280 GCGAACATTAACCCTCACCCCAGCCCTCAC 7 57 1 ACCCTCACCC 0.924198 -244 CCTCACCCCAGCCCTCACCCTGGAAGGGAG 7 69 1 GCCCTCACCC 0.977381 -232 GCCGTTCTGCCCCCTCTCCCTTCCAGGGTG 7 84 0 CCCCTCTCCC 0.984398 -217 TCGGGTAACTCCCCTCTCCTCGCTGTGATA 8 38 1 CCCCTCTCCT 0.952722 -129 ATCAGATACCCAGCCCGCCTAATGAGCGGG 12 42 1 CAGCCCGCCT 0.558485 -50 GGCGCACTCCCGTTCTGGATA 13 2 1 GCGCACTCCC 0.959232 -136 CTAACCGCTATCCCTCTACTGTAT 15 5 1 CCGCTATCCC 0.769322 -142 ATTGCACGCGGACCTCTCCCTGTTAAAAGC 17 63 0 GACCTCTCCC 0.887219 -238 AGCGCCCGCCTGGCCAACAAA 18 176 0 GCGCCCGCCT 0.931917 -11 CTCCGCTTCCGCGCACACCTTTTCAATGAT 31 17 1 GCGCACACCT 0.815863 -242 ATTACGCAAAACGCACGCCTTTGACAAGTG 31 85 1 ACGCACGCCT 0.710666 -174 GCCCGCGCTTCTGCTCTCCCGGCGTAACCC 34 34 1 CTGCTCTCCC 0.79342 -71 CCCTACGGTTGCCCTCGCCAGCACGGGCAT 37 55 1 GCCCTCGCCA 0.86995 -57 ********** Masking position 4 Map Score: 19.3664 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 565 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 ACGCGTGGCGTCAGTCGGCTTGCCTGACT 1 6 1 TGGCGCAGGC 0.995355 -53 ATGTGATGTCCTGCGCCGTTCTGCCCCCTCTCCC 7 94 0 CTGCGCGTGC 0.858861 -207 TTTGCCAACCTGGCTACATAATGCCGCGCATGTC 10 22 1 TGGCTCATGC 0.757025 -38 CCGGAATCTCTTGCGACAAATGGCGCAGTAGATT 17 113 0 TTGCGCAGGC 0.994623 -188 CAAGAGATTCCGGCGACACCCGGCATTCGGGTTA 17 134 1 CGGCGCAGGC 0.986713 -167 GAGGAAATGATTGCGTCGCCACGCAATGGAGAGC 18 91 0 TTGCGCGCGC 0.911498 -96 TTTGCGCCTGTCGGCAAAGGGATTT 22 2 1 TTGCGCTGGC 0.980924 -92 AAATGGTCCGTGGTGACTGTCGGCGCAGTAAGCT 22 67 0 TGGTGCTGGC 0.882856 -27 TGAATCGATGTGGCGTCCATCTGCCGTGAAGAGC 23 244 1 TGGCGCCTGC 0.917027 -57 TTTTATGCCTTTGCGGCATCGGGCAATGCGT 26 8 0 TTGCGCAGGC 0.994623 -158 GACTGCTAAAGCGTCAAAAGGCCGGATTTTCC 32 9 1 AAGCGCAGGC 0.808137 -100 CCGCTTATACTTGTGGCAAATGGACACGTTCAGG 34 71 1 TTGTGCAGGA 0.606541 -34 GGGTAAGTTGTTGCGTCAGGAGGCGTT 35 124 1 TTGCGCAGGC 0.994623 -17 ***** ** *** Masking position 7 Map Score: 14.5526 Number of sites scoring better than the average of aligned sites = 637 Number in coding regions = 592 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 TAGCCATTAACGCGTCCACGAGGTTAATAATAATTA 3 203 1 CCGCACGGTA 0.869146 -98 GTACGTTAGTCTCTGACCGTTTGTCACGCGCAACGT 5 200 1 CCTCCGTGCA 0.813689 -55 CCTAAAAGCAAACGCGCACTATGTCAACTCTTGAGG 7 212 0 ACGCACTGCA 0.947729 -89 AAGGCTGAAGACCGAGCTGGCGGACAAGAATTTTAT 8 121 0 ACGCTGGGCA 0.961608 -46 TTTATTGCATATCTTTCAGTGTGACAACTTTTGTTC 9 243 1 ACTCAGTGCA 0.921393 -58 AACGGGTAATCGCGCCCAGGACGACAGCTTCTTCAT 17 267 0 CCGCAGGGCA 0.996069 -34 TAGAATGCGCCCCGAACAGGATGACAGGGCGTAAAA 26 127 1 CCGCAGGGCA 0.996069 -39 GGCAAATGGACACGTTCAGGGAGGCATCAA 34 85 1 CCGCAGGGCA 0.996069 -20 GTGCTGTACAAACGTCCAGTTGGAAAGGCATTTCCT 35 73 0 ACGCAGTGAA 0.869234 -68 TAGGGGCATCACCGTCCAGGATGCCAGGAACGGTGA 37 24 0 ACGCAGGGCA 0.993746 -88 * ** **** * ** Masking position 16 Map Score: 8.34749 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 341 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 AACGCAATCTGCAACTCGGGGTTGCATCTGGT 7 179 0 GAATCGGGGT 0.562242 -122 ATAATGCCGCGCATGTCGCGGCATTGTTTTC 10 39 1 GATTCGCGGC 0.830096 -21 GTAGCATGAAATAATTAGCGCCAACAATTTAG 14 23 0 AAATAGCGCC 0.775134 -51 ACGTAAAACGGGTAATCGCGCCCAGGACGACA 17 277 0 GTATCGCGCC 0.957372 -24 AAACCAGAGCGAAACCAGCGCCGCGTTAAGCC 18 147 0 GAACAGCGCC 0.636603 -40 AGAATTCGTTGAAAATCCGGTCCTGACGGGAC 19 45 1 GAATCCGGTC 0.733149 -45 TATTCCTTGTAAAAGTCCCGTCAGGACCGGAT 19 59 0 AAATCCCGTC 0.632735 -31 CTTACTCATCAAAAGTAGCGCCAGATTCACTG 23 277 0 AAATAGCGCC 0.775134 -24 ACCCTGACTTGCAACTCCCGCCGAAATCCTGC 24 38 1 GAATCCCGCC 0.976682 -57 GTTAAATTGAGAAAGTCTCGCCA 27 44 1 GAATCTCGCC 0.866308 -13 GCTTCCGAAAGGAATGCGCGGCTTATTTTCGT 30 63 1 GAAGCGCGGC 0.938229 -48 ATGAATTGCTAAAAATCGGGGCCT 30 97 1 AAATCGGGGC 0.873648 -14 CGTTTTGCGTAATATTCGCGCCCTATTGTGAA 31 66 0 ATATCGCGCC 0.857063 -193 TTCACAGTAAGGTAATCGGGGCGAAAAGCCCG 31 228 1 GTATCGGGGC 0.865601 -31 TAATCGGGGCGAAAAGCCCGGCTTTTGCG 31 240 1 GAAGCCCGGC 0.875694 -19 AAAAAGGCCGGAAAATCCGGCCTTTTGACGCT 32 20 0 GAATCCGGCC 0.946903 -89 TTGCGCTCAGGTGAATCGCGCCAGCAAATTAC 38 76 1 GGATCGCGCC 0.929447 -100 * ** ******* Masking position 10 Map Score: 14.047 Number of sites scoring better than the average of aligned sites = 1218 Number in coding regions = 1140 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 CCGTGCCTAACACCACTGACGCTATTCGGACA 5 141 1 CACCACTGCC 0.932353 -114 ACCTTCACATCATCAGGGGCGACGATTATACA 11 13 0 CATCAGGGCA 0.972149 -28 GCATCACAACCACCACCGTCAAGCCGACGATC 18 61 0 CACCACCGCA 0.981684 -126 ACCAGAGCGAAACCAGCGCCGCGTTAAGCCCA 18 145 0 AACCAGCGCC 0.826139 -42 CGCCGACAGTCACCACGGACCATTTGCA 22 76 1 CACCACGGCA 0.987528 -18 TCCATTGCTTCACAACGGACACGATTCAACAA 23 14 1 CACAACGGCC 0.893304 -287 TGTCTCTTCTCATCAGGGTAGCTATAGTGTCG 29 72 0 CATCAGGGAC 0.80363 -90 TTTTCTGGTCCACCAGGGCCCAAAGTGGTAGC 29 109 1 CACCAGGGCA 0.985161 -53 TTTCTTCACCCATCAGGGACAAAAA 32 94 1 CATCAGGGCA 0.972149 -15 TAAAGGAAAACATCACCGTTCCTGGCATCCTG 37 12 1 CATCACCGTC 0.767653 -100 ACCGTAGGGGCATCACCGTCCAGGATGCCAGG 37 32 0 CATCACCGCA 0.965729 -80 ******** * * Masking position 5 Map Score: 8.789 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 546 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 TGATATCCGTGTGTCGATTTGGGGAATAT 5 2 0 GGTTGGGAAA 0.96446 -253 GGTAAAAGCACCTTTATATTGTGGGAGATAGCCCTGAT 5 36 0 CTTTGGGGAA 0.757319 -219 TTTTCCGGCTGCGGTCAATTGTGGGACATCGCCTATAA 5 75 1 GGGTGGGGAA 0.958845 -180 TTTGGGGAGAGGGTTAGGGTGAGGGGAACAGCCAGCAC 7 15 1 GGTGGGGGGA 0.956307 -286 CGTGGAGAATGAGTAAAAGTGGGGGAAAAGTATATCAC 8 62 0 GGTGGGGGAA 0.993379 -105 TTTGAATCCGGGATACAGTAGAGGGATAGCGGTTAG 15 9 0 GATTGGGGAA 0.860057 -138 GGCATCAAAAGCGTCTTTGAGAGGGAAAGGAATATCGA 17 168 0 GGTGGGGGAA 0.993379 -133 ATAACCGAGAGCGTAGCGTTGAGGAAATGATTGCGTCG 18 107 0 GGTTGGGAAT 0.685501 -80 ACGCCACATCGATTCATGGGGAGGAATAAAAAAAACCT 23 222 0 GTTGGGGAAA 0.904365 -79 GCTCTGAGATGTGGCTTAACGAGGAAAAAGACGT 25 13 1 GGGAGGGAAA 0.516489 -24 GGATGACAGGGCGTAAAATCGTGGGACACAT 26 145 1 GGTTGGGGAA 0.989396 -21 GGAGTTCCGTTATGGGACAATTAAGGTCA 27 2 1 GGTTAGGGAA 0.822296 -55 TCGTCGTCAAAGGGAGGAATATTCATGATAT 29 141 0 TGTGGGGAAA 0.711743 -21 TGATTTCTCGCGCGGGCAATCTTGCCCGC 34 2 1 GTTGGGGGCA 0.927018 -103 TACGCCGGGAGAGCAGAAGCGCGGGCAAGATTGCCCGC 34 22 0 GGCGGGGGCA 0.8884 -83 CGGATTTGCCGCTTATACTTGTGGCAAATGGACACGTT 34 63 1 GTTTGGGCAA 0.682569 -42 TTACCGATGCCCGTGCTGGCGAGGGCAACCGTAGGGGC 37 53 0 CGTGGGGGCA 0.900547 -59 * ** * * **** * Masking position 13 Map Score: 14.252 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 237 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 GCTTTTACCGTTTTCCGGCTGCGGTCAATT 5 65 1 TTTTCCGGCT 0.915203 -190 CGCTTCTCCGTTACCCGGCTCCTGGTCGGG 8 13 1 TTACCCGGCT 0.96206 -154 AAGAGAACTTTCTCCCGGCCAGCACTGCTC 9 181 0 TCTCCCGGCC 0.964369 -120 TTATTTCATGCTACCCGGCACATAGCCAGT 14 41 1 CTACCCGGCA 0.950614 -33 GATTCCGGCGACACCCGGCATTCGGGTTAT 17 139 1 ACACCCGGCA 0.75213 -162 ATTCACTGCTCTTCACGGCAGATGGACGCC 23 255 0 CTTCACGGCA 0.726992 -46 GCCACCTTCCTGCTGATTGACTGC 29 5 1 CCTTCCTGCT 0.647021 -157 AAAGGCCGGATTTTCCGGCCTTTTTTATTA 32 27 1 TTTTCCGGCC 0.878974 -82 GCGCTTCTGCTCTCCCGGCGTAACCCGGAT 34 38 1 TCTCCCGGCG 0.936333 -67 CCCTAGATTTCTACCCGGCTTAACTACTCC 36 18 0 CTACCCGGCT 0.959538 -77 AAAACTTTCCCTGCAATGTTTATGG 38 6 1 TTTCCCTGCA 0.897545 -170 CATGCGTTATTTTCCCTGCTTCGAACGATT 40 25 0 TTTCCCTGCT 0.915203 -81 ********** Masking position 6 Map Score: 7.45086 Number of sites scoring better than the average of aligned sites = 1074 Number in coding regions = 990 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 9 TTTTGTTCGTTTGTTATTGGGCGGG 1 44 0 TGCGTTTGTT 0.977398 -15 TTATTTTGCGTTCCCGTTTGTTTTATTTTTGT 3 251 0 TTCGTTTGTT 0.828443 -50 ATAGCCCTGATATCCGTGTGTCGATTTGGGGA 5 15 0 TACGTGTGTC 0.785604 -240 CGTTAGTCTCTGACCGTTTGTCACGCGCAACG 5 203 1 TGCGTTTGTC 0.985706 -52 GTTGACATAGTGCGCGTTTGCTTTTAGGTTAG 7 220 1 TGCGTTTGCT 0.943171 -81 ATAAAAAATATGCACGTTTATTGCATATCTTT 9 227 1 TGCGTTTATT 0.773103 -74 TGACAACTTTTGTTCGTTTGTTAACGAACTTT 9 264 1 TGCGTTTGTT 0.977398 -37 ATGCCTGATATACTCGTTTGTCTTGCCAATTA 15 109 1 TACGTTTGTC 0.951119 -38 CTCCTTTCTATAACCTTTTGTCAACTTTAACA 23 140 0 TACTTTTGTC 0.629625 -161 TCCCTGAACGTGTCCATTTGCCACAAGTATAA 34 75 0 TGCATTTGCC 0.698098 -30 CCTTTCCAACTGGACGTTTGTACAGCACAATT 35 81 1 TGCGTTTGTA 0.914298 -60 ** ******** Masking position 7 Map Score: 6.27828 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 169 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 CCCCTTTGGGGAGAGGGTTAGGG 7 2 1 CCCTTTGGAG 0.977195 -299 GAAGAAAAATCCCTTTGCCGACAGGCGCAAA 22 10 0 CCCTTTGGAC 0.988116 -84 CTTTCTATAACCTTTTGTCAACTTTAACAAAA 23 137 0 CCTTTTGAAC 0.787121 -164 TGCCTTCGCTGAGGGTGCCGGTC 24 2 1 GCCTTCGGAG 0.931176 -93 GGAAGGAAATCCCTACGCAAACGTTTTCTTTT 26 90 1 CCCTACGAAC 0.809142 -76 ATAGTGTCGCCCCTTCGCAGACCATGGGTCTA 29 49 0 CCCTTCGGAC 0.983141 -113 GAATATTCCTCCCTTTGACGACGA 29 148 1 CCCTTTGGAC 0.988112 -14 CAAAACGCACGCCTTTGACAAGTGCTACAGTC 31 91 1 GCCTTTGAAG 0.906336 -168 ACCCTAAGTTGCCTTTGTTCACAGTAAGGTAA 31 211 1 GCCTTTGCAC 0.894276 -48 CTTCCACCCTTTGAAAATTTGAGACTTA 40 88 0 CCCTTTGAAT 0.845904 -18 ******* *** Masking position 4 Map Score: 6.30417 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 74 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ATGCTCTGTTGTGAGTAAAAAATAACATCT 3 65 0 GTGAGTAAAA 0.81818 -236 TCCGTGGAGAATGAGTAAAAGTGGGGGAAA 8 72 0 ATGAGTAAAA 0.877821 -95 TAGAGCAAATATGCATAAAAATTTGTTAAA 9 81 1 ATGCATAAAA 0.790236 -220 TGTATTCACCATGCGTAAAGCAATCAGATA 12 20 1 ATGCGTAAAG 0.87256 -72 GGCATTGGATGTGAATAAAGCGTATAGGTT 15 84 0 GTGAATAAAG 0.62626 -63 GACTTTTACAAGGAATAAAGATCGCC 19 74 1 AGGAATAAAG 0.810681 -16 GGTTATAGAAAGGAGTAAAAAACCACATCA 23 157 1 AGGAGTAAAA 0.919997 -144 ATTCATGGGGAGGAATAAAAAAAACCTTAC 23 219 0 AGGAATAAAA 0.838844 -82 GATGCCGCAAAGGCATAAAAAGTCGATGGC 26 22 1 AGGCATAAAA 0.857746 -144 CAGGATGACAGGGCGTAAAATCGTGGGACA 26 143 1 GGGCGTAAAA 0.892971 -23 GCAATGTTTATGGAGTAAAGCGACCGCAAC 38 23 1 TGGAGTAAAG 0.598606 -153 TGCCCGACATATGCGTAAAATGAGCGGCAG 38 135 1 ATGCGTAAAA 0.892736 -41 ********** Masking position 7 Map Score: 7.61338 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 219 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 ATGTTCGCACCAGTGCTGGCTGTTCCCCTCA 7 34 0 CATGCTGGCT 0.929264 -267 GGTAACTCCCCTCTCCTCGCTGTGATATACT 8 41 1 CTTCCTCGCT 0.784143 -126 TCCCGGCCAGCACTGCTCGCTATATAAAAGC 9 168 0 CATGCTCGCT 0.982846 -133 ATGGTGAATACACTGCCCGTT 12 1 0 CATGCCCGTT 0.957762 -91 TATTCACATCCAATGCCTGATATACTCGTTT 15 97 1 CATGCCTGAT 0.916022 -50 ACGCATTGCCCGATGCCGCAAAGG 26 4 1 CATGCCCGAT 0.975601 -162 CCATAAGGTACAATCCCCGCTTTCTTCACCC 32 74 1 CATCCCCGCT 0.981082 -35 CTCAATGCCTGCTCATCAAAAAA 36 82 0 CATGCCTGCT 0.975601 -13 ** ******** Masking position 4 Map Score: 4.88549 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 337 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 AGTCATGCGCTACATAAATTTTTCAGGAGC 2 8 1 CGCAATAATT 0.972715 -28 CAAACGGGAACGCAAAATAAATATTCGTTTTCA 3 263 1 CGCAATAATA 0.960553 -38 ATGATGTCGGCGCAAAAAACATTATCCAGAACG 13 21 0 CGCAAAAATT 0.972715 -117 AAGTATAAGGAGCTACAAAAATAGATTATTGAT 16 38 0 AGCAAAAATA 0.680249 -51 TATACTTAGCCGCAATATTGATACCGGACAAAC 16 64 1 CGCAATTATA 0.793331 -25 CAGTAAGCTTCGCGAAATAGATTTAGGAATAAG 22 43 0 CGCAATAATT 0.972715 -51 GGCAGATGGACGCCACATCGATTCATGGGGAGG 23 236 0 CGCAATCATT 0.892812 -65 ATAAAAATGGCGCTGAAAAAATATTCAACGCCA 26 48 0 CGCGAAAATA 0.835479 -118 ATTCAGAGTGCGCTATAAATATTCACAATAGGG 31 45 1 CGCAAAAATT 0.972715 -214 GGTCGCTTTACTCCATAAACATTGCAGGGAAAG 38 15 0 CTCAAAAATT 0.756966 -161 *** * *** *** Masking position 7 Map Score: 3.20296 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 82 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 GGGCGCTAGTCAGGCAAGCCGACTGACGCCACG 1 14 0 CGCAAGCGAC 0.924732 -45 CCCCCTCTCCCTTCCAGGGTGAGGGCTGGGGTG 7 72 0 CTCAGGGGAG 0.807948 -229 GGCTGAAGACCGAGCTGGCGGACAAGAATTTTA 8 122 0 CACTGGCGAC 0.87625 -45 TATTGCATATCTTTCAGTGTGACAACTTTTGTT 9 245 1 CTCAGTGGAC 0.739482 -56 GGTATGTTTGCTGACTGGCCAGCCAGCTCAAGG 17 204 0 CGCTGGCAGC 0.660459 -97 CGGGTAATCGCGCCCAGGACGACAGCTTCTTCA 17 268 0 CCCAGGAGAC 0.869534 -33 ACAACCACCACCGTCAAGCCGACGATCAGCAAC 18 55 0 CGCAAGCGAC 0.924732 -132 AGCGCCCGCCTGGCCAACAAACCAGAGC 18 169 0 CGCTGGCAAC 0.848772 -18 CGGGAGTTGCAAGTCAGGGTGCCAGACCGGCAC 24 25 0 AGCAGGGGCC 0.6517 -70 CCCTGTCAGACTTGCAGGCAGACTTTGCAGGAT 24 63 0 CTCAGGCGAC 0.982337 -32 GCCTGCAAGTCTGACAGGGCAACTATTT 24 77 1 CGCAGGGAAC 0.94145 -18 GAATGCGCCCCGAACAGGATGACAGGGCGTAAA 26 129 1 CACAGGAGAC 0.888012 -37 CAAATGGACACGTTCAGGGAGGCATCAA 34 87 1 CTCAGGGGGC 0.941729 -18 GGGGCATCACCGTCCAGGATGCCAGGAACGGTG 37 25 0 CTCAGGAGCC 0.863335 -87 * * ***** *** Masking position 5 Map Score: 5.34868 Number of sites scoring better than the average of aligned sites = 1380 Number in coding regions = 1312 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 15 TAATCCGCAGTGCGGTTAATTGAAATGGAAA 4 28 1 TGCGGTTATT 0.945782 -25 GTTTTCCGGCTGCGGTCAATTGTGGGACATC 5 74 1 TGCGGTCATT 0.957371 -181 GACATCACATTGCGCTTATGCGAATCCATCA 7 118 1 TGCGCTTAGC 0.814805 -183 GTATCAATATTGCGGCTAAGTATAAGGAGCT 16 57 0 TGCGGCTAGT 0.942454 -32 CCAGTAGAATTGCGGGTATGTTTGCTGACTG 17 220 0 TGCGGGTAGT 0.967887 -81 ACGGTAGCAGTGCGATCAGGTTTTGTGGAGT 18 26 0 TGCGATCAGT 0.89887 -161 TTCTATTTTGTGCGGGTAAGTTGTTGCGTCA 35 111 1 TGCGGGTAGT 0.967887 -30 TTAAGATTGTTGCGGTCGCTTTACTCCATAA 38 30 0 TGCGGTCGTT 0.839929 -146 ATCTCAATGTTGCGCTCAGGTGAATCGCGCC 38 67 1 TGCGCTCAGT 0.960386 -109 ******** ** Masking position 1 Map Score: 3.19082 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 199 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