AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i303_ecoli_bsub_100.orf -o303_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 msrA 205 peptide methionine sulfoxide reductase #2 ccdA 219 integral membrane protein #3 yppP 131 similar to peptide methionine sulfoxide reductase Motif number 1 AGCAGACTAAACCCCAAATATTTCTTATGTTTTACTTTAG 1 92 1 ACAAATATTT 0.918418 -114 CACAATAACCACCGTGAATAGGTCTAAAGTAAAACATAAG 1 115 0 ACGAATATTT 0.962087 -91 TTAGATCTTCAAAGTGAATGTTTATATTATATCCATATTT 2 32 1 AAGAATGTTT 0.990428 -188 CTAATTTTCAAATGAGAAGGAGTATAATGTCTCAATGTCA 2 75 1 AAGAAGGTTT 0.975982 -145 ATGTCAAATTAAATTATATAAGTTTTTTCTGAAAATAGAA 2 109 1 AAATATATTT 0.897828 -111 AGTGTTAAAAAAATGAAATGATTTTGTCATAACTTGAAGG 2 163 1 AAAAATGTTT 0.972137 -57 ATTTTGTCATAACTTGAAGGAATGTCAAATCATGAAGGGA 2 183 1 AAGAAGGTTT 0.978631 -37 TATAGGTTTTAAGCAATATGCTTATGTAATGGAGGTTCAC 3 15 0 AAATATGTTT 0.925568 -117 GTAAAAATAGAATGAAAATGATTCTGCTTTTCAATAAAAT 3 56 0 AAAAATGTTT 0.972137 -76 CTTTGTTAATACGTGGTATTATTATATTATAGCATGTAAA 3 91 0 ACGTATTTTT 0.81986 -41 ** ***** * * * Masking position 8 Map Score: 10.1941 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 98 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 ACGCCGTTAAACGGCTTAACAAAAATCCAGTAA 1 47 1 AGGTAACAAA 0.99059 -159 ATCCAGTAATATGGATTAAAAAGCAGACTAAAC 1 71 1 AGGTAAAAAG 0.942063 -135 ATTGGGGTTAAGGTTGTAACAAGAGGCGTATTT 1 158 0 AGTTAACAAG 0.983824 -48 CTTCAAGTGAAAGTGTTAAAAAAATGAAATGAT 2 152 1 AGTTAAAAAA 0.966996 -68 ACATTCCTTCAAGTTATGACAAAATCATTTCAT 2 175 0 AGTTGACAAA 0.983824 -45 TCATAACTTGAAGGAATGTCAAATCATGAAGGG 2 189 1 AGGTGTCAAA 0.914407 -31 TAAAATCTATAGGTTTTAAGCAATATGCTTATG 3 29 0 AGTTAAGCAA 0.867388 -103 TAATAATACCACGTATTAACAAAGGAGGCACCA 3 107 1 AGTTAACAAA 0.990775 -25 * ** ******* Masking position 12 Map Score: 8.50052 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 69 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 AAAAGGATATTCAGGAGAAAAT 1 3 0 TCAGGAGAAA 0.975149 -203 CGTTCCAGGGGCAGGAAAAAAGGATATTCA 1 20 0 GCAGGAAAAA 0.948455 -186 TGAATAGGTCTAAAGTAAAACATAAGAAAT 1 111 0 TAAAGTAAAA 0.787326 -95 ATACTCCTTCTCATTTGAAAATTAGTATAA 2 70 0 TCATTTGAAA 0.812108 -150 TGTCTCAATGTCAAATTAAATTATATAAGT 2 102 1 TCAAATTAAA 0.733242 -118 ATTTCTATTTTCAGAAAAAACTTATATAAT 2 121 0 TCAGAAAAAA 0.898624 -99 TAGAAATCCTTCAAGTGAAAGTGTTAAAAA 2 144 1 TCAAGTGAAA 0.97563 -76 TTATATTATAGCATGTAAAAATAGAATGAA 3 80 0 GCATGTAAAA 0.929084 -52 ********** Masking position 3 Map Score: 4.0018 Number of sites scoring better than the average of aligned sites = 890 Number in coding regions = 746 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 4 AAATATGGATATAATATAAACATTCACTTT 2 42 0 ATAATATAAA 0.930169 -178 AAAAACTTATATAATTTAATTTGACATTGA 2 106 0 ATAATTTAAT 0.872611 -114 GTTTTTTCTGAAAATAGAAATCCTTCAAGT 2 130 1 AAAATAGAAA 0.955433 -90 AAAGTGTTAAAAAAATGAAATGATTTTGTC 2 161 1 AAAAATGAAA 0.739234 -59 ATAGCATGTAAAAATAGAATGAAAATGATT 3 73 0 AAAATAGAAT 0.95536 -59 TTTACATGCTATAATATAATAATACCACGT 3 91 1 ATAATATAAT 0.902968 -41 ********** Masking position 4 Map Score: 3.21788 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 97 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 CTGGATTTTTGTTAAGCCGTTTAACGGCGTTCCA 1 43 0 GTAACGTTAA 0.964647 -163 CAAAAATCCAGTAATATGGATTAAAAAGCAGACT 1 66 1 GTATTGTTAA 0.948649 -140 AATAACCACCGTGAATAGGTCTAAAGTAAAACAT 1 118 0 GTAAAGCTAA 0.87226 -88 ATTCACGGTGGTTATTGTGTGCAAATACGCCTCT 1 136 1 GTATGGGCAA 0.931421 -70 CCGAAAATCGGTCATTGGGGTTAAGGTTGTAACA 1 170 0 GTATGGTTAA 0.991783 -36 ATTTTCAAATGAGAAGGAGTATAATGTCTCAATG 2 78 1 GAAAGGATAA 0.842202 -142 AATCCTTCAAGTGAAAGTGTTAAAAAAATGAAAT 2 148 1 GTAAGGTAAA 0.96152 -72 ATATGCTTATGTAATGGAGGTTCACAAAT 3 6 0 GTATGGTTCA 0.969755 -126 ** ** * * **** Masking position 4 Map Score: 1.55772 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 303 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 TCTCCTGAATATCCTTTTTTCCTGCCCCTG 1 15 1 ATCCTTTTTT 0.967474 -191 AGGGATGTATCCTTTCATACATTAGATC 2 9 1 ATCCTTTCAT 0.989629 -211 TTTATATTATATCCATATTTATACTAATTT 2 52 1 ATCCATATTT 0.781575 -168 TTATGACAAAATCATTTCATTTTTTTAACA 2 165 0 ATCATTTCAT 0.947587 -55 GTCATCATCCCTTCATGATTTGACAT 2 204 0 ATCCCTTCAT 0.982494 -16 ********** Masking position 6 Map Score: 2.47197 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 74 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ********** No masking Map Score: -1.01364e-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: -1.01364e-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: -1.01364e-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