AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_tpal_reg_100.orf -o00500_tpal_100.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 TP0060 105 ribosomal protein L9 (rplI) #2 TP0085 80 PTS system, nitrogen regulatory IIA component (ptsN-1) #3 TP0102_TP0103 64 TP0102: rep helicase, single-stranded DNA-dependent ATPase (rep), TP0103: ATP-dependent DNA helicase, putative #4 TP0413 102 phosphoglucomutase #5 TP0475 63 glucose-6-phosphate isomerase (gpi) #6 TP0476 66 acetate kinase (ack) #7 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #8 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #9 TP0479 111 T. pallidum predicted coding region TP0479 #10 TP0505 300 hexokinase (hxk) #11 TP0755 199 PTS system, nitrogen regulatory IIA component (ptsN-2) #12 TP0900 38 T. pallidum predicted coding region TP0900 #13 TP0901 40 conserved hypothetical integral membrane protein #14 TP1028 82 DNA helicase II (uvrD) #15 TP1030 27 T. pallidum predicted coding region TP1030 #16 TP1036 152 cation-transporting ATPase, P-type Motif number 1 CGTTTTGTCCCCTCCTACGCAGGAATAAAAGT 1 83 0 CCTCCTCCAG 0.973166 -23 TTTGGAAAAGCTCCCCACGCTCTTTCCGCTCC 2 20 0 CTCCCCCCTC 0.918342 -61 AGTCTATGCCCTTCCACATACGGATATTCTT 3 10 1 CCTTCCCTAC 0.689462 -55 TTCTTTTTTCCGCCCTATTTTGCTACGCTTGT 3 37 1 CGCCCTTTTG 0.606898 -28 TCCTACCTCTCCCCCGCCCCTAC 4 2 1 CCTACCCCCC 0.965065 -101 CCTCTCCCCCGCCCCTACACCCGACCACACCT 4 16 1 GCCCCTCCCC 0.969803 -87 GTCAAGACCACCACCTCCCTTGCACTTCCTTC 4 59 1 CCACCTCTTG 0.684093 -44 CTCCCTTGCACTTCCTTCACCCGCGCCCTATC 4 73 1 CTTCCTCCCC 0.945584 -30 CCTTCACCCGCGCCCTATCCTCCGCGC 4 86 1 CGCCCTTCTC 0.871544 -17 CTCCTTTTATCGTTCTACCCCGTAGGGTTTAC 5 34 0 CGTTCTCCCG 0.946024 -30 CCTCCTCTCTCCCGCTACGTTCTAGTGTCGTT 7 29 0 CCCGCTCTTC 0.925125 -32 GGGCGAACATCCTCCTCTCTCCCGCTACG 7 42 0 CATCCTCCTC 0.758362 -19 CGCAGGCAGACTCTCCGCTCCCTAAGGCA 8 8 0 CTCTCCCCCC 0.832044 -65 TTCAACGGTGCGACCTACACCGGATGTGCCGC 8 37 0 CGACCTCCCG 0.925066 -36 AAACCGCCCCTTCTTTCAACGGTGCGA 8 56 0 GCCCCTCTTC 0.799744 -17 GCCCTCCCCCCTTCCTTGCGAAGAGGAG 9 94 0 CCCCCTCTTG 0.958734 -18 TATCGTCGCGTCCCACGCACCTCCTCTTTT 10 9 1 CGTCCCCCAC 0.966379 -292 CAGTCAATCCCCTACTACGCCCCTGTTGTGTT 10 96 0 CCTACTCCCC 0.967318 -205 TTGCCGTACTCGTTCCGCATAGGCCCTGTCTT 10 174 1 CGTTCCCTAG 0.56799 -127 GTATAAACTCCCTGCCCCATACGCCGGCACCC 10 209 1 CCTGCCCTAC 0.830652 -92 ACGAGCTATCCGTGCTACCCTGGCAGCCGACC 10 266 1 CGTGCTCCTG 0.946441 -35 ACGCGCCCTCCCTGGTCGGCTGCCAGGG 10 283 0 CCTCCCGTCG 0.568969 -18 AAACCAACCTCCCCTTTCTCTGTAACAAGACA 11 66 0 CCCCTTCCTG 0.885269 -134 GGAATCTTCCCCTTTTGCGCCCACTCATACAC 11 159 0 CCTTTTCCCC 0.728154 -41 TACGTGTTACGTCCTTCGGGTAAG 12 3 1 CGTGTTCTCC 0.533464 -36 TCCATGCTCCGTGCCTTACCCGAAGGACGTA 12 18 0 CGTGCCTCCC 0.802193 -21 GCCCGGGCGGCGCCCTGCACTGACGGCATGTT 14 13 0 CGCCCTCCTG 0.98373 -70 CGCACCGAGTGCCACCGCGCCCGGGCGGCGCC 14 31 0 GCCACCCCCC 0.857659 -52 CGAAAACTGCCGCACCGCACCGAGTGCCACCG 14 46 0 CGCACCCCCG 0.961326 -37 GCCTGAGCGCGCCCCGCCGCGACGCAG 15 8 1 CGCGCCCCCG 0.982116 -20 TCGTTGAGCTCCCATTTCACAGCAGATAGGAT 16 14 1 CCCATTCCAG 0.500627 -139 GTCACTGCCAGCCGCTCCTCCCCAGAGCTTTT 16 90 1 GCCGCTCCCC 0.934481 -63 GAAAGACTACCTCCTATTCAGGACGGGTTTT 16 132 0 CCTCCTTCAG 0.772646 -21 ****** * *** Masking position 5 Map Score: 42.7072 Number of sites scoring better than the average of aligned sites = 4118 Number in coding regions = 3564 Number in noncoding regions = 554 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 2 CGCTCTTTCCGCTCCCAGGATATC 2 5 0 GCTCCCAGGA 0.860818 -76 AGAGTTTTTAGCTTGGGGGA 2 71 1 GCTTGGGGGA 0.941143 -10 TCGGGTGTAGGGGCGGGGGAGAGGTAGGA 4 10 0 GGGCGGGGGA 0.985043 -93 GGAGGATAGGGCGCGGGTGAAGGAAGTGCA 4 79 0 GCGCGGGTGA 0.950043 -24 GCGCGGAGGATAGGGCGCGG 4 93 0 GCGCGGAGGA 0.987843 -10 TTTTCTAAAGGCTGCGAGGCAATTATTAGG 9 22 1 GCTGCGAGGC 0.885067 -90 GGCGTTTAGCGCGCGCCGTCAAGTTTTTCT 9 50 1 GCGCGCCGTC 0.952094 -62 CGCAAGGAAGGGGGGAGGGC 9 102 1 GGGGGAGGGC 0.786882 -10 TGCAAAAAAGGGGTGCCGGCGTATGGGGCA 10 221 0 GGGTGCCGGC 0.951796 -80 CGCCCTCCCTGGTCGGCTGCCAGGGTAGCA 10 278 0 GGTCGGCTGC 0.796706 -23 TACGCATCATGCGTTGCGTAGAAATCTCAC 11 27 0 GCGTTGCGTA 0.639359 -173 GAGTGCCACCGCGCCCGGGCGGCGCCCTGC 14 27 0 GCGCCCGGGC 0.915299 -56 GGCACTCGGTGCGGTGCGGCAGTTTTCGGT 14 50 1 GCGGTGCGGC 0.976564 -33 GCGGCGGGGCGCGCTCAGGC 15 1 0 GCGCTCAGGC 0.96304 -27 CTGCGTCGCGGCGGGGCGCGCT 15 16 0 GCGTCGCGGC 0.976428 -12 GTATCCAAAAGCTCTGGGGAGGAGCGGCTG 16 98 0 GCTCTGGGGA 0.947269 -55 ********** Masking position 1 Map Score: 21.0574 Number of sites scoring better than the average of aligned sites = 1842 Number in coding regions = 1691 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 3 ACGTTTTGTCCCCTCCTACGCAGGA 1 91 0 ACGTGTCCCC 0.935667 -15 CTTCCTTCACCCGCGCCCTATCCTCCGCGC 4 83 1 CCGCCTTCCC 0.808298 -20 TCGTTCTACCCCGTAGGGTTTACCTACAGACATAT 5 22 0 CCGTGTTACT 0.929299 -42 TTCTCGGACACCGTAGCATACACGCAAAATGCGCC 6 17 0 CCGTATCACC 0.969037 -50 CTTCTTTCAACGGTGCGACCTACACCGGATGTGCC 8 39 0 CGGTACTACC 0.785695 -34 CAATTATTAGGCGTTTAGCGCGCGCCGTCAAGTTT 9 41 1 GCGTGCCGCC 0.863322 -71 GTTTTTCTCACCGTTTGGCATACTCCTCTTCGCAA 9 72 1 CCGTGCTACC 0.993464 -40 TATCGTCGCGTCCCACGCACCTCCTCTTTTCG 10 8 1 GCGTACCACT 0.789184 -293 GTCACTGGGTCCGTCGGGTTCACCCTACAAGGAAC 10 132 1 CCGTGTCACC 0.989142 -169 AAGGAACACTCCGTTTGCCGTACTCGTTCCGCATA 10 160 1 CCGTCCTACC 0.989725 -141 GGTATAAACTCCCTGCCCCATACGCCGGCACCCCT 10 208 1 CCCTCCTACC 0.933824 -93 CGGAATCTTCCCCTTTTGCGCCCACTCATACACGG 11 157 0 CCCTGCCCCC 0.963378 -43 TACGTGTTACGTCCTTCGGGTAAGGC 12 2 1 ACGTACTCCT 0.664952 -37 TGTTACGTGATGTCTACCCAAAAGGGAGT 13 5 1 ACGTGTTACC 0.915891 -36 CCGTGCACCGCACTCCCTTTTGGGT 13 26 0 CCGTCCCACC 0.989499 -15 AATTCGTTGAGCTCCCATTTCACAGCAG 16 4 1 TCGTGCCCCT 0.777545 -149 GGATAAAAAACCGTACACTTTTCATCCTATCTGCT 16 34 0 CCGTCTTTCT 0.593955 -119 **** ** *** * Masking position 13 Map Score: 19.6868 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 698 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 TACCTCTCCCCCGCCCCTACACCCGACCACA 4 14 1 CCGCCCTACA 0.846148 -89 ACCTCCCTTGCACTTCCTTCACCCGCGCCCT 4 71 1 CACTCCTTCA 0.829449 -32 TTTCGCTCAACATTTCCTTCAATCAGTCCAA 10 38 1 CATTCCTTCA 0.766428 -263 CCGACGGACCCAGTGACTGCACAGTCAATCC 10 118 0 CAGTACTGCA 0.956141 -183 GTTTAGGAAACCGTTCCTGCAAAAAAGGGGT 10 237 0 CCGTCCTGCA 0.995578 -64 AGAGGTTGCGCGGTACCTGCGAATTTCTGAA 11 122 1 CGGTCCTGCG 0.97 -78 CACTCATACACGGTACGTTCAGAAATTCGCA 11 139 0 CGGTCGTTCA 0.940448 -61 TCCATGCTCCGTGCCTTACCCGAAGGACG 12 20 0 CCGTCCTTAC 0.764999 -19 GGAACATGCCGTCAGTGCAGGGCGCCGCC 14 9 1 CCGTAGTGCA 0.937159 -74 GTTTTTTATCCGGTACATGCAAGTTTCTTGC 16 58 1 CGGTCATGCA 0.93135 -95 AAGTTTCTTGCCGTCACTGCCAGCCGCTCCT 16 78 1 CCGTACTGCC 0.959969 -75 **** ****** Masking position 8 Map Score: 7.06062 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 509 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 AGTAGAAGTTGCTGTGCATAGGCAGAGTGGC 1 43 1 GCTGGCATAG 0.857303 -63 AGGCAGAGTGGCTCTGCGTGGACTTTTATTC 1 62 1 GCTCGCGTGG 0.960596 -44 GCGCGGAGGATAGGGCGCGGGTG 4 90 0 GCGGGGATAG 0.791966 -13 CGGTAATGCCGAGCCTTGAACGACACTA 7 8 1 GCCGGCCTTG 0.911402 -53 GAAAAACTTGACGGCGCGCGCTAAACGCCTA 9 48 0 ACGGGCGCGC 0.868553 -64 GCGAAAAGAGGAGGTGCGTGGGACGCGACGA 10 13 0 GAGGGCGTGG 0.953209 -288 ACGCGCCCTCCCTGGTCGGCTGCCA 10 286 0 GCCCCCCTGG 0.748225 -15 TACGCATCATGCGTTGCGTAGAAATCTCACG 11 26 0 GCGTGCGTAG 0.882507 -174 CGGGTAAGGCACGGAGCATGGA 12 27 1 ACGGGCATGG 0.952196 -12 AAAAGGGAGTGCGGTGCACGG 13 30 1 GCGGGCACGG 0.99368 -11 TCAGTGCAGGGCGCCGCCCGGGCGCGGTGGC 14 22 1 GCGCGCCCGG 0.982666 -61 GCGCAGCCCTGCAACCGAAAA 14 72 0 GCGCGCCCTG 0.957354 -11 CTGCGTCGCGGCGGGGCGCGCTCAGGC 15 7 0 GCGGGCGCGC 0.577127 -21 **** ****** Masking position 2 Map Score: 15.3613 Number of sites scoring better than the average of aligned sites = 1264 Number in coding regions = 1145 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 ACGTTTTGTCCCCTCCTACGCA 1 94 0 ACGTTTGTCC 0.939178 -12 TGCGACCTACACCGGATGTGCCGCAGGCAGAC 8 29 0 ACCGATGTCC 0.986893 -44 AGTACGGCAAACGGAGTGTTCCTTGTAGGGTG 10 152 0 ACGGGTGTCC 0.993286 -149 CCACTCATACACGGTACGTTCAGAAATTCGCA 11 139 0 ACGGACGTCA 0.948917 -61 ACTTTTCCTGACGGAATCTTCCCCTTTTGCGC 11 171 0 ACGGATCTCC 0.986893 -29 CCCTGCACTGACGGCATGTTCC 14 1 0 ACGGATGTCC 0.996964 -82 **** **** ** Masking position 9 Map Score: 4.49838 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 45 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 AATCAGGTGTGGTCGGGTGTAGGGGCGGGG 4 22 0 GGTCGGGTGT 0.987832 -81 CGTTCTACCCCGTAGGGTTTACCTACAGAC 5 26 0 CGTAGGGTTT 0.947716 -38 TTGCGTGTATGCTACGGTGTCCGAGAAATT 6 25 1 GCTACGGTGT 0.887181 -42 GCCTGCGGCACATCCGGTGTAGGTCGCACC 8 33 1 CATCCGGTGT 0.851342 -40 TCACTGGGTCCGTCGGGTTCACCCTACAAG 10 133 1 CGTCGGGTTC 0.947649 -168 CTTTTTTGCAGGAACGGTTTCCTAAACGAG 10 241 1 GGAACGGTTT 0.887928 -60 CGCCCTCCCTGGTCGGCTGCCAGGGTAGCA 10 278 0 GGTCGGCTGC 0.855886 -23 AATTTCTGAACGTACCGTGTATGAGTGGGC 11 143 1 CGTACCGTGT 0.827642 -57 GGTGGCACTCGGTGCGGTGCGGCAGTTTTC 14 47 1 GGTGCGGTGC 0.932759 -36 GGATGAAAAGTGTACGGTTTTTTATCCGGT 16 42 1 TGTACGGTTT 0.805549 -111 CTCCTATTCAGGACGGGTTTTTTATGTATC 16 123 0 GGACGGGTTT 0.913629 -30 ********** Masking position 8 Map Score: 6.76166 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 361 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TGAACTAGGAAAAACAACCGCTGTATACCAG 1 13 0 AAAACACCGC 0.990093 -93 TCATCCTGTCAAGACCACCACCTCCCTTGCA 4 52 1 AAGACACCAC 0.97534 -51 TTCTTCGGACAAACCAACCTCCCCTTTCTCT 11 77 0 AAACCACCTC 0.966782 -123 CCTGCAACCGAAAACTGCCGCACCGCACCGA 14 55 0 AAAACGCCGC 0.97827 -28 GAAAGACTACCTCCTATTCAGGA 16 140 0 AAGACACCTC 0.985858 -13 ***** ***** Masking position 2 Map Score: 2.24181 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 CTATGCACAGCAACTTCTACTGAACTAGGAA 1 33 0 CACTTCTACT 0.86256 -73 CCAAAAAGCTTGACTTTTCCTTTGAGAGTTT 2 47 1 TACTTTTCCT 0.811744 -34 TCCTACCTCTCCCCCGCCCCTAC 4 3 1 CACCTCTCCC 0.900227 -100 CCTTCACCCGCGCCCTATCCTCCGCGC 4 86 1 CCCCTATCCT 0.921054 -17 TGCGCGTTCTCCTTTTATCGTTC 5 51 0 CCGTTCTCCT 0.933296 -13 GAGCTCCTCCTTTTTCTAAAGGCTGCG 9 7 1 CCCTTTTTCT 0.962372 -105 CGCGCGCCGTCAAGTTTTTCTCACCGTTTGG 9 59 1 CAGTTTTTCT 0.825939 -53 GCCCTCCCCCCTTCCTTGCGAAGAGG 9 96 0 CCCCCTTCCT 0.917872 -16 TCTTTTCGCTCAACATTTCCTTCAATCAGTC 10 35 1 CACATTTCCT 0.915034 -266 AAACCAACCTCCCCTTTCTCTGTAACAAGAC 11 67 0 CCCTTTCTCT 0.814493 -133 AGGTACCGCGCAACCTCTTCTATCGTGAGAA 11 109 0 CACCTCTTCT 0.950764 -91 GGTGCCCACTTTTCCTGACGGAATCT 11 184 0 CACTTTTCCT 0.983632 -16 * ********* Masking position 10 Map Score: 9.27906 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 391 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 AGCTTTTTGGAAAAGCTCCCCACGCTCTTT 2 27 0 AAAAGCTCCC 0.881426 -54 CCCCCAAGCTAAAAACTCTCAAAGGAAAAG 2 60 0 AAAAACTCTC 0.914729 -21 ACGGTGTCCGAGAAATTACCAAAACGGTGG 6 38 1 AGAAATTACC 0.842517 -29 GTCTTTAGGTATAAACTCCCTGCCCCATAC 10 201 1 ATAAACTCCC 0.932008 -100 GTTTGTCCGAAGAAATTCTCACGATAGAAG 11 94 1 AGAAATTCTC 0.938844 -106 CGGTACGTTCAGAAATTCGCAGGTACCGCG 11 130 0 AGAAATTCGC 0.959633 -70 AGTGACGGCAAGAAACTTGCATGTACCGGA 16 66 0 AGAAACTTGC 0.883619 -87 ********** Masking position 4 Map Score: 1.38361 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 100 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 11 GTGGTGGTCTTGACAGGATGAAATCAGGTG 4 43 0 TGACAGGATG 0.930192 -60 GAGAAAAACTTGACGGCGCGCGCTAAACGC 9 51 0 TGACGGCGCG 0.980102 -61 CCACTTTTCCTGACGGAATCTTCCCCTTTT 11 175 0 TGACGGAATC 0.930192 -25 CGCCCTGCACTGACGGCATGTTCC 14 5 0 TGACGGCATG 0.994664 -78 CGGCTGGCAGTGACGGCAAGAAACTTGCAT 16 74 0 TGACGGCAAG 0.986626 -79 ********** Masking position 3 Map Score: 1.73951 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 19 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 ********** No masking Map Score: -1.4755e-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: -1.4755e-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: -1.4755e-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