AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_tpal_reg_100.orf -o00030_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 TP0261 114 catabolite gene activator, putative #2 TP0284 104 T. pallidum predicted coding region TP0284 #3 TP0289 22 T. pallidum predicted coding region TP0289 #4 TP0290 54 conserved hypothetical protein #5 TP0291 36 T. pallidum predicted coding region TP0291 #6 TP0413 102 phosphoglucomutase #7 TP0475 63 glucose-6-phosphate isomerase (gpi) #8 TP0476 66 acetate kinase (ack) #9 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #10 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #11 TP0479 111 T. pallidum predicted coding region TP0479 #12 TP0560 110 transketolase A (tktA) #13 TP0611 141 ABC transporter, ATP-binding protein #14 TP0612 80 conserved hypothetical protein #15 TP0613 26 conserved hypothetical protein #16 TP0615 50 nitrogen fixation protein (nifU) #17 TP0662 266 fructose-bisphosphate aldolase (cbbA) #18 TP0945 151 ribulose-phosphate 3-epimerase (cfxE) Motif number 1 ACGCCTTTTCCAGGAAAGGTGG 1 2 0 CGGAAAGGTG 0.816503 -113 CTGCAGGTGTGCGCGCAGGAGCGCGTGACGT 1 44 1 GGCGCAGGAG 0.991136 -71 GTTGAGTGATCTTCGGGGCTGTGCTTTTAAA 2 52 1 CTCGGGGCTG 0.730332 -53 ACTTGTTCAAGTTCAGAGGTGATGTTG 4 38 1 GTCAGAGGTG 0.837847 -17 TCGGGTGTAGGGGCGGGGGAGAGGTAGGA 6 9 0 GGCGGGGGAG 0.99111 -94 AGGTGGTGGTCTTGACAGGATGAAATCAGGT 6 44 0 CTGACAGGAT 0.573208 -59 GGTGAAGGAAGTGCAAGGGAGGTGGTGGTCT 6 63 0 GGCAAGGGAG 0.959665 -40 GCGGAGGATAGGGCGCGGGTGAAGGAAGTGC 6 80 0 GGCGCGGGTG 0.971941 -23 GCGCGGAGGATAGGGCGCGGG 6 92 0 GGCGGAGGAT 0.937669 -11 GGGGTAGAACGATAAAAGGAGAACGCGCA 7 45 1 GTAAAAGGAG 0.788529 -19 ATTACCAAAACGGTGGAGGTGTATT 8 52 1 CGTGGAGGTG 0.884538 -15 GACACTAGAACGTAGCGGGAGAGAGGAGGAT 9 32 1 CTAGCGGGAG 0.942117 -29 CCCCTTCCTTGCGAAGAGGAGTATGCCAAAC 11 84 0 GGAAGAGGAG 0.944631 -28 TCTTCGCAAGGAAGGGGGGAGGGC 11 98 1 GAGGGGGGAG 0.899767 -14 ACCGTGCTGTGCTAGGAGCAG 12 1 0 GTAGGAGCAG 0.789427 -110 TATGTGTTTCCTGTGCAGGATGCGTGGTCTC 13 53 1 CGTGCAGGAT 0.768384 -89 AAGGAGTAAACTGAGCAGGAGTATACGTACA 13 108 0 CGAGCAGGAG 0.976647 -34 TCAGTTTACTCCTTGCAGGAGCCGCTC 13 125 1 CTTGCAGGAG 0.905875 -17 GGTCTGCTGGCGTGGGGGCAGCGCGCCTCCA 14 32 0 CTGGGGGCAG 0.848578 -49 TGTGCGCCCTCAGGAAGGGAG 15 1 0 CGGAAGGGAG 0.934559 -26 CTTCCTGAGGGCGCACAGCAGT 15 15 1 GGCACAGCAG 0.901401 -12 GCAGCGAATGCCAGGAAGGCGCACTGGC 16 8 0 CAGGAAGGCG 0.546863 -43 GATCTCCTTAGAGAAAGGCAGCGAATGCCAG 16 25 0 GGAAAGGCAG 0.671467 -26 GTTAGGGGTGGTGAAAAGGAGTTTGCGA 17 8 0 GGAAAAGGAG 0.905245 -259 GCCTGCGAGGCGTTAGGGGTGGTGAAAAGGA 17 19 0 CTTAGGGGTG 0.531879 -248 ACCCCTAACGCCTCGCAGGCGCCAGCTCGCC 17 30 1 CTCGCAGGCG 0.912645 -237 TGGACAGGTACCACGCGGGAGGTTTGACAAG 17 85 0 CACGCGGGAG 0.928831 -182 GTCAACCGAAGCGCGAAGGCTTGAGTCCACA 17 146 0 GGCGAAGGCT 0.683419 -121 CAGCCTACCCGCGGGAAGGATATTTTTCTAT 18 19 1 GGGGAAGGAT 0.844059 -133 * ********* Masking position 8 Map Score: 34.0442 Number of sites scoring better than the average of aligned sites = 3811 Number in coding regions = 3366 Number in noncoding regions = 445 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 2 ACCTTTCCTGGAAAAGGCGTGCGAACGATCT 1 13 1 GAAAGGCGTG 0.615925 -102 ATCTCTGCAGGTGTGCGCGCAGGAGCGCGTG 1 40 1 GTGGCGCGCA 0.976811 -75 GTGTGGTCGGGTGTAGGGGCGGGGGAGAGGT 6 15 0 GTGAGGGGCG 0.988972 -88 GCGCGGAGGATAGGGCGCGGGTGAAGGAA 6 84 0 GATGGGCGCG 0.958811 -19 ACGATAAAAGGAGAACGCGCA 7 53 1 GAGACGCGCA 0.983448 -11 GCACCGTTGAAAGAAGGGGCGGTTT 10 58 1 AAGAGGGGCG 0.935213 -15 AGAAAAACTTGACGGCGCGCGCTAAACGCCT 11 49 0 GACGCGCGCG 0.889442 -63 GTTTCTTTTTCTGTACGGGCAGTCTCTCTTG 12 30 1 CTGACGGGCA 0.891039 -81 TTATCCTTTTGTGGAGGCGCGCTGCCCCCAC 14 21 1 GTGAGGCGCG 0.994353 -60 CGGTCTGCTGGCGTGGGGGCAGCGCGCCTCC 14 33 0 GCGGGGGGCA 0.941367 -48 CCACCGCTTAGAGGAAGCGCGT 14 69 1 GAGAAGCGCG 0.941427 -12 CTCCCTTCCTGAGGGCGCACAGCAGT 15 9 1 CTGGGGCGCA 0.969762 -18 AGCGAATGCCAGGAAGGCGCACTGGC 16 6 0 AGGAGGCGCA 0.842085 -45 CCACCCTCGGCAAGAGGGGCATGGTAGGGCG 17 191 0 CAAAGGGGCA 0.76197 -76 TTTTCTATCGGTTTAGGCGCAAATAAAACAG 18 42 1 GTTAGGCGCA 0.945446 -110 *** ******* Masking position 7 Map Score: 19.4052 Number of sites scoring better than the average of aligned sites = 1350 Number in coding regions = 1232 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 TGCCTTAGGGAGCGGAGAGTCT 10 3 1 CCTTAGGGAG 0.937175 -70 ACCGGATGTGCCGCAGGCAGACTCTCCGCT 10 21 0 CCGCAGGCAG 0.989911 -52 CTCCCCCCTTCCTTGCGAAGAGGAGTATGC 11 89 0 CCTTGCGAAG 0.941055 -23 TTTTCCCGTGCGTCACCGAGCACACTATAG 12 73 0 CGTCACCGAG 0.809362 -38 AGGTTTAATACCGTGCGCAGTGTATGTCCT 13 22 0 CCGTGCGCAG 0.952247 -120 TGCTGTGCGCCCTCAGGAAGGGAG 15 5 0 CCTCAGGAAG 0.98735 -22 GGCGTTGGAACGGCAGCAAGACGATTTGGA 17 112 0 CGGCAGCAAG 0.923076 -155 AGGCTTGAGTCCACACGCAGGCGTTGGAAC 17 131 0 CCACACGCAG 0.927723 -136 AGCGTGCCACCCTCGGCAAGAGGGGCATGG 17 198 0 CCTCGGCAAG 0.974157 -69 GTCAGCCTACCCGCGGGAAGGATATTTTTC 18 17 1 CCGCGGGAAG 0.989193 -135 ********** Masking position 9 Map Score: 11.8878 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 256 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 4 CACACCTGCAGAGATCGTTCGCACGCCTTTTC 1 23 0 GAGATGTCGC 0.904372 -92 TGGTGCAGTACGCTGAAGTAAT 3 10 0 GGTGCGACGC 0.969039 -13 TTTTAGGGAAAAGGAAGATCGC 5 25 1 AAGGAGTCGC 0.898457 -12 GCGCGGAGGATAGGGCGCGGGTGAAGGA 6 85 0 AGGATGGCGC 0.875919 -18 TAAACCCTACGGGGTAGAACGATAAAAGGAGA 7 35 1 GGGGTGACGA 0.951206 -29 CGGGAGAGAGGAGGATGTTCGCCC 9 47 1 GAGGAGTCGC 0.972758 -14 CGGCACATCCGGTGTAGGTCGCACCGTTGAAA 10 38 1 GGTGTGTCGC 0.985527 -35 TAGTGTGCTCGGTGACGCACGGGAAAAGCATA 12 76 1 GGTGAGACGG 0.789663 -35 TGCTGGCGTGGGGGCAGCGCGCCTCCACAAAA 14 27 0 GGGGCGGCGC 0.990544 -54 CCTCTTGCCGAGGGTGGCACGCTTCTCTATTT 17 205 1 AGGGTGACGC 0.982229 -62 TTGAATGTTTGGGGTTGTTCACGCCAGTATCC 18 91 1 GGGGTGTCAC 0.955861 -61 ***** * **** Masking position 10 Map Score: 13.2947 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 427 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 AACCGAGTGAGAAAAAGAATCATCACATACTC 2 23 0 GAAAAAGACA 0.944866 -82 GCTTTTTTAGGGAAAAGGAAGATCGC 5 21 1 GGAAAAGAGA 0.980742 -16 TAGGGGCGGGGGAGAGGTAGGA 6 1 0 GGAGAGGAGA 0.95011 -102 GCAGCCTTTAGAAAAAGGAGGAGCTC 11 5 0 GAAAAAGAGA 0.934934 -107 TGCCCGTACAGAAAAAGAAACCGTGCTGTGCT 12 19 0 GAAAAAGACC 0.746321 -92 GTGACGCACGGGAAAAGCATAAGGAGTGAGAA 12 87 1 GGAAAAGAAA 0.887366 -24 AACGCCAAGGTAGGACATACACTGC 13 4 1 GCCAAGGAGA 0.809958 -138 CACGCATCCTGCACAGGAAACACATACAGGTT 13 47 0 GCACAGGACA 0.927177 -95 ATGTTGCAAGGGAAAGAGACCACGCATCCTGC 13 67 0 GGAAAGAACA 0.874612 -75 AAGACGATTTGGACAGGTACCACGCGGGAGGT 17 93 0 GGACAGGACA 0.976636 -174 CGCAGGCGTTGGAACGGCAGCAAGACGATTTG 17 114 0 GGAACGGACA 0.943466 -153 AAATAAAACAGGATAAGCAGGACACTGTCTTG 18 62 1 GGATAAGAGA 0.889233 -90 ******* * ** Masking position 9 Map Score: 8.52956 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 143 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 GCTCCTGCGCGCACACCTGCAGAGATCGTT 1 36 0 GCACACCTGC 0.977159 -79 AACTTTAAAAGCACAGCCCCGAAGATCACT 2 56 0 GCACAGCCCC 0.904151 -49 TTGAACAAGTGCACACCCAAAAAACAACAC 4 18 0 GCACACCCAA 0.920177 -37 TCCCCCGCCCCTACACCCGACCACACCTGA 6 20 1 CTACACCCGA 0.823433 -83 CTACACCCGACCACACCTGATTTCATCCTG 6 30 1 CCACACCTGA 0.747716 -73 CTTGCACTTCCTTCACCCGCGCCCTATCCT 6 77 1 CTTCACCCGC 0.76907 -26 GGACACCGTAGCATACACGCAAAATGCGCC 8 17 0 GCATACACGC 0.9305 -50 TCTGCCTGCGGCACATCCGGTGTAGGTCGC 10 30 1 GCACATCCGG 0.859102 -43 GCCCTCCCCCCTTCCTTGCG 11 102 0 GCCCTCCCCC 0.885015 -10 GAGGCGCGCTGCCCCCACGCCAGCAGACCG 14 34 1 GCCCCCACGC 0.905035 -47 CCAGCAGACCGCATATCCACCGCTTAGAGG 14 53 1 GCATATCCAC 0.59082 -28 GAAGGCTTGAGTCCACACGCAGGCGTTGGA 17 133 0 GTCCACACGC 0.91703 -134 GACGGGGTCAGCCTACCCGCGGGAAGGATA 18 11 1 GCCTACCCGC 0.982303 -141 ********** Masking position 8 Map Score: 7.36369 Number of sites scoring better than the average of aligned sites = 1633 Number in coding regions = 1484 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 7 ATGATTCTTTTTCTCACTCGGTTGAGTGATCTT 2 32 1 TTCTCCTGGT 0.966869 -73 AAACCGCCCCTTCTTTCAACGGTGCGACCTACA 10 50 0 TTCTTCACGT 0.846496 -23 AGCTCCTCCTTTTTCTAAAGGCTGCGAGGCAAT 11 12 1 TTTTCAAGGT 0.91754 -100 GCCGTCAAGTTTTTCTCACCGTTTGGCATACTC 11 64 1 TTTTCCACGT 0.946835 -48 GCAGCGCGCCTCCACAAAAGGATAACTTACTTT 14 13 0 TCCACAAGGT 0.727749 -68 ACGCGCTTCCTCTAAGCGGTGGATATGCGG 14 61 0 TCCTCAACGT 0.961605 -20 GACAAGCTATTTCTCCATGCGCTAGAATGCGGC 17 58 0 TTCTCATCGT 0.975486 -209 GACTCAAGCCTTCGCGCTTCGGTTGACTAGAGC 17 150 1 TTCGCCTCGT 0.909691 -117 TTCGTGACTCTTCTCGAAGCAATCCTAACAAAG 17 235 1 TTCTCAACAT 0.835795 -32 GGAAGGATATTTTTCTATCGGTTTAGGCGCAAA 18 32 1 TTTTCATGGT 0.883725 -120 ***** ** ** * Masking position 1 Map Score: 3.59861 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 145 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CTGGAAAAGGCGTGCGAACGATCTCTGCAG 1 20 1 CGTGCGAACG 0.543703 -95 AGTGCATGACCGTTCTATCGAAAATGTACC 1 95 1 CGTTCTATCG 0.872352 -20 TCTCCCGCTACGTTCTAGTGTCGTTCAAGG 9 24 0 CGTTCTAGTG 0.928007 -37 TTGCAACATACATTCGAATGTACGTATACT 13 90 1 CATTCGAATG 0.495313 -52 CAGCTCGCCGCATTCTAGCGCATGGAGAAA 17 52 1 CATTCTAGCG 0.928007 -215 GTCTTGCTGCCGTTCCAACGCCTGCGTGTG 17 120 1 CGTTCCAACG 0.574062 -147 ********** Masking position 7 Map Score: 2.52233 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 47 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: 5.92755e-14 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 10 ********** No masking Map Score: 5.92755e-14 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: 5.92755e-14 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