AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i337_weak_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 yjjK 183 putative ATP-binding component of a transport system #2 HI1252 162 ABC transporter, ATP-binding protein #3 HI1603 207 conserved hypothetical protein #4 HI1604 24 phosphate permease, putative #5 HI1605 65 conserved hypothetical protein Motif number 1 TACGCCACGTTACGGACACTTTTTTACTTTTACTG 1 63 1 TCACCTTTTT 0.937914 -121 AGTGGTTAGGTTTCGCCAAACTTTTGCAAAATCTG 2 67 1 TTCCAATTTT 0.990883 -96 TCTGTCCACTTGTTTCCTATATTTTCGCCCTATTT 2 98 1 TTCCATTTTT 0.982762 -65 TAAACCTTTTTTCTTACAAATTTTTTTGAAAAATT 3 114 1 TCACAATTTT 0.967085 -94 TTCGTGCGCATATTACCCGATTTTTGTTGATAGTT 3 151 0 TTCCGATTTT 0.975454 -57 TCGGGTAATATGCGCACGAATTTTTAACCCCTTAA 3 166 1 TCACAATTTT 0.967085 -42 AGTTTATTTCCTATGTTTTGTTGA 4 6 0 TTCCATTTTT 0.982762 -19 TGCGGTTAAAATTAACCGCACTTTTTATTGAGATC 5 13 0 ATCCCATTTT 0.9438 -53 TGCGGTTAATTTTAACCGCACTTTTGTTGTGATGT 5 28 1 TTCCCATTTT 0.9907 -38 * * ** ** **** Masking position 12 Map Score: 12.2438 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 156 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 2 AAAGGCTACACTTCGCCTTTGAAAACTCAT 1 133 1 CTTCGCCTTT 0.98409 -51 GTTGGACTTCGCCTCTATGTTTATCG 1 168 0 CTTCGCCTCT 0.950081 -16 TTAGGGAATACTTCACTCTAAATATTTACA 2 37 1 CTTCACTCTA 0.808386 -126 AGTGGTTAGGTTTCGCCAAACTTTTGCAAA 2 67 1 TTTCGCCAAA 0.912146 -96 TTTCCTATATTTTCGCCCTATTTTCCAGTA 2 110 1 TTTCGCCCTA 0.991794 -53 TCACAAAAAAATTCGCCCTATTCTACTGGA 2 133 0 ATTCGCCCTA 0.973518 -30 TCAATACACTTTTCGCTTTAAAAGCGAGAA 3 29 0 TTTCGCTTTA 0.960468 -179 AAAGGTTTATCTTCGACTAAGTAAGCAACT 3 93 0 CTTCGACTAA 0.875388 -115 TTTTTCCCCTTAAACATCACAA 5 54 0 TTTCCCCTTA 0.953324 -12 ********** Masking position 3 Map Score: 10.2042 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 865 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 AAACGGCAATGACTGGTTAGCATAAATCTA 1 34 0 GACTGGTTAG 0.904431 -150 TGTCCGTAACGTGGCGTAAACGGCAATGAC 1 51 0 GTGGCGTAAA 0.904431 -133 AAATATTTACAAGTGGTTAGGTTTCGCCAA 2 56 1 AAGTGGTTAG 0.957175 -107 ATATTTCCTAGTGTGGTAAGATAAGTAACT 3 58 0 GTGTGGTAAG 0.97271 -150 ACTCCAAATTAAGGGGTTAAAAATTCGTGC 3 179 0 AAGGGGTTAA 0.972867 -29 TCAATAAAAAGTGCGGTTAATTTTAACCGC 5 17 1 GTGCGGTTAA 0.984369 -49 CACAACAAAAGTGCGGTTAAAATTAACCGC 5 29 0 GTGCGGTTAA 0.984369 -37 TGTGATGTTTAAGGGGAAAAA 5 55 1 AAGGGGAAAA 0.800217 -11 ********** Masking position 9 Map Score: 6.07466 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 701 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 4 CTTTTTTACTTTTACTGCGAGGGTGATCGAC 1 81 1 TTTACTGGAG 0.974693 -103 CGCCTCTATGTTTATCGTGATAATGAGTTTT 1 154 0 TTTATCGGAT 0.960794 -30 TAGGGCGAATTTTTTTGTGAGGAATTATTA 2 143 1 TTTTTTGGAG 0.976586 -20 TTACCCGATTTTTGTTGATAGTTAAAATTTT 3 143 0 TTTGTTGTAG 0.946236 -65 AACCGCACTTTTTATTGAGATCAA 5 4 0 TTTATTGGAT 0.985299 -62 TAACCGCACTTTTGTTGTGATGTTTAAGGGG 5 40 1 TTTGTTGGAT 0.986367 -26 ******* *** Masking position 3 Map Score: 5.4141 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 65 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 GTTACGGACACTTTTTTACTTTTACTGCGA 1 71 1 CTTTTTTACT 0.825954 -113 CGAAGTGTAGCCTTTTTCCCCGCCTAATCC 1 118 0 CCTTTTTCCC 0.96919 -66 AATCTGTCCACTTGTTTCCTATATTTTCGC 2 96 1 CTTGTTTCCT 0.942797 -67 ATATTTTCGCCCTATTTTCCAGTAGAATAG 2 116 1 CCTATTTTCC 0.927018 -47 TTTTTTACCTTTCAAATTTT 3 1 1 TTTTTTACCT 0.666961 -207 TTTTACCTTTCAAATTTTCTCGCTTTTAAA 3 13 1 CAAATTTTCT 0.61485 -195 GCAACTGGGTAATATTTCCTAGTGTGGTAA 3 69 0 AATATTTCCT 0.794478 -139 CGAAGATAAACCTTTTTTCTTACAAATTTT 3 108 1 CCTTTTTTCT 0.935401 -100 AATTCGTGCGCATATTACCCGATTTTTGTT 3 158 0 CATATTACCC 0.872634 -50 AGTTTATTTCCTATGTTTTGTT 4 13 0 TTTATTTCCT 0.898743 -12 ********** Masking position 5 Map Score: 5.05097 Number of sites scoring better than the average of aligned sites = 950 Number in coding regions = 742 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 6 CGTGATAATGAGTTTTCAAAGGCGAAGTGT 1 140 0 AGTTTTCAAA 0.979204 -44 AAGTGGACAGATTTTGCAAAAGTTTGGCGA 2 79 0 ATTTTGCAAA 0.970461 -84 TTTTTTACCTTTCAAATTTTCTCGCT 3 7 1 ACCTTTCAAA 0.965059 -201 GATAGTTAAAATTTTTCAAAAAAATTTGTA 3 128 0 ATTTTTCAAA 0.982456 -80 ********** Masking position 5 Map Score: 1.52672 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 33 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 CAGCGTCATGCCGCGTAATAGATTTATGCT 1 16 1 CCGCGTAATA 0.89816 -168 GCCTTTTTCCCCGCCTAATCCCAGCCGGTC 1 109 0 CCGCCTAATC 0.989466 -75 CCTATATTTTCGCCCTATTTTCCAGTAGAA 2 113 1 CGCCCTATTT 0.957162 -50 CAAAAAAATTCGCCCTATTCTACTGGAAAA 2 130 0 CGCCCTATTC 0.980523 -33 GAATTTTTAACCCCTTAATTTGGAGTAAAT 3 183 1 CCCCTTAATT 0.972528 -25 TTTTTCCCCTTAAACATCACAACAA 5 51 0 CCCCTTAAAC 0.951638 -15 ********** Masking position 6 Map Score: 3.39252 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 116 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 8 ********** No masking Map Score: -9.70439e-14 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: -9.70439e-14 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: -9.70439e-14 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