AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i194_dna_replication_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 ybaN 69 putative gene 58 #2 apt 152 adenine phosphoribosyltransferase #3 dnaX 128 DNA polymerase III, tau and gamma subunits; DNA elongation factor III #4 ybaB 52 orf, hypothetical protein #5 HI0440 98 penicillin-binding protein 1A (ponA) #6 HI0441 87 orfJ protein #7 HI0442 116 conserved hypothetical protein #8 HI0443 61 recombination protein (recR) #9 HI1230 147 adenine phosphoribosyltransferase (apt) #10 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #11 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #12 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) Motif number 1 ATTACACACTAAAGTGCGGTCATTT 6 6 0 AAAGTGCGGT 0.99914 -82 TTTAAGCTATAAAGTGCGGTGAAATTTAGT 7 29 0 AAAGTGCGGT 0.99914 -88 TTATAGCTTAAAAGTGCGGTAAGATTTTCT 7 47 1 AAAGTGCGGT 0.99914 -70 ATAATGCTCAAAAGTGCGGTAAAAAAAGAA 9 126 0 AAAGTGCGGT 0.99914 -22 AAAGACCGTAAAAGTGCGGTCAATATTTTT 10 74 1 AAAGTGCGGT 0.99914 -40 TTGATGAAAACTGCGGTCAAAAAACAT 11 8 1 AAACTGCGGT 0.994829 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 11 39 0 AAAGTGCGGT 0.99914 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 12 106 0 AAAGTGCGGT 0.99914 -194 ********** Masking position 3 Map Score: 40.8725 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 TTGTTTAACCTTTGACCGCCTGCGCCTGTGC 2 69 0 TTGACCGCCT 0.944027 -84 AAATGACCGCACTTTAGTGTGT 6 2 1 ATGACCGCAC 0.99706 -86 CGCCACTAAATTTCACCGCACTTTATAGCTT 7 25 1 TTCACCGCAC 0.993298 -92 TCTTAGAAAATCTTACCGCACTTTTAAGCTA 7 50 0 TTTACCGCAC 0.996058 -67 ACGTTTCTTTTTTTACCGCACTTTTGAGCAT 9 122 1 TTTACCGCAC 0.996058 -26 CGTTAAAAATATTGACCGCACTTTTACGGTC 10 77 0 ATGACCGCAC 0.99706 -37 CACAATGTTTTTTGACCGCAGTTTTCATCAA 11 11 0 TTGACCGCAG 0.99074 -52 CATTGTGTTTTATGACCGCACTTTAAAAGGA 11 35 1 TTGACCGCAC 0.998455 -28 AACACAAAAAAATTACCGCACTTTCAAATAA 12 102 1 ATTACCGCAC 0.992512 -198 * ********* Masking position 5 Map Score: 26.9931 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 76 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 3 GGGATTTATTTAAAATCTTAGAAAATCTTACCGCACTT 7 58 0 TAAATAAAAT 0.962081 -59 ATTTACAATTTAAGATGAATTAAAACTTC 9 2 0 TAAATAAAAT 0.962081 -146 AAATAATGCTCAAAAGTGCGGTAAAAAA 9 130 0 AAAAAAAAAG 0.888661 -18 TTTTACCTCGTAAAAACGTTAAAAATATTGACCGCACT 10 86 0 TAAAAAAAAT 0.945445 -28 CCTTTTTGAAAAAAATCTGAAAAAACTTTAAAACAAAG 12 19 1 AAAATAAAAT 0.98246 -281 TTGTTCGCTAAAATAACCAGTAAAATATTGCATTCCAT 12 61 0 AAAAAAAAAT 0.974536 -239 TTAGCGAACAAAAAAACACAAAAAAATTACCGCACTTT 12 88 1 AAAAAAAAAT 0.974537 -212 CTTTATCTCAAAAAATCTTCTAAAATTTACAAGATTTG 12 184 1 AAAATAAAAT 0.982256 -116 TGCTTTTCACAAACATTTAACAAATCTTGTAAATTTTA 12 204 0 AAAATAAATT 0.887397 -96 TTCACTCAAAACAGATTAAGGAAAACCT 12 282 1 ACAATAAAAT 0.921169 -18 *** ** **** * Masking position 12 Map Score: 8.57541 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 63 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 GTGCTCGAAAACGCCAGAATGTACTGGCTG 2 43 0 ACGCCAGAAT 0.974065 -110 TCAGAACGGCGAGGCTGAATGCACATCTTG 3 49 0 GAGGCTGAAT 0.950767 -80 CTATTCTTTAAAGGCTGAATCTTTTATACT 5 19 1 AAGGCTGAAT 0.958838 -80 TTCATTAACGAAGCGAGAATTTTACG 5 83 1 AAGCGAGAAT 0.959816 -16 TTATTAGGCGCGTGAATATAAGATTCA 8 8 1 GCGCGTGAAT 0.983079 -54 CTGAGAGATGACGCGTGAATCTTATATTCA 8 23 0 ACGCGTGAAT 0.98593 -39 ********** Masking position 8 Map Score: 5.18289 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 234 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 GGTAATGCTAACACAGCCCCGTCAGAACGG 3 70 0 ACACAGCCCC 0.950661 -59 AAGATTTTAAATAAATCCCACAGTTCCCAA 7 77 1 ATAAATCCCA 0.94352 -40 CCACAGTTCCCAAAAGCCCATTTTTTCGCT 7 94 1 CAAAAGCCCA 0.929329 -23 AAACTTAAATAAAAATCCCCAATTGGGGAT 9 42 1 AAAAATCCCC 0.963327 -106 AGAGGAAAATAAAAATCCCCAATTGGGGAT 9 56 0 AAAAATCCCC 0.963327 -92 ATCGGTGGGCTTAAAGCCCACCTACAGA 10 9 0 TTAAAGCCCA 0.898708 -105 AACCCATCCTATAAAGACCGTAAAAGTGCG 10 62 1 ATAAAGACCG 0.837446 -52 AAACTTTAAAACAAAGCCCGATGGAATGCA 12 41 1 ACAAAGCCCG 0.980316 -259 ********** Masking position 5 Map Score: 4.77851 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 383 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 AGCACAACAATCGCAGTTGCAAT 2 1 1 AGCACAACAG 0.990975 -152 GGCGTTTTCGAGCACAGGCGCAGGCGGTCAAAG 2 58 1 AGCACAGGCG 0.990223 -95 TAGCGTGGGCAGCACAAGACTGGCGATAA 3 7 0 AGCACAAGAG 0.993787 -122 CGCTACGGACAGCACAAGATGTGCATTCAGCCT 3 35 1 AGCACAAGAG 0.993787 -94 TCGTAAGCACAGCTTACGTTCGTCATCC 4 6 1 AGCACAGCTG 0.979129 -47 ********* * Masking position 6 Map Score: 3.04957 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 AACAATTATCATTTTCATTGAGGTCTTATC 1 11 0 ATTTTCATTG 0.820902 -59 CTTGACAAGAATATTCATTAACGAAGCGAG 5 70 1 ATATTCATTA 0.886544 -29 TATTCCTTATATATTCCTTATTTGTTTAAT 6 64 0 ATATTCCTTA 0.938846 -24 AATATATTCCTTATATATTCCTT 6 75 0 ATATTCCTTA 0.938846 -13 GTCATCTCTCAGTTTCCTCTCATTAATCAC 8 41 1 AGTTTCCTCT 0.763192 -21 GGGGATTTTTATTTTCCTCTCTTTCTATTT 9 66 1 ATTTTCCTCT 0.932404 -82 TTTGACCGCAGTTTTCATCAA 11 2 0 GTTTTCATCA 0.903608 -61 AAGATAGTGAATTTTCATCAAATCATCATA 12 157 0 ATTTTCATCA 0.950441 -143 AGGTTTTCCTTAATCTGTTTTG 12 288 0 GTTTTCCTTA 0.934665 -12 ********** Masking position 5 Map Score: 6.51665 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 217 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 8 CCAATTGGGGATTTTTATTTAAGTTTGAATTT 9 36 0 ATTTATTTAA 0.562641 -112 CTCTCTTTCTATTTTTTTATGATAGAATGCCA 9 82 1 ATTTTTATGA 0.729968 -66 TAAAAAAAGAAACGTTTTTAGATTGGCATTCT 9 105 0 AATTTTTAGA 0.798293 -43 CATAAAACACAATGTTTTTTGACCGCAGTTTT 11 17 0 AATTTTTTGA 0.965667 -46 GCTTTGTTTTAAAGTTTTTTCAGATTTTTTTC 12 26 0 AATTTTTTCA 0.803412 -274 TTTGCCATAAATAATTATTTGAAAGTGCGGTA 12 115 0 ATTTATTTGA 0.929191 -185 ATTTATGGCAAAGCTGATTTGATATGATGATT 12 135 1 AATGATTTGA 0.931875 -165 CTGATTTGATATGATGATTTGATGAAAATTCA 12 148 1 ATTGATTTGA 0.903318 -152 TAAATTTTAGAAGATTTTTTGAGATAAAGATA 12 181 0 AATTTTTTGA 0.965667 -119 GGTTTTCCTTAATCTGTTTTGAGTGAATATTA 12 277 0 AATGTTTTGA 0.95244 -23 ** ******** Masking position 5 Map Score: 7.28245 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 103 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 ********** No masking Map Score: -7.64954e-13 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: -7.64954e-13 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 11 ********** No masking Map Score: -7.64954e-13 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