AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_bsub_mtub_100.orf -o320_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ndk 115 nucleoside diphosphate kinase #2 hisS 300 histidyl-tRNA synthetase #3 ndkA 42 ndkA #4 valS 87 valS #5 Rv2449c 89 hypothetical protein Rv2449c #6 Rv2450c 81 hypothetical protein Rv2450c #7 aspS 239 aspS #8 Rv2581c 50 hypothetical protein Rv2581c Motif number 1 ATTAATCAATCCGGGGCGGAGAAATTTCTT 1 25 0 CCGGGGCGGA 0.877184 -91 TGTTACGATTTCGGTGTGCAGTGTGAAAGC 1 66 1 TCGGTGTGCA 0.804206 -50 CGCTTTCAGCCTGGGGCGGGTTCCTCTCTA 2 30 0 CTGGGGCGGG 0.981944 -271 TACGTTCATATTCCCGCTCGATCCTTTAAC 2 149 0 TTCCCGCTCG 0.577911 -152 TCATGTATAGTAGGGGCGGGAGTTTTTTTC 2 223 1 TAGGGGCGGG 0.932136 -78 ATCCGGGCGGTTTCGGGCGCT 4 2 1 TCCGGGCGGT 0.928216 -86 TCCGGGCGGTTTCGGGCGCTTTCATGCCGG 4 12 1 TTCGGGCGCT 0.848725 -76 CTAGAATTGATCGGTGACCGCCAGCCCTCA 4 55 1 TCGGTGACCG 0.692431 -33 AGCCCTCACCCTGCCGCCGAT 4 77 1 CTGCCGCCGA 0.743513 -11 TGACGCTACTCCGGGGTGCGCGAGCAGACG 5 65 0 CCGGGGTGCG 0.990485 -25 TGGGTTGGCTTTGGCGCGCGCGCACCGCGA 6 51 1 TTGGCGCGCG 0.986189 -31 GTTGTTCCTTTCGCGGTGCGCGCGCGCCAA 6 61 0 TCGCGGTGCG 0.977255 -21 CGCCGTCTCGCCGGAGCTCGATCCCGGCGC 7 22 1 CCGGAGCTCG 0.89716 -218 GAGCTCGATCCCGGCGCGCGGAGTGTGGCC 7 35 1 CCGGCGCGCG 0.822527 -205 GGCCGGGTATTCGCCGCTGTTGTGCGGCCA 7 60 0 TCGCCGCTGT 0.836007 -180 GGAACGACGGTCGCCGCGCTGTTGCACAAG 7 89 0 TCGCCGCGCT 0.982507 -151 CTAGTCGGACCCGGTGCCGTCGGAACGACG 7 110 0 CCGGTGCCGT 0.881258 -130 CTAGAGGTGCCCGCGGCGCACATCGGTCAC 7 188 0 CCGCGGCGCA 0.987209 -52 GTTCGCGGCCCGCCTCGTCCCC 8 3 1 TCGCGGCCCG 0.990543 -48 TTTCCCATCCCCGGCGTCCGGGGACGAGGC 8 22 0 CCGGCGTCCG 0.952454 -29 ********** Masking position 6 Map Score: 35.8096 Number of sites scoring better than the average of aligned sites = 2247 Number in coding regions = 2056 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 TAAGAAATTTCTCCGCCCCGGATTGATTAAT 1 24 1 CTCGCCCCGG 0.987379 -92 TTTCTCGAAACAACACTCCGGAGGTTTCCTG 2 74 1 CAAACTCCGG 0.87385 -227 CAAGATGTATGCCCAAACCGG 3 1 0 GCCAAACCGG 0.949018 -42 CATGAAAGCGCCCGAAACCGCCCGGAT 4 7 0 CCCAAACCGC 0.926896 -81 CTAGGAACCGCTTCACACCGGCATGAAAGCG 4 28 0 CTTACACCGG 0.936423 -60 CGCAAAAGCTCCCAAATCCGGTCGGATTTGG 5 25 1 CCCAATCCGG 0.993164 -65 CGCAAAAGCTCCCAAATCCGACCGGATTTGG 5 36 0 CCCAATCCGA 0.89932 -54 GGGTTTGACGCTACTCCGGGGTGCGCGAG 5 71 0 CGCACTCCGG 0.994523 -19 GGGTCTGCGCCGTCTCGCCGGAGCTCGATCC 7 15 1 CGTTCGCCGG 0.823006 -225 CTCGCCGGAGCTCGATCCCGGCGCGCGGAGT 7 28 1 CTCATCCCGG 0.956641 -212 TGTTGTGCGGCCACACTCCGCGCGCCGGGAT 7 42 0 CCAACTCCGC 0.898649 -198 ACAACAGCGGCGAATACCCGGCCTTGTGCAA 7 67 1 CGATACCCGG 0.929734 -173 CATTGCCCTAGTCGGACCCGGTGCCGTCGGA 7 116 0 GTCGACCCGG 0.911893 -124 CTGAGCAGTCGGTTAATCCGGTTGAAGGGGA 7 219 1 GGTAATCCGG 0.82707 -21 CGCGGCCCGCCTCGTCCCCGGACGCCGGGGA 8 14 1 CTCTCCCCGG 0.989511 -37 TTCCCAGTTTCCCATCCCCGGCGTCCGGGGA 8 28 0 CCCTCCCCGG 0.994456 -23 *** ******* Masking position 8 Map Score: 24.4551 Number of sites scoring better than the average of aligned sites = 837 Number in coding regions = 781 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 GCATACATCTTGCGGCATCTAGTGTTGGGCAC 3 20 1 TGCGCTCTAG 0.964256 -23 TTGATCGGTGACCGCCAGCCCTCACCCTGCCG 4 61 1 ACCGCGCCCT 0.927463 -27 TGGGAGCTTTTGCGTCTTTTCGCGGTGG 5 7 0 TGCGCTTTCG 0.982221 -83 TGGGAGCTTTTGCGTCTGCTCGCGCACCCCGG 5 53 1 TGCGCGCTCG 0.997371 -37 GATGGGGTCTGCGCCGTCTCGCCGGAGCTCG 7 10 1 TGCGCTCTCG 0.972518 -230 CCCGGCCTTGTGCAACAGCGCGGCGACCGTCG 7 83 1 TGCACGCGCG 0.936614 -157 CAGCGCGGCGACCGTCGTTCCGACGGCACCGG 7 98 1 ACCGCTTCCG 0.934406 -142 AACCGGATTAACCGACTGCTCAGTCTAGAGGT 7 210 0 ACCGCGCTCA 0.949953 -30 **** * ***** Masking position 6 Map Score: 6.19286 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 455 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 GTATGTATAGGCTTTCACACTGCACACCGAAA 1 74 0 GCTTCACACG 0.967429 -42 AATGGGATCCGCTTTCAGCCTGGGGCGGGTTC 2 37 0 GCTTCAGCCG 0.988751 -264 CGTTATTCACGCGTTCAGCAGGAAACCTCCGG 2 91 0 GCGTCAGCAG 0.950602 -210 CGTGAATAACGCCATTAGGCAGTGAACGTGAA 2 112 1 GCCTTAGGCG 0.930487 -189 GGTTTCGGGCGCTTTCATGCCGGTGTGAAGCG 4 19 1 GCTTCATGCG 0.907543 -69 GTGACCGCCAGCCCTCACCCTGCCGCCGAT 4 68 1 GCCTCACCCG 0.9968 -20 TTGCGTCTGCTCGCGCACCCCGGAGTAGCGTC 5 62 1 TCGGCACCCG 0.972376 -28 GCTTTGGCGCGCGCGCACCGCGAAAGGAACAA 6 58 1 GCGGCACCGG 0.944323 -24 TGGGGTCTGCGCCGTCTCGCCGGAGCTCGATC 7 13 1 GCCTCTCGCG 0.954603 -227 CACAACAGCGGCGAATACCCGGCCTTGTGCAA 7 66 1 GCGATACCCG 0.880838 -174 GCGGCGACCGTCGTTCCGACGGCACCGGGTCC 7 102 1 TCGTCCGACG 0.666822 -138 GCGGCGCACATCGGTCACGCAGGATAATTTCG 7 174 0 TCGTCACGCG 0.983389 -66 TCCCCTTCAACCGGATTAACCGAC 7 226 0 CCCTCAACCG 0.817942 -14 *** ****** * Masking position 2 Map Score: 12.9947 Number of sites scoring better than the average of aligned sites = 1206 Number in coding regions = 1111 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 ATTATGTATGTATAGGCTTTCACACTGCACACCG 1 77 0 TTGCTTTACA 0.730278 -39 GCGGATCCCATTGCGTCTTTCTCGAAACAACACT 2 57 1 TGTCTTTTCG 0.878049 -244 ATATTCCCGCTCGATCCTTTAACGCAGGTTCACG 2 138 0 TGCCTTTACG 0.980246 -163 CGGGCGGTTTCGGGCGCTTTCATGCCGGTGTGAA 4 14 1 CGGCTTTATG 0.880031 -74 CGACCGGATTTGGGAGCTTTTGCGTCTTTTCGCG 5 15 0 TGGCTTTGCG 0.997221 -75 CGGTCGGATTTGGGAGCTTTTGCGTCTGCTCGCG 5 43 1 TGGCTTTGCG 0.997221 -47 CATGCCCGTGGGTTGGCTTTGGCGCGCGCGCACC 6 43 1 GTGCTTTGCG 0.949409 -39 CGTTGTTCCTTTCGCGGTGCGCGCGC 6 66 0 TGCCTTTGCG 0.992184 -16 GGCCGGGTATTCGCCGCTGTTGTGCGGCCACACT 7 56 0 TGGCTGTGTG 0.942883 -184 * * ***** *** Masking position 8 Map Score: 8.31814 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 330 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TAGGGTGGCACCACGGGTATAACTCTCGTC 2 186 1 CCACGGGTAT 0.989539 -115 CTAGATGCCGCAAGATGTATGCCCAAACCG 3 12 0 CAAGATGTAT 0.501147 -31 GAACCGCTTCACACCGGCATGAAAGCGCCC 4 25 0 ACACCGGCAT 0.925921 -63 GGGTTAGCTGCCAGGTGCATTCGAGGGTGC 6 14 0 CCAGGTGCAT 0.975581 -68 CAAAGCCAACCCACGGGCATGGGTTAGCTG 6 34 0 CCACGGGCAT 0.997124 -48 ACAAACATTGCAACAGGCATTGCCCTAGTC 7 134 0 CAACAGGCAT 0.969668 -106 CCGATGTGCGCCGCGGGCACCTCTAGACTG 7 192 1 CCGCGGGCAC 0.970464 -48 ********** Masking position 9 Map Score: 4.86032 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 266 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 AGACGCAAAAGCTCCCAAATCCGGTCGGAT 5 22 1 GCTCCCAAAT 0.991334 -68 AGACGCAAAAGCTCCCAAATCCGACCGGAT 5 40 0 GCTCCCAAAT 0.991334 -50 GCATGGGTTAGCTGCCAGGTGCATTCGAGG 6 18 0 GCTGCCAGGT 0.982297 -64 GGTTCCCAGTTTCCCATCCCC 8 40 0 GTTCCCAGTT 0.961919 -11 ********** Masking position 7 Map Score: 1.40394 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 42 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GTATAGGCTTTCACACTGCACACCGAAATC 1 72 0 TCACACTGCA 0.951538 -44 GTAGGTCAGATTGCATGATTAGAGA 2 6 1 TCAGATTGCA 0.840477 -295 GGATCCGCTTTCAGCCTGGGGCGGGTTCCT 2 35 0 TCAGCCTGGG 0.954385 -266 TGAAAGCGGATCCCATTGCGTCTTTCTCGA 2 52 1 TCCCATTGCG 0.881954 -249 GCAGTGAACGTGAACCTGCGTTAAAGGATC 2 130 1 TGAACCTGCG 0.899091 -171 GTTTGGGCATACATCTTGCGGCATCTAGTG 3 14 1 ACATCTTGCG 0.851299 -29 CCGCCAGCCCTCACCCTGCCGCCGAT 4 72 1 TCACCCTGCC 0.976863 -16 TGAGCCGAAATTATCCTGCGTGACCGATGT 7 169 1 TTATCCTGCG 0.913798 -71 ********** Masking position 7 Map Score: 0.288447 Number of sites scoring better than the average of aligned sites = 913 Number in coding regions = 806 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 ********** No masking Map Score: -7.43638e-13 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: -7.43638e-13 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: -7.43638e-13 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