AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_hpyl_reg_100.orf -o00970_hpyl_100.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 Purged sequences: HP1141 23 methionyl-tRNA formyltransferase (fmt) HP1253 31 tryptophanyl-tRNA synthetase (trpS) Input sequences: #1 HP0122 186 H. pylori predicted coding region HP0122 #2 HP0123 39 threonyl-tRNA synthetase (thrS) #3 HP0181 257 H. pylori predicted coding region HP0181 #4 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #5 HP0320 71 conserved hypothetical secreted protein #6 HP0322 141 poly E-rich protein #7 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #8 HP0417 168 methionyl-tRNA synthetase (metS) #9 HP0476 117 glutamyl-tRNA synthetase (gltX) #10 HP0616 77 chemotaxis protein (cheV) #11 HP0617 34 aspartyl-tRNA synthetase (aspS) #12 HP0643 164 glutamyl-tRNA synthetase (gltX) #13 HP0774 23 tyrosyl-tRNA synthetase (tyrS) #14 HP0777 107 uridine 5'-monophosphate (UMP) kinase (pyrH) #15 HP0885 167 virulence factor mviN protein (mviN) #16 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #17 HP0972 111 glycyl-tRNA synthetase, beta subunit (glyS) #18 HP1142 39 H. pylori predicted coding region HP1142 #19 HP1143 243 H. pylori predicted coding region HP1143 #20 HP1153 130 valyl-tRNA synthetase (valS) #21 HP1190 61 histidyl-tRNA synthetase (hisS) #22 HP1241 119 alanyl-tRNA synthetase (alaS) #23 HP1254 116 biotin synthesis protein (bioC) #24 HP1422 24 isoleucyl-tRNA synthetase (ileS) #25 HP1423 101 conserved hypothetical protein #26 HP1483 26 gerC2 protein (gerC2) #27 HP1490 103 hemolysin #28 HP1550 62 protein-export membrane protein (secD) #29 HP1551 47 conserved hypothetical secreted protein #30 HP1552 23 Na+/H+ antiporter (nhaA) #31 HP1553 248 helicase Motif number 1 TATCATTGTTATATTTTTGTTTTAAGAAACTTAATGATC 1 27 0 ATTTTTAAAA 0.801986 -160 TTTTGAAACCTTGAGATTGTTTTAGTGTATTATAGCTAT 3 18 1 TTTTTTAGTA 0.931525 -240 TTAGTGTATTATAGCTATATTTTAATTTAAGAATTTTAG 3 39 1 ATTTTTAATA 0.901339 -219 AGAATTTTAGATTGATTTTTTTAAGGGTAGTTTTTTTTA 3 68 1 ATTTTAAGTA 0.950593 -190 AGAGTGTGAATTGGCATGATTTAAGAGTAATGGGTGTTT 3 140 1 TTTTTAAGTA 0.931524 -118 ATTTAATATTATTTAATCTTTTTAAAATTTTGTTTTATA 4 46 0 ATTTTTAATT 0.76641 -160 AGTCCTTTTTTTAAAATTGTTTTAGGCTTTTATTTTCAT 4 173 0 TTTTTTAGTT 0.829959 -33 TTTGTTTGAATTATAGCTTTTTTAAAAAATAATTGATAG 5 14 0 TTTTTTAAAA 0.741183 -58 TTTTGATTATAATAAAAGATTTAAAAAAAGCGATAAAAT 6 67 1 AATTTAAAAA 0.801987 -75 ATTTGATAAGAAACGCTTCTTTAAGCCTATCCATTTTAT 6 99 0 AATTTAAGTA 0.950593 -43 GCTTTTTTGCTCCCTTTTAAGGTTTTTCTTTTATT 7 7 1 TTTTTAAGTT 0.829959 -74 TAAAGTTGTATTATAGCTTTTTAAAAATAAAATATAAGG 7 45 1 TTTTTAAATA 0.866058 -36 AGCGTTAATTATAATGAATTTTAAGCTAAAAACACCCCA 8 45 1 ATTTTAAGAA 0.894972 -124 CTCTTAATTTTAACATGCTTTTAAAAATTTAGAGAATAG 8 106 0 TATTTAAATT 0.698785 -63 ATTAAGAGATTTAAACAAATTTAAGGTAACACGATTATA 8 137 1 TTTTTAAGAA 0.857652 -32 ACAATAAGAGTATTTTATTTTTAAGGTTAGAACA 9 94 1 TATTTAAGTA 0.931523 -24 GTTTGTAAAAACCTTTTAAACTAAATTAGGGTAG 10 6 1 TATTTAAAAA 0.741183 -72 ATTTAATTTTTGTTTTAATTTAAAGGGATAAA 11 4 1 TATTTTAATA 0.866056 -31 CAAACATGAATAGGCATCATTTAAGAGATTAGCACTTGG 12 59 0 TATTTAAGAT 0.683715 -106 AAAAACCCTTTATTTAAAAATAGTTTTTGATT 12 143 0 AATTTAAATA 0.901229 -22 AAAAACACCCTTTCTGAATTTTAAGCCTACATTCTCAGC 14 17 0 TTTTTAAGTA 0.931524 -91 TTCTCATTAATTAATAAAATTTTAATAAAACTTGTGATT 14 73 0 TTTTTTAAAA 0.741088 -35 AAATTCTTATATTATACCATTTAAGGATTAAAAA 15 6 0 ATTTTAAGTT 0.873467 -162 TGTTGGTTAAAAATATTTTTTTTAGCATACTGGTTGTAT 15 92 0 AATTTTAGTA 0.950593 -76 TATACATATTAAATAATATTTTAAAATTAAAAAGCG 16 8 0 AATTTAAATA 0.901426 -124 TTTTGAATGTAAGGGCTATTTTAAACTTATTATTGTAAA 16 67 1 AATTTAAATA 0.901426 -65 CCTAAAAAACAAAATCACTTTTAAGACTAAATCATGTTA 17 70 0 AATTTAAGTA 0.950593 -42 GTTGTCCCAAAAGCACAAGTTTTAGAGAACCATACG 19 8 0 AATTTTAGAA 0.894972 -236 AAAATTATACAACAAAGCATTTAAATTAAAAAGGATAGT 20 14 0 AATTTAAAAA 0.801987 -117 TTTTTTAAGGAACGCTCTATTTTAGGATAATA 20 109 1 AATTTTAGTA 0.95059 -22 CAATAGCCCTTTTTTAAAGATTTTAAGCTAAA 21 4 1 TATTTAAATT 0.698785 -58 TAAAGATTTTAAGCTAAAATTTTAGCATACAAATACAAG 21 25 1 AATTTTAGTA 0.950494 -37 TCTCCTTTAATTTTGGATGTTTAAAGTATAATAAACTAT 22 16 1 TTTTTAAAAT 0.506775 -104 AAAGTATAATAAACTATCTTTTTAAAAAAATAACTTAAA 22 38 1 AATTTTAAAA 0.801987 -82 TAAGGCTATTTTATAGCTCTTTTAAGTTATTTTTTTAAA 22 58 0 TTTTTTAATA 0.866058 -62 TTGTTGTTTTATCGCGTATTTTAAGGCTATTTTATAGCT 22 79 0 ATTTTAAGTA 0.950592 -41 AAGCGTGATTTTTTCTAAATTTTAGGCATTTAAGGAATC 23 12 0 TTTTTTAGAT 0.649522 -105 GCTTGAAATTAAAACTAAATTTTAGTGTATTCTTAGCAA 23 66 0 AATTTTAGTA 0.921486 -51 TATCCATAACTTATAAGGGTTTTAGTTTTAGCATGTTAG 25 43 0 TTTTTTAGTT 0.829959 -59 AATATATAAAATCTCAGAATTTTAACATAAAAGATTAAG 27 42 0 ATTTTTAATA 0.901425 -62 TTTTATATTTATCGTTAGGTTTTAGGTTTAAAGTT 27 79 1 ATTTTTAGTT 0.873466 -25 ATTTGAGATTAAAACATCTTTTAAGGAAATTAA 29 25 1 AATTTAAGAA 0.894972 -23 AATTAAAAATTTTAAGGTTGTCT 30 1 1 AATTTTAATT 0.766408 -23 ATAGCAAAAGATTAAGGTTTTTTAGCTTAAGTAAAAAAG 31 171 1 ATTTTTAGTA 0.950593 -78 TAGCTTAAGTAAAAAAGGCTTTTAGGTTATAATAAAGAC 31 193 1 AATTTTAGTA 0.950593 -56 AATAAAGACAAAATTAGAATTTTAGGATAGATCTCA 31 223 1 AATTTTAGTA 0.950591 -26 ** ****** ** Masking position 10 Map Score: 67.9147 Number of sites scoring better than the average of aligned sites = 1145 Number in coding regions = 883 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 2 TTAAGTTTCTTAAAACAAAAATATAACAAT 1 32 1 TAAAACAAAA 0.858948 -155 ACAAACTAGCTAAAACTAAAGCTCTATCAT 1 68 0 TAAAACTAAA 0.93548 -119 AATAAAATCATAAACCAAAAAGAATACACC 1 121 0 TAAACCAAAA 0.820576 -66 TCCTTTCTTCAAACCTTAAAAT 2 3 0 AAACCTTAAA 0.730119 -37 TATAGCTATAATACACTAAAACAATCTCAA 3 28 0 ATACACTAAA 0.812437 -230 TCTAAAATTCTTAAATTAAAATATAGCTAT 3 49 0 TTAAATTAAA 0.803081 -209 AATATAATTCAAACCCTAAACCCAAACCTT 3 223 0 AAACCCTAAA 0.848264 -35 AAGTAACGCTAAATCAATATAAT 3 245 0 TAACGCTAAA 0.746664 -13 AGTTTTACTATAAAACAAAATTTTAAAAAG 4 38 1 TAAAACAAAA 0.858948 -168 AAAATTTTAAAAAGATTAAATAATATTAAA 4 54 1 AAAGATTAAA 0.731366 -152 TATGAAAATAAAAGCCTAAAACAATTTTAA 4 172 1 AAAGCCTAAA 0.80862 -34 AATAAAAGAAAAACCTTAAAAGGGAGCAAA 7 16 0 AAACCTTAAA 0.730119 -65 ATAGCTTTTTAAAAATAAAATATAAGGATC 7 57 1 AAAAATAAAA 0.755621 -24 ATAATGAATTTTAAGCTAAAAACACCCCAC 8 55 1 TTAAGCTAAA 0.777881 -114 TATAATCGTGTTACCTTAAATTTGTTTAAA 8 146 0 TTACCTTAAA 0.600061 -23 TTCTAACCTTAAAAATAAAATACTCTTATT 9 96 0 AAAAATAAAA 0.755621 -22 TAAAAACCTTTTAAACTAAATTAGGGTAGT 10 16 1 TTAAACTAAA 0.893951 -62 AAGCCCTATCAAAGATTAAATGCTATAATA 10 45 0 AAAGATTAAA 0.731366 -33 AAATTAAAACAAAAATTAAAT 11 2 0 AAAAATTAAA 0.880412 -33 TTTTATCCCTTTAAATTAAAACAAAAATTA 11 14 0 TTAAATTAAA 0.803081 -21 AATCCCGTAAAAAGCCAAAAATCCTAGAGC 15 146 0 AAAGCCAAAA 0.639582 -22 AATAATATTTTAAAATTAAAAAGCG 16 6 0 TAAAATTAAA 0.875257 -126 GTATTAAGAAATAAACTAAACTGAGTGTAA 17 25 1 ATAAACTAAA 0.898504 -87 AAATCACTTTTAAGACTAAATCATGTTAGA 17 68 0 TAAGACTAAA 0.842815 -44 ATTCTCCCTAAAAAACAAAATCACTTTTAA 17 85 0 AAAAACAAAA 0.864671 -27 AAACTACATTATAAATAAAAAAAATGAAGA 19 75 0 ATAAATAAAA 0.642763 -169 ACAAACAACAAAAAATAAAAAAGGCAAAAA 19 120 0 AAAAATAAAA 0.755621 -124 TAAAACCTGCTTAAGTTAAATTGATCTCAT 19 183 1 TTAAGTTAAA 0.628817 -61 AACAAAGCATTTAAATTAAAAAGGATAGTC 20 13 0 TTAAATTAAA 0.803081 -118 TTAAAAGCGTAAAAGCAAAAGGCGTTCCAA 20 70 1 AAAAGCAAAA 0.726361 -61 TTTAAAGATTTTAAGCTAAAATTTTAGCAT 21 23 1 TTAAGCTAAA 0.777881 -39 TTTTAAAAAAATAACTTAAAAGAGCTATAA 22 57 1 ATAACTTAAA 0.762887 -63 TTTGCTAAGAATACACTAAAATTTAGTTTT 23 65 1 ATACACTAAA 0.812437 -52 CGCTTGAAATTAAAACTAAATTTTAGTGTA 23 76 0 TAAAACTAAA 0.93548 -41 GCTAACATGCTAAAACTAAAACCCTTATAA 25 42 1 TAAAACTAAA 0.93548 -60 GTTATGGATAAAAACTTAAAGAATAGGGTA 25 72 1 AAAACTTAAA 0.846838 -30 CTCAGAATTTTAACATAAAAGATTAAGCCT 27 39 0 TAACATAAAA 0.590483 -65 AACTTTAAACCTAAAACCTAACGAT 27 89 0 TAAACCTAAA 0.91589 -15 CCTTTTTTACTTAAGCTAAAAAACCTTAAT 31 181 0 TTAAGCTAAA 0.777881 -68 TGTCTTTATTATAACCTAAAAGCCTTTTTT 31 203 0 ATAACCTAAA 0.869256 -46 AGGTTATAATAAAGACAAAATTAGAATTTT 31 216 1 AAAGACAAAA 0.702634 -33 ********** Masking position 3 Map Score: 50.3188 Number of sites scoring better than the average of aligned sites = 1445 Number in coding regions = 1132 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 224 Fraction of orfs with sites within 600 bp upstream = 0.0359782 Motif number 3 CTAACCGCCCATTATACAATAAAATCATAAACCA 1 134 0 ATTAAAATAA 0.770529 -53 TTAGTTAGGTATTTTTGAATAGAAAGGGTGGTT 1 164 1 ATTTTAATAA 0.868957 -23 CTATATTTTAATTTAAGAATTTTAGATTGATTTT 3 53 1 ATTTAAATTA 0.479947 -205 TAGACTTGAAATTTGAAAATAATAACACAACTTA 3 105 0 ATTTAAATAA 0.95663 -153 TTTTAAAAAGATTAAATAATATTAAATTGAATGG 4 58 1 ATTAAAATAA 0.770542 -148 GTTTATCAATATTTGACAAAAATAAGATCAAAAA 4 93 1 ATTTAAAAAA 0.930406 -113 CCTAAAACAATTTTAAAAAAAGGACTTTTG 4 186 1 TTTTAAAAAA 0.686529 -20 AATTATAGCTTTTTTAAAAAATAATTGATAGGTT 5 11 0 TTTTAAAAAA 0.686518 -61 ATAGAGTGTAATTTAAAATAAGGATCATTTG 6 8 0 ATTTAATAAA 0.762265 -134 AACCAAGTGGATTTTTGATTATAATAAAAGATTT 6 55 1 ATTTTATTAA 0.613944 -87 TATAATACAACTTTAATAAAAGAAAAACCTTAAA 7 26 0 CTTTAAAAAA 0.496614 -55 TATTATAGCTTTTTAAAAATAAAATATAAGGATC 7 53 1 TTTTAAATAA 0.781094 -28 CTATTCTCTAAATTTTTAAAAGCATGTTAAAATT 8 106 1 AATTTAAAAA 0.312238 -63 GATTGAGATTATTTTTGATTAGGATCAACC 9 7 0 ATTTTATTAA 0.614009 -111 TTTTTAAGCCATTTTTGAATACAATAAGAGTATT 9 74 1 ATTTTAATAA 0.868957 -44 GCCTATTCATGTTTGATAAAAACAGAACTACCAC 12 83 1 GTTTAAAAAA 0.496626 -82 AAAACCCTTTATTTAAAAATAGTTTTTGATTATA 12 140 0 ATTTAAATAT 0.479947 -25 ATCCCTTCTCATTAATTAATAAAATTTTAATAAA 14 83 0 ATTATAATAA 0.501483 -25 TAATATAAGAATTTGAAAAAAGAAATATGCTAAC 15 31 1 ATTTAAAAAA 0.930407 -137 CGCTTTTTAATTTTAAAATATTATTTAATATGT 16 10 1 ATTTAAATAA 0.95663 -122 AAAACTCACCATTTTACAATAATAAGTTTAAAAT 16 84 0 ATTTAAATAA 0.956583 -48 AGTTTAGTTTATTTCTTAATACAAAAGGTAGGCG 17 13 0 ATTTTAATAA 0.868979 -99 TCCTAATTCACAATATCATCTCAAAGCA 18 22 0 AATTAAATAA 0.713547 -18 AAAATGAAGAAATTGAGATAACGATCGATCAGCT 19 51 0 AATTAATAAA 0.265838 -193 TAAAAACTACATTATAAATAAAAAAAATGAAGAA 19 74 0 ATTAAATAAA 0.328021 -170 GATTTTTTATATTTTATAATAGAATGAGATCAAT 19 202 0 ATTTAAATAA 0.95657 -42 TTGTTGTATAATTTTGAAAAAATACGCAACAATT 20 38 1 ATTTGAAAAA 0.516386 -93 GGAACGCTCTATTTTAGGATAATA 20 117 1 ATTTAGATAA 0.593633 -14 TTAAGCTAAAATTTTAGCATACAAATACAAGGAA 21 33 1 ATTTACATAA 0.72892 -29 ATAAACTATCTTTTTAAAAAAATAACTTAAAAGA 22 46 1 TTTTAAAAAA 0.6864 -74 AAATCTCAGAATTTTAACATAAAAGATTAAGCCT 27 39 0 ATTTACATAA 0.728874 -65 AAATGCTATAATTTGAGATTAAAACATCTTTTAA 29 15 1 ATTTAATTAA 0.840964 -33 **** * **** * Masking position 3 Map Score: 29.8411 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 409 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 4 CAACTTAAAAAAAACTACCCTTAAAAAAAT 3 82 0 AAAACTACCC 0.929723 -176 GCGTCTTAAAACAAACACCCATTACTCTTA 3 161 0 ACAAACACCC 0.951452 -97 AATTCAAACAAAAACCAACCAATAAGATTA 5 41 1 AAAACCAACC 0.969512 -31 ACTCTATGATAAAAACAACCAACCAAGTGG 6 35 1 AAAAACAACC 0.974782 -107 ATTTTAAGCTAAAAACACCCCACAAATAAG 8 62 1 AAAAACACCC 0.984135 -107 AAAACACCCCACAAATAAGCATAAATGCAA 8 73 1 ACAAATAAGC 0.565549 -96 TAGCTTTTTGATAACCAACCATAAAAAGCT 12 20 1 ATAACCAACC 0.786474 -145 AATCTTGCTTAAAAACACCCTTTCTGAATT 14 36 0 AAAAACACCC 0.984135 -72 ATTAGGTAATAAATACAACCAGTATGCTAA 15 80 1 AAATACAACC 0.878842 -88 AAAAAAGGCAAAAAATACCCTTCGCATAAA 19 104 0 AAAAATACCC 0.941456 -140 ATAATTTTGAAAAAATACGCAACAATTAAA 20 45 1 AAAAATACGC 0.868635 -86 AAGGCGTTCCAAATCCAACCATTTTTTAAG 20 88 1 AAATCCAACC 0.856473 -43 AAATTTAGAAAAAATCACGCTTGATCTTAT 23 29 1 AAAATCACGC 0.876398 -88 CCTAACTTTAAAAATCAAGCCTTCAAAAAC 27 12 0 AAAATCAAGC 0.81544 -92 ********** Masking position 7 Map Score: 16.3039 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 451 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 AGCTATATTTTAATTTAAGAATTTTAGATTG 3 51 1 TAATTAAGAA 0.854603 -207 AAAACAATTTTAAAAAAAGGACTTTTG 4 189 1 TAAAAAAGGA 0.952677 -17 GAGTGTAATTTAAAATAAGGATCATTTG 6 8 0 TAAAAAAGGA 0.952677 -134 GCGTTTCTTATCAAATAAGGAGTCCCTAAA 6 122 1 TCAAAAAGGA 0.745976 -20 AATACAACTTTAATAAAAGAAAAACCTTAAA 7 26 0 TAATAAAGAA 0.926032 -55 TTTAAAAATAAAATATAAGGATCGTTA 7 64 1 AAATAAAGGA 0.904321 -17 TAAGCCCTAATTAAGGAATGAAC 13 8 1 TAATTAGGAA 0.594758 -16 TTAAATGGTATAATATAAGAATTTGAAAAAA 15 21 1 TAATAAAGAA 0.926032 -147 TATAAGAATTTGAAAAAAGAAATATGCTAAC 15 34 1 TGAAAAAGAA 0.77069 -134 ATAAATAAAAAAAATGAAGAAATTGAGATAA 19 64 0 AAAATAAGAA 0.734014 -180 ATAAGTTCAGTAAAATAGGGATTTTAAATAC 19 148 0 TAAAAAGGGA 0.834072 -96 TTTAGCATACAAATACAAGGAAATGGA 21 45 1 AAATAAAGGA 0.904321 -17 TAAACATCCAAAATTAAAGGAGAAAACC 22 8 0 AAATTAAGGA 0.816091 -112 AGACAAGCCATGAAAAAAGAAAAGTC 26 11 1 TGAAAAAGAA 0.77069 -16 TGTTCTTAAGAAAATTAAGAATCAAATGAGC 31 51 0 AAAATAAGAA 0.734014 -198 TAAGAACACCTAATACAAGGATTAGCATGTG 31 74 1 TAATAAAGGA 0.952677 -175 ***** ***** Masking position 7 Map Score: 13.6398 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 137 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 AAATATAACAATGATAGCATGATAGAGCTT 1 50 1 ATGATAGCAT 0.897423 -137 GTTTTAGTGTATTATAGCTATATTTTAATT 3 36 1 ATTATAGCTA 0.647166 -222 TAATTTAAGAATTTTAGATTGATTTTTTTA 3 61 1 ATTTTAGATT 0.680707 -197 TTTTGTTTGAATTATAGCTTTTTTAAAAAA 5 24 0 ATTATAGCTT 0.891507 -48 TTAAAGTTGTATTATAGCTTTTTAAAAATA 7 44 1 ATTATAGCTT 0.891507 -37 TTGTGGGGTGTTTTTAGCTTAAAATTCATT 8 57 0 TTTTTAGCTT 0.703073 -112 AAATCTCTTAATTTTAACATGCTTTTAAAA 8 119 0 ATTTTAACAT 0.552551 -50 TTAGGGTAGTATTATAGCATTTAATCTTTG 10 36 1 ATTATAGCAT 0.947798 -42 AAATTCTTATATTATACCATTTAAGGATTA 15 15 0 ATTATACCAT 0.519125 -153 CAGTGTTTTTTTGTTAGCATATTTCTTTTT 15 47 0 TTGTTAGCAT 0.71801 -121 AAAAATATTTTTTTTAGCATACTGGTTGTA 15 93 0 TTTTTAGCAT 0.840135 -75 AGACTAAATCATGTTAGAATTATACTTGAA 17 56 0 ATGTTAGAAT 0.674772 -56 TTTATATTTTATAATAGAATGAGATCAATT 19 201 0 ATAATAGAAT 0.218086 -43 GGAACGCTCTATTTTAGGATAATA 20 117 1 ATTTTAGGAT 0.761905 -14 TTAAGCTAAAATTTTAGCATACAAATACAA 21 33 1 ATTTTAGCAT 0.955846 -29 TTCTTAGCAAATTTTAGATAAGATCAAGCG 23 46 0 ATTTTAGATA 0.322485 -71 TAGTTTTAGCATGTTAGCATTCAGCCACCA 25 30 0 ATGTTAGCAT 0.903757 -72 AAATCTCAGAATTTTAACATAAAAGATTAA 27 43 0 ATTTTAACAT 0.552551 -61 TTAATCTCAAATTATAGCATTTTTAG 29 7 0 ATTATAGCAT 0.947798 -41 TCCTATTAAAATGATAGAAAAACGACAAAA 31 131 1 ATGATAGAAA 0.286627 -118 AAACCCTACGATTATAGCAAAAGATTAAGG 31 158 1 ATTATAGCAA 0.80354 -91 AGATTAAGGTTTTTTAGCTTAAGTAAAAAA 31 179 1 TTTTTAGCTT 0.703073 -70 CAAAATTAGAATTTTAGGATAGATCTCA 31 231 1 ATTTTAGGAT 0.761905 -18 ********** Masking position 5 Map Score: 23.6851 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 316 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 7 GAAAGGAAACATAAGTTTTAAAGA 2 26 1 ATAAGTTTTA 0.648539 -14 CCCCTTAAAAATGAGTTTTACTATAAAACA 4 25 1 ATGAGTTTTA 0.643822 -181 CAAAATTTTAAAAAGATTAAATAATATTAA 4 53 1 AAAAGATTAA 0.898105 -153 TTTGACAAAAATAAGATCAAAAAAATTTTT 4 104 1 ATAAGATCAA 0.893669 -102 AAACCAACCAATAAGATTAAGGAGTAAAGT 5 52 1 ATAAGATTAA 0.918203 -20 TGATTATAATAAAAGATTTAAAAAAAGCGA 6 70 1 AAAAGATTTA 0.755262 -72 AAAATTGAAAAAGAGTTCAAGGAATAGACA 8 12 0 AAGAGTTCAA 0.75217 -157 TGTTAAAATTAAGAGATTTAAACAAATTTA 8 130 1 AAGAGATTTA 0.751428 -39 GGCATCATTTAAGAGATTAGCACTTGGCTA 12 56 0 AAGAGATTAG 0.771495 -109 TTTTACAATAATAAGTTTAAAATAGCCCTT 16 77 0 ATAAGTTTAA 0.840518 -55 TTTACAATCAATGAGATTAGGAATTTA 16 115 1 ATGAGATTAG 0.81132 -17 GTTTTATCCAATAAGTTCAGTAAAATAGGG 19 159 0 ATAAGTTCAG 0.606768 -85 TTATAATAGAATGAGATCAATTTAACTTAA 19 193 0 ATGAGATCAA 0.891693 -51 CAAATTTTAGATAAGATCAAGCGTGATTTT 23 39 0 ATAAGATCAA 0.893669 -78 ATTTTAACATAAAAGATTAAGCCTAACTTT 27 33 0 AAAAGATTAA 0.898105 -71 CGATTATAGCAAAAGATTAAGGTTTTTTAG 31 166 1 AAAAGATTAA 0.898105 -83 ********** Masking position 4 Map Score: 16.1099 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 170 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 ACTTAATGATCATTTTAAGGGAGTTTT 1 8 0 CATTTTAAGG 0.884329 -179 TATTACTAAGCTTTTTAATAAGAGGGTGTA 1 97 1 CTTTTTAATA 0.23897 -90 TTTGGTTTATGATTTTATTGTATAATGGGC 1 132 1 GATTTTATTG 0.345176 -55 TTAGATTGATTTTTTTAAGGGTAGTTTTTT 3 74 1 TTTTTTAAGG 0.772782 -184 AGTAAAACTCATTTTTAAGGGGGATAGTTA 4 17 0 ATTTTTAAGG 0.905358 -189 AGCGATCAAGGTTTTTATGAAAATAAAAGC 4 157 1 GTTTTTATGA 0.702543 -49 TTGGTTGGTTGTTTTTATCATAGAGTGTAA 6 31 0 GTTTTTATCA 0.477221 -111 TAAGCCTATCCATTTTATCGCTTTTTTTAA 6 87 0 CATTTTATCG 0.588435 -55 TTTTTTGCTCCCTTTTAAGGTTTTTCTTTT 7 13 1 CCTTTTAAGG 0.567513 -68 AATTATAATGAATTTTAAGCTAAAAACACC 8 51 1 AATTTTAAGC 0.770267 -118 TAAATCTCTTAATTTTAACATGCTTTTAAA 8 120 0 AATTTTAACA 0.329683 -49 AAGTGAAACCATTTTTAAGCCATTTTTGAA 9 63 1 ATTTTTAAGC 0.857569 -55 AGAGTATTTTATTTTTAAGGTTAGAACA 9 100 1 ATTTTTAAGG 0.905358 -18 TAACGCCAAGCTTTTTATGGTTGGTTATCA 12 28 0 CTTTTTATGG 0.869159 -137 TGGTAGTTCTGTTTTTATCAAACATGAATA 12 86 0 GTTTTTATCA 0.477221 -79 ACCCTTTCTGAATTTTAAGCCTACATTCTC 14 20 0 AATTTTAAGC 0.770267 -88 CAGAAAGGGTGTTTTTAAGCAAGATTAGGT 14 40 1 GTTTTTAAGC 0.927862 -68 TAAAAAAAATATTTTTAACCAACAGCTTAG 15 107 1 ATTTTTAACC 0.699439 -61 ACAGCTTAGGGATTTTATGCTCTAGGATTT 15 128 1 GATTTTATGC 0.776056 -40 GGATTTTTGGCTTTTTACGGGATTTG 15 152 1 CTTTTTACGG 0.555749 -16 AAGTGATTTTGTTTTTTAGGGAGAATTGAG 17 89 1 GTTTTTTAGG 0.608992 -23 TTATAATGTAGTTTTTATGCGAAGGGTATT 19 91 1 GTTTTTATGC 0.861554 -153 AATCCAACCATTTTTTAAGGAACGCTCTAT 20 99 1 TTTTTTAAGG 0.772782 -32 CTTTTTTAAAGATTTTAAGCTAAAATTTTA 21 19 1 GATTTTAAGC 0.877483 -43 TTTTATCGCGTATTTTAAGGCTATTTTATA 22 82 0 TATTTTAAGG 0.654449 -38 AGCCACCACTCTTTTTAAGGAATTTGT 25 8 0 CTTTTTAAGG 0.932112 -94 TATTCTTTAAGTTTTTATCCATAACTTATA 25 67 0 GTTTTTATCC 0.706333 -35 AAAATCTCAGAATTTTAACATAAAAGATTA 27 44 0 AATTTTAACA 0.329683 -60 AACTTTTTAACGCTCGTTTAAT 28 3 1 CTTTTTAACG 0.841441 -60 TCGTTTAATCGTTTTTATTGGCGCGCTTCT 28 24 1 GTTTTTATTG 0.486282 -39 AATTAAAAATTTTAAGGTTGTCT 30 8 1 AATTTTAAGG 0.841949 -16 AAAGATTAAGGTTTTTTAGCTTAAGTAAAA 31 177 1 GTTTTTTAGC 0.495022 -72 ********** Masking position 5 Map Score: 29.2007 Number of sites scoring better than the average of aligned sites = 1921 Number in coding regions = 1623 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 9 ATTAAGTTTCTTAAAACAAAAATATAACAAT 1 31 1 TTAAAAAAAA 0.889652 -156 AAAAAGCTTAGTAATACAAACTAGCTAAAAC 1 82 0 GTAATAAAAC 0.777133 -105 AAAACTACCCTTAAAAAAATCAATCTAAAAT 3 71 0 TTAAAAAATC 0.404703 -187 ATAACACAACTTAAAAAAAACTACCCTTAAA 3 87 0 TTAAAAAAAC 0.917074 -171 TCATAGCGTCTTAAAACAAACACCCATTACT 3 165 0 TTAAAAAAAC 0.917074 -93 AAAATGAGTTTTACTATAAAACAAAATTTTA 4 32 1 TTACTAAAAA 0.464363 -174 ACCAAAAGAGTTAATAAAAAATTTTTTTGAT 4 119 0 TTAATAAAAA 0.912344 -87 GGCTTTTATTTTCATAAAAACCTTGATCGCT 4 157 0 TTCATAAAAC 0.554066 -49 TATAGCTTTTTTAAAAAATAATTGATAGGTT 5 11 0 TTAAAAATAA 0.454972 -61 AATAAAAGATTTAAAAAAAGCGATAAAATGG 6 77 1 TTAAAAAAGC 0.649654 -65 TAATACAACTTTAATAAAAGAAAAACCTTAA 7 27 0 TTAATAAAGA 0.635727 -54 TATAGCTTTTTAAAAATAAAATATAAGGATC 7 56 1 TAAAAAAAAA 0.689152 -25 TACACTAATTTTAATAGAAAAAAGTGAAACC 9 42 1 TTAATAAAAA 0.912344 -76 GTTCTAACCTTAAAAATAAAATACTCTTATT 9 96 0 TAAAAAAAAA 0.689152 -22 TCCCTTTAAATTAAAACAAAAATTAAAT 11 8 0 TTAAAAAAAA 0.889652 -27 CTATTCATGTTTGATAAAAACAGAACTACCA 12 85 1 TTGATAAAAC 0.554066 -80 TGAAAATTAGGTAATAAATACAACCAGTATG 15 75 1 GTAATAATAC 0.265271 -93 AGTTTATTTCTTAATACAAAAGGTAGGCGTT 17 11 0 TTAATAAAAA 0.912344 -101 AACTACATTATAAATAAAAAAAATGAAGAAA 19 73 0 TAAATAAAAA 0.741074 -171 ATAGGGATTTTAAATACAAACAACAAAAAAT 19 134 0 TAAATAAAAC 0.796994 -110 AAAGAATAGGGTAAAATAAACGC 25 89 1 GTAAAAAAAC 0.729806 -13 TCTCAGAATTTTAACATAAAAGATTAAGCCT 27 39 0 TTAACAAAAA 0.602904 -65 AACCTAACGATAAATATAAAATATATAAAAT 27 69 0 TAAATAAAAA 0.741074 -35 TTCTATCATTTTAATAGGAACAAGGCAAAGA 31 119 0 TTAATAGAAC 0.543208 -130 ****** **** Masking position 6 Map Score: 19.4986 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 190 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 10 AACCACCCTTTCTATTCAAAAATACCTAAC 1 167 0 TTTATTCAAA 0.921458 -20 AGTTGTGTTATTATTTTCAAATTTCAAGTCT 3 107 1 TTTTTTCAAA 0.777954 -151 AAATCTTTTATTATAATCAAAAATCCACTTG 6 58 0 TTTAATCAAA 0.953667 -84 AAAGAAGCGTTTCTTATCAAATAAGGAGTCC 6 116 1 TTTTATCAAA 0.860001 -26 GGTTGATCCTAATCAAAAATAATCTCA 9 7 1 TCTAATCAAA 0.753817 -111 TTTCACTTTTTTCTATTAAAATTAGTGTATG 9 40 0 TTTATTAAAA 0.554835 -78 AATACTCTTATTGTATTCAAAAATGGCTTAA 9 77 0 TTTATTCAAA 0.921458 -41 GGTAGTTCTGTTTTTATCAAACATGAATAGG 12 84 0 TTTTATCAAA 0.85924 -81 TATTCTTTAGGTATAATCAAAAACTATTTTT 12 129 1 GTTAATCAAA 0.753817 -36 CAAGATTAGGTTACAATCACAAGTTTTATTA 14 59 1 TTCAATCACA 0.670022 -49 ATTAATAAAATTTTAATAAAACTTGTGATTG 14 72 0 TTTAATAAAA 0.482529 -36 TATGTATATGTTTCAATCAAAGACAGCGTTT 16 39 1 TTCAATCAAA 0.9278 -93 AAAATAGCCCTTACATTCAAAACGCTGTCTT 16 58 0 TTCATTCAAA 0.887944 -74 ATGGTGAGTTTTACAATCAATGAGATTAGGA 16 106 1 TTCAATCAAT 0.57806 -26 ** ******** Masking position 9 Map Score: 10.9825 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 230 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 11 TGATAGCATGATAGAGCTTTAGTTTTAGCT 1 61 1 ATAGAGCTTT 0.588394 -126 AGGTTTGGGTTTAGGGTTTGAATTATATTG 3 224 1 TTAGGGTTTG 0.571274 -34 TAAAATTGTTTTAGGCTTTTATTTTCATAA 4 171 0 TTAGGCTTTT 0.462543 -35 AATTTTAAAAAAAGGACTTTTG 4 194 1 AAAGGACTTT 0.413583 -12 TTGCTCCCTTTTAAGGTTTTTCTTTTATTA 7 17 1 TTAAGGTTTT 0.669325 -64 ATTTAGTTTAAAAGGTTTTTACAAAC 10 7 0 AAAGGTTTTT 0.347382 -71 TTAATCTTTGATAGGGCTTTAGGGGAAAAT 10 56 1 ATAGGGCTTT 0.951176 -22 ATTTTTAAATAAAGGGTTTTT 12 154 1 AAAGGGTTTT 0.926858 -11 CATTCCTTAATTAGGGCTTA 13 1 0 TTAGGGCTTA 0.543702 -23 TAAAATTCAGAAAGGGTGTTTTTAAGCAAG 14 33 1 AAAGGGTGTT 0.552737 -75 AACCAACAGCTTAGGGATTTTATGCTCTAG 15 123 1 TTAGGGATTT 0.740048 -45 GTTTTGAATGTAAGGGCTATTTTAAACTTA 16 66 1 TAAGGGCTAT 0.784023 -66 GTTTTTATGCGAAGGGTATTTTTTGCCTTT 19 101 1 GAAGGGTATT 0.296246 -143 GTTCAGTAAAATAGGGATTTTAAATACAAA 19 145 0 ATAGGGATTT 0.759173 -99 AATCTTTAAAAAAGGGCTATTG 21 3 0 AAAGGGCTAT 0.792047 -59 AAATAACTTAAAAGAGCTATAAAATAGCCT 22 65 1 AAAGAGCTAT 0.218821 -55 ATCGCGTATTTTAAGGCTATTTTATAGCTC 22 78 0 TTAAGGCTAT 0.387087 -42 CCATAACTTATAAGGGTTTTAGTTTTAGCA 25 49 0 TAAGGGTTTT 0.921012 -53 TCTTTTAGGGGTAGGGTTTTCT 28 51 1 GTAGGGTTTT 0.88626 -12 TGCTATAATCGTAGGGTTTTGTCGTTTTTC 31 147 0 GTAGGGTTTT 0.88626 -102 TAGCAAAAGATTAAGGTTTTTTAGCTTAAG 31 172 1 TTAAGGTTTT 0.669325 -77 GCTTAAGTAAAAAAGGCTTTTAGGTTATAA 31 195 1 AAAAGGCTTT 0.7081 -54 ********** Masking position 3 Map Score: 11.6053 Number of sites scoring better than the average of aligned sites = 2262 Number in coding regions = 2032 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 12 ATAAAATCATAAACCAAAAAGAATACACCC 1 120 0 AAACCAAAAA 0.678415 -67 GAGTTTTACTATAAAACAAAATTTTAAAAA 4 37 1 ATAAAACAAA 0.649444 -169 TCTATGATAAAAACAACCAACCAAGTGGAT 6 37 1 AAACAACCAA 0.859255 -105 AGCTAAAAACACCCCACAAATAAGCATAAA 8 68 1 ACCCCACAAA 0.740364 -101 AATTCTCCCTAAAAAACAAAATCACTTTTA 17 86 0 AAAAAACAAA 0.835 -26 ATCTCAAAGCACACCACAAAAA 18 3 0 ACACCACAAA 0.931849 -37 TTTTAAATACAAACAACAAAAAATAAAAAA 19 128 0 AAACAACAAA 0.966968 -116 TTTCAAAATTATACAACAAAGCATTTAAAT 20 27 0 ATACAACAAA 0.914652 -104 ATACGCGATAAAACAACAAAAAGGAATACC 22 99 1 AAACAACAAA 0.966968 -21 AATGATAGAAAAACGACAAAACCCTACGAT 31 140 1 AAACGACAAA 0.900076 -109 ********** Masking position 6 Map Score: 5.00646 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 133 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 TGATTTTTTTAAGGGTAGTTTTTTTTAAGTTG 3 80 1 AAGGTAGTTT 0.648382 -178 TATCTCGCATAAAGATAGTCATAGCGTCTTAA 3 182 0 AAAGTAGTCT 0.873825 -76 ATATGAGAGAAAGGTTTGGGTTTAGGGTTTGA 3 213 1 AAGGTTGGGT 0.890226 -45 AAGCGATAAAATGGATAGGCTTAAAGAAGCGT 6 94 1 ATGGTAGGCT 0.954299 -48 CCAACCATAAAAAGCTTGGCGTTAGCCAAGTG 12 34 1 AAAGTTGGCT 0.917642 -131 TTTATCAAACATGAATAGGCATCATTTAAGAG 12 71 0 ATGATAGGCT 0.624012 -94 TCTTAATACAAAAGGTAGGCGTT 17 2 0 AAAGTAGGCT 0.965485 -110 TTAAATTAAAAAGGATAGTCCA 20 1 0 AAGGTAGTCA 0.705563 -130 CTTGATTTTTAAAGTTAGGCTTAATCTTTTAT 27 23 1 AAAGTAGGCT 0.965241 -81 CGCTTCTTTTAGGGGTAGGGTTTTCT 28 47 1 AGGGTAGGGT 0.826285 -16 CACCTAATACAAGGATTAGCATGTGTGAATTT 31 80 1 AAGGTTAGCT 0.704982 -169 **** ***** * Masking position 1 Map Score: 2.12759 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 185 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 TTATAGCTATATTTTAATTTAAGAATTTTAGA 3 47 1 ATTTAATTAA 0.702556 -211 TAAATCTTTTATTATAATCAAAAATCCACTTG 6 58 0 ATTTAATCAA 0.741643 -84 AAATGCTATAATACTACCCTAATTTAGTTTAA 10 26 0 ATATACCCAA 0.649497 -52 CTATTTTCCCCTAAAGCCCTATCA 10 64 0 ATTTCCCCAA 0.943264 -14 ATAGTTTTTGATTATACCTAAAGAATACTTAA 12 124 0 ATTTACCTAA 0.94336 -41 AAAACTTGTGATTGTAACCTAATCTTGCTTAA 14 54 0 ATTTAACCAA 0.839935 -54 TCATGTTAGAATTATACTTGAATTTACACTCA 17 46 0 ATTTACTTAA 0.901101 -66 AATCTCAATTCTCCCTAAAAAACAAAATC 17 93 0 ATTTCCCTAA 0.931878 -19 GATTTTCCTTTAAGATTTGATTT 19 231 0 ATTTCCTTAA 0.882123 -13 TATTATCCTAAAATAGAGCGTTC 20 118 0 ATTTCCTAAA 0.54122 -13 GTATGCTAAAATTTTAGCTTAAAATCTTTAAA 21 23 0 ATTTAGCTAA 0.660446 -39 AAGATAGTTTATTATACTTTAAACATCCAAAA 22 26 0 ATTTACTTAA 0.901101 -94 GCGTTTATTTTACCCTATTCTTTAAGTT 25 84 0 ATTTACCCAT 0.649497 -18 GAGAATTCTCCTTAAAGTTATTTTGG 31 5 1 ATTTCCTTAA 0.882123 -244 TTTTGTCTTTATTATAACCTAAAAGCCTTTTT 31 204 0 ATTTAACCAA 0.839935 -45 *** ***** ** Masking position 11 Map Score: 12.1387 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 106 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 15 ********** No masking Map Score: -1.56076e-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