AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ihipB_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 hipB 222 persistence to inhibition of murein or DNA biosynthesis; regulatory protein #2 b1509 43 putative ATP-binding component of a transport system and adhesin protein #3 ydeK 300 orf, hypothetical protein Motif number 1 ATATCCGCGATCGCGGATAAAAAGGAGGAT 1 88 0 TCGCGGATAA 0.991616 -135 TTATCCGCGATCGCGGATATCGCAGCGTTT 1 98 1 TCGCGGATAT 0.977425 -125 TTATCCGCTCTACGGGATAAACGCTGCGAT 1 116 0 TACGGGATAA 0.946411 -107 TTATCCCGTAGAGCGGATAAGATGTGTTTC 1 126 1 GAGCGGATAA 0.993184 -97 TTATCCTTTAGTGAGGATAAGTCAATCTGG 1 155 0 GTGAGGATAA 0.923935 -68 TTATCCTCACTAAAGGATAAAACTTATAAT 1 165 1 TAAAGGATAA 0.885101 -58 TTATCCGCTTAAGGGGATATTATAAGTTTT 1 183 0 AAGGGGATAT 0.947436 -40 ATATCCCCTTAAGCGGATAAACTTGCTGTG 1 193 1 AAGCGGATAA 0.989496 -30 ********** Masking position 7 Map Score: 10.6964 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 450 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 CGCATCAACGCCTTATTTAAATCCTCCTTT 1 68 1 CCTTATTTAA 0.952364 -155 ATTATCATCATCATATTTAACAAAGAATAG 3 36 0 TCATATTTAA 0.980289 -265 ATGATAATTTTCCTATTGAAAGAAACAGTT 3 58 1 TCCTATTGAA 0.914547 -243 GAAACAGTTTTCTTATTAAGCAACAATAAC 3 79 1 TCTTATTAAG 0.882463 -222 AACTCATAGTTCATATTTAAATAAAATAAG 3 106 1 TCATATTTAA 0.980289 -195 ATTGCATAGTTCTTATTTTATTTAAATATG 3 117 0 TCTTATTTTA 0.920895 -184 TAAAAATGAAACTTATTAAATTGTCAGAGG 3 226 0 ACTTATTAAA 0.854419 -75 TTAATAAGTTTCATTTTTAATGTCTGACGA 3 237 1 TCATTTTTAA 0.899432 -64 ********** Masking position 6 Map Score: 7.45245 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 75 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 ATGCCATCTCGACATGCGGCTTATACGGT 1 10 0 GACATGCGGC 0.984667 -213 ATGTCGAGATGGCATGCGGCTTAATATTGC 1 25 1 GGCATGCGGC 0.991529 -198 GTCATACGTCCACAGCAAGT 1 213 0 GTCATACGTC 0.900704 -10 GCAACCTGGAGAATGGCGGCACGGTTCAA 2 25 1 GAATGGCGGC 0.950305 -19 GTTGGAGGTGGGAAGGTGTCAATTTGGCTA 3 180 0 GGAAGGTGTC 0.869888 -121 TTATTAAATTGTCAGAGGTCTGTATTGAGT 3 214 0 GTCAGAGGTC 0.93475 -87 CATTTTTAATGTCTGACGACTCATCTCTTT 3 248 1 GTCTGACGAC 0.921972 -53 ********** Masking position 8 Map Score: 4.1307 Number of sites scoring better than the average of aligned sites = 1962 Number in coding regions = 1840 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 TCTCGACATGCGGCTTATACGGT 1 2 0 CGCTTTACGG 0.74546 -221 TCCTTTTTATCCGCGATCGCGGATATCGCAGC 1 92 1 CCCGACGCGG 0.499976 -131 CAGCGTTTATCCCGTAGAGCGGATAAGATGTG 1 120 1 CCGTAAGCGG 0.974261 -103 TAAGTTTTATCCTTTAGTGAGGATAAGTCAAT 1 159 0 CCTTATGAGG 0.79959 -64 CTTATAATATCCCCTTAAGCGGATAAACTTGC 1 187 1 CCCTTAGCGG 0.550075 -36 TCCAGGTTGCCGCCGATAGTGGTT 2 3 0 CGCGAAGTGG 0.900661 -41 TCGGCGGCAACCTGGAGAATGGCGGCACGGTT 2 19 1 CCGGAAATGG 0.921416 -25 AACAATACAGCCACGAAAGAGATGAGTCGTCA 3 261 0 CCCGAAGAGA 0.778113 -40 ** *** ***** Masking position 11 Map Score: 3.41466 Number of sites scoring better than the average of aligned sites = 1889 Number in coding regions = 1688 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 CATGCGGCTTAATATTGCCGACTTCAAACGGCGCATCA 1 37 1 AAATCATCAA 0.984192 -186 TTTAACAAAGAATAGCACTAATTGCTAAAAATCGAAGT 3 13 0 AAACCATCTA 0.989975 -288 ATTAAGCAACAATAACTCATAGTTCATATTTAAATAAA 3 93 1 AAACCATCAA 0.994602 -208 TGATAGATTAAAAATTGCATAGTTCTTATTTTATTTAA 3 122 0 AAATCATCTA 0.970904 -179 CCCACCTCCAACTAACACTCAATACAGACCTCTGACAA 3 198 1 ACACCATCAA 0.985374 -103 ATAAACGCTCCATATACAAACAATACAGCC 3 281 0 AACCCTTCAA 0.94325 -20 ** * * * * * ** * Masking position 13 Map Score: 2.25334 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 20 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TTGCCGACTTCAAACGGCGCATCAACGCCT 1 51 1 CAAACGGCGC 0.955331 -172 ACGCCTTATTTAAATCCTCCTTTTTATCCG 1 75 1 TAAATCCTCC 0.932725 -148 CTCTACGGGATAAACGCTGCGATATCCGCG 1 109 0 TAAACGCTGC 0.993522 -114 TTGAACCGTGCCGCCATTCTC 2 33 0 TGAACCGTGC 0.970229 -11 ATAAACGCTCCATATACAAAC 3 290 0 TAAACGCTCC 0.990563 -11 ********** Masking position 4 Map Score: 1.39336 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 447 Number in noncoding regions = 30 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: 1.72962e-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 8 ********** No masking Map Score: 1.72962e-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 9 ********** No masking Map Score: 1.72962e-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