AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_hpyl_reg_100.orf -o00400_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 Input sequences: #1 HP0153 98 recombinase (recA) #2 HP0282 50 H. pylori predicted coding region HP0282 #3 HP0289 66 toxin-like outer membrane protein #4 HP0290 47 diaminopimelate decarboxylase (dap decarboxylase) (lysA) #5 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #6 HP0654 296 conserved hypothetical protein #7 HP0655 82 protective surface antigen D15 #8 HP0774 23 tyrosyl-tRNA synthetase (tyrS) #9 HP0777 107 uridine 5'-monophosphate (UMP) kinase (pyrH) #10 HP1038 128 3-dehydroquinase type II (aroQ) #11 HP1253 31 tryptophanyl-tRNA synthetase (trpS) #12 HP1254 116 biotin synthesis protein (bioC) #13 HP1279 300 anthranilate isomerase (trpC) #14 HP1282 222 anthranilate synthase component I (trpE) #15 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #16 HP1361 56 competence locus E (comE3) #17 HP1365 83 response regulator #18 HP1368 300 type IIS restriction enzyme M2 protein (mod) #19 HP1378 300 competence lipoprotein (comL) #20 HP1379 41 ATP-dependent protease (lon) #21 HP1380 38 prephenate dehydrogenase (tyrA) Motif number 1 GGTAAGTCCTTTTATTATAATAGATTTTAGG 1 32 1 TTTATATAAT 0.735547 -67 TAGGCTAGGATTTGATAGAATAAACAAATCA 1 59 1 TTTGTAGAAT 0.898055 -40 AGCCTTAATCTTGGATATAATGGCGTAATCA 2 17 1 TTGGTATAAT 0.746285 -34 AACTCTCTCATTTGATTAAATCAAAGGGA 3 9 0 TTTGTTAAAT 0.544026 -58 CTTTTTTGCTATAATGCTTCGTTCA 4 5 1 TTTGTATAAT 0.954202 -43 GTATTATAGCTTTTTAAAAATAAAATATAAG 5 52 1 TTTTAAAAAT 0.859521 -29 CATTATCATTTATGCTATAATTATGGGACAA 6 36 0 TATGTATAAT 0.849399 -261 TTTTTGTAAATTTTTAAAAATTTTCATACTC 6 80 0 TTTTAAAAAT 0.859521 -217 TTTTTAAAAATTTACAAAAATGAGAAAGAAC 6 91 1 TTTAAAAAAT 0.606064 -206 AATAGATTTTTATGATAAAATCTAAGCTTTA 6 139 0 TATGTAAAAT 0.881975 -158 AAGGGGATATTTTTATATAATATGTAAAAAG 6 217 1 TTTTTATAAT 0.917956 -80 ATTTTTAGCGTTTTTAAGAATGATTAGTTAT 7 13 1 TTTTAAGAAT 0.663756 -70 TTAAGAATGATTAGTTATAATAACGCTACTA 7 26 1 TTAGTATAAT 0.780123 -57 AATCACAAGTTTTATTAAAATTTTATTAATT 9 73 1 TTTATAAAAT 0.786253 -35 GATAAAAACTTATGCTATAATGTGGTCTCAT 10 81 1 TATGTATAAT 0.849399 -48 TGCCTAAAATTTAGAAAAAATCACGCTTGAT 12 23 1 TTAGAAAAAT 0.662355 -94 ACGCTTGATCTTATCTAAAATTTGCTAAGAA 12 45 1 TTATTAAAAT 0.716279 -72 CCCCCTATGATTTGAAAGAATTACAGATTGA 13 71 1 TTTGAAGAAT 0.786147 -230 CTTGCCTTTATTTTCTAAAATATCTAAACAC 13 126 0 TTTTTAAAAT 0.936804 -175 TGAGTGAGCGTTTTCAAAAATTCCAAGACAT 14 133 0 TTTTAAAAAT 0.86084 -90 TTTATCTATTTCTTGTAAAATACGAGTTTAT 14 183 1 TCTTTAAAAT 0.694429 -40 AAGGGAGTGTTTTTTTATAACCGCTTTTAGT 17 34 1 TTTTTATAAC 0.576914 -50 TATGAAAAGGTTTTCTAAAACTTCATAAAAT 18 12 1 TTTTTAAAAC 0.643788 -289 ATGAGCGGGCTTTGTTATAATACTTCCTATG 18 82 0 TTTGTATAAT 0.9542 -219 ACTGACTCATTTTTTTAAAATACCCCCATTT 18 222 1 TTTTTAAAAT 0.936204 -79 CAAACAATTTTGGTAAAATCAATTTTCGC 19 9 1 TTTGTAAAAT 0.965041 -292 TTCGCTAGTTTTGGATATAATCCCAATAACT 19 35 1 TTGGTATAAT 0.746285 -266 CTCCTTATTATATTTTATAATGATTCGGTTA 19 83 0 TATTTATAAT 0.751798 -218 ATAAGAAAGATAAGAAAAAATAACCATGAGT 19 247 1 TAAGAAAAAT 0.346844 -54 AACCATGAGTTATTCAAAAATTTAACTTTAT 19 268 1 TATTAAAAAT 0.62613 -33 TTTTCATCTCTCTGTTATAATGTGTATGGTT 20 21 0 TCTGTATAAT 0.761553 -21 **** ****** Masking position 9 Map Score: 35.4403 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 823 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 2 TATCAAATCCTAGCCTAAAATCTATTATAAT 1 45 0 TACCTAAAAT 0.58856 -54 ATCCAAGATTAAGGCTTAAACG 2 2 0 AAGCTTAAAC 0.471084 -49 ACTTCCTAAAAAATGATTACGC 2 39 0 CTCCTAAAAA 0.810492 -12 ACGAAGCATTATAGCAAAAAAG 4 2 0 ATGCAAAAAA 0.721128 -46 AGAAAAACCTAACCATAAAATTTGAACGAA 4 28 0 TACCATAAAA 0.56734 -20 AATAAAAGAAAAACCTTAAAAGGGAGCAAAA 5 15 0 AACCTTAAAA 0.775979 -66 TCCCATAATTATAGCATAAATGATAATGAAA 6 39 1 ATGCATAAAT 0.590682 -258 AGCTTAGATTTTATCATAAAAATCTATTTAA 6 142 1 TTTCATAAAA 0.450327 -155 AAGCATTCTTAAATCTAAAAATGCTACAATG 6 245 1 AATCTAAAAA 0.650558 -52 CATTCTTAAAAACGCTAAAAATTA 7 4 0 AAGCTAAAAA 0.872299 -79 TAACAACACTCAAGCTAAAATCTATTAAGGA 7 55 1 CAGCTAAAAT 0.824768 -28 GCTGAGAATGTAGGCTTAAAATTCAGAAAGG 9 17 1 TAGCTTAAAA 0.888151 -91 GTAACCTAATCTTGCTTAAAAACACCCTTTC 9 42 0 CTGCTTAAAA 0.919336 -66 TGATTCCTTAAATGCCTAAAATT 12 3 1 ATCCTTAAAT 0.624466 -114 ACGCTTGATCTTATCTAAAATTTGCTAAGAA 12 45 1 TTTCTAAAAT 0.471946 -72 TTTAACGCACCACGCTTGAAATTAAAACTAA 12 87 0 CAGCTTGAAA 0.466466 -30 GCTCAAGTCATACTCTAAAATTCCGTTATTT 13 21 0 TATCTAAAAT 0.471946 -280 CTTGCCTTTATTTTCTAAAATATCTAAACAC 13 126 0 TTTCTAAAAT 0.471886 -175 CTTTAGCTTTATGGCTTAAATACAACAAACT 13 193 0 ATGCTTAAAT 0.792188 -108 CTTATGCGCATTTGCAAAAAATCATAAGGCT 13 275 1 TTGCAAAAAA 0.721125 -26 TTAGATTGTAAAAGCATAAAAAGGAATTTTC 14 45 1 AAGCATAAAA 0.750374 -178 AGACATTCTGCTCTCTTAAAAATGTGGTTGT 14 108 0 CTTCTTAAAA 0.756468 -115 CAATTTCTTTACGCTAAAAATAAACTCGTA 14 203 0 TAGCTAAAAA 0.872299 -20 TAAAAAAACACTCCCTTAAAAAAGACACCGC 17 20 0 CTCCTTAAAA 0.832543 -64 ACAATACCCCCATGCAAAAAAAGATTTTTTT 18 121 1 CAGCAAAAAA 0.787753 -180 CCTTAACGCTCTCGCTTAAAAGGTAATCGTC 18 159 0 CTGCTTAAAA 0.919336 -142 ** ******** Masking position 9 Map Score: 18.2559 Number of sites scoring better than the average of aligned sites = 2926 Number in coding regions = 2519 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 3 ATAGTAGCCAAAAACTCTCTCATTTGATTAAA 3 20 0 AAAACTCCTA 0.942288 -47 AATGAGAAAGAACACCGGCTAATGGCTTGATA 6 109 1 AACACCGCTA 0.878385 -188 CTTGCTTAAAAACACCCTTTCTGAATTTTAAG 9 31 0 AACACCCTTT 0.86766 -77 TGACTAATGTCAAACCCCTTGATG 10 3 0 CAAACCCTTA 0.909247 -126 CTTACCCCTTAAATCCCCCTAAGAACGAATCA 10 50 0 AAATCCCCTA 0.866442 -79 AAGTCATGCTCACACCCTCTTTTAAATCTTTA 13 219 0 CACACCCCTT 0.86467 -82 AATTTTTGAAAACGCTCACTCATTAGCGTATT 14 142 1 AACGCTCCTA 0.950593 -81 AAGAAGTTCAAACGCCCCCTGAAAAGTTTTGT 16 14 0 AACGCCCCTA 0.981927 -43 GTTATAAAAAAACACTCCCTTAAAAAAGACAC 17 23 0 AACACTCCTA 0.963238 -61 GAAGTTTTAGAAAACCTTTTCATAG 18 4 0 AAAACCTTTA 0.589151 -297 TTTTCATTATAACGCTCCTTAAAAAACATAGG 18 56 1 AACGCTCTTA 0.900848 -245 GTATTATAACAAAGCCCGCTCATTAAGCGCTA 18 90 1 AAAGCCCCTA 0.971302 -211 TTCAATGAGTCAAACTCCTTAACGCTCTCGCT 18 174 0 CAAACTCTTA 0.780127 -127 TCTTTCATGCAAAACCCATTGAAGTTTAATAA 18 264 1 AAAACCCTTA 0.956085 -37 ******* ** * Masking position 2 Map Score: 14.3301 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 718 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 AAATCTATTATAATAAAAGGACTTACCCTATC 1 27 0 TAAAAAGGAC 0.874277 -72 CCCTTTGATTTAATCAAATGAGAGAGTTTTTG 3 12 1 TAAAAATGAG 0.92637 -55 AACTTAAACCAACACAAAGGAGATACT 6 6 0 AACAAAGGAG 0.852888 -291 TGATAATGAAAAAGTAAATGAGAGTATGAAAA 6 59 1 AAAAAATGAG 0.895039 -238 TTTAAAAATTTACAAAAATGAGAAAGAACACC 6 93 1 TACAAATGAG 0.84176 -204 GAGAATTAGGTAAAAAAAGGGGTTGGCATCAA 6 174 1 TAAAAAGGGG 0.970178 -123 TTTATCTTTAAAACGAAAGGGCAATTTAACC 6 276 1 AAAAAAGGGC 0.883434 -21 TAAAATCTATTAAGGAAATCAGT 7 70 1 TAAAAATCAG 0.812191 -13 TAATTCTTTCAAATCATAGGGGGGCAAATCAA 13 62 0 AAAATAGGGG 0.653577 -239 GAGCATTTAAAAACCAAAGCGCCTTATGCGCA 13 253 1 AAAAAAGCGC 0.722611 -48 TTACAAGAAATAGATAAATGGGCAATAAATAC 14 169 0 TAGAAATGGG 0.761391 -54 ATTTGATCCCTAATAAAATGACTTTT 15 5 0 TAAAAATGAC 0.812191 -24 TAAAATAAAGCGGTGTCTTTTTT 17 2 1 AAAAAAGCGG 0.883434 -82 ATTGCCTTTATACTAAAAGCGGTTATAAAAAA 17 44 0 TACAAAGCGG 0.825415 -40 GGGGGTATTTTAAAAAAATGAGTCAGTCAAGG 18 217 0 TAAAAATGAG 0.92637 -84 AAGAATTTTACAATGAAATGGGGGTATTTTAA 18 236 0 CAAAAATGGG 0.808399 -65 *** ******* Masking position 6 Map Score: 14.3115 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 381 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 GATTTAATCAAATGAGAGAGTTTTTGGCTA 3 18 1 AATGAGAGAG 0.982146 -49 CTATCTAGGAAATGAGAGGGTAGCATTTA 3 48 1 AATGAGAGGG 0.971794 -19 CATAAATGATAATGAAAAAGTAAATGAGAG 6 53 1 AATGAAAAAG 0.712233 -244 TGAAAAAGTAAATGAGAGTATGAAAATTTT 6 65 1 AATGAGAGTA 0.656861 -232 AATTTACAAAAATGAGAAAGAACACCGGCT 6 99 1 AATGAGAAAG 0.971826 -198 TTTATTAATTAATGAGAAGGGATC 9 94 1 AATGAGAAGG 0.955761 -14 TAAATACGCTAATGAGTGAGCGTTTTCAAA 14 146 0 AATGAGTGAG 0.961402 -77 TGTAGCGCTTAATGAGCGGGCTTTGTTATA 18 94 0 AATGAGCGGG 0.943948 -207 CTAAATTTTCAATGAGTCAAACTCCTTAAC 18 183 0 AATGAGTCAA 0.698811 -118 ATTTTAAAAAAATGAGTCAGTCAAGGCAAT 18 213 0 AATGAGTCAG 0.913121 -88 GGAGTTGAGGAATGAGCAAAATAAAACCAC 19 110 1 AATGAGCAAA 0.788229 -191 ATTTGGTGGGAATAAGAAAGATAAGAAAAA 19 236 1 AATAAGAAAG 0.712233 -65 ********** Masking position 5 Map Score: 12.8902 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 149 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 TTTTGCTCCCTTTTAAGGTTTTTCTTTTATTAA 5 15 1 TTTAATTTTT 0.622303 -66 TAAAGTTGTATTATAGCTTTTTAAAAATAAAAT 5 45 1 TTTAGTTTTA 0.835794 -36 TAACGATCCTTATATTTTATTTTTAAAAA 5 62 0 TCTTATTTTA 0.722337 -19 TTTCTCATTTTTGTAAATTTTTAAAAATTTTCA 6 85 0 TTTAATTTTA 0.9535 -212 TTAAGAATGCTTTTTACATATTATATAAAAATA 6 224 0 TTTTATATTA 0.622303 -73 CATTGTAGCATTTTTAGATTTAAGAATGCTTTT 6 243 0 TTTTATTTAA 0.622303 -54 ACTGATTTCCTTAATAGATTTTAGCTTGAGTGT 7 60 0 TTATATTTTA 0.65251 -23 AAAAACACCCTTTCTGAATTTTAAGCCTACATT 9 23 0 TTCTGTTTTA 0.561209 -85 TCTCATTAATTAATAAAATTTTAATAAAACTTG 9 78 0 TATAATTTTA 0.636305 -30 CTAATTTTAATATTTTAATTTATCTTA 11 15 0 TTTAATTTTA 0.953516 -17 AGCGTGATTTTTTCTAAATTTTAGGCATTTAAG 12 17 0 TTCTATTTTA 0.836659 -100 TCACACCCTCTTTTAAATCTTTAGCTTTATGGC 13 209 0 TTTAACTTTA 0.709467 -92 TTGCGTTATAAGTTTTTAGAGGATAACT 14 6 1 TTTAATTTTA 0.952531 -217 GAAAATTCCTTTTTATGCTTTTACAATCTAAAG 14 43 0 TTTATTTTTA 0.652522 -180 AAGCGCAATTTTATGAAGTTTTAGAAAACCTTT 18 17 0 TTTGATTTTA 0.827372 -284 TCTTATTTTTACCTTTTATTAAACTTCA 18 283 0 TTTTATTTTA 0.953518 -18 CCTCAACTCCTTATTATATTTTATAATGATTCG 19 87 0 TTTTATTTTA 0.953516 -214 ** *** ***** Masking position 11 Map Score: 12.1639 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 201 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 TATATCCAAGATTAAGGCTTAAACG 2 6 0 ATTAAGGCTT 0.825116 -45 TAATTTTTAGCGTTTTTAAGAATGA 7 6 1 TTTAGCGTTT 0.824338 -77 TCATTCCTTAATTAGGGCTTA 8 2 0 ATTAGGGCTT 0.976879 -22 AATCAAAATCTTTAGCGCTCAAGTCATACT 13 38 0 TTTAGCGCTC 0.959672 -263 AATCTTTAGCTTTATGGCTTAAATACAACA 13 197 0 TTTATGGCTT 0.853217 -104 AAGTCATTTTATTAGGGATCAAATCA 15 13 1 ATTAGGGATC 0.727647 -16 TATAAAGGCAATTAGCGCTACAATACCCCC 17 64 1 ATTAGCGCTA 0.876259 -20 ATGGGGGTATTGTAGCGCTTAATGAGCGGG 18 104 0 TGTAGCGCTT 0.907566 -197 GCATTATTGGTTTAGGGCTT 21 29 1 TTTAGGGCTT 0.981151 -10 ********** Masking position 4 Map Score: 4.65761 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 535 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 AGTATCTCCTTTGTGTTGGTTTAAGTTGTC 6 10 1 TTTGTGTTGT 0.182803 -287 AGGGGGTTAAAAGGGGATATTTTTATATAAT 6 207 1 AAGGGGATTT 0.708209 -90 AAAATTCAGAAAGGGTGTTTTTAAGCAAGAT 9 34 1 AAGGGTGTTT 0.708209 -74 GATTCGTTCTTAGGGGGATTTAAGGGGTAAG 10 51 1 TAGGGGGATT 0.696987 -78 TGGTGCGTTAAAGGCGGTGGT 12 106 1 AAGGCGGTGT 0.885517 -11 TTCGCATACAATGGTGGTTGTGGCGAATGTG 13 159 1 ATGGTGGTGT 0.960795 -142 AGCTTTCAATTTGGTGGTGGTTAGAAAATTC 14 68 0 TTGGTGGTGT 0.939974 -155 CTCTCTTAAAAATGTGGTTGTGCGAAAAGAA 14 98 0 AATGTGGTGT 0.808118 -125 CAGGTATTCTTTGGGGGTCGTAAGAAGTTCA 16 36 0 TTGGGGGTGT 0.971907 -21 TGTCTTTTTTAAGGGAGTGTTTTTTTATAAC 17 24 1 AAGGGAGTTT 0.708209 -60 CTTTTTTTGCATGGGGGTATTGTAGCGCTTA 18 113 0 ATGGGGGTTT 0.975116 -188 TTACAATGAAATGGGGGTATTTTAAAAAAAT 18 230 0 ATGGGGGTTT 0.975116 -71 TTTTTCTTGATTTGTGGTTTTATTTTGCTCA 19 122 0 TTTGTGGTTT 0.692925 -179 ******** ** Masking position 11 Map Score: 8.23305 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 650 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 9 AAATTACCTTATTGAATTTGATTTGTTTATTCT 1 75 0 ATTGTTGATT 0.592444 -24 ATAAAAATCTATTTAATGAGAATTAGGTAAAAA 6 157 1 ATTTTGGAAT 0.975028 -140 TGATTCGCTGAGAATGTAGGCTTAA 9 3 1 ATTCTGGAAT 0.733876 -105 TCAAGCGGTAGTTTCTTGTGATTCGTTCTTAGG 10 32 1 GTTTTGGATT 0.86351 -97 CTTATCTAAAATTTGCTAAGAATACACTAAAAT 12 54 1 ATTTTAGAAT 0.789656 -63 CACAACCACCATTGTATGCGAATCCTTGCCTTT 13 148 0 ATTGTGGAAT 0.95528 -153 TAGCCTTATGATTTTTTGCAAATGCGCATAAGG 13 274 0 ATTTTGAAAT 0.786231 -27 ATCATGGTTAAGTTATTGGGATTATATCCAAAA 19 43 0 AGTTTGGATT 0.863508 -258 CTAAAATGAGATTTACTGGGATTATTTTTCTTG 19 144 0 ATTTTGGATT 0.967092 -157 TGCTGACATTATTTGGTGGGAATAAGAAAGATA 19 226 1 ATTTTGGAAT 0.977278 -75 **** ** **** Masking position 7 Map Score: 4.96221 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 72 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 10 AGTAAAATCCTTTTGTGATAGGG 1 4 1 AAAATCCTTT 0.93904 -95 TTAATAAAAGAAAAACCTTAAAAGGGAGCA 5 18 0 AAAAACCTTA 0.684386 -63 ATTTTATCATAAAAATCTATTTAATGAGAA 6 149 1 AAAAATCTAT 0.666631 -148 GGGGGCAAATCAAAATCTTTAGCGCTCAAG 13 45 0 CAAAATCTTT 0.87395 -256 GGTGGTTAGAAAATTCCTTTTTATGCTTTT 14 54 0 AAATTCCTTT 0.810732 -169 CAATTTCTTTACGCTAAAAA 14 213 0 CAATTTCTTT 0.659031 -10 TGAAGTTTTAGAAAACCTTTTCATAG 18 7 0 GAAAACCTTT 0.803655 -294 CTTCTAATAAAAAAATCTTTTTTTGCATGG 18 130 0 AAAAATCTTT 0.924297 -171 ATTTCATTGTAAAATTCTTTCATGCAAAAC 18 249 1 AAAATTCTTT 0.933818 -52 TGATTTTACCAAAATTGTTTG 19 2 0 AAAATTGTTT 0.647791 -299 ********** Masking position 3 Map Score: 2.104 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 750 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 11 TAAAATTCAGAAAGGGTGTTTTTAAGCAAG 9 33 1 AAAGGGTGTT 0.903953 -75 TAGATAAGATCAAGCGTGATTTTTTCTAAA 12 32 0 CAAGCGTGAT 0.975945 -85 GTTTTAATTTCAAGCGTGGTGCGTTAAAGG 12 90 1 CAAGCGTGGT 0.991044 -27 AGAAAGCACTCAAGCGTGTTTAGATATTTT 13 111 1 CAAGCGTGTT 0.986211 -190 GATTCGCATACAATGGTGGTTGTGGCGAAT 13 157 1 CAATGGTGGT 0.935727 -144 ********** Masking position 7 Map Score: 1.84888 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 53 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 ATTAGGTAAAAAAAGGGGTTGGCATCAATA 6 178 1 AAAAGGGGTT 0.899792 -119 GTTGGCATCAATAGGGGGTTAAAAGGGGAT 6 195 1 ATAGGGGGTT 0.933696 -102 ATAGGGGGTTAAAAGGGGATATTTTTATAT 6 205 1 AAAAGGGGAT 0.713962 -92 CATCAAGGGGTTTGACATTAGT 10 3 1 TCAAGGGGTT 0.964568 -126 TGATTCGTTCTTAGGGGGATTTAAGGGGTA 10 50 1 TTAGGGGGAT 0.883005 -79 TTAGGGGGATTTAAGGGGTAAGATAAAAAC 10 60 1 TTAAGGGGTA 0.838782 -69 ACAAAACTTTTCAGGGGGCGTTTGAACTTC 16 14 1 TCAGGGGGCG 0.857777 -43 GTGTCTTTTTTAAGGGAGTGTTTTTTTATA 17 23 1 TAAGGGAGTG 0.742081 -61 CCTATGTTTTTTAAGGAGCGTTATAATGAA 18 58 0 TTAAGGAGCG 0.741389 -243 AGCGAGAGCGTTAAGGAGTTTGACTCATTG 18 174 1 TTAAGGAGTT 0.914127 -127 TTATTAAACTTCAATGGGTTTTGCATGAAA 18 266 0 TCAATGGGTT 0.661395 -35 ATAAAATATAATAAGGAGTTGAGGAATGAG 19 96 1 ATAAGGAGTT 0.846652 -205 ********** Masking position 3 Map Score: 5.65958 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 798 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 13 TTGATAGAATAAACAAATCAAATTCAATAA 1 70 1 AAACAAATCA 0.884251 -29 CATAAAATTTGAACGAAGCATTATAGCAAA 4 15 0 GAACGAAGCA 0.968137 -33 ATCCCCCTAAGAACGAATCACAAGAAACTA 10 40 0 GAACGAATCA 0.968749 -89 CTAAAATTTAGAAAAAATCACGCTTGATCT 12 26 1 GAAAAAATCA 0.685774 -91 AGCATTTAAAAACCAAAGCGCCTTATGCGC 13 254 1 AACCAAAGCG 0.74048 -47 TTTTATTAGGGATCAAATCA 15 19 1 GATCAAATCA 0.828223 -10 TAATGAAAACGAACGAAGCGCAATTTTATG 18 35 0 GAACGAAGCG 0.945073 -266 ATGGAAGTTTAACCGAATCATTATAAAATA 19 74 1 AACCGAATCA 0.890756 -227 ********** Masking position 6 Map Score: 2.04071 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 75 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: -7.07457e-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 ********** No masking Map Score: -7.07457e-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