AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i227_rna_methyltransferase_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 cysS 173 cysteine tRNA synthetase #2 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #3 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #4 hflK 85 protease specific for phage lambda cII repressor #5 yjeT 81 orf, hypothetical protein #6 purA 103 adenylosuccinate synthetase #7 yjeB 204 orf, hypothetical protein #8 BIME224 57 BIME #9 yjfH 88 orf, hypothetical protein #10 HI0078 102 cysteinyl-tRNA synthetase (cysS) #11 HI0860 55 conserved hypothetical protein #12 HI0861 191 virulence-associated protein (vacB) #13 HI0862 135 conserved hypothetical protein Motif number 1 GCACGATACGTCTCAATTGTACACAT 2 7 0 TCTCAATTGT 0.678782 -79 GACGTATCGTGCGCAATTTTTTCAGAATCG 2 25 1 GCGCAATTTT 0.833577 -61 TCTCTCTTTTCCTTATATGC 2 76 0 TCTCTCTTTT 0.703848 -10 TTCAGAGTTACAGCACTTTTTGCACTCAAA 6 38 0 CAGCACTTTT 0.969853 -66 TGGATTCTACCATCGCTTTTTCAGAGTTAC 6 57 0 CATCGCTTTT 0.951607 -47 AGTGTTAAATCCTCGCTTTTTTCCTTCCCC 7 98 1 CCTCGCTTTT 0.985593 -107 ATAATACAACCCTTAATTTTTTAGAGGGAA 10 17 0 CCTTAATTTT 0.710705 -86 AGCACTTTTACCTCGATTGTGGAATAATAC 10 40 0 CCTCGATTGT 0.885435 -63 CGCACTTTTATAGCACTTTTACCTCGATTG 10 51 0 TAGCACTTTT 0.85364 -52 TAAAAACAAACCGCACTTTTATAGCACTTT 10 62 0 CCGCACTTTT 0.991144 -41 AATTTTTACCGCGCTTTTCATACTTTAA 12 9 1 CCGCGCTTTT 0.986704 -183 TATAAAAAGTCATCACTGTTATAGTGCTGG 12 46 1 CATCACTGTT 0.800945 -146 TCGTTAAGTTCTTCAATTTTAAAATATCCT 12 83 1 CTTCAATTTT 0.791375 -109 GTCAAACTCTCCGCACTTTTTAAAACTGTA 12 165 1 CCGCACTTTT 0.991144 -27 TCGTCAATTTTCATAAAATAT 13 2 1 CGTCAATTTT 0.848991 -134 ********** Masking position 7 Map Score: 19.2411 Number of sites scoring better than the average of aligned sites = 944 Number in coding regions = 796 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 2 AAACGGAACAGGATGCAAAA 1 1 0 GGATGCAAAA 0.635173 -173 GCTGATTCGCGCGGGAAATATGGGTATTAT 1 113 1 GCGGGAAATA 0.885732 -61 AATAAGCATATAAGGAAAAGAGAGA 2 71 1 TAAGGAAAAG 0.725255 -15 GGTCATTTTTGAGTGCAAAAAGTGCTGTAA 6 31 1 GAGTGCAAAA 0.900558 -73 TGTTCGCCCGGCAGGCAAAATATCTGCCAG 7 22 0 GCAGGCAAAA 0.971749 -183 TCAGTTCGGGGAAGGAAAAAAGCGAGGATT 7 105 0 GAAGGAAAAA 0.968902 -100 AAAAGGGAAATCGGGAAAAAATACATTTAT 7 176 0 TCGGGAAAAA 0.936601 -29 ACGTAGTGCATCAGGCAAAACGTAAACAAC 9 59 1 TCAGGCAAAA 0.883629 -30 TAATTTTTTAGAGGGAAAACAAA 10 4 0 GAGGGAAAAC 0.91228 -99 TTCCACAATCGAGGTAAAAGTGCTATAAAA 10 46 1 GAGGTAAAAG 0.808614 -57 TTGTAAGAATGAATTAAAAATTCAAATAAG 11 22 1 GAATTAAAAA 0.602909 -34 TATGAAAAGCGCGGTAAAAATT 12 3 0 GCGGTAAAAA 0.936601 -189 ********** Masking position 7 Map Score: 7.57479 Number of sites scoring better than the average of aligned sites = 2624 Number in coding regions = 2315 Number in noncoding regions = 309 Number of orfs with sites within 600 bp upstream = 321 Fraction of orfs with sites within 600 bp upstream = 0.051558 Motif number 3 TGATCTATTTAGAGGGTTATACGC 3 62 1 AGAGGGTTAA 0.966576 -14 CATCGCTTTTTCAGAGTTACAGCACTTTTTG 6 46 0 TCAGAGTTAA 0.87324 -58 TGCCGGGCGAACAGTGTGATACATTGCTGTG 7 39 1 ACAGTGTGAA 0.968672 -166 GCTATCCGACACAGTGTTAAATCCTCGCTTT 7 86 1 ACAGTGTTAA 0.984438 -119 CTTTAAAAGAAGAGGGTTAGATTGCTGACAA 8 21 1 AGAGGGTTAA 0.966576 -37 TAAAAAGTCATCACTGTTATAGTGCTGGGGA 12 48 1 TCACTGTTAA 0.82822 -144 AAAAGTGCGGAGAGTTTGACACTGTAAGGAG 12 154 0 AGAGTTTGAA 0.891083 -38 TATTTTTTACAGTTTTAAAAAGTGCGGAG 12 173 0 ACAGTTTTAA 0.953985 -19 CGATTGCATTTGAGTTTTATATTTTATGAAA 13 19 0 TGAGTTTTAA 0.897748 -117 ********* * Masking position 7 Map Score: 6.72411 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 89 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 CGGTTATGCTATAACACCACCCTATATATGA 1 56 0 AAACACCACC 0.941731 -118 TCCCCGTGTAAAAAAACAGCCCGAAACC 3 8 0 AAAAACAGCC 0.981317 -68 GTACAGGTCAATAAAGCCACCGCATCCTCAG 5 24 1 AAAAGCCACC 0.950508 -58 TTATAGAAAAAGAAAACCACCGACATCCCTG 5 52 0 AAAAACCACC 0.981317 -30 ACAAAAAACAGACTGATCGAGGT 6 3 1 AAAAACAGAC 0.854342 -101 TATATTGATGATAAACCAGCCACAAGCTGTG 7 148 0 AAAACCAGCC 0.972485 -57 CGATTGTGGAATAATACAACCCTTAATTTTT 10 26 0 AAATACAACC 0.917526 -77 AAAATGAAATAAAAACAAACCGCACTTTTAT 10 70 0 AAAACAAACC 0.801063 -33 * ********* Masking position 4 Map Score: 5.73568 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 308 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 TTTTGCATCCTGTTCCGTTTGATTGGT 1 6 1 CTCCTGTTCG 0.939676 -168 ATGATCCGATCGTGCGGTTATGCTATAACACC 1 69 0 CTGCGGTTTG 0.945687 -105 GCATACATTGCGTGATGATCCGATCGTGCGGT 1 83 0 CTGATGATCG 0.985343 -91 TCACGCAATGTATGCTGATTCGCGCGGGAAAT 1 100 1 TTGCTGATCG 0.936506 -74 TCTTTCGACGCCAGAGGATATGACTCCACGCT 4 26 0 CAGAGGATTG 0.851364 -60 CACCGACATCCCTGAGGATGCGGTGGCTTTAT 5 34 0 CTGAGGATCG 0.982286 -48 AGTGTGATACATTGCTGTGTCGGGTAAGCCAT 7 51 1 ATGCTGTGCG 0.854055 -154 AAACCAGCCACAAGCTGTGTCGCTAATTTATT 7 135 0 CAGCTGTGCG 0.964897 -70 ATATAGGGGGCTAGATGATACGCATATTTCTA 13 64 0 CAGATGATCG 0.972425 -72 * ******* ** Masking position 7 Map Score: 4.84653 Number of sites scoring better than the average of aligned sites = 1126 Number in coding regions = 1058 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 TTCGGGTCATATATAGGGTGGTGTTATAGC 1 50 1 ATATAGGGTG 0.956619 -124 GGCTGTTTTTTTACACGGGGAGCCAGCGAT 3 18 1 TTACACGGGG 0.914305 -58 CCGCTGATCTATTTAGAGGGTTATACGC 3 58 1 ATTTAGAGGG 0.928675 -18 TCCATATTTGTTATGCGGTGATCCCTGTTG 4 58 0 TTATGCGGTG 0.782608 -28 CCCTCTTCTTTTAAAGAGGGTATTGA 8 7 0 TTAAAGAGGG 0.880723 -51 ACCCTTAATTTTTTAGAGGGAAAACAAA 10 9 0 TTTTAGAGGG 0.928675 -94 TATCCTTAAAATATACAGTGATAATTTTAT 12 107 1 ATATACAGTG 0.895234 -85 CCGAGGTTGAATATAGGGGGCTAGATGATA 13 76 0 ATATAGGGGG 0.982583 -60 ********** Masking position 2 Map Score: 3.53518 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 60 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 TTTTTTTACACGGGGAGCCAGCGATCCTGC 3 23 1 CGGGGAGCCA 0.950154 -53 AATAGATCAGCGGGGAACGCAGGATCGCTG 3 41 0 CGGGGAACGC 0.990332 -35 CGAAAGACAACAGGGATCACCGCATAACAA 4 51 1 CAGGGATCAC 0.902795 -35 ACCGCATCCTCAGGGATGTCGGTGGTTTTC 5 42 1 CAGGGATGTC 0.800397 -40 ATTGCTGTGTCGGGTAAGCCATTACGCTAT 7 61 1 CGGGTAAGCC 0.884327 -144 TATTTCAGTTCGGGGAAGGAAAAAAGCGAG 7 109 0 CGGGGAAGGA 0.975425 -96 GTTATAGTGCTGGGGAAAGATCGTTAAGTT 12 63 1 TGGGGAAAGA 0.776231 -129 TAATGCAAGACGGGGATAAAATTATCACTG 12 122 0 CGGGGATAAA 0.829751 -70 AAATCGGGGTTAGGGAACCCGAGGTTGAAT 13 94 0 TAGGGAACCC 0.8686 -42 ********** Masking position 6 Map Score: 3.19486 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 663 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 8 GCGCGGGAAATATGGGTATTATACGCAACT 1 121 1 TATGGGTATT 0.799429 -53 TTTAGACATGTGTGGGTAATTGAGTTGCGT 1 143 0 TGTGGGTAAT 0.906084 -31 TGATCTATTTAGAGGGTTATACGC 3 62 1 AGAGGGTTAT 0.827968 -14 TTTCGACGCCAGAGGATATGACTCCACGCT 4 26 0 AGAGGATATG 0.74664 -60 TCTTTTTCTATAAGGATAATGA 5 70 1 TAAGGATAAT 0.887758 -12 ATCAACCTCAAAAGGGAAATCGGGAAAAAA 7 185 0 AAAGGGAAAT 0.710116 -20 CTTCTTTTAAAGAGGGTATTGA 8 3 0 AGAGGGTATT 0.961212 -55 CTGTATATTTTAAGGATATTTTAAAATTGA 12 95 0 TAAGGATATT 0.865225 -97 GACACTGTAAGGAGGATAATGCAAGACGGG 12 138 0 GGAGGATAAT 0.875004 -54 ********** Masking position 5 Map Score: 1.78025 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 293 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 9 TGGGTTGAAGCACCAATCAAACGGAACAGG 1 19 0 CACCAATCAA 0.886873 -155 TATGCTATAACACCACCCTATATATGACCC 1 53 0 CACCACCCTA 0.886605 -121 TTACCCGACACAGCAATGTATCACACTGTT 7 48 0 CAGCAATGTA 0.964223 -157 GCTGGTTTATCATCAATATAAATGTATTTT 7 159 1 CATCAATATA 0.898005 -46 CGCATTTTGTCAGCAATCTAACCCTCTTCT 8 28 0 CAGCAATCTA 0.986347 -30 TACATGATCTCTGCAATATATTGAATTTGC 9 19 0 CTGCAATATA 0.905113 -70 GATCTTTCCCCAGCACTATAACAGTGATGA 12 55 0 CAGCACTATA 0.96867 -137 ********** Masking position 5 Map Score: 2.96581 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 81 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 CGTGATGATCCGATCGTGCGGTTATGCTAT 1 75 0 CGATCGTGCG 0.985487 -99 CAATTGAGACGTATCGTGCGCAATTTTTTC 2 18 1 GTATCGTGCG 0.955517 -68 GGGGAGCCAGCGATCCTGCGTTCCCCGCTG 3 34 1 CGATCCTGCG 0.968126 -42 GGCAAAATATCTGCCAGGCGTACCAGAA 7 9 0 CTGCCAGGCG 0.959499 -196 GATATTTTGCCTGCCGGGCGAACAGTGTGA 7 28 1 CTGCCGGGCG 0.978058 -177 ********** Masking position 5 Map Score: 0.171295 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 150 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ********** No masking Map Score: -7.29427e-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 12 CGAAGATTCCGTTTAGACATGTGT 1 160 0 AGATTCGTTT 0.752476 -14 GGGATGTCGGTGGTTTTCTTTTTCTATAAGGA 5 54 1 TGTTTCTTTT 0.787627 -28 AAAGCGATGGTAGAATCCATTTTTAAGCAAAC 6 68 1 TGAATCATTT 0.842977 -36 GTGTCGCTAATTTATTTCAGTTCGGGGAAGGA 7 119 0 TTATTCAGTT 0.894433 -86 ATCTCTGCAATATATTGAATTTGCGTGATTAT 9 11 0 TTATTAATTT 0.62953 -78 AATGTACTCGTTGTTTACGTTTTGCCTGATGC 9 66 0 TGTTTCGTTT 0.910039 -23 GCGGTTTGTTTTTATTTCATTTTACGAGCTTA 10 78 1 TTATTCATTT 0.945455 -25 TATTTTTTACAGTTTTAAAAAGTG 12 178 0 TTTTTCAGTT 0.816326 -14 ATTGCAAGAGTCGATTGCATTTGAGTTTTATA 13 29 0 TGATTCATTT 0.971473 -107 * **** ***** Masking position 6 Map Score: 1.14834 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 188 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 13 ********** No masking Map Score: -7.29427e-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 14 ********** No masking Map Score: -7.29427e-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 15 ********** No masking Map Score: -7.29427e-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