AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_hpyl_reg_300.orf -o00330_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: HP1157 22 H. pylori predicted coding region HP1157 Input sequences: #1 HP0056 300 delta-1-pyrroline-5-carboxylate dehydrogenase {Synechocystis sp.) #2 HP0090 300 malonyl coenzyme A-acyl carrier protein transacylase (fabD) #3 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #4 HP0246 188 flagellar basal-body P-ring protein (flgI) #5 HP0320 71 conserved hypothetical secreted protein #6 HP0322 141 poly E-rich protein #7 HP0417 168 methionyl-tRNA synthetase (metS) #8 HP0830 58 amidase #9 HP0832 91 spermidine synthase (speE) #10 HP0833 76 H. pylori predicted coding region HP0833 #11 HP1054 63 H. pylori predicted coding region HP1054 #12 HP1057 148 H. pylori predicted coding region HP1057 #13 HP1100 65 6-phosphogluconate dehydratase #14 HP1154 130 H. pylori predicted coding region HP1154 #15 HP1156 107 H. pylori predicted coding region HP1156 #16 HP1399 201 arginase (rocF) #17 HP1483 26 gerC2 protein (gerC2) #18 HP1490 103 hemolysin #19 HP1491 138 phosphate permease Motif number 1 TGTAAATCCGTTTAATTTAAAATCGTTTCGTTCAAT 1 18 1 TTTATAAAAT 0.557227 -283 AATGTTATAATTTATTATTAAACGAAAAGTAAATGA 1 75 1 TTTATTAAAA 0.768021 -226 CGAAAAGTAAATGAAGCTAAAAACAATACAAATTAT 1 97 1 ATGATAAAAA 0.781868 -204 ACCGCTAGAACAAAATTTAAAATTAAAAAACATTAC 1 200 1 CAAATAAAAA 0.917823 -101 TTACCAATAAATGAGACTTAAAGCCACCCGCTTAAA 1 232 1 ATGATTAAAA 0.756239 -69 ACAATCAAGTCAAATTCTTAAATAAAAGGTAAGCTC 1 275 1 CAAATTAAAA 0.906809 -26 ACAAAGTAGAATTATAGTAAAAATAAGTTAAAATAA 2 185 1 ATTATAAAAA 0.901607 -116 ATAAGTTAAAATAAACCTTAAACTTTAATGGTTTCT 2 207 1 ATAATTAAAT 0.832434 -94 TTTATTAATCCATAATTTAAAATTGTAATATAAAAG 2 258 0 CATATAAAAT 0.660643 -43 TTATGGATTAATAAAACTTAAAGGATAACACC 2 279 1 ATAATTAAAT 0.832434 -22 AAAATTTTGTTTTATAGTAAAACTCATTTTTAAGGG 3 26 0 TTTATAAAAA 0.792749 -180 TACTATAAAACAAAATTTTAAAAAGATTAAATAATA 3 43 1 CAAATTAAAA 0.906811 -163 AAAAAGATTAAATAATATTAAATTGAATGGGGTTTA 3 62 1 AATATTAAAA 0.872884 -144 TTATGAAAATAAAAGCCTAAAACAATTTTAAAAAAA 3 171 1 AAAATAAAAT 0.832434 -35 TTAGCTTTTTATAAAGTTTCAAATTAAATTGAGGTA 4 21 0 ATAATTCAAA 0.77868 -168 AAAAGCTAATAAAAGGCTAAAATTAAAATCTTTGAT 4 48 1 AAAATAAAAA 0.937835 -141 CAAAAATCTTATAAACTTTAAATCAAAGATTTTAAT 4 69 0 ATAATTAAAA 0.937836 -120 AGCCTTTTATAAAAACTTTAAACCTAATTGAGCGTA 4 120 0 AAAATTAAAA 0.928865 -69 TTATAAAAGGCTTATGCTAAAATAATTAGAATTTAG 4 144 1 CTTATAAAAT 0.692239 -45 TGATTATAATAAAAGATTTAAAAAAAGCGATAAAAT 6 70 1 AAAATTAAAA 0.928865 -72 AAAAAATTGAAAAAGAGTTCAAGGAATAGACAG 7 8 0 AAAATTCAAA 0.752796 -161 GTGGGGTGTTTTTAGCTTAAAATTCATTATAATTAA 7 49 0 TTTATAAAAA 0.792746 -120 CTCTATTCTCTAAATTTTTAAAAGCATGTTAAAATT 7 104 1 TAAATTAAAA 0.844939 -65 TGTTAAAATTAAGAGATTTAAACAAATTTAAGGTAA 7 130 1 AAGATTAAAA 0.728645 -39 TTTAATCAAAATTAGATTACAATATTATAGTTATTT 10 28 1 ATTATACAAT 0.413054 -49 ATTAAAACGACTAACGCTAAAATTTTAAACCTTAAC 11 25 0 CTAATAAAAT 0.810507 -39 TAAAAATCCTAAGTGTTAAATATAGTGGCATTGT 12 9 1 CTAATTAAAA 0.918318 -140 CAATTATACTAAAATAATTAAAATGACCGGTTAAAA 12 83 0 AAAATTAAAA 0.928865 -66 AAACTTTTAACAAACAATTCAAGGGATTTGGCGATT 12 123 1 CAAATTCAAA 0.69413 -26 TATTATCCTAAAATAGAGCGTTCCTTA 14 2 1 ATTATAAAAA 0.901634 -129 CGCAACAATTAAAAGCGTAAAAGCAAAAGGCGTTCC 14 54 0 AAAATAAAAA 0.937836 -77 GTATTTTTTCAAAATTATACAACAAAGCATTTAAAT 14 89 1 AAAATACAAA 0.778617 -42 CAACAAAGCATTTAAATTAAAAAGGATAGTCCA 14 108 1 TTTATAAAAA 0.79275 -23 AATTAAGCGACTAACCATTAAACTTAAGCGATAAAT 15 31 1 CTAATTAAAA 0.918319 -77 TTAAGCGATAAATAAGATAAAATTTAGGATAGCTCA 15 54 1 AATATAAAAA 0.888063 -54 TTCATTGTGTAAAAGAGTAAAACCATTCAAGTTTTT 16 83 0 AAAATAAAAT 0.832434 -119 AAGATTAAGCCTAACTTTAAAAATCAAGCCTTCAAA 18 15 0 CTAATAAAAA 0.928517 -89 GGCTTAATCTTTTATGTTAAAATTCTGAGATTTTAT 18 40 1 TTTATAAAAT 0.556427 -64 AAACCTAACGATAAATATAAAATATATAAAATCTCA 18 65 0 ATAATAAAAA 0.945676 -39 AACTTTAAACCTAAAACCTAACGATAAATA 18 84 0 TTAATAAAAA 0.879135 -20 TATCTTAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 19 11 0 TAAATTAAAA 0.844939 -128 **** ***** * Masking position 8 Map Score: 51.3569 Number of sites scoring better than the average of aligned sites = 1202 Number in coding regions = 809 Number in noncoding regions = 393 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 2 GATTTTAAATTAAACGGATTTACAAAAAATT 1 4 0 TAAATTAAAA 0.917385 -297 TCGTGTAATTTAAAACCATTGAACGAAACGATTTTAAA 1 33 0 TAAATTAGAA 0.822373 -268 TTACACAATGATAAGAATTTGAGTGATAATTTGTATTG 1 120 0 AAATTTAGAA 0.920613 -181 TGATAAACTCAAAAAGGTTGGAATGAGAATTAATTACC 1 165 1 AAATTGAGAA 0.780387 -136 TACAATCAAGTCAAATTCTTAAATAAAAGGTAAGCTC 1 274 1 TAACTTAAAA 0.746796 -27 ATTCTAAACAAAAAGTTTTTAAAGGCAAAAAGGCTGGC 2 53 1 AAATTTAGCA 0.63998 -248 TATTACAATTTTAAATTATGGATTAATAAAACTTAAAG 2 264 1 TAAATGAAAA 0.772864 -37 AACAAAATTTTAAAAAGATTAAATAATATTAAATTGAA 3 51 1 TAAATTAAAA 0.917385 -155 AATGGGGTTTATCAATATTTGACAAAAATAAGATCAAA 3 87 1 ACATTTAAAA 0.803467 -119 ATAAGATCAAAAAAATTTTTTATTAACTCTTTTGGTGT 3 114 1 AAATTTAAAT 0.590098 -92 AGGATAGCGATCAAGGTTTTTATGAAAATAAAAGCCTA 3 152 1 TAATTTAAAA 0.965295 -54 ATAAAAGCCTAAAACAATTTTAAAAAAAGGACTTTTG 3 179 1 AAATTTAAAA 0.965295 -27 AGGCTAAAATTAAAATCTTTGATTTAAAGTTTATAAGA 4 61 1 TAATTTATAA 0.642092 -128 TTATTTTAGCATAAGCCTTTTATAAAAACTTTAAACCT 4 131 0 AAATTTAAAA 0.965295 -58 TTTGATTATAATAAAAGATTTAAAAAAAGCGATAAAAT 6 68 1 AAAATTAAAA 0.917385 -74 TAATTAACGCTCAAAAAATTGAAAAAGAGTTCAAGGAA 7 18 0 TAAATTAAAA 0.917385 -151 CTAAAAAATCTAAATTATTGTAACAAAAGC 9 3 0 TAATTGAAAA 0.89499 -89 ACCGGTCATTTTAATTATTTTAGTATAATTGAAAGAAA 12 88 1 TAATTTAATA 0.609851 -61 TATAATTGAAAGAAACTTTTAACAAACAATTCAAGGGA 12 111 1 AAATTTAAAA 0.965295 -38 GAATACCCCTTTAATTAAGATTTAATATAT 13 46 0 AACTTTAAAA 0.803467 -20 AATAGCCCATTTTAATCAACAATTAAGCGAC 15 4 1 ACCTTTAAAA 0.37535 -104 TTAGGATAGCTCAAATCTTTTAAAAAGAAAAGGATAAC 15 77 1 TAATTTAAAA 0.965295 -31 GTTAATCCTTTAAATAATAGTGTCAGTTA 16 2 1 TAATTTAAAA 0.965295 -200 GTAAAACCATTCAAGTTTTTGATAGAAAAACACCCCAA 16 65 0 TAATTTAGAA 0.920613 -137 AGACAAGCCATGAAAAAAGAAAAGTC 17 3 1 AAAATGAAAA 0.772864 -24 CACTATTAGAACAAGGTTTTTATGACGAT 19 120 1 AAATTTAACA 0.810015 -19 * ** *** * ** * Masking position 9 Map Score: 28.5882 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 566 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 TGAGTGATAATTTGTATTGTTTTTAGCTTCATTT 1 105 0 TTTGTTTTTT 0.958653 -196 GTCTCATTTATTGGTAATGTTTTTTAATTTTAAA 1 215 0 TTGGTTTTTT 0.906701 -86 ATTTGACTTGATTGTAGCATGTTTTAAGCGGGTG 1 256 0 ATTGTTGTTT 0.661612 -45 CCTTTTTGCCTTTAAAAACTTTTTGTTTAGAATG 2 52 0 TTTAATTTTT 0.797056 -249 TAAGGTTTATTTTAACTTATTTTTACTATAATTC 2 193 0 TTTAATTTTT 0.797056 -108 AAAAATTTTTTTGATCTTATTTTTGTCAAATATT 3 100 0 TTGATTTTTT 0.910697 -106 AAAAAAATTTTTTATTAACTCTTTTGGTGTAGGA 3 122 1 TTTATTCTTT 0.743345 -84 ATTTTAGCCTTTTATTAGCTTTTTATAAAGTTTC 4 37 0 TTTATTTTTT 0.960521 -152 TGATTTAAAGTTTATAAGATTTTTGAGTATAGCA 4 80 1 TTTATTTTTT 0.960521 -109 TTAAACCTAATTGAGCGTATTTTTATGCTATACT 4 105 0 TTGAGTTTTT 0.829695 -84 TTTTGTTTGAATTATAGCTTTTTTAAAAAATAAT 5 20 0 ATTATTTTTT 0.865398 -52 CCTTAATCTTATTGGTTGGTTTTTGTTTGAATTA 5 40 0 ATTGGTTTTT 0.745354 -32 AAAAATCCACTTGGTTGGTTGTTTTTATCATAGA 6 37 0 TTGGTTGTTT 0.75617 -105 GCCTATCCATTTTATCGCTTTTTTTAAATCTTTT 6 80 0 TTTATTTTTT 0.960521 -62 CCTTGAACTCTTTTTCAATTTTTTGAGCGTTAAT 7 20 1 TTTTTTTTTT 0.721381 -149 TTTATGCTTATTTGTGGGGTGTTTTTAGCTTAAA 7 64 0 TTTGTTGTTT 0.880936 -105 CAATAACCCTTTTAGAGTGTTTTTGAGTTATTAT 13 11 1 TTTAGTTTTT 0.92078 -55 TATCCTAAATTTTATCTTATTTATCGCTTAAGTT 15 51 0 TTTATTTTAT 0.754268 -57 CAATAAGACTATTGGGGTGTTTTTCTATCAAAAA 16 54 1 ATTGGTTTTT 0.745354 -148 ATTCTGAGATTTTATATATTTTATATTTATCGTT 18 61 1 TTTATTTTAT 0.754268 -43 ***** ***** Masking position 10 Map Score: 19.4742 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 905 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 4 GAATGTTATAATTTATTATTAAACGAAAAGTAA 1 74 1 ATTATTTAAA 0.751307 -227 CTAGAACAAAATTTAAAATTAAAAAACATTACC 1 204 1 ATTAATTAAA 0.385435 -97 AAAAGCCCTTAGTTTTGTTTAGAAACCATTAAA 2 230 0 ATTTGTTAGA 0.668127 -71 TACAATTTTAAATTATGGATTAATAAAACTTAA 2 267 1 ATTAGATTAA 0.364343 -34 ATCTTTTTAAAATTTTGTTTTATAGTAAAACTC 3 37 0 ATTTGTTTAT 0.729962 -169 ACCCCATTCAATTTAATATTATTTAATCTTTTT 3 62 0 ATTATTTATT 0.496929 -144 TTTAAAATTGTTTTAGGCTTTTATTTTCATAAA 3 170 0 TTTAGTTTTA 0.606511 -36 AAATACGCTCAATTAGGTTTAAAGTTTTTATAA 4 117 1 ATTAGTTAAA 0.937462 -72 AACCTATCAATTATTTTTTAAAAAAGCTATA 5 9 1 ATTATTTTAA 0.690575 -63 AACCAAGTGGATTTTTGATTATAATAAAAGATT 6 55 1 ATTTGTTATA 0.853133 -87 TTGTGGGGTGTTTTTAGCTTAAAATTCATTATA 7 54 0 TTTTGTTAAA 0.609006 -115 TAGAGGTTGCATTTATGCTTATTTGTGGGGTGT 7 76 0 ATTAGTTATT 0.830552 -93 TTGTTACAATAATTTAGATTTTTTAGCTAGCAT 9 15 1 ATTTGTTTTT 0.660738 -77 ATTGTAATCTAATTTTGATTAAATTGAAGCGAT 10 18 0 ATTTGTTAAA 0.889656 -59 CTAGACCCTTATTTAAGCTTTAAATAACTATAA 10 52 0 ATTAGTTTAA 0.917178 -25 TTGATCTTGGAGTTAAGGTTTAAAATTTTAGCG 11 14 1 ATTAGTTTAA 0.917178 -50 TATATTTAACACTTAGGATTTTTA 12 2 0 ATTAGTTTTT 0.783601 -147 AGTGTTTTTGAGTTATTATTATATATTAAATCT 13 26 1 ATTATTTATA 0.685202 -40 ATACCCCTTTAATTAAGATTTAATATATAATAA 13 41 0 ATTAGTTTAA 0.917178 -25 CGCCTTTTGCTTTTACGCTTTTAATTGTTGCGT 14 58 1 TTTAGTTTTA 0.606511 -73 GCTATCCTAAATTTTATCTTATTTATCGCTTAA 15 54 0 ATTTTTTATT 0.346966 -54 TAATAGTGTCAGTTATGATTATATTCGCTCAAT 16 25 1 ATTAGTTATA 0.915257 -177 TTGGTTGTTAATTTTGGTTTAGAATAGAACATT 16 154 1 ATTTGTTAGA 0.668127 -48 TGATTTTTAAAGTTAGGCTTAATCTTTTATGTT 18 25 1 ATTAGTTAAT 0.871853 -79 GATTTTATATATTTTATATTTATCGTTAGGTTT 18 68 1 ATTTTTTTAT 0.352658 -36 TATCGTTAGGTTTTAGGTTTAAAGTT 18 88 1 TTTAGTTAAA 0.743324 -16 * *** * ***** Masking position 4 Map Score: 23.6021 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 321 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 AATGCGTGATAAACTCAAAAAGGTTGGAAT 1 159 1 AAACTCAAAA 0.633319 -142 AACAAAATTTAAAATTAAAAAACATTACCA 1 208 1 AAAATTAAAA 0.888712 -93 TGGATTAATAAAACTTAAAGGATAACACC 2 282 1 AAACTTAAAG 0.484767 -19 TGACAAAAATAAGATCAAAAAAATTTTTTA 3 106 1 AAGATCAAAA 0.76372 -100 ATAAAAGGCTAAAATTAAAATCTTTGATTT 4 56 1 AAAATTAAAA 0.888712 -133 ACCAACCAATAAGATTAAGGAGTAAAGT 5 54 1 AAGATTAAGG 0.716492 -18 AAAGCATGTTAAAATTAAGAGATTTAAACA 7 124 1 AAAATTAAGA 0.919755 -45 GATATTGTTAAAAAGTAAGCTAAGGAGTGT 9 70 1 AAAAGTAAGC 0.792401 -22 CCTTAACTCCAAGATCAAGCC 11 2 0 AAGATCAAGC 0.819642 -62 ATAACCCCCTAAAATTAAAACGACTAACGC 11 44 0 AAAATTAAAA 0.888712 -20 TTAAAAGCGTAAAAGCAAAAGGCGTTCCAA 14 52 0 AAAAGCAAAA 0.633319 -79 AAAATACGCAACAATTAAAAGCGTAAAAGC 14 66 0 ACAATTAAAA 0.636296 -65 ATTTTAATCAACAATTAAGCGACTAACCAT 15 19 1 ACAATTAAGC 0.710963 -89 ACTAACCATTAAACTTAAGCGATAAATAAG 15 40 1 AAACTTAAGC 0.792401 -68 CATTGTGTAAAAGAGTAAAACCATTCAAGT 16 87 0 AAGAGTAAAA 0.633319 -115 ATTCTAAACCAAAATTAACAACCAATTATT 16 149 0 AAAATTAACA 0.624821 -53 CCTAACTTTAAAAATCAAGCCTTCAAAAAC 18 12 0 AAAATCAAGC 0.877198 -92 TTTAACATAAAAGATTAAGCCTAACTTTAA 18 31 0 AAGATTAAGC 0.877198 -73 ********** Masking position 7 Map Score: 13.0092 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 562 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 6 ATTCTTATCATTGTGTAAAAATGCGTGATA 1 140 1 TTGTGTAAAA 0.846021 -161 TAAAAACTTTTTGTTTAGAATGTATTAACG 2 44 0 TTGTTTAGAA 0.901257 -257 GCCCTTAGTTTTGTTTAGAAACCATTAAAG 2 229 0 TTGTTTAGAA 0.901257 -72 ATTAAAATCTTTGATTTAAAGTTTATAAGA 4 69 1 TTGATTTAAA 0.576154 -120 ATTACACTCTATGATAAAAACAACCAACCA 6 30 1 ATGATAAAAA 0.52414 -112 AAGTGGATTTTTGATTATAATAAAAGATTT 6 59 1 TTGATTATAA 0.775618 -83 GACTCCTTATTTGATAAGAAACGCTTCTTT 6 116 0 TTGATAAGAA 0.815123 -26 TACCTTAAATTTGTTTAAATCTCTTAATTT 7 135 0 TTGTTTAAAT 0.695054 -34 GGCATGGATATTGTTAAAAAGTAAGCTAAG 9 64 1 TTGTTAAAAA 0.865253 -28 TAATCTAATTTTGATTAAATTGAAGCGATA 10 17 0 TTGATTAAAT 0.718595 -60 CTTGGAGTTAAGGTTTAAAATTTTAGCGTT 11 19 1 AGGTTTAAAA 0.539321 -45 CCGGTTAAAATGGAGTAAAATTTTTACCCA 12 63 0 TGGAGTAAAA 0.759714 -86 CGCTTAATTGTTGATTAAAATGGGCTATT 15 10 0 TTGATTAAAA 0.944207 -98 AACAATTTCATTGTGTAAAAGAGTAAAACC 16 95 0 TTGTGTAAAA 0.846021 -107 AATAAGCAAATGGATAATAAATAGAACAAT 16 119 0 TGGATAATAA 0.433701 -83 TTGTTAATTTTGGTTTAGAATAGAACATTA 16 158 1 TGGTTTAGAA 0.824252 -44 AAAGCGTTGTTTGATAAAAATGGCTCATTA 19 52 0 TTGATAAAAA 0.879386 -87 ********** Masking position 9 Map Score: 12.772 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 474 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 AAAACATGCTACAATCAAGTCAAATTCTTA 1 265 1 ACAATCAAGT 0.742871 -36 TGTTTAGAAACCATTAAAGTTTAAGGTTTA 2 218 0 CCATTAAAGT 0.79671 -83 TTGATAAACCCCATTCAATTTAATATTATT 3 72 0 CCATTCAATT 0.950845 -134 AACCTATCAATTATTTTTTAAA 5 3 1 CCTATCAATT 0.704559 -69 CAAACAAAAACCAACCAATAAGATTAAGGA 5 45 1 CCAACCAATA 0.76716 -27 ATAAAAACAACCAACCAAGTGGATTTTTGA 6 43 1 CCAACCAAGT 0.969277 -99 TTCTTTAAGCCTATCCATTTTATCGCTTTT 6 92 0 CTATCCATTT 0.520781 -50 TGTTAAACTACCATTAAATTTTTTGTAAGG 8 31 1 CCATTAAATT 0.793859 -28 TTTACCCACCCTAATAAAGTCATGCTACAA 12 41 0 CTAATAAAGT 0.475094 -108 CGTTCCAAATCCAACCATTTTTTAAGGAAC 14 30 0 CCAACCATTT 0.863455 -101 AAGAGTAAAACCATTCAAGTTTTTGATAGA 16 77 0 CCATTCAAGT 0.951707 -125 ACCAAAATTAACAACCAATTATTAATAAGC 16 142 0 ACAACCAATT 0.796637 -60 TGGTCTTATTCTATCCAATTAGCCCTTGAG 19 92 0 CTATCCAATT 0.841791 -47 ********** Masking position 7 Map Score: 6.82412 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 275 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 TGTAGCATGTTTTAAGCGGGTGGCTTTAAG 1 248 0 TTTAAGCGGG 0.840344 -53 AAAACTCATTTTTAAGGGGGATAGTTATCC 3 14 0 TTTAAGGGGG 0.958256 -192 TTATGCTTATTTGTGGGGTGTTTTTAGCTT 7 67 0 TTGTGGGGTG 0.795165 -102 GTCGTTTTAATTTTAGGGGGTTAT 11 50 1 TTTTAGGGGG 0.977659 -14 AGCATGACTTTATTAGGGTGGGTAAAAATT 12 45 1 TATTAGGGTG 0.946895 -104 CAATAACCCTTTTAGAGTGTTTTTGAGTT 13 10 1 TTTTAGAGTG 0.930005 -56 TCAATAAGACTATTGGGGTGTTTTTCTATC 16 53 1 TATTGGGGTG 0.897073 -149 TAGAATAGAACATTAGAGGGGATTTAAAGG 16 173 1 CATTAGAGGG 0.677056 -29 AACAACGCTTTTTAAGAGTGGCTCAAGGGC 19 71 1 TTTAAGAGTG 0.874525 -68 ********** Masking position 6 Map Score: 4.38 Number of sites scoring better than the average of aligned sites = 664 Number in coding regions = 580 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 ATTTATTATTAAACGAAAAGTAAATGAAGC 1 84 1 AAACGAAAAG 0.902143 -217 ATTCTTAAATAAAAGGTAAGCTC 1 288 1 AAAAGGTAAG 0.919747 -13 TCGTAAAAGGAATGCTTAGAAACT 2 5 1 AAAAGGAATG 0.877136 -296 AATACATTCTAAACAAAAAGTTTTTAAAGG 2 48 1 AAACAAAAAG 0.61445 -253 GGTTTTTATGAAAATAAAAGCCTAAAACAA 3 166 1 AAAATAAAAG 0.677618 -40 AAAAGCGATAAAATGGATAGGCTTAAAGAA 6 92 1 AAATGGATAG 0.643705 -50 GGATATTGTTAAAAAGTAAGCTAAGGAGTG 9 69 1 AAAAAGTAAG 0.664564 -23 ATTTAAATTAAAAAGGATAGTCCA 14 117 1 AAAAGGATAG 0.919747 -14 TTTTCTTTTTAAAAGATTTGAGCTATCCTA 15 78 0 AAAAGATTTG 0.457704 -30 AAATCTTTTAAAAAGAAAAGGATAACCCC 15 89 1 AAAAGAAAAG 0.955438 -19 AAGCCATGAAAAAAGAAAAGTC 17 15 1 AAAAGAAAAG 0.955438 -12 ********** Masking position 3 Map Score: 5.59561 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 267 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 ATAATTTGTATTGTTTTTAGCTTCATTTACTT 1 101 0 TTTTTTTGCT 0.687148 -200 GGAATGAGAATTAATTACCGCTAGAACAAAAT 1 184 1 TTATTACGCT 0.762582 -117 AAAAAAATTTTTTATTAACTCTTTTGGTGTAG 3 122 1 TTATTAATCT 0.714193 -84 TTTTTTAAAATTGTTTTAGGCTTTTATTTTCA 3 174 0 TTTTTTAGCT 0.772637 -32 TATAAGATTTTTGAGTATAGCATAAAAATACG 4 92 1 TTAGTATGCA 0.418808 -97 GGTTTTTGTTTGAATTATAGCTTTTTTAAAAA 5 25 0 TGATTATGCT 0.561813 -47 TTTTATCGCTTTTTTTAAATCTTTTATTATAA 6 73 0 TTTTTAATCT 0.772775 -69 TAAGAAACGCTTCTTTAAGCCTATCCATTTTA 6 100 0 TTTTTAACCT 0.666099 -42 AAAATTCATTATAATTAACGCTCAAAAAATTG 7 35 0 ATATTAAGCT 0.572397 -134 TACCTTAAATTTGTTTAAATCTCTTAATTTTA 7 133 0 TTTTTAATCT 0.772762 -36 CCATTAAATTTTTTGTAAGGCTAAAAAC 8 41 1 TTTGTAAGCT 0.919164 -18 ATGTTAGCAATTCATTAAGGCATGGATATTGT 9 46 1 TTATTAAGCA 0.71396 -46 CTTTTTTATCGCTTCAATTTAAT 10 2 1 TTTTTATGCT 0.942722 -75 AATATTATAGTTATTTAAAGCTTAAATAAGGG 10 48 1 TTTTTAAGCT 0.962181 -29 CAACCATTTTTTAAGGAACGCTCTATTTTAGG 14 17 0 TTAGGAAGCT 0.739598 -114 AAATTTTATCTTATTTATCGCTTAAGTTTAAT 15 47 0 TTTTTATGCT 0.942722 -61 TAAGATAAAATTTAGGATAGCTCAAATCTTTT 15 66 1 TTAGGATGCT 0.647355 -42 GACTTTTCTTTTTTCATGGCTTGTCT 17 6 0 TTTTCATGCT 0.676088 -21 GGTTTTTGAAGGCTTGATTTTTAA 18 3 1 TTTTGAAGCT 0.896448 -101 ** ***** *** Masking position 11 Map Score: 13.9116 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 748 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 11 TTAAACGGATTTACAAAAAATT 1 2 0 TTAAAAAAAT 0.880272 -299 GCCTTTTTGCCTTTAAAAACTTTTTGTTTAG 2 56 0 CTTAAAAACT 0.665282 -245 AAATTATGGATTAATAAAACTTAAAGGATAA 2 276 1 TTATAAAACT 0.520768 -25 AAAACAAAATTTTAAAAAGATTAAATAATAT 3 49 1 TTTAAAAGAT 0.799115 -157 CCAAAAGAGTTAATAAAAAATTTTTTTGATC 3 118 0 TAAAAAAAAT 0.525914 -88 CCTAAAACAATTTTAAAAAAAGGACTTTTG 3 186 1 TTTAAAAAAA 0.593034 -20 CATAAGCCTTTTATAAAAACTTTAAACCTAA 4 129 0 TTAAAAAACT 0.878081 -60 ATTATAGCTTTTTTAAAAAATAATTGATAGG 5 13 0 TTTAAAAAAT 0.944576 -59 TAATAAAAGATTTAAAAAAAGCGATAAAATG 6 76 1 TTTAAAAAAG 0.683699 -66 TTTAACATGCTTTTAAAAATTTAGAGAATAG 7 106 0 TTTAAAAATT 0.684113 -63 AATTAAGAGATTTAAACAAATTTAAGGTAAC 7 136 1 TTTAACAAAT 0.683699 -33 GTTTTTAGCCTTACAAAAAATTTAATGGTAG 8 38 0 TTAAAAAAAT 0.880272 -21 TTATTTAAGCTTTAAATAACTATAATATTGT 10 46 0 TTTAATAACT 0.588246 -31 GTTGTATAATTTTGAAAAAATACGCAACAAT 14 81 0 TTTAAAAAAT 0.944581 -50 ATCCTTTTCTTTTTAAAAGATTTGAGCTATC 15 81 0 TTTAAAAGAT 0.799115 -27 GGTGTTTTTCTATCAAAAACTTGAATGGTTT 16 69 1 TATAAAAACT 0.715844 -133 TTTTTAAAACTCTCTTTAAAA 19 1 1 TTTTAAAACT 0.715843 -138 *** ******* Masking position 6 Map Score: 10.89 Number of sites scoring better than the average of aligned sites = 836 Number in coding regions = 629 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 12 ACGAAACGATTTTAAATTAAACGGATTTACA 1 18 0 TTTAATTAAA 0.769045 -283 GTTCAATGGTTTTAAATTACACGATGCGAAT 1 47 1 TTTAATTACA 0.926814 -254 TGGTAATGTTTTTTAATTTTAAATTTTGTTC 1 207 0 TTTAATTTTA 0.873185 -94 ACTAAGGGCTTTTATATTACAATTTTAAATT 2 250 1 TTTTATTACA 0.583257 -51 ATATTACAATTTTAAATTATGGATTAATAAA 2 263 1 TTTAATTATG 0.787683 -38 AAATCAAAGATTTTAATTTTAGCCTTTTATT 4 55 0 TTTAATTTTA 0.873185 -134 TTGGTTTTTGTTTGAATTATAGCTTTTTTAA 5 28 0 TTTAATTATA 0.95917 -44 TGATCCTTATTTTAAATTACACTCTATGATA 6 15 1 TTTAATTACA 0.926814 -127 CCAAGTGGATTTTTGATTATAATAAAAGATT 6 57 1 TTTGATTATA 0.787725 -85 GCGTTAGTCGTTTTAATTTTAGGGGGTTAT 11 44 1 TTTAATTTTA 0.873185 -20 TAACCGGTCATTTTAATTATTTTAGTATAAT 12 86 1 TTTAATTATT 0.714593 -63 TAAAAGTTTCTTTCAATTATACTAAAATAAT 12 101 0 TTTAATTATA 0.95917 -48 CAACAAAGCATTTAAATTAAAAAGGATAGTC 14 108 1 TTTAATTAAA 0.769045 -23 GTTAATCCTTTAAATAATAGTGTCAGTTA 16 9 1 TTTAATAATA 0.696505 -193 *** ******* Masking position 6 Map Score: 16.7356 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 31 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 CCATTGAACGAAACGATTTTAAATTAAACGGA 1 24 0 AAACATTTAA 0.862721 -277 GTTTTAAATTACACGATGCGAATGTTATAATT 1 55 1 ACACATGGAA 0.917557 -246 ACGCATTTTTACACAATGATAAGAATTTGAGT 1 134 0 ACACATGTAA 0.962802 -167 TTATAGTAAAACTCATTTTTAAGGGGGATAGT 3 19 0 ACTCTTTTAA 0.698451 -187 TTACTATAAAACAAAATTTTAAAAAGATTAAA 3 42 1 ACAAATTTAA 0.76054 -164 TAAAAGCCTAAAACAATTTTAAAAAAAGGACT 3 180 1 AAACATTTAA 0.862719 -26 TTTAAATTACACTCTATGATAAAAACAACCAA 6 25 1 ACTCATGTAA 0.921385 -117 ATTTAAGGTAACACGATTATAAAG 7 155 1 ACACATTTAA 0.973229 -14 TAAAAATTTTACTCCATTTTAACCGGTCATTT 12 67 1 ACTCATTTAA 0.94273 -82 TAGAATAAGACCACTATTAGAACAAGGTTTTT 19 109 1 CCACATTGAA 0.765252 -30 **** *** *** Masking position 7 Map Score: 5.36992 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 70 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 ATTAAAGTTTAAGGTTTATTTTAACTTATT 2 206 0 AAGGTTTATT 0.773296 -95 AAACAAAACTAAGGGCTTTTATATTACAAT 2 243 1 AAGGGCTTTT 0.965862 -58 ATTTTAAAAAAAGGACTTTTG 3 195 1 AAGGACTTTT 0.814493 -11 AACACTCTAAAAGGGTTATTG 13 2 0 AAGGGTTATT 0.956598 -64 ATCTTAATTAAAGGGGTATTC 13 55 1 AAGGGGTATT 0.948799 -11 GTTGATTAAAATGGGCTATT 15 1 0 ATGGGCTATT 0.931236 -107 AGAGTGGCTCAAGGGCTAATTGGATAGAAT 19 85 1 AAGGGCTAAT 0.931236 -54 ********** Masking position 1 Map Score: 3.41134 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 154 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 15 CCACCCGCTTAAAACATGCTACAATCAAGT 1 255 1 AAAACATGCT 0.898912 -46 TCTCTTAATTTTAACATGCTTTTAAAAATT 7 116 0 TTAACATGCT 0.975382 -53 TAATGGTAGTTTAACATGCTTAGAGATAAA 8 17 0 TTAACATGCT 0.975382 -42 TAATGAATTGCTAACATGCTAGCTAAAAAA 9 33 0 CTAACATGCT 0.970846 -59 ********** Masking position 6 Map Score: 0.830887 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 21 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617