AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -igalR_mthe_opreg_100.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH412 300 conserved protein #2 MTH451 132 magnesium chelatase subunit ChlI #3 MTH452 45 unknown #4 MTH625 107 unknown #5 MTH631 143 UDP-glucose 4-epimerase Motif number 1 ATCCCAGATCCACTTTCTGGACACACAAAAAATT 1 55 0 CCTTTGGCAC 0.972198 -246 TTGATCAATGCCCCTACTGGACTGATAGACAATC 1 93 0 CCCTTGGCTG 0.996459 -208 TCATATATGTCTTTTTTTGGGCTGAAAAATCGCA 1 187 1 CTTTTGGCTG 0.995084 -114 CTTCTTAGTACCCCTGATGACCAGGGTGTAGGGT 4 75 0 CCCTTGACAG 0.940745 -33 CCTTTGCATAGCTTTAATGGTCTGATTTCATATA 5 29 0 GTTTTGGCTG 0.993554 -115 TTGTGGGTAGGTCTTTGTGGTCTGCCTTTGCATA 5 53 0 GCTTTGGCTG 0.996869 -91 ATGTAAATAAGGTTTGGTGGCCTGTTTTTGTGGG 5 80 0 GTTTTGGCTG 0.993554 -64 * *** *** *** Masking position 8 Map Score: 9.90934 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 58 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 GCTCTCTGACGGTCTATTTTAATTTAAAAA 1 155 1 GGTCTATTTT 0.974324 -146 AGCTCATATATGTCTTTTTTTGGGCTGAAA 1 184 1 TGTCTTTTTT 0.893751 -117 ATAATAAAGGGGTCTGTCCTGTATATAACC 2 19 0 GGTCTGTCCT 0.968385 -114 AATATGTACCTGACTGTATTAAAAGTAATA 2 46 0 TGACTGTATT 0.858161 -87 TAGCTTTAATGGTCTGATTTCATATATTAA 5 25 0 GGTCTGATTT 0.966532 -119 AGGTCTTTGTGGTCTGCCTTTGCATAGCTT 5 49 0 GGTCTGCCTT 0.972591 -95 AAGGTTTGGTGGCCTGTTTTTGTGGGTAGG 5 76 0 GGCCTGTTTT 0.97717 -68 GATATGATTCTGTCTATATTTCTGTTAACA 5 113 0 TGTCTATATT 0.888268 -31 ********** Masking position 5 Map Score: 6.57606 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 156 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 TATCAGTCCAGTAGGGGCATTGATCAAGCA 1 100 1 GTAGGGGCAT 0.992874 -201 ACAGTGCCCGGTAGGGTCACTGTGACATTA 1 252 0 GTAGGGTCAC 0.992559 -49 TGACCAGGGTGTAGGGTGAGATGAGCAGCG 4 62 0 GTAGGGTGAG 0.989208 -46 GGGGTACTAAGAAGGGGCAGAAC 4 95 1 GAAGGGGCAG 0.993396 -13 ********** Masking position 3 Map Score: 3.50844 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 23 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 GGATTTCCATCGAATCCCATTTTAAATATAA 1 8 0 CATCCTTTTA 0.988366 -293 CGATGGAAATCCTATCGCCATTTAAAATTTTTTG 1 30 1 CATCCATTTA 0.991033 -271 GCATTGATCAAGCATATCCATTTATCTCAAAAAT 1 116 1 AATACATTTA 0.79654 -185 AATAGACCGTCAGAGAGCTTTTTATTTTTGAGAT 1 139 0 CAGACTTTTA 0.894439 -162 ATTAGTAATACTCATCTTTTTTTAGAAATTATTA 2 73 1 CATCTTTTTA 0.976269 -60 AGTGGTTGGTCTAATCATTATTTAATAATTTCTA 2 95 0 CATCTATTTA 0.980884 -38 AAACAGGCCACCAAACCTTATTTACATGTTAACA 5 87 1 CAACTATTTA 0.929603 -57 * *** * ***** Masking position 4 Map Score: 3.14802 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 14 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TCGAATCCCATTTTAAATATAA 1 1 0 TTTTAATATA 0.971593 -300 GAGCTTTTTATTTTTGAGATAAATGGATATGC 1 127 0 TTTTTAGATA 0.875433 -174 CTGACGGTCTATTTTAATTTAAAAAGCTCATA 1 160 1 ATTTTATTTA 0.77842 -141 AAATCGCAATATTTATATATGATTTGAGATTC 1 213 1 ATTTAATATA 0.957993 -88 GAGATTCAAGTTTTTAATGTCACAGTGACCCT 1 238 1 TTTTTATGTA 0.938917 -63 ACTCATCTTTTTTTAGAAATTATTAAATAATG 2 82 1 TTTTAAAATA 0.883793 -51 AATGGTCTGATTTCATATATTAATCTGAGGTG 5 16 0 TTTCAATATA 0.905678 -128 ACCAAACCTTATTTACATGTTAACAGAAATAT 5 96 1 ATTTAATGTA 0.93892 -48 ***** **** * Masking position 7 Map Score: 2.46772 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 38 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 CAAAAAAAGACATATATGAGCTTTTTAAAT 1 176 0 CATATATGAG 0.920987 -125 AATTTCTAAAAAAAGATGAGTATTACTAAT 2 73 0 AAAAGATGAG 0.871871 -60 GTGGAACCGCCAGAGATGAGGAATTTCATG 4 17 0 CAGAGATGAG 0.994501 -91 AGGGTGTAGGGTGAGATGAGCAGCGCAGCC 4 57 0 GTGAGATGAG 0.965655 -51 ATATATTAATCTGAGGTGATGTT 5 4 0 CTGAGGTGAT 0.924609 -140 TTTATCACACAGATATGATTCTGTCTATA 5 125 0 CAGATATGAT 0.954466 -19 ********** Masking position 4 Map Score: 2.33443 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 274 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 CAGTCCAGTAGGGGCATTGATCAAGCATAT 1 103 1 GGGGCATTGA 0.987879 -198 GTGCCCGGTAGGGTCACTGTGACATTAAAA 1 249 0 GGGTCACTGT 0.987879 -52 GTGACCCTACCGGGCACTGTGGATTGGAGG 1 262 1 CGGGCACTGT 0.991789 -39 CTGGTCATCAGGGGTACTAAGAAGGGGCAG 4 85 1 GGGGTACTAA 0.953512 -23 ********** Masking position 6 Map Score: 0.747768 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 132 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: 1.67931e-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 9 ********** No masking Map Score: 1.67931e-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 10 ********** No masking Map Score: 1.67931e-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