AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00120_ctra_reg_300.orf -o00120_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #2 cutE 63 Apolipoprotein N-Acetyltransferase #3 yciA 135 Acyl-CoA Thioester Hydrolase #4 CT538 300 hypothetical protein Motif number 1 AGGATAATATACGGGGTCTCTTTGTCAGGGTTT 1 75 1 ACGGGGTCTT 0.95176 -26 GTAACTTCTAAGGGGATTCTTTTTCTCTCATC 2 10 1 AAGGGGTCTT 0.755105 -54 TAAAGGGGCTCCCTTACTAGCTTAC 2 49 0 AAGGGGCCTT 0.502836 -15 TCCTCCAAGGAATTTCTTGATTTTCTTCT 3 7 1 AAGGAATCTG 0.950427 -129 CTTGTGCCTAACGGAAAATCATGATAGCATGTA 4 82 1 ACGGAATCTG 0.969617 -219 GCTCTAGGGGTAGGGGCATCCTGAATCGACTAC 4 112 0 TAGGGGTCTG 0.979536 -189 CCTCCTTCTAAAGGGAAGCCTTTCCGCCCATAT 4 219 0 AAGGGACCTT 0.891222 -82 TTCCCTTTAGAAGGAGGCTGGTGATTAAAAGAA 4 235 1 AAGGAGTGTG 0.957944 -66 ****** ** ** Masking position 12 Map Score: 12.2386 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 79 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 2 GTAACTTCTAAGGGGATTCTTTTTCT 2 5 1 CTTCTAAGGA 0.989974 -59 TCTTGATTTTCTTCTATATCGAGACTACTATC 3 25 1 CTTCTATTGA 0.995351 -111 AGTCTAATAGCCTCTATCTTGACTAGTCTCAG 3 98 0 CCTCTATTGA 0.987804 -38 ATCACCCTTCTATATGAGTCTAATAGCC 3 118 0 CTTCTATTAG 0.912289 -18 AAATGAAAAACTTCTATGTCGAGCAAGAAAAT 4 18 0 CTTCTATTGA 0.995518 -283 CACCAGCCTCCTTCTAAAGGGAAGCCTTTCCG 4 226 0 CTTCTAAGGA 0.989708 -75 ******* * ** Masking position 6 Map Score: 8.30702 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 29 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 3 GATAGCAAGTGTTTTAGAACT 1 1 1 GTAGCAAGTG 0.989892 -100 GTGTTTTAGAACTAGGTAGTAATTTTTTGAT 1 19 1 ATAGGTAGTA 0.901936 -82 TTTTTTTTTAGCAAGCAAGCGATATCAAAAA 1 42 0 GAAGCAAGCG 0.95858 -59 CATCTTGAATGTAAGCTAGTAAGGGAGCCCC 2 39 1 GAAGCTAGTA 0.967105 -25 GAAAAACGTAATGAGCTTGTGCCTAACGGAA 4 67 1 AGAGCTTGTG 0.863262 -234 GGAAAATCATGATAGCATGTAGTCGATTCAG 4 94 1 GTAGCATGTA 0.933397 -207 AAATACTTTTGCAAGGAAGTGAGAGTAGGTA 4 178 1 GAAGGAAGTG 0.978827 -123 AGGAAGTGAGAGTAGGTAGAGAACAGGGATA 4 191 1 ATAGGTAGAG 0.830074 -110 * ********* Masking position 4 Map Score: 3.97109 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 134 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 TATTATCCTTTTTTTTTTTTAGCAAGCAAG 1 54 0 TTTTTTTTTT 0.927293 -47 TCTAAGGGGATTCTTTTTCTCTCATCTTGA 2 17 1 TTCTTTTTCT 0.803523 -47 GAATTTCTTGATTTTCTTCTATATCGAGAC 3 20 1 ATTTTCTTCT 0.920378 -116 GACATAGAAGTTTTTCATTTGAATTCAAAG 4 30 1 TTTTTCATTT 0.960408 -271 TGCTATCATGATTTTCCGTTAGGCACAAGC 4 81 0 ATTTTCCGTT 0.808672 -220 GTTAGGCCTGTTTTGCTTTTTGTAAAAATA 4 153 1 TTTTGCTTTT 0.93675 -148 GGCAAACTGATTCTTCTTTTAATCACCAGC 4 251 0 TTCTTCTTTT 0.969302 -50 TATCCTTACTTTTTTCAGTTGCTTAATGGC 4 278 0 TTTTTCAGTT 0.93214 -23 ********** Masking position 4 Map Score: 4.36356 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 731 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 5 AGATGACTGGGGAGTAGAGGTGGGCCTGTA 3 65 1 GGAGTAGAGG 0.985486 -71 GAGACTAGTCAAGATAGAGGCTATTAGACT 3 100 1 AAGATAGAGG 0.852395 -36 CCATGCTCTAGGGGTAGGGGCATCCTGAAT 4 119 0 GGGGTAGGGG 0.997107 -182 CCCTACCCCTAGAGCATGGGGAGGTTAGGC 4 130 1 AGAGCATGGG 0.931393 -171 GTAGAGAACAGGGATATGGGCGGAAAGGCT 4 206 1 GGGATATGGG 0.985486 -95 ********** Masking position 6 Map Score: 1.54037 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 107 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 6 AAAAAAAAAAGGATAATATACGGGGTCTCTTTGT 1 66 1 GGATATATCG 0.964219 -35 TCTCTGTAATGGATAGTAGTCTCGATATAGAAGA 3 34 0 GGATATAGCG 0.994568 -102 AGAGATGACTGGGGAGTAGAGGTGGGCCTGTAAC 3 63 1 GGGGATAGGG 0.972954 -73 CCTGTAACTCTGAGACTAGTCAAGATAGAGGCTA 3 89 1 TGAGATAGCG 0.98506 -47 TCAAGATAGAGGCTATTAGACTCATATAGAAGGG 3 108 1 GGCTATAGCA 0.953741 -28 TAGAGCATGGGGAGGTTAGGCCTGTTTTGCTTTT 4 139 1 GGAGGTAGCG 0.992475 -162 TGCAAGGAAGTGAGAGTAGGTAGAGAACAGGGAT 4 187 1 TGAGATAGTA 0.831648 -114 ***** *** * * Masking position 8 Map Score: 2.44075 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 51 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 7 ********** No masking Map Score: -7.36532e-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: -7.36532e-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: -7.36532e-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