AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i209_rpod_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 rpsU 237 30S ribosomal subunit protein S21 #2 dnaG 110 DNA biosynthesis; DNA primase #3 rpoD 194 RNA polymerase, sigma(70) factor; regulation of proteins induced at high temperatures #4 HI0531 231 ribosomal protein S21 (rpS21) #5 HI0532 133 DNA primase (dnaG) #6 HI0533 69 RNA polymerase sigma-70 factor (rpoD) Motif number 1 CGCCCCTGGAGAAAGCCTCGTGTATACTCCTCACCCTTA 1 78 1 GAAGCGTATC 0.968291 -160 CCCTTTCAAAAAAGGCCGCGGTGCTTTACAAAGCAGCAG 1 124 1 AAAGCGTTAC 0.995911 -114 GCTTATTTCAAAATGGTGCGGAATTTTACTGCAATTGCT 1 161 0 AAAGCGTTAC 0.995911 -77 CTTCCGAAAGGAATGCGCGGCTTATTTTCGTTTATGAAT 2 64 1 GAAGGGTTTC 0.933421 -47 GTTAACGCTGAAATCCAACGGTTGTTTACCGCCAACGAT 3 102 0 AAACCGTTAC 0.9867 -93 TTATTACCTAAAATGTTGCGCGATTTTACCCTGTTTAAG 4 24 1 AAAGCGTTAC 0.995911 -208 CAAATTTAATAAAGGACGCAATTCTAATCTATTTTTAGG 4 126 0 AAAGCATATC 0.924825 -106 CCGTGAGTCCAAAGGATTCACGGTTTGTCTTAACTCGAG 5 28 0 AAAGCATTTC 0.974956 -106 ATCTACGCCAAAAACGACCGCACTTTCACACCACGATCA 5 92 1 AAACCGTTAC 0.9867 -42 *** * ** ** ** Masking position 15 Map Score: 11.315 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 153 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 TAAAACTTTGTTCGCCCCTGGAGAAAGCCT 1 66 1 TTCGCCCCTG 0.94999 -172 TTTTACTGCAATTGCTGCTGCTTTGTAAAG 1 147 0 ATTGCTGCTG 0.927305 -91 ATTAATTCGGTTTGCCGCTGGCATCAACGC 1 202 0 TTTGCCGCTG 0.992829 -36 CCGAAAGGAATGCGCGGCTTATTTTCGTTT 2 67 1 TGCGCGGCTT 0.95128 -44 TTTAACGGCTTAAGTGCCGAA 3 2 1 TTAACGGCTT 0.836027 -193 GCTGCCTCTCAGTGCGGCTGTCGGGGGCTT 3 43 0 AGTGCGGCTG 0.974157 -152 TACTTATATATTTGCCGCTGCCTCTCAGTG 3 59 0 TTTGCCGCTG 0.992829 -136 GATTTCAGCGTTAACGGCTGAAGGACATCG 3 126 1 TTAACGGCTG 0.957066 -69 ********** Masking position 9 Map Score: 8.632 Number of sites scoring better than the average of aligned sites = 1597 Number in coding regions = 1534 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 GCGCGGTAATAAAGCGAGGTAAAACAAGTC 1 11 0 AAAGCGAGGT 0.936906 -227 TTGGTCCTACACTGCGCGGTAATAAAGCGA 1 24 0 ACTGCGCGGT 0.934861 -214 GTGTAGGACCAATGCGGGTTGATGTAAAAC 1 42 1 AATGCGGGTT 0.817003 -196 GCTTTGTAAAGCACCGCGGCCTTTTTTGAA 1 128 0 GCACCGCGGC 0.8975 -110 ATTCCTTTCGGAAGCACGGCCTTACAACTA 2 48 0 GAAGCACGGC 0.924372 -63 TTCCGAAAGGAATGCGCGGCTTATTTTCGT 2 65 1 AATGCGCGGC 0.985836 -46 GAATTGCTAAAAATCGGGGCCT 2 99 1 AAATCGGGGC 0.948866 -12 CGACAGCCGCACTGAGAGGCAGCGGCAAAT 3 50 1 ACTGAGAGGC 0.668141 -145 CGGCTGAAGGACATCGGGTCAATCGCCCAA 3 140 1 ACATCGGGTC 0.727559 -55 GAGTCCAAAGGATTCACGGTTTGTCTTAAC 5 33 0 GATTCACGGT 0.60658 -101 TCGTGGTGTGAAAGTGCGGTCGTTTTTGGC 5 98 0 AAAGTGCGGT 0.853674 -36 ********** Masking position 8 Map Score: 6.92673 Number of sites scoring better than the average of aligned sites = 4953 Number in coding regions = 4661 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 4 GTGCGGAATTTTACTGCAATTGCTGCTGCTTT 1 153 0 TTCTGAATTG 0.888829 -85 TCACCTTTGATTAATTCGGTTTGCCGCTGGCA 1 209 0 TTATTGGTTT 0.876214 -29 CCACACTTATTTCATGAGGTTGGTGTTGGGCG 3 163 0 TTATGGGTTG 0.985052 -32 TTTTACCCTGTTTAAGCGGTTTTAACCAGTTG 4 47 1 TTAAGGGTTT 0.79468 -185 AATTGCGTCCTTTATTAAATTTGTCATTTACA 4 142 1 TTATTAATTT 0.786126 -90 CTCAATGAGTTTAATTTAATTGCAATTTAAAA 4 199 0 TTATTAATTG 0.918135 -33 ATTAAACTCATTGAGGTGATTGGCTT 4 216 1 TTAGGGATTG 0.94697 -16 GATAAGATTTTTTATGAACTTGAGATTCTACC 6 15 0 TTATGACTTG 0.925993 -55 CTCGTTTTGCTTGATGTGATTGAGAAGATAAG 6 41 0 TTATGGATTG 0.985344 -29 ** *** ***** Masking position 10 Map Score: 3.94305 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 399 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 AGGGACTTTTATAAGGGTGAGGAGTATACAC 1 97 0 ATAAGGTGAG 0.967484 -141 TCCCTTTCAAAAAAGGCCGCGGTGCTTTACA 1 123 1 AAAAGCCGCG 0.941134 -115 AGCTTATTTCAAAATGGTGCGGAATTTTACT 1 170 0 AAAAGGTGCG 0.993547 -68 ACCGAATTAATCAAAGGTGAGAGGCAC 1 221 1 TCAAGGTGAG 0.915834 -17 TTTATTACCTAAAATGTTGCGCGATTTTACC 4 23 1 AAAAGTTGCG 0.967215 -209 TTAAAGTAACAAAACCGTGAGTCCAAAGGAT 5 50 0 AAAACGTGAG 0.957348 -84 **** ****** Masking position 4 Map Score: 1.31956 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 307 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 AAACTTTGTTCGCCCCTGGAGAAAGCCTCG 1 68 1 CGCCCCTGGA 0.968028 -170 CGGAGAGCAACGCTCTCGGGGAA 2 4 0 CGCTCTCGGG 0.994996 -107 CCGAGAGCGTTGCTCTCCGATCAGACCGAG 2 15 1 TGCTCTCCGA 0.950981 -96 GCTTCCCGATCGCTCTTCGGCACTTAAGCC 3 17 0 CGCTCTTCGG 0.972322 -178 TATATAAGTACGCCCTCGTAATTATCGTTG 3 79 1 CGCCCTCGTA 0.968525 -116 TTTCACACCACGATCACGGAGGCTCGACA 5 115 1 CGATCACGGA 0.918577 -19 ********** Masking position 5 Map Score: 2.33496 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 433 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 ********** No masking Map Score: -3.39396e-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 GTTTATGAATTGCTAAAAATCGGGGCCT 2 93 1 TGCTAAAAAT 0.818078 -18 TGAGAGGCAGCGGCAAATATATAAGTACGC 3 62 1 CGGCAAATAT 0.947498 -133 CCAGTTGAAACCACAAATATTAAGGTGAAT 4 72 1 CCACAAATAT 0.859118 -160 TTTACTTTTTCCCTAAAAATAGATTAGAAT 4 115 1 CCCTAAAAAT 0.896006 -117 ACAGGTGCTTTGGCAAAAATAAAATTTTAA 4 175 1 TGGCAAAAAT 0.91881 -57 ACTTTAAGCACAACAAAAATCTACGCCAAA 5 74 1 CAACAAAAAT 0.837113 -60 CAAAAATCTACGCCAAAAACGACCGCACTT 5 87 1 CGCCAAAAAC 0.948963 -47 ********** Masking position 5 Map Score: 0.256903 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 1016 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 9 ********** No masking Map Score: -3.39396e-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: -3.39396e-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: -3.39396e-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