AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_hpyl_reg_300.orf -o00240_hpyl_300.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 HP0105 37 conserved hypothetical protein #4 HP0106 24 cystathionine gamma-synthase (metB) #5 HP0107 38 cysteine synthetase (cysK) #6 HP0194 214 triosephosphate isomerase (tpi) #7 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #8 HP0198 66 nucleoside diphosphate kinase (ndk) #9 HP0262 157 H. pylori predicted coding region HP0262 #10 HP0263 111 adenine specific DNA methyltransferase (hpaim) #11 HP0264 72 ATP-dependent protease binding subunit (clpB) #12 HP0265 53 cytochrome c biogenesis protein (ccdA) #13 HP0349 259 CTP synthetase (pyrG) #14 HP0364 205 ribonucleoside diphosphate reductase, beta subunit (nrdB) #15 HP0372 123 deoxycytidine triphosphate deaminase (dcd) #16 HP0497 228 sodium- and chloride-dependent transporter #17 HP0500 57 DNA polymerase III beta-subunit (dnaN) #18 HP0584 81 flagellar switch protein (fliN) #19 HP0585 228 endonuclease III (nth) #20 HP0680 171 ribonucleoside-diphosphate reductase 1 alpha subunit (nrdA) #21 HP0681 39 H. pylori predicted coding region HP0681 #22 HP0682 153 H. pylori predicted coding region HP0682 #23 HP0683 300 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #24 HP0717 68 DNA polymerase III gamma and tau subunits (dnaX) #25 HP0718 207 conserved hypothetical integral membrane protein #26 HP0813 132 conserved hypothetical protein #27 HP0818 68 osmoprotection protein (proWX) #28 HP0820 173 H. pylori predicted coding region HP0820 #29 HP0824 88 thioredoxin (trxA) #30 HP0866 40 transcription elongation factor GreA (greA) #31 HP0869 58 hydrogenase expression/formation protein (hypA) #32 HP0870 207 flagellar hook (flgE) #33 HP0871 300 CDP-diglyceride hydrolase (cdh) #34 HP1010 300 polyphosphate kinase (ppk) #35 HP1011 36 dihydroorotate dehydrogenase (pyrD) #36 HP1084 66 aspartate transcarbamoylase (pyrB) #37 HP1180 300 pyrimidine nucleoside transport protein (nupC) #38 HP1198 223 DNA-directed RNA polymerase, beta subunit (rpoB) #39 HP1199 45 ribosomal protein L7/L12 (rpl7/l12) #40 HP1200 108 ribosomal protein L10 (rpl10) #41 HP1201 44 ribosomal protein L1 (rpl1) #42 HP1203 300 transcription termination factor NusG (nusG) #43 HP1215 35 H. pylori predicted coding region HP1215 #44 HP1217 48 H. pylori predicted coding region HP1217 #45 HP1218 119 glycinamide ribonucleotide synthetase (purD) #46 HP1255 116 protein translocation protein, low temperature (secG) #47 HP1295 22 ribosomal protein S11 (rps11) #48 HP1297 78 ribosomal protein L36 (rpl36) #49 HP1300 42 preprotein translocase subunit (secY) #50 HP1318 34 ribosomal protein L4 (rpl4) #51 HP1319 36 ribosomal protein L3 (rpl3) #52 HP1320 164 ribosomal protein S10 (rps10) #53 HP1386 70 D-ribulose-5-phosphate 3 epimerase (rpe) #54 HP1460 147 DNA polymerase III alpha-subunit (dnaE) #55 HP1470 67 DNA polymerase I (polA) #56 HP1471 65 type IIS restriction enzyme R protein (BCGIB) #57 HP1483 26 gerC2 protein (gerC2) #58 HP1490 103 hemolysin #59 HP1491 138 phosphate permease Motif number 1 TTTTAATCAAAATGAGATTTAAGGGTTAAAGA 1 10 0 AAGATTTAAG 0.653341 -112 TTAGCTATGATAAGCGTTTTAAAAACAAACGAA 1 43 0 TAGTTTTAAA 0.924405 -79 GAAAGCCCTTTAAAGTGTAAAATA 1 108 0 AAGCTTTAAA 0.848161 -14 TTAGGTTAATTTTGAGTTTTTAGGAGCAGTTTT 6 12 0 TTGTTTTTAG 0.402078 -203 GTTTAAAATTTACATTTTTTAAACGCTATTAGA 6 149 1 TAATTTTAAA 0.782656 -66 AAAAATATTTTAAGGGTAATATTT 8 2 1 AAATTTTAAG 0.853685 -65 TGATTATACAAAAATTTTTTAAAATATTACCCT 8 23 0 AAATTTTAAA 0.897977 -44 TTATAATAAAAATGAAATTTAAATTTTAGATAT 9 88 0 AAGATTTAAA 0.739795 -70 AAAAGCCTTTTTAAATCTTCTAAT 10 98 0 AAGTTTTTAA 0.943265 -14 TTTAACCCTCAAAGGTTTTTAAAACGC 11 5 0 AAGTTTTAAA 0.967626 -68 TGTAAAATAGTAAAGATTTTAAAACTCAAAAAG 11 42 1 TAATTTTAAA 0.782655 -31 ACTACTAAAAAAAGGGTTTTAAATA 13 3 0 AAGTTTTAAA 0.967626 -257 ATTATACGCCAACGAATTTTAAAATTGCTCTTA 13 51 1 AAGTTTTAAA 0.967626 -209 TTCATTGTCTTAAAACTTTTAAGAGCAATTTTA 13 70 0 TAATTTTAAG 0.704759 -190 GTTTTAAGACAATGAAGTTTAAACACATAAAAG 13 87 1 AAGGTTTAAA 0.848161 -173 AAAAAGGGTTAAAAAGCTTTAAAAGAGGGCAAA 13 193 0 AAACTTTAAA 0.62192 -67 ACTGAAAAATTGAAGTTTTTTAAAATTTGGAGT 14 92 1 TGATTTTTAA 0.46362 -114 TCTGGCTTTTAGGGGGTTTTAAATTCTTTTAAG 14 129 1 AGGTTTTAAA 0.928045 -77 TTACTAGCCATAAGCGTTTTTAGCAAAAAATTA 15 60 1 TAGTTTTTAG 0.818479 -64 CATAATTATTAACAAACTTTAAAGGCTTT 15 105 1 AAACTTTAAA 0.62192 -19 CTGTATTTTTTAGGTATTTTTAAAGTGGGTTTT 16 94 1 TAGTTTTTAA 0.871828 -135 TTAAGATCTTTAAAGATTTTAAAAACTAATACA 16 137 1 TAATTTTAAA 0.782655 -92 AAAAGCGTTCTTTTAYGCTATAATTA 17 4 1 AGGCTTTTAY 0.572794 -54 AAAGAGAGAAAGCGTTTTTTAAGGGCTTCATCG 19 71 0 AGGTTTTAAG 0.895284 -158 TATTAATGAGAATAAGTTTTAAAGTTTTTTAAT 20 50 0 AAATTTTAAA 0.897977 -122 AATTAAATCGTTTGTTTTTTAAATTTGGAATTG 20 131 0 TTGTTTTAAA 0.645855 -41 TAGGATCATTAGGAGCGTTTAAAGAGAGATTGA 23 112 1 AGAGTTTAAA 0.415142 -189 AAACTCATTTTAGGGAATTTTAACATGCCTTAT 23 268 0 TAGATTTTAA 0.392845 -33 AATACTCCTAAATGAGTTTTAAGGATTACAATC 24 43 1 AAGTTTTAAG 0.951953 -26 TAGCGCTCTTAGTGGCGTTTAAGAATAAGTTAA 25 18 0 AGGGTTTAAG 0.615063 -190 CGCTAAAAAATGGGGTTTTTAAATTTTCGCGCA 25 46 1 TGGTTTTAAA 0.840681 -162 TTTATTTATAAAGGTCGTTTTAAACCCTAAAAT 25 105 1 AAGGTTTTAA 0.756524 -103 TCATTCAAAAATGGTATTTTAAAATTTTAGGGT 25 128 0 ATGTTTTAAA 0.816769 -80 TTTCAATAATAATGACTTTTTAAAACTAGTTTG 26 95 1 AAGTTTTTAA 0.943265 -38 TATTTGGATAAAGGGGTTTTAAAATGCTAAAGG 27 34 0 AAGTTTTAAA 0.967626 -35 ACCACCCCATAACGCTTTTTAAAGGTTATCGCT 32 34 0 AAGTTTTAAA 0.967626 -174 AATGATTGGTTGCGGATTTTAAAGTTTTGTTAA 32 113 0 TGGTTTTAAA 0.840681 -95 GTTGTTCCTAAATAGCTTTTTAGAATGATTGGT 32 136 0 AAATTTTTAG 0.764456 -72 AAAAAGCTAAAAGAATTTTTTAAAAAATTAAAT 33 90 0 AAATTTTTAA 0.830393 -211 AAAAATTCTTTTAGCTTTTTTAATGTTATCAAT 33 103 1 TTGTTTTTAA 0.503583 -198 AAACGCTAAAAAAATTTTAAGCGATCTTTTA 34 9 1 AAATTTTAAG 0.853685 -292 GTTTTACAAAAAAGAGTTTTTAAACAACAACTA 34 73 1 AAGTTTTTAA 0.943265 -228 TACTCCGACCATGACTTTTTAAAAAAGCTTCAA 34 207 1 ATATTTTAAA 0.567599 -94 ATGTAATTTTAATGGATTTTTAAGAAAGGTTTT 37 68 1 AAGTTTTTAA 0.943265 -233 ACGGATATTAAATGAAGTTTAAATCAAAATCAT 37 205 0 AAGGTTTAAA 0.848161 -96 AGCATTGCAAAAGGATCTTTAAACTTTAGAACC 38 148 0 AAGCTTTAAA 0.848161 -76 CGTTAGGAGTTTTTAATCTTAGGCTG 40 4 1 TAGTTTTTAA 0.871828 -105 CTTTTTAAAAAAGAAATTTTAAGCTTTTTAGCT 40 48 0 AAATTTTAAG 0.853685 -61 CCTCTGCAAGATTATCTTTTTAAAAAAGAAATT 40 63 0 ATATTTTTAA 0.422024 -46 TTGGAATTGAAAGAAATTTTTAAGGATTAGAAT 41 21 1 AAATTTTTAA 0.830393 -24 TTATACATTAAAAGAATTTTTAATTCTATCCAA 42 38 0 AAGTTTTTAA 0.943265 -263 TATGTTAATATAAAAGTTTTTAGTAGTGCCTAA 48 35 1 TAATTTTTAG 0.570411 -44 TTGCTATTTTTAGGGCTTTTTAGAGATTTTTAC 52 37 0 TAGTTTTTAG 0.818479 -128 TATTATTTTTAATGCTATTTTAGGAGTTCATC 54 10 0 AAGATTTTAG 0.511803 -138 AATCTAATAAAGAGTTTTTTAAAGAGCGATAGG 54 91 1 AGGTTTTAAA 0.928045 -57 AAGGGGTTTTAAGCGCGCTAGCT 55 1 1 AAGTTTTAAG 0.951953 -67 TCTTCAATCAAGCGAATTTTAAGTTTATTGTAA 55 38 0 AGGTTTTAAG 0.895284 -30 AAAATTTTAAAGAGAGTTTTAAAAA 59 3 0 AGGTTTTAAA 0.928045 -136 TTTATCAAACAACGCTTTTTAAGAGTGGCTCAA 59 64 1 AAGTTTTAAG 0.951953 -75 ** * ******* Masking position 8 Map Score: 72.7932 Number of sites scoring better than the average of aligned sites = 2278 Number in coding regions = 1914 Number in noncoding regions = 364 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 2 ATTCATAACATTAATTTTTACACAATATTAACAC 2 109 0 TTATTTTAAA 0.576209 -46 GGTTTTTCCTTTTTTATTGAATTT 4 8 0 TTTCTTTTTT 0.702661 -17 AATCGCAAAATTGAATTTTATTGTTTGTTATAGG 5 11 1 TTATTTTATT 0.872048 -28 TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA 6 94 0 TTAGTTTTTT 0.808438 -121 AAAATGAAATTTAAATTTTAGATATTCTGCTTAA 9 79 0 TTATTTTAAA 0.576209 -79 AAATTTAAATTTCATTTTTATTATAAGCTTGTTT 9 95 1 TTATTTTATT 0.872048 -63 TCAATCCTTTTTGAGTTTTAAAATCTTTACTATT 11 47 0 TTATTTTAAT 0.82055 -26 ACTGAAATTGTTTTTTTTTTTTTTTGAAATCGCT 13 153 1 TTTTTTTTTT 0.775553 -107 GAAGCAGTATTTTAGCTTTTTAATCCTTTAAAAA 14 57 1 TTACTTTTAT 0.823356 -149 TTTAAAAAACTTCAATTTTTCAGTATTTTTAAAG 14 82 0 TTATTTTTAT 0.872048 -124 GACATCGCTCTTTAATTTTAATCATTGACAAGGA 16 190 1 TTATTTTATA 0.669592 -39 TTTAAAGTTTTTTAATTTTTTTATACCCCCTCCA 20 32 0 TTATTTTTTT 0.910381 -140 CAAATCCAACTTGAACTTTTCTTTTTCTTAAGTT 20 86 1 TTACTTTTTT 0.874172 -86 TTTCTTTTTCTTAAGTTTTTTATTGATACAATTC 20 103 1 TTATTTTTAT 0.872048 -69 ATTAAATCGTTTGTTTTTTAAATTTGGAATTGTA 20 129 0 TTTTTTTAAT 0.608668 -43 TTTGCGTTTTTTCATTTTTTTAATCCTCATTTGC 23 191 0 TTATTTTTAT 0.872048 -110 TGTATCATCATTTAATTTTTATTTATAAAGGTCG 25 88 1 TTATTTTTTT 0.910381 -120 TTAGAGCTGTTTGAAGTTTTTTTAGCGGGTTTTT 28 71 1 TTAGTTTTTA 0.556519 -103 ACTAAACCTTAATCTTTAAATTAGCCCCTATT 31 37 0 TTACTTTAAT 0.757706 -22 GTTGCGGATTTTAAAGTTTTGTTAATCAAAAAGA 32 104 0 TTAGTTTTTA 0.556519 -104 TAGGAACAACTTTTGCTTTATTTTGCATAGATTG 32 159 1 TTTCTTTATT 0.613226 -49 GGTTATCCTTTAATTTAAAGAAATTC 32 192 0 TTTCTTTATT 0.613226 -16 GTGCAAGCTATTTAATTTTTTAAAAAATTCTTTT 33 81 1 TTATTTTTAA 0.669592 -220 AAAAAATTCTTTTAGCTTTTTTAATGTTATCAAT 33 102 1 TTACTTTTTA 0.673821 -199 ATGTTATCAATTTAATTTTTTTCTAGTTAGTATT 33 125 1 TTATTTTTTT 0.910381 -176 TTTGTAAAACTTCATTTTTTGAATAAAACTTCAT 34 49 0 TTATTTTTAT 0.872048 -252 TAAAATTACATTAAACTTTTATTATCAATCCTAC 37 45 0 TTACTTTTTA 0.673821 -256 AATCTCATTCTTTTATTTTTTTGTCAAGGTAGCT 37 106 1 TTTTTTTTTT 0.775553 -195 TAATATCCGTTTAATCTTTTTTTTAGCAAAACTA 37 228 1 TTACTTTTTT 0.874172 -73 TGCAAGGCTATTGTAGTTTAGTTTTGCTAAAAAA 37 246 0 TTTGTTTATT 0.490606 -55 GCAAAGGCCTTTCTGTTTTTAAGTC 38 2 0 TTTTTTTTAT 0.698639 -222 CTCTGCAAGATTATCTTTTTAAAAAAGAAATTTT 40 61 0 TTTTTTTTAA 0.408052 -48 AATTTTTTAATTTTAGTTTAAGCTATTTT 42 6 1 TTATTTTATT 0.872048 -295 TACACTAAAATTTAGTTTTAATTTCAAGCGTGGT 46 28 0 TTATTTTATT 0.872048 -89 TGAGTAGTATTTCAGTTTTTATTTTATTGTTTTA 52 95 1 TTATTTTTTT 0.910381 -70 TATTGTTTTATTCTGTTTTTTAGTAACGGATAAA 52 119 1 TTTTTTTTAT 0.698639 -46 TCAAGCGAATTTTAAGTTTATTGTAACACAAGCT 55 30 0 TTAGTTTATT 0.739001 -38 TTTTGAAGGCTTGATTTTTAAAGTTAGGCTTAAT 58 14 1 TTATTTTAAT 0.82055 -90 AAAGTTAGGCTTAATCTTTTATGTTAAAATTCTG 58 33 1 TTACTTTTTT 0.874172 -71 ATCGTTAGGTTTTAGGTTTAAAGTT 58 89 1 TTAGTTTAAT 0.655132 -15 ** * ***** * * Masking position 7 Map Score: 42.8363 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 372 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TTAAATCTCATTTTGATTAAAATTCGTTTGTTT 1 21 1 TTTATTAAAT 0.893483 -101 AATGCAAGAATTTTAGCTATGATAAGCGTTTTA 1 55 0 TTTGCTAGAT 0.779546 -67 CTTGCATTTCTTTTTGTTATAATGGCGTTATTT 1 80 1 TTTGTTAAAT 0.944096 -42 GAATCATATATTTTCACTAAAATAATATTGAAA 9 33 0 TTTACTAAAT 0.925596 -125 TTATCAAAATTTTGTATTATAATTTG 9 142 1 TTTATTAAAT 0.893374 -16 TTTAACCCTTTTTAGACTACAATTTAAGAAGCA 13 213 1 TTTACTAAAT 0.925596 -47 TAGCAAAAAATTATTGTTATAATAACATAATTA 15 80 1 TTAGTTAAAT 0.606509 -44 AAAGCGTTCTTTTAYGCTATAATTAAGACCAAA 17 12 1 TTTGCTAAAT 0.961602 -46 TGTTATAAAATTTATAGTAAAATTAAGATTTTA 18 21 1 TTTAGTAAAT 0.778713 -61 AAAGCCACGCTTTCGGTTAAAATCAACCGCATT 19 153 1 TTTGTTAAAT 0.944097 -76 TTAATTCAAATTTAAGGAAAAATT 20 158 1 TTTGGAAAAT 0.514417 -14 CATCAAAGATTTAAGGCTAGAATTTTGCGTTTT 23 215 0 TTAGCTAAAT 0.695682 -86 TTTAAGTCATTTTGCATTACAATACTCCTAAAT 24 23 1 TTTATTAAAT 0.893483 -46 ACACAATGGCTTTGCGCGAAAATTTAAAAACCC 25 58 0 TTTGCGAAAT 0.800462 -150 AATAAGGCGATTTTGACTAGAATAGCGCTTCTA 26 49 0 TTTACTAAAT 0.925596 -84 TCGCCTTATTTTTGCGCTATGATTTTCAATAAT 26 72 1 TTTGCTAGAT 0.779546 -61 GCGCTATGATTTTCAATAATAATGACTTTTTAA 26 85 1 TTTATAAAAT 0.554471 -48 TCGCATTTACTTTCTGTAAAAAT 29 1 0 TTTGTAAAAT 0.714742 -88 TTTTTACTATAATCTCTACTGAA 30 1 1 TTTACTAAAT 0.925145 -40 CCCATGCCATTTTTAGCTAAAATAAAATCTATA 36 23 1 TTTGCTAAAT 0.961608 -44 AAAACCCCCTTTTAGTTATAATATAGATTTTA 36 45 0 TTTGTTAAAT 0.944097 -22 TCCAAAATAGCTTAAACTAAAATTAAAAAATT 42 10 0 CTTACTAAAT 0.6372 -291 GTTTAAGCTATTTTGGATAGAATTAAAAATTCT 42 26 1 TTTGATAAAT 0.642499 -275 TTAAGGGTTATTTCAATGAAAATATGTTAATAT 48 13 1 TTTATGAAAT 0.573282 -66 TTTTCAATGTTTTCAAGTAAAATATTAGCATCT 53 36 0 TTTAGTAAAT 0.780041 -35 AGCGCGCTAGCTTGTGTTACAATAAACTTAAAA 55 22 1 CTTGTTAAAT 0.704508 -46 GGCTTAATCTTTTATGTTAAAATTCTGAGATTT 58 40 1 TTTGTTAAAT 0.944096 -64 *** **** *** Masking position 9 Map Score: 29.3715 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 93 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 AAAATGAGATTTAAGGGTTAAAGA 1 3 0 TTAAGGGTAA 0.868918 -119 CTCTTGTATTAAAAGGACTTCA 2 143 1 AAAAGGATTA 0.701951 -12 AATTTATGAATAAAGGAGTTAAAAAC 3 22 1 TAAAGGATTA 0.687631 -16 AATTCAATTCAAAGGGGCTATTGTTTAAAATT 6 127 1 AAAGGGGTAT 0.756477 -88 ATTAGATATAATAAGGGATAGTTACCACCTAT 6 176 1 ATAAGGGTAT 0.814151 -39 AACTACTAAAAAAAGGGTTTTAAATA 13 5 0 AAAAGGGTTA 0.860728 -255 TTGTAGTCTAAAAAGGGTTAAAAAGCTTTAAA 13 203 0 AAAAGGGTAA 0.834532 -57 TCAGTATTTTTAAAGGATTAAAAAGCTAAAAT 14 65 0 TAAAGGATAA 0.642405 -141 TTTCTGGCTTTTAGGGGGTTTTAAATTCTTTT 14 127 1 TTAGGGGTTT 0.833418 -79 TTAAAATAATATAAGGAATAGATCGTT 15 6 0 ATAAGGATAA 0.729924 -118 AAAGCGTTTTTTAAGGGCTTCATCGCAGTTAG 19 64 0 TTAAGGGTTA 0.890377 -165 TAAACTCATTTTAGGGAATTTTAACATGCCTT 23 270 0 TTAGGGATTT 0.655953 -31 TAAAATGAGTTTAAGGATTTTA 23 289 1 TTAAGGATTA 0.755828 -12 AAAGGGGCTAGTTTTAAGTCAT 24 1 1 AAAGGGGTAT 0.756477 -68 TAAATGAGTTTTAAGGATTACAATCAAT 24 51 1 TTAAGGATAA 0.716403 -18 TTATTTGGATAAAGGGGTTTTAAAATGCTAAA 27 36 0 AAAGGGGTTA 0.860384 -33 ATACAATATAATAGGGGCTAATTTAAAGATTA 31 28 1 ATAGGGGTAT 0.813715 -31 TCATAAGAAAATAGGGGGTTTTGCAACACCAC 32 62 0 ATAGGGGTTT 0.842586 -146 CCATGCGATCTTAGGGGGTTGATACTTGTCAA 33 28 0 TTAGGGGTTA 0.890104 -273 CATGATGATTTAAAGGATTTCTA 34 288 1 TAAAGGATTT 0.576231 -13 ATCATAAAAGATAAGGATTTAA 35 25 1 ATAAGGATTA 0.768078 -12 ATTATAACTAAAAGGGGGTTTT 36 55 1 AAAGGGGTTT 0.79195 -12 ATTTCTTGCATTAGGGATTTGACG 37 287 1 TTAGGGATTA 0.755298 -14 AAAGAAATTTTTAAGGATTAGAATC 41 30 1 TTAAGGATAA 0.716403 -15 ATTTAAGGGTTATTTCAATGAAAA 48 3 1 TTAAGGGTAT 0.803713 -76 GAATATAATATAAAGGGTTTGAT 50 22 1 TAAAGGGTTA 0.852433 -13 AGATAATAAAATAAGGGTTAGAT 51 24 1 ATAAGGGTAA 0.876421 -13 ATCAAATCATAAAAGGGTTTTT 53 1 0 AAAAGGGTTT 0.792423 -70 TTAAATCCAAATAGGGGTTAGACA 54 134 1 ATAGGGGTAA 0.876109 -14 ******* ** * Masking position 9 Map Score: 35.1483 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 965 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 5 TATAAGAAAAATTATTTCAAATGTAGTAGA 6 75 0 ATTATTTCAA 0.76207 -140 AATACGAATGATTATTTTAATAAGGACAAT 7 43 1 ATTATTTTAA 0.908959 -22 AAAAATATTTTAAGGGTAATATT 8 4 1 AATATTTTAA 0.866588 -63 TTTTAAGGGTAATATTTTAAAAAATTTTTG 8 18 1 AATATTTTAA 0.866588 -49 CTTTGATTAAATTCTTTCAATATTATTTTA 9 19 1 ATTCTTTCAA 0.708483 -139 TTCATTAGCAATACTTTTAAGCAGAATATC 9 63 1 ATACTTTTAA 0.751523 -95 ACTATTTTACACTATTTTAACCCTCAAAGG 11 23 0 ACTATTTTAA 0.713712 -50 CATTGTCTTAAAACTTTTAAGAGCAATTTT 13 71 0 AAACTTTTAA 0.663043 -189 GGGGTTTTAAATTCTTTTAAGGTATTCTAA 14 141 1 ATTCTTTTAA 0.883393 -65 TATTCCTTATATTATTTTAAAATATGCCAC 15 18 1 ATTATTTTAA 0.908959 -106 TACATATTGTATAATTTTAAGAAAATTTCA 16 32 0 ATAATTTTAA 0.799438 -197 ATTCAAGGGGATTATTTTAACT 17 46 1 ATTATTTTAA 0.908959 -12 AAAACTCTACTCTTTCAAGAATGATTTG 18 64 0 ACTCTTTCAA 0.377663 -18 GCGTTTTTTCATTTTTTTAATCCTCATTTG 23 192 0 ATTTTTTTAA 0.825578 -109 TTTAAACCCTAAAATTTTAAAATACCATTT 25 123 1 AAAATTTTAA 0.721701 -85 AAGCTAAAAGAATTTTTTAAAAAATTAAAT 33 90 0 AATTTTTTAA 0.754867 -211 AATCATTATGATTATTTTAATGAATTTTAA 33 204 0 ATTATTTTAA 0.908959 -97 AAACGCTAAAAAAATTTTAAGCGATCTTTT 34 11 1 AAAATTTTAA 0.721701 -290 AATCCTTCACATTTTTTTAAATTAAAGCCA 39 21 0 ATTTTTTTAA 0.825578 -25 GAATTGAAAGAAATTTTTAAGGATTAGAAT 41 24 1 AAATTTTTAA 0.551451 -21 AATTTTTTAATTTTAGTTTA 42 1 1 AATTTTTTAA 0.754867 -300 AGAATTAAAAATTCTTTTAATGTATAAATG 42 44 1 ATTCTTTTAA 0.883393 -257 GTAGTGCCTAATTTTTTCAAAGGAGAAAAA 48 57 1 ATTTTTTCAA 0.602928 -22 TTAGTGGTGAATTATTTTAAAATGGTGGTT 54 59 0 ATTATTTTAA 0.908959 -89 ATCTTAAAGTAAAATTTTAAAGAGAGTTTT 59 16 0 AAAATTTTAA 0.721701 -123 ********** Masking position 5 Map Score: 26.449 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 329 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 AACAAACGAATTTTAATCAAAATGAGATTTA 1 22 0 TTTTATCAAA 0.946837 -100 TATTCATAAATTGTAATGAAACT 3 3 0 TTGTATGAAA 0.557276 -35 TATTGAAAGAATTTAATCAAAGGGCTAGAC 9 10 0 ATTTATCAAA 0.825868 -148 CCAAAAACCATTTTGATCAAAGCTCTAAAAT 10 49 1 TTTTATCAAA 0.947219 -63 AAGCTTTTCATTTTAATCAAACCTAGCTAAT 13 117 1 TTTTATCAAA 0.946837 -143 TGTTTTTTTTTTTTTTTGAAATCGCTTTAAT 13 161 1 TTTTTTGAAA 0.538309 -99 ATTGAGATAGTTTTAAGGAAATTAAGGAACA 14 183 1 TTTTAGGAAA 0.71617 -23 GCCATAAGCGTTTTTAGCAAAAAATTATTGT 15 66 1 TTTTAGCAAA 0.857976 -58 AATTAAGATTTTATAATCAAAGTCAAATCAT 18 41 1 TTATATCAAA 0.524562 -41 TTAAAGACAAAGTTTATGAAATCGTAGAAAT 19 31 1 AGTTATGAAA 0.400387 -198 GCACAATACCTTGTCATCAAAGAAAGCGT 19 210 1 TTGTATCAAA 0.750589 -19 TTTAATTCAAATTTAAGGAAAAATT 20 157 1 ATTTAGGAAA 0.400385 -15 AGCCTTAAATCTTTGATGAAACGAAGTCAAA 23 230 1 CTTTATGAAA 0.758839 -71 GATTTTCCTTTCATCAAACTCATCTCAA 26 8 1 CTTTATCAAA 0.882668 -125 AGCTTAAGAATGTTAATGAAATCGCATTTAC 29 24 0 TGTTATGAAA 0.71646 -65 ATATAATTCTCGTTAATCAAAATCATATATT 29 56 1 CGTTATCAAA 0.716892 -33 TTTAAAGTTTTGTTAATCAAAAAGATCGACC 32 98 0 TGTTATCAAA 0.857977 -110 TTAAATGAAGTTTTATTCAAAAAATGAAGTT 34 45 1 TTTTTTCAAA 0.734066 -256 TTAAATGAAGTTTAAATCAAAATCATGGTGT 37 200 0 TTTAATCAAA 0.501953 -101 TTTAATCTTTTTTTTAGCAAAACTAAACTAC 37 237 1 TTTTAGCAAA 0.857976 -64 AACTCAAAATTTTTGATCAAAGGCTTGAAAT 38 203 1 TTTTATCAAA 0.947219 -21 GTAGTGCCTAATTTTTTCAAAGGAGAAAAAT 48 57 1 ATTTTTCAAA 0.424194 -22 ATATTAGCATCTTTAATCAAATCATAAAAGG 53 17 0 CTTTATCAAA 0.882665 -54 TAATGAGCCATTTTTATCAAACAACGCTTTT 59 52 1 TTTTATCAAA 0.947219 -87 **** ****** Masking position 9 Map Score: 22.0268 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 495 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 TAAGGCAGTGTTTTTGCGTCAAGCGATTTT 6 43 0 TTTTTGCGTC 0.7837 -172 ATGCTCTTGATTTTAGAGCTTTGATCAAAA 10 59 0 TTTTAGAGCT 0.731499 -53 TATCAATCCTTTTTGAGTTTTAAAATCTT 11 54 0 TTTTTGAGTT 0.481291 -19 ATCGCTTTAATTTTTGCCCTCTTTTAAAGC 13 181 1 TTTTTGCCCT 0.74974 -79 GTTCCTTTAATTTTTGCTTCTTAAATTGTA 13 230 0 TTTTTGCTTC 0.644251 -30 AGAAGCAGTATTTTAGCTTTTTAATCCTTT 14 56 1 TTTTAGCTTT 0.887221 -150 TCCCCTTGAATTTTTGGTCTTAATTATAGC 17 27 0 TTTTTGGTCT 0.732728 -31 ACGCTTTTAGTTTTAGCCCCGTCATTGATT 23 44 0 TTTTAGCCCC 0.695713 -257 AAACCCCATTTTTTAGCGCTCTTAGTGGCG 25 34 0 TTTTAGCGCT 0.962094 -174 TATTTTAAAATTTTAGGGTTTAAAACGACC 25 117 0 TTTTAGGGTT 0.860978 -91 AATCGCCTTATTTTTGCGCTATGATTTTCA 26 70 1 TTTTTGCGCT 0.933064 -63 TTAACATGCTTTTTAGCGCTTGTAGCAATA 28 145 0 TTTTAGCGCT 0.962094 -29 TAAAAAATTCTTTTAGCTTTTTTAATGTTA 33 101 1 TTTTAGCTTT 0.887221 -200 CTTTTTTGCTCCTTGTTTTTAA 33 289 0 TTTTTGCTCC 0.744921 -12 CTTAAAATTTTTTTAGCGTTT 34 2 0 TTTTAGCGTT 0.94026 -299 TTAAGCGATCTTTTAGGGTTAAATGAAGTT 34 27 1 TTTTAGGGTT 0.860978 -274 ATTTTAAGCTTTTTAGCTCTTACGATCTTC 40 36 0 TTTTAGCTCT 0.926933 -73 ATCACGCTGTTTTTAGCTTTGTTGGATTTT 42 222 1 TTTTAGCTTT 0.887221 -79 CTTTTGCTATTTTTAGGGCTTTTTAGAGAT 52 43 0 TTTTAGGGCT 0.908983 -122 TATCGTTAGGTTTTAGGTTTAAAGTT 58 88 1 TTTTAGGTTT 0.755828 -16 ********** Masking position 4 Map Score: 23.7116 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 854 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 TTAAGGACATCGCTCTTTAATTTTAATCAT 16 185 1 CGCTCTTTAA 0.979146 -44 TTAAAACTTATTCTCATTAATAGAACAAAT 20 61 1 TTCTCATTAA 0.602363 -111 TAGCGTCAATCTCTCTTTAAACGCTCCTAA 23 120 0 CTCTCTTTAA 0.961069 -181 GCGCTATCAGCGCTCATTAAAGGGCATATT 23 156 1 CGCTCATTAA 0.949244 -145 CACCCCATAACGCTTTTTAAAGGTTATCGC 32 35 0 CGCTTTTTAA 0.920826 -173 ATTCAAAAATCTCTTTTTAAAAATAGGTTA 33 156 1 CTCTTTTTAA 0.859451 -145 TTTGCAAAAACTCTCATTAAAAACAAGGAG 33 273 1 CTCTCATTAA 0.907689 -28 GTTGCGTATCTGCTCTTTAATAGGAAATAT 42 159 0 TGCTCTTTAA 0.878545 -142 TTATACCTATCGCTCTTTAAAAAACTCTTT 54 99 0 CGCTCTTTAA 0.979146 -49 TTTTTAAAACTCTCTTTAAAATTTTACTT 59 10 1 CTCTCTTTAA 0.961069 -129 TATCAAACAACGCTTTTTAAGAGTGGCTCA 59 66 1 CGCTTTTTAA 0.920826 -73 ********** Masking position 9 Map Score: 15.861 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 95 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 GAATCTCTTGTATTAAAAGGACTTCA 2 139 1 TTTAAAAGGA 0.645998 -16 CGCTATTAGATATAATAAGGGATAGTTACCA 6 172 1 TTAATAAGGG 0.851266 -43 TTACCACCTATAAAATAAGGATCGTTCA 6 197 1 TAAATAAGGA 0.86498 -18 GAATGATTATTTTAATAAGGACAATCA 7 48 1 TTAATAAGGA 0.834165 -17 ATGGTTATTTTTGAAAAAGGATTGA 12 39 1 TGAAAAAGGA 0.599487 -15 AATGAACTACTAAAAAAAGGGTTTTAAATA 13 10 0 TAAAAAAGGG 0.890907 -250 TAAATTGTAGTCTAAAAAGGGTTAAAAAGCT 13 208 0 TTAAAAAGGG 0.865087 -52 TATTTTAAAATAATATAAGGAATAGATCGTT 15 11 0 TATATAAGGA 0.674742 -113 ATTTCATTATTTAAGTAAGGGGAATTA 16 7 0 TAAGTAAGGG 0.72612 -222 GAGATGAGTTTGATGAAAGGAAAATC 26 6 0 TATGAAAGGA 0.458086 -127 TCTAATACAATATAATAGGGGCTAATTTAAA 31 24 1 TTAATAGGGG 0.571876 -35 TACTCCGCAATCAAAAAGGGAGATTGTAGCG 34 116 0 TAAAAAGGGA 0.626179 -185 AGAGGTCTAGTCTAGAAAGGAGGAAAAG 40 91 1 TTAGAAAGGA 0.672096 -18 GTTGGTGGCTTTAAATAAGGAGAATA 42 285 1 TAAATAAGGA 0.86498 -16 ATTGAGATAATAAAATAAGGGTTAGAT 51 20 1 TAAATAAGGG 0.879363 -17 TATATTTCCTTATAAAAAGGAAGTAAAAATC 52 15 1 TTAAAAAGGA 0.849294 -150 TTTAATCAAATCATAAAAGGGTTTTT 53 6 0 TATAAAAGGG 0.72561 -65 * ********* Masking position 7 Map Score: 11.0657 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 241 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 10 AGTGTAAAATAACGCCATTATAACAAAAAG 1 89 0 AACGCCATTA 0.874505 -33 ACATTTTTTAAACGCTATTAGATATAATAA 6 160 1 AACGCTATTA 0.947799 -55 AAATTAAAGGAACGCAATAACTT 13 247 1 AACGCAATAA 0.502331 -13 AATACAGAGCAACGCCCTTAGATTATACTA 16 71 0 AACGCCCTTA 0.905905 -158 GATCTATAACAACGCTTTTAATAGGGTTGT 22 113 1 AACGCTTTTA 0.764915 -41 TCTCTCTTTAAACGCTCCTAATGATCCTAA 23 111 0 AACGCTCCTA 0.785373 -190 CGCTAGGCAAAGCGCTATCAGCGCTCATTA 23 145 1 AGCGCTATCA 0.884361 -156 CCCATTTTTTAGCGCTCTTAGTGGCGTTTA 25 30 0 AGCGCTCTTA 0.968241 -178 CAATAATAGAAGCGCTATTCTAGTCAAAAT 26 43 1 AGCGCTATTC 0.762972 -90 TTATGAGACCAGCGCTCTAAACCAGCTGAG 37 138 0 AGCGCTCTAA 0.872298 -163 GCAGATACGCAACGCACTTATTTCTGTTTT 42 176 1 AACGCACTTA 0.861575 -125 GGTGGTGGTGAGCGCTATCACGCTGTTTTT 42 206 1 AGCGCTATCA 0.884361 -95 AACACAAGCTAGCGCGCTTAAAACCCCTT 55 10 0 AGCGCGCTTA 0.864093 -58 TAGCCAACTCAACGCTATTAAGTGGGGCGA 56 21 1 AACGCTATTA 0.947799 -45 ********** Masking position 1 Map Score: 9.33256 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 280 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TATTTAAAACCCTTTTTTTAGTAG 13 5 1 TAAAACCCTT 0.523674 -255 TAAAACCCCCTAAAAGCCAGAAAAAACTCC 14 120 0 TAAAAGCCAG 0.804074 -86 TAAAAGAATTTAAAACCCCCTAAAAGCCAG 14 130 0 TAAAACCCCC 0.955535 -76 AGATTTAAGAAAAAACCCACTTTAAAAATA 16 108 0 AAAAACCCAC 0.929539 -121 TATTCCATGAAAAAAGCCACGCTTTCGGTT 19 141 1 AAAAAGCCAC 0.894476 -88 TCATGGGATCTTAAAGCCACTTGAATGCGG 19 179 0 TTAAAGCCAC 0.901121 -50 AACTTATTCTTAAACGCCACTAAGAGCGCT 25 20 1 TAAACGCCAC 0.7078 -188 TTTAGCATTTTAAAACCCCTTTATCCAAAT 27 36 1 TAAAACCCCT 0.851573 -33 CCATTCAATGAAAAACCCGCTAAAAAAACT 28 85 0 AAAAACCCGC 0.858576 -89 GCTTGCGGTTATAAAGCCCCTCCATTCAAT 28 106 0 ATAAAGCCCC 0.671492 -68 AACAAAACTTTAAAATCCGCAACCAATCAT 32 115 1 TAAAATCCGC 0.539999 -93 GTAGCGGGATTCAAACCCACGACCTCACCC 34 180 0 TCAAACCCAC 0.838348 -121 TCCTTGCTAAAACCCATGCCATTTTTA 36 8 1 TAAAACCCAT 0.904687 -59 TAAAAATACCAAAAACCCACCTGCAATACT 38 110 0 AAAAACCCAC 0.929539 -114 TTTTTTTAAATTAAAGCCATCACAGGCTC 39 10 0 TTAAAGCCAT 0.70872 -36 TTCTCCTTATTTAAAGCCACCAACCTATAG 42 279 0 TTAAAGCCAC 0.901121 -22 AAGTCGTTGCTAAAACCCGCCT 43 3 0 TAAAACCCGC 0.942399 -33 GTGGTTGTTTTTAAACCCAGATGACCGCTA 45 86 0 TTAAACCCAG 0.718162 -34 CTAGCGCGCTTAAAACCCCTT 55 2 0 TAAAACCCCT 0.851573 -66 ********** Masking position 4 Map Score: 13.733 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 475 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 TTTGATTAAAATTCGTTTGTTTTTAAAACGCT 1 32 1 ATCGTTGTTT 0.931741 -90 ATTAACACCGATACGATGGTTTTTGATTGGAA 2 85 0 ATCGTGGTTT 0.604907 -70 GCAAAATTGAATTTTATTGTTTGTTATAGGAG 5 15 1 ATTTTTGTTT 0.66755 -24 CCCATTTTGAATACGAATGATTATTTTAATAA 7 34 1 ATCGATGATT 0.479725 -31 CATTTTTATTATAAGCTTGTTTCAAACACCAG 9 107 1 ATAGTTGTTT 0.894802 -51 TAAATTTTCTATGCTCTTGATTTTAGAGCTTT 10 67 0 ATCTTTGATT 0.829883 -45 AGCCACTTGAATGCGGTTGATTTTAACCGAAA 19 163 0 ATCGTTGATT 0.92415 -66 ATTTGAATTAAATCGTTTGTTTTTTAAATTTG 20 137 0 AACGTTGTTT 0.508112 -35 CTTTATCCAAATAAGTTTGGTTATA 27 54 1 ATAGTTGGTT 0.639494 -15 TCCTAAATATATGATTTTGATTAACGAGAATT 29 60 0 ATATTTGATT 0.752465 -29 AATTTGGTCGATCTTTTTGATTAACAAAACTT 32 93 1 ATTTTTGATT 0.641871 -115 ATGTTTAAAAATCAGTTTGTTTGGTGTGATTA 34 259 0 ATAGTTGTTT 0.894802 -42 TCTTGACACCATGATTTTGATTTAAACTTCAT 37 195 1 ATATTTGATT 0.752465 -106 ATTTTGCTCCATGATTTTGTTTGTGAGCGTGT 38 64 1 ATATTTGTTT 0.773018 -160 CTTTCCTGCAATGTGGTTGTTTTTAAACCCAG 45 96 0 ATTGTTGTTT 0.833751 -24 CCCCTGTTGTATCAGCTTGATTTAAGAGGAAT 49 13 1 ATAGTTGATT 0.883616 -30 TTCAGTTTTTATTTTATTGTTTTATTCTGTTT 52 105 1 ATTTTTGTTT 0.66755 -60 TAAACTTAAAATTCGCTTGATTGAAGAGGGTT 55 44 1 ATCGTTGATT 0.92415 -24 ** ** ****** Masking position 11 Map Score: 14.0255 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 140 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 AATTTTAATCAAAATGAGATTTAAGGGTTAA 1 14 0 AAATGAGATT 0.760614 -108 TCAACAATTCACAAGGAGTTTAAA 8 53 1 AAAGGAGTTT 0.919545 -14 GAACTACTAAAAAAAGGGTTTTAAATA 13 7 0 AAAAGGGTTT 0.846743 -253 TTAATCATTGACAAGGAGTTTGGTAGTTAAG 16 207 1 AAAGGAGTTT 0.919545 -22 ACCAAAAGAGAGAAAGCGTTTTTTAAGGGCT 19 77 0 AAAAGCGTTT 0.929045 -152 AGGAGCGTTTAAAGAGAGATTGACGCTAGGC 23 122 1 AAGAGAGATT 0.731807 -179 AAAATTCCCTAAAATGAGTTTAAGGATTTTA 23 280 1 AAATGAGTTT 0.878124 -21 ACAATACTCCTAAATGAGTTTTAAGGATTAC 24 41 1 TAATGAGTTT 0.340167 -28 TAGCGCAAAAATAAGGCGATTTTGACTAGAA 26 60 0 AAAGGCGATT 0.762263 -73 GATAACCTTTAAAAAGCGTTATGGGGTGGTG 32 37 1 AAAAGCGTTA 0.483679 -171 ACTTGTCAAAATAAAGCGTTTTATAA 33 6 0 AAAAGCGTTT 0.929045 -295 ACCTATTTTTAAAAAGAGATTTTTGAATACT 33 153 0 AAAAGAGATT 0.900744 -148 AAGTTTTACAAAAAAGAGTTTTTAAACAACA 34 71 1 AAAAGAGTTT 0.953662 -230 CCGCAATCAAAAAGGGAGATTGTAGCGCGAG 34 112 0 AAGGGAGATT 0.602441 -189 AAAAAATAAAAGAATGAGATTATACAAAAAC 37 96 0 AAATGAGATT 0.760614 -205 TTAAGACAAACCAAAGAGTTTGTCTTGTTTG 44 21 1 CAAAGAGTTT 0.685767 -28 TGAATATAATATAAAGGGTTTGAT 50 21 1 AAAAGGGTTT 0.846743 -14 AAATAATCTAATAAAGAGTTTTTTAAAGAGC 54 87 1 AAAAGAGTTT 0.953662 -61 GTAAAATTTTAAAGAGAGTTTTAAAAA 59 7 0 AAGAGAGTTT 0.860881 -132 AGCCACTCTTAAAAAGCGTTGTTTGATAAAA 59 63 0 AAAAGCGTTG 0.581313 -76 * ********* Masking position 10 Map Score: 17.7569 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 319 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 14 AAATTCAATAAAAAAGGAAAAA 4 2 1 AATCAATAAA 0.693533 -23 TATCCTAAAAAAGACAAGAAATGGTTATTTT 12 19 1 AAGCAAGAAA 0.541191 -35 TTAGCTTTTTAATCCTTTAAAAATACTGAAA 14 68 1 AATCTTTAAA 0.769139 -138 GTCTTGTTAGAATACCTTAAAAGAATTTAAA 14 146 0 AATCCTTAAA 0.734187 -60 AAAGCCTTTAAAGTTTGTTAAT 15 112 0 AAGCTTTAAA 0.769839 -12 ACGCTCAATGAAGCCATTAAAGACAAAGTTT 19 15 1 AAGCATTAAA 0.922369 -214 AACTGCGATGAAGCCCTTAAAAAACGCTTTC 19 66 1 AAGCCTTAAA 0.734956 -163 AATGCAAAAGAATGCATTGAACCCCTTCATG 19 111 0 AATCATTGAA 0.530815 -118 CTTTTGCATTATTCCATGAAAAAAGCCACGC 19 132 1 ATTCATGAAA 0.604723 -97 TTTAACCCAAATGTCATTAAATGGAGGGGGT 20 11 1 ATGCATTAAA 0.747368 -161 AATAAGTTAAAATTCATTAAAATAATCATAA 33 198 1 AATCATTAAA 0.922086 -103 TAGAAATCCTTTAAATCATCATGTT 34 286 0 AATCTTTAAA 0.769139 -15 ATCCATTAAAATTACATTAAACTTTTATTAT 37 54 0 ATTCATTAAA 0.746623 -247 CTTTCTTAAAAATCCATTAAAATTACATTAA 37 65 0 AATCATTAAA 0.922086 -236 TCAAATCCCTAATGCAAGAAATTAAAAGATG 37 278 0 AATCAAGAAA 0.540211 -23 TACTTGAATTAATGCATTAAATAACTCAAAA 38 181 1 AATCATTAAA 0.922086 -43 TTTTTGATCAAAGGCTTGAAAT 38 212 1 AAGCTTGAAA 0.634578 -12 TTAATACATTTATACATTAAAAGAATTTTTA 42 49 0 TATCATTAAA 0.432892 -252 ATTTGCTAAGAATACACTAAAATTTAGTTTT 46 43 0 AATCACTAAA 0.570341 -74 GATAGGTATAATGGCATTAAATCCAAATAGG 54 118 1 ATGCATTAAA 0.747368 -30 AGACAAGCCATGAAAAAAGAAAAGT 57 5 1 AAGCATGAAA 0.860503 -22 *** ******* Masking position 10 Map Score: 15.5517 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 379 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 15 ATTTTGAGTTTTTAGGAGCAGTTTTT 6 4 0 TTTAGGAGCT 0.959778 -211 AAACCCTTTTTTTAGTAGTTCATTCAAAACGGA 13 17 1 TTTAGTAGTT 0.893031 -243 TCTTAAAACTTTTAAGAGCAATTTTAAAATTCG 13 63 0 TTTAAGAGCT 0.704217 -197 GTTTAGGATCATTAGGAGCGTTTAAAGAGAGAT 23 109 1 ATTAGGAGCT 0.685974 -192 TTAAAACTCATTTAGGAGTATTGTAATGCAAAA 24 32 0 TTTAGGAGTG 0.73612 -37 AAATCATATATTTAGGAGTAACTA 29 75 1 TTTAGGAGTT 0.956516 -14 TAAAAAGCTATTTAGGAACAACTTTTGCTTTAT 32 147 1 TTTAGGAACT 0.785875 -61 ATTAGTAACTTTTAGTAACCTATTTTTAAAAAG 33 168 0 TTTAGTAACT 0.582105 -133 CGTTAGGAGTTTTTAATCTTAGGC 40 2 1 GTTAGGAGTT 0.74903 -107 TATAAAAGTTTTTAGTAGTGCCTAATTTTTTCA 48 43 1 TTTAGTAGTT 0.893031 -36 ATGGCGCATTTTGAGTAGTATTTCAGTTTTTAT 52 84 1 TTGAGTAGTT 0.514266 -81 TATTCTGTTTTTTAGTAACGGATAAAACGAGTT 52 127 1 TTTAGTAACT 0.582105 -38 AACGAGTTCTTTTAGGAGAGTTT 52 152 1 TTTAGGAGAT 0.75581 -13 TTAATGCTATTTTAGGAGTTCATC 54 2 0 TTTAGGAGTT 0.956516 -146 TATTAGATTATTTAGTGGTGAATTATTTTAAAA 54 67 0 TTTAGTGGTT 0.514266 -81 AACAACGCTTTTTAAGAGTGGCTCAAGGGCTAA 59 71 1 TTTAAGAGTT 0.686986 -68 ********* * Masking position 4 Map Score: 7.16378 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 182 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789