AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ilexA_tpal_opreg_100.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 TP0102 64 rep helicase, single-stranded DNA-dependent ATPase (rep) #2 TP0116 150 excinuclease ABC, subunit B (uvrB) #3 TP0162 174 Holliday junction DNA helicase (ruvB) #4 TP0438 29 conserved hypothetical protein #5 TP0439 86 purine-binding chemotaxis protein (cheW-2) #6 TP0440 89 spore coat polysaccharide biosynthesis protein, putative #7 TP0514 113 excinuclease ABC, subunit A (uvrA) #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 TP0692 260 recA protein (recA) #13 TP0944 170 conserved hypothetical protein #14 TP0999 71 cell division protein, putative #15 TP1028 82 DNA helicase II (uvrD) #16 TP1030 27 T. pallidum predicted coding region TP1030 Motif number 1 GCGCAGTTACCTGCAAGGAGC 4 2 0 CTGCAAGGAG 0.983028 -28 TTGCAGGTAACTGCGCCGTGAAAA 4 16 1 CTGCGCCGTG 0.901097 -14 TGCTCTGCAAGGTGCGTGAGCGAA 5 5 1 CTGCAAGGTG 0.95335 -82 AGGTGCGTGAGCGAACGGAGTGCAGGACAC 5 20 1 GCGAACGGAG 0.946003 -67 TTGACTGCAGCTGAGAGGAGGGATTGTACG 5 54 1 CTGAGAGGAG 0.940376 -33 GCGCTTGGAGCTGCAGGCAGGAGACAGACA 6 22 0 CTGCAGGCAG 0.843656 -68 GGGATGGACCCCGCACGGCGCTTGGAGCTG 6 39 0 CCGCACGGCG 0.991524 -51 GCGGTCTGCCGCGAAGGGAGTGGAATTGCA 7 12 1 GCGAAGGGAG 0.952281 -102 TACACTGCGCGTGAGGAGTGTCCT 9 9 1 GCGTGAGGAG 0.91142 -16 CCTGATACCCGCGCGAGGAATATAGAAA 10 9 0 GCGCGAGGAA 0.897545 -76 GTATCAGGGTGTGAGGGGAAAGAAGTGTCA 10 31 1 GTGAGGGGAA 0.649888 -54 GGTCATGCAAGGGCGCGGCGTGGTGGTGAG 11 62 0 GGGCGCGGCG 0.984837 -82 AAGAAAACTGGCGCGCCGAGTGTACCAAAG 11 99 0 GCGCGCCGAG 0.969396 -45 GACTCATAATCCGCGGGTCGCCGGTTCAAG 12 159 1 CCGCGGGTCG 0.899816 -102 GAAAAACCCCGCGCAAGGCGCAAGAGACGC 12 227 0 GCGCAAGGCG 0.985444 -34 GGTGTTCAGGTGTAAGGAGACCCTGTCGC 13 10 1 GTGTAAGGAG 0.815273 -161 GCTTGTTTTTCTGCGGGGATACTGCTTCTT 13 57 1 CTGCGGGGAT 0.881812 -114 TTAGTTTTTGCTGCGTGGTGCTTGCACGCG 13 101 1 CTGCGTGGTG 0.864586 -70 GGTCGGTAGCCTGCAGGGCGTGCAAGCTAA 14 28 1 CTGCAGGGCG 0.990202 -44 CATGCCGTCAGTGCAGGGCGCCGCCCGGGC 15 15 1 GTGCAGGGCG 0.9894 -68 GGCGCCGCCCGGGCGCGGTGGCACTCGGTG 15 31 1 GGGCGCGGTG 0.960558 -52 AACTGCCGCACCGCACCGAGTGCCACCGCG 15 44 0 CCGCACCGAG 0.951507 -39 CTGCGTCGCGGCGGGGCGCGCTCAGGC 16 10 0 CGGCGGGGCG 0.987483 -18 ********** Masking position 3 Map Score: 40.3223 Number of sites scoring better than the average of aligned sites = 1774 Number in coding regions = 1601 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 AGGTCCGCGCCAGAGTGCCGTTTTCTTTTC 3 90 0 CAGAGTGCCG 0.798133 -85 CCTTGCAGGTAACTGCGCCGTGAAAA 4 14 1 AACTGCGCCG 0.836548 -16 GCAGTCAAGCGCGTGTCCTGCACTCCGTTC 5 32 0 GCGTGTCCTG 0.569205 -55 TGCCCCACCGCTGTCTGTCTCCT 6 4 1 CCCACCGCTG 0.721166 -86 GCCTGCAGCTCCAAGCGCCGTGCGGGGTCC 6 34 1 CCAAGCGCCG 0.975599 -56 CATCCCCGTCCACAGCCCCGCCATCCGAAG 6 63 1 CACAGCCCCG 0.975327 -27 GCGAACGTCCTGCGACACGTTC 7 102 0 GAACGTCCTG 0.707672 -12 TGTCAAATCAGAATGCGCTGGTGAACATGA 10 56 1 GAATGCGCTG 0.833107 -29 AAGAACTCACCACCACGCCGCGCCCTTGCA 11 57 1 CACCACGCCG 0.928331 -87 CATCCTATCCCCATACCCCGATCTACGAAA 12 20 0 CCATACCCCG 0.914106 -241 AAAACGCTGTACAAACCCCGGGGAACACCC 12 53 0 ACAAACCCCG 0.84446 -208 GTCAATTCTTCAAAACGCTGTACAAACCCC 12 64 0 CAAAACGCTG 0.81083 -197 GTTTCGTGCTACAAGTCCCGCCGGAAGGGC 12 103 1 ACAAGTCCCG 0.719519 -158 CGCGGATTATGAGTCCGCTGCTCTAACCAA 12 144 0 GAGTCCGCTG 0.407629 -117 GCCTCCCATGAAAAACCCCGCGCAAGGCGC 12 236 0 AAAAACCCCG 0.800792 -25 TCAGGTGTAAGGAGACCCTGTCGCTCATAG 13 16 1 GGAGACCCTG 0.397549 -155 CCTGCAGGCTACCGACCCCGACAGAAGGAG 14 15 0 ACCGACCCCG 0.758927 -57 CTGTTAGCTTGCACGCCCTGCAGGCTACCG 14 31 0 GCACGCCCTG 0.950635 -41 GGAACATGCCGTCAGTGCAGG 15 2 1 GAACATGCCG 0.625471 -81 GCCGTCAGTGCAGGGCGCCGCCCGGGCGCG 15 18 1 CAGGGCGCCG 0.523277 -65 CCGAGTGCCACCGCGCCCGGGCGGCGCCCT 15 29 0 CCGCGCCCGG 0.533853 -54 AAAACTGCCGCACCGCACCGAGTGCCACCG 15 46 0 CACCGCACCG 0.743766 -37 GCGCAGCCCTGCAACCGAAAA 15 72 0 CGCAGCCCTG 0.821602 -11 GCCTGAGCGCGCCCCGCCGCGACGCA 16 7 1 GCGCGCCCCG 0.974426 -21 ********** Masking position 8 Map Score: 19.015 Number of sites scoring better than the average of aligned sites = 3249 Number in coding regions = 2937 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 3 TATCCGTATGTGGAAGGGCATAGACT 1 4 0 TGGAGGGATG 0.99615 -61 CAAAATCAAAGGGAAAGGCACAGCATGTACTAC 2 85 1 GGGAAGGACG 0.972704 -66 TTTCTTTTCCTGAAAGGGTACTGAAAAATTGAC 3 66 0 TGAAGGGACG 0.977377 -109 GGCGGGGCTGTGGACGGGGATGGACCCCGCACG 6 52 0 TGGAGGGATG 0.99615 -38 CTGCCGCGAAGGGAGTGGAATTGCATAAAGCAT 7 17 1 GGGATGGATG 0.979923 -97 TGCCCTCTTATGGATGGGGATCGCGTAGAAAGG 7 67 1 TGGAGGGATG 0.99615 -47 ACCCAGGTCATGCAAGGGCGCGGCGTGGTGGTG 11 64 0 TGCAGGGGCG 0.937347 -80 CGTAGATCGGGGTATGGGGATAGGATGAGAGGG 12 23 1 GGTAGGGATG 0.965132 -238 TGGGCCCAGCTGGACTTGAACCGGCGACCCGCG 12 170 0 TGGATTGACG 0.881917 -91 **** *** ** * Masking position 4 Map Score: 12.7402 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 70 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 GAAAAATTGACGTTTCCTGCGTGATCCGCT 3 47 0 CGTTTCCTGC 0.99335 -128 GTGCCGTTTTCTTTTCCTGAAAGGGTACTG 3 76 0 CTTTTCCTGA 0.775642 -99 CAGTCAAGCGCGTGTCCTGCACTCCGTTCG 5 31 0 CGTGTCCTGC 0.975416 -56 CACCGCTGTCTGTCTCCTGCCTGCAGCTCC 6 16 1 TGTCTCCTGC 0.988673 -74 AGACACGTTGCTTTTCCTGCGCGA 11 5 0 CTTTTCCTGC 0.979667 -139 ACGCGTGTGTTGTTTCGTGCTACAAGTCCC 12 92 1 TGTTTCGTGC 0.97642 -169 GGTGGTAGCGCGTCTCTTGCGCCTTGCGCG 12 218 1 CGTCTCTTGC 0.964924 -43 GCGGGGATACTGCTTCTTGCTATGCATAGG 13 69 1 TGCTTCTTGC 0.793079 -102 TAGGGGTTAGTTTTTGCTGCGTGGTGCTTG 13 95 1 TTTTTGCTGC 0.761982 -76 GAACAACCACTGTCGCGTGCAAGCACCACG 13 114 0 TGTCGCGTGC 0.869247 -57 GCGACAGTGGTTGTTCGTGCAAGTTATGGT 13 128 1 TTGTTCGTGC 0.836762 -43 TCGGCTCCTTCTGTCGGGGTC 14 2 1 CGGCTCCTTC 0.793694 -70 ********** Masking position 8 Map Score: 12.7786 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 514 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 AGCGTAGCAAAATAGGGCGGAAAAAAGAATA 1 35 0 AATAGGGCGA 0.931469 -30 GACCCCGCTTAAGAGGAGGCACGTT 2 5 0 AAGAGGAGGA 0.988689 -146 CAGAGGTTCTAAGAGAGCAAAATCAAAGGGA 2 68 1 AAGAGAGCAA 0.873707 -83 AAGAGGGCGCAACTGTAGCTG 3 164 0 AAGAGGGCGA 0.992839 -11 GACTGCAGCTGAGAGGAGGGATTGTACGAAG 5 56 1 GAGAGGAGGA 0.97713 -31 CCCCATCCATAAGAGGGCAGACTATGCGCAA 7 55 0 AAGAGGGCAA 0.986027 -59 GCCACACATAAAGAGGAGATA 8 31 1 AAGAGGAGAA 0.978017 -11 GTATCAGGGTGTGAGGGGAAAGAAGTGTCAA 10 31 1 GTGAGGGGAA 0.931043 -54 GCTGGTGAACATGAGGAGGAAAT 10 72 1 ATGAGGAGGA 0.965062 -13 ********* * Masking position 4 Map Score: 12.2266 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 86 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 CCTCCTCTTAAGCGGGGTCCACTCTATTCA 2 17 1 AGCGGGGTCC 0.74848 -134 GCATCAAAGTAGCGGATCACGCAGGAAACG 3 37 1 AGCGGATCAC 0.384079 -138 AGAGGTCCGCGCCAGAGTGCCGTTTTCTTT 3 92 0 GCCAGAGTGC 0.566878 -83 AAGCAGCTACAGTTGCGCCCTCTT 3 161 1 AGTTGCGCCC 0.885705 -14 TGCAGCTCCAAGCGCCGTGCGGGGTCCATC 6 37 1 AGCGCCGTGC 0.76826 -53 CCTCTTTATGTGTGGCGCACTGAAGCGAAC 8 17 0 TGTGGCGCAC 0.594567 -25 CCTCATGTTCACCAGCGCATTCTGATTTGA 10 58 0 ACCAGCGCAT 0.566306 -27 AGAAGAACTCACCACCACGCCGCGCCCTTG 11 55 1 ACCACCACGC 0.714334 -89 CCCTTGCATGACCTGGGTGCCTTTGGTACA 11 79 1 ACCTGGGTGC 0.781531 -65 CCGGAAGAAAACTGGCGCGCCGAGTGTACC 11 103 0 ACTGGCGCGC 0.97967 -41 ATCACTCACTGGGGCACTAAACCGGAA 11 127 0 ACTGGGGCAC 0.908 -17 AGTTGGTTAGAGCAGCGGACTCATAATCCG 12 142 1 AGCAGCGGAC 0.639221 -119 CTGGACTTGAACCGGCGACCCGCGGATTAT 12 164 0 ACCGGCGACC 0.774956 -97 GTTCAAGTCCAGCTGGGCCCATACTATTTG 12 182 1 AGCTGGGCCC 0.900096 -79 ACGCGCTACCACCTGCACACAAATAGTATG 12 201 0 ACCTGCACAC 0.870928 -60 GTCTCCTTACACCTGAACACC 13 2 0 ACCTGAACAC 0.607476 -169 CTCATAGGGTACTAGAGCGCTTGTTTTTCT 13 39 1 ACTAGAGCGC 0.829336 -132 GCTGCGTGGTGCTTGCACGCGACAGTGGTT 13 110 1 GCTTGCACGC 0.686159 -61 ATGTTTGTAAAGCAGAGCACTT 13 159 1 AGCAGAGCAC 0.861334 -12 TAATCTGTTAGCTTGCACGCCCTGCAGGCT 14 35 0 GCTTGCACGC 0.686159 -37 ACCGCGCCCGGGCGGCGCCCTGCACTGACG 15 20 0 GGCGGCGCCC 0.970311 -63 CGCACCGAGTGCCACCGCGCCCGGGCGGCG 15 33 0 GCCACCGCGC 0.89075 -50 GCAACCGAAAACTGCCGCACCGCACCGAGT 15 53 0 ACTGCCGCAC 0.848486 -30 CTGCGTCGCGGCGGGGCGCGCTCAGGC 16 9 0 GGCGGGGCGC 0.959138 -19 ********** Masking position 10 Map Score: 23.6718 Number of sites scoring better than the average of aligned sites = 4310 Number in coding regions = 3994 Number in noncoding regions = 316 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 7 AAATTCACCCAAGGAGTGTCAC 3 3 0 AAGGAGTGTC 0.947769 -172 GCTGCAGTCAAGCGCGTGTCCTGCACTCCG 5 35 0 AGCGCGTGTC 0.980673 -52 GTAGAAAGGGAGAACGTGTCGCAGGACGTT 7 91 1 AGAACGTGTC 0.812892 -23 CACTGCGCGTGAGGAGTGTCCT 9 13 1 GAGGAGTGTC 0.950625 -12 TGTGAGGGGAAAGAAGTGTCAAATCAGAAT 10 40 1 AAGAAGTGTC 0.835991 -45 CGCAGGAAAAGCAACGTGTCTTTTTCAAAA 11 14 1 GCAACGTGTC 0.817873 -130 AAACTGGCGCGCCGAGTGTACCAAAGGCAC 11 95 0 GCCGAGTGTA 0.79115 -49 TTGAAGAATTGACGCGTGTGTTGTTTCGTG 12 81 1 GACGCGTGTG 0.864557 -180 TGCAGGTGGTAGCGCGTCTCTTGCGCCTTG 12 214 1 AGCGCGTCTC 0.879328 -47 GCCGCACCGCACCGAGTGCCACCGCGCCCG 15 40 0 ACCGAGTGCC 0.881488 -43 ********** Masking position 7 Map Score: 3.90295 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 406 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 CATACGGATATTCTTTTTTCCGCCCTATTTT 1 27 1 TTCTTTTTCC 0.957875 -38 TGCCTTTCCCTTTGATTTTGCTCTCTTAGAA 2 74 0 TTTGTTTTGC 0.959845 -77 CAGAGTGCCGTTTTCTTTTCCTGAAAGGGTA 3 79 0 TTTTTTTTCC 0.964824 -96 TAAAGAAGCATTTGATCTTCCTCGCATAAGC 3 134 1 TTTGTCTTCC 0.953945 -41 TTTCTATATTCCTCGCGCGGGT 10 2 1 TTCTTATTCC 0.84871 -83 AAAAAGACACGTTGCTTTTCCTGCGCGA 11 8 0 GTTGTTTTCC 0.945743 -136 TGCATAGGGGTTAGTTTTTGCTGCGTGGTGC 13 91 1 TTAGTTTTGC 0.879014 -80 **** ****** Masking position 6 Map Score: 0.879368 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 62 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 GTATGTGGAAGGGCATAGACT 1 2 0 GGGCATAGAC 0.966451 -63 GCAAAATCAAAGGGAAAGGCACAGCATGTA 2 84 1 AGGGAAAGGC 0.918346 -67 GCTGCAGGCAGGAGACAGACAGCGGTGGGG 6 13 0 GGAGACAGAC 0.919371 -77 GGCTGTGGACGGGGATGGACCCCGCACGGC 6 50 0 GGGGATGGAC 0.978694 -40 CAGGGTGTGAGGGGAAAGAAGTGTCAAATC 10 35 1 GGGGAAAGAA 0.967354 -50 ATCGGGGTATGGGGATAGGATGAGAGGGTG 12 28 1 GGGGATAGGA 0.972376 -233 ********** Masking position 5 Map Score: 1.75694 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 86 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 ********** No masking Map Score: -2.44894e-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 11 ********** No masking Map Score: -2.44894e-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 ********** No masking Map Score: -2.44894e-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