AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i149_bsub_mtub_300.orf -o149_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 trxA 300 thioredoxin #2 Rv3908 300 hypothetical protein Rv3908 #3 sigM 34 sigM #4 trxB2 93 trxB2 Motif number 1 CATGCCGGCGCTCTTTTTCAGGTT 1 3 1 TGCGCGCTCT 0.947619 -298 GTTTTAAAACAGCTCCGGCAGGGCATGGTAAA 1 32 1 AGCCGGCAGG 0.959759 -269 CGTCGCATTGGCCGGTGTCGGGACG 2 4 1 CGCTGGCCGG 0.963608 -297 GGATTCTTAATATTGTCGCCGGCTGTTTGTCG 2 61 0 TATGCGCCGG 0.92921 -240 GCGCACGATTTGCCCACCTTCGAGCGACAAGA 2 108 0 TGCCCCTTCG 0.872234 -193 GTGGGCAAATCGTGCGCCCCCGACACAGCGAC 2 123 1 CGTCCCCCCG 0.736739 -178 GCGGGTCGCCTGCACCGCCCCGCTCCCTCGCC 2 195 1 TGCCGCCCCG 0.991086 -106 GTGTTCCCGATGTACTCGCCGTCTGAGCGCCC 2 252 0 TGTCCGCCGT 0.96749 -49 GTACATCGGGAACACCCGCCCGTACCAGCTAC 2 269 1 AACCCGCCCG 0.968658 -32 CCGTACCAGCTACTATCGCTGGG 2 288 1 TACACGCTGG 0.891311 -13 TGGCTGGCCGTGCCCGGCCCGG 3 1 0 TGCCGCCCGG 0.993024 -34 AGCACTTCACCCTGGCTGGCCGTGCCCGG 3 16 0 CACCGGCTGG 0.956922 -19 TGGGTCTGGGTGCTGTCGCTCGCCTGCGGGAA 4 11 1 TGCGCGCTCG 0.99157 -83 TAGGCACTGCTGTTCCCGCAGGCGAGCGACAG 4 23 0 TGTCCGCAGG 0.981988 -71 GGAACAGCAGTGCCTACGCTGGCGTTCGTTGT 4 39 1 TGCTCGCTGG 0.985235 -55 TCTCAAGATCTGCCCTCGCACTCGAAAGGCTC 4 70 1 TGCCCGCACT 0.968065 -24 *** * ****** Masking position 9 Map Score: 24.7667 Number of sites scoring better than the average of aligned sites = 1962 Number in coding regions = 1827 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 ATTAAAATAGCGTGAACGAATGGGAGATGC 1 241 1 CGTGAACGAA 0.630095 -60 GAGGTATCGTCGTGCCCATCTCCGCGCGAC 2 35 1 CGTGCCCATC 0.949378 -266 CCCATCTCCGCGCGACAAACAGCCGGCGAC 2 49 1 CGCGACAAAC 0.975657 -252 ACAAACAGCCGGCGACAATATTAAGAATCC 2 63 1 GGCGACAATA 0.695246 -238 AGCGACAAGACGCGACCGCACCCAAGGATT 2 88 0 CGCGACCGCA 0.981235 -213 CCCACCTTCGAGCGACAAGACGCGACCGCA 2 98 0 AGCGACAAGA 0.805902 -203 GCAAATCGTGCGCCCCCGACACAGCGACTT 2 127 1 CGCCCCCGAC 0.919615 -174 CCAATTGAGTCGCGCCAGTCACATCTATCA 2 160 0 CGCGCCAGTC 0.982277 -141 GGGCGGTGCAGGCGACCCGCGCTGACCAAT 2 185 0 GGCGACCCGC 0.904606 -116 GCCCCGCTCCCTCGCCCAACGAATAAGTCC 2 211 1 CTCGCCCAAC 0.911667 -90 TCGCCGTCTGAGCGCCCATCGTCGGCCAGG 2 239 0 AGCGCCCATC 0.949377 -62 GCGAGTACATCGGGAACACCCGCCCGTACC 2 265 1 CGGGAACACC 0.843949 -36 CCTGGCTGGCCGTGCCCGGCCCGG 3 5 0 CGTGCCCGGC 0.981135 -30 CCCGCAGGCGAGCGACAGCACCCAGACCCA 4 11 0 AGCGACAGCA 0.782733 -83 CGCTCGCCTGCGGGAACAGCAGTGCCTACG 4 27 1 CGGGAACAGC 0.897952 -67 TGCCCTCGCACTCGAAAGGCTCGC 4 80 1 CTCGAAAGGC 0.706182 -14 ********** Masking position 4 Map Score: 15.6842 Number of sites scoring better than the average of aligned sites = 2799 Number in coding regions = 2620 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 3 AGGTTTTAAAACAGCTCCGGCAGGGCATGG 1 30 1 ACAGCTCCGG 0.955074 -271 GCATAAGATCACATCTCCTCTTCACTGTCA 1 69 0 ACATCTCCTC 0.90014 -232 TAAAAAAAGAGCATATCCCATTCAACCATA 1 164 1 GCATATCCCA 0.771856 -137 TTTTAGTATAGCATCTCCCATTCGTTCACG 1 251 0 GCATCTCCCA 0.974826 -50 ATCGTCGTGCCCATCTCCGCGCGACAAACA 2 40 1 CCATCTCCGC 0.972301 -261 ACAAGACGCGACCGCACCCAAGGATTCTTA 2 84 0 ACCGCACCCA 0.972599 -217 GCGCGGGTCGCCTGCACCGCCCCGCTCCCT 2 193 1 CCTGCACCGC 0.933311 -108 CCTGCACCGCCCCGCTCCCTCGCCCAACGA 2 203 1 CCCGCTCCCT 0.964663 -98 AGCACTTCACCCTGGCTGGCCGT 3 22 0 ACTTCACCCT 0.885221 -13 CAGGCGAGCGACAGCACCCAGACCCA 4 7 0 ACAGCACCCA 0.984297 -87 ********** Masking position 7 Map Score: 8.91087 Number of sites scoring better than the average of aligned sites = 1309 Number in coding regions = 1140 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 4 CGAAGCATAAGATCACATCTCCTCTTCACT 1 73 0 GATCACATCT 0.931661 -228 TTTAAAAAAAGAGCATATCCCATTCAACCA 1 162 1 GAGCATATCC 0.83343 -139 ATTTTTTCCTGATCACAGCCGGTTTACTCA 1 200 0 GATCACAGCC 0.946909 -101 GCGCGGAGATGGGCACGACGATACCTCGTC 2 32 0 GGGCACGACG 0.941987 -269 GCTCGAAGGTGGGCAAATCGTGCGCCCCCG 2 115 1 GGGCAAATCG 0.947059 -186 GAGTCGCGCCAGTCACATCTATCACAGAAG 2 154 0 AGTCACATCT 0.851106 -147 CGACTCAATTGGTCAGCGCGGGTCGCCTGC 2 178 1 GGTCAGCGCG 0.837627 -123 CTCAGACGGCGAGTACATCGGGAACACCCG 2 257 1 GAGTACATCG 0.822615 -44 CCGGGCCGGGCACGGCCAGCCAGGGTG 3 8 1 GGGCACGGCC 0.98452 -27 ACGCCAGCGTAGGCACTGCTGTTCCCGCAG 4 34 0 AGGCACTGCT 0.751301 -60 TCGAGTGCGAGGGCAGATCTTGAGACAACG 4 65 0 GGGCAGATCT 0.968514 -29 ********** Masking position 5 Map Score: 7.48347 Number of sites scoring better than the average of aligned sites = 1124 Number in coding regions = 1027 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 CCCTGCCGGAGCTGTTTTAAAACCTGAAAA 1 25 0 GCTGTTTTAA 0.909001 -276 TATGCTTCGTACCATTTTAATGATTATTGG 1 94 1 ACCATTTTAA 0.94938 -207 ATCCCATTCAACCATATAAAAATGAGTAAA 1 178 1 ACCATATAAA 0.822279 -123 ATTCGTTCACGCTATTTTAATGCTTACAAA 1 232 0 GCTATTTTAA 0.964688 -69 AATGGGAGATGCTATACTAAAAATCATCAT 1 259 1 GCTATACTAA 0.908997 -42 ACAGCCGGCGACAATATTAAGAATCCTTGG 2 67 1 ACAATATTAA 0.872991 -234 ********** Masking position 5 Map Score: 0.525429 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 155 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 ********** No masking Map Score: 4.92707e-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 7 ********** No masking Map Score: 4.92707e-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 8 ********** No masking Map Score: 4.92707e-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