AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 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 Motif number 1 GCTATCCCTTCTTTCTGTCTTTTCA 1 6 1 CCCTTCTTTC 0.976203 -145 AATCGGTGAACTTTTCCTTCATTTTCAAAA 1 71 1 CTTTTCCTTC 0.970615 -80 GACTTTCCCCTGCCTTCCACTTGTTAT 1 134 0 CCCTGCCTTC 0.943378 -17 ACTTGAGTGTCTTTTCTTTCTGTAAATAGA 2 82 1 CTTTTCTTTC 0.978253 -32 CAGCGAGCCTTTCTTCATTCAATGTAACAA 4 117 0 TTCTTCATTC 0.826694 -62 CTTATTGTATCGTTGCATGCGTGTGAATAC 5 45 1 CGTTGCATGC 0.721692 -65 TTCATGTCTTCCTTGTATTCACACGCATGC 5 59 0 CCTTGTATTC 0.797576 -51 TCCCATTTTACTCTGTCTTCTTCATGTCTT 5 79 0 CTCTGTCTTC 0.891623 -31 CACTTTTTTTTCGTCGAATTAA 7 3 1 CTTTTTTTTC 0.938573 -88 GCACTCCTTTTCTTTCCCTTCCCGTT 8 21 0 CTTTTCTTTC 0.978253 -16 TAAACGAGTATCTTTTTTTCTTAAGCAAAC 9 115 1 TCTTTTTTTC 0.553657 -38 AAAGTCTTGTTCTTTTTTTCTTTGCCTGTG 10 52 1 TCTTTTTTTC 0.553657 -82 TTCTTGTCGGCTTTTCATGCTACACACTTT 10 84 0 CTTTTCATGC 0.917279 -50 TTCCGCTTCCTCCCTTCATTTGC 10 121 0 CGCTTCCTCC 0.870703 -13 AAGATTCTGCCGTTTTTTTCATGTGTAAAA 11 39 1 CGTTTTTTTC 0.865957 -101 CGGCTTCTCTCTCTGCATGCGCCTTTTTTG 13 54 0 CTCTGCATGC 0.890484 -247 AATTTCTCTACTCTTCTTTCAAGAAATTAT 13 133 0 CTCTTCTTTC 0.983508 -168 CGCGAAAGAGCTTTTCGTCCTTTTACAGGG 13 227 1 CTTTTCGTCC 0.773346 -74 GAAAAAAGAGCTCTTCATCCCTGTAAAAGG 13 245 0 CTCTTCATCC 0.93631 -56 GGATGAAGAGCTCTTTTTTCGTTCTCAGCC 13 255 1 CTCTTTTTTC 0.952956 -46 ********** Masking position 4 Map Score: 27.3255 Number of sites scoring better than the average of aligned sites = 2378 Number in coding regions = 2052 Number in noncoding regions = 326 Number of orfs with sites within 600 bp upstream = 337 Fraction of orfs with sites within 600 bp upstream = 0.0541279 Motif number 2 TTTTTTTGCCAAAAAGGGGTTATCTGTAG 2 10 1 CAAAAAGGGG 0.873577 -104 TTATCTGTAGAAAAAAGTCGAAAAAACCTT 2 30 1 AAAAAAGTCG 0.86985 -84 TTCTGTAAATAGAAAAGGTGATGTT 2 99 1 AGAAAAGGTG 0.989546 -15 ACTAAGGGATAGTAAAGGGGAGTCAGTA 3 16 1 AGTAAAGGGG 0.945681 -18 GGAGTTCAATAGAAGAGGTGTAACACG 6 14 1 AGAAGAGGTG 0.977558 -17 AATTCGACGAAAAAAAAGTG 7 1 0 AAAAAAAGTG 0.731239 -90 GGGAAGGGAAAGAAAAGGAGTGC 8 24 1 AGAAAAGGAG 0.97629 -13 AACGTTTTTTGGACAAGGCGACAAAAGTCT 10 29 1 GGACAAGGCG 0.848001 -105 GAACTCAATGAGTAAAGGTGTGTTGTCT 11 122 1 AGTAAAGGTG 0.946701 -18 CTCTTTTATAAGACAAGGCGGTTTCTCTAG 12 30 0 AGACAAGGCG 0.972506 -30 CTTGTCTTATAAAAGAGGGGATTATCA 12 43 1 AAAAGAGGGG 0.952743 -17 GGAAGAGTACAAAAAAGGCGCATGCAGAGA 13 45 1 AAAAAAGGCG 0.982919 -256 ATTTCTTGAAAGAAGAGTAGAGAAATTCGG 13 136 1 AGAAGAGTAG 0.687583 -165 TGAGTTCATGAAAAAAGGTGGTACCGCGAA 13 203 1 AAAAAAGGTG 0.978117 -98 ********** Masking position 6 Map Score: 21.7016 Number of sites scoring better than the average of aligned sites = 903 Number in coding regions = 682 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 3 ATCTCCTATCGTTTGCTGTAGACTATTTGAA 1 32 0 GTTTGCTGAG 0.880831 -119 AGTTCACCGATTTTGCAGAAATCTCCTATCG 1 52 0 TTTTGCAGAA 0.944008 -99 GCGTGCAAGATTTTTTTGAAAATGAAGGAAA 1 83 0 TTTTTTTGAA 0.703445 -68 TTTTTTTGCCAAAAAGGGGTTATC 2 4 1 TTTTGCCAAA 0.758201 -110 TTTTTCGACTTTTTTCTACAGATAACCCCTT 2 24 0 TTTTTCTAAG 0.919925 -90 GAGTGTCTTTTCTTTCTGTAAATAGAAAAGG 2 86 1 TCTTTCTGAA 0.918517 -28 TTTAGGGTATTTTTGCTTTAAGAAAGGAAGA 7 61 1 TTTTGCTTAA 0.92781 -30 GAAAAAGTTATTTTTCTGAAATTGTGACAAG 9 66 1 TTTTTCTGAA 0.97627 -87 CGAGTATCTTTTTTTCTTAAGCAAACCCTGA 9 119 1 TTTTTCTTAG 0.87747 -34 GTTCGTCAAATTTTTCAGCAG 10 1 0 TTTTTCAGAG 0.913863 -133 AGGATGTCCATTTTGCTACAATCCATACCAG 11 92 1 TTTTGCTAAA 0.953712 -48 GACAAGGCGGTTTCTCTAGAAACCGCCCCGG 12 18 0 TTTCTCTAAA 0.720464 -42 GAGAGAAGCCGTTTGCTGAAAGGCTTCTTAT 13 73 1 GTTTGCTGAA 0.9244 -228 TCTCTACTCTTCTTTCAAGAAATTATGCTCC 13 128 0 TCTTTCAAAA 0.680791 -173 GGTACCACCTTTTTTCATGAACTCAATCAGT 13 197 0 TTTTTCATAA 0.831975 -104 ******** ** Masking position 10 Map Score: 13.7774 Number of sites scoring better than the average of aligned sites = 1627 Number in coding regions = 1378 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 4 TATTTGAAAAGACAGAAAGAAGGGATAGC 1 10 0 GACAGAAAGA 0.850824 -141 GATTTTTTTGAAAATGAAGGAAAAGTTCAC 1 76 0 AAAATGAAGG 0.72824 -75 AAAAACCTTTAAAATGAAAACTGGCACTCT 2 51 1 AAAATGAAAA 0.517248 -63 CTTTTCTATTTACAGAAAGAAAAGACACTC 2 86 0 TACAGAAAGA 0.566073 -28 GTTTAGCTAGGAAGTGAAGATA 5 3 0 GAAGTGAAGA 0.937345 -107 ATACAAGGAAGACATGAAGAAGACAGAGTA 5 71 1 GACATGAAGA 0.926164 -39 GACAGAGTAAAATGGGAGGATGGAAGCT 5 92 1 AATGGGAGGA 0.691059 -18 AAAATACCCTAAAGGGAAAAACTCATAAAC 7 44 0 AAAGGGAAAA 0.831184 -47 TTTGCTTTAAGAAAGGAAGATACATACAT 7 72 1 GAAAGGAAGA 0.98317 -19 CGGTTCTATAAACGGGAAGGGAAAGAAAAG 8 11 1 AACGGGAAGG 0.918034 -26 AGCCTGTCACTAAAGGACGAAGGCTCAGGG 9 20 0 TAAAGGACGA 0.822408 -133 AGCAAACCCTGAAAGGATGACGAAC 9 138 1 GAAAGGATGA 0.881275 -15 TCAAGCAAATGAAGGGAGGAAGCGGAA 10 117 1 GAAGGGAGGA 0.956452 -17 ACCTGCTTAGAACGGGAAGAGTACAAAAAA 13 31 1 AACGGGAAGA 0.976592 -270 TCATCCCTGTAAAAGGACGAAAAGCTCTTT 13 231 0 AAAAGGACGA 0.93612 -70 ********** Masking position 7 Map Score: 11.9465 Number of sites scoring better than the average of aligned sites = 1762 Number in coding regions = 1366 Number in noncoding regions = 396 Number of orfs with sites within 600 bp upstream = 438 Fraction of orfs with sites within 600 bp upstream = 0.0703501 Motif number 5 GAAATGCTGGCGGCAGGTTTAAT 4 4 1 ATGCTGGCGG 0.995058 -175 TCTTTTTTTGATTCTGCCGGAGCCGGATGC 11 13 0 ATTCTGCCGG 0.992395 -127 TCAAAAAAAGATTCTGCCGTTTTTTTCATG 11 32 1 ATTCTGCCGT 0.961547 -108 TCAAGAAATTATGCTCCCGGGCGACCTTCC 13 115 0 ATGCTCCCGG 0.988166 -186 ATTTTTAAACATGCTGGAGGGTTATG 13 285 1 ATGCTGGAGG 0.974794 -16 ********** Masking position 5 Map Score: 5.42656 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 112 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTATCTGTAGAAAAAAGTCGAAAAAACCTT 2 30 1 AAAAAAGTCG 0.760509 -84 TTGTAATCAATGAAAAAGCTCACGATTTGG 4 78 0 TGAAAAAGCT 0.660292 -101 TGACAAAATAAAAAAAGCCTGTCACTAAAG 9 35 0 AAAAAAGCCT 0.912646 -118 TCTGAAATTGTGACAAGCCTCGTGATTTGG 9 80 1 TGACAAGCCT 0.941528 -73 AACGTTTTTTGGACAAGGCGACAAAAGTCT 10 29 1 GGACAAGGCG 0.876699 -105 GTGTGTAGCATGAAAAGCCGACAAGAACGG 10 87 1 TGAAAAGCCG 0.987245 -47 TGAAAAGCCGGGGCGGTTTC 12 1 1 TGAAAAGCCG 0.987245 -59 GGCGGTTTCTAGAGAAACCGCCTTGTCTTA 12 22 1 AGAGAAACCG 0.907711 -38 GGAAGAGTACAAAAAAGGCGCATGCAGAGA 13 45 1 AAAAAAGGCG 0.92656 -256 GCATGCAGAGAGAGAAGCCGTTTGCTGAAA 13 64 1 AGAGAAGCCG 0.984578 -237 TCAGACAACATAAGAAGCCTTTCAGCAAAC 13 83 0 TAAGAAGCCT 0.896025 -218 ********** Masking position 5 Map Score: 11.6833 Number of sites scoring better than the average of aligned sites = 1493 Number in coding regions = 1313 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 7 GCGTGCAAGATTTTTTTGAAAATGAAGGAA 1 84 0 TTTTTTTGAA 0.550472 -67 CTTCCACTTGTTATTTTCTCTTAATTGAAT 1 118 0 TTATTTTCTC 0.811973 -33 TTTTTTTGCCAAAAAGGGGT 2 1 1 TTTTTTTGCC 0.967202 -113 ATTTTAAAGGTTTTTTCGACTTTTTTCTAC 2 36 0 TTTTTTCGAC 0.903712 -78 CACTTTTTTTTCGTCGAATTAAGCT 7 6 1 TTTTTTCGTC 0.940893 -85 GCACTCCTTTTCTTTCCCTTCCCGTTTA 8 19 0 TTTCTTTCCC 0.863952 -18 CAGGCTTTTTTTATTTTGTCATGAAAAAGT 9 44 1 TTATTTTGTC 0.8945 -109 AACGAGTATCTTTTTTTCTTAAGCAAACCC 9 117 1 TTTTTTTCTT 0.650998 -36 TTGACGAACGTTTTTTGGACAAGGCGACAA 10 23 1 TTTTTTGGAC 0.777836 -111 AGAACAAGACTTTTGTCGCCTTGTCCAAAA 10 35 0 TTTTGTCGCC 0.899984 -99 TTGTTCTTTTTTTCTTTGCCTGTGCTAAAG 10 58 1 TTTCTTTGCC 0.925751 -76 CGGCAGAATCTTTTTTTGATTCTGCCGGAG 11 21 0 TTTTTTTGAT 0.683477 -119 CATGCGCCTTTTTTGTACTCTTCCCGTTCT 13 39 0 TTTTGTACTC 0.552264 -262 GAAAGGCTTCTTATGTTGTCTGATTGGAAG 13 90 1 TTATGTTGTC 0.836733 -211 AGAGCTCTTTTTTCGTTCTCAGCCATTTTT 13 261 1 TTTCGTTCTC 0.804092 -40 ********** Masking position 6 Map Score: 10.4016 Number of sites scoring better than the average of aligned sites = 1700 Number in coding regions = 1414 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 296 Fraction of orfs with sites within 600 bp upstream = 0.0475426 Motif number 8 AGGAGATTTCTGCAAAATCGGTGAACTTTT 1 56 1 TGCAAAATCG 0.962156 -95 ACCTTTAAAATGAAAACTGGCACTCTTACT 2 55 1 TGAAAACTGG 0.869158 -59 CGCTGAAATGAGCCAAATCGTGAGCTTTTT 4 66 1 AGCCAAATCG 0.857303 -113 AAGAAGACAGAGTAAAATGGGAGGATGGAA 5 87 1 AGTAAAATGG 0.943116 -23 TTTTTTCATGTGTAAAATTGAATATTCCCA 11 52 1 TGTAAAATTG 0.805331 -88 TATGGATTGTAGCAAAATGGACATCCTGAG 11 89 0 AGCAAAATGG 0.973929 -51 ATTGAGTTCATGAAAAAAGGTGGTACCGCG 13 201 1 TGAAAAAAGG 0.817584 -100 ********** Masking position 5 Map Score: 0.925713 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 401 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 9 ********** No masking Map Score: -3.0529e-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: -3.0529e-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: -3.0529e-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