AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i185_4_6_1_10_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 ybaX 64 orf, hypothetical protein #2 ybaE 87 orf, hypothetical protein #3 ygcM 300 putative 6-pyruvoyl tetrahydrobiopterin synthase #4 ygcF 223 orf, hypothetical protein #5 HI1190 89 6-pyruvoyl tetrahydrobiopterin synthase, putative #6 HI1191 155 conserved hypothetical protein Motif number 1 ATAGCTGGTCCGGGTTAATCGCAGGCGTTA 1 10 1 CCGGTTAATC 0.890103 -55 TATTGTTCAAGCAGGATTATCT 1 53 1 GCGGATTATC 0.973746 -12 AGTAAGCAAAGCTGTTTCTGCGCCCTGTCAG 3 11 1 GCGTTTCTGC 0.922805 -290 AATCGACTAACCTGTTTTAGCAATAGTCTTT 3 123 1 CCGTTTTAGC 0.95052 -178 TTTTCATTAGGTTGGTTAATCTATTTTGTTG 3 156 0 GTGGTTAATC 0.837422 -145 GCGCAAAATCGCTGATTTATCTTAATGATTG 3 202 0 GCGATTTATC 0.942425 -99 GCGCAACAAAGTCGTTTTAGATAATGCGAAA 3 229 1 GTGTTTTAGA 0.812279 -72 TACCGGAAAGGCTGTTTTTTCGCATTATCTA 3 246 0 GCGTTTTTTC 0.985848 -55 GTACTCTACGGCGGTTTTATCGTCCTGTAGA 3 274 1 GCGTTTTATC 0.989222 -27 TCTGTTACAGGCAGGTTTAAAGAAAAATGCG 4 132 0 GCGGTTTAAA 0.863365 -92 GATTGTTGTGGCAGGATCTGCAATAATTAAC 4 178 1 GCGGATCTGC 0.824952 -46 AAATGCCCAAGCTGTATTTTACGCAATAAAG 5 33 1 GCGTATTTTA 0.878391 -57 GCTACAATTCGCAGGTTTTTAATTTAGCAAA 6 22 0 GCGGTTTTTA 0.971509 -134 ATTTTACCTAGTTTTTTATTGTAGGAGG 6 138 0 CTGTTTTTTA 0.560553 -18 ** ******** Masking position 7 Map Score: 14.0666 Number of sites scoring better than the average of aligned sites = 3324 Number in coding regions = 3051 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 2 TCAGCGCCCATAAAACAGAAGAGAAGGTAAGGTTAACGG 3 38 1 TCAAAGAAGA 0.96939 -263 GGGATAGCGATAACTAATAACCAAATCGACTAACCTGTT 3 100 1 TAAAAAAATA 0.973083 -201 TTAGCAATAGTCTTTAACAACAAAATAGATTAACCAACC 3 139 1 TAAAAAAATA 0.973086 -162 ACCAACCTAATGAAAAACAAATGAATTTAGCCAATCATT 3 171 1 TAAAAGAATA 0.967556 -130 TAAAAACTAATACAGAAAAAATAAATATAATTTTGGTGA 4 11 1 TAAAAAAATA 0.973086 -213 TGGTGAATGTTTTGACATGATTAAATCCATTTTCTTTAT 4 44 1 TCAGAAAATA 0.915794 -180 AGTAACGTATTATGTCAGAAGAAAATAAAGAAAATGGAT 4 68 0 TCAAAAAATA 0.978969 -156 GCGAAACATATCGTTAATAATTAAAGGGAGTAACGTATT 4 96 0 TAAAAAAAGA 0.967555 -128 AAGAAATATTTGACTCAAAAAGGTAGAAAAA 5 69 1 TCAAAGTAGA 0.83312 -21 * ** ** **** * Masking position 10 Map Score: 6.65159 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 87 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 TAATAGTGAATAGTTAAATAATATTGTTCC 2 60 1 TAGTTAAATA 0.715175 -28 TTAACCAACCTAATGAAAAACAAATGAATT 3 168 1 TAATGAAAAA 0.94224 -133 TATCGTCCTGTAGAGAAATT 3 291 1 TAGAGAAATT 0.834799 -10 TAAAAACTAATACAGAAAAAATAAATATAA 4 11 1 TACAGAAAAA 0.880231 -213 CAGAAGAAAATAAAGAAAATGGATTTAATC 4 62 0 TAAAGAAAAT 0.863976 -162 CAGGCAGGTTTAAAGAAAAATGCGAAACAT 4 126 0 TAAAGAAAAA 0.952606 -98 AATAAAGGTTTAAAGAAATATTTGACTCAA 5 57 1 TAAAGAAATA 0.94224 -33 CCTTTTTGCTAAATTAAAAACCTGCGAATT 6 18 1 AAATTAAAAA 0.503741 -138 TTAGCAAGACAAGTGAAATATTTCGTTGGA 6 67 0 AAGTGAAATA 0.803942 -89 ********** Masking position 6 Map Score: 4.97203 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 330 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 4 ATAACGCTTTTATTGTTCAAGCAGGATTAT 1 43 1 TATTGTTCAA 0.85998 -22 TGTTAAAGACTATTGCTAAAACAGGTTAGT 3 128 0 TATTGCTAAA 0.98065 -173 TAATCTATTTTGTTGTTAAAGACTATTGCT 3 141 0 TGTTGTTAAA 0.798601 -160 AAATCAGCGATTTTGCGCAACAAAGTCGTT 3 215 1 TTTTGCGCAA 0.943995 -86 TCGTTTTAGATAATGCGAAAAAACAGCCTT 3 240 1 TAATGCGAAA 0.956974 -61 GTTTAAAGAAAAATGCGAAACATATCGTTA 4 119 0 AAATGCGAAA 0.779369 -105 TTTAAACCTTTATTGCGTAAAATACAGCTT 5 41 0 TATTGCGTAA 0.935938 -49 AAGTAAACCTTTTTGCTAAATTAAAAACCT 6 11 1 TTTTGCTAAA 0.919108 -145 ATTTCACTTGTCTTGCTAAAATAGAACTTC 6 78 1 TCTTGCTAAA 0.951224 -78 ********** Masking position 4 Map Score: 7.62177 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 301 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 ATAGCTGGTCCGGGTTAATCGCAG 1 5 1 CTGGTCCGGG 0.973482 -60 TCTGTGACACGGTTAATGGTG 2 2 1 CTGTGACACG 0.947199 -86 TTAAATAATATTGTTCCGGGTTTAT 2 73 1 TTGTTCCGGG 0.984625 -15 TAAAACGACTTTGTTGCGCAAAATCGCTGA 3 218 0 TTGTTGCGCA 0.838147 -83 TATTAACATTCTGTTACAGGCAGGTTTAAA 4 142 0 CTGTTACAGG 0.976414 -82 GACATGATTGTTGTGGCAGGATCTGCAATA 4 173 1 TTGTGGCAGG 0.971236 -51 ********** Masking position 2 Map Score: 0.62602 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 1023 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 ********** No masking Map Score: 1.63668e-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 7 ********** No masking Map Score: 1.63668e-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: 1.63668e-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