AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_bsub_mtub_300.orf -o316_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 pbpC 150 penicillin-binding protein 3 #2 pbpA 113 penicillin-binding protein 2A #3 yqgE 33 similar to hypothetical proteins #4 sodA 178 superoxide dismutase #5 yqgC 109 yqgC #6 mreC 30 cell-shape determining protein #7 mreB 90 cell-shape determining protein #8 ysxA 36 similar to DNA repair protein #9 maf 152 maf #10 spoIIB 133 spoIIB #11 comC 139 DNA-binding protein #12 folC 59 folyl-polyglutamate synthetase #13 valS 300 valyl-tRNA synthetase #14 ppp 88 ppp #15 Rv0019c 123 hypothetical protein Rv0019c #16 Rv0020c 300 hypothetical protein Rv0020c #17 accD5 49 accD5 Motif number 1 AAGCATCCGGCTCCGGCAGAATCAAAA 11 8 1 CGGCTCCGGC 0.92037 -132 TCTCTAGAAACCGCCCCGGCTTTTCA 12 7 0 CCGCCCCGGC 0.996677 -53 AAGAAATTATGCTCCCGGGCGACCTTCCAA 13 113 0 GCTCCCGGGC 0.816246 -188 CCCGCGCTGGCGACGATGCAG 14 2 1 CCGCGCTGGC 0.990716 -87 TTGTGGGGGCGCGCCCCCACCGCTTCTCTG 14 36 0 GCGCCCCCAC 0.985127 -53 CAAGTGGGGGGTACCCCCACCCGCTTGCGG 14 63 1 GTACCCCCAC 0.791457 -26 TCTCCCCCGCAAGCGGGTGG 14 79 0 TCTCCCCCGC 0.908703 -10 CGGCGCGGGTCAACCCCGGCAGCTTCGAGC 15 20 0 CAACCCCGGC 0.927724 -104 CGGGGTTGACCCGCGCCGACCACCGTCAAA 15 32 1 CCGCGCCGAC 0.995308 -92 TGCTCCGGCCCCGCGCTGCCGAGCACGTCA 15 77 0 CCGCGCTGCC 0.91925 -47 CCTGCACCGTCTGCTCCGGCCCCGCGCTGC 15 88 0 CTGCTCCGGC 0.933073 -36 TCAAGTCCCCCTTCGCCCACCGTACTGTGA 16 18 0 CTTCGCCCAC 0.922953 -283 AGGGGGACTTGAACCCCCACGTCCCGAAGG 16 36 1 GAACCCCCAC 0.744552 -265 GGAATGGCAGACGCGCTGGCTTCAGGTGCC 16 71 0 ACGCGCTGGC 0.936977 -230 CCATTCCGCCACTCGCCCGCAACAACCGGA 16 94 1 ACTCGCCCGC 0.939326 -207 CCGCTGCCAGGGGCGCCGGCGGGCTCAGTG 16 157 1 GGGCGCCGGC 0.981973 -144 AAAGGGCCGGCCACGCCCACTGAGCCCGCC 16 174 0 CCACGCCCAC 0.976289 -127 GGCCCTTTCCGCTCGCTCACACTGTCCCGA 16 196 1 GCTCGCTCAC 0.875301 -105 GTCGTTTGCCTTGCGCCGACGATGCACCAG 16 258 1 TTGCGCCGAC 0.874501 -43 CTTTCAGCGCTCGCCTCACTGTTC 16 287 0 CAGCGCTCGC 0.940939 -14 ********** Masking position 6 Map Score: 30.4605 Number of sites scoring better than the average of aligned sites = 1677 Number in coding regions = 1567 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 GCTATCCCTTCTTTCTGTCTTTTCAAATAGT 1 11 1 CTTTCTGTCT 0.939714 -140 ATCGGTGAACTTTTCCTTCATTTTCAAAAAA 1 72 1 TTTTCCTTCT 0.811882 -79 ACTTGAGTGTCTTTTCTTTCTGTAAATAGAA 2 82 1 CTTTTCTTTT 0.798769 -32 TCACAGCGAGCCTTTCTTCATTCAATGTAAC 4 119 0 CCTTTCTTCT 0.950084 -60 TATCTTCACTTCCTAGCTAAACTA 5 4 1 CTTCACTTCT 0.872724 -106 ACTCTGTCTTCTTCATGTCTTCCTTGTATTC 5 69 0 CTTCATGTCT 0.745074 -41 CACTTTTTTTTCGTCGAATTAAGC 7 4 1 TTTTTTTTCT 0.82362 -87 ATGTATGTATCTTCCTTTCTTAAAGCAAAAA 7 70 0 CTTCCTTTCT 0.960956 -21 GCACTCCTTTTCTTTCCCTTCCCG 8 23 0 CTCCTTTTCT 0.765335 -14 TAGTGACAGGCTTTTTTTATTTTGTCATGAA 9 38 1 CTTTTTTTAT 0.648886 -115 AAACGAGTATCTTTTTTTCTTAAGCAAACCC 9 116 1 CTTTTTTTCT 0.975349 -37 AAGTCTTGTTCTTTTTTTCTTTGCCTGTGCT 10 53 1 CTTTTTTTCT 0.975349 -81 TTCCGCTTCCTCCCTTCATTTGCTTGACC 10 115 0 CCTCCCTTCT 0.922117 -19 ACGGCAGAATCTTTTTTTGATTCTGCCGGAG 11 21 0 CTTTTTTTGT 0.732554 -119 AGATTCTGCCGTTTTTTTCATGTGTAAAATT 11 40 1 GTTTTTTTCT 0.732554 -100 TTTTTGTACTCTTCCCGTTCTAAGCAGGTGT 13 29 0 CTTCCCGTTT 0.561776 -272 CCGAATTTCTCTACTCTTCTTTCAAGAAATT 13 135 0 CTACTCTTCT 0.728284 -166 CGCGGTACCACCTTTTTTCATGAACTCAATC 13 200 0 CCTTTTTTCT 0.939855 -101 CGCGAAAGAGCTTTTCGTCCTTTTACAGGGA 13 227 1 CTTTTCGTCT 0.961571 -74 GATGAAGAGCTCTTTTTTCGTTCTCAGCCAT 13 256 1 TCTTTTTTCT 0.648404 -45 CTGGCGTCCTTTCCGTCCTGCACCGTCTG 15 105 0 CTTTCCGTCT 0.949966 -19 ********* * Masking position 8 Map Score: 21.6741 Number of sites scoring better than the average of aligned sites = 1931 Number in coding regions = 1583 Number in noncoding regions = 348 Number of orfs with sites within 600 bp upstream = 361 Fraction of orfs with sites within 600 bp upstream = 0.0579827 Motif number 3 TTTTTTTGCCAAAAAGGGGTTATCTGTAG 2 10 1 CAAAAAGGGG 0.736152 -104 TTATCTGTAGAAAAAAGTCGAAAAAACCTT 2 30 1 AAAAAAGTCG 0.68534 -84 TTCTGTAAATAGAAAAGGTGATGTT 2 99 1 AGAAAAGGTG 0.974584 -15 ACTAAGGGATAGTAAAGGGGAGTCAGTA 3 16 1 AGTAAAGGGG 0.907563 -18 GGAGTTCAATAGAAGAGGTGTAACACG 6 14 1 AGAAGAGGTG 0.905435 -17 GGGAAGGGAAAGAAAAGGAGTGC 8 24 1 AGAAAAGGAG 0.920979 -13 AACGTTTTTTGGACAAGGCGACAAAAGTCT 10 29 1 GGACAAGGCG 0.826936 -105 GTGTGTAGCATGAAAAGCCGACAAGAACGG 10 87 1 TGAAAAGCCG 0.880003 -47 GAACTCAATGAGTAAAGGTGTGTTGTCT 11 122 1 AGTAAAGGTG 0.860917 -18 TGAAAAGCCGGGGCGGTTTC 12 1 1 TGAAAAGCCG 0.880003 -59 CTCTTTTATAAGACAAGGCGGTTTCTCTAG 12 30 0 AGACAAGGCG 0.968046 -30 CTTGTCTTATAAAAGAGGGGATTATCA 12 43 1 AAAAGAGGGG 0.815397 -17 GGAAGAGTACAAAAAAGGCGCATGCAGAGA 13 45 1 AAAAAAGGCG 0.968107 -256 GCATGCAGAGAGAGAAGCCGTTTGCTGAAA 13 64 1 AGAGAAGCCG 0.918987 -237 TGAGTTCATGAAAAAAGGTGGTACCGCGAA 13 203 1 AAAAAAGGTG 0.917712 -98 TGCAGAGCGCAGAGAAGCGGTGGGGGCGCG 14 27 1 AGAGAAGCGG 0.868604 -62 ********** Masking position 6 Map Score: 19.7623 Number of sites scoring better than the average of aligned sites = 969 Number in coding regions = 787 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 TCTCCTATCGTTTGCTGTAGACTATTTGAA 1 32 0 TTTGCTGTAG 0.905375 -119 GTTCACCGATTTTGCAGAAATCTCCTATCG 1 52 0 TTTGCAGAAA 0.898547 -99 TTTTCCTTCATTTTCAAAAAAATCTTGCAC 1 82 1 TTTTCAAAAA 0.57137 -69 TTTTTTTGCCAAAAAGGGGTTATC 2 5 1 TTTGCCAAAA 0.731949 -109 TTTTCGACTTTTTTCTACAGATAACCCCTT 2 24 0 TTTTCTACAG 0.765151 -90 TTAGGGTATTTTTGCTTTAAGAAAGGAAGA 7 62 1 TTTGCTTTAA 0.613004 -29 AAAAAGTTATTTTTCTGAAATTGTGACAAG 9 67 1 TTTTCTGAAA 0.877355 -86 CCTTTCAGGGTTTGCTTAAGAAAAAAAGAT 9 124 0 TTTGCTTAAG 0.887295 -29 TTCGTCAAATTTTTCAGCAG 10 1 0 TTTTCAGCAG 0.687807 -133 TTTCTTTGCCTGTGCTAAAGTGTGTAGCAT 10 68 1 TGTGCTAAAG 0.740552 -66 GGATGTCCATTTTGCTACAATCCATACCAG 11 93 1 TTTGCTACAA 0.891349 -47 AGAGAAGCCGTTTGCTGAAAGGCTTCTTAT 13 74 1 TTTGCTGAAA 0.961403 -227 GTATCGTGACTTTGCTGACGTGCTCGGCAG 15 62 1 TTTGCTGACG 0.844452 -62 ********** Masking position 3 Map Score: 6.65949 Number of sites scoring better than the average of aligned sites = 1503 Number in coding regions = 1372 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 5 CTCGTTTATCCTACCAAATCACGAGGCTTGTCACAATT 9 85 0 CCCAGAGGCT 0.982872 -68 TTTTTTGATTCTGCCGGAGCCGGATGCTT 11 2 0 CCCAGATGCT 0.833835 -138 AAGAGCTTTTCGTCCTTTTACAGGGATGAAGAGCTCTT 13 232 1 CCCTGGGATG 0.816625 -69 GTGGGGGTACCCCCCACTTGTGGGGGCGCGCCCCCACC 14 45 0 CCCTGGGGCG 0.78528 -44 GGGGTACCCCCACCCGCTTGCGGGGGAGA 14 70 1 CCCTGGGGAG 0.723584 -19 CCCCCTTCGCCCACCGTACTGTGAGACGAGT 16 4 0 CCCAGAGACG 0.982815 -297 TGGTATGGTCCTCCGGTTGTTGCGGGCGAGTGGCGGAA 16 97 0 CCGTCGGGCG 0.761601 -204 CCGCAGGCCCCATCCGCTGCCAGGGGCGCCGGCGGGCT 16 144 1 CCCTGGGGCG 0.915676 -157 GCCGACGATGCACCAGAACAGTGAGGCGAGCGCTGAAA 16 272 1 CCAAGAGGCG 0.969815 -29 CCGCACACTACTTCCTTAGGCTGGGGCG 17 1 0 CCCAGGGGCG 0.983303 -49 * ** * ****** Masking position 4 Map Score: 13.3249 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 120 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 GACTTTCCCCTGCCTTCCACTTGTTATT 1 133 0 TCCCTGCCTC 0.987172 -18 GCACTCCTTTTCTTTCCCTTCCCGTTT 8 20 0 TCCTTTCTTC 0.593565 -17 GTTCGTCATCCTTTCAGGGTTTGCT 9 138 0 TCGCATCCTC 0.91205 -15 TTCCGCTTCCTCCCTTCATTTGCT 10 120 0 TCCCTTCCCC 0.976978 -14 AAGTCCCCCTTCGCCCACCGTACTGTGAGACGA 16 13 0 TCGCCACCTC 0.895803 -288 TGAAGCCAGCGCGTCTGCCATTCCGCCACTCGC 16 77 1 GCGCTGCCTC 0.987797 -224 GGCGTGGCCGGCCCTTTCCGCTCGCTCACACTG 16 187 1 GCCTTTCCCC 0.928029 -114 TACAGGCGAGTCGTTTGCCTTGCGCCGACGATG 16 249 1 TCGTTGCCTC 0.979805 -52 CTTTCAGCGCTCGCCTCACTGTTCTGGTG 16 282 0 GCGTCGCCCC 0.948171 -19 GTCGATGTTATCGGCTGCCGCACACTACTTCCT 17 23 0 TCGCTGCCCC 0.991947 -27 *** ***** * * Masking position 8 Map Score: 8.56558 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 376 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 AATCTGCCCCATTAAACCTGCCGCCAGCATTT 4 12 0 AAAACCTGCC 0.786338 -167 GACGCTTCACAGCGAGCCTTTCTTCATTCAAT 4 124 0 AGAGCCTTTC 0.972432 -55 GACAAAATAAAAAAAGCCTGTCACTAAAGGAC 9 32 0 AAAGCCTGTC 0.972914 -121 CTACCAAATCACGAGGCTTGTCACAATTTCAG 9 81 0 AAGGCTTGTC 0.886475 -72 CAGACAACATAAGAAGCCTTTCAGCAAACGGC 13 80 0 AAAGCCTTTC 0.943018 -221 TGGTACCGCGAAAGAGCTTTTCGTCCTTTTAC 13 221 1 AGAGCTTTTC 0.915162 -80 GAGAACGAAAAAAGAGCTCTTCATCCCTGTAA 13 249 0 AGAGCTCTTC 0.84004 -52 CTGGCAGCGGATGGGGCCTGCGGCTACTACAG 16 135 0 AGGGCCTGCG 0.900984 -166 GGCCACGCCCACTGAGCCCGCCGGCGCCCCTG 16 164 0 AGAGCCCGCC 0.979687 -137 GAGCGAGCGGAAAGGGCCGGCCACGCCCACTG 16 182 0 AGGGCCGGCC 0.948908 -119 * ********* Masking position 1 Map Score: 4.93095 Number of sites scoring better than the average of aligned sites = 643 Number in coding regions = 589 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 GAAAATGAAGGAAAAGTTCACCGATTTTGCA 1 66 0 GAAAAGTTCC 0.843873 -85 GTAATCAATGAAAAAGCTCACGATTTGGCTC 4 75 0 AAAAAGCTCC 0.915631 -104 ATTGAATGAAGAAAGGCTCGCTGTGAAGCGT 4 124 1 GAAAGGCTCC 0.985713 -55 ACCCTAAAGGGAAAAACTCATAAACTCTATT 7 38 0 GAAAAACTCT 0.867616 -53 GTCCTTTAGTGACAGGCTTTTTTTATTTTGT 9 32 1 GACAGGCTTT 0.791674 -121 AAGAGTACAAAAAAGGCGCATGCAGAGAGAG 13 47 1 AAAAGGCGCT 0.798384 -254 GCCGTTTGCTGAAAGGCTTCTTATGTTGTCT 13 80 1 GAAAGGCTTT 0.942287 -221 GTAAAAGGACGAAAAGCTCTTTCGCGGTACC 13 222 0 GAAAAGCTCT 0.985033 -79 TTACAGGGATGAAGAGCTCTTTTTTCGTTCT 13 249 1 GAAGAGCTCT 0.939825 -52 ********* * Masking position 2 Map Score: 3.73508 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 572 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 GTACTGAAATGACGCTTCACAGCGAGCCTT 4 136 0 GACGCTTCAC 0.869762 -43 ACTAAAGGACGAAGGCTCAGGGCACTATCT 9 12 0 GAAGGCTCAG 0.87778 -141 CCGCGCTGGCGACGATGCAGAGCGCAGAGA 14 12 1 GACGATGCAG 0.966896 -77 TACTGGGCTCGAAGCTGCCGGGGTTGACCC 15 14 1 GAAGCTGCCG 0.92432 -110 TTTGACGGTGGTCGGCGCGGGTCAACCCCG 15 32 0 GTCGGCGCGG 0.926121 -92 GGCCGGAGCAGACGGTGCAGGACGGAAAGG 15 97 1 GACGGTGCAG 0.988563 -27 TACCACTGTAGTAGCCGCAGGCCCCATCCG 16 130 1 GTAGCCGCAG 0.910438 -171 CACTGAGCCCGCCGGCGCCCCTGGCAGCGG 16 157 0 GCCGGCGCCC 0.909031 -144 GCCTTGCGCCGACGATGCACCAGAACAGTG 16 265 1 GACGATGCAC 0.937703 -36 ********** Masking position 8 Map Score: 4.02785 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 809 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 GGTTTAATGGGGCAGATTATCGGTTAAAGT 4 26 1 GGCAGATTAT 0.890689 -153 GAAGGCTCAGGGCACTATCTC 9 2 0 GGCACTATCT 0.902673 -151 ATCCGGCTCCGGCAGAATCAAAAAAAGATT 11 15 1 GGCAGAATCA 0.922492 -125 TGAAAAAAACGGCAGAATCTTTTTTTGATT 11 30 0 GGCAGAATCT 0.979693 -110 GAAAAGCCGGGGCGGTTTCTAGAGAAACCG 12 12 1 GGCGGTTTCT 0.97689 -48 TATAAGACAAGGCGGTTTCTCTAGAAACCG 12 24 0 GGCGGTTTCT 0.97689 -36 GGTCAACCCCGGCAGCTTCGAGCCCAGTAG 15 13 0 GGCAGCTTCG 0.930848 -111 ********** Masking position 8 Map Score: 4.04282 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 206 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 TCGCTGTGAAGCGTCATTTCAGTACATATA 4 141 1 GCGTCATTTC 0.946536 -38 AGCTTCCATCCTCCCATTTTA 5 99 0 GCTTCCATCC 0.97971 -11 ATGTATGTATCTTCCTTTCTTAAAGCAAA 7 72 0 TCTTCCTTTC 0.874544 -19 TTCCGCTTCCTCCCTTCATTTGCT 10 120 0 GCTTCCTCCC 0.971552 -14 TGTCCATTTTGCTACAATCCATACCAGAAC 11 96 1 GCTACAATCC 0.85142 -44 ATGCTCCCGGGCGACCTTCCAATCAGACAA 13 105 0 GCGACCTTCC 0.983139 -196 CTGGCGTCCTTTCCGTCCTGCAC 15 111 0 GCGTCCTTTC 0.984825 -13 ********** Masking position 5 Map Score: 4.69109 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 205 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 ********** No masking Map Score: -4.98558e-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: -4.98558e-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 ********** No masking Map Score: -4.98558e-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