AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoE_ecoli_hinf_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 HI0266 82 conserved hypothetical protein #8 HI0267 41 nitrate/nitrite sensor protein (narQ) #9 HI0269 125 RNA polymerase sigma-32 factor (rpoH) #10 HI0622 300 polypeptide deformylase (def) #11 HI0623 92 methionyl-tRNA formyltransferase (fmt) #12 HI0626 72 large conductance mechanosensitive channel (mscL) #13 HI0627 89 conserved hypothetical protein #14 HI0628 107 RNA polymerase sigma-E factor (rpoE) #15 HI0629 24 sigma-E factor negative regulatory protein (mclA) #16 HI1259 193 periplasmic serine protease Motif number 1 CCAGGCTTTTGTAAAGACGAA 2 2 1 CAGGCTTTTG 0.981775 -128 AGAGAAGTTACTGGCTGGTGGAGGATTAGG 4 26 1 CTGGCTGGTG 0.918861 -275 GTTAGAGTGTCTCGTTTTTGTAAAGTTCCG 4 200 0 CTCGTTTTTG 0.860783 -101 AAGAGTATAACACGCTTTTA 5 1 0 CACGCTTTTA 0.860777 -244 AAGTTCAATGCAAGCTTGTGAATAAATTAC 5 111 0 CAAGCTTGTG 0.936239 -134 GACTACACTCCTCGCTGTTGCTTCATGGCA 6 126 0 CTCGCTGTTG 0.971904 -24 CTTCTTTATTTTGGCTTTTGCCAATCAATG 9 99 0 TTGGCTTTTG 0.903048 -27 ATATGGGGTTTTAGCTTTTGGGAATTTATT 10 138 1 TTAGCTTTTG 0.855566 -163 ACTTTTTTAACACGCTTTTGTCTGAACAAG 14 31 1 CACGCTTTTG 0.986022 -77 ATCAAGACAGCAAGCTCTTGTTGCTTGTTC 14 54 0 CAAGCTCTTG 0.895965 -54 ********** Masking position 6 Map Score: 9.8131 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 472 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 GTCCTCTCCCGCGTGAGAAATACGCTTCCC 1 64 0 CGCGTGAAAA 0.981596 -20 AGGGCGGCGAGAAAAAGAGAAGTTAC 4 5 1 CGCGAGAAAA 0.985806 -296 GATCCGTCTACAGCATGACAAACAAAAACAGA 4 161 1 CGCATGAAAA 0.980162 -140 GATAAAATCACGGTCTGATAAAACAGTGAATG 5 144 1 CGTCTGAAAA 0.935691 -101 ATTGCTCAATCCGCCAGATAACACATACTTGC 6 16 1 CGCCAGAAAC 0.955297 -134 TTTGCACTCCAGCAAGAAAAACTGTTCGTTA 7 62 0 CGCAAGAAAA 0.984694 -21 ATAACGTGGTCTGTAAGACAAAAAAATAAAAA 16 149 0 CGTAAGAAAA 0.946093 -45 * ****** *** Masking position 8 Map Score: 6.41137 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 182 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 TTCACCACCTAATCCTCCACCAGCCAGTAA 4 33 0 AATCCTCCAC 0.857115 -268 CTATCATTATAAGTCTACAGAATCTGAACA 4 126 0 AAGTCTACAG 0.829562 -175 CCGAGGTAAAGTCTCCCCAAACCAAATT 4 283 0 AAGTCTCCCC 0.95973 -18 AACTGTTCGTTATTCTACCCAAAATTGATA 7 44 0 TATTCTACCC 0.750276 -39 CACATGGGGAAACCCCACACTACCATCGGC 10 36 0 AACCCCACAC 0.902607 -265 ATCCCACTAAAATTCTACCCTTAAAAACAA 10 273 1 AATTCTACCC 0.950146 -28 TTGCTGGCTAAAGCCCACCCTACGTT 11 7 0 AAGCCCACCC 0.991957 -86 GGGTGGGCTTAAGCCCACCGTTTTTTGAAA 11 40 0 AAGCCCACCG 0.97407 -53 CGGTGGGCTTAAGCCCACCCTACTTCCTAT 11 50 1 AAGCCCACCC 0.991957 -43 ********** Masking position 2 Map Score: 7.64377 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 178 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AGCCCGATTTGAAGGCATAGTTTACCATGC 1 27 1 GAAGGCATAG 0.880725 -57 TGCAATTTGAGCAAGCAAAGGGTTAGAGTG 4 221 0 GCAAGCAAAG 0.84782 -80 GGAACCCATTGCAGGGAAAGAGTATAACAC 5 18 0 GCAGGGAAAG 0.990271 -227 GGGTTCCGTAGCAGGGAAAGAGACCCCGTT 5 41 1 GCAGGGAAAG 0.990271 -204 CCAAAATAAAGAAGGGAAACG 9 115 1 GAAGGGAAAC 0.984656 -11 GAACTCAGAAGTGAAACGCTGTAATGC 10 8 1 GAAGTGAAAC 0.892748 -293 TGTAATTTTTGAAGGGGAACATTATT 12 57 1 GAAGGGGAAC 0.951798 -16 ********** Masking position 3 Map Score: 5.60259 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 202 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 TCAAATCCTCTCAATCGATATCTTC 5 230 0 TCCTCTCAAT 0.961101 -15 AAGGTTTCCTCTAAAATTATTGTAGG 7 7 1 TCCTCTAAAA 0.751562 -76 TGTAGGCGTATGCTATCAATTTTGGGTAGA 7 31 1 TGCTATCAAT 0.877437 -52 TTTACCGCACTTTTCTAAATTTCCACTGGA 8 15 1 TTTTCTAAAT 0.704061 -27 ATAAGACAGATTTTATCAATTGAAAGTTCA 9 23 0 TTTTATCAAT 0.75751 -103 GAAGTCACATTCCTATAAATGTTTTATTAG 10 233 1 TCCTATAAAT 0.951394 -68 CCACCCTACTTCCTATCAATTACCATAACG 11 64 1 TCCTATCAAT 0.961842 -29 CTAACTTTCATTCTTTAAATA 13 2 0 TTCTTTAAAT 0.752788 -88 AAGTAGCAAATTCTATAAATTTATGTTCTA 16 48 0 TTCTATAAAT 0.924667 -146 ********** Masking position 6 Map Score: 4.40248 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 31 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 AAGTTTCTGCAAAAGGTAAAAATTTATTGTTCG 2 28 0 AAGTAAAAAT 0.656801 -102 CTATGTACATAGCAGCTAAAAAAATGATGAAAT 6 82 0 AAGTAAAAAA 0.93774 -68 GTGACTTCATATGAGTTGAAAAATTACTTACTT 10 208 0 AAGTGAAAAA 0.846326 -93 TTAGCCAGCAATCATTTCAAAAAACGGTGGGCT 11 26 1 AATTCAAAAA 0.856106 -67 AATCACTCTGAAAAGTAAAAAAA 12 1 0 AAGAAAAAAA 0.947085 -72 TTCCCCTTCAAAAATTACATAAAAAGAGCGACT 12 43 0 AATACATAAA 0.636922 -30 TAGCTTAAAAAATAGTAATAAAAAAAGTCAGCA 13 38 0 AAGAATAAAA 0.694579 -52 CTAGTCAATAAAAAGGTCAAAAA 16 1 0 AAGTCAAAAA 0.960031 -193 AATTGCGCGTATTAGAACATAAATTTATAGAAT 16 36 1 AAGACATAAA 0.876263 -158 AGGAAATCGGAGCAGTACAAAAACGGTCTTACA 16 77 0 AAGACAAAAA 0.96615 -117 GTAAGACAAAAAAATAAAAAAAATGTTCAATAA 16 136 0 AATAAAAAAA 0.815956 -58 * ** ******* Masking position 4 Map Score: 4.79185 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 221 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 AATGCCGATGGTAGTGTGGGGTTTCCCCAT 10 33 1 GTAGTGTGGG 0.993506 -268 AACGTAGGGTGGGCTTTAGCCAG 11 4 1 GTAGGGTGGG 0.997609 -89 TTGATAGGAAGTAGGGTGGGCTTAAGCCCA 11 53 0 GTAGGGTGGG 0.997609 -40 ********** Masking position 3 Map Score: 3.58978 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 1 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 AATAAGCTATCTTATTGAACCAATTTGTTA 9 53 0 CTTATTGAAC 0.971392 -73 TCCTTCTGTTTTTATTTAACTTAGATAAGT 10 94 0 TTTATTTAAC 0.817269 -207 AAATTACTTACTTATTGAAAATTAAAATTA 10 191 0 CTTATTGAAA 0.942643 -110 AAGCCCACCGTTTTTTGAAATGATTGCTGG 11 30 0 TTTTTTGAAA 0.706209 -63 AGCGAATGAACTTTTTTAACACGCTTTTGT 14 22 1 CTTTTTTAAC 0.898085 -86 AGCAAATTATCTTGTTTAAAAGGAAATCGG 16 100 0 CTTGTTTAAA 0.781932 -94 TTGCTCTCCTCTTATTGAACATTTTTTTTA 16 125 1 CTTATTGAAC 0.971392 -69 ********** Masking position 8 Map Score: 2.73909 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 81 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 AGCAATTTTGCGTTATCTGTTAATCGAGAC 2 102 1 CGTTATCTGT 0.955375 -28 CTGAACATCGCATTATCTGTGTAGAAATGC 4 103 0 CATTATCTGT 0.974232 -198 GTAGACGGATCATTATCTATCATTATAAGT 4 142 0 CATTATCTAT 0.896346 -159 AACGCCACTCCATTAGCTGCAATTTGAGCA 4 238 0 CATTAGCTGC 0.943484 -63 ACGAGGTTATCATTCACTGTTTTATCAGAC 5 156 0 CATTCACTGT 0.866795 -89 ATAAATGTTTTATTAGCTGTGCTATAATCC 10 247 1 TATTAGCTGT 0.836022 -54 TAAAAAAGTTCATTCGCTAATCAATAATT 14 10 0 CATTCGCTAA 0.720082 -98 TTACAGACCACGTTATCTGAAATTTATTTT 16 165 1 CGTTATCTGA 0.903041 -29 ********** Masking position 4 Map Score: 1.99133 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 278 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 AGATTTACTCGCGATAAGCCCGATTTGAAGG 1 11 1 GCGATAACCC 0.973455 -73 GGAACTTCAGGCTATAAAACGAATCTGAAGA 2 67 1 GCTATAAACG 0.950757 -63 AGCTTATTGTGCTATAACTAGGTACATTGAT 9 75 1 GCTATAATAG 0.867097 -51 ATTCCCAAAAGCTAAAACCCCATATCTTTCG 10 132 0 GCTAAAACCC 0.961327 -169 TATTAGCTGTGCTATAATCCCACTAAAATTC 10 257 1 GCTATAACCC 0.989696 -44 TATTTTTTAAGCTATAATCAGCCCTCAATTT 13 57 1 GCTATAACAG 0.971453 -33 ******* *** Masking position 6 Map Score: 1.54305 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 94 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CCAGTAACTTCTCTTTTTCTCGCCGCCCT 4 10 0 CTCTTTTTCT 0.865618 -291 TAACCCAACGGCCTTTTTATTTCACCACCT 4 53 0 GCCTTTTTAT 0.689254 -248 CGTAACGCATCTGTTTTTGTTTGTCATGCT 4 172 0 CTGTTTTTGT 0.93852 -129 TTAGAGTGTCTCGTTTTTGTAAAGTTCCGT 4 199 0 TCGTTTTTGT 0.66759 -102 GAATAACGAACAGTTTTTCTTGCTGGAGTG 7 59 1 CAGTTTTTCT 0.62356 -24 CGTTTCCCTTCTTTATTTTGGCTTTT 9 110 0 CCTTCTTTAT 0.559247 -16 CGGGGTCCTTCTGTTTTTATTTAACTTAGA 10 99 0 CTGTTTTTAT 0.933732 -202 ATAATAGTCGCTCTTTTTATGTAATTTTTG 12 38 1 CTCTTTTTAT 0.919194 -35 GAAATGCTGACTTTTTTTATTACTATTTTT 13 34 1 CTTTTTTTAT 0.846336 -56 TTTTTGACCTTTTTATTGACTAGAAA 16 7 1 ACCTTTTTAT 0.725195 -187 ACTTGTAAGACCGTTTTTGTACTGCTCCGA 16 74 1 CCGTTTTTGT 0.953458 -120 CATTTTTTTTATTTTTTTGTCTTACAGACC 16 144 1 ATTTTTTTGT 0.50776 -50 ********** Masking position 6 Map Score: 4.39647 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 451 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 12 ACGAATCTGAAGAACACAGCAATTTTGCGT 2 85 1 AGAACACAGC 0.894073 -45 CTCTTAAGCTCTGGCACAGTTGTTGCTACC 5 188 1 CTGGCACAGT 0.927459 -57 CTGTTGCTTCATGGCACAGCGTTAACGCTA 6 112 0 ATGGCACAGC 0.990428 -38 GTACCTAGTTATAGCACAATAAGCTATCTT 9 70 0 ATAGCACAAT 0.774763 -56 ATGTGAGAGTAGGGCACCGCCAGGTTACCA 10 61 1 AGGGCACCGC 0.969104 -240 TAGTGGGATTATAGCACAGCTAATAAAACA 10 252 0 ATAGCACAGC 0.985032 -49 ********** Masking position 6 Map Score: 1.21816 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 348 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TGAAGAACACAGCAATTTTGCGTTATCTGTT 2 92 1 AGCAATTTGC 0.954253 -38 TCCACCAGCCAGTAACTTCTCTTTTTCTCGC 4 17 0 AGTAACTTTC 0.918756 -284 TGGCGGATTGAGCAATTTATC 6 1 0 AGCAATTTTC 0.982732 -149 TCAATAAGTAAGTAATTTTTCAACTCATATG 10 203 1 AGTAATTTTC 0.950682 -98 TCTTACAAGTAGCAAATTCTATAAATTTATG 16 53 0 AGCAAATTTA 0.860327 -141 ATAAGAGGAGAGCAAATTATCTTGTTTAAAA 16 109 0 AGCAAATTTC 0.97544 -85 ******** ** Masking position 5 Map Score: 1.59918 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 93 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 ATGCGCTTACGGGGAAGCGTATTTCTCACG 1 53 1 GGGGAAGCGT 0.980619 -31 AGCAAGCAAAGGGTTAGAGTGTCTCGTTTT 4 212 0 GGGTTAGAGT 0.926011 -89 ACCCATTGCAGGGAAAGAGTATAACACGCT 5 15 0 GGGAAAGAGT 0.986415 -230 TTCCGTAGCAGGGAAAGAGACCCCGTTGTC 5 44 1 GGGAAAGAGA 0.980648 -201 GATGAAATACCGGGAAGAGACAACGGGGTC 5 62 0 CGGGAAGAGA 0.957011 -183 ********** Masking position 6 Map Score: 1.11694 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 52 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 ATTTGAGCAAGCAAAGGGTTAGAGTGTCTC 4 217 0 GCAAAGGGTT 0.929624 -84 CTCTTTCCCTGCAATGGGTTCCGTAGCAGG 5 26 1 GCAATGGGTT 0.958836 -219 CCGGGAAGAGACAACGGGGTCTCTTTCCCT 5 53 0 ACAACGGGGT 0.959472 -192 GAGCTTAAGAGCAACGAGGTTATCATTCAC 5 169 0 GCAACGAGGT 0.960017 -76 CATATCTTTCGACACGGGGTCCTTCTGTTT 10 113 0 GACACGGGGT 0.95911 -188 CGTGTCGAAAGATATGGGGTTTTAGCTTTT 10 127 1 GATATGGGGT 0.876234 -174 ********** Masking position 4 Map Score: 0.30721 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 188 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282