AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_tpal_reg_100.orf -o00550_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 TP0246 145 T. pallidum predicted coding region TP0246 #2 TP0247 50 N-acetylmuramoyl-L-alanine amidase (amiA) #3 TP0345 152 phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) #4 TP0382 83 T. pallidum predicted coding region TP0382 #5 TP0383 27 conserved hypothetical protein #6 TP0524 135 ATP-dependent protease LA (lon-2) #7 TP0671 30 sn-1,2-diacylglycerol cholinephosphotransferase, putative #8 TP0672 134 glycyl-tRNA synthetase (glyS) #9 TP0933 135 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase (murE) Motif number 1 CGAAAATGCGCATCCCCCGCAAAGGTGGCG 1 74 0 CATCCCCCGC 0.98196 -72 CCCCTCCTGCGGAACAAACA 1 136 0 CCCCTCCTGC 0.982255 -10 ACCTGTCCCCTCTCCCTACTCACAAT 2 35 0 CCCCTCTCCC 0.909203 -16 CGTGTGTCAACACGCGCTCAAGAAATGCAC 3 29 0 CACGCGCTCA 0.752427 -124 CCTCCCTTGCCCTCTCCTGCTGCATCCTTC 3 104 0 CCTCTCCTGC 0.965118 -49 TTCCTGTTCTCCTCCCTTGCCCTCTCCTGC 3 114 0 CCTCCCTTGC 0.980812 -39 ACGTCCACCCCCCCCCCCCCGACGAGA 4 8 1 CCCCCCCCCC 0.99672 -76 GATTTCCTACCTTCCCCTATATTTT 5 13 0 CCTACCTTCC 0.750026 -15 CGGTATACTGCGCCCCCGCAGGTCGTGCAA 6 42 0 CGCCCCCGCA 0.955777 -94 AAAAAATATACCTGCGCGGTATACTGCGCC 6 58 0 CCTGCGCGGT 0.712038 -78 ATTGACTTTTCGTCCCTTGCCTGGATACTA 6 108 1 CGTCCCTTGC 0.941183 -28 TTTCCCCGCGCGCAGAGAGCGGAC 7 17 0 CCCGCGCGCA 0.897443 -14 CCTTTGAACACATCCCCTGCATACCTCTTT 8 39 0 CATCCCCTGC 0.985111 -96 TCACAGAGATCGCGCCCGCCTTTGAACACA 8 57 0 CGCGCCCGCC 0.983273 -78 ATACTGTCAGCACCCGCGGCGACCTCACAG 8 81 0 CACCCGCGGC 0.984344 -54 CGCTCACCTTCCCCCCTGTCTAGCATACTG 8 105 0 CCCCCCTGTC 0.915674 -30 ATTAACTTACACTCCGCCGC 9 1 0 ACTCCGCCGC 0.757995 -135 TATCTGATTGCACGCCCTCGGGGAACAATC 9 102 0 CACGCCCTCG 0.819177 -34 ********** Masking position 1 Map Score: 26.6814 Number of sites scoring better than the average of aligned sites = 2587 Number in coding regions = 2206 Number in noncoding regions = 381 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 ATGCGAAGCGTGCGCAAGAGAATTTTGCGC 1 16 1 TGCGCAAGAG 0.690042 -130 ATGCGCATCCCCCGCAAAGGTGGCGATATT 1 69 0 CCCGCAAAGG 0.876534 -77 TTGTGTTTGTTCCGCAGGAGGGG 1 133 1 TCCGCAGGAG 0.930676 -13 TTATTGTGAGTAGGGAGAGGGGACAGGT 2 33 1 TAGGGAGAGG 0.950851 -18 TGCACGCTCGTACCCAGGAGCCT 3 4 0 TACCCAGGAG 0.75813 -149 AAGGATGCAGCAGGAGAGGGCAAGGGAGGA 3 105 1 CAGGAGAGGG 0.888593 -48 AGGAGAGGGCAAGGGAGGAGAACAGGAAGG 3 116 1 AAGGGAGGAG 0.662707 -37 GGGAGGAGAACAGGAAGGAGCACCGGTAGT 3 128 1 CAGGAAGGAG 0.83234 -25 CTTTTTCTCGTCGGGGGGGGGGGGGTGGAC 4 13 0 TCGGGGGGGG 0.983835 -71 TACTGGACAACCGGCAACGGTATGGGTGAC 4 49 0 CCGGCAACGG 0.949666 -35 GAAAAATATAGGGGAAGGTAGGAAATC 5 9 1 TAGGGGAAGG 0.887818 -19 TCTTGCACGACCTGCGGGGGCGCAGTATAC 6 40 1 CCTGCGGGGG 0.749676 -96 GCCTAGTATCCAGGCAAGGGACGAAAAGTC 6 111 0 CAGGCAAGGG 0.985226 -25 TCCCCGCGCGCAGAGAGCGGACAACAAC 7 9 0 CAGAGAGCGG 0.609037 -22 ACGCGGGCTATAGGGAAAAGAGGTATGCAG 8 23 1 TAGGGAAAAG 0.75336 -112 GGAAAAGAGGTATGCAGGGGATGTGTTCAA 8 36 1 TATGCAGGGG 0.9241 -99 CTCTGTGAGGTCGCCGCGGGTGCTGACAGT 8 79 1 TCGCCGCGGG 0.710507 -56 GACAGTATGCTAGACAGGGGGGAAGGTGAG 8 103 1 TAGACAGGGG 0.919184 -32 TCGCAAACGGTGGGGAAAGGCCATCTCGTT 9 46 0 TGGGGAAAGG 0.791242 -90 TCAAAGAAGATCGCAAACGGTGGGGAAAGG 9 56 0 TCGCAAACGG 0.519536 -80 AATAGATTGTTCCCCGAGGGCGTGCAATCA 9 98 1 TCCCCGAGGG 0.853197 -38 ********** Masking position 10 Map Score: 20.8536 Number of sites scoring better than the average of aligned sites = 2586 Number in coding regions = 2276 Number in noncoding regions = 310 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 3 CGCAAAATTCTCTTGCGCACGCTTCGCATCA 1 14 0 TCTTGCGCAG 0.899758 -132 CGCAAGAGAATTTTGCGCGTTTTTTTTCCGC 1 28 1 TTTTGCGCGT 0.911235 -118 ATATCGCCACCTTTGCGGGGGATGCGCATTT 1 70 1 CTTTGCGGGG 0.979728 -76 AGCGTGCATTTCTTGAGCGCGTGTTGACACA 3 26 1 TCTTGAGCGG 0.966653 -127 GAGCACTGTGCCTTGTGCTAGTCCCTGAGCG 3 72 1 CCTTGTGCTG 0.879564 -81 TTGTGCTAGTCCCTGAGCGAGAAGGATGCAG 3 84 1 CCCTGAGCGG 0.990841 -69 TCCAGTAAATTTTTGCGATAGG 4 72 1 TTTTGCGATG 0.58519 -12 GTCTTGCACGACCTGCGGGGGCGCAGTATAC 6 39 1 ACCTGCGGGG 0.975045 -97 TAAAAAATATACCTGCGCGGTATACTGCGCC 6 58 0 ACCTGCGCGT 0.951112 -78 GTTGTCCGCTCTCTGCGCGCGGGGAAA 7 14 1 CTCTGCGCGG 0.994299 -17 CGGGCGCGATCTCTGTGAGGTCGCCGCGGGT 8 69 1 CTCTGTGAGT 0.59815 -66 ATAGATTGTTCCCCGAGGGCGTGCAATCAGA 9 99 1 CCCCGAGGGG 0.892216 -37 ********* * Masking position 5 Map Score: 13.8225 Number of sites scoring better than the average of aligned sites = 2057 Number in coding regions = 1910 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 TGCTTCAGCGGAAAAAAAACGCGCAAAATT 1 36 0 GAAAAAAAAC 0.918908 -110 GGTACACAACGAAAATGCGCATCCCCCGCA 1 83 0 GAAAATGCGC 0.906777 -63 CCCTCCTGCGGAACAAACACAAACCGATCA 1 125 0 GAACAAACAC 0.94927 -21 TCCCTACTCACAATAAGCACATACGTCCAC 2 19 0 CAATAAGCAC 0.898965 -32 AGGAGAACAGGAAGGAGCACCGGTAGTAGT 3 131 1 GAAGGAGCAC 0.954765 -22 CCCCCGACGAGAAAAAGAACATTGTCACCC 4 26 1 GAAAAAGAAC 0.976492 -58 GATCTTCTTTGAAAAAGCATTGACAATAGA 9 74 1 GAAAAAGCAT 0.95181 -62 ********** Masking position 3 Map Score: 1.56946 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 340 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 GTGATGCGAAGCGTGCGCAAGAGAATTTTG 1 13 1 GCGTGCGCAA 0.939565 -133 TGGCGATATTCCGTGCTTCAGCGGAAAAAA 1 49 0 CCGTGCTTCA 0.949553 -97 TTACACTCGGCCGTGTGTCAACACGCGCTC 3 40 0 CCGTGTGTCA 0.98597 -113 TGACACACGGCCGAGTGTAACGGAGCACTG 3 50 1 CCGAGTGTAA 0.97597 -103 TTTCCCCGCGCGCAGAGAGCGGACA 7 16 0 CCGCGCGCAG 0.904502 -15 GGAAGGTGAGCGGCGCGTCACC 8 123 1 CGGCGCGTCA 0.974401 -12 GCGGCGGAGTGTAAGTTAATCACT 9 5 1 CGGAGTGTAA 0.944865 -131 ********** Masking position 5 Map Score: 4.94732 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 402 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 GAAATGCACGCTCGTACCCAGGAGCCT 3 7 0 CTCGTACCAG 0.957805 -146 AGGGCGCCTAGTATCCAGGCAAGGGACG 6 118 0 CTAGTACCAG 0.950479 -18 TTTCCCCGCGCGCAGAGAGCGGACAACAA 7 12 0 CGCGCAAGAG 0.933965 -19 CCCTATAGCCCGCGTTAACTGAGAATA 8 7 0 CGCGTTACTG 0.96212 -128 GCACCCGCGGCGACCTCACAGAGATCGCGCC 8 71 0 CGACCTACAG 0.867917 -64 TCCCCCCTGTCTAGCATACTGTCAGCACCCG 8 95 0 CTAGCAACTG 0.941285 -40 GAAAGGCCATCTCGTTGACAGCCTTTTAGTG 9 31 0 CTCGTTACAG 0.966694 -105 ****** **** Masking position 1 Map Score: 2.04039 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 383 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 CCTATTTTACAAGCTGATCGGTTTGTGTTTG 1 111 1 AAGCGATCGG 0.966547 -35 TATTGTGAGTAGGGAGAGGGGACAGGT 2 34 1 AGGGGAGGGG 0.982952 -17 AAGGATGCAGCAGGAGAGGGCAAGGGAGGAG 3 105 1 CAGGGAGGGC 0.982952 -48 GATGTGTTCAAAGGCGGGCGCGATCTCTGTG 8 55 1 AAGGGGGCGC 0.991016 -80 GACAGGGGGGAAGGTGAGCGGCGCGTCACC 8 115 1 AAGGGAGCGG 0.996692 -20 TGCTTTTTCAAAGAAGATCGCAAACGGTGGG 9 62 0 AAGAGATCGC 0.951302 -74 **** ****** Masking position 6 Map Score: 3.78348 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 157 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 ********** No masking Map Score: 1.72905e-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 9 ********** No masking Map Score: 1.72905e-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 10 ********** No masking Map Score: 1.72905e-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