AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_tpal_reg_100.orf -o00400_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 TP0015 190 phenylalanyl-tRNA synthetase beta subunit (pheT) #2 TP0223 267 aspartate aminotransferase (tpaaT) #3 TP0818 26 T. pallidum predicted coding region TP0818 #4 TP0819 27 conserved hypothetical protein #5 TP0820 95 hypothetical protein #6 TP0821 80 lipoprotein (tpn32) #7 TP0822 87 conserved hypothetical protein #8 TP0823 300 desulfoferrodoxin (rbo) #9 TP0834 86 tyrosyl-tRNA synthetase (tyrS) #10 TP0835 140 ankyrin, putative #11 TP0973 87 phenylalanyl-tRNA synthetase alpha subunit (pheS) Motif number 1 TCATGCCTTTGTGCGCACGGTACTTATGCC 1 13 1 GTGCGCACGG 0.953072 -178 GAGCGCTCATATGCGCACGGCATAAGTACC 1 31 0 ATGCGCACGG 0.570489 -160 CCACTACACGGCACACGTGCTCTACACTTT 1 90 0 GCACACGTGC 0.743503 -101 GGCATCCTCTGCAAAGACGGTGTGGTGGCT 1 118 1 GCAAAGACGG 0.903928 -73 CGTATACTGAGCACGGTCGGAGGGCTC 1 174 1 GCACGGTCGG 0.913 -17 CGACTTCAGAGCACACAAGCCCGCGCAGCC 2 53 0 GCACACAAGC 0.701599 -215 GTCTCACAGTGTAGACACGCCCCCTGACCC 2 116 0 GTAGACACGC 0.894094 -152 AGCGTTTAACGCACGCGCGCCTTCAGAGAG 2 152 0 GCACGCGCGC 0.509675 -116 AGGAACGGTGGTGCACGCGCTGTTATCTCC 2 190 1 GTGCACGCGC 0.958918 -78 CGTGGGGAAAATACGCGCGCAAACCAAGAG 2 219 0 ATACGCGCGC 0.870717 -49 TGCACAGAATGCAGAGGCGCGG 2 256 1 GCAGAGGCGC 0.985591 -12 CGGAGTATTGCAACGGCGCGTTATAT 3 8 0 GCAACGGCGC 0.702168 -19 TGCATCCTACGCAAGGGCGTACTGCGCGCA 7 65 0 GCAAGGGCGT 0.750271 -23 CTCGTGCGTAGCACAGGCTCGGAAGGAGCG 8 115 1 GCACAGGCTC 0.900937 -186 TACGCATTCAGTAAACTCGCTCCTTCCGAG 8 132 0 GTAAACTCGC 0.645707 -169 TACTGAATGCGTACAGGTGGGTGACGCTTT 8 149 1 GTACAGGTGG 0.875354 -152 GCACAGCCCCGCAGAGGCGCTGATTCTACC 8 197 0 GCAGAGGCGC 0.985591 -104 CTGTGCTCTGGCGCGGGCGGTTTCCGCACG 8 221 1 GCGCGGGCGG 0.624614 -80 CGGGCGGTTTCCGCACGCGGAGGCACGACA 8 234 1 CCGCACGCGG 0.765684 -67 TTTTGTTCTCGTGCGGACGCCTGTCGTGCC 8 255 0 GTGCGGACGC 0.981501 -46 CGGGGCGACGGTGGGGGTGCATCAGCGCGT 9 18 1 GTGGGGGTGC 0.817278 -69 CCCCGATCCAGGGCAGGCGGTTCAGTCCCG 9 61 0 GGGCAGGCGG 0.931666 -26 GGACGCAACCGCGCAGGCGCGTTCCCATTT 10 11 0 GCGCAGGCGC 0.745598 -130 CCACTCTCCCGTGAGGACGCAACCGCGCAG 10 25 0 GTGAGGACGC 0.924782 -116 TACACACACTGTACAGACGCGGCACCATAC 10 104 1 GTACAGACGC 0.979845 -37 ********** Masking position 9 Map Score: 46.1137 Number of sites scoring better than the average of aligned sites = 4164 Number in coding regions = 3872 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 CGGCATAAGTACCGTGCGCACAAAGGCATG 1 14 0 ACCGTGCGCA 0.913368 -177 CGGTACTTATGCCGTGCGCATATGAGCGCT 1 30 1 GCCGTGCGCA 0.965353 -161 TGGTGGCTGGCCCTTGTGGTGTCCTTTTTT 1 140 1 CCCTTGTGGT 0.630193 -51 ACGGATGAGCTTCCTGCGGCAAATGGTTAC 2 21 0 TTCCTGCGGC 0.875616 -247 AGGAAGCTCATCCGTGTGGCTGCGCGGGCT 2 36 1 TCCGTGTGGC 0.892745 -232 GTGCAACAATCCCGTGGGGAAAATACGCGC 2 231 0 CCCGTGGGGA 0.991402 -37 ACCATCCCCATCCTTGAGTATGCAGAAGAA 5 53 0 TCCTTGAGTA 0.819652 -43 GCGCAGTACGCCCTTGCGTAGGATGCAGGC 7 68 1 CCCTTGCGTA 0.972575 -20 GTTTCTACGTGCCCTGCGGAAAGAAAAGAA 8 26 0 GCCCTGCGGA 0.979423 -275 CCAGCTTGGATTCCTGAGGAGTTTCTACGT 8 46 0 TTCCTGAGGA 0.894337 -255 TCAAGGTATACTCGTGCGTAGCACAGGCTC 8 105 1 CTCGTGCGTA 0.980886 -196 CTAAATCAGGTCCGTGGGTAAAGCGTCACC 8 168 0 TCCGTGGGTA 0.944347 -133 GTCGTGCCTCCGCGTGCGGAAACCGCCCGC 8 233 0 CGCGTGCGGA 0.981257 -68 TGATTTTGTTCTCGTGCGGACGCCTGTCGT 8 258 0 CTCGTGCGGA 0.993127 -43 CGCCCACTCTCCCGTGAGGACGCAACCGCG 10 28 0 CCCGTGAGGA 0.993008 -113 GCAGCGGATCCTCCTGAGTATGGTGCCGCG 10 121 0 CTCCTGAGTA 0.882994 -20 ********** Masking position 5 Map Score: 25.1673 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 538 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 AAGTACCGTGCGCACAAAGGCATGAGC 1 7 0 CGCACAAGGC 0.766763 -184 GAGCCCTCCGACCGTGCTCAGTAT 1 177 0 CCCTCGACCG 0.675673 -14 AGCACACAAGCCCGCGCAGCCACACGGATGA 2 43 0 CCCGCCAGCC 0.981867 -225 TGTAGACACGCCCCCTGACCCTGTCAATTTA 2 106 0 CCCCCGACCC 0.993337 -162 CAGCGCGTGCACCACCGTTCCTTCAAGAGCA 2 181 0 ACCACGTTCC 0.789376 -87 ATATAACGCGCCGTTGCAATACTCCG 3 7 1 CGCGCGTTGC 0.924058 -20 AAGACACACCCACACCATCCCCATCCTTGAG 5 65 0 CACACATCCC 0.746624 -31 CATTCGGCCTCCCCCTGTCCCTCTATCCATC 6 58 0 CCCCCGTCCC 0.990605 -23 CGCAAATATGCCCCCAATCTCCTGCTCCCCT 7 38 0 CCCCCATCTC 0.626301 -50 TGACGCTTTACCCACGGACCTGATTTAGGTA 8 170 1 CCCACGACCT 0.872065 -131 AGAGCACAGCCCCGCAGAGGCGCTGATTCTA 8 199 0 CCCGCGAGGC 0.991906 -102 GCGTGCGGAAACCGCCCGCGCCAGAGCACAG 8 221 0 ACCGCCGCGC 0.682466 -80 GCGGTTTCCGCACGCGGAGGCACGACAGGCG 8 237 1 CACGCGAGGC 0.955418 -64 CTGATGCACCCCCACCGTCGCCCCGCGTGTC 9 12 0 CCCACGTCGC 0.988175 -75 AAAGACAAAACGCGCTGATGCACCCCCACCG 9 26 0 CGCGCGATGC 0.94495 -61 CGCACACCCCGATCCAGGGCAGGCG 9 72 0 CACCCGATCC 0.877134 -15 TGAGGACGCAACCGCGCAGGCGCGTTCCCAT 10 13 0 ACCGCCAGGC 0.865685 -128 TCTTTAGACGCCCACTCTCCCGTGAGGACGC 10 35 0 CCCACCTCCC 0.973381 -106 ***** ***** Masking position 5 Map Score: 22.7645 Number of sites scoring better than the average of aligned sites = 1163 Number in coding regions = 1022 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 GCAGAGGATGCCACTACACGGCACACGTGCTCTAC 1 95 0 CCCAGGCACA 0.998255 -96 CCAGCCACCACACCGTCTTTGCAGAGGATGCCACT 1 115 0 CCCTTGCAGA 0.837276 -76 CAAGCCCGCGCAGCCACACGGATGAGCTTCCTGCG 2 33 0 CCCAGGATGA 0.806951 -235 ATCGACAGCCCGACTTCAGAGCACACAAGCCCGCG 2 58 0 CCCAAGCACA 0.992983 -210 TTTTCTTTTCTTTCCGCAGGGCACGTAGAAACTCC 8 24 1 TCCAGGCACG 0.933712 -277 TCAAGGTATACTCGTGCGTAGCACAGGCTCGGAAG 8 105 1 CGCGAGCACA 0.757128 -196 CGGAAACCGCCCGCGCCAGAGCACAGCCCCGCAGA 8 212 0 CCCAAGCACA 0.992986 -89 CGCACACCCCGATCCAGGGCAGGCGGTTCAGTC 9 64 0 CACAGGCAGG 0.918494 -23 TGCGCGGTTGCGTCCTCACGGGAGAGTGGGCGTCT 10 26 1 CCCAGGGAGA 0.980588 -115 CTACCGGTTTCGGCGATAAGGCACAGAATCTTTAG 10 59 0 CCTAGGCACA 0.987579 -82 CTATTTCTCCACACTACGGCAGATGTACCCTGA 11 9 1 CCTAGGCAGA 0.982874 -79 ATTTTTCGTTCTGCATCAGGGTACATCTGCCGTAG 11 24 0 CCCAGGTACA 0.98039 -64 * * ** ****** Masking position 11 Map Score: 14.0923 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 166 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 5 CGGCATAAGTACCGTGCGCACAAAGGCATGAGC 1 8 0 ACGGCGCAAG 0.995395 -183 ACACTCTTAAACTGAGCGCTCATATGCGCACGGCAT 1 38 0 ACGGCGCAAG 0.995499 -153 TTGGACATTGACAGGATGGATAGAGGGACAGGGGGA 6 44 1 ACGATGTAAG 0.985017 -37 GCAAGGGCGTACTGCGCGCAAATATGCCCCCAATCT 7 49 0 ACGGCGAAAG 0.993054 -39 GAGCGAGTTTACTGAATGCGTACAGGTGGGTGACGC 8 140 1 ACGATGTAAG 0.981723 -161 GCGATAAGGCACAGAATCTTTAGACGCCCACTCTCC 10 46 0 ACGATCTAAG 0.915831 -95 CCGCGTCTGTACAGTGTGTGTAAAAGCGTATCCTAC 10 90 0 ACGGTGTAAG 0.994089 -51 CTACATCTAAACGGCGCGAAAATACGTT 11 70 1 ACGGCGAAAG 0.993055 -18 ** * *** ** * * Masking position 12 Map Score: 13.3345 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CACGGCACACGTGCTCTACACTTTAGTCATAA 1 82 0 GTCTTACACT 0.699384 -109 GTGCCGTGTAGTGGCATCCTCTGCAAAGACGG 1 106 1 GTGCTCCTCT 0.977098 -85 GCTGGCCCTTGTGGTGTCCTTTTTTTGACCGT 1 145 1 GTGTTCCTTT 0.932371 -46 TGCACGCGCTGTTATCTCCTCTTGGTTTGCGC 2 201 1 GTATTCCTCT 0.906783 -67 GGTGCAAGTTCTTTCCGTTTAAAACCTAC 5 8 1 GTCTTCCGTT 0.918627 -88 GGGTGTAGTGCTCTCCTGTTTTTAGGAAG 7 8 1 GTCTTCCTGT 0.855664 -80 GACCATTTGGGTAGTTTCCGCTACGCTCCTGC 8 75 0 GTGTTCCGCT 0.993742 -226 ATGCGTACAGGTGGGTGACGCTTTACCCACGG 8 155 1 GTGGGACGCT 0.775953 -146 CGCCTCTGCGGGGCTGTGCTCTGGCGCGGGCG 8 208 1 GGCTTGCTCT 0.69495 -93 TCTGGCGCGGGCGGTTTCCGCACGCGGAGGCA 8 227 1 GCGTTCCGCA 0.859325 -74 CGCCTGCGCGGTTGCGTCCTCACGGGAGAGTG 10 22 1 GTGCTCCTCA 0.897058 -119 GCCGAAACCGGTAGGATACGCTTTTACACACA 10 80 1 GTGGTACGCT 0.956201 -61 ACCATACTCAGGAGGATCCGCTGC 10 127 1 GGGGTCCGCT 0.963686 -14 ** ** ****** Masking position 9 Map Score: 7.65683 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 247 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 ACGGCACACGTGCTCTACACTTTAGTCATA 1 83 0 TGCTCTACAC 0.792672 -108 TGCAGAGGATGCCACTACACGGCACACGTG 1 101 0 GCCACTACAC 0.974448 -90 ACAAGGGCCAGCCACCACACCGTCTTTGCA 1 127 0 GCCACCACAC 0.991479 -64 TCAAAAAAAGGACACCACAAGGGCCAGCCA 1 143 0 GACACCACAA 0.791616 -48 ACAAGCCCGCGCAGCCACACGGATGAGCTT 2 39 0 GCAGCCACAC 0.703725 -229 TGTCAATTTATGCACCCCAGTGAATCGACA 2 86 0 TGCACCCCAG 0.888308 -182 TAACAGCGCGTGCACCACCGTTCCTTCAAG 2 185 0 TGCACCACCG 0.888308 -83 AAAACAGGAGAGCACTACACCC 7 3 0 AGCACTACAC 0.905648 -85 CGCACGCGGAGGCACGACAGGCGTCCGCAC 8 245 1 GGCACGACAG 0.95721 -56 GTACAGACGCGGCACCATACTCAGGAGGAT 10 114 1 GGCACCATAC 0.951753 -27 ********** Masking position 5 Map Score: 4.72982 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 342 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 ATTGTTGCACAGAATGCAGAGGCGCGG 2 251 1 AGAATGCAGA 0.909142 -17 CCCATCCTTGAGTATGCAGAAGAACCGTCA 5 47 0 AGTATGCAGA 0.909142 -49 TGCATACTCAAGGATGGGGATGGTGTGGGT 5 59 1 AGGATGGGGA 0.989205 -37 GGACATTGACAGGATGGATAGAGGGACAGG 6 46 1 AGGATGGATA 0.874651 -35 TCCTGTTTTTAGGAAGGGGAGCAGGAGATT 7 24 1 AGGAAGGGGA 0.935256 -64 GGGGAGCAGGAGATTGGGGGCATATTTGCG 7 39 1 AGATTGGGGG 0.810629 -49 GCCCTTGCGTAGGATGCAGGC 7 77 1 AGGATGCAGG 0.968006 -11 ACGCGGGGCGACGGTGGGGGTGCATCAGCG 9 15 1 ACGGTGGGGG 0.861476 -72 CATCTGCCGTAGTGTGGAGAAATAG 11 6 0 AGTGTGGAGA 0.916632 -82 ********** Masking position 1 Map Score: 6.10531 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 216 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 AAATGGTTACACAAACACCG 2 1 0 ACAAACACCG 0.953205 -267 ACTTCAGAGCACACAAGCCCGCGCAGCCAC 2 51 0 ACACAAGCCC 0.820802 -217 CTCACAGTGTAGACACGCCCCCTGACCCTG 2 114 0 AGACACGCCC 0.969704 -154 TTGAGTATGCAGAAGAACCGTCAGGACTGG 5 40 0 AGAAGAACCG 0.817825 -56 TTCTTTCAAAAGACACACCCACACCATCCC 5 75 0 AGACACACCC 0.988151 -21 GCGCACATCAAGACTCACCCTGCATT 6 7 0 AGACTCACCC 0.958648 -74 CAATGTCCAAAGAAAAAGCGCACATCAAGA 6 24 0 AGAAAAAGCG 0.89501 -57 TGATTTAGGTAGAATCAGCGCCTCTGCGGG 8 190 1 AGAATCAGCG 0.865769 -111 CCCGAGAAAAAGACAAAACGCGCTGATGCA 9 35 0 AGACAAAACG 0.803184 -52 ATACGCTTTTACACACACTGTACAGACGCG 10 95 1 ACACACACTG 0.753247 -46 CGAAAAATTGAGAAACAGCCTACATCTAAA 11 51 1 AGAAACAGCC 0.95111 -37 ********** Masking position 3 Map Score: 10.1281 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 284 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 ACGGCATAAGTACCGTGCGCACAAAGGCAT 1 15 0 TACCGTGCGC 0.83477 -176 CTGAGCGCTCATATGCGCACGGCATAAGTA 1 33 0 ATATGCGCAC 0.640194 -158 AACACTCTTAAACTGAGCGCTCATATGCGC 1 45 0 AACTGAGCGC 0.970793 -146 TTTGACCGTATACTGAGCACGGTCGGAGGG 1 168 1 TACTGAGCAC 0.745066 -23 GGACCTCTCTGAAGGCGCGCGTGCGTTAAA 2 148 1 GAAGGCGCGC 0.940955 -120 AAGAGGAGATAACAGCGCGTGCACCACCGT 2 194 0 AACAGCGCGT 0.935315 -74 CCCGTGGGGAAAATACGCGCGCAAACCAAG 2 221 0 AAATACGCGC 0.83314 -47 GGAGTATTGCAACGGCGCGTTATAT 3 6 0 AACGGCGCGT 0.970219 -21 TGTCCAAAGAAAAAGCGCACATCAAGACTC 6 21 0 AAAAGCGCAC 0.869838 -60 CGCAAGGGCGTACTGCGCGCAAATATGCCC 7 56 0 TACTGCGCGC 0.988497 -32 CGCGTGCGGAAACCGCCCGCGCCAGAGCAC 8 223 0 AACCGCCCGC 0.939168 -78 CCTACATCTAAACGGCGCGAAAATACGTT 11 69 1 AACGGCGCGA 0.948654 -19 ********** Masking position 8 Map Score: 12.0636 Number of sites scoring better than the average of aligned sites = 1360 Number in coding regions = 1274 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 ********** No masking Map Score: 2.51775e-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: 2.51775e-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: 2.51775e-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