AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i011_bsub_mtub_300.orf -o011_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 ctrA 241 CTP synthetase #2 rpoE 182 RNA polymerase (delta subunit) #3 ywjF 154 similar to hypothetical proteins #4 lprJ 300 lprJ #5 Rv1691 38 hypothetical protein Rv1691 #6 Rv1697 95 hypothetical protein Rv1697 #7 Rv1698 21 hypothetical protein Rv1698 #8 pyrG 139 pyrG Motif number 1 TAGTACGTTATGCTCCCTTTCAAGAAATTGAAAG 1 100 1 TGCCTTTCAG 0.757383 -142 TTCGTTTGCTCCTCTCTTCGCTCTTAGCTA 1 222 0 TGCCCTCTCG 0.960642 -20 ACCGGCACTCCTTTCCGTAGTAAAGGT 3 4 1 GGCCCTTTCG 0.984292 -151 GTCCCCCGATTGGTGGACTTCACGATCCACCGGA 4 112 0 TGGGCTTCCG 0.856033 -189 GGGCACCGCGGGCCGATCGTCCCCCGATTGGTGG 4 130 0 GGCGCGTCCC 0.961393 -171 CGGCCCGCGGTGCCCCCCTACCCGGTTAACGCGC 4 149 1 TGCCCTACCG 0.994945 -152 GATAAAGGTTTGCACACTAACGCGTTTCGTGTGG 4 190 0 TGCCTAACCG 0.907235 -111 CGTCATTTAAGGCACCTCGACAACAGTGGCCAAC 4 249 0 GGCCCGACAC 0.883025 -52 TAGTTACGGGGCGCAGCAACCCCCGTAACCTCT 5 10 1 GGCCCAACCC 0.974907 -29 CTAATGTTACGGCGCGCCTCCACGCACCTGCCCA 6 50 1 GGCCCTCCCG 0.997172 -46 TCCACGCACCTGCCCAGCTTCACCGCCAGAATCC 6 68 1 TGCCCTTCCC 0.99279 -28 TAACATCCACGGCGCCTCACCGCGGGGAACACGC 8 23 0 GGCCCACCCG 0.993555 -117 TGGGTCGGCAGGCCCAGCAAGGCCAGAGAAATCT 8 70 1 GGCCCAAGCC 0.914349 -70 AGACGGGCAGGGCTGTTCTTGACGCTGCCAAGAT 8 100 0 GGCGCTTGCG 0.962072 -40 AGAACAGCCCTGCCCGTCTTCACGGAGGTCGCTC 8 115 1 TGCCCTTCCG 0.996323 -25 *** * **** ** Masking position 2 Map Score: 26.4365 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 507 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 TATACAGATTCGGGGGTAGGGGATCGCGGTCTT 3 108 1 CGGGGGGGGA 0.992046 -47 ATCAGTAAAAAGGGGGAATTGGA 3 142 1 AGGGGGTGGA 0.708822 -13 CACGACTAGTCGGTGGCCGGGGGAAATGCCGAA 4 72 1 CGGTGGGGGG 0.99524 -229 TCCACCGGATGCGGGATTCGGCATTTCCCCCGG 4 88 0 GCGGGAGGCA 0.897177 -213 ATCCCGCATCCGGTGGATCGTGAAGTCCACCAA 4 104 1 CGGTGGGTGA 0.917791 -197 GTCCACCAATCGGGGGACGATCGGCCCGCGGTG 4 128 1 CGGGGGATCG 0.848187 -173 TGCGCGTTAACCGGGTAGGGGGGCACCGCGGGC 4 151 0 CCGGGTGGGG 0.986957 -150 TAGAGGTTACGGGGGTTGCTGCGCCCCGTAACT 5 12 0 GGGGGTTGCG 0.885169 -27 CTGGGCAGGTGCGTGGAGGCGCGCCGTAACATT 6 52 0 GCGTGGCGCG 0.962864 -44 GGGATTCTGGCGGTGAAGCTGGGCAGGTGCGTG 6 70 0 CGGTGATGGG 0.919908 -26 GGGGGGATTCTGGCGGTGAAGCT 6 83 0 GGGGGGCTGG 0.912348 -13 GCCCGCGTTAGGGCGTGTTCCCCGC 8 3 1 CCGCGTGGCG 0.952852 -137 GGCGTGTTCCCCGCGGTGAGGCGCCGTGGATGT 8 22 1 CCGCGGGGCG 0.989204 -118 GGGTGGGTTTCCGTGGGTCGGCAGGCCCAGCAA 8 57 1 CCGTGGGGCA 0.981017 -83 TGAGCGACCTCCGTGAAGACGGGCAGGGCTGTT 8 117 0 CCGTGACGGG 0.940672 -23 ****** **** Masking position 5 Map Score: 19.7446 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 776 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 GCTCTTCAAAAACGAAGAGAGAACATAGTAC 1 75 1 ACGAAGAGAG 0.965976 -167 TTTCAATTTCTTGAAAGGGAGCATAACGTAC 1 102 0 TGAAAGGGAG 0.990313 -140 TTTCAAGAAATTGAAAGGGAGCTTTCTTATT 1 117 1 TGAAAGGGAG 0.990313 -125 TGTAGCTAAGAGCGAAGAGAGGAGCAAACGA 1 220 1 ACGAAGAGAG 0.965976 -22 ATATAAGTAATAGAAAGGGAGTGTCCGACC 2 163 1 TGAAAGGGAG 0.990313 -20 TACCTTTACTACGGAAAGGAGTGCCGGT 3 8 0 AGGAAAGGAG 0.961343 -147 * ********* Masking position 6 Map Score: 6.102 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 49 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 ACCCCTCATTTTTCTTATAAATCATTTAAAA 1 151 1 TTTTTATAAA 0.836198 -91 GGCTAAATGATTTTTTATAAAATAGTACATT 1 182 1 TTTTTATAAA 0.836198 -60 ATCGCTTTCATTATTGATAAAACAGATACAT 2 134 1 TTATGATAAA 0.961786 -49 TAAGATTATCTTTATGATAAATAATGAATGA 3 79 0 TTTTGATAAA 0.566226 -76 TTCCCCCTTTTTACTGATAAAGACCGCGATC 3 129 0 TTATGATAAA 0.961786 -26 *** ******* Masking position 5 Map Score: 3.84664 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 107 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 AATATGCTACCCTTAACAGCGTTAATTTAAA 2 50 0 CCTTACAGCG 0.971233 -133 GGGCACACTACCTTTACTACGGAAAGGAGTG 3 16 0 CCTTACTACG 0.912581 -139 AAGTGGAAATCGACTACAACG 4 1 0 CGACACAACG 0.983224 -300 ACAAGAGTCACGTTCACAGCACAGTGGGATA 4 220 0 CGTTACAGCA 0.954901 -81 ATTTAAGGCACCTCGACAACAGTGGCCAACA 4 248 0 CCTCACAACA 0.980453 -53 GACGCAAGTGCGACAACAACGAGAAGCGGGA 4 279 1 CGACACAACG 0.983224 -22 ATCTTGGCAGCGTCAAGAACAGCCCTGCCCG 8 100 1 CGTCAGAACA 0.927053 -40 **** ****** Masking position 6 Map Score: 4.4245 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 247 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GTAATAGAAAGGGAGTGTCCGACC 2 169 1 GGGAGTGTCC 0.907912 -14 GACTTATCTTTGGCGGGTTTGGACTCCGCT 4 35 1 TGGCGGGTTT 0.943109 -266 CGGTGAAGCTGGGCAGGTGCGTGGAGGCGC 6 63 0 GGGCAGGTGC 0.949024 -33 GGGGGGATTCTGGCGGTGAA 6 86 0 GGGGGGATTC 0.950017 -10 TTTTCTTGGACGGTGGGTTC 7 12 1 CGGTGGGTTC 0.975594 -10 GCCCGCGTTAGGGCGTGTTCCCCGCGGTGA 8 11 1 GGGCGTGTTC 0.990734 -129 GTGGATGTTAGGGTGGGTTTCCGTGGGTCG 8 47 1 GGGTGGGTTT 0.979406 -93 ********** Masking position 8 Map Score: 3.75927 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 152 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TTTAGCCTTTTAAATGATTTATAAGAAAAA 1 159 0 TAAATGATTT 0.920322 -83 TTTAAAAGGCTAAATGATTTTTTATAAAAT 1 175 1 TAAATGATTT 0.920322 -67 AGCGTTAATTTAAATAATTTTACAAGAGTG 2 34 0 TAAATAATTT 0.931557 -149 ATCTGTTTTATCAATAATGAAAGCGATTTT 2 131 0 TCAATAATGA 0.885554 -52 GAGTGTTCAGTCAATAATTAAATTCCTGCT 3 51 0 TCAATAATTA 0.896125 -104 ATCTTTATGATAAATAATGAATGAGTGTTC 3 73 0 TAAATAATGA 0.896125 -82 ********** Masking position 5 Map Score: 2.68395 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 29 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TCTTATTTTCACCCCTCATTTTTCTTATAA 1 141 1 ACCCCTCATT 0.984495 -101 CGGAAAACATCTCTCAGTCGGATCACTC 2 9 1 ATCTCTCAGT 0.94202 -174 TACAAACCATACCTCTCATTATAAACAAAA 2 89 0 ACCTCTCATT 0.986936 -94 TTATTGACTGAACACTCATTCATTATTTAT 3 64 1 AACACTCATT 0.940147 -91 ********** Masking position 6 Map Score: 0.00596537 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 11 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: -2.58394e-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: -2.58394e-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 11 ********** No masking Map Score: -2.58394e-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