AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_ecoli_mtub_300.orf -o320_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 aspS 276 aspartate tRNA synthetase #2 hisS 110 histidine tRNA synthetase #3 gcpE 26 orf, hypothetical protein #4 yfgA 284 putative membrane protein #5 yfgB 149 orf, hypothetical protein #6 ndk 148 nucleoside diphosphate kinase #7 b2520 47 orf, hypothetical protein #8 ndkA 42 ndkA #9 valS 87 valS #10 Rv2449c 89 hypothetical protein Rv2449c #11 Rv2450c 81 hypothetical protein Rv2450c #12 aspS 239 aspS #13 Rv2581c 50 hypothetical protein Rv2581c Motif number 1 GGTAACGAGGCGTTCCAGCGCGGGCCAGGCTCT 1 125 1 CGCAGCGCGG 0.94461 -152 GCTAACGCTGCGACTTGGTCACCTGCGCAGCAG 1 218 1 CGTGGTCACC 0.576052 -59 CGCAGCAGGGGGCATCCGCCGGCAGCTAAGTTA 1 243 1 GGCCGCCGGC 0.783021 -34 ATCATACACGGGAAGCGAGGCGCTTCCCATCAC 2 15 0 GGCGAGGCGC 0.954714 -96 TCAATGTTTCGGGAGCCATGCGGGTTCAATCAT 2 43 0 GGCCATGCGG 0.88075 -68 AAACATTGAGGGAAGCGTTGAGGGTTCATTTTT 2 67 1 GGCGTTGAGG 0.755791 -44 AGTATAAGACCGTCTGTGTGCTCGTGACAAAGC 4 167 0 CGGTGTGCTC 0.665651 -118 GATGTTTCGCGGTGTGGGTGAGCATGATGGTTC 4 223 1 GGGGGTGAGC 0.9714 -62 ACGGATGCCACGTTTGCACGCGGCATTTACGAA 5 15 0 CGGCACGCGG 0.869516 -135 GTGCAAACGTGGCATCCGTGCGCCAGAATTTGT 5 29 1 GGCCGTGCGC 0.99245 -121 AGCGGCTGCTCGTCCGGGGGCGCTGCATTGTAC 5 60 0 CGGGGGGCGC 0.991426 -90 AAAAAAGAAACGCCCCGGTGAGCGGCTGCTCGT 5 80 0 CGCGGTGAGC 0.980326 -70 TACCAGCGTACGAGATGGCGCGGATTATAATGA 6 93 0 CGTGGCGCGG 0.990162 -56 ATCCGGGCGGTTTCGGGCGCTTTCATGCCG 9 8 1 CGTCGGGCGC 0.984089 -80 AGAATTGATCGGTGACCGCCAGCCCTCACCCTG 9 57 1 GGCCGCCAGC 0.929534 -31 ATCGGCGGCAGGGTGAGGGCTGGCGGTC 9 70 0 CGGGGTGAGG 0.961192 -18 GGAGCTTTTGCGTCTTTTCGCGGTGG 10 4 0 CGTTTCGCGG 0.643741 -86 CAAATCCGACCGGATTTGGGAGCTTTTGCGTCT 10 22 0 CGTTGGGAGC 0.914813 -68 CAAATCCGGTCGGATTTGGGAGCTTTTGCGTCT 10 37 1 CGTTGGGAGC 0.914813 -53 ACGCTACTCCGGGGTGCGCGAGCAGACGCAAAA 10 60 0 GGGCGCGAGC 0.97391 -30 CCCGTGGGTTGGCTTTGGCGCGCGCGCACCGCG 11 47 1 GGTGGCGCGC 0.992628 -35 GATGGGGTCTGCGCCGTCTCGCCGGA 12 4 1 GGCTGCGCCG 0.914221 -236 GCCGGAGCTCGATCCCGGCGCGCGGAGTGTGGC 12 31 1 GACGGCGCGC 0.8958 -209 GGGTATTCGCCGCTGTTGTGCGGCCACACTCCG 12 53 0 CGTTGTGCGG 0.943544 -187 TCGGAACGACGGTCGCCGCGCTGTTGCACAAGG 12 88 0 GGCCGCGCTG 0.625957 -152 TGCCCTAGTCGGACCCGGTGCCGTCGGAACGAC 12 111 0 GGCGGTGCCG 0.763149 -129 GACCGATGTGCGCCGCGGGCACCTCTAGACTGA 12 190 1 CGCGGGCACC 0.515107 -50 CGTCCGGGGACGAGGCGGGCCGCGAAC 13 5 0 CGCGGGCCGC 0.983672 -46 ** ******** Masking position 2 Map Score: 42.1481 Number of sites scoring better than the average of aligned sites = 8628 Number in coding regions = 8230 Number in noncoding regions = 398 Number of orfs with sites within 600 bp upstream = 320 Fraction of orfs with sites within 600 bp upstream = 0.0513974 Motif number 2 GCGATTAGCCGATGGCGGAACGACAAATTT 1 19 1 GATGGCGGAA 0.833431 -258 CTATAAAGGTGTTGCCCGAACTCATAAAAA 1 55 0 GTTGCCCGAA 0.535075 -222 GGCGTTCCAGCGCGGGCCAGGCTCTTACGG 1 133 1 CGCGGGCCAG 0.625589 -144 AGGCTCTTACGGTGCGGCAGAATTTCCAGT 1 151 1 GGTGCGGCAG 0.954351 -126 CCTTAACTTAGCTGCCGGCGGATGCCCCCT 1 249 0 GCTGCCGGCG 0.934777 -28 CAGACGGGTAACGCGGGAGATTTTTC 3 10 1 AACGCGGGAG 0.842087 -17 ATAAAGTAACCGTGGCGTAATGGCTA 4 7 0 CGTGGCGTAA 0.44872 -278 CTTTATGTACCGTGGCGTAATGTTTTATGA 4 31 1 CGTGGCGTAA 0.44872 -254 TGAGAATTGAGATGCCGGTGAACCATCATG 4 245 0 GATGCCGGTG 0.935344 -40 ACGTGGCATCCGTGCGCCAGAATTTGTACA 5 35 1 CGTGCGCCAG 0.899536 -115 TGTACAATGCAGCGCCCCCGGACGAGCAGC 5 59 1 AGCGCCCCCG 0.924285 -91 TGAAAAAAGAAACGCCCCGGTGAGCGGCTG 5 85 0 AACGCCCCGG 0.890256 -65 GTGTAATAACGAGGCCGGAATAGCAT 5 134 1 GAGGCCGGAA 0.779515 -16 ATCAATAGTCAACGGCCCTGTTGCTCATTA 6 69 1 AACGGCCCTG 0.479522 -80 CAGCGTACGAGATGGCGCGGATTATAATGA 6 93 0 GATGGCGCGG 0.907383 -56 CCCAACACTAGATGCCGCAAGATGTATGCC 8 19 0 GATGCCGCAA 0.928319 -24 AGCGCCCGAAACCGCCCGGAT 9 2 0 ACCGCCCGGA 0.607997 -86 CCGGCATGAAAGCGCCCGAAACCGCCCGGA 9 12 0 AGCGCCCGAA 0.886734 -76 CGGGCGCTTTCATGCCGGTGTGAAGCGGTT 9 24 1 CATGCCGGTG 0.903508 -64 CAGCCCTCACCCTGCCGCCGAT 9 76 1 CCTGCCGCCG 0.881599 -12 GCTACTCCGGGGTGCGCGAGCAGACGCAAA 10 61 0 GGTGCGCGAG 0.945754 -29 GCAGCTAACCCATGCCCGTGGGTTGGCTTT 11 33 1 CATGCCCGTG 0.854827 -49 GGTTGGCTTTGGCGCGCGCGCACCGCGAAA 11 53 1 GGCGCGCGCG 0.861326 -29 GCTCCGGCGAGACGGCGCAGACCCCATC 12 9 0 GACGGCGCAG 0.931293 -231 CCACACTCCGCGCGCCGGGATCGAGCTCCG 12 33 0 CGCGCCGGGA 0.954715 -207 CTTGTGCAACAGCGCGGCGACCGTCGTTCC 12 89 1 AGCGCGGCGA 0.719314 -151 AGTCGGACCCGGTGCCGTCGGAACGACGGT 12 108 0 GGTGCCGTCG 0.894903 -132 TCAGTCTAGAGGTGCCCGCGGCGCACATCG 12 193 0 GGTGCCCGCG 0.976738 -47 GGGGACGAGGCGGGCCGCGAAC 13 3 0 CGGGCCGCGA 0.752826 -48 CTCGTCCCCGGACGCCGGGGATGGGAAACT 13 24 1 GACGCCGGGG 0.979579 -27 ********** Masking position 4 Map Score: 32.3326 Number of sites scoring better than the average of aligned sites = 17182 Number in coding regions = 16442 Number in noncoding regions = 740 Number of orfs with sites within 600 bp upstream = 509 Fraction of orfs with sites within 600 bp upstream = 0.0817539 Motif number 3 CACCTTTATAGCAAACTGGCGTAGAGTCTG 1 74 1 GCAAACTGGC 0.709256 -203 CCTGGCCCGCGCTGGAACGCCTCGTTACCA 1 124 0 GCTGGAACGC 0.832633 -153 GTGACATACAGCTAACGCTGCGACTTGGTC 1 208 1 GCTAACGCTG 0.797118 -69 GGTCACCTGCGCAGCAGGGGGCATCCGCCG 1 234 1 GCAGCAGGGG 0.839008 -43 CTTAAAGTCAGCAAAAACGCACCGTTAATA 4 92 0 GCAAAAACGC 0.923208 -193 CCCCGGACGAGCAGCCGCTCACCGGGGCGT 5 74 1 GCAGCCGCTC 0.966791 -76 CCTGATTGTTGCTAAAACTCATTTTATTTT 6 22 1 GCTAAAACTC 0.827198 -127 ATTATAATGAGCAACAGGGCCGTTGACTAT 6 73 0 GCAACAGGGC 0.969597 -76 ATTCGACGTTGCTAACGGGCCATTGTGGCA 7 18 1 GCTAACGGGC 0.951953 -30 CAGGGTGAGGGCTGGCGGTCACCGATCAAT 9 60 0 GCTGGCGGTC 0.888867 -28 GCGAAAAGACGCAAAAGCTCCCAAATCCGG 10 16 1 GCAAAAGCTC 0.974113 -74 GCGAGCAGACGCAAAAGCTCCCAAATCCGA 10 46 0 GCAAAAGCTC 0.974113 -44 GCGCCGTCTCGCCGGAGCTCGATCCCGGCG 12 21 1 GCCGGAGCTC 0.850602 -219 CCGGCCTTGTGCAACAGCGCGGCGACCGTC 12 84 1 GCAACAGCGC 0.982601 -156 ********** Masking position 2 Map Score: 15.5138 Number of sites scoring better than the average of aligned sites = 3925 Number in coding regions = 3781 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 4 CTTACGGTGCGGCAGAATTTCCAGTATAAT 1 156 1 GGCAGAATTT 0.940456 -121 AATGAAAAAAGGCGGCTATTATACTGGAAA 1 173 0 GGCGGCTATT 0.909936 -104 CGGGTAACGCGGGAGATTTTTC 3 15 1 GGGAGATTTT 0.953392 -12 CACGTTTGCACGCGGCATTTACGAAATTA 5 10 0 CGCGGCATTT 0.953679 -140 GCATCCGTGCGCCAGAATTTGTACAATGCA 5 40 1 GCCAGAATTT 0.6965 -110 AGCCGCTCACCGGGGCGTTTCTTTTTTCAA 5 86 1 CGGGGCGTTT 0.906976 -64 TACGAGATGGCGCGGATTATAATGAGCAAC 6 88 0 CGCGGATTAT 0.726035 -61 GACCGGATTTGGGAGCTTTTGCGTCTTTTC 10 18 0 GGGAGCTTTT 0.975722 -72 GGTCGGATTTGGGAGCTTTTGCGTCTGCTC 10 44 1 GGGAGCTTTT 0.975722 -46 ********** Masking position 10 Map Score: 4.92423 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 797 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 5 AGCGAGGCGCTTCCCATCACGTTA 2 5 0 TTCCCATCAC 0.919085 -106 ACCCGCATGGCTCCCGAAACATTGAGGGAA 2 51 1 CTCCCGAAAC 0.966023 -60 GCAAGATGTATGCCCAAACCGG 8 3 0 TGCCCAAACC 0.962579 -40 GGTGCCCAACACTAGATGCCGC 8 31 0 TGCCCAACAC 0.968165 -12 GGCATGAAAGCGCCCGAAACCGCCCGGAT 9 10 0 CGCCCGAAAC 0.96536 -78 GACGCAAAAGCTCCCAAATCCGGTCGGATT 10 23 1 CTCCCAAATC 0.964171 -67 GACGCAAAAGCTCCCAAATCCGACCGGATT 10 39 0 CTCCCAAATC 0.964171 -51 GGTTCCCAGTTTCCCATCCCCGGCGTCCGG 13 31 0 TTCCCATCCC 0.904001 -20 ********** Masking position 5 Map Score: 8.53185 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 142 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 AAGTTGCAATTGTCTGGTCAATATTAACGGT 4 71 1 TGTCGGTCAA 0.742717 -214 ATGTGGGCTTTGTCACGAGCACACAGACGGT 4 161 1 TGTCCGAGCA 0.949865 -124 ATTTCGTAAATGCCGCGTGCAAACGTGGCAT 5 13 1 TGCCCGTGCA 0.948992 -137 GTTCTGTTGTTGTCTGTACCAGCGTACGAGA 6 111 0 TGTCGTACCA 0.720033 -38 ATGGGTTAGCTGCCAGGTGCATTCGAGGGTG 11 15 0 TGCCGGTGCA 0.81791 -67 GCGAATACCCGGCCTTGTGCAACAGCGCGGC 12 76 1 GGCCTGTGCA 0.916742 -164 ACTAGGGCAATGCCTGTTGCAATGTTTGTTG 12 135 1 TGCCGTTGCA 0.943463 -105 GACCGATGTGCGCCGCGGGCACCTCTAGACT 12 190 1 CGCCCGGGCA 0.877792 -50 **** ****** Masking position 11 Map Score: 2.77207 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 755 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 GCGTTCCAGCGCGGGCCAGGCTCTTACGGTG 1 134 1 GCGGGCCGGC 0.919129 -143 ACGTGATGGGAAGCGCCTCGCTTCCCGTGTA 2 13 1 AAGCGCCCGC 0.940307 -98 GTATGATTGAACCCGCATGGCTCCCGAAACA 2 41 1 ACCCGCAGGC 0.972933 -70 ATAAAAATGAACCCTCAACGCTTCCCTCAAT 2 71 0 ACCCTCACGC 0.975483 -40 CATCATGCTCACCCACACCGCGAAACATCCG 4 221 0 ACCCACACGC 0.936156 -64 GGACGAGCAGCCGCTCACCGGGGCGTTTCTT 5 78 1 CCGCTCACGG 0.864554 -72 TCTTTTTTCAACCCTCCAGGGGCCATAACGT 5 105 1 ACCCTCCGGG 0.956825 -45 AAGCGCCCGAAACCGCCCGGAT 9 2 0 AACCGCCGGA 0.421452 -86 GCGTCTGCTCGCGCACCCCGGAGTAGCGTCA 10 64 1 GCGCACCCGG 0.929535 -26 AAGCCAACCCACGGGCATGGGTTAGCTGCCA 11 31 0 ACGGGCAGGG 0.834765 -51 GCTTTGGCGCGCGCGCACCGCGAAAGGAACA 11 58 1 GCGCGCACGC 0.840729 -24 TTGTGCGGCCACACTCCGCGCGCCGGGATCG 12 40 0 ACACTCCCGC 0.891893 -200 CGTCGGAACGACGGTCGCCGCGCTGTTGCAC 12 92 0 ACGGTCGCGC 0.83905 -148 GTCTAGAGGTGCCCGCGGCGCACATCGGTCA 12 189 0 GCCCGCGCGC 0.960557 -51 GTTCGCGGCCCGCCTCGTCCCCGGACGC 13 8 1 GCCCGCCCGT 0.887278 -43 TTCCCAGTTTCCCATCCCCGGCGTCCGGGGA 13 28 0 CCCATCCCGG 0.536592 -23 ******* *** Masking position 6 Map Score: 18.2194 Number of sites scoring better than the average of aligned sites = 4033 Number in coding regions = 3827 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 8 CGTTCCGCCATCGGCTAATCGCATTAAGGT 1 11 0 TCGGCTAATC 0.991722 -266 CAGGATAATTTCGGCTCATCTCAACAAACA 12 157 0 TCGGCTCATC 0.990166 -83 GACTGAGCAGTCGGTTAATCCGGTTGAAGG 12 217 1 TCGGTTAATC 0.977739 -23 ********** Masking position 8 Map Score: 0.641082 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 20 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 TAGCCGATGGCGGAACGACAAATTTTGTTA 1 24 1 CGGAACGACA 0.980378 -253 CAGGCTCTTACGGTGCGGCAGAATTTCCAG 1 150 1 CGGTGCGGCA 0.903004 -127 ATAACGAGGCCGGAATAGCAT 5 139 1 CGGAATAGCA 0.89418 -11 CCACCGCGAAAAGACGCAAAAGCTCC 10 7 1 CGAAAAGACG 0.818939 -83 TCGCGCACCCCGGAGTAGCGTCAAACCC 10 72 1 CGGAGTAGCG 0.922515 -18 GCACCGCGAAAGGAACAACG 11 72 1 AGGAACAACG 0.84801 -10 CGAGCTCCGGCGAGACGGCGCAGACCCCAT 12 12 0 CGAGACGGCG 0.934438 -228 CCGGTGCCGTCGGAACGACGGTCGCCGCGC 12 100 0 CGGAACGACG 0.99216 -140 ********** Masking position 2 Map Score: 2.15025 Number of sites scoring better than the average of aligned sites = 1752 Number in coding regions = 1674 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 10 ********** No masking Map Score: 2.53196e-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: 2.53196e-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: 2.53196e-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