AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_hpyl_reg_100.orf -o00240_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: HP1472 30 type IIS restriction enzyme M protein (mod) Input sequences: #1 HP0005 121 orotidine 5'-phosphate decarboxylase (pyrF) #2 HP0104 154 2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB) #3 HP0194 214 triosephosphate isomerase (tpi) #4 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #5 HP0198 66 nucleoside diphosphate kinase (ndk) #6 HP0263 111 adenine specific DNA methyltransferase (hpaim) #7 HP0264 72 ATP-dependent protease binding subunit (clpB) #8 HP0265 53 cytochrome c biogenesis protein (ccdA) #9 HP0349 259 CTP synthetase (pyrG) #10 HP0364 205 ribonucleoside diphosphate reductase, beta subunit (nrdB) #11 HP0372 123 deoxycytidine triphosphate deaminase (dcd) #12 HP0497 228 sodium- and chloride-dependent transporter #13 HP0500 57 DNA polymerase III beta-subunit (dnaN) #14 HP0584 81 flagellar switch protein (fliN) #15 HP0585 228 endonuclease III (nth) #16 HP0680 171 ribonucleoside-diphosphate reductase 1 alpha subunit (nrdA) #17 HP0717 68 DNA polymerase III gamma and tau subunits (dnaX) #18 HP0718 207 conserved hypothetical integral membrane protein #19 HP0820 173 H. pylori predicted coding region HP0820 #20 HP0824 88 thioredoxin (trxA) #21 HP0866 40 transcription elongation factor GreA (greA) #22 HP0869 58 hydrogenase expression/formation protein (hypA) #23 HP0870 207 flagellar hook (flgE) #24 HP1010 300 polyphosphate kinase (ppk) #25 HP1011 36 dihydroorotate dehydrogenase (pyrD) #26 HP1084 66 aspartate transcarbamoylase (pyrB) #27 HP1180 300 pyrimidine nucleoside transport protein (nupC) #28 HP1198 223 DNA-directed RNA polymerase, beta subunit (rpoB) #29 HP1215 35 H. pylori predicted coding region HP1215 #30 HP1217 48 H. pylori predicted coding region HP1217 #31 HP1218 119 glycinamide ribonucleotide synthetase (purD) #32 HP1255 116 protein translocation protein, low temperature (secG) #33 HP1295 22 ribosomal protein S11 (rps11) #34 HP1297 78 ribosomal protein L36 (rpl36) #35 HP1300 42 preprotein translocase subunit (secY) #36 HP1318 34 ribosomal protein L4 (rpl4) #37 HP1319 36 ribosomal protein L3 (rpl3) #38 HP1320 164 ribosomal protein S10 (rps10) #39 HP1386 70 D-ribulose-5-phosphate 3 epimerase (rpe) #40 HP1460 147 DNA polymerase III alpha-subunit (dnaE) #41 HP1470 67 DNA polymerase I (polA) #42 HP1471 65 type IIS restriction enzyme R protein (BCGIB) #43 HP1483 26 gerC2 protein (gerC2) #44 HP1490 103 hemolysin Motif number 1 TTAGCTATGATAAGCGTTTTAAAAACAAACGAA 1 43 0 TAGTTTTAAA 0.936441 -79 GAAAGCCCTTTAAAGTGTAAAATA 1 108 0 AAGCTTTAAA 0.90704 -14 GTTTAAAATTTACATTTTTTAAACGCTATTAGA 3 149 1 TAATTTTAAA 0.778534 -66 AAAAATATTTTAAGGGTAATATTT 5 2 1 AAATTTTAAG 0.840001 -65 TGATTATACAAAAATTTTTTAAAATATTACCCT 5 23 0 AAATTTTAAA 0.893277 -44 CAACAATTCACAAGGAGTTTAAA 5 54 1 CAGGTTTAAA 0.656139 -13 AAAAGCCTTTTTAAATCTTCTAAT 6 98 0 AAGTTTTTAA 0.924413 -14 TTTAACCCTCAAAGGTTTTTAAAACGC 7 5 0 AAGTTTTAAA 0.972284 -68 TGTAAAATAGTAAAGATTTTAAAACTCAAAAAG 7 42 1 TAATTTTAAA 0.778534 -31 ACTACTAAAAAAAGGGTTTTAAATA 9 3 0 AAGTTTTAAA 0.972284 -257 ATTATACGCCAACGAATTTTAAAATTGCTCTTA 9 51 1 AAGTTTTAAA 0.972284 -209 TTCATTGTCTTAAAACTTTTAAGAGCAATTTTA 9 70 0 TAATTTTAAG 0.687985 -190 GTTTTAAGACAATGAAGTTTAAACACATAAAAG 9 87 1 AAGGTTTAAA 0.89108 -173 AAAAAGGGTTAAAAAGCTTTAAAAGAGGGCAAA 9 193 0 AAACTTTAAA 0.699528 -67 CTGAAAAATTGAAGTTTTTTAAAATTTGGAGTT 10 93 1 GAGTTTTAAA 0.810483 -113 TCTGGCTTTTAGGGGGTTTTAAATTCTTTTAAG 10 129 1 AGGTTTTAAA 0.92995 -77 TTACTAGCCATAAGCGTTTTTAGCAAAAAATTA 11 60 1 TAGTTTTTAG 0.763132 -64 CATAATTATTAACAAACTTTAAAGGCTTT 11 105 1 AAACTTTAAA 0.699528 -19 CTGTATTTTTTAGGTATTTTTAAAGTGGGTTTT 12 94 1 TAGTTTTTAA 0.837039 -135 TCTTAAATCTTAAGATCTTTAAAGATTTTAAAA 12 128 1 TAGCTTTAAA 0.803845 -101 CTATTGCTGTATTAGTTTTTAAAATCTTTAAAG 12 144 0 ATATTTTAAA 0.505358 -85 AAAAGCGTTCTTTTAYGCTATAATTA 13 4 1 AGGCTTTTAY 0.562806 -54 AAAGAGAGAAAGCGTTTTTTAAGGGCTTCATCG 15 71 0 AGGTTTTAAG 0.892784 -158 TATTAATGAGAATAAGTTTTAAAGTTTTTTAAT 16 50 0 AAATTTTAAA 0.893277 -122 AATTAAATCGTTTGTTTTTTAAATTTGGAATTG 16 131 0 TTGTTTTAAA 0.64265 -41 AATACTCCTAAATGAGTTTTAAGGATTACAATC 17 43 1 AAGTTTTAAG 0.956528 -26 TAGCGCTCTTAGTGGCGTTTAAGAATAAGTTAA 18 18 0 AGGGTTTAAG 0.660087 -190 CGCTAAAAAATGGGGTTTTTAAATTTTCGCGCA 18 46 1 TGGTTTTAAA 0.847924 -162 TTTATTTATAAAGGTCGTTTTAAACCCTAAAAT 18 105 1 AAGGTTTTAA 0.740403 -103 TCATTCAAAAATGGTATTTTAAAATTTTAGGGT 18 128 0 ATGTTTTAAA 0.810675 -80 AGCACCACGCCAGAATTTTTAAATCAGCCTTAA 19 13 0 CAATTTTAAA 0.661275 -161 AGAGCTGTTTGAAGTTTTTTTAGCGGGTTTTTC 19 73 1 GAGTTTTTAG 0.483248 -101 ACCACCCCATAACGCTTTTTAAAGGTTATCGCT 23 34 0 AAGTTTTAAA 0.972284 -174 AATGATTGGTTGCGGATTTTAAAGTTTTGTTAA 23 113 0 TGGTTTTAAA 0.847924 -95 GTTGTTCCTAAATAGCTTTTTAGAATGATTGGT 23 136 0 AAATTTTTAG 0.64668 -72 AAACGCTAAAAAAATTTTAAGCGATCTTTTA 24 9 1 AAATTTTAAG 0.840001 -292 GTTTTACAAAAAAGAGTTTTTAAACAACAACTA 24 73 1 AAGTTTTTAA 0.924413 -228 CTACTCCGACCATGACTTTTTAAAAAAGCTTCA 24 206 1 CAGTTTTTAA 0.740428 -95 ATGTAATTTTAATGGATTTTTAAGAAAGGTTTT 27 68 1 AAGTTTTTAA 0.924413 -233 ACGGATATTAAATGAAGTTTAAATCAAAATCAT 27 205 0 AAGGTTTAAA 0.89108 -96 AGCATTGCAAAAGGATCTTTAAACTTTAGAACC 28 148 0 AAGCTTTAAA 0.90704 -76 TATGTTAATATAAAAGTTTTTAGTAGTGCCTAA 34 35 1 TAATTTTTAG 0.434617 -44 TTGCTATTTTTAGGGCTTTTTAGAGATTTTTAC 38 37 0 TAGTTTTTAG 0.763132 -128 AATCTAATAAAGAGTTTTTTAAAGAGCGATAGG 40 91 1 AGGTTTTAAA 0.92995 -57 AAGGGGTTTTAAGCGCGCTAGCT 41 1 1 AAGTTTTAAG 0.956528 -67 TCTTCAATCAAGCGAATTTTAAGTTTATTGTAA 41 38 0 AGGTTTTAAG 0.892784 -30 TTTTTGAAGGCTTGATTTTTAAAGTTAGGCTTA 44 13 1 CTGTTTTAAA 0.49968 -91 ** * ******* Masking position 8 Map Score: 58.7987 Number of sites scoring better than the average of aligned sites = 2023 Number in coding regions = 1703 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 2 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 3 23 0 TTTTTAATTT 0.784789 -192 TTCTACTACATTTGAAATAATTTTTCTTATAAAC 3 74 1 TTTGTATTTT 0.700269 -141 TTGAATTGAATTTTTTCTCAATTTAGGTTTTGTT 3 105 0 TTTTTAATTT 0.784789 -110 AAATATTACCCTTAAAATATTTTT 5 1 0 CTTATTTTTT 0.702532 -66 ATCTTTACTATTTTACACTATTTTAACCCTCAAA 7 25 0 TTTTCATTTT 0.691553 -48 AAAATAACCATTTCTTGTCTTTTTTAGGATAACA 8 16 0 TTTCTTTTTT 0.648109 -38 CTGAAATTGTTTTTTTTTTTTTTTGAAATCGCTT 9 154 1 TTTTTTTTTT 0.948234 -106 TTTTAAAGCTTTTTAACCCTTTTTAGACTACAAT 9 202 1 TTTTCTTTTT 0.764858 -58 AAACTTCAATTTTTCAGTATTTTTAAAGGATTAA 10 76 0 TTTTTTTTTT 0.948234 -130 TTTAGGGGGTTTTAAATTCTTTTAAGGTATTCTA 10 136 1 TTTATTTTTA 0.524822 -70 GCTCTGTATTTTTTAGGTATTTTTAAAGTGGGTT 12 91 1 TTTTTTTTTT 0.948234 -138 AAATCTTAATTTTACTATAAATTTTATAACAAAT 14 18 0 TTTATAATTT 0.660671 -64 GTTTTAAAGTTTTTTAATTTTTTTATACCCCCTC 16 34 0 TTTTTTTTTT 0.948234 -138 AATTTTTCCTTAAATTTGAATTAAATC 16 155 0 TTTTTAATTT 0.784789 -17 AAGGGGCTAGTTTTAAGTCATTTTGCATTACAAT 17 12 1 TTTTTATTTT 0.92661 -57 TGTATCATCATTTAATTTTTATTTATAAAGGTCG 18 88 1 TTTATTATTT 0.73854 -120 TGTTGGTAGTTTTTAGCTTATTTTGAGTGAAAGG 18 174 1 TTTTTATTTT 0.92661 -34 ATTAGAGCTGTTTGAAGTTTTTTTAGCGGGTTTT 19 70 1 TTTGTTTTTT 0.772184 -104 TAGGAACAACTTTTGCTTTATTTTGCATAGATTG 23 159 1 TTTTTATTTT 0.92661 -49 TAAAAGATCGCTTAAAATTTTTTTAGCGTTT 24 8 0 CTTATTTTTT 0.702532 -293 ATAATAAAAGTTTAATGTAATTTTAATGGATTTT 27 54 1 TTTATATTTT 0.870822 -247 TTAATATCCGTTTAATCTTTTTTTTAGCAAAACT 27 227 1 TTTATTTTTT 0.907236 -74 TGCAGGTGGGTTTTTGGTATTTTTATCATGGATG 28 115 1 TTTTTTTTTT 0.948234 -109 TGATCAAAAATTTTGAGTTATTTAATGCATTAAT 28 188 0 TTTTTATTTA 0.587774 -36 TTAGCAACGACTTTGGCTATTTTTCC 29 20 1 CTTTTTTTTT 0.815611 -16 TACACTAAAATTTAGTTTTAATTTCAAGCGTGGT 32 28 0 TTTATAATTT 0.660671 -89 TCAAGCGTGATTTTTTCTAAATTTTAGGCATTTA 32 85 1 TTTTTAATTT 0.784789 -32 TTTAGAGATTTTTACTTCCTTTTTATAAGGAAAT 38 18 0 TTTACTTTTT 0.634597 -147 TAGTCAATAACTTTTGCTATTTTTAGGGCTTTTT 38 49 0 CTTTTTTTTT 0.815611 -116 ATTTTATTGTTTTATTCTGTTTTTTAGTAACGGA 38 115 1 TTTATTTTTT 0.907236 -50 AATAAGAAAGTTTTTATTATTTTTAATGCTATTT 40 23 0 TTTTTTTTTT 0.948234 -125 AATTCTGAGATTTTATATATTTTATATTTATCGT 44 60 1 TTTTTTTTTA 0.67412 -44 **** * ***** Masking position 3 Map Score: 39.5174 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 712 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 3 CCCTTAAATCTCATTTTGATTAAAATTCGTTTGTTT 1 18 1 TTTTTAAAAT 0.964355 -104 ATTCTTGCATTTCTTTTTGTTATAATGGCGTTATTT 1 77 1 TTTTTATAAT 0.711749 -45 AAACAAAACCTAAATTGAGAAAAAATTCAATTCAAA 3 104 1 TATTAAAAAT 0.411075 -111 TTGTGAATTGTTGATTATACAAAAATTTTTTAAAAT 5 31 0 TATTCAAAAT 0.673786 -36 GAGATGGCCTTTATTTAGCCAAAAACCATTTTGATC 6 31 1 TTTTCAAAAC 0.767085 -81 GTGTTTAAACTTCATTGTCTTAAAACTTTTAAGAGC 9 77 0 TATTTAAAAC 0.709643 -183 TAAAAGCTTTTCATTTTAATCAAACCTAGCTAATAA 9 114 1 TTTTTAAACC 0.829544 -146 AAATTGTTTTTTTTTTTTTTTGAAATCGCTTTAATT 9 157 1 TTTTTGAAAT 0.666278 -103 TTTGTTCCTTAATTTCCTTAAAACTATCTCAATGA 10 181 0 TTTTTAAACT 0.927651 -25 ATCTATTCCTTATATTATTTTAAAATATGCCACAAA 11 15 1 TATTTAAAAT 0.865576 -109 TATAACAATAATTTTTTGCTAAAAACGCTTATGGCT 11 65 0 ATTTTAAAAC 0.477272 -59 AAAAGCGTTCTTTTAYGCTATAATTAAGACCAAA 13 9 1 TTTTCATAAT 0.442004 -49 TGGCTTTATTTGTTATAAAATTTATAGTAAA 14 6 1 TTTTAAAAAT 0.74572 -76 AAAAAAGCCACGCTTTCGGTTAAAATCAACCGCATT 15 150 1 CTTTTAAAAT 0.68362 -79 CTTGCTTAATCCTTTCACTCAAAATAAGCTAAAAA 18 183 0 TTTTTAAAAT 0.964355 -25 AAATCGCATTTACTTTCTGTAAAAAT 20 1 0 TTTTTAAAAT 0.964354 -88 TAAAACTTCATTTTTTGAATAAAACTTCATTTAACC 24 43 0 TTTTTAAACT 0.917268 -258 GTTTAAAAACTCTTTTTTGTAAAACTTCATTTTTTG 24 62 0 TTTTTAAACT 0.927599 -239 ATATAGATTTTATTTTAGCTAAAAATGGCATGGGTT 26 21 0 TTTTTAAAAT 0.963854 -46 ATATTAAATGAAGTTTAAATCAAAATCATGGTGTCA 27 198 0 ATTTTAAAAT 0.719945 -103 CGTTTAATCTTTTTTTTAGCAAAACTAAACTACAAT 27 235 1 TTTTCAAACT 0.801344 -66 ACAAACTCTTTGGTTTGTCTTAAACTTTAACCT 30 8 0 TTTTTAAACT 0.92765 -41 ATTTAAGGGTTATTTCAATGAAAATATGTTAATAT 34 10 1 TTTTTAAAAT 0.964355 -69 AACCCTTTTATGATTTGATTAAAGATGCTAATATTT 39 14 1 TTTTTAAGAT 0.666236 -57 AAGATGCTAATATTTTACTTGAAAACATTGAAAATA 39 35 1 TTTTTAAAAC 0.911257 -36 TATTTAGTGGTGAATTATTTTAAAATGGTGGTTATA 40 56 0 TATTTAAAAT 0.865577 -92 TTAGGCTTAATCTTTTATGTTAAAATTCTGAGATTT 44 37 1 TTTTTAAAAT 0.964349 -67 * *** * ***** Masking position 6 Map Score: 28.2673 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 261 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 TCTTTAACCCTTAAATCTCATTTTG 1 6 1 AACCCTTAAA 0.930572 -116 GAAAGCCCTTTAAAGTGTAAAAT 1 109 0 AGCCCTTTAA 0.589472 -13 TATATCTAATAGCGTTTAAAAAATGTAAAT 3 156 0 AGCGTTTAAA 0.735126 -59 TTTAAAATATTACCCTTAAAATATTTTT 5 9 0 TACCCTTAAA 0.359301 -58 TTTTGATCAAAGCTCTAAAATCAAGAGCAT 6 59 1 AGCTCTAAAA 0.870855 -53 ACACTATTTTAACCCTCAAAGGTTTTTAAA 7 15 0 AACCCTCAAA 0.898862 -58 AGGGTTAAAAAGCTTTAAAAGAGGGCAAAA 9 192 0 AGCTTTAAAA 0.726118 -68 AAAGGATTAAAAAGCTAAAATACTGCTTCT 10 56 0 AAAGCTAAAA 0.516329 -150 AAAGCCTTTAAAGTTTGTTAAT 11 112 0 AGCCTTTAAA 0.881058 -12 CACTTTAAAAATACCTAAAAAATACAGAGC 12 91 0 ATACCTAAAA 0.44509 -138 CGCTCAATGAAGCCATTAAAGACAAAGTTT 15 16 1 AGCCATTAAA 0.440804 -213 ACTGCGATGAAGCCCTTAAAAAACGCTTTC 15 67 1 AGCCCTTAAA 0.949598 -162 AAAATTAAAAAACTTTAAAACTTATTCTCA 16 47 1 AACTTTAAAA 0.653513 -125 ATTGATTGTAATCCTTAAAACTCATTTAGG 17 49 0 ATCCTTAAAA 0.72487 -20 CGCCACTAAGAGCGCTAAAAAATGGGGTTT 18 34 1 AGCGCTAAAA 0.926126 -174 GGTCGTTTTAAACCCTAAAATTTTAAAATA 18 117 1 AACCCTAAAA 0.959684 -91 TTTTTAAATCAGCCTTAAAA 19 1 0 AGCCTTAAAA 0.929355 -173 CCCGCTAAAAAAACTTCAAACAGCTCTAAT 19 70 0 AAACTTCAAA 0.294904 -104 TATTGCTACAAGCGCTAAAAAGCATGTTAA 19 145 1 AGCGCTAAAA 0.926126 -29 CTTGAGCGATAACCTTTAAAAAGCGTTATG 23 30 1 AACCTTTAAA 0.840504 -178 TGATTAACAAAACTTTAAAATCCGCAACCA 23 110 1 AACTTTAAAA 0.653513 -98 AAACGCTAAAAAAATTTTAAG 24 2 1 AACGCTAAAA 0.89918 -299 ACCCTAAAAGATCGCTTAAAATTTTTTTAG 24 16 0 ATCGCTTAAA 0.585707 -285 AACTTCATTTAACCCTAAAAGATCGCTTAA 24 27 0 AACCCTAAAA 0.959684 -274 TTATGAGACCAGCGCTCTAAACCAGCTGAG 27 138 0 AGCGCTCTAA 0.262933 -163 TCATTGAAATAACCCTTAAAT 34 2 0 AACCCTTAAA 0.930572 -77 GGAAGTAAAAATCTCTAAAAAGCCCTAAAA 38 33 1 ATCTCTAAAA 0.574558 -132 ATCTCTAAAAAGCCCTAAAAATAGCAAAAG 38 43 1 AGCCCTAAAA 0.970981 -122 GTGTTACAATAAACTTAAAATTCGCTTGAT 41 35 1 AAACTTAAAA 0.528348 -33 TTAAAAATCAAGCCTTCAAAAACC 44 5 0 AGCCTTCAAA 0.830844 -99 GATTAAGCCTAACTTTAAAAATCAAGCCTT 44 19 0 AACTTTAAAA 0.653513 -85 AACTTTAAACCTAAAACCTAACGATA 44 88 0 AAACCTAAAA 0.740206 -16 ********** Masking position 6 Map Score: 37.1684 Number of sites scoring better than the average of aligned sites = 1759 Number in coding regions = 1544 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 5 GGGTAAGGGGATAGGGGGGTAAAAATCATTCC 2 20 0 ATAGGGGGTA 0.548482 -135 GCTTATGGGCAAAATGGGTAAAATAATGGGTA 2 47 0 AAAATGGTAA 0.450366 -108 AATTCAATTCAAAGGGGCTATTGTTTAAAATT 3 127 1 AAAGGGGTAT 0.966014 -88 ATTAGATATAATAAGGGATAGTTACCACCTAT 3 176 1 ATAAGGGTAT 0.868573 -39 TTCGTATTCAAAATGGGCTTATTATAGCTTAT 4 19 0 AAATGGGTTT 0.797773 -46 AGCTTTGATCAAAATGGTTTTTGGCTAAATAA 6 41 0 AAAATGGTTT 0.685618 -71 AACTACTAAAAAAAGGGTTTTAAATA 9 5 0 AAAAGGGTTA 0.853999 -255 TTGTAGTCTAAAAAGGGTTAAAAAGCTTTAAA 9 203 0 AAAAGGGTAA 0.842075 -57 TTTCTGGCTTTTAGGGGGTTTTAAATTCTTTT 10 127 1 TTAGGGGTTT 0.519362 -79 AGGTATTTTTAAAGTGGGTTTTTTCTTAAATC 12 105 1 AAAGTGGTTT 0.827335 -124 ACCAAAAATTCAAGGGGATTATTTTAACT 13 39 1 CAAGGGGTTT 0.758171 -19 AAAGGGGCTAGTTTTAAGTCAT 17 1 1 AAAGGGGTAT 0.966014 -68 GAGCGCTAAAAAATGGGGTTTTTAAATTTTCG 18 43 1 AAATGGGTTT 0.79778 -165 ATACAATATAATAGGGGCTAATTTAAAGATTA 22 28 1 ATAGGGGTAT 0.935566 -31 TCATAAGAAAATAGGGGGTTTTGCAACACCAC 23 62 0 ATAGGGGTTT 0.940926 -146 TCCGCAATCAAAAAGGGAGATTGTAGCGCGAG 24 112 0 AAAAGGGGAT 0.705358 -189 ATTATAACTAAAAGGGGGTTTT 26 55 1 AAAGGGGTTT 0.968925 -12 CGTGTGGCCTAAAGTGGTTAGTATTGCAGGTG 28 91 1 AAAGTGGTAT 0.813708 -133 AGATAATAAAATAAGGGTTAGAT 37 24 1 ATAAGGGTAA 0.731458 -13 ATCAAATCATAAAAGGGTTTTT 39 1 0 AAAAGGGTTT 0.934165 -70 TTAAATCCAAATAGGGGTTAGACA 40 134 1 ATAGGGGTAA 0.856822 -14 ******* ** * Masking position 3 Map Score: 24.7573 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 716 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 6 TTTGATTAAAATTCGTTTGTTTTTAAAACGCT 1 32 1 ATTGTTGTTT 0.914983 -90 TAAATTTTCTATGCTCTTGATTTTAGAGCTTT 6 67 0 ATGTTTGATT 0.927301 -45 AGCCACTTGAATGCGGTTGATTTTAACCGAAA 15 163 0 ATGGTTGATT 0.953423 -66 TTTTTGAATGATTGGTTTGTATGGTGTTGGTA 18 150 1 ATTGTTGTAT 0.668829 -58 TCCTAAATATATGATTTTGATTAACGAGAATT 20 60 0 ATGTTTGATT 0.927301 -29 ATTAGCCCCTATTATATTGTATTAGAGTAATC 22 18 0 ATTTTTGTAT 0.557222 -41 AATTTGGTCGATCTTTTTGATTAACAAAACTT 23 93 1 ATCTTTGATT 0.86796 -115 ATGTTTAAAAATCAGTTTGTTTGGTGTGATTA 24 259 0 ATCGTTGTTT 0.913413 -42 TCTTGACACCATGATTTTGATTTAAACTTCAT 27 195 1 ATGTTTGATT 0.927301 -106 ATTTTGCTCCATGATTTTGTTTGTGAGCGTGT 28 64 1 ATGTTTGTTT 0.927301 -160 CTTTCCTGCAATGTGGTTGTTTTTAAACCCAG 31 96 0 ATGGTTGTTT 0.953423 -24 CCCCTGTTGTATCAGCTTGATTTAAGAGGAAT 35 13 1 ATCGTTGATT 0.913413 -30 TTCAGTTTTTATTTTATTGTTTTATTCTGTTT 38 105 1 ATTTTTGTTT 0.870238 -60 TAAACTTAAAATTCGCTTGATTGAAGAGGGTT 41 44 1 ATTGTTGATT 0.914983 -24 *** * ****** Masking position 1 Map Score: 14.2525 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 152 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 GATAAGCGTTTTAAAAACAAACGAATTTTA 1 38 0 TTAAAAACAA 0.906214 -84 TCCTAAAAACTCAAAATTAACCTAAAATCG 3 20 1 TCAAAATTAA 0.706626 -195 ATAATTTTTCTTATAAACAAAACCTAAATT 3 90 1 TTATAAACAA 0.690894 -125 CAATCCTTTTTCAAAAATAACCATTTCTTG 8 33 0 TCAAAAATAA 0.797401 -21 TTTTAATCCTTTAAAAATACTGAAAAATTG 10 74 1 TTAAAAATAC 0.797401 -132 AAAACCCACTTTAAAAATACCTAAAAAATA 12 97 0 TTAAAAATAC 0.797401 -132 TTGTCAATGATTAAAATTAAAGAGCGATGT 12 191 0 TTAAAATTAA 0.866747 -38 AATTAAGATTTTATAATCAAAGTCAAATCA 14 41 1 TTATAATCAA 0.577668 -41 ACGCTTTCGGTTAAAATCAACCGCATTCAA 15 159 1 TTAAAATCAA 0.855337 -70 TAAGAATAAGTTAAGATTAAC 18 2 0 TTAAGATTAA 0.605745 -206 TTAGTGGCGTTTAAGAATAAGTTAAGATTA 18 13 0 TTAAGAATAA 0.71597 -195 AAAACGACCTTTATAAATAAAAATTAAATG 18 96 0 TTATAAATAA 0.713897 -112 TAAAAATCCATTAAAATTACATTAAACTTT 27 60 0 TTAAAATTAC 0.706626 -241 TCAAAAACAAACAAGACAAA 30 39 0 TCAAAAACAA 0.778505 -10 TCATCTGGGTTTAAAAACAACCACATTGCA 31 92 1 TTAAAAACAA 0.906214 -28 ACGCTTGAAATTAAAACTAAATTTTAGTGT 32 31 1 TTAAAACTAA 0.670798 -86 TAAAATAGCATTAAAAATAATAAAAACTTT 40 21 1 TTAAAAATAA 0.914903 -127 ********** Masking position 6 Map Score: 10.0714 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 299 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 8 GATTAAAATTCGTTTGTTTTTAAAACGCTTA 1 35 1 CGTTGTTTTT 0.610515 -87 TTAGGTTAATTTTGAGTTTTTAGGAGCAGTT 3 14 0 TTTAGTTTTT 0.744991 -201 GCCCCTTTGAATTGAATTTTTTCTCAATTTA 3 114 0 ATTAATTTTT 0.559235 -101 ATCAATCCTTTTTGAGTTTTAAAATCTTTAC 7 51 0 TTTAGTTTTA 0.333677 -22 ATAACCATTTCTTGTCTTTTTTAGGATAACA 8 16 0 CTTTCTTTTT 0.820086 -38 TTTGAAATCGCTTTAATTTTTGCCCTCTTTT 9 175 1 CTTAATTTTT 0.89873 -85 TATTGCGTTCCTTTAATTTTTGCTTCTTAAA 9 235 0 CTTAATTTTT 0.89873 -25 TTTTAAAAAACTTCAATTTTTCAGTATTTTT 10 86 0 CTTAATTTTT 0.89873 -120 GGACATCGCTCTTTAATTTTAATCATTGACA 12 189 1 CTTAATTTTA 0.603368 -40 AAATAATCCCCTTGAATTTTTGGTCTTAATT 13 32 0 CTTAATTTTT 0.89873 -26 TTTTAAAGTTTTTTAATTTTTTTATACCCCC 16 36 0 TTTAATTTTT 0.670556 -136 CCAACTTGAACTTTTCTTTTTCTTAAGTTTT 16 91 1 CTTTCTTTTT 0.820086 -81 TTTTCTTTTTCTTAAGTTTTTTATTGATACA 16 102 1 CTTAGTTTTT 0.927208 -70 TGAATTAAATCGTTTGTTTTTTAAATTTGGA 16 135 0 CGTTGTTTTT 0.610515 -37 GTGTATCATCATTTAATTTTTATTTATAAAG 18 87 1 ATTAATTTTT 0.559235 -121 TTTTGTAAAACTTCATTTTTTGAATAAAACT 24 53 0 CTTATTTTTT 0.555306 -248 TTAAATCCTTATCTTTTATGATTTGAAC 25 19 0 CTTTCTTTTA 0.438624 -18 TAATCTCATTCTTTTATTTTTTTGTCAAGGT 27 105 1 CTTTATTTTT 0.861257 -196 CGCAAAGGCCTTTCTGTTTTTAAGTC 28 6 0 TTTTGTTTTT 0.671427 -218 TTGAGTAGTATTTCAGTTTTTATTTTATTGT 38 94 1 TTTAGTTTTT 0.744991 -71 TTATTGTTTTATTCTGTTTTTTAGTAACGGA 38 118 1 ATTTGTTTTT 0.560207 -47 GACTTTTCTTTTTTCATGGCTTG 43 14 0 CTTTCTTTTT 0.820086 -13 *** ******* Masking position 7 Map Score: 20.1745 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 358 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 CGAATGATTATTTTAATAAGGACAATCA 4 47 1 TTTTAAAGGA 0.962423 -18 AATGGTTATTTTTGAAAAAGGATTGA 8 38 1 TTTGAAAGGA 0.898749 -16 ATTTTTCAGTATTTTTAAAGGATTAAAAAGCT 10 70 0 ATTTTAAGGA 0.683035 -136 AAAGCGTGGCTTTTTTCATGGAATAATGCAAA 15 134 0 TTTTTATGGA 0.868673 -95 AATATATGATTTTGATTAACGAGAATTATATT 20 55 0 TTTGAAACGA 0.679002 -34 CCTAAATAGCTTTTTAGAATGATTGGTTGCGG 23 131 0 TTTTTAATGA 0.619109 -77 ATGGCATGGGTTTTAGCAAGGA 26 1 0 TTTTAAAGGA 0.962423 -66 TTTTTGGTATTTTTATCATGGATGGTTCTAAA 28 125 1 TTTTAATGGA 0.901048 -99 AGGCGGGTTTTAGCAACGACTTTGGCTAT 29 8 1 TTTTAAACGA 0.859223 -28 AGTGCCTAATTTTTTCAAAGGAGAAAAATC 34 59 1 TTTTTAAGGA 0.948988 -20 TTTTACTTCCTTTTTATAAGGAAATATAAAAA 38 11 0 TTTTTAAGGA 0.948988 -154 TGGTGAATTATTTTAAAATGGTGGTTATAATA 40 53 0 TTTTAATGGT 0.513313 -95 ***** ***** Masking position 8 Map Score: 6.01605 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 139 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 ATTTTGAGTTTTTAGGAGCAGTTTTT 3 4 0 TTTAGGAGCT 0.970894 -211 AAACCCTTTTTTTAGTAGTTCATTCAAAACGGA 9 17 1 TTTAGTAGTT 0.934097 -243 TCTTAAAACTTTTAAGAGCAATTTTAAAATTCG 9 63 0 TTTAAGAGCT 0.687217 -197 TTTTCTGGCTTTTAGGGGGTTTTAAATTCTTTT 10 126 1 TTTAGGGGGT 0.749565 -80 TTAAAACTCATTTAGGAGTATTGTAATGCAAAA 17 32 0 TTTAGGAGTG 0.849075 -37 AAATCATATATTTAGGAGTAACTA 20 75 1 TTTAGGAGTT 0.972729 -14 TAAAAAGCTATTTAGGAACAACTTTTGCTTTAT 23 147 1 TTTAGGAACT 0.808448 -61 TATAAAAGTTTTTAGTAGTGCCTAATTTTTTCA 34 43 1 TTTAGTAGTT 0.934097 -36 ATGGCGCATTTTGAGTAGTATTTCAGTTTTTAT 38 84 1 TTGAGTAGTT 0.690935 -81 TATTCTGTTTTTTAGTAACGGATAAAACGAGTT 38 127 1 TTTAGTAACT 0.626466 -38 AACGAGTTCTTTTAGGAGAGTTT 38 152 1 TTTAGGAGAT 0.86472 -13 TTAATGCTATTTTAGGAGTTCATC 40 2 0 TTTAGGAGTT 0.972729 -146 TATTAGATTATTTAGTGGTGAATTATTTTAAAA 40 67 0 TTTAGTGGTT 0.81745 -81 ********* * Masking position 4 Map Score: 5.81369 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 151 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 GTATAATCTAAGGGCGTTGCTCTGTATTTTT 12 73 1 AGGGGTTGCT 0.888699 -156 ATGTCATTAAATGGAGGGGGTATAAAAAAAT 16 21 1 ATGGGGGGGT 0.978997 -151 ATTGGTTTGTATGGTGTTGGTAGTTTTTAGC 18 160 1 ATGGGTTGGT 0.948349 -48 TTTTCATTGAATGGAGGGGCTTTATAACCGC 19 101 1 ATGGGGGGCT 0.953876 -73 GCGCGCACCCTTGGGGTGGGTGAGGTCGTGG 24 163 1 TTGGGTGGGT 0.858234 -138 GGGGTGGGTGAGGTCGTGGGTTTGAATCCCG 24 175 1 AGGTGTGGGT 0.922474 -126 TTAGCTAAAAATGGCATGGGTTTTAGCAAGG 26 12 0 ATGGATGGGT 0.789867 -55 CATAAGCCGGAGGTCGGGGGTTCAAGTCCCC 27 163 1 AGGTGGGGGT 0.928013 -138 AAAATAGCCAAAGTCGTTGCTAAAACCCGCC 29 12 0 AAGTGTTGCT 0.499978 -24 TGGTGCGTTAAAGGCGGTGGT 32 1 0 AAGGGGTGGT 0.896413 -116 **** ****** Masking position 11 Map Score: 3.4431 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 189 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 CGCCAACGAATTTTAAAATTGCTCTTAAAA 9 57 1 TTTTAAAATT 0.631823 -203 TTAAAATTGCTCTTAAAAGTTTTAAGACAA 9 69 1 TCTTAAAAGT 0.595275 -191 AATTGAAGTTTTTTAAAATTTGGAGTTTTT 10 99 1 TTTTAAAATT 0.631823 -107 AATGAAATTTTCTTAAAATTATACAATATG 12 30 1 TCTTAAAATT 0.938975 -199 TCTTTAAAGATCTTAAGATTTAAGAAAAAA 12 123 0 TCTTAAGATT 0.882727 -106 AGGACATCGCTCTTTAATTTTAATCATTGA 12 188 1 TCTTTAATTT 0.366308 -41 TTCTACGATTTCATAAACTTTGTCTTTAAT 15 30 0 TCATAAACTT 0.39175 -199 CTTTTCTTTTTCTTAAGTTTTTTATTGATA 16 101 1 TCTTAAGTTT 0.531771 -71 AATTTTTCCTTAAATTTGAATTAAAT 16 156 0 TCCTTAAATT 0.602079 -16 AAAAATGGTATTTTAAAATTTTAGGGTTTA 18 125 0 TTTTAAAATT 0.631823 -83 TCATTAACATTCTTAAGCTAATATAATTCT 20 36 1 TCTTAAGCTA 0.32135 -53 TTAATCTCCTAAGCTTATTCAGTAGA 21 25 0 TCCTAAGCTT 0.621814 -16 TAAACCTTAATCTTTAAATTAGCCCCTATT 22 37 0 TCTTTAAATT 0.792989 -22 CGAGTTAGATTCTTAAGCTTGAGCGATAAC 23 13 1 TCTTAAGCTT 0.806323 -195 AGATTGAATTTCTTTAAATTAAAGGATAAC 23 187 1 TCTTTAAATT 0.792989 -21 CTAAAAGATCGCTTAAAATTTTTTTAGCGT 24 13 0 GCTTAAAATT 0.595297 -288 CAATCCTACTTCCTCAAATTGATGACAAAA 27 24 0 TCCTCAAATT 0.405331 -277 CAAAAACCTTTCTTAAAAATCCATTAAAAT 27 73 0 TCTTAAAAAT 0.498106 -228 CTTTGGTTTGTCTTAAACTTTAACCT 30 7 0 TCTTAAACTT 0.894852 -42 GATGAACTCCTAAAATAGCATTAAAAA 40 8 1 TCCTAAAATA 0.40869 -140 GTTACAATAAACTTAAAATTCGCTTGATTG 41 37 1 ACTTAAAATT 0.498106 -31 TAATCTTTTATGTTAAAATTCTGAGATTTT 44 44 1 TGTTAAAATT 0.50165 -60 ********** Masking position 4 Map Score: 5.45254 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 343 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 13 AAACACTGCCTTAATTCTACTACATTTGAAAT 3 60 1 TTAATTCATA 0.78009 -155 AGGGCAAAAATTAAAGCGATTTCAAAAAAAAA 9 169 0 TTAAAGCATT 0.857682 -91 TCATGGGATCTTAAAGCCACTTGAATGCGGTT 15 177 0 TTAAAGCATT 0.857682 -52 CCCCCTCCATTTAATGACATTTGGGTTAAA 16 9 0 TTAATGAATT 0.807648 -163 ATTTGTTCTATTAATGAGAATAAGTTTTAAAG 16 59 0 TTAATGAATA 0.712282 -113 AACAAACGATTTAATTCAAATTTAAGGAAAAA 16 148 1 TTAATTCATT 0.857478 -24 TTACAGAAAGTAAATGCGATTTCATTAACATT 20 15 1 TAAATGCATT 0.75527 -74 TAATAAAAGTTTAATGTAATTTTAATGGATTT 27 55 1 TTAATGTATT 0.704241 -246 ATTTAATGCATTAATTCAAGTAAGCATTGCAA 28 171 0 TTAATTCATA 0.78009 -53 TTTATTATTTTTAATGCTATTTTAGGAGTTCA 40 13 0 TTAATGCATT 0.960456 -135 CTATTTGGATTTAATGCCATTATACCTATCGC 40 116 0 TTAATGCATA 0.934728 -32 ******* * ** Masking position 4 Map Score: 3.31378 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 104 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 TTGGTTTGGGGAATGATTTTTACCCCCCTATC 2 9 1 GGGTGTTTTA 0.690324 -146 CAATTCAAAGGGGCTATTGTTTAAAATTTACATT 3 131 1 GGGATGTTAA 0.85783 -84 AATATTTTAAGGGTAATATTTTAAAAAATTTTTG 5 14 1 GGGATTTTAA 0.957403 -53 AGACAAGAAATGGTTATTTTTGAAAAAGGATTGA 8 30 1 TGGATTTTAA 0.55981 -24 TTATGTGTTTGTGGCATATTTTAAAATAATATAA 11 24 0 GTGATTTTAA 0.802949 -100 TTTTTAAAGTGGGTTTTTTCTTAAATCTTAAGAT 12 110 1 GGGTTTCTAA 0.818162 -119 AAAAATTCAAGGGGATTATTTTAACT 13 42 1 GGGTTTTTAA 0.970728 -16 CCACTTGAATGCGGTTGATTTTAACCGAAAGCGT 15 159 0 GCGTGTTTAA 0.721416 -70 AAAGGGGCTAGTTTTAAGTCATTTTGC 17 4 1 GGGTATTTAA 0.891636 -65 CAATATAATAGGGGCTAATTTAAAGATTAAGGTT 22 31 1 GGGTATTTAA 0.891636 -28 GGGTTATCGTTCAAATCATAAAAG 25 1 1 GGGATGTTAA 0.85783 -36 GATTTTCTTAGGGGCAGATTTAAAAA 31 3 0 GGGAGTTTAA 0.942871 -117 TTCCTGCAATGTGGTTGTTTTTAAACCCAGATGA 31 92 0 GTGTGTTTAA 0.815318 -28 TTATTTAGTGGTGAATTATTTTAAAATGGTGGTT 40 59 0 GTGTTTTTAA 0.857389 -89 TTCAGATTGGGGGATTTGTTTGAA 42 52 1 GGGTTTTTAA 0.970728 -14 *** ** *** ** Masking position 14 Map Score: 11.974 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 325 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 AACGAATTTTAATCAAAATGAGATTTAAGGG 1 18 0 AACAAAATGA 0.679639 -104 CCTAAATTGAGAAAAAATTCAATTCAAAGGG 3 112 1 GAAAAATTCA 0.59747 -103 AAAAAAAAAAAAACAATTTCAGTTTCTTATT 9 145 0 AACAATTTCA 0.697723 -115 AAGATTTTATAATCAAAGTCAAATCATTCTT 14 45 1 AACAAAGTCA 0.869151 -37 CTCATTAATAGAACAAATCCAACTTGAACTT 16 73 1 GACAAATCCA 0.76187 -99 AATTCTCGTTAATCAAAATCATATATTTAGG 20 60 1 AACAAAATCA 0.947825 -29 CAAAAAGATCGACCAAATTCATAAGAAAATA 23 81 0 GACAAATTCA 0.944411 -127 CCTTTAATTTAAAGAAATTCAATCTATGCAA 23 181 0 AAGAAATTCA 0.701699 -27 ATGAAGTTTAAATCAAAATCATGGTGTCAAG 27 196 0 AACAAAATCA 0.947825 -105 CAAAATCATGGAGCAAAATCATCTGCCGCAC 28 52 0 GACAAAATCA 0.944411 -172 ACACGCTCACAAACAAAATCATGGAGCAAAA 28 65 0 AACAAAATCA 0.947825 -159 ** ******** Masking position 6 Map Score: 3.81846 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 137 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419