AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imalT_mthe_opreg_300.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 MTH478 49 sulfate transport system permease protein #2 MTH479 136 conserved protein #3 MTH480 91 unknown #4 MTH922 67 unknown #5 MTH923 21 unknown #6 MTH925 32 conserved protein #7 MTH927 139 ferredoxin #8 MTH928 300 cobalamin biosynthesis protein N Motif number 1 GTTAACATACTACTTTATTTTTAAGACCCCGA 1 16 1 TATTATTTTT 0.936832 -34 AGAGTAGTCCTTCTTTATCTTTCAGGACGATC 2 31 1 TTTTATCTTT 0.905708 -106 CTCTCCCCAATAATGTATTTTTTCACTGAACA 3 48 0 TATTATTTTT 0.936772 -44 TTTCAATTTTTTTATTTTTCAGGAAATAC 7 8 1 TTTTATTTTT 0.944999 -132 ACAGGTCCATATATAAATCTTTCTTAATGGAC 7 106 0 ATTAATCTTT 0.688276 -34 GATTGATCGATTCAGAATTTTTCTGAAACGTT 8 35 1 TTAAATTTTT 0.944999 -266 ACTCAAGAAATTAAAAATTTTTATAAATATAA 8 88 0 TTAAATTTTT 0.944988 -213 ATTGCATAATTAATGAATATTTTATCTGCATT 8 141 0 TATAATATTT 0.818438 -160 GTGATGAATGTATTAAATTTTCATATAATTAT 8 178 1 TATAATTTTC 0.910082 -123 ATATAATTATTACTTAATTTTTATTAGAGCAA 8 200 1 TATAATTTTT 0.969731 -101 TTAAGACTTTTTATTAATTTTTTTATTACATA 8 235 0 TTTAATTTTT 0.973763 -66 TAAAAAGTCTTAAATAATCTTCATACCATATC 8 254 1 TAAAATCTTC 0.723717 -47 CTCCTTTATAGTTTTTACAATTGTGG 8 285 0 TTAAGTTTTT 0.730454 -16 ** * ******* Masking position 8 Map Score: 14.2241 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 67 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 CTTCAGAAAAAGTCGGGGTC 1 40 0 CTTCAGAAAA 0.897786 -10 GTTCTGGGAATAACTCCCTC 2 1 1 GTTCTGGGAA 0.977218 -136 ATACATATCGGTTCTGTGAAGGAATGAGAA 2 68 0 GTTCTGTGAA 0.975505 -69 TGAATCTGATGTTCAGTGAAAAAATACATT 3 39 1 GTTCAGTGAA 0.989194 -53 AGCGTTTCCAGTGCAGTGAACTGTCCTA 4 9 0 GTGCAGTGAA 0.965718 -59 TTTTTTTATTTTTCAGGAAATACGTGAGGA 7 17 1 TTTCAGGAAA 0.919413 -123 CCTTTAAACGTTTCAGAAAAATTCTGAATC 8 43 0 TTTCAGAAAA 0.912085 -258 ********** Masking position 9 Map Score: 7.30305 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 196 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 ATATCGACATGGACATATATACATATCGGT 2 86 0 GGACATATAT 0.861894 -51 ATATGTCCATGTCGATATAGGTGTTCTGAG 2 98 1 GTCGATATAG 0.943182 -39 TTATCAGTTTGTCCATGAATCTGATGTTCA 3 24 1 GTCCATGAAT 0.933274 -68 GTTATCACCATTCCATATATCTCTCTCCCC 3 72 0 TTCCATATAT 0.902663 -20 TTTTCATGAGGTCCATTAAGAAAGATTTAT 7 96 1 GTCCATTAAG 0.952678 -44 TATTCCACAGGTCCATATATAAATCTTTCT 7 114 0 GTCCATATAT 0.986192 -26 CAACTGAAGAGGCCATTTAGTGCCA 8 6 0 GGCCATTTAG 0.968888 -295 ********** Masking position 5 Map Score: 4.37014 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 142 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 TAAGACCCCGACTTTTTCTGAAG 1 37 1 ATTTTCTGAA 0.886232 -13 ATATATACATATCGGTTCTGTGAAGGAATGAG 2 70 0 ACGTTCTGTG 0.912164 -67 ATGTCGATATAGGTGTTCTGAGTTAATGGAGG 2 106 1 AGTTTCTGAG 0.971041 -31 CTGCACTGGAAACGCTCCTGAAAGGTGTGCTG 4 23 1 ACGTCCTGAA 0.9609 -45 CGCTCCTGAAAGGTGTGCTGAATTACTTTCAG 4 35 1 AGTTGCTGAA 0.958368 -33 TTCAAGGTAATCTGAAAGTAATTCAG 4 52 0 AGTATCTGAA 0.927778 -16 ACTGTTTTACATGGCAGCTGAGGACCCCCGCA 7 60 0 AGGAGCTGAG 0.921806 -80 CAGTTGATTGATCGATTCAGAATTTTTCTGAA 8 30 1 ACGTTCAGAA 0.961888 -271 AAGCCCTTTAAACGTTTCAGAAAAATTCTGAA 8 45 0 ACGTTCAGAA 0.961889 -256 * ** ******* Masking position 1 Map Score: 5.6748 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 311 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 AGGACGATCCCATGTTCTCATTCCTTCACA 2 54 1 CATGTTCTCA 0.902225 -83 TGTCGATATAGGTGTTCTGAGTTAATGGAG 2 107 1 GGTGTTCTGA 0.98536 -30 AACTGATAAAGATATCCGGAAG 3 3 0 GATATCCGGA 0.841776 -89 GCTCCTGAAAGGTGTGCTGAATTACTTTCA 4 36 1 GGTGTGCTGA 0.968072 -32 TTCAAGGTAATCTGAAAGTAATTCA 4 53 0 GGTAATCTGA 0.90594 -15 TTTAAACCAGGATCTGATACC 5 8 1 CAGGATCTGA 0.756823 -14 AGTTATAATGGATATCCTCACGTATTTCCT 7 31 0 GATATCCTCA 0.924877 -109 TATAACTGCGGGGGTCCTCAGCTGCCATGT 7 54 1 GGGGTCCTCA 0.965858 -86 ********** Masking position 10 Map Score: 2.95546 Number of sites scoring better than the average of aligned sites = 907 Number in coding regions = 853 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 TATCTGCATTTATGTATTACCGATGTATGT 8 121 0 TATGTATTAC 0.870872 -180 GCAGATAAAATATTCATTAATTATGCAATA 8 144 1 TATTCATTAA 0.766832 -157 ATTCATTAATTATGCAATAACGCGTGATGA 8 155 1 TATGCAATAA 0.934974 -146 ACGCGTGATGAATGTATTAAATTTTCATAT 8 174 1 AATGTATTAA 0.940576 -127 TAATAAAAATTAAGTAATAATTATATGAAA 8 196 0 TAAGTAATAA 0.940235 -105 AGAGCAAGAATATGTAATAAAAAAATTAAT 8 225 1 TATGTAATAA 0.962097 -76 TGTAATAAAAAAATTAATAAAAAGTCTTAA 8 237 1 AAATTAATAA 0.692794 -64 AAATTAATAAAAAGTCTTAAATAATCTTCA 8 247 1 AAAGTCTTAA 0.723803 -54 ********** Masking position 2 Map Score: 2.74858 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 28 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AAAAAGTCGGGGTCTTAAAAATAAAGTAGT 1 24 0 GGTCTTAAAA 0.965041 -26 GGTCTTTAACCTCCATTAAC 2 127 0 GGTCTTTAAC 0.986886 -10 AACGTTTAAAGGGCTTTAACCTTGCCGTTA 8 61 1 GGGCTTTAAC 0.977859 -240 ATTAATAAAAAGTCTTAAATAATCTTCATA 8 249 1 AGTCTTAAAT 0.874183 -52 ********** Masking position 5 Map Score: 0.096099 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ATAGCACCAGTATAATGGCAATTTCGGGCA 6 12 0 TATAATGGCA 0.9661 -21 GGATATCCATTATAACTGCGGGGGTCCTCA 7 44 1 TATAACTGCG 0.973853 -96 TTTTTATAAATATAACGGCAAGGTTAAAGC 8 73 0 TATAACGGCA 0.9873 -228 ATCGGTAATACATAAATGCAGATAAAATAT 8 127 1 CATAAATGCA 0.909487 -174 TTGTAAAAACTATAAAGGAG 8 291 1 TATAAAGGAG 0.912254 -10 ********** Masking position 5 Map Score: 0.825451 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 70 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ********** No masking Map Score: -1.56076e-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: -1.56076e-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 11 ********** No masking Map Score: -1.56076e-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