AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_bsub_mtub_300.orf -o146_bsub_mtub_300.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 yufT 300 similar to NADH dehydrogenase #2 Rv0079 300 hypothetical protein Rv0079 #3 Rv0081 94 hypothetical protein Rv0081 #4 nuoA 300 nuoA #5 nuoH 115 nuoH Motif number 1 AAAGCCTACTGGGCGCACGTGTGGCAACGAG 2 116 1 GGGCGCACGG 0.9437 -185 TCGGCTAGTCCGCGGCCCAACGGCGGCATTT 2 159 0 CGCGGCCCAC 0.962753 -142 CCGACACGGACGCGGACAGGGCCGAAAGTCC 2 226 0 CGCGGACAGG 0.896922 -75 AAGCTTGTCTGGCCGACACGGACGCGGACAG 2 238 0 GGCCGACACG 0.98411 -63 GATGCGTGCGGGCCGCCCGCGGCCAATCGG 3 10 0 GGCCGCCCGG 0.698342 -85 CTGGGGATTGCGCGTCCCGGCGAATTGTATG 4 68 0 CGCGTCCCGC 0.812583 -233 AGCGACCGACGCCGGACCCAGCCACGGGTTC 4 110 1 GCCGGACCCG 0.863544 -191 CCCACATTCCCGGGGTCAGGCTGGTGCATAC 4 158 0 CGGGGTCAGC 0.691292 -143 GTCGCGCAACGGCCACCCCACATTCCCGGGG 4 174 0 GGCCACCCCC 0.950169 -127 CGGGGCTTCGGGCCGTCACAGTGACCTTCAA 4 209 0 GGCCGTCACG 0.970725 -92 CCGCCAGCGCGGCGGCCGGGCGGTGACCGGG 4 254 0 GGCGGCCGGC 0.658853 -47 CGTCGTACGGGGCCGCCAGCGCGGCGGCCGG 4 266 0 GGCCGCCAGG 0.981667 -35 CACGCGCGCTCGCGGCAAGGGGAGACGC 5 8 0 CGCGGCAAGG 0.974617 -108 GCGCGTGTTCCCCCGCAAGCGGGAGGTGCCC 5 32 1 CCCCGCAAGG 0.841739 -84 TCGGCGTACTGGGGGCACCTCCCGCTTGCGG 5 44 0 GGGGGCACCC 0.936917 -72 GCCCCCAGTACGCCGACACACCGATTTTGAT 5 59 1 CGCCGACACC 0.98175 -57 GATGTACCAGTGCGGACCCTCGCGCAAGGAG 5 87 1 TGCGGACCCC 0.895654 -29 GGCCGCCACTCCTTGCGCGAG 5 105 0 GGCCGCCACC 0.996229 -11 ********* * Masking position 2 Map Score: 33.231 Number of sites scoring better than the average of aligned sites = 1775 Number in coding regions = 1663 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 TGGGCCGTTCACGACCCAGCCTCATGCGCTG 2 12 1 ACGACCCGCC 0.741441 -289 GTGGCAGTTTCCGTCGCTGCGCAGAAGCTGA 2 81 0 CCGTCGCGCG 0.977435 -220 CGACTCGTTGCCACACGTGCGCCCAGTAGGC 2 119 0 CCACACGGCG 0.659007 -182 ACACGAAATGCCGCCGTTGGGCCGCGGACTA 2 154 1 CCGCCGTGGG 0.827063 -147 CCGGAAAATTCGGCTAGTCCGCGGCCCAACG 2 168 0 CGGCTAGCCG 0.70725 -133 GACACGGACGCGGACAGGGCCGAAAGTCCCA 2 224 0 CGGACAGGCC 0.93935 -77 GCTTGTCTGGCCGACACGGACGCGGACAGGG 2 236 0 CCGACACGAC 0.742299 -65 TGCGTGCGGGCCGCCCGCGGCCAATCGG 3 8 0 CCGCCCGGGC 0.981261 -87 TGGGGATTGCGCGTCCCGGCGAATTGTATGA 4 67 0 GCGTCCCGCG 0.872607 -234 GGTCCGGCGTCGGTCGCTGCGAAGCAAAACT 4 97 0 CGGTCGCGCG 0.951709 -204 CGACCGACGCCGGACCCAGCCACGGGTTCTG 4 112 1 CGGACCCGCC 0.971989 -189 ATGCACCAGCCTGACCCCGGGAATGTGGGGT 4 160 1 CTGACCCGGG 0.829483 -141 AGTCGCGCAACGGCCACCCCACATTCCCGGG 4 175 0 CGGCCACCCA 0.806662 -126 GGGCTTCGGGCCGTCACAGTGACCTTCAACA 4 207 0 CCGTCACGTG 0.828002 -94 CTGTGACGGCCCGAAGCCCCGGTTCGTCACG 4 219 1 CCGAAGCCCG 0.927044 -82 CGGTTCGTCACGGCAGCCCGGTCACCGCCCG 4 238 1 CGGCAGCCGG 0.845797 -63 AGCCCGGTCACCGCCCGGCCGCCGCGCTGGC 4 252 1 CCGCCCGCCG 0.510004 -49 TCGTACGGGGCCGCCAGCGCGGCGGCCGGGC 4 264 0 CCGCCAGGCG 0.994986 -37 GCTGGCGGCCCCGTACGACGGATCATGGAGC 4 277 1 CCGTACGCGG 0.552306 -24 TCTCCCCTTGCCGCGAGCGCGCGTGTTCCCC 5 14 1 CCGCGAGGCG 0.933354 -102 GCGTGTTCCCCCGCAAGCGGGAGGTGCCCCC 5 34 1 CCGCAAGGGG 0.947828 -82 CCCCAGTACGCCGACACACCGATTTTGATGT 5 61 1 CCGACACCCG 0.973571 -55 TGTACCAGTGCGGACCCTCGCGCAAGGAGTG 5 89 1 CGGACCCCGC 0.79562 -27 GGCCGCCACTCCTTGCGCGAGGG 5 103 0 CCGCCACCCT 0.903009 -13 ******* *** Masking position 3 Map Score: 34.434 Number of sites scoring better than the average of aligned sites = 2837 Number in coding regions = 2662 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 ACCCAGCCTCATGCGCTGCATCTGCTCGCCAACCT 2 25 1 ACCGATCTGC 0.996741 -276 GTCCAGAGCGAGCCTCAGCTTCTGCGCAGCGACGG 2 67 1 ACCGTTCTGC 0.996741 -234 GCCCGCACGCATCCGCACTATCTGATAAATTCTTC 3 28 1 ACCCATCTGA 0.941309 -67 ATTTGTTGTTAATCTCGGCATTTGCC 4 2 0 ACCGATTTGC 0.99484 -299 ACCCCCTGATAAGCGCAGCATTTGTTGTTAATCTC 4 21 0 ACCGATTTGT 0.967562 -280 CGGGACGCGCAATCCCCAGTTTTGCTTCGCAGCGA 4 80 1 ACCATTTTGC 0.961552 -221 CGCCGGACCCAGCCACGGGTTCTGCTTCGACTCGC 4 119 1 ACCGTTCTGC 0.996741 -182 CAGTACGCCGACACACCGATTTTGATGTACCAGTG 5 64 1 ACCGTTTTGA 0.981342 -52 * * * * ****** Masking position 1 Map Score: 12.5265 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 57 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 AGGTTGGCGAGCAGATGCAGCGCATGAGGCTG 2 28 0 GCAGATGCGG 0.99468 -273 CCGTCGCTGCGCAGAAGCTGAGGCTCGCTCTG 2 70 0 GCAGAAGCGG 0.996677 -231 CGGGCCACAATCGAAAGCCGAGCAG 2 286 1 TCGAAAGCGG 0.956847 -15 GGCAAATGCCGAGATTAACAACA 4 2 1 GCAAATGCGG 0.994785 -299 GAGATTAACAACAAATGCTGCGCTTATCAGGG 4 21 1 ACAAATGCGG 0.967225 -280 TCGCTGCGAAGCAAAACTGGGGATTGCGCGTC 4 83 0 GCAAAACTGG 0.935149 -218 GCGAGTCGAAGCAGAACCCGTGGCTGGGTCCG 4 122 0 GCAGAACCGG 0.992161 -179 CACTGGTACATCAAAATCGGTGTGTCGGCGTA 5 67 0 TCAAAATCGG 0.928134 -49 ******** * * Masking position 5 Map Score: 10.7267 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 416 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TCCATTACAGCAGTTCGAAGCGTGGCAGCTTG 1 102 1 CATTCGAACG 0.610966 -199 GCATTTCGTGTGGATCGACTCGTTGCCACACG 2 133 0 TGATCGACCG 0.879561 -168 GAAATGCCGCCGTTGGGCCGCGGACTAGCCGA 2 158 1 CGTGGGCCCG 0.957587 -143 ACACAGCCCACATTTGGCATGGGACTTTCGGC 2 205 1 CATTGGCAGG 0.862386 -96 CCGATTGGCCGCGGGCGGCCCGC 3 2 1 CGTTGGCCCG 0.986411 -93 AACATTCATACAATTCGCCGGGACGCGCAATC 4 62 1 CATTCGCCGG 0.973462 -239 TCCCCAGTTTTGCTTCGCAGCGACCGACGCCG 4 92 1 TGTTCGCACG 0.822365 -209 CCACGGGTTCTGCTTCGACTCGCACAGGTATG 4 131 1 TGTTCGACCG 0.945931 -170 CCCGAAGCCCCGGTTCGTCACGGCAGCCCGGT 4 228 1 CGTTCGTCCG 0.925408 -73 ** ****** ** Masking position 7 Map Score: 9.95312 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 240 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 ACAGCAGTTCGAAGCGTGGCAGCTTGCAGA 1 108 1 GAAGCGTGGC 0.738132 -193 GCAGATGCAGCGCATGAGGCTGGGTCGTGA 2 20 0 CGCATGAGGC 0.930929 -281 CAGTAGGCTTTGAGTGTGGCAGTTTCCGTC 2 97 0 TGAGTGTGGC 0.96344 -204 CTACTGGGCGCACGTGTGGCAACGAGTCGA 2 121 1 CACGTGTGGC 0.968539 -180 AGTCCCATGCCAAATGTGGGCTGTGTCACC 2 201 0 CAAATGTGGG 0.966912 -100 GATTGTGGCCCGATTGTGGCCAATGCCCAA 2 268 0 CGATTGTGGC 0.988386 -33 GCTCGGCTTTCGATTGTGGCCCGATTGTGG 2 279 0 CGATTGTGGC 0.988386 -22 AGATTAACAACAAATGCTGCGCTTATCAGG 4 22 1 CAAATGCTGC 0.76867 -279 GCGAATTGTATGAATGTTGGTCTAACCCCC 4 50 0 TGAATGTTGG 0.707063 -251 CCTGACCCCGGGAATGTGGGGTGGCCGTTG 4 169 1 GGAATGTGGG 0.960354 -132 GGGCACCTCCCGCTTGCGGGGGAACACGCG 5 33 0 CGCTTGCGGG 0.930337 -83 ********** Masking position 6 Map Score: 11.3799 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 558 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 CTGCATCTGCTCGCCAACCTCGTACATGTC 2 40 1 TCGCCAACCT 0.814881 -261 GTGGGCTGTGTCACCACCCGGAAAATTCGG 2 186 0 TCACCACCCG 0.986314 -115 GGATGCGTGCGGGCCGCCCGCGGCCAATCG 3 12 0 GGGCCGCCCG 0.969097 -83 ATTCTTCAACTCGTCAACCGATGTAACGCT 3 56 1 TCGTCAACCG 0.88965 -39 CGCGTCTCCTGAGAGCTTCAG 3 84 0 GCGTCTCCTG 0.854582 -11 ACTGGGGATTGCGCGTCCCGGCGAATTGTA 4 70 0 GCGCGTCCCG 0.971346 -231 GTTTTGCTTCGCAGCGACCGACGCCGGACC 4 98 1 GCAGCGACCG 0.942928 -203 GCGAGTCGAAGCAGAACCCGTGGCTGGGTC 4 124 0 GCAGAACCCG 0.842829 -177 GCACAGGTATGCACCAGCCTGACCCCGGGA 4 152 1 GCACCAGCCT 0.83338 -149 GGCAGCCCGGTCACCGCCCGGCCGCCGCGC 4 249 1 TCACCGCCCG 0.986041 -52 GCGTCTCCCCTTGCCGCGAG 5 1 1 GCGTCTCCCC 0.913391 -115 CGTACTGGGGGCACCTCCCGCTTGCGGGGG 5 41 0 GCACCTCCCG 0.994516 -75 ********** Masking position 8 Map Score: 14.0587 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 889 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 TAAGTCTAACAAAAAAGAGGTTATTTGTAT 1 45 0 AAAAAAGAGG 0.709361 -256 GCAGCTTGCAGAAAAGTGCGATATAATTTG 1 126 1 GAAAAGTGCG 0.974486 -175 CGCTATGTATAAAATATACGGTCAAACGAC 1 162 0 AAAATATACG 0.777703 -139 GTTCTCAATTGAAAAATGCGCTATGTATAA 1 180 0 GAAAAATGCG 0.972417 -121 TTGAGAACGAGAAAAGGAGGTCTTATCTTT 1 202 1 GAAAAGGAGG 0.903583 -99 AAAAGCAAATAAAAAAGGCGATAAAATAGC 1 248 0 AAAAAAGGCG 0.876274 -53 TCCCTTCTTGGCAAAATACGCAAAAAGA 1 283 1 GCAAAATACG 0.879125 -18 GCTCGCTCTGGACATGTACGAGGTTGGCGA 2 50 0 GACATGTACG 0.736945 -251 GTCACCACCCGGAAAATTCGGCTAGTCCGC 2 177 0 GGAAAATTCG 0.767528 -124 CCTGACCCCGGGAATGTGGGGTGGCCGTTG 4 169 1 GGAATGTGGG 0.789496 -132 ********** Masking position 4 Map Score: 2.46692 Number of sites scoring better than the average of aligned sites = 1956 Number in coding regions = 1757 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 9 TGTACGAGGTTGGCGAGCAGATGCAGCGCA 2 36 0 TGGCGAGCAG 0.843334 -265 CAGTTTCCGTCGCTGCGCAGAAGCTGAGGC 2 78 0 CGCTGCGCAG 0.989576 -223 CACAATCGAAAGCCGAGCAG 2 291 1 AGCCGAGCAG 0.979652 -10 CGGCGTCGGTCGCTGCGAAGCAAAACTGGG 4 94 0 CGCTGCGAAG 0.916653 -207 TTCTGCTTCGACTCGCACAGGTATGCACCA 4 138 1 ACTCGCACAG 0.800978 -163 CCTTCAACATAGTCGCGCAACGGCCACCCC 4 186 0 AGTCGCGCAA 0.95877 -115 ACCGCCCGGCCGCCGCGCTGGCGGCCCCGT 4 261 1 CGCCGCGCTG 0.983171 -40 CAGTGCGGACCCTCGCGCAAGGAGTGGCGG 5 94 1 CCTCGCGCAA 0.941329 -22 ********** Masking position 5 Map Score: 5.71121 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 624 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 ATTTTTATGAGTTCTTTTGACCTCAAAATAAG 1 71 0 GTCTTTGACC 0.899493 -230 ATTTGGACTAGGTCGTTTGACCGTATATTTTA 1 151 1 GGCGTTGACC 0.982237 -150 CACGAAATGCCGCCGTTGGGCCGCGGACTAGC 2 155 1 CGCGTTGGCC 0.972604 -146 ATTTGGCATGGGACTTTCGGCCCTGTCCGCGT 2 216 1 GGCTTTGGCC 0.977421 -85 GCGCTTATCAGGGGGTTAGACCAACATTCATA 4 40 1 GGGGTTGACC 0.981597 -261 AATGTGGGGTGGCCGTTGCGCGACTATGTTGA 4 181 1 GGCGTTCGCG 0.938781 -120 TGACGAACCGGGGCTTCGGGCCGTCACAGTGA 4 216 0 GGCTTCGGCC 0.97667 -85 CATCAAAATCGGTGTGTCGGCGTACTGGGGGC 5 59 0 GGGTGTGGCG 0.930081 -57 CCTCGCGCAAGGAGTGGCGGCC 5 104 1 GGGTGGGGCC 0.93265 -12 ** **** **** Masking position 11 Map Score: 10.945 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 157 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: 1.36667e-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: 1.36667e-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: 1.36667e-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