AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_protease_clp_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 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 CTGCGGGCCGTTTTGTTTTGTCTGGATTTTGCGCTTTTTG 1 30 1 TTTTTTTATT 0.971801 -271 GGTGGTGGGCTTTTTTTTGTCATGAATTTTGCATGGAACC 2 59 1 TTTTTTTATT 0.971801 -187 TTATCTCCCCTTTAATTTTTCCTCTATTCTCGGCGTTGAA 4 53 1 TTTATTTATT 0.929242 -135 TCTCTCTTAGTTTAATTTCCGCCAGGTAATCAGATGACAC 4 153 0 TTTATTTGTT 0.847371 -35 CAAAATTCTTTTTTGTTTAAAACCCACTTTATAACTCAGA 5 75 1 TTTTTTTACT 0.823813 -118 TGGTCTCTCTTATAATTTCGTTCCGATAATTTGGGTAAAT 5 160 0 TATATTTATT 0.695049 -33 AAATAAATTGAATTATTTAATATGTATAATAATTATTATC 6 31 0 AATTTTTATT 0.616595 -270 CTTATTATACTTTTTTTTGATATTGATTAAATAAATTGAA 6 59 0 TTTTTTTATA 0.946664 -242 TCAAAAATGATTTTCTTTTATGCTCATATAAAGCAATTAG 6 107 0 TTTTTTTATA 0.946664 -194 TTGACCGCACTTTTGTTTGTAAGTCATATTTTAAAATTAT 6 143 1 TTTTTTTATT 0.971801 -158 GACTGCGTAGATTTCTTTCGTTATAATTGAGCGTCTTTTT 6 213 1 ATTTTTTATA 0.826763 -88 TTGAGCGTCTTTTTATTTAACAAACGTGTTCGGTGTGGAT 6 239 1 TTTTTTTGTT 0.935777 -62 TGTTACCTCAATTAATTTGCACTCGGTCAAAATCCACACC 6 270 0 ATTATTTGTA 0.434694 -31 GCGACCGCACTTTTATTCAATCATAATAATATTACTTA 7 9 0 TTTTTTCATT 0.823796 -114 GCGATCGCATTTTTATTTGTGGGTTATTTACGATAAAATA 7 63 1 TTTTTTTATA 0.946664 -60 **** *** ** * Masking position 7 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 TCTGGATTTTGCGCTTTTTGCCCAGCATTC 1 50 1 GCGCTTTTTG 0.895149 -251 TATAGCGGCATCACTTTTATGAGTCGAGAA 1 134 0 TCACTTTTAT 0.957106 -167 GCCAGGTGGTGGGCTTTTTTTTGTCATGAA 2 55 1 GGGCTTTTTT 0.723732 -191 GCAGGTTTTTTCAATTTTATCCAGGAGACG 2 223 1 TCAATTTTAT 0.615535 -23 AGAGCTCTCTCTTAGTTTAATTTCC 4 173 0 TCTCTCTTAG 0.734575 -15 AATTGGTCTCTCTTATAATTTCGTTC 5 177 0 TCTCTCTTAT 0.888709 -16 ATTTTTGACCGCACTTTTGTTTGTAAGTCA 6 139 1 GCACTTTTGT 0.849583 -162 CAATTTTTAATCACTCTTTTATCGACTGCG 6 190 1 TCACTCTTTT 0.939199 -111 AAGAGCGACCGCACTTTTATTCAATCATAA 7 23 0 GCACTTTTAT 0.948337 -100 AAAAGTGCGGTCGCTCTTTTTAATAAAAGC 7 35 1 TCGCTCTTTT 0.960989 -88 AAAAATGCGATCGCTTTTATTAAAAAGAGC 7 47 0 TCGCTTTTAT 0.972665 -76 ATAAAAGCGATCGCATTTTTATTTGTGGGT 7 57 1 TCGCATTTTT 0.776202 -66 ********** Masking position 7 Map Score: 9.27498 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 465 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 GTCGAGAACGGTTATTGCGCGCTGTCGCGT 1 112 0 GTTATTGCGC 0.88104 -189 ACTCATAAAAGTGATGCCGCTATAATGCCG 1 140 1 GTGATGCCGC 0.99227 -161 TGATGCCGCTATAATGCCGCGTCCTATTTG 1 151 1 ATAATGCCGC 0.915188 -150 AATTTAGCGCGTTATGCTGCGTAAA 2 6 0 GTTATGCTGC 0.957041 -240 ACAATCTTTTGTTGTTACGCTAACACCGAA 2 114 0 GTTGTTACGC 0.865471 -132 TTGAAATATGGTGATGCCGTACCCATAACA 2 149 1 GTGATGCCGT 0.92655 -97 CAGAGGCGCAACTGTGCCGCTATACTTATC 3 14 1 ACTGTGCCGC 0.939813 -112 CGCTTACAGCGTTGTGCCGCCCTGGATAAG 3 38 0 GTTGTGCCGC 0.996577 -88 TTCTTTGTTCTTTGTGCCGCACACGACGAC 3 93 0 TTTGTGCCGC 0.974325 -33 ********** Masking position 5 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 GCAGGCCGTTTTTCATAAAATCT 1 2 0 TTTATAAATC 0.820516 -299 TGTCGCGTATTTTTTCACAATTCCCGGGCAAT 1 88 0 TTTTCAAATT 0.871252 -213 CACATTCCCTGTTACCAGAATCATCCCGAAAG 1 185 0 GTTCCAAATC 0.957118 -116 GAACCGGGATGTTCTTATAATCAATCACATTC 1 210 0 GTTTTAAATC 0.89152 -91 GGTACAGCAGGTTTTTTCAATTTTATCCAGGA 2 217 1 GTTTTTAATT 0.837591 -29 TTTTGTGAAATTTAATAAAATTTTTCATTATT 5 20 1 TTTATAAATT 0.817731 -173 TATCACTTCATTTGCCAAAATTCTTTTTTGTT 5 60 1 TTTCCAAATT 0.940678 -133 TAACTCAGATTTTGTTATAATCTTTTCCTTGA 5 106 1 TTTTTAAATC 0.856171 -87 GTTATAATCTTTTCCTTGAATTCCTTTTTCCC 5 119 1 TTTCTTAATT 0.897405 -74 TTATAATTTCGTTCCGATAATTTGGGTAAATA 5 159 0 GTTCGAAATT 0.833977 -34 AGGTTTCCTTAATTTTTAATGATA 6 3 1 GTTCCTAATT 0.933329 -298 TTGTTACCTCAATTAATTTGCACT 6 287 0 GTTCCTAATT 0.933329 -14 GCGACCGCACTTTTATTCAATCATAATAATAT 7 17 0 TTTATTAATC 0.744977 -106 *** *** **** Masking position 9 Map Score: 8.7804 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 194 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 AAACGGCCCGCAGGCCGTTTTTCATAAAATC 1 12 0 CAGGCCTTTT 0.907879 -289 AAACGGCCTGCGGGCCGTTTTGTTTTGTCTG 1 23 1 CGGGCCTTTT 0.988796 -278 TCACAATTCCCGGGCAATTTTCGTCTGAATG 1 75 0 CGGGCATTTT 0.978904 -226 TGCGCGCTGTCGCGTATTTTTTCACAATTCC 1 96 0 CGCGTATTTT 0.93417 -205 GCTATAATGCCGCGTCCTATTTGAATGCTTT 1 158 1 CGCGTCTATT 0.757644 -143 CTGGCGGTGACGGGCCTTTGTGCGAATTTAG 2 29 0 CGGGCCTTGT 0.938083 -217 CGCCAGGTGGTGGGCTTTTTTTTGTCATGAA 2 54 1 TGGGCTTTTT 0.561083 -192 GAGATAAAATCCCCCCTTTTTGGTTAACTAA 4 29 0 CCCCCCTTTT 0.852261 -159 ATCATTTTTGACCGCACTTTTGTTTGTAAGT 6 136 1 ACCGCATTTT 0.91288 -165 GTTATAATTGAGCGTCTTTTTATTTAACAAA 6 232 1 AGCGTCTTTT 0.908393 -69 AAAAAGAGCGACCGCACTTTTATTCAATCAT 7 25 0 ACCGCATTTT 0.91288 -98 AATAAAAGCGATCGCATTTTTATTTGTGGGT 7 56 1 ATCGCATTTT 0.725075 -67 ****** **** Masking position 8 Map Score: 8.63744 Number of sites scoring better than the average of aligned sites = 1578 Number in coding regions = 1336 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 6 GAAAAAATACGCGACAGCGCGCAATAACCG 1 104 1 GCGACAGCGC 0.970939 -197 GGGGTAAGAGTTGACCGAGCACTGTGATTT 1 267 1 TTGACCGAGC 0.96099 -34 AAAATCATTTTTGACCGCACTTTTGTTTGT 6 133 1 TTGACCGCAC 0.977637 -168 CACTCTTTTATCGACTGCGTAGATTTCTTT 6 201 1 TCGACTGCGT 0.9332 -100 GGTGTGGATTTTGACCGAGTGCAAATTAAT 6 270 1 TTGACCGAGT 0.922646 -31 ATTAAAAAGAGCGACCGCACTTTTATTCAA 7 29 0 GCGACCGCAC 0.990777 -94 TTTAATAAAAGCGATCGCATTTTTATTTGT 7 53 1 GCGATCGCAT 0.87256 -70 ********** Masking position 4 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 CAAAAAGCGCAAAATCCAGACAAAACAAAA 1 40 0 AAAATCCAGA 0.942781 -261 TGTTACCAGAATCATCCCGAAAGCATTCAA 1 178 0 ATCATCCCGA 0.90364 -123 TGATTATAAGAACATCCCGGTTCCGCGAAG 1 219 1 AACATCCCGG 0.903536 -82 AAGGGGAGATAAAATCCCCCCTTTTTGGTT 4 35 0 AAAATCCCCC 0.939567 -153 ATGTGGGGGAAACATCCCCATATACTGACG 4 92 1 AACATCCCCA 0.976568 -96 TTTTTTGTTTAAAACCCACTTTATAACTCA 5 83 1 AAAACCCACT 0.789249 -110 GCACTCGGTCAAAATCCACACCGAACACGT 6 262 0 AAAATCCACA 0.964038 -39 TTTATCGTAAATAACCCACAAATAAAAATG 7 70 0 ATAACCCACA 0.847494 -53 ********** Masking position 4 Map Score: 3.89268 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 221 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 AAACAAAACGGCCCGCAGGCCGTTTTTCAT 1 18 0 GCCCGCAGGC 0.897099 -283 GCGCTTTTTGCCCAGCATTCAGACGAAAAT 1 60 1 CCCAGCATTC 0.88311 -241 GTTCCGCGAAGCCAACAACCTGTGCTTGCG 1 238 1 GCCAACAACC 0.952819 -63 TCAACTCTTACCCCGCAAGCACAGGTTGTT 1 251 0 CCCCGCAAGC 0.987574 -50 TCGCACAAAGGCCCGTCACCGCCAGGTGGT 2 35 1 GCCCGTCACC 0.930272 -211 ACAAAAAAAAGCCCACCACCTGGCGGTGAC 2 49 0 GCCCACCACC 0.980316 -197 GGGATGTTTCCCCCACATTCAACGCCGAGA 4 80 0 CCCCACATTC 0.930601 -108 ********** Masking position 3 Map Score: 2.21499 Number of sites scoring better than the average of aligned sites = 1213 Number in coding regions = 1157 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 GTGATTTTTTGAGGTAACAAG 1 290 1 GAGGTAACAA 0.989153 -11 ATCCGTCCATAAGGTTACAATCGGTACAGC 2 195 1 AAGGTTACAA 0.958937 -51 CAAATTAATTGAGGTAACAA 6 291 1 GAGGTAACAA 0.989153 -10 TTTAATGAAAAAGGTAAGAAA 7 112 1 AAGGTAAGAA 0.956544 -11 ********** Masking position 5 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 10 TTAATAAAATTTTTCATTATTTTAGCCATTATCA 5 31 1 TTATATTTTA 0.971596 -162 TTTTTAATGATAATAATTATTATACATATTAAAT 6 23 1 TTATATTATA 0.948221 -278 CAATTAGATTTTGTACTTATTATACTTTTTTTTG 6 80 0 TTCTATTATA 0.87019 -221 AAAAATTGCATTTTGATAATTTTAAAATATGACT 6 164 0 TTATATTTTA 0.971595 -137 TTTTATTCAATCATAATAATATTACTTA 7 5 0 TTATATATTA 0.892995 -118 TCATTAAAACTGCTAATTATTTTATCGTAAATAA 7 86 0 TTATATTTTA 0.971596 -37 * * ** ****** Masking position 7 Map Score: 0.690829 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 GAAAATTGCCCGGGAATTGTGAAAAAATAC 1 84 1 CGGGAATTGT 0.867051 -217 TTTTATGAGTCGAGAACGGTTATTGCGCGC 1 120 0 CGAGAACGGT 0.956945 -181 CCCTGTGTTATGGGTACGGCATCACCATAT 2 154 0 TGGGTACGGC 0.942375 -92 GGCTTGCGCCTGAGAATGGCATTTGCGTCG 3 67 1 TGAGAATGGC 0.980714 -59 ACTAATTGTATGGGAATGGTTAA 4 4 0 TGGGAATGGT 0.980714 -184 GCAAATGAAGTGATAATGGCTAAAATAATG 5 45 0 TGATAATGGC 0.887217 -148 ********** Masking position 6 Map Score: 1.47299 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 388 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 ********** 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 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