AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i158_CYD_operon_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 cydD 122 ATP-binding component of cytochrome-related transport, Zn sensitive #2 trxB 300 thioredoxin reductase #3 HI1157 71 ATP-binding protein protein (cydD) #4 HI1158 73 thioredoxin reductase (trxB) #5 HI1159 284 conserved hypothetical protein #6 HI1161 300 conserved hypothetical protein Motif number 1 ATCGGCTTATAAAGCGGGAAATTTAAGTAG 2 136 1 AAAGCGGGAA 0.839345 -165 CAGAGGTGATAATGACGGGAGAATTTGACC 2 166 1 AATGACGGGA 0.903706 -135 AAAAGAGTTAAAAGAGGGGAATTGGTTAGA 3 15 0 AAAGAGGGGA 0.98464 -57 TAACTCTTTTAAAGAGGGGAACTTTTTCTA 3 35 1 AAAGAGGGGA 0.98464 -37 TGATTTTAGCAAAGTGCGGAAGATTTTAGA 5 32 0 AAAGTGCGGA 0.871533 -253 ACGCATAAAGAATCGGCGGATTTTTTGGCA 5 193 1 AATCGGCGGA 0.898929 -92 TCCACCCATTTATGGGGGGA 6 1 0 TATGGGGGGA 0.993873 -300 TCCCCCCATAAATGGGTGGAGCCAAGATTA 6 11 1 AATGGGTGGA 0.981841 -290 TTCCCCTGCTTGTGGGGGAAGGTGCCCGAA 6 103 1 TGTGGGGGAA 0.886509 -198 CTGCCGAAGGTGAGGGGGGATAAATGTTCA 6 228 0 TGAGGGGGGA 0.976099 -73 TCCACCCATTTATGGGGGGAGCTGCCGAAG 6 249 0 TATGGGGGGA 0.993873 -52 TCCCCCCATAAATGGGTGGAGCCAAGATAA 6 259 1 AATGGGTGGA 0.981841 -42 ********** Masking position 10 Map Score: 20.818 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 188 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 ATAAAGGCGACCCATAGTCGCATGGTGTCGCCTTC 1 37 0 CCCATGCTGG 0.980025 -86 CTTTGACAATCCCCTGGTGTTTTGCGAAAACATTC 2 36 0 CCCCTTTTGC 0.983561 -265 GTCTGTAAATTCCCTACAATCCTGCCCATTGTCTG 2 256 1 TCCCTTCTGC 0.797928 -45 GAGATCCCCATAGTTGTTGGCAGACAATGGG 2 280 0 CCCATGTGGC 0.989443 -21 CTTGGCTCCACCCATTTATGGGGGGA 6 2 0 CCCATGGGGG 0.963925 -299 AACTTGCCTTCCCCTGCTTGTGGGGGAAGGTGCCC 6 95 1 CCCCTGTGGG 0.968075 -206 TCCCTATATCCCCCTTCCCTTCGGGCACCTTCCCC 6 117 0 CCCCTTTGGG 0.994449 -184 ACATTTATCCCCCCTCACCTTCGGCAGCTCCCCCC 6 231 1 CCCCTTTGGC 0.993826 -70 CTTGGCTCCACCCATTTATGGGGGGAGCTGCCGAA 6 250 0 CCCATGGGGG 0.963925 -51 ***** ** *** Masking position 5 Map Score: 14.6124 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 112 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 CAGATATTCATTAACAGGGGCGTTTATTCA 2 99 1 TTAACAGGGG 0.928014 -202 AATCGGCTTATAAAGCGGGAAATTTAAGTA 2 135 1 TAAAGCGGGA 0.86465 -166 GCAGAGGTGATAATGACGGGAGAATTTGAC 2 165 1 TAATGACGGG 0.894662 -136 TAAAAGAGTTAAAAGAGGGGAATTGGTTAG 3 16 0 AAAAGAGGGG 0.928087 -56 TTAACTCTTTTAAAGAGGGGAACTTTTTCT 3 34 1 TAAAGAGGGG 0.986304 -38 CTCCACCCATTTATGGGGGGA 6 2 0 TTATGGGGGG 0.991322 -299 CTTCCCCTGCTTGTGGGGGAAGGTGCCCGA 6 102 1 TTGTGGGGGA 0.91663 -199 GCTGCCGAAGGTGAGGGGGGATAAATGTTC 6 229 0 GTGAGGGGGG 0.948109 -72 CTCCACCCATTTATGGGGGGAGCTGCCGAA 6 250 0 TTATGGGGGG 0.991322 -51 ********** Masking position 8 Map Score: 8.93954 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 126 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 GTCGCCTTTATTTTTTCCCCGTTGTAACATTGCTCTG 1 61 1 TTTTTCTTAA 0.973417 -62 TAACAGGGGCGTTTATTCATCATTTAATCGGCTTATA 2 110 1 GTTATATTAA 0.72209 -191 CGTCATACTCTTTTTTTACGTCTGTAAATTCCCTACA 2 237 1 TTTTTCTTAA 0.973417 -64 CCAATTCCCCTCTTTTAACTCTTTTAAAGAGGGGAAC 3 20 1 TTTTTCTTAA 0.973417 -52 CAGCCATTATTTTTTTCACAAGGATAAAACATGGCTG 5 60 1 TTTTTCGTAA 0.87335 -225 TCGCTCTTTTTCACAATTTACTTTTCCAAGA 5 264 0 TTTTTATTAC 0.912834 -21 TATCATTATTTATTTTAGAACCTCTAATCTTGGCTCC 6 28 0 TTTTTATTAA 0.964647 -273 GGGAAGGCAAGTTTTTAAAACCTCTAATAAGCAGAAG 6 71 0 GTTTTATTAA 0.912834 -230 CACTCCAAAATTTTATTTCGCATATCCCTATATCCCC 6 139 0 TTTATCTTCC 0.685863 -162 ACATTATCTATGTTTTTTAATATTTCATCACTCCAAA 6 167 0 TTTTTATTCA 0.94472 -134 TTAATCTATTCCATATTATCAATTATCTTGG 6 280 0 TTATTATTCA 0.684688 -21 * **** * * *** Masking position 6 Map Score: 5.76939 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 74 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 ATGAATATCTGGCATGTTGTACTAAAAATC 2 80 0 GGCATGTTGT 0.937892 -221 GCTAAAATCAGCCATTATTTTTTTCACAAG 5 52 1 GCCATTATTT 0.814335 -233 AGGAAAATCAGCCATGTTTTATCCTTGTGA 5 75 0 GCCATGTTTT 0.977793 -210 AATGGGTGGAGCCAAGATTAGAGGTTCTAA 6 21 1 GCCAAGATTA 0.950383 -280 ATAAGCAGAAGGCAAGTTATCATTATTTAT 6 52 0 GGCAAGTTAT 0.959007 -249 AGCAGGGGAAGGCAAGTTTTTAAAACCTCT 6 83 0 GGCAAGTTTT 0.977603 -218 AATGGGTGGAGCCAAGATAATTGATAATAT 6 269 1 GCCAAGATAA 0.911237 -32 ********** Masking position 4 Map Score: 4.00611 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 272 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 GTCGCCTTTATTTTTTCCCCGTTGTAACATT 1 61 1 TTTTTCCCCG 0.89696 -62 TACTGTTTTTTTTCTTCCTCGAATGTTTTCG 2 16 1 TTTTTCCTCG 0.970391 -285 AAAAATCGATGTTTTGCTTTGACAATCCCCT 2 56 0 GTTTGCTTTG 0.764773 -245 ATCAGCCATGTTTTATCCTTGTGAAAAAAAT 5 68 0 TTTATCCTTG 0.946894 -217 CTGATTTTCCTTTTATCGTTGAGATCAACGA 5 94 1 TTTATCGTTG 0.946894 -191 TCAGTAAGATTTTGTTCGTTGATCTCAACGA 5 109 0 TTTTTCGTTG 0.979881 -176 CCGCCGATTCTTTATGCGTTGGCGCGTAAAA 5 181 0 TTTTGCGTTG 0.965011 -104 TCAAGGACAATTTATTCTTGGAAAAGTAAAT 5 249 1 TTTTTCTTGG 0.887691 -36 *** ******* Masking position 3 Map Score: 4.08089 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 157 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 GTTATCAGAATTATTTGCAGAGCAATGTTAC 1 84 0 TTATTGCAGA 0.882182 -39 TGCACGCTTAGCAGGTGAGTTATCA 1 108 0 CGCTAGCAGG 0.850975 -15 ATTTCCCGCTTTATAAGCCGATTAAATGATG 2 127 0 TTATAGCCGA 0.782112 -174 GCGGGAAATTTAAGTAGCAGAGGTGATAATG 2 149 1 TAAGAGCAGA 0.922316 -152 TCGGCAGCATCGATAAGCAGGTCAAATTCTC 2 184 0 CGATAGCAGG 0.960692 -117 ACAATTTGTGCAATCGGCAGCATCGATAAGC 2 197 0 CAATGGCAGC 0.929974 -104 TGTTGGCAGACAATGGGCAGGATTGTAGGGA 2 266 0 CAATGGCAGG 0.972678 -35 ATCCCCATAGTTGTTGGCAGACAATGGGCAG 2 277 0 TTGTGGCAGA 0.797643 -24 ACTACTTGAGCAAGTTGCAGAACAATATCAA 5 222 1 CAAGTGCAGA 0.891735 -63 TTAAAACCTCTAATAAGCAGAAGGCAAGTTA 6 63 0 TAATAGCAGA 0.96505 -238 **** ****** Masking position 8 Map Score: 3.15899 Number of sites scoring better than the average of aligned sites = 774 Number in coding regions = 713 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 TTACTTTTGTTACTGATTTGTAAAA 1 6 0 TACTGATTTG 0.870957 -117 AAGAATACTGTTTTTTTTCTTCCTC 2 6 1 TACTGTTTTT 0.940618 -295 AAAATCGTCATACTCTTTTTTTACGTCTGT 2 232 1 TACTCTTTTT 0.848581 -69 AGTTGCATTTTACTGATTATAAACTTTTTG 4 12 0 TACTGATTAT 0.819945 -62 AAAAAATAATGGCTGATTTTAGCAAAGTGC 5 45 0 GGCTGATTTT 0.979869 -240 GATAAAACATGGCTGATTTTCCTTTTATCG 5 82 1 GGCTGATTTT 0.979869 -203 ATAAAGAATCGGCGGATTTTTTGGCACTAC 5 197 1 GGCGGATTTT 0.928202 -88 TCGCTCTTTTTCACAATTTAC 5 274 0 CGCTCTTTTT 0.800175 -11 ********** Masking position 7 Map Score: 4.02823 Number of sites scoring better than the average of aligned sites = 820 Number in coding regions = 693 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 9 ********** No masking Map Score: 2.75223e-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 10 ********** No masking Map Score: 2.75223e-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 11 ********** No masking Map Score: 2.75223e-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