AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_mthe_reg_300.orf -o047_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 RTH00627 31 M.thermo #2 RTH00736 144 M.thermo #3 RTH01945 83 M.thermo #4 RTH00865 19 M.thermo #5 RTH00262 31 M.thermo #6 RTH01033 203 M.thermo #7 RTH00235 158 M.thermo #8 RTH01020 117 M.thermo Motif number 1 TAAAGATGTTGAAAAAAAATTAAATGGTTTAA 2 17 0 GAAAAAAATA 0.954394 -128 AAGATTGTTATAATAAAAATGAACATTTTAGT 2 51 0 TAAAAAAATA 0.975401 -94 TTTTTTTGAATAAAAAAAATTAGGTGCATTAC 3 45 0 TAAAAAAATA 0.977035 -39 TTTTTTTTATTCAAAAAAATAAAAGGAGGAAG 3 58 1 TCAAAAAATA 0.988242 -26 CAGCAGGGAGTAATAATAATCATCCTCTGGTC 6 84 0 TAAAATAATA 0.955666 -120 TTTGGGATGATCACAAAAATCAACGCCACCAT 6 128 1 TCAAAAAATA 0.98825 -76 GTCCCCCCGTGCAGAAAAATCAATAAACTTGA 7 72 0 GCAAAAAATA 0.976258 -87 CACTCCCACTTCAAAATATTTATTAATGCCGG 8 18 1 TCAAATATTA 0.870911 -100 CGGTCATGTATCACACTAATCATCCGGCATTA 8 41 0 TCAACTAATA 0.911579 -77 *** ****** * Masking position 5 Map Score: 14.4995 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 27 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 GTCTGGTGGGTGAGGGTTTGTTG 1 2 0 TGAGGTTGTT 0.72969 -30 CAAACTTTTAAGTGCCAGTATTCAATTATTAT 2 116 1 AGTGCGTATT 0.813671 -29 AAAAATAAAAGGAGGAAGAAAT 3 72 1 GGAGGGAAAT 0.97782 -12 TCCGGGGGAGGTGTAGATT 4 7 1 GGAGGTAGAT 0.968559 -13 CTCTCTGTGGAGAGCTCTAAATATAATTTATT 6 17 1 AGAGCTAAAT 0.801116 -187 CCATGGGTCCAGAGCCGGTAATAAATTATATT 6 36 0 AGAGCGTAAT 0.948966 -168 AGTATCATCAGCAGGGAGTAATAATAATCATC 6 92 0 GCAGGGTAAT 0.897244 -112 TTTTTTATATGGTGGCGTTGATTTTTGTGATC 6 136 0 GGTGGTTGAT 0.968559 -68 ATAAACTTGAGGTGGGAGAGATGCCGGCCTTT 7 50 0 GGTGGGAGAT 0.980173 -109 AATATTTTGAAGTGGGAGTGTTGAATT 8 6 0 AGTGGGTGTT 0.934438 -112 GGTAAGTATCGGAGCTGGTGATGG 8 104 1 GGAGCGTGAT 0.988077 -14 ***** ***** Masking position 12 Map Score: 10.9051 Number of sites scoring better than the average of aligned sites = 1059 Number in coding regions = 998 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 ACAAACTTTTAAGTGCCAGTATTCAATTATTA 2 115 1 AAGGCAGTAT 0.893018 -30 AAAAAATAAAAGGAGGAAGAAAT 3 71 1 AGGGGAGAAA 0.951306 -13 TCCGGGGGAGGTGTAGATT 4 3 1 CGGGGGGTGT 0.982913 -17 GAGCTCTCCACAGAGAGAGTGAC 6 2 0 CAGGAAGTGA 0.921749 -202 CCCATGGGTCCAGAGCCGGTAATAAATTATAT 6 37 0 CAGGCGGTAA 0.934299 -167 CTCTGGACCCATGGGGCAGTGACTGTGAATGA 6 54 1 ATGGGAGTGA 0.962232 -150 GAGTATCATCAGCAGGGAGTAATAATAATCAT 6 93 0 AGCGGAGTAA 0.900996 -111 AATAAACTTGAGGTGGGAGAGATGCCGGCCTT 7 51 0 AGGGGAGAGA 0.978623 -108 AAATATTTTGAAGTGGGAGTGTTGAATT 8 7 0 AAGGGAGTGT 0.974329 -111 AGGTAAGTATCGGAGCTGGTGATGG 8 103 1 CGGGCGGTGA 0.984955 -15 *** ** ***** Masking position 5 Map Score: 9.28424 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 562 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 AATTTTTTTTCAACATCTTTAATACTAAAA 2 28 1 CAACATCTTT 0.969319 -117 TTTTTATTATAACAATCTTTAAATACAAGA 2 64 1 AACAATCTTT 0.779109 -81 AAGAAAACGGCAACATATTTCCGACACAAA 2 90 1 CAACATATTT 0.925217 -55 ATATTTCCGACACAAACTTTTAAGTGCCAG 2 104 1 CACAAACTTT 0.965673 -41 TTGTGCAATGCACCTTCGTTAAT 3 4 0 CACCTTCGTT 0.901256 -80 AGGTGCATTGCACAAACTTTTTAAGTGTAA 3 19 1 CACAAACTTT 0.965673 -65 AAGTGTAATGCACCTAATTTTTTTTATTCA 3 41 1 CACCTAATTT 0.921192 -43 TATGTAAAAACACCTTTTTTTGGGTTTTCT 6 171 0 CACCTTTTTT 0.922573 -33 GGGGGACGGGCATCAATTTTTAAGTGCCAG 7 97 1 CATCAATTTT 0.700315 -62 ACTCCCACTTCAAAATATTTATTAATGCCG 8 19 1 CAAAATATTT 0.840341 -99 ********** Masking position 2 Map Score: 9.03142 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 255 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 GAGCAGTTAAACCATTTAATTTTTTTTCAAC 2 11 1 ACCTTTAATT 0.922389 -134 AATAAAAATGAACATTTTAGTATTAAAGATG 2 41 0 AACTTTTAGT 0.948635 -104 TTATTATAACAATCTTTAAATACAAGAAAAC 2 67 1 AATTTTAAAT 0.901229 -78 TTCCGACACAAACTTTTAAGTGCCAGTATTC 2 108 1 AACTTTAAGT 0.986777 -37 CATTGCACAAACTTTTTAAGTGTAATGCACC 3 24 1 ACTTTTAAGT 0.970772 -60 GACGGGCATCAATTTTTAAGTGCCAGCACGA 7 101 1 AATTTTAAGT 0.978555 -58 *** ******* Masking position 6 Map Score: 4.2379 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 11 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 CACAAACTTTTAAGTGCCAGTATTCAATTAT 2 114 1 TAAGGCCAGT 0.928775 -31 TAAATATAATTTATTACCGGCTCTGGACCCA 6 34 1 TTATACCGGC 0.892227 -170 ATCACAAAAATCAACGCCACCATATAAAAAA 6 137 1 TCAAGCCACC 0.919778 -67 TTCACTGTTAAAGCCGGCAACATCCCTT 7 8 1 TTAAGCCGGC 0.99526 -151 CATGGAACATTAAAGGCCGGCATCTCTCCCA 7 39 1 TAAAGCCGGC 0.99526 -120 CATCAATTTTTAAGTGCCAGCACGATATAGT 7 107 1 TAAGGCCAGC 0.988275 -52 AAAATATTTATTAATGCCGGATGATTAGTGT 8 30 1 TTAAGCCGGA 0.970137 -88 **** ****** Masking position 3 Map Score: 6.65052 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 81 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TAATCATCCTCTGGTCATTCACAGTCACTG 6 70 0 CTGGTCATTC 0.963133 -134 GGGAGTAATAATAATCATCCTCTGGTCATT 6 81 0 ATAATCATCC 0.973145 -123 GTTGATTTTTGTGATCATCCCAAAGCAGAG 6 122 0 GTGATCATCC 0.985637 -82 ATGTATCACACTAATCATCCGGCATTAATA 8 38 0 CTAATCATCC 0.982472 -80 AAAAAAACTCATGGTCATCAGGTAAGTATC 8 84 1 ATGGTCATCA 0.944101 -34 ********** Masking position 5 Map Score: 2.44354 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 64 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 ********** No masking Map Score: 4.85601e-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: 4.85601e-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 10 ********** No masking Map Score: 4.85601e-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