AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icpxR_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 HP0166 235 response regulator (ompR) #2 HP0168 46 H. pylori predicted coding region HP0168 #3 HP0170 74 H. pylori predicted coding region HP0170 #4 HP0171 60 peptide chain release factor RF-2 (prfB) #5 HP0174 300 H. pylori predicted coding region HP0174 #6 HP0392 56 histidine kinase (cheA) #7 HP0395 22 conserved hypothetical protein #8 HP0398 28 H. pylori predicted coding region HP0398 #9 HP0399 120 ribosomal protein S1 (rps1) #10 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #11 HP0600 163 multidrug resistance protein (spaB) #12 HP0813 132 conserved hypothetical protein #13 HP0977 128 conserved hypothetical secreted protein #14 HP1010 300 polyphosphate kinase (ppk) #15 HP1011 36 dihydroorotate dehydrogenase (pyrD) #16 HP1015 111 H. pylori predicted coding region HP1015 #17 HP1017 97 amino acid permease (rocE) #18 HP1018 47 H. pylori predicted coding region HP1018 #19 HP1206 300 multidrug resistance protein (hetA) #20 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 TTTTTTAATGTTTTTAAACAATTCCTTTGA 1 18 0 TTTTTAAACA 0.884533 -218 TTGAATTTTTATTTTTAAGATATTTTCAAG 1 117 1 ATTTTTAAGA 0.607852 -119 AAGTTAATCGTTTTTAAAGTTGCAGAAATC 1 195 1 TTTTTAAAGT 0.620007 -41 TGCCAATTGGTTTTAAAAAGCGTTTTATAG 3 45 0 TTTTAAAAAG 0.734899 -30 TTATATTTGGTTTTTTAGCATTGCATGTTA 5 206 1 TTTTTTAGCA 0.761212 -95 TTCTTTTTATAAAATTGTAAAATA 6 5 1 TTTTATAAAA 0.353038 -52 AGAGTGATTTTAAAAGCATGAGAATG 8 7 1 ATTTTAAAAG 0.635609 -22 ATTAGCGGTTTTTTTAAAGAAAATTTTCAA 9 17 0 TTTTTAAAGA 0.891372 -104 TAATTGTTAGTTTTTAAACGATTTTGTAAG 9 43 1 TTTTTAAACG 0.942052 -78 GTATTATAGCTTTTTAAAAATAAAATATAA 10 52 1 TTTTTAAAAA 0.493378 -29 CCTTTGGGTTTTTTATAACAAGGAGTTACA 11 14 0 TTTTATAACA 0.683698 -150 AAGTTTGAAATTTTAAAGGGCTTTGTTTTA 11 78 1 TTTTAAAGGG 0.868796 -86 TAAATTTTGCTTTTAAAACAAAGCCCTTTA 11 91 0 TTTTAAAACA 0.890408 -73 TAAAAGCAAAATTTAAAGGAGCATGAAAAT 11 106 1 ATTTAAAGGA 0.695766 -58 TTCAAACTAGTTTTAAAAAGTCATTATTAT 12 100 0 TTTTAAAAAG 0.734899 -33 TATTTTTGATTTTTTAAAGGGATTAGAGTT 13 106 1 TTTTTAAAGG 0.950921 -23 CGCTTAAAATTTTTTTAGCGTTT 14 4 0 TTTTTTAGCG 0.7234 -297 CGCTAAAAAAATTTTAAGCGATCTTTTAGG 14 14 1 ATTTTAAGCG 0.764552 -287 CAAAAAAGAGTTTTTAAACAACAACTAAGC 14 79 1 TTTTTAAACA 0.884533 -222 CGACCATGACTTTTTAAAAAAGCTTCAATG 14 212 1 TTTTTAAAAA 0.493378 -89 AACAAACTGATTTTTAAACATGATGATTTA 14 270 1 TTTTTAAACA 0.884533 -31 AAACATGATGATTTAAAGGATTTCTA 14 285 1 ATTTAAAGGA 0.695766 -16 CAACAAGCATTTTTTAATGAATTGCAACTC 16 53 0 TTTTTAATGA 0.621244 -59 TATTTTAAAAGAAGTTTTTAGC 17 3 1 TTTTAAAAGA 0.904179 -95 TTTTAAGGTTTTTTTAAAGAACGCTAAAAA 17 25 0 TTTTTAAAGA 0.891372 -73 AAGCGATAGTTTTTTAAGCGTTTTAAGGTT 17 45 0 TTTTTAAGCG 0.919867 -53 TTTTTAAAGATTAAATAGTA 17 88 0 TTTTTAAAGA 0.891372 -10 AGTTTAGCAAATTTTAAGGAAGTAACCATG 18 28 1 ATTTTAAGGA 0.825839 -20 ********** Masking position 4 Map Score: 39.2371 Number of sites scoring better than the average of aligned sites = 2032 Number in coding regions = 1600 Number in noncoding regions = 432 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 AAAACGATCAAAGGAATTGTTTAA 1 2 1 AAACTCAAAG 0.935208 -234 AATTGTTTAAAAACATTAAAAAATAAGACTTTA 1 25 1 AAACTAAAAA 0.961483 -211 CTTAAAAATAAAAATTCAAAACATTATCATAGT 1 103 0 AAAACAAAAA 0.763099 -133 AAGGTATCTTTAATAATAAAATGCTAGAATTAG 1 144 1 TAATTAAAAG 0.763983 -92 TAGTCCCCTAAAACATTAACAAAGTTAATCGTT 1 174 1 AAACTAACAA 0.694598 -62 TAAATTATGGTTACTATAAAACGCTTTTTAAAA 3 32 1 TTACTAAAAG 0.558667 -43 AGAATAAAACTAACACCAAAAAAGACAATAAAT 5 54 0 TAACCAAAAA 0.816516 -247 ATGCAATGCTAAAAAACCAAATATAAAGAATAA 5 199 0 AAAACCAAAA 0.666067 -102 TCTTTTTATAAAATTGTAAAATACTCTTATCTC 6 12 1 AAATTAAAAA 0.878937 -45 CTCTTATCTCAAACGCTAAAAAGGGGTTTTAA 6 35 1 AAACTAAAAG 0.958865 -22 TGACTGCCTTACTATAAAATAAATATAAAAT 9 100 0 TTACTAAAAA 0.575481 -21 AATAAAAGAAAAACCTTAAAAGGGAGCAAAAAA 10 13 0 AAACTAAAAG 0.958865 -68 TATAGCTTTTTAAAAATAAAATATAAGGATCGT 10 56 1 TAAATAAAAA 0.804661 -25 CCTTGTTATAAAAAACCCAAAGGCATCCTTGCT 11 21 1 AAAACCAAAG 0.650663 -143 TAATCCCTTTAAAAAATCAAAAATATGAAATTC 13 98 0 AAAATCAAAA 0.842328 -31 AAACGCTAAAAAAATTTTAAGCG 14 1 1 AAACTAAAAA 0.961483 -300 AAACTTCATTTAACCCTAAAAGATCGCTTAAAA 14 25 0 TAACTAAAAA 0.922593 -276 GTTATCGTTCAAATCATAAAAGATAAGGATTTA 15 13 1 AAATTAAAAA 0.878937 -24 TTCTTTAAAAAAACCTTAAAACGCTTAAAAAAC 17 34 1 AAACTAAAAG 0.958865 -64 TTTAAAGATTAAATAGTAAAAGAGCTTGATCAA 17 73 0 AAATTAAAAA 0.878937 -25 CCAGCAACTAAAATAATCAAAGACTTGGGATTA 19 117 1 AAATTCAAAA 0.818037 -184 ACTTACCGCTTAAATTTCAAAAGTATCCTACAA 20 17 1 TAAATCAAAG 0.704307 -104 **** ***** * Masking position 9 Map Score: 25.0859 Number of sites scoring better than the average of aligned sites = 964 Number in coding regions = 735 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 3 GGAATATTGAAAAATAAAGTCTTATTTTTT 1 42 0 AAAATAAAGT 0.782363 -194 ATATTCCATGAAAACAAAGCCTTAAATTTC 1 65 1 AAAACAAAGC 0.897308 -171 TAAAAAACCAAATATAAAGAATAATAACCC 5 193 0 AATATAAAGA 0.731092 -108 TATTTATTTTATAGTAAGGCAGTCA 9 106 1 ATAGTAAGGC 0.665499 -15 TTAAAAATAAAATATAAGGATCGTTA 10 65 1 AATATAAGGA 0.832491 -16 TGGGTTTTTTATAACAAGGAGTTACAACA 11 10 0 ATAACAAGGA 0.89235 -154 GTTCCAACCAAAAGCAAGGATGCCTTTGGG 11 36 0 AAAGCAAGGA 0.853792 -128 TTTTGCTTTTAAAACAAAGCCCTTTAAAAT 11 87 0 AAAACAAAGC 0.897308 -77 AAAATGGGCTATAATAAAGAAAATTTATAC 11 131 1 ATAATAAAGA 0.846653 -33 TCATAGCGCAAAAATAAGGCGATTTTGACT 12 64 0 AAAATAAGGC 0.951094 -69 AAAACTCTCTATAATAAGGATAATTTTAAT 13 15 1 ATAATAAGGA 0.90985 -114 ACCTTTGGTTAAAATAAGGTTATTTGATTT 13 46 1 AAAATAAGGT 0.867922 -83 CAAATCATAAAAGATAAGGATTTAA 15 22 1 AAGATAAGGA 0.806845 -15 CACATCCACCAAAACAAAGAGTTGCAATTC 16 35 1 AAAACAAAGA 0.922478 -77 GCTAAACTTCAAAATTAAGAAAAGA 18 6 0 AAAATTAAGA 0.570135 -42 ********** Masking position 7 Map Score: 12.9754 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 407 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 4 AAATGGCGTTTAGAGATTAGG 2 2 1 AATGGCGTTT 0.925296 -45 AATGGCTTTTAACAATGCTA 4 1 1 AATGGCTTTT 0.818146 -60 AACCTTTATGAGTGGGGTTTTGAACTTATC 4 35 0 AGTGGGGTTT 0.870684 -26 AAAAAATGTTAAAGAAGATTCAAAAATTCT 5 99 1 AAAGAAGATT 0.624456 -202 CAAACGCTAAAAAGGGGTTTTAA 6 44 1 AAAGGGGTTT 0.955393 -13 TTGAAATTTTAAAGGGCTTTGTTTTAAAAG 11 82 1 AAAGGGCTTT 0.711259 -82 TTTCAATAATAATGACTTTTTAAAACTAGT 12 95 1 AATGACTTTT 0.764145 -38 AACTAGTTTGAAGGGAGTTTGGAGT 12 118 1 AAGGGAGTTT 0.884511 -15 TCCTTATTATAGAGAGTTTTTAAC 13 5 0 AGAGAGTTTT 0.593166 -124 TTTAGGGTTAAATGAAGTTTTATTCAAAAA 14 38 1 AATGAAGTTT 0.917353 -263 TTATTCAAAAAATGAAGTTTTACAAAAAAG 14 57 1 AATGAAGTTT 0.917353 -244 GTTTTACAAAAAAGAGTTTTTAAACAACAA 14 73 1 AAAGAGTTTT 0.844481 -228 CGCAATCAAAAAGGGAGATTGTAGCGCGAG 14 112 0 AAGGGAGATT 0.570688 -189 TATTTTAAAAGAAGTTTTTAGCGTTCT 17 8 1 AAAGAAGTTT 0.905472 -90 TCAATAATGTAATGAGTTTTGAGCTGTGTT 19 258 0 AATGAGTTTT 0.862855 -43 ********** Masking position 1 Map Score: 12.2275 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 703 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 ATCGGCTGTCATTTTAGCGCAC 3 3 0 ATTTTAGCGC 0.81943 -72 AATATAAAGAATAATAACCCTGGTAACCAA 5 183 0 ATAATAACCC 0.757243 -118 AGAATAGCCATAAAGAAGAA 7 1 1 AGAATAGCCA 0.771665 -22 AATTTTCTTTATTATAGCCCATTTTCATGC 11 126 0 ATTATAGCCC 0.964338 -38 GATTTTGACTAGAATAGCGCTTCTATTATT 12 44 0 AGAATAGCGC 0.980826 -89 ATTATTGAAAATCATAGCGCAAAAATAAGG 12 75 0 ATCATAGCGC 0.935603 -58 AAAAAGGGAGATTGTAGCGCGAGTTTGCTT 14 105 0 ATTGTAGCGC 0.870565 -196 TTGATTGCGGAGTATGGCGCAGCCTGATTA 14 133 1 AGTATGGCGC 0.868076 -168 AAGGGGCGAAAAAATAGCCCAACAAGCATT 16 72 0 AAAATAGCCC 0.891528 -40 TAACAGAATAGCCCCACACAAAGG 16 98 0 AGAATAGCCC 0.977216 -14 ATTTGTTGCTATAATAGAGCATTTGAATGA 20 79 1 ATAATAGAGC 0.788152 -42 ********** Masking position 1 Map Score: 8.33951 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 171 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TAGGGGACTAATTCTAGCATTTTATTATTAA 1 153 0 ATTTAGCATT 0.948133 -83 TGAACTTATCATTATAGCATTGTTAAAAGCC 4 14 0 ATTTAGCATT 0.948133 -47 TATATTTGGTTTTTTAGCATTGCATGTTATC 5 207 1 TTTTAGCATT 0.934867 -94 TTAAAACCCCTTTTTAGCGTTTGAGATAAGA 6 36 0 TTTTAGCGTT 0.964664 -21 TTAAAGTTGTATTATAGCTTTTTAAAAATAA 10 44 1 ATTTAGCTTT 0.948133 -37 GCTTAAAATTTTTTTAGCGTTT 14 2 0 TTTTAGCGTT 0.964664 -299 GCTAAAAAAATTTTAAGCGATCTTTTAGGGT 14 15 1 TTTAAGCGAT 0.69978 -286 AATGATAATCATTGAAGCTTTTTTAAAAAGT 14 220 0 ATTAAGCTTT 0.884284 -81 TTAAAAGAAGTTTTTAGCGTTCTTTAAAAAA 17 15 1 TTTTAGCGTT 0.964664 -83 AGCGATAGTTTTTTAAGCGTTTTAAGGTTTT 17 43 0 TTTAAGCGTT 0.919435 -55 AAGACTTGGGATTATAGCAGTTTTATACTTG 19 136 1 ATTTAGCAGT 0.893757 -165 CCATACGAATAATTTAGCTTTCCGTCATCAT 19 179 0 AATTAGCTTT 0.746893 -122 CATGGTTAAAATTTTAGCTATAATCTAGCTC 19 217 1 ATTTAGCTAT 0.788746 -84 ATGTAATGAGTTTTGAGCTGTGTTAAGCCAA 19 251 0 TTTGAGCTGT 0.695973 -50 TACTTTTGAAATTTAAGCGGTAAGTTGGATA 20 11 0 ATTAAGCGGT 0.869939 -110 TTGTTGCTATAATAGAGCATTTGAATGACAA 20 81 1 AATGAGCATT 0.505611 -40 *** ******* Masking position 6 Map Score: 20.4661 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 669 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 ATTATTGTTGTATGCATTCTCTTTCCTTGGT 5 157 1 TTGCATTCTC 0.715332 -144 TATACTCTATTAATCAATCTCATATTGATAA 5 255 1 TATCAATCTC 0.939268 -46 TTATAGCCCATTTTCATGCTCCTTTAAATTT 11 114 0 TTTCATGCTC 0.903826 -50 GATTTTCCTTTCATCAAACTCATCTCAACCA 12 11 1 TATCAAACTC 0.939268 -122 AAACAACAACTAAGCAAACTCGCGCTACAAT 14 94 1 TAGCAAACTC 0.938116 -207 AACTATCGCTTGATCAAGCTCTTTTACTATT 17 64 1 TATCAAGCTC 0.982667 -34 TTCAAGTCCCTTAGCCAGCTCCAGTTGAAAT 19 38 0 TAGCCAGCTC 0.936547 -263 GCTAAAATTTTAACCATGCTCTGTGCCATAC 19 204 0 TACCATGCTC 0.915783 -97 ATTTTAGCTATAATCTAGCTCAATTTGGCTT 19 227 1 TATCTAGCTC 0.910394 -74 * ********* Masking position 10 Map Score: 5.1354 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 172 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TCTTATTTTTTAATGTTTTTAAACAATTCC 1 23 0 TAATGTTTTT 0.757366 -213 TTGGTTTTAAAAAGCGTTTTATAGTAACCA 3 39 0 AAAGCGTTTT 0.765325 -36 AAAAGACAATAAATATTATTACAACATCTG 5 38 0 AAATATTATT 0.45034 -263 GCGTTTGAGATAAGAGTATTTTACAATTTT 6 21 0 TAAGAGTATT 0.735947 -36 CAAACGCTAAAAAGGGGTTTTAA 6 44 1 AAAGGGGTTT 0.700174 -13 ATAAAATCCTTAAGGGTATTGTATCCTTTT 9 77 0 TAAGGGTATT 0.938925 -44 TGCTCCCTTTTAAGGTTTTTCTTTTATTAA 10 18 1 TAAGGTTTTT 0.914763 -63 TTGAAATTTTAAAGGGCTTTGTTTTAAAAG 11 82 1 AAAGGGCTTT 0.692095 -82 AATTTATACCAAATCTTATTGC 11 152 1 AAATCTTATT 0.469337 -12 TATTTTAACCAAAGGTTATTAAAATTATCC 13 32 0 AAAGGTTATT 0.939532 -97 TTGGTTAAAATAAGGTTATTTGATTTTACT 13 50 1 TAAGGTTATT 0.924246 -79 GATTTTACTATAAGGTTGTTTAAACCTGAA 13 71 1 TAAGGTTGTT 0.7403 -58 GTTTTACAAAAAAGAGTTTTTAAACAACAA 14 73 1 AAAGAGTTTT 0.752829 -228 TTAAGCGTTTTAAGGTTTTTTTAAAGAACG 17 32 0 TAAGGTTTTT 0.914763 -66 GCTCCAGTTGAAATGTTATTTTGCGAAGTT 19 22 0 AAATGTTATT 0.818817 -279 AAATTAAAACAAATGGTATTTTAGCCGATA 20 53 0 AAATGGTATT 0.850624 -68 ********** Masking position 3 Map Score: 12.8177 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 757 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 9 GATAATGTTTTGAATTTTTATTTTTAAGAT 1 108 1 TGAATTTTTA 0.912126 -128 AATTGCATCGAGAATTTTTGAATCTTCTTT 5 109 0 AGAATTTTTG 0.823864 -192 AATAGAGTATAGAAGTTATTTAATATGGGA 5 236 0 AGAAGTTATT 0.492405 -65 GGTTAAAGTTTGAAATTTTAAAGGGCTTTG 11 73 1 TGAAATTTTA 0.593437 -91 TCAATAATAATGACTTTTTAAAACTAGTTT 12 97 1 TGACTTTTTA 0.735918 -36 CTTATTATAGAGAGTTTTTAAC 13 3 0 AGAGTTTTTA 0.713252 -126 TTCATATTTTTGATTTTTTAAAGGGATTAG 13 102 1 TGATTTTTTA 0.505359 -27 TAGGGTTAAATGAAGTTTTATTCAAAAAAT 14 40 1 TGAAGTTTTA 0.937075 -261 ATTCAAAAAATGAAGTTTTACAAAAAAGAG 14 59 1 TGAAGTTTTA 0.937075 -242 TTTACAAAAAAGAGTTTTTAAACAACAACT 14 75 1 AGAGTTTTTA 0.713252 -226 ACTCCGACCATGACTTTTTAAAAAAGCTTC 14 208 1 TGACTTTTTA 0.735918 -93 TGATAATCATTGAAGCTTTTTTAAAAAGTC 14 219 0 TGAAGCTTTT 0.46244 -82 TAGCCCAACAAGCATTTTTTAATGAATTGC 16 58 0 AGCATTTTTT 0.51111 -54 TATTTTAAAAGAAGTTTTTAGCGTTCTTT 17 10 1 AGAAGTTTTT 0.872588 -88 TTCTTAATTTTGAAGTTTAGCAAATTTTAA 18 15 1 TGAAGTTTAG 0.362735 -33 TGTTATTTTGCGAAGTTTTTGGTGAGAT 19 9 0 CGAAGTTTTT 0.61542 -292 TTGGGATTATAGCAGTTTTATACTTGACTT 19 141 1 AGCAGTTTTA 0.744471 -160 CATTATTGAAAGAATTTATGGACACTTAAA 19 279 1 AGAATTTATG 0.398486 -22 ********** Masking position 7 Map Score: 6.56373 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 698 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 ATGATTTCTGCAACTTTAAAAACGATTAAC 1 197 0 CAACTTTAAA 0.693978 -39 AGAATGCATACAACAATAATTACGAATATT 5 147 0 CAACAATAAT 0.947733 -154 AGCTATAATACAACTTTAATAAAAGAAAAA 10 33 0 CAACTTTAAT 0.926763 -48 CTTTTGGTTGGAACTATAATCGGTTAAAGT 11 52 1 GAACTATAAT 0.911437 -112 TCATCTCAACCAACAATAATAGAAGCGCTA 12 30 1 CAACAATAAT 0.947733 -103 CTATGATTTTCAATAATAATGACTTTTTAA 12 88 1 CAATAATAAT 0.669403 -45 AAGAACTCTAATCCCTTTAAAA 13 117 0 GAACTCTAAT 0.790049 -12 GCTAAGCCAGCAACTAAAATAATCAAAGAC 19 111 1 CAACTAAAAT 0.839043 -190 ********** Masking position 3 Map Score: 2.01945 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 27 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 ACAAAGCCTTAAATTTCCATTAATAACTATGATAAT 1 78 1 ATTTCTTATA 0.891182 -158 ATAATGTTTTGAATTTTTATTTTTAAGATATTTTCA 1 109 1 GTTTTTTTTA 0.708987 -127 GCGTTTCTCTTAATCATTTTCAATAC 2 31 0 GTTTCTTATA 0.97652 -16 CCCTTTTAAGGTTTTTCTTTTATTAAAGTTGTATTA 10 22 1 GTTTCTTTTA 0.956173 -59 AAGCAAGGATGCCTTTGGGTTTTTTATAACAAGGAG 11 19 0 GTTTGTTTTA 0.78312 -145 GATTTTCCTTTCATCAAACTCATCTC 12 1 1 GTTTCTTATA 0.97652 -132 AAGCTTCAATGATTATCATTTCATTATATAATCACA 14 231 1 GTATCTTATA 0.929292 -70 CCAAAACAAAGAGTTGCAATTCATTAAAAAATGCTT 16 43 1 GTTGCTTATA 0.906693 -69 ACGCTTAAAAAACTATCGCTTGATCAAGCTCTTTTA 17 54 1 ATATCTTATA 0.721292 -44 * **** ** ** * Masking position 10 Map Score: 1.615 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 83 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TAAGGCTTTGTTTTCATGGAATATTGAAAAA 1 58 0 TTTTCATGGA 0.742994 -178 TGAATTTTTATTTTTAAGATATTTTCAAGGT 1 118 1 TTTTTAAGAA 0.706528 -118 TTTTAAGATATTTTCAAGGTATCTTTAATAA 1 129 1 TTTTCAAGGA 0.934013 -107 TTAAAACCAATTGGCAAGGAACGACA 3 59 1 TTGGCAAGGA 0.855586 -16 TTTATTCTTTTTGGAAAGAAAAAAAATGTTA 5 79 1 TTGGAAAGAA 0.864723 -222 TTAGCGGTTTTTTTAAAGAAAATTTTCAAAA 9 15 0 TTTTAAAGAA 0.93854 -106 AAGTTTGAAATTTTAAAGGGCTTTGTTTTAA 11 78 1 TTTTAAAGGC 0.814417 -86 ATTTTTGATTTTTTAAAGGGATTAGAGTTCT 13 107 1 TTTTAAAGGA 0.932843 -22 TCTTTTATGATTTGAACGATAACCC 15 5 0 TTTGAACGAA 0.704542 -32 TGGATAATGTTTTGCAAGAAATATCT 16 6 0 TTTGCAAGAA 0.934012 -106 TTTAAGGTTTTTTTAAAGAACGCTAAAAACT 17 23 0 TTTTAAAGAC 0.828321 -75 TTTTTAAAGATTAAATAGTAAA 17 86 0 TTTTAAAGAT 0.638845 -12 TATACTTGACTTGTCAAGAAATGATGACGGA 19 159 1 TTGTCAAGAA 0.877473 -142 TAATAGAGCATTTGAATGACAAAAGCTTATC 20 90 1 TTTGAATGAA 0.739383 -31 ********* * Masking position 6 Map Score: 9.92268 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 324 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 ********** No masking Map Score: -5.68902e-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: -5.68902e-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 AAAAATTCAAAACATTATCATAGTTATTAA 1 97 0 AACATTATCA 0.944291 -139 AGTCCCCTAAAACATTAACAAAGTTAATCG 1 175 1 AACATTAACA 0.727675 -61 CTTACATAGTAAGCTTATCAATATGAGATT 5 270 0 AAGCTTATCA 0.863164 -31 AAAGGTTATTAAAATTATCCTTATTATAGA 13 22 0 AAAATTATCC 0.826038 -107 AAAAGCTTCAATGATTATCATTTCATTATA 14 229 1 ATGATTATCA 0.670441 -72 TTTCTTGCAAAACATTATCCACATCCACCA 16 16 1 AACATTATCC 0.933566 -96 AAACGCTTAAAAAACTATCGCTTGATCAAG 17 52 1 AAAACTATCG 0.771734 -46 AGTATCCTACAACACTATCGGCTAAAATAC 20 38 1 AACACTATCG 0.909136 -83 TGAATGACAAAAGCTTATCGCAAAGGTTT 20 102 1 AAGCTTATCG 0.883957 -19 ********** Masking position 6 Map Score: 0.606406 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 119 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542