AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_hpyl_reg_100.orf -o00790_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: HP1552 23 Na+/H+ antiporter (nhaA) Input sequences: #1 HP0791 24 cadmium-transporting ATPase, P-type (cadA) #2 HP0795 111 trigger factor (tig) #3 HP0906 259 H. pylori predicted coding region HP0906 #4 HP0907 50 hook assembly protein, flagella (flgD) #5 HP0909 51 H. pylori predicted coding region HP0909 #6 HP0925 155 recombinational DNA repair protein (recR) #7 HP1038 128 3-dehydroquinase type II (aroQ) #8 HP1228 150 invasion protein (invA) #9 HP1365 83 response regulator #10 HP1368 300 type IIS restriction enzyme M2 protein (mod) #11 HP1483 26 gerC2 protein (gerC2) #12 HP1490 103 hemolysin #13 HP1503 25 cation-transporting ATPase, P-type (copA) #14 HP1506 127 glutamate permease (gltS) #15 HP1523 81 DNA recombinase (recG) #16 HP1550 62 protein-export membrane protein (secD) #17 HP1551 47 conserved hypothetical secreted protein #18 HP1553 248 helicase Motif number 1 AAGGATTTTTATAAGGGAGAA 1 1 1 AAGGTTTTTA 0.977371 -24 AGTTTATAAAAAGCGGTTTTAATTCTAGTTT 2 27 0 AAGCGTTTTA 0.97951 -85 TCTCTAAAATTATCGTTTTTATTTAATTGTA 3 18 1 TATCTTTTTA 0.853021 -242 AAAAATGCTAAAGGTGTTTTTAAAACGAAAA 3 146 0 AAGGGTTTTT 0.934516 -114 AAAACACCTTTAGCATTTTTAGATTTGATCA 3 157 1 TAGCTTTTTA 0.961327 -103 GGTTATCCTTTTTAAAACAACTCT 3 246 0 TATCTTTTTA 0.853021 -14 TATGGTAAAATATCCTTTTTAATAAGGATAT 5 28 1 TATCTTTTTA 0.853021 -24 CCTTTTTAATAAGGATATTTA 5 41 1 AAGGTATTTA 0.699475 -11 ACGCTTCATTAAGCGCTTTTTCATATTATTT 6 57 1 AAGCCTTTTT 0.875758 -99 TGTTTTTTAAAAGGGGGTTTAATTAAATAAT 6 81 0 AAGGGGTTTA 0.750678 -75 AAAACAATAAAAGCCCTTTTAGTGGCTTTCA 6 106 1 AAGCCTTTTA 0.949031 -50 CATCAAGGGGTTTGACATTAGTCAA 7 5 1 AAGGGTTTGA 0.893814 -124 AATGAGTTTCAAGCCCTTTTTTCTTAATTTT 8 50 1 AAGCCTTTTT 0.875757 -101 TTTATACTAAAAGCGGTTATAAAAAAACACT 9 39 0 AAGCGTTATA 0.728747 -45 CTATGAAAAGGTTTTCTAAAACTTCATA 10 8 1 AAGGTTTCTA 0.868781 -293 TAATACTTCCTATGTTTTTTAAGGAGCGTTA 10 65 0 TATGTTTTTA 0.820682 -236 CTAATAAAAAAATCTTTTTTTGCATGGGGGT 10 126 0 AATCTTTTTT 0.828794 -175 CGAGAGCGTTAAGGAGTTTGACTCATTGAAA 10 176 1 AAGGGTTTGA 0.893814 -125 GCCAATCCTTAATCATTTTTATGATAAGATA 15 46 0 AATCTTTTTA 0.927471 -36 ACGCTCGTTTAATCGTTTTTATTGGCGCGCT 16 20 1 AATCTTTTTA 0.927472 -43 TCTCAAATTATAGCATTTTTAG 17 2 0 TAGCTTTTTA 0.961327 -46 ATTTCCTTAAAAGATGTTTTAATCTCAAATT 17 24 0 AAGAGTTTTA 0.730078 -24 ATCCTTGTATTAGGTGTTCTTAAGAAAATTA 18 65 0 TAGGGTTCTT 0.498153 -184 GCTATAATCGTAGGGTTTTGTCGTTTTTCTA 18 145 0 TAGGTTTTGT 0.623629 -104 GCAAAAGATTAAGGTTTTTTAGCTTAAGTAA 18 174 1 AAGGTTTTTA 0.977372 -75 TATAACCTAAAAGCCTTTTTTACTTAAGCTA 18 193 0 AAGCTTTTTT 0.95399 -56 **** ****** Masking position 8 Map Score: 34.0779 Number of sites scoring better than the average of aligned sites = 2247 Number in coding regions = 1916 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 2 TAAAACAAATTAAGCTATAATGATACAAAAA 2 63 1 TAGCTATAAT 0.975833 -49 TTAATTAAATTTCGCTACAATTAAATAAAAA 3 33 0 TTGCTACAAT 0.893775 -227 TAAGCAAGTTTGCTCTATAATAAGACATCTT 4 14 1 TGTCTATAAT 0.772516 -37 TTTAAATGGAAGTGTTATAATGTGCTATCTC 6 27 0 AGGTTATAAT 0.928289 -129 GATAAAAACTTATGCTATAATGTGGTCTCAT 7 81 1 TAGCTATAAT 0.975833 -48 AAAGCTAGTATACACTATAATACCATCTTAA 8 100 1 TAACTATAAT 0.812533 -51 CAAACAAGAAAGAGCTAAAATAAAGACCT 8 132 1 AGGCTAAAAT 0.874586 -19 AAAGGCAATTAGCGCTACAATACCCCC 9 67 1 AGGCTACAAT 0.940164 -17 TTTTTTAAGGAGCGTTATAATGAAAACGAAC 10 51 0 AGGTTATAAT 0.928358 -250 ATGAGCGGGCTTTGTTATAATACTTCCTATG 10 82 0 TTGTTATAAT 0.873978 -219 CCGCTCATTAAGCGCTACAATACCCCCATGC 10 105 1 AGGCTACAAT 0.940164 -196 CTTAATCTTTTATGTTAAAATTCTGAGATTT 12 42 1 TAGTTAAAAT 0.757872 -62 AGGGGGGTATTATATTATAATAAGATAAATT 14 87 1 TAATTATAAT 0.621924 -41 CTAAAAATGCTATAATTTGAGATTAA 17 6 1 AAGCTATAAT 0.961108 -42 ACCTTAATCTTTTGCTATAATCGTAGGGTTT 18 158 0 TTGCTATAAT 0.948142 -91 AAAAGGCTTTTAGGTTATAATAAAGACAAAA 18 205 1 TAGTTATAAT 0.938745 -44 ** ******** Masking position 6 Map Score: 20.447 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 128 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 AAGGATTTTTATAAGGGAGAAAAA 1 9 1 TTATAAGGGG 0.88306 -16 TTTTAAGCAAGTTTGCTCTAT 4 1 1 TTTTAAGCAG 0.615517 -50 AAAATATCCTTTTTAATAAGGATATTTA 5 34 1 TTTTAATAAG 0.540306 -18 CTATCTCAATTTTAAGGAATAAC 6 3 0 TTTAAGGAAA 0.373223 -153 TAATGAAGCGTTTAAATGGAAGTGTTATAAT 6 37 0 TTTAAATGGA 0.811877 -119 TTATTGTTTTTTAAAAGGGGGTTTAATTAAA 6 85 0 TTAAAAGGGG 0.744995 -71 ATAAAAGCCCTTTTAGTGGCTTTCAAGTCAA 6 112 1 TTTTAGTGGT 0.611776 -44 TGTGATTCGTTCTTAGGGGGATTTAAGGGGT 7 48 1 TCTTAGGGGA 0.739775 -81 CTTAGGGGGATTTAAGGGGTAAGATAAAAAC 7 59 1 TTTAAGGGGA 0.923497 -70 ACCCTCTCCGTTTTAATAGCGTTATTTGGGC 8 11 1 TTTTAATAGG 0.890046 -140 TTGAAACTCATTTTAATAGCGCCCAAATAAC 8 31 0 TTTTAATAGG 0.890046 -120 TAATTTTTGATTTTAATGGCATTCTTAAAGC 8 74 1 TTTTAATGGA 0.91773 -77 GCGGTGTCTTTTTTAAGGGAGTGTTTTTTTA 9 20 1 TTTTAAGGGG 0.985162 -64 TCCTATGTTTTTTAAGGAGCGTTATAATGAA 10 58 0 TTTAAGGAGG 0.897536 -243 GACGATTACCTTTTAAGCGAGAGCGTTAAGG 10 159 1 TTTTAAGCGG 0.916831 -142 TTAATCCTTAATTTAAGGGCG 13 1 0 ATTTAAGGGG 0.803206 -25 GATCTCGTTCTTTTAGGGGGGTATTATATTA 14 73 1 TTTTAGGGGG 0.985219 -55 GTTTAATCGTTTTTATTGGCGCGCTTCTTTT 16 26 1 TTTTATTGGG 0.701089 -37 GGCGCGCTTCTTTTAGGGGTAGGGTTTTCT 16 43 1 TTTTAGGGGA 0.968946 -20 TTAAAACATCTTTTAAGGAAATTAA 17 33 1 TTTTAAGGAA 0.818611 -15 CCAAAATAACTTTAAGGAGAATTCTC 18 6 0 TTTAAGGAGA 0.803934 -243 TTTTCTATCATTTTAATAGGAACAAGGCAAA 18 121 0 TTTTAATAGA 0.791134 -128 ********* * Masking position 5 Map Score: 24.4625 Number of sites scoring better than the average of aligned sites = 2110 Number in coding regions = 1841 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 4 TTTTTTAAATTTTTGAAAACTAGAAT 2 2 1 TTTAATTTTA 0.591334 -110 AATGATACAAAAATTTAATTTTTTAGCCATTAAGG 2 81 1 ATTTATTTTA 0.921624 -31 CTCTAAAATTATCGTTTTTATTTAATTGTAGCGAA 3 19 1 AGTTTTTTTA 0.635371 -241 GAATAACGACAACTTTTATTTTTAAAAAATGGGGT 3 111 1 ATTTATTTTA 0.921624 -149 GTCTTAAGGAACTCTTTTTGCTTAACTCCCACCAT 3 191 1 ACTTTTCTTA 0.830349 -69 AACTCTTTTATTTCTTTATATTTTACATGGTGGGA 3 217 0 TCTTATTTTA 0.944756 -43 ATATTTTACCATACTTCTTATTTCAGCCTT 5 6 0 ACTTTTTTTA 0.930829 -46 TATTTATTTCTCCTTGTTTAATATGGAATGA 7 108 0 TCTCTTTTTA 0.719212 -21 CAAGCCCTTTTTTCTTAATTTTTGATTTTAATGGC 8 59 1 TCTTATTTTA 0.944756 -92 TTGCCTTGACTGACTCATTTTTTTAAAATACCCCC 10 214 1 TCTCTTTTTA 0.719211 -87 GACTTTTCTTTTTTCATGGCTTGTCT 11 11 0 ATTTTTTTTA 0.867734 -16 GGTTTTTGAAGGCTTGATTTTTAAAGTTAGGCTT 12 10 1 ACTTATTTTA 0.960191 -94 TTTTAAAGTTAGGCTTAATCTTTTATGTTAAAATT 12 29 1 ACTTATTTTA 0.960191 -75 AAATTCTGAGATTTTATATATTTTATATTTATCGT 12 59 1 ATTAATTTTA 0.671142 -45 TTTTTTAATCCTTAATTTAAGGGCG 13 11 0 TTTTATCTTA 0.75201 -15 TCCTCCATGCTCATTTGATTCTTAATTTTCTTAAG 18 43 1 TTTTATCTTA 0.75201 -206 TAAGCTAAAAAACCTTAATCTTTTGCTATAATCGT 18 165 0 ACTTATTTTG 0.741689 -84 * *** ** *** * Masking position 9 Map Score: 14.3149 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 457 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 GCGTTTAAATGGAAGTGTTATAATGTGCTAT 6 30 0 GGAAGTGTTT 0.889161 -126 TTTTTTAAAAGGGGGTTTAATTAAATAATAT 6 79 0 GGGGGTTTAT 0.86082 -77 GTTTGATTAAGATGGTATTATAGTGTATACT 8 106 0 GATGGTATTT 0.706152 -45 TCTTTTTTAAGGGAGTGTTTTTTTATAACCG 9 26 1 GGGAGTGTTT 0.972279 -58 GGGGGTATTGTAGCGCTAATT 9 73 0 GGGGGTATTT 0.994736 -11 AAAAAACATAGGAAGTATTATAACAAAGCCC 10 76 1 GGAAGTATTT 0.934066 -225 TTTTTTGCATGGGGGTATTGTAGCGCTTAAT 10 111 0 GGGGGTATTT 0.994736 -190 ACAATGAAATGGGGGTATTTTAAAAAAATGA 10 228 0 GGGGGTATTT 0.994736 -73 GTTCTTTTAGGGGGGTATTATATTATAATAA 14 79 1 GGGGGTATTT 0.994736 -49 ********* * Masking position 6 Map Score: 15.8023 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 95 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 CCTCTGTTCTCATTAAGCGCGAATAACGAC 3 91 1 CATTAAGCGC 0.992011 -169 TTAAACGCTTCATTAAGCGCTTTTTCATAT 6 53 1 CATTAAGCGC 0.992011 -103 AGTATAAAGGCAATTAGCGCTACAATACCC 9 62 1 CAATTAGCGC 0.955315 -22 AATGAAAACGAACGAAGCGCAATTTTATGA 10 34 0 AACGAAGCGC 0.95328 -267 AAAGCCCGCTCATTAAGCGCTACAATACCC 10 100 1 CATTAAGCGC 0.992011 -201 CCTACCCCTAAAAGAAGCGCGCCAATAAAA 16 36 0 AAAGAAGCGC 0.960436 -27 ********** Masking position 6 Map Score: 7.99498 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 29 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 GGTTTTAATTCTAGTTTTCAAAAATTTAAAAAA 2 11 0 CAGTTTAAAA 0.963187 -101 TGTTTTAATTCCAGTTTATAAAAAGCGGTTTTA 2 37 0 CAGTTAAAAA 0.751894 -75 AAACGAAACCATAGTTTTAAAAACCTCTGTTCT 3 68 1 AAGTTTAAAA 0.784264 -192 ACGAAAAACCCCATTTTTTAAAAATAAAAGTTG 3 120 0 CATTTTAAAA 0.905774 -140 CTATAATAAGACATCTTTAAGAAGGAAGAGATC 4 28 1 AATCTTAGAA 0.505593 -23 ATAGTGTATACTAGCTTTAAGAATGCCATTAAA 8 85 0 CAGCTTAGAA 0.952456 -66 TTCATTATAACGCTCCTTAAAAAACATAGGAAG 10 58 1 CCTCTTAAAA 0.799974 -243 TTGACTGACTCATTTTTTTAAAATACCCCCATT 10 219 1 CTTTTTAAAA 0.549837 -82 AGACAAGCCATGAAAAAAGAAAAGTC 11 4 1 CAGCATAAAA 0.870048 -23 CTTTAAAAATCAAGCCTTCAAAAACC 12 4 0 CAGCTTAAAA 0.982994 -100 AAGATTAAGCCTAACTTTAAAAATCAAGCCTTC 12 18 0 CAACTTAAAA 0.86586 -86 AACGATTAAACGAGCGTTAAAAAGTT 16 4 0 CAGCTTAAAA 0.982994 -59 * *** ** **** Masking position 10 Map Score: 8.68145 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 692 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 8 TCTCTAAAATTATCGTTTTTATTTAATTGT 3 18 1 TATCGTTTTT 0.784559 -242 AAATAAAAGTTGTCGTTATTCGCGCTTAAT 3 102 0 TGTCGTTATT 0.947584 -158 GATCTCTTCCTTCTTAAAGATG 4 39 0 TCTCTTCCTT 0.770812 -12 CTTTATTTTAGCTCTTTCTTGTTTGATTAA 8 127 0 GCTCTTTCTT 0.873965 -24 AGGTCTTTATTTTAGCTCTTT 8 140 0 GGTCTTTATT 0.877673 -11 AATAAAGCGGTGTCTTTTTTAAGGGAGTGT 9 14 1 TGTCTTTTTT 0.956 -70 GACTTTTCTTTTTTCATGGCTTGT 11 13 0 TTTCTTTTTT 0.770709 -14 TTCTAACTGATCTCGTTCTTTTAGGGGGGT 14 65 1 TCTCGTTCTT 0.945864 -63 CGTAGGGTTTTGTCGTTTTTCTATCATTTT 18 138 0 TGTCGTTTTT 0.95925 -111 ATTCTAATTTTGTCTTTATTATAACCTAAA 18 213 0 TGTCTTTATT 0.943459 -36 ********** Masking position 6 Map Score: 6.86237 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 194 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 TAAACTGGAATTAAAACAAATTAAGCTATAATGA 2 52 1 TTAACAATAA 0.951514 -60 GTAGCGAAATTTAATTAAACCTAAACGAAACCAT 3 46 1 TTAAAAATAA 0.954732 -214 AAACCCCCTTTTAAAAAACAATAAAAGCCCTTTT 6 92 1 TTAAAACTAA 0.930797 -64 TTAGTGGCTTTCAAGTCAAGTTAAGTTTGATATA 6 124 1 TCAACAATAA 0.884473 -32 ATCTTACCCCTTAAATCCCCCTAAGAACGAATCA 7 50 0 TTAACCCTAA 0.82778 -79 AATGAGTCAGTCAAGGCAATCTAAATTTTCAATG 10 199 0 TCAACAATAA 0.885195 -102 CCATTGAAGTTTAATAAAAGGTAAAAATAAGA 10 279 1 TTAAAAATAA 0.955495 -22 TGCATCCTTATTAATCAAATTTATCTTATTATAA 14 101 0 TTAAAAATAT 0.731867 -27 ATACATTGACTTAAGGAAATTTAATTG 15 4 0 TTAAAAATAA 0.938048 -78 CTTAATTTTCTTAAGAACACCTAATACAAGGATT 18 63 1 TTAAACATAA 0.891814 -186 TTTACTTAAGCTAAAAAACCTTAATCTTTTGCTA 18 172 0 CTAAAACTAA 0.717015 -77 **** *** *** Masking position 4 Map Score: 7.81697 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 61 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 GCCAATCTCTCTAAAATTATCGTTTTTATT 3 11 1 CTAAAATTAT 0.896934 -249 CCATTTCATTGTAAAATTCTTTCATGCAAA 10 247 1 GTAAAATTCT 0.947316 -54 ATCTTTTATGTTAAAATTCTGAGATTTTAT 12 46 1 TTAAAATTCT 0.819028 -58 TGATAAGATAGTCAAATTATACATTGACTT 15 26 0 GTCAAATTAT 0.913146 -56 ATGTTTTAATCTCAAATTATAGCATTTTTA 17 12 0 CTCAAATTAT 0.913146 -36 CAAAGACAGCGTCAAATTCACACATGCTAA 18 95 0 GTCAAATTCA 0.81845 -154 GAGATCTATCCTAAAATTCTAATTTTGTCT 18 228 0 CTAAAATTCT 0.947316 -21 ********** Masking position 5 Map Score: 3.42784 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 39 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 CGAAATTTAATTAAACCTAAACGAAACCAT 3 50 1 TTAAACCTAA 0.947395 -210 AGACGCGTGATCAAATCTAAAAATGCTAAA 3 165 0 TCAAATCTAA 0.705218 -95 TGTTAGTATATCAAACTTAACTTGACTTGA 6 134 0 TCAAACTTAA 0.874644 -22 TTACCTTTTATTAAACTTCAATGGGTTTTG 10 273 0 TTAAACTTCA 0.640367 -28 ACATAAAAGATTAAGCCTAACTTTAAAAAT 12 27 0 TTAAGCCTAA 0.824719 -77 AACTTTAAACCTAAAACCTAACGA 12 90 0 TTAAACCTAA 0.947395 -14 ATTAAGGTTTTTTAGCTTAAGTAAAAAAGG 18 181 1 TTTAGCTTAA 0.628903 -68 TTGTCTTTATTATAACCTAAAAGCCTTTTT 18 204 0 TATAACCTAA 0.763737 -45 TGAGATCTATCCTAAAATTCTAATT 18 234 0 TCTATCCTAA 0.727262 -15 ********** Masking position 4 Map Score: 2.42897 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 211 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 12 TATCATTATAGCTTAATTTGTTTTAATTCC 2 58 0 GCTTAATTTG 0.941183 -54 TAATGTGCTATCTCAATTTTAAGGAATAAC 6 11 0 TCTCAATTTT 0.873126 -145 CGTTTTAATAGCGTTATTTGGGCGCTATTA 8 19 1 GCGTTATTTG 0.682567 -132 AGCCCTTTTTTCTTAATTTTTGATTTTAAT 8 61 1 TCTTAATTTT 0.952054 -90 AGGTCTTTATTTTAGCTCTTTCT 8 138 0 TCTTTATTTT 0.90189 -13 AAAAGACACCGCTTTATTTTA 9 2 0 GCTTTATTTT 0.917845 -82 AACGAACGAAGCGCAATTTTATGAAGTTTT 10 28 0 GCGCAATTTT 0.708259 -273 AATAAAAAAATCTTTTTTTGCATGGGGGTA 10 125 0 TCTTTTTTTG 0.64079 -176 GTCAAGGCAATCTAAATTTTCAATGAGTCA 10 194 0 TCTAAATTTT 0.81648 -107 TCTTATTTTTACCTTTTATT 10 291 0 TCTTATTTTT 0.853186 -10 GTTTTTGAAGGCTTGATTTTTAAAGTTAGG 12 12 1 GCTTGATTTT 0.834241 -92 TTAAAGTTAGGCTTAATCTTTTATGTTAAA 12 31 1 GCTTAATCTT 0.778778 -73 CTCATTTGATTCTTAATTTTCTTAAGAACA 18 52 1 TCTTAATTTT 0.952054 -197 ATCCTAAAATTCTAATTTTGTCTTTATTAT 18 221 0 TCTAATTTTG 0.463335 -28 ********** Masking position 7 Map Score: 11.3466 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 501 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 13 ********** No masking Map Score: -7.8627e-13 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: -7.8627e-13 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 TATAAACTGGAATTAAAACAAATTAAGCTATA 2 50 1 AATTAAACAA 0.75331 -62 ATTAAGCTATAATGATACAAAAATTTAATTTT 2 71 1 AATGAACAAA 0.956666 -41 ATTAAACCTAAACGAAACCATAGTTTTAAAAA 3 59 1 AACGAACCAA 0.910185 -201 ATTCGCGCTTAATGAGAACAGAGGTTTTTAAA 3 83 0 AATGAAACAA 0.964721 -177 TTTAATATGGAATGAGACCACATTATAGCATA 7 91 0 AATGAACCAA 0.977464 -38 ATACCATCTTAATCAAACAAGAAAGAGCTAAA 8 119 1 AATCAACAAA 0.785125 -32 GGAGCGTTATAATGAAAACGAACGAAGCGCAA 10 42 0 AATGAAACGA 0.864666 -259 AGACAAGCCATGAAAAAAGAAAAGTC 11 9 1 CATGAAAAAA 0.764813 -18 TTCCTATTAAAATGATAGAAAAACGACAAAAC 18 130 1 AATGAAGAAA 0.862448 -119 ***** **** * Masking position 7 Map Score: 1.47734 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 80 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185