AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_ctra_reg_100.orf -o00051_ctra_100.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 kdsB 300 CMP-2-keto-3-deoxyoctulosonic acid synthetase #2 CT203 213 hypothetical protein #3 ybhI 29 Dicarboxylate Translocator #4 dut 36 dUTP Nucleotidohydrolase #5 accD 71 AcCoA Carboxylase/Transferase Beta #6 sodM 131 Superoxide Dismutase (Mn) #7 yhxB 151 Phosphomannomutase #8 tpiS 196 Triosephosphate Isomerase #9 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #10 kdsA 300 KDO Synthetase #11 mraY 145 Muramoyl-Pentapeptide Transferase #12 mrsA 245 Phosphoglucomutase Motif number 1 ATAATCTTGATTGTTAACGATCTCCTTGTTAGGATGGTCGG 1 170 1 TGTTGCCTTA 0.895616 -131 GGTCGGGTTCTGTGTACTAGATCCCTAGTCATATGAATATG 1 205 1 TTGTACCTTA 0.947696 -96 CATATGAATATGTTTGGTAAGGGCCTACTGTATAAGAAGTT 1 234 1 TTTTACCTTT 0.962431 -67 ATCCTGTAGCTCTTTGTTAATGCTTTTTTTTGTCATAAATC 2 23 1 TTTTATTTTT 0.710173 -191 CAACTTAATGTTGTTTAGATTCGCCTTGTCTGCTTAGACTC 2 107 1 TGTTACCTTT 0.961678 -107 AGAAGGCCCTCTTTTTGAAGAGCCTCCTATGATCTT 4 7 0 TTTTACCTTT 0.962431 -30 CAGGCTTCTGTTTTTGTAAAAAACTTGCTTAACTTAGAAAG 7 37 0 TTTTACTTTA 0.95303 -115 GCTTAAATAGTTGGTTTTAGCCCCTTTGTTAT 8 2 0 TGGTACTTTA 0.916929 -195 CTTGTCTTACTTTTTTCTGTGAATTTGCTTAAATAGTTGGT 8 28 0 TTTTGTTTTA 0.455866 -169 TTATATGATTTATTTTCTATTGCTTTGATATAAATCTCTTG 8 83 0 TTTTATTTTT 0.710173 -114 AATTACTACCTAGTTCTAAAACACTTGCTATC 9 2 0 TGTTACTTTT 0.939781 -99 TTGCGTTTGATTGGTACGAGAAACCTTATAAAATCCTAGGA 10 180 0 TGGTACCTTA 0.946664 -121 TGTAAGATGCTCTTTTTAACTTGCCTTTTGAAAGCTTAAGT 11 63 1 TTTTACCTTA 0.970262 -83 TTTCGATAATTATTTTCTTACTTCTTATTTAAAAAGTGAAT 12 38 1 TTTTTCTTTA 0.666332 -208 AACATCAATCTGGGTATCAATAGCTTACTATTTATAACCAA 12 97 0 TGGTACTTTT 0.896552 -149 TTTATCAAAATCTTTGCAATTCGCCTTCTTAAGACCTTTCC 12 141 0 TTTTACCTTA 0.970262 -105 * *** * *** * * Masking position 16 Map Score: 14.8628 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 166 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 CCTAACAAGGAGATCGTTAACAATCAAGAT 1 173 0 AGATCGTTAA 0.707673 -128 TAACAGTTCGAGAGCGTGCAACGCTATTAT 2 65 0 AGAGCGTGCA 0.675376 -149 GGACTCTCAGAAAACGAGCAGGCCGTAGCA 2 169 0 AAAACGAGCA 0.874309 -45 TCTTTACAAAAAATTGAGCAATAATTTTAT 5 42 0 AAATTGAGCA 0.703061 -30 AGCCTGTAGAAAATAGAGAAGGTGGCGAGG 6 85 1 AAATAGAGAA 0.939436 -47 TCCTTGCAAGAAATCGAGTATTACGCTTTG 8 134 1 AAATCGAGTA 0.703059 -63 GTATTTTGTAAGATAGATCAAAGCGTAATA 8 152 0 AGATAGATCA 0.781263 -45 TTTAAAGAGGAAATAGTGAATCCAAGGAAT 10 141 0 AAATAGTGAA 0.913143 -160 TCAGCTGAGAAGATCGTTAAGAACTCTGAC 10 243 1 AGATCGTTAA 0.707673 -58 TTTAGAATAGAAATAGTTAACTTTCAAGTC 11 31 1 AAATAGTTAA 0.694959 -115 AAGGCAAGTTAAAAAGAGCATCTTACAGCG 11 60 0 AAAAAGAGCA 0.865091 -86 CTTAAGTTTAAGATAGAGAATTTCTTATAG 11 97 1 AGATAGAGAA 0.938252 -49 TTCCCATAATAAAACGAGAAAACAG 11 131 1 AAAACGAGAA 0.865091 -15 CTTCTTATTTAAAAAGTGAATGGCCGTTTG 12 58 1 AAAAAGTGAA 0.800254 -188 ATTTTGATAAAAATAGGGAATATTTATCTC 12 171 1 AAATAGGGAA 0.763867 -75 ATATTCTTAGGGATAGAGCA 12 236 1 GGATAGAGCA 0.676415 -10 ********** Masking position 3 Map Score: 11.9291 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 333 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 3 GATAATGTATTTGATTATTTTTCACGAATGAA 1 107 0 TGATTTTTTT 0.684694 -194 CCCTAGTCATATGAATATGTTTGGTAAGGGCC 1 227 1 AGAATTGTTT 0.701248 -74 CTCTTTGTTAATGCTTTTTTTTGTCATAAATC 2 32 1 AGCTTTTTTT 0.976425 -182 CAAAAAATTGAGCAATAATTTTATTGTAATTT 5 34 0 ACAATATTTT 0.609367 -38 CGAGGATAGTAACCTTATTTTTTAGGATGGCT 6 110 1 ACCTTTTTTT 0.953985 -22 ACTATACGTCAGGCTTCTGTTTTTGTAAAAAA 7 55 0 AGCTTTGTTT 0.9586 -97 TTATTTTTATATGATTTATTTTCTATTGCTTT 8 98 0 AGATTATTTT 0.93159 -99 CTTGCAAGGAAGGCTTATTTTTATATGATTTA 8 112 0 AGCTTTTTTT 0.976401 -85 CCCGTATATTATCCTTTTTTTTTTTTAGCAAG 9 58 0 ACCTTTTTTT 0.954934 -43 TGCCTTTTGAAAGCTTAAGTTTAAGATAGAGA 11 84 1 AGCTTAGTTT 0.934792 -62 CGAAAACTAAATGATTTATTTTTTTTGTTTTT 12 11 0 AGATTATTTT 0.93159 -235 AAACTAACTGATCCTTGATTTTCAGAGATAAA 12 193 0 ACCTTATTTT 0.938993 -53 * **** ***** Masking position 6 Map Score: 12.2234 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 147 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 CTCATAGGCTCTCTTCGTTCCTATATTCGA 1 65 1 CTCTTCGTTC 0.922114 -236 TTTCTGAGAGTCCTTCCTTCCGTGAAAGGC 2 186 1 TCCTTCCTTC 0.971386 -28 ATAAAAATAAGCCTTCCTTGCAAGAAATCG 8 120 1 GCCTTCCTTG 0.952184 -77 TCTGGAAGCACTCTTCCTTCTTCTATTCCT 10 62 1 CTCTTCCTTC 0.986213 -239 CTTCCTTCTTCTATTCCTTGAGATGCTTGT 10 74 1 CTATTCCTTG 0.942401 -227 TGCCCATAACCCATTCCTTGGATTCACTAT 10 129 1 CCATTCCTTG 0.941305 -172 TTAAAAAACCTTCTTCCTAGGATTTTATAA 10 166 1 TTCTTCCTAG 0.861243 -135 GATAATTATTTTCTTACTTCTTATTTAAAA 12 42 1 TTCTTACTTC 0.794563 -204 ********** Masking position 5 Map Score: 4.37237 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 192 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 GTGAATAATCTTGATTGTTAACGATCTCCTTGT 1 166 1 TTGTTGTTAG 0.936255 -135 TCATATGAATATGTTTGGTAAGGGCCTACTGTA 1 233 1 ATGTTGGTAG 0.940872 -68 TAGATTCGCCTTGTCTGCTTAGACTCCGAGCTC 2 122 1 TTGCTGCTAA 0.914209 -92 TTTTATTATTGATTGGTTAAAAAAAATTACA 5 9 1 TTGTTGGTAA 0.98714 -63 TTGATATCGCTTGCTTGCTAAAAAAAAAAAAGG 9 45 1 TTGTTGCTAA 0.975681 -56 ATTCCTTGAGATGCTTGTTCAAACTGCTAATCC 10 86 1 ATGTTGTTAA 0.904719 -215 CCATTTGCGTTTGATTGGTACGAGAAACCTTAT 10 192 0 TTGTTGGTCA 0.953245 -109 GTTTGAATTTTTGTTTGGTTATAAATAGTAAGC 12 83 1 TTGTTGGTAA 0.98714 -163 *** ***** * * Masking position 6 Map Score: 4.81083 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 TACAGTAGGCCCTTACCAAACATATTCATA 1 236 0 CCTTACCAAA 0.928955 -65 TCATAGGAGGCTCTTCAAAAAGAGGGCCTT 4 15 1 CTCTTCAAAA 0.877382 -22 AAACCATCCTCTTTACAAAAAATTGAGCAA 5 51 0 CTTTACAAAA 0.975622 -21 TAAGCAAGTTTTTTACAAAAACAGAAGCCT 7 47 1 TTTTACAAAA 0.892474 -105 CTCATCCACGCTCTACCAAATACAGATACA 7 104 0 CTCTACCAAA 0.957686 -48 CTTTGATCTATCTTACAAAATACATGCACA 8 159 1 TCTTACAAAA 0.840422 -38 ACTATTTCCTCTTTAAAAAACCTTCTTCCT 10 154 1 CTTTAAAAAA 0.901444 -147 CACAATTCCACTCTAAAAAAGGATACCCTT 10 279 1 CTCTAAAAAA 0.901335 -22 ********** Masking position 8 Map Score: 4.31055 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 130 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 CATCCTAACAAGGAGATCGTTAACAATCAAG 1 175 0 AGAGATCGTT 0.934215 -126 AGCGTGGATGAGTGTTTCGTTCTGATCGGAA 7 122 1 AGGTTTCGTT 0.960907 -30 GCACTATGGAAGTGTTTCCTT 10 1 0 AGGTTTCCTT 0.960907 -300 CTGTCAGCTGAGAAGATCGTTAAGAACTCTG 10 240 1 AGAGATCGTT 0.934216 -61 AAAAGGGTATCCTTTTTTAGAGTG 10 287 0 AGGTATCCTT 0.960872 -14 GTAAAAGATCAGAATTTCTTTTTAGAATAGA 11 11 1 AGATTTCTTT 0.917563 -135 TTTAAGATAGAGAATTTCTTATAGGAGCTTC 11 103 1 AGATTTCTTA 0.666073 -43 TCTATCCCTAAGAATATCCTTTGGCTCAAAA 12 222 0 AGATATCCTT 0.961654 -24 ** ******** Masking position 1 Map Score: 4.56422 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 48 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: 4.152e-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 CAAGATTATTCACAGAGCTACTAGCTTTCTTAACTT 1 143 0 CAAGGCTAGT 0.992019 -158 AAAGCATTAACAAAGAGCTACAGGATAACGATAGAT 2 13 0 CAAGGCTGGT 0.974519 -201 GAGCAACGACCATGGAGCTCGGAGTCTAAGCAGACA 2 133 0 CAGGGCTAGC 0.970023 -81 GAAACACTTCCATAGTGCTGGAAGATACTATACCTT 10 14 1 CAAGGCTAGT 0.992019 -287 GGTGTATAGTCAAATTTCTGTCAGCTGAGAAGATCG 10 223 1 CAATTCTAGT 0.917441 -78 TGCCTTTAGTCAGAGTTCTTAACGATCTTCTCAGCT 10 245 0 CAAGTCTCGT 0.937302 -56 AGTTAACTTTCAAGTCGCTGTAAGATGCTCTTTTTA 11 45 1 CAGTGCTAGT 0.965356 -101 CTCTGAAAATCAAGGATCAGTTAGTTTTGAGCCAAA 12 198 1 CAGGTCAAGT 0.895113 -48 ** ** *** ** * Masking position 2 Map Score: 4.13559 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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: 4.152e-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 TGAGAAGGCTTGTAAATATCTAGAAGTGTAT 1 38 0 TGTAAATACT 0.835216 -263 AAATATTCACTGTCAAGAGCTATCCACATCT 6 24 0 TGTCAAGACT 0.915957 -108 CTTCTGTTTTTGTAAAAAACTTGCTTAACTT 7 43 0 TGTAAAAACT 0.920955 -109 AAGCAAGCGATATCAAAAAATTACTACCTAG 9 30 0 TATCAAAAAT 0.772511 -71 CGAGAAACCTTATAAAATCCTAGGAAGAAGG 10 174 0 TATAAAATCT 0.68053 -127 AGAAAATAATTATCGAAAACTAAATGATTTA 12 25 0 TATCGAAACT 0.889831 -221 TCAATCTGGGTATCAATAGCTTACTATTTAT 12 103 0 TATCAATACT 0.929721 -143 TCCCTATTTTTATCAAAATCTTTGCAATTCG 12 159 0 TATCAAAACT 0.968163 -87 ******** ** Masking position 6 Map Score: 0.854644 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 106 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 12 ********** No masking Map Score: 4.152e-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 13 ********** No masking Map Score: 4.152e-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 14 ********** No masking Map Score: 4.152e-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