AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iglpR_tpal_opreg_300.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0231 100 conserved hypothetical protein #2 TP0232 99 T. pallidum predicted coding region TP0232 #3 TP0233 30 anti-sigma F factor antagonist, putative #4 TP0234 234 ribosomal protein L33 (rpmG) #5 TP0235 149 preprotein translocase subunit (secE) #6 TP0237 106 ribosomal protein L11 (rplK) #7 TP0240 108 ribosomal protein L7/L12 (rplL) #8 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #9 TP0243 102 ribosomal protein S12 (rpsL) #10 TP0244 21 ribosomal protein S7 #11 TP0245 23 T. pallidum predicted coding region TP0245 #12 TP0246 145 T. pallidum predicted coding region TP0246 #13 TP0247 50 N-acetylmuramoyl-L-alanine amidase (amiA) #14 TP0248 66 T. pallidum predicted coding region TP0248 #15 TP0249 78 flagellar filament outer layer protein (flaA-1) #16 TP0250 50 T. pallidum predicted coding region TP0250 #17 TP0251 153 DNA-binding protein II #18 TP0254 236 transcription termination factor Rho (rho) #19 TP0255 118 ribosomal protein L31 (rpmE) #20 TP0256 44 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (pgsA) #21 TP0257 96 glycerophosphoryldiester phosphodiesterase (glpQ) #22 TP0976 47 T. pallidum predicted coding region TP0976 #23 TP0979 169 conserved hypothetical protein #24 TP0981 59 sensory transduction histidine kinase, putative Motif number 1 AGGTGCGGGACGGAAAGGAGAGAGGAT 1 84 1 CGGAAGGAGG 0.772686 -17 GCATTCTGGTAGGCGGTGTGTGGTTTTGAGTT 2 25 1 AGGGGTGTGG 0.918008 -75 CTGCCCCAGAAAGAAAGGCGCGTCAC 4 5 0 AAGAAGGCGG 0.754126 -230 CGTGCTTGATGTGTGAGGTGAGGCGTTATACA 4 68 1 GTGGAGGTGG 0.899826 -167 GCCGGCCTCCGGGCGGCTCGGGGAGTCCTGTC 4 106 1 GGGGGCTCGG 0.693679 -129 CCGTCTGTGGATGTGAGGAGGGGTGGT 4 218 1 ATGGAGGAGG 0.809257 -17 TCTTCTTCCAGGGTGGAGAGTGTTGCAATGCG 6 14 1 GGGGGAGAGG 0.978976 -93 TTTTTTGCATGCGTCCGGCGCGTCGTTGTGTG 8 20 1 GCGCCGGCGG 0.766665 -243 TTTCGTGTGGGAGGGCGTCGCGCTTTTGAGTA 8 64 1 GAGGCGTCGG 0.790981 -199 TCGCGCTTTTGAGTAGAGCGTGGGCTTCTATT 8 81 1 GAGAGAGCGG 0.848803 -182 CCCTCCACTCAAGTGAGGAGAACGCGACCCAA 8 150 0 AAGGAGGAGA 0.40166 -113 CTTGAGTGGAGGGGACGGCGTCTCCCCTGTGT 8 169 1 GGGACGGCGC 0.802813 -94 CGTCTCCCCTGTGTGGGGAGTATTACGGTAGA 8 187 1 GTGGGGGAGA 0.822362 -76 GGGAGTATTACGGTAGAGCGTGTGGTATAGGG 8 202 1 CGGAGAGCGG 0.756889 -61 GTGTGGTATAGGGAGCACCGTGTCGGTTCGGT 8 221 1 GGGGCACCGG 0.843048 -42 GGTGCAGCTTGAGGGGGGAGTGC 8 250 1 GAGGGGGAGG 0.980675 -13 TCCTAGCCGCGTGTGCTGTGTGCGGCAAGGTT 9 41 1 GTGGCTGTGG 0.870466 -62 GATTTTTTTGGGGAAGTGAGCGAAAAGA 9 85 1 GGGAGTGAGG 0.96007 -18 GGGCTGGGGAGAGGAGTTGGT 10 2 1 GGCGGGGAGG 0.878039 -20 ATGTGATGCGAAGCGTGCGCAAGAGAA 12 6 1 ATGGAAGCGG 0.639421 -140 CCACCTTTGCGGGGGATGCGCATTTTCGTTGT 12 76 1 GGGGATGCGA 0.911735 -70 TGCTTATTGTGAGTAGGGAGAGGGGACAGGT 13 30 1 GAGAGGGAGG 0.930706 -21 ACGGTGTAGTGAGGGCGGTGTGTTGGACTCTC 14 32 1 GAGGCGGTGG 0.957463 -35 TTGACAAAATAGGCGGTGAGCGTATACTCGAA 15 22 1 AGGGGTGAGG 0.956366 -57 ATCTTATTGTGCGAAAGGAGCGTTTGA 15 62 1 GCGAAGGAGG 0.724936 -17 CCTAGGGAGAGGGGGCGGTGGGGTTCTAGGCG 16 23 1 GGGGCGGTGG 0.990337 -28 GCACCACCTCGGGTGAAGAGAACACACCGTTG 17 93 0 GGGGAAGAGA 0.718547 -61 TCTTCACCCGAGGTGGTGCGCGTTTGAGGCGG 17 106 1 AGGGGTGCGG 0.978475 -48 TGGTGTATACAGGAACTGTGCGCCTCTTTTAG 18 41 0 AGGACTGTGG 0.720142 -196 GTAGCGTGCACGGTGCTGCGTGCTGTTCAAAC 18 187 1 CGGGCTGCGG 0.952211 -50 ACCTTTTTAAGGGCGCGGCGCGCTGTAGAATG 19 79 1 GGGGCGGCGG 0.997602 -40 CTGTAGAATGGGGAAAGGAGCGATTCAG 19 101 1 GGGAAGGAGG 0.965407 -18 ATTCTATAACAGGGGAGGAGAGAAGTTT 21 79 1 AGGGAGGAGG 0.962179 -18 GCAAGGGAACAGGTGGTGCGTAGGTTTGCGCG 22 11 0 AGGGGTGCGA 0.845233 -37 AGCTGGGCCGTGCGCGCATGTCCGCG 23 5 1 GGGCGTGCGG 0.940313 -165 TACCGCGCGTGTGTGCCGCGCGTTGCGCTTCC 23 95 1 GTGGCCGCGG 0.887882 -75 CGGCGTACCAGGGCGGTACGCGCGAGCGCCTC 23 126 1 GGGGGTACGG 0.815645 -44 CTAATATCCTGAGTGCTGTGAGGCGCTCGCGC 23 145 0 GAGGCTGTGG 0.898476 -25 AGTAAGTTGGGGTACGCCGGAAGCGTACGTT 24 39 0 GGGACGCCGA 0.458739 -21 *** ****** * Masking position 10 Map Score: 56.4203 Number of sites scoring better than the average of aligned sites = 2533 Number in coding regions = 2199 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 TCAAAACCACACACCGCCTACCAGAATGCCCTGCTACAGG 2 14 0 ACCCAGAGCC 0.952704 -86 AGTGTGCGAAACCGCTAGTGGGGATGGCCT 3 9 1 AACCGGGGGC 0.864752 -22 AGCCAACCAGCCTGCCCCAGAAAGAAAGGCGCGTCAC 4 8 0 CCCCGGAGGC 0.931209 -227 AGCACGAAACACCTCCCTAAACAGGCAGCCAACCAGCCTG 4 34 0 ACCCAGGGCC 0.951768 -201 AGGACTCCCCGAGCCGCCCGGAGGCCGGCCCGCATTGTAT 4 95 0 GACCGGCGCC 0.971791 -140 TGTCTGTGTTGCTTCTGTAGCTCAGTTGGCAGAGCGCAAC 4 134 1 GCCGGAGGGC 0.855875 -101 CTCACATCCACAGACGGAAGCTTCCGAGCGGGATTGAACC 4 195 0 CACGGCCGCG 0.784125 -40 TCCCCGGAAAACACCAGAAAACCCCGTGCGTAACAGATAT 5 20 0 ACCGACCGCG 0.89659 -130 AGAGTGTTGCAATGCGCATGATTGCCTGCCGCTTACGCGT 6 30 1 AACCGGCGCC 0.97677 -77 GGAAGACAGCACCCCAGAAGCCTGACCGCCTAACACATAC 7 36 0 ACCGGGAGCC 0.983373 -73 AAGGGTGTCAGAGGCACACAACGACGCGCCGGACGCATGC 8 26 0 GACCAACGCC 0.728695 -237 GCCTCTGACACCCTTTCGTGTGGGAGGGCGTCGCGCTTTT 8 51 1 CCTCGGAGCG 0.636532 -212 AACGCGACCCAACCCGCATGCCAAAATGCCGAGAACAAGT 8 122 0 AACCGAAGCC 0.886087 -141 GGTCGCGTTCTCCTCACTTGAGTGGAGGGGACGGCGTCTC 8 153 1 TCCCGGGGGG 0.587599 -110 CGTAATACTCCCCACACAGGGGAGACGCCGTCCCCTCCAC 8 174 0 CCCCGGACCG 0.653607 -89 ACGCCCCAGGAAGAGACGCGTAT 11 4 0 ACCCGAGGCG 0.954836 -20 ACGAAAATGCGCATCCCCCGCAAAGGTGGCGATATTCCGT 12 65 0 GCCCGAGGGC 0.907429 -81 GCCCCGCGCCTAGAACCCCACCGCCCCCTCTCCCT 16 26 0 GCCAACAGCC 0.457711 -25 CACATTCGGGACTTCTGGCGAGCCACAGCCTTTCTAGCGA 17 44 0 ACCGGCAGCC 0.973491 -110 GTGCGCGTTTGAGGCGGCTGTTTGCCCGCGTGTGTTTCTT 17 121 1 GACGGGCGCG 0.919614 -33 AGAAAAACCGACGTCCAACGAGTACACGCCCAAGAACACT 18 137 0 ACCAGACGCC 0.868823 -100 ACCGGTTTGAACAGCACGCAGCACCGTGCACGCTACAACC 18 183 0 ACCCACCGCA 0.535412 -54 TGTGTCGGTTACACCCGGCGTGTACGAGCCTTCTGGAAGA 19 28 1 ACCGGACGCC 0.979453 -91 ACAGATCGTCACCGTGCATAGTAGCACGCCGCATATCTCC 21 37 0 ACTCAGCGCC 0.765097 -60 GCAAACCTACGCACCACCTGTTCCCTTGCGCAACAAGGAA 22 14 1 GCCCGCCGCG 0.98343 -34 GCGAACTAGAACGGCCGACGCGGACATGCGCGCACGGCCC 23 15 0 ACCGGACGCG 0.963905 -155 GAACAAAGCAACCATTGCGGGCACAGGGGCACGCGAACTA 23 47 0 ACTGGCAGGC 0.479215 -123 CTCCGCAAATACCGCGCGTGTGTGCCGCGCGTTGCGCTTC 23 86 1 ACCCGGCCGC 0.843888 -84 CGCGCGTTGCGCTTCCGGCGTACCAGGGCGGTACGCGCGA 23 111 1 GCCGGCAGCG 0.943937 -59 ** * * * ** *** Masking position 18 Map Score: 31.9003 Number of sites scoring better than the average of aligned sites = 2371 Number in coding regions = 2162 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 ACGCGCCTTTCTTTCTGGGGCAGGCTGGTT 4 14 1 CTTTCTGGGG 0.988511 -221 TGCGGGCCGGCCTCCGGGCGGCTCGGGGAG 4 101 1 CCTCCGGGCG 0.959562 -134 CAGACGGAAGCTTCCGAGCGGGATTGAACC 4 195 0 CTTCCGAGCG 0.852673 -40 ACGCACGGGGTTTTCTGGTGTTTTCCGGGG 5 29 1 TTTTCTGGTG 0.801744 -121 TTTTCTGGTGTTTTCCGGGGATTTGTGGGT 5 39 1 TTTTCCGGGG 0.958527 -111 GGTTCGAGTCCTTCCTGGCCTGAGTGCTTT 5 116 1 CTTCCTGGCC 0.865635 -34 TTTTCTTCTTCCAGGGTGGAGAGTGT 6 7 1 TCTTCCAGGG 0.813587 -100 TTACGCGTTGGTTTCGGGTGTTTTGTTGTT 6 62 1 GTTTCGGGTG 0.764047 -45 AGGCGGTCAGGCTTCTGGGGTGCTGTCTTC 7 45 1 GCTTCTGGGG 0.965981 -64 ATACGCGTCTCTTCCTGGGGCGT 11 11 1 CTTCCTGGGG 0.986985 -13 ATATCGCCACCTTTGCGGGGGATGCGCATT 12 70 1 CTTTGCGGGG 0.858579 -76 CCCCTCCTGCGGAACAAACACA 12 134 0 CCTCCTGCGG 0.805593 -12 TGCAGTAGTCTTCCTAGGGAGAGGGGGCG 16 10 1 CTTCCTAGGG 0.942023 -41 GCGAAAACACCTTTCCGGGCAGCGGTGTCA 17 18 0 CTTTCCGGGC 0.921797 -136 GAGCCACAGCCTTTCTAGCGAAAACACCTT 17 35 0 CTTTCTAGCG 0.928612 -119 CACATTCGGGACTTCTGGCGAGCCACAGCC 17 54 0 ACTTCTGGCG 0.793366 -100 CGTCTTCTGTTTTCCTGGTGTTCTAGTCTT 18 90 1 TTTCCTGGTG 0.780906 -147 GTCGGTTTTTCTTTCCAGGGTTGTAGCGTG 18 165 1 CTTTCCAGGG 0.954495 -72 CGCGCGTTGCGCTTCCGGCGTACCAGGGCG 23 111 1 GCTTCCGGCG 0.95798 -59 AAAAACGTACGCTTCCGGCGTACCCCAACT 24 36 1 GCTTCCGGCG 0.95798 -24 ********** Masking position 3 Map Score: 28.6611 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 378 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 CGGTAACAGAAAGAGTGTCGTGTGAATTTC 2 61 1 AAGAGTGTCG 0.942945 -39 CATCCCCACTAGCGGTTTCGCACACT 3 7 0 AGCGGTTTCG 0.963905 -24 CTGTTTAGGGAGGTGTTTCGTGCTTGATGT 4 50 1 AGGTGTTTCG 0.922193 -185 TCCCACACGAAAGGGTGTCAGAGGCACACA 8 46 0 AAGGGTGTCA 0.961671 -217 ATGCAGGGGTGTTGACAAAATAGG 15 5 1 AGGGGTGTTG 0.962685 -74 CTTTCCGGGCAGCGGTGTCAAGTCGCT 17 8 0 AGCGGTGTCA 0.963905 -146 ACGTGAAGTTAAGGGTGTCGTCTTCTGTTT 18 72 1 AAGGGTGTCG 0.992213 -165 TGCTGTTCAAACCGGTGTCGGTAATCTCGG 18 207 1 ACCGGTGTCG 0.986089 -30 GGAGACTGGAACGTGTGTCGGTTACACCCG 19 15 1 ACGTGTGTCG 0.969193 -104 ********** Masking position 6 Map Score: 11.0125 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 65 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 ATACCAGGCACCGCATACTACCGGTCAACCAA 1 52 0 CCGCATCTAC 0.578796 -49 AAACCACACACCGCCTACCAGAATGCCCTGCT 2 19 0 CCGCCTCCAA 0.981892 -81 GGCAGCCAACCAGCCTGCCCCAGAAAGAAAGG 4 19 0 CAGCCTCCCA 0.917161 -216 AAGCACGAAACACCTCCCTAAACAGGCAGCCA 4 43 0 CACCTCCTAA 0.715494 -192 ACCACCCCTCCTCACATCCACAGA 4 221 0 CACCCCCCTA 0.790505 -14 AGAAGCCTGACCGCCTAACACATACCCCGTAA 7 29 0 CCGCCTACAA 0.694074 -80 GACAGGAAGACAGCACCCCAGAAGCCTGACCG 7 48 0 CAGCACCCAA 0.905553 -61 AGCGCGACGCCCTCCCACACGAAAGGGTGTCA 8 56 0 CCTCCCCACA 0.754248 -207 GCGACCCAACCCGCATGCCAAAATGCCGAGAA 8 127 0 CCGCATCCAA 0.958018 -136 AGACGCCGTCCCCTCCACTCAAGTGAGGAGAA 8 160 0 CCCTCCCTCA 0.837495 -103 ACACGGTGCTCCCTATACCACACGCTCTACCG 8 212 0 CCCTATCCAA 0.852826 -51 GCACTCCCCCCTCAAGCTGCACCGAAC 8 246 0 CCCCCCCAAC 0.884441 -17 TCTTTTCGCTCACTTCCCCAAAAAAATCCTCA 9 81 0 CACTTCCCAA 0.672008 -22 ACCAACTCCTCTCCCCAGCCC 10 3 0 CCTCTCCCAC 0.690369 -19 ACCTGTCCCCTCTCCCTACTCACAATAA 13 33 0 CCCCTCCCCA 0.982411 -18 TACAATGCTGCCCCATCCCCTA 14 1 0 CCCCATCCCA 0.971301 -66 GTCCAACACACCGCCCTCACTACACCGTACAA 14 28 0 CCGCCCCACA 0.939709 -39 ACCCCACCGCCCCCTCTCCCTAGGAAGACTAC 16 15 0 CCCCTCCCCA 0.982411 -36 GTTACATCCACCCTCTTCCAGAAGGCTCGTAC 19 49 0 CCCTCTCCAA 0.932294 -70 TCGCTCCTTTCCCCATTCTACAGCGCGCCGCG 19 92 0 CCCCATCTAA 0.876736 -27 ****** *** * Masking position 1 Map Score: 19.622 Number of sites scoring better than the average of aligned sites = 917 Number in coding regions = 754 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 TTCTGGTAGGCGGTGTGTGGTTTTGAGTTC 2 28 1 CGGTGTGTGG 0.634147 -72 CACGGGGTTTTCTGGTGTTTTCCGGGGATT 5 32 1 TCTGGTGTTT 0.47281 -118 CTGGTGTTTTCCGGGGATTTGTGGGTCAGT 5 43 1 CCGGGGATTT 0.330329 -107 CGCGTTGGTTTCGGGTGTTTTGTTGTTTTT 6 65 1 TCGGGTGTTT 0.538124 -42 AACTTAGTTACGGGGTATGTGTTAGGCGGT 7 22 1 CGGGGTATGT 0.856416 -87 CGGTCAGGCTTCTGGGGTGCTGTCTTCCTG 7 48 1 TCTGGGGTGC 0.845251 -61 ATTATCTTCTCCTTGTATGCGAAATAACCC 7 89 0 CCTTGTATGC 0.778424 -20 TCCGGCGCGTCGTTGTGTGCCTCTGACACC 8 33 1 CGTTGTGTGC 0.944542 -230 AGTATCCTAGCCGCGTGTGCTGTGTGCGGC 9 37 1 CCGCGTGTGC 0.919983 -66 CGCGTCTCTTCCTGGGGCGT 11 14 1 CCTGGGGCGT 0.886772 -10 GCCACCTTTGCGGGGGATGCGCATTTTCGT 12 75 1 CGGGGGATGC 0.866656 -71 TGCGCATTTTCGTTGTGTACCTATTTTACA 12 92 1 CGTTGTGTAC 0.712098 -54 TGTGGTGCGTGGACGTATGT 13 1 1 TGTGGTGCGT 0.815365 -50 GACTGTACAACGGTGTGTTCTCTTCACCCG 17 86 1 CGGTGTGTTC 0.798333 -68 CTTCACCCGAGGTGGTGCGCGTTTGAGGCG 17 107 1 GGTGGTGCGC 0.873258 -47 GGCTGTTTGCCCGCGTGTGTTTCTTGTC 17 136 1 CCGCGTGTGT 0.83992 -18 CTTAACTTCACGTGGTGTATACAGGAACTG 18 55 0 CGTGGTGTAT 0.750296 -182 CTTCTGTTTTCCTGGTGTTCTAGTCTTTAG 18 93 1 CCTGGTGTTC 0.882908 -144 GTGAGAGTGTTCTTGGGCGTGTACTCGTTG 18 132 1 TCTTGGGCGT 0.434001 -105 GGCGTGTACTCGTTGGACGTCGGTTTTTCT 18 147 1 CGTTGGACGT 0.412576 -90 CGGTTACACCCGGCGTGTACGAGCCTTCTG 19 33 1 CGGCGTGTAC 0.642385 -86 GAGTACACCTGTGGTGTACCATTACGTCT 20 10 1 TGTGGTGTAC 0.631826 -35 CAAGGGAACAGGTGGTGCGTAGGTTTGCGC 22 12 0 GGTGGTGCGT 0.758703 -36 AGCTGGGCCGTGCGCGCATGTCCGCGT 23 8 1 CCGTGCGCGC 0.615087 -162 CAAATACCGCGCGTGTGTGCCGCGCGTTGC 23 91 1 GCGTGTGTGC 0.79238 -79 CGCGTACCGCCCTGGTACGCCGGAAGCGCA 23 118 0 CCTGGTACGC 0.884507 -52 AGTAAGTTGGGGTACGCCGGAAGCGTA 24 43 0 TGGGGTACGC 0.736124 -17 ********** Masking position 5 Map Score: 22.4568 Number of sites scoring better than the average of aligned sites = 3156 Number in coding regions = 2885 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 7 TGGTATAGGTGCGGGACGGAAAGGAGAGAG 1 78 1 GCGGGACGGA 0.959482 -23 GACTCCCCGAGCCGCCCGGAGGCCGGCCCG 4 103 0 GCCGCCCGGA 0.961121 -132 AGCTACAGAAGCAACACAGACAGGACTCCC 4 126 0 GCAACACAGA 0.795328 -109 CCCCCCTCAAGCTGCACCGAACCGACACGG 8 238 0 GCTGCACCGA 0.954346 -25 CACAGCACACGCGGCTAGGATACTCAGAAT 9 31 0 GCGGCTAGGA 0.888064 -72 TGTGCTGTGTGCGGCAAGGTTTACGGTGTT 9 52 1 GCGGCAAGGT 0.925856 -51 TTTTTCCGCTGAAGCACGGAATATCGCCAC 12 50 1 GAAGCACGGA 0.909852 -96 ACTTGACACCGCTGCCCGGAAAGGTGTTTT 17 15 1 GCTGCCCGGA 0.967207 -139 TGAACAGCACGCAGCACCGTGCACGCTACA 18 186 0 GCAGCACCGT 0.90637 -51 GTTCCCTTGCGCAACAAGGAAACAG 22 33 1 GCAACAAGGA 0.830168 -15 AGCGCAACGCGCGGCACACACGCGCGGTAT 23 94 0 GCGGCACACA 0.8237 -76 ********** Masking position 1 Map Score: 6.90539 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 344 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TACCAGGCACCGCATACTACCGGTCAACCAAA 1 51 0 CGCATCTACG 0.941722 -50 TAGTATGCGGTGCCTGGTATAGGTGCGGGACG 1 64 1 TGCCTGTAAG 0.513788 -37 AACCACACACCGCCTACCAGAATGCCCTGCTA 2 18 0 CGCCTCCAAA 0.927806 -82 GAGGCCGGCCCGCATTGTATAACGCCTCACCT 4 83 0 CGCATGTAAA 0.9571 -152 GGCAATCATGCGCATTGCAACACTCTCCACCC 6 24 0 CGCATGCACA 0.957636 -83 GGGGTTATTTCGCATACAAGGAGAAGATAAT 7 88 1 CGCATCAAGA 0.750319 -21 ACGCGCCGGACGCATGCAAAAAAAACCAGACA 8 11 0 CGCATCAAAA 0.918796 -252 CGACCCAACCCGCATGCCAAAATGCCGAGAAC 8 126 0 CGCATCCAAA 0.971002 -137 CTCTTGCGCACGCTTCGCATCACAT 12 4 0 CGCTTGCACA 0.760765 -142 CGCTCCTTTCCCCATTCTACAGCGCGCCGCGC 19 91 0 CCCATCTAAG 0.647578 -28 ATCGTCACCGTGCATAGTAGCACGCCGCATAT 21 41 0 TGCATGTACA 0.821611 -56 TGACGATCTGTGCATTCTATAACAGGGGAGGA 21 66 1 TGCATCTAAA 0.87217 -31 ***** *** ** Masking position 9 Map Score: 4.98607 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 172 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 TTTTGGAGACCGACGCTCTGCCATTAGAGCT 5 73 0 CGCGCTCTGC 0.681518 -77 TTGCAACACTCTCCACCCTGGAAGAAGAAAA 6 11 0 CTCACCCTGG 0.954491 -96 GACAGGAAGACAGCACCCCAGAAGCCTGACC 7 49 0 CACACCCCAG 0.727239 -60 GTGAGGAGAACGCGACCCAACCCGCATGCCA 8 139 0 CGGACCCAAC 0.840549 -124 ACGCCGTCCCCTCCACTCAAGTGAGGAGAAC 8 159 0 CTCACTCAAG 0.714383 -104 TGCACCGAACCGACACGGTGCTCCCTATACC 8 225 0 CGCACGGTGC 0.744533 -38 CCCCCTCAAGCTGCACCGAACCGACACGGTG 8 236 0 CTCACCGAAC 0.946488 -27 AAAAAATCCTCAACACCGTAAACCTTGCCGC 9 62 0 CACACCGTAA 0.522846 -41 ACCGCCCTCACTACACCGTACAATGCTGCCC 14 20 0 CTCACCGTAC 0.94645 -47 GGTGTGTTCTCTTCACCCGAGGTGGTGCGCG 17 97 1 CTCACCCGAG 0.849526 -57 GGCATTCAGTCAAGACCCAACCATATCTACG 18 11 0 CAGACCCAAC 0.829516 -226 GAACAGCACGCAGCACCGTGCACGCTACAAC 18 184 0 CACACCGTGC 0.964981 -53 CGTGTGTCGGTTACACCCGGCGTGTACGAGC 19 26 1 TTCACCCGGC 0.523065 -93 CGCCGCATATCTCCACTGAGCGCTGATCCTA 21 20 0 CTCACTGAGC 0.873698 -77 ATGCACAGATCGTCACCGTGCATAGTAGCAC 21 50 0 CGCACCGTGC 0.967589 -47 GACATGCGCGCACGGCCCAGCT 23 2 0 CAGGCCCAGC 0.672024 -168 GAGCGCCTCACAGCACTCAGGATATTAGCCC 23 149 1 CACACTCAGG 0.796961 -21 ** ******** Masking position 6 Map Score: 8.99618 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 903 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 10 ACAGAAGCAACACAGACAGGACTCCCCGAGC 4 121 0 CACAACAGGA 0.956058 -114 TCCTCACATCCACAGACGGAAGCTTCCGAGC 4 206 0 CACAACGGAA 0.956057 -29 TAATACTCCCCACACAGGGGAGACGCCGTCC 8 181 0 CACAAGGGGA 0.986068 -82 GTACAGTCTACACATTCGGGACTTCTGGCGA 17 63 0 CACATCGGGA 0.976405 -91 GACAAGAAACACACGCGGGCAAACAGCCGC 17 134 0 CACAGCGGGC 0.976343 -20 ACTCACCTAGGGGAAAGACGTAAT 20 31 0 CACCAGGGGA 0.956098 -14 CAACGCGCGGCACACACGCGCGGTATTTGCG 23 89 0 CACAACGCGC 0.955945 -81 **** ****** Masking position 2 Map Score: 4.26231 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 52 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 GGCCAGGAAGGACTCGAACCTTCAACATTC 5 106 0 GACTCGAACC 0.964213 -44 ATGCCAAAATGCCGAGAACAAGTATGAAAA 8 115 0 GCCGAGAACA 0.886614 -148 GCCCCGCGCCTAGAACCCCACCGCCCC 16 34 0 GCCTAGAACC 0.97519 -17 GCAAACAGCCGCCTCAAACGCGCACCACCT 17 116 0 GCCTCAAACG 0.860281 -38 ATTGGCTAAAGACTAGAACACCAGGAAAAC 18 98 0 GACTAGAACA 0.954636 -139 GTAAGGAGACTGGAACGTGTGTCGGTT 19 8 1 GACTGGAACG 0.955277 -111 GGGGCACGCGAACTAGAACGGCCGACGCGG 23 32 0 AACTAGAACG 0.860144 -138 ********** Masking position 7 Map Score: 1.73187 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 29 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 CTTCCGAGCGGGATTGAACCGCTGACCTCAAC 4 183 0 GGATTGACGC 0.990141 -52 TGGATTGACCTGGTTTGGCTATT 9 2 1 GGATTGACGG 0.950758 -101 GATCGGTTTGTGTTTGTTCCGCAGGAGGGG 12 126 1 TGTTTGTCGC 0.807129 -20 TAGGGGATGGGGCAGCATTGTACGGT 14 5 1 GGATGGGCGC 0.961107 -62 TACCGACACCGGTTTGAACAGCACGCAGCACC 18 198 0 GGTTTGACGC 0.99241 -39 AACTGAAGGTAGGATCAGCGCTCAGTGGA 21 8 1 GGTAGGACGC 0.948105 -89 TTTTTCACGCGGTTTGAAAAGCCGTGCAAC 24 9 0 GGTTTGAAGC 0.944312 -51 ******* * ** Masking position 6 Map Score: 2.64629 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 59 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 ********** No masking Map Score: -4.90742e-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: -4.90742e-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 15 ********** No masking Map Score: -4.90742e-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