AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i032_Pyruvate_Synthase_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv2455c 231 hypothetical protein Rv2455c #2 clpX 290 clpX Motif number 1 AGCGAGGGCTGGCGGTAGCGACGACACAGA 1 24 0 GGCGGTAGCG 0.935727 -208 TTGGTCGGTTACCGGCCGCATATATGGCAT 1 65 1 ACCGGCCGCA 0.799414 -167 ATTTCATTTCGGGTGTAAGGCGGTCTCCGA 1 94 0 GGGTGTAAGG 0.781919 -138 TTGTGTCACTGGCGGTAGCGATTATGACAT 1 122 0 GGCGGTAGCG 0.935727 -110 GTGACACAAGCCGTGCGGCGCGGGGGTGTC 1 143 1 CCGTGCGGCG 0.720063 -89 TGCGGCGCGGGGGTGTCGCTCCGACGACGC 1 156 1 GGGTGTCGCT 0.880314 -76 CGTAACCTGAAGCTGCAGCGCGGAGTGCCT 1 185 1 AGCTGCAGCG 0.60231 -47 AGCGCGGAGTGCCTGTCCGATAACACATGG 1 201 1 GCCTGTCCGA 0.649815 -31 AACGCCACTGTAGGGTGGTCAGCTG 2 6 1 CACTGTAGGG 0.793301 -285 GTGGTCAGCTGGCGGTCGGGCCGCTGCCGG 2 25 1 GGCGGTCGGG 0.865016 -266 GCGTCGCGGACCCGGCAGCGGCCCGACCGC 2 36 0 CCCGGCAGCG 0.50222 -255 ACCGAGGCCCGCGCGTCGCGGACCCGGCAG 2 48 0 GCGCGTCGCG 0.978032 -243 ACGCGCGGGCCTCGGTGGGGTTACGACCGC 2 62 1 CTCGGTGGGG 0.770465 -229 CGTGTCTCTGGCGTGTCGCGGTCGTAACCC 2 79 0 GCGTGTCGCG 0.990965 -212 CGCCAGAGACACGGATCGCGCGTCTCGGCG 2 96 1 ACGGATCGCG 0.851041 -195 GCGCGTCTCGGCGAGTGGGGCGCAGTCGGG 2 113 1 GCGAGTGGGG 0.936554 -178 GCGAGTGGGGCGCAGTCGGGCTATATGTTT 2 123 1 CGCAGTCGGG 0.794046 -168 ACCGTTAGCACCGAATAGCGTCCTAGAGAT 2 183 0 CCGAATAGCG 0.674457 -108 ATTCGGTGCTAACGGTCGCGGGGGGCCGGA 2 197 1 AACGGTCGCG 0.927217 -94 AACGGTCGCGGGGGGCCGGAGCAAGCGGGT 2 207 1 GGGGGCCGGA 0.935354 -84 GCCGGAGCAAGCGGGTAGCGTCGGGGCATA 2 221 1 GCGGGTAGCG 0.990165 -70 GTTCGTGTTGCCGTGCCCCGTGTATGCCCC 2 243 0 CCGTGCCCCG 0.515349 -48 CAACACGAACGGCGATCAGGAAGTAGGCCA 2 263 1 GGCGATCAGG 0.670473 -28 ********** Masking position 5 Map Score: 40.0888 Number of sites scoring better than the average of aligned sites = 50075 Number in coding regions = 46508 Number in noncoding regions = 3567 Number of orfs with sites within 600 bp upstream = 1439 Fraction of orfs with sites within 600 bp upstream = 0.231128 Motif number 2 GCTGGCGGTAGCGACGACACAGAACTGTGG 1 17 0 GCGACGACAC 0.833486 -215 CCGCCAGCCCTCGCTGACTTCGCCTTTTGG 1 39 1 TCGCTGACTT 0.846794 -193 TGTAAGGCGGTCTCCGATGCCATATATGCG 1 81 0 TCTCCGATGC 0.913536 -151 AAGCCGTGCGGCGCGGGGGTGTCGCTCCGA 1 150 1 GCGCGGGGGT 0.956975 -82 CGGGGGTGTCGCTCCGACGACGCGTAACCT 1 163 1 GCTCCGACGA 0.905869 -69 TGAAGCTGCAGCGCGGAGTGCCTGTCCGAT 1 192 1 GCGCGGAGTG 0.882168 -40 GTCTCCGCCTTCCATGTGTTA 1 221 0 TCTCCGCCTT 0.716768 -11 GGCCCGCGCGTCGCGGACCCGGCAGCGGCC 2 43 0 TCGCGGACCC 0.989295 -248 GGTCCGCGACGCGCGGGCCTCGGTGGGGTT 2 54 1 GCGCGGGCCT 0.980642 -237 CTCTGGCGTGTCGCGGTCGTAACCCCACCG 2 74 0 TCGCGGTCGT 0.971321 -217 GCGATCCGTGTCTCTGGCGTGTCGCGGTCG 2 85 0 TCTCTGGCGT 0.861371 -206 TGCGCCCCACTCGCCGAGACGCGCGATCCG 2 107 0 TCGCCGAGAC 0.915236 -184 GGCGAGTGGGGCGCAGTCGGGCTATATGTT 2 122 1 GCGCAGTCGG 0.836905 -169 CCCTGAAATCTCTAGGACGCTATTCGGTGC 2 176 1 TCTAGGACGC 0.865129 -115 CTACCCGCTTGCTCCGGCCCCCCGCGACCG 2 209 0 GCTCCGGCCC 0.940796 -82 CCCCGTGTATGCCCCGACGCTACCCGCTTG 2 228 0 GCCCCGACGC 0.673916 -63 TACTTCCTGATCGCCGTTCGTGTTGCCGTG 2 258 0 TCGCCGTTCG 0.692223 -33 ********** Masking position 6 Map Score: 19.0761 Number of sites scoring better than the average of aligned sites = 45942 Number in coding regions = 43212 Number in noncoding regions = 2730 Number of orfs with sites within 600 bp upstream = 1224 Fraction of orfs with sites within 600 bp upstream = 0.196595 Motif number 3 GAAGTCAGCGAGGGCTGGCGGTAGCGACGA 1 30 0 AGGGCTGGCG 0.987315 -202 CCCGCGCCGCACGGCTTGTGTCACTGGCGG 1 137 0 ACGGCTTGTG 0.892042 -95 CGTGCGGCGCGGGGGTGTCGCTCCGACGAC 1 154 1 GGGGGTGTCG 0.946518 -78 CGCTGCAGCTTCAGGTTACGCGTCGTCGGA 1 175 0 TCAGGTTACG 0.800028 -57 TGTAGGGTGGTCAGCTGGCGGTCGGGCCGC 2 19 1 TCAGCTGGCG 0.95483 -272 CGGGCCTCGGTGGGGTTACGACCGCGACAC 2 67 1 TGGGGTTACG 0.936432 -224 TCCGTGTCTCTGGCGTGTCGCGGTCGTAAC 2 81 0 TGGCGTGTCG 0.754386 -210 CGCCAGAGACACGGATCGCGCGTCTCGGCG 2 96 1 ACGGATCGCG 0.924823 -195 ATCGCGCGTCTCGGCGAGTGGGGCGCAGTC 2 110 1 TCGGCGAGTG 0.688781 -181 TTTCATTCAGACGAGAGGCGTGAACACCCT 2 150 1 ACGAGAGGCG 0.743227 -141 GCCGGAGCAAGCGGGTAGCGTCGGGGCATA 2 221 1 GCGGGTAGCG 0.97956 -70 CGGGGCATACACGGGGCACGGCAACACGAA 2 242 1 ACGGGGCACG 0.922659 -49 ********** Masking position 10 Map Score: 8.07136 Number of sites scoring better than the average of aligned sites = 15606 Number in coding regions = 14233 Number in noncoding regions = 1373 Number of orfs with sites within 600 bp upstream = 882 Fraction of orfs with sites within 600 bp upstream = 0.141664 Motif number 4 TCTGTGTCGTCGCTACCGCCAGCCCTCGCT 1 24 1 CGCTACCGCC 0.967675 -208 ATATGCGGCCGGTAACCGACCAAAAGGCGA 1 58 0 GGTAACCGAC 0.85914 -174 ATATGGCATCGGAGACCGCCTTACACCCGA 1 86 1 GGAGACCGCC 0.977301 -146 ATGTCATAATCGCTACCGCCAGTGACACAA 1 122 1 CGCTACCGCC 0.967675 -110 AAGCTGCAGCGCGGAGTGCCTGTCCGATAA 1 194 1 GCGGAGTGCC 0.519335 -38 CCGACCGCCAGCTGACCACCCTACAGTGGC 2 14 0 GCTGACCACC 0.966119 -277 CCGGCAGCGGCCCGACCGCCAGCTGACCAC 2 25 0 CCCGACCGCC 0.992683 -266 GCCTCGGTGGGGTTACGACCGCGACACGCC 2 70 1 GGTTACGACC 0.875603 -221 CGAGTGGGGCGCAGTCGGGCTATATGTTTC 2 124 1 GCAGTCGGGC 0.395006 -167 AGACGAGAGGCGTGAACACCCTGAAATCTC 2 158 1 CGTGAACACC 0.725677 -133 GCTATTCGGTGCTAACGGTCGCGGGGGGCC 2 194 1 GCTAACGGTC 0.78673 -97 ATGCCCCGACGCTACCCGCTTGCTCCGGCC 2 220 0 GCTACCCGCT 0.519828 -71 TGGCCTACTTCCTGATCGCCGTTCGTGTTG 2 263 0 CCTGATCGCC 0.964812 -28 AATGCTGATGGCCTACTTCCTGA 2 278 0 GCTGATGGCC 0.953885 -13 ********** Masking position 10 Map Score: 12.685 Number of sites scoring better than the average of aligned sites = 26916 Number in coding regions = 25247 Number in noncoding regions = 1669 Number of orfs with sites within 600 bp upstream = 971 Fraction of orfs with sites within 600 bp upstream = 0.155959 Motif number 5 ********** No masking Map Score: 1.50878e-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 6 ********** No masking Map Score: 1.50878e-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: 1.50878e-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