AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00053_mtub_reg_100.orf -o00053_mtub_100.ace -a/home/amcguire/genomes/ORF_mtub.txt -z/home/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 Rv0144 101 hypothetical protein Rv0144 #2 Rv0145 88 hypothetical protein Rv0145 #3 Rv0146 42 hypothetical protein Rv0146 #4 Rv0147 94 hypothetical protein Rv0147 #5 Rv0223c 98 hypothetical protein Rv0223c #6 Rv0224c 35 hypothetical protein Rv0224c #7 Rv1880c 49 hypothetical protein Rv1880c #8 lppE 40 lppE #9 Rv1882c 27 hypothetical protein Rv1882c #10 Rv1883c 38 hypothetical protein Rv1883c #11 fbpB 300 fbpB #12 Rv3292 30 hypothetical protein Rv3292 #13 aldB 26 aldB Motif number 1 GCCATGGTTGCGCTGCTGATCGTCGGATAGCG 1 26 0 CGCGCTATCG 0.990019 -76 CGCCGCACAGCGGCGGTGATCGCGTACGTCCA 1 65 0 CGGGGTATCG 0.995141 -37 CGTTTCGGATCTCCTCGCCGCACAGCG 1 85 0 CGGTCTCTCG 0.9876 -17 CACTACGCTTCGGGGCCGCCGGTTAGGTCTCG 2 12 0 CGGGCCCCGG 0.992129 -77 CCTGTGCTCCCTCTGGTTCTCGTGATGCCGGT 3 12 0 CTCGGTCTCG 0.926589 -31 TAAGGTCAGTCGGATGCGCTCG 4 1 0 CGGTGCCTCG 0.973334 -94 CGGTGATAACCGCGATCCTAGT 4 83 0 CGGGATACCG 0.508589 -12 GCATCGTCGCCGGCGGTCATGGCGTCACCCTA 5 47 0 CGGGGTATGG 0.989646 -52 ATGCGCCGCTCCTCCTCATCGCTGC 5 84 0 CGCGCTCTCC 0.975788 -15 GGGCGGTTCGGCTATTCCGGATTCCGC 9 9 1 CGGTATCCGG 0.939948 -19 AGACCGCACACGCCGCCAACCG 10 1 0 CGCGCCACCG 0.988694 -38 CCGGAACAGACCGGGATAGCGTG 11 2 1 CGGACAACCG 0.874445 -299 GGGCTACCGGCTGTGCTCCCCCAGGGAGGCCG 11 81 0 CTGGCTCCCC 0.954652 -220 AATCGCGGCCCGGGGCTACCGGCTGTGCTCCC 11 93 0 CGGGCTCCGG 0.984847 -208 GCTCTGTCCGCGGCGGTAACCGATACGGAAAT 11 185 1 CGGGGTACCG 0.752965 -116 GGCCGGAGACTATCGCAACGGCAGT 12 4 1 CGGGACATCG 0.952599 -27 ACTATCGCAACGGCAGTGCCGC 12 19 1 CGGAGTCCGC 0.895344 -12 *** *** **** Masking position 1 Map Score: 37.7968 Number of sites scoring better than the average of aligned sites = 17738 Number in coding regions = 16744 Number in noncoding regions = 994 Number of orfs with sites within 600 bp upstream = 664 Fraction of orfs with sites within 600 bp upstream = 0.10665 Motif number 2 GGATAGCGCTGGCCAACTCTGGG 1 1 0 GGCCACCGGG 0.95897 -101 TCCAGACCTGGGCCATGGTTGCGCTGCTGATCG 1 36 0 GGCCTGTGCG 0.99443 -66 GCCGCACAGCGGCGGTGATCGCGTACGTCCAGA 1 63 0 GGCGTGTGCG 0.980306 -39 CCGAGACCTAACCGGCGGCCCCGAAGC 2 5 1 GACCAACGCG 0.940823 -84 TCAACCGGGTGACTAGGATCGCGGTTATCACCG 4 72 1 GACTGGTGCG 0.987172 -23 TTTCGCGTTCGGCTTGGGTAGGGTGACGCCATG 5 29 1 GGCTGGTGGG 0.973909 -70 CATCGTCGCCGGCGGTCATGGCGTCACCCTACC 5 45 0 GGCGTCTGCG 0.958391 -54 CGGCGACGATGCCGAGCGCAGCGATGAGGAGGA 5 67 1 GCCGGCCGCG 0.990831 -32 CACACCCTACGGCCCGCTAGGCTATCGACCA 6 9 0 GGCCGCAGCT 0.888556 -27 ACAATGCTCAGGCCCGAATGGAGGTGGCTG 8 21 1 GGCCGATGAG 0.9599 -20 TGCGGTCTATGACCAGGTCGACGT 10 25 1 GACCGGCACG 0.97452 -14 CCGGAACAGACCGGGATAGCGTGGTCTTCGT 11 9 1 GACCGGTGCG 0.995822 -292 GGTCTTCGTCGGCTTGCTTCGAGCGAGCCTACG 11 33 1 GGCTGCTGAG 0.958847 -268 CCCCCAGGGAGGCCGAACTTGCGTTCACCGCGT 11 63 0 GGCCAATGCG 0.975168 -238 ACAGCCGGTAGCCCCGGGCCGCGATTCTGAGAA 11 99 1 GCCCGGCGCG 0.99746 -202 ATCGGTTACCGCCGCGGACAGAGCAAGTGTGCT 11 176 0 GCCGGGCGAG 0.95851 -125 GTATGTTCTGGCCCGAGCACACGACGACATACA 11 260 1 GCCCAGAACG 0.766326 -41 GGCCGGAGACTATCGCAACGGCAGTGCCGC 12 8 1 GACTTCCACG 0.660147 -23 CTGGGCTCGTAACGCGTCAGTGGTTA 13 11 0 GGCTGTAGCG 0.882644 -16 **** ** * *** Masking position 3 Map Score: 34.7904 Number of sites scoring better than the average of aligned sites = 23163 Number in coding regions = 21867 Number in noncoding regions = 1296 Number of orfs with sites within 600 bp upstream = 770 Fraction of orfs with sites within 600 bp upstream = 0.123675 Motif number 3 GAGTTGGCCAGCGCTATCCGACGATCAGCA 1 15 1 GCGCTATCCG 0.986074 -87 GTCTGGACGTACGCGATCACCGCCGCTGTG 1 62 1 ACGCGATCAC 0.906694 -40 CACCGGCATCACGAGAACCAGA 3 3 1 CCGGCATCAC 0.897751 -40 CGGTGATAACCGCGATCCTAGTCACCCGG 4 76 0 CCGCGATCCT 0.984157 -19 CCCAAGCCGAACGCGAAACGAGAACGTGTT 5 17 0 ACGCGAAACG 0.891477 -82 CAGCCACCTCCATTCGGGCCTGAGCA 8 25 0 CCTCCATTCG 0.704885 -16 GCGGAATCCGGAATAGCCGA 9 18 0 GCGGAATCCG 0.899027 -10 ACCGCACACGCCGCCAACCG 10 1 0 CCGCCAACCG 0.987916 -38 GACGAAGACCACGCTATCCCGGTCTGTTCC 11 13 0 ACGCTATCCC 0.977046 -288 GGGAGCACAGCCGGTAGCCCCGGGCCGCGA 11 93 1 CCGGTAGCCC 0.899351 -208 TAGCCCCGGGCCGCGATTCTGAGAAATCCG 11 107 1 CCGCGATTCT 0.905398 -194 TAGATCCATACCGCCATACCGTTTGTGAGC 11 140 1 CCGCCATACC 0.975953 -161 TCTGTCCGCGGCGGTAACCGATACGGAAAT 11 187 1 GCGGTAACCG 0.903878 -114 TAACCACTGACGCGTTACGAGCCCAG 13 10 1 ACGCGTTACG 0.715774 -17 ********** Masking position 2 Map Score: 13.9105 Number of sites scoring better than the average of aligned sites = 8834 Number in coding regions = 8065 Number in noncoding regions = 769 Number of orfs with sites within 600 bp upstream = 604 Fraction of orfs with sites within 600 bp upstream = 0.0970125 Motif number 4 CTGGGCCATGGTTGCGCTGCTGATCGTCGG 1 32 0 GTTGCGCTGC 0.913518 -70 GAAGCGTAGTGATGTGCCACACAAATCGTA 2 33 1 GATGTGCCAC 0.915931 -56 GGCGCTCATCCTGTGCTCCCTCTGGTTCT 3 24 0 CCTGTGCTCC 0.985822 -19 AGGTCAGTCGGATGCGCTCG 4 1 0 GATGCGCTCG 0.981359 -94 CCTCCTCATCGCTGCGCTCGGCATCGTCGC 5 69 0 GCTGCGCTCG 0.983353 -30 CGGGCCGTAGGGTGTGCCAG 6 26 1 GGTGTGCCAG 0.959997 -10 GGGCCTGAGCATTGTGCTCGGGACA 8 6 0 ATTGTGCTCG 0.936628 -35 GGGGCTACCGGCTGTGCTCCCCCAGGGAGG 11 84 0 GCTGTGCTCC 0.99251 -217 CCATACCGTTTGTGAGCCCCCTAAGCACAC 11 153 1 TGTGAGCCCC 0.867211 -148 ATGAGACGACTTTGCGCCCGAATCGACATT 11 215 1 TTTGCGCCCG 0.965473 -86 TGTATGTCGTCGTGTGCTCGGGCCAGAACA 11 263 0 CGTGTGCTCG 0.985009 -38 ACTTGTGCCCCTTTGTCCTGT 11 290 0 CTTGTGCCCC 0.985188 -11 ********** Masking position 3 Map Score: 19.7447 Number of sites scoring better than the average of aligned sites = 2739 Number in coding regions = 2529 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 5 CCAGCGCTATCCGACGATCAGCAGCGCAAC 1 22 1 CCGACGATCA 0.956508 -80 CCGCACAGCGGCGGTGATCGCGTACGTCCA 1 65 0 GCGGTGATCG 0.989363 -37 CCGCCGCTGTGCGGCGAGGAGATCCGAAAC 1 81 1 GCGGCGAGGA 0.987128 -21 GACTAGGATCGCGGTTATCACCG 4 82 1 GCGGTTATCA 0.835954 -13 ATCGTCGCCGGCGGTCATGGCGTCACCCTA 5 47 0 GCGGTCATGG 0.909898 -52 ATGACCGCCGGCGACGATGCCGAGCGCAGC 5 59 1 GCGACGATGC 0.945167 -40 GCCGAGCGCAGCGATGAGGAGGAGCGGCGC 5 77 1 GCGATGAGGA 0.953556 -22 CGCGCCTCCGTCGATCGAGTGGCTTTT 7 33 0 CCGTCGATCG 0.949256 -17 TCGAAGCAAGCCGACGAAGACCACGCTATC 11 25 0 CCGACGAAGA 0.870891 -276 TCGTCGGCTTGCTTCGAGCGAGCCTACGCG 11 38 1 GCTTCGAGCG 0.757935 -263 GCGAGCCTACGCGGTGAACGCAAGTTCGGC 11 55 1 GCGGTGAACG 0.97147 -246 ********** Masking position 7 Map Score: 11.2225 Number of sites scoring better than the average of aligned sites = 13694 Number in coding regions = 12820 Number in noncoding regions = 874 Number of orfs with sites within 600 bp upstream = 593 Fraction of orfs with sites within 600 bp upstream = 0.0952457 Motif number 6 ATCCGGATATATGGCTGGATCTTTTCTATTG 4 36 1 ATGCTGGATC 0.963518 -59 GATCTTTTCTATTGCTGGTTCAACCGGGTGA 4 53 1 ATGCTGGTTC 0.983794 -42 GGTGACTAGGATCGCGGTTATCACCG 4 79 1 ATGCGGTTAT 0.814145 -16 ATTGCGGGTTCTAGTCTTGAA 7 1 1 ATGCGGGTTC 0.996245 -49 CGGTTCGGCTATTCCGGATTCCGC 9 14 1 ATCCGGATTC 0.93688 -14 ACAGACCGGGATAGCGTGGTCTTCGTCGGCT 11 16 1 ATGCGTGGTC 0.915526 -285 GTATGGATCTATCGCGGATTTCTCAGAATCG 11 120 0 ATGCGGATTT 0.960727 -181 CACAAACGGTATGGCGGTATGGATCTATCGC 11 136 0 ATGCGGTATG 0.89946 -165 ** ******** Masking position 1 Map Score: 5.56009 Number of sites scoring better than the average of aligned sites = 879 Number in coding regions = 820 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 CAATAGAAAAGATCCAGCCATATATCCGGA 4 37 0 GATCCAGCCA 0.934074 -58 TCACCCGGTTGAACCAGCAATAGAAAAGAT 4 54 0 GAACCAGCAA 0.990429 -41 TACCCAAGCCGAACGCGAAACGAGAACGTG 5 19 0 GAACGCGAAA 0.943385 -80 TTCAAGACTAGAACCCGCAAT 7 2 0 GAACCCGCAA 0.995729 -48 GCGGAATCCGGAATAGCCGAACC 9 15 0 GAATCCGGAA 0.943395 -13 ********** Masking position 2 Map Score: 2.20444 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 323 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 CGATCACCGCCGCTGTGCGGCGAGGAGATCC 1 75 1 CGCGTGCGGC 0.990445 -27 AGGGAGCACAGGATGAGCGCC 3 32 1 GGAGAGCGCC 0.982513 -11 GCAGCGATGAGGAGGAGCGGCGCAT 5 84 1 GGAGAGCGGC 0.99042 -15 CCACTCGATCGACGGAGGCGCG 7 38 1 GACGAGGCGC 0.953384 -12 GGGCGGTTCGGCTATTCCGGAT 9 2 1 GGCGTTCGGC 0.963574 -26 CGGGGCTACCGGCTGTGCTCCCCCAGGGAGG 11 84 0 GGCGTGCTCC 0.978536 -217 GAAATGAGACGACTTTGCGCCCGAATCGACA 11 212 1 GACTTGCGCC 0.930572 -89 CGACATACAGGACAAAGGGGCACAAGT 11 284 1 GACAAGGGGC 0.865854 -17 CTATCGCAACGGCAGTGCCGC 12 20 1 GGCGTGCCGC 0.996051 -11 *** ******* Masking position 11 Map Score: 13.0416 Number of sites scoring better than the average of aligned sites = 6678 Number in coding regions = 6169 Number in noncoding regions = 509 Number of orfs with sites within 600 bp upstream = 413 Fraction of orfs with sites within 600 bp upstream = 0.0663347 Motif number 9 CCGCTGTGCGGCGAGGAGATCCGAAACG 1 84 1 GAGAGATCGA 0.834898 -18 GAAGCGTAGTGATGTGCCACACAAATCGTATAGG 2 33 1 GGGCCACCAA 0.73625 -56 AAGTAAGTTAGGTAACCTATACGATTTGTGTGGC 2 48 0 GACCTATCGA 0.961935 -41 GGCATGCCATGCTACCTAAGTAAG 2 75 0 GAGCCATCTA 0.844696 -14 CGGTCATGGCGTCACCCTACCCAAGCCGAACGCG 5 32 0 GACCTACCAA 0.922515 -67 TGGTCGATAGCCTAGCGGGCCGTAGGGTG 6 6 1 GACCTAGGGG 0.770747 -30 TAGTCTTGAAGAAAAGCCACTCGATCGACGGAGG 7 22 1 GAGCCACCGA 0.983564 -28 CTCGCTCGAAGCAAGCCGACGAAGACCACGCTAT 11 26 0 GACCGACAAG 0.715834 -275 CTTGCTTCGAGCGAGCCTACGCGGTGAACGCAAG 11 45 1 GACCTACCGG 0.988932 -256 GCCTCCCTGGGGGAGCACAGCCGGTAGCCCCGGG 11 83 1 GACACAGCGG 0.925183 -218 CGGTAGCCCCGGGCCGCGATTCTGAGAAATCCGC 11 104 1 GCGCGATCTG 0.605885 -197 TGTCCGCGGCGGTAACCGATACGGAAATGAGACG 11 189 1 GACCGATCGG 0.986758 -112 TCGACATTTGGCCTCCACACACGGTATGTTCTGG 11 237 1 GTCACACCGG 0.816211 -64 * * ***** *** Masking position 9 Map Score: 5.36907 Number of sites scoring better than the average of aligned sites = 6993 Number in coding regions = 6413 Number in noncoding regions = 580 Number of orfs with sites within 600 bp upstream = 477 Fraction of orfs with sites within 600 bp upstream = 0.0766142 Motif number 10 ********** No masking Map Score: 6.77448e-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: 6.77448e-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 12 ********** No masking Map Score: 6.77448e-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