AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00071_mthe_reg_300.orf -o00071_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 MTH657 96 long-chain-fatty-acid-CoA ligase #2 MTH659 216 epoxidase #3 MTH660 119 unknown Motif number 1 GAGGTATAGGCTTCTTTCTCTGCTCTATGAAG 1 8 0 CTCTTCTTTC 0.993254 -89 GCTCCTCAAGCTGCTTCCTTATCTCGGGAGGTATA 1 35 0 CTCTTCTATC 0.997053 -62 GTTAAGTAATCTCCTAAATGATCTCCGGTTATCTG 2 86 0 CTCTAATATC 0.96577 -131 TAAGCTGTATCTATTATCTAAAATCTCAGTTTAAA 2 171 0 CTTTACTATC 0.950246 -46 ATCACTCTCCTTTTGGATGTGCCTAACATAT 3 7 1 CTCTTTGATG 0.936689 -113 TGCCGGTAACCTACTTCCGAAAATCTACCAACATT 3 63 1 CTCTTCGATC 0.995617 -57 CTCTCTACTTTTTTTATTCTCATGATATT 3 101 0 CTCTTTTTTC 0.980297 -19 ** *** ** * ** Masking position 5 Map Score: 6.56477 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 132 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 CTGCTTCCTTATCTCGGGAGGTATAGGCTTC 1 29 0 ATCTCGGAGG 0.995217 -68 TCCATGTAATATCTGAGGGGGTAATGGATTC 2 14 0 ATCTGGGGGG 0.976784 -203 GAATGGTTGCATCTCTGCAGGGATGTGAACA 2 43 1 ATCTCGCAGG 0.986598 -174 ATATTTTCAGATAACCGGAGATCATTTAGGA 2 79 1 ATAACGGAGA 0.936987 -138 TTCGTCATGCATATGCTGATGCTCTGCACAT 2 123 1 ATATGTGATG 0.894233 -94 TGCTGTTTAAAAATGTGCAGAGCATCAGCAT 2 135 0 AAATGGCAGA 0.800211 -82 GCAATCACCAATATAAGGATGCCGGTAACCT 3 44 1 ATATAGGATG 0.902948 -76 AACATTATAAATATCATGAGAATAAAAAAAG 3 92 1 ATATCTGAGA 0.949946 -28 ***** ***** Masking position 1 Map Score: 4.62819 Number of sites scoring better than the average of aligned sites = 929 Number in coding regions = 852 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 TGCTTCCTTATCTCGGGAGGTATAGGCTTC 1 29 0 TCTCGGGAGG 0.929129 -68 AAGATTAACTTATAAGGGTGGATTT 1 82 1 TATAAGGGTG 0.93391 -15 CCATGTAATATCTGAGGGGGTAATGGATTC 2 14 0 TCTGAGGGGG 0.94585 -203 TCCTAAATGATCTCCGGTTATCTGAAAATA 2 80 0 TCTCCGGTTA 0.799941 -137 TCGTCATGCATATGCTGATGCTCTGCACAT 2 124 1 TATGCTGATG 0.860068 -93 TTATCTAAAATCTCAGTTTAAAAAAATTGC 2 163 0 TCTCAGTTTA 0.747971 -54 ATCACTCTCCTTTTGGATGTGCCTA 3 6 1 TCTCCTTTTG 0.807931 -114 CAATCACCAATATAAGGATGCCGGTAACCT 3 45 1 TATAAGGATG 0.924587 -75 TCATGATATTTATAATGTTGGTAGATTTTC 3 81 0 TATAATGTTG 0.879509 -39 ACATTATAAATATCATGAGAATAAAAAAAG 3 93 1 TATCATGAGA 0.458871 -27 ********** Masking position 3 Map Score: 2.87683 Number of sites scoring better than the average of aligned sites = 2559 Number in coding regions = 2375 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 4 GTTGCATCTCTGCAGGGATGTGAACATTGACAT 2 48 1 TGCAGATGTA 0.994831 -169 TCCGGTTATCTGAAAATATGTCAATGTTCACAT 2 65 0 TGAAAATGTA 0.887112 -152 AGCATATGCATGACGAACTGTTAAGTAATCTCC 2 107 0 TGACGCTGTA 0.94621 -110 AGATACAGCTTACCATAATGTTAAGGTGATCAC 2 194 1 TACCAATGTA 0.721606 -23 TATTGGTGATTGCAGATATGTTAGGCACATCCA 3 24 0 TGCAGATGTA 0.994865 -96 ***** **** * Masking position 9 Map Score: 1.50939 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 38 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 5 AGCAGAGAAAGAAGCCTATACCTCCCGAGATA 1 19 1 GAAGCCTACC 0.994251 -78 TACGAATCCATTACCCCCTCAGATA 2 4 1 GAATCCTACC 0.977549 -213 GTGATCACCTTAACATTATGGTAA 2 203 0 GATCACTAAC 0.955382 -14 TCTCCTTTTGGATGTGCCTAACATATCTGCAA 3 16 1 GATGTGTAAC 0.942514 -104 CCAATATAAGGATGCCGGTAACCTACTTCCGA 3 51 1 GATGCCTAAC 0.991355 -69 ****** **** Masking position 9 Map Score: 0.704268 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 87 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 CTTCATAGAGCAGAGAAAGAAGCCTA 1 7 1 AGAGCAGAGA 0.972687 -90 TGTTCACATCCCTGCAGAGATGCAACCATT 2 44 0 CCTGCAGAGA 0.981639 -173 CATTGACATATTTTCAGATAACCGGAGATC 2 72 1 TTTTCAGATA 0.865627 -145 TGTTTAAAAATGTGCAGAGCATCAGCATAT 2 133 0 TGTGCAGAGC 0.981405 -84 TATATTGGTGATTGCAGATATGTTAGGCAC 3 29 0 ATTGCAGATA 0.971114 -91 ********** Masking position 6 Map Score: 0.765159 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 336 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 ********** No masking Map Score: 7.76924e-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: 7.76924e-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: 7.76924e-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