AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_ecoli_mtub_100.orf -o259_ecoli_mtub_100.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 flgB 154 flagellar biosynthesis, cell-proximal portion of basal-body rod #2 flgE 24 flagellar biosynthesis, hook protein #3 BIME65 28 BIME #4 flgG 44 flagellar biosynthesis, cell-distal portion of basal-body rod #5 flhB 130 putative part of export apparatus for flagellar proteins #6 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #7 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #8 fliL 104 flagellar biosynthesis #9 fliO 62 flagellar biosynthesis Motif number 1 TCCGCAATGACCATCAACGGCATAAATAGCGACCC 1 50 1 CCAAGGCAAA 0.911285 -105 CTTTACGCGCGCGTTATCGGCGGAATAAACGCAAA 1 87 0 GCGAGGCGAA 0.993124 -68 GTCCTGTAGTGGATTAGTGACAAAGTGCATATGTC 4 15 0 GGAAGACAAG 0.887805 -30 TGAGTAAGGGGCAAAACAGGCGGGATTTAGGGCTT 5 43 0 GCAAGGCGGA 0.986968 -88 ACGTGCTTCCCCGCCACCGGCGGGGTTTTTTTCTG 6 35 1 CCGAGGCGGG 0.994183 -144 TGCGTTATATGAGTTATCGGCATGATTATCCGTTT 6 142 0 GAGAGGCAGA 0.929038 -37 ATTATGGACGGCGTTATTGGCAAAGTGGAACAAGA 7 173 0 GCGAGGCAAG 0.995091 -42 GCAACAAAGCGGGGAAAAGACGCGGATTACGGTGC 8 22 0 GGGAGACGGG 0.978137 -83 CCGCTTTGTTGCGCTCAAGACGCAGGATAATTAGC 8 45 1 GCGCGACGAG 0.961232 -60 TAGCCGATAAGCAGTAGCGACACAGGAAGACCGCA 8 76 1 GCAAGACAAG 0.967312 -29 AGTGGCGCAGCAGAAACCGGCGCGGAAGATTGCAC 9 31 0 CAGAGGCGGG 0.968863 -32 CTGCAGCAGTGGCGCAGCAGAAACCGG 9 46 0 GCAAGGCGAG 0.995091 -17 *** * **** ** Masking position 11 Map Score: 20.2663 Number of sites scoring better than the average of aligned sites = 2537 Number in coding regions = 2437 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 AATTGTACCTGTCCGCAATGACCATCAACG 1 39 1 GTCCGCAATG 0.83517 -116 CTCCTCCGCAGGTATCAAAATTCTGCCATC 1 133 0 GGTATCAAAA 0.667353 -22 CTTGATGTGTGGCAGCAAAAGCCCTAAATC 5 25 1 GGCAGCAAAA 0.984966 -106 AATGATGCCAGAGCGCAAAGCGTTCAATGG 5 80 0 GAGCGCAAAG 0.928699 -51 AGCGCAATTTGTCAGCAACGTGCTTCCCCG 6 18 1 GTCAGCAACG 0.969823 -161 GTAAATTCCAGGCAGAAAAAAACCCCGCCG 6 52 0 GGCAGAAAAA 0.901022 -127 GATAATTTCTGGTAGCAAAGCCTACCAGTA 7 23 1 GGTAGCAAAG 0.973996 -192 TTTATTGGCGGATAGAAAAAAACGAAAGCA 7 95 1 GATAGAAAAA 0.664128 -120 TCACTCCCGGGTCAGCAAACTCGAAAAATT 7 142 0 GTCAGCAAAC 0.887315 -73 CGTCAGAGGTAGCACCGTAATCCGCGT 8 8 1 GGTAGCACCG 0.857549 -97 CCTGCGTCTTGAGCGCAACAAAGCGGGGAA 8 41 0 GAGCGCAACA 0.900762 -64 GACACAGGAAGACCGCAACAC 8 94 1 GACCGCAACA 0.962485 -11 ********** Masking position 7 Map Score: 10.9282 Number of sites scoring better than the average of aligned sites = 2679 Number in coding regions = 2505 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 3 GTTTATTCCGCCGATAACGCGCGCGTAAAG 1 92 1 CCGATAACGC 0.947166 -63 CAGCAAAAGCCCTAAATCCCGCCTGTTTTG 5 37 1 CCTAAATCCC 0.734113 -94 TTACTCAAACCATTGAACGCTTTGCGCTCT 5 71 1 CATTGAACGC 0.960307 -60 CGCTCTGGCATCATTCACGCTTAATACTCT 5 95 1 TCATTCACGC 0.717171 -36 AACATAAAGCGCAATTTGTCAG 6 3 1 CATAAAGCGC 0.926087 -176 CTGGAATTTACCTGTAACCCCCAAATAACC 6 71 1 CCTGTAACCC 0.938111 -108 CTGTAACCCCCAAATAACCCCTCATTTCAC 6 82 1 CAAATAACCC 0.9487 -97 AATAACCCCTCATTTCACCCACTAATCGTC 6 94 1 CATTTCACCC 0.918466 -85 GCCGATAACTCATATAACGCAGGGCTGTTT 6 156 1 CATATAACGC 0.982538 -23 TTTTTGTTGCTATTTAGCGCCTTTGTCTTA 7 59 0 TATTTAGCGC 0.862306 -156 TTCTATCCGCCAATAAACCCGTTTTTTTGT 7 82 0 CAATAAACCC 0.88047 -133 TTCCACTTTGCCAATAACGCCGTCCATAAT 7 178 1 CCAATAACGC 0.975788 -37 TTATCCTGCGTCTTGAGCGCAACAAAGCGG 8 45 0 TCTTGAGCGC 0.788149 -60 ********** Masking position 8 Map Score: 10.0586 Number of sites scoring better than the average of aligned sites = 2345 Number in coding regions = 2179 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 4 GTAGAAATGGCTGGGGGCGAAA 1 2 0 CTGGGGGGAA 0.963918 -153 AATTTTGATACCTGCGGAGGAGAT 1 141 1 CCTGCGGGGA 0.987267 -14 AAAATGTCCTGTAGTGGATTAGTGACAA 4 27 0 CCTGTAGGGA 0.969336 -18 GTCGCCAATCCTGGAAAGAGTATTAAGCGT 5 111 0 CCTGGAAGAG 0.882337 -20 AAAAACCCCGCCGGTGGCGGGGAAGCACGTT 6 34 0 CCGGTGGGGG 0.985327 -145 CAGAAATTATCCGGGAGACGAGA 7 3 0 CCGGGAGCGA 0.97523 -212 GTTTGCTGACCCGGGAGTGAGTCTTGTTCCA 7 152 1 CCGGGAGGAG 0.993258 -63 GCAGCAGAAACCGGCGCGGAAGATTGCACAG 9 29 0 CCGGCGCGAA 0.960073 -34 ******* *** Masking position 4 Map Score: 6.48391 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 1141 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 5 CAAAATGGGTCGCTATTTATGCCGTTGATG 1 61 0 CGCTATTTAT 0.936226 -94 CTGCAGAAACGGATAATCATGCCGATAACT 6 136 1 GGATAATCAT 0.910485 -43 TATAACGCAGGGCTGTTTATC 6 168 1 GGCTGTTTAT 0.981509 -11 CGCACCTCGTGGCTGATTATGGACGGCGTT 7 193 0 GGCTGATTAT 0.981509 -22 ACTGCTTATCGGCTAATTATCCTGCGTCTT 8 61 0 GGCTAATTAT 0.984621 -44 ACAGTAGCGTGGTTATTCATCA 9 3 0 GGTTATTCAT 0.910485 -60 ********** Masking position 4 Map Score: 4.74503 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 86 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 AATTCACGTTGTAGAAATGGCTGGGGGCGA 1 13 0 GTAGAAATGG 0.918582 -142 TTGATGTGTGGCAGCAAAAGCCCTAAATCC 5 26 1 GCAGCAAAAG 0.895347 -105 TAAAAACCCTGCAGAAACGGATAATCATGC 6 128 1 GCAGAAACGG 0.993951 -51 TAGCCGATAAGCAGTAGCGACACAGGAAGA 8 76 1 GCAGTAGCGA 0.89294 -29 CAGTGGCGCAGCAGAAACCGGCGCGGAAGA 9 37 0 GCAGAAACCG 0.979022 -26 CTGCAGCAGTGGCGCAGCAGAA 9 51 0 GCAGCAGTGG 0.984907 -12 ********** Masking position 6 Map Score: 2.31128 Number of sites scoring better than the average of aligned sites = 1027 Number in coding regions = 963 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 AGGGCTTTTGCTGCCACACATCAAGCATAG 5 20 0 CTGCCACACA 0.862038 -111 GGGTTTTTTTCTGCCTGGAATTTACCTGTA 6 57 1 CTGCCTGGAA 0.954754 -122 TGCCTGGAATTTACCTGTAACCCCCAAATA 6 68 1 TTACCTGTAA 0.89098 -111 GTAGGCTTTGCTACCAGAAATTATCCGGGA 7 18 0 CTACCAGAAA 0.964303 -197 GTAGCAAAGCCTACCAGTAAGTCAATAAGA 7 34 1 CTACCAGTAA 0.979501 -181 TTGTTCCACTTTGCCAATAACGCCGTCCAT 7 175 1 TTGCCAATAA 0.76123 -40 GATTACGGTGCTACCTCTGACG 8 3 0 CTACCTCTGA 0.881151 -102 ********** Masking position 10 Map Score: 0.8214 Number of sites scoring better than the average of aligned sites = 957 Number in coding regions = 894 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 8 GATGGTCATTGCGGACAGGTACAATTCACGT 1 34 0 GCGGAAGGTA 0.965414 -121 GATAACGCGCGCGTAAAGGCATTTAAGCTGA 1 104 1 GCGTAAGGCA 0.975608 -51 TATGCTTGATGTGTGGCAGCAAAAGCCCTAA 5 21 1 GTGTGCAGCA 0.83466 -110 CCCGCCGGTGGCGGGGAAGCACGTTGCTGAC 6 28 0 GCGGGAAGCA 0.990322 -151 TGGTAGCAAAGCCTACCAGTAAGTCAATAAG 7 32 1 GCCTACAGTA 0.838378 -183 GGGTTTATTGGCGGATAGAAAAAAACGAAAG 7 92 1 GCGGAAGAAA 0.732369 -123 AGACTCACTCCCGGGTCAGCAAACTCGAAAA 7 145 0 CCGGGCAGCA 0.95035 -70 AGGATAATTAGCCGATAAGCAGTAGCGACAC 8 68 1 GCCGAAAGCA 0.974217 -37 TGCAGCAGTGGCGCAGCAGAAACCGGCGCGG 9 41 0 GCGCACAGAA 0.909006 -22 ***** ***** Masking position 11 Map Score: 3.58736 Number of sites scoring better than the average of aligned sites = 2385 Number in coding regions = 2267 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 9 CATTTAAGCTGATGGCAGAATTTTGATACC 1 123 1 GATGGCAGAA 0.983873 -32 TAGGGCTTTTGCTGCCACACATCAAGCATA 5 21 0 GCTGCCACAC 0.950585 -110 AAGCGTGAATGATGCCAGAGCGCAAAGCGT 5 87 0 GATGCCAGAG 0.974688 -44 CAGGTAAATTCCAGGCAGAAAAAAACCCCG 6 55 0 CCAGGCAGAA 0.860362 -124 GGTAGGCTTTGCTACCAGAAATTATCCGGG 7 19 0 GCTACCAGAA 0.949881 -196 AGAAAAAAACGAAAGCACAAATAATGGGAG 7 108 1 GAAAGCACAA 0.872247 -107 CGGCGCGGAAGATTGCACAGTAGCGTGGTT 9 19 0 GATTGCACAG 0.880644 -44 ********** Masking position 7 Map Score: 0.635593 Number of sites scoring better than the average of aligned sites = 1581 Number in coding regions = 1502 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 10 ********** No masking Map Score: 1.73616e-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: 1.73616e-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 12 ********** No masking Map Score: 1.73616e-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