AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_bsub_mtub_300.orf -o066_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 lysA 105 diaminopimelate decarboxylase #2 spoVAA 121 mutants lead to the production of immature spores (stage V sporulation) #3 spoIIAA 95 anti-anti-sigma factor (antagonist of SpoIIAB) #4 dacF 154 D-alanyl-D-alanine carboxypeptidase (penicilin binding protein) #5 drm 160 phosphodeoxyribomutase #6 ripX 300 integrase/recombinase #7 yutL 122 similar to diaminopimelate epimerase #8 yutK 136 similar to Na+/nucleoside cotransporter #9 yuzB 262 yuzB #10 argS 300 argS #11 dapF 24 dapF #12 Rv2728c 108 hypothetical protein Rv2728c #13 Rv2729c 66 hypothetical protein Rv2729c Motif number 1 CCGCAGGTGGCTGCGGCTTTTTTGTTTAGAGCGA 5 4 1 CGGGCGCGTG 0.994278 -157 GTATGATAAACCGGAAGCTCCGCTGTAAAAGTTGTTGAAAT 6 199 1 CGAGCCCGAG 0.993969 -102 GCGCCACCCGCGAGGGCGGCCGCATAGTTGGCTTCGTGGTC 10 40 0 CGGCGCCGTG 0.991936 -261 GCCGCCCTCGCGGGTGGCGCCGATCACATTGTTGTAGCCAT 10 61 1 CGGGCCCGTG 0.999031 -240 TAGATCAACCCTTGTGCCCCCGGCAGGATTCGAACCTGCGG 10 111 1 CGGCCCCGTC 0.991946 -190 GGGGATAGAGCGTCTGCCTCCGGAGCAGAAGGCCGCAGGTT 10 143 0 CCGCCCCGAG 0.946793 -158 AACGTGTCGTCGTGCGCCCCCGTAGCTCAGGGGATAGAGCG 10 172 0 CGGCCCCGAG 0.80009 -129 CACGTTGCGCCATGGGGCCCCGCCAGAGTAGCGCATCGCGG 10 207 1 CGGGCCCGTG 0.998689 -94 GATTCGGCCTCGTGGAGCAACGGCTGCAAAGAGACCGTGCT 12 51 0 CGAGCACGAG 0.949344 -58 * * *** *** * * Masking position 11 Map Score: 15.4166 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 30 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 ATAAAACTGTCCTTTCATCCATAAGCGGAG 1 71 1 CCTTTCATCC 0.848996 -35 GCAGGCTAGCTTTTTTGTGCAAAAGCGTGG 2 19 1 TTTTTTGTGC 0.645268 -103 GATTTTGTTCTCATTCATCCGCTCGAAAAG 2 60 0 TCATTCATCC 0.732124 -62 ACAGCTGTCTTTTTTTATGCCCAAAATTCG 4 56 1 TTTTTTATGC 0.871397 -99 AGTATAAACCGTTTTCATTCCCGTTGACAA 5 82 0 GTTTTCATTC 0.728789 -79 TGCATTGAAAGTTTTCATCCTGTTTACCGG 6 106 1 GTTTTCATCC 0.933436 -195 ACCGCTTTGTTCTATTATGCTATGATATGG 6 140 1 TCTATTATGC 0.720045 -161 ACCGATGATAGTTTTCATACTCTTGATTCA 6 171 0 GTTTTCATAC 0.937469 -130 GAGCTTCCGGTTTATCATACCGATGATAGT 6 189 0 TTTATCATAC 0.85877 -112 ACCATCCGCCTTTTTCATCCTGATCCATTT 6 236 0 TTTTTCATCC 0.954851 -65 TTATCCCCCGTTTTTCATACATAAAAGCTC 7 40 0 TTTTTCATAC 0.957652 -83 GCTTATAATAGCTTTTATACTAAGAAAAAG 7 83 1 GCTTTTATAC 0.899065 -40 TTTTTTTAGTTCTTTTGTACGGCAAAATAA 8 37 0 TCTTTTGTAC 0.782919 -100 TAAAAAAATATCTTTTATACGATAACAATA 8 88 0 TCTTTTATAC 0.930721 -49 CTTCAATGTATCTATCATACTCTTCGGATT 9 25 0 TCTATCATAC 0.895658 -238 ********** Masking position 5 Map Score: 13.2325 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 573 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 3 GGAAAATGTTTCGAATTTTGGGCATAAAAAAAG 4 64 0 TCGAATTTGC 0.735297 -91 GATCAACCGGTCGAACCATCCGCCTTTTTCATC 6 247 0 TCGAACCTGC 0.971159 -54 TGAGGCTAGATCAACCCTTGTGCCCCCGGCAGG 10 105 1 TCAACCCTGC 0.958333 -196 CCGGCAGGATTCGAACCTGCGGCCTTCTGCTCC 10 130 1 TCGAACCGGC 0.989022 -171 GTGTCGTCGTGCGCCCCCGTAGCTCAGGGGATA 10 177 0 GCGCCCCGGC 0.941363 -124 TGGTTGGGCTTCGAATCCGTTGCGGTGGTCAGT 10 254 0 TCGAATCGGC 0.939643 -47 CCCAACCACCTCAGCCCATAGGATGGACGTTC 10 279 1 TCAGCCCTGA 0.836907 -22 CGGGACAGTGTCGGCCTCTCAGCACGGTCTCTT 12 31 1 TCGGCCTTGC 0.979731 -78 GCGGGCGGATTCGGCCTCGTGGAGCAACGGCTG 12 66 0 TCGGCCTGGA 0.929898 -43 CCACCGACATTCGGCCCGGAAGCTGACTGATAC 13 34 0 TCGGCCCGGC 0.99609 -33 ******* * ** Masking position 2 Map Score: 8.19988 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 398 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 GTCTATTGTATCGCTAAGAGGTCTGACAACTCA 5 112 0 TCGCTGGGTC 0.988768 -49 GCCGCATAGTTGGCTTCGTGGTCTCGCTCTCAA 10 30 0 TGGCTGGGTC 0.935827 -271 TCTATCCCCTGAGCTACGGGGGCGCACGACGAC 10 175 1 GAGCTGGGGC 0.927628 -126 ACGACACGTTGCGCCATGGGGCCCCGCCAGAGT 10 203 1 GCGCCGGGCC 0.996394 -98 CGCCAGAGTAGCGCATCGCGGCTACCCACTGAC 10 227 1 GCGCAGGGCT 0.90795 -74 ACACTGTCCCGCGCTCATTGGCCAGAGACGG 12 9 0 GCGCTTGGCC 0.980634 -100 CAAAGAGACCGTGCTGAGAGGCCGACACTGTCC 12 33 0 GTGCTGGGCC 0.985957 -76 CTCAGCACGGTCTCTTTGCAGCCGTTGCTCCAC 12 48 1 TCTCTGAGCC 0.802392 -61 TGCAGCCGTTGCTCCACGAGGCCGAATCCGCCC 12 64 1 GCTCCGGGCC 0.980819 -45 GGGCCGAATGTCGGTGGGAGGTCACCT 13 50 1 TCGGTGGGTC 0.919418 -17 ***** * **** Masking position 11 Map Score: 8.04082 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 189 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 TGATATCAGACACAGCTGTCTTTTGGTCCTG 4 24 0 CACAGTGTCT 0.988498 -131 TCTGATATCACACAGCTGTCTTTTTTTATGC 4 45 1 CACAGTGTCT 0.988498 -110 CCGCAGGTGGCTGCGGCTTTTT 5 2 1 CGCAGTGGCT 0.991677 -159 GATTCCTGAAAACAGCTGTCGATGCATTGAA 6 84 1 AACAGTGTCG 0.882372 -217 AGGGCGGCCGCATAGTTGGCTTCGTGGTCTC 10 38 0 CATAGTGGCT 0.958375 -263 CGGCCGCCCTCGCGGGTGGCGCCGATCACAT 10 59 1 CGCGGTGGCG 0.981688 -242 GATCTAGCCTCACGCATGGCTACAACAATGT 10 86 0 CACGCTGGCT 0.958268 -215 ***** ***** Masking position 7 Map Score: 5.2617 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 84 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ACGATAAAAGCTCCTTGCGTCAGTG 7 6 1 AAAAGCTCCT 0.984386 -117 TTTCATACATAAAAGCTCCTTGCACTGACG 7 28 0 AAAAGCTCCT 0.984386 -95 AGAAAAGGGCCTGGACAGGCCC 8 3 1 AAAAGGGCCT 0.990299 -134 GGCAAAATAAAAAAGGGCCTGTCCAGGCCC 8 17 0 AAAAGGGCCT 0.990299 -120 ********** Masking position 4 Map Score: 3.97455 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 48 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 CCTCCATTTCATAATCCTTTTTATTTTTTCC 4 125 0 ATAACCTTTT 0.856603 -30 CAACTCAAGTATAAACCGTTTTCATTCCCGT 5 88 0 ATAACCGTTT 0.904532 -73 CTTGAAAGCCTCCTTTTTTTCTATACG 5 144 0 AGCCCCTTTT 0.919533 -17 CGGTCGAACCATCCGCCTTTTTCATCCTGAT 6 242 0 ATCCCCTTTT 0.977276 -59 TCTTGATCTACTCCCCGTTTTGGTAAAAAA 6 281 0 ACTCCCGTTT 0.83178 -20 CAATACAATTATCCCCCGTTTTTCATACATA 7 47 0 ATCCCCGTTT 0.985558 -76 TTGAATTCCCCTTTAATCCGAAGAG 9 5 1 ATTCCCTTTA 0.709018 -258 TAAATTTTGAATCATCCGTTGTCTTTGACGA 9 197 1 ATCACCGTTG 0.951618 -66 GTGAGGCTAGATCAACCCTTGTGCCCCCGGC 10 104 1 ATCACCCTTG 0.848167 -197 **** ****** Masking position 9 Map Score: 2.26906 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 313 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 8 TCACACAGCTGTCTTTTTTTATGCCCAAAAT 4 52 1 GTTTTTTTTA 0.873755 -103 CGACCGGTTGATCTTTTTTTACCAAAACGGG 6 267 1 ATTTTTTTTA 0.957434 -34 TGATGTCTACACATTTTTTTAGTTCTTTTGT 8 49 0 ACTTTTTTTA 0.938026 -88 GATAACAATAATATTTTTTGATGTCTACACA 8 67 0 ATTTTTTTGA 0.938026 -70 CGTATAAAAGATATTTTTTTAAATAAAATTT 8 97 1 ATTTTTTTTA 0.957434 -40 ATAATTCTAGATGTTATTTTACATAGTTCGT 9 60 0 ATTTATTTTA 0.90728 -203 AATTAGTAAAACGTTATTTGAGAAATAATAT 9 156 1 ACTTATTTGA 0.815865 -107 ** ******** Masking position 11 Map Score: 2.65695 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 123 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 9 CGACCGGTTGATCTTTTTTTACCAAAACGG 6 267 1 ATCTTTTTTT 0.726414 -34 AGGTGCCTCCAACTTTTTTTCTTTTTCTTA 7 103 0 AACTTTTTTT 0.859182 -20 TGATGTCTACACATTTTTTTAGTTCTTTTG 8 50 0 ACATTTTTTT 0.832736 -87 AGACATCAAAAAATATTATTGTTATCGTAT 8 72 1 AAATATTATT 0.826228 -65 CGTATAAAAGATATTTTTTTAAATAAAATT 8 97 1 ATATTTTTTT 0.762961 -40 TACACCTCTTAAATTTTATTTAAAAAAATA 8 108 0 AAATTTTATT 0.901121 -29 GTTATTTTGAAACTATTATTGTGATTTTAG 9 103 0 AACTATTATT 0.797698 -160 TATTATCGTAACATATTATTTCTCAAATAA 9 169 0 ACATATTATT 0.762893 -94 CGGATGATTCAAAATTTATTATCGTAACAT 9 185 0 AAAATTTATT 0.589092 -78 ********** Masking position 6 Map Score: 1.4785 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 203 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 10 GAAACTGACTGAAGAGTATGATAATGTATG 1 18 1 GAAGAGTATG 0.99053 -88 ATGGGTGAATCAAGAGTATGAAAACTATCA 6 166 1 CAAGAGTATG 0.982697 -135 CCTTTAATCCGAAGAGTATGATAGATACAT 9 20 1 GAAGAGTATG 0.99053 -243 ********** Masking position 5 Map Score: 1.23242 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 TGTCATTCCCTCTTTCTCCGCTTATGGAT 1 87 0 CCTCTTCTCC 0.925513 -19 TCGATTTTGTTCTCATTCATCCGCTCGAAAA 2 61 0 TCTCTTCATC 0.829687 -61 GACGGAATGAATTCCTTCACCGTGACAAAAC 3 30 0 ATTCTTCACC 0.893894 -66 GCTCATTCCTCCTTGATATGA 3 85 0 GCTCTTCCTC 0.940899 -11 TTTTCATACTCTTGATTCACCCATATCATAG 6 159 0 CTTGTTCACC 0.871373 -142 GAACCATCCGCCTTTTTCATCCTGATCCATT 6 237 0 CCTTTTCATC 0.713655 -64 GAATACTCGTACACCTCTTAAATTT 8 122 0 ACTCTACACC 0.931357 -15 GCGGTTTCACCTCACATATGT 9 252 0 GCGGTTCACC 0.839901 -11 GGTTCTTACCCCGACGAATTTG 10 2 1 GTTCTACCCC 0.794848 -299 GGAGGCAGACGCTCTATCCCCTGAGCTACGG 10 163 1 GCTCATCCCC 0.917074 -138 CTGCGCCACTCCTCAATCACCAGA 11 4 0 CCTCATCACC 0.946406 -21 CCGGAAGCTGACTGATACATCTCGATTTAAG 13 21 0 ACTGTACATC 0.630221 -46 **** ****** Masking position 8 Map Score: 3.0115 Number of sites scoring better than the average of aligned sites = 1088 Number in coding regions = 965 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 12 GATGGTTTTATACGCCACTGATGGAAAATG 4 89 0 TACGCCACTG 0.964499 -66 AAAAGCTCCTTGCGTCAGTGCAAGGAGCTT 7 16 1 TGCGTCAGTG 0.861676 -107 CAATGTGATCGGCGCCACCCGCGAGGGCGG 10 62 0 GGCGCCACCC 0.976005 -239 CGTGTCGTCGTGCGCCCCCGTAGCTCAGGG 10 181 0 TGCGCCCCCG 0.981627 -120 GACGACACGTTGCGCCATGGGGCCCCGCCA 10 202 1 TGCGCCATGG 0.935886 -99 GTAGCCGCGATGCGCTACTCTGGCGGGGCC 10 222 0 TGCGCTACTC 0.953884 -79 CTGCGCCACTCCTCAATCACC 11 14 0 TGCGCCACTC 0.993768 -11 ********** Masking position 4 Map Score: 3.5082 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 167 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: -5.68191e-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 CCGCAGGTGGCTGCGGCTTTTTTGTTTAGA 5 8 1 TGGCGGCTTT 0.988131 -153 CTTTCTGATTTGGCATATGGTTTATATAACTGG 6 17 1 TGGCTGGTTT 0.967563 -284 AGGATGAAAAAGGCGGATGGTTCGACCGGTTGA 6 245 1 AGGCGGGTTC 0.989671 -56 CCGGAGCAGAAGGCCGCAGGTTCGAATCCTGCC 10 132 0 AGGCGGGTTC 0.989641 -169 TCTGCTCCGGAGGCAGACGCTCTATCCCCTGAG 10 155 1 AGGCGGCTCT 0.970854 -146 GCTAACGCCTTGGCGGGCGGATTCGGCCTCGTG 12 78 0 TGGCGGGATT 0.957806 -31 CCGCCCGCCAAGGCGTTAGCTTTGTGTT 12 91 1 AGGCTGCTTT 0.967289 -18 **** * ***** Masking position 9 Map Score: 5.36039 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 151 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 ********** No masking Map Score: -5.68191e-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