AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ifruR_ctra_opreg_300.orf -g0.413 -x5 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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 CT196 223 hypothetical protein #2 gcp_1 75 O-Sialoglycoprotein Endopeptidase #3 oppB_1 158 Oligopeptide Permease #4 oppC_1 31 Oligopeptide Permease #5 CT203 213 hypothetical protein #6 ybhI 29 Dicarboxylate Translocator #7 tpiS 196 Triosephosphate Isomerase #8 CT330 208 hypothetical protein #9 pykF 96 Pyruvate Kinase #10 ptsH 136 PTS Phosphocarrier Protein Hpr #11 CT338 283 hypothetical protein #12 CT646 100 hypothetical protein #13 CT691 160 hypothetical protein #14 pgk 127 Phosphoglycerate Kinase Motif number 1 AAAAACCGTTTTATTTCTAAGTCGACTAATC 1 97 1 TTATTTCAAG 0.701145 -127 CTATTTCATTTCTTTTGCAAAAACTCTCTAC 1 174 1 TCTTTTGAAA 0.895654 -50 AATGTTTCCCTCTTTTTTAAGTGTTCGCT 2 57 1 TCTTTTTAAG 0.958461 -19 AAAGAGAGAATCTTTTCTACGCACGGAGTAA 3 20 0 TCTTTTCACG 0.935478 -139 GAAAAGATTCTCTCTTTAAAATGCGGAGAGG 3 34 1 TCTCTTTAAA 0.773979 -125 TAATACTCGATTTCTTGCAAGGAAGGCTTAT 7 126 0 TTTCTTGAAG 0.806807 -71 CCTGTGCATGTATTTTGTAAGATAGATCAAA 7 160 0 TATTTTGAAG 0.79632 -37 TCAAAAGAGATTTTTTCCACGTTT 8 4 0 TTTTTTCACG 0.872553 -205 AGGTCTATGATCTCTTCCAAACGTTTCATAG 8 40 0 TCTCTTCAAA 0.896023 -169 AAAGCGTACTTTTTTTCTAAAACTAGCCTT 10 10 0 TTTTTTCAAA 0.912327 -127 CCTTAGAGCTTCTTTTCAAAGCTAAAGAGAA 10 43 0 TCTTTTCAAG 0.983069 -94 AATAAAAACATCTTTTTCAAGAAAAACATTA 12 32 0 TCTTTTTAAG 0.958461 -69 AAGATGTTTTTATTTTTTAAAATGAGCGCTC 12 49 1 TATTTTTAAA 0.602204 -52 TTTTTCTTTATCTTTTTAAAATGAAGAGCGC 12 74 0 TCTTTTTAAA 0.897509 -27 AATTTTTTGTTTTTTTCTAAGATTTTTCACG 13 48 0 TTTTTTCAAG 0.964812 -113 TTGGGAGCATTTTTCTCAAAGACAATTAAAA 13 131 1 TTTTCTCAAG 0.776623 -30 ******* *** Masking position 6 Map Score: 16.7064 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 404 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 CTTGGGACAAAAGAATGGCTTCAACTTTGTA 1 42 0 AAGAATGGTT 0.870501 -182 TTACTAATTAAAAAAACCGTTTTATTTCTAA 1 86 1 AAAAAACCTT 0.769437 -138 AGTTGAAAACATAAAAGGCCTTTGCCAAGAG 3 92 0 ATAAAAGGCT 0.714245 -67 TAATTTAATAAAGGATTTCTAAAACAA 4 7 1 AATAAAGGTT 0.916917 -25 TTTATGACAAAAAAAAGCATTAACAAAGAGC 5 31 0 AAAAAAGCTT 0.936883 -183 CCTTTCACGGAAGGAAGGACTCTCAGAAAAC 5 184 0 AAGGAAGGCT 0.940268 -30 CCTTCCTTCCGTGAAAGGCTTGAAGGT 5 197 1 GTGAAAGGTT 0.841098 -17 GATTTCTTGCAAGGAAGGCTTATTTTTATAT 7 118 0 AAGGAAGGTT 0.968375 -79 TGAAGACGCTATGAAACGTTTGGAAGAGATC 8 32 1 ATGAAACGTT 0.698501 -177 ATCCGAAATGAAAGAAGCCTTCAACTATACA 9 33 0 AAAGAAGCTT 0.910095 -64 TTAGCTTTGAAAAGAAGCTCTAAGGGTTTAT 10 49 1 AAAGAAGCCT 0.839863 -88 AGAATACGATAATAAACCCTTAGAGCTTCTT 10 60 0 AATAAACCTT 0.636428 -77 ATCTGCTCGAGAGAAAGCACTTCTACCGGTT 11 26 0 GAGAAAGCCT 0.892395 -258 ACTTCTTCCCAAGAAAGCGTTCTGCGCATCT 11 53 0 AAGAAAGCTT 0.96917 -231 CGGTTGCCCAGAGGATGGTTTGAGTTGGTAG 11 100 1 GAGGATGGTT 0.703711 -184 AAAGACAATTAAAAAAGGCTTAT 13 148 1 AAAAAAGGTT 0.954625 -13 GTGGCACTGAGATAAAGGCTTGAGTTTTCCT 14 63 1 GATAAAGGTT 0.85004 -65 ******** ** Masking position 5 Map Score: 14.9351 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 528 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 TCTCGAACTGTTATCTTTTGCGTGTCAACTTAA 5 82 1 TTTCTTGCGT 0.905155 -132 GCTAATCTTCTTGTCTTACTTTTTTCTGTGAAT 7 45 0 TTTCTATTTT 0.84696 -152 ATATGATTTATTTTCTATTGCTTTGATATAAAT 7 89 0 TTTCATGCTT 0.865575 -108 TACGCTTTTCTTCTCTTTAGCTTTGAAAAGAAG 10 33 1 TTTCTTGCTT 0.980649 -104 TAAGGGTTTATTATCGTATTCTTTTGATTGGAT 10 69 1 TTTCTATCTT 0.937746 -68 TGGATTTAGCTTATCATCATTTTGTTTTTACAC 10 97 1 TTTCTCTTTT 0.823059 -40 TCCCTGGTATTTGTCATTTTTTTCCTCTTTGAG 11 206 1 TTTCTTTTTT 0.952174 -78 TTAGCGTTTTTCTTTATCTTTTTAAAATGA 12 81 0 TTTCTTTCTT 0.98188 -20 GAACCAAAATTTTTTGTTTTTTTCTAAGATTTT 13 53 0 TTTTTTTTTT 0.634955 -108 ATAAGCCTTTTTTAATTGTCTTTGAGAAAAAT 13 139 0 TTTATTTCTT 0.825611 -22 AAGGCTTGAGTTTTCCTTTGCTTAGGCCTATAA 14 77 1 TTTCTTGCTT 0.980649 -51 ** ** ** **** Masking position 4 Map Score: 7.65747 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 TTCTTTTGCAAAAACTCTCTACTTTAAATT 1 183 1 AAAACTCTCT 0.954057 -41 TTGCTTGATTAACAATCTCATGATACGATC 2 15 1 AACAATCTCA 0.788205 -61 CGCACGGAGTAAAAACATCTT 3 2 0 AAAAACATCT 0.825702 -157 GTGATAATTTAACACTCTCTAGACAAGACC 3 63 0 AACACTCTCT 0.910321 -96 TTGCTTTGATATAAATCTCTTGGATATGCT 7 75 0 ATAAATCTCT 0.870061 -122 AAACGTGGAAAAAATCTCTTTTGAAGACG 8 10 1 AAAAATCTCT 0.976975 -199 GCAGAAAACCAAAAATCTCGAAATAGCTCG 11 153 0 AAAAATCTCG 0.918594 -131 TTAAAAAACTCTGTTTATAATT 12 3 1 AAAAAACTCT 0.898168 -98 TTTAAAAAATAAAAACATCTTTTTCAAGAA 12 40 0 AAAAACATCT 0.825702 -61 ********** Masking position 4 Map Score: 5.83026 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 155 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 CATGGAGCTCGGAGTCTAAGCAGACAAGGCGAATC 5 124 0 GGCTAGCAAC 0.978316 -90 ACGGAAGGAAGGACTCTCAGAAAACGAGCAGGCCG 5 174 0 GGCTAGAAAC 0.972483 -40 AAGTAAGACAAGAAGATTAGCATATCCAAGAGATT 7 57 1 AGATAGCAAT 0.621231 -140 TACATGCACAGGTTATTCAGCAAATCTC 7 179 1 GGTTAGCAAT 0.97123 -18 CACTTCTACCGGTTGTTTAGAACAAGCTG 11 5 0 GGTTAGAAAA 0.94812 -279 GGGCAACCGTGGAACTTTAGCAAACACTTCTTCCC 11 74 0 GGTTAGCAAC 0.985861 -210 TTTCTGCATTGGGTGTTGAGAATACTGATTTCCCT 11 176 1 GGTTAGAAAC 0.981217 -108 CTTTTTTAATTGTCTTTGAGAAAAATGCTCCCAAA 13 130 0 TGTTAGAAAA 0.671453 -31 CCTTTGCTTAGGCCTATAAGAAAATTTAGGTTAAG 14 91 1 GGATAGAAAT 0.919407 -37 ** ** **** ** Masking position 7 Map Score: 4.79716 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 6 TTTTGGAAGGAGAGGATCGTATCATGAGAT 2 29 0 AGAGGATCGT 0.968757 -47 CATTTTAAAGAGAGAATCTTTTCTACGCAC 3 27 0 AGAGAATCTT 0.899252 -132 TCATAAATCTATAATAGCGTTGCACGCTCT 5 55 1 ATAATAGCGT 0.61777 -159 TGTAAGATAGATCAAAGCGTAATACTCGAT 7 146 0 ATCAAAGCGT 0.72567 -51 ATACAAGGCAAGAGAAGCTTCTAAAGACGT 8 87 0 AGAGAAGCTT 0.906281 -122 CGACCAACGGAGCGAATCGTAGCCGGTC 8 191 1 AGCGAATCGT 0.957489 -18 ATTAGTGAGTAGAATATCTTCTAGAATATC 9 61 0 AGAATATCTT 0.708867 -36 GCTAAAGAGAAGAAAAGCGTACTTTTTTTC 10 24 0 AGAAAAGCGT 0.955539 -113 ACGGTTGCCCAGAGGATGGTTTGAGTTGGT 11 99 1 AGAGGATGGT 0.800599 -185 GTCTGTCTCAAGCAGATCGTATCGAGCTAT 11 131 1 AGCAGATCGT 0.932631 -153 ********** Masking position 6 Map Score: 4.42899 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 235 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ATACGATCCTCTCCTTCCAAAATGTTTCCC 2 37 1 CTCCTTCCAA 0.969004 -39 CGTTTCATAGCGTCTTCAAAAGAGATTTTT 8 20 0 CGTCTTCAAA 0.926334 -189 AGGTCTATGATCTCTTCCAAACGTTTCATA 8 41 0 TCTCTTCCAA 0.840765 -168 AATTGATCAGCCTCTTCATACAAGGCAAGA 8 104 0 CCTCTTCATA 0.947552 -105 TTAGCAAACACTTCTTCCCAAGAAAGCGTT 11 63 0 CTTCTTCCCA 0.921023 -221 CGCTCGAGGTCCCCTTCAAATAGTAGGAGA 13 20 0 CCCCTTCAAA 0.976023 -141 CAAAATATACCTCCTTCATATATATATTTG 13 104 0 CTCCTTCATA 0.932772 -57 ********** Masking position 10 Map Score: 2.51944 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 108 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 AATATCAACCGCTGGTTTAATAAAACCCAA 1 132 1 GCTGGTTTAA 0.919646 -92 CGCCTTGCTTGATTAACAATCTCATG 2 7 1 GCTTGATTAA 0.685164 -69 GAGTTTGTTTTAGAAATCCTTT 4 20 0 GTTTGTTTTA 0.89586 -12 GCTACGGCCTGCTCGTTTTCTGAGAGTCCT 5 170 1 GCTCGTTTTC 0.946534 -44 TGCTTAAATAGTTGGTTTTAGCCCCTTTGT 7 14 0 GTTGGTTTTA 0.877025 -183 AAGGCTAGTTTTAGAAAAAAAGT 10 4 1 GCTAGTTTTA 0.929963 -133 AACCCTTAGAGCTTCTTTTCAAAGCTAAAG 10 47 0 GCTTCTTTTC 0.779457 -90 CAGCTTGTTCTAAACAACCGGT 11 3 1 GCTTGTTCTA 0.91077 -281 AATGAAGAGCGCTCATTTTAAAAAATAAAA 12 56 0 GCTCATTTTA 0.801761 -45 ********** Masking position 7 Map Score: 1.19058 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 129 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 9 TACTTTTACAAAGTTGAAGCCATTCTTTTG 1 36 1 AAGTTGAAGC 0.740719 -188 AAAACATAAAAGGCCTTTGCCAAGAGTGAT 3 88 0 AGGCCTTTGC 0.923521 -71 ATGGAGCTCGGAGTCTAAGCAGACAAGGCG 5 128 0 GAGTCTAAGC 0.776157 -86 CCGAGCTCCATGGTCGTTGCTCTGCTACGG 5 147 1 TGGTCGTTGC 0.873416 -67 GAAAACGAGCAGGCCGTAGCAGAGCAACGA 5 160 0 AGGCCGTAGC 0.967359 -54 CTTAAATAGTTGGTTTTAGCCCCTTTGTTA 7 12 0 TGGTTTTAGC 0.667976 -185 TTGATTCATAAGGTCTATGATCTCTTCCAA 8 51 0 AGGTCTATGA 0.638753 -158 CGCATTCAAGAAGTCGAAGCACGTATTAAA 8 153 1 AAGTCGAAGC 0.935517 -56 ATTTTCTTATAGGCCTAAGCAAAGGAAAAC 14 86 0 AGGCCTAAGC 0.965941 -42 ********** Masking position 3 Map Score: 1.21017 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 104 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: -2.81132e-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: -2.81132e-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 12 ********** No masking Map Score: -2.81132e-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