AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_ecoli_reg_100.orf -o00790_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 folA 191 dihydrofolate reductase type I; trimethoprim resistance #2 yacA 155 orf, hypothetical protein #3 secA 61 preprotein translocase; secretion protein #4 mutT 59 7,8-dihydro-8-oxoguanine-triphosphatase, prefers dGTP, causes AT-GC transversions #5 pcnB 92 poly(A) polymerase I #6 yadB 36 putative tRNA synthetase #7 dksA 177 dnaK suppressor protein #8 yaiB 300 orf, hypothetical protein #9 phoA 31 alkaline phosphatase #10 nfnB 93 oxygen-insensitive NAD(P)H nitroreductase #11 ybdF 64 orf, hypothetical protein #12 ybdJ 65 orf, hypothetical protein #13 ybdK 300 orf, hypothetical protein #14 lipB 166 protein of lipoate biosynthesis #15 helD 122 DNA helicase IV #16 rnt 102 RNase T, degrades tRNA #17 lhr 92 member of ATP-dependent helicase superfamily II #18 ntpA 117 dATP pyrophosphohydrolase #19 folE 257 GTP cyclohydrolase I #20 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #21 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #22 hmpA 300 dihydropteridine reductase, ferrisiderophore reductase activity #23 ygcM 300 putative 6-pyruvoyl tetrahydrobiopterin synthase #24 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #25 ygiG 101 putative kinase #26 folP 44 7,8-dihydropteroate synthase #27 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #28 ftsJ 125 cell division protein #29 yhhN 140 putative enzyme #30 zntA 73 zinc-transporting ATPase #31 gmk 251 guanylate kinase #32 rpoZ 54 RNA polymerase, omega subunit #33 rep 174 rep helicase, a single-stranded DNA dependent ATPase #34 dapF 300 diaminopimelate epimerase #35 uvrD 83 DNA-dependent ATPase I and helicase II #36 recQ 126 ATP-dependent DNA helicase #37 dnaB 82 replicative DNA helicase; part of primosome #38 mgtA 300 Mg2+ transport ATPase, P-type 1 #39 lplA 27 lipoate-protein ligase A #40 smp 105 orf, hypothetical protein Motif number 1 CGTCGATTATCGCCGTACTTCGCGGCATACTTTGCTT 11 12 1 CGTTGCGGCA 0.613063 -53 CCCCACTTTTACTCATTCTCCACGGAGATGCCGTTTT 14 76 1 ACTTACGGAG 0.734638 -91 AGAATTTTATCCTGATACAAAACGGCATCTCCGTGGA 14 94 0 CCTAACGGCA 0.836664 -73 TTCTCTTAATACGGATAAATTGCAGCGCGCATTATGA 16 72 0 ACTAGCAGCG 0.606017 -31 TTTAACATCTGCTGATGAAAGGCAGCGGCAATTACAA 19 107 1 GCTAGCAGCG 0.70408 -151 ATAACTTTGCCCCCACGCAGGGCGGAGGCGTCACACC 19 214 1 CCCAGCGGAG 0.927062 -44 TATAGGCGGTCCTGTTGGACAACGGCGAACAGTATAA 22 25 1 CCTAACGGCG 0.980893 -276 AAACAGCCTTTCCGGTACTCTACGGCGGTTTTATCGT 23 260 1 TCTTACGGCG 0.886741 -41 TGTATATCTGCCTGACTATCTACAGCGGAG 31 4 0 CCCTACAGCG 0.92129 -248 CTACATACGAGCTTATTATACACGGCGCGGCCATGTG 31 191 0 GCTTACGGCG 0.955322 -61 ACATCCGCAGCCAACCGGTTAGCGGCTTACACGCGGT 33 88 1 CCCTGCGGCT 0.893146 -87 GCGTCTCTACCGGTTTGGTCGGCGGCGGTGCGTTTTT 34 170 0 CGTTGCGGCG 0.968626 -131 GTATATATACCCAGCTTTTTGGCGGAGGGCGTTGCGC 35 22 1 CCTTGCGGAG 0.977277 -62 CTCCGCCCAACCTATTTTTACGCGGCGGTGCCA 35 61 1 CCTTGCGGCG 0.995365 -23 ATTGGATTCTCCTTATTATTTGCGGCGCTTTTTTCAC 38 66 1 CCTTGCGGCG 0.995364 -235 TGATCCCACGCCTCTCCCTCGACGGAGATTAAAACTT 38 125 1 CCCTACGGAG 0.942515 -176 TTCCGGTAAGCCCGTCTTTTCACGGCGTTACCGGATG 38 162 1 CCCTACGGCG 0.987905 -139 ** * * ****** Masking position 15 Map Score: 19.9451 Number of sites scoring better than the average of aligned sites = 1346 Number in coding regions = 1282 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 GTGAACCAGTCGTTTTTTTTTGAATTTTATA 2 69 1 CGTTTTTTTT 0.906879 -87 ACGGTGCGAACGCTGTTTTCTTAAGCACTTT 2 113 1 CGCTTTTTCT 0.983154 -43 TATGATTAGCCGCTATTTTTTTGTCCTGAAT 5 13 1 CGCTTTTTTT 0.96249 -80 TTACCCGAGTCGCTAATTTTTGCCGCAAG 5 74 1 CGCTATTTTT 0.673306 -19 AAATCTATAGCGCATTTTTCTCGCTTACCAT 10 16 1 CGCATTTTCT 0.824174 -78 AAGCTGAACCCGTTTTTTTCTGCATGACTCA 13 95 1 CGTTTTTTCT 0.956803 -206 TACATTGCAGGGCTATTTTTTATAAGATGCA 22 239 1 GGCTTTTTTT 0.78721 -62 GTACCGGAAAGGCTGTTTTTTCGCATTATCT 23 247 0 GGCTTTTTTT 0.78721 -54 GCATTTCAATCGCTGTTCTCTTTCAGCGAAA 24 108 1 CGCTTTCTCT 0.887871 -43 AGTATCCTGACGCTGTTTTTAACACAGTTGT 27 53 1 CGCTTTTTTA 0.873411 -47 TCCTTGAATTCGTTATTTTTTCGTAAGCGGA 29 114 0 CGTTTTTTTT 0.906879 -27 CGTTACGACCCGATATTTTCTAAGTCTAATG 33 13 1 CGATTTTTCT 0.821376 -162 GGCGGCGGTGCGTTTTTATCTGCAGGCGGGA 34 156 0 CGTTTTATCT 0.781445 -145 GTGGCGCGATCGTTTTTATCCGGCACCGTGG 34 216 0 CGTTTTATCC 0.509285 -85 TAAAAACAGGCGCTATTTTCAGCGCCTGCGC 36 91 0 CGCTTTTTCA 0.940092 -36 TTATTTGCGGCGCTTTTTTCACTTACCGGAG 38 81 1 CGCTTTTTCA 0.940092 -220 TAGCCTCATGCGTTATTTTCCCTGCTTCGAA 40 30 0 CGTTTTTTCC 0.865396 -76 **** ****** Masking position 7 Map Score: 17.0576 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 496 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 AGAGCGTGGACTCGCCAGCAGAATATAAAAT 1 86 1 CCGCCAGCAG 0.973633 -106 AGTAATTTTGCGTGCCAGCAGATTACAAGGT 10 57 0 CTGCCAGCAG 0.969584 -37 GTGAACTGATGGTGCCTGAAGCAATTTGGCT 13 184 0 GTGCCTGAAG 0.976261 -117 GTGAACTCATCGCGCCCGCATCTTTACTGCA 16 24 1 CCGCCCGCAT 0.811758 -79 TCGAGTCGATGCCTGATGACATGCAATG 17 8 1 GTGCCTGATG 0.893611 -85 CCTCACTATAGATGCCTGAATCATTGCATGT 17 29 0 GTGCCTGAAT 0.891156 -64 GCGGAGGCGTCACACCTGCAGGAGAAATCAT 19 235 1 CCACCTGCAG 0.929284 -23 AAAGCCTTGCGTAGCCTGAAGGTAATCGTTT 22 106 0 GAGCCTGAAG 0.880523 -195 GTCCTGCCTGCTTTTTGGCTAAC 25 89 0 CTGCCTGCTT 0.784753 -13 CGCTCTATTTCCCGCCTGCAGATAAAAACGC 34 147 1 CCGCCTGCAG 0.990464 -154 GTGGCGAAGCCTTACCTGAAGGTAATAAAGC 38 232 0 CTACCTGAAG 0.891434 -69 AAGGCTTCGCCACGCCTGAAGACATTTCTGT 38 250 1 CCGCCTGAAG 0.986872 -51 GAGACTTAATGTTGCCAGAAGCAATGGATAC 40 65 0 GTGCCAGAAG 0.935984 -41 * ********* Masking position 6 Map Score: 13.2848 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 914 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 TTCTTAAGCACTTTTCCGCACAACTTATCT 2 130 1 CTTTTCCGCA 0.931359 -26 AAGGCGCAGGATTCTGCGCCTTTTTTATAG 4 30 1 ATTCTGCGCC 0.78714 -30 AGTCGCTAATTTTTGCCGCAAG 5 81 1 TTTTGCCGCA 0.848856 -12 AGGAAAAGCGTATTTGCGCACGCGACCAGA 7 38 0 TATTTGCGCA 0.854516 -140 AGCGGCCTCATTTTTCCCCCGAACATGGGG 7 129 1 TTTTTCCCCC 0.90706 -49 AAACAAAAAATATTTGCGCAAAGTATTTCC 8 194 1 TATTTGCGCA 0.854516 -107 CTGTGATATACTTTTCCCCCACTTTTACTC 14 60 1 CTTTTCCCCC 0.889084 -107 GGATAAAATTCTTGTCCGCCAGCTCGGTCT 14 119 1 CTTGTCCGCC 0.879339 -48 AAAACGTTACAATTGCCGCCCATTACTGAA 15 33 0 AATTGCCGCC 0.590023 -90 AATACTGGATTATGTGCGCCGCCTCACGCA 19 158 1 TATGTGCGCC 0.759309 -100 AGCTTAATAACTTTGCCCCCACGCAGGGCG 19 208 1 CTTTGCCCCC 0.731546 -50 CATAATGCCATTTTTGCCCCCAACAGACCA 21 83 0 TTTTTGCCCC 0.896882 -73 AGCAAAGCTGTTTCTGCGCCCTGTCAGCGC 23 15 1 TTTCTGCGCC 0.920117 -286 TAAATCAGCGATTTTGCGCAACAAAGTCGT 23 214 1 ATTTTGCGCA 0.825379 -87 GGAAAGGCTGTTTTTTCGCATTATCTAAAA 23 243 0 TTTTTTCGCA 0.590723 -58 AGGGTATGCTTATTTCCGCATTTTCCGATG 29 21 0 TATTTCCGCA 0.868261 -120 TTGCTCACACTTTTTGCGCAAAGTTGTTGC 31 152 0 TTTTTGCGCA 0.936398 -100 GGGCGTTGCGCTTCTCCGCCCAACCTATTT 35 48 1 CTTCTCCGCC 0.913908 -36 ********** Masking position 3 Map Score: 13.6723 Number of sites scoring better than the average of aligned sites = 1713 Number in coding regions = 1557 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 5 AATGCGGCGAGTCCAGGGAGAGAGCGTGGACTCGC 1 66 1 GCAGGAGAGC 0.927315 -126 TGGTTCACCTGGCCGGAGAGAGTGCCAGATTTGCC 2 42 0 GCGGGAGAGC 0.952519 -114 GAGCTATAAAAAACGGTGCGAACGCTGTTTTCTTA 2 101 1 ACGGGCGAGC 0.911218 -55 AGTTATGGCAGTGCTGACTGGTGGCGAAGAATTTT 13 132 0 GCTGCTGGGC 0.952595 -169 TCAGTATAGAAGTCGGAGCGGCTGGGCGAGATGCG 13 248 0 ACGGGCGGGG 0.899368 -53 AGCCTGGGAGATTGGCTCGTAAGGC 14 152 0 ACTGGAGAGG 0.861484 -15 CTATGTGAATGGGATGAGCGAAGGCAGTCAACGAA 18 85 1 GATGGCGAGC 0.678707 -33 TGACGCCTCCGCCCTGCGTGGGGGCAAAGTTATTA 19 212 0 GCTGGTGGGC 0.972628 -46 ATCGAACCAGGTTCAGACAGAAAGGTCCCTA 21 135 1 GCAGCAGAGG 0.747647 -21 TGTTTTATGGGCGCTGACAGGGCGCAGAAACAGCT 23 20 0 GCTGCAGGGC 0.97445 -281 AGCACAAGGGGACCTGGCTGGTTGCCGGATACCGT 24 35 0 GCTGCTGGGC 0.952595 -116 GCAAAAACGGAGTCTGCGAGGACGCTTCCTGAAAA 31 65 1 ACTGGAGGGC 0.969725 -187 TACTCTCTTCAGCCTGACGGGCTGCGGTCTGAAAG 34 109 1 ACTGCGGGGC 0.847702 -192 GTACTGTTTCAGACAGTGCGGAGGGACTCCTT 38 279 1 ACAGGCGGGG 0.850382 -22 * *** **** ** Masking position 6 Map Score: 8.36945 Number of sites scoring better than the average of aligned sites = 1078 Number in coding regions = 1026 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 TTAGATAATTGCTATCCGGAAAAGCATCTG 7 91 1 GCTATCCGGA 0.946636 -87 GGTATCCGCTGATTCGTTAC 20 60 0 GGTATCCGCT 0.845118 -10 AAAAGAAATCCGTTTCCGGTTGCAAGCTCT 22 146 0 CGTTTCCGGT 0.938707 -155 ATTAGTTATCGCTATCCCGTCTTTAATCCA 23 88 0 GCTATCCCGT 0.820629 -213 GAAAAAACAGCCTTTCCGGTACTCTACGGC 23 256 1 CCTTTCCGGT 0.92775 -45 ATCTTTTAACGGTATCCGGCAACCAGCCAG 24 27 1 GGTATCCGGC 0.92543 -124 CGCCGGAAGTGGTATCCGGTTAGCCAAAAA 25 71 1 GGTATCCGGT 0.979046 -31 GCCCCGGGGTTTTCGGTACAAATACAG 26 28 0 GGTTTTCGGT 0.755986 -17 CGTGTAAGCCGCTAACCGGTTGGCTGCGGA 33 91 0 GCTAACCGGT 0.939775 -84 GAAAAGACGGGCTTACCGGAAAAGTTTTAA 38 153 0 GCTTACCGGA 0.856032 -148 CTTTTCACGGCGTTACCGGATGCGTAAGGC 38 177 1 CGTTACCGGA 0.734198 -124 ********** Masking position 3 Map Score: 6.74879 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 556 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 TTTAGGCGAAGGAGAATAAGCAAAGTATGCCGC 11 33 0 GGAATAAGAA 0.827225 -32 GAGCGGCTGGGCGAGATGCGGAAGTTCTGGAAT 13 235 0 GCGATGCGAA 0.896878 -66 GCATCTCCGTGGAGAATGAGTAAAAGTGGGGGA 14 74 0 GGAATGAGAA 0.923364 -93 AACATCGTTATGCAAATACGGAAGTGAAAGTTA 19 75 0 TGAATACGAA 0.654565 -183 CCCCACGCAGGGCGGAGGCGTCACACCTGCAGG 19 224 1 GGGAGGCGCA 0.779657 -34 AAGTCGTTTTAGATAATGCGAAAAAACAGCCTT 23 237 1 AGAATGCGAA 0.893715 -64 ATGAATCTGTGGATAATACGCACATTTCGCCGG 25 44 1 GGAATACGAC 0.791367 -58 ATCCCTCATCGGAAAATGCGGAAATAAGCATAC 29 15 1 GGAATGCGAA 0.983745 -126 TGTATCCTTCGGTTAATGAGAAAAAACTTAACC 30 41 1 GGAATGAGAA 0.923364 -33 GTGAATGACAGGCAAATGCGGAAGCAGCTACGC 31 114 1 GGAATGCGAA 0.983745 -138 TATCATCGCAGGAGAAGACGTAAAAG 34 4 0 GGAAGACGAA 0.9239 -297 CGACCAAACCGGTAGAGACGCAAACGCAATCCA 34 186 1 GGGAGACGAA 0.899141 -115 TCACGGCGTTACCGGATGCGTAAGGCCGTGACG 38 181 1 ACGATGCGAA 0.547184 -120 ** ****** ** Masking position 6 Map Score: 6.10543 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 556 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 AAACGTGATGGAACGGCTGTAA 6 1 0 GACGGCTGAA 0.948751 -36 ATATCATGCAGGATGCGTGGAATAGCCTCACT 17 53 0 GGTGCGTGAA 0.868881 -40 TGTCCAACAGGACCGCCTATAAAGGCCAAAAA 22 14 0 GACGCCTAAA 0.935519 -287 CGCACCTTTGGAGCGCCTGAAACCTGCGGCGC 24 76 1 GACGCCTGAA 0.991139 -75 ATTTGAATGTGACCGCGTGTAAGCCGCTAACC 33 104 0 GACGCGTGAA 0.975353 -71 TTTCATTATGGATTGCCTGTAAAGTTCATCGC 34 48 0 GATGCCTGAA 0.986018 -253 GTAATACAGTGAGTGCCTTAAACACGTTTTTC 34 76 0 GATGCCTTAA 0.901448 -225 CCCGATTGCCTGAAATAAAAACAGG 36 112 0 GATGCCTGAA 0.986018 -15 ** ****** ** Masking position 11 Map Score: 5.83634 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 131 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CTCTCCCTGGACTCGCCGCATTACAATGAA 1 58 0 ACTCGCCGCA 0.944128 -134 AGAGAAAAAAACTCACCGCATGGCCATTTA 8 42 0 ACTCACCGCA 0.987809 -259 CCGAAACAGGACTCACTGTATAAATAAACA 13 38 0 ACTCACTGTA 0.931113 -263 CCGGGCGTGAACTCATCGCGCCCGCATCTT 16 18 1 ACTCATCGCG 0.857609 -85 AGTGAAAGTTACTCACAGCACATTGAATAA 19 56 0 ACTCACAGCA 0.956717 -202 ATAATCCAGTATTCACAGCGATAATTATTG 19 141 0 ATTCACAGCG 0.621645 -117 CTTTTGCTATTCTCACCGTAACGAATCAGC 20 43 1 TCTCACCGTA 0.829514 -27 CATGGGGATAACTCATCGTAACCAATTGCG 28 96 0 ACTCATCGTA 0.856686 -30 TTTGCCTGTCATTCACTGCAATAAAGACGA 31 100 0 ATTCACTGCA 0.845567 -152 TGTTTAAGGCACTCACTGTATTACTTACTC 34 84 1 ACTCACTGTA 0.931113 -217 ********** Masking position 3 Map Score: 5.29458 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 257 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 AGAAGTCGGAGCGGCTGGGCGAGATGCGGAA 13 245 0 GCGGCGGGCG 0.994199 -56 CCGTTACCCGGCTCCTGGTCGGGTAACTCCC 14 20 1 GCTCCGGTCG 0.945179 -147 AAATTCTTGTCCGCCAGCTCGGTCTTCAGCC 14 124 1 CCGCCGCTCG 0.964282 -43 TCTCCTGCCGGGCGTGAACTCATC 16 4 1 CCTGCGGGCG 0.984312 -99 GCGCCTGAAACCTGCGGCGCGCATTTCAATC 24 88 1 CCTGCGCGCG 0.984276 -63 GGTTTGGTCGGCGGCGGTGCGTTTTTATCTG 34 165 0 GCGGCGTGCG 0.977353 -136 GCTATTTTCAGCGCCTGCGCGAGAAACTGCA 36 80 0 GCGCCGCGCG 0.992394 -47 ***** ***** Masking position 5 Map Score: 6.23197 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 548 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 GAGGTGTACTATTTTTACCCGAGTCGCTAATTTTTGCCG 5 60 1 ATACCGTCGA 0.687122 -33 CCGTTCCATCACGTTTACCACAGGCGGGAA 6 17 1 ATACCGGCGA 0.970882 -20 GTTAATTTACATTCTGGTCGCGTGCGCAAATACGCTTTT 7 26 1 ATGTCTGCGA 0.933887 -152 GGTGGCGAAGAATTTTGACGATTGAGTCATGCAGAAAAA 13 109 0 ATGACTGAGA 0.52674 -192 ATTTCTTATCAGTGTAACCGTCAGAGAAAACGTGCTCCA 15 70 0 ATACCAGAGA 0.685093 -53 GCGTAGCCTGAAGGTAATCGTTTGCGTAAATTCCTTTGT 22 90 0 ATATCTGCGA 0.955163 -211 CGGTACAAATACAGTCATCTGATGCGGGAAC 26 3 0 ATATCTGCGA 0.955163 -42 TTGTAATAAGAGGTTAATCCCTTGAGTGAC 27 80 1 ATATCTGAGA 0.846686 -20 GGGATAACTCATCGTAACCAATTGCGTAAATTTTTACGC 28 83 0 ATACCTGCGA 0.985085 -43 CCTGGGATGGACCATCGCCAGTGGCGCGATCGTTTTTAT 34 228 0 ATGCCGGCGA 0.956726 -73 TCCAGCATCCAGGATTACCCTCTCAGAGACTAAAAGCAT 36 41 1 ATACCTCAGA 0.625673 -86 AACAGGCGCTATTTTCAGCGCCTGCGCGAGAAACTGCAA 36 79 0 ATAGCTGCGA 0.905631 -48 GTCTTTTCACGGCGTTACCGGATGCGTAAGGCCGTGACG 38 175 1 GTACCTGCGA 0.905968 -126 CAATGGATACAAGGTAGCCTCATGCGTTATTTTCCCTGC 40 36 0 ATGCCTGCGA 0.977676 -70 * * *** **** * Masking position 19 Map Score: 8.75865 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 325 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 AGATAAGTTGTGCGGAAAAGTGCTTAAGAAAA 2 128 0 TCGGAAAATG 0.6231 -28 GACAACTGTGTGAGGAAAAGCGTATTTGCGCA 7 48 0 TAGGAAAACG 0.931039 -130 ATAATTGCTATCCGGAAAAGCATCTGCTATTT 7 95 1 TCGGAAAACA 0.960986 -83 TAGTGCGTGTTAAGGAGAAGCAAC 7 164 1 TAGGAGAACA 0.676345 -14 ATACTTTGGATAAGGAAATACAGAC 8 286 1 TAGGAAATCA 0.605462 -15 TGCCGCCCATTACTGAAAACCACAGTAAAGCG 15 18 0 TCTGAAAACA 0.929821 -105 TAACATCTGCTGATGAAAGGCAGCGGCAATTA 19 109 1 TATGAAAGCA 0.550242 -149 ATCACATTCTTTCTGAAAAACACCAAAGAACC 22 204 1 TCTGAAAACA 0.929821 -97 TTAACCAACCTAATGAAAAACAAATGAATTTA 23 168 1 TATGAAAACA 0.876947 -133 ACGACTTTGTTGCGCAAAATCGCTGATTTATC 23 212 0 TCGCAAAACG 0.727464 -89 TTTTAGATAATGCGAAAAAACAGCCTTTCCGG 23 243 1 TCGAAAAACA 0.638648 -58 CGAGGACGCTTCCTGAAAATCGTCTTTATTGC 31 81 1 TCTGAAAACG 0.931039 -171 AGGCAATCCATAATGAAAAACGTGTTTAAGGC 34 62 1 TATGAAAACG 0.878964 -239 * ******* ** Masking position 6 Map Score: 5.02625 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 310 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 13 GAGAGAGTGCCAGATTTGCCAGTCGAATTT 2 32 0 CAGATTTGCC 0.976979 -124 GGCGCAGAAACAGCTTTGCTTACT 23 5 0 CAGCTTTGCT 0.95722 -296 TTTTGCCACTCGGCTTTGCTTTCATCACGT 31 41 0 CGGCTTTGCT 0.948849 -211 TAGCTGCTTCCGCATTTGCCTGTCATTCAC 31 114 0 CGCATTTGCC 0.88968 -138 GGTATATATACAGATTTGCTGA 35 3 0 CAGATTTGCT 0.964272 -81 TGCTGGATTCCAGATTTGCCAACCACTCAA 36 18 0 CAGATTTGCC 0.976979 -109 ********** Masking position 5 Map Score: 3.34235 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 105 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 14 GAATGAAGATAAGTTGTGCGGA 2 144 0 AAGAAGATAA 0.690521 -12 GTTAACTTATAATTAAGAGAAAAAAACTCAC 8 56 0 AATAAGAGAA 0.920536 -245 ATTATAAGTTAACGAAGAGAATATATTTCAT 8 74 1 AAGAAGAGAA 0.957912 -227 GTAATTATTTAAATAAGAGAAACGTTTCGCT 8 156 1 AATAAGAGAA 0.920536 -145 CGACTTCTATACTGAATAGAAAACGCCAACA 13 268 1 ACGAATAGAA 0.741775 -33 GAAAACGCCAACATAAGAGAAACCT 13 286 1 ACTAAGAGAA 0.937162 -15 AATTTATCCGTATTAAGAGAATCAG 16 88 1 TATAAGAGAA 0.646163 -15 TTATGCAAATACGGAAGTGAAAGTTACTCAC 19 70 0 ACGAAGTGAA 0.822038 -188 CGCCCATAAAACAGAAGAGAAGGTAAGGTTA 23 42 1 ACGAAGAGAA 0.966999 -259 ** ******** Masking position 6 Map Score: 3.19612 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 82 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 AAACCGTCGTCGACTGGTGCGAGGATGATG 1 126 0 CGACTGGTGC 0.935772 -66 CAAAAAAAAACGACTGGTTCACCTGGCCGG 2 61 0 CGACTGGTTC 0.881252 -95 ATCACGTTTACCACAGGCGGGAA 6 24 1 CCACAGGCGG 0.902939 -13 AAGGGCAGGGCCACTGGCTCTGCCCTTTTG 20 19 1 CCACTGGCTC 0.952599 -51 TTCAGGCGCTCCAAAGGTGCGAATAATAGC 24 67 0 CCAAAGGTGC 0.852538 -84 CTGTCACCACAAGTTCTTGTTATTTC 24 135 0 CCACAAGTTC 0.746285 -16 TGCGTATTATCCACAGATTCATCGTTGAAC 25 36 0 CCACAGATTC 0.746372 -66 TTAAAAAGCTCCACAGGTGAAGAAATGACT 32 33 0 CCACAGGTGA 0.930688 -22 AACGATCGCGCCACTGGCGATGGTCCATCC 34 233 1 CCACTGGCGA 0.90027 -68 ********** Masking position 3 Map Score: 1.18437 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 865 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454