AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i262_3_5_1_28_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 b2817 141 putative amidase #2 HI0063 247 poly(A) polymerase (pcnB) #3 HI0065 75 conserved hypothetical protein Motif number 1 CATTACTGATAAAAAAGTCGCTCTCGCATA 1 87 0 AAAAAAGTCG 0.92476 -55 TGAAAAATACAAAAGTGCGGTTAAAATTAA 2 21 1 AAAAGTGCGG 0.998878 -227 TTAAATGCAAAAAAGTGCGGTTAATTTTAA 2 41 0 AAAAGTGCGG 0.998878 -207 TTTTGCATTTAAAAATGCAGGAAAATCCAC 2 59 1 AAAAATGCAG 0.981757 -189 TCTTTACAAGAAAAGAGCCAAGTCATTTAT 2 98 1 AAAAGAGCCA 0.938843 -150 TGAGGTTCATAAAAGTGCGGTGAAATTT 3 9 0 AAAAGTGCGG 0.998878 -67 TATGAACCTCAAAAGTGCGGTAGAATCAGC 3 28 1 AAAAGTGCGG 0.998878 -48 ATGAATGAAGAAAAATGTGGGCTGATTCTA 3 48 0 AAAAATGTGG 0.987587 -28 ********** Masking position 4 Map Score: 23.599 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 294 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 TTTATCAGTAATGCCGTGAATATAAAAAGA 1 104 1 ATGCCGTGAA 0.975634 -38 AAATACAAAAGTGCGGTTAAAATTAACCGC 2 25 1 GTGCGGTTAA 0.997902 -223 ATGCAAAAAAGTGCGGTTAATTTTAACCGC 2 37 0 GTGCGGTTAA 0.997902 -211 GTTCATAAAAGTGCGGTGAAATTT 3 5 0 GTGCGGTGAA 0.998643 -71 AACCTCAAAAGTGCGGTAGAATCAGCCCAC 3 32 1 GTGCGGTAGA 0.991839 -44 ********** Masking position 7 Map Score: 11.6988 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 65 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 GCGAAAAAACAGAATAAAAATACACTAATT 1 38 0 AGAATAAAAA 0.96453 -104 TAATGCCGTGAATATAAAAAGAATGTTTAC 1 112 1 AATATAAAAA 0.912416 -30 ATTCTATTGAAAAATACAAAAGTGCGGTTA 2 14 1 AAAATACAAA 0.94157 -234 CTGCATTTTTAAATGCAAAAAAGTGCGGTT 2 49 0 AAATGCAAAA 0.846597 -199 TCTTTTCTTGTAAAGAAAAAGGCAAGTGGA 2 84 0 TAAAGAAAAA 0.957014 -164 TATTCTTACTTATATCAAAAATTTGTTTGG 2 152 1 TATATCAAAA 0.818369 -96 TTGTTTGGCAAGAAGACAAAAAAATCAAAA 2 174 1 AGAAGACAAA 0.94479 -74 AGAAGACAAAAAAATCAAAAGAGGTTGCCA 2 184 1 AAAATCAAAA 0.96453 -64 GGGTCATGAATGAAGAAAAATGTGGGCTGA 3 53 0 TGAAGAAAAA 0.948357 -23 ********** Masking position 8 Map Score: 10.0656 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 440 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 4 CTTTGCATGATTATTCGAAATTAGTGTATTTTT 1 20 1 TTTTCAAATA 0.95145 -122 TACACTTGCACCCTGCGAAAAAACAGAATAAAA 1 49 0 CCTGCAAAAA 0.957622 -93 TTCATTCTATTGAAAAATACAAAAGTGCG 2 7 1 CTTTGAAATA 0.9189 -241 CTTGGCTCTTTTCTTGTAAAGAAAAAGGCAAGT 2 87 0 TTTTGAAAAA 0.902836 -161 CTCCGTTTTGTTGTTGGAAATAAATGACTTGGC 2 114 0 TTTTGAAAAA 0.902836 -134 TTTTTTGTCTTCTTGCCAAACAAATTTTTGATA 2 164 0 TCTGCAAAAA 0.969653 -84 AAACAAGTGCTCATTCTAAACGAGTTGAGCGTT 2 214 1 TCTTCAAAGA 0.91939 -34 ** *** *** ** Masking position 8 Map Score: 3.27002 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 65 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 ACACCTCTTTGCATGATTATTCGAAATTAG 1 14 1 GCATGATTAT 0.88938 -128 TTCGCAGGGTGCAAGTGTAAATTTTATGCG 1 63 1 GCAAGTGTAA 0.941797 -79 AATATAAAAAGAATGTTTACCGTTTATTAG 1 122 1 GAATGTTTAC 0.845173 -20 AAAGAAAAAGGCAAGTGGATTTTCCTGCAT 2 73 0 GCAAGTGGAT 0.93168 -175 TTTGATATAAGTAAGAATAATTTACTCCGT 2 141 0 GTAAGAATAA 0.759731 -107 AATTTGTTTGGCAAGAAGACAAAAAAATCA 2 171 1 GCAAGAAGAC 0.969079 -77 AACTCGTTTAGAATGAGCACTTGTTTTGGC 2 210 0 GAATGAGCAC 0.89902 -38 AACGGGTCATGAATGAAGAAAAATGTGGGC 3 56 0 GAATGAAGAA 0.906125 -20 ********** Masking position 3 Map Score: 1.48044 Number of sites scoring better than the average of aligned sites = 964 Number in coding regions = 840 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 ********** No masking Map Score: -8.28903e-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 7 ********** No masking Map Score: -8.28903e-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 8 ********** No masking Map Score: -8.28903e-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