AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__mthe_reg_100.orf -o056_mthe_100.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 RTH00661 61 M.thermo #2 RTH01407 25 M.thermo #3 RTH01538 300 M.thermo #4 RTH01353 75 M.thermo #5 RTH00151 64 M.thermo #6 RTH00311 135 M.thermo #7 RTH00569 142 M.thermo Motif number 1 TGTTCTATCTGGTCCATGAAAAACATCATCA 1 24 0 GGTCCATGAA 0.920363 -38 GGTCCCTCACTTGATTAATAA 3 1 1 GGTCCCTCAT 0.966163 -300 GTCCCCATATGTTCACTGGATAACTGTCTTT 3 178 0 GTTCACTGGT 0.810323 -123 TCCAGCAAGTGGTCCATGGGGCAGTCTGTGA 3 236 0 GGTCCATGGG 0.980886 -65 GTTCATAAAGGTTCCAGCAAGTGGTCCATGG 3 248 0 GTTCCAGCAG 0.966473 -53 CGATCCCTCCTGAGGGCCTGCG 6 2 1 GATCCCTCCG 0.956224 -134 CACTGACATAGTTCCCGGCCACATCCACCTG 6 85 1 GTTCCCGGCA 0.960977 -51 GCCTCTGCAAGTTCCCTCAGGTGGATGTGGC 6 102 0 GTTCCCTCAG 0.990723 -34 TATAACCCGGGTTCCCGGGTGCCAGGTAATT 7 23 0 GTTCCCGGGG 0.992448 -120 ********* * Masking position 3 Map Score: 7.77662 Number of sites scoring better than the average of aligned sites = 1047 Number in coding regions = 1007 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 ACCCCAAGATGACTGATGATGTTTTTCATGGA 1 9 1 ATGACTGATT 0.973415 -53 ATATATAGTAATAACTTATTAGTTTTCAGGAGCT 3 62 0 ATAACTTATT 0.98509 -239 CGGGACTCCCATAAATTTTATTTTAAATGAGCTG 4 41 1 ATAAATTTTT 0.730631 -35 CATATTTCCTATAAAATATATACTTTCAAATAA 5 10 0 ATAAAATATT 0.901714 -55 ATTATTATTAATGACATATTTCCTATAAAATATA 5 24 0 ATGACATATT 0.777625 -41 ATTAATAATAATGACAGATTCCGTTCAAG 5 46 1 ATGACAGATT 0.957641 -19 AACCCGGGTTATAACTTATAAGATATAACTTATA 7 41 1 ATAACTTATT 0.985016 -102 CTTATAAGATATAACTTATAACATACTGTGTGTA 7 55 1 ATAACTTATT 0.983422 -88 ********* * Masking position 4 Map Score: 6.93459 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 14 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 CTGTTAATCTGGATGTTAAAATGCA 2 6 0 CTGGTGTTAA 0.931266 -20 GGAGCTCACCAAGTCTTTTATAGACGGGGCGT 3 36 0 AAGTTTTTAA 0.668324 -265 AAAAACTCGTCTGAATTTTACATCTATATTTT 3 133 0 CTGATTTTAA 0.894584 -168 GTTTTTCAGTATGAAGGCGAAAGACAGTTATC 3 159 1 ATGAGGCGAA 0.876425 -142 ATGGGGACATCAGAAGGTTAAAGAGGCTCTAA 3 201 1 CAGAGGTTAA 0.957002 -100 GTCCATGGGGCAGTCTGTGAAAATTAGAGCCT 3 224 0 CAGTTGTGAA 0.947426 -77 CTGACAGATGATGACTTCGAGAAACCATTCAT 6 35 1 ATGATTCGAA 0.648761 -101 GTCAGTGTAACTGTTGGCTATACCTATGAATG 6 60 0 CTGTGGCTAA 0.977525 -76 CTTTTACACACAGTATGTTATAAGTTATATCT 7 61 0 CAGTTGTTAA 0.961992 -82 GCTTAAATTTCTGTGGGCTACAATTAAAAGCT 7 91 0 CTGTGGCTAA 0.977525 -52 **** ***** * Masking position 10 Map Score: 5.43404 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 275 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 GACTTGGTGAGCTCCTGAAAACTAATAAGT 3 53 1 GCTCCTGAAA 0.928114 -248 GCCTCTTTAACCTTCTGATGTCCCCATATG 3 198 0 CCTTCTGATG 0.94682 -103 CTTCTATCCTCCTTTAGCAGAATAATT 3 284 0 CCTCCTTTAG 0.960731 -17 CGATCCCTCCTGAGGGCCTGCGGCC 6 6 1 CCTCCTGAGG 0.753085 -130 CCGGCCACATCCACCTGAGGGAACTTGCAG 6 99 1 CCACCTGAGG 0.893087 -37 ACCCTCCTTAACAGCCTCTGCA 6 124 0 CCTCCTTAAC 0.965705 -12 ********** Masking position 6 Map Score: 3.98736 Number of sites scoring better than the average of aligned sites = 971 Number in coding regions = 943 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 CTTTTATAGACGGGGCGTGATATTATTAAT 3 24 0 CGGGGCGTGA 0.972192 -277 TATATTTTCACCCGGCCCTATAAATACTTT 3 111 0 CCCGGCCCTA 0.981914 -190 TTATGGGAGTCCCGGTCTGATCCGGAATTT 4 25 0 CCCGGTCTGA 0.988675 -51 CCTGAGGGCCTGCGGCCTGACAGATGATGA 6 19 1 TGCGGCCTGA 0.863729 -117 TGACATAGTTCCCGGCCACATCCACCTGAG 6 88 1 CCCGGCCACA 0.981914 -48 ACCCGGGTTCCCGGGTGCCAGGTAATTTAC 7 20 0 CCGGGTGCCA 0.947097 -123 ********** Masking position 10 Map Score: 2.71227 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 179 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 CTATCTGGTCCATGAAAAACATCATCAGTCATCT 1 17 0 CATAAAACCA 0.918859 -45 TTTCATGGACCAGATAGAACACCAGTAAGGGAGA 1 34 1 CAGTAAACCA 0.962286 -28 TGCATTTTAACATCCAGATTAACAG 2 11 1 CATCAATTCA 0.894415 -15 TCCCTCACTTGATTAATAATATCACGCCCCGTCT 3 13 1 GATAAAATCA 0.793147 -288 CTGAATTTTACATCTATATTTTCACCCGGCCCTA 3 121 0 CATTAATTCA 0.964949 -180 ATTAACAGCTCATTTAAAATAAAATTTATGGGAG 4 46 0 CATTAAATAA 0.861188 -30 TTTCCTATAAAATATATACTTTCAAATAA 5 6 0 AATTAACTCA 0.826249 -59 GTATAGCCAACAGTTACACTGACATAGTTCCCGG 6 69 1 CAGTAACTCA 0.972319 -67 GAAATTTAAGCAGATAAAATGCCAGACCACGGGG 7 112 1 CAGTAAATCA 0.981203 -31 *** ** *** ** Masking position 8 Map Score: 3.13022 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 212 Number in noncoding regions = 24 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: -1.61761e-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 8 ********** No masking Map Score: -1.61761e-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: -1.61761e-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