AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoE_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dgt 83 deoxyguanosine triphosphate triphosphohydrolase #2 htrA 129 periplasmic serine protease Do; heat shock protein HtrA #3 rseA 32 sigma-E factor, negative regulatory protein #4 rpoE 300 RNA polymerase, sigma-E factor; heat shock and oxidative stress #5 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #6 ftsY 149 cell division membrane protein #7 sigW 300 RNA polymerase ECF-type sigma factor (sigma-W) #8 htrA 168 serine protease Do (heat-shock protein) #9 yyxA 68 alternate gene name: yycK; similar to serine protease Do #10 yycJ 21 yycJ #11 yycF 300 similar to two-component response regulator [YycG] Motif number 1 GTCCTCTCCCGCGTGAGAAATACGC 1 69 0 TCTCCCGCTG 0.992184 -15 ACCACCTAATCCTCCACCAGCCAGTAACTTCTCT 4 26 0 CCCCCCGCAG 0.994997 -275 AGATAATGATCCGTCTACAGCATGACAAACAAAA 4 154 1 CCTCACGCTG 0.993386 -147 TTAATTCACATCACCGCCTGCAAGTATGTGTTAT 6 33 0 TCCCCCGCAG 0.978521 -117 TCACGAATTACCATCTACACCCTGCCAAAAATTT 7 191 1 CCTCACCCTG 0.961629 -110 CTAACCTCTGCCTTCACCGGTCTGTATGTATACG 7 271 0 CCTCCCGTTG 0.988436 -30 TTGAAACCTCCCCTCACCGGAGTGCGTCTTTATC 11 56 0 CCTCCCGATG 0.992529 -245 TTTTGATTTTCCTCCTGCCGAATGACTTCATTTC 11 275 0 CCCCGCGATG 0.966351 -26 ** ** ** ** ** Masking position 8 Map Score: 8.94456 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 544 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 GCACAAAATGTGACATAGAGATGAAATACCGGGAAG 5 75 0 TGATATGAAA 0.981416 -170 AATCACGGTCTGATAAAACAGTGAATGATAACCTCG 5 149 1 TGAAATGAAT 0.915971 -96 ACATAGCAGCTAAAAAAATGATGAAATAGTCTATCA 6 73 0 TAAAATGAAA 0.930515 -77 ATCTACACCCTGCCAAAAATTTGATAAACTTATTTT 7 203 1 TGAAATGATA 0.904025 -98 AAACTTATTTTATAAAAAAATTGAAACCTTTTGAAA 7 228 1 TAAAATGAAA 0.930386 -73 TGGGAAATTGTGAAAAAGTGCGGAAAACGGTACACT 8 39 0 TGAAAGGAAA 0.947645 -130 ACAAAAACTGTGGGATAAAAATGAAAAGATTATGGG 8 71 0 TGATATGAAA 0.981452 -98 TAAATAGACATGTGAAAATAGAGAAACGGAGTGAAC 8 140 1 TGAAAAGAAA 0.924314 -29 ATAAACAACTGGCGATAAAGGTGAAACATGTGTTTT 11 133 1 GGATATGAAA 0.916911 -168 ATGAAACGAATGTTATATAGATGAAATGAAGTCATT 11 253 1 TGATATGAAA 0.98143 -48 ** *** ***** Masking position 7 Map Score: 8.50473 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 66 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 GAATCTGAAGAACACAGCAATTTTGCGTTATCT 2 87 1 AACCGCATTT 0.802759 -43 ACCAGCCAGTAACTTCTCTTTTTCTCGCCGCCC 4 12 0 AACTTCTTTT 0.979011 -289 ACAGAATCTGAACATCGCATTATCTGTGTAGAA 4 107 0 AACTGCATAT 0.724602 -194 AAAGTTCCGTAACGCATCTGTTTTTGTTTGTCA 4 176 0 AACCTCTTTT 0.941747 -125 CTTTGATCAAAAGGTGTCTTTTTTCTTTTCGGA 7 91 1 AAGTTCTTTT 0.941818 -210 TTCGTTTCAAAAGGTTTCAATTTTTTTATAAAA 7 235 0 AAGTTCATTT 0.921603 -66 ATTTCCCATAATCTTTTCATTTTTATCCCACAG 8 67 1 ATCTTCATTT 0.796936 -102 TCAAGTCATAAACCTATCAATATAAATAGACAT 8 118 1 AACTTCATAT 0.883612 -51 TCTCTATTTTCACATGTCTATTTATATTGATAG 8 131 0 CACTTCTTTT 0.888986 -38 GGTTTCAATAAAGTTATCTTTTTTAAAAAAAGT 11 82 1 AAGTTCTTTT 0.941833 -219 ATAAAGGTGAAACATGTGTTTTTTTTCTAAACC 11 147 1 AACTTGTTTT 0.844888 -154 TTTTTTTCTAAACCTTTATTTTTTTTATCTTTT 11 166 1 AACTTATTTT 0.786117 -135 *** * *** *** Masking position 11 Map Score: 7.64874 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 185 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 CCAGGCTTTTGTAAAGACGAACAATAAAT 2 9 1 TTGTAAGACG 0.768952 -121 ACTTCAGGCTATAAAACGAATCTGAAGAACA 2 70 1 ATAAAAGAAT 0.807855 -60 TTGAAACCTTTTGAAACGAAGCTCGTATACA 7 248 1 TTGAAAGAAG 0.931082 -53 CATATTGTATATGAAAGGACTGAGTCG 8 7 0 ATGAAAGACT 0.962028 -162 TGGGATAAAAATGAAAAGATTATGGGAAATT 8 66 0 ATGAAAGATT 0.902804 -103 CTTATGGCCCATGTAAAGAATGGGTCCTTGT 11 220 0 ATGTAAGAAT 0.932356 -81 GCCATAAGTGATGAAACGAATGTTATATAGA 11 243 1 ATGAAAGAAT 0.974127 -58 TGTTATATAGATGAAATGAAGTCATTCGGCA 11 263 1 ATGAAAGAAG 0.973618 -38 ****** **** Masking position 6 Map Score: 5.60106 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 71 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 CGAGACACTCTAACCCTTTGCTTGCTCAAA 4 216 1 TAACCCTTTG 0.941964 -85 CCCTGCTACGGAACCCATTGCAGGGAAAGA 5 27 0 GAACCCATTG 0.911326 -218 CAGGGAAAGAGACCCCGTTGTCTCTTCCCG 5 52 1 GACCCCGTTG 0.964883 -193 CCCAGTCACAGACACCTTTGATCAAAAGGT 7 76 1 GACACCTTTG 0.976557 -225 AAAGAAAAAAGACACCTTTTGATCAAAGGT 7 89 0 GACACCTTTT 0.933671 -212 TAAAAAAATTGAAACCTTTTGAAACGAAGC 7 240 1 GAAACCTTTT 0.934866 -61 GTTTTTTTTCTAAACCTTTATTTTTTTTAT 11 164 1 TAAACCTTTA 0.846251 -137 CTTTTGACCTTAAACCGTTATAATAGACAA 11 194 1 TAAACCGTTA 0.78836 -107 ********** Masking position 2 Map Score: 4.80602 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 295 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GCATGGTAAACTATGCCTTCAAATCGGGCTTA 1 25 0 CTTGCCTTCA 0.974754 -59 CACTCTAACCCTTTGCTTGCTCAAATTGCAGC 4 221 1 CTTGCTTGCC 0.926498 -80 GTGTTATACTCTTTCCCTGCAATGGGTTCCGT 5 18 1 CTTCCCTGCA 0.964686 -227 AACGGGGTCTCTTTCCCTGCTACGGAACCCAT 5 39 0 CTTCCCTGCA 0.964686 -206 GTAGCAACAACTGTGCCAGAGCTTAAGAGCAA 5 185 0 CTTGCCAGAC 0.940037 -60 ATGAAATAGTCTATCACTTAACTTAATTCACA 6 57 0 CTTCACTTAC 0.730631 -93 AGCGTTAACGCTGTGCCATGAAGCAACAGCGA 6 113 1 CTTGCCATGA 0.819129 -37 AGTCAAAGTCCGTTGCCTTACCGCTTGGCTAT 7 15 0 CGTGCCTTAC 0.8806 -286 TCAAAGGTGTCTGTGACTGGGCTAGCTGGATT 7 65 0 CTTGACTGGC 0.913227 -236 TTTATCTAACCTCTGCCTTCACCGGTCTGTAT 7 278 0 CTTGCCTTCC 0.989068 -23 ** ******* * Masking position 4 Map Score: 6.03905 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 874 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 TTCACCACCTAATCCTCCACCAGCCAGTAA 4 33 0 AATCCTCCAC 0.848865 -268 ACGCGCTATCGAAACGCCACTCCATTAGCT 4 250 0 GAAACGCCAC 0.93797 -51 TGCTACCACTGAAGCGCCAGAAGATATCGA 5 211 1 GAAGCGCCAG 0.944636 -34 TAAATTGCTCAATCCGCCAGATAACACATA 6 13 1 AATCCGCCAG 0.940031 -137 AGGGAGAACCGGCCCTGCGGCCGGT 11 6 1 GAACCGGCCC 0.980128 -295 CTTCTTCTTTGAACCGGCCGCAGGGCCGGT 11 18 0 GAACCGGCCG 0.974299 -283 AACTTTATTGAAACCTCCCCTCACCGGAGT 11 67 0 AAACCTCCCC 0.939727 -234 ********** Masking position 2 Map Score: 1.83845 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 796 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 TCGGGCTTATCGCGAGTAAATCT 1 3 0 CGCGAGTAAT 0.831994 -81 TCCCCGTAAGCGCATGGTAAACTATGCCTTC 1 37 0 CGCATGGAAA 0.951011 -47 GTCCTCTCCCGCGTGAGAAATACGCTTCCC 1 64 0 CGCGTGAAAA 0.962261 -20 ATCCGTCTACAGCATGACAAACAAAAACAGA 4 162 1 AGCATGAAAA 0.862707 -139 GTTTCGATAGCGCGTGGAAATTTGGTTTGGG 4 265 1 CGCGTGGAAT 0.980157 -36 TAAAAGCGTGTTATACTCTTTCCCT 5 5 1 AGCGTGTATA 0.671688 -240 GTTCAATGCAAGCTTGTGAATAAATTACGCA 5 108 0 AGCTTGTAAT 0.843818 -137 GTTGCCTTACCGCTTGGCTATAGCC 7 5 0 CGCTTGGTAT 0.72461 -296 AAAGTTGACCAGCATGACAATAGATAAACAA 11 110 1 AGCATGAAAT 0.885605 -191 ******* *** Masking position 3 Map Score: 1.5164 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 559 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 AATTGCAGCTAATGGAGTGGCGTTTCGATA 4 244 1 AATGGAGTGG 0.97299 -57 AGAAGATATCGATTGAGAGGATTTGA 5 229 1 GATTGAGAGG 0.711293 -16 ACCAACGCATGACGGAGTCAAAGTCCGTTG 7 32 0 GACGGAGTCA 0.970692 -269 TATATGAAAGGACTGAGTCG 8 1 0 GACTGAGTCG 0.916041 -168 AAAATAGAGAAACGGAGTGAACATG 8 154 1 AACGGAGTGA 0.97299 -15 AAATAATGGAGTGAGACAAAC 10 5 1 AATGGAGTGA 0.967565 -17 ATATAGATGAAATGAAGTCATTCGGCAGGA 11 267 1 AATGAAGTCA 0.746573 -34 ********** Masking position 6 Map Score: 1.48111 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 129 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 ATGCAAGCTTGTGAATAAATTACGCACAAAA 5 103 0 GTGAATAAAT 0.982481 -142 CATTGAACTTGTGGATAAAATCACGGTCTGA 5 131 1 GTGGATAAAT 0.970499 -114 AGGCGGTGATGTGAATTAAGTTAAGTGATAG 6 48 1 GTGAATTAAT 0.956889 -102 ATGGTAATTCGTGAATAAACTACCTTAACAT 7 174 0 GTGAATAAAT 0.982481 -127 ********* * Masking position 6 Map Score: 0.79639 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TTGAAGGCATAGTTTACCATGCGCTTACGG 1 35 1 AGTTTACCAT 0.953008 -49 AAGAGCAACGAGGTTATCATTCACTGTTTT 5 163 0 AGGTTATCAT 0.952802 -82 ATGATGAAATAGTCTATCACTTAACTTAAT 6 62 0 AGTCTATCAC 0.922468 -88 TTATAAAATAAGTTTATCAAATTTTTGGCA 7 213 0 AGTTTATCAA 0.946865 -88 TTATGACTTGAGTTTATCATAAACAAAAAC 8 99 0 AGTTTATCAT 0.978265 -70 ********** Masking position 5 Map Score: 0.701177 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 35 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 TTTAGTTCGGAACTTCAGGCTATAAAACGA 2 59 1 AACTTCAGGC 0.974927 -71 CGTTGGGTTACTCTTCAGGCAGTTAAATGG 4 73 1 CTCTTCAGGC 0.983637 -228 CTCAATCGATATCTTCTGGCGCTTCAGTGG 5 216 0 ATCTTCTGGC 0.97495 -29 TTCGTTTCATCACTTATGGCCCATGTAAAG 11 233 0 CACTTATGGC 0.938071 -68 ********** Masking position 5 Map Score: 0.317262 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 133 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 13 ********** No masking Map Score: -5.39769e-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: -5.39769e-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: -5.39769e-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