AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_ecoli_mtub_100.orf -o316_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mrdA 30 cell elongation, e phase; peptidoglycan synthetase; penicillin-binding protein 2 #2 ybeB 300 orf, hypothetical protein #3 mreC 65 rod shape-determining protein #4 mreB 244 regulator of ftsI, penicillin binding protein 3, septation function #5 ppp 88 ppp #6 Rv0019c 123 hypothetical protein Rv0019c #7 accD5 49 accD5 Motif number 1 ATCATCCCACCCCGCGCCGCAGATTGCATC 2 67 0 CCCGCGCCGC 0.993342 -234 GGAGTGCTTTACCCTGCAAGTTTTCCCCCT 2 192 0 ACCCTGCAAG 0.827256 -109 ACAGACACTTCCCCTGCCTGCATCCGA 3 8 0 CCCCTGCCTG 0.990378 -58 GTGTCTGTTTACCCTGCCTGGTCTGATACG 3 30 1 ACCCTGCCTG 0.928747 -36 CCCGCGCTGGCGACGATGCA 5 1 1 CCCGCGCTGG 0.83994 -88 TGGGGGCGCGCCCCCACCGCTTCTCTGCGC 5 33 0 CCCCCACCGC 0.99324 -56 TGGGGGCGCGCCCCCACAAGTGGGGGGTAC 5 47 1 CCCCCACAAG 0.968163 -42 GTGGGGGGTACCCCCACCCGCTTGCGGGGG 5 66 1 CCCCCACCCG 0.979815 -23 TCTCCCCCGCAAGCGGGTGGGGG 5 76 0 CCCCCGCAAG 0.993453 -13 CGCGGGTCAACCCCGGCAGCTTCGAGCCCA 6 17 0 CCCCGGCAGC 0.975294 -107 CCGGGGTTGACCCGCGCCGACCACCGTCAA 6 31 1 CCCGCGCCGA 0.98762 -93 CTGCTCCGGCCCCGCGCTGCCGAGCACGTC 6 78 0 CCCGCGCTGC 0.981505 -46 CGCCCCAGCCTAAGGAAGTAGT 7 3 1 CCCCAGCCTA 0.889241 -47 ********** Masking position 7 Map Score: 28.5123 Number of sites scoring better than the average of aligned sites = 1370 Number in coding regions = 1251 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 ACCCCGCGCCGCAGATTGCATCGCCATTTTTGTAA 2 54 0 GCTGCATCGC 0.992348 -247 AGCACTCCAGGATTTTGTTATCGACAAAATTGATG 2 214 1 GATTTATCGC 0.740407 -87 CCTCAAAGGTCAGGACATCATCGCCTTAGACGTTC 2 250 1 CACTCATCGC 0.938594 -51 TCAGGGCAAATCCAGCATCACCGACTGC 2 283 1 TCCTCACCGC 0.957533 -18 ATGGGAGTGTGCTTGTCTGCTCGCCAGATTGTTGC 4 58 1 GCTTGCTCGC 0.969031 -187 TAATGCATCAGCAGCATTCCTCGCCTGTTTGCAAC 4 123 0 GCATCCTCGC 0.985995 -122 GCGACAAGGCGCAAAAATCATCTGCTACGGTGAAA 4 212 0 GCATCATCTC 0.900236 -33 CCGCTTCTCTGCGCTCTGCATCGTCGCCAGCGCGG 5 12 0 GCCGCATCGC 0.996967 -77 GGGTTGACCCGCGCCGACCACCGTCAAAGTATCGT 6 34 1 GCGCCACCGC 0.940172 -90 TCGTGACTTTGCTGACGTGCTCGGCAGCGCGGGGC 6 65 1 GCCTGCTCGC 0.973671 -59 GGCGTCCTTTCCGTCCTGCACCGTCTGCTCCGGCC 6 97 0 CCCGCACCGC 0.977673 -27 GTGTGCGGCAGCCGATAACATCGACTCCC 7 31 1 GCTACATCGC 0.766116 -19 ** * ****** * Masking position 12 Map Score: 12.4568 Number of sites scoring better than the average of aligned sites = 2676 Number in coding regions = 2596 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 CACCCCGCGCCGCAGATTGCATCGCCATTTT 2 59 0 CGCAGTTGCA 0.769516 -242 CAATCTGCGGCGCGGGGTGGGATGATAGCCC 2 71 1 CGCGGGTGGG 0.986711 -230 GGACAATTGTCGCCGAATCGGCTTTCGAAAG 2 103 0 CGCCGATCGG 0.786149 -198 TCCCATGAGACGCAGCGCGCATTATTCTACG 4 33 0 CGCAGGCGCA 0.935489 -212 AATGACCTTACGCGGTTGCAAACAGGCGAGG 4 109 1 CGCGGTGCAA 0.831946 -136 ACGCAGCAGCGACAAGGCGCAA 4 233 0 CGCAGAGCGA 0.967017 -12 CCCGCGCTGGCGACGATGCAGAG 5 3 1 CGCGCGGCGA 0.947639 -86 CTGGCGACGATGCAGAGCGCAGAGAAGCGGT 5 17 1 TGCAGGCGCA 0.868651 -72 AGCGCAGAGAAGCGGTGGGGGCGCGCCCCCA 5 32 1 AGCGGGGGGG 0.979993 -57 CTCCCCCGCAAGCGGGTGGGGGTACCCCCCA 5 67 0 AGCGGTGGGG 0.932558 -22 CCCACCCGCTTGCGGGGGAGA 5 78 1 TGCGGGGAGA 0.893635 -11 TGCTCGGCAGCGCGGGGCCGGAGCAGACGGT 6 82 1 CGCGGGCCGG 0.992986 -42 GAGCAGACGGTGCAGGACGGAAAGGACGCCA 6 102 1 TGCAGACGGA 0.864844 -22 GGAAGTAGTGTGCGGCAGCCGATAACATCGA 7 24 1 TGCGGAGCCG 0.929468 -26 ***** ***** Masking position 3 Map Score: 16.7199 Number of sites scoring better than the average of aligned sites = 4951 Number in coding regions = 4718 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 4 TGCAGGGTAAAGCACTCCAGGATTTTGTTA 2 204 1 AGCACTCCAG 0.98514 -97 CTCAAAGGTCAGGACATCATCGCCTTAGAC 2 251 1 AGGACATCAT 0.851562 -50 GTATTCTCGTATCAGACCAGGCAGGGTAAA 3 37 0 ATCAGACCAG 0.92271 -29 CAATCTGGCGAGCAGACAAGCACACTCCCA 4 59 0 AGCAGACAAG 0.961697 -186 AGATTGTTGCAGCACATATGCAGATGAATG 4 83 1 AGCACATATG 0.856754 -162 CGCGCTGCCGAGCACGTCAGCAAAGTCACG 6 66 0 AGCACGTCAG 0.98866 -58 CAGGACGGAAAGGACGCCAG 6 114 1 AGGACGCCAG 0.98701 -10 ********** Masking position 4 Map Score: 3.57063 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 1001 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TTGATTCACCCAGGGGGAAAACTTGCAGGG 2 181 1 CAGGGGGAAA 0.970579 -120 GGAAAACTTGCAGGGTAAAGCACTCCAGGA 2 196 1 CAGGGTAAAG 0.985949 -105 CTTAGACGTTCAGGGCAAATCCAGCATCAC 2 274 1 CAGGGCAAAT 0.985949 -27 CGGATGCAGGCAGGGGAAGTGTCTGTTTAC 3 12 1 CAGGGGAAGT 0.9831 -54 TCAGACCAGGCAGGGTAAACAGACACTTCC 3 26 0 CAGGGTAAAC 0.985949 -40 ********** Masking position 8 Map Score: 3.1984 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 214 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 CGCGGGGTGGGATGATAGCCCACTTTCGAAAGC 2 81 1 GATGTGCCCC 0.91375 -220 ATTCACCCAGGGGGAAAACTTGCAGGGTAAAGC 2 184 1 GGGGAACTTC 0.894712 -117 AAAACTTGCAGGGTAAAGCACTCCAGGATTTTG 2 198 1 GGGTAGCACC 0.929926 -103 AGAAGCGGTGGGGGCGCGCCCCCACAAGTGGGG 5 39 1 GGGGGGCCCC 0.908123 -50 CCCCACAAGTGGGGGGTACCCCCACCCGCTTGC 5 58 1 GGGGGACCCC 0.508535 -31 CGAAGCTGCCGGGGTTGACCCGCGCCGACCACC 6 23 1 GGGGTACCCC 0.801388 -101 **** * **** * Masking position 9 Map Score: 2.60539 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 89 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 CCGCTGCGTTTTCTACTCAAAGC 1 18 0 CTGCGTTTTC 0.98877 -13 CCTGAACCAGAGGCGATTTCGGGACAATTG 2 125 0 AGGCGATTTC 0.972103 -176 AAGTTATGCGTATTCTCGTATCAGA 3 51 0 ATGCGTATTC 0.983445 -15 CTGCCGTTTAATCCGTTTTCACGTAGAATA 4 12 1 ATCCGTTTTC 0.982454 -233 ********** Masking position 8 Map Score: 0.823027 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 101 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GACTTTTTCCGCCAGACACGACTTTGTAGAA 2 17 1 GCCAGACCGA 0.969684 -284 GTATACCTGAACCAGAGGCGATTTCGGGACA 2 129 0 ACCAGAGCGA 0.977879 -172 GGACATCATCGCCTTAGACGTTCAGGGCAAA 2 262 1 GCCTTAGCGT 0.887919 -39 ACAAATCTCTGCCTGAGTCCAGAAAGGCTTA 4 156 0 GCCTGAGCCA 0.969686 -89 ACTAATTTTCACCGTAGCAGATGATTTTTGC 4 206 1 ACCGTAGAGA 0.890864 -39 CCCGCGCTGGCGACGATGCAGAGCGC 5 6 1 GCTGGCGCGA 0.95158 -83 GCTCGAAGCTGCCGGGGTTGACCCGCGCCGA 6 20 1 GCCGGGGTGA 0.964573 -104 GCAGCGCGGGGCCGGAGCAGACGGTGCAGGA 6 88 1 GCCGGAGAGA 0.993631 -36 ******* *** Masking position 2 Map Score: 4.04496 Number of sites scoring better than the average of aligned sites = 1694 Number in coding regions = 1576 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 9 ********** No masking Map Score: -5.58897e-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 10 ********** No masking Map Score: -5.58897e-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 11 ********** No masking Map Score: -5.58897e-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