AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -inarP_tpal_opreg_100.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 CGTGTAGAACACTCCATCGCCCCGTGCACGCTG 1 86 0 ACCCTCCCCC 0.994851 -109 GCGCTCGTCTTCCTCGGAAGACTG 2 2 1 CGTCTCTCCT 0.880219 -126 CATGGACTGCCGCTTATTTGCCACAGTCTTCCG 2 25 0 CGTTTTGCCA 0.849561 -103 TCACCAGCGCACTCCCTTCCCCACATGGACTGC 2 48 0 ACCCTTCCCA 0.958792 -80 TCCATCATCCGCCCATGAGTGTTC 2 114 0 CCTCTCGCCC 0.996958 -14 CTTCCGTTTTCTGCCCTGTACTTCCC 3 4 1 CCTTTCGCCC 0.991763 -42 TTCCCTTCTTCGTTTTTCACCCCT 3 32 1 CGTTTCCCCC 0.990629 -14 ACGTCCACCCCCCCCCCCCCGAC 4 1 1 ACTCACCCCC 0.985367 -83 GAGAAAAAGAACATTGTCACCCATACCGTTGCC 4 34 1 ACTTTCCCCA 0.970308 -50 GATTTCCTACCTTCCCCTATATTTTTC 5 10 0 CCACTTCCCT 0.917519 -18 TCCCCTCCCATTCCCCTACACCGCGT 6 30 0 CCCCATCCCC 0.979569 -16 ** ** ** **** Masking position 11 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 GGATCCAAAGGGTCTCTTTGCGTTACGATGC 1 26 0 GGTCTCTTGC 0.902864 -169 TTGGATCCAGGCCCTGTGTGTATCTGGCATT 1 49 1 GCCCTGGTGT 0.904477 -146 GTGCACGCTGGGACGCAATGCCAGATACACA 1 65 0 GGACGCATGC 0.745255 -130 ACAAGAACTAGGAGTCTGTGTCGCCCGTGTA 1 113 0 GGAGTCGTGT 0.985705 -82 CCTAGTTCTTGTATTCTGTGCAAAAACCGAC 1 132 1 GTATTCGTGC 0.95396 -63 TCTAGTGAGTGTTCTCTGTGC 1 184 1 GTTCTCGTGC 0.971198 -11 CAAATAAGCGGCAGTCCATGTGGGGAAGGGA 2 38 1 GCAGTCATGT 0.934626 -90 TCCATGTGGGGAAGGGAGTGCGCTGGTGATC 2 52 1 GAAGGGGTGC 0.805933 -76 ACCGCGTGCCGCATGCTGTGCGCGGT 6 6 0 GCATGCGTGC 0.673528 -40 ACAGCATGCGGCACGCGGTGTAGGGGAATGG 6 18 1 GCACGCGTGT 0.921754 -28 ****** **** Masking position 9 Map Score: 11.208 Number of sites scoring better than the average of aligned sites = 1110 Number in coding regions = 1011 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 TCGCCCGTGTAGAACACTCCATCGCCCCGT 1 94 0 AGAACACTCC 0.942833 -101 ACAGAATACAAGAACTAGGAGTCTGTGTCG 1 121 0 AGAACTAGGA 0.873494 -74 AACACTCACTAGACTACGGAGATACAGTTT 1 167 0 AGACTACGGA 0.94813 -28 GCACAGAGAACACTCACTAGACTACG 1 179 0 AGAACACTCA 0.98415 -16 GCTGGTGATCAGACAACAGACGAGGAGCGC 2 73 1 AGACAACAGA 0.89848 -55 AAACAGTCTCAGAACACTCATGGGCGGATG 2 103 1 AGAACACTCA 0.98415 -25 AGTACAGGGCAGAAAACGGAAG 3 3 0 AGAAAACGGA 0.987888 -43 CCCCCCGACGAGAAAAAGAACATTGTCACC 4 25 1 AGAAAAAGAA 0.78141 -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 GTTACGATGCCGGCGAGAGGGTTTC 1 6 0 CGGCGAGAGG 0.991902 -189 CCAGCGTGCACGGGGCGATGGAGTGTTCTA 1 85 1 CGGGGCGATG 0.929005 -110 ATGGAGTGTTCTACACGGGCGACACAGACT 1 102 1 CTACACGGGC 0.728817 -93 CTTCCGAGGAAGACGAGCGC 2 1 0 AGACGAGCGC 0.900716 -127 GCAGTCCATGTGGGGAAGGGAGTGCGCTGG 2 48 1 TGGGGAAGGG 0.894714 -80 AGACAACAGACGAGGAGCGCAAACAGTCTC 2 83 1 CGAGGAGCGC 0.984849 -45 GGGTGAAAAACGAAGAAGGGAAGTACAGGG 3 24 0 CGAAGAAGGG 0.831277 -22 TTTTTCTCGTCGGGGGGGGGGGGGTGGACG 4 12 0 CGGGGGGGGG 0.994255 -72 GTGCCGCATGCTGTGCGCGGT 6 2 0 CTGTGCGCGG 0.925797 -44 GCACAGCATGCGGCACGCGGTGTAGGGGAA 6 16 1 CGGCACGCGG 0.976376 -30 GTGTAGGGGAATGGGAGGGGA 6 35 1 ATGGGAGGGG 0.960149 -11 ********** Masking position 9 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 0.99157 -163 CTTTGGATCCAGGCCCTGTGTGTATCTGGC 1 47 1 AGGCCCTGTG 0.98814 -148 CGGGCGACACAGACTCCTAGTTCTTGTATT 1 117 1 AGACTCCTAG 0.890455 -78 AATAAGCGGCAGTCCATGTGGGGAAGGGAG 2 40 1 AGTCCATGTG 0.933988 -88 GAGTGTTCTGAGACTGTTTGCGCTCCTCGT 2 92 0 AGACTGTTTG 0.964645 -36 CCATTCCCCTACACCGCGTGCCGCATGCTG 6 19 0 ACACCGCGTG 0.960216 -27 ********** Masking position 1 Map Score: 3.06835 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 115 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GAAACCCTCTCGCCGGCATCGTAACGCAA 1 10 1 TCGCCGGCAT 0.902758 -185 GAACACTCCATCGCCCCGTGCACGCTGGGA 1 83 0 TCGCCCCGTG 0.929284 -112 GGAGTCTGTGTCGCCCGTGTAGAACACTCC 1 104 0 TCGCCCGTGT 0.968455 -91 TACAGTTTTTACGTCGGTTTTTGCACAGAA 1 145 0 ACGTCGGTTT 0.909187 -50 GCGCTCGTCTTCCTCGGAAGACTGTGGCAA 2 11 1 TCCTCGGAAG 0.794141 -117 TTTGCGCTCCTCGTCTGTTGTCTGATCACC 2 76 0 TCGTCTGTTG 0.956779 -52 GTTCTTTTTCTCGTCGGGGGGGGGGGGGTG 4 16 0 TCGTCGGGGG 0.989365 -68 ACCCATACCGTTGCCGGTTGTCCAGTAAAT 4 52 1 TTGCCGGTTG 0.961986 -32 ********** Masking position 5 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