AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_tpal_reg_100.orf -o00330_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 TP0055 206 T. pallidum predicted coding region TP0055 #2 TP0162 174 Holliday junction DNA helicase (ruvB) #3 TP0223 267 aspartate aminotransferase (tpaaT) #4 TP0568 121 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase (eda) #5 TP0797 50 1-pyrroline-5-carboxylate reductase (proC) #6 TP0798 32 methionyl-tRNA synthetase (metG) #7 TP0831 22 arginyl-tRNA synthetase (argS) #8 TP0832 66 T. pallidum predicted coding region TP0832 Motif number 1 AATTGGTTTTGCAGTGCGTGTTGACGTGCGT 1 55 1 GCGTGCGTGT 0.861703 -152 AGTGCGTGTTGACGTGCGTCCGCGTGTGCCT 1 67 1 GAGTGCGTCC 0.982796 -140 TGCGTTCTCAGAGGCACACGCGGACGCACGT 1 78 0 GAGCACACGC 0.929661 -129 CATCACGTAGGAGTTGCCCGC 1 196 1 GATTGCCCGC 0.960012 -11 TGTAGCTCGAGAGGTCCGCGCCAGAGTGCCG 2 100 0 GAGTCCGCGC 0.990904 -75 TAAGCAGCTACAGTTGCGCCCTCTT 2 160 1 CATTGCGCCC 0.837502 -15 CATCCGTGTGGCTGCGCGGGCTTGTGTGCTC 3 44 1 GCGCGCGGGC 0.985384 -224 TCACAGTGTAGACACGCCCCCTGACCCTGTC 3 112 0 GAACGCCCCC 0.867507 -156 CCTCTCTGAAGGCGCGCGTGCGTTAAACGCT 3 151 1 GGGCGCGTGC 0.98869 -117 AAGGAACGGTGGTGCACGCGCTGTTATCTCC 3 189 1 GGGCACGCGC 0.983893 -79 ATCTCCTCTTGGTTTGCGCGCGTATTTTCCC 3 214 1 GGTTGCGCGC 0.986304 -54 GACACCACATGCAGTGCACCCGCCTAAGCTA 4 68 0 GCGTGCACCC 0.976024 -54 TGTCTGAAAAGATGTCCGCGGGCAAGAGGAG 4 95 1 GAGTCCGCGG 0.914236 -27 GCTGCGCTCCCCCTATCCGAC 5 40 0 GCGCGCTCCC 0.966081 -11 ** ******** Masking position 7 Map Score: 18.0058 Number of sites scoring better than the average of aligned sites = 3044 Number in coding regions = 2836 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 GAGTAGGGAAAGTAGACGGG 1 1 1 GAGTAGGGAA 0.965576 -206 CTCTGTTGTCGCGTAGGAAAACTTGTAAAG 1 114 1 GCGTAGGAAA 0.957925 -93 GAACGGGGTCGAGGGTAAAAAAAAAAGACG 1 157 0 GAGGGTAAAA 0.85659 -50 CGCAAACCAAGAGGAGATAACAGCGCGTGC 3 202 0 GAGGAGATAA 0.96694 -66 CAACAATCCCGTGGGGAAAATACGCGCGCA 3 228 0 GTGGGGAAAA 0.929557 -40 CCGCGGGCAAGAGGAGGGAATT 4 110 1 GAGGAGGGAA 0.986256 -12 GTTTAAATCAGAGTAGGAAACGCT 6 19 1 GAGTAGGAAA 0.971292 -14 TTTTTGCAAGGCGGGGATAAGGGACGT 8 50 1 GCGGGGATAA 0.950717 -17 ********** Masking position 9 Map Score: 9.039 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 187 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TGTGAGGTATGGAACCTACAGCGCAATTGGT 1 31 1 GGAACTACAG 0.846414 -176 CACGCGGACGCACGTCAACACGCACTGCAAA 1 62 0 CACGCAACAC 0.922589 -145 AGTTTTCCTACGCGACAACAGAGCAGGCTGC 1 106 0 CGCGCAACAG 0.994422 -101 TCCTCGCATAAGCAGCTACAGTTGCGCCCTC 2 152 1 AGCACTACAG 0.942052 -23 CACAAGCCCGCGCAGCCACACGGATGAGCTT 3 39 0 CGCACCACAC 0.964829 -229 GAATCGACAGCCCGACTTCAGAGCACACAAG 3 64 0 CCCGCTTCAG 0.969676 -204 GGTCAGGGGGCGTGTCTACACTGTGAGACAT 3 117 1 CGTGCTACAC 0.950296 -151 TTAACGCACGCGCGCCTTCAGAGAGGTCCAT 3 146 0 CGCGCTTCAG 0.989057 -122 GCGTATAACACCAATCAACAGGAAAACG 4 8 0 CCAACAACAG 0.880145 -114 **** ****** Masking position 10 Map Score: 6.86039 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 279 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 TGCTCTGTTGTCGCGTAGGAAAACTTGTAA 1 112 1 TCGCGTAGGA 0.986408 -95 CCTGAATTCATCACGTAGGAGTTGCCCGC 1 188 1 TCACGTAGGA 0.987772 -19 AAGTAGCGGATCACGCAGGAAACGTCAATT 2 43 1 TCACGCAGGA 0.886306 -132 TGTAACCATTTGCCGCAGGAAGCTCATCCG 3 20 1 TGCCGCAGGA 0.87883 -248 TGTGCAACAATCCCGTGGGGAAAATACGCG 3 232 0 TCCCGTGGGG 0.828853 -36 ********** Masking position 1 Map Score: 5.51361 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 38 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GCAACTGTAGCTGCTTATGCGAGGAAGATC 2 147 0 CTGCTTATGC 0.906722 -28 GCGTTAAACGCTGCTCTTGAAGGAACGGTG 3 170 1 CTGCTCTTGA 0.968672 -98 GAGGAGATAACAGCGCGTGCACCACCGTTC 3 192 0 CAGCGCGTGC 0.94016 -76 GCGCTGTTATCTCCTCTTGGTTTGCGCGCG 3 206 1 CTCCTCTTGG 0.962948 -62 GTGTTATACGCAGATCTTGATTTTTGATCA 4 28 1 CAGATCTTGA 0.775425 -94 TCTTTTCAGACACCACATGCAGTGCACCCG 4 77 0 CACCACATGC 0.947567 -45 AATTCCCTCCTCTTGCCCGCGGACAT 4 106 0 CTCCTCTTGC 0.991255 -16 TGCCTCACCTCATACCAAGCTA 7 8 0 CACCTCATAC 0.906722 -15 ********** Masking position 8 Map Score: 4.28583 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 600 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 GAGTAGGGAAAGTAGACGGGTGTGAGGT 1 6 1 GGGAAAAGAG 0.91742 -201 AACACGCACTGCAAAACCAATTGCGCTGTAGGT 1 44 0 GCAAAAAATG 0.968494 -163 GGGGTCGAGGGTAAAAAAAAAAGACGCTTTGTG 1 150 0 GTAAAAAAAG 0.949084 -57 TACCCTTTCAGGAAAAGAAAACGGCACTCTGGC 2 79 1 GGAAAAAAAG 0.989825 -96 GCTTATGCGAGGAAGATCAAATGCTTCTTTATC 2 132 0 GGAAGAAAAG 0.957856 -43 AAATACGCGCGCAAACCAAGAGGAGATAACAGC 3 208 0 GCAAACAGAG 0.91742 -60 TATCCGACACGGAAAACCAAATGCTCTGTGAAT 5 15 0 GGAAAAAAAG 0.989825 -36 AAAAATATAGGCAAAAAGAAAATAAAGCAGCCG 8 21 0 GCAAAAAAAT 0.905091 -46 TCCCCGCCTTGCAAAAAATATAGGCAAAAAGAA 8 34 0 GCAAAATATG 0.828939 -33 ****** *** * Masking position 4 Map Score: 7.60217 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 106 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 GAGTAGGGAAAGTAGACGGGTGTGAGGT 1 9 1 AAAGTAGACG 0.87398 -198 TGCCTCTGAGAACGCAGCCTGCTCTGTTGT 1 93 1 AACGCAGCCT 0.941431 -114 CTACGTGATGAATTCAGGCGAACGGGGTCG 1 176 0 AATTCAGGCG 0.776938 -31 TTGATGCATCAAAGTAGCGGATCACGCAGG 2 32 1 AAAGTAGCGG 0.954876 -143 CGTTCCTTCAAGAGCAGCGTTTAACGCACG 3 167 0 AGAGCAGCGT 0.973818 -101 TGTTGCACAGAATGCAGAGGCGCGG 3 253 1 AATGCAGAGG 0.954638 -15 TCAAAAATCAAGATCTGCGTATAACACCAA 4 25 0 AGATCTGCGT 0.596234 -97 CACCACATGCAGTGCACCCGCCTAAGCTAA 4 67 0 AGTGCACCCG 0.855481 -55 AGTCTTGTTTAAATCAGAGTAGGAAACGCT 6 13 1 AAATCAGAGT 0.828495 -20 AAAAGAAAATAAAGCAGCCGATATTGGGTC 8 11 0 AAAGCAGCCG 0.991897 -56 ********** Masking position 1 Map Score: 5.02585 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 655 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 GAGTAGGGAAAGTAGACGGGTGTGA 1 6 1 GGGAAAGTAG 0.776484 -201 CAGGCGAACGGGGTCGAGGGTAAAAAAAAA 1 162 0 GGGTCGAGGG 0.965485 -45 TAAATTGACAGGGTCAGGGGGCGTGTCTAC 3 106 1 GGGTCAGGGG 0.994432 -162 TGCTCTTGAAGGAACGGTGGTGCACGCGCT 3 181 1 GGAACGGTGG 0.949775 -87 AGATGTCCGCGGGCAAGAGGAGGGAATT 4 104 1 GGGCAAGAGG 0.927357 -18 TTTCCGTGTCGGATAGGGGGAGCGCAGC 5 33 1 GGATAGGGGG 0.988567 -18 TGCAAGGCGGGGATAAGGGACGT 8 54 1 GGATAAGGGA 0.902796 -13 ********** Masking position 2 Map Score: 3.54375 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 320 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 GGGAAAGTAGACGGGTGTGAGGTATGGAAC 1 16 1 ACGGGTGTGA 0.944445 -191 TGACGTGCGTCCGCGTGTGCCTCTGAGAAC 1 76 1 CCGCGTGTGC 0.983049 -131 GTGACACTCCTTGGGTGAATTTTGATGC 2 9 1 CCTTGGGTGA 0.904516 -166 GTGATCCGCTACTTTGATGCATCAAAATTC 2 27 0 ACTTTGATGC 0.579848 -148 GGCTGCGCGGGCTTGTGTGCTCTGAAGTCG 3 53 1 GCTTGTGTGC 0.949405 -215 CTGTCGATTCACTGGGGTGCATAAATTGAC 3 85 1 ACTGGGGTGC 0.991182 -183 CTCTCTGAAGGCGCGCGTGCGTTAAACGCT 3 152 1 GCGCGCGTGC 0.934274 -116 TCTTGAAGGAACGGTGGTGCACGCGCTGTT 3 184 1 ACGGTGGTGC 0.977523 -84 ACATTAGCTTAGGCGGGTGCACTGCATGTG 4 64 1 AGGCGGGTGC 0.96978 -58 ********** Masking position 8 Map Score: 7.76251 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 824 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 10 CCTCTGAGAACGCAGCCTGCTCTGTTGTCG 1 95 1 CGCAGCCTGC 0.98223 -112 AAAAAAAAGACGCTTTGTGCAAGCTCTTTA 1 139 0 CGCTTTGTGC 0.905537 -68 ATCACGTAGGAGTTGCCCGC 1 197 1 AGTTGCCCGC 0.94625 -10 GAAAAATTGACGTTTCCTGCGTGATCCGCT 2 47 0 CGTTTCCTGC 0.994215 -128 CACACGGATGAGCTTCCTGCGGCAAATGGT 3 24 0 AGCTTCCTGC 0.989168 -244 AGCGTTTCCTACTCTGATTTAA 6 21 0 CGTTTCCTAC 0.963753 -12 ********** Masking position 2 Map Score: 4.92522 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 355 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 ********** No masking Map Score: 1.37435e-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 12 ********** No masking Map Score: 1.37435e-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 13 ********** No masking Map Score: 1.37435e-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