AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i292_3_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 ybgI 270 orf, hypothetical protein #2 ybgJ 22 putative carboxylase #3 HI1731 300 conserved hypothetical protein Motif number 1 TTGCGCGGCGTGCTTGTGTTTCCTTAAAGTT 1 47 1 TGCTGTGTTT 0.913748 -224 ATCATCACGCTTCAGCTAATGTATATTTATG 1 126 0 TTCGCTAATG 0.739046 -145 ATAAACAATTTGCGTCTTTTGGCGTCGGGTT 1 157 1 TGCTCTTTTG 0.972449 -114 TTTCGATCCCTCTGATTATTCG 2 6 0 TCCTCTGATT 0.943935 -17 AAACAGGCGTTGCAGCTGGTGTTGGTTACCA 3 41 1 TGCGCTGGTG 0.980604 -260 AAGCGGCAAATGCCGCTTTTTAAAAGAGATA 3 88 0 TGCGCTTTTT 0.972449 -213 AAGCGGCATTTGCCGCTTTTTTTATGGGTGG 3 101 1 TGCGCTTTTT 0.972449 -200 TTAACACAAATTCATTTGGTTGAAACAATAA 3 134 0 TTCTTTGGTT 0.768268 -167 GTGTTAAATTTCCTTTTGATGGTTAAAGCGT 3 158 1 TCCTTTGATG 0.782223 -143 AGTCTTTATTTTCATCTTTTTAATTCAATTT 3 198 0 TTCTCTTTTT 0.927193 -103 *** ******* Masking position 7 Map Score: 6.60365 Number of sites scoring better than the average of aligned sites = 2108 Number in coding regions = 1972 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 ATCTGTATCAAAGTTTTAACTTTAAGGAAA 1 65 0 AAGTTTTAAC 0.891599 -206 TTATATCATCACGCTTCAGCTAATGTATAT 1 131 0 ACGCTTCAGC 0.986206 -140 CGCTATGTTAACGGTGTAGCTATCAGAATA 1 237 1 ACGGTGTAGC 0.980614 -34 GGTAAAACAGGCGTTGCAGCTGGTGTTGGT 3 37 1 GCGTTGCAGC 0.976383 -264 TAAAAACATTACGCTTTAACCATCAAAAGG 3 169 0 ACGCTTTAAC 0.982093 -132 CTTTAAAAGAGAGCTGTAACAAAAAAATAA 3 249 1 GAGCTGTAAC 0.960252 -52 ********** Masking position 5 Map Score: 3.72309 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 677 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 ATAATCAGATCTGTATCAAAGTTTTAACTT 1 73 0 CTGTATCAAA 0.960322 -198 CGAGGTAACGCTATGTTAACGGTGTAGCTA 1 229 1 CTATGTTAAC 0.852765 -42 GCTGCAACGCCTGTTTTACCTTGACTATTG 3 27 0 CTGTTTTACC 0.923045 -274 TTTGGATTATCTCTTTTAAAAAGCGGCATT 3 81 1 CTCTTTTAAA 0.951079 -220 GGTGGTATTATTGTTTCAACCAAATGAATT 3 127 1 TTGTTTCAAC 0.910106 -174 CCAAATGAATTTGTGTTAAATTTCCTTTTG 3 146 1 TTGTGTTAAA 0.897292 -155 TGTTACAGCTCTCTTTTAAAGGATATTTAT 3 240 0 CTCTTTTAAA 0.951079 -61 TAAAAGAGAGCTGTAACAAAAAAATAACAA 3 252 1 CTGTAACAAA 0.812644 -49 ********** Masking position 8 Map Score: 3.20551 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 425 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 ATACAGATCTGATTATTTATGCAATATGCT 1 87 1 GATTATTTAT 0.966736 -184 TTCAGCTAATGTATATTTATGCAATCAGAC 1 117 0 GTATATTTAT 0.868942 -154 AAAAGACGCAAATTGTTTATATCATCACGC 1 147 0 AATTGTTTAT 0.736331 -124 TTGGCGTCGGGTTTGTTTCTTAATATGTCA 1 175 1 GTTTGTTTCT 0.896691 -96 TATGTCAAAAGATTGGCTATCGACGAACTG 1 198 1 GATTGGCTAT 0.950934 -73 TATGTTAACGGTGTAGCTATCAGAATACGG 1 240 1 GTGTAGCTAT 0.791342 -31 GTAAAGTTTGGATTATCTCTTTTAAAAAGC 3 75 1 GATTATCTCT 0.921368 -226 CTCTTTTAAAGGATATTTATAGATTTTGTC 3 230 0 GGATATTTAT 0.795496 -71 GATGTTATGTGATTTGTTATTTTTTTGTTA 3 265 0 GATTTGTTAT 0.855364 -36 ********** Masking position 4 Map Score: 2.16852 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 470 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 5 GATCTGATTATTTATGCAATATGCTGTCTG 1 92 1 TTTATGCAAT 0.972707 -179 CTAATGTATATTTATGCAATCAGACAGCAT 1 112 0 TTTATGCAAT 0.972707 -159 ACGCAAATTGTTTATATCATCACGCTTCAG 1 142 0 TTTATATCAT 0.922115 -129 TTTATATGATGTTATGTGATTTGTTATTTT 3 272 0 GTTATGTGAT 0.958449 -29 AAGATACCCTTTATATGATGTTATGTGAT 3 282 0 TTTATATGAT 0.954615 -19 ********** Masking position 5 Map Score: 1.95384 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 59 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 ********** No masking Map Score: -1.48971e-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: -1.48971e-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: -1.48971e-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