AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i185_4_6_1_10_ecoli_hinf_reg_100.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 TAACGCCTGCGATTAACCCGGACCAGCTAT 1 10 0 GATTAACCGG 0.872105 -55 AGATAATCCTGCTTGAACAATA 1 53 0 GATAATCCGC 0.968974 -12 CTGACAGGGCGCAGAAACAGCTTTGCTTACT 3 11 0 GCAGAAACGC 0.917217 -290 AAAGACTATTGCTAAAACAGGTTAGTCGATT 3 123 0 GCTAAAACGG 0.941771 -178 CAACAAAATAGATTAACCAACCTAATGAAAA 3 156 1 GATTAACCAC 0.812612 -145 CAATCATTAAGATAAATCAGCGATTTTGCGC 3 202 1 GATAAATCGC 0.93243 -99 TTTCGCATTATCTAAAACGACTTTGTTGCGC 3 229 0 TCTAAAACAC 0.784619 -72 TAGATAATGCGAAAAAACAGCCTTTCCGGTA 3 246 1 GAAAAAACGC 0.983237 -55 TCTACAGGACGATAAAACCGCCGTAGAGTAC 3 274 0 GATAAAACGC 0.987224 -27 CGCATTTTTCTTTAAACCTGCCTGTAACAGA 4 132 1 TTTAAACCGC 0.841766 -92 GTTAATTATTGCAGATCCTGCCACAACAATC 4 178 0 GCAGATCCGC 0.813721 -46 CTTTATTGCGTAAAATACAGCTTGGGCATTT 5 33 0 TAAAATACGC 0.858779 -57 TTTGCTAAATTAAAAACCTGCGAATTGTAGC 6 22 1 TAAAAACCGC 0.966339 -134 CCTCCTACAATAAAAAACTAGGTAAAAT 6 138 1 TAAAAAACAG 0.517819 -18 ******** ** Masking position 5 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 CGTTACCATAACGCTTTTATTGTTCAAGCAGGATTAT 1 36 1 ACTTTTGTAA 0.985154 -29 GGTTGGTTAATCTATTTTGTTGTTAAAGACTATTGCT 3 141 0 TCTTTTGTAA 0.981773 -160 ATTATCTAAAACGACTTTGTTGCGCAAAATCGCTGAT 3 217 0 ACTTTTGGAA 0.988431 -84 AGAAAAAATAAATATAATTTTGGTGAATGTTTTGACA 4 24 1 AAATTTGTAA 0.795815 -200 TGTTAATAAGACATGATTGTTGTGGCAGGATCTGCAA 4 164 1 ACTTTTGGCA 0.976614 -60 ATATTTCTTTAAACCTTTATTGCGTAAAATACAGCTT 5 41 0 AATTTTGGAA 0.965518 -49 TTTTTCTACCTTTTTGAGTCAAATATTTCTT 5 69 0 TCTTTTGGCA 0.971343 -21 AAGTAAACCTTTTTGCTAAATTAAAAACCT 6 4 1 TATTTTGTAA 0.946389 -152 ACGAAATATTTCACTTGTCTTGCTAAAATAGAACTTC 6 71 1 TCGTTTGTAA 0.934667 -85 ** ** *** * ** Masking position 8 Map Score: 7.06767 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 138 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 AATTCATTTGTTTTTCATTAGGTTGGTTAA 3 168 0 TTTTTCATTA 0.90679 -133 AATTTCTCTACAGGACGATA 3 291 0 AATTTCTCTA 0.875817 -10 TTATATTTATTTTTTCTGTATTAGTTTTTA 4 11 0 TTTTTCTGTA 0.974905 -213 GATTAAATCCATTTTCTTTATTTTCTTCTG 4 62 1 ATTTTCTTTA 0.972964 -162 ATGTTTCGCATTTTTCTTTAAACCTGCCTG 4 126 1 TTTTTCTTTA 0.979106 -98 CAGCTTGGGCATTTTCTGCATCCACCTTCG 5 17 0 ATTTTCTGCA 0.901771 -73 TTGAGTCAAATATTTCTTTAAACCTTTATT 5 57 0 TATTTCTTTA 0.953239 -33 ********** Masking position 10 Map Score: 6.13667 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 98 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 GACACGGTTAATGGTGATTGAGTATCACCTGAT 2 16 1 ATGTGATTGT 0.841092 -72 TACGGAAGTAATAGTGAATAGTTAAATAATATT 2 52 1 ATGTGAATTT 0.957724 -36 GTTAGTCGATTTGGTTATTAGTTATCGCTATCC 3 101 0 TTGTTATTTT 0.962722 -200 TTTCATTAGGTTGGTTAATCTATTTTGTTGTTA 3 153 0 TTGTTAATAT 0.802775 -148 GCTAAATTCATTTGTTTTTCATTAGGTTGGTTA 3 169 0 TTGTTTTTTT 0.877734 -132 CACCAAAATTATATTTATTTTTTCTGTATTAGT 4 16 0 ATTTTATTTT 0.735435 -208 AAATATAATTTTGGTGAATGTTTTGACATGATT 4 33 1 TTGTGAATTT 0.948421 -191 TGCGAAACATATCGTTAATAATTAAAGGGAGTA 4 103 0 ATGTTAATTT 0.969525 -121 GAAGTGGATAATTGTTAATTATTGCAGATCCTG 4 189 0 ATGTTAATTT 0.969528 -35 ATTTTACCTAGTTTTTTATTGTAGGAGGTT 6 136 0 CTGTTTTTTT 0.763815 -20 ** ****** ** Masking position 5 Map Score: 5.51629 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 119 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 AGTAAGCAAAGCTGTTTCTG 3 1 1 AGTAAGCAAA 0.915372 -300 AAACAAATGAATTTAGCCAATCATTAAGAT 3 185 1 ATTTAGCCAA 0.923418 -116 AAACGACTTTGTTGCGCAAAATCGCTGATT 3 216 0 GTTGCGCAAA 0.838231 -85 TTAAACCTTTATTGCGTAAAATACAGCTTG 5 40 0 ATTGCGTAAA 0.849558 -50 CAGGTTTTTAATTTAGCAAAAAGGTTTACT 6 12 0 ATTTAGCAAA 0.970396 -144 TACCCCCCGTAGTTCGCAAACCTCCTACAA 6 118 1 AGTTCGCAAA 0.976987 -38 ********** Masking position 3 Map Score: 1.66632 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 301 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 CATAAAACAGAAGAGAAGGTAAGGTTAACG 3 46 1 AAGAGAAGGT 0.92353 -255 AAAGTCGTTTTAGATAATGCGAAAAAACAG 3 236 1 TAGATAATGC 0.881138 -65 GAAGAAAATAAAGAAAATGGATTTAATCAT 4 60 0 AAGAAAATGG 0.924932 -164 ACCTGCCTGTAACAGAATGTTAATAAGACA 4 147 1 AACAGAATGT 0.883357 -77 ATCCACTTCACAGAGAATGCT 4 213 1 CAGAGAATGC 0.987705 -11 AAGGTGGATGCAGAAAATGCCCAAGCTGTA 5 19 1 CAGAAAATGC 0.972719 -71 ********** Masking position 6 Map Score: 0.566731 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 299 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 ATAGCTGGTCCGGGTTAATCGCAG 1 5 1 CTGGTCCGGG 0.970951 -60 TCTGTGACACGGTTAATGGTG 2 2 1 CTGTGACACG 0.942281 -86 TTAAATAATATTGTTCCGGGTTTAT 2 73 1 TTGTTCCGGG 0.983131 -15 TAAAACGACTTTGTTGCGCAAAATCGCTGA 3 218 0 TTGTTGCGCA 0.824946 -83 TATTAACATTCTGTTACAGGCAGGTTTAAA 4 142 0 CTGTTACAGG 0.974143 -82 GACATGATTGTTGTGGCAGGATCTGCAATA 4 173 1 TTGTGGCAGG 0.968482 -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 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 Motif number 9 ********** 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 10 ********** 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