AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -isoxS_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 TP0135 300 T. pallidum predicted coding region TP0135 #2 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #3 TP0479 111 T. pallidum predicted coding region TP0479 Motif number 1 CCCAACATGCAGCCGCGTTTCTGC 1 1 0 AGCCGGTTGC 0.8364 -300 CAAACCCGTTAGCGCCCAACATGCAGCCGCGTTT 1 15 0 AGCGCCATGC 0.992552 -286 GTGTAAACCAAGCGCTCTGCCCGCTGAGCTAAGC 1 66 1 AGCGCCTCGC 0.997349 -235 TTGGTATGCGACCGCGCGCGACGCACAAGCGCGC 1 115 1 ACCGCCGCGC 0.998499 -186 ACAGGCACTGCGTGCACGGCGCGCTTGTGCGTCG 1 133 0 CGTGCCGCGC 0.997372 -168 CCGTGCACGCAGTGCCTGTACCGCCTTCCATGAT 1 148 1 AGTGCTGCGC 0.9857 -153 TTCCATGATACCCCGACASTGCGCGACGCACAAG 1 173 1 CCCCGCACGC 0.982346 -128 CAAGCGCGACCGTGCACGCAGTGCCTGTACCGCC 1 203 1 CGTGCCGTGC 0.992614 -98 ATACCCCGACACTGCGCGGCGCGCAACACGATGT 1 244 1 ACTGCCGCGC 0.995758 -57 CCGCCGAGTCCTGGGCATGCCGCCGAATGCAGT 1 278 0 CCTGGCACGC 0.985709 -23 TGCCTTAGGGAGCGGAGAGTCTGCCTGCGGCACA 2 11 1 AGCGGGATGC 0.947184 -62 TGCGACCTACACCGGATGTGCCGCAGGCAGACTC 2 27 0 ACCGGTGCGC 0.988047 -46 AACTTGACGGCGCGCGCTAAACGCCTAATAATTG 3 41 0 CGCGCCTCGC 0.997818 -71 GCCCTCCCCCCTTCCTTGCGAAGAGGAGT 3 93 0 CCCCCTTTGC 0.885097 -19 ***** ** *** Masking position 14 Map Score: 34.099 Number of sites scoring better than the average of aligned sites = 2118 Number in coding regions = 1965 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GCTCAGCGGGCAGAGCGCTTGGTTTACACCCA 1 63 0 CAGGCGCTGG 0.608657 -238 AAACAATACGCAGGGCGCTTAGCTCAGCGGGC 1 84 0 CAGGCGCTAG 0.9445 -217 TGGTATGCGACCGCGCGCGACGCACAAGCGCG 1 116 1 CCGGCGCGCG 0.680464 -185 CACAAGCGCGCCGTGCACGCAGTGCCTGTACC 1 138 1 CCGGCACGAG 0.930807 -163 GATACCCCGACASTGCGCGACGCACAAGCGCG 1 179 1 CASGCGCGCG 0.99375 -122 ACAAGCGCGACCGTGCACGCAGTGCCTGTACC 1 202 1 CCGGCACGAG 0.930807 -99 GATACCCCGACACTGCGCGGCGCGCAACACGA 1 243 1 CACGCGCGCG 0.978316 -58 CCGCCGAGTCCTGGGCATGCCGCCGAATGCAG 1 279 0 CTGGCATGCG 0.944662 -22 TGCCTTAGGGAGCGGAGAGTCTGCCTG 2 6 1 TAGGAGCGAG 0.962916 -67 ATTAGGCGTTTAGCGCGCGCCGTCAAGTTTTT 3 46 1 TAGGCGCGCG 0.906026 -66 *** ***** ** Masking position 5 Map Score: 28.1373 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 481 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 CCCAACATGCAGCCGCGTTTCTGC 1 5 0 AGCCGCGTTT 0.835114 -296 ACCAAGCGCTCTGCCCGCTGAGCTAAGCGC 1 72 1 CTGCCCGCTG 0.799517 -229 CTGAGCTAAGCGCCCTGCGTATTGTTTTGG 1 89 1 CGCCCTGCGT 0.872165 -212 TTGTGCGTCGCGCGCGGTCGCATACCAAAA 1 113 0 CGCGCGGTCG 0.823936 -188 ACTGCGTGCACGGCGCGCTTGTGCGTCGCG 1 131 0 CGGCGCGCTT 0.917402 -170 GCGCCGTGCACGCAGTGCCTGTACCGCCTT 1 145 1 CGCAGTGCCT 0.962419 -156 TTGTGCGTCGCGCATGTCGGGGTATCATG 1 176 0 CGCATGTCG 0.379862 -125 CGACCGTGCACGCAGTGCCTGTACCGCCTT 1 209 1 CGCAGTGCCT 0.962419 -92 TTGCGCGCCGCGCAGTGTCGGGGTATCATG 1 240 0 CGCAGTGTCG 0.963294 -61 CCGCCGAGTCCTGGGCATGCC 1 290 0 CGCCGAGTCC 0.839651 -11 CAGGCAGACTCTCCGCTCCCTAAGGCA 2 8 0 CTCCGCTCCC 0.773715 -65 CGGTGTAGGTCGCACCGTTGAAAGAAGGGG 2 47 1 CGCACCGTTG 0.980158 -26 AAACCGCCCCTTCTTTCAACGGTG 2 59 0 CGCCCCTTCT 0.97235 -14 GAGCTCCTCCTTTTTCTAAAGGC 3 4 1 CTCCTCCTTT 0.668438 -108 ATAATTGCCTCGCAGCCTTTAGAAAAAGGA 3 18 0 CGCAGCCTTT 0.924267 -94 GCGTTTAGCGCGCGCCGTCAAGTTTTTCTC 3 51 1 CGCGCCGTCA 0.862445 -61 TCAAGTTTTTCTCACCGTTTGGCATACTCC 3 68 1 CTCACCGTTT 0.936694 -44 GTTTGGCATACTCCTCTTCGCAAGGAAGGG 3 84 1 CTCCTCTTCG 0.715298 -28 GCCCTCCCCCCTTCCTTGCGAAG 3 99 0 CTCCCCCCTT 0.885793 -13 ********** Masking position 1 Map Score: 23.2891 Number of sites scoring better than the average of aligned sites = 4581 Number in coding regions = 4192 Number in noncoding regions = 389 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 4 CAGGCACTGCGTGCACGGCGCGCTTGTGCG 1 136 0 GTGCACGGCG 0.94231 -165 TCGGGGTATCATGGAAGGCGGTACAGGCAC 1 159 0 ATGGAAGGCG 0.995079 -142 TGCGTCGCGCATGTCGGGGTATCATGGAA 1 173 0 ATGTCGGGG 0.961137 -128 TCGGGGTATCATGGAAGGCGGTACAGGCAC 1 223 0 ATGGAAGGCG 0.995079 -78 CGCGCCGCGCAGTGTCGGGGTATCATGGAA 1 237 0 AGTGTCGGGG 0.954102 -64 CGCACCGTTGAAAGAAGGGGCGGTTT 2 57 1 AAAGAAGGGG 0.943998 -16 GTGAGAAAAACTTGACGGCGCGCGCTAAAC 3 53 0 CTTGACGGCG 0.979501 -59 TCCTCTTCGCAAGGAAGGGGGGAGGGC 3 95 1 AAGGAAGGGG 0.98876 -17 ********** Masking position 7 Map Score: 12.8473 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 163 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TACCGCCTTCCATGATACCCCGACASTGCG 1 166 1 CATGATACCC 0.997396 -135 TACCGCCTTCCATGATACCCCGACACTGCG 1 230 1 CATGATACCC 0.997396 -71 ********** Masking position 5 Map Score: 1.42333 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 GCAGAAACGCGGCTGCATGTTGG 1 4 1 GAAACGCGGC 0.988654 -297 TAACGGGTTTGAACCGCTGACCTCTTGGGT 1 38 1 GAACCGCTGA 0.798466 -263 GCCCCTTCTTTCAACGGTGCGACCTACACC 2 48 0 TCAACGGTGC 0.666559 -25 CTCCTTTTTCTAAAGGCTGCGAGGCAATTA 3 17 1 TAAAGGCTGC 0.966105 -95 AGGAGTATGCCAAACGGTGAGAAAAACTTG 3 69 0 CAAACGGTGA 0.966564 -43 TCTTCGCAAGGAAGGGGGGAGGGC 3 98 1 GAAGGGGGGA 0.939331 -14 ********** Masking position 3 Map Score: 1.57925 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 260 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 ********** No masking Map Score: -6.1574e-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: -6.1574e-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: -6.1574e-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