AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i026_ecoli_bsub_100.orf -o026_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #2 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #3 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) Motif number 1 AATTTAATTACTAAACCATCAGATCGTGCTT 1 84 0 CTAACCATCA 0.867706 -211 TCAGTGATAATTTAGCCCTCTTGCGCACTAA 1 123 1 TTTACCCTCT 0.972993 -172 AAATTTCAGACTTATCCATCAGACTATACTG 1 170 1 CTTACCATCA 0.937799 -125 CCAGATTGTTTTTATCCCACAGCCACGTACT 1 265 0 TTTACCCACA 0.872459 -30 GATAGCCCCTCTCCCTCTAGTAATCTAG 2 16 0 CCTCCCCTCT 0.984227 -18 ATCTGTCTCCCCTCTCTCCTGCGTATA 3 7 1 CTCCCTCTCT 0.962438 -286 TTCTGTAATCCTCCCCCCTGTTTGAGCTATA 3 39 0 CTCCCCCTGT 0.987409 -254 TTTCATTTTACTCCTCCCTCAAAAGGGCGTC 3 180 0 CTCCCCCTCA 0.995033 -113 TGCTAAATCTCTTCCCCCACTTCTTTCAATT 3 240 0 CTTCCCCACT 0.98812 -53 TACTTTACCCCCTGTTTGATAAGTG 3 278 0 TTACCCCTGT 0.907583 -15 **** ****** Masking position 6 Map Score: 12.8145 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 598 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 AGACAAATTTTACGCAGGAATCAAACAGCG 1 36 1 TACGCAGGAA 0.993967 -259 ATTTTTTTAGTGCGCAAGAGGGCTAAATTA 1 130 0 TGCGCAAGAG 0.989781 -165 AGCTATAATATACGCAGGAGAGAGGGGAGA 3 16 0 TACGCAGGAG 0.996099 -277 TATGAAAAATTAAGCAAGAAATATATATTG 3 85 1 TAAGCAAGAA 0.964119 -208 ********** Masking position 6 Map Score: 4.24112 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 43 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 ACTGCCCACCGCTGTTTGATTCCTGCGTAA 1 45 0 GCTGTTTGAT 0.98995 -250 GAAGTACGTGGCTGTGGGATAAAAACAATC 1 263 1 GCTGTGGGAT 0.952359 -32 AATCCTCCCCCCTGTTTGAGCTATAATATA 3 34 0 CCTGTTTGAG 0.993585 -259 TTTCTTGACGCCCTTTTGAGGGAGGAGTAA 3 174 1 CCCTTTTGAG 0.930413 -119 TACTTTACCCCCTGTTTGATAAGTGCGAAA 3 273 0 CCTGTTTGAT 0.993079 -20 ********** Masking position 5 Map Score: 4.15754 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 154 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 4 GGGCAGTGACTAAAAAAAGCACGATCTGAT 1 68 1 TAAAAAAAGC 0.846119 -227 GTTTAGTAATTAAATTAATCATCTTCAGTG 1 99 1 TAAATTAATC 0.920311 -196 TCTTGCGCACTAAAAAAATCGATCTCGTCA 1 141 1 TAAAAAAATC 0.937647 -154 CCCCTCTCCCTCTAGTAATCTAGTACTC 2 9 0 TCTAGTAATC 0.884523 -25 AATTTTTCAATCAACTAATCAATTCGGAAA 3 124 1 TCAACTAATC 0.95249 -169 CAAAAGGGCGTCAAGAAAACGCGTACATAA 3 162 0 TCAAGAAAAC 0.922192 -131 AATGAAATTGTCAATAAATCTTAATAAAGT 3 204 1 TCAATAAATC 0.968807 -89 ********** Masking position 4 Map Score: 3.69879 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 166 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 ACGGCGAGACAAATTTTACGCAGGAATCAA 1 30 1 AAATTTTACG 0.97802 -265 GATAAGTCTGAAATTTGACGAGATCGATTT 1 156 0 AAATTTGACG 0.952481 -139 ATTTCTTGCTTAATTTTTCATAAGAATTAC 3 77 0 TAATTTTTCA 0.93235 -216 TGATAAAATAAAATTTTTCAATCAACTAAT 3 113 1 AAATTTTTCA 0.951803 -180 ACATAAATTATAATTTTCCGAATTGATTAG 3 138 0 TAATTTTCCG 0.9631 -155 ********** Masking position 5 Map Score: 2.67357 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 95 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TCATCTTCAGTGATAATTTAGCCCTCTTGC 1 117 1 TGATAATTTA 0.962879 -178 TGGATAAGTCTGAAATTTGACGAGATCGAT 1 158 0 TGAAATTTGA 0.811895 -137 GTAATTCTTATGAAAAATTAAGCAAGAAAT 3 77 1 TGAAAAATTA 0.816975 -216 ATTCGGAAAATTATAATTTATGTACGCGTT 3 145 1 TTATAATTTA 0.876389 -148 TAAGATTTATTGACAATTTCATTTTACTCC 3 197 0 TGACAATTTC 0.94973 -96 AATAAAGTGCTTACAATTGAAAGAAGTGGG 3 226 1 TTACAATTGA 0.902302 -67 ACCCCCTGTTTGATAAGTGCGAAATGTGCT 3 267 0 TGATAAGTGC 0.88543 -26 ********** Masking position 5 Map Score: 0.921844 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 226 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 7 ********** No masking Map Score: -6.01529e-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 8 ********** No masking Map Score: -6.01529e-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 9 ********** No masking Map Score: -6.01529e-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