AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i135_ecoli_mtub_300.orf -o135_ecoli_mtub_300.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 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 ybgE 127 orf, hypothetical protein #3 ybgC 149 orf, hypothetical protein #4 tolA 64 membrane spanning protein, required for outer membrane integrity #5 tolB 132 periplasmic protein involved in the tonb-independent uptake of group A colicins #6 pal 34 peptidoglycan-associated lipoprotein Motif number 1 AACCCCGTTAGAAAGGGTCACACGCATGCCCC 1 244 0 GAAGGTCACA 0.877513 -57 TACCCCAAACGAACAGGCAAGAAGCGTTCCCA 2 47 0 GACAGCAAGA 0.980327 -81 AATCAGGCAAAGCCGGTCAAGAAGACATCTG 2 107 1 AGCGGCAAGA 0.941185 -21 TATGGGCCTGGAGCGGCCCATAATTTTTTAAA 3 23 0 GACGGCCATA 0.981731 -127 GCTTGAAAGAGAGCGGGTAACAGGCGAACAGT 4 28 1 GACGGTAACA 0.984952 -37 TTGACCGTCCGAACAGTCAACATCGCGA 5 7 0 GACAGCAACA 0.984952 -126 TTGACTGTTCGGACGGTCAACATCAGGCACCG 5 19 1 GGCGGCAACA 0.993866 -114 TATCGTGGGCCATCGGTCCAGATAAGGGAGAT 5 108 1 CACGGCCAGA 0.976221 -25 ** *** ***** Masking position 10 Map Score: 7.83715 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 318 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 AGATAAATTGTTCTCGATCAAATTG 1 5 1 AAATTGTTCC 0.986601 -296 ATTTAGCTATAAATTGATCACCGTCGAAAAA 1 50 1 AAATTGATCC 0.969726 -251 ATAAAAACTCAAATTGATCCCACGTATATAT 1 132 0 AAATTGATCC 0.969726 -169 TGGTATGATGAAAGTGTTCAAACAAATTTCT 1 210 1 AAAGTGTTCA 0.96931 -91 GAACAGGCAAGAAGCGTTCCCAGAATCCATG 2 38 0 GAAGCGTTCC 0.959956 -90 TGCCTGATTCGACGTGTTCAAGCGCCAGCGC 2 85 0 GACGTGTTCA 0.867367 -43 CGGTTTCCAAAAACTGTTCGCCTGTTACCCG 4 41 0 AAACTGTTCC 0.977371 -24 ********* * Masking position 2 Map Score: 6.08382 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 193 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 AATAGAAATTTGTTTGAACACTTTCATCATAC 1 212 0 TGTGAACACT 0.9486 -89 CCTTGCTCATCGCATGAAGACTCCGAGAGTGA 1 275 0 CGTGAAGACT 0.94871 -26 GTGATTACCCCAAACGAACAGGCAAGAAGCGT 2 52 0 CACGAACAGG 0.978766 -76 ACCGCGCTGGCGCTTGAACACGTCGAATCAGG 2 82 1 CGTGAACACG 0.978524 -46 ACCTCAATCGCGCGCGTATAGTAGCAGCGTTT 3 91 1 CGCGTATAGT 0.910556 -59 GAGCGGGTAACAGGCGAACAGTTTTTGGAAAC 4 38 1 CACGAACAGT 0.987864 -27 TGATGTTGACCGTCCGAACAGTCAACATCGCG 5 12 0 CGCGAACAGT 0.99522 -121 TAATAATTAATTGAATAGTAAAGGAATCA 6 8 1 TATGAATAGT 0.762019 -27 ** ******** Masking position 8 Map Score: 5.27327 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 419 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 AGCTAAATTACCGCCTTTCAGCCAATTTGA 1 28 0 CCGCCTTTCA 0.958963 -273 CGAGAGTGAACCCCGTTAGAAAGGGTCACA 1 254 0 CCCCGTTAGA 0.837991 -47 GTCTTCTTGACCGGCTTTGCCTGATTCGAC 2 103 0 CCGGCTTTGC 0.926983 -25 AATTTTTACGCTCCCTTAACTTGCCCTCAT 3 55 1 CTCCCTTAAC 0.897129 -95 CCTTAACTTGCCCTCATTCCCAAACCTCAA 3 68 1 CCCTCATTCC 0.856111 -82 ACATCTGCGTTTCCCTTGCTTGAA 4 5 1 CTGCGTTTCC 0.966149 -60 CTGTTACCCGCTCTCTTTCAAGCAAGGGAA 4 21 0 CTCTCTTTCA 0.905732 -44 TCTCGGTTTCCAAAAACTGTT 4 54 0 CTCGGTTTCC 0.958965 -11 CATATCTCCCTTATCTGGACCGATG 5 118 0 CTCCCTTATC 0.897129 -15 ********** Masking position 7 Map Score: 2.94088 Number of sites scoring better than the average of aligned sites = 1433 Number in coding regions = 1255 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 5 GCATTTTTCGACGGTGATCAATTTATAGCT 1 54 0 ACGGTGATCA 0.969388 -247 TAAGGATTTTGCGGCGTAATATATACGTGG 1 114 1 GCGGCGTAAT 0.846776 -187 GCACACAAAAACGGCGTAAAGAAAGGTTGC 1 173 0 ACGGCGTAAA 0.931431 -128 ACCCTTTCTAACGGGGTTCACTCTCGGAGT 1 258 1 ACGGGGTTCA 0.983961 -43 AAGCGCCAGCGCGGTGATTACCCCAAACGA 2 67 0 GCGGTGATTA 0.917504 -61 GCGTATAGTAGCAGCGTTTAAAAGCTCTAA 3 104 1 GCAGCGTTTA 0.678689 -46 TTGAAAGAGAGCGGGTAACAGGCGAACAGT 4 30 1 GCGGGTAACA 0.853172 -35 GACTGTTCGGACGGTCAACATCAGGCACCG 5 21 1 ACGGTCAACA 0.809675 -112 ACCGGTTGCCACGGGGTTCTGGTAGTTTTG 5 47 1 ACGGGGTTCT 0.950947 -86 ********** Masking position 2 Map Score: 3.32346 Number of sites scoring better than the average of aligned sites = 3281 Number in coding regions = 2992 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 6 ********** No masking Map Score: -1.41155e-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 7 ********** No masking Map Score: -1.41155e-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 8 AAATTTCTATTGGGGCATGCGTGTGACCCTT 1 233 1 TGGGGCAGCG 0.985463 -68 CTTCATGCGATGAGCAAGGAGTC 1 288 1 TGAGCAAGAG 0.887214 -13 TAAAAATTTATGGGCCTGGAGCGGCCCATAA 3 32 0 TGGGCCTGAG 0.963915 -118 CGCGCGCGATTGAGGTTTGGGAATGAGGGCA 3 76 0 TGAGGTTGGG 0.93008 -74 CCGCTCTCTTTCAAGCAAGGGAAACGCAGAT 4 13 0 TCAAGCAGGG 0.915385 -52 ACGGTCAACATCAGGCACCGGTTGCCACGGG 5 31 1 TCAGGCACGG 0.97237 -102 TAAATTATCGTGGGCCATCGGTCCAGATAAG 5 103 1 TGGGCCACGG 0.987127 -30 ******* *** Masking position 1 Map Score: 0.334214 Number of sites scoring better than the average of aligned sites = 922 Number in coding regions = 861 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 ********** No masking Map Score: -1.41155e-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: -1.41155e-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: -1.41155e-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