AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -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 aceE 160 pyruvate dehydrogenase (decarboxylase component) #2 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #3 sdhC 300 succinate dehydrogenase, cytochrome b556 Motif number 1 AAACGTAGAACCTGTCTTATTGAGCTTTCCGGCGAG 1 77 1 CCGTATAGCT 0.75793 -84 GGGACAGGTTCCAGAAAACTCAACGTTATTAGATAG 1 121 1 CCGACTACGT 0.932678 -40 GAAGTAATACCCTAACCACCACCGGGTCGTTCTATC 2 117 0 CCAACCCGGG 0.985549 -184 CTTGCTGCACCCAGAAATCCATAGGGTATGTGAAGT 2 148 0 CCGACCAGGG 0.962412 -153 GTAGCAAGCGCCAGAATCCCCAGGAGCTTACATAAG 2 184 1 CCGACCGGAG 0.960208 -117 GCCGCTGCGGCCTGAAAGACGACGGGTATGACCGCC 2 251 1 CCGAACCGGG 0.562623 -50 GCAGGGTGTTCCGGAGACCTGGCGGCAGTATAGGCT 3 73 0 CCGACTCGGC 0.986144 -228 ACCCTGCAATCCCGAGCCACCCAGCGTTGTAACGTG 3 102 1 CCGAACAGCG 0.98147 -199 TTTCCTTCCTCCGGTCTGCTTGCGGGTCAGACAGCG 3 191 0 CCGTCTCGGG 0.900998 -110 GGAAGGAAATCCCGACGTCTCCAGGTAACAGAAAGT 3 218 1 CCGACTAGGT 0.989143 -83 AACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAGA 3 255 1 CCGTCCAGGG 0.882285 -46 ** ** ** **** Masking position 2 Map Score: 18.1759 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 670 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 TCTTATTGAGCTTTCCGGCGAGAGTTCAATG 1 91 1 CTTCCGGCGA 0.935411 -70 CCGGGTCGTTCTATCCGTCGGTATTTTACAA 2 101 0 CTTCCGTCGG 0.965887 -200 ACGGATAGAACGACCCGGTGGTGGTTAGGGT 2 114 1 CGCCCGGTGG 0.983895 -187 ATTACTTCACATACCCTATGGATTTCTGGGT 2 145 1 ATCCCTATGG 0.731884 -156 TACCCTATGGATTTCTGGGTGCAGCAAGGTA 2 156 1 ATTCTGGGTG 0.683464 -145 CTGGCGCTTGCTACCTTGCTGCACCCAGAAA 2 167 0 CTCCTTGCTG 0.849326 -134 TACTTATGTAAGCTCCTGGGGATTCTGGCGC 2 191 0 AGTCCTGGGG 0.963254 -110 GTGAAGCTAACGCCGCTGCGGCCTGAAAGAC 2 240 1 CGCGCTGCGG 0.941452 -61 TCCGGCGGTCATACCCGTCGTCTTTCAGGCC 2 259 0 ATCCCGTCGT 0.80971 -42 CTATATATTTATCTCCGGCGGTCATACCCGT 2 272 0 ATTCCGGCGG 0.993719 -29 GGTGTTCCGGAGACCTGGCGGCAGTATAGGC 3 74 0 AGCCTGGCGG 0.984445 -227 TGTTCTTATTATTCCCTGGGGACTACGGGCA 3 263 0 ATCCCTGGGG 0.985994 -38 ** ******** Masking position 5 Map Score: 11.928 Number of sites scoring better than the average of aligned sites = 4257 Number in coding regions = 3994 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 3 TGATTTTTCTGGTAAAAATTATCCA 1 5 1 TTTCTGGTAA 0.973606 -156 ATTTACAACATCTTCTGGATAATTTTTACCA 1 20 0 TTTCTGGATA 0.877049 -141 TAACGTTGAGTTTTCTGGAACCTGTCCCATT 1 118 0 TTTCTGGAAC 0.932812 -43 GCTTTTTTCTGGTAATCTCATGAAT 2 5 1 TTTCTGGTAA 0.973606 -296 CTCATGAATGTATTGAGGTTATTAGCGAATA 2 27 1 TTTGAGGTTA 0.858406 -274 ATCACTGTTCAGGATAAAACCCGACA 3 6 1 TTTCAGGATA 0.94805 -295 GATTGCAGGGTGTTCCGGAGACCTGGCGGCA 3 82 0 TTTCCGGAGA 0.92478 -219 AATCCCGACGTCTCCAGGTAACAGAAAGTTA 3 225 1 TTCCAGGTAA 0.763755 -76 * ********* Masking position 3 Map Score: 8.33389 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 276 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 AAGATGTTGTAAATCAAGCGCATATAAAAGC 1 37 1 AATCAAGCGC 0.896331 -124 GTGCAGCAAGGTAGCAAGCGCCAGAATCCCC 2 174 1 GAGCAAGCGC 0.953628 -127 AGCGGCGTTAGCTTCACGCCCTCACCCCAGT 2 226 0 GTTCACGCCC 0.976257 -75 AAGACGACGGGTATGACCGCCGGAGATAAAT 2 266 1 GATGACCGCC 0.93248 -35 TCACTGTTCAGGATAAAACCCGACAAACTAT 3 12 1 GATAAAACCC 0.841672 -289 GCAGTGTTTTGCATGACGCGCAGTTATAGAA 3 156 1 GATGACGCGC 0.994914 -145 AAAGGACGCTGTCTGACCCGCAAGCAGACCG 3 185 1 GCTGACCCGC 0.962464 -116 GAATAACGCCCACATGCTGTT 3 290 0 GATAACGCCC 0.988753 -11 * ********* Masking position 6 Map Score: 3.92368 Number of sites scoring better than the average of aligned sites = 1201 Number in coding regions = 1115 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 GACAGGTTCTACGTTTAGTTGCCGCGCTTT 1 63 0 ACGTTTAGTT 0.973994 -98 CTATCTAATAACGTTGAGTTTTCTGGAACC 1 127 0 ACGTTGAGTT 0.956466 -34 CAATTAACCTACATATAGTTTGTCGGGTTT 3 27 0 ACATATAGTT 0.833566 -274 CAGCGTTGTAACGTGTCGTTTTCGCATCTG 3 123 1 ACGTGTCGTT 0.963677 -178 GTTTTGCATGACGCGCAGTTATAGAAAGGA 3 161 1 ACGCGCAGTT 0.966089 -140 ACAGAGGTTAACTTTCTGTTACCTGGAGAC 3 234 0 ACTTTCTGTT 0.858133 -67 AATAACGCCCACATGCTGTTCTTATTATTC 3 280 0 ACATGCTGTT 0.943726 -21 ********** Masking position 1 Map Score: 3.13773 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 279 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 ********** No masking Map Score: -9.70439e-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 7 ********** No masking Map Score: -9.70439e-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 8 ********** No masking Map Score: -9.70439e-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