AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 pcnB 92 poly(A) polymerase I #2 yadB 36 putative tRNA synthetase #3 dksA 177 dnaK suppressor protein #4 rpsB 300 30S ribosomal subunit protein S2 #5 tsf 257 protein chain elongation factor EF-Ts #6 pyrH 146 uridylate kinase #7 frr 291 ribosome releasing factor #8 yaeM 91 putative ATP-binding component of a transport system #9 yaeS 185 orf, hypothetical protein #10 cdsA 120 CDP-diglyceride synthetase #11 yaeT 29 orf, hypothetical protein #12 hlpA 121 histone-like protein, located in outer membrane or nucleoid #13 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #14 dnaE 36 DNA polymerase III, alpha subunit #15 ldcC 98 lysine decarboxylase 2, constitutive #16 yaeR 29 orf, hypothetical protein #17 mesJ 64 cell cycle protein #18 ychF 116 putative GTP-binding protein #19 pth 277 peptidyl-tRNA hydrolase #20 prsA 150 phosphoribosylpyrophosphate synthetase #21 hemM 213 an enzyme in main pathway of synthesis of 5-aminolevulinate, possibly glutamyl-tRNA dehydrogenase #22 yejH 148 putative ATP-dependent helicase #23 rplY 124 50S ribosomal subunit protein L25 #24 folP 44 7,8-dihydropteroate synthase #25 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #26 ftsJ 125 cell division protein #27 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase Motif number 1 TCAGGACAAAAAAATAGCGGCTAATCATAGC 1 11 0 AAAATGCGGC 0.909599 -82 TGTTCGGGGGAAAAATGAGGCCGCTATAAAT 3 123 0 AAAAAGAGGC 0.868201 -55 TTCGAGTTGCAGAAAGGCGGCAAGCTCGAGA 5 38 1 AGAAAGCGGC 0.894259 -220 TATAAAAGTGAAAAAGGGGGCCATATGCAGG 5 190 0 AAAAAGGGGC 0.986911 -68 TTATCAAAAAGGAGCCGCCTGAGGG 6 5 1 CAAAAGGAGC 0.829915 -142 ATGGGCACAAAAAGAAGCCGCCCTCAGGCGG 6 25 0 AAAGAGCCGC 0.865337 -122 CTTGAACGACAAAAACGCCGCTCAGTAGATC 8 14 1 AAAAAGCCGC 0.983766 -78 GAATAAAAAGCAAAACGCCGCCAGCCGATCC 8 50 0 CAAAAGCCGC 0.980304 -42 GCCTATACAAAAAAAAGCCGTGTAAAACCAC 9 118 0 AAAAAGCCGT 0.727881 -68 CGGCAACAGAAACAACGCCGCGATGACGACG 10 64 0 AACAAGCCGC 0.865337 -57 CAAAAGTTCTGAAAAAGGGTCACTTCGGTGG 15 15 1 GAAAAGGGTC 0.81385 -84 CCGTGGCGATAAAAAAGGGCCACCGAAGTGA 15 34 0 AAAAAGGGCC 0.84714 -65 ACGTTACCGGGCAAATGCGGCGATGACAAGC 17 12 0 GCAAAGCGGC 0.848661 -53 GGCACTCGGCAAAAATGCCGCAGACAACGAC 18 11 0 AAAAAGCCGC 0.983766 -106 GCAATTACTCCAAAAGGGGGCGCTCTCTTTT 21 81 0 CAAAAGGGGC 0.984109 -133 TTTGCGTATGCAAAAGCGGGCGAGATTCTAT 23 45 0 CAAAACGGGC 0.802031 -80 CGTTGGGATTGAAAACGGGTCATTCTACCGC 26 26 1 GAAAAGGGTC 0.81385 -100 CATATATCACCAAATAGGCGCGTAAAAATTT 26 64 1 CAAATGGCGC 0.869145 -62 GACGATGGTCGAAAATGGCGCTTTCGTCAGC 27 166 1 GAAAAGGCGC 0.975718 -135 ***** ***** Masking position 4 Map Score: 22.3756 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 546 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 2 TGCGCAAATACGCTTTTCCTCACACAGTTGTCAAGT 3 48 1 CGCTTCACAA 0.980254 -130 AAAATGAGGCCGCTATAAATAGCAGATGCTTTTCCG 3 107 0 CGCTTAGCAA 0.907955 -71 TAATTGTTGGCGCTGTGTACAGCATCAGACGTCGAA 4 77 0 CGCTTTGCAC 0.980061 -224 AAGTCCGGCGCGCTTTATACCACAAATACGTCGTGG 4 120 0 CGCTTTACAA 0.96032 -181 GCGACAATCTCACTTTGTGTAACAACACACACGTAT 4 189 1 CACTTTACAC 0.698771 -112 CATTGTACGTCGCTTTTCAGCGCAGCCCCACAAGGG 6 73 0 CGCTTCGCAC 0.990179 -74 GGTTGCTGCGCGCTGGCCGTGACCAAACTGCCTGCA 7 89 0 CGCTGCACCA 0.85613 -203 GTTTAATCAGGGCTATACTTAGCACACTTCCACTGT 7 219 1 GGCTTCGCAA 0.962095 -73 AATATAAGATCGCCGGGCCACGCAAAGAACTGCACC 12 63 1 CGCCGCGCAA 0.954735 -59 CAAAGAACTGCACCCTCCGGTGCAAATGGGATGGTA 12 85 1 CACCTCGCAA 0.815086 -37 GGCTTGTCATCGCCGCATTTGCCCGG 17 1 1 GGCTGCGCCC 0.730962 -64 ACTGGGTGTTGTCTATACTTTACACATAAGGAAGAG 19 53 0 GTCTTCACAA 0.545018 -225 CGTTGCATCGCGCTCTTTAATACACCGCCTGGAAAG 20 55 1 CGCTTTACAC 0.955774 -96 GTTATTAGACCGCTATACTGGGCAGACAACAGTTCA 22 61 0 CGCTTCGCAA 0.991221 -88 TATAGAATCTCGCCCGCTTTTGCATACGCAAAGCAG 23 44 1 CGCCGTGCAA 0.91137 -81 CGTCAGGATACTCTATATCCAGCATCTTTCAAACTT 25 29 0 CTCTTTGCAC 0.840663 -71 AGTATCCTGACGCTGTTTTTAACACAGTTGTAATAA 25 53 1 CGCTTTACAA 0.96032 -47 **** * * *** * Masking position 13 Map Score: 17.1535 Number of sites scoring better than the average of aligned sites = 1073 Number in coding regions = 1007 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 ATAAAGCGCGCCGGACTTCCGATCCATTTCGTA 4 138 1 CCGGTCCGAT 0.854706 -163 GGCACATATTCCGGGGTGCCCTTTGGGGTCGGT 4 226 1 CCGGGCCCTT 0.976636 -75 AAATATGAAGGGGGAGAGCCCTTATAGACCAGG 5 135 1 GGGGGCCCTT 0.967375 -123 CCGGTTGCTGCGCGCTGGCCGTGACCAAACTGC 7 94 0 CGCGGCCGTG 0.978223 -198 AAAGCAAAACGCCGCCAGCCGATCCGCAAGGAT 8 42 0 GCCGGCCGAT 0.973628 -50 TGCCGCCGGTGGGGTTCGCCATTGTAACGCTGG 10 90 1 GGGGGCCATT 0.88184 -31 TCTTACGATTGCGGCAGGCCGTGTTATTATTGT 13 52 1 GCGGGCCGTG 0.991893 -53 GTTACTCGCCCGGAAGCCGCTCTGGCAAG 16 9 0 CCCGGCCGCT 0.945903 -21 CGGCATTTTTGCCGAGTGCCGTGTATAATAGGC 18 22 1 GCCGGCCGTG 0.991896 -95 ATAAGGAAGAGGGGTATTCCCTGTTACAACCCA 19 31 0 GGGGTCCCTG 0.843357 -247 TGGAGTAATTGCCGAAAGCCGTTAGATTCTGGC 21 100 1 GCCGGCCGTT 0.993324 -114 CGGGTCAATGCCCGACCTCCGTTTTTACAGGCA 22 22 0 CCCGTCCGTT 0.959495 -127 **** ****** Masking position 9 Map Score: 14.1133 Number of sites scoring better than the average of aligned sites = 932 Number in coding regions = 886 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 CATCACGTTTACCACAGGCGGGAA 2 23 1 ACCACAGGCG 0.972171 -14 AAAGAAGCCGCCCTCAGGCGGCTCCTTTTT 6 16 0 CCCTCAGGCG 0.994478 -131 TCAGCGCAGCCCCACAAGGGTTAGCTGAAT 6 63 0 CCCACAAGGG 0.962399 -84 AATGGCGAACCCCACCGGCGGCAACAGAAA 10 83 0 CCCACCGGCG 0.988781 -38 GCAGACCACCAGCGTTACAATGGC 10 107 0 ACCACCAGCG 0.913901 -14 AAGAACTGCACCCTCCGGTGCAAATGGGAT 12 87 1 CCCTCCGGTG 0.943378 -35 TCTAATAGTCCACTCAGGCAATTATTACGT 19 169 1 CACTCAGGCA 0.84416 -109 GAGAAGAACCTCAGGCATGCGTCCATT 20 134 0 ACCTCAGGCA 0.898388 -17 CTAATAACATCCCTCAAGGGAAAAAGATCC 22 89 1 CCCTCAAGGG 0.946624 -60 GTCACTCAAGGGATTAACCTCT 25 88 0 CACTCAAGGG 0.866467 -12 ********** Masking position 5 Map Score: 11.2588 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 492 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 AATTTCGCCAAACGTGCCACTGAAGGTTTT 4 34 1 AACGTGCCAC 0.458581 -267 TGTGGTATAAAGCGCGCCGGACTTCCGATC 4 132 1 AGCGCGCCGG 0.987303 -169 GGAATTCTCGAGCTTGCCGCCTTTCTGCAA 5 44 0 AGCTTGCCGC 0.684925 -214 CTTACTGATGTAAGCTCCCGGGAATTCTCG 5 64 0 TAAGCTCCCG 0.362517 -194 CCCTTCATATTTCGCGCCGCAGATGCGTTA 5 117 0 TTCGCGCCGC 0.89859 -141 GGGGGCCATATGCAGGCCCCCTAACCAAAC 5 176 0 TGCAGGCCCC 0.640152 -82 CGGAGATGTGATCTGCCCGGCATTAAACCG 5 227 0 ATCTGCCCGG 0.279836 -31 TAACCAGACTTACGCCCCCGCGATACTTAC 7 45 0 TACGCCCCCG 0.871261 -247 CTCCGGTTGCTGCGCGCTGGCCGTGACCAA 7 99 0 TGCGCGCTGG 0.711621 -193 CGTACTTTTGTACGCTCCGGTTGCTGCGCG 7 113 0 TACGCTCCGG 0.769079 -179 TTGAACGACAAAAACGCCGCTCAGTAGATC 8 15 1 AAAACGCCGC 0.483903 -77 AATAAAAAGCAAAACGCCGCCAGCCGATCC 8 50 0 AAAACGCCGC 0.483903 -42 GATCAATATAAGATCGCCGGGCCACGCAAA 12 59 1 AGATCGCCGG 0.823655 -63 GTTACTCGCCCGGAAGCCGCTC 16 18 0 TACTCGCCCG 0.920446 -12 TTTGCCCGGTAACGTGCCGGGCATTGCTAC 17 28 1 AACGTGCCGG 0.899881 -37 TGTAATTGTGATCACGCCCGCACATAACCC 19 89 0 ATCACGCCCG 0.813722 -189 GTTTACTGGTTGCGGCCCCGCTTGACAAAA 19 221 0 TGCGGCCCCG 0.762944 -57 ACCAGTAAACTACGCGCCAGTTATGTACAC 19 241 1 TACGCGCCAG 0.88951 -37 ACCGAAACTCAGCTTGCCCGGC 20 3 0 AGCTTGCCCG 0.805519 -148 CCGAAAACTGTGCGGGCCAGGCATGATCCT 20 89 0 TGCGGGCCAG 0.792897 -62 TCAATAAAAGAGAGCGCCCCCTTTTGGAGT 21 76 1 AGAGCGCCCC 0.862716 -138 TGAGTATAGAATCTCGCCCGCTTTTGCATA 23 40 1 ATCTCGCCCG 0.86478 -85 ********** Masking position 7 Map Score: 12.897 Number of sites scoring better than the average of aligned sites = 6613 Number in coding regions = 6249 Number in noncoding regions = 364 Number of orfs with sites within 600 bp upstream = 295 Fraction of orfs with sites within 600 bp upstream = 0.0473819 Motif number 6 TGTCAAACATCATTCAGGACAAAAAAATAGC 1 24 0 CATCAGGACA 0.977559 -69 GGTTAATTTACATTCTGGTCGCGTGCGCAAA 3 25 1 CATCTGGTCG 0.934096 -153 TTCGTATACACAGACTGGACGGAAGCGACAA 4 165 1 CAACTGGACG 0.968011 -136 GTTATGTACACACTCAGGACAAAAAAAC 19 260 1 CATCAGGACA 0.97763 -18 CTGCTTGCATCATACAGGATGCGTAAGATCA 21 48 1 CAACAGGATG 0.888213 -166 ATGTGAACGCTATTCAGGACGGGTCACACGC 27 13 0 TATCAGGACG 0.95394 -288 TCTCAAATTACAGTCAGGACGCGT 27 287 1 CATCAGGACG 0.993769 -14 ** ******** Masking position 2 Map Score: 5.4633 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 138 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 CTTGCGGCAAAAATTAGCGACTC 1 80 0 GCGGCAAAAA 0.662617 -13 GAAAAATGAGGCCGCTATAAATAGCAGATG 3 115 0 GCCGCTATAA 0.584066 -63 GCTGTACACAGCGCCAACAATTATTGGTGT 4 90 1 GCGCCAACAA 0.692195 -211 TGTGATCTGCCCGGCATTAAACCGCACAGA 5 221 0 CCGGCATTAA 0.523279 -37 GACCAAACTGCCTGCAACAATAACGCCTTA 7 75 0 CCTGCAACAA 0.811638 -217 CGGCCAGCGCGCAGCAACCGGAGCGTACAA 7 106 1 GCAGCAACCG 0.888957 -186 GGATAATCCGGCTACAGAGAGTCGCGC 9 8 1 CCGGCTACAG 0.943432 -178 AACCCCACCGGCGGCAACAGAAACAACGCC 10 76 0 GCGGCAACAG 0.981408 -45 AACACGGCCTGCCGCAATCGTAAGAATGAG 13 47 0 GCCGCAATCG 0.825076 -58 CTTGCCAGAGCGGCTTCCGGGCGAGTAAC 16 10 1 GCGGCTTCCG 0.810683 -20 GTCAAGCGGGGCCGCAACCAGTAAACTACG 19 225 1 GCCGCAACCA 0.917949 -53 TACAGGCGACCCAGCAACAGGTAAGTGATC 23 79 0 CCAGCAACAG 0.901235 -46 TTAAATTAATCCTGCTACAGGCGACCCAGC 23 94 0 CCTGCTACAG 0.792299 -31 GTTCCCGCATCAGATGACTGTAT 24 4 1 CCCGCATCAG 0.887682 -41 ********** Masking position 5 Map Score: 8.40887 Number of sites scoring better than the average of aligned sites = 2889 Number in coding regions = 2519 Number in noncoding regions = 370 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 8 ACACAGACTGGACGGAAGCGACAATCTCAC 4 172 1 GACGGAAGCG 0.952993 -129 ATGAGCGAGCGAAGATAACGCATCTGCGGC 5 102 1 GAAGATAACG 0.895546 -156 TTTCTTGAACGACAAAAACGCCGCTCAGTA 8 11 1 GACAAAAACG 0.731702 -81 GCCGCATTTGCCCGGTAACGTGCCGGGCAT 17 22 1 CCCGGTAACG 0.772592 -43 CAAAAATGCCGCAGACAACGAC 18 3 0 GCAGACAACG 0.80795 -114 CGTATCAAATGCAGATAACGTAATAATTGC 19 186 0 GCAGATAACG 0.920036 -92 GAAAGAATCTGCCGAAAACTGTGCGGGCCA 20 100 0 GCCGAAAACT 0.802297 -51 TGGAGTAATTGCCGAAAGCCGTTAGATTCT 21 100 1 GCCGAAAGCC 0.849053 -114 CTTGAACATAGACGATAGCGGACGGTAACG 21 144 1 GACGATAGCG 0.970032 -70 GACGATAGCGGACGGTAACGCTAGCATTAA 21 154 1 GACGGTAACG 0.955905 -60 TATCCCCGCTGACGAAAGCGCCATTTTCGA 27 174 0 GACGAAAGCG 0.970032 -127 ********** Masking position 7 Map Score: 5.6959 Number of sites scoring better than the average of aligned sites = 1661 Number in coding regions = 1588 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 9 AAAAAAATAGCGGCTAATCATAGC 1 2 0 CGGCAATTAG 0.890223 -91 ATTAGCGACTCGGGTAAAAATAGTACACCTCGG 1 58 0 CGGGAAATAG 0.816737 -35 CTTGCGGCAAAAATTAGCGACTCGGGT 1 76 0 CGGCAAATAG 0.63684 -17 ACACACGTATCGGCACATATTCCGGGGTGCCCT 4 215 1 CGGCCATTCC 0.870697 -86 ATGTAAGCTCCCGGGAATTCTCGAGCTTGCCGC 5 54 0 CCGGAATTCG 0.824976 -204 GCGATACTTACGCGGAATCTTACCCTTATTTAT 7 23 0 CGCGAATTAC 0.66914 -269 ATTTTGGCCCCGGGCAGTGCTCGCCATCCTCAC 7 142 0 CGGGAGTTCG 0.833388 -150 AAACATATTACGGGTAATCGTCTGGATTATTAG 7 190 0 CGGGAATTCT 0.787147 -102 GCGATGACGACGGGTATTAACACAAAAGCAGAT 10 43 0 CGGGATTCAC 0.911762 -78 GGTAACGTGCCGGGCATTGCTACTGTAAAATCG 17 35 1 CGGGATTTAC 0.926445 -30 TGGGTTGTAACAGGGAATACCCCTCTTCCTTAT 19 31 1 CAGGAATCCC 0.669407 -247 GTGATCACGCCCGCACATAACCCACTGGGTGTT 19 79 0 CCGCCATCCC 0.443361 -199 GTCTGCGGGAAATAATACCAACGTTGAT 21 6 1 CGGGAATTAC 0.966903 -208 TAACGGCTTTCGGCAATTACTCCAAAAGGGGGC 21 91 0 CGGCATTTCC 0.885941 -123 AAACGGAGGTCGGGCATTGACCCGAAAATCTGA 22 31 1 CGGGATTCCC 0.939514 -118 CCGGGAGATTTCAGACGAAAGTTT 25 2 1 CGGGGATCAG 0.696446 -98 GGATTGAAAACGGGTCATTCTACCGCCATCTCC 26 31 1 CGGGCATTAC 0.913984 -95 CTTTCGTCAGCGGGGATAATCCGTTATTGAACA 27 186 1 CGGGATACCG 0.71155 -115 **** *** *** Masking position 1 Map Score: 10.7319 Number of sites scoring better than the average of aligned sites = 1466 Number in coding regions = 1313 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 10 CTGCAACAATAACGCCTTATAACCAGACTT 7 64 0 AACGCCTTAT 0.76758 -228 ATTACGGGTAATCGTCTGGATTATTAGGCT 7 187 0 ATCGTCTGGA 0.922703 -105 TTGCTGAAGTATCGCCTGATATCTGCTTTT 10 23 1 ATCGCCTGAT 0.958605 -98 TCTTATATTGATCGCCTAAAGTCATCGCTA 12 42 0 ATCGCCTAAA 0.85136 -80 TTTACAAATAAACGCCTGAACACCTTGACT 19 138 1 AACGCCTGAA 0.964944 -140 AGCGCGATGCAACGTCTGGAACAAGGTGAC 20 39 0 AACGTCTGGA 0.881532 -112 TCTTTAATACACCGCCTGGAAAGGATCATG 20 68 1 ACCGCCTGGA 0.930157 -83 TCTATACTCAATCGCCTTATACATCAATCA 23 20 0 ATCGCCTTAT 0.841221 -105 CTTTCAAACTTTCGTCTGAAATCTCCCGG 25 10 0 TTCGTCTGAA 0.695251 -90 ********** Masking position 7 Map Score: 3.50818 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 959 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 11 AATTTACATTCTGGTCGCGTGCGCAAATAC 3 29 1 CTGGTCGCGT 0.92248 -149 ACGATTGCGGCAGGCCGTGTTATTATTGTC 13 56 1 CAGGCCGTGT 0.947351 -49 TATATTTTGACAGGAAGAGTATC 13 92 1 CAGGAAGAGT 0.884448 -13 TTGCATCATACAGGATGCGTAAGATCAATA 21 52 1 CAGGATGCGT 0.968163 -162 GAACGCTATTCAGGACGGGTCACACGCGC 27 10 0 CAGGACGGGT 0.983389 -291 AAATTACAGTCAGGACGCGT 27 291 1 CAGGACGCGT 0.993738 -10 ********** Masking position 10 Map Score: 2.48777 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 104 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 AGCCGCTATTTTTTTGTCCTGAATGATGTTTG 1 20 1 TTTTTCCTGA 0.961135 -73 AGCGGCCTCATTTTTCCCCCGAACATGGGGAT 3 129 1 TTTTCCCCGA 0.919042 -49 GTTTCTTTCCTGAGACTGTCAAC 6 134 0 TTTTTCCTGA 0.961135 -13 GGCGTTTTGCTTTTTATTCTGTCTCAACTCTG 8 62 1 TTTTTTCTGT 0.719197 -30 GCGTTTTTTATTCCCTGACAGGGTTTAC 9 168 0 TTTTCCCTGA 0.979833 -18 GTTTTTTTGTCCTGAGTGTGTACAT 19 263 0 TTTTTCCTGA 0.961135 -15 GCCATGGATCTTTTTCCCTTGAGGGATGTTAT 22 92 0 TTTTCCTTGA 0.826486 -57 CAGGTGGATGTTTTTGCTCTTATTTCGATCAA 27 87 0 TTTTCTCTTA 0.609542 -214 TATTGAACAATTTATCCTCTGTCCATTTCACG 27 210 1 TTTTCTCTGT 0.834219 -91 *** * ****** Masking position 5 Map Score: 4.7953 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 179 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 13 TTCCCCCGAACATGGGGATCGATAGTGCGTG 3 142 1 CATGGGGATG 0.980499 -36 TACAAAAGTACGTGAGGATGGCGAGCACTGC 7 131 1 CGTGAGGATG 0.980503 -161 TCAGTAGATCCTTGCGGATCGGCTGGCGGCG 8 35 1 CTTGCGGATG 0.889952 -57 CTGCTCAAACCGTGGCGATAAAAAAGGGCCA 15 43 0 CGTGGCGATA 0.94485 -56 TTTTTGCTTACGTTGGGATTGAAAACGGGTC 26 16 1 CGTTGGGATG 0.950716 -110 TTAACTTTCCCATGGGGATAACTCATCGTAA 26 105 0 CATGGGGATA 0.932061 -21 AGACAAAAGGCGTGACGATGGTCGAAAATGG 27 153 1 CGTGACGATG 0.954997 -148 ********* * Masking position 8 Map Score: 1.62354 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 206 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 TGCGCAAATACGCTTTTCCTCACACAGTTG 3 48 1 CGCTTTTCCT 0.966312 -130 AAATAGCAGATGCTTTTCCGGATAGCAATT 3 97 0 TGCTTTTCCG 0.887192 -81 GTTGCTTCTCCTTAACACGCAC 3 166 0 TGCTTCTCCT 0.843072 -12 GCGAAGATAACGCATCTGCGGCGCGAAATA 5 110 1 CGCATCTGCG 0.919389 -148 CCGGGCAGATCACATCTCCGAGGATTTTAG 5 237 1 CACATCTCCG 0.661018 -21 CATTGTACGTCGCTTTTCAGCGCAGCCCCA 6 79 0 CGCTTTTCAG 0.798997 -68 TGGGGGTCGCTTTTGCTGAAGTATCGC 10 8 1 CGCTTTTGCT 0.950957 -113 TTGTCATCGCCGCATTTGCCCGGTAACGTG 17 14 1 CGCATTTGCC 0.798031 -51 GAATCTCGCCCGCTTTTGCATACGCAAAGC 23 48 1 CGCTTTTGCA 0.854678 -77 GAATTTAAACCGCTTCACCTTGAAAAAACT 27 255 0 CGCTTCACCT 0.813877 -46 ********** Masking position 5 Map Score: 2.78844 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 925 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 15 TATGATTAGCCGCTATTTTTTTGTCCTGAA 1 13 1 CGCTATTTTT 0.846408 -80 GGAAGTCCGGCGCGCTTTATACCACAAATA 4 128 0 CGCGCTTTAT 0.903735 -173 TACAGAGAGTCGCGCTATTTGTTAGCGTAG 9 23 1 CGCGCTATTT 0.932178 -163 GCATTTGATACGCAGTTTTTTGTCAAGCGG 19 204 1 CGCAGTTTTT 0.856092 -74 GACGTTGCATCGCGCTCTTTAATACACCGC 20 53 1 CGCGCTCTTT 0.974019 -98 CAAAAGGGGGCGCTCTCTTTTATTGATCTT 21 72 0 CGCTCTCTTT 0.959745 -142 AGTATCCTGACGCTGTTTTTAACACAGTTG 25 53 1 CGCTGTTTTT 0.937621 -47 ********** Masking position 6 Map Score: 2.11192 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 224 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344