AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00770_ctra_reg_300.orf -o00770_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 AAACCCTGACAAAGAGACCCCGTATATTATCCT 1 75 0 AAGACCCCGT 0.949818 -26 GATGAGAGAAAAAGAATCCCCTTAGAAGTTAC 2 10 0 AAGACCCCTT 0.747613 -54 GTAAGCTAGTAAGGGAGCCCCTTTA 2 49 1 AAGGCCCCTT 0.502672 -15 AGAAGAAAATCAAGAAATTCCTTGGAGGA 3 7 0 CAGATTCCTT 0.949506 -129 TACATGCTATCATGATTTTCCGTTAGGCACAAG 4 82 0 CAGATTCCGT 0.97137 -219 GTAGTCGATTCAGGATGCCCCTACCCCTAGAGC 4 112 1 CAGACCCCTA 0.980054 -189 ATATGGGCGGAAAGGCTTCCCTTTAGAAGGAGG 4 219 1 AAGGTCCCTT 0.887612 -82 TTCTTTTAATCACCAGCCTCCTTCTAAAGGGAA 4 235 0 CACACTCCTT 0.960121 -66 ** ** ****** Masking position 2 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 0.988701 -59 TCTTGATTTTCTTCTATATCGAGACTACTATC 3 25 1 CTTCTATTGA 0.994798 -111 AGTCTAATAGCCTCTATCTTGACTAGTCTCAG 3 98 0 CCTCTATTGA 0.986269 -38 ATCACCCTTCTATATGAGTCTAATAGCC 3 118 0 CTTCTATTAG 0.905278 -18 AAATGAAAAACTTCTATGTCGAGCAAGAAAAT 4 18 0 CTTCTATTGA 0.994946 -283 CACCAGCCTCCTTCTAAAGGGAAGCCTTTCCG 4 226 0 CTTCTAAGGA 0.988466 -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 GATAGCAAGTGTTTTAGAACTAGGTAGTAATTTTTT 1 11 1 GTTTTATAGA 0.968178 -90 TATCCTTTTTTTTTTTTAGCAAGCAAGCGATATCAA 1 45 0 TTTTTAAAGA 0.987129 -56 AGCTCATTACGTTTTTCAATAAGACTTTGAATTCAA 4 48 0 GTTTTAAAGT 0.968177 -253 TGCAAAAGTATTTTTACAAAAAGCAAAACAGGCCTA 4 155 0 TTTTTAAAGA 0.987341 -146 GTAAAAATACTTTTGCAAGGAAGTGAGAGTAGGTAG 4 174 1 TTTTGAAAGA 0.984853 -127 AGAAGAATCAGTTTGCCATTAAGCAACTGAAAAAAG 4 264 1 GTTTGAAAGA 0.990313 -37 ***** * *** * Masking position 8 Map Score: 3.64184 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 58 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 4 TATATTATCCTTTTTTTTTTTTAGCAAGCA 1 56 0 TTTTTTTTTT 0.915689 -45 TCTAAGGGGATTCTTTTTCTCTCATCTTGA 2 17 1 TTCTTTTTCT 0.776917 -47 GAATTTCTTGATTTTCTTCTATATCGAGAC 3 20 1 ATTTTCTTCT 0.90778 -116 GACATAGAAGTTTTTCATTTGAATTCAAAG 4 30 1 TTTTTCATTT 0.953825 -271 TGCTATCATGATTTTCCGTTAGGCACAAGC 4 81 0 ATTTTCCGTT 0.782574 -220 GTTAGGCCTGTTTTGCTTTTTGTAAAAATA 4 153 1 TTTTGCTTTT 0.926536 -148 GGCAAACTGATTCTTCTTTTAATCACCAGC 4 251 0 TTCTTCTTTT 0.964143 -50 TATCCTTACTTTTTTCAGTTGCTTAATGGC 4 278 0 TTTTTCAGTT 0.921243 -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 GATAGCAAGTGTTTTAGAACT 1 1 1 GATAGCAAGG 0.986238 -100 TTTTTTTTTAGCAAGCAAGCGATATCAAAAA 1 42 0 GCAAGCAAGG 0.959006 -59 TTCAAGATGAGAGAAAAAGAATCCCCTTAGA 2 17 0 GAGAAAAAGA 0.784347 -47 TTGAATGTAAGCTAGTAAGGGAGCCCCTTTA 2 43 1 GCTAGTAAGG 0.931128 -21 AACTTCTATGTCGAGCAAGAAAATCATTTCT 4 11 0 TCGAGCAAGA 0.958556 -290 GGAAAATCATGATAGCATGTAGTCGATTCAG 4 94 1 GATAGCATGA 0.96034 -207 CCCCTACCCCTAGAGCATGGGGAGGTTAGGC 4 129 1 TAGAGCATGG 0.940136 -172 GCAAGGAAGTGAGAGTAGGTAGAGAACAGGG 4 188 1 GAGAGTAGGA 0.956364 -113 AGAGTAGGTAGAGAACAGGGATATGGGCGGA 4 199 1 GAGAACAGGA 0.949669 -102 ********* * Masking position 7 Map Score: 6.73939 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 324 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 6 ACAAAGAGACCCCGTATATTATCCTTTTTTTTTT 1 66 0 CGATATATCC 0.959295 -35 TCTTCTATATCGAGACTACTATCCATTACAGAGA 3 34 1 CGCTATATCC 0.993965 -102 GTTACAGGCCCACCTCTACTCCCCAGTCATCTCT 3 63 0 CCCTATCCCC 0.969194 -73 TAGCCTCTATCTTGACTAGTCTCAGAGTTACAGG 3 89 0 CGCTATCTCA 0.984666 -47 CCCTTCTATATGAGTCTAATAGCCTCTATCTTGA 3 108 0 TGCTATAGCC 0.947512 -28 AAAAGCAAAACAGGCCTAACCTCCCCATGCTCTA 4 139 0 CGCTACCTCC 0.991407 -162 ATCCCTGTTCTCTACCTACTCTCACTTCCTTGCA 4 187 0 TACTATCTCA 0.812035 -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