AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_bsub_reg_100.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 ddlA 174 D-alanyl-D-alanine ligase A #2 murF 71 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase #3 yllB 125 similar to hypothetical proteins #4 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #5 ftsL 39 cell-division protein #6 spoVD 116 penicillin-binding protein #7 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #8 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #9 spoVE 60 spoVE #10 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #11 murB 26 UDP-N-acetylenolpyruvoylglucosamine reductase #12 ftsA 173 cell-division protein #13 ftsZ 35 cell-division initiation protein #14 murC 249 UDP-N-acetyl muramate-alanine ligase Motif number 1 ATGTCACATCTCCTTTTCAATGCCATTTTA 1 11 1 TCCTTTTCAA 0.841062 -164 TGTATGTAATTCCTTTTTATTTTATATTAA 1 38 0 TCCTTTTTAT 0.966642 -137 TACTATCTTATCATTTTCACCGGAAAATGA 1 105 0 TCATTTTCAC 0.814095 -70 AGTTCAGGGTTTCTTTTTATGGGTAAACAG 3 36 1 TTCTTTTTAT 0.947526 -90 GCTCCACAACTTCATTTTACACTGTTTACC 3 57 0 TTCATTTTAC 0.792046 -69 GCTGATGACCTCCTTTTAATTTTGCGTTCG 5 18 0 TCCTTTTAAT 0.929186 -22 TATGCAGGCTTTCTTTTTTTATGCCTTCAG 6 26 1 TTCTTTTTTT 0.902913 -91 TTAGGCTTGTTTCATTTTATGCCTGAATTT 6 78 0 TTCATTTTAT 0.758097 -39 GGGCTGCCTATTCTTTTATTGCAGAAAAAA 7 14 1 TTCTTTTATT 0.808103 -162 GCTGGATGTATCCTTTTATTTACGCTAAAA 7 65 1 TCCTTTTATT 0.8711 -111 TTCTAATTCGTTCTTTTTATCATTGAAGTC 7 137 0 TTCTTTTTAT 0.947526 -39 TGTCCTTTTCTCCTCCTGTTTC 8 101 0 TCCTTTTCTC 0.95457 -12 TTCTTTTTTCCCCCAGTCTA 10 113 0 TTCTTTTTTC 0.918717 -10 TATTTTTATGTGCTTTTCACATTTTATGTT 12 49 0 TGCTTTTCAC 0.871004 -125 TATGGGTTCATTTTCACACCAAACATG 14 8 1 TCATTTTCAC 0.814095 -242 ********** Masking position 5 Map Score: 17.006 Number of sites scoring better than the average of aligned sites = 1600 Number in coding regions = 1225 Number in noncoding regions = 375 Number of orfs with sites within 600 bp upstream = 391 Fraction of orfs with sites within 600 bp upstream = 0.0628012 Motif number 2 TGAACTAGTCAGGGTTCTTTAAAACTTTATT 3 9 0 AGGTCTTTAA 0.889454 -117 TTACTGAATAATGGAGCTTGAAAAAGATTTTTC 8 21 1 ATGGCTTGAA 0.98983 -92 ATAACTACGTATGTCGTTTGAAAGAAACAGGAG 8 78 1 ATGGTTTGAA 0.915743 -35 CATGTTAGACAGGAGGCTTGGAAATACATTCG 10 10 0 AGGGCTTGAA 0.987697 -113 CCTGTCTAACATGAAGCTTGGAAACAATTGATG 10 30 1 ATGGCTTGAA 0.98983 -93 TTCACATTTTATGTTTATTGAAAATATTCGTTA 12 31 0 ATGTATTGAA 0.681543 -143 AATACAATGAATGTGGCTTTACAAGTGTGTAAC 12 96 0 ATGGCTTTCA 0.976111 -78 TTTAACAGCTATGCCGCTTTACAGCAGCTGTGC 14 58 1 ATGGCTTTCA 0.976111 -192 ACGCCGCTAAGGGAGGCTTTTCAGCCGCCGCGG 14 165 1 GGGGCTTTCA 0.887319 -85 *** ***** ** Masking position 8 Map Score: 8.10348 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 259 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 TCTAATTATTTTTGGGCATGCTGATGTTGA 1 75 0 TTTGGGCATG 0.907716 -100 TTTTTAGAGTGTTATACACGAAGAATCA 4 9 0 GTTATACACG 0.802568 -61 GAAAGCCGTCGTTATGCAGGCTTTCTTTTT 6 14 1 GTTATGCAGG 0.945586 -103 TATGCCTGAATTTGGACAGGTAGAACGATG 6 61 0 TTTGGACAGG 0.973527 -56 TCACTCCTTATTTAGGCTTGTTTCATTTTA 6 89 0 TTTAGGCTTG 0.786039 -28 CAAGCTTCATGTTAGACAGGAGGCTTGGAA 10 20 0 GTTAGACAGG 0.987263 -103 ACCCTGTTTTGTTGGACAGGGTTATCGCAT 10 60 0 GTTGGACAGG 0.987 -63 TATAGAGAAACTTAGACTGGGGGAAAAAAG 10 101 1 CTTAGACTGG 0.889616 -22 ********** Masking position 3 Map Score: 4.71426 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 145 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AAAATAATTAGATCATTTTCCGGTGAAAAT 1 93 1 GATCATTTTC 0.953225 -82 TTTACTATCTTATCATTTTCACCGGAAAAT 1 107 0 TATCATTTTC 0.847716 -68 GTAAGGTCCCTCTCTTTCTTTTGTATAT 2 54 0 CCTCTCTTTC 0.87632 -18 GATCTCTTGCCCCACTTTCT 3 116 0 GATCTCTTGC 0.937452 -10 AAAAAATGCTGATATCTTTCAAGATTAGCT 7 38 1 GATATCTTTC 0.889192 -138 TATTCAGTAACATCTCTTTC 8 1 0 CATCTCTTTC 0.968077 -112 CCATATGAAAAATCTTTTTCAAGCTCCATT 8 30 0 AATCTTTTTC 0.874558 -83 TCATATTCATGATTTTTTTCCATATGAAAA 8 49 0 GATTTTTTTC 0.898722 -64 TATGGGTTCATTTTCACACCAAACA 14 6 1 GTTCATTTTC 0.762855 -244 AGTATCAGGTTATTTCTTTCCGATTAAACC 14 112 0 TATTTCTTTC 0.79426 -138 ********** Masking position 7 Map Score: 5.5119 Number of sites scoring better than the average of aligned sites = 957 Number in coding regions = 837 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 CCCTGAACTAGTCAGGGTTCTTTAAAACTT 3 15 0 GTCAGGGTTC 0.908124 -111 CCCACCTTTTATCAGGATGAATTGAAATTG 4 39 0 ATCAGGATGA 0.876726 -31 GTTTGAAAGAAACAGGAGGAGAAAAGGACA 8 93 1 AACAGGAGGA 0.951789 -20 CTTCATGTTAGACAGGAGGCTTGGAAATAC 10 16 0 GACAGGAGGC 0.964825 -107 TGTTTTGTTGGACAGGGTTATCGCATCAAT 10 56 0 GACAGGGTTA 0.971236 -67 TGTCCAACAAAACAGGGTTATCGTTATGTT 10 72 1 AACAGGGTTA 0.942358 -51 GAGAAACTTAGACTGGGGGAAAAAAGAA 10 105 1 GACTGGGGGA 0.945896 -18 ********** Masking position 5 Map Score: 3.20423 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 251 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 ATTCCTTTTTATTTTATATTAAAATGGCAT 1 30 0 ATTTTATATT 0.776536 -145 TCAGGGTTTCTTTTTATGGGTAAACAGTGT 3 39 1 TTTTTATGGG 0.779997 -87 GCAGGCTTTCTTTTTTTATGCCTTCAGAGG 6 29 1 TTTTTTTATG 0.874381 -88 AGATATCAGCATTTTTTCTGCAATAAAAGA 7 25 0 ATTTTTTCTG 0.751517 -151 TTACCACATCATTTGATGTGACTTCAATGA 7 118 1 ATTTGATGTG 0.905834 -58 TGAAAAAGATTTTTCATATGGAAAAAAATC 8 39 1 TTTTCATATG 0.733922 -74 TGCTTTTCACATTTTATGTTTATTGAAAAT 12 39 0 ATTTTATGTT 0.847133 -135 CAACAGAATATTTTTATGTGCTTTTCACAT 12 57 0 TTTTTATGTG 0.949562 -117 TTCTGTTGTTATTTTTTGTTACACACTTGT 12 79 1 ATTTTTTGTT 0.765664 -95 ATTTTATATGTTTTGTTATGTTTAGTATCA 14 135 0 TTTTGTTATG 0.749558 -115 TTAGCGGCGTATTTTATATGTTTTGTTATG 14 145 0 ATTTTATATG 0.933461 -105 ********** Masking position 4 Map Score: 6.01441 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 570 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 7 ACTTGTTTTCAATGGATACTCCCCCCACTACA 1 144 0 AATGTACTCC 0.953597 -31 GCAATAAAAGAATAGGCAGCCCGAA 7 4 0 AATGCAGCCC 0.985317 -172 TCTTGAAGTAAATCGGCAGCCCTAATGACTTT 9 18 1 AATGCAGCCC 0.985317 -43 AGCAATCGACACCCCAAGCTTAAAG 9 46 0 AATGCACCCC 0.992271 -15 TCTATGGCACCTCCTCACATTTCG 12 160 0 TATGACCTCC 0.881116 -14 AATTGTACCTCCAACAAACGTC 14 238 0 AATGACCTCC 0.967786 -12 *** * ****** Masking position 3 Map Score: 1.41383 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 45 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 ATGGATACTCCCCCCACTACAATTCATCTT 1 135 0 CCCCCACTAC 0.980683 -40 CCACTTCGCTCCACAACTTCATTTTACACT 3 64 0 CCACAACTTC 0.855284 -62 TCACCACTATTCACCACTTCGCTCCACAAC 3 77 0 TCACCACTTC 0.955352 -49 TCTCCTTAACTCACCACTATTCACCACTTC 3 87 0 TCACCACTAT 0.94371 -39 GATCTCTTGCCCCACTTTCTCTCCTTAA 3 108 0 GCCCCACTTT 0.961771 -18 ATTGTGTTGGTCCCACCTTTTATCAGGATG 4 50 0 TCCCACCTTT 0.772353 -20 TTCTTTTTTCCCCCAGTCTAAGTTTCTCT 10 104 0 CCCCCAGTCT 0.914884 -19 GTCTATCTGTTCCCCAGTATATGACGCTCA 14 211 0 TCCCCAGTAT 0.938173 -39 ********** Masking position 8 Map Score: 2.25162 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 161 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 TTTTATTTTATATTAAAATGGCATTGAAAA 1 24 0 TATTAAAATG 0.671173 -151 ATATAAAATAAAAAGGAATTACATACAAAT 1 41 1 AAAAGGAATT 0.350925 -134 TATCAGGATGAATTGAAATTGTTTTTAGAG 4 30 0 AATTGAAATT 0.795073 -40 GCGAACGCAAAATTAAAAGGAGGTCATCAG 5 17 1 AATTAAAAGG 0.8618 -23 ATTTTAGCGTAAATAAAAGGATACATCCAG 7 66 0 AAATAAAAGG 0.80991 -110 AAAAAGAACGAATTAGAATGTTGAGAGGTT 7 149 1 AATTAGAATG 0.911543 -27 AAAAGCAAATGGAATGCGAGGTTACG 11 7 1 AAATGGAATG 0.918368 -20 TTTTCAATAAACATAAAATGTGAAAAGCAC 12 40 1 ACATAAAATG 0.673893 -134 CAAATAATAGAATAGAAATGATCGAAATGT 12 138 1 AATAGAAATG 0.865422 -36 CGCGGTCGCAAATTGAAATGAGCGTCATAT 14 193 1 AATTGAAATG 0.958368 -57 ********** Masking position 7 Map Score: 2.69153 Number of sites scoring better than the average of aligned sites = 860 Number in coding regions = 694 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 10 ********** No masking Map Score: 2.74513e-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: 2.74513e-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 12 ********** No masking Map Score: 2.74513e-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