AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i177_cobalamin_biosynthesis_2_mthe_reg_300.orf -o177_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01110 300 M.thermo #2 RTH01626 132 M.thermo Motif number 1 AAATGACACATCCATTATCAGCATATTTGAAA 1 34 1 TCCATTATCC 0.993093 -267 ACAAAGTTCTTCCATCCTCCGCATCATGGGAA 1 275 0 TCCATCCTCC 0.99705 -26 GTCTCTAAACTCCATCATCTTCTGTCGGCCGC 2 15 1 TCCATCATCC 0.998669 -118 GCTGATGGAATGCATCAGCCCCGTAAGATACC 2 49 0 TGCATCAGCC 0.995672 -84 GCTGATGCATTCCATCAGCTCCGGTCATTTTT 2 62 1 TCCATCAGCC 0.998767 -71 ********* * Masking position 5 Map Score: 10.2144 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 57 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 ATGCCTTATTTTTTGATTTGGAGGCAAAATATTT 1 105 1 TTTGAGGAGG 0.992122 -196 TTATCGTTCCCTCTGGATGGTAGGAATATAACTG 1 152 0 CTTGGGTAGG 0.995293 -149 ATAAACGTATTTCTGGATTGGAGGCGGTACAATT 1 182 1 TTTGGGGAGG 0.997325 -119 CCTGCTGCTACCATGGGAAGGAGGAACAGGGATG 1 232 0 CCTGGGGAGG 0.998876 -69 TGGCTGCTTCCCATGATGCGGAGGATGGAAGAAC 1 268 1 CCTGAGGAGG 0.996074 -33 CCATCATCTTCTGTCGGCCGCAGGGTATCTTACG 2 26 1 CTTCGGCAGG 0.985582 -107 ** *** ***** Masking position 4 Map Score: 10.0431 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 184 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 GATGTGTCATTTTTATTTCCCCTTTAAACCT 1 15 0 TTTATTTCCC 0.789672 -286 GAAATAAAAATGACACATCCATTATCAGCAT 1 27 1 TACACATCCA 0.702394 -274 TATATAAATATTTTGCCTCCAAATCAAAAAA 1 113 0 TTTGCCTCCA 0.969246 -188 TTCGCAGTTATATTCCTACCATCCAGAGGGA 1 148 1 TTTCCTACCA 0.932475 -153 AGAAATACGTTTATCGTTCCCTCTGGATGGT 1 165 0 TATCGTTCCC 0.833325 -136 CGCTTAATTGTACCGCCTCCAATCCAGAAAT 1 190 0 TCCGCCTCCA 0.93966 -111 AGCGATTTTTTATTACATCCCTGTTCCTCCT 1 217 1 TTTACATCCC 0.957523 -84 ACATCCCTGTTCCTCCTTCCCATGGTAGCAG 1 231 1 TCTCCTTCCC 0.991325 -70 CAGCCACACCTGCTGCTACCATGGGAAGGAG 1 243 0 TCTGCTACCA 0.946289 -58 CAGCAGGTGTGGCTGCTTCCCATGATGCGGA 1 259 1 GCTGCTTCCC 0.955588 -42 GTTACAAAGTTCTTCCATCCTCCGCATCATG 1 279 0 TTTCCATCCT 0.878088 -22 * ********* Masking position 9 Map Score: 8.6028 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 889 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 TATTTCCCCTTTAAACCTCTTT 1 1 0 TTAACTCTTT 0.964531 -300 CACATCCATTATCAGCATATTTGAAAAAGGAT 1 40 1 ATAGCTATTT 0.940926 -261 CTTTTTTTCAATTAAAACCTTTTAATCCTTTT 1 64 0 ATAAACCTTT 0.940927 -237 ATAAGGCATCATAAAACTCTTTTTTTCAATTA 1 82 0 ATAAATCTTT 0.981029 -219 GCGAAGCCATATATAAATATTTTGCCTCCAAA 1 121 0 ATTAATATTT 0.897952 -180 AGAGGGAACGATAAACGTATTTCTGGATTGGA 1 172 1 ATAACTATTT 0.979688 -129 GCTCAATTTATTTAAATTATTTGTAACAAACA 2 97 0 TTAAATATTT 0.949103 -36 ** *** ***** Masking position 10 Map Score: 5.20848 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 17 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 AAAGGGGAAATAAAAATGACACATCCATTA 1 21 1 TAAAAATGAC 0.967658 -280 GTTTTAATTGAAAAAAAGAGTTTTATGATG 1 78 1 AAAAAAAGAG 0.840473 -223 TCCAAATCAAAAAATAAGGCATCATAAAAC 1 97 0 AAAATAAGGC 0.950896 -204 GCAAAATATTTATATATGGCTTCGCAGTTA 1 128 1 TATATATGGC 0.861505 -173 GGGATGTAATAAAAAATCGCTTAATTGTAC 1 208 0 AAAAAATCGC 0.939235 -93 AACAAACAGAGAAAAATGACCGGAGCTGAT 2 75 0 GAAAAATGAC 0.96175 -58 ********** Masking position 6 Map Score: 0.861941 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 117 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 ********** No masking Map Score: -2.03625e-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: -2.03625e-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: -2.03625e-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