AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_hpyl_reg_300.orf -o00251_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: HP0406 25 H. pylori predicted coding region HP0406 Input sequences: #1 HP0056 300 delta-1-pyrroline-5-carboxylate dehydrogenase {Synechocystis sp.) #2 HP0329 248 NH(3)-dependent NAD+ synthetase (nadE) #3 HP0380 65 glutamate dehydrogenase (gdhA) #4 HP0382 182 zinc-metallo protease (YJR117W) #5 HP0404 80 protein kinase C inhibitor (SP:P16436) #6 HP0407 103 biotin sulfoxide reductase (bisC) #7 HP0408 165 H. pylori predicted coding region HP0408 #8 HP0417 168 methionyl-tRNA synthetase (metS) #9 HP0476 117 glutamyl-tRNA synthetase (gltX) #10 HP0512 290 glutamine synthetase (glnA) #11 HP0549 37 glutamate racemase (glr) #12 HP0550 263 transcription termination factor Rho (rho) #13 HP0640 62 poly(A) polymerase (papS) #14 HP0643 164 glutamyl-tRNA synthetase (gltX) #15 HP0919 98 carbamoyl-phosphate synthase (glutamine-hydrolysing) (pyrAb) #16 HP0920 143 conserved hypothetical integral membrane protein #17 HP1234 300 conserved hypothetical integral membrane protein #18 HP1236 78 H. pylori predicted coding region HP1236 #19 HP1530 152 purine nucleoside phosphorylase (punB) #20 HP1531 42 H. pylori predicted coding region HP1531 Motif number 1 ACGAAAAGTAAATGAAGCTAAAAACAATACAAAT 1 96 1 AAACTAAAAA 0.930555 -205 AAAATGCGTGATAAACTCAAAAAGGTTGGAATGA 1 157 1 ATACAAAAAG 0.64726 -144 CTAGAACAAAATTTAAAATTAAAAAACATTACCA 1 204 1 ATAATTAAAA 0.578596 -97 ATTACCAATAAATGAGACTTAAAGCCACCCGCTT 1 231 1 AAACTTAAAG 0.932477 -70 GTGTTACAATAAAAACACTTAAAACAATAAAGGA 3 34 1 AAACTTAAAA 0.972955 -32 TTTGAGCGTTTTTAATCCTAAAAAGCTGTGTTAT 4 40 0 TTACTAAAAA 0.87655 -143 AAAATTTACCATAAAACCATAAAATTAAATAAAT 4 96 0 ATACATAAAA 0.927704 -87 TTTAATAAAAGAAAAACCTTAAAAGGGAGCAAAA 5 53 1 GAACTTAAAA 0.749783 -28 TGTTTTCAATATTGACGCTTATAAGGATAAAAG 7 143 1 ATACTTATAA 0.803056 -23 ATTCATTATAATTAACGCTCAAAAAATTGAAAAA 8 30 0 ATACTCAAAA 0.823221 -139 TTATAATGAATTTTAAGCTAAAAACACCCCACAA 8 53 1 TTACTAAAAA 0.618312 -116 ATTGTATTCAAAAATGGCTTAAAAATGGTTTCAC 9 65 0 AATCTTAAAA 0.60083 -53 TGTTCTAACCTTAAAAATAAAATACT 9 102 0 TTACTTAAAA 0.949064 -16 TTATTTTTAAATTTAAACTTAAAATTATAGCATA 12 21 1 ATACTTAAAA 0.980314 -243 AGTGTAACCAAAAGATGCTAATAAGTGGCCCATG 12 156 0 AAACTAATAA 0.505257 -108 CAAAAAGCTAAAGCATTCTTAAAAAATTAGTGTA 12 184 0 AAACTTAAAA 0.972955 -80 CAATTAAGATAAAAATACAAAAAGCTAAAGCATT 12 201 0 AAACAAAAAG 0.552303 -63 AAAATTCCTTAAAAATTCTAAAAAGATATAATAA 13 12 1 AAACTAAAAA 0.930556 -51 GCTTTTTACTCTTAAAATTTCTTTGTG 13 46 0 TTACTTAAAA 0.944757 -17 GCTTTTTGATAACCAACCATAAAAAGCTTGGCGT 14 22 1 AAACATAAAA 0.896137 -143 AAACCTAATAAAAAATACTTTAAAATATTGATAA 15 41 1 AAACTTTAAA 0.732747 -58 AACTAATCCTTAAAGAAAGAATGTA 15 84 0 ACACTTAAAG 0.800338 -15 AAAATTGAAATTGAAGTCTGAAAATAGGATAATA 16 17 0 TTACTGAAAA 0.624083 -127 GGGATTTAAAAAGCTTAAAAAGAGTTTTCT 17 7 1 TAACTTAAAA 0.926684 -294 TTATAGAAATATGAAAACATAAAAACACGAATCC 17 93 0 ATACATAAAA 0.927711 -208 CTTTTATGCGTTTAAAGCTTAAAAACTTTAAGTC 17 225 1 TTACTTAAAA 0.603437 -76 AAAATCTCTAATTAAGACTTAAAGTTTTTAAGCT 17 240 0 ATACTTAAAG 0.953576 -61 GCATTTTACCCATAAAGATTTTAGGGT 17 284 0 TTACATAAAG 0.637153 -17 ATTAATTCTTTAAAAAGCGTTTTA 18 1 1 ATACTTTAAA 0.802993 -78 AAACGATAAAATACACTCTAAAAATAAATAAAAT 18 41 1 ATACTAAAAA 0.952225 -38 TGAAATGTGAATGAAGCCTTAAAATTAAGGTGTT 19 63 1 ATACTTAAAA 0.981655 -90 AGCATTATAGACAAACCCTTAAAAGAAACACCTT 19 89 0 ACACTTAAAA 0.912606 -64 ** * ******* Masking position 13 Map Score: 38.7318 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 675 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 ATTAAACGGATTTACAAAAAATT 1 3 0 TTTACAAAAA 0.545055 -298 AACGAAACGATTTTAAATTAAACGGATTTAC 1 19 0 TTTTAATTAA 0.89449 -282 TTACTTTTCGTTTAATAATAAATTATAACAT 1 76 0 TTTAAAATAA 0.854 -225 TAGAACAAAATTTAAAATTAAAAAACATTAC 1 205 1 TTTAAATTAA 0.912085 -96 CAAGTCAAATTCTTAAATAAAAGGTAAGCTC 1 280 1 TCTTAATAAA 0.395688 -21 CAAGTATTTATTTTACCATAATGGGAGCGAT 2 36 1 TTTTACATAA 0.904535 -213 AAAAGCTAATTTTTCACTTAAACGATGCGTT 2 207 1 TTTTCCTTAA 0.898442 -42 ATTAAAACTTAATTACCCTTTT 3 2 1 TTAAACTTAA 0.778076 -64 TTTGAGCGTTTTTAATCCTAAAAAGCTGTGT 4 43 0 TTTAACCTAA 0.686407 -140 TTTTCAAAAATTTACCATAAAACCATAAAAT 4 105 0 TTTACATAAA 0.679897 -78 CTCCATTAAATTTACCAATAAAAGTGTAGGA 4 147 0 TTTACAATAA 0.754736 -36 ATTATAGCTTTTTAAAAATAAAATATAAGGA 5 17 0 TTTAAAATAA 0.854 -64 TTTTAAATTAACGCCCATGCT 6 1 1 TTTTAATTAA 0.89449 -103 TGTGGGGTGTTTTTAGCTTAAAATTCATTAT 8 55 0 TTTTACTTAA 0.943844 -114 GGTTTCACTTTTTTCTATTAAAATTAGTGTA 9 42 0 TTTTCATTAA 0.816852 -76 TGTTCTAACCTTAAAAATAAAATA 9 104 0 TCTAACTTAA 0.803283 -14 TAAGTTTAAATTTAAAAATAAAGGATACTTG 12 11 0 TTTAAAATAA 0.854 -253 TATTTTTAAATTTAAACTTAAAATTATAGCA 12 22 1 TTTAACTTAA 0.953581 -242 AAACTTAAAATTATAGCATAAGTCATAATAA 12 35 1 TTATACATAA 0.617461 -229 CTTTTTGTATTTTTATCTTAATTGCAACAAA 12 211 1 TTTTACTTAA 0.943844 -53 TAAATTTCCTTTTAACAAAAAGAGATTTCT 12 244 0 TTTTACAAAA 0.786707 -20 GCTTTTTACTCTTAAAATTTCTTTG 13 48 0 TTTACCTTAA 0.915436 -15 TAGTTTTTGATTATACCTAAAGAATACTTAA 14 124 0 TTATACTAAA 0.526998 -41 CAAAAACTATTTTTAAATAAAGGGTTTTT 14 146 1 TTTTAATAAA 0.767411 -19 TTTTATGCGTTTAAAGCTTAAAAACTTTAAG 17 226 1 TTAAACTTAA 0.778076 -75 TTTAGGGTAGTTTAACCTAAAATCTCTAATT 17 261 0 TTTAACTAAA 0.888333 -40 GCATTTTACCCATAAAGATTTTAGG 17 286 0 TTTACCATAA 0.85923 -15 TTAAAAAGCGTTTTATCTAAAAAACGATAAA 18 20 1 TTTTACTAAA 0.867241 -59 TAAAATACACTCTAAAAATAAATAAAATATG 18 47 1 TCTAAAATAA 0.536731 -32 ***** ***** Masking position 10 Map Score: 31.8037 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 444 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 3 CCACCCGCTTAAAACATGCTACAATCAAGTCAA 1 255 1 AAAAATCTCA 0.812402 -46 ATAATGTTTAAAAACATGCAGAATATTAAGAAA 2 65 1 AAAAATCAAA 0.736817 -184 AGTGTTACAATAAAAACACTTAAAACAATAAAG 3 33 1 TAAAACCTAA 0.923399 -33 TTTTTAGGATTAAAAACGCTCAAAAATAGTCTC 4 50 1 TAAAACCTAA 0.923399 -133 TAACGATCCTTATATTTTATTTT 5 1 1 TAACATCTAT 0.385703 -80 GCATTCTGTTAAAACACCCCAAATTCTAACATA 6 64 0 AAAAACCCAA 0.884642 -40 AAGTCTTTCTAAAACACCCTCATGCTAGTATGT 7 20 0 AAAAACCTAT 0.923399 -146 TTTTAAGCTAAAAACACCCCACAAATAAGCATA 8 63 1 AAAAACCCCA 0.599444 -106 ATCCTAATCAAAAATAATCTCAATCATACACTA 9 16 1 AAAAAACTAA 0.738194 -102 CCTTAAAAATAAAATACTCTTATTGTATTCAAA 9 87 0 AAAAACCTAT 0.923396 -31 GATTTTCTTCAAAAAATCCTAATAGTGTGGTTG 10 118 1 AAAAATCTAT 0.871915 -173 TGCATGCGGTAAAATCCGCTAAATCAAGGAGTG 10 169 0 AAAACCCTAA 0.873634 -122 TAATAAATTAAAACCACTCTAAAGTTAAATAAA 12 60 1 AAACACCTAA 0.921971 -204 TAGTGTAACCAAAAGATGCTAATAAGTGGCCCA 12 158 0 AAAAATCTAT 0.871912 -106 ACAAAAAGCTAAAGCATTCTTAAAAAATTAGTG 12 186 0 AAAGATCTAA 0.820811 -78 GCAATTAAGATAAAAATACAAAAAGCTAAAGCA 12 203 0 TAAAATCAAA 0.462023 -61 CAAAATTCCTTAAAAATTCTAAAAAGATATAAT 13 11 1 TAAAATCTAA 0.871915 -52 GATTATACCTAAAGAATACTTAATTGTGTTGTG 14 114 0 AAAGATCTAA 0.820812 -51 AAAACCTAATAAAAAATACTTTAAAATATTGAT 15 40 1 AAAAATCTTA 0.736814 -59 AATACCAAACAAAACCCCCTAAAATTGAAATTG 16 38 0 AAAACCCTAA 0.873634 -106 ATTTTAGGTTAAACTACCCTAAAATCTTTATGG 17 269 1 AAACACCTAA 0.921971 -32 AAAAAACGATAAAATACACTCTAAAAATAAATA 18 38 1 AAAAACCTTA 0.83215 -41 **** ** ** ** Masking position 3 Map Score: 19.6366 Number of sites scoring better than the average of aligned sites = 1035 Number in coding regions = 877 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 CACGATGCGAATGTTATAATTTATTATTAA 1 66 1 ATGTTATAAT 0.963769 -235 CGCTTAAAACATGCTACAATCAAGTCAAAT 1 260 1 ATGCTACAAT 0.903482 -41 TTAGCTTTTCTTGCTATAATCATCGTTTCA 2 186 0 TTGCTATAAT 0.910836 -63 TTTTGAAAAATTGTTATAATTCCTACACTT 4 127 1 TTGTTATAAT 0.846042 -56 TATTTTTAAAAAGCTATAATACAACTTTAA 5 28 1 AAGCTATAAT 0.852801 -53 AGGTGAATCTATGTTAGAATTTGGGGTGTT 6 55 1 ATGTTAGAAT 0.822561 -49 CTCAATTTTTATATTATAATACCCAATCAA 7 100 1 ATATTATAAT 0.639241 -66 TTTTAAAAGCATGTTAAAATTAAGAGATTT 8 119 1 ATGTTAAAAT 0.767317 -50 TGCCCCATAAATGCTATAATCACCCCTATC 10 236 1 ATGCTATAAT 0.979802 -55 ATTATGACTTATGCTATAATTTTAAGTTTA 12 34 0 ATGCTATAAT 0.979802 -230 ATTCTTTGCTATGCTATCATAATTTTTTTA 12 105 0 ATGCTATCAT 0.855351 -159 TGGTAAAATCATGTTATAACAATGTTCTAG 17 185 0 ATGTTATAAC 0.809293 -116 CCACTTATTCACGCTATAATAACGCC 19 7 0 ACGCTATAAT 0.895685 -146 ********** Masking position 6 Map Score: 12.6255 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 44 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 AATGTTTTTTAATTTTAAATTTTGTTCTAG 1 204 0 AATTTTAAAT 0.361285 -97 ATCAAGTCAAATTCTTAAATAAAAGGTAAG 1 278 1 ATTCTTAAAT 0.616804 -23 GACAAACCTTTTTGTTTATAGCGGGTT 4 8 1 CTTTTTGTTT 0.561086 -175 TTTATGGTAAATTTTTGAAAAATTGTTATA 4 115 1 ATTTTTGAAA 0.858031 -68 CTTATATTTTATTTTTAAAAAGCTATAATA 5 19 1 ATTTTTAAAA 0.857521 -62 GTAATTCTCAATTTTTATATTATAATACCC 7 94 1 ATTTTTATAT 0.736576 -72 TCCTTGAACTCTTTTTCAATTTTTTGAGCG 8 19 1 CTTTTTCAAT 0.763783 -150 TATTCTCTAAATTTTTAAAAGCATGTTAAA 8 107 1 ATTTTTAAAA 0.857521 -62 GATTGAGATTATTTTTGATTAGGATCAACC 9 11 0 ATTTTTGATT 0.779183 -107 TTTTTAAGCCATTTTTGAATACAATAAGAG 9 74 1 ATTTTTGAAT 0.906114 -44 ATTCCCACCAATTTTTATAATATCATCCCA 10 17 1 ATTTTTATAA 0.635822 -274 GACACTATTTTTAATTTAATGGGATT 11 22 0 ATTTTTAATT 0.778438 -16 AGTATCCTTTATTTTTAAATTTAAACTTAA 12 13 1 ATTTTTAAAT 0.904498 -251 AAGCTAAAGCATTCTTAAAAAATTAGTGTA 12 184 0 ATTCTTAAAA 0.502332 -80 AATGCTTTAGCTTTTTGTATTTTTATCTTA 12 201 1 CTTTTTGTAT 0.778115 -63 CTAGAAATCTCTTTTTGTTAAAAGGAAATT 12 242 1 CTTTTTGTTA 0.443866 -22 ACGCTGTTAGCTTTTTGATAACCAACCATA 14 13 1 CTTTTTGATA 0.733484 -152 ATCAAAAACTATTTTTAAATAAAGGGTTTT 14 144 1 ATTTTTAAAT 0.904498 -21 TCTTTTTAAGCTTTTTAAATCCC 17 4 0 CTTTTTAAAT 0.922918 -297 CTCCTAGACCCTTTTTAAAGGGTTTGAATG 17 49 0 CTTTTTAAAG 0.763352 -252 AACACGAATCCTTTTTGAAAATAAACTCCT 17 74 0 CTTTTTGAAA 0.883036 -227 AGATAAAACGCTTTTTAAAGAATTAAT 18 8 0 CTTTTTAAAG 0.763352 -71 CATGTTATTCCTTTTTCATTCACCACTTAT 19 29 0 CTTTTTCATT 0.541011 -124 ********** Masking position 5 Map Score: 19.0488 Number of sites scoring better than the average of aligned sites = 1372 Number in coding regions = 1063 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 6 ATTATCACTCAAATTCTTATCATTGTGTAA 1 128 1 AAATTCTTAT 0.430902 -173 CAATCAAGTCAAATTCTTAAATAAAAGGTA 1 276 1 AAATTCTTAA 0.715418 -25 AATCAAATCTCCTAGCGTGTTTAAG 2 6 1 AATCTCCTAG 0.739287 -243 GTTACAATAAAAACACTTAAAACAATAAAG 3 36 1 AAACACTTAA 0.717352 -30 ATTCCAAACTCCTTTCTCCATTAAA 4 168 0 AAACTCCTTT 0.836627 -15 AATTTGTTTAAATCTCTTAATTTTAACATG 8 128 0 AATCTCTTAA 0.79323 -41 TTTTCTTCAAAAAATCCTAATAGTGTGGTT 10 120 1 AAAATCCTAA 0.577359 -171 TTCCATAATAACACTCCTTGATTTAGCGGA 10 158 1 ACACTCCTTG 0.466836 -133 ACAAACTAGAAATCTCTTTTTGTTAAAAGG 12 237 1 AATCTCTTTT 0.557053 -27 CAAAATTCCTTAAAAATTCTAA 13 3 1 AAATTCCTTA 0.773645 -60 TTACTCTTAAAATTTCTTTGTGTTATTATA 13 38 0 AATTTCTTTG 0.331857 -25 GCCAAGTGCTAATCTCTTAAATGATGCCTA 14 58 1 AATCTCTTAA 0.79323 -107 AAAAACCCTTTATTTAAAAATA 14 153 0 AAACCCTTTA 0.850864 -12 ACCTAATAAAAAATACTTTAAAATATTGAT 15 43 1 AAATACTTTA 0.357034 -56 TACCAAACAAAACCCCCTAAAATTGAAATT 16 39 0 AACCCCCTAA 0.423438 -105 CACTATTAGAAAACTCTTTTTAAGCTTTTT 17 18 0 AAACTCTTTT 0.803907 -283 AGTGGCATTCAAACCCTTTAAAAAGGGTCT 17 44 1 AAACCCTTTA 0.850864 -257 TTTTGAAAATAAACTCCTAGACCCTTTTTA 17 62 0 AAACTCCTAG 0.902381 -239 TCAGCATTTCAAACTCCTTATAGAAATATG 17 114 0 AAACTCCTTA 0.944452 -187 ACAAAAGGTAAAACTCCTAGAACATTGTTA 17 169 1 AAACTCCTAG 0.902381 -132 AAACTACCCTAAAATCTTTATGGGTAAAAT 17 279 1 AAAATCTTTA 0.543447 -22 CCCTTAAAAGAAACACCTTAATTTTAAGGC 19 78 0 AAACACCTTA 0.775308 -75 CATTATAGACAAACCCTTAAAAGAAACACC 19 91 0 AAACCCTTAA 0.83979 -62 ********** Masking position 8 Map Score: 17.3506 Number of sites scoring better than the average of aligned sites = 1046 Number in coding regions = 864 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 7 AATGATAAGAATTTGAGTGATAATTTGTATTG 1 120 0 ATTGAGTGAA 0.879099 -181 ACTCAAAAAGGTTGGAATGAGAATTAATTACC 1 171 1 GTGGAATGAA 0.980121 -130 AAAACGCATCGTTTAAGTGAAAAATTAGCTTT 2 208 0 GTTAAGTGAA 0.692446 -41 CAATAAAAGTGTAGGAATTATAACAATTTTTC 4 131 0 GTGGAATTAA 0.81159 -52 TAAAATTAGTGTATGATTGAGATTATTTTTGA 9 23 0 GTTGATTGAA 0.943375 -95 ATAAAAATTGGTGGGAATGATAAG 10 3 0 GTGGAATGAA 0.980121 -288 CCTCTGATAGATAGGAATGACAAATTGATTGT 10 83 1 ATGGAATGAA 0.932938 -208 TATGAATTGAGTTTGATTGATAGGGGTGATTA 10 252 0 GTTGATTGAA 0.943375 -39 TTTTTAAAGGGTTTGAATGCCACTATTAGAAA 17 36 0 GTTGAATGCA 0.904678 -265 AAGGAATAACATGTGAATGAAATGTGAATGAA 19 46 1 ATTGAATGAA 0.927749 -107 ** ******* * Masking position 6 Map Score: 7.04526 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 48 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 AATGAGAATTAATTACCGCTAGAACAAAAT 1 186 1 AATTACCGCT 0.973058 -115 ATTAAAACTTAATTACCCTTTTAGTGTTAC 3 11 1 AATTACCCTT 0.82337 -55 TTTTAAATTAACGCCCATGCTGAGG 6 6 1 AATTAACGCC 0.758198 -98 ATTCACCTAAAATTACCGCTAATAAGCCCT 6 33 0 AATTACCGCT 0.973058 -71 CATTCTGTTAAAACACCCCAAATTCTAACA 6 66 0 AAACACCCCA 0.847084 -38 AAAAATTGAGAATTACCCCACGCTTCAGCT 7 80 0 AATTACCCCA 0.965504 -86 AATTCATTATAATTAACGCTCAAAAAATTG 8 35 0 AATTAACGCT 0.910639 -134 TTTAAGCTAAAAACACCCCACAAATAAGCA 8 64 1 AAACACCCCA 0.847084 -105 TAAATGCTATAATCACCCCTATCAATCAAA 10 243 1 AATCACCCCT 0.974352 -48 AAATAATTTTAATTAACCCTACAGCTAGGT 16 98 0 AATTAACCCT 0.937713 -46 ********** Masking position 5 Map Score: 9.5549 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 170 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 ATCATTGTGTAAAAATGCGTGATAAACTCAAAAAGG 1 146 1 AAATTGAAAA 0.939132 -155 GCCTTAAATTATAATAGAAAAAACGCATCGTT 2 227 0 AAATAGAAAA 0.95792 -22 AAAATTAAATAAATATGGTAGAAAAAAGAGACTATT 4 74 0 AAATAGAAAA 0.95792 -109 TAGGAATTATAACAATTTTTCAAAAATTTACCATAA 4 116 0 AAATTCAAAA 0.66643 -67 ATAATACAACTTTAATAAAAGAAAAACCTTAAAAGG 5 43 1 TTATAGAAAA 0.622048 -38 ATTGATTGGGTATTATAATATAAAAATTGAGAATTA 7 95 0 TAATATAAAA 0.574691 -71 ATCATACACTAATTTTAATAGAAAAAAGTGAAACCA 9 38 1 AATTAGAAAA 0.67574 -80 TATTGTATTCAAAAATGGCTTAAAAATGGTTTCACT 9 64 0 AAATTTAAAA 0.773035 -54 CAAAAAGCTAAAGCATTCTTAAAAAATTAGTGTAAC 12 182 0 AAATTAAAAA 0.703877 -82 AATGATGCCTATTCATGTTTGATAAAAACAGAACTA 14 77 1 ATATTGAAAA 0.805774 -88 CAAAATGTAGTAAAATACCAAACAAAACCCCCTAAA 16 48 0 TAATAAAAAA 0.485333 -96 AAGCTTCTAGAATGATTCTAGACAAAACAAAAGGTA 17 143 1 AAATAGAAAA 0.95792 -158 ATTAATTCTTTAAAAAGCGTTTTATC 18 1 1 ATATTTAAAA 0.47803 -78 AAAATAAATAAAATATGCGAGAAAAATC 18 61 1 AAATAGAAAA 0.95792 -18 ATTATAAAGCAAGCATTATAGACAAACCCTTAAAAG 19 98 0 AAATAGAAAA 0.95792 -55 ** ** *** *** Masking position 12 Map Score: 9.84653 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 154 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 AAAAACATTACCAATAAATGAGACTTAAAG 1 225 1 CCAATAAATG 0.956521 -76 ATTAAATTTACCAATAAAAGTGTAGGAATT 4 144 0 CCAATAAAAG 0.831329 -39 ACTCCTTTCTCCATTAAATTTACCAATAAA 4 156 0 CCATTAAATT 0.829348 -27 ATTATAATACCCAATCAATGCGTTTAATTT 7 112 1 CCAATCAATG 0.884136 -54 ATAATATCATCCCATAATTGTTCGCATTAT 10 33 1 CCCATAATTG 0.894518 -258 CTTTTTTTGCCCCATAAATGCTATAATCAC 10 229 1 CCCATAAATG 0.959763 -62 TAACCACCTTTAATTGTTATGAATTG 10 275 0 CCTTTAATTG 0.7332 -16 CTAATTAATCCCATTAAATTAAAAATAGTG 11 16 1 CCATTAAATT 0.829348 -22 AAGTGCTAATCTCTTAAATGATGCCTATTC 14 61 1 CTCTTAAATG 0.630573 -104 CATGATTTTACCAATCAATGCAACTTTTAT 17 202 1 CCAATCAATG 0.884136 -99 TATAGACAAACCCTTAAAAGAAACACCTTA 19 88 0 CCCTTAAAAG 0.841902 -65 GTGATCGCCTTTAATTTAGAATGCTCC 20 26 0 CCTTTAATTT 0.387421 -17 ********** Masking position 7 Map Score: 8.16522 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 245 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 AAGGTTGGAATGAGAATTAATTACCGCTAG 1 178 1 TGAGAATTAA 0.85381 -123 TACCAATAAATGAGACTTAAAGCCACCCGC 1 233 1 TGAGACTTAA 0.931906 -68 ATTAAAACTTAATTACCCTTTT 3 3 1 TAAAACTTAA 0.561116 -63 GTTACAATAAAAACACTTAAAACAATAAAG 3 36 1 AAACACTTAA 0.692477 -30 GGTGTTTTAGAAAGACTTAAGCGCTAAAGA 7 35 1 AAAGACTTAA 0.945622 -131 CTTAAGCGCTAAAGACTTGAGCGCTAGCCA 7 50 1 AAAGACTTGA 0.766074 -116 ATATAAAAATTGAGAATTACCCCACGCTTC 7 84 0 TGAGAATTAC 0.691505 -82 GTTAAAATTAAGAGATTTAAACAAATTTAA 8 131 1 AGAGATTTAA 0.678401 -38 ATAGCATAGCAAAGAATTACGAAATTCAAC 12 118 1 AAAGAATTAC 0.740141 -146 AATCTCTAATTAAGACTTAAAGTTTTTAAG 17 242 0 TAAGACTTAA 0.936036 -59 AACGCTTTTTAAAGAATTAAT 18 2 0 AAAGAATTAA 0.881252 -77 ********** Masking position 5 Map Score: 3.77142 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 75 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 TATAACATTCGCATCGTGTAATTTAAAACCATTG 1 50 0 GCATCTGTAT 0.934252 -251 ATTGTTTTTAGCTTCATTTACTTTTCGTTTAATA 1 90 0 GCTTCTTTAT 0.97489 -211 CTTGATTGTAGCATGTTTTAAGCGGGTGGCTTTA 1 250 0 GCATGTTTAG 0.829926 -51 AAACATTATCGCTCCCATTATGGTAAAATAAATA 2 40 0 GCTCCATTAT 0.555692 -209 TAGAAAAAACGCATCGTTTAAGTGAAAAATTAGC 2 211 0 GCATCTTTAG 0.957816 -38 GAGCGGCATCCTTTATTGTTTTAAGTGTT 3 47 0 GCATCTTTAT 0.97825 -19 CAAGTATCCTTTATTTTTAAATTTAAA 12 4 1 GTATCTTTAT 0.747631 -260 GAATGCTTTAGCTTTTTGTATTTTTATCTTAATT 12 200 1 GCTTTTGTAT 0.491471 -64 ACATGAATAGGCATCATTTAAGAGATTAGCACTT 14 61 0 GCATCTTTAG 0.957816 -104 TATTGATAACGCTTCGTTTACATTCTTTCTTTAA 15 66 1 GCTTCTTTAT 0.97489 -33 TAATTTTAAGGCTTCATTCACATTTCATTCACAT 19 56 0 GCTTCTTCAT 0.85962 -97 TGTCTATAATGCTTGCTTTATAATAAGCTAATGG 19 110 1 GCTTGTTTAT 0.892979 -43 TCCTTTTTTCGCATCCATTAGCTTATTATAAAGC 19 124 0 GCATCATTAT 0.901829 -29 ***** **** * Masking position 10 Map Score: 10.921 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 71 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ********** No masking Map Score: -2.06525e-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 14 AACCATTGAACGAAACGATTTTAAATTAAA 1 28 0 CGAAACGATT 0.565296 -273 TTATAACATTCGCATCGTGTAATTTAAAAC 1 55 0 CGCATCGTGT 0.962543 -246 CCTACAGGACCGCAACCTGTTGCTCTATTC 2 128 1 CGCAACCTGT 0.852224 -121 ATAGAAAAAACGCATCGTTTAAGTGAAAAA 2 216 0 CGCATCGTTT 0.983543 -33 GAGCGGCATCCTTTATTGTTTTAA 3 52 0 GGCATCCTTT 0.928067 -14 AGAAATTAAACGCATTGATTGGGTATTATA 7 114 0 CGCATTGATT 0.70276 -52 AACATGAATAGGCATCATTTAAGAGATTAG 14 66 0 GGCATCATTT 0.712005 -99 ATATTGATAACGCTTCGTTTACATTCTTTC 15 65 1 CGCTTCGTTT 0.893723 -34 CATAAAAACACGAATCCTTTTTGAAAATAA 17 80 0 CGAATCCTTT 0.892943 -221 ATCCTTTTTTCGCATCCATTAGCTTATTAT 19 129 0 CGCATCCATT 0.956231 -24 ********** Masking position 10 Map Score: 6.49668 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 157 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 ********** No masking Map Score: -2.06525e-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