AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_tpal_reg_300.orf -o00330_tpal_300.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 TP0054 170 conserved hypothetical protein #2 TP0055 206 T. pallidum predicted coding region TP0055 #3 TP0162 174 Holliday junction DNA helicase (ruvB) #4 TP0218 300 sigma factor SigB regulation protein, putative #5 TP0220 28 anti-sigma F factor antagonist (spoIIAA-1) #6 TP0223 267 aspartate aminotransferase (tpaaT) #7 TP0568 121 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase (eda) #8 TP0569 24 aminopeptidase P #9 TP0570 26 T. pallidum predicted coding region TP0570 #10 TP0797 50 1-pyrroline-5-carboxylate reductase (proC) #11 TP0798 32 methionyl-tRNA synthetase (metG) #12 TP0831 22 arginyl-tRNA synthetase (argS) #13 TP0832 66 T. pallidum predicted coding region TP0832 Motif number 1 CAGACATTTTTACGCCCGCCGCAATTGAGAATTCAA 1 61 0 TACGCCGCAT 0.919479 -110 TTCCATACCTCACACCCGTCTACTTTCCCTACTC 2 9 0 CACACCGTCT 0.750675 -198 CACGTCAACACGCACTGCAAAACCAATTGCGCTGTA 2 47 0 CGCACGCACA 0.866274 -160 CGTTCTCAGAGGCACACGCGGACGCACGTCAACACG 2 71 0 GGCACCGCCA 0.975412 -136 TCGAGAGGTCCGCGCCAGAGTGCCGTTTTCTTTTCC 3 89 0 CGCGCAGACT 0.895883 -86 GTAGTTGGAATACGCACCAATACCTTT 4 2 0 TACGCCCACT 0.931613 -299 GCTAAGAGCGCACGCGACCGTGCAGAAAGCGTAGTT 4 32 0 CACGCACCCA 0.973101 -269 AAAGAAACACCACGCACGCGAGAATAATCCTTTTAC 4 157 0 CACGCCGCAA 0.978681 -144 CTCATCCTGCGACACACGAGAAAGAAACACCACGCA 4 177 0 GACACCGAAA 0.610356 -124 TCAGATAGCACACGCACCCATCACGATGAAGCCAAC 4 212 0 CACGCCCCAA 0.981805 -89 ACGGCGCTCCCGAACTTTTCCTCATTTC 5 11 0 GGCGCCCCCT 0.990419 -18 CACACAAGCCCGCGCAGCCACACGGATGAGCTTCCT 6 36 0 CGCGCGCCCA 0.98806 -232 ACAGTGTAGACACGCCCCCTGACCCTGTCAATTTAT 6 105 0 CACGCCCCCT 0.994248 -163 GCGTTTAACGCACGCGCGCCTTCAGAGAGGTCCATG 6 145 0 CACGCCGCCA 0.995308 -123 TAACAGCGCGTGCACCACCGTTCCTTCAAGAGCAGC 6 179 0 TGCACACCCT 0.796671 -89 GTGGGGAAAATACGCGCGCAAACCAAGAGGAGATAA 6 212 0 TACGCCGCCA 0.985455 -56 CCACATGCAGTGCACCCGCCTAAGCTAATGTCCTTT 7 59 0 TGCACCGCAT 0.840481 -63 CGCTCTTGGCGCGGCAACGCACACAC 9 4 0 GGCGCGCACA 0.89357 -23 GCTGCGCTCCCCCTATCCGACACGGAAAAC 10 31 0 CGCTCCCCCA 0.957514 -20 ***** *** * * Masking position 5 Map Score: 27.7705 Number of sites scoring better than the average of aligned sites = 2401 Number in coding regions = 2235 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 AAGTATACTACCCTGTGCCCGCACTCAGGAGG 1 21 0 CCTGGCCCGC 0.996216 -150 CACACAAGACACAGAGCCCTGCAGACAGACAT 1 90 0 ACGACCCTGC 0.708009 -81 AGGTTCCATACCTCACACCCGTCTACTTTCCC 2 16 0 CCCAACCCGT 0.901648 -191 GTGCGTGTTGACGTGCGTCCGCGTGTGCCTCT 2 68 1 ACTGGTCCGC 0.905509 -139 TTTTTTTTACCCTCGACCCCGTTCGCCTGAAT 2 163 1 CCCGCCCCGT 0.99122 -44 CTAAGAGCGCACGCGACCGTGCAGAAAGCGTA 4 35 0 ACCGCCGTGC 0.881129 -266 TCCTTTTACCCCACGCGCCCCTTTCTGTAGCC 4 134 0 CCCGGCCCCT 0.916675 -167 GGAAGCTCATCCGTGTGGCTGCGCGGGCTTGT 6 37 1 CCTGGGCTGC 0.891447 -231 ACTTCAGAGCACACAAGCCCGCGCAGCCACAC 6 49 0 ACCAGCCCGC 0.984339 -219 TAGACACGCCCCCTGACCCTGTCAATTTATGC 6 103 0 CCTGCCCTGT 0.944739 -165 GCAGCGTTTAACGCACGCGCGCCTTCAGAGAG 6 152 0 ACCAGCGCGC 0.873534 -116 CCGCGCCTCTGCATTCTGTGCA 6 256 0 CCCGCTCTGC 0.945422 -12 ACACCACATGCAGTGCACCCGCCTAAGCTAAT 7 66 0 CATGACCCGC 0.745845 -56 AATTCCCTCCTCTTGCCCGCGGACATCTTT 7 102 0 CCCTGCCCGC 0.979892 -20 ACGTCCCTTATCCCCGCCTTGCAAAAA 13 50 0 CCTACCCCGC 0.9877 -17 ** ** ****** Masking position 2 Map Score: 20.4776 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 839 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 GATGAAACCTCCTCCTGAGTGCGGGCACAGG 1 9 1 CCTCCTGAGG 0.941147 -162 AACGGATTTCCTACGTCTCTGTTAGGT 1 154 0 GTTCCTACGC 0.846371 -17 CTCTTTACAAGTTTTCCTACGCGACAACAGAGC 2 113 0 GTTCCTACGG 0.90702 -94 AAAAAAAAGACGCTTTGTGCAAGCTCTTTACAA 2 136 0 CTTTGTGCAG 0.816596 -71 GCGGGCAACTCCTACGTGATGAATTCAG 2 189 0 CCTCCTACGG 0.961778 -18 GAAAAATTGACGTTTCCTGCGTGATCCGCTACT 3 44 0 CTTCCTGCGG 0.996022 -131 GTGCCGTTTTCTTTTCCTGAAAGGGTACTGAAA 3 73 0 CTTCCTGAAG 0.937335 -102 GCAACTGTAGCTGCTTATGCGAGGAAGATCAAA 3 144 0 CCTTATGCGG 0.849922 -31 ATTCCAACTACGCTTTCTGCACGGTCGCGTGCG 4 27 1 CTTTCTGCAG 0.976673 -274 CCCCACGCGCCCCTTTCTGTAGCCTACTTGAGA 4 125 0 CTTTCTGTAC 0.629158 -176 ATGAAGCCAACTCATCCTGCGACACACGAGAAA 4 190 0 CATCCTGCGC 0.947273 -111 CACACGGATGAGCTTCCTGCGGCAAATGGTTAC 6 21 0 ATTCCTGCGC 0.910276 -247 CTGACCCTGTCAATTTATGCACCCCAGTGAATC 6 90 0 CTTTATGCAC 0.749478 -178 GCGTGCACCACCGTTCCTTCAAGAGCAGCGTTT 6 175 0 CTTCCTTCAG 0.903058 -93 * ******** * Masking position 8 Map Score: 11.8494 Number of sites scoring better than the average of aligned sites = 1188 Number in coding regions = 1082 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 CGCCGCAATTGAGAATTCAAAGTCCATCAAGT 1 49 0 GAGATCAAAG 0.839061 -122 GTGAGGTATGGAACCTACAGCGCAATTGGTTT 2 32 1 GAACACAGCG 0.801969 -175 AGAGCAGGCTGCGTTCTCAGAGGCACACGCGG 2 86 0 GCGTTCAGAG 0.954229 -121 GTTTTCCTACGCGACAACAGAGCAGGCTGCGT 2 104 0 GCGAACAGAG 0.982743 -103 GACGTTTCCTGCGTGATCCGCTACTTTGATGC 3 37 0 GCGTTCCGCT 0.751559 -138 CATGTAGCTCGAGAGGTCCGCGCCAGAGTGCC 3 101 0 GAGATCCGCG 0.980118 -74 ACGGTCGCGTGCGCTCTTAGCGGAGATTTCTC 4 47 1 GCGCTTAGCG 0.844931 -254 ACTGTGGGAAGAAAACTCAGATAGCACACGCA 4 232 0 GAAATCAGAT 0.445023 -69 AATCGACAGCCCGACTTCAGAGCACACAAGCC 6 62 0 CCGATCAGAG 0.956499 -206 TAACGCACGCGCGCCTTCAGAGAGGTCCATGT 6 144 0 GCGCTCAGAG 0.987084 -124 AAACCAAGAGGAGATAACAGCGCGTGCACCAC 6 197 0 GAGAACAGCG 0.978082 -71 GAAAATACGCGCGCAAACCAAGAGGAGATAAC 6 211 0 GCGCACCAAG 0.794635 -57 GATTGTTGCACAGAATGCAGAGGCGCGG 6 250 1 CAGAGCAGAG 0.740374 -18 GGTGTCTGAAAAGATGTCCGCGGGCAAGAGGA 7 93 1 AAGATCCGCG 0.764535 -29 ACTACGCAGAACACCGATTCAATT 8 7 0 CAGAACCGAT 0.516265 -18 GTGCGTTGCCGCGCCAAGAGCG 9 15 1 GCGCAGAGCG 0.845522 -12 **** ****** Masking position 3 Map Score: 9.96711 Number of sites scoring better than the average of aligned sites = 1423 Number in coding regions = 1326 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 CGTCTTTTTTTTTTACCCTCGACCCCGTTC 2 157 1 TTTTACCCTC 0.821109 -50 AAGCATTTGATCTTCCTCGCATAAGCAGCT 3 139 1 TCTTCCTCGC 0.967585 -36 CGGATGGGCGTTTTCCCCTTCCTCTTGAGA 4 75 0 TTTTCCCCTT 0.897599 -226 GAATAATCCTTTTACCCCACGCGCCCCTTT 4 142 0 TTTACCCCAC 0.893494 -159 GGTAAAAGGATTATTCTCGCGTGCGTGGTG 4 156 1 TTATTCTCGC 0.812802 -145 GCGTGGTGTTTCTTTCTCGTGTGTCGCAGG 4 178 1 TCTTTCTCGT 0.707884 -123 TATCTGAGTTTTCTTCCCACAGTTTAAAAG 4 241 1 TTCTTCCCAC 0.834869 -60 GCTCCCGAACTTTTCCTCATTTC 5 4 0 TTTTCCTCAT 0.857321 -25 TGCGCGCGTATTTTCCCCACGGGATTGTTG 6 228 1 TTTTCCCCAC 0.98508 -40 AATTCCCTCCTCTTGCCCGCGGACATCTTT 7 102 0 TCTTGCCCGC 0.939829 -20 ACGTCCCTTATCCCCGCCTTGCAAAAA 13 50 0 TTATCCCCGC 0.973016 -17 ********** Masking position 1 Map Score: 7.97595 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 380 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 GAGTAGGGAAAGTAGACGGGTGTGAGGT 2 9 1 AAAGTAGACG 0.887591 -198 ACGCGACAACAGAGCAGGCTGCGTTCTCAG 2 98 0 AGAGCAGGCT 0.921271 -109 CTACGTGATGAATTCAGGCGAACGGGGTCG 2 176 0 AATTCAGGCG 0.817229 -31 TTGATGCATCAAAGTAGCGGATCACGCAGG 3 32 1 AAAGTAGCGG 0.929409 -143 CGTTCCTTCAAGAGCAGCGTTTAACGCACG 6 167 0 AGAGCAGCGT 0.947575 -101 TGTTGCACAGAATGCAGAGGCGCGG 6 253 1 AATGCAGAGG 0.944388 -15 CACCACATGCAGTGCACCCGCCTAAGCTAA 7 67 0 AGTGCACCCG 0.83887 -55 AGTCTTGTTTAAATCAGAGTAGGAAACGCT 11 13 1 AAATCAGAGT 0.676297 -20 AAAAGAAAATAAAGCAGCCGATATTGGGTC 13 11 0 AAAGCAGCCG 0.98807 -56 ********** Masking position 6 Map Score: 2.5165 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 439 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 TTGGGGAAACCTAACAGAGACGTAGGAAAT 1 146 1 CTAACAGAGA 0.899642 -25 AGGTATGGAACCTACAGCGCAATTGGTTTT 2 35 1 CCTACAGCGC 0.984361 -172 TTCCTACGCGACAACAGAGCAGGCTGCGTT 2 103 0 ACAACAGAGC 0.970467 -104 GAAATCTCCGCTAAGAGCGCACGCGACCGT 4 47 0 CTAAGAGCGC 0.884109 -254 CGACAGCCCGACTTCAGAGCACACAAGCCC 6 61 0 ACTTCAGAGC 0.916518 -207 CGCACGCGCGCCTTCAGAGAGGTCCATGTC 6 143 0 CCTTCAGAGA 0.860832 -125 CCAAGAGGAGATAACAGCGCGTGCACCACC 6 196 0 ATAACAGCGC 0.950528 -72 ********** Masking position 6 Map Score: 3.05938 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 250 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CGCACTGCAAAACCAATTGCGCTGTAGGTT 2 43 0 AACCAATTGC 0.983069 -164 ATGCGAGGAAGATCAAATGCTTCTTTATCA 3 131 0 GATCAAATGC 0.903398 -44 GTGTTTGTGTAACCATTTGCCGCAGGAAGC 6 13 1 AACCATTTGC 0.958298 -255 TCTTTTCAGACACCACATGCAGTGCACCCG 7 77 0 CACCACATGC 0.966247 -45 CGACACGGAAAACCAAATGCTCTGTGAATA 10 14 0 AACCAAATGC 0.988123 -37 ********** Masking position 5 Map Score: 1.50612 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ********** No masking Map Score: -1.90893e-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 GGATCACGCAGGAAACGTCAATTTTTCAGT 3 50 1 GGAAACGTCA 0.872754 -125 TTCTTTTCCTGAAAGGGTACTGAAAAATTG 3 68 0 GAAAGGGTAC 0.89328 -107 TTCAGGAAAAGAAAACGGCACTCTGGCGCG 3 85 1 GAAAACGGCA 0.818457 -90 CGACCGTGCAGAAAGCGTAGTTGGAATACG 4 24 0 GAAAGCGTAG 0.941856 -277 TTTCTCAAGAGGAAGGGGAAAACGCCCATC 4 73 1 GGAAGGGGAA 0.934788 -228 GTAGGCTACAGAAAGGGGCGCGTGGGGTAA 4 131 1 GAAAGGGGCG 0.980795 -170 CCATACAAAGGGAACGGTAG 4 291 1 GGAACGGTAG 0.943459 -10 GAAATGAGGAAAAGTTCGGGAGCGCCGT 5 9 1 GAAAAGTTCG 0.710115 -20 TGCATAAATTGACAGGGTCAGGGGGCGTGT 6 102 1 GACAGGGTCA 0.883909 -166 TGCTCTTGAAGGAACGGTGGTGCACGCGCT 6 181 1 GGAACGGTGG 0.882603 -87 ********** Masking position 4 Map Score: 1.93281 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 379 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 11 ********** No masking Map Score: -1.90893e-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: -1.90893e-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: -1.90893e-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