AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icysB_ecoli_opreg_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 topA 300 DNA topoisomerase type I, omega protein #2 cysB 209 positive transcriptional regulator for cysteine regulon #3 cysZ 229 required for sulfate transport #4 cysK 184 cysteine synthase A, O-acetylserine sulfhydrolase A Motif number 1 CAGAGTCACGACAAGGGGTTGATATCCGCAGA 1 190 1 ACAAGGGTGA 0.992665 -111 GTTTTTATAAACAAAGGGTCGCGAAAGCGGCC 2 27 1 ACAAGGGTGC 0.997158 -183 ATATGCAATAAAAAAGGGCCGCTTTCGCGACC 2 43 0 AAAAGGGCGC 0.985346 -167 GGTTTACAAAATAACCGGTAGATTG 4 4 0 ATAACGGTGA 0.951208 -181 CCTGTTTCACACAAACGGTTTACAAAATAACC 4 20 0 ACAACGGTTA 0.864811 -165 GTTTGTGTGAAACAGGGGTGGCTTATGCCGCC 4 36 1 AACAGGGTGC 0.969265 -149 GCAAGATGGAATAAGGGGCGGCATAAGCCACC 4 52 0 ATAAGGGCGC 0.985346 -133 AAATTGGGATACAACAGGTAGCATACCCGCTC 4 143 0 ACAAAGGTGC 0.981743 -42 **** **** ** Masking position 4 Map Score: 9.53583 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 193 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 TCTATTGCCAGATTGACGAAAGCGTCACACT 1 73 0 GTTGACGAAA 0.98538 -228 GTCGTGACTCTGTTCACGAAAATTCAGGTGA 1 171 0 TTTCACGAAA 0.869386 -130 TTCGTGAACAGAGTCACGACAAGGGGTTGAT 1 182 1 GGTCACGACA 0.983017 -119 TATAAACAAAGGGTCGCGAAAGCGGCCCTTT 2 32 1 GGTCGCGAAA 0.983017 -178 TAGTGTATAGGTGTGAAGAAAAAATAATATG 2 70 0 GGTGAAGAAA 0.969743 -140 CACACCTGGCGGGTGACTAATACGATTTAAT 2 145 0 GGTGACTAAT 0.869346 -65 CACCCGCCAGGTGTGACGAAAAAACGATGTT 2 161 1 GGTGACGAAA 0.995968 -49 * ********* Masking position 9 Map Score: 6.19773 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 276 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 TGCGTATCGGATTTTATCAGGTACAGTGTGA 1 49 1 ATTTTTCAGG 0.965049 -252 ACCTAATTTGATTCTTCCAGGAATGCGTCGC 1 271 0 ATTCTCCAGG 0.992278 -30 CCTTTAATTCTGTCAGGTTTTTATAAA 2 7 1 ATTCTTCAGG 0.977486 -203 AATTCTGCGTATTTTACCGGGTAATTGCGCA 3 174 0 ATTTTCCGGG 0.992278 -56 AATACGCAGAATTTTCCTGGGATTGGTCAAA 3 192 1 ATTTTCTGGG 0.952103 -38 CAATCTACCGGTTATTTTGTAA 4 2 1 AATCTCCGGT 0.885205 -183 ***** ***** Masking position 5 Map Score: 4.42119 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 275 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 GTCTTGGCCTACAGGCGCTATAGCACGACG 1 129 0 ACAGGCGCTA 0.904354 -172 CTTCCACTGGCAACGAGTTACCGATATGGA 1 229 0 CAACGAGTTA 0.855199 -72 GAAGGTTTATCAACGTGCGACGCATTCCTG 1 255 1 CAACGTGCGA 0.954826 -46 GCCTTAGTGTATAGGTGTGAAGAAAAAATA 2 75 0 ATAGGTGTGA 0.854207 -135 TAATAATAAAAAAGGTGCTAACTATAACCA 2 119 0 AAAGGTGCTA 0.974639 -91 TAGTCACCCGCCAGGTGTGACGAAAAAACG 2 157 1 CCAGGTGTGA 0.962044 -53 GCCGTGGTGGCAAGGTGTTAGAACAACAGA 3 18 0 CAAGGTGTTA 0.974635 -212 GGATTGGTCAAAAGGAGCTCATCCTGATT 3 211 1 AAAGGAGCTC 0.816198 -19 ********** Masking position 3 Map Score: 4.11719 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 358 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 GGGTTGATATCCGCAGAGAGCGAGTCCATA 1 205 1 CCGCAGAGAG 0.990847 -96 TTAACTTTCACAGCACAAAGATAGATGAAA 3 101 1 CAGCACAAAG 0.988132 -129 TTCGAAAAAACAGCAAAAAGCACGATTTCA 3 126 0 CAGCAAAAAG 0.96828 -104 GGTAGCATACCCGCTCAGAGAATATGCGGA 4 129 0 CCGCTCAGAG 0.987475 -56 ********** Masking position 7 Map Score: 1.44666 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 74 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 6 AGAAAAAATAATATGCAATAAAAAAGGGCC 2 55 0 ATATGCAATA 0.90533 -155 ACCCGGTAAAATACGCAGAATTTTCCTGGG 3 183 1 ATACGCAGAA 0.969175 -47 TAGCATATCTATATACAGAAGGGAAATAAT 4 89 0 ATATACAGAA 0.931438 -96 CTGTATATAGATATGCTAAATCCTTACTTC 4 101 1 ATATGCTAAA 0.925642 -84 CGCTCAGAGAATATGCGGAAGTAAGGATTT 4 118 0 ATATGCGGAA 0.976159 -67 ********** Masking position 3 Map Score: 0.777442 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 148 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 TTGACGAAAGCGTCACACTGTACCTGATAA 1 62 0 CGTCACACTG 0.995335 -239 GTGACGCTTTCGTCAATCTGGCAATAGATT 1 76 1 CGTCAATCTG 0.985093 -225 AACCCCTTGTCGTGACTCTGTTCACGAAAA 1 180 0 CGTGACTCTG 0.9769 -121 ATCGTTTTTTCGTCACACCTGGCGGGTGAC 2 159 0 CGTCACACCT 0.948502 -51 GTTCTGATGGCGTCTAAGTGGATGGTTTAA 2 189 1 CGTCTAAGTG 0.890997 -21 ********** Masking position 3 Map Score: 1.26261 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 344 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 ********** No masking Map Score: 6.63809e-14 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 9 ACTGGCAACTTTGGATTTTGCATGCTAATAA 1 15 1 TTGGATTTGC 0.792209 -286 GCTAATAAAGTTGCGTATCGGATTTTATCAG 1 38 1 TTGCGTTCGG 0.94369 -263 TCGACCAAAATTCCGTCGTGCTATAGCGCCT 1 116 1 TTCCGTGTGC 0.977954 -185 CAGAGAGCGAGTCCATATCGGTAACTCGTTG 1 218 1 GTCCATTCGG 0.956768 -83 AGTAAATGTTTGCCGTGGTGGCAAGGTGTTA 3 28 0 TGCCGTGTGG 0.878671 -202 AGATGAAATCGTGCTTTTTGCTGTTTTTTCG 3 123 1 GTGCTTTTGC 0.872816 -107 TATCCTAACTGTCCATTGCGCAATTACCCGG 3 158 1 GTCCATGCGC 0.9724 -72 CCGCCCCTTATTCCATCTTGCATGTCATTAT 4 63 1 TTCCATTTGC 0.974011 -122 ****** **** Masking position 6 Map Score: 1.47725 Number of sites scoring better than the average of aligned sites = 857 Number in coding regions = 792 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 10 ********** No masking Map Score: 6.63809e-14 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: 6.63809e-14 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 ********** No masking Map Score: 6.63809e-14 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