AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ipurR_tpal_opreg_300.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 TP0278 127 T. pallidum predicted coding region TP0278 #2 TP0279 45 ribosomal protein S1 (rpsA) #3 TP0283 177 lipopolysaccharide core biosynthesis protein (kdtB) #4 TP0284 104 T. pallidum predicted coding region TP0284 #5 TP0289 22 T. pallidum predicted coding region TP0289 #6 TP0290 54 conserved hypothetical protein #7 TP0291 36 T. pallidum predicted coding region TP0291 #8 TP0319 28 membrane lipoprotein (tmpC) #9 TP0321 75 ribose/galactose ABC transporter, ATP-binding protein (rbsA-2) #10 TP0324 103 T. pallidum predicted coding region TP0324 #11 TP0327 56 cationic outer membrane protein (ompH) #12 TP0328 55 DNA mismatch repair protein (mutS) #13 TP0329 117 serine hydroxymethyltransferase (glyA) #14 TP0694 159 5,10-methenyltetrahydrofolate synthetase, putative #15 TP0695 87 phosphoribosylglycinamide formyltransferase, putative Motif number 1 GCGCTCGTCTTCCTCGGAAGACTGTGGCAAAT 1 3 1 GCCCTTCGAC 0.947948 -125 CGCACTCCCTTCCCCACATGGACTGCCGCTTATTTGCCAC 1 34 0 TCCCTACTCT 0.871378 -94 GAGACTGTTTGCGCTCCTCGTCTGTTGTCTGATCACCAGC 1 73 0 GCCCCCTGCT 0.987688 -55 GCCCTGTACTTCCCTTCTTCGTTTTTCACCCCT 2 23 1 TCCCTTTTCC 0.695983 -23 CGTGCGCACCGCACGGCGCGAACGCTTCTCCTC 3 4 0 GCCCCACGTC 0.97444 -174 TCACGCGAGCTCTCTACGCTTCCTAGCTACACAACGTGCG 3 38 0 TCCCCCCTAC 0.962878 -140 CTATTTATATTCGCACCCACTCCGTCAACTCCTCGCGGAA 3 87 0 TCCCACCGCT 0.961104 -91 GCACGGCAACCCCTCACGTTGTTCAGGAAC 3 158 0 GCCCACCTTT 0.819582 -20 AACTTTAAAAGCACAGCCCCGAAGATCACTCAACCGAGTG 4 46 0 GCCCCAAGCT 0.925034 -59 AAGAATCCTCCCCCCTTTATCGACAAAC 8 1 0 TCCCTTCGAC 0.879409 -28 GGGGCGTGTGTCTCGACCCGCCCGTGGTCAGTGGGTATGG 9 14 1 TCCCCCCGCA 0.961954 -62 AGCCCCTCCCTCAAGTTCATTACTGGACGTC 9 55 0 GCCCCAAGTT 0.727817 -21 AATAGGTGCCACCCAACTCACCCTTCTTCCAAAAA 10 6 0 ACCCCCCTCC 0.974243 -98 CCGGAATACAGAACCCCCTACCCGGGTGCTCATTGCAAAG 10 46 0 GACCTCCGCT 0.912331 -58 ATCACTCCTTGCCTGGTGGACGCAGCCCCGG 11 36 0 TCCCTCTGAC 0.904717 -21 TGCACCGTGAGCACCGCGTCTCCTGCCTCCTACGTGTTGG 12 11 1 GCCCTCCTCC 0.994641 -45 AAAACGCCGCGCGCCGCATGCCCGATACCCGTCGTGCGTA 13 27 0 GCCCTCCGCC 0.998172 -91 ATTCTGCAGCGCACACCACAGCCGCGTGCTAAAGTACCGT 14 30 1 GCCCCCCGCT 0.99751 -130 ACCGTCACGGGCCCTTCGTTACAGCCACCCTACGATATCC 14 65 1 GCCCTCAGCC 0.988237 -95 TCCACCAAAGACACATCACGTCTTCTTTTCGTTAGGGACG 14 102 1 ACCCCCTTTC 0.621438 -58 ** * * * *** ** Masking position 7 Map Score: 31.0561 Number of sites scoring better than the average of aligned sites = 1303 Number in coding regions = 1168 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 2 GTCTGATCACCAGCGCACTCCCTTCCCCACA 1 56 0 CAGGCACTCC 0.940182 -72 TTCTGAGACTGTTTGCGCTCCTCGTCTGTTG 1 86 0 GTTGCGCTCC 0.803589 -42 CAAACAGTCTCAGAACACTCATGGGCGGATG 1 102 1 CAGACACTCA 0.824539 -26 GCTACACAACGTGCGCACCGCACGGCGCGAA 3 22 0 GTGGCACCGC 0.991489 -156 GAGAGCTCGCGTGAACACCGATTTTCCGCGA 3 64 1 GTGACACCGA 0.972091 -114 TGGTGCAGTACGCTGAAGTAAT 5 7 0 CAGACGCTGA 0.923178 -16 ACTTGAACAAGTGCACACCCAAAAAACAACA 6 19 0 GTGACACCCA 0.960901 -36 AGAGGGCAGTGCTTTTTTAGGG 7 2 1 GAGGCAGTGC 0.869893 -35 AAGTTCATTACTGGACGTCCCCATACCCACT 9 43 0 CTGACGTCCC 0.907938 -33 TCCTTGCCTGGTGGACGCAGCCCCGGACCGT 11 31 0 GTGACGCAGC 0.953631 -26 TGCACCGTGAGCACCGCGTCTCCTGCC 12 7 1 GTGGCACCGC 0.991489 -49 GTGGACGCTCCTGGGCCAACA 12 45 0 GTGACGCTCC 0.987801 -11 AAAGAATGGACAAAACGCCGCGCGCCGCATG 13 47 0 CAAACGCCGC 0.839331 -71 CGCGGCTGTGGTGTGCGCTGCAGAATAAAGA 14 25 0 GTGGCGCTGC 0.990336 -135 CGGCGTCGTCCTGCACGTCCCTAACGAAAAG 14 126 0 CTGACGTCCC 0.907938 -34 GGACGTGCAGGACGACGCCGACACCACCCAT 14 137 1 GACACGCCGA 0.78889 -23 CATGCACCAAGAGGACAGCGCCGTGCTATCT 15 43 1 GAGACAGCGC 0.938867 -45 *** ******* Masking position 6 Map Score: 24.5351 Number of sites scoring better than the average of aligned sites = 2196 Number in coding regions = 2026 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 TTATTTGCCACAGTCTTCCGAGGAAGACGAGC 1 13 0 CTCTTCCGAG 0.949025 -115 CACCAGCGCACTCCCTTCCCCACATGGACTGC 1 48 0 CCCTTCCCCA 0.862614 -80 TCCATCATCCGCCCATGAGTGTT 1 115 0 CTCATCCGCC 0.953871 -13 CTTCCGTTTTCTGCCCTGTACTTCC 2 4 1 CTTTTCTGCC 0.962461 -42 TTCCCTTCTTCGTTTTTCACCCCT 2 32 1 CTTTTCACCC 0.775656 -14 GCGTGAACACCGATTTTCCGCGAGGAGTTGAC 3 72 1 CTTTTCCGCG 0.979269 -106 CCACCCAACTCACCCTTCTTCCAAAAA 10 6 0 CCCTTCTTCC 0.817394 -98 GTAGGGGGTTCTGTATTCCGGGCGCGTTTTTT 10 65 1 CTATTCCGGG 0.88845 -39 ACAGAGCGAACAATATTCTGCCTACCTGAGGA 13 87 1 CTATTCTGCC 0.970917 -31 ATCTACACCTCTTTATTCTGCAGCGCACACCA 14 16 1 CTATTCTGCA 0.884205 -144 TGCCTTATTCCTCCATTCTAATCA 15 3 1 CTATTCCTCC 0.94707 -85 CAGCGCCGTGCTATCTTCCCAGAAAGGAGGAT 15 58 1 CTCTTCCCAG 0.892009 -30 * ********* Masking position 7 Map Score: 9.4496 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 315 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 AAGCGGCAGTCCATGTGGGGAAGGGAGTGC 1 43 1 CCATGTGGGG 0.837915 -85 CGTGCGCACCGCACGGCGCGAACGCTTCTC 3 14 0 GCACGGCGCG 0.970994 -164 CACCGATTTTCCGCGAGGAGTTGACGGAGT 3 79 1 CCGCGAGGAG 0.79562 -99 TTGTTCAGGAACATGCGGCGAACTACACAA 3 140 0 ACATGCGGCG 0.906066 -38 TTCCTGAACAACGTGAGGGGTTGCCGTGC 3 159 1 ACGTGAGGGG 0.795746 -19 GGGTCGAGACACACGCCCCACT 9 3 0 ACACGCCCCA 0.732906 -73 TACCCACTGACCACGGGCGGGTCGAGACAC 9 21 0 CCACGGGCGG 0.816755 -55 TTTGCAATGAGCACCCGGGTAGGGGGTTCT 10 47 1 GCACCCGGGT 0.836917 -57 GTAGCAAAAAACGCGCCCGGAATACAGAAC 10 72 0 ACGCGCCCGG 0.75996 -32 CGTTCCGTGCCCGTTTTGAAACGG 11 5 1 CCGTGCCCGT 0.824755 -52 GGGGCTGCGTCCACCAGGCAAGGAGTGAT 11 38 1 CCACCAGGCA 0.497159 -19 CCCCTGTTACGCACGACGGGTATCGGGCAT 13 20 1 GCACGACGGG 0.971552 -98 GGACAAAACGCCGCGCGCCGCATGCCCGAT 13 41 0 CCGCGCGCCG 0.727496 -77 CGGTACTTTAGCACGCGGCTGTGGTGTGCG 14 39 0 GCACGCGGCT 0.972695 -121 AACGAAGGGCCCGTGACGGTACTTTAGCAC 14 55 0 CCGTGACGGT 0.799195 -105 GCGTCGTCCTGCACGTCCCTAACGAAAAGA 14 125 0 GCACGTCCCT 0.775716 -35 TGGGAAGATAGCACGGCGCTGTCCTCTTGG 15 49 0 GCACGGCGCT 0.933719 -39 ********** Masking position 2 Map Score: 15.4628 Number of sites scoring better than the average of aligned sites = 3884 Number in coding regions = 3527 Number in noncoding regions = 357 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 5 CTCGGAAGACTGTGGCAAATAAGCGGCAGTCC 1 23 1 TGGCAAATAA 0.925927 -105 CTCAACCGAGTGAGAAAAAGAATCATCACATA 4 26 0 TGAAAAAGAA 0.83538 -79 AGTGCTTTTTTAGGGAAAAGGAAGATCGC 7 18 1 TAGAAAAGGA 0.908831 -19 CCCGGGTGCTCATTGCAAAGAATAGGTGCCAC 10 34 0 CAGCAAAGAA 0.953679 -70 GCCCGCTAAGTGTAGCAAAAAACGCGCCCGGA 10 81 0 TGGCAAAAAA 0.925927 -23 GCTCTGTTTCTAGCGCAAAGAATGGACAAAAC 13 62 0 TAGCAAAGAA 0.985275 -56 TGCACGTCCCTAACGAAAAGAAGACGTGATGT 14 114 0 TAGAAAAGAA 0.970057 -46 ** ******** Masking position 7 Map Score: 1.29928 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 84 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 GTCTCAGAACACTCATGGGCGGATGATGGA 1 108 1 ACTCATGGGC 0.8936 -20 GAAGAAGGGAAGTACAGGGCAGAAAACGGA 2 13 0 AGTACAGGGC 0.925449 -33 GTGGTCAGTGGGTATGGGGACGTCCAGTAA 9 37 1 GGTATGGGGA 0.85226 -39 GTTTTGAAACGGTCCGGGGCTGCGTCCACC 11 23 1 GGTCCGGGGC 0.992631 -34 GTGGACGCTCCTGGGCCAACACGTAG 12 40 0 GCTCCTGGGC 0.943355 -16 ACGCACGACGGGTATCGGGCATGCGGCGCG 13 28 1 GGTATCGGGC 0.978008 -90 GCTAAAGTACCGTCACGGGCCCTTCGTTAC 14 57 1 CGTCACGGGC 0.96308 -103 ********** Masking position 3 Map Score: 2.92439 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 124 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 TACGCTTCCTAGCTACACAACGTGCGCACCG 3 33 0 ACTACACAAC 0.836621 -145 CACCCACTCCGTCAACTCCTCGCGGAAAATC 3 83 0 GCAACTCCTC 0.906889 -95 ACATGCGGCGAACTACACAAAAAACAGGCAG 3 129 0 ACTACACAAA 0.559167 -49 GCACGGCAACCCCTCACGTTGTTCA 3 163 0 GCAACCCCTC 0.935218 -15 GAGAAAAAGAATCATCACATACTCAGCTCAT 4 16 0 ACATCACATA 0.711332 -89 ACACCCAAAAAACAACACGGCAACT 6 5 0 ACAACACGGC 0.912513 -50 CAACATCACCTCTGAACTTGAA 6 43 0 ACATCACCTC 0.962192 -12 ACGCTCCTGGGCCAACACGTAGGAGGCAGGA 12 31 0 GCAACACGTA 0.913337 -25 GTATAATCTACACCTCTTTATTCTGC 14 6 1 ACTACACCTC 0.96659 -154 CCACCAAAGACACATCACGTCTTCTTTTCGT 14 103 1 CCATCACGTC 0.827953 -57 GCAGGACGACGCCGACACCACCCATAC 14 143 1 GCGACACCAC 0.892721 -17 * ********* Masking position 6 Map Score: 4.3144 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 296 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 GCTGTGCTTTTAAAGTTCAGAAAAGTTTTG 4 69 1 TAAAGTTCAG 0.981628 -36 GTGCACTTGTTCAAGTTCAGAGGTGATGTT 6 34 1 TCAAGTTCAG 0.988045 -21 AGCCCCTCCCTCAAGTTCATTACTGGACGT 9 56 0 TCAAGTTCAT 0.954132 -20 AGCCGCGTGCTAAAGTACCGTCACGGGCCC 14 49 1 TAAAGTACCG 0.925394 -111 ********** Masking position 6 Map Score: 0.591038 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 8 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 TCCATCATCCGCCCATGAGTGTTCT 1 113 0 CATCCGCCCA 0.951483 -15 CAAAGAATAGGTGCCACCCAACTCACCCTT 10 21 0 GTGCCACCCA 0.940591 -83 ACCGCGTCTCCTGCCTCCTACGTGTTGGCC 12 23 1 CTGCCTCCTA 0.970958 -33 GAACAATATTCTGCCTACCTGAGGAGAGAA 13 94 1 CTGCCTACCT 0.938676 -24 CCCTTCGTTACAGCCACCCTACGATATCCA 14 76 1 CAGCCACCCT 0.985725 -84 GTGTTTTCATCCTCCTTTCTGGGAAGA 15 71 0 CATCCTCCTT 0.91868 -17 ********** Masking position 5 Map Score: 1.67943 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 108 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 ********** No masking Map Score: 2.16248e-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: 2.16248e-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: 2.16248e-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