AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icrp_hpyl_opreg_100.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 HP0097 104 H. pylori predicted coding region HP0097 #2 HP0133 180 serine transporter (sdaC) #3 HP0166 235 response regulator (ompR) #4 HP0360 216 UDP-glucose 4-epimerase #5 HP0473 225 molybdenum ABC transporter, periplasmic molybdate-binding protein (modA) #6 HP0474 21 molybdenum ABC transporter, permease protein (modB) #7 HP0588 184 ferrodoxin-like protein #8 HP0654 296 conserved hypothetical protein #9 HP0655 82 protective surface antigen D15 #10 HP0664 37 H. pylori predicted coding region HP0664 #11 HP0723 128 L-asparaginase II (ansB) #12 HP0745 300 conserved hypothetical protein #13 HP0813 132 conserved hypothetical protein #14 HP0818 68 osmoprotection protein (proWX) #15 HP0942 40 D-alanine glycine permease (dagA) #16 HP0943 21 D-amino acid dehydrogenase (dadA) #17 HP0944 300 translation initiation inhibitor, putative #18 HP1027 159 ferric uptake regulation protein (fur) #19 HP1075 134 conserved hypothetical secreted protein #20 HP1112 109 adenylosuccinate lyase (purB) #21 HP1113 65 outer membrane protein (omp24) #22 HP1180 300 pyrimidine nucleoside transport protein (nupC) #23 HP1430 37 conserved hypothetical ATP-binding protein #24 HP1431 253 16S rRNA (adenosine-N6,N6-)-dimethyltransferase (ksgA) #25 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 ATTAAACTGAATGAAAGGAGTTTGA 1 90 1 ATAAGGGTTT 0.97693 -15 AAAGCTTTTTATGATTGGGGTTTTTTGAGATTA 2 110 0 ATATGGGTTT 0.932901 -71 TTATGCTACAATGAAAGCTCTTTAACACGATAA 2 141 1 ATAAGCCTTT 0.69149 -40 TAATTTCATCTTTATTGGCTTTTAAGGGCTTAT 4 105 0 TTATGGTTTT 0.942577 -112 CCATTTATTATTTAAGGATTTTTTAAGAAAATT 4 145 0 TTAAGATTTT 0.936972 -72 TTTTTTCATTTTAAAAGGGGTTTT 4 203 1 TTAAGGGTTT 0.978233 -14 AGTTCCTACTATTAAAGCATTTTAGAATTTATT 7 84 1 ATAAGCTTTT 0.927221 -101 TAATTCTCATTAAATAGATTTTTATGATAAAAT 8 149 0 TAATGATTTT 0.615755 -148 TTTTAGATTTAAGAATGCTTTTTACATATTATA 8 232 0 AAAAGCTTTT 0.806862 -65 TTAAATTTATTTTAACGATGTTTTACTATACTA 11 20 1 TTAAGAGTTT 0.930379 -109 AAAATATTCATGATTGGTTTTTCTTTTTTAAT 12 10 1 ATATGGTTTT 0.939268 -291 TCATGAGAAATTGAATGGCGTTTTGCGCAAGTT 12 110 0 TTAAGGGTTT 0.978233 -191 CAAATCATTTTTAAAAGGGGTTTTATAATGGAA 12 154 0 TTAAGGGTTT 0.978233 -147 TTTTGAGTAAAATAATGGTTTTTAAAAAAGCAA 12 266 1 AAAAGGTTTT 0.93904 -35 GATTTTCAATAATAATGACTTTTTAAAACTAGT 13 92 1 AAAAGATTTT 0.821392 -41 TAAAACTAGTTTGAAGGGAGTTTGGAGT 13 115 1 TTAAGGGTTT 0.978233 -18 ACTTATTTGGATAAAGGGGTTTTAAAATGCTAA 14 37 0 ATAAGGTTTT 0.97921 -32 ACCCTAGTTTATTAAGGAGTTTTT 15 27 1 ATAAGATTTT 0.933365 -14 TTAGAAATTCTTAAACGGGTTTTGTTTGAGTTT 17 145 0 TTAAGGTTTT 0.98039 -156 AAGATGAAAATTCATGGCGTTTTGCGCTCATTT 17 210 1 TTATGCTTTT 0.816157 -91 ATAACACATCATCATAGGAGTTTCAATC 17 283 1 ATATGGGTTT 0.932901 -18 TCAATCCAAAAATATTGATTTTTTATTACCATT 18 37 0 AAATGATTTT 0.60144 -123 GAATTAAAATAATAATGAGTTTTATCTATGTTT 18 68 1 AAAAGATTTT 0.821392 -92 TCCTTATCCGTAAAATGATTTTTATAACTAGAA 18 127 0 TAAAGATTTT 0.829755 -33 TCAATTCTATTTAAAAGGTTTTTT 19 2 0 TTAAGGTTTT 0.98039 -133 TAAAAACCTTTTTAAGGGGGTTTTTTAAAGTTT 19 68 0 TTAAGGGTTT 0.978233 -67 CTTTAATTAAATCAAGGGGCTTTTTTGCGCCTT 20 13 1 ATAAGGCTTT 0.892329 -97 TTTATGTTACTTTAAAGGGGTTTAAAGAATCAA 20 61 0 TTAAGGGTTT 0.978233 -49 AAATTGAAGTTTTAAGGGGTTTT 21 53 1 TTAAGGTTTT 0.98039 -13 TTAATGTAATTTTAATGGATTTTTAAGAAAGGT 22 65 1 TTAAGGTTTT 0.98039 -236 ATGGATTTTTAAGAAAGGTTTTTGTATAATCTC 22 79 1 AAAAGGTTTT 0.939263 -222 TAAACGGATATTAAATGAAGTTTAAATCAAAAT 22 208 0 TTAAGAGTTT 0.930379 -93 CAACTTCTTTATTATAGCTTTTTTCATTCAAAG 24 166 0 ATATGCTTTT 0.80706 -88 ** ** ** **** Masking position 4 Map Score: 65.5807 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 956 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 2 GGAATAAGGGCTTAAAAAAGAT 1 2 0 CTTAAAAAGA 0.94071 -103 ATAATAACGCTTAAAAAAAGATTAATAAAGG 2 20 0 TTAAAAAAGA 0.890023 -161 GTATCTTTAATAATAAAATGCTAGAATTAGT 3 147 1 TAATAAAAGC 0.439078 -89 TTTCTGCAACTTTAAAAACGATTAACTTTGT 3 192 0 TTTAAAAAGA 0.952957 -44 CCCCAAAGATTGTAAAAATGGTGGGCTTAGG 4 18 1 TGTAAAAAGG 0.708816 -199 TTAAATTTTCTTAAAAAATCCTTAAATAATA 4 142 1 TTAAAAAACC 0.742028 -75 AAAACCCCTTTTAAAATGAAAAAATAACA 4 198 0 TTTTAAAAGA 0.820888 -19 AACGCATAAAAAAGGCGAGCA 6 5 1 CATAAAAAGG 0.698579 -17 TCAATTCAAAAGAAAAAACGCCCCATTTACC 7 17 0 AGAAAAAAGC 0.393345 -168 TTAGAATTTATTAAAAAAGGCTTGCTACAAT 7 105 1 TTAAAAAAGC 0.916347 -80 GAGAATTAGGTAAAAAAAGGGGTTGGCATCA 8 174 1 TAAAAAAAGG 0.541734 -123 TTATATAATATGTAAAAAGCATTCTTAAATC 8 229 1 TGTAAAAACA 0.580207 -68 CATTCTTAAATCTAAAAATGCTACAATGTTT 8 248 1 TCTAAAAAGC 0.669251 -49 CAATGTTTATCTTTAAAACGAAAGGGCAATT 8 271 1 CTTTAAAAGA 0.782119 -26 ACTAATCATTCTTAAAAACGCTAAAAATTA 9 10 0 CTTAAAAAGC 0.955508 -73 ATACAATCAGCTTAAAAAGGATATAAA 10 21 1 CTTAAAAAGA 0.94071 -17 TTAAAATAAATTTAAAAAGGGTTA 11 4 0 TTTAAAAAGG 0.903553 -125 GCGCGAAGCCATTAAAAAAGAAAAACCAATC 12 22 0 ATTAAAAAGA 0.821892 -279 TTGTTTTCCATTATAAAACCCCTTTTAAAAA 12 149 1 TTATAAAACC 0.394222 -152 TAAAACCCCTTTTAAAAATGATTTGAGCCAC 12 162 1 TTTAAAAAGA 0.952957 -139 TACTCAAAACCTTAAAAATCATGTTTTTATT 12 244 0 CTTAAAAACA 0.806435 -57 AATAATGGTTTTTAAAAAAGCAAAAAAGAGT 12 276 1 TTTAAAAAGC 0.964813 -25 GATAAAGGGGTTTTAAAATGCTAAAGGCATT 14 30 0 TTTTAAAAGC 0.861178 -39 TAAACTAGGGTTTAAAAAAGAAATTCC 15 7 0 TTTAAAAAGA 0.952957 -34 AATGAGTGTCTGTAAAAATGCTCAAAAGCAT 17 42 1 TGTAAAAAGC 0.876916 -259 TAATAAAGAAATAAAAAATGAGCGCAAAACG 17 227 0 ATAAAAAAGA 0.648326 -74 TTATAAGTTACATTAAAATGCGACAATGGTA 18 13 1 CATTAAAAGC 0.60547 -147 GACAATGGTAATAAAAAATCAATATTTTTGG 18 34 1 ATAAAAAACA 0.326184 -126 ATATTCTAGTTATAAAAATCATTTTACGGAT 18 124 1 TATAAAAACA 0.626875 -36 TTAAAGTTTTCATAAAAAGGAACGAAAAATG 19 46 0 CATAAAAAGA 0.833648 -89 TTATGAAAACTTTAAAAAACCCCCTTAAAAA 19 62 1 TTTAAAAACC 0.878047 -73 AAAAAACCCCCTTAAAAAGGTTTTTAGGTAT 19 75 1 CTTAAAAAGT 0.531651 -60 GTTTTGTTTTTATAAAAACGCGCC 21 4 0 TATAAAAAGC 0.896484 -62 AAAAACCTTTCTTAAAAATCCATTAAAATTA 22 71 0 CTTAAAAACC 0.84938 -230 TTAGTTTTGCTAAAAAAAAGATTAAACGGAT 22 232 0 TAAAAAAAGA 0.718795 -69 ATTTCAATTTTTTAAAAAGGCA 23 2 0 TTTAAAAAGC 0.964813 -36 AGATTTTGCATTATAAAATGAAATCCTAGCT 24 49 0 TTATAAAAGA 0.646764 -205 AAGAAGTTGCATTAAAAAGGAAAGACAAATC 24 190 1 ATTAAAAAGA 0.821892 -64 CATATTATACCTTAAAAAGGGGATTTGTCTT 24 211 0 CTTAAAAAGG 0.880063 -43 ******** ** Masking position 6 Map Score: 47.0936 Number of sites scoring better than the average of aligned sites = 2335 Number in coding regions = 1921 Number in noncoding regions = 414 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 3 GTAGTTTGACTTAAAATTAAGATTTTATTAGG 1 31 0 TTAAATAAGA 0.711214 -74 TTAAAAACATTAAAAAATAAGACTTTATTTTT 3 31 1 TAAAATAAGA 0.660611 -205 TGAAAATATCTTAAAAATAAAAATTCAAAACA 3 113 0 TTAAATAAAA 0.922665 -123 AAAACCCCTTTTAAAATGAAAAAATAACAACT 4 195 0 TTAAAGAAAA 0.868402 -22 CATCTTTGATAAAAAATTAAAACTTTTAGAAA 5 59 0 AAAAATAAAA 0.910679 -167 TTTTACTCAATTCAAAAGAAAAAACGCCCCAT 7 22 0 TTAAAGAAAA 0.868402 -163 TAGTAGGAACTTAAAATTAAAATGAGAAGATA 7 63 0 TTAAATAAAA 0.922645 -122 GGACCACCTTTTGAAATTAAAAGATTTTATAG 11 50 0 TTAAATAAAA 0.922645 -79 TGCCCCTTCAAACAAAATAAAAGAATCAACAA 11 103 0 AAAAATAAAA 0.910679 -26 GCGAAGCCATTAAAAAAGAAAAACCAATCATG 12 19 0 TAAAAGAAAA 0.839111 -282 TAAACCAACTAATAAATTAATAAATAAAAACA 12 222 1 AAAAATAATA 0.757724 -79 AATGGTTTTTAAAAAAGCAAAAAAGAGTTTGG 12 279 1 AAAAACAAAA 0.849378 -22 GATGAGTTTGATGAAAGGAAAATC 13 3 0 ATAAAGAAAA 0.877074 -130 TTATTATGCAATCAAATTAATAAAGAAATAAA 17 243 0 ATAAATAATA 0.798273 -58 CAATGGTAATAAAAAATCAATATTTTTGGATT 18 36 1 AAAAACAATA 0.633681 -124 TTTGGATTGAATTAAAATAATAATGAGTTTTA 18 60 1 ATAAATAATA 0.798273 -100 TCTCTACTATTTGAAACTAAAAGATCGCTAAT 19 107 0 TTAAATAAAA 0.922665 -28 TTTAAACCCCTTTAAAGTAACATAAATCCCAT 20 68 1 TTAAATAACA 0.572325 -42 CGACAATCCTTAAAATCAAAATGGGATTTAT 20 89 0 TTAAACAAAA 0.868402 -21 GCGCGTTTTTATAAAAACAAAACTATAAAATA 21 12 1 ATAAACAAAA 0.877074 -54 CTACCTTGACAAAAAAATAAAAGAATGAGATT 22 106 0 AAAAATAAAA 0.910679 -195 TTAAATGAAGTTTAAATCAAAATCATGGTGTC 22 199 0 TTAAACAAAA 0.868383 -102 TCCCTAATGCAAGAAATTAAAAGATGCAAGGC 22 272 0 AAAAATAAAA 0.910679 -29 AAAAAATTGAAATAAAGGAATAAAAGTT 23 20 1 AAAAAGAATA 0.633681 -18 CTATTATAGCAACAAATTAAAACAAATGGTAT 25 64 0 AAAAATAAAA 0.910679 -57 ** *** ***** Masking position 6 Map Score: 30.8543 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 554 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 TAACCCGCACAAGCTATAATAACGCTTAAA 2 36 0 AAGCTATAAT 0.941307 -145 ACGCATTTATTTTCTAAAATCCACGATTTA 2 64 0 TTTCTAAAAT 0.486591 -117 AAAAAGCTTTATGCTACAATGAAAGCTCTT 2 133 1 ATGCTACAAT 0.892921 -48 TAATAATAAAATGCTAGAATTAGTCCCCTA 3 154 1 ATGCTAGAAT 0.755226 -82 AAGAAAATTTAATCTATAATTTCATCTTTA 4 124 0 AATCTATAAT 0.825351 -93 TGGGATTAAGATGTTATAATAGTTGTTATT 4 175 1 ATGTTATAAT 0.78575 -42 AAGATACAAATAGGTATAATCACCAATTCC 5 182 1 TAGGTATAAT 0.773064 -44 TTTTTAATAAATTCTAAAATGCTTTAATAG 7 92 0 ATTCTAAAAT 0.558157 -93 TAAAAAAGGCTTGCTACAATTTTAGGCAAA 7 116 1 TTGCTACAAT 0.835237 -69 ATTATCATTTATGCTATAATTATGGGACAA 8 36 0 ATGCTATAAT 0.962359 -261 AAATCTAAAAATGCTACAATGTTTATCTTT 8 255 1 ATGCTACAAT 0.892921 -42 TAAGAATGATTAGTTATAATAACGCTACTA 9 27 1 TAGTTATAAT 0.571105 -56 AACAACACTCAAGCTAAAATCTATTAAGGA 9 56 1 AAGCTAAAAT 0.776142 -27 TTGGTTTAATACGCTATAATCTGTGTGCCA 12 200 0 ACGCTATAAT 0.789353 -101 TCAAAAGCATTTTCTATAATAAGCCATAAT 17 63 1 TTTCTATAAT 0.81467 -238 TCGCATTATTATTGTATAATAATATTCTAG 18 103 1 ATTGTATAAT 0.711402 -57 AAAAGGTTTTTAGGTATAATTAGCGATCTT 19 89 1 TAGGTATAAT 0.773064 -46 AAGAAAGGTTTTTGTATAATCTCATTCTTT 22 89 1 TTTGTATAAT 0.616463 -212 CTAGGATTTCATTTTATAATGCAAAATCTA 24 51 1 ATTTTATAAT 0.509265 -203 TGAATGAAAAAAGCTATAATAAAGAAGTTG 24 169 1 AAGCTATAAT 0.941307 -85 TCCCCTTTTTAAGGTATAATATGAGGAATT 24 219 1 AAGGTATAAT 0.854352 -35 TTTTAATTTGTTGCTATAATAGAGCATTTG 25 74 1 TTGCTATAAT 0.937175 -47 ********** Masking position 5 Map Score: 22.1039 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 140 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 5 AATTAAACTGAATGAAAGGAGTTTGA 1 89 1 AATGAAAGGA 0.456996 -16 GGTTTTTTGAGATTAAGGGGTGGTTTTGGG 2 95 0 GATTAAGGGG 0.937917 -86 TCTTTAACACGATAAAAGGGCGGTTTAATA 2 159 1 GATAAAAGGG 0.947714 -22 AAAACGATCAAAGGAATTGTTTAAA 3 6 1 GATCAAAGGA 0.64691 -230 ATCCTTAAATAATAAATGGGATTAAGATGT 4 159 1 AATAAATGGG 0.593213 -58 ATTTTTTCATTTTAAAAGGGGTTTT 4 202 1 TTTAAAAGGG 0.813768 -15 CCAATCATTTAATCAAAGGGAGTTCT 5 210 1 AATCAAAGGG 0.921243 -16 AGAATTAGGTAAAAAAAGGGGTTGGCATCA 8 175 1 AAAAAAAGGG 0.483303 -122 TCAATAGGGGGTTAAAAGGGGATATTTTTA 8 202 1 GTTAAAAGGG 0.890395 -95 TCAAATCATTTTTAAAAGGGGTTTTATAAT 12 158 0 TTTAAAAGGG 0.813768 -143 AGATGAGTTTGATGAAAGGAAAATC 13 6 0 GATGAAAGGA 0.489172 -127 AACTTATTTGGATAAAGGGGTTTTAAAATG 14 41 0 GATAAAGGGG 0.944214 -28 TTTATTAAAGGGACTATCAGC 16 3 1 TATTAAAGGG 0.896932 -19 AATAAGCCATAATAAAAGGGCTTGCAAGCG 17 80 1 AATAAAAGGG 0.940933 -221 CTAAAAACCTTTTTAAGGGGGTTTTTTAAA 19 72 0 TTTTAAGGGG 0.78458 -63 CCCTTGATTTAATTAAAGGG 20 1 0 AATTAAAGGG 0.934292 -109 CCTTTAATTAAATCAAGGGGCTTTTTTGCG 20 12 1 AATCAAGGGG 0.916128 -98 GGGTTTAAAGAATCAAGGGGAAAAATCGCA 20 47 0 AATCAAGGGG 0.916128 -63 TTTATGTTACTTTAAAGGGGTTTAAAGAAT 20 64 0 TTTAAAGGGG 0.803164 -46 AAAATTGAAGTTTTAAGGGGTTTT 21 52 1 TTTTAAGGGG 0.78458 -14 CTAAAAAAAAGATTAAACGGATATTAAATG 22 224 0 GATTAAACGG 0.625759 -77 TTTAAATTTCAATTAAAGGAGTCATC 24 7 0 AATTAAAGGA 0.661854 -247 TACTTTTGAAATTTAAGCGGTAAGTTGGAT 25 12 0 ATTTAAGCGG 0.380815 -109 ********** Masking position 5 Map Score: 27.1566 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 646 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 TAGAAAATAAATGCGTGCCCAAAACCACCCCTTAAT 2 78 1 AGGCCAAACC 0.978321 -103 CGCTCTAACCACCTGAGCTATAAGCCCTTAAAAGCC 4 86 1 AGGCAAAGCC 0.993272 -131 TTAAATACTAATAAGTGGGATACACCCACAAAACAA 5 115 1 AGGGAACACC 0.888024 -111 TCATTCTCCTTTGTGCTAAAAGCTGCATTTAAAG 7 161 0 CGGCAAAGCT 0.841827 -24 TGAATATGGAAAAATTGCGCGAAGCCATTAAAAAAG 12 33 0 ATGCCAAGCC 0.965091 -268 TCGCCTAAAAACTTGCGCAAAACGCCATTCAATTTC 12 101 1 AGGCAACGCC 0.990576 -200 CATTGCCACTAAAAGAGGGCAAAGCCGCAATCTGT 17 10 0 AGGGCAAGCC 0.977152 -291 GAAATAAAAAATGAGCGCAAAACGCCATGAATTTTC 17 215 0 AGGCAACGCC 0.990576 -86 GGCTTATGAGACCAGCGCTCTAAACCAGCTGAGCTA 22 135 0 AGGCCAAACC 0.978321 -166 AAACCTTTGCGATAAGCTTTTGTCATTC 25 103 0 ATGCAAAGCT 0.813865 -18 * * ** * ***** Masking position 12 Map Score: 6.99456 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 133 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ATTGTAGCATAAAGCTTTTTATGATTGGGGT 2 122 0 AAACTTTTTA 0.723234 -59 ATAAAAAATTAAAACTTTTAGAAAAATAACC 5 52 0 AAACTTTTAG 0.898944 -174 CAAACCGCCTCAAACTTTTAAAATACAAATT 5 148 1 CAACTTTTAA 0.961327 -78 TTTTAAAATACAAATTTTTAAGATACAAATA 5 163 1 CAATTTTTAA 0.904162 -63 TCACCAATTCCAATCATTTAATCAAAGGGAG 5 201 1 CAACATTTAA 0.666287 -25 TGAGAGTATGAAAATTTTTAAAAATTTACAA 8 77 1 AAATTTTTAA 0.867955 -220 ACTCAAGCTAAAATCTATTAAGGAAATCAGT 9 62 1 AAACTATTAA 0.581775 -21 CTATACTATAAAATCTTTTAATTTCAAAAGG 11 45 1 AAACTTTTAA 0.945413 -84 GCGTTTTGCGCAAGTTTTTAGGCGATGCGTT 12 95 0 CAATTTTTAG 0.828935 -206 AAAAAACCTTTTAAATAGAATTGA 19 4 1 AAACTTTTAA 0.945413 -131 CCTTTTTATGAAAACTTTAAAAAACCCCCTT 19 57 1 AAACTTTAAA 0.581775 -78 TTATACCTAAAAACCTTTTTAAGGGGGTTTT 19 77 0 AAACTTTTTA 0.723234 -58 GTATAATTAGCGATCTTTTAGTTTCAAATAG 19 102 1 CGACTTTTAG 0.618201 -33 CTTAAAACTTCAATTTTTTAGCGCTTATTTT 21 38 0 CAATTTTTAG 0.828935 -28 TCCTTTATTTCAATTTTTTAAAAAGGCA 23 8 0 CAATTTTTAA 0.904164 -30 TATTAACGAAAAAGATTTTAATACTAATTTT 24 87 1 AAAATTTTAA 0.577102 -167 GATTTTAATACTAATTTTTAATACGAGCGTT 24 100 1 CTATTTTTAA 0.446671 -154 *** ******* Masking position 8 Map Score: 11.9866 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 448 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 ACTGAATGAAAGGAGTTTGA 1 95 1 AGGAGTTTGA 0.937937 -10 TTATTATTTAAGGATTTTTTAAGAAAATTT 4 144 0 AGGATTTTTT 0.591364 -73 CATTTTTAAAAGGGGTTTTATAATGGAAAA 12 152 0 AGGGGTTTTA 0.940041 -149 AAATAAAAACATGATTTTTAAGGTTTTGAG 12 243 1 ATGATTTTTA 0.841664 -58 GAGTAAAATAATGGTTTTTAAAAAAGCAAA 12 270 1 ATGGTTTTTA 0.78525 -31 GTTGGTTGAGATGAGTTTGATGAAAGGAAA 13 14 0 ATGAGTTTGA 0.89334 -119 TTTTTGCGCTATGATTTTCAATAATAATGA 13 80 1 ATGATTTTCA 0.648168 -53 ATTTGGATAAAGGGGTTTTAAAATGCTAAA 14 36 0 AGGGGTTTTA 0.940041 -33 TAGTTTATTAAGGAGTTTTT 15 31 1 AGGAGTTTTT 0.774716 -10 CGGGTTTTGTTTGAGTTTTAGGCTTTGTTG 17 133 0 TTGAGTTTTA 0.503609 -168 ACATCATCATAGGAGTTTCAATC 17 288 1 AGGAGTTTCA 0.887627 -13 TAAAATAATAATGAGTTTTATCTATGTTTC 18 72 1 ATGAGTTTTA 0.92664 -88 TATCCGTAAAATGATTTTTATAACTAGAAT 18 126 0 ATGATTTTTA 0.841664 -34 GTTACTTTAAAGGGGTTTAAAGAATCAAGG 20 59 0 AGGGGTTTAA 0.665784 -51 TCTTGACACCATGATTTTGATTTAAACTTC 22 195 1 ATGATTTTGA 0.778991 -106 TTCTTGCATTAGGGATTTGACG 22 289 1 AGGGATTTGA 0.615616 -12 GTATAATATGAGGAATTTTAGAAGCGTTTC 24 232 1 AGGAATTTTA 0.778333 -22 ********** Masking position 6 Map Score: 17.4647 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 413 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 TTAAAATTAAGATTTTATTAGGAATAAGGGCTTA 1 19 0 GATTTTTAGA 0.776982 -86 CTAATTCTAGCATTTTATTATTAAAGATACCTTG 3 143 0 CATTTTTATA 0.809724 -93 ATTATTTAAGGATTTTTTAAGAAAATTTAATCTA 4 138 0 GATTTTTAGA 0.776982 -79 TTGTAGCAAGCCTTTTTTAATAAATTCTAAAATG 7 101 0 CCTTTTTATA 0.872497 -84 ATAAAGCTTAGATTTTATCATAAAAATCTATTTA 8 138 1 GATTTTTATA 0.937216 -159 GTTAAAAGGGGATATTTTTATATAATATGTAAAA 8 212 1 GATATTTATA 0.865576 -85 GAAATTAAAAGATTTTATAGTATAGTAAAACATC 11 36 0 GATTTTTGTA 0.844464 -93 TTTTAAAAGGGGTTTTATAATGGAAAACAACGAA 12 145 0 GGTTTTTATA 0.777171 -156 TAATAGAAGCGCTATTCTAGTCAAAATCGCCTTA 13 46 1 GCTATTTGTA 0.79018 -87 TGTTATGTCAGCTATTATTATGCAATCAAATTAA 17 255 0 GCTATTTATA 0.911928 -46 TTATAACTAGAATATTATTATACAATAATAATGC 18 105 0 AATATTTATA 0.538613 -55 AAAATGCCCAACTTTTGTCATCAATTTGAGGAAG 22 12 1 ACTTTTTATA 0.813149 -289 ATTACATTAAACTTTTATTATCAATCCTACTTCC 22 41 0 ACTTTTTATA 0.813149 -260 AAGATGCAAGGCTATTGTAGTTTAGTTTTGCTAA 22 250 0 GCTATTTGTA 0.79018 -51 GCTAGGATTTCATTTTATAATGCAAAATCTAACC 24 50 1 CATTTTTATA 0.809724 -204 CTTTATTATAGCTTTTTTCATTCAAAGATGTTAG 24 159 0 GCTTTTTATA 0.960006 -95 TTTGCGATAAGCTTTTGTCATTCAAATGCTCTAT 25 92 0 GCTTTTTATA 0.960006 -29 ****** * ** * Masking position 8 Map Score: 15.8785 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 205 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 TTTTATGATTGGGGTTTTTTGAGATTAAGGG 2 106 0 GGGTTTTTTG 0.947191 -75 AAACGATCAAAGGAATTGTTTAAAAACATTA 3 12 1 AGGATTGTTT 0.521685 -224 TGGAAATTTAAGGCTTTGTTTTCATGGAATA 3 66 0 AGGTTTGTTT 0.911103 -170 TTATTATTTAAGGATTTTTTAAGAAAATTTA 4 143 0 AGGTTTTTTA 0.635314 -74 AAAGTTTGAGGCGGTTTGTTTTGTGGGTGTA 5 135 0 GCGTTTGTTT 0.874658 -91 GGTAAATGGGGCGTTTTTTCTTTTGAATTGA 7 17 1 GCGTTTTTCT 0.654559 -168 GGGTTAAAAGGGGATATTTTTATATAATATG 8 210 1 GGGTATTTTT 0.671156 -87 TTTGAGTTTTAGGCTTTGTTGTCATCAATTT 17 123 0 AGGTTTGTTG 0.905526 -178 ATTCTTAAACGGGTTTTGTTTGAGTTTTAGG 17 141 0 GGGTTTGTTT 0.972719 -160 CCTTTTTAAGGGGGTTTTTTAAAGTTTTCAT 19 64 0 GGGTTTTTTA 0.858369 -71 TTAAATCAAGGGGCTTTTTTGCGCCTTGTGC 20 19 1 GGGTTTTTTG 0.947191 -91 TCTTGCATTAGGGATTTGACG 22 290 1 GGGTTTGACG 0.641754 -11 CCTTAAAAAGGGGATTTGTCTTTCCTTTTTA 24 202 0 GGGTTTGTCT 0.947368 -52 *** ******* Masking position 7 Map Score: 8.07006 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 878 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 11 CATTCAGTTTAATTTTCGTTTAGAATTTCC 1 73 0 AATTTTCGTT 0.838087 -32 TTAGAGTGAAAATGTTGGTTAAATACTAAT 5 97 1 AATGTTGGTT 0.95629 -129 ATTTTAGGCAAATTTTGATTGCTAGGGCTT 7 134 1 AATTTTGATT 0.769921 -51 TATTTTTGAAATTGTTGATTCTTTTATTTT 11 92 1 ATTGTTGATT 0.777619 -37 CGCTTCTATTATTGTTGGTTGAGATGAGTT 13 27 0 ATTGTTGGTT 0.946691 -106 GGCATTCTTTAATGTTGGTTGCAGG 14 6 0 AATGTTGGTT 0.95629 -63 TTATCCAAATAAGTTTGGTTATA 14 56 1 AAGTTTGGTT 0.798818 -13 AAAAATCAATATTTTTGGATTGAATTAAAA 18 47 1 ATTTTTGGAT 0.684988 -113 ATTCACAAGCATTTTTCGTTCCTTTTTATG 19 37 1 ATTTTTCGTT 0.807746 -98 ********** Masking position 5 Map Score: 3.06731 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 73 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 AAGACTTTATTTTTCAATATTCCATGAAAA 3 49 1 TTTTCAATAT 0.673898 -187 AGTTGTTATTTTTTCATTTTAAAAGGGGTT 4 195 1 TTTTCATTTT 0.869283 -22 GTTTAGTATCTTCTCATTTTAATTTTAAGT 7 57 1 TTCTCATTTT 0.91383 -128 CTCATTTACTTTTTCATTATCATTTATGCT 8 51 0 TTTTCATTAT 0.936251 -246 CCGGTGTTCTTTCTCATTTTTGTAAATTTT 8 97 0 TTCTCATTTT 0.91383 -200 TTTTACCTAATTCTCATTAAATAGATTTTT 8 159 0 TTCTCATTAA 0.767198 -138 TTCAAAAATATTCTCATTATGGACCACCTT 11 72 0 TTCTCATTAT 0.959051 -57 GCCATTCAATTTCTCATGATTTTCGTTGTT 12 124 1 TTCTCATGAT 0.830057 -177 TTTTCGTTGTTTTCCATTATAAAACCCCTT 12 143 1 TTTCCATTAT 0.774338 -158 TTGGTTAGATTTTGCATTATAAAATGAAAT 24 56 0 TTTGCATTAT 0.774338 -198 ********** Masking position 6 Map Score: 6.00348 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 53 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 CTTATTCCTAATAAAATCTTAATTTTAAGT 1 25 1 ATAAAATCTT 0.539529 -80 ACCCCAATCATAAAAAGCTTTATGCTACAA 2 122 1 TAAAAAGCTT 0.479676 -59 AGGAATTGTTTAAAAACATTAAAAAATAAG 3 22 1 TAAAAACATT 0.811259 -214 TTCCATGAAAACAAAGCCTTAAATTTCCAT 3 68 1 ACAAAGCCTT 0.576312 -168 AAATAAAAATTCAAAACATTATCATAGTTA 3 101 0 TCAAAACATT 0.68453 -135 AATTAGTCCCCTAAAACATTAACAAAGTTA 3 171 1 CTAAAACATT 0.761743 -65 CATTTTCACTCTAAAATCTTCATCTTTGAT 5 81 0 CTAAAATCTT 0.690261 -145 GTTCCTACTATTAAAGCATTTTAGAATTTA 7 85 1 TTAAAGCATT 0.540158 -100 TATAATATGTAAAAAGCATTCTTAAATCTA 8 232 1 AAAAAGCATT 0.550846 -65 TTACTATACTATAAAATCTTTTAATTTCAA 11 42 1 ATAAAATCTT 0.539529 -87 TCAACAATTTCAAAAATATTCTCATTATGG 11 80 0 CAAAAATATT 0.623682 -49 ATTATTTTACTCAAAACCTTAAAAATCATG 12 252 0 TCAAAACCTT 0.826608 -49 TTTGCTTTTTTAAAAACCATTATTTTACTC 12 270 0 TAAAAACCAT 0.403212 -31 TAAAAATGCTCAAAAGCATTTTCTATAATA 17 54 1 CAAAAGCATT 0.699933 -247 TAATTCAATCCAAAAATATTGATTTTTTAT 18 44 0 CAAAAATATT 0.623682 -116 AAAAAACCTTTTAAATAGAA 19 1 1 AAAAAACCTT 0.857839 -134 TAATTATACCTAAAAACCTTTTTAAGGGGG 19 81 0 TAAAAACCTT 0.904246 -54 TGAGATTATACAAAAACCTTTCTTAAAAAT 22 83 0 CAAAAACCTT 0.919853 -218 AAAATTAGTATTAAAATCTTTTTCGTTAAT 24 88 0 TTAAAATCTT 0.6471 -166 ********** Masking position 10 Map Score: 9.21345 Number of sites scoring better than the average of aligned sites = 1151 Number in coding regions = 1010 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 14 AGATTTTATTAGGAATAAGGGCTTAAAAAAGAT 1 9 0 AAAAGGGTTA 0.959929 -96 TTAAAAAAAGATTAATAAAGGATTATAGAA 2 6 0 AAAAAGGTTA 0.575453 -175 ATCCTTAAATAATAAATGGGATTAAGATGTTATAA 4 159 1 AAAGGGATAA 0.642373 -58 ATTTTTTCATTTTAAAAGGGGTTTT 4 202 1 TAAGGGGTTT 0.808876 -15 ACTTTAATTCAACAAGAAGGATTTATT 5 3 0 AAAAGGATTA 0.894554 -223 ATTAAATGATTGGAATTGGTGATTATACCTATTTG 5 188 0 TAAGGTGTTA 0.707677 -38 TTTTGAATTGAGTAAAAAGTGTTTAGTATCTTCTC 7 37 1 AAAAGTGTTA 0.719994 -148 AGAATTAGGTAAAAAAAGGGGTTGGCATCAATAGG 8 175 1 AAAGGGGTGG 0.760675 -122 AGGGGTTGGCATCAATAGGGGGTTAAAAGGGGATA 8 191 1 AAAGGGGTTA 0.977674 -106 CTTGATGGGAAAGAAGGAGGATTGAATATGGAAAA 12 56 0 AAAAGGATGA 0.796085 -245 CAAATCATTTTTAAAAGGGGTTTTATAATGGAAAA 12 152 0 TAAGGGTTTA 0.663344 -149 AAACTCCTTAATAAACTAGGGTTTAAAAAAGAAAT 15 14 0 AAAAGGGTTA 0.959927 -27 ATCCTTAAAATCAAAATGGGATTTATGTTACTTTA 20 80 0 TAAGGGATTA 0.888726 -30 CATCAATTTGAGGAAGTAGGATTGATAATAAAAGT 22 30 1 AAAAGGATGA 0.796085 -271 ATATTATACCTTAAAAAGGGGATTTGTCTTTCCTT 24 206 0 TAAGGGGTTT 0.808876 -48 * ** **** *** Masking position 5 Map Score: 4.70742 Number of sites scoring better than the average of aligned sites = 807 Number in coding regions = 680 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 15 TATTATAGCTTGTGCGGGTTAAATCGTGGATTTTA 2 45 1 TGGGTTAATC 0.983788 -136 TGTTAATGTTTTAGGGGACTAATTCTAGCATTTTA 3 160 0 TGGGCTAATC 0.96471 -76 AAGGGTGAGGTCGGAGGTTCAACTCCTCCTAAGCC 4 41 0 TGGGTCAATC 0.992739 -176 GTGCCAACATTGTGTGGCTCAAATCATTTTTAAAA 12 171 0 TGGGTCAATC 0.992739 -130 AAGCCGGAGGTCGGGGGTTCAAGTCCCCCTCTTGA 22 166 1 TGGGTCAATC 0.992739 -135 * * ** **** ** Masking position 11 Map Score: 1.07612 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 6 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555