AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_hpyl_reg_300.orf -o00360_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 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #4 HP0246 188 flagellar basal-body P-ring protein (flgI) #5 HP0830 58 amidase #6 HP0832 91 spermidine synthase (speE) #7 HP0833 76 H. pylori predicted coding region HP0833 #8 HP0943 21 D-amino acid dehydrogenase (dadA) #9 HP0944 300 translation initiation inhibitor, putative #10 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #11 HP1377 300 H. pylori predicted coding region HP1377 #12 HP1483 26 gerC2 protein (gerC2) #13 HP1490 103 hemolysin #14 HP1491 138 phosphate permease Motif number 1 AAATCAATATAATTCAAACCCTAAACCCAAACCTT 1 21 1 AATACCTAAA 0.889622 -237 ATAAAGATAGTCATAGCGTCTTAAAACAAACACCC 1 73 1 TCACCTTAAA 0.686111 -185 ATTATTTTCAAATTTCAAGTCTAAAGAGTGTGAAT 1 128 0 AATATCTAAA 0.706183 -130 TTGAAAATAATAACACAACTTAAAAAAAACTACCC 1 152 1 TAAATTAAAA 0.813479 -106 CAACTTAAAAAAAACTACCCTTAAAAAAATCAATC 1 167 1 AAAACTTAAA 0.955625 -91 TACCCTTAAAAAAATCAATCTAAAATTCTTAAATT 1 182 1 AAAACTAAAA 0.958232 -76 AAAATATAGCTATAATACACTAAAACAATCTCAAG 1 217 1 TATACTAAAA 0.890642 -41 AAAAACTGCTCCTAAAAACTCAAAATT 2 3 1 AAACCTAAAA 0.901521 -212 CTAAAAACTCAAAATTAACCTAAAATCGCTTGACG 2 22 1 AAAACTAAAA 0.958232 -193 ATTTTTCTTATAAACAAAACCTAAATTGAGAAAAA 2 93 1 TAAACCTAAA 0.902216 -122 GCGTTTAAAAAATGTAAATTTTAAACAATAGCCCC 2 140 0 AATATTTAAA 0.781476 -75 TTATTATATCTAATAGCGTTTAAAAAATGTAAATT 2 155 0 TAACTTAAAA 0.63507 -60 TTTGGATAACTATCCCCCTTAAAAATGAGTTTT 3 9 1 ACTCCTTAAA 0.656294 -197 TTTTACTATAAAACAAAATTTTAAAAAGATTAAAT 3 40 1 AAAATTTAAA 0.865264 -166 ATATTTGACAAAAATAAGATCAAAAAAATTTTTTA 3 101 1 AAAATCAAAA 0.821364 -105 CCTTGATCGCTATCCTACACCAAAAGAGTTAATAA 3 133 0 TATACCAAAA 0.845527 -73 GTTTTTATGAAAATAAAAGCCTAAAACAATTTTAA 3 167 1 AAAACCTAAA 0.935373 -39 ATAAAAAGCTAATAAAAGGCTAAAATTAAAATCTT 4 45 1 AATACTAAAA 0.927406 -144 ATAAGCCTTTTATAAAAACTTTAAACCTAATTGAG 4 124 0 TATATTTAAA 0.695099 -65 CAATTTAATCAAAATTAGATTACAATATTATAGTT 7 25 1 AAAATTACAA 0.557085 -52 ATATTATAGTTATTTAAAGCTTAAATAAGGGTCTA 7 49 1 TATACTTAAA 0.884324 -28 TTACAGACACTCATTGCCACTAAAAGAGGGCAAAG 9 22 0 TCACCTAAAA 0.699582 -279 AAAATTGATGACAACAAAGCCTAAAACTCAAACAA 9 122 1 ACAACCTAAA 0.852405 -179 TTTTTTAGAATAACCAACGCTAAAAATAGCGCTTT 10 118 1 TAAACTAAAA 0.936 -54 AATAGCGCTTTAATTGAATCCAAAACAAGGAGTTT 10 142 1 TAAACCAAAA 0.907658 -30 AGGAATGAGCAAAATAAAACCACAAATCAAGAAAA 11 113 0 AAAACCACAA 0.739223 -188 AAAAGACCGCCTTAAAACCAGCGCTC 11 285 0 AAACCTTAAA 0.895759 -16 CTAACTTTAAAAATCAAGCCTTCAAAAACC 13 6 0 AAAACTTCAA 0.798353 -98 TTAGGCTTAATCTTTTATGTTAAAATTCTGAGATT 13 37 1 TCTATTAAAA 0.492159 -67 AACTTTAAACCTAAAACCTAACGATA 13 88 0 ACTACTAAAA 0.836006 -16 GTAAAATTTTAAAGAGAGTTTTAAAAA 14 3 0 AAAATTTAAA 0.865264 -136 *** * ****** Masking position 14 Map Score: 34.4352 Number of sites scoring better than the average of aligned sites = 2664 Number in coding regions = 2179 Number in noncoding regions = 485 Number of orfs with sites within 600 bp upstream = 307 Fraction of orfs with sites within 600 bp upstream = 0.0493093 Motif number 2 TAGACTTGAAATTTGAAAATAATAACACAACTT 1 140 1 ATTAAATAAT 0.929639 -118 CAAAACCTAAATTGAGAAAAAATTCAATTCAAA 2 107 1 ATTGAAAAAT 0.82141 -108 TTTTAAAAAGATTAAATAATATTAAATTGAATG 3 58 1 ATTAAATATT 0.638625 -148 GTTTATCAATATTTGACAAAAATAAGATCAAAA 3 93 1 ATTAAAAAAT 0.956929 -113 GCCTAAAACAATTTTAAAAAAAGGACTTTTG 3 185 1 ATTAAAAAAG 0.958397 -21 TTAATTTGAAACTTTATAAAAAGCTAATAAAAG 4 30 1 ACTAAAAAAG 0.721796 -159 ATTTTTGAGTATAGCATAAAAATACGCTCAATT 4 98 1 ATAAAAAAAT 0.614723 -91 AATTCTAATTATTTTAGCATAAGCCTTTTATAA 4 144 0 ATTACATAAG 0.927211 -45 AATCTAAATTATTGTAACAAAAGC 6 2 0 ATTACAAAAG 0.956556 -90 TATCGCTTCAATTTAATCAAAATTAGATTACAA 7 17 1 ATTACAAAAT 0.95329 -60 ATTATGGCTTATTATAGAAAATGCTTTTGAGCA 9 60 0 ATTAAAAATG 0.755306 -241 TATTAATTTGATTGCATAATAATAGCTGACATA 9 253 1 ATTAAATAAT 0.929786 -48 ACACCGATGCATTGCGCCATAAGCTTCAAGAAA 10 37 0 ATTGCATAAG 0.729856 -135 AATAACCGCTATTATACCATAAGAAAACCGCTC 10 86 0 ATTACATAAG 0.927947 -86 AGCGTTGGTTATTCTAAAAAAATAACCGCTATT 10 106 0 ATTAAAAAAT 0.956841 -66 TAAAACCACAAATCAAGAAAAATAATCCCAGTA 11 101 0 AATAAAAAAT 0.627935 -200 GCGAAAATTGATTTTACCAAAATTGTTTGATAT 11 225 1 ATTACAAAAT 0.865579 -76 AAATCTCAGAATTTTAACATAAAAGATTAAGCC 13 40 0 ATTACATAAA 0.592624 -64 AAAAAGCGTTGTTTGATAAAAATGGCTCATTAT 14 51 0 GTTAAAAAAT 0.7028 -88 *** * ****** Masking position 9 Map Score: 19.3274 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 198 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 GACTTGAAATTTGAAAATAATAACACAACTT 1 142 1 TTAAAATAAT 0.66835 -116 TTTAAGAATTTTAGATTGATTTTTTTAAGGG 1 184 0 TTGATTGATT 0.699382 -74 TTCTACTACATTTGAAATAATTTTTCTTATA 2 74 1 TTGAAATAAT 0.85056 -141 AATAGCCCCTTTGAATTGAATTTTTTCTCAA 2 118 0 TTAATTGAAT 0.893223 -97 TTAAACGCTATTAGATATAATAAGGGATAGT 2 167 1 TTGATATAAT 0.951099 -48 TTAAATAATATTAAATTGAATGGGGTTTATC 3 69 1 TTAATTGAAT 0.893282 -137 AATTAAAATCTTTGATTTAAAGTTTATAAGA 4 68 1 TTGATTTAAA 0.652088 -121 TTTTTATCGCTTCAATTTAATCAAAATTAGA 7 13 1 TTAATTTAAT 0.873127 -64 TCTTTATTAATTTGATTGCATAATAATAGCT 9 249 1 TTGATTGCAT 0.872785 -52 AAAATAGCGCTTTAATTGAATCCAAAACAAG 10 140 1 TTAATTGAAT 0.893064 -32 TTCGCTAGTTTTGGATATAATCCCAATAACT 11 199 0 TTGATATAAT 0.951098 -102 ACCAAAATTGTTTGATATAATACAGAGTTTA 11 240 1 TTGATATAAT 0.951096 -61 AGAGTTTAGCTTAGAAATCATTGAGCGCTGG 11 263 1 TTGAAATCAT 0.622957 -38 CAAGGGCTAATTGGATAGAATAAGACCACTA 14 94 1 TTGATAGAAT 0.959412 -45 ** ******** Masking position 5 Map Score: 13.2306 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 122 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 TCAATATAATTCAAACCCTAAACCCAAACC 1 24 1 TCAAACCCTA 0.927895 -234 GTGTTTGTTTTAAGACGCTATGACTATCTT 1 76 0 TAAGACGCTA 0.833346 -182 TTTCTTATAAACAAAACCTAAATTGAGAAA 2 96 1 ACAAAACCTA 0.69635 -119 AATTCAATTCAAAGGGGCTATTGTTTAAAA 2 127 1 AAAGGGGCTA 0.573919 -88 TTTACATTTTTTAAACGCTATTAGATATAA 2 157 1 TTAAACGCTA 0.717879 -58 TTTATTTTCATAAAAACCTTGATCGCTATC 3 154 0 TAAAAACCTT 0.789213 -52 TTTATGAAAATAAAAGCCTAAAACAATTTT 3 170 1 TAAAAGCCTA 0.955958 -36 TGAAACTTTATAAAAAGCTAATAAAAGGCT 4 36 1 TAAAAAGCTA 0.910659 -153 AAAAAGCTAATAAAAGGCTAAAATTAAAAT 4 47 1 TAAAAGGCTA 0.96521 -142 AAAGTTTTTATAAAAGGCTTATGCTAAAAT 4 137 1 TAAAAGGCTT 0.928701 -52 TCAAACCCTTTCTTATTCCC 4 179 0 TCAAACCCTT 0.85799 -10 AAGCCATAATAAAAGGGCTTGCAAGCGAGT 9 83 1 AAAAGGGCTT 0.716928 -218 ATTGATGACAACAAAGCCTAAAACTCAAAC 9 125 1 ACAAAGCCTA 0.861914 -176 TGGATTCAATTAAAGCGCTATTTTTAGCGT 10 134 0 TAAAGCGCTA 0.917501 -38 TAAGAGTGGCTCAAGGGCTAATTGGATAGA 14 83 1 TCAAGGGCTA 0.926764 -56 ATCGTCATAAAAACCTTGTTCTAATAG 14 122 0 TAAAAACCTT 0.789213 -17 ********** Masking position 3 Map Score: 14.5713 Number of sites scoring better than the average of aligned sites = 1122 Number in coding regions = 983 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 TTGAATTTTTTCTCAATTTAGGTTTTGTTT 2 104 0 TCTCAATTTA 0.548703 -111 GGTAACTATCCCTTATTATATCTAATAGCG 2 172 0 CCTTATTATA 0.931092 -43 TGAACGATCCTTATTTTATAGGTGGTAA 2 197 0 CCTTATTTTA 0.952236 -18 ATTTTTTTGATCTTATTTTTGTCAAATATT 3 100 0 TCTTATTTTT 0.576552 -106 CAAAAGTCCTTTTTTTAAAATTGTTTT 3 189 0 CCTTTTTTTA 0.775786 -17 GAGATTCATACCTCAATTTAATTTGAAACT 4 13 1 CCTCAATTTA 0.728709 -176 CCTTTTATTAGCTTTTTATAAAGTTTCAAA 4 34 0 GCTTTTTATA 0.628635 -155 GCTCGTTTTATCTCTAAGCA 5 1 1 GCTCGTTTTA 0.775271 -58 CGCTAGACCCTTATTTAAGCTTTAAATA 7 59 0 CCTTATTTAA 0.615571 -18 TTTTATTATGGCTTATTATAGAAAATGCTT 9 67 0 GCTTATTATA 0.907007 -234 TGAATTTTCATCTTATTATAAGGTATTGTA 9 194 0 TCTTATTATA 0.859475 -107 GGCGTTTTGCGCTCATTTTTTATTTCTTTA 9 225 1 GCTCATTTTT 0.659737 -76 TCCCAGTAAATCTCATTTTAGCGGTAGGTG 11 79 0 TCTCATTTTA 0.889603 -222 TTCCTCAACTCCTTATTATATTTTATAATG 11 143 1 CCTTATTATA 0.931092 -158 GATAAAAATGGCTCATTATATGGTATCTTA 14 40 0 GCTCATTATA 0.897009 -99 CTAATAGTGGTCTTATTCTATCCAATTAGC 14 99 0 TCTTATTCTA 0.775956 -40 GTCATAAAAACCTTGTTCTAATAGTGGTCT 14 116 0 CCTTGTTCTA 0.672571 -23 ********** Masking position 7 Map Score: 15.8889 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 254 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 GTCTTAAAACAAACACCCATTACTCTTAAATC 1 90 1 AAACCCCTTA 0.989153 -168 AACTTAAAAAAAACTACCCTTAAAAAAATCAA 1 168 1 AAACACCTTA 0.977846 -90 TGAACGATCCTTATTTTATAGGT 2 202 0 GAACATCTTA 0.820398 -13 AAATATTGATAAACCCCATTCAATTTAATATT 3 75 0 AAACCCATCA 0.852212 -131 TAAGCATGTTAAACTACCATTAAATTTTTTGT 5 25 1 AAACACCTTA 0.977846 -34 AAACACTCCTTAGCTTACTTTT 6 80 0 AAACCTCTTA 0.97271 -12 TGATTCGGTTAAACTTCCATCATGGTTAAGTT 11 171 1 AAACTCCTCA 0.908216 -130 TTTTTAAAACTCTCTTTAAAATTTTACT 14 7 1 AAACCTCTTA 0.972705 -132 **** *** *** Masking position 3 Map Score: 5.7779 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 201 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 TAAAATTCTTAAATTAAAATATAGCTATAATAC 1 202 1 AATAAATATA 0.892181 -56 TTTTGTTTATAAGAAAAATTATTTCAAATGTAG 2 79 0 AAAAAATATT 0.801979 -136 GCGTTTAAAAAATGTAAATTTTAAACAATAGCC 2 142 0 AATAAATTTA 0.919299 -73 TTTTACTATAAAACAAAATTTTAAAAAGATTAA 3 40 1 AAAAAATTTA 0.940055 -166 CAAAAGAGTTAATAAAAAATTTTTTTGATCTTA 3 115 0 AAAAAATTTT 0.84788 -91 TAAAATCTTTGATTTAAAGTTTATAAGATTTTT 4 71 1 GATAAATTTA 0.703762 -118 ATAAGCCTTTTATAAAAACTTTAAACCTAATTG 4 126 0 TAAAAATTTA 0.795543 -63 TTTTTAGCCTTACAAAAAATTTAATGGTAGTTT 5 35 0 TAAAAATTTA 0.795543 -24 CTAGCTAAAAAATCTAAATTATTGTAACAAAAG 6 12 0 AATAAATATT 0.746318 -80 GCTTCAATTTAATCAAAATTAGATTACAATATT 7 21 1 AAAAAATAGA 0.661656 -56 CCTAACGATAAATATAAAATATATAAAATCTCA 13 65 0 AATAAATATA 0.892171 -39 TGGTATCTTAAAGTAAAATTTTAAAGAGAGTTT 14 17 0 AAAAAATTTA 0.940055 -122 ** **** **** Masking position 7 Map Score: 6.29957 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 61 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 ATATTGATTTAGCGTTACTT 1 1 0 AGCGTTACTT 0.852425 -257 AGTTTTTAGGAGCAGTTTTT 2 1 0 AGCAGTTTTT 0.84651 -214 AACCTAATTGAGCGTATTTTTATGCTATAC 4 106 0 AGCGTATTTT 0.744895 -83 AATGCTCAAAAGCATTTTCTATAATAAGCC 9 58 1 AGCATTTTCT 0.52119 -243 TGCATAAGCGGTTTCTATGCAAAGCG 10 7 1 AGCGGTTTCT 0.937506 -165 TTCTATGCAAAGCGTTTCTTGAAGCTTATG 10 23 1 AGCGTTTCTT 0.927307 -149 GGCGCAATGCATCGGTGTTTTTGCAAATAC 10 52 1 ATCGGTGTTT 0.729962 -120 AATACAAGCGAGCGGTTTTCTTATGGTATA 10 77 1 AGCGGTTTTC 0.873845 -95 ATGGTATAATAGCGGTTATTTTTTTAGAAT 10 99 1 AGCGGTTATT 0.882152 -73 CGCTATTTTTAGCGTTGGTTATTCTAAAAA 10 119 0 AGCGTTGGTT 0.945585 -53 ATTCAATTAAAGCGCTATTTTTAGCGTTGG 10 131 0 AGCGCTATTT 0.883816 -41 ATCTCATTTTAGCGGTAGGTGGCGTCTTTT 11 70 0 AGCGGTAGGT 0.698051 -231 GAAATCATTGAGCGCTGGTTTTAAGGCGGT 11 276 1 AGCGCTGGTT 0.907752 -25 ACTCTTAAAAAGCGTTGTTTGATAAAAATG 14 60 0 AGCGTTGTTT 0.965212 -79 ********** Masking position 1 Map Score: 8.84127 Number of sites scoring better than the average of aligned sites = 1184 Number in coding regions = 1048 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 9 AAATCAATATAATTCAAACCCTAAACCCAA 1 21 1 AATTCAAACC 0.357346 -237 TAGCGTCTTAAAACAAACACCCATTACTCT 1 86 1 AAACAAACAC 0.649047 -172 CATTACTCTTAAATCATGCCAATTCACACT 1 107 1 AAATCATGCC 0.878011 -151 TGAAATTTGAAAATAATAACACAACTTAAA 1 146 1 AAATAATAAC 0.579781 -112 TAATACACTAAAACAATCTCAAGGTTTCAA 1 229 1 AAACAATCTC 0.709854 -29 CTTGACGCAAAAACACTGCCTTAATTCTAC 2 50 1 AAACACTGCC 0.580962 -165 TTTTTCTTATAAACAAAACCTAAATTGAGA 2 94 1 AAACAAAACC 0.926569 -121 TATTTGACAAAAATAAGATCAAAAAAATTT 3 102 1 AAATAAGATC 0.406084 -104 GTTTTTATGAAAATAAAAGCCTAAAACAAT 3 167 1 AAATAAAAGC 0.620577 -39 AAATTGATGACAACAAAGCCTAAAACTCAA 9 123 1 CAACAAAGCC 0.661636 -178 CCTAAAACTCAAACAAAACCCGTTTAAGAA 9 141 1 AAACAAAACC 0.926569 -160 AAAATAAACTCCTTGTTTTGG 10 161 0 AAATAAACTC 0.807908 -11 TATTCCCACCAAATAATGTCAGCACCATTT 11 15 1 AAATAATGTC 0.780538 -286 CCATTTCTCCAAATCAAGCCCAGCCGCACC 11 39 1 AAATCAAGCC 0.910324 -262 AAATCAAGAAAAATAATCCCAGTAAATCTC 11 95 0 AAATAATCCC 0.926643 -206 GGAATGAGCAAAATAAAACCACAAATCAAG 11 117 0 AAATAAAACC 0.93895 -184 CTAGTTTTGGATATAATCCCAATAACTTAA 11 196 0 ATATAATCCC 0.488746 -105 CTAACTTTAAAAATCAAGCCTTCAAAAACC 13 11 0 AAATCAAGCC 0.910324 -93 ********** Masking position 10 Map Score: 10.3648 Number of sites scoring better than the average of aligned sites = 1024 Number in coding regions = 901 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 10 TAAAAAAAACTACCCTTAAAAAAATCAATCT 1 172 1 TACCTTAAAA 0.563463 -86 AATTAAAATATAGCTATAATACACTAAAACA 1 213 1 TACTATAATA 0.873572 -45 TAAACGCTATTAGATATAATAAGGGATAGTT 2 168 1 TAATATAATA 0.53487 -47 GGATAGTTACCACCTATAAAATAAGGATCGT 2 191 1 CACTATAAAA 0.588376 -24 AAAATGAGTTTTACTATAAAACAAAATTTTA 3 32 1 TTCTATAAAA 0.884903 -174 TATTATTTAATCTTTTTAAAATTTTGTTTTA 3 48 0 TCTTTTAAAA 0.70559 -158 TAAACCCCATTCAATTTAATATTATTTAATC 3 67 0 TCATTTAATA 0.485723 -139 CAAAAGTCCTTTTTTTAAAATTGTTTTAGG 3 186 0 TTTTTTAAAA 0.599511 -20 AGGTTTAAAGTTTTTATAAAAGGCTTATGCT 4 131 1 TTTTATAAAA 0.623785 -58 GCTAACATGCTAGCTAAAAAATCTAAATTAT 6 23 0 TACTAAAAAA 0.490939 -69 AAGCTTTAAATAACTATAATATTGTAATCTA 7 40 0 TACTATAATA 0.873572 -37 GCTGATAGTCCCTTTAATAAA 8 3 0 TCCTTTAATA 0.85019 -19 TCAAAAGCATTTTCTATAATAAGCCATAATA 9 63 1 TTCTATAATA 0.79757 -238 AAGCGAGTGGTAGCTTTAAAATTGATGACAA 9 105 1 TACTTTAAAA 0.924084 -196 TTTAACCGAATCATTATAAAATATAATAAGG 11 153 0 TCTTATAAAA 0.726543 -148 AGATTAAGCCTAACTTTAAAAATCAAGCCTT 13 19 0 TACTTTAAAA 0.924084 -85 AACCTAACGATAAATATAAAATATATAAAAT 13 69 0 TAATATAAAA 0.69168 -35 TTTTTAAAACTCTCTTTAAAATTTTACTTTA 14 11 1 TCCTTTAAAA 0.917155 -128 CTTTAAAATTTTACTTTAAGATACCATATAA 14 24 1 TTCTTTAAGA 0.522676 -115 ** ******** Masking position 8 Map Score: 14.415 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 461 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 11 TACCCTTAAAAAAATCAATCTAAAATTCTT 1 182 1 AAAATCAATC 0.779849 -76 TTCTTAAATTAAAATATAGCTATAATACAC 1 207 1 AAAATATAGC 0.690072 -51 TCAAGGTTTCAAAATTTAGCC 1 247 1 AAAATTTAGC 0.900251 -11 CTAAAAACTCAAAATTAACCTAAAATCGCT 2 22 1 AAAATTAACC 0.858334 -193 GATATTGTTAAAAAGTAAGCTAAGGAGTGT 6 70 1 AAAAGTAAGC 0.841119 -22 GTTATTCTAAAAAAATAACCGCTATTATAC 10 102 0 AAAAATAACC 0.627454 -70 ACCATTTCTCCAAATCAAGCCCAGCCGCAC 11 38 1 CAAATCAAGC 0.957683 -263 AATAAAACCACAAATCAAGAAAAATAATCC 11 106 0 CAAATCAAGA 0.6407 -195 GGATTATATCCAAAACTAGCGAAAATTGAT 11 207 1 CAAAACTAGC 0.714758 -94 CCTAACTTTAAAAATCAAGCCTTCAAAAAC 13 12 0 AAAATCAAGC 0.97307 -92 TTTAACATAAAAGATTAAGCCTAACTTTAA 13 31 0 AAGATTAAGC 0.81014 -73 ********** Masking position 4 Map Score: 3.49329 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 561 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 12 ********** No masking Map Score: -2.42052e-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 13 ********** No masking Map Score: -2.42052e-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 ********** No masking Map Score: -2.42052e-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