AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_protease_clp_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 tig 300 trigger factor; a molecular chaperone involved in cell division #2 clpP 245 ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 #3 clpX 125 ATP-dependent specificity component of clpP serine protease, chaperone #4 lon 187 DNA-binding, ATP-dependent protease La; heat shock K-protein #5 HI0462 192 ATP-dependent proteinase (lon) #6 HI0713 300 trigger factor (tig) #7 HI0714 122 ATP-dependent Clp protease, proteolytic subunit (clpP) Motif number 1 CAAAAAGCGCAAAATCCAGACAAAACAAAACGGCCCGCAG 1 30 0 AATAAAAAAA 0.978392 -271 GGTTCCATGCAAAATTCATGACAAAAAAAAGCCCACCACC 2 59 0 AATAAAAAAA 0.978392 -187 TTCAACGCCGAGAATAGAGGAAAAATTAAAGGGGAGATAA 4 53 0 AATAAATAAA 0.945221 -135 GTGTCATCTGATTACCTGGCGGAAATTAAACTAAGAGAGA 4 153 1 AACAAATAAA 0.87943 -35 TCTGAGTTATAAAGTGGGTTTTAAACAAAAAAGAATTTTG 5 75 0 AGTAAAAAAA 0.860013 -118 ATTTACCCAAATTATCGGAACGAAATTATAAGAGAGACCA 5 160 1 AATAAATATA 0.749667 -33 GATAATAATTATTATACATATTAAATAATTCAATTTATTT 6 31 1 AATAAAAATT 0.67877 -270 TTCAATTTATTTAATCAATATCAAAAAAAAGTATAATAAG 6 59 1 TATAAAAAAA 0.958883 -242 CTAATTGCTTTATATGAGCATAAAAGAAAATCATTTTTGA 6 107 1 TATAAAAAAA 0.958882 -194 ATAATTTTAAAATATGACTTACAAACAAAAGTGCGGTCAA 6 143 0 AATAAAAAAA 0.978392 -158 AAAAAGACGCTCAATTATAACGAAAGAAATCTACGCAGTC 6 213 0 TATAAAAAAT 0.862459 -88 ATCCACACCGAACACGTTTGTTAAATAAAAAGACGCTCAA 6 239 0 AACAAAAAAA 0.950359 -62 GGTGTGGATTTTGACCGAGTGCAAATTAATTGAGGTAACA 6 270 1 TACAAATAAT 0.50257 -31 TAAGTAATATTATTATGATTGAATAAAAGTGCGGTCGC 7 9 1 AATGAAAAAA 0.859991 -114 TATTTTATCGTAAATAACCCACAAATAAAAATGCGATCGC 7 63 0 TATAAAAAAA 0.958883 -60 * ** *** **** Masking position 14 Map Score: 13.6809 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 121 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 2 GATTTTATGAAAAACGGCCTGCGGGCCGTTT 1 12 1 AAAAGGCCTG 0.916195 -289 CAGACAAAACAAAACGGCCCGCAGGCCGTTT 1 23 0 AAAAGGCCCG 0.988274 -278 CATTCAGACGAAAATTGCCCGGGAATTGTGA 1 75 1 AAAATGCCCG 0.977932 -226 GGAATTGTGAAAAAATACGCGACAGCGCGCA 1 96 1 AAAATACGCG 0.949587 -205 AAAGCATTCAAATAGGACGCGGCATTATAGC 1 158 0 AATAGACGCG 0.819887 -143 CTAAATTCGCACAAAGGCCCGTCACCGCCAG 2 29 1 ACAAGGCCCG 0.940731 -217 TTAGTTAACCAAAAAGGGGGGATTTTATCTC 4 29 1 AAAAGGGGGG 0.896953 -159 ACTTACAAACAAAAGTGCGGTCAAAAATGAT 6 136 0 AAAATGCGGT 0.935056 -165 TTTGTTAAATAAAAAGACGCTCAATTATAAC 6 232 0 AAAAGACGCT 0.929391 -69 ATGATTGAATAAAAGTGCGGTCGCTCTTTTT 7 25 1 AAAATGCGGT 0.935056 -98 ACCCACAAATAAAAATGCGATCGCTTTTATT 7 56 0 AAAATGCGAT 0.783729 -67 **** ****** Masking position 4 Map Score: 9.8764 Number of sites scoring better than the average of aligned sites = 1435 Number in coding regions = 1222 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 3 ACGCGACAGCGCGCAATAACCGTTCTCGAC 1 112 1 GCGCAATAAC 0.87756 -189 CGGCATTATAGCGGCATCACTTTTATGAGT 1 140 0 GCGGCATCAC 0.992016 -161 CAAATAGGACGCGGCATTATAGCGGCATCA 1 151 0 GCGGCATTAT 0.912608 -150 TTTACGCAGCATAACGCGCTAAATT 2 6 1 GCAGCATAAC 0.955673 -240 TTCGGTGTTAGCGTAACAACAAAAGATTGT 2 114 1 GCGTAACAAC 0.861607 -132 TGTTATGGGTACGGCATCACCATATTTCAA 2 149 0 ACGGCATCAC 0.924287 -97 GATAAGTATAGCGGCACAGTTGCGCCTCTG 3 14 0 GCGGCACAGT 0.937935 -112 CTTATCCAGGGCGGCACAACGCTGTAAGCG 3 38 1 GCGGCACAAC 0.996465 -88 GTCGTCGTGTGCGGCACAAAGAACAAAGAA 3 93 1 GCGGCACAAA 0.973492 -33 ********** Masking position 6 Map Score: 9.21057 Number of sites scoring better than the average of aligned sites = 1142 Number in coding regions = 1060 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 AGATTTTATGAAAAACGGCCTGC 1 4 1 TTTTATGAAA 0.934511 -297 AACTCAATATTTTGTGAAATTTAATAAAA 5 10 1 TTTTGTGAAA 0.949436 -183 TAATGAAAAATTTTATTAAATTTCACAAAA 5 20 0 TTTTATTAAA 0.797549 -173 CAAAATTCTTTTTTGTTTAAAACCCACTTT 5 75 1 TTTTGTTTAA 0.798223 -118 ATAACTCAGATTTTGTTATAATCTTTTCCT 5 105 1 TTTTGTTATA 0.850002 -88 TTCCTTAATTTTTAATGATAATAATTATTA 6 15 1 TTTAATGATA 0.713568 -286 TATTATACTTTTTTTTGATATTGATTAAAT 6 67 0 TTTTTTGATA 0.657093 -234 TTGAGCGTCTTTTTATTTAACAAACGTGTT 6 239 1 TTTTATTTAA 0.842004 -62 GCGACCGCACTTTTATTCAATCATAATAAT 7 19 0 TTTTATTCAA 0.818339 -104 ATGCGATCGCTTTTATTAAAAAGAGCGACC 7 43 0 TTTTATTAAA 0.797549 -80 AATTAGCAGTTTTAATGAAAAAGGTAAGAA 7 102 1 TTTAATGAAA 0.631347 -21 ********** Masking position 10 Map Score: 9.82158 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 87 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 TTTTGTTTTGTCTGGATTTTGCGCTTTTTGC 1 40 1 TCTGGATTTG 0.878493 -261 GCAATTTTCGTCTGAATGCTGGGCAAAAAGC 1 62 0 TCTGAATGTG 0.913969 -239 CCGCGTCCTATTTGAATGCTTTCGGGATGAT 1 167 1 TTTGAATGTT 0.789717 -134 TTGAATGCTTTCGGGATGATTCTGGTAACAG 1 178 1 TCGGGATGTT 0.944264 -123 TAACAGGGAATGTGATTGATTATAAGAACAT 1 203 1 TGTGATTGTT 0.901471 -98 GACCGAGCACTGTGATTTTTTGAGGTAACAA 1 279 1 TGTGATTTTT 0.796107 -22 ACTAATTGTATGGGAATGGTTAA 4 3 0 TGGGAATGTT 0.953735 -185 CGTCAGTATATGGGGATGTTTCCCCCACATT 4 91 0 TGGGGATGTT 0.970479 -97 ACGTGTTCGGTGTGGATTTTGACCGAGTGCA 6 262 1 TGTGGATTTG 0.933463 -39 CATTTTTATTTGTGGGTTATTTACGATAAAA 7 70 1 TGTGGGTTTT 0.839576 -53 ******** ** Masking position 7 Map Score: 5.59475 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 436 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 CGGTTATTGCGCGCTGTCGCGTATTTTTTC 1 104 0 GCGCTGTCGC 0.973959 -197 AAATCACAGTGCTCGGTCAACTCTTACCCC 1 267 0 GCTCGGTCAA 0.965388 -34 ACAAACAAAAGTGCGGTCAAAAATGATTTT 6 133 0 GTGCGGTCAA 0.980197 -168 AAAGAAATCTACGCAGTCGATAAAAGAGTG 6 201 0 ACGCAGTCGA 0.940537 -100 ATTAATTTGCACTCGGTCAAAATCCACACC 6 270 0 ACTCGGTCAA 0.931057 -31 TTGAATAAAAGTGCGGTCGCTCTTTTTAAT 7 29 1 GTGCGGTCGC 0.991812 -94 ACAAATAAAAATGCGATCGCTTTTATTAAA 7 53 0 ATGCGATCGC 0.885735 -70 ********** Masking position 7 Map Score: 4.44619 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 811 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 GTCGCGTATTTTTTCACAATTCCCGGGCAAT 1 88 0 TTTTCAAATT 0.883875 -213 ACATTCCCTGTTACCAGAATCATCCCGAAAG 1 185 0 TTACCAAATC 0.871597 -116 CCCTTTAATTTTTCCTCTATTCTCGGCGTTG 4 60 1 TTTCCTTATT 0.903436 -128 TTAATAAAATTTTTCATTATTTTAGCCATTA 5 31 1 TTTTCATATT 0.735898 -162 ATCACTTCATTTGCCAAAATTCTTTTTTGTT 5 61 1 TTGCCAAATT 0.937465 -132 ACCCCAATATTTACCCAAATTATCGGAACGA 5 152 1 TTACCCAATT 0.920082 -41 AGGTTTCCTTAATTTTTAATGATA 6 4 1 TTTCCTAATT 0.962344 -297 TTGTTACCTCAATTAATTTGCACT 6 287 0 TTACCTAATT 0.95152 -14 ****** **** Masking position 9 Map Score: 2.13223 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 103 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 CTTGTTACCTCAAAAAATCAC 1 290 0 TTGTTACCTC 0.989153 -11 GCTGTACCGATTGTAACCTTATGGACGGAT 2 195 0 TTGTAACCTT 0.958937 -51 TTGTTACCTCAATTAATTTG 6 291 0 TTGTTACCTC 0.989153 -10 TTTCTTACCTTTTTCATTAAA 7 112 0 TTCTTACCTT 0.956544 -11 ********** Masking position 6 Map Score: 2.0014 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AAACAAAACGGCCCGCAGGCCGTTTTTCAT 1 18 0 GCCCGCAGGC 0.834958 -283 ACCAGAATCATCCCGAAAGCATTCAAATAG 1 174 0 TCCCGAAAGC 0.895985 -127 GTTCCGCGAAGCCAACAACCTGTGCTTGCG 1 238 1 GCCAACAACC 0.92457 -63 TCAACTCTTACCCCGCAAGCACAGGTTGTT 1 251 0 CCCCGCAAGC 0.985004 -50 TCGCACAAAGGCCCGTCACCGCCAGGTGGT 2 35 1 GCCCGTCACC 0.973801 -211 ACAAAAAAAAGCCCACCACCTGGCGGTGAC 2 49 0 GCCCACCACC 0.984972 -197 ********** Masking position 3 Map Score: 1.67947 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 869 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 CAGGCCGTTTTTCATAAAATCT 1 3 0 TTCATAAAAT 0.946962 -298 CCGTTCTCGACTCATAAAAGTGATGCCGCT 1 131 1 CTCATAAAAG 0.876972 -170 AACCGGGATGTTCTTATAATCAATCACATT 1 211 0 TTCTTATAAT 0.747444 -90 CTTGTTACCTCAAAAAATCACAGTGCTC 1 283 0 CTCAAAAAAT 0.753558 -18 TTTATTAAATTTCACAAAATATTGAGTT 5 9 0 TTCACAAAAT 0.910003 -184 TTTGTGAAATTTAATAAAATTTTTCATTAT 5 21 1 TTAATAAAAT 0.854057 -172 AATTGGTCTCTCTTATAATTTCGTTCCGA 5 174 0 CTCTTATAAT 0.709118 -19 TATTTTAAAATTATCAAAATGCAATTTTTA 6 169 1 TTATCAAAAT 0.63482 -132 GTCGCTCTTTTTAATAAAAGCGATCGCATT 7 44 1 TTAATAAAAG 0.740895 -79 ********** Masking position 6 Map Score: 1.62967 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 145 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 11 ********** No masking Map Score: -1.49681e-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 12 TAAAATTGAAAAAACCTGCTGTACCGATTGTA 2 210 0 AAAACTGCGT 0.766054 -36 AAACATCCCCATATACTGACGTACATGTTAAT 4 101 1 ATATATGAGT 0.739361 -87 AAATTTCACAAAATATTGAGTT 5 1 0 AAATATGATT 0.848079 -192 GGGTTTTAAACAAAAAAGAATTTTGGCAAATG 5 68 0 CAAAAAGATT 0.48663 -125 AATCTGAGTTATAAAGTGGGTTTTAAACAAAA 5 85 0 ATAAATGGTT 0.774231 -108 AGATTATAACAAAATCTGAGTTATAAAGTGGG 5 97 0 AAAATTGATT 0.795776 -96 TAATTTGGGTAAATATTGGGGTAGGGAAAAAG 5 142 0 AAATATGGGT 0.744753 -51 TATTGATTAAATAAATTGAATTATTTAATATG 6 47 0 ATAAATGATT 0.888585 -254 AAAGTGCGGTCAAAAATGATTTTCTTTTATGC 6 124 0 CAAAATGATT 0.905927 -177 GACTTACAAACAAAAGTGCGGTCAAAAATGAT 6 136 0 CAAAATGCGT 0.905921 -165 TGATAATTTTAAAATATGACTTACAAACAAAA 6 153 0 AAAATTGATT 0.795768 -148 AAGAGTGATTAAAAATTGCATTTTGATAATTT 6 176 0 AAAAATGCTT 0.940101 -125 CCGAGTGCAAATTAATTGAGGTAACAA 6 284 1 ATTAATGAGT 0.488228 -17 TATGATTGAATAAAAGTGCGGTCGCTCTTTTT 7 24 1 TAAAATGCGT 0.707913 -99 ***** *** ** Masking position 12 Map Score: 3.46137 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 477 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 13 ********** No masking Map Score: -1.49681e-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 14 ********** No masking Map Score: -1.49681e-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 15 ********** No masking Map Score: -1.49681e-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