AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_tpal_reg_300.orf -o00530_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 Purged sequences: TP0244 21 ribosomal protein S7 Input sequences: #1 TP0027 225 hemolysin, putative #2 TP0029 107 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) #3 TP0085 80 PTS system, nitrogen regulatory IIA component (ptsN-1) #4 TP0090 181 UDP-N-acetylmuramate dehydrogenase (murB) #5 TP0231 100 conserved hypothetical protein #6 TP0232 99 T. pallidum predicted coding region TP0232 #7 TP0233 30 anti-sigma F factor antagonist, putative #8 TP0234 234 ribosomal protein L33 (rpmG) #9 TP0235 149 preprotein translocase subunit (secE) #10 TP0237 106 ribosomal protein L11 (rplK) #11 TP0240 108 ribosomal protein L7/L12 (rplL) #12 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #13 TP0243 102 ribosomal protein S12 (rpsL) #14 TP0245 23 T. pallidum predicted coding region TP0245 #15 TP0246 145 T. pallidum predicted coding region TP0246 #16 TP0247 50 N-acetylmuramoyl-L-alanine amidase (amiA) #17 TP0248 66 T. pallidum predicted coding region TP0248 #18 TP0249 78 flagellar filament outer layer protein (flaA-1) #19 TP0250 50 T. pallidum predicted coding region TP0250 #20 TP0251 153 DNA-binding protein II #21 TP0413 102 phosphoglucomutase #22 TP0417 26 apolipoprotein N-acyltransferase (cutE) #23 TP0505 300 hexokinase (hxk) #24 TP0755 199 PTS system, nitrogen regulatory IIA component (ptsN-2) #25 TP0757 40 polypeptide deformylase (def) #26 TP0758 118 ribosomal protein S21 (rpsU) #27 TP0861 236 glucosamine-fructose-6-phosphate aminotransferase (glmS) #28 TP0862 134 peptidyl-prolyl cis-trans isomerase, FKBP-type, 22 kDa (fklB) Motif number 1 AGTTCATTGTAGTGGAGGGTGTGCTCTTGAC 1 44 1 AGTGGAGGGG 0.979138 -182 CCTCCCCGCTGGGGGGGGGCACCTTTTAAGG 1 90 0 GGGGGGGGGA 0.971587 -136 GCCCCCCCCCAGCGGGGAGGGGTCCAAGGAT 1 101 1 AGCGGGGAGG 0.867503 -125 GTAAGTACACAGGATGGGGCCGTACTTTTGC 2 18 1 AGGATGGGGC 0.654651 -90 GTGTGCGCAAAGGGGTGAGAGC 2 96 1 AGGGGTGAGG 0.895018 -12 GAGCGGAAAGAGCGTGGGGAGCTTTTCCAAA 3 21 1 AGCGTGGGGG 0.831545 -60 GCGCGACAATGGGGCTGGGCGTGGTCCGCAC 4 52 0 GGGGCTGGGG 0.937737 -130 GGTAGACTGAAGCGCAGGCGGGCAAAGGCGT 4 85 0 AGCGCAGGCG 0.749003 -97 GTTTCGAGGGAGGGTAGACTGAAGCGCAGGC 4 97 0 AGGGTAGACG 0.715357 -85 CGGGACGGAAAGGAGAGAGGAT 5 89 1 AGGAGAGAGA 0.665888 -12 AGGGCATTCTGGTAGGCGGTGTGTGGTTTTG 6 22 1 GGTAGGCGGG 0.542753 -78 CGAAACCGCTAGTGGGGATGGCCT 7 17 1 AGTGGGGATG 0.461268 -14 CTTTCTTTCTGGGGCAGGCTGGTTGGCTGCC 8 20 1 GGGGCAGGCG 0.9656 -215 TAGCTCAGTTGGCAGAGCGCAACCATGGTAA 8 151 1 GGCAGAGCGA 0.584615 -84 TGTGGATGTGAGGAGGGGTGGT 8 223 1 AGGAGGGGTG 0.876308 -12 TAGCTCTAATGGCAGAGCGTCGGTCTCCAAA 9 72 1 GGCAGAGCGC 0.723493 -78 CTTCTTCCAGGGTGGAGAGTGTTGCAATGCG 10 15 1 GGTGGAGAGG 0.949992 -92 TTACGTCATAAGGAGAGGCCAGT 10 94 1 AGGAGAGGCA 0.762213 -13 CCTTTCGTGTGGGAGGGCGTCGCGCTTTTGA 12 62 1 GGGAGGGCGC 0.896476 -201 CGCGCTTTTGAGTAGAGCGTGGGCTTCTATT 12 82 1 AGTAGAGCGG 0.86474 -181 ACTTGAGTGGAGGGGACGGCGTCTCCCCTGT 12 168 1 AGGGGACGGG 0.922614 -95 GGAGTATTACGGTAGAGCGTGTGGTATAGGG 12 203 1 GGTAGAGCGG 0.924982 -60 TAGAGCGTGTGGTATAGGGAGCACCGTGTCG 12 215 1 GGTATAGGGG 0.838856 -48 GTGTCGGTTCGGTGCAGCTTGAGGGGGGAGT 12 240 1 GGTGCAGCTG 0.455243 -23 GTGCAGCTTGAGGGGGGAGTGC 12 251 1 AGGGGGGAGG 0.969635 -12 CCACCTTTGCGGGGGATGCGCATTTTCGTTG 15 76 1 GGGGGATGCC 0.608989 -70 ATTGTGAGTAGGGAGAGGGGACAGGT 16 35 1 GGGAGAGGGA 0.948229 -16 TAGGGGATGGGGCAGCATTGTA 17 2 1 AGGGGATGGG 0.916973 -65 TGACAAAATAGGCGGTGAGCGTATACTCGAA 18 23 1 GGCGGTGAGG 0.771233 -56 AGTCTTCCTAGGGAGAGGGGGCGGTGGGGTT 19 17 1 GGGAGAGGGG 0.993678 -34 CTTCACCCGAGGTGGTGCGCGTTTGAGGCGG 20 107 1 GGTGGTGCGG 0.860058 -47 GTAGGGGCGGGGGAGAGGTAGGA 21 3 0 GGGAGAGGTG 0.952687 -100 GGTGTGGTCGGGTGTAGGGGCGGGGGAGAGG 21 16 0 GGTGTAGGGC 0.756259 -87 GGAAGTGCAAGGGAGGTGGTGGTCTTGACAG 21 57 0 GGGAGGTGGG 0.840087 -46 GCGCGGAGGATAGGGCGCGGGTGAAGG 21 86 0 AGGATAGGGG 0.928034 -17 GCCGGCGTATGGGGCAGGGAGTTTATACCTA 23 206 0 GGGGCAGGGG 0.988118 -95 CCTGCAAAAAAGGGGTGCCGGCGTATGGGGC 23 222 0 AGGGGTGCCG 0.837102 -79 CAGCCGACCAGGGAGGGCGCGT 23 289 1 GGGAGGGCGG 0.975594 -12 TTACAGAGAAAGGGGAGGTTGGTTTGTCCGA 24 73 1 AGGGGAGGTG 0.966359 -127 GTGTGCGTGCAGGGGAGGCAGGAGTGCTTTC 26 21 1 AGGGGAGGCG 0.98696 -98 CAGCCTACCAGGGGTAGGCTAGCGCAAAAGA 26 76 0 GGGGTAGGCA 0.72909 -43 TGTTTTTTTCAGGGGAGGGTCG 26 107 1 AGGGGAGGGC 0.979829 -12 ACCTCCCCCAAGGGGAGACCCGACGAACGAG 27 71 0 AGGGGAGACC 0.774818 -166 GTCTCCCCTTGGGGGAGGTGGTGAGTCTCCC 27 83 1 GGGGGAGGTG 0.98227 -154 AAGTACGGATGGGGTAGGCTGGTCGCCTCGG 28 84 1 GGGGTAGGCG 0.9585 -51 TGGTCGCCTCGGGGCGGCGCGGATGAGCGCG 28 103 1 GGGGCGGCGG 0.954816 -32 ********* * Masking position 2 Map Score: 70.3541 Number of sites scoring better than the average of aligned sites = 2483 Number in coding regions = 2092 Number in noncoding regions = 391 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 2 TGTAGTGGAGGGTGTGCTCTTGACACAAGGGC 1 51 1 GGGGCTCTTG 0.737373 -175 GCGACAATGGGGCTGGGCGTGGTCCGCACGTG 4 49 0 GGTGGCGTGG 0.902471 -133 TGGCCTTCTTTGCGTTTCGAGGGAGGGTAGAC 4 109 0 TGGTTCGAGG 0.779035 -73 ATGCTACAATGGCGCGGTCTTGGCCTTCTTTG 4 129 0 GGGGGTCTTG 0.927845 -53 ACCGGTAGTATGCGGTGCCTGGTATAGGTGCG 5 59 1 TGGTGCCTGG 0.95867 -42 CATTCTGGTAGGCGGTGTGTGGTTTTGAGTTC 6 26 1 GGGTGTGTGG 0.992227 -74 TGTTTAGGGAGGTGTTTCGTGCTTGATGTGTG 8 51 1 GGGTTCGTGC 0.934914 -184 GTGCTTGATGTGTGAGGTGAGGCGTTATACAA 8 69 1 TGGGGTGAGG 0.869605 -166 CCGGCCTCCGGGCGGCTCGGGGAGTCCTGTCT 8 107 1 GGGCTCGGGG 0.919113 -128 TGTTACGCACGGGGTTTTCTGGTGTTTTCCGG 9 25 1 GGGTTTCTGG 0.922871 -125 GGTGTTTTCCGGGGATTTGTGGGTCAGTAGCT 9 45 1 GGGTTTGTGG 0.97133 -105 GTTGGTTTCGGGTGTTTTGTTGTTTTTTACGT 10 68 1 GGGTTTGTTG 0.917737 -39 AGGCTTCTGGGGTGCTGTCTTCCTGTCCGTTT 11 53 1 GGGTGTCTTC 0.784849 -56 GCATGCGTCCGGCGCGTCGTTGTGTGCCTCTG 12 26 1 GGGGTCGTTG 0.943418 -237 GCATGCGGGTTGGGTCGCGTTCTCCTCACTTG 12 141 1 TGGCGCGTTC 0.722206 -122 CCCACACAGGGGAGACGCCGTCCCCTCCACTC 12 172 0 GGGCGCCGTC 0.550073 -91 CCTAGCCGCGTGTGCTGTGTGCGGCAAGGTTT 13 42 1 TGGTGTGTGC 0.90342 -61 ATGTGATGCGAAGCGTGCGCAAG 15 2 1 TGGTGCGAAG 0.49496 -144 TGTGGTGCGTGGACGTATGTGC 16 1 1 TGGTGCGTGG 0.985003 -50 GTGTAGTGAGGGCGGTGTGTTGGACTCTCTTG 17 35 1 GGGTGTGTTG 0.976762 -32 CTAGGGAGAGGGGGCGGTGGGGTTCTAGGCGC 19 24 1 GGGGGTGGGG 0.977747 -27 GATGAAATCAGGTGTGGTCGGGTGTAGGGGCG 21 25 0 GGGGGTCGGG 0.939458 -78 AGCGAAAAGAGGAGGTGCGTGGGACGCGACGA 23 13 0 GGGTGCGTGG 0.99548 -288 GTACGCATCATGCGTTGCGTAGAAATCTCACG 24 26 0 TGGTGCGTAG 0.828932 -174 GACACGTAGGGTGTGCGTGCAGGGGAGGCA 26 9 1 GGTTGCGTGC 0.72414 -110 ACAGGTCACAGGCGATCCCATGCCCATCCGTT 27 28 0 GGGTCCCATG 0.530755 -209 TGGGATCGCCTGTGACCTGTGGGTTACCTTGC 27 40 1 TGGCCTGTGG 0.802603 -197 TCTCCCCTTGGGGGAGGTGGTGAGTCTCCCTG 27 84 1 GGGGGTGGTG 0.935352 -153 TAGCCTGCGAGGCGGCTCGTGGCTTGGTTGAG 27 132 1 GGGCTCGTGG 0.966211 -105 TACGCGTGCGTGTGTTCTGTGGGTTTGAGTTT 27 177 1 TGGTCTGTGG 0.892606 -60 TGGTCGCCTCGGGGCGGCGCGGATGAGCGCGC 28 103 1 GGGGGCGCGG 0.945599 -32 ** * ******* Masking position 2 Map Score: 44.1508 Number of sites scoring better than the average of aligned sites = 1327 Number in coding regions = 1178 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 GGACTCCGCGCGGTCTCCGGACACGCAGTT 1 18 1 CGGTCTCCGG 0.821756 -208 CCCCCCCCAGCGGGGAGGGGTCCAAGGATG 1 103 1 CGGGGAGGGG 0.97097 -123 CCGCTGCGTTCGGTGTGTTGGTAGTGCTGC 1 204 1 CGGTGTGTTG 0.878701 -22 GATATCCTGGGAGCGGAAAGAGCGTG 3 7 1 CTGGGAGCGG 0.924465 -74 CGCACGTGTTCTGCGCCCGGTTGGGAGAAA 4 27 0 CTGCGCCCGG 0.829819 -155 GACAATGGGGCTGGGCGTGGTCCGCACGTG 4 49 0 CTGGGCGTGG 0.940828 -133 TGTTATCCTGCTGTTTGCGTGTTTGGTTGA 5 30 1 CTGTTTGCGT 0.330623 -71 CGGTAGTATGCGGTGCCTGGTATAGGTGCG 5 61 1 CGGTGCCTGG 0.944536 -40 TTCTGGTAGGCGGTGTGTGGTTTTGAGTTC 6 28 1 CGGTGTGTGG 0.97648 -72 GACACTCTTTCTGTTACCGGCAGAACTCAA 6 50 0 CTGTTACCGG 0.355904 -50 CAATGCGGGCCGGCCTCCGGGCGGCTCGGG 8 98 1 CGGCCTCCGG 0.761352 -137 GGCCTCCGGGCGGCTCGGGGAGTCCTGTCT 8 109 1 CGGCTCGGGG 0.896139 -126 TCGGGGAGTCCTGTCTGTGTTGCTTCTGTA 8 123 1 CTGTCTGTGT 0.28265 -112 GGTAAGGTTGAGGTCAGCGGTTCAATCCCG 8 177 1 AGGTCAGCGG 0.602586 -58 GTCAGGCTTCTGGGGTGCTGTCTTCCTGTC 11 50 1 TGGGGTGCTG 0.539049 -59 TGCATGCGTCCGGCGCGTCGTTGTGTGCCT 12 25 1 CGGCGCGTCG 0.745534 -238 TTTTGGCATGCGGGTTGGGTCGCGTTCTCC 12 136 1 CGGGTTGGGT 0.581217 -127 GGCGTCTCCCCTGTGTGGGGAGTATTACGG 12 185 1 CTGTGTGGGG 0.922247 -78 AGCACCGTGTCGGTTCGGTGCAGCTTGAGG 12 234 1 CGGTTCGGTG 0.685265 -29 GCCGCGTGTGCTGTGTGCGGCAAGGTTTAC 13 46 1 CTGTGTGCGG 0.94647 -57 ACAAGCTGATCGGTTTGTGTTTGTTCCGCA 15 119 1 CGGTTTGTGT 0.53699 -27 TGTGGTGCGTGGACGTATGTGC 16 3 1 TGGTGCGTGG 0.850337 -48 GTAGTGAGGGCGGTGTGTTGGACTCTCTTG 17 37 1 CGGTGTGTTG 0.878701 -30 ATGCAGGGGTGTTGACAAAATAGG 18 5 1 AGGGGTGTTG 0.497122 -74 ACAAAATAGGCGGTGAGCGTATACTCGAAG 18 25 1 CGGTGAGCGT 0.887709 -54 GTGGGGTTCTAGGCGCGGGGC 19 40 1 AGGCGCGGGG 0.869897 -11 AACACCTTTCCGGGCAGCGGTGTCAAGTCG 20 13 0 CGGGCAGCGG 0.921776 -141 TCACCCGAGGTGGTGCGCGTTTGAGGCGGC 20 109 1 TGGTGCGCGT 0.616397 -45 GGTCGGGTGTAGGGGCGGGGGAGAGGTAGG 21 12 0 AGGGGCGGGG 0.908702 -91 AAATGCTTTTCTGGCAGGGGAAAGTT 22 11 1 CTGGCAGGGG 0.660377 -16 CGAAAAGAGGAGGTGCGTGGGACGCGACGA 23 13 0 AGGTGCGTGG 0.892682 -288 CTGTTGTGTTCGGCGACTTGGATATCTTCC 23 76 0 CGGCGACTTG 0.478001 -225 TGTGCAGTCACTGGGTCCGTCGGGTTCACC 23 126 1 CTGGGTCCGT 0.446519 -175 AAAGGGGTGCCGGCGTATGGGGCAGGGAGT 23 215 0 CGGCGTATGG 0.433129 -86 TGTTTTTTTCAGGGGAGGGTCG 26 107 1 AGGGGAGGGT 0.419901 -12 ATGGGATCGCCTGTGACCTGTGGGTTACCT 27 39 1 CTGTGACCTG 0.360444 -198 GTCTCCCTGTTGGTGCGCTGGACCGTAGCC 27 107 1 TGGTGCGCTG 0.631938 -130 GCCTGCGAGGCGGCTCGTGGCTTGGTTGAG 27 134 1 CGGCTCGTGG 0.881336 -103 CTGGTCGCCTCGGGGCGGCGCGGATGAGCG 28 102 1 CGGGGCGGCG 0.843116 -33 ********** Masking position 3 Map Score: 39.5073 Number of sites scoring better than the average of aligned sites = 3052 Number in coding regions = 2721 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 4 CCTTTTAAGGTGCTCACGCCCTTGTGTCAAG 1 69 0 TGCTCACGCC 0.40452 -157 GTGTTCTTTCCGTTTCCGCTGCGTTCGGTGT 1 189 1 CGTTTCCGCG 0.914693 -37 GCTCTCACCCCTTTGCGCACACATTCCTGT 2 88 0 CCTTTGCGCC 0.98956 -20 CTCCCCACGCTCTTTCCGCTCCCAGGATATC 3 11 0 TCTTTCCGCC 0.977862 -70 CGGGCAAAGGCGTTTGCGCGACAATGGGGCT 4 67 0 CGTTTGCGCA 0.83849 -115 CGCGCAAACGCCTTTGCCCGCCTGCGCTTCA 4 78 1 CCTTTGCCCC 0.942587 -104 TCTCTCCTTTCCGTCCCGCACCTATACCAGG 5 76 0 CCGTCCCGCC 0.952023 -25 TCCCCACTAGCGGTTTCGCACACT 7 4 0 CGGTTTCGCC 0.90101 -27 AACCTTACCATGGTTGCGCTCTGCCAACTGA 8 155 0 TGGTTGCGCC 0.929977 -80 GTCGTCATATCTGTTACGCACGGGGTTTTCT 9 14 1 CTGTTACGCC 0.800763 -136 ACACCGTAAACCTTGCCGCACACAGCACACG 13 50 0 CCTTGCCGCC 0.891877 -53 TCTTTTCGCTCACTTCCCCAA 13 92 0 TCTTTTCGCC 0.933807 -11 GCGCAAAATTCTCTTGCGCACGCTTCGCATC 15 15 0 CTCTTGCGCC 0.931811 -131 TTGCGCGTTTTTTTTCCGCTGAAGCACGGAA 15 40 1 TTTTTCCGCG 0.779718 -106 AATATCGCCACCTTTGCGGGGGATGCGCATT 15 69 1 CCTTTGCGGG 0.621902 -77 CGGTTTGTGTTTGTTCCGCAGGAGGGG 15 129 1 TTGTTCCGCG 0.661293 -17 TCAAACGCTCCTTTCGCACAATAAGATAA 18 60 0 TCCTTTCGCC 0.840439 -19 AGCGAAAACACCTTTCCGGGCAGCGGTGTCA 20 18 0 CCTTTCCGGC 0.887964 -136 CCCGGAAAGGTGTTTTCGCTAGAAAGGCTGT 20 29 1 TGTTTTCGCA 0.43589 -125 TTGAGGCGGCTGTTTGCCCGCGTGTGTTTCT 20 129 1 TGTTTGCCCC 0.806598 -25 TCCTACCTCTCCCCCGCCCCTACACCC 21 7 1 CTCTCCCCCC 0.473239 -96 CCTTGCACTTCCTTCACCCGCGCCCTATCCT 21 76 1 CCTTCACCCC 0.55369 -27 ACGCACCTCCTCTTTTCGCTCAACATTTCCT 23 25 1 TCTTTTCGCC 0.933807 -276 TTTGCCGTACTCGTTCCGCATAGGCCCTGTC 23 173 1 TCGTTCCGCT 0.492098 -128 GAATCTTCCCCTTTTGCGCCCACTCATACAC 24 159 0 CTTTTGCGCC 0.973404 -41 CGCCTCTTCCCGCTCTTACCCAAGA 25 26 0 TCTTCCCGCC 0.94371 -15 CAGGGGACGTCTTTTGCGCTAGCCTACCCCT 26 67 1 CTTTTGCGCA 0.786214 -52 CGCTCCTTTTGCGCGCTCATCCGCGC 28 119 0 CTTTTGCGCC 0.973404 -16 ********* * Masking position 4 Map Score: 32.2849 Number of sites scoring better than the average of aligned sites = 1173 Number in coding regions = 1081 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 5 CGCCCTTGTGTCAAGAGCACACCCTCCACT 1 54 0 TCAAGAGCAC 0.884317 -172 TGACACAAGGGCGTGAGCACCTTAAAAGGT 1 71 1 GCGTGAGCAC 0.408655 -155 GCAAAGAAGGCCAAGACCGCGCCATTGTAG 4 128 1 CCAAGACCGC 0.860757 -54 CGCCATTGTAGCATAAGCGCGTGAAATCGT 4 147 1 GCATAAGCGC 0.791169 -35 TACCGGTCAACCAAACACGCAAACAGCAGG 5 36 0 CCAAACACGC 0.626261 -65 CCGGCAGAACTCAAAACCACACACCGCCTA 6 34 0 TCAAAACCAC 0.914365 -66 AGTGTGCGAAACCGCTAGTGGGGAT 7 6 1 GCGAAACCGC 0.787273 -25 AGGCCATCCCCACTAGCGGTTTC 7 18 0 CCATCCCCAC 0.653487 -13 GGTCAGCGGTTCAATCCCGCTCGGAAGCTT 8 188 1 TCAATCCCGC 0.720538 -47 AAACACCTTTTCGAAAGCACTCAGGCCAGG 9 129 0 TCGAAAGCAC 0.871152 -21 CACGCTCTACTCAAAAGCGCGACGCCCTCC 12 73 0 TCAAAAGCGC 0.953485 -190 GAGAACGCGACCCAACCCGCATGCCAAAAT 12 135 0 CCCAACCCGC 0.814467 -128 TCAAACGCTCCTTTCGCACA 18 69 0 TCAAACGCTC 0.736746 -10 AACAGCCGCCTCAAACGCGCACCACCTCGG 20 113 0 TCAAACGCGC 0.975003 -41 TTTCATCCTGTCAAGACCACCACCTCCCTT 21 50 1 TCAAGACCAC 0.855191 -53 TGCACTTCCTTCACCCGCGCCCTATCCTCC 21 79 1 TCACCCGCGC 0.743911 -24 CAAGAGAAACTCATACCCGC 25 1 0 TCATACCCGC 0.920997 -40 ATCGTTTCTTCCGAAAGCACTCCTGCCTCC 26 34 0 CCGAAAGCAC 0.826742 -85 CAGGCTACGGTCCAGCGCACCAACAGGGAG 27 109 0 TCCAGCGCAC 0.750157 -128 AACGTTAAACTCAAACCCACAGAACACACG 27 185 0 TCAAACCCAC 0.953089 -52 CCTTTTCAGTGCAAAAGCACACGGGAGAAC 27 212 0 GCAAAAGCAC 0.868468 -25 TTTTCAGGCATCGTACGCACC 28 2 0 TCGTACGCAC 0.832697 -133 CTTCCTTGAGCCACACCCACTTTTCAGGCA 28 22 0 CCACACCCAC 0.758533 -113 TTTTGCGCGCTCATCCGCGCCGCCCCGAGG 28 109 0 TCATCCGCGC 0.836865 -26 ********** Masking position 8 Map Score: 24.016 Number of sites scoring better than the average of aligned sites = 864 Number in coding regions = 790 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 AGAAAGAGGACTCCGCGCGGTCTCCGG 1 8 1 GGACTCCGCG 0.866927 -218 CACCTTTTAAGGTGCTCACGCCCTTGTGTC 1 72 0 GGTGCTCACG 0.60372 -154 CACCTTAAAAGGTGCCCCCCCCCAGCGGGG 1 88 1 GGTGCCCCCC 0.860975 -138 ATACATCCTTGGACCCCTCCCCGCTGGGGG 1 106 0 GGACCCCTCC 0.767449 -120 TTTTGGAAAAGCTCCCCACGCTCTTTCCGC 3 23 0 GCTCCCCACG 0.956269 -58 GGCTGGGCGTGGTCCGCACGTGTTCTGCGC 4 41 0 GGTCCGCACG 0.892431 -141 AACACAGACAGGACTCCCCGAGCCGCCCGG 8 114 0 GGACTCCCCG 0.895363 -121 AAAAGAAATAGAAGCCCACGCTCTACTCAA 12 89 0 GAAGCCCACG 0.935433 -174 CAAGTGAGGAGAACGCGACCCAACCCGCAT 12 143 0 GAACGCGACC 0.707803 -120 TCACTTGAGTGGAGGGGACGGCGTCTCCCC 12 166 1 GGAGGGGACG 0.697941 -97 GCACTCCCCCCTCAAGCTGC 12 253 0 GCACTCCCCC 0.630458 -10 ACGAAAATGCGCATCCCCCGCAAAGGTGGC 15 75 0 GCATCCCCCG 0.589087 -71 CCCGCGCCTAGAACCCCACCGCCCCCTCTC 19 29 0 GAACCCCACC 0.921144 -22 CCCCGCCCCTACACCCGACCACACCTGATT 21 22 1 ACACCCGACC 0.484541 -81 GAGGTGCGTGGGACGCGACGATA 23 4 0 GGACGCGACG 0.951778 -297 CTTGTAGGGTGAACCCGACGGACCCAGTGA 23 133 0 GAACCCGACG 0.930878 -168 GCAAAAAAGGGGTGCCGGCGTATGGGGCAG 23 220 0 GGTGCCGGCG 0.885691 -81 TGCTACCCTGGCAGCCGACCAGGGAGGGCG 23 278 1 GCAGCCGACC 0.890391 -23 AGCCGACCAGGGAGGGCGCGT 23 290 1 GGAGGGCGCG 0.643966 -11 GGTGCCCACTTTTCCTGACG 24 190 0 GGTGCCCACT 0.61808 -10 CCCCAAGGGGAGACCCGACGAACGAGCAAG 27 67 0 AGACCCGACG 0.824909 -170 GGGGTAGGCTGGTCGCCTCGGGGCGGCGCG 28 94 1 GGTCGCCTCG 0.730672 -41 ********** Masking position 9 Map Score: 16.2857 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 641 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 AAAGGTGCCCCCCCCCAGCGGGGAGGGGTC 1 95 1 CCCCCCAGCG 0.626358 -131 AACGCCTTTGCCCGCCTGCGCTTCAGTCTA 4 84 1 CCCGCCTGCG 0.973138 -98 GCGCTTCAGTCTACCCTCCCTCGAAACGCA 4 101 1 CTACCCTCCC 0.919224 -81 AAAACCACACACCGCCTACCAGAATGCCCT 6 22 0 ACCGCCTACC 0.862971 -78 AGGCAGCCAACCAGCCTGCCCCAGAAAGAA 8 22 0 CCAGCCTGCC 0.98556 -213 ACAATGCGGGCCGGCCTCCGGGCGGCTCGG 8 97 1 CCGGCCTCCG 0.720469 -138 AGGTTCGAGTCCTTCCTGGCCTGAGTGCTT 9 115 1 CCTTCCTGGC 0.5771 -35 GCAACACTCTCCACCCTGGAAGAAGAAAA 10 10 0 CCACCCTGGA 0.38723 -97 AATGCGCATGATTGCCTGCCGCTTACGCGT 10 40 1 ATTGCCTGCC 0.588903 -67 CGCGACCCAACCCGCATGCCAAAATGCCGA 12 130 0 CCCGCATGCC 0.781285 -133 CCCCTCCTGCGGAACAAACAC 15 135 0 CCCTCCTGCG 0.857734 -11 ACCTGTCCCCTCTCCCTACTCACAAT 16 35 0 CCCCTCTCCC 0.837226 -16 ACCCCACCGCCCCCTCTCCCTAGGAAGACT 19 17 0 CCCCTCTCCC 0.837226 -34 TCCTACCTCTCCCCCGCCCCTACACCCG 21 9 1 CTCCCCCGCC 0.653162 -94 TGTCAAGACCACCACCTCCCTTGCACTTCC 21 58 1 ACCACCTCCC 0.782782 -45 CACCCGCGCCCTATCCTCCGCGC 21 90 1 CTATCCTCCG 0.345681 -13 AACTTTCCCCTGCCAGAAAAGCAT 22 13 0 TTCCCCTGCC 0.509907 -14 TTAGGTATAAACTCCCTGCCCCATACGCCG 23 205 1 ACTCCCTGCC 0.871386 -96 GCTATCCGTGCTACCCTGGCAGCCGACCAG 23 270 1 CTACCCTGGC 0.786903 -31 ACGCGCCCTCCCTGGTCGGCTGCCAG 23 285 0 CCTCCCTGGT 0.228806 -16 GTAGAAATCTCACGCCTGGCGTGTATCAC 24 10 0 CACGCCTGGC 0.557362 -190 TTCGGACAAACCAACCTCCCCTTTCTCTGT 24 75 0 CCAACCTCCC 0.899571 -125 CCCTGCACGCACACCCTACGTGTC 26 5 0 ACACCCTACG 0.480051 -114 CGAAAGCACTCCTGCCTCCCCTGCACGCAC 26 23 0 CCTGCCTCCC 0.961933 -96 GTCTTTTGCGCTAGCCTACCCCTGGTAGGC 26 75 1 CTAGCCTACC 0.767967 -44 TGAAAAAAACACAGCCTACCAGGGGTAGGC 26 88 0 ACAGCCTACC 0.767967 -31 CGACCCTCCCCTGAAAAAAA 26 109 0 CGACCCTCCC 0.751402 -10 AGGGAGACTCACCACCTCCCCCAAGGGGAG 27 85 0 ACCACCTCCC 0.782782 -152 CAAGCCACGAGCCGCCTCGCAGGCTACGGT 27 128 0 GCCGCCTCGC 0.595421 -109 CCCGAGGCGACCAGCCTACCCCATCCGTAC 28 86 0 CCAGCCTACC 0.939953 -49 ********** Masking position 6 Map Score: 27.1448 Number of sites scoring better than the average of aligned sites = 1069 Number in coding regions = 889 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 8 TTTTAGCCCTTCGGGGGAATTACGTGTGAGTGT 1 160 1 TCGGGGATTC 0.907793 -66 GGAAAGAGCGTGGGGAGCTTTTCCAAAAAGCTT 3 25 1 TGGGAGCTTC 0.929787 -56 AGAAAGAGTGTCGTGTGAATTTCAATAGTTTTT 6 68 1 TCGGTGATTC 0.96419 -32 CACGGGGTTTTCTGGTGTTTTCCGGGGATTTGT 9 32 1 TCTGTGTTTC 0.824108 -118 TCTTCCAGGGTGGAGAGTGTTGCAATGCGCATG 10 17 1 TGGGAGTTTC 0.980337 -90 CGCGTTGGTTTCGGGTGTTTTGTTGTTTTTTAC 10 65 1 TCGGTGTTTT 0.824108 -42 CTCCCCTGTGTGGGGAGTATTACGGTAGAGCGT 12 190 1 TGGGAGTTTC 0.980337 -73 GGCTGTTTGCCCGCGTGTGTTTCTTGTC 20 136 1 CCGGTGTTTC 0.91802 -18 ATCTCACGCCTGGCGTGTATCAC 24 1 0 TGGGTGTTCC 0.950335 -199 ACCTCTTCTATCGTGAGAATTTCTTCGGACAAA 24 95 0 TCGGAGATTC 0.96419 -105 TTGGGGGAGGTGGTGAGTCTCCCTGTTGGTGCG 27 91 1 TGGGAGTTCC 0.950331 -146 *** **** ** * Masking position 10 Map Score: 9.13626 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 76 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ACCAACACACCGAACGCAGCGGAAACGGAAA 1 195 0 CGAACGCACG 0.969741 -31 CCGCACCTATACCAGGCACCGCATACTACCG 5 61 0 ACCAGGCACG 0.674865 -40 AGAACTCAAAACCACACACCGCCTACCAGAA 6 28 0 ACCACACACG 0.764254 -72 ACAAATCCCCGGAAAACACCAGAAAACCCCG 9 34 0 GGAAAACACA 0.350206 -116 TAAACGGACAGGAAGACAGCACCCCAGAAGC 11 55 0 GGAAGACACA 0.828363 -54 GGGTGTCAGAGGCACACAACGACGCGCCGGA 12 33 0 GGCACACACG 0.977263 -230 TAAACCTTGCCGCACACAGCACACGCGGCTA 13 44 0 CGCACACACA 0.904317 -59 AATTCTCTTGCGCACGCTTCGCATCACAT 15 9 0 CGCACGCTCG 0.933672 -137 TTGTAAAATAGGTACACAACGAAAATGCGCA 15 92 0 GGTACACACG 0.881379 -54 GCAAGAGAGTCCAACACACCGCCCTCACTAC 17 37 0 CCAACACACG 0.909892 -30 CCTCTCCCTAGGAAGACTACTGCA 19 4 0 GGAAGACTCT 0.421312 -47 TCGGGTGAAGAGAACACACCGTTGTACAGTC 20 86 0 AGAACACACG 0.879817 -68 ATCGTCGCGTCCCACGCACCTCCTCTTTTCG 23 12 1 CCCACGCACT 0.60395 -289 TCCAAGTCGCCGAACACAACAGGGGCGTAGT 23 84 1 CGAACACACA 0.879404 -217 CACCCTACAAGGAACACTCCGTTTGCCGTAC 23 152 1 GGAACACTCG 0.920011 -149 ACACACTTGGGGTACGCATCATGCGTTGCGT 24 38 0 GGTACGCACA 0.665563 -162 TTCAGAAATTCGCAGGTACCGCGCAACCTCT 24 122 0 CGCAGGTACG 0.65622 -78 GCGCAAAAGGGGAAGATTCCGTCAGGAAAAG 24 171 1 GGAAGATTCG 0.345562 -29 GCGATGTGCAGCAAGGCAACGGATGGGCATG 27 11 1 GCAAGGCACG 0.878856 -226 CGAGCCGCCTCGCAGGCTACGGTCCAGCGCA 27 120 0 CGCAGGCTCG 0.866336 -117 ******** ** Masking position 4 Map Score: 17.0534 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 1019 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 10 AGGACTCCGCGCGGTCTCCGGACACGCAGT 1 17 1 GCGGTCTCCG 0.598939 -209 CCCGCTGGGGGGGGGCACCTTTTAAGGTGC 1 87 0 GGGGGCACCT 0.119472 -139 GCTCTCACCCCTTTGCGCAC 2 98 0 GCTCTCACCC 0.867207 -10 GCCCCTTCGAAGTTTCTCCCAACCGGGCGC 4 15 1 AGTTTCTCCC 0.51261 -167 CCGCATACTACCGGTCAACCAAACACGCAA 5 44 0 CCGGTCAACC 0.705779 -57 ATCCTCTCTCCTTTCCGTCCCG 5 89 0 CCTCTCTCCT 0.730129 -12 TACCATGGTTGCGCTCTGCCAACTGAGCTA 8 151 0 GCGCTCTGCC 0.895507 -84 TTGGAGACCGACGCTCTGCCATTAGAGCTA 9 72 0 ACGCTCTGCC 0.790271 -78 CTTCTGGGGTGCTGTCTTCCTGTCCGTTTA 11 56 1 GCTGTCTTCC 0.612955 -53 CAAAAGCGCGACGCCCTCCCACACGAAAGG 12 62 0 ACGCCCTCCC 0.879538 -201 ATAGAAGCCCACGCTCTACTCAAAAGCGCG 12 82 0 ACGCTCTACT 0.369968 -181 GGGTTGGGTCGCGTTCTCCTCACTTGAGTG 12 147 1 GCGTTCTCCT 0.673814 -116 TGGAGGGGACGGCGTCTCCCCTGTGTGGGG 12 175 1 GGCGTCTCCC 0.759497 -88 CCTATACCACACGCTCTACCGTAATACTCC 12 203 0 ACGCTCTACC 0.848477 -60 CGAACCGACACGGTGCTCCCTATACCACAC 12 221 0 CGGTGCTCCC 0.770812 -42 ATACGCGTCTCTTCCTGGGGCGT 14 6 1 CGTCTCTTCC 0.666877 -18 ACCTGTCCCCTCTCCCTACTCACAAT 16 35 0 CCCCTCTCCC 0.955003 -16 ACCCCACCGCCCCCTCTCCCTAGGAAGACT 19 17 0 CCCCTCTCCC 0.955003 -34 TCCTACCTCTCCCCCGCCCCTACAC 21 6 1 CCTCTCCCCC 0.691854 -97 TGGGTCCGTCGGGTTCACCCTACAAGGAAC 23 137 1 GGGTTCACCC 0.73286 -164 AACGAGCTATCCGTGCTACCCTGGCAGCCG 23 265 1 CCGTGCTACC 0.582969 -36 ACGCGCCCTCCCTGGTCGGCTG 23 289 0 GCGCCCTCCC 0.943202 -12 TTCGCAGGTACCGCGCAACCTCTTCTATCG 24 115 0 CCGCGCAACC 0.623371 -85 CGCCTCTTCCCGCTCTTACC 25 31 0 CGCCTCTTCC 0.622197 -10 CCTCCCCTGCACGCACACCCTACGTGTC 26 9 0 ACGCACACCC 0.375834 -110 CGAAAGCACTCCTGCCTCCCCTGCACGCAC 26 23 0 CCTGCCTCCC 0.727736 -96 CCCTGTCAATCGTTTCTTCCGAAAGCACTC 26 42 0 CGTTTCTTCC 0.356496 -77 GCTCGTTCGTCGGGTCTCCCCTTGGGGGAG 27 70 1 CGGGTCTCCC 0.946654 -167 TTTGAGTTTAACGTTCTCCCGTGTGCTTTT 27 200 1 ACGTTCTCCC 0.896491 -37 CTCCTTTTGCGCGCTCATCCGCGCCGCCCC 28 113 0 GCGCTCATCC 0.806687 -22 ********** Masking position 6 Map Score: 27.7588 Number of sites scoring better than the average of aligned sites = 1289 Number in coding regions = 1156 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 11 CTCACCCCTTTGCGCACACATTCCTGTAGA 2 85 0 TGCGCACACA 0.973443 -23 CACTAGCGGTTTCGCACACT 7 1 0 TTCGCACACT 0.986113 -30 TAGGGGTTATTTCGCATACAAGGAGAAGAT 11 86 1 TTCGCATACA 0.800306 -23 TCTTTTCGCTCACTTCCCCAAAAA 13 89 0 TTCGCTCACT 0.946007 -14 AAAATTCTCTTGCGCACGCTTCGCATCACA 15 12 0 TGCGCACGCT 0.962769 -134 AAACGCTCCTTTCGCACAATAAGATAACCA 18 57 0 TTCGCACAAT 0.902079 -22 CTTCCCCTTTTGCGCCCACTCATACACGGT 24 156 0 TGCGCCCACT 0.969079 -44 ********** Masking position 1 Map Score: 5.20365 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 171 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 GCTCTCACCCCTTTGCGCACACATTC 2 92 0 ACCCCTTTGC 0.826373 -16 AAAGCTCCCCACGCTCTTTCCGCTCCCAGG 3 16 0 ACGCTCTTTC 0.88098 -65 GTGCGCCCCTTCGAAGTTTCTC 4 3 1 GCGCCCCTTC 0.853892 -179 TGTCGCGCAAACGCCTTTGCCCGCCTGCGC 4 75 1 ACGCCTTTGC 0.961176 -107 AATTCACACGACACTCTTTCTGTTACCGGC 6 59 0 ACACTCTTTC 0.842706 -41 GAAACACCTTTTCGAAAGCACTC 9 137 0 ACACCTTTTC 0.956106 -13 TGTGCCTCTGACACCCTTTCGTGTGGGAGG 12 48 1 ACACCCTTTC 0.978781 -215 CAAAAGCGCGACGCCCTCCCACACGAAAGG 12 62 0 ACGCCCTCCC 0.812104 -201 CGGAATATCGCCACCTTTGCGGGGGATGCG 15 66 1 CCACCTTTGC 0.754674 -80 TATTTTGTCAACACCCCTGCAT 18 3 0 ACACCCCTGC 0.91677 -76 TCTAGCGAAAACACCTTTCCGGGCAGCGGT 20 22 0 ACACCTTTCC 0.90353 -132 CTGGCGAGCCACAGCCTTTCTAGCGAAAAC 20 40 0 ACAGCCTTTC 0.806264 -114 TCCTTCACCCGCGCCCTATCCTCCGCGC 21 85 1 GCGCCCTATC 0.681796 -18 AGACGCCTTTTCAGTGCAAAAG 27 225 0 ACGCCTTTTC 0.96784 -12 ********** Masking position 2 Map Score: 13.7161 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 196 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 ********** No masking Map Score: 1.18259e-11 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: 1.18259e-11 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: 1.18259e-11 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