AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i043_5_1_3_1_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 dam 106 DNA adenine methylase #2 damX 91 putative membrane protein; interferes with cell division #3 aroB 56 3-dehydroquinate synthase #4 aroK 199 shikimate kinase I #5 yrfD 68 orf, hypothetical protein #6 yjeQ 64 orf, hypothetical protein Motif number 1 TCAAGGTTATCTCCCGCAATGGTTTATCGTT 1 11 1 CTCCCGCATG 0.976046 -96 CTTCAGGCAACTCCCGCAACGATAAACCATT 1 28 0 CTCCCGCACG 0.991997 -79 GTGGAGAAAGCTCCGACAGCATCCAGCGCTT 1 56 0 CTCCGACGCA 0.96904 -51 ATTACACCTTCTCCGGCTGTGGAGAAAGCTC 1 74 0 CTCCGGCGTG 0.984853 -33 AACAAGAAAGGTCAGGCCGCTTATCAAGCGG 2 12 1 GTCAGGCGCT 0.958217 -80 CATCATGGAACGCAGGCAGCGAAGAGCACCA 4 106 0 CGCAGGCGCG 0.602809 -94 TGATTTATCATTCAGGCGGCATTTTGCTGTC 4 138 1 TTCAGGCGCA 0.937661 -62 CGCTCTGGCGATAAATCACCGGG 4 187 0 CTCTGGCATA 0.874377 -13 ACTCTCCAAAGGCCAGCAGCGCCGC 6 50 1 GGCCAGCGCG 0.958723 -15 ******* *** Masking position 7 Map Score: 10.5231 Number of sites scoring better than the average of aligned sites = 3451 Number in coding regions = 3297 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 TAAACCATTGCGGGAGATAACCTTGA 1 7 0 CGGGAGATAA 0.846825 -100 TTTATCGTTGCGGGAGTTGCCTGAAGCGCT 1 33 1 CGGGAGTTGC 0.933492 -74 ACCTTTTAGTGGGGTGTTAA 2 82 1 GGGGTGTTAA 0.944281 -10 TACCCGCAGACGAGTGTATATAAAGCCAGA 3 12 0 CGAGTGTATA 0.915094 -45 TTGACGCGCGCAGGTATTTAGCATACAAGG 4 59 1 CAGGTATTTA 0.753389 -141 TAATCTTACCCGGTGATTTATCGCCAGAGC 4 179 1 CGGTGATTTA 0.800004 -21 TTGGGCAGTTTATAAACAAACG 5 3 1 GGGCAGTTTA 0.909832 -66 TACTACCGCGCGTTTGTTTATAAACTGCCC 5 13 0 CGTTTGTTTA 0.81237 -56 AACAAACGCGCGGTAGTATAAAGGCAAGCC 5 25 1 CGGTAGTATA 0.946212 -44 TCTGACGGGTATATCAATGCGTCTG 5 54 0 CGGGTATATC 0.855641 -15 GCTGGCCTTTGGAGAGTTTATTTTTACTCA 6 37 0 GGAGAGTTTA 0.913339 -28 ********** Masking position 7 Map Score: 3.49177 Number of sites scoring better than the average of aligned sites = 2382 Number in coding regions = 2103 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 282 Fraction of orfs with sites within 600 bp upstream = 0.0452939 Motif number 3 CGGGAGTTGCCTGAAGCGCTGGATGCTGTC 1 43 1 CTGAAGCGCT 0.944399 -64 GCTGACTAACTAATTACACCT 1 96 0 CTGACTAACT 0.767051 -11 ACTGTACCCGCAGACGAGTGTATATAAAGC 3 16 0 CAGACGAGTG 0.976705 -41 TTTCATCTATTTGACGCGCGCAGGTATTTA 4 49 1 TTGACGCGCG 0.972284 -151 AGTTTATAAACAAACGCGCGGTAGTATAAA 5 17 1 CAAACGCGCG 0.978551 -52 AAAGGCAAGCCAGACGCATTGATATACCCG 5 44 1 CAGACGCATT 0.965325 -25 CTCAATCGTACAGACTCCTGGTCGCCCCTG 6 11 0 CAGACTCCTG 0.920744 -54 ********** Masking position 4 Map Score: 2.99462 Number of sites scoring better than the average of aligned sites = 3311 Number in coding regions = 3163 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 4 AGCGGTAATGTTTTTACGCTGAACGTGTTT 4 22 1 TTTTTACGCT 0.992514 -178 TTTGCTGTCTTTTTTACGCTAATCTTACCC 4 160 1 TTTTTACGCT 0.992514 -40 GGAGAGTTTATTTTTACTCAATCGTACAGA 6 27 0 TTTTTACTCA 0.964983 -38 ********** Masking position 6 Map Score: 2.15588 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 56 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 CAACAAGAAAGGTCAGGCCGCTTATC 2 7 1 GAAAGGTCAG 0.970705 -85 ACGAGTGTATATAAAGCCAGAA 3 3 0 ATAAAGCCAG 0.954811 -54 GATTAGCGTAAAAAAGACAGCAAAATGCCG 4 154 0 AAAAAGACAG 0.945937 -46 CGCGGTAGTATAAAGGCAAGCCAGACGCAT 5 33 1 TAAAGGCAAG 0.944509 -36 ATAAACTCTCCAAAGGCCAGCAGCGCCGC 6 46 1 CAAAGGCCAG 0.992461 -19 ********** Masking position 4 Map Score: 1.57639 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 343 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 AGCGCTTCAGGCAACTCCCGCAACGATAAA 1 33 0 GCAACTCCCG 0.885169 -74 AGCTCCGACAGCATCCAGCGCTTCAGGCAA 1 49 0 GCATCCAGCG 0.883372 -58 ACTAATTACACCTTCTCCGGCTGTGGAGAA 1 79 0 CCTTCTCCGG 0.945265 -28 AGGTCAGGCCGCTTATCAAGCGGTCTATTA 2 20 1 GCTTATCAAG 0.874374 -72 AAAGGTTAATGCTTACCACGTTGCAATTAA 2 58 0 GCTTACCACG 0.977716 -34 AAACATTACCGCTTTTACGGCTGT 4 5 0 GCTTTTACGG 0.898926 -195 CAGGTATTTAGCATACAAGGAGTACCGATT 4 69 1 GCATACAAGG 0.933134 -131 TTTACGCTAATCTTACCCGGTGATTTATCG 4 172 1 TCTTACCCGG 0.939169 -28 ********** Masking position 2 Map Score: 0.729662 Number of sites scoring better than the average of aligned sites = 2576 Number in coding regions = 2305 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 7 GGAGTTGCCTGAAGCGCTGGATGCTGTCGG 1 45 1 GAAGCGCTGG 0.903429 -62 ATCTATTTGACGCGCGCAGGTATTTAGCAT 4 53 1 CGCGCGCAGG 0.992368 -147 TCATCATCATGGAACGCAGGCAGCGAAGAG 4 111 0 GGAACGCAGG 0.989291 -89 GTAGTATAAAGGCAAGCCAGACGCATTGAT 5 37 1 GGCAAGCCAG 0.923884 -32 CAGGGGCGACCAGGAGTCTGTACG 6 5 1 GGCGACCAGG 0.989008 -60 ACTCTCCAAAGGCCAGCAGCGCCGC 6 50 1 GGCCAGCAGC 0.971069 -15 ********** Masking position 7 Map Score: 1.78209 Number of sites scoring better than the average of aligned sites = 2491 Number in coding regions = 2405 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 8 ********** No masking Map Score: -8.85746e-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: -8.85746e-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: -8.85746e-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