AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i024_Formate_Dehydrogenase_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 fdoG 193 formate dehydrogenase-O, major subunit #2 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #3 HI0009 69 fdhE protein (fdhE) Motif number 1 ACACCAACATTATGGTATTCTGTTACAAAC 1 37 1 TATGGTATTC 0.937397 -157 AGCGGCAGAAAAAGGCATCCAAAAAGGCGA 2 21 1 AAAGGCATCC 0.943263 -280 CTTTAAGACGTTTTGTAACCACGGCGACCG 2 89 0 TTTTGTAACC 0.718102 -212 CGTACACCATATAGGTCTTCCAATTCACTG 2 141 1 ATAGGTCTTC 0.896501 -160 CTTTGCCATTTAATGCCTTCATATTCCAGT 2 167 0 TAATGCCTTC 0.891433 -134 ATTAAATGGCAAAGGTAACCGTGGATTCTC 2 183 1 AAAGGTAACC 0.880276 -118 AAGATGGTGTTAAGGTATTCGTAGAGAATC 2 206 0 TAAGGTATTC 0.970525 -95 CATCTTGGGGTGAGGCAATCACGCAAACAC 2 230 1 TGAGGCAATC 0.852293 -71 ACCAAGAATGTTTTGTATTCTGGTGTTTGC 2 252 0 TTTTGTATTC 0.838515 -49 ATTATGCCTCCCCAACTTTTT 2 290 0 TTATGCCTCC 0.905057 -11 ********** Masking position 10 Map Score: 6.87753 Number of sites scoring better than the average of aligned sites = 830 Number in coding regions = 656 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 2 CCAGATAAGAACACACACACCAACATTATGGT 1 21 1 ACCCACACCA 0.996407 -173 GTATTCTGTTACAAACCCTTCCTGGATGGAGG 1 51 1 ACACCCTTCC 0.900457 -143 GAATTGGCTCAATTTCCCTCCATCCAGGAAGG 1 67 0 AATCCCTCCA 0.918508 -127 AAGAAAAATAACTCCCACTCCCTGCACACGCA 1 123 1 ACCCACTCCC 0.99307 -71 ATGGTGTACGACACGCCCATCAATTTCGAGAT 2 119 0 ACCCCCATCA 0.989171 -182 CTCTACGAATACCTTAACACCATCTTGGGGTG 2 210 1 ACTAACACCA 0.962349 -91 TGAGGCAATCACGCAAACACCAGAATACAAAA 2 240 1 ACCAACACCA 0.986953 -61 ** * ******* Masking position 1 Map Score: 5.45098 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 444 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 GTAAATATTGAAAAAGTTGGGGAGGCATAA 2 280 1 AAAAAGTTGG 0.969455 -21 CCTGAAAAAGAAAAAGTGCGGTTAAAATTG 3 19 1 AAAAAGTGCG 0.99571 -51 CTTTTATAATAAAAAGTGCGGTCAATTTTA 3 41 0 AAAAAGTGCG 0.99571 -29 CTTTTTATTATAAAAGTGAGAGAAT 3 55 1 TAAAAGTGAG 0.971163 -15 ********** Masking position 5 Map Score: 4.47067 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 50 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 ACACACACCAACATTATGGTATTCTGTTACAAA 1 33 1 ACAATGGTTT 0.955472 -161 TTCCCTCCATCCAGGAAGGGTTTGTAACAGAAT 1 53 0 CCAAAGGGTT 0.994431 -141 CCGCAAAGGTCCAGAATTGGCTCAATTTCCCTC 1 79 0 CCAATTGGTC 0.920077 -115 AAAAAGGCATCCAAAAAGGCGATATGGTAAAAA 2 29 1 CCAAAGGCAT 0.952709 -272 GTGTCGTACACCATATAGGTCTTCCAATTCACT 2 137 1 CCATAGGTTT 0.978128 -164 TTGCCTCACCCCAAGATGGTGTTAAGGTATTCG 2 215 0 CCAATGGTTT 0.993991 -86 TCAATATTTACCAAGAATGTTTTGTATTCTGGT 2 258 0 CCAAATGTTT 0.983257 -43 *** ***** ** Masking position 3 Map Score: 5.15898 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 275 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 ACCATAATGTTGGTGTGTGTGTTCTTATCTG 1 22 0 TGTGTGTGTG 0.98768 -172 TGGGAGTTATTTTTCTTTGCGGAAGGGGCCG 1 109 0 TTTCTTTGCG 0.902702 -85 TACATTCGCTTGCTGCGTGTGCAGGGAGTGG 1 137 0 TGTGCGTGTG 0.988576 -57 GGATTGCTCCTTGTTTCGACATTGT 1 179 0 TGTCCTTGTT 0.87619 -15 TAAAAATTACTTCTCGTCGTGGCTATATTAA 2 56 1 TTTCGTCGTG 0.909218 -245 ATCTCGAAATTGATGGGCGTGTCGTACACCA 2 119 1 TGTGGGCGTG 0.983118 -182 TTTTGTATTCTGGTGTTTGCGTGATTGCCTC 2 241 0 TGTGTTTGCG 0.978104 -60 ** ******** Masking position 4 Map Score: 3.67909 Number of sites scoring better than the average of aligned sites = 1046 Number in coding regions = 1007 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 TTTGCGGAAGGGGCCGCAAAGGTCCAGAAT 1 95 0 GGGCCGCAAA 0.987097 -99 TTTGCGGCCCCTTCCGCAAAGAAAAATAAC 1 105 1 CTTCCGCAAA 0.95696 -89 ATGCCTTTTTCTGCCGCTAATTTTTCGC 2 9 0 CTGCCGCTAA 0.991455 -292 AAAAGAAAAAGTGCGGTTAAAATTGACCGC 3 24 1 GTGCGGTTAA 0.981057 -46 ATAATAAAAAGTGCGGTCAATTTTAACCGC 3 36 0 GTGCGGTCAA 0.977506 -34 ********** Masking position 9 Map Score: 2.46868 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 418 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 ********** No masking Map Score: 1.4022e-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 CCTCCATCCAGGAAGGGTTTGTAACAGAATA 1 52 0 GGAAGGGTTG 0.976818 -142 TTTTCTTTGCGGAAGGGGCCGCAAAGGTCCA 1 99 0 GGAAGGGGCG 0.99508 -95 TTGCTGCGTGTGCAGGGAGTGGGAGTTATTT 1 128 0 TGCAGGGATG 0.949849 -66 TGCACACGCAGCAAGCGAATGTAAATGGGAC 1 145 1 GCAAGCGATG 0.899072 -49 CAAGCGAATGTAAATGGGACGTGACAATGTC 1 156 1 TAAATGGGCG 0.880102 -38 GTGGCTATATTAAAGCGGTCGCCGTGGTTAC 2 74 1 TAAAGCGGCG 0.959804 -227 ATCTCGAAATTGATGGGCGTGTCGTACACCA 2 119 1 TGATGGGCTG 0.914827 -182 ******** ** Masking position 7 Map Score: 0.321904 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 830 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 ********** No masking Map Score: 1.4022e-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: 1.4022e-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: 1.4022e-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