AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_hpyl_reg_300.orf -o00051_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0004 121 carbonic anhydrase (icfA) #2 HP0031 108 H. pylori predicted coding region HP0031 #3 HP0032 30 conserved hypothetical protein #4 HP0038 126 H. pylori predicted coding region HP0038 #5 HP0042 62 trbI protein #6 HP0043 69 mannose-6-phosphate isomerase (pmi) or (algA) #7 HP0044 41 GDP-D-mannose dehydratase (rfbD) #8 HP0175 300 cell binding factor 2 #9 HP0194 214 triosephosphate isomerase (tpi) #10 HP0230 107 CTP:CMP-3-deoxy-D-manno-octulosonate-cytidylyl-transferase (kdsB) #11 HP0866 40 transcription elongation factor GreA (greA) #12 HP0869 58 hydrogenase expression/formation protein (hypA) #13 HP0870 207 flagellar hook (flgE) #14 HP0871 300 CDP-diglyceride hydrolase (cdh) #15 HP1101 65 glucose-6-phosphate dehydrogenase (g6pD) #16 HP1154 130 H. pylori predicted coding region HP1154 #17 HP1255 116 protein translocation protein, low temperature (secG) #18 HP1259 69 conserved hypothetical protein #19 HP1260 101 NADH-ubiquinone oxidoreductase, NQO7 subunit (NQO7) #20 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #21 HP1377 300 H. pylori predicted coding region HP1377 #22 HP1385 70 fructose-1,6-bisphosphatase Motif number 1 TCTCATTTTGATTAAAATTCGTTTGTTTTTAAAACG 1 81 0 ATTAAATTGT 0.755084 -41 TCTTTAACCCTTAAATCTCATTTTGATTAAAATTC 1 97 0 CTTAAATTTG 0.843488 -25 TCAGCGGGTCATTAGGGTTTATTTGGTATAATACCA 2 59 1 ATTAGGTTGG 0.61911 -50 AAGAACCAACCTTAAATGAAGTTTTGGTATTATACC 2 83 0 CTTAAATTTG 0.843488 -26 ATAAATAGGAATTTAATGAGAATTTTTTTTGTTATT 4 11 1 ATTTAATTTT 0.892178 -116 CTTCGTAATTTTTAGGGCCTTGTTTGAAAGGGGTGA 5 20 0 TTTAGGTTTG 0.852508 -43 TTTGAATCTTCTTTAACATTTTTTTTCTTTCCAAAA 8 69 1 CTTTAATTTT 0.880795 -232 TTATTGTCTTTTTTGGTGTTAGTTTTATTCTTTTTG 8 100 0 TTTTGGTTTT 0.887951 -201 ATTTCTTACTCTTTAATGTGAGTTTTCTGTGATCAT 8 200 1 CTTTAATTTT 0.880795 -101 ATTTTGAGTTTTTAGGAGCAGTTTTT 9 1 0 TTTAGGTTTT 0.913041 -214 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAGG 9 21 0 TTTTAGTTTG 0.827717 -194 ATGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGC 9 49 0 ATTAAGTTTT 0.920403 -166 ATTCTACTACATTTGAAATAATTTTTCTTATAAACA 9 73 1 ATTTGATTTT 0.882539 -142 ACAATAGCCCCTTTGAATTGAATTTTTTCTCAATTT 9 115 0 CTTTGATTTT 0.870286 -100 ATTATATTGTATTAGAGTAATCTTTTAGC 12 4 0 ATTAGATTTT 0.908716 -55 TTTCTTATGAATTTGGTCGATCTTTTTGATTAACAA 13 84 1 ATTTGGTTTT 0.887951 -124 TAAAAAGCTATTTAGGAACAACTTTTGCTTTATTTT 13 147 1 TTTAGGTTTT 0.913041 -61 TATTTAATTTTTTAAAAAATTCTTTTAGCTTTTTTA 14 89 1 TTTAAATTTT 0.916411 -212 GTAACCTATTTTTAAAAAGAGATTTTTGAATACTAA 14 151 0 TTTAAATTTT 0.916411 -150 TGATTAAAGATTTTAACCACTATTGTAGAAAAATAA 14 229 1 TTTTAATTGT 0.699423 -72 TGCTCCTTGTTTTTAATGAGAGTTTTTGCAAACCCT 14 269 0 TTTTAATTTT 0.892178 -32 CAATAACCCTTTTAGAGTGTTTTTGAGTTATTATT 15 41 0 TTTTAGTTTG 0.827717 -25 TAGAGCGTTCCTTAAAAAATGGTTGGATTTGGAACG 16 24 1 CTTAAATTGG 0.602472 -107 AAATGGTTGGATTTGGAACGCCTTTTGCTTTTACGC 16 40 1 ATTTGGTTTT 0.887951 -91 CACGCTTGAAATTAAAACTAAATTTTAGTGTATTCT 17 30 1 ATTAAATTTT 0.916411 -87 GACAAAGCCAATTAAACCATGTTTTTGCTAATCGTT 19 43 0 ATTAAATTTT 0.916411 -59 TTTGGATTCAATTAAAGCGCTATTTTTAGCGTTGGT 20 130 0 ATTAAATTTT 0.916411 -42 GAGCGCTGGTTTTAAGGCGGTCTTTT 21 285 1 TTTAAGTTTT 0.920403 -16 ****** **** Masking position 13 Map Score: 32.0857 Number of sites scoring better than the average of aligned sites = 2655 Number in coding regions = 2120 Number in noncoding regions = 535 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 2 ATTTTACACTTTAAAGGGCTTTC 1 3 0 TTAAAGGCTT 0.938804 -119 CGTTTGTTTTTAAAACGCTTATCATAGCTAA 1 67 0 TAAAAGCTTA 0.924763 -55 TCATTTTGATTAAAATTCGTTTGTTTTTAAA 1 84 0 TAAAATCGTT 0.624186 -38 AAAATTCTCATTAAATTCCTATTTAT 4 6 0 TTAAATCCTA 0.784615 -121 AATCCCCAATTAAAAACGCTATAATAACCCT 6 17 1 TAAAACGCTA 0.852357 -53 AAAATTAACCTAAAATCGCTTGACGCAAAAA 9 32 1 TAAAACGCTT 0.841374 -183 TAAAACTCCTAAAGTTCAATA 10 1 1 TAAAATCCTA 0.798583 -107 ATTATACCCATTAAAAGCTTATTTCTTATTA 10 48 0 TTAAAGCTTA 0.918659 -60 TATTTTGGCTTAAAAAGGTTTAAAG 10 93 1 TAAAAGGTTT 0.912029 -15 CGATAACCTTTAAAAAGCGTTATGGGGTGGT 13 36 1 TAAAAGCGTT 0.892393 -172 TTATAAAACGCTTTATTTTGACAA 14 4 1 TAAAAGCTTT 0.918659 -297 TTTTAAAAAATTAAATAGCTTGCACTAAGCA 14 75 0 TTAAAAGCTT 0.622167 -226 TTGATAACATTAAAAAAGCTAAAAGAATTTT 14 104 0 TAAAAAGCTA 0.661102 -197 ACAATAGTGGTTAAAATCTTTAATCATTATG 14 224 0 TTAAATCTTT 0.675128 -77 TAAATCTTAATTAAAGGGGTATTC 15 4 0 TTAAAGGGTA 0.883893 -62 AAAAACACTCTAAAAGGGTTATTG 15 52 1 TAAAAGGTTA 0.918588 -14 TACGCAACAATTAAAAGCGTAAAAGCAAAAG 16 61 0 TTAAAGCGTA 0.892393 -70 CCTTTTTAATTTAAATGCTTTGTTGTATAAT 16 102 0 TTAAAGCTTT 0.912099 -29 GCATTTAAATTAAAAAGGATAGTCCA 16 115 1 TAAAAGGATA 0.613567 -16 TGATTCCTTAAATGCCTAAAATTTAGAA 17 99 0 TTAAAGCCTA 0.947888 -18 GAAAGCGGGATTAAAACCTTTAGAGACGCTG 18 49 1 TTAAACCTTT 0.767238 -21 TTGGATTCAATTAAAGCGCTATTTTTAGCGT 20 134 0 TTAAACGCTA 0.841374 -38 AATCAAATCATAAAAGGGTTTTT 22 58 1 TAAAAGGTTT 0.912029 -13 ***** ***** Masking position 10 Map Score: 24.3628 Number of sites scoring better than the average of aligned sites = 1247 Number in coding regions = 1044 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 TTTAAAGTGTAAAATAACGCCATTATAACA 1 19 1 AAAATAACGC 0.808606 -103 CACAAGTCCCATAATAACAAAAAAAATTCT 4 29 0 ATAATAACAA 0.558564 -98 GCTATTAGATATAATAAGGGATAGTTACCA 9 173 1 ATAATAAGGG 0.965581 -42 TACCACCTATAAAATAAGGATCGTTCA 9 198 1 AAAATAAGGA 0.958477 -17 AATCCTTACAATAATAAGAAATAAGCTTTT 10 37 1 ATAATAAGAA 0.771651 -71 TTTTTAAGCCAAAATAGGGGATTTTATGGT 10 79 0 AAAATAGGGG 0.971907 -29 CTAATACAATATAATAGGGGCTAATTTAAA 12 25 1 ATAATAGGGG 0.968186 -34 AATTCATAAGAAAATAGGGGGTTTTGCAAC 13 67 0 AAAATAGGGG 0.971907 -141 TTGTAGAAAAATAACAAGAGGGTTTGCAAA 14 251 1 ATAACAAGAG 0.663751 -50 ACTCTCATTAAAAACAAGGAGCAAAAAAG 14 282 1 AAAACAAGGA 0.907059 -19 TTCTTATGGTATAATAGCGGTTATTTTTTT 20 94 1 ATAATAGCGG 0.919323 -78 ACCAACGCTAAAAATAGCGCTTTAATTGAA 20 130 1 AAAATAGCGC 0.820887 -42 AATTGAATCCAAAACAAGGAGTTTATTTT 20 153 1 AAAACAAGGA 0.907059 -19 ATTATAAAATATAATAAGGAGTTGAGGAAT 21 142 0 ATAATAAGGA 0.953063 -159 GAAAACATTGAAAATAGGGAAGTATT 22 7 0 AAAATAGGGA 0.961598 -64 ********** Masking position 6 Map Score: 17.0485 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 337 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 AAATAACGCCATTATAACAAAAAGAAATGCA 1 30 1 ATTATACAAA 0.948906 -92 AAATGCAAGAATTTTAGCTATGATAAGCGTT 1 54 1 ATTTTACTAT 0.601497 -68 AAGTTTTGGTATTATACCAAATAAACCCTAA 2 70 0 ATTATACAAA 0.948912 -39 TTAAATTCACATTATAGCAAATTTAAAACAA 8 247 0 ATTATACAAA 0.948912 -54 TATAAGAAAAATTATTTCAAATGTAGTAGAA 9 74 0 ATTATTCAAA 0.877839 -141 AAAAATGTAAATTTTAAACAATAGCCCCTTT 9 137 0 ATTTTAACAA 0.681713 -78 ACTATCCCTTATTATATCTAATAGCGTTTAA 9 167 0 ATTATACTAA 0.898017 -48 ATTTTATGGTATTATACCCATTAAAAGCTTA 10 58 0 ATTATACCAT 0.554568 -50 AAGCTATTTAATTTTTTAAAAAATTCTTTTA 14 85 1 ATTTTTAAAA 0.679313 -216 TTAAAAAGAGATTTTTGAATACTAACTAGAA 14 145 0 ATTTTTAATA 0.450545 -156 TTAGTAACCTATTTTTAAAAAGAGATTTTTG 14 159 0 ATTTTTAAAA 0.670847 -142 ATTTTAATGAATTTTAACTTATTAGTAACTT 14 190 0 ATTTTACTTA 0.773073 -111 TTGAGTTATTATTATATATTAAATCTTAATT 15 23 0 ATTATAATTA 0.5012 -43 ATTGTTGCGTATTTTTTCAAAATTATACAAC 16 81 1 ATTTTTCAAA 0.877835 -50 TTCTTAGCAAATTTTAGATAAGATCAAGCGT 17 62 1 ATTTTAATAA 0.722007 -55 ATCAAGCGTGATTTTTTCTAAATTTTAGGCA 17 84 1 ATTTTTCTAA 0.773072 -33 AATAAAAATTATTTTAACATTTC 19 3 0 ATTTTACATT 0.551848 -99 AATAACCGCTATTATACCATAAGAAAACCGC 20 88 0 ATTATACATA 0.877839 -84 TAACCGAATCATTATAAAATATAATAAGGAG 21 151 0 ATTATAAATA 0.679434 -150 AGTTATTGGGATTATATCCAAAACTAGCGAA 21 199 1 ATTATACCAA 0.878981 -102 GCGAAAATTGATTTTACCAAAATTGTTTGAT 21 225 1 ATTTTACAAA 0.94891 -76 TAAACTCTGTATTATATCAAACAATTTTGGT 21 240 0 ATTATACAAA 0.948912 -61 ****** **** Masking position 5 Map Score: 21.7149 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 405 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 5 TATTTTACACTTTAAAGGGCTTTC 1 5 0 TTTAAAGGGC 0.587969 -117 TCAAAATGAGATTTAAGGGTTAAAGA 1 106 1 ATTTAAGGGT 0.912109 -16 CCAAAACTTCATTTAAGGTTGGTTCTT 2 92 1 ATTTAAGGTT 0.824482 -17 ATAAATAGGAATTTAATGAGAATTTTTTTT 4 11 1 ATTTAATGAG 0.765879 -116 TTCTTCGTAATTTTTAGGGCCTTGTTTGAA 5 28 0 TTTTTAGGGC 0.636959 -35 TCTCTTTTGTTTTTTAGGGTTATTATAGCG 6 33 0 TTTTTAGGGT 0.83505 -37 TATAATGTGAATTTAATGATGAAAATTAGT 8 262 1 ATTTAATGAT 0.71623 -39 TAATTTTGAGTTTTTAGGAGCAGTTTTT 9 9 0 TTTTTAGGAG 0.852214 -206 GCGTCAAGCGATTTTAGGTTAATTTTGAGT 9 28 0 ATTTTAGGTT 0.677975 -187 CGATCCTTATTTTATAGGTGGTAACTATCC 9 191 0 TTTATAGGTG 0.519841 -24 AGAAATAAGCTTTTAATGGGTATAATACCA 10 53 1 TTTTAATGGG 0.802031 -55 AAAATAGGGGATTTTATGGTATTATACCCA 10 69 0 ATTTTATGGT 0.562774 -39 CATAACGCTTTTTAAAGGTTATCGCTCAAG 13 30 0 TTTAAAGGTT 0.650808 -178 ATTTCTTTAAATTAAAGGATAACC 13 194 1 ATTAAAGGAT 0.768772 -14 CTTTTAGCTTTTTTAATGTTATCAATTTAA 14 110 1 TTTTAATGTT 0.5859 -191 ATTATGATTATTTTAATGAATTTTAACTTA 14 200 0 TTTTAATGAA 0.468641 -101 TGCTCCTTGTTTTTAATGAGAGTTTTTGCA 14 275 0 TTTTAATGAG 0.780728 -26 TTAAATCTTAATTAAAGGGGTATTC 15 6 0 ATTAAAGGGG 0.830597 -60 GGAACGCTCTATTTTAGGATAATA 16 5 0 ATTTTAGGAT 0.803451 -126 TCCAACCATTTTTTAAGGAACGCTCTATTT 16 21 0 TTTTAAGGAA 0.761168 -110 AATTTTAGGCATTTAAGGAATCA 17 104 1 ATTTAAGGAA 0.745427 -13 TTTGCTAGTAATTAAAGGAGTTTGAGAGTC 19 80 1 ATTAAAGGAG 0.811645 -22 TGAGCGCTGGTTTTAAGGCGGTCTTTT 21 284 1 TTTTAAGGCG 0.707857 -17 ********** Masking position 3 Map Score: 16.6498 Number of sites scoring better than the average of aligned sites = 1584 Number in coding regions = 1285 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 6 CCCTTTAAAGTGTAAAATAACGCCATTATAACAAA 1 16 1 TGTAAAAACA 0.551089 -106 CGCCATTATAACAAAAAGAAATGCAAGAATTTTAG 1 36 1 ACAAAAAAGA 0.451592 -86 AATCTCGCTTAGAAAAAGGACACAAA 2 2 0 AGAAAAAACA 0.86752 -107 TTGGTATTATACCAAATAAACCCTAATGACCCGCT 2 61 0 ACCAAATACA 0.887328 -48 TAAAGAAAATTTAATAAATAAAATTCAA 7 4 1 AGAAAATAAA 0.573368 -38 TTTTTTTCTTTCCAAAAAGAATAAAACTAACACCA 8 88 1 TCCAAAAAAA 0.805408 -213 TTCACATTATAGCAAATTTAAAACAAAATCAGCTA 8 238 0 AGCAAATAAA 0.809017 -63 GAAAAATTATTTCAAATGTAGTAGAATTAAGGCAG 9 65 0 TTCAAATAAA 0.215356 -150 TAGGGGGTTTTGCAACACCACCCCATAACGCTTTT 13 48 0 TGCAACAACA 0.664021 -160 AAAAAGATCGACCAAATTCATAAGAAAATAGGGGG 13 76 0 ACCAAATAAA 0.731315 -132 ATTCAATCTATGCAAAATAAAGCAAAAGTTGTTCC 13 161 0 TGCAAAAACA 0.949079 -47 CCACTATTGTAGAAAAATAACAAGAGGGTTTGCAA 14 245 1 AGAAAAAAAA 0.693551 -56 TGTATAATTTTGAAAAAATACGCAACAATTAAAAG 16 75 0 TGAAAAAACA 0.855348 -56 TCGGTGTTTTTGCAAATACAAGCGAGCGGTTTTCT 20 63 1 TGCAAATACA 0.917135 -109 GCACCATTTCTCCAAATCAAGCCCAGCCGCACCAA 21 36 1 TCCAAATACA 0.876718 -265 GCCCAGCCGCACCAAAAAGACGCCACCTACCGCTA 21 56 1 ACCAAAAACA 0.929884 -245 CCACAAATCAAGAAAAATAATCCCAGTAAATCTCA 21 94 0 AGAAAAAACA 0.86752 -207 TTGAGGAATGAGCAAAATAAAACCACAAATCAAGA 21 116 0 AGCAAAAACA 0.953789 -185 TGGGATTATATCCAAAACTAGCGAAAATTGATTTT 21 205 1 TCCAAAAAGA 0.700936 -96 ******* * * * Masking position 10 Map Score: 15.1916 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 381 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TCAGCGGGTCATTAGGGTTTATTTGGTATAATA 2 59 1 ATTGGTTTAT 0.576179 -50 GGGGAAAATCAGGTTTTCTTCGTAATTTT 5 44 0 AATAGTTTTT 0.72575 -19 AATTTTATTTATTAAATTTTCTTTA 7 3 0 ATTATTTTCT 0.75398 -39 TTTTTCCTTTATTGAATTTTATTTATTAAATTT 7 17 0 ATTATTTTAT 0.856753 -25 CAGATGTTGTAATAATATTTATTGTCTTTTTTG 8 121 0 AATAATTTAT 0.707213 -180 CTACATTTGAAATAATTTTTCTTATAAACAAAA 9 79 1 AATATTTTCT 0.700096 -136 TTTTTTCTCAATTTAGGTTTTGTTTATAAGAAA 9 96 0 ATTAGTTTTT 0.822688 -119 ATTGTTTAAAATTTACATTTTTTAAACGCTATT 9 146 1 ATTAATTTTT 0.745197 -69 TAATTTAAAGATTAAGGTTTAGT 12 46 1 ATTAGTTTAT 0.908997 -13 AATGTTATCAATTTAATTTTTTTCTAGTTAGTA 14 124 1 ATTATTTTTT 0.831025 -177 TTAACTTATTAGTAACTTTTAGTAACCTATTTT 14 175 0 AGTATTTTAT 0.687964 -126 TACCCCTTTAATTAAGATTTAATATATAATAAT 15 14 1 ATTAATTTAT 0.735772 -52 ATACACTAAAATTTAGTTTTAATTTCAAGCGTG 17 30 0 ATTATTTTAT 0.912296 -87 GAAATGTTAAAATAATTTTTATTTTTTCAGCTA 19 11 1 AATATTTTAT 0.805239 -91 CTACCGCTAAAATGAGATTTACTGGGATTATTT 21 82 1 AATAATTTAT 0.782076 -219 *** * ***** * Masking position 1 Map Score: 10.6079 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 102 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 GTTATTATAGCGTTTTTAATTGGGGATTTT 6 15 0 CGTTTTTAAT 0.856072 -55 CACTTTTACCCGCTTTGAATGGAATGAATA 8 161 1 CGCTTTGAAT 0.974255 -140 AAACAATAGCCCCTTTGAATTGAATTTTTT 9 123 0 CCCTTTGAAT 0.936466 -92 ATAAGAAATAAGCTTTTAATGGGTATAATA 10 50 1 AGCTTTTAAT 0.7526 -58 GAATACCCCTTTAATTAAGATTTAAT 15 7 1 CCCTTTAATT 0.78875 -59 TTTGCTTTTACGCTTTTAATTGTTGCGTAT 16 63 1 CGCTTTTAAT 0.974752 -68 TGGACTATCCTTTTTAATTTAAATGCTT 16 113 0 CCTTTTTAAT 0.698496 -18 TAACGCACCACGCTTGAAATTAAAACTAAA 17 22 1 CGCTTGAAAT 0.902311 -95 CTTCAAGAAACGCTTTGCATAGAAACCGCT 20 17 0 CGCTTTGCAT 0.876946 -155 GAAAACCGCTCGCTTGTATTTGCAAAAACA 20 67 0 CGCTTGTATT 0.855116 -105 CTAAAAATAGCGCTTTAATTGAATCCAAAA 20 137 1 CGCTTTAATT 0.905535 -35 ********** Masking position 5 Map Score: 8.42816 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 469 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 TTCGTTTGTTTTTAAAACGCTTATCATAGCT 1 69 0 TTAAAACGCT 0.975 -53 AAATCCCCAATTAAAAACGCTATAATAACCC 6 16 1 TAAAAACGCT 0.946407 -54 AGGCGAACACTTTTACCCGCTTTGAATGGAA 8 154 1 TTTACCCGCT 0.809339 -147 AATTTACATTTTTTAAACGCTATTAGATATA 9 155 1 TTTAAACGCT 0.939519 -60 AGCTTAAGAATCTAACTCGCT 13 1 0 TTAACTCGCT 0.728434 -207 AACCAATCATTCTAAAAAGCTATTTAGGAAC 13 135 1 TTAAAAAGCT 0.85731 -73 TTATAAAACGCTTTATTTTGAC 14 2 1 TTAAAACGCT 0.975 -299 ATTGATAACATTAAAAAAGCTAAAAGAATTT 14 105 0 TAAAAAAGCT 0.731222 -196 TGATTAAAGATTTTAACCACTATTGTAGAAA 14 229 1 TTTAACCACT 0.630169 -72 TAATAATAACTCAAAAACACTCTAAAAGGGT 15 40 1 TAAAAACACT 0.731222 -26 ACGCTTTGCATAGAAACCGCTTATGCA 20 7 0 TGAAACCGCT 0.880601 -165 * ********* Masking position 5 Map Score: 7.23492 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 734 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 10 AAACAAACGAATTTTAATCAAAATGAGATTTAA 1 89 1 ATTTAATCAA 0.662728 -33 TTGTGTCCTTTTTCTAAGCGAGATTGTAGCGCT 2 12 1 TTCTAAGCAA 0.911485 -97 CTTTAAGCATTTCTTACTCTTTAATGTGAGTTT 8 192 1 TTTTACTCTA 0.710214 -109 CTTTAAACCTTTTTAAGCCAAAATAGGGGATT 10 86 0 TTTTAAGCAA 0.935327 -22 GCGAGTTAGATTCTTAAGCTTGAGCGATAACCT 13 12 1 TTTTAAGCTA 0.924075 -196 TTTTAAAGTTTTGTTAATCAAAAAGATCGACCA 13 97 0 TTTTAATCAA 0.939254 -111 GTGGTTAAAATCTTTAATCATTATGATTATTTT 14 216 0 TCTTAATCTA 0.710209 -85 TGGACTATCCTTTTTAATTTAAATGCTTTGTTG 16 108 0 TTTTAATTAA 0.549248 -23 AAAATTTAGTAATCTTAAGCGGGGCTGG 18 6 1 TTGTAATCTA 0.775609 -64 AACCATGTTTTTGCTAATCGTTAGCTGAAAAAA 19 32 0 TTCTAATCTA 0.902592 -70 CGCTCAATGATTTCTAAGCTAAACTCTGTATTA 21 257 0 TTCTAAGCAA 0.911486 -44 ** ****** * * Masking position 6 Map Score: 1.24294 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 113 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 CTTTAAAGTGTAAAATAACGCCATTATAACAA 1 18 1 TAAATACGCC 0.780989 -104 CTCAAAAATCCCCAATTAAAAAC 6 2 1 TAAAAACCCC 0.962411 -68 GCAAATTTAAAACAAAATCAGCTATCATGATC 8 230 0 ACAAAACAGC 0.723288 -71 GTAAATTTTAAACAATAGCCCCTTTGAATTGA 9 130 0 ACAATACCCC 0.902892 -85 CCTTAATCTTTAAATTAGCCCCTATTATATTG 12 31 0 TAATTACCCC 0.73245 -28 GGGGTGGTGTTGCAAAACCCCCTATTTTCTTA 13 59 1 TCAAAACCCC 0.965204 -149 TTAACAAAACTTTAAAATCCGCAACCAATCAT 13 113 1 TTAAAACCGC 0.81674 -95 CGCTTTCTGCTGAAATACCAGCCCCGCTTAAG 18 24 0 TAAATACAGC 0.835989 -46 CGCTTGTATTTGCAAAAACACCGATGCATTGC 20 55 0 TCAAAACACC 0.886708 -117 TATTATACCATAAGAAAACCGCTCGCTTGTAT 20 78 0 TAGAAACCGC 0.801693 -94 GTTATTCTAAAAAAATAACCGCTATTATACCA 20 100 0 AAAATACCGC 0.877983 -72 * ***** **** Masking position 7 Map Score: 2.64347 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 604 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 ATAATGGCGTTATTTTACACTTTAAAGGGC 1 15 0 TATTTTACAC 0.537186 -107 GTGCAAGGGCTTTTTTTCATCTCATGCACC 4 79 0 TTTTTTTCAT 0.727934 -48 TATTTTTCCTTTATTGAATT 7 32 0 TATTTTTCCT 0.751615 -10 TCTTTAACATTTTTTTTCTTTCCAAAAAGA 8 78 1 TTTTTTTCTT 0.87042 -223 CATTTGAAATAATTTTTCTTATAAACAAAA 9 82 1 AATTTTTCTT 0.600018 -133 ACTTTTGCTTTATTTTGCATAGATTGAATT 13 167 1 TATTTTGCAT 0.786006 -41 ATCAATTTAATTTTTTTCTAGTTAGTATTC 14 130 1 TTTTTTTCTA 0.679763 -171 ACCCTCTTGTTATTTTTCTACAATAGTGGT 14 244 0 TATTTTTCTA 0.80364 -57 CTTTTTTGCTCCTTGTTTTTA 14 290 0 TTTTTTGCTC 0.773 -11 TTACTGGGATTATTTTTCTTGATTTGTGGT 21 100 1 TATTTTTCTT 0.928322 -201 TTTGTGGTTTTATTTTGCTCATTCCTCAAC 21 122 1 TATTTTGCTC 0.867824 -179 AAGATGCTAATATTTTACTTGAAAACATTG 22 27 0 TATTTTACTT 0.80364 -44 ********** Masking position 5 Map Score: 5.49316 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 335 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 ********** No masking Map Score: 6.61048e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 6.61048e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 6.61048e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0