AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_ctra_reg_100.orf -o00950_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 ubiA 111 4-hydroxybenzoate octaphenyltransferase #2 CT355 300 hypothetical protein #3 CT389 181 hypothetical protein #4 aspC 89 Aspartate Aminotransferase #5 CT426 196 Fe-S oxidoreductase #6 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #7 tyrB 187 Aromatic AA Aminotransferase #8 ygcA 85 rRNA Methyltransferse #9 hctA 300 Histone-Like Developmental Protein Motif number 1 TTTTCTTGCTGAAAAAAGTACGTTGAAGTTCGTT 1 26 0 GAAAAAGACT 0.929476 -86 AAGCCAAAGGAAACAAAAATGTATTTTTCTGGAA 2 58 0 AAAAAAATGT 0.861927 -243 AGAACACTTTTAACAAAAAAGCGTTATATCCTCA 2 91 0 TAAAAAAAGT 0.845619 -210 GCAAACACCCAAACAAAGCAGCTTATATTCTAAA 2 181 0 AAAAAAGAGT 0.983089 -120 CGGAAGTAGAGAAAAAACAAGATTTTTAGGAGAA 3 123 0 GAAAAACAGT 0.959719 -59 AGACGAGTAGAAATAAAGAAGTCATGAAGGCCTT 5 14 0 AAAAAAGAGA 0.86085 -183 GACTGCTGTCAGAAAAAGAAGTCTTGTCCCCGTG 5 143 1 AGAAAAGAGT 0.901663 -54 TGCTTGCTAAAAAAAAAAAAGGATAATATACGGG 6 56 1 AAAAAAAAGT 0.96832 -45 TACCCCGAGGGAAGAAACTAGGTTATCATGTTTA 7 86 1 GAAAAACAGT 0.959719 -102 CATCTTACTGGAAAAAAAGACAGTAAGCAGCAGT 7 143 1 GAAAAAAACT 0.873888 -45 TTTAGAAAAGAAAGAAAGGAGCTTGTTCTCTTGT 9 21 0 AAAAAAGAGT 0.983089 -280 AGGAGATGTCAAATAAAGCTGCTTTAGGATCCTT 9 174 1 AAAAAAGTGT 0.922321 -127 AATTAAAACTGAAAAAAATAGTTTAAAACAACAA 9 260 1 GAAAAAAAGT 0.972532 -41 *** **** ** * Masking position 7 Map Score: 16.4236 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 120 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 AGTACGTTGAAGTTCGTTTCAACGTACAGA 1 14 0 AGTTCGTTTC 0.477933 -98 CAGCAAGAAAAGCTCCTTCTGATTACAATA 1 49 1 AGCTCCTTCT 0.943949 -63 TCTGACGGCTGGGTCCCTCCTCCCCTATAG 2 122 1 GGGTCCCTCC 0.970607 -179 GGACGAGGGTAGGTTCTTTTTTAGAATATA 2 162 1 AGGTTCTTTT 0.77156 -139 TAAGAATTTTGGGTTGTTCCTCCTCCCCTT 2 249 0 GGGTTGTTCC 0.752171 -52 AAAATTCTTAAGGTTTTTCTACCTAAAAAC 2 269 1 AGGTTTTTCT 0.835876 -32 CTCGAGTGTCGGCTTCTTTCGGATTTGACT 3 88 0 GGCTTCTTTC 0.759208 -94 CCGACACTCGAGCGCTCTTCTCCTAAAAAT 3 106 1 AGCGCTCTTC 0.819192 -76 CTTTTCTCAGTGCTCTCTAAAAATTACG 4 9 1 AGTGCTCTCT 0.783398 -81 TGTTTTGATAGGGTCTTTCCTACTAGGAAG 5 85 1 GGGTCTTTCC 0.950507 -112 CCTTTAGATAGGGGTCTTCCTAGTAGGAAA 5 100 0 GGGGTCTTCC 0.92388 -97 ATAATATACGGGGTCTCTTTGTCAGGGTTT 6 78 1 GGGTCTCTTT 0.822228 -23 ATGATAACCTAGTTTCTTCCCTCGGGGTAT 7 85 0 AGTTTCTTCC 0.793457 -103 TATTTTAGCGCTTTCTCTTTTTTATA 8 7 1 AGCGCTTTCT 0.898933 -79 TGTTGATAAAAGTGCCCTCTATAAAAAAGA 8 26 0 AGTGCCCTCT 0.867117 -60 TTTTATCAACAGGGCCCTCTTTCCTCTTCT 8 45 1 AGGGCCCTCT 0.95779 -41 CAAGAGAACAAGCTCCTTTCTTTCTTTTCT 9 22 1 AGCTCCTTTC 0.900019 -279 AACAAGGTTCAGCGCTTTCTATTAAAAGAA 9 53 1 AGCGCTTTCT 0.898933 -248 GGTCTGAATAGGGTTTCTTTTAATAGAAAG 9 67 0 GGGTTTCTTT 0.629622 -234 ********** Masking position 8 Map Score: 18.7413 Number of sites scoring better than the average of aligned sites = 746 Number in coding regions = 743 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 GCTCTTAGTTACCCCTCTTTTCGATATTTAA 2 18 1 ACCCCTCTTT 0.97953 -283 CTGGGTCCCTCCTCCCCTATAGCTTTTACCT 2 130 1 CCTCCCCTTA 0.782935 -171 GGTTGTTCCTCCTCCCCTTTTTCTTTGGATC 2 237 0 CCTCCCCTTT 0.918266 -64 GGCCTTCATGACTTCTTTATTTCTACTCGTC 5 16 1 ACTTCTTTTT 0.65061 -181 CTTTATTTCTACTCGTCTGTTGCGCTACAGC 5 30 1 ACTCGTCTTT 0.834366 -167 AACAGCTGTTACTCCTATACTGAGAAGGGCT 5 58 0 ACTCCTATCT 0.826807 -139 TACTAGGAAGACCCCTATCTAAAGGATGTGG 5 105 1 ACCCCTATTA 0.849496 -92 GACAAAGAGACCCCGTATATTATCCTTTTTT 6 70 0 CCCCGTATTT 0.826201 -31 GCGGTTCGATCCCGCTATGCTCCAATTTCTG 7 12 0 CCCGCTATCT 0.788802 -176 AATAAAACCTCTCTATAGCGCACTGCT 7 171 0 ACCTCTCTTA 0.849496 -17 ATCAACAGGGCCCTCTTTCCTCTTCTCATTG 8 49 1 CCCTCTTTCT 0.707137 -37 CTCATTGATCCCTTCTCTTTTTT 8 73 1 CCTTCTCTTT 0.928903 -13 ATCTCCTTGTACCGCTCTGTTTATCAATAGG 9 150 0 ACCGCTCTTT 0.935796 -151 ******** ** Masking position 8 Map Score: 6.45008 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 475 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 GGAGCTTTTCTTGCTGAAAAAAGTACGTTGA 1 34 0 TTCTGAAAAA 0.950079 -78 AGTGAAAAAATTCCAGAAAAATACATTTTTG 2 48 1 TTCAGAAAAA 0.728722 -253 CAGAACACTTTTAACAAAAAAGCGTTATATC 2 95 0 TTACAAAAAA 0.700182 -206 AGCAGCTTATATTCTAAAAAAGAACCTACCC 2 168 0 ATCTAAAAAA 0.883198 -133 TATCGCTTGCTTGCTAAAAAAAAAAAAGGAT 6 49 1 TTCTAAAAAA 0.968085 -52 AGCTGTCATCTTACTGGAAAAAAAGACAGTA 7 137 1 TTCTGGAAAA 0.922817 -51 AAAAGTGCCCTCTATAAAAAAGAGAAAGCGC 8 18 0 TCATAAAAAA 0.678332 -68 CTTTCTTTCTTTTCTAAACAAGGTTCAGCGC 9 37 1 TTCTAAACAA 0.850936 -264 AGCACATAGTTTTATAAAAAATTTTTCTATT 9 103 1 TTATAAAAAA 0.91727 -198 TTTTCCTCTGTTAATAGAAAAATTTTTTATA 9 115 0 TTATAGAAAA 0.875214 -186 CCTTACCTAGATTCTAGAAAATGGTTGCATG 9 204 1 ATCTAGAAAA 0.825684 -97 ** ******** Masking position 8 Map Score: 7.37761 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 244 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 TTGTTAAAAGTGTTCTGACGGCTGGGTCCCTCCT 2 109 1 TGTTCACGCG 0.985267 -192 CTTTTTCTTTGGATCTTACCGCCTCCCTAGAGAT 2 218 0 GGATCACGCT 0.976293 -83 TTAGTGTGGGTTATGAGACAGCCGCGTTATAACT 3 157 0 TTATGACGCG 0.94651 -25 CCTATCTAAAGGATGTGGCCGCAGCGACTGCTGT 5 118 1 GGATGGCGCG 0.976316 -79 CAAGACTTCTTTTTCTGACAGCAGTCGCTGCGGC 5 135 0 TTTTCACGCG 0.948033 -62 GAGCATAGCGGGATCGAACCGCTGACCTCAACAA 7 21 1 GGATCACGCG 0.99686 -167 ATCTAGGTAAGGATCCTAAAGCAGCTTTATTTGA 9 182 0 GGATCAAGCG 0.976293 -119 ***** ** ** * Masking position 4 Map Score: 3.4435 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 32 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 TCAGAACACTTTTAACAAAAAAGCGTTATATCCT 2 93 0 TTAACAAAGC 0.920643 -208 GCAGCTTATATTCTAAAAAAGAACCTACCCTCGT 2 164 0 TTTAAAAAAC 0.79936 -137 TAGAGATGTGGCAAACACCCAAACAAAGCAGCTT 2 191 0 GCAACACAAC 0.907284 -110 TCTTGTCCCCGTGAAAAGCAAAACTCACAAACTG 5 164 1 GTAAAAAAAC 0.954225 -33 CCTAAATCGTGTAAACATGATAACCTAGTTTCTT 7 97 0 GTAACAAAAC 0.974293 -91 GAATCTTCTAACAAGAGAACAAGCTCCTTT 9 7 1 TCAACAAAAC 0.960429 -294 TTGCATGAATTTGAACAAACAAACTAATTAAAAA 9 228 1 TTAACACAAC 0.960429 -73 AACAAACTAATTAAAAATTAAAACTGAAAAAAAT 9 245 1 TTAAAAAAAC 0.961935 -56 AAAAAAATAGTTTAAAACAACAACTAGAGGATAT 9 271 1 TTAAAAAAAC 0.961938 -30 ** **** * *** Masking position 7 Map Score: 5.41798 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 62 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 AGGATATAACGCTTTTTTGTTAAAAGTGTTC 2 93 1 GCTTTTTGTT 0.899641 -208 AAACAAAGCAGCTTATATTCTAAAAAAGAAC 2 174 0 GCTTATATCT 0.649936 -127 GAATGAGTATGCTTGTTGGTTAGTTAATTGT 3 30 0 GCTTGTTGTT 0.97512 -152 CTCCTAAAAATCTTGTTTTTTCTCTACTTCC 3 125 1 TCTTGTTTTT 0.759644 -57 TTTTGATATCGCTTGCTTGCTAAAAAAAAAA 6 43 1 GCTTGCTGCT 0.978022 -58 TAAGATGACAGCTTGTTGTCCTAAATCGTGT 7 119 0 GCTTGTTTCC 0.923259 -69 GCGCACTGCTGCTTACTGTCTTTTTTTCCAG 7 150 0 GCTTACTTCT 0.903797 -38 TATTTTAGCGCTTTCTCTTTTTTATAGAGG 8 10 1 GCTTTCTTTT 0.854887 -76 AAAGAAAGGAGCTTGTTCTCTTGTTAGAAGA 9 14 0 GCTTGTTTCT 0.982961 -287 TTTTTAATTAGTTTGTTTGTTCAAATTCATG 9 231 0 GTTTGTTGTT 0.773966 -70 ******* *** Masking position 4 Map Score: 6.38674 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 187 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 TTTTCTTGCTGAAAAAAGTACGTTGAAGTTC 1 29 0 GAAAAAGTAC 0.94263 -83 ATATTTAAGTGAAAAAATTCCAGAAAAATAC 2 41 1 GAAAAATTCC 0.941868 -260 GTTTTTCTACCTAAAAACTACAAATCAAGG 2 281 1 CAAAAACTAC 0.926017 -20 TCAGTGCTCTCTAAAAATTACGCTGGACAGA 4 17 1 CAAAAATTAC 0.97153 -73 CAAGCGATATCAAAAAATTACTACCTAGTTC 6 27 0 CAAAAATTAC 0.971596 -74 TATTAACAGAGGAAAAATAACCTATTGATAA 9 130 1 GAAAAATAAC 0.951313 -171 GAAAAAATATCCTCTAGTTGT 9 290 0 GAAAAATATC 0.828319 -11 * ********* Masking position 6 Map Score: 3.32455 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 9 TCCCATAATATTCGAAGGGTTT 1 100 1 TTCAGGGTTT 0.983165 -12 ATAAGCTGCTTTGTTTGGGTGTTTGCCACATC 2 189 1 TTGTGGGTGT 0.919003 -112 CCTCCCCTTTTTCTTTGGATCTTACCGCCTCC 2 226 0 TTCTGGATCT 0.838236 -75 CAACCCAAAATTCTTAAGGTTTTTCTACCTAA 2 263 1 TTCAAGGTTT 0.883385 -38 AACAGCTGTTTTGATAGGGTCTTTCCTACTAG 5 79 1 TTGAGGGTCT 0.985899 -118 CGGGGTCTCTTTGTCAGGGTTTTGC 6 86 1 TTGAGGGTTT 0.978004 -15 AACTATGTGCTGCATAGGGTCTGAATAGGGTT 9 82 0 TGCAGGGTCT 0.96582 -219 *** ******* Masking position 10 Map Score: 2.27249 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 35 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 GCTTTTCTTGCTGAAAAAAGTACGTTGAAG 1 32 0 CTGAAAAAAG 0.788287 -80 ATCCCATAATATTCGAAGGGTTT 1 99 1 ATTCGAAGGG 0.734376 -13 CAAGATTTTTAGGAGAAGAGCGCTCGAGTG 3 110 0 AGGAGAAGAG 0.886359 -72 TTAGAGAGCACTGAGAAAAG 4 1 0 CTGAGAAAAG 0.919099 -89 TACTCCTATACTGAGAAGGGCTGTAGCGCA 5 50 0 CTGAGAAGGG 0.991255 -147 GAAGGGATCAATGAGAAGAGGAAAGAGGGC 8 58 0 ATGAGAAGAG 0.967068 -28 AAAAAAGAGAAGGGATCAATGAGA 8 72 0 AAGAGAAGGG 0.911811 -14 TGCATAGGGTCTGAATAGGGTTTCTTTTAA 9 74 0 CTGAATAGGG 0.921505 -227 AAACTATGTGCTGCATAGGGTCTGAATAGG 9 85 0 CTGCATAGGG 0.851597 -216 ********** Masking position 7 Map Score: 5.30905 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 164 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 11 GAATATTATGGGATTATAGGTGTAAAAGAT 1 83 0 GGATTATAGG 0.93946 -29 AAAACCTTAAGAATTTTGGGTTGTTCCTCC 2 256 0 GAATTTTGGG 0.955169 -45 CTTGATTTGTAGTTTTTAGGTAGAAAAACC 2 280 0 AGTTTTTAGG 0.872249 -21 ATTTGACTAAGAATTTTAGGAGGCAATGAA 3 66 0 GAATTTTAGG 0.979294 -116 GAAAAAACAAGATTTTTAGGAGAAGAGCGC 3 117 0 GATTTTTAGG 0.970594 -65 ********** Masking position 5 Map Score: 0.98197 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 31 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: -2.75447e-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: -2.75447e-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: -2.75447e-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