AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -itrpR_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 TP0708 65 T. pallidum predicted coding region TP0708 #2 TP0823 300 desulfoferrodoxin (rbo) #3 TP0943 48 flagellar protein (fliS) #4 TP0944 170 conserved hypothetical protein #5 TP0945 151 ribulose-phosphate 3-epimerase (cfxE) Motif number 1 GTCAAGGACCTGTTTCCAAGCGTGTAGTGTGAGCT 1 10 0 TGTTCGCGGA 0.996846 -56 AAATGGTCAAGGTATACTCGTGCGTAGCACAGGCTC 2 99 1 GGTTCGTGGA 0.980988 -202 GTTTACTGAATGCGTACAGGTGGGTGACGCTTTACC 2 146 1 TGCTCGTGGG 0.993664 -155 TCTGCGGGGCTGTGCTCTGGCGCGGGCGGTTTCCGC 2 212 1 TGTCCGCGGG 0.9938 -89 ACGCCTGTCGTGCCTCCGCGTGCGGAAACCGCCCGC 2 233 0 TGCTCGTGGA 0.990558 -68 GGTCTGATTTTGTTCTCGTGCGGACGCCTGTCGTGC 2 256 0 TGTCCGCGAG 0.95613 -45 GGTGTTCAGGTGTAAGGAGACCCTGT 4 1 1 GGTTCGTGAG 0.941431 -170 CTAGAGCGCTTGTTTTTCTGCGGGGATACTGCTTCT 4 50 1 TGTTTGCGGA 0.979757 -121 TGCTGCGTGGTGCTTGCACGCGACAGTGGTTGTTCG 4 109 1 TGCTCGCGCG 0.982967 -62 CACGCGACAGTGGTTGTTCGTGCAAGTTATGGTAAT 4 125 1 TGGTTGTGAG 0.74149 -46 GACGGGGTCAGCCTACCCGCGGGAAGGATATTTTT 5 10 1 AGCTCGCGGA 0.97672 -142 CCTGTAAATATGGATACTGGCGTGAACAACCCCAAA 5 98 0 TGGTCGCGGA 0.989252 -54 GTGCTCGATTTGTTTGCTAGCATGGACCT 5 133 1 TGTTCGCAGA 0.899304 -19 *** * * *** * * Masking position 10 Map Score: 25.4739 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 494 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 GTTTCGTCAAGGACCTGTTTCCAAGCGTGTA 1 20 0 GGCCTGTTTC 0.974396 -46 GAGCTAGTCTGCAGCTGGTTTTTTGTTTCGT 1 44 0 GCGCTGGTTT 0.96532 -22 GGAGCTAGTCTGCAGCTGGTT 1 55 0 GGGCTAGTCT 0.969204 -11 AGGCTCGGAAGGAGCGAGTTTACTGAATGCG 2 129 1 GGGCGAGTTT 0.966138 -172 CTTTACCCACGGACCTGATTTAGGTAGAATC 2 175 1 GGCCTGATTT 0.95635 -126 GCCCCGCAGAGGCGCTGATTCTACCTAAATC 2 191 0 GGGCTGATTC 0.964115 -110 GCGCCTCTGCGGGGCTGTGCTCTGGCGCGGG 2 207 1 GGGCTGTGCT 0.930607 -94 TGCTCTGGCGCGGGCGGTTTCCGCACGCGGA 2 224 1 CGGCGGTTTC 0.807331 -77 CTCCTATGTTGGTCTGATTTTGTTCTCGTGC 2 271 0 GGCTGATTTT 0.799942 -30 GGTCGATATTGGCGCTATTGTTTTGCTACGA 3 17 1 GGGCTATTGT 0.926493 -32 GGGTACTAGAGCGCTTGTTTTTCTGCGGGGA 4 45 1 GCCTTGTTTT 0.79596 -126 GCTATGCATAGGGGTTAGTTTTTGCTGCGTG 4 87 1 GGGTTAGTTT 0.942018 -84 TTGAATGTTTGGGGTTGTTCACGCCAGTATC 5 91 1 GGGTTGTTCA 0.774724 -61 ** ******** Masking position 9 Map Score: 10.1501 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 707 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 ACGCTTGGAAACAGGTCCTTGACGAAACAA 1 23 1 ACAGGTCCTT 0.974632 -43 CGTGCGTAGCACAGGCTCGGAAGGAGCGAG 2 117 1 ACAGGCTCGG 0.963732 -184 CTGAATGCGTACAGGTGGGTGACGCTTTAC 2 151 1 ACAGGTGGGT 0.857635 -150 TCTACCTAAATCAGGTCCGTGGGTAAAGCG 2 173 0 TCAGGTCCGT 0.95353 -128 TTAGGTAGAATCAGCGCCTCTGCGGGGCTG 2 194 1 TCAGCGCCTC 0.887456 -107 GCGCCAGAGCACAGCCCCGCAGAGGCGCTG 2 205 0 ACAGCCCCGC 0.979919 -96 GGGGCTGTGCTCTGGCGCGGGCGGTTTCCG 2 217 1 TCTGGCGCGG 0.844771 -84 CCTATGAGCGACAGGGTCTCCTTACACCTG 4 17 0 ACAGGGTCTC 0.960951 -154 CCGCAGAAAAACAAGCGCTCTAGTACCCTA 4 43 0 ACAAGCGCTC 0.884555 -128 CTGCGGGGATACTGCTTCTTGCTATGCATA 4 67 1 ACTGCTTCTT 0.642718 -104 ATCCATATTTACAGGTGCTCGATTTGTTTG 5 119 1 ACAGGTGCTC 0.986934 -33 ********** Masking position 2 Map Score: 8.51335 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 767 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 AGCTCACACTACACGCTTGGAAAC 1 2 1 GCTCAACTAC 0.903838 -64 CAGGAGCGTAGCGGAAACTACCCAAATGGTCAA 2 76 1 GCGGAACTCC 0.980479 -225 CTACCCAAATGGTCAAGGTATACTCGTGCGTAG 2 93 1 GGTCAGGTAC 0.807761 -208 CGTACAGGTGGGTGACGCTTTACCCACGGACCT 2 158 1 GGTGAGCTAC 0.954755 -143 GCCTCCGCGTGCGGAAACCGCCCGCGCCAGAGC 2 225 0 GCGGAACCCC 0.939134 -76 GTTTCCGCACGCGGAGGCACGACAGGCGTCCGC 2 240 1 GCGGAGCAAC 0.987169 -61 GACCAACATAGGAGATGCTTGCC 2 288 1 GGAGAGCTCC 0.971745 -13 GGTGTTCAGGTGTAAGGAGACCCTGTCGCTCA 4 10 1 GTGTAGGACC 0.670995 -161 GCACCACGCAGCAAAAACTAACCCCTATGCATA 4 89 0 GCAAAACTCC 0.717061 -82 CCACTGTCGCGTGCAAGCACCACGCAGCAAAAA 4 105 0 GTGCAGCAAC 0.933348 -66 TCCTTCCCGCGGGTAGGCTGACCCCGTC 5 6 0 GGGTAGCTCC 0.704536 -146 ATCGGTTTAGGCGCAAATAAAACAGGATAAGCA 5 48 1 GCGCAATAAC 0.660673 -104 AAATAAAACAGGATAAGCAGGACACTGTCTTGA 5 62 1 GGATAGCAAC 0.876865 -90 ***** *** ** Masking position 5 Map Score: 9.07187 Number of sites scoring better than the average of aligned sites = 1092 Number in coding regions = 1009 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 CTTTTCTTTCCGCAGGGCACGTAGAAACTC 2 28 1 CGCAGGGCAC 0.982461 -273 AATCCAAGCTGGCAGGAGCGTAGCGGAAAC 2 64 1 GGCAGGAGCG 0.987228 -237 GCACAGGCTCGGAAGGAGCGAGTTTACTGA 2 125 1 GGAAGGAGCG 0.888363 -176 AGCACAGCCCCGCAGAGGCGCTGATTCTAC 2 198 0 CGCAGAGGCG 0.968859 -103 CCCGCGCCAGAGCACAGCCCCGCAGAGGCG 2 208 0 AGCACAGCCC 0.915613 -93 GCTGTGCTCTGGCGCGGGCGGTTTCCGCAC 2 220 1 GGCGCGGGCG 0.892461 -81 CGCACGCGGAGGCACGACAGGCGTCCGCAC 2 245 1 GGCACGACAG 0.974774 -56 GACAGGCGTCCGCACGAGAACAAAATCAGA 2 260 1 CGCACGAGAA 0.819945 -41 ATGTTTGTAAAGCAGAGCACTT 4 159 1 AGCAGAGCAC 0.909519 -12 AAACAGGATAAGCAGGACACTGTCTTGAAT 5 67 1 AGCAGGACAC 0.957155 -85 ********** Masking position 2 Map Score: 9.80302 Number of sites scoring better than the average of aligned sites = 1189 Number in coding regions = 1083 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 ********** No masking Map Score: -1.51102e-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 7 ********** No masking Map Score: -1.51102e-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 8 ********** No masking Map Score: -1.51102e-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