AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_ctra_reg_300.orf -o00760_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 valS 126 Valyl tRNA Synthetase #2 atpK 41 ATP Synthase Subunit K #3 CT309 166 hypothetical protein #4 atpE 108 ATP Synthase Subunit E #5 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #6 cutE 63 Apolipoprotein N-Acetyltransferase #7 yciA 135 Acyl-CoA Thioester Hydrolase #8 CT538 300 hypothetical protein Motif number 1 GAGCTATAAGTACGAGGTGACTTTAACGGAGAACATA 1 50 0 TAGAGGCTTC 0.967081 -77 GATCTAACCTTAGGGGCTAACCGGATCATAATTGATC 4 43 1 TAGGGCCCGC 0.996734 -66 AAGGATAATATACGGGGTCTCTTTGTCAGGGTTTTGC 5 74 1 TAGGGGCTTC 0.996598 -27 GTAACTTCTAAGGGGATTCTTTTTCTCTCATCTTG 6 9 1 TAGGGGCTTC 0.996598 -55 TAAAGGGGCTCCCTTACTAGCTTACAT 6 47 0 TAAGGGCCCC 0.980953 -17 GTCTCAGAGTTACAGGCCCACCTCTACTCCCCAGTCA 7 68 0 TAAGGCCCTC 0.991848 -68 GCTCTAGGGGTAGGGGCATCCTGAATCGACTACATGC 8 108 0 TAGGGCCTGC 0.995801 -193 AGCCTCCTTCTAAAGGGAAGCCTTTCCGCCCATATCC 8 217 0 TAAGGGCCTC 0.993291 -84 TTCAGTTGCTTAATGGCAAACTGATTCTTCTTTTAAT 8 258 0 TATGGCCTGC 0.973469 -43 ** **** *** * Masking position 2 Map Score: 16.0131 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 13 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 ATTATGATCAAGCAAGAGGTGCC 1 1 0 AGCAAGAGCC 0.974205 -126 TAACGATTTAACCAACATAGCCCCTTAAGCCAA 3 18 0 ACCAACAACC 0.970756 -149 CTCAACGCATACAAAAAAACTCCGAGTTTGCGG 3 79 0 ACAAAAAACC 0.948841 -88 TACACCTTCAACTAAGAAACTCTCTAGACAGCT 3 134 0 ACTAAGAACT 0.818089 -33 ATCTGATACCAAGAAAAACAACGTTTATCT 4 89 0 ACCAAGAACA 0.971966 -20 CAAAACCCTGACAAAGAGACCCCGTATATTATC 5 77 0 ACAAAGAACC 0.985015 -24 TCAAGATGAGAGAAAAAGAATCCCCTTAGAAGT 6 14 0 AGAAAAAACC 0.948841 -50 AATGTAAGCTAGTAAGGGAGCCCCTTTA 6 46 1 AGTAAGGACC 0.896254 -18 ATAGAAGAAAATCAAGAAATTCCTTGGAGGA 7 9 0 ATCAAGAACC 0.968777 -127 TTCTATGTCGAGCAAGAAAATCATTTCT 8 6 0 AGCAAGAACA 0.971966 -295 TTTTACAAAAAGCAAAACAGGCCTAACCTCCCC 8 147 0 AGCAAAAACC 0.982636 -154 ******* * ** Masking position 5 Map Score: 13.5859 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 140 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 AGAAGGTTGATGTGCGTTTTTTTGAAAAAAATA 2 15 1 TTCGTTTTTT 0.950298 -27 CTCCGCAAACTCGGAGTTTTTTTGTATGCGTTG 3 77 1 TGAGTTTTTT 0.87121 -90 TCTCCAGAGATAGTTCTTCTTTTCTCAACGCAT 3 102 0 TGTCTTTTTT 0.905927 -65 TATTTGATTTTAAACGTTGTTATGATCTAACCT 4 20 1 TACGTTTTAT 0.935556 -89 GGATCATAATTGATCGTTTTTTTAAGATAAACG 4 65 1 TACGTTTTTT 0.989259 -44 TTTTTTAAGATAAACGTTGTTTTTCTTGGTATC 4 82 1 TACGTTTTTT 0.989254 -27 ACCCCGTATATTATCCTTTTTTTTTTTTAGCAA 5 59 0 TACCTTTTTT 0.986729 -42 AATGGCAAACTGATTCTTCTTTTAATCACCAGC 8 251 0 TATCTTTTTT 0.944463 -50 ACTTATCCTTACTTTTTTCAGTTGC 8 286 0 TACCTTCTTT 0.945569 -15 * * **** **** Masking position 7 Map Score: 8.93291 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 49 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 TTTCTATTTTTTTCAAAAAAACGCA 2 27 0 TATTTTTTCA 0.977835 -15 AACTAGGTAGTAATTTTTTGATATCGCTTGC 5 28 1 TATTTTTTGA 0.958434 -73 TCCTCCAAGGAATTTCTTGATTTTCTTCTA 7 10 1 GATTTCTTGA 0.87484 -126 GCTCGACATAGAAGTTTTTCATTTGAATTCA 8 26 1 GAGTTTTTCA 0.968073 -275 ACAAGCTCATTACGTTTTTCAATAAGACTTT 8 56 0 TAGTTTTTCA 0.973386 -245 ACTTATCCTTACTTTTTTCAGTTGCTTAAT 8 281 0 TATTTTTTCA 0.977835 -20 ** ******** Masking position 6 Map Score: 4.13871 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 42 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 GCCTTACTTCCATATGTTGTGACTAT 1 111 0 CTTCCATATG 0.965467 -16 GTAACTTCTAAGGGGATTCTTTTT 6 5 1 CTTCTAAGGG 0.965713 -59 TCTTGATTTTCTTCTATATCGAGACTACTA 7 25 1 CTTCTATATC 0.975591 -111 ATCACCCTTCTATATGAGTCTAATAG 7 120 0 CTTCTATATG 0.986513 -16 AAATGAAAAACTTCTATGTCGAGCAAGAAA 8 20 0 CTTCTATGTC 0.970725 -281 CACCAGCCTCCTTCTAAAGGGAAGCCTTTC 8 228 0 CTTCTAAAGG 0.970852 -73 ********** Masking position 6 Map Score: 6.67454 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 49 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 CCATATGTTGTGACTATTCTCGCATCTCTAA 1 97 0 TGACTATCTC 0.980235 -30 GCCTCTATCTTGACTAGTCTCAGAGTTACAG 7 90 0 TGACTATCTC 0.980235 -46 AGGCCTAACCTCCCCATGCTCTAGGGGTAGG 8 131 0 TCCCCAGCTC 0.976971 -170 CCCTGTTCTCTACCTACTCTCACTTCCTTGC 8 188 0 TACCTATCTC 0.966206 -113 TCCGCCCATATCCCTGTTCTCTACCTACTCT 8 199 0 TCCCTGTCTC 0.97649 -102 CTTCTTTTAATCACCAGCCTCCTTCTAAAGG 8 238 0 TCACCACCTC 0.96426 -63 ****** **** Masking position 10 Map Score: 2.55246 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 37 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 AGAACTATCTCTGGAGAGCTGTCTAGAGAG 3 118 1 CTGGAGAGCT 0.967386 -49 GGAGAGCTGTCTAGAGAGTTTCTTAGTTGA 3 130 1 CTAGAGAGTT 0.956988 -37 TGTTTTAGAACTAGGTAGTAATTTTTTGAT 5 20 1 CTAGGTAGTA 0.922006 -81 CATCTCTGTAATGGATAGTAGTCTCGATAT 7 40 0 ATGGATAGTA 0.882602 -96 ACAGAGATGACTGGGGAGTAGAGGTGGGCC 7 61 1 CTGGGGAGTA 0.990434 -75 CCCCTAGAGCATGGGGAGGTTAGGCCTGTT 8 135 1 ATGGGGAGGT 0.940335 -166 ********** Masking position 7 Map Score: 1.50519 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 116 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GGCACCTCTTGCTTGATCATAATCAA 1 6 1 CTCTTGCTTA 0.922579 -121 AGTTCTAAAACACTTGCTATC 5 1 0 CACTTGCTAC 0.987184 -100 TTTTTGATATCGCTTGCTTGCTAAAAAAAAA 5 42 1 CGCTTGCTTC 0.984789 -59 GGGGCTCCCTTACTAGCTTACATTCAAGATG 6 39 0 TACTAGCTTC 0.909321 -25 CTGAATCGACTACATGCTATCATGATTTTCC 8 94 0 TACATGCTAC 0.813517 -207 TACCTACTCTCACTTCCTTGCAAAAGTATTT 8 178 0 CACTTCCTTC 0.971461 -123 TTACTTTTTTCAGTTGCTTAATGGCAAACTG 8 272 0 CAGTTGCTTA 0.90278 -29 ********* * Masking position 8 Map Score: 2.09151 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 94 Number in noncoding regions = 1 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: -1.84498e-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 10 ********** No masking Map Score: -1.84498e-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 11 ********** No masking Map Score: -1.84498e-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