AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_tpal_reg_300.orf -o00051_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0085 80 PTS system, nitrogen regulatory IIA component (ptsN-1) #2 TP0108 101 pyrophosphate--fructose 6-phosphate 1-phosphotransferase (pfk) #3 TP0109 300 rRNA methylase, putative #4 TP0505 300 hexokinase (hxk) #5 TP0524 135 ATP-dependent protease LA (lon-2) #6 TP0537 150 triosephosphate isomerase (tpi) #7 TP0542 59 pyrophosphate--fructose 6-phosphate 1-phosphotransferase, beta subunit #8 TP0543 41 Holliday junction DNA helicase (ruvA) #9 TP0544 24 T. pallidum predicted coding region TP0544 #10 TP0545 84 methylgalactoside ABC transporter, periplasmic galactose-binding protein (mglB-1) #11 TP0547 143 penicillin tolerance protein (lytB) #12 TP0642 140 phosphomannomutase (manB) #13 TP0662 266 fructose-bisphosphate aldolase (cbbA) #14 TP0755 199 PTS system, nitrogen regulatory IIA component (ptsN-2) #15 TP0757 40 polypeptide deformylase (def) #16 TP0758 118 ribosomal protein S21 (rpsU) Motif number 1 GGAGCGGAAAGAGCGTGGGGAGCTTTTCCAAAA 1 20 1 GGCTGGGAGC 0.86216 -61 ATTACACAACCAGGGAGGGAGGCCCAGGCTAGT 3 36 1 CGGAGGAGGC 0.937444 -265 CCTTGTATCGCAGCCAGGCGCGCTTTGCAATAG 3 259 0 CGCAGGGCGC 0.919786 -42 AAAAGAGGAGGTGCGTGGGACGCGACGATA 4 8 0 GGCTGGACGC 0.981636 -293 AACACAACAGGGGCGTAGTAGGGGATTGACTGT 4 96 1 GGCTAGAGGG 0.983185 -205 AAAGGGGTGCCGGCGTATGGGGCAGGGAGTTTA 4 212 0 CGCTATGGGC 0.796314 -89 GGTCGGCTGCCAGGGTAGCACGGATAGCTCGTT 4 265 0 CGGTAGACGG 0.942705 -36 CCCTGGCAGCCGACCAGGGAGGGCGCGT 4 283 1 CACAGGAGGG 0.799387 -18 ACGTCTTGCACGACCTGCGGGGGCGCAGTATAC 5 37 1 CACTGCGGGG 0.920731 -99 CGTCCCTTGCCTGGATACTAGGCGCCCT 5 118 1 CGGTACAGGC 0.933237 -18 ACGAAAGGATGTGCTAAGGAGGGGAT 6 135 1 GGCAAGAGGG 0.928827 -16 GTTGTGGGGGTGCGGCGGTGCGGTCGTG 7 6 1 GGGTGCGCGG 0.972051 -54 GCGCGGGTATCAGGGTGTGAGGGGAAAGAAGTG 10 25 1 CGGTGTAGGG 0.917545 -60 TGCAAGGGCGCGGCGTGGTGGTGAGTTCTTCTT 11 54 0 CGCTGGGGTG 0.858534 -90 AAGGCACCCAGGTCATGCAAGGGCGCGGCGTGG 11 69 0 GTCTGCAGGG 0.826967 -75 TACGGCACCACAGGATAGAGGGGCATTGTAATG 12 83 0 CGGTAGGGGG 0.973278 -58 CGGCGAGCTGGCGCCTGCGAGGCGTTAGGGGTG 13 29 0 GGCTGCAGGC 0.98594 -238 TCCACACGCAGGCGTTGGAACGGCAGCAAGACG 13 119 0 GCGTGGACGG 0.777635 -148 TCGGCAAGAGGGGCATGGTAGGGCGATCGGGAC 13 183 0 GGCTGGAGGG 0.994298 -84 CCCTCTTGCCGAGGGTGGCACGCTTCTCTATTT 13 204 1 GGGTGGACGC 0.971926 -63 TCAGAAATTCGCAGGTACCGCGCAACCTCTTCT 14 119 0 GAGTACGCGC 0.457204 -81 CACGTAGGGTGTGCGTGCAGGGGAGGCAGGAGT 16 13 1 GGCTGCGGGG 0.991263 -106 GAAAAAAACACAGCCTACCAGGGGTAGGCTAGC 16 84 0 CGCTACAGGG 0.970868 -35 * ** *** **** Masking position 12 Map Score: 33.4291 Number of sites scoring better than the average of aligned sites = 1243 Number in coding regions = 1082 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 GATATCCTGGGAGCGGAAAGAGC 1 1 1 GTATCCGGGG 0.756078 -80 AAGATGCGAAGATGCCCTGGGTGTTT 2 4 0 GTGCCCGGGG 0.960052 -98 ACCCCATTGCGTTAGCCTGAGGGAGTCTCTACG 2 57 1 GTAGCCGAGG 0.866849 -45 GGGGTCCTCCGCGTACCGCGTGCGTAGAGACT 2 80 0 CCGTACGCGG 0.639143 -22 GCTACCATTACACAACCAGGGAGGGAGGCCCAG 3 30 1 CCAACCGGGG 0.977275 -271 TCAGCAGCCCCACAGCACACGCGCATTCCGGCA 3 166 1 CCAGCAACGG 0.867906 -135 TCCTTGTATCGCAGCCAGGCGCGCTTTGCAATA 3 260 0 GAGCCAGCGG 0.785934 -41 AGTCGCCGAACACAACAGGGGCGTAGTAGGGGA 4 88 1 CCAACAGGGG 0.963738 -213 GAACGAGTACGGCAAACGGAGTGTTCCTTGTAG 4 156 0 GCAAACGAGG 0.792611 -145 TACCCTGGCAGCCGACCAGGGAGGGCGCGT 4 281 1 GCGACCGGGG 0.981305 -20 AAACGTCTTGCACGACCTGCGGGGGCGCAGTAT 5 35 1 CCGACCGCGG 0.977715 -101 GAGATCTCGCCCCAACCCAAGGGAAAATCTCAC 6 25 0 CCAACCAAGG 0.924614 -126 GAGACATACCCTCGCCAGGAGATCTCGCCCCAA 6 43 0 CCGCCAGAGT 0.764639 -108 TACACTGCGCGTGAGGAGTGTCCT 9 8 1 CCGTGAGAGG 0.617667 -17 CGCGCCCTTGCATGACCTGGGTGCCTTTGGTAC 11 75 1 CTGACCGGGG 0.933833 -69 GAAGAAAACTGGCGCGCCGAGTGTACCAAAGGC 11 97 0 GCGCGCGAGG 0.927107 -47 CTGTGCAATGCTCACAAAAAGTGCATGTCTTGA 12 37 0 CCACAAAAGG 0.649527 -104 GACTATTTACGGCACCACAGGATAGAGGGGCAT 12 90 0 GCACCAAGGT 0.459464 -51 GATTTGGACAGGTACCACGCGGGAGGTTTGACA 13 87 0 GTACCAGCGG 0.892099 -180 GGACGCTCTAGTCAACCGAAGCGCGAAGGCTTG 13 154 0 GCAACCAAGG 0.914164 -113 GCGTGCCACCCTCGGCAAGAGGGGCATGGTAGG 13 194 0 CCGGCAGAGG 0.965396 -73 TCGAAGCAATCCTAACAAAGGGGGTTCTC 13 248 1 CTAACAAGGG 0.683127 -19 GTGATACACGCCAGGCGTGAGATTTCTAC 14 7 1 CCGCCAGCGG 0.634658 -193 ACGCATGATGCGTACCCCAAGTGTGTCTTGTTA 14 43 1 CTACCCAAGG 0.84884 -157 TGTATGAGTGGGCGCAAAAGGGGAAGATTCCGT 14 160 1 GCGCAAAGGG 0.733712 -40 GGAAGATTCCGTCAGGAAAAGTGGGCACC 14 181 1 GCAGGAAAGG 0.474056 -19 CCCCTGCACGCACACCCTACGTGTC 16 3 0 CCACCCACGG 0.957486 -116 TGCGTGCAGGGGAGGCAGGAGTGCTTTCGGAAG 16 24 1 GAGGCAGAGG 0.641241 -95 * ***** *** * Masking position 11 Map Score: 32.0048 Number of sites scoring better than the average of aligned sites = 1977 Number in coding regions = 1773 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 ACCAGAATCTGCGGTGCTACCATTACACAA 3 15 1 GCGGTGCTAC 0.778185 -286 CGTCGGTCAAGTGGAGGTACCGGGTAAGTT 3 119 0 GTGGAGGTAC 0.923816 -182 CGCGTGTGCTGTGGGGCTGCTGATGGCAGC 3 159 0 GTGGGGCTGC 0.942413 -142 TTGCCGGAATGCGCGTGTGCTGTGGGGCTG 3 170 0 GCGCGTGTGC 0.596777 -131 TATCGGCAATGTGCAGTTGTGTGTCTTTGC 3 196 0 GTGCAGTTGT 0.799479 -105 CGATACAATTGTGCAGTCGCTCCTTCCAGT 3 221 1 GTGCAGTCGC 0.910888 -80 TGAGCGAAAAGAGGAGGTGCGTGGGACGCG 4 17 0 GAGGAGGTGC 0.877549 -284 GGGATTGACTGTGCAGTCACTGGGTCCGTC 4 117 1 GTGCAGTCAC 0.753819 -184 CAAAAAAGGGGTGCCGGCGTATGGGGCAGG 4 219 0 GTGCCGGCGT 0.734337 -82 TGCACGACCTGCGGGGGCGCAGTATACCGC 5 43 1 GCGGGGGCGC 0.951412 -93 GCAGTATACCGCGCAGGTATATTTTTTAAA 5 61 1 GCGCAGGTAT 0.863597 -75 AAGGCCTCGAATGGAGGCATTGACTTTTCG 5 90 1 ATGGAGGCAT 0.404749 -46 GATATAGTGGTGCCGTGAGATTTTCC 6 7 1 GTGGTGCCGT 0.907852 -144 GTATGTCTCTGCGGTGGCTCTATAGAACAG 6 67 1 GCGGTGGCTC 0.71405 -84 ACAGTTTCTCGTGGAGCTATCGGCGGGGTG 6 93 1 GTGGAGCTAT 0.715642 -58 GTTGTGGGGGTGCGGCGGTGCGG 7 4 1 GTGGGGGTGC 0.978088 -56 GGGTGCGGCGGTGCGGTCGTGCTATTTTTC 7 18 1 GTGCGGTCGT 0.865104 -42 TATATTCCTCGCGCGGGTATCAGGGTGTGA 10 15 1 GCGCGGGTAT 0.873045 -70 AAATCAGAATGCGCTGGTGAACATGAGGAG 10 60 1 GCGCTGGTGA 0.790905 -25 AGGGCGCGGCGTGGTGGTGAGTTCTTCTTC 11 53 0 GTGGTGGTGA 0.804093 -91 CCTCTATCCTGTGGTGCCGTAAATAGTCCA 12 95 1 GTGGTGCCGT 0.907852 -46 AGAATGCGGCGAGCTGGCGCCTGCGAGGCG 13 38 0 GAGCTGGCGC 0.879934 -229 TTGAGTCCACACGCAGGCGTTGGAACGGCA 13 127 0 ACGCAGGCGT 0.670061 -140 ********** Masking position 3 Map Score: 25.8131 Number of sites scoring better than the average of aligned sites = 2432 Number in coding regions = 2218 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 AAGCTCCCCACGCTCTTTCCGCTCCCAGGA 1 15 0 CGCTCTTTCC 0.96689 -66 CCACAGCACACGCGCATTCCGGCAAAGACA 3 175 1 CGCGCATTCC 0.855959 -126 ATTGTGCAGTCGCTCCTTCCAGTCAGTAGC 3 228 1 CGCTCCTTCC 0.988303 -73 CGCAGCCAGGCGCGCTTTGCAATAGCGCTA 3 254 0 CGCGCTTTGC 0.948432 -47 TATCGTCGCGTCCCACGCACCTCCTCTT 4 9 1 CGTCCCACGC 0.688706 -292 ACGCGCCCTCCCTGGTCGGCT 4 290 0 CGCGCCCTCC 0.923555 -11 ATTGACTTTTCGTCCCTTGCCTGGATACTA 5 108 1 CGTCCCTTGC 0.964742 -28 CAGGAGATCTCGCCCCAACCCAAGGGAAAA 6 31 0 CGCCCCAACC 0.917456 -120 TGCACAGAGCAGCACCTTCCCATTACAATG 12 63 1 AGCACCTTCC 0.631928 -78 ATTACAATGCCCCTCTATCCTGTGGTGCCG 12 84 1 CCCTCTATCC 0.665091 -57 CCCTACCATGCCCCTCTTGCCGAGGGTGGC 13 193 1 CCCCTCTTGC 0.901018 -74 ACTTGGGGTACGCATCATGCGTTGCGTAGA 14 35 0 CGCATCATGC 0.708149 -165 ACGGAATCTTCCCCTTTTGCGCCCACTCAT 14 163 0 CCCCTTTTGC 0.758808 -37 CGCCTCTTCCCGCTCTTACCCAAGAGAAAC 15 21 0 CGCTCTTACC 0.824993 -20 CGCCTCTTCCCGCTCTTACC 15 31 0 CGCCTCTTCC 0.985393 -10 CCCTGTCAATCGTTTCTTCCGAAAGCACTC 16 42 0 CGTTTCTTCC 0.842983 -77 TGACAGGGGACGTCTTTTGCGCTAGCCTAC 16 64 1 CGTCTTTTGC 0.750017 -55 CGACCCTCCCCTGAAAAAAA 16 109 0 CGACCCTCCC 0.7637 -10 ********** Masking position 10 Map Score: 17.5126 Number of sites scoring better than the average of aligned sites = 1269 Number in coding regions = 1131 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 GGGGTCCTCCGCGTACCGCGTGCGTAGAG 2 83 0 CGCGTACCGC 0.956484 -19 CGGTCAAGTGGAGGTACCGGGTAAGTTTTT 3 116 0 GAGGTACCGG 0.86095 -185 CTGCTGATGGCAGCTGCCAGTCTGCGTCGG 3 143 0 CAGCTGCCAG 0.858929 -158 TATCGTCGCGTCCCACGCACCTCCTC 4 7 1 CGCGTCCCAC 0.775714 -294 CTATGCGGAACGAGTACGGCAAACGGAGTG 4 166 0 CGAGTACGGC 0.573916 -135 CTGCAAAAAAGGGGTGCCGGCGTATGGGGC 4 222 0 GGGGTGCCGG 0.959285 -79 CCTCCCTGGTCGGCTGCCAGGGTAGCACGG 4 275 0 CGGCTGCCAG 0.957153 -26 CGTCTTGCACGACCTGCGGGGGCGCAGTAT 5 38 1 GACCTGCGGG 0.427158 -98 GTTTCTCGTGGAGCTATCGGCGGGGTGTTT 6 96 1 GAGCTATCGG 0.387506 -55 GTTGTGGGGGTGCGGCGGTGCGGTCG 7 7 1 GGGGTGCGGC 0.873965 -53 ATTCCTCGCGCGGGTATCAGGGTGTGAGGG 10 18 1 CGGGTATCAG 0.919868 -67 GTCTTGAAAAAGTGTACCAGAGCCACTACA 12 14 0 AGTGTACCAG 0.640363 -127 GGCGAGCTGGCGCCTGCGAGGCGTTAGGGG 13 31 0 CGCCTGCGAG 0.855489 -236 ACGATTTGGACAGGTACCACGCGGGAGGTT 13 92 0 CAGGTACCAC 0.900863 -175 GAAATAGAGAAGCGTGCCACCCTCGGCAAG 13 208 0 AGCGTGCCAC 0.776712 -59 TCACGCCTGGCGTGTATCAC 14 1 0 CGTGTATCAC 0.60632 -199 CAGAAATTCGCAGGTACCGCGCAACCTCTT 14 121 0 CAGGTACCGC 0.907457 -79 CTGAACGTACCGTGTATGAGTGGGCGCAAA 14 148 1 CGTGTATGAG 0.499992 -52 GCGGGTATGAGTTTCTCTTGG 15 2 1 CGGGTATGAG 0.83384 -39 AAAAAAACACAGCCTACCAGGGGTAGGCTA 16 86 0 AGCCTACCAG 0.703262 -33 ********** Masking position 5 Map Score: 14.8678 Number of sites scoring better than the average of aligned sites = 1534 Number in coding regions = 1389 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 6 AAACTCTCAAAGGAAAAGTCAAGCTTTTTGGA 1 46 0 AGAAAGTCAA 0.862214 -35 CCCCCAAGCTAAAAACTCTCAAAGGAAAAGTC 1 58 0 AAAATCTCAA 0.800868 -23 CAAGCAGATAACGAACACTCACTCAGATCAAA 3 87 1 AGAAACTCAC 0.974305 -214 GCGCATTCCGGCAAAGACACACAACTGCACAT 3 186 1 GAAAACACAC 0.650275 -115 ATACAAGGAGGAGAACACTTACTCCGT 3 284 1 GGAAACTTAC 0.71784 -17 CAGGCAAGGGACGAAAAGTCAATGCCTCCATT 5 99 0 AGAAAGTCAA 0.862214 -37 CCAACCCAAGGGAAAATCTCACGGCACCACTA 6 15 0 GAAATCTCAC 0.920847 -136 TGTGAGGGGAAAGAAGTGTCAAATCAGAATGC 10 40 1 AGAATGTCAA 0.819677 -45 AAATAAAAGAAGAAGAACTCACCACCACGCCG 11 45 1 AAAGACTCAC 0.746491 -99 GGATTGCTTCGAGAAGAGTCACGAAATAGAGA 13 228 0 GGAAAGTCAC 0.947742 -39 ATGCGTTGCGTAGAAATCTCACGCCTGGCGTG 14 17 0 TGAATCTCAC 0.830862 -183 GTTTGTCCGAAGAAATTCTCACGATAGAAGAG 14 94 1 AAAATCTCAC 0.92575 -106 * *** ****** Masking position 4 Map Score: 5.42812 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 116 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 CTCCCTCCCTGGTTGTGTAATGGTAGCACC 3 27 0 GGTTGTGTAA 0.91888 -274 CGCCCCCGCAGGTCGTGCAAGACGTTTACT 5 32 0 GGTCGTGCAA 0.992548 -104 GTGAACGAAAGGATGTGCTAAGGAGGGGAT 6 131 1 GGATGTGCTA 0.886572 -20 GCGGCGGTGCGGTCGTGCTATTTTTCGTAT 7 22 1 GGTCGTGCTA 0.986185 -38 AAGGCACCCAGGTCATGCAAGGGCGCGGCG 11 72 0 GGTCATGCAA 0.953713 -72 AGGCGTTAGGGGTGGTGAAAAGGAGTTTGC 13 13 0 GGTGGTGAAA 0.904951 -254 ********** Masking position 6 Map Score: 3.16348 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 25 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 TAGGTATAAACTCCCTGCCCCATACGCCGG 4 206 1 CTCCCTGCCC 0.960982 -95 ACCTGCGCGGTATACTGCGCCCCCGCAGGT 5 49 0 TATACTGCGC 0.939243 -87 TAGTGTTCGCTTCAGTGCGCCACACATAAA 8 13 1 TTCAGTGCGC 0.961019 -29 TACACTGCGCGTGAGGAGTG 9 1 1 TACACTGCGC 0.979239 -24 AGTGTCAAATCAGAATGCGCTGGTGAACAT 10 54 1 CAGAATGCGC 0.802779 -31 ACACGTTGCTTTTCCTGCGCGA 11 3 0 TTTCCTGCGC 0.943657 -141 TTTCTTCCGGTTTAGTGCCCCAGTGAGTGA 11 123 1 TTTAGTGCCC 0.845424 -21 ACCTTCCCATTACAATGCCCCTCTATCCTG 12 76 1 TACAATGCCC 0.952672 -65 CAAGCTATTTCTCCATGCGCTAGAATGCGG 13 59 0 CTCCATGCGC 0.958227 -208 CCGATCGCCCTACCATGCCCCTCTTGCCGA 13 186 1 TACCATGCCC 0.956156 -81 ********** Masking position 6 Map Score: 9.76781 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 345 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 GTTTTTGATCTGAGTGAGTGTTCGTTATCT 3 92 0 TGAGTGAGTG 0.925069 -209 CTGACTGGAAGGAGCGACTGCACAATTGTA 3 224 0 GGAGCGACTG 0.960869 -77 ACGGAGTAAGTGTTCTCCTCCT 3 289 0 GGAGTAAGTG 0.91816 -12 GCGTAGTAGGGGATTGACTGTGCAGTCACT 4 108 1 GGATTGACTG 0.948059 -193 CCCGACGGACCCAGTGACTGCACAGTCAAT 4 120 0 CCAGTGACTG 0.973742 -181 GATAGCTCCACGAGAAACTGTTCTATAGAG 6 84 0 CGAGAAACTG 0.8327 -67 GTTTAGTGCCCCAGTGAGTGAT 11 132 1 CCAGTGAGTG 0.957972 -12 TCGGAAGAAACGATTGACAGGGGACGTCTT 16 50 1 CGATTGACAG 0.81119 -69 ********** Masking position 7 Map Score: 2.54828 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 95 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 GATATCCTGGGAGCGGAAAG 1 1 1 GATATCCTGG 0.874023 -80 AAGATGCGAAGATGCCCTGGGTGTTT 2 7 0 GATGCCCTGG 0.968055 -95 CGTGCGTAGAGACTCCCTCAGGCTAACGCA 2 64 0 GACTCCCTCA 0.713616 -38 GCCTGGGCCTCCCTCCCTGGTTGTGTAATG 3 35 0 CCCTCCCTGG 0.97414 -266 AGCTATCCGTGCTACCCTGGCAGCCGACCA 4 269 1 GCTACCCTGG 0.981192 -32 ACGCGCCCTCCCTGGTCGGCTGCCA 4 286 0 CCCTCCCTGG 0.97414 -15 GTTGGGGCGAGATCTCCTGGCGAGGGTATG 6 42 1 GATCTCCTGG 0.823591 -109 ACCGCAGAGACATACCCTCGCCAGGAGATC 6 52 0 CATACCCTCG 0.939876 -99 TCTTTCCCCTCACACCCTGATACCCGCGCG 10 24 0 CACACCCTGA 0.920103 -61 CGCGCCCTTGCATGACCTGGGTGCCTTTGG 11 75 1 CATGACCTGG 0.725846 -69 AGAGAAGCGTGCCACCCTCGGCAAGAGGGG 13 203 0 GCCACCCTCG 0.954497 -64 CGACCCTCCCCTGAAAAAAACACA 16 105 0 CCTCCCCTGA 0.885706 -14 ********** Masking position 8 Map Score: 12.9969 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 125 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 ********** No masking Map Score: -2.72605e-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 12 TGGAGGTACCGGGTAAGTTTTTGATCTGAGTG 3 106 0 GGGAGTTTTT 0.761215 -195 GGCGTAGTAGGGGATTGACTGTGCAGTCACTG 4 107 1 GGGTGACTGT 0.89983 -194 GTTCCGCATAGGCCCTGTCTTTAGGTATAAAC 4 185 1 GGCTGTCTTT 0.982545 -116 CGGCGTATGGGGCAGGGAGTTTATACCTAAAG 4 203 0 GGCGGAGTTT 0.930468 -98 CTCGAATGGAGGCATTGACTTTTCGTCCCTTG 5 95 1 GGCTGACTTT 0.97465 -41 CTCCTGGCGAGGGTATGTCTCTGCGGTGGCTC 6 55 1 GGGTGTCTCT 0.929336 -96 TGGAGCTATCGGCGGGGTGTTTGTGGTGTGAA 6 104 1 GGCGGTGTTT 0.951436 -47 GCGGGTATGAGTTTCTCTTGGGTA 15 3 1 GGGTGAGTTT 0.959402 -38 ACGATTGACAGGGGACGTCTTTTGCGCTAGCC 16 59 1 GGGCGTCTTT 0.945415 -60 ACCCCTGGTAGGCTGTGTTTTTTTCAGGGGAG 16 92 1 GGCTGTTTTT 0.938858 -27 *** ******* Masking position 10 Map Score: 8.09686 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 73 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 ACCCCATTGCGTTAGCCTGAGGGAGTCTCTAC 2 57 1 GTTAGCGAGG 0.685611 -45 GTCTGCGTCGGTCAAGTGGAGGTACCGGGTAA 3 122 0 GTCAAGGAGG 0.821092 -179 TCCTTGTAGGGTGAACCCGACGGACCCAGTGA 4 133 0 GTGAACGACG 0.986875 -168 TGTTTGTGGTGTGAACGAAAGGATGTGCTAAG 6 121 1 GTGAACAAGG 0.957703 -30 GCGCACTGAAGCGAACACTACG 8 1 0 GCGAACTACG 0.78598 -41 GAATGCGCTGGTGAACATGAGGAGGAAAT 10 66 1 GTGAACGAGG 0.993242 -19 GGCGCGCCGAGTGTACCAAAGGCACCCAGGTC 11 88 0 GTGTACAAGG 0.862902 -56 TCTTGAAAAAGTGTACCAGAGCCACTACACTG 12 11 0 GTGTACGAGC 0.82672 -130 GTTAGGGGTGGTGAAAAGGAGTTTGCGA 13 7 0 GTGAAAGAGT 0.666876 -260 GCATGGTAGGGCGATCGGGACGCTCTAGTCAA 13 172 0 GCGATCGACG 0.842296 -95 TAGGGTGTGCGTGCAGGGGAGGCAGGAGTGCT 16 17 1 GTGCAGGAGG 0.944128 -102 GGGTAGGCTAGCGCAAAAGACGTCCCCTGTCA 16 64 0 GCGCAAGACG 0.757546 -55 ****** **** Masking position 10 Map Score: 3.0658 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 312 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 ********** No masking Map Score: -2.72605e-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: -2.72605e-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