AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i235_sensory_cassete1_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 ygiX 151 putative 2-component transcriptional regulator #2 HI1708 62 transcriptional regulatory protein (ygiX) #3 HI1709 114 conserved hypothetical protein #4 HI1710 254 H. influenzae predicted coding region HI1710 #5 HI1711 59 PTS system, glucose-specific IIA component (crr) #6 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #7 HI1713 158 phosphocarrier protein HPr (ptsH) #8 HI1714 70 conserved hypothetical protein Motif number 1 ACAGCACTAAATTTTATTTTTTTCCCTTAAGA 1 70 0 ATTTTTTTTT 0.959675 -82 TAGCTCGCTGTTTTTGTTTATAAAGTGCGGTC 2 33 1 TTTTTTTATA 0.700809 -30 TTTTATTAAGATTTATTTGTTTTAATACACAC 3 46 1 ATTTATTTTT 0.817048 -69 TTCCTTTTTAAGTTAGTTAATTTCAAGCTCCA 3 88 0 AGTTATTATT 0.813937 -27 TTGTGCGGATTTTTTATTTATTATAGTTACCT 4 38 1 TTTTTTTATT 0.959675 -217 AAATACTCGCACTTTGTGCTTTTAAATGATGT 4 225 0 ACTTTTGTTT 0.807816 -30 TTATGGCTATTGTTTATTTATTACTTTGTTAA 6 40 1 TGTTTTTATT 0.930093 -40 TTTATTTATTACTTTGTTAATTGTTTCGGAAG 6 52 1 ACTTTTTATT 0.941224 -28 TAAGCTAAATAGTTTATTTATTATTCACAATC 7 18 0 AGTTTTTATT 0.95889 -141 ATTTAGCTTATTTTTATGATTTAATTCAGGCT 7 40 1 TTTTTTGTTT 0.862002 -119 TTTTTAGTGTTTATTCTTGATTATTTTGCTTT 7 71 1 TTATTTTATT 0.817048 -88 TACTAGGGCAATTTTCTGGTTTTATATTTTTA 7 112 1 ATTTTTGTTT 0.916332 -47 TTCTGGTTTTATATTTTTAATTATTGATTAGT 7 125 1 ATATTTTATT 0.886749 -34 CTATGCAAAAATTTTTTTCATTTTACCAAAAA 8 24 1 ATTTTTTATT 0.976595 -47 ***** ** *** Masking position 7 Map Score: 14.6621 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 350 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 2 ACGCGCTCTGTACAGCACTAAATTTTATTTTTTTCC 1 77 0 TAAGCCATTT 0.845204 -75 AAATGCGAGCATTAGCTCGCTGTTTTTGTTTATAAA 2 21 1 ATAGCCCTTT 0.929424 -42 TTTGTTTATAAAGTGCGGTCAATTTTTT 2 45 1 AATGCGCTTT 0.908674 -18 ATAAAAGATTAAGAGGACTATACTTTTTTGAAAAGA 3 16 0 AAAGGCATTT 0.871444 -99 AAAATCCGCACAAAGGCGGACTTTTTTTACCGTAAA 4 15 0 CAAGGGATTT 0.839064 -240 AGGCTAATTTAAGTGCTACCCCGTTGGGGTAGTTTG 4 86 1 AATGCACTTG 0.863373 -169 GAATATTTTGCAAAGCGAAATCTTTTGCTGACGTGG 4 170 0 CAAGCAATTT 0.963553 -85 TTTAAAAGCACAAAGTGCGAGTATTTTATTAGTA 4 231 1 CAAGTCATTT 0.6682 -24 TTTACGTTAAAATAGCAACCATCTTGAATGGATAGG 5 26 1 AAAGCACTTG 0.939401 -34 TTCTTACTTAGCCATAAAATTGTGAAATTTTA 6 7 1 CTAGCAATTG 0.87894 -73 ATAAATAAACAATAGCCATAAAATTTCACAATTTTA 6 25 0 AAAGCAATTT 0.973699 -55 AATCATAAAAATAAGCTAAATAGTTTATTTATTATT 7 25 0 ATAGCAATTT 0.93933 -134 ATCAGGTATCCTATGCAAAAATTTTTTTCATTTTAC 8 14 1 CTTGCAATTT 0.868341 -57 AAAAGTGCGGTCGTTTTTTCCCTTGTTT 8 53 0 AATGCGCTTT 0.900604 -18 ** *** * * *** Masking position 14 Map Score: 9.72605 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 817 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 AGCGAGCTAATGCTCGCATTTTCAGAAATGA 2 10 0 TGCGCATTTT 0.98978 -53 AAAAAATTGACCGCACTTTATAAACAAAA 2 44 0 TGCGCACTTT 0.996518 -19 AATCCGCACAAAGGCGGACTTTTTTTACCGTA 4 17 0 AACGGACTTT 0.93891 -238 AGTCCGCCTTTGTGCGGATTTTTTATTTATTA 4 29 1 TGCGGATTTT 0.980628 -226 ACTAATAAAATACTCGCACTTTGTGCTTTTAA 4 232 0 TACGCACTTT 0.989776 -23 AGGGAAAAAACGACCGCACTTTT 8 58 1 CGCGCACTTT 0.99231 -13 ** ******** Masking position 8 Map Score: 6.76252 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 55 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 CATTAAAGGGAGTAATAAAC 1 1 0 AGTAATAAAC 0.897255 -151 GCTCGGAAACAGACATTAAAGGGAGTAATA 1 14 0 AGACATTAAA 0.669571 -138 TCTGTTTCCGAGCATTTAACAAGATAGTCC 1 31 1 AGCATTTAAC 0.724163 -121 TTAACAAGATAGTCCTTAACAACTTCTTAA 1 46 1 AGTCCTTAAC 0.863374 -106 CGCTCTGTACAGCACTAAATTTTATTTTTT 1 80 0 AGCACTAAAT 0.842843 -72 CCAACGGGGTAGCACTTAAATTAGCCTAGG 4 83 0 AGCACTTAAA 0.936101 -172 TTCTTACTTAGCCATAAAATTGTGAAATT 6 10 1 AGCCATAAAA 0.954591 -70 AATAAACAATAGCCATAAAATTTCACAATT 6 28 0 AGCCATAAAA 0.954591 -52 CAATTAACAAAGTAATAAATAAACAATAGC 6 45 0 AGTAATAAAT 0.746857 -35 TACCTTCCGAAACAATTAACAAAGTAATAA 6 57 0 AACAATTAAC 0.8272 -23 GCCTGAATTAAATCATAAAAATAAGCTAAA 7 41 0 AATCATAAAA 0.732274 -118 ATCAAGAATAAACACTAAAAAGCCTGAATT 7 62 0 AACACTAAAA 0.829884 -97 TCGACTAATCAATAATTAAAAATATAAAAC 7 130 0 AATAATTAAA 0.6985 -29 ********** Masking position 8 Map Score: 11.4089 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 820 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 5 GACTATACTTTTTTGAAAAGACTTTA 3 7 0 TTTTGAAAAG 0.883083 -108 ATATTGAATATTTTGCAAAGCGAAATCTTT 4 181 0 TTTTGCAAAG 0.759538 -74 CCTAGTATCCTTTTTCAAAGCAAAATAATC 7 89 0 TTTTTCAAAG 0.883083 -70 TGAAAAAAATTTTTGCATAGGATACCTGAT 8 14 0 TTTTGCATAG 0.952313 -57 ********** Masking position 4 Map Score: 3.64016 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 13 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTAACAACTTCTTAAGGGAAAAAAATAAAAT 1 61 1 CTTAGGGAAA 0.954858 -91 TTTGTTTACGGTAAAAAAAGTCCGC 4 5 1 TTTAGGTAAA 0.650787 -250 ATTATAGTTACCTAGGGTAAGTATACCCTAG 4 57 1 CCTAGGTAAG 0.948062 -198 CTTAAATTAGCCTAGGGTATACTTACCCTAG 4 68 0 CCTAGGTATA 0.925539 -187 CGTAAGTATACCTACGGTTAATTATAGTCGT 4 139 0 CCTAGGTTAA 0.9617 -116 ATTATTTGATTTTACGTTAAAATAGCAACCA 5 16 1 TTTAGTTAAA 0.569852 -44 ATTTCACAATTTTATGGCTAAGTAAGAA 6 8 0 TTTAGGCTAA 0.834033 -72 TTTTCCCTTGTTTTTGGTAAAATGAAAAAAA 8 35 0 TTTTGGTAAA 0.887659 -36 **** ****** Masking position 3 Map Score: 2.6631 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 163 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TCTTTTCAAAAAAGTATAGTCCTCTTAATC 3 16 1 AAAGTATAGT 0.827607 -99 ACTAACTTAAAAAGGAAACGTT 3 103 1 AAAGGAAACG 0.872233 -12 TTACCTAGGGTAAGTATACCCTAGGCTAAT 4 64 1 TAAGTATACC 0.961954 -191 TGACGTGGCGTAAGTATACCTACGGTTAAT 4 148 0 TAAGTATACC 0.961954 -107 TTGCTTTGAAAAAGGATACTAGGGCAATTT 7 96 1 AAAGGATACT 0.970521 -63 AAATTTTTGCATAGGATACCTGATATT 8 8 0 ATAGGATACC 0.948187 -63 ********** Masking position 6 Map Score: 1.63237 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 82 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: -1.02785e-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: -1.02785e-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: -1.02785e-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