AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -ipdhR_mtub_opreg_100.orf -g0.656 -x5 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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0458 67 hypothetical protein Rv0458 #2 Rv0460 59 hypothetical protein Rv0460 #3 Rv0461 37 hypothetical protein Rv0461 #4 Rv0462 63 hypothetical protein Rv0462 #5 aceA 274 aceA #6 sucB 263 sucB #7 aceE 51 aceE Motif number 1 CTCACACTACCGCCGGGGCCACAATGGCTT 1 13 0 CGCCGGGGCC 0.906325 -55 CCGCAGTAAGGTCGTAGACCGTG 2 4 1 CAGTAAGGTC 0.546198 -56 GCCATGACCGCGGAAGGGGGATCACGGTCT 2 26 0 CGGAAGGGGG 0.584404 -34 CGCGCTGGTCAGCTGCCATGACCGCG 2 44 0 GGTCAGCTGC 0.892183 -16 CAACGATTACCGGTCGGCACCCGGAACCGA 3 11 1 CGGTCGGCAC 0.632896 -27 AAACGGCTCGGTTCCGGGTGCCGA 3 24 0 GGCTCGGTTC 0.765574 -14 TGACCCAGTAGGTCAAGTCCGACAACCGA 4 10 0 GGTCAAGTCC 0.865307 -54 TTGACCTACTGGGTCAGGCCGACGAGCACT 4 24 1 GGGTCAGGCC 0.927219 -40 CTACCCTAATGGTCGAGTGCTCGTCGGCCT 4 39 0 GGTCGAGTGC 0.957873 -25 TCGACCATTAGGGTAGGGGCC 4 53 1 GGGTAGGGGC 0.9677 -11 TAAACCCACGGATCGACGTCCTGCGGATCC 5 13 0 GATCGACGTC 0.462384 -262 CGTTACTGGCGGGTAGCTTCTGAAACGGTT 5 56 1 GGGTAGCTTC 0.741643 -219 TTCAGTTTTTGGGCGACTTCGCAAAATTTG 5 84 1 GGGCGACTTC 0.923688 -191 TTGCGAATTTCGGCAACGGCCTGCGGACTT 5 118 0 CGGCAACGGC 0.973699 -157 GCCCTACCGTCGTCCAGGCGGTGTCAACGG 5 214 0 CGTCCAGGCG 0.818345 -61 GCCTGGACGACGGTAGGGCGTCAGCGTTTT 5 225 1 CGGTAGGGCG 0.844617 -50 CAGCAAGTCCCGGTGGGCGGAGGTGCG 6 8 0 CGGTGGGCGG 0.859626 -256 CTGGTTGCAACAGCAAGTCCCGGTGGGCGG 6 18 0 CAGCAAGTCC 0.774708 -246 GCTACGGTTTGGGCGACTGGTTGCAACAGC 6 34 0 GGGCGACTGG 0.88915 -230 TAGCAAGGACGGCCGACTGCACCGATGTCC 6 60 1 GGCCGACTGC 0.922986 -204 GCCGACACCTCGGCGGGGACATCGGTGCAG 6 76 0 CGGCGGGGAC 0.96602 -188 GCCGAGGTGTCGGCAACGGCCGCCGGGGCC 6 92 1 CGGCAACGGC 0.973699 -172 CGGCAACGGCCGCCGGGGCCACCAACTCGC 6 102 1 CGCCGGGGCC 0.906325 -162 ATCCAGGGCGCGGCGAGTTGGTGGCCCCGG 6 114 0 CGGCGAGTTG 0.90298 -150 GAGCGACACACATCCAGGGCGCGGCGAGTT 6 125 0 CATCCAGGGC 0.818033 -139 CCTGTCACTGCGCCCGGAGCGACACACATC 6 141 0 CGCCCGGAGC 0.77322 -123 CACGGTCGCGCACCGGGTGCGGAACCCAGG 6 188 0 CACCGGGTGC 0.882784 -76 GGTCGGCGCAGGTCCACCTCTGGCCTATCA 6 218 0 GGTCCACCTC 0.586832 -46 GATCGATCGTCGGTCGGCGCAGGTCCACCT 6 229 0 CGGTCGGCGC 0.941063 -35 ACCCGAACTCGGTCGGGTTCGCTTGCGCTG 7 19 0 GGTCGGGTTC 0.934186 -33 ********** Masking position 2 Map Score: 37.7331 Number of sites scoring better than the average of aligned sites = 115028 Number in coding regions = 108215 Number in noncoding regions = 6813 Number of orfs with sites within 600 bp upstream = 1762 Fraction of orfs with sites within 600 bp upstream = 0.283007 Motif number 2 GGAAGCCATTGTGGCCCCGGCGGTAGTGTG 1 11 1 GTGGCCCCGG 0.969352 -57 TGATTTTGACGAGGAGCCGAATACG 1 53 1 GAGGAGCCGA 0.913273 -15 GATTACCGGTCGGCACCCGGAACCGAGCCG 3 15 1 CGGCACCCGG 0.963182 -23 TCAGGCCGACGAGCACTCGACCATTAGGGT 4 37 1 GAGCACTCGA 0.940569 -27 TCGACGTCCTGCGGATCCGG 5 1 0 GCGGATCCGG 0.616336 -274 TGCAAATTTTGCGAAGTCGCCCAAAAACTG 5 86 0 GCGAAGTCGC 0.620651 -189 TCACTGGTGTGCTAACTCGACCATGGCACA 5 177 0 GCTAACTCGA 0.785652 -98 CAGTGAAGCTGCGCCGTTGACACCGCCTGG 5 201 1 GCGCCGTTGA 0.691159 -74 CGCACCTCCGCCCACCGGGACTTGCTGTT 6 10 1 GCCCACCGGG 0.873013 -254 GGGGACATCGGTGCAGTCGGCCGTCCTTGC 6 62 0 GTGCAGTCGG 0.965526 -202 CGGCGAGTTGGTGGCCCCGGCGGCCGTTGC 6 104 0 GTGGCCCCGG 0.969352 -160 CCAACTCGCCGCGCCCTGGATGTGTGTCGC 6 123 1 GCGCCCTGGA 0.92935 -141 TATCCTGTCACTGCGCCCGGAGCGACACAC 6 144 0 CTGCGCCCGG 0.90509 -120 CACCTGGGTTCCGCACCCGGTGCGCGACCG 6 186 1 CCGCACCCGG 0.964845 -78 CAGAGGTGGACCTGCGCCGACCGACGATCG 6 226 1 CCTGCGCCGA 0.691444 -38 AACAGCGCAAGCGAACCCGACCGAGTTCGG 7 17 1 GCGAACCCGA 0.984564 -35 CGCGGATCACCCGAACTCGGTCGGGTTCGC 7 27 0 CCGAACTCGG 0.757172 -25 ********** Masking position 9 Map Score: 21.7452 Number of sites scoring better than the average of aligned sites = 32409 Number in coding regions = 30396 Number in noncoding regions = 2013 Number of orfs with sites within 600 bp upstream = 1029 Fraction of orfs with sites within 600 bp upstream = 0.165275 Motif number 3 CCGGATCCGCAGGACGTCGATCC 5 4 1 GATCCGCAGG 0.998324 -271 GCAGGACGTCGATCCGTGGGTTTACCTGCG 5 19 1 GATCCGTGGG 0.98711 -256 AGTAACGACAAATCCGCAGGTAAACCCACG 5 33 0 AATCCGCAGG 0.99737 -242 ATTTGCAAAAAGTCCGCAGGCCGTTGCCGA 5 109 1 AGTCCGCAGG 0.992845 -166 CCGTTGCCGAAATTCGCAAGTGAAATGGGT 5 129 1 AATTCGCAAG 0.952034 -146 GAGTTCGGGTGATCCGCGAGGGT 7 39 1 GATCCGCGAG 0.994057 -13 ********** Masking position 3 Map Score: 11.9377 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 400 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 CGTAGACCGTGATCCCCCTTCCGCGGTCATGG 2 23 1 GATCCCTTCC 0.581524 -37 CGGTCATGGCAGCTGACCAGCGCG 2 46 1 AGCGCCAGCG 0.756057 -14 GTCGAGTGCTCGTCGGCCTGACCCAGTAGGTC 4 26 0 CGTGCCTGAC 0.934258 -38 ACCCACGGATCGACGTCCTGCGGATCCGG 5 8 0 CGAGCCTGCG 0.974556 -267 TCGATCCGTGGGTTTACCTGCGGATTTGTCGT 5 27 1 GGTTCCTGCG 0.988546 -248 CGAATTTCGGCAACGGCCTGCGGACTTTTTGC 5 113 0 CAAGCCTGCG 0.961157 -162 AAGTGAAATGGGTGGACCAGCGTTGACACGCT 5 146 1 GGTGCCAGCG 0.992214 -129 CTAACTCGACCATGGCACAGCGTGTCAACGCT 5 164 0 CATGACAGCG 0.873397 -111 GACGCCCTACCGTCGTCCAGGCGGTGTCAACG 5 215 0 CGTGCCAGGC 0.96309 -60 CGACTGCACCGATGTCCCCGCCGAGGTGTCGG 6 73 1 GATTCCCGCC 0.857029 -191 GCGGCGAGTTGGTGGCCCCGGCGGCCGTTGCC 6 103 0 GGTGCCCGGC 0.955965 -161 CGAAACCTATCCTGTCACTGCGCCCGGAGCGA 6 149 0 CCTTACTGCG 0.546182 -115 TAGGTTTCGACATCCACCTGGGTTCCGCACCC 6 172 1 CATCCCTGGG 0.932186 -92 ATAGGCCAGAGGTGGACCTGCGCCGACCGACG 6 220 1 GGTGCCTGCG 0.995141 -44 AACTCGGTCGGGTTCGCTTGCGCTGTTTGAGT 7 12 0 GGTCCTTGCG 0.885067 -40 *** * ****** Masking position 8 Map Score: 18.257 Number of sites scoring better than the average of aligned sites = 11712 Number in coding regions = 10963 Number in noncoding regions = 749 Number of orfs with sites within 600 bp upstream = 566 Fraction of orfs with sites within 600 bp upstream = 0.0909091 Motif number 5 CCGCAGTAAGGTCGTAGACCGTGATCCCC 2 10 1 GGTCGTAGAC 0.866007 -50 GCTCGGTTCCGGGTGCCGACCGGTAATCGT 3 13 0 GGGTGCCGAC 0.992402 -25 TCGGTTGTCGGACTTGACCTAC 4 3 1 GGTTGTCGGA 0.967884 -61 ATGGTCGAGTGCTCGTCGGCCTGACCCAGT 4 31 0 GCTCGTCGGC 0.935485 -33 CGGATCCGCAGGACGTCGATCCGTGGGTTT 5 12 1 GGACGTCGAT 0.830777 -263 GTCCGCAGGCCGTTGCCGAAATTCGCAAGT 5 120 1 CGTTGCCGAA 0.829943 -155 CCATGGCACAGCGTGTCAACGCTGGTCCAC 5 157 0 GCGTGTCAAC 0.917251 -118 GTCGTCCAGGCGGTGTCAACGGCGCAGCTT 5 206 0 CGGTGTCAAC 0.924761 -69 GACGACGGTAGGGCGTCAGCGTTTTCGGCA 5 230 1 GGGCGTCAGC 0.972149 -45 GTCCCCGCCGAGGTGTCGGCAACGGCCGCC 6 86 1 AGGTGTCGGC 0.943798 -178 GAACCCAGGTGGATGTCGAAACCTATCCTG 6 167 0 GGATGTCGAA 0.951536 -97 GTCGCGCACCGGGTGCGGAACCCAGGTGGA 6 184 0 GGGTGCGGAA 0.848582 -80 ********** Masking position 5 Map Score: 13.7307 Number of sites scoring better than the average of aligned sites = 15559 Number in coding regions = 14662 Number in noncoding regions = 897 Number of orfs with sites within 600 bp upstream = 594 Fraction of orfs with sites within 600 bp upstream = 0.0954064 Motif number 6 TGGCCCCGGCGGTAGTGTGAGCTGTATTACAT 1 22 1 GGAGTTGAGC 0.583067 -46 CCATGACCGCGGAAGGGGGATCACGGTCTACG 2 23 0 GGAGGGGATC 0.481171 -37 CCCCTTCCGCGGTCATGGCAGCTGACCAGCGC 2 37 1 GGCATGCAGC 0.95886 -23 CGGATCCGCAGGACGTCGATCCGTGGGTTTAC 5 12 1 GGCGTGATCC 0.691424 -263 CCTGCGGATTTGTCGTTACTGGCGGGTAGCTT 5 43 1 TGCGTACTGG 0.64219 -232 AAAGTCCGCAGGCCGTTGCCGAAATTCGCAAG 5 117 1 GGCGTGCCGA 0.928989 -158 AATTCGCAAGTGAAATGGGTGGACCAGCGTTG 5 139 1 TGAATGGTGG 0.710875 -136 TGGCACAGCGTGTCAACGCTGGTCCACCCATT 5 152 0 TGCAAGCTGG 0.65769 -123 GACACCGCCTGGACGACGGTAGGGCGTCAGCG 5 219 1 GGCGAGGTAG 0.775744 -56 AAGTCCCGGTGGGCGGAGGTGCG 6 2 0 GGCGGGGTGC 0.993145 -262 CGGTGCAGTCGGCCGTCCTTGCTACGGTTTGG 6 52 0 GGCGTCTTGC 0.691192 -212 ACCTCGGCGGGGACATCGGTGCAGTCGGCCGT 6 68 0 GGCATGGTGC 0.985416 -196 TGGCCCCGGCGGCCGTTGCCGACACCTCGGCG 6 91 0 GGCGTGCCGA 0.928989 -173 CCAGGGCGCGGCGAGTTGGTGGCCCCGGCGGC 6 110 0 GCAGTGGTGG 0.811528 -154 CCGTGTGATAGGCCAGAGGTGGACCTGCGCCG 6 213 1 GGCAGGGTGG 0.979965 -51 ATCGATCGTCGGTCGGCGCAGGTCCACCTCTG 6 226 0 GGCGGGCAGG 0.981528 -38 ** *** ***** Masking position 2 Map Score: 10.7749 Number of sites scoring better than the average of aligned sites = 26413 Number in coding regions = 24791 Number in noncoding regions = 1622 Number of orfs with sites within 600 bp upstream = 948 Fraction of orfs with sites within 600 bp upstream = 0.152265 Motif number 7 AAACGGCTCGGTTCCGGGTGC 3 27 0 AACGGCTCGG 0.973885 -11 TAGCTTCTGAAACGGTTCAGTTTTTGGGCG 5 69 1 AACGGTTCAG 0.961553 -206 GAGTTAGCACACCAGTGAAGCTGCGCCGTT 5 189 1 ACCAGTGAAG 0.62262 -86 AGGCGGTGTCAACGGCGCAGCTTCACTGGT 5 199 0 AACGGCGCAG 0.997426 -76 CGGCGGGGACATCGGTGCAGTCGGCCGTCC 6 66 0 ATCGGTGCAG 0.982223 -198 GACACACATCCAGGGCGCGGCGAGTTGGTG 6 121 0 CAGGGCGCGG 0.969013 -143 GTGTGTCGCTCCGGGCGCAGTGACAGGATA 6 144 1 CCGGGCGCAG 0.968732 -120 TCGATCGTCGGTCGGCGCAGGTCCACCTCT 6 227 0 GTCGGCGCAG 0.981076 -37 AACTCAAACAGCGCAAGCGAACCCGA 7 7 1 AACAGCGCAA 0.882089 -45 ********** Masking position 5 Map Score: 11.284 Number of sites scoring better than the average of aligned sites = 7403 Number in coding regions = 6880 Number in noncoding regions = 523 Number of orfs with sites within 600 bp upstream = 381 Fraction of orfs with sites within 600 bp upstream = 0.061195 Motif number 8 ********** No masking Map Score: -1.36181e-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 9 ********** No masking Map Score: -1.36181e-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 10 ********** No masking Map Score: -1.36181e-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