AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i198_ecoli_mtub_300.orf -o198_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 eno 87 enolase #2 pyrG 227 CTP synthetase #3 mazG 70 orf, hypothetical protein #4 chpR 77 suppressor of inhibitory function of ChpA, PemI-like, autoregulated #5 relA 47 (p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor #6 ygcA 56 putative enzyme #7 Rv1019 254 hypothetical protein Rv1019 #8 mfd 58 mfd #9 lpqU 87 lpqU #10 eno 96 eno Motif number 1 AGACAAACAACGCGTACCCAGGGTACGCGTTGC 1 28 0 CGTCCCAGGG 0.950685 -60 CATTATCCCTCCTCTTCGCCAGCGCACTATTGA 2 116 0 CCTCGCCAGC 0.961669 -112 TTCGGCAGGTCTGGTCCCTAAAGGAGAGGACG 5 26 1 CGTCCTAAAG 0.478785 -22 CTCCTTGAAGCTCCGTCGCCAGGACTCGAACCT 7 16 1 CCGCGCCAGG 0.997587 -239 TAGACGGTGTCAACGCCGTCAGCACAGTCAACG 7 117 1 CCGCGTCAGC 0.961305 -138 GCCGTCTACCCACCGGCCCCACGCAAACCGATA 7 155 1 CCGCCCCACG 0.976666 -100 TGGCGCGCGTCACCCGCGTCGGGTTTTCCGGCG 7 230 0 CCCCGTCGGG 0.986078 -25 CGGGCGGGGAAGCCGGGCCCAATGTTG 8 5 1 CGGAGCCGGG 0.980249 -54 TGCGGCCATTCTAGGGCGCCGAGGTTAGTCAAC 8 34 0 CGGCGCCGAG 0.911511 -25 TTGACTACCCCGTCGCACTCGGGGCGG 9 5 0 CCGACTCGGG 0.974018 -83 CCGTCACGATCATCGTCCCATGGGTTTGTTGAC 9 33 0 CCGCCCATGG 0.953932 -55 AACTCTCCCTCGTAGGGCACCTATACC 9 71 0 CCCCGTAGGG 0.957666 -17 CAGGATGAACCGCTAACCCAGGCTTTACGCTA 10 10 1 CCTACCCAGG 0.969055 -87 CGGTCGGGGCCAGCCAACCCAAGACCGTCCGTG 10 47 1 CCCACCCAAG 0.87271 -50 CGTGCAGCAGCTACGACGCAAGGAGAACCCA 10 76 1 CCGCGCAAGG 0.993359 -21 * ** ******* Masking position 1 Map Score: 24.0774 Number of sites scoring better than the average of aligned sites = 3689 Number in coding regions = 3513 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 2 ACAAACAACGCGTACCCAGGGTACGCGTTG 1 29 0 CGTACCCAGG 0.931249 -59 TATCCCTCCTCTTCGCCAGCGCACTATTGA 2 116 0 CTTCGCCAGC 0.773255 -112 GATGGAATAACCAAGACGGGAAAGCAGTAT 2 178 0 CCAAGACGGG 0.907161 -50 CTTGAAGCTCCGTCGCCAGGACTCGAACCT 7 19 1 CGTCGCCAGG 0.989863 -236 GCCGATTACACCACGACGGATTGCACATCG 7 78 1 CCACGACGGA 0.797101 -177 GGTGGGTAGACGGCGACAGCGTTGACTGTG 7 139 0 CGGCGACAGC 0.899658 -116 GTCTACCCACCGGCCCCACGCAAACCGATA 7 158 1 CGGCCCCACG 0.925725 -97 GGGCCGGATAAGGCGCCGGAAAACCCGACG 7 217 1 AGGCGCCGGA 0.752658 -38 CGCGCGTCACCCGCGTCGGGTTTTCCGGCG 7 230 0 CCGCGTCGGG 0.979375 -25 CGCGGGTGACGCGCGCCAGG 7 245 1 GCGCGCCAGG 0.985581 -10 CGGGCGGGGAAGCCGGGCCCAATGTTG 8 8 1 GGAAGCCGGG 0.941775 -51 GGCCATTCTAGGGCGCCGAGGTTAGTCAAC 8 34 0 GGGCGCCGAG 0.945426 -25 CCGCCCCGAGTGCGACGGGG 9 1 1 CCGCCCCGAG 0.963994 -87 AACTCTCCCTCGTAGGGCACCTATACC 9 71 0 CCTCGTAGGG 0.619196 -17 GGATGAACCGCTAACCCAGGCTTTACGCTA 10 13 1 CTAACCCAGG 0.774243 -84 TCGGGGCCAGCCAACCCAAGACCGTCCGTG 10 50 1 CCAACCCAAG 0.72817 -47 GCAGCAGCTACGACGCAAGGAGAACCCA 10 79 1 CGACGCAAGG 0.94203 -18 ********** Masking position 7 Map Score: 16.5025 Number of sites scoring better than the average of aligned sites = 9943 Number in coding regions = 9497 Number in noncoding regions = 446 Number of orfs with sites within 600 bp upstream = 400 Fraction of orfs with sites within 600 bp upstream = 0.0642467 Motif number 3 GAGTTTCAGTTTAACTAGTGACTTGAGGAAAACCTA 1 62 1 TACGATTAGG 0.98867 -26 GAAAGTTTGTGGCACAGGTCATGTTCGGGTATACTGCT 2 148 1 GACGAGTCGG 0.992021 -80 GCTGAACCTGAGAAGTTAGGTTGAAAAGAC 2 208 0 TACGAGTAGG 0.980165 -20 TGAATTGTCCTGAAAATTGCGGGTCTGTCAGG 3 49 0 TTCGATTCGG 0.980647 -22 CTACATTGTAGATACGAGCAAATTTCGGC 4 2 0 GACGATTCGG 0.995466 -76 TTGCGATTTGCCGATTTCGGCAGGTCTGGT 5 3 1 GATGGTTCGG 0.957972 -45 GGAGTTCCGTTATGGGACAATTAAGGTCACACTGTT 6 9 1 GATGATTAGG 0.981853 -48 CCTCTGATTTTGGTTCAGATAGTTCAGGTTCGAGTCCT 7 36 0 TTTGATTAGG 0.925857 -219 * ** * * ** *** Masking position 14 Map Score: 6.50511 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 166 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 4 AAAAGTTAGAGCGGCAACGCGTACCCTGGGTAC 1 15 1 GCGAACGCTA 0.984439 -73 CACAAATGGCGCTTGACCGCGTAATTCCC 2 7 0 GCTACCGCTA 0.984445 -221 GCTGAACCTGAGAAGTTAGGTTG 2 215 0 GCGACCTGGA 0.987341 -13 GGTGTAATCGGCAGCACCTCTGATTTTGGTTCA 7 57 0 GCGACCTCGA 0.993307 -198 TGTTGATGTGGCCGGACCGGATAAAGGGCCGGA 7 192 1 GCGACCGGTA 0.995345 -63 CAGGATGAACCGCTAACCCAGGCTTT 10 4 1 GAGACCGCAA 0.961608 -93 ** * ***** ** Masking position 6 Map Score: 3.84818 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 397 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TAAAAAATGACACAAATGGCGCTTGACCGC 2 20 0 CACAAATGGC 0.809025 -208 ATGTTTTTGACGCAAATCAAGCGCTTGTCA 2 52 0 CGCAAATCAA 0.899454 -176 AACCCTTTCCTCAAACCGCTATCATATGT 4 59 0 CTCAAACCGC 0.974463 -19 TGCCGAAATCGGCAAATCGCAA 5 3 0 GGCAAATCGC 0.958261 -45 ACCGGCCCCACGCAAACCGATACCCTTGTT 7 166 1 CGCAAACCGA 0.991696 -89 CAGGATGAACCGCTAACCCAGGCTTTACGC 10 11 1 CGCTAACCCA 0.922556 -86 CCAGGCTTTACGCTAACAGCGGTCGGGGCC 10 28 1 CGCTAACAGC 0.943183 -69 ********** Masking position 5 Map Score: 2.39774 Number of sites scoring better than the average of aligned sites = 1392 Number in coding regions = 1333 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 ACGCGGTCAAGCGCCATTTGTGTCATTTTTTA 2 18 1 GCCCATTGTG 0.828831 -210 TGAGAAAATAGCCCCTTTGGGGTAAATGTTTT 2 75 0 GCCCTTTGGG 0.977002 -153 AGACGGGAAAGCAGTATACCCGAACATGACCT 2 163 0 GCGTATACCG 0.837295 -65 CGTCCTCTCCTTTAGGGACCAGACCTG 5 31 0 TCCCTTTGGG 0.880164 -17 GACCTTAATTGTCCCATAACGGAACTCC 6 7 0 GTCCATACGG 0.791161 -50 GCCTTATCCGGCCCTTTATCCGGTCCGGCCAC 7 199 0 GCCTTTACCG 0.977012 -56 GGGTTTTCCGGCGCCTTATCCGGCCCTTTATC 7 211 0 GCCCTTACCG 0.994647 -44 GTCACCCGCGTCGGGTTTTCCGGCGCCTTATC 7 223 0 TCGGTTTCCG 0.752413 -32 CCTGGCGCGCGTCACCCGCGTCGGGTTT 7 237 0 GCCGTCACCG 0.938877 -18 CCCTCGTAGGGCACCTATACCGGCTTCCGTCA 9 60 0 GCCCTATCCG 0.966989 -28 ** ***** *** Masking position 12 Map Score: 3.62425 Number of sites scoring better than the average of aligned sites = 2828 Number in coding regions = 2422 Number in noncoding regions = 406 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 7 ********** No masking Map Score: -2.59815e-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 ********** No masking Map Score: -2.59815e-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 9 ********** No masking Map Score: -2.59815e-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