AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ipurR_hpyl_opreg_300.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0181 257 H. pylori predicted coding region HP0181 #2 HP0252 300 outer membrane protein (omp7) #3 HP0255 99 adenylosuccinate synthetase (purA) #4 HP0404 80 protein kinase C inhibitor (SP:P16436) #5 HP0406 25 H. pylori predicted coding region HP0406 #6 HP0407 103 biotin sulfoxide reductase (bisC) #7 HP0408 165 H. pylori predicted coding region HP0408 #8 HP0417 168 methionyl-tRNA synthetase (metS) #9 HP0584 81 flagellar switch protein (fliN) #10 HP0585 228 endonuclease III (nth) #11 HP0737 146 conserved hypothetical integral membrane protein #12 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #13 HP0742 64 phosphoribosylpyrophosphate synthetase (prsA) #14 HP0830 58 amidase #15 HP0832 91 spermidine synthase (speE) #16 HP0833 76 H. pylori predicted coding region HP0833 #17 HP0919 98 carbamoyl-phosphate synthase (glutamine-hydrolysing) (pyrAb) #18 HP0920 143 conserved hypothetical integral membrane protein #19 HP1010 300 polyphosphate kinase (ppk) #20 HP1011 36 dihydroorotate dehydrogenase (pyrD) #21 HP1108 259 pyruvate ferredoxin oxidoreductase, gamma subunit #22 HP1112 109 adenylosuccinate lyase (purB) #23 HP1218 119 glycinamide ribonucleotide synthetase (purD) #24 HP1234 300 conserved hypothetical integral membrane protein #25 HP1236 78 H. pylori predicted coding region HP1236 #26 HP1483 26 gerC2 protein (gerC2) #27 HP1490 103 hemolysin #28 HP1491 138 phosphate permease Motif number 1 AGATTGATTTTTTTAAGGGTAGTTTTTTTTAA 1 76 1 TTTTAAGGAG 0.898513 -182 AGGGTAGTTTTTTTTAAGTTGTGTTATTATTT 1 91 1 TTTTTAAGGT 0.788015 -167 AATTGACATCTTTTAAGCAAAATGTTATAATG 2 170 0 TTTTAAGCAA 0.786853 -131 AAACTTTCTAATTTTAAGATAATCATTCTTAA 2 232 0 ATTTTAAGAA 0.719726 -69 GCTCTTTTTAGGGCTTATAAAGAGGC 3 5 1 TTTTTAGGTT 0.929779 -95 ATCTACTTTGTTTTAAGGATAATATTTT 3 82 1 TTTTAAGGAA 0.894174 -18 TTTTGCTCCCTTTTAAGGTTTTTCTTTTATTA 4 55 0 TTTTAAGGTT 0.926725 -26 CTAAAACTATTTTTAAGGAAAAAT 5 12 1 TTTTAAGGAA 0.894174 -14 ATTAGCGGTAATTTTAGGTGAATCTATGTTAG 6 40 1 ATTTTAGGAA 0.827107 -64 TTGTGGGGTGTTTTTAGCTTAAAATTCATTAT 8 55 0 TTTTTAGCAA 0.794443 -114 AAATTAAGAGATTTAAACAAATTTAAGGTAAC 8 135 1 ATTTAAACAT 0.603327 -34 AGAAAGCGTTTTTTAAGGGCTTCATCGCAGTT 10 66 0 TTTTAAGGTT 0.926725 -163 AATGCGGTTGATTTTAACCGAAAGCGTGGCTT 10 154 0 ATTTTAACAA 0.528731 -75 TAAGGCTTAATTTTAAGCACGTTTTAGTATGA 11 50 0 TTTTAAGCGT 0.742929 -97 AAATCATGGCATTTTAGCATTTTATTTGCATT 11 104 0 ATTTTAGCTT 0.757778 -43 TTTAAAAAGAATTTAAGGCAATGA 11 133 1 ATTTAAGGAT 0.866407 -14 CAAAAGCCTTTTTTTAGGTAAATATAGATAGA 12 24 1 TTTTTAGGAA 0.898436 -54 ATTGCAATCGTTTTTAGGGAGTTTGATC 12 60 1 TTTTTAGGGT 0.873819 -18 ATTTTAATTCATTTTAGGGAGTGTAAGCG 13 46 1 ATTTTAGGGT 0.789256 -19 GTTTTTAGCCTTACAAAAAATTT 14 46 0 TTTTTAGCTA 0.802991 -13 CTTAGCTTACTTTTTAACAATATCCATGCCTT 15 62 0 TTTTTAACTA 0.686312 -30 TATTATAGTTATTTAAAGCTTAAATAAGGGTC 16 50 1 ATTTAAAGTA 0.7212 -27 GTTATCAATATTTTAAAGTATTTTTTATTAGG 17 44 0 TTTTAAAGTT 0.871612 -55 TTCAATTTCAATTTTAGGGGGTTTTGTTTGGT 18 36 1 ATTTTAGGGT 0.789256 -108 GCTTAAAATTTTTTTAGCGTTT 19 1 0 TTTTTAGCTT 0.852613 -300 CGCTAAAAAAATTTTAAGCGATCTTTTAGGGT 19 14 1 ATTTTAAGAT 0.784698 -287 ACAAACTGATTTTTAAACATGATGATTTAAAG 19 271 1 TTTTAAACGA 0.52222 -30 AAACATGATGATTTAAAGGATTTCTA 19 285 1 ATTTAAAGTT 0.785932 -16 CTTTGTTATTATTTAAGGTGTGATTTGATTTT 21 29 0 ATTTAAGGTG 0.834696 -231 CTAATATTTATTTTAAACTTTGTTATTATTTA 21 46 0 TTTTAAACTG 0.686495 -214 TAACAATATCTTTTTAGGAATTTTTATAGGAA 21 157 0 TTTTTAGGTT 0.929779 -103 CCCATTTTGATTTTAAGGATTGTCG 22 95 1 TTTTAAGGTG 0.903261 -15 ATGTGGTTGTTTTTAAACCCAGATGACCGCTA 23 86 0 TTTTAAACAG 0.674938 -34 TAGAAAACTCTTTTTAAGCTTTTTAAATCCC 24 10 0 TTTTTAAGTT 0.876657 -291 CCTAGACCCTTTTTAAAGGGTTTGAATGCCAC 24 45 0 TTTTAAAGTT 0.871612 -256 AGACTTAAAGTTTTTAAGCTTTAAACGCATAA 24 228 0 TTTTTAAGTT 0.876657 -73 TTAATTAGAGATTTTAGGTTAAACTACCCTAA 24 259 1 ATTTTAGGAA 0.827107 -42 ACCCATAAAGATTTTAGGGTAGTTTAACCTAA 24 272 0 ATTTTAGGAG 0.833684 -29 ATAAAACGCTTTTTAAAGAATTAAT 25 4 0 TTTTAAAGTT 0.871612 -75 AAGGCTTGATTTTTAAAGTTAGGCTTAATCTT 27 19 1 TTTTAAAGAG 0.826161 -85 AAATCTCAGAATTTTAACATAAAAGATTAAGC 27 41 0 ATTTTAACAA 0.528731 -63 TAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 28 10 0 TTTTAAAGAG 0.826161 -129 CAAACAACGCTTTTTAAGAGTGGCTCAAGGGC 28 69 1 TTTTTAAGTG 0.839928 -70 ******** ** Masking position 6 Map Score: 49.4401 Number of sites scoring better than the average of aligned sites = 2720 Number in coding regions = 2221 Number in noncoding regions = 499 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 2 GATATATGAGAGAAAGGTTTGGGTTTAGGG 1 210 1 AGAAAGGTTT 0.607238 -48 TACTAGCAAGAAAACGGGTTTGATCCATAA 2 25 1 AAAACGGGTT 0.690737 -276 AAGCGTTTCAAAAAAGCATCAAATTGACAT 2 193 0 AAAAAGCATC 0.836802 -108 AAAAAAAAGTAAAAAGCCTCTTTATAAGCC 3 22 0 AAAAAGCCTC 0.939922 -78 TTTTATTTTTAAAAAGCTATAATACAACTT 4 25 1 AAAAAGCTAT 0.687395 -56 AGGGTGTTTTAGAAAGACTTAAGCGCTAAA 7 33 1 AGAAAGACTT 0.660867 -133 CAAAAAATTGAAAAAGAGTTCAAGGAATAG 8 15 0 AAAAAGAGTT 0.935163 -154 ACCAAAAGAGAGAAAGCGTTTTTTAAGGGC 10 78 0 AGAAAGCGTT 0.910657 -151 TATTCCATGAAAAAAGCCACGCTTTCGGTT 10 141 1 AAAAAGCCAC 0.777381 -88 TTTCTTAAACAATAAGGCTTAATTTTAAGC 11 64 0 AATAAGGCTT 0.605655 -83 TATTTGCATTAAAAAGCGATTTTCTTAAAC 11 84 0 AAAAAGCGAT 0.903052 -63 GCCATGATTTAAAAAGAATTTAAGGCAATG 11 126 1 AAAAAGAATT 0.723368 -21 ATTTACCTAAAAAAAGGCTTTTGAATTTTC 12 17 0 AAAAAGGCTT 0.936842 -61 GCACCCAAACTAAAAGCGTTTGTTT 13 6 0 TAAAAGCGTT 0.701077 -59 TTAAAGCTTAAATAAGGGTCTAGCG 16 62 1 AATAAGGGTC 0.652971 -15 AAGTTTTACAAAAAAGAGTTTTTAAACAAC 19 71 1 AAAAAGAGTT 0.935163 -230 TGACTTTTTAAAAAAGCTTCAATGATTATC 19 218 1 AAAAAGCTTC 0.869734 -83 AAAAATTCCTAAAAAGATATTGTTATAAGA 21 164 1 AAAAAGATAT 0.431812 -96 ACAAGGCGCAAAAAAGCCCCTTGATTTAAT 22 18 0 AAAAAGCCCC 0.61136 -92 TAAAAAGCTTAAAAAGAGTTTTCTAATAGT 24 17 1 AAAAAGAGTT 0.935163 -284 CAAACCCTTTAAAAAGGGTCTAGGAGTTTA 24 53 1 AAAAAGGGTC 0.947842 -248 GTTTATTTTCAAAAAGGATTCGTGTTTTTA 24 78 1 AAAAAGGATT 0.829394 -223 TTAATTCTTTAAAAAGCGTTTTATCTAAAA 25 12 1 AAAAAGCGTT 0.976599 -67 AGCCACTCTTAAAAAGCGTTGTTTGATAAA 28 64 0 AAAAAGCGTT 0.976599 -75 ********** Masking position 4 Map Score: 23.8298 Number of sites scoring better than the average of aligned sites = 1403 Number in coding regions = 1205 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 3 ATAGCTATATTTTAATTTAAGAATTTTAGA 1 49 1 TTTAATTTAA 0.793828 -209 TGTGAATTGGCATGATTTAAGAGTAATGGG 1 144 1 CATGATTTAA 0.715229 -114 GTAATGGGTGTTTGTTTTAAGACGCTATGA 1 166 1 TTTGTTTTAA 0.716915 -92 ATAATGCTCGCTTAATTTTATTTGGGGTGT 2 146 0 CTTAATTTTA 0.91094 -155 TCCAATCTACTTTGTTTTAAGGATAATATT 3 78 1 TTTGTTTTAA 0.716915 -22 ATCCTTATATTTTATTTTTAAAAAGCTATA 4 16 1 TTTATTTTTA 0.686391 -65 CAGCATGGGCGTTAATTTAAAA 6 3 0 GTTAATTTAA 0.778398 -101 GTTTAAATCTCTTAATTTTAACATGCTTTT 8 123 0 CTTAATTTTA 0.91094 -46 ATTATAAAATCTTAATTTTACTATAAATTT 9 28 0 CTTAATTTTA 0.91094 -54 CTTGAATGCGGTTGATTTTAACCGAAAGCG 10 160 0 GTTGATTTTA 0.916608 -69 AAAATTAAAGGTTAATTTTA 11 1 0 GTTAATTTTA 0.852431 -146 AAAATTAACCTTTAATTTTTGAGAGAATTT 11 12 1 TTTAATTTTT 0.396708 -135 AACAATAAGGCTTAATTTTAAGCACGTTTT 11 57 0 CTTAATTTTA 0.91094 -90 GCTAAAATGCCATGATTTAAAAAGAATTTA 11 118 1 CATGATTTAA 0.715229 -29 GTGCGCTACAATTGATTTTAATTCATTTTA 13 32 1 ATTGATTTTA 0.629687 -33 TTTTAAACATGATGATTTAAAGGATTTCTA 19 281 1 GATGATTTAA 0.586505 -20 TAAGGTGTGATTTGATTTTAGTCTGTATGG 21 18 0 TTTGATTTTA 0.923573 -242 ACCACTAATATTTATTTTAAACTTTGTTAT 21 52 0 TTTATTTTAA 0.570985 -208 AAAAAAGCCCCTTGATTTAATTAAAGGG 22 9 0 CTTGATTTAA 0.92209 -101 TAAATCCCATTTTGATTTTAAGGATTGTCG 22 90 1 TTTGATTTTA 0.923573 -20 CTGCAATGTGGTTGTTTTTAAACCCAGATG 23 93 0 GTTGTTTTTA 0.791141 -27 ATTGTTATAACATGATTTTACCAATCAATG 24 192 1 CATGATTTTA 0.805077 -109 GCATATTTTATTTATTTTTAGAGTGTATTT 25 49 0 TTTATTTTTA 0.686391 -30 TTTTTGAAGGCTTGATTTTTAAAGTTAGGC 27 13 1 CTTGATTTTT 0.668348 -91 ********** Masking position 6 Map Score: 24.2127 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 657 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 4 ACAACTTAAAAAAAACTACCCTTAAAAAAA 1 83 0 AAAAACTACC 0.898018 -175 GCGTCTTAAAACAAACACCCATTACTCTTA 1 161 0 ACAAACACCC 0.933005 -97 TGCATTCTGTTAAAACACCCCAAATTCTAA 6 68 0 TAAAACACCC 0.955052 -36 TAAGTCTTTCTAAAACACCCTCATGCTAGT 7 24 0 TAAAACACCC 0.955052 -142 ATTTTAAGCTAAAAACACCCCACAAATAAG 8 62 1 AAAAACACCC 0.949914 -107 GATCAAACTCCCTAAAAACGAT 12 66 0 TCAAACTCCC 0.973097 -12 CGCTTACACTCCCTAAAATGAAT 13 52 0 TTACACTCCC 0.841827 -13 TCTAAGCATGTTAAACTACCATTAAATTTT 14 23 1 TTAAACTACC 0.820372 -36 AAACACTCCTTAGCTTACTT 15 82 0 AAACACTCCT 0.732595 -10 GTTGTTGTTTAAAAACTCTTTTTTGTAAAA 19 74 0 AAAAACTCTT 0.522472 -227 AACTCGCGCTACAATCTCCCTTTTTGATTG 19 110 1 ACAATCTCCC 0.721692 -191 ATCTGGGTTTAAAAACAACCACATTGCAGG 23 94 1 AAAAACAACC 0.791596 -26 CTTTTTGAAAATAAACTCCTAGACCCTTTT 24 64 0 ATAAACTCCT 0.844584 -237 CTTCAGCATTTCAAACTCCTTATAGAAATA 24 116 0 TCAAACTCCT 0.906164 -185 AAACAAAAGGTAAAACTCCTAGAACATTGT 24 167 1 TAAAACTCCT 0.929335 -134 AGATTTTAGGTTAAACTACCCTAAAATCTT 24 267 1 TTAAACTACC 0.820372 -34 TTTTTAAAACTCTCTTTAAAATTT 28 5 1 TAAAACTCTC 0.821149 -134 ********** Masking position 3 Map Score: 16.9326 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 808 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 AATATAATTCAAACCCTAAACCCAAACCTT 1 223 0 AAACCCTAAA 0.928848 -35 AAGTAACGCTAAATCAATATAAT 1 245 0 TAACGCTAAA 0.955443 -13 TGCTTTTTTGAAACGCTTAATAGCAAATTA 2 205 1 AAACGCTTAA 0.920735 -96 GCCTCTTTATAAGCCCTAAAAAGAGC 3 7 0 AAGCCCTAAA 0.931226 -93 AGAAAGACTTAAGCGCTAAAGACTTGAGCG 7 43 1 AAGCGCTAAA 0.971761 -123 TCAGCTTGGCTAGCGCTCAAGTCTTTAGCG 7 56 0 TAGCGCTCAA 0.865878 -110 TCATTATAATTAACGCTCAAAAAATTGAAA 8 32 0 TAACGCTCAA 0.861576 -137 ACGCTCAATGAAGCCATTAAAGACAAAGTT 10 15 1 AAGCCATTAA 0.468804 -214 AACTGCGATGAAGCCCTTAAAAAACGCTTT 10 66 1 AAGCCCTTAA 0.825808 -163 AATGCAAATAAAATGCTAAAATGCCATGAT 11 104 1 AAATGCTAAA 0.621974 -43 AAATTTTTTGTAAGGCTAAAAAC 14 46 1 TAAGGCTAAA 0.611819 -13 GATTAAATTGAAGCGATAAAAAAG 16 5 0 AAGCGATAAA 0.864976 -72 TCCAATATAATAGCGCAAAATGTAGTAAAA 18 69 0 TAGCGCAAAA 0.75904 -75 AAACGCTAAAAAAATTTTAA 19 1 1 AAACGCTAAA 0.97074 -300 AAACTTCATTTAACCCTAAAAGATCGCTTA 19 28 0 TAACCCTAAA 0.894039 -273 TTTAAGCTTTAAACGCATAAAAGTTGCATT 24 218 0 AAACGCATAA 0.621952 -83 TTTATCTAAAAAACGATAAAATACACTCTA 25 31 1 AAACGATAAA 0.86065 -48 ACCTAAAACCTAACGATAAATATAAAATAT 27 76 0 TAACGATAAA 0.799674 -28 ********** Masking position 2 Map Score: 21.3892 Number of sites scoring better than the average of aligned sites = 1421 Number in coding regions = 1284 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 TCAATCTAAAATTCTTAAATTAAAATATAGCTATA 1 48 0 ATTCTAAAAA 0.737198 -210 AGTAAAATCACTTATCAAAGCAAAAAGGATATTT 2 277 1 CTTATAAAAA 0.77057 -24 TTGATTGGGTATTATAATATAAAAATTGAGAATTA 7 95 0 ATTATAAAAA 0.930775 -71 TTTTACTATAAATTTTATAACAAATAAAGCCA 9 8 0 AATTTAAAAT 0.480609 -74 TAAAATTAAGATTTTATAATCAAAGTCAAATCATT 9 38 1 ATTTTAAAAG 0.729396 -44 ATTCTTTTGCATTATTCCATGAAAAAAGCCACGCT 10 129 1 ATTATAAAAA 0.9308 -100 GAATTTAAAAGTTATCATACTAAAACGTGCTTAAA 11 36 1 GTTATAAAAA 0.770571 -111 ATTAAGCCTTATTGTTTAAGAAAATCGCTTTTTAA 11 71 1 ATTGTAAAAT 0.664255 -76 AAAAATCTAAATTATTGTAACAAAAGC 15 3 0 ATTATAAAAA 0.9308 -89 GTAAAACTTCATTTTTTGAATAAAACTTCATTTAA 19 45 0 ATTTTAAAAA 0.899742 -256 GTTTGGTGTGATTATATAATGAAATGATAATCATT 19 238 0 ATTATAAAAT 0.862241 -63 GAACGCTTGTCTTTTTAGAATAAATGGCCATAAAA 21 91 1 CTTTTAAAAT 0.51619 -169 GTATGCCCCCATTTTCCTATAAAAATTCCTAAAAA 21 144 1 ATTTTAAAAA 0.899742 -116 TCAGCCTAGAATTATACAAGAAAAACTATTAATGT 21 195 0 ATTATAAAAA 0.930775 -65 ATGTCTCCTTAATATCGTATAAAATAAATTGAATT 21 229 0 AATATAAAAT 0.577213 -31 AAATAAATAAAATATGCGAGAAAAATC 25 62 1 AATATAAAAA 0.744118 -17 AAATCTCAGAATTTTAACATAAAAGATTAAGCCTA 27 38 0 ATTTTAAAAG 0.729396 -66 CTTAAAAAGCGTTGTTTGATAAAAATGGCTCATTA 28 52 0 GTTGTAAAAA 0.563084 -87 ***** * **** Masking position 5 Map Score: 10.3727 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 177 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 AATTCTTAAATTAAAATATAGCTATAATAC 1 44 0 TTAAAATATA 0.559603 -214 AACACCCCAAATAAAATTAAGCGAGCATTA 2 145 1 ATAAAATTAA 0.587376 -156 TACTTAATCCATAAAAGAAACTTTCTAATT 2 251 0 ATAAAAGAAA 0.919593 -50 CTTTTTAAAAATAAAATATAAGGATCGTTA 4 11 0 ATAAAATATA 0.899717 -70 TACAACTTTAATAAAAGAAAAACCTTAAAA 4 47 1 ATAAAAGAAA 0.919593 -34 ATTGGGTATTATAATATAAAAATTGAGAAT 7 97 0 ATAATATAAA 0.432027 -69 TTTATTTGTTATAAAATTTATAGTAAAATT 9 15 1 ATAAAATTTA 0.559602 -67 ATACCTTGTCATCAAAGAAAGCGT 10 215 1 ATCAAAGAAA 0.561944 -14 CAAAAACCTAATAAAAAATACTTTAAAATA 17 38 1 ATAAAAAATA 0.532702 -61 CGTTCAAATCATAAAAGATAAGGATTTAA 20 18 1 ATAAAAGATA 0.910781 -19 ATAACAAAGTTTAAAATAAATATTAGTGGT 21 52 1 TTAAAATAAA 0.587386 -208 GCCTAGAATTATACAAGAAAAACTATTAAT 21 197 0 ATACAAGAAA 0.561944 -63 TTAATATCGTATAAAATAAATTGAATTCAG 21 226 0 ATAAAATAAA 0.909513 -34 CTAAAAAACGATAAAATACACTCTAAAAAT 25 36 1 ATAAAATACA 0.677023 -43 CTAAAAATAAATAAAATATGCGAGAAAAAT 25 58 1 ATAAAATATG 0.516445 -21 ACAAGCCATGAAAAAAGAAAAGTC 26 13 1 AAAAAAGAAA 0.463957 -14 GAATTTTAACATAAAAGATTAAGCCTAACT 27 35 0 ATAAAAGATT 0.450526 -69 AACGATAAATATAAAATATATAAAATCTCA 27 65 0 ATAAAATATA 0.899717 -39 ********** Masking position 6 Map Score: 7.64489 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 147 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 AACCTTGAGATTGTTTTAGTGTATTATAGCTA 1 24 1 TTGTTAGTGT 0.7603 -234 TTAGATTGATTTTTTTAAGGGTAGTTTTTTTT 1 74 1 TTTTTAGGGT 0.820476 -184 CTCGCTTAATTTTATTTGGGGTGTTAGCTCAG 2 138 0 TTTTTGGGGT 0.961845 -163 CTTTTTACTTTTTTTTTGGTATTCTAACAAGC 3 36 1 TTTTTGGTAT 0.937917 -64 ATTAAACGCATTGATTGGGTATTATAATATAA 7 108 0 TTGTTGGTAT 0.874251 -58 TTTATGCTTATTTGTGGGGTGTTTTTAGCTTA 8 66 0 TTTTGGGTGT 0.847231 -103 TGGCTTTATTTGTTATAAAATTTATA 9 5 1 TTTTTGTTAT 0.636979 -77 AGAGAAAGCGTTTTTTAAGGGCTTCATCGCAG 10 68 0 TTTTTAGGGC 0.590816 -161 TCAAAAGCCTTTTTTTAGGTAAATATAGATAG 12 23 1 TTTTTGGTAA 0.636345 -55 TAAAGTATTTTTTATTAGGTTTTTGCGTGGCG 17 31 0 TTTTTGGTTT 0.788454 -68 TTTAGGGGGTTTTGTTTGGTATTTTACTACAT 18 48 1 TTTTTGGTAT 0.937917 -96 TAGCGCGAGTTTGCTTAGTTGTTGTTTAAAAA 19 89 0 TTGTTGTTGT 0.670187 -212 TAAAAATCAGTTTGTTTGGTGTGATTATATAA 19 254 0 TTTTTGGTGT 0.974371 -47 CTAGGAGGATTTTCTTAGGGGCAGATTTAAAA 23 12 0 TTTTTGGGGC 0.888446 -108 *** ** ***** Masking position 5 Map Score: 7.80789 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 421 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 GGCTAAATTTTGAAACCTTGAGATT 1 6 1 AATTTTGAAA 0.854925 -252 TTTAGACTTGAAATTTGAAAATAATAACAC 1 111 0 AAATTTGAAA 0.890261 -147 GATTATCTTAAAATTAGAAAGTTTCTTTTA 2 240 1 AAATTAGAAA 0.807973 -61 TTATAATATAAAAATTGAGAATTACCCCAC 7 89 0 AAAATTGAGA 0.827649 -77 TATAAGCGTCAATATTGAAAACAGAAATTA 7 136 0 AATATTGAAA 0.890261 -30 TAACGCTCAAAAAATTGAAAAAGAGTTCAA 8 22 0 AAAATTGAAA 0.917818 -147 TGCTTTTAAAAATTTAGAGAATAGAGGTTG 8 100 0 AATTTAGAGA 0.567886 -69 TTTTTAGGTAAATATAGATAGACTTTATTG 12 34 1 AATATAGATA 0.53909 -44 AATACTTTAAAATATTGATAACGCTTCGTT 17 54 1 AATATTGATA 0.692791 -45 AAAACCCCCTAAAATTGAAATTGAAGTCTG 18 31 0 AAAATTGAAA 0.917818 -113 CTCCTTATAGAAATATGAAAACATAAAAAC 24 101 0 AAATATGAAA 0.645095 -200 ACAAGCCATGAAAAAAGAAAAGTC 26 13 1 AAAAAAGAAA 0.564803 -14 ********** Masking position 8 Map Score: 5.2556 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 302 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 TAGATTGATTTTTTTAAGGGTAGTTTTTTT 1 75 1 TTTTTAAGGG 0.86788 -183 GCTATGACTATCTTTATGCGAGATATATGA 1 189 1 TCTTTATGCG 0.691702 -69 TTATTCTCTTTCTTTATGGATCAAACCCGT 2 38 0 TCTTTATGGA 0.892128 -263 TTAGAAAGTTTCTTTTATGGATTAAGTAAA 2 253 1 TCTTTTATGG 0.80187 -48 GCTCTTTTTAGGGCTTATAAAG 3 3 1 TCTTTTTAGG 0.656839 -97 GCTAAAACTATTTTTAAGGAAAAAT 5 11 1 TTTTTAAGGA 0.676904 -15 ATAAACTTTGTCTTTAATGGCTTCATTGAG 10 18 0 TCTTTAATGG 0.88648 -211 GAGAAAGCGTTTTTTAAGGGCTTCATCGCA 10 69 0 TTTTTAAGGG 0.86788 -160 TTACATTCTTTCTTTAAGGATTAGTT 17 83 1 TCTTTAAGGA 0.895905 -16 TTTTAAGCGATCTTTTAGGGTTAAATGAAG 19 25 1 TCTTTTAGGG 0.953104 -276 TAAATCCTTATCTTTTATGATTTGAACGAT 20 16 0 TCTTTTATGA 0.563429 -21 TTGATTTTAGTCTGTATGGGGCAAGT 21 7 0 TCTGTATGGG 0.796027 -253 TATAACAATATCTTTTTAGGAATTTTTATA 21 161 0 TCTTTTTAGG 0.656839 -99 TTTTCATATTTCTATAAGGAGTTTGAAATG 24 110 1 TCTATAAGGA 0.541266 -191 TACCCTAAAATCTTTATGGGTAAAATGC 24 283 1 TCTTTATGGG 0.963901 -18 ********** Masking position 5 Map Score: 13.822 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 576 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 GATTCTCCTTCAAGCTTGCATT 6 92 0 TTCTCCTTCA 0.62785 -12 CTGTCTATTCCTTGAACTCTTTTTC 8 6 1 TATTCCTTGA 0.635613 -163 GAATGCATTGAACCCCTTCATGGATACCAA 10 103 0 AACCCCTTCA 0.923469 -126 GGGATCTTAAAGCCACTTGAATGCGGTTGA 10 175 0 AGCCACTTGA 0.634768 -54 GTTTTACTCCTTGAATTCAACTCA 18 130 0 TACTCCTTGA 0.952303 -14 GGCGCAAAAAAGCCCCTTGATTTAATTAAA 22 14 0 AGCCCCTTGA 0.95663 -96 TGTGCGATTTTTCCCCTTGATTCTTTAAAC 22 45 1 TTCCCCTTGA 0.923077 -65 TGATTCTTTAAACCCCTTTAAAGTAACATA 22 62 1 AACCCCTTTA 0.815629 -48 TTTGAAAATAAACTCCTAGACCCTTTTTAA 24 61 0 AACTCCTAGA 0.854795 -240 CAAAAGGTAAAACTCCTAGAACATTGTTAT 24 170 1 AACTCCTAGA 0.854795 -131 TCTATCCAATTAGCCCTTGAGCCACTCTTA 28 83 0 TAGCCCTTGA 0.831001 -56 ********** Masking position 10 Map Score: 3.58391 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 260 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 GTTTGGGTTTAGGGTTTGAATTATATTGAT 1 226 1 AGGGTTTGAA 0.687361 -32 TGGAGTGTAGGGGGTTCGAACCCCTGACCT 2 80 1 GGGGTTCGAA 0.95449 -221 TTAAAATTAAGAGATTTAAACAAATTTAAG 8 132 1 GAGATTTAAA 0.508975 -37 TATCCATGAAGGGGTTCAATGCATTCTTTT 10 107 1 GGGGTTCAAT 0.809699 -122 TCGGAGTAGCGGGATTCAAACCCACGACCT 19 185 0 GGGATTCAAA 0.924829 -116 TTACTTTAAAGGGGTTTAAAGAATCAAGGG 22 58 0 GGGGTTTAAA 0.972831 -52 AGCGGTCATCTGGGTTTAAAAACAACCACA 23 87 1 TGGGTTTAAA 0.860916 -33 GGGATTTAAAAAGCTTAAAA 24 1 1 GGGATTTAAA 0.929356 -300 TTCTAATAGTGGCATTCAAACCCTTTAAAA 24 37 1 GGCATTCAAA 0.766889 -264 ATTTCTATAAGGAGTTTGAAATGCTGAAGC 24 117 1 GGAGTTTGAA 0.687361 -184 GCAACTTTTATGCGTTTAAAGCTTAAAAAC 24 221 1 TGCGTTTAAA 0.623377 -80 ********** Masking position 9 Map Score: 5.31837 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 610 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 13 CAGCTGAGCTAACACCCCAAATAAAATTAAGC 2 135 1 AAACCCCAAT 0.902839 -166 TTCACCTAAAATTACCGCTAATAAGCCCTCAG 6 30 0 ATACCGCTAT 0.924519 -74 ATTCTGTTAAAACACCCCAAATTCTAACATAG 6 63 0 AAACCCCAAT 0.902839 -41 CGTGGGTTTGAATCCCGCTACTCCGACCATGA 19 189 1 AACCCGCTAT 0.919157 -112 GTTCTTAATAAAAACCACTAATATTTATTTTA 21 63 0 AAACCACTAT 0.9592 -197 TTAAACCCAGATGACCGCTACTTTTACATGCG 23 74 0 ATACCGCTAT 0.931168 -46 AAAGGGTTTGAATGCCACTATTAGAAAACTCT 24 31 0 AAGCCACTAT 0.878547 -270 TGGATAGAATAAGACCACTATTAGAACAAGGT 28 105 1 AAACCACTAT 0.959189 -34 ** ******* * Masking position 10 Map Score: 2.93226 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 61 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 ********** No masking Map Score: 1.27638e-11 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: 1.27638e-11 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