AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iompR_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 TP0135 300 T. pallidum predicted coding region TP0135 Motif number 1 CCCGTTAGCGCCCAACATGCAGCCGCGTTTCTG 1 12 0 CCACATGCGC 0.941976 -289 TGGTTTACACCCAAGAGGTCAGCGGTTCAAACC 1 43 0 CCGAGGTCGC 0.990082 -258 TGGGTGTAAACCAAGCGCTCTGCCCGCTGAGCT 1 63 1 CCGCGCTCGC 0.998237 -238 GCGCTCTGCCCGCTGAGCTAAGCGCCCTGCGTA 1 77 1 CGGAGCTAGC 0.948325 -224 CGCGCTTGTGCGTCGCGCGCGGTCGCATACCAA 1 115 0 CGGCGCGCGT 0.998172 -186 CACAAGCGCGCCGTGCACGCAGTGCCTGTACCG 1 138 1 CCGCACGCGT 0.998698 -163 GTCGGGGTATCATGGAAGGCGGTACAGGCACTG 1 157 0 CAGAAGGCGT 0.982965 -144 GATACCCCGACASTGCGCGACGCACAAGCGCGA 1 179 1 CAGCGCGAGC 0.991511 -122 ACAAGCGCGACCGTGCACGCAGTGCCTGTACCG 1 202 1 CCGCACGCGT 0.998698 -99 GTCGGGGTATCATGGAAGGCGGTACAGGCACTG 1 221 0 CAGAAGGCGT 0.982965 -80 GATACCCCGACACTGCGCGGCGCGCAACACGAT 1 243 1 CAGCGCGGGC 0.989917 -58 CTGGGCATGCCGCCGAATGCAGTACATCGTGTT 1 268 0 CGGAATGCGT 0.968678 -33 CGGCGGCATGCCCAGGACTCGGCGG 1 286 1 CCGGACTCGC 0.985472 -15 ** ****** ** Masking position 1 Map Score: 33.6224 Number of sites scoring better than the average of aligned sites = 1532 Number in coding regions = 1418 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GCAGAAACGCGGCTGCATGTTGGGC 1 5 1 AAACGCGGCG 0.964984 -296 TTACACCCAAGAGGTCAGCGGTTCAAACCCG 1 41 0 GAGGTCAGCG 0.945239 -260 TGTAAACCAAGCGCTCTGCCCGCTGAGCTAA 1 67 1 GCGCTCTGCC 0.949362 -234 TCTGCCCGCTGAGCTAAGCGCCCTGCGTATT 1 81 1 GAGCTAAGCC 0.560234 -220 CTTGTGCGTCGCGCGCGGTCGCATACCAAAA 1 113 0 GCGCGCGGTG 0.996701 -188 CGACGCACAAGCGCGCCGTGCACGCAGTGCC 1 133 1 GCGCGCCGTC 0.547251 -168 GGGTATCATGGAAGGCGGTACAGGCACTGCG 1 155 0 GAAGGCGGTC 0.984146 -146 CCCCGACASTGCGCGACGCACAAGCGCGACC 1 183 1 GCGCGACGCC 0.800836 -118 CGCGACGCACAAGCGCGACCGTGCACGCAGT 1 194 1 AAGCGCGACG 0.780442 -107 GCGCGACCGTGCACGCAGTGCCTGTACCGCC 1 206 1 GCACGCAGTC 0.72779 -95 GGGTATCATGGAAGGCGGTACAGGCACTGCG 1 219 0 GAAGGCGGTC 0.984146 -82 ACATCGTGTTGCGCGCCGCGCAGTGTCGGGG 1 247 0 GCGCGCCGCC 0.523616 -54 GCATGCCGCCGAATGCAGTACATCGTGTTGC 1 266 0 GAATGCAGTC 0.868784 -35 GGCATGCCCAGGACTCGGCGG 1 290 1 GGACTCGGCG 0.941298 -11 ********* * Masking position 8 Map Score: 30.5587 Number of sites scoring better than the average of aligned sites = 3388 Number in coding regions = 3121 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 GCAGAAACGCGGCTGCATGTT 1 2 1 CAGAAACGCG 0.905557 -299 ACGCGGCTGCATGTTGGGCGCTAACGGGTT 1 17 1 ATGTTGGGCG 0.946733 -284 TTGGGTGTAAACCAAGCGCTCTGCCCGCTG 1 62 1 ACCAAGCGCT 0.915711 -239 CCAAAACAATACGCAGGGCGCTTAGCTCAG 1 89 0 ACGCAGGGCG 0.983701 -212 GCGCTTGTGCGTCGCGCGCGGTCGCATACC 1 117 0 GTCGCGCGCG 0.938029 -184 GCGCGCGACGCACAAGCGCGCCGTGCACGC 1 128 1 CACAAGCGCG 0.975827 -173 TCGGGGTATCATGGAAGGCGGTACAGGCAC 1 159 0 ATGGAAGGCG 0.935132 -142 TGATACCCCGACASTGCGCGACGCACAAGC 1 178 1 ACASTGCGCG 0.970313 -123 STGCGCGACGCACAAGCGCGACCGTGCACG 1 191 1 CACAAGCGCG 0.975827 -110 CACAAGCGCGACCGTGCACGCAGTGCCTGT 1 201 1 ACCGTGCACG 0.910386 -100 TCGGGGTATCATGGAAGGCGGTACAGGCAC 1 223 0 ATGGAAGGCG 0.935132 -78 TGATACCCCGACACTGCGCGGCGCGCAACA 1 242 1 ACACTGCGCG 0.956508 -59 GCAGTACATCGTGTTGCGCGCCGCGCAGTG 1 253 0 GTGTTGCGCG 0.943699 -48 ********** Masking position 9 Map Score: 18.6539 Number of sites scoring better than the average of aligned sites = 4451 Number in coding regions = 4172 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 4 AGAAACGCGGCTGCATGTTGGGCGCTAACG 1 13 1 CTGCATGTTG 0.783989 -288 ACCAAGCGCTCTGCCCGCTGAGCTAAGCGC 1 72 1 CTGCCCGCTG 0.549127 -229 GCTAAGCGCCCTGCGTATTGTTTTGGTATG 1 93 1 CTGCGTATTG 0.975857 -208 GGTACAGGCACTGCGTGCACGGCGCGCTTG 1 140 0 CTGCGTGCAC 0.666821 -161 GGTACAGGCACTGCGTGCACGGTCGCGCTT 1 204 0 CTGCGTGCAC 0.666821 -97 TACCCCGACACTGCGCGGCGCGCAACACGA 1 245 1 CTGCGCGGCG 0.782031 -56 GAATGCAGTACATCGTGTTGCGCGCCGCGC 1 257 0 CATCGTGTTG 0.895592 -44 ********** Masking position 4 Map Score: 10.0609 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 780 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 ********** No masking Map Score: 7.91135e-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 6 ********** No masking Map Score: 7.91135e-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 7 ********** No masking Map Score: 7.91135e-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