AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -inarL_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 TP0100 194 thioredoxin, putative #2 TP0278 127 T. pallidum predicted coding region TP0278 #3 TP0279 45 ribosomal protein S1 (rpsA) #4 TP0382 83 T. pallidum predicted coding region TP0382 #5 TP0383 27 conserved hypothetical protein #6 TP0390 45 cell division protein (ftsZ) Motif number 1 CAGCGTGCACGGGGCGATGGAGTGTTCTACACG 1 86 1 GGGGGAGGGT 0.99538 -109 CAGTCTTCCGAGGAAGACGAGCGC 2 2 0 AGGAGAGACG 0.891242 -126 CGGAAGACTGTGGCAAATAAGCGGCAGTCCATG 2 25 1 TGGCAAAACG 0.862965 -103 GCAGTCCATGTGGGGAAGGGAGTGCGCTGGTGA 2 48 1 TGGGAAGGGT 0.962889 -80 GAACACTCATGGGCGGATGATGGA 2 114 1 GGGCGAGAGG 0.997271 -14 GGGAAGTACAGGGCAGAAAACGGAAG 3 4 0 GGGCGAAAGG 0.992608 -42 AGGGGTGAAAAACGAAGAAGGGAA 3 32 0 GGGGGAAACG 0.991588 -14 GTCGGGGGGGGGGGGGTGGACGT 4 1 0 GGGGGTGAGT 0.986858 -83 GGCAACGGTATGGGTGACAATGTTCTTTTTCTC 4 34 0 TGGGGAAAGT 0.973292 -50 GAAAAATATAGGGGAAGGTAGGAAATC 5 10 1 AGGGAAGTGG 0.9254 -18 ACGCGGTGTAGGGGAATGGGAGGGGA 6 30 1 GGGGATGGGG 0.98164 -16 **** ** ** ** Masking position 3 Map Score: 15.2869 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 651 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 GCATCGTAACGCAAAGAGACCCTTTGGATCC 1 26 1 GCAAAGAGAC 0.868036 -169 AATGCCAGATACACACAGGGCCTGGATCCAA 1 49 0 ACACACAGGC 0.845409 -146 TGTGTATCTGGCATTGCGTCCCAGCGTGCAC 1 65 1 GCATTGCGTC 0.876897 -130 TACACGGGCGACACAGACTCCTAGTTCTTGT 1 113 1 ACACAGACTC 0.988099 -82 GTCGGTTTTTGCACAGAATACAAGAACTAGG 1 132 0 GCACAGAATC 0.97437 -63 GCACAGAGAACACTCACTAGA 1 184 0 GCACAGAGAC 0.983597 -11 CGCTTATTTGCCACAGTCTTCCGAGGAAGAC 2 17 0 CCACAGTCTC 0.88605 -111 TCCCTTCCCCACATGGACTGCCGCTTATTTG 2 38 0 ACATGGACTC 0.790869 -90 GATCACCAGCGCACTCCCTTCCCCACATGGA 2 52 0 GCACTCCCTC 0.918256 -76 ACCGCGCACAGCATGCGGCACGCGGT 6 6 1 GCACAGCATC 0.729159 -40 CCATTCCCCTACACCGCGTGCCGCATGCTGT 6 18 0 ACACCGCGTC 0.955357 -28 ********* * Masking position 3 Map Score: 11.192 Number of sites scoring better than the average of aligned sites = 1015 Number in coding regions = 920 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 TCGCCCGTGTAGAACACTCCATCGCCCCGT 1 94 0 AGAACACTCC 0.952383 -101 ACAGAATACAAGAACTAGGAGTCTGTGTCG 1 121 0 AGAACTAGGA 0.893318 -74 AACACTCACTAGACTACGGAGATACAGTTT 1 167 0 AGACTACGGA 0.956836 -28 GCACAGAGAACACTCACTAGACTACG 1 179 0 AGAACACTCA 0.986893 -16 GCTGGTGATCAGACAACAGACGAGGAGCGC 2 73 1 AGACAACAGA 0.914771 -55 AAACAGTCTCAGAACACTCATGGGCGGATG 2 103 1 AGAACACTCA 0.986893 -25 AGTACAGGGCAGAAAACGGAAG 3 3 0 AGAAAACGGA 0.989991 -43 CCCCCCGACGAGAAAAAGAACATTGTCACC 4 25 1 AGAAAAAGAA 0.812568 -59 ********** Masking position 3 Map Score: 6.93392 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 203 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 GAAACCCTCTCGCCGGCATCGTAAC 1 6 1 CCTCTCGCCG 0.990704 -189 TAGAACACTCCATCGCCCCGTGCACGCTGG 1 85 0 CATCGCCCCG 0.919072 -110 AGTCTGTGTCGCCCGTGTAGAACACTCCAT 1 102 0 GCCCGTGTAG 0.699857 -93 GCGCTCGTCTTCCTCGGAAG 2 1 1 GCGCTCGTCT 0.887273 -127 CCAGCGCACTCCCTTCCCCACATGGACTGC 2 48 0 CCCTTCCCCA 0.880567 -80 GAGACTGTTTGCGCTCCTCGTCTGTTGTCT 2 83 0 GCGCTCCTCG 0.982578 -45 CCCTGTACTTCCCTTCTTCGTTTTTCACCC 3 24 1 CCCTTCTTCG 0.810412 -22 CGTCCACCCCCCCCCCCCCGACGAGAAAAA 4 12 1 CCCCCCCCCG 0.993385 -72 ACCGCGCACAGCATGCGGCAC 6 2 1 CCGCGCACAG 0.921734 -44 TTCCCCTACACCGCGTGCCGCATGCTGTGC 6 16 0 CCGCGTGCCG 0.974971 -30 TCCCCTCCCATTCCCCTACAC 6 35 0 CCCCTCCCAT 0.954346 -11 ********** Masking position 2 Map Score: 9.88056 Number of sites scoring better than the average of aligned sites = 2160 Number in coding regions = 1901 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 5 TAACGCAAAGAGACCCTTTGGATCCAGGCC 1 32 1 AGACCCTTTG 0.98823 -163 CTTTGGATCCAGGCCCTGTGTGTATCTGGC 1 47 1 AGGCCCTGTG 0.993092 -148 GAACACTCCATCGCCCCGTGCACGCTGGGA 1 83 0 TCGCCCCGTG 0.938306 -112 CGGGCGACACAGACTCCTAGTTCTTGTATT 1 117 1 AGACTCCTAG 0.851685 -78 AATAAGCGGCAGTCCATGTGGGGAAGGGAG 2 40 1 AGTCCATGTG 0.909912 -88 GAGTGTTCTGAGACTGTTTGCGCTCCTCGT 2 92 0 AGACTGTTTG 0.92291 -36 CCATTCCCCTACACCGCGTGCCGCATGCTG 6 19 0 ACACCGCGTG 0.978808 -27 ********** Masking position 4 Map Score: 4.3595 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 183 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TTGCGTTACGATGCCGGCGAGAGGGTTTC 1 10 0 ATGCCGGCGA 0.902945 -185 TCCCAGCGTGCACGGGGCGATGGAGTGTTC 1 83 1 CACGGGGCGA 0.92688 -112 GGAGTGTTCTACACGGGCGACACAGACTCC 1 104 1 ACACGGGCGA 0.96736 -91 TTCTGTGCAAAAACCGACGTAAAAACTGTA 1 145 1 AAACCGACGT 0.906175 -50 TTGCCACAGTCTTCCGAGGAAGACGAGCGC 2 11 0 CTTCCGAGGA 0.788191 -117 GGTGATCAGACAACAGACGAGGAGCGCAAA 2 76 1 CAACAGACGA 0.955265 -52 CACCCCCCCCCCCCCGACGAGAAAAAGAAC 4 16 1 CCCCCGACGA 0.98902 -68 ATTTACTGGACAACCGGCAACGGTATGGGT 4 52 0 CAACCGGCAA 0.96065 -32 ********** Masking position 6 Map Score: 3.44396 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 414 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 ********** No masking Map Score: 5.21128e-13 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 8 ********** No masking Map Score: 5.21128e-13 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: 5.21128e-13 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