AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_hpyl_reg_300.orf -o00190_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 HP0031 108 H. pylori predicted coding region HP0031 #2 HP0032 30 conserved hypothetical protein #3 HP0144 300 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound (fixN) #4 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #5 HP0620 300 inorganic pyrophosphatase (ppa) #6 HP0828 121 ATP synthase F0, subunit a (atpB) #7 HP0830 58 amidase #8 HP0832 91 spermidine synthase (speE) #9 HP0833 76 H. pylori predicted coding region HP0833 #10 HP1010 300 polyphosphate kinase (ppk) #11 HP1067 290 chemotaxis protein (cheY) #12 HP1132 22 ATP synthase F1, subunit beta (atpD) #13 HP1137 110 ATP synthase F0, subunit b' (atpF') #14 HP1141 23 methionyl-tRNA formyltransferase (fmt) #15 HP1142 39 H. pylori predicted coding region HP1142 #16 HP1143 243 H. pylori predicted coding region HP1143 #17 HP1212 132 ATP synthase F0, subunit c (atpE) #18 HP1215 35 H. pylori predicted coding region HP1215 #19 HP1217 48 H. pylori predicted coding region HP1217 #20 HP1218 119 glycinamide ribonucleotide synthetase (purD) #21 HP1255 116 protein translocation protein, low temperature (secG) #22 HP1259 69 conserved hypothetical protein #23 HP1260 101 NADH-ubiquinone oxidoreductase, NQO7 subunit (NQO7) #24 HP1422 24 isoleucyl-tRNA synthetase (ileS) #25 HP1423 101 conserved hypothetical protein Motif number 1 AAAGCTTAATTTTTAATCTTTTTCTGTAACA 3 214 0 TTTTAATCTT 0.724625 -87 AATTTACATTTTTTAAACGCTATTAGATATA 4 50 0 TTTTAAACCT 0.928383 -165 AAAATGTAAATTTTAAACAATAGCCCCTTTG 4 69 1 TTTTAAACAT 0.922732 -146 TGTGAAAGGCTTTTAAGCACTTTCTAGTGTT 5 182 0 TTTTAAGCCT 0.923693 -119 AAGCCCGCTCTTTTTAAACCTCTTTAGGGGT 5 242 0 TTTTTAAACT 0.834915 -59 TTTAACGAGTTTTTTAACGATTTGTCTTGTT 6 23 0 TTTTTAACAT 0.936917 -99 TAAACCAAGCTTTTTAACGAGTTTTTTAACG 6 35 0 TTTTTAACAG 0.924027 -87 GTTTAATGAGTTTTTAAAACTTAATTGCTAC 6 61 1 TTTTTAAACT 0.834915 -61 GTTTTTAGCCTTACAAAAAATT 7 47 0 TTTTTAGCTT 0.891725 -12 TAATTTAGATTTTTTAGCTAGCATGTTAGCA 8 24 1 TTTTTAGCAG 0.919077 -68 CTTAGCTTACTTTTTAACAATATCCATGCCT 8 63 0 TTTTTAACAT 0.936917 -29 CTTTTTTATCGCTTCAATTTAAT 9 3 1 TTTTTATCCT 0.856784 -74 GCTTAAAATTTTTTTAGCGTTT 10 2 0 TTTTTAGCTT 0.891725 -299 GCTAAAAAAATTTTAAGCGATCTTTTAGGGT 10 15 1 TTTTAAGCAT 0.917705 -286 CATTGAAGCTTTTTTAAAAAGTCATGGTCGG 10 211 0 TTTTTAAAAG 0.792323 -90 ACAAACTGATTTTTAAACATGATGATTTAAA 10 271 1 TTTTAAACTG 0.853097 -30 ATTTTATTACTTTTAAACGATTATCATAGCA 11 79 1 TTTTAAACAT 0.922732 -212 AATTAGGCTCTTTTTAAACAGCCAAAGCGTC 11 242 0 TTTTTAAAAG 0.792331 -49 GTGCTTCTCCTTTTAAGATTGCATTTAAATT 11 269 0 TTTTAAGATG 0.629781 -22 TATTCTCAAATTTTAAGCGATTTTTTGTTAA 13 19 1 TTTTAAGCAT 0.917705 -92 AAGATTTGATTTTTTATATTTTATAATAGAA 16 212 0 TTTTTATATT 0.50657 -32 TAAAAAACGCTTTTTAAAATT 17 1 0 TTTTTAAATT 0.734515 -132 AAAAAGCGTTTTTTAAAAGCGTTTTTAAGCT 17 17 1 TTTTAAAACG 0.769057 -116 TTAAAAGCGTTTTTAAGCTAGTTTGTATTAA 17 29 1 TTTTAAGCAG 0.901302 -104 TTTTTAAATCTGCCCCTAAGA 20 1 1 TTTTTAAACT 0.834915 -119 TCTCTAAAGGTTTTAATCCCGCTTTCTGCTG 22 44 0 TTTTAATCCG 0.797535 -26 ATTCTTTAAGTTTTTATCCATAACTTATAAG 25 65 0 TTTTTATCAT 0.846419 -37 ******** ** Masking position 6 Map Score: 35.1207 Number of sites scoring better than the average of aligned sites = 1600 Number in coding regions = 1360 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 GATGAGGGTTTGTTTAATCATGTTTAACCTTTAGCCAAAGAT 3 121 1 TGTTTATTTT 0.923491 -180 TGAATGGCATTTTTAAGCCAAATTGCTACTATCTTTGGCTAA 3 151 0 TTTTAATTAT 0.690853 -150 AAAATTAAGCTTTTTGAAAAAGATAAAATTTTATAATTATGT 3 232 1 TTTTTATTTT 0.943763 -69 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAGGAGCAGT 4 179 1 TTTTAATTTT 0.974397 -36 TTCTAGGGGGTTTTAATGAAATGTCAGGCTTTTTTGCATTTT 5 105 0 TTTTAATTTT 0.974397 -196 AGCCCGCTCTTTTTAAACCTCTTTAGGGGTTTTTAAAGGAGC 5 230 0 TTTTATTTTT 0.894677 -71 AAAGAGCGGGCTTTATGTTAGAATAAGTCTTTTTATTCAAAG 5 260 1 CTTTAATTTT 0.930909 -41 TTAACGAGTTTTTTAACGATTTGTCTTGTTTTCTTTTACAAT 6 11 0 TTTTATTTTT 0.894677 -111 TCTCTAAGCATGTTAAACTACCATTAAATTTTTTGTAAGGCT 7 21 1 TGTTAATTTT 0.964756 -38 GCTTTTGTTACAATAATTTAGATTTTTTAGCTAGCAT 8 6 1 TGTTAATTTT 0.964756 -86 TTAAGCGATCTTTTAGGGTTAAATGAAGTTTTATTCAAAAAA 10 27 1 TTTTATTTTT 0.894677 -274 TAAAAACTCTTTTTTGTAAAACTTCATTTTTTGAATAAAACT 10 53 0 TTTTTATTTT 0.943763 -248 GACCATGACTTTTTAAAAAAGCTTCAATGATTATCATTTCAT 10 213 1 TTTTAATATT 0.690853 -88 CTAAATGGAGCGTTCAATGAGCGTTCTTATTTGTAAAAAAAT 11 120 0 CGTTCATTTT 0.778994 -171 AGCGATTTTTTGTTAAGATAGAGTTAATGTTTTTATAACAAA 13 34 1 TGTTAATTTT 0.964756 -77 GCTGATCGATCGTTATCTCAATTTCTTCATTTTTTTTATTTA 16 52 1 CGTTAATTTT 0.906464 -192 TTCTTCATTTTTTTTATTTATAATGTAGTTTTTATGCGAAGG 16 74 1 TTTTTATTTT 0.943763 -170 GCGAAGGGTATTTTTTGCCTTTTTTATTTTTTGTTGTTTGTA 16 109 1 TTTTTTTTTT 0.789283 -135 GATTTTCCTTTAAGATTTGATTTTTTATATTTTA 16 220 0 TTTTCATTTT 0.932625 -24 GTCTTTCCTGCAATGTGGTTGTTTTTAAACCCAG 20 96 0 CTTTCATTTT 0.830525 -24 CAAGCGTGATTTTTTCTAAATTTTAGGCATTTAAGGAATCA 21 86 1 TTTTTATTTT 0.943763 -31 GAAATGTTAAAATAATTTTTATTTTTTCAGCTAACG 23 5 1 TGTTAATTTT 0.964756 -97 GCGTTTATTTTACCCTATTCTTTAAGTTTTTATCCATAA 25 73 0 TTTTAATTTT 0.974397 -29 ***** * * *** Masking position 14 Map Score: 36.0585 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 333 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 GTATAATACCAAAACTTCATTTAAGGTTGGTTCTT 1 84 1 AACAAATCTT 0.942195 -25 TTGTAATAACTCAATCCCATTTGAATGGCATTTTTAAGCCAAATT 3 169 0 TACAGATTTT 0.891014 -132 AATTTTAAACAATAGCCCCTTTGAATTGAATTTTTTCTCAATTTA 4 77 1 AACCGATTTT 0.886974 -138 ACATTTCATTAAAACCCCCTAGAAAATCCTATTTTGATAATCTTT 5 123 1 AACCAATTTT 0.956894 -178 GCCTTTCACAAATACAGCAGACGATACGCTCCTTTAAAAACCCCT 5 203 1 AACAGACTTT 0.756515 -98 ATTAAGTTTTAAAAACTCATTAAACCAAGCTTTTTAACGAGTTTT 6 41 0 AACAAATTTT 0.984972 -81 TCATTATATAATCACACCAAACAAACTGATTTTTAAACATGATGA 10 251 1 AACAAATTTA 0.897506 -50 CCAATGACCCTTTATCGCACTCAAAGAGTTATTTTATTACTTTTA 11 49 1 TACAAATTTT 0.948646 -242 TTAAACGATTATCATAGCAAACAAACTGAATTTTTTTACAAATAA 11 91 1 AACAAATTTT 0.984983 -200 ATAATAATAAATCGTTCCAAATAATAGCATGTTTTGATTAAAATT 11 186 0 AGCAAATTTT 0.880386 -105 TTCTCCTTTTAAGATTGCATTTAAATTAGGCTCTTTTTAAACAGC 11 251 0 AACAAATCTT 0.950449 -40 GATCAGCTGCAAGTTGTCCCAAAAGCACAAGTTTTAGAGAACCAT 16 14 0 ATCCAATTTT 0.628007 -230 GTTTTATCCAATAAGTTCAGTAAAATAGGGATTTTAAATACAAAC 16 144 0 AACAAATTTT 0.984961 -100 AAACTAGCTTAAAAACGCTTTTAAAAAACGCTTTTTAAAATT 17 8 0 AACTAATTTT 0.847869 -125 CTCTACTTTCAAAAATACAAGCAAGAATTTATTTTAATACAAACT 17 48 0 AACAAATTTT 0.984972 -85 TCAAAAACAAACAAGACAAACTCTTTGGTTTGTCT 19 24 0 TACAAATCTT 0.854966 -25 GTGGTTGTTTTTAAACCCAGATGACCGCTACTTTTACATGCGCAT 20 71 0 TACAGATTTT 0.891867 -49 AAAATTTGCTAAGAATACACTAAAATTTAGTTTTAATTTCAAGCG 21 32 0 AACAAATTTA 0.897491 -85 CTAGCAAATGACAAAGCCAATTAAACCATGTTTTTGCTAATCGTT 23 43 0 AACAAATTTT 0.984985 -59 * * ** ** **** Masking position 24 Map Score: 24.4442 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 271 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 TCCTTTTTCTAAGCGAGATTGTAGCGCTTT 1 17 1 AAGCGAGATT 0.841797 -92 GCGGGTCATTAGGGTTTATTTGGTATAATA 1 62 1 AGGGTTTATT 0.444534 -47 GGCAAGAATGATGAGGGTTTGTTTAATCAT 3 112 1 ATGAGGGTTT 0.520354 -189 TTTTTGCGTCAAGCGATTTTAGGTTAATTT 4 173 1 AAGCGATTTT 0.899193 -42 TATTGAAAGCATGCTTGTTTAAAGAAACAG 5 66 0 ATGCTTGTTT 0.731806 -235 ATGAAATGTCAGGCTTTTTTGCATTTTGAA 5 102 0 AGGCTTTTTT 0.821277 -199 AGGATTTTCTAGGGGGTTTTAATGAAATGT 5 123 0 AGGGGGTTTT 0.776533 -178 AAACCTCTTTAGGGGTTTTTAAAGGAGCGT 5 228 0 AGGGGTTTTT 0.871226 -73 GCTTGGTTTAATGAGTTTTTAAAACTTAAT 6 56 1 ATGAGTTTTT 0.585666 -66 AAAAAATTTAATGGTAGTTTAACATGCTTA 7 25 0 ATGGTAGTTT 0.426326 -34 AAGTAAGCTAAGGAGTGTTT 8 82 1 AGGAGTGTTT 0.841655 -10 TTTTACAAAAAAGAGTTTTTAAACAACAAC 10 74 1 AAGAGTTTTT 0.766186 -227 CGCAATCAAAAAGGGAGATTGTAGCGCGAG 10 112 0 AAGGGAGATT 0.698923 -189 ATAATCATTGAAGCTTTTTTAAAAAGTCAT 10 217 0 AAGCTTTTTT 0.808911 -84 ATCGCACTCAAAGAGTTATTTTATTACTTT 11 62 1 AAGAGTTATT 0.566772 -229 CTCAAATTTTAAGCGATTTTTTGTTAAGAT 13 23 1 AAGCGATTTT 0.899193 -88 TTTATAACAAATGCGAGTTTCAAATATTTT 13 65 1 ATGCGAGTTT 0.851847 -46 TTTTATGCGAAGGGTATTTTTTGCCTTTTT 16 103 1 AGGGTATTTT 0.555858 -141 AATTTTAAAAAGCGTTTTTTAAAAGCGTT 17 10 1 AAGCGTTTTT 0.934587 -123 CGTTTTTTAAAAGCGTTTTTAAGCTAGTTT 17 23 1 AAGCGTTTTT 0.934587 -110 AAGCGTTTTTAAGCTAGTTTGTATTAAAAT 17 33 1 AAGCTAGTTT 0.797554 -100 TTCAAAAATTAGGCTTGATTTTCATTTCGA 17 100 0 AGGCTTGATT 0.73272 -33 AGGCGGGTTTTAGCAACGAC 18 1 1 AGGCGGGTTT 0.922501 -35 AGATAAGATCAAGCGTGATTTTTTCTAAAT 21 77 1 AAGCGTGATT 0.894997 -40 TTTCAGCAGAAAGCGGGATTAAAACCTTTA 22 41 1 AAGCGGGATT 0.814053 -29 ********** Masking position 9 Map Score: 28.645 Number of sites scoring better than the average of aligned sites = 1912 Number in coding regions = 1713 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 5 TTTGTGTCCTTTTTCTAAGCGAGATTGTA 1 10 1 TTTTTCTAAG 0.921111 -99 TTTTAATCTTTTTCTGTAACATTGTAATAA 3 205 0 TTTCTGTAAC 0.7219 -96 AAAATTAAGCTTTTTGAAAAAGATAAAATT 3 232 1 TTTTTGAAAA 0.842535 -69 ATAAAAAGACTTATTCTAACATAAAGCCCG 5 266 0 TTATTCTAAC 0.83738 -35 ATAAGTCTTTTTATTCAAAGGAGATTGCA 5 282 1 TTATTCAAAG 0.837371 -19 GTTTAATGAGTTTTTAAAACTTAATTGCTA 6 61 1 TTTTTAAAAC 0.807586 -61 TCTCTAAGCCTTATTGAAAATTTCCTTAAT 6 93 0 TTATTGAAAA 0.758822 -29 GAAAAAGTTTCTCTAAGCCTTATTGAA 6 105 0 TTTCTCTAAG 0.695018 -17 ACCATTAAATTTTTTGTAAGGCTAAAAAC 7 40 1 TTTTTGTAAG 0.930069 -19 AAAATCTAAATTATTGTAACAAAAGC 8 7 0 TTATTGTAAC 0.854344 -85 AAATGAAGTTTTATTCAAAAAATGAAGTTT 10 47 1 TTATTCAAAA 0.734245 -254 TAAAAACTCTTTTTTGTAAAACTTCATTTT 10 65 0 TTTTTGTAAA 0.876731 -236 CGACCATGACTTTTTAAAAAAGCTTCAATG 10 212 1 TTTTTAAAAA 0.466148 -89 TTGTCTTTCTTTTTTCAAACCATCCAATGA 11 26 1 TTTTTCAAAC 0.920512 -265 GAACGATTTATTATTATAAGGCGTTAGAGA 11 214 1 TTATTATAAG 0.699764 -77 AGAGTTAATGTTTTTATAACAAATGCGAGT 13 53 1 TTTTTATAAC 0.840296 -58 TAAAAAGCGTTTTTTAAAAGCGTTTTTAAG 17 16 1 TTTTTAAAAG 0.807586 -117 CTTGCTTGTATTTTTGAAAGTAGAGGAACG 17 68 1 TTTTTGAAAG 0.929464 -65 TCAAGCCTAATTTTTGAAACGGAGTGCGAA 17 112 1 TTTTTGAAAC 0.929464 -21 CAAGCGTGATTTTTTCTAAATTTTAGGCAT 21 86 1 TTTTTCTAAA 0.862029 -31 ********** Masking position 5 Map Score: 22.3507 Number of sites scoring better than the average of aligned sites = 1575 Number in coding regions = 1344 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 6 GAAAATACAAAAATAAAGCCAAGCGTTAGGTCT 3 28 1 AAAAAGCAAG 0.964808 -273 GTTGCGATAAAAAAAGGGGCAAGAATGATGAGG 3 95 1 AAAAGGCAAG 0.880382 -206 GCACCATTCAAAATGCAAAAAAGCCTGACATTT 5 96 1 AAAGAAAAAG 0.585787 -205 ATTGTAAAAGAAAACAAGACAAATCGTT 6 6 1 AAAGAACAAG 0.924106 -116 TGGTTTGAAAAAAGAAAGACAAGGATTTTACAA 11 15 0 AAAAAGCAAG 0.964808 -276 TTGAATTAAAAACAAGGAATAAC 14 4 1 AATAAACAAG 0.887284 -20 CATTATAAATAAAAAAAATGAAGAAATTGAGAT 16 66 0 AAAAAAGAAG 0.815762 -178 ACAAACAACAAAAAATAAAAAAGGCAAAAAATA 16 117 0 AAAAAAAAAG 0.840458 -127 TAGGGATTTTAAATACAAACAACAAAAAATAAA 16 131 0 AAAAAACAAC 0.803616 -113 CTACTTTCAAAAATACAAGCAAGAATTTATTTT 17 58 0 AAAAAACAAG 0.978428 -75 AACGATTCGAAATGAAAATCAAGCCTAATTTTT 17 94 1 AATAAACAAG 0.887284 -39 GGAAAAATAGCCAAAGTCGTTGCTA 18 21 0 AAAAAGCAAA 0.625308 -15 TCAAAAACAAACAAGACAAACTCTT 19 34 0 AAAAAACAAG 0.978428 -15 AGCAAATTTTAGATAAGATCAAGCGTGATTTTT 21 67 1 AGAAGACAAG 0.765743 -50 CCTAAAATTTAGAAAAAATCACGCTTGATCTTA 21 80 0 AGAAAACACG 0.622937 -37 *** * ** **** Masking position 11 Map Score: 14.0556 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 379 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 AACGCTGTTGTATTTTTTAGGCGCACCGGAT 3 67 0 TATTTTTAGG 0.97274 -234 GAACGATCCTTATTTTATAGGTGGTAACTAT 4 12 1 TATTTTTAGG 0.972739 -203 GGTTAATTTTGAGTTTTTAGGAGCAGTTTTT 4 194 1 GAGTTTTAGG 0.943256 -21 ATCAAAATAGGATTTTCTAGGGGGTTTTAAT 5 130 0 GATTTTTAGG 0.974785 -171 ATTTTGATAATCTTTTTTATGATCAATTAAA 5 153 1 TCTTTTTATG 0.726207 -148 CAATAATTTAGATTTTTTAGCTAGCATGTTA 8 21 1 GATTTTTAGC 0.833499 -71 AATTTTAAGCGATCTTTTAGGGTTAAATGAA 10 23 1 GATCTTTAGG 0.889654 -278 GAGTTTCAAATATTTTGTAGGATTTTAGGAA 13 79 1 TATTTTTAGG 0.97274 -32 ATTTATAATGTAGTTTTTATGCGAAGGGTAT 16 89 1 TAGTTTTATG 0.726207 -155 CAGCCACCACTCTTTTTAAGGAATTTGT 25 8 0 TCTTTTAAGG 0.683436 -94 ****** **** Masking position 6 Map Score: 6.58764 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 173 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 AAGAACCAACCTTAAATGAAGTTTTGGTATTA 1 87 0 ACCCTTATAT 0.971051 -22 TAATAACTCAATCCCATTTGAATGGCATTTTTAAGCCAA 3 172 0 ACCTTGAGAT 0.794113 -129 GCAATACTCCTATTTGTAGTAAATTCAACAAAGAT 3 276 0 CCCTTGATAT 0.781056 -25 TTTAAACAATAGCCCCTTTGAATTGAATTTTTTCTCAAT 4 80 1 ACCTTGATAT 0.960704 -135 TGACGCAAAAACACTGCCTTAATTCTACTACATTTGAAA 4 145 0 AACCTTATAT 0.795757 -70 TTTTAACAATATCCATGCCTTAATGAATTGCTAACATGC 8 44 0 ACCCCTATAT 0.830319 -48 TAATATTGTAATCTAATTTTGATTAAATTGAAGCGATAA 9 16 0 ACTTTTATAT 0.880125 -61 TCCAAATAATAGCATGTTTTGATTAAAATTACCTTGACC 11 177 0 ACATTTATAT 0.743984 -114 GTTTAAAAAGAGCCTAATTTAAATGCAATCTTAAAAGGA 11 254 1 ACCTTTATAT 0.973595 -37 TGTATTTAAAATCCCTATTTTACTGAACTTATTGGATAA 16 147 1 ACCTTTATAT 0.973602 -97 TTATTGGATAAAACCTGCTTAAGTTAAATTGATCTCATT 16 175 1 AACCTTATAT 0.795757 -69 AGCGTTTTTAAGCTAGTTTGTATTAAAATAAATTCTTGC 17 34 1 ACTTTGATAT 0.829606 -99 TTGAAATTAAAACTAAATTTTAGTGTATTCTTAGCAAAT 21 35 1 ACTTTTATAT 0.880134 -82 CTGAAATACCAGCCCCGCTTAAGATTACTAAATTTT 22 8 0 ACCCTTAAAT 0.781173 -62 * ** *** * * * * Masking position 12 Map Score: 7.91205 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 62 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 AACCAACCTTAAATGAAGTTTTGGTATTATA 1 85 0 AAATGAAGTT 0.766595 -24 AAGATAGTAGCAATTTGGCTTAAAAATGCCA 3 158 1 CAATTTGGTT 0.3678 -143 AAAAGATTAAAAATTAAGCTTTTTGAAAAAG 3 223 1 AAATTAAGTT 0.906153 -78 CTATTGTTTAAAATTTACATTTTTTAAACGC 4 61 0 AAATTTACTT 0.819119 -154 AATTTTTTCTCAATTTAGGTTTTGTTTATAA 4 105 1 CAATTTAGTT 0.838365 -110 TTAATTGTAGCAATTAAGTTTTAAAAACTCA 6 67 0 CAATTAAGTT 0.778463 -55 TTTGTTACAATAATTTAGATTTTTTAGCTAG 8 14 1 TAATTTAGTT 0.566251 -78 CAATTTAATCAAAATTAGATTACAATATTAT 9 25 1 AAAATTAGTT 0.901879 -52 TTTTAGGGTTAAATGAAGTTTTATTCAAAAA 10 37 1 AAATGAAGTT 0.766595 -264 TTTATTCAAAAAATGAAGTTTTACAAAAAAG 10 56 1 AAATGAAGTT 0.766595 -245 ATCATGTTTAAAAATCAGTTTGTTTGGTGTG 10 263 0 AAAATCAGTT 0.83681 -38 TAAAAGTAATAAAATAACTCTTTGAGTGCGA 11 63 0 AAAATAACCT 0.402692 -228 ATTTGTAAAAAAATTCAGTTTGTTTGCTATG 11 103 0 AAATTCAGTT 0.888381 -188 TGTTTTGATTAAAATTACCTTGACCGACAAT 11 171 0 AAAATTACTT 0.745211 -120 CTCCGTTTCAAAAATTAGGCTTGATTTTCAT 17 105 0 AAAATTAGCT 0.758066 -28 GAATACACTAAAATTTAGTTTTAATTTCAAG 21 34 0 AAATTTAGTT 0.930934 -83 AAATTTAGAAAAAATCACGCTTGATCTTATC 21 78 0 AAAATCACCT 0.357518 -39 TGAAAAAATAAAAATTATTTTAACATTTC 23 9 0 AAAATTATTT 0.303359 -93 ******** ** Masking position 11 Map Score: 7.8048 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 241 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 10 ATGCCCATGAAAATACAAAAATAAAGCCAA 3 20 1 AAATACAAAA 0.769881 -281 TGCGCCTAAAAAATACAACAGCGTTGCGAT 3 73 1 AAATACAACA 0.811578 -228 TATTTGTAGTAAATTCAACAAAGATAAACA 3 271 0 AAATTCAACA 0.557632 -30 AATTTTTCTTATAAACAAAACCTAAATTGA 4 114 0 ATAAACAAAA 0.426432 -101 TTCATAAACAACCCCACTTACCA 5 4 1 ATAAACAACC 0.769051 -297 AAATTTGAGAATATTCAAGCG 13 2 0 ATATTCAAGC 0.613862 -109 TTGAATTAAAAACAAGGAATAAC 14 8 1 AAAAACAAGG 0.646015 -16 TAGGGATTTTAAATACAAACAACAAAAAAT 16 134 0 AAATACAAAC 0.92088 -110 GAATTTATTTTAATACAAACTAGCTTAAAA 17 39 0 TAATACAAAC 0.533917 -94 CTACTTTCAAAAATACAAGCAAGAATTTAT 17 61 0 AAATACAAGC 0.948877 -72 ATTCGAAATGAAAATCAAGCCTAATTTTTG 17 98 1 AAAATCAAGC 0.804866 -35 TCAAAAACAAACAAGACAAACT 19 37 0 AAAAACAAAC 0.898352 -12 ATCTGGGTTTAAAAACAACCACATTGCAGG 20 94 1 AAAAACAACC 0.919213 -26 CTTTCTGCTGAAATACCAGCCCCGCTTAAG 22 24 0 AAATACCAGC 0.730279 -46 ********** Masking position 3 Map Score: 6.86367 Number of sites scoring better than the average of aligned sites = 735 Number in coding regions = 641 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 11 CTAAAGGTTAAACATGATTAAACAAACCCT 3 125 0 AACATGATTA 0.811996 -176 TCTTTAAACAAGCATGCTTTCAATAGCACC 5 71 1 AGCATGCTTT 0.871665 -230 ATGGTAGTTTAACATGCTTAGAGATAAAAC 7 15 0 AACATGCTTA 0.970844 -44 ATGAATTGCTAACATGCTAGCTAAAAAATC 8 31 0 AACATGCTAG 0.903384 -61 TTTTAATCAAAACATGCTATTATTTGGAAC 11 188 1 AACATGCTAT 0.940969 -103 TATTGGATAAAACCTGCTTAAGTTAAATTG 16 176 1 AACCTGCTTA 0.898416 -68 GATTAGCAAAAACATGGTTTAATTGGCTTT 23 46 1 AACATGGTTT 0.83097 -56 GCTGAATGCTAACATGCTAAAACTAAAACC 25 35 1 AACATGCTAA 0.954036 -67 ********** Masking position 1 Map Score: 4.55318 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 72 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 TGAAAGCTCAAAGATAAAGCGCTACAATCT 1 32 0 AAGATAAAGC 0.858977 -77 TGAAAATACAAAAATAAAGCCAAGCGTTAG 3 27 1 AAAATAAAGC 0.925712 -274 AAAAAGATTAAAAATTAAGCTTTTTGAAAA 3 222 1 AAAATTAAGC 0.959604 -79 CTAAAAACTCAAAATTAACCTAAAATCGCT 4 184 0 AAAATTAACC 0.863985 -31 GCAAATAGGTAAAATTAGCCACATCATGGT 5 30 0 AAAATTAGCC 0.81893 -271 GACTTATTCTAACATAAAGCCCGCTCTTTT 5 259 0 AACATAAAGC 0.767968 -42 GATATTGTTAAAAAGTAAGCTAAGGAGTGT 8 70 1 AAAAGTAAGC 0.832048 -22 AGATTGCATTTAAATTAGGCTCTTTTTAAA 11 255 0 TAAATTAGGC 0.704135 -36 CTCCGTTTCAAAAATTAGGCTTGATTTTCA 17 106 0 AAAATTAGGC 0.944177 -27 AATTTTAGATAAGATCAAGCGTGATTTTTT 21 71 1 AAGATCAAGC 0.78132 -46 ********** Masking position 4 Map Score: 5.44199 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 239 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 13 CCAAGTAGCCAAATAGCATGGATAA 2 6 1 TAGCCAAATA 0.895858 -25 GTTTAACCTTTAGCCAAAGATAGTAGCAAT 3 142 1 TAGCCAAAGA 0.977622 -159 TTTTTCAAACCATCCAATGACCCTTTATCG 11 36 1 CATCCAATGA 0.727111 -255 ACGCTCCATTTAGCCAATGATTATTGTCGG 11 149 1 TAGCCAATGA 0.972572 -142 TCTTTTTAAACAGCCAAAGCGTCTCTAACG 11 235 0 CAGCCAAAGC 0.886466 -56 GGAAAAATAGCCAAAGTCGTTGCTAAA 18 19 0 TAGCCAAAGT 0.886734 -17 AGTTTAAGACAAACCAAAGAGTTTGTCTTG 19 18 1 AAACCAAAGA 0.679716 -31 GCAAATGACAAAGCCAATTAAACCATGTTT 23 55 0 AAGCCAATTA 0.752322 -47 CTTTAATTACTAGCAAATGACAAAGCCAAT 23 67 0 TAGCAAATGA 0.776595 -35 ********** Masking position 6 Map Score: 2.95443 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 207 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 CCTATAATCATGCCCATGAAAAT 3 3 1 TTAATCATGC 0.890894 -298 TGAGGGTTTGTTTAATCATGTTTAACCTTTA 3 123 1 TTAATCATGT 0.935148 -178 GATAAAATTTTATAATTATGTTTATCTTTGT 3 253 1 TTAATTATGT 0.616893 -48 ATGGTGCTATTGAAAGCATGCTTGTTTAAAG 5 72 0 TAAAGCATGC 0.913138 -229 TCGTTTTATCTCTAAGCATGTTAAACTACCA 7 13 1 TTAAGCATGT 0.967513 -46 TCGTTCCAAATAATAGCATGTTTTGATTAAA 11 189 0 TATAGCATGT 0.871732 -102 ACAAAGCCAATTAAACCATGTTTTTGCTAAT 23 47 0 TAAACCATGT 0.840574 -55 AGGGTTTTAGTTTTAGCATGTTAGCATTCAG 25 36 0 TTTAGCATGT 0.915985 -66 * ********* Masking position 5 Map Score: 1.28837 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 148 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 ********** No masking Map Score: 2.53907e-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