AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ioxyR_rpxx_opreg_100.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP805 249 DIHYDROLIPOAMIDE DEHYDROGENASE (pdhD) #2 RP806 300 unknown Motif number 1 ATTTGTATCGTTGTTTTATATTTTTTAGTTTT 1 19 1 TTTTTATATT 0.978879 -231 AAAGAGCTAAATGTTTTATATTTCTTAACTGC 1 69 0 ATTTTATATT 0.889428 -181 TTTATTTTTATTTTATTGGTTC 1 238 0 TTTTTTTATT 0.842964 -12 TTCCGTCATATTATTTTATATATGGTAATTCA 2 37 1 TTTTTATATA 0.985587 -264 ATACAAAACATTTGATTGTCTTGAATTACCAT 2 58 0 TTATTGTCTT 0.795116 -243 ATCAAATGTTTTGTATTAGATAATTTTCTTAG 2 74 1 TTATTAGATA 0.955215 -227 ATTAGATAATTTTCTTAGTATTATCCTATTTG 2 88 1 TTTTAGTATT 0.787301 -213 TTGAAGCATATTAATTTAGCTATAATTATATT 2 117 1 TTTTTAGCTA 0.894157 -184 TTAACTATTAATTAATAATATAATTATAGCTA 2 133 0 ATATAATATA 0.582423 -168 TAATTAATAGTTAATTTATATATCATTTTGCT 2 151 1 TTTTTATATA 0.985585 -150 CATTTTGCTATTCCTTTGTATTTAAAAATTTT 2 174 1 TTTTTGTATT 0.955215 -127 TTTAAAAATTTTTAATTAAATAATTAATATAT 2 194 1 TTATTAAATA 0.842964 -107 TTATATAATTTTCTATTATATATTAATTATTT 2 211 0 TTATTATATA 0.97888 -90 TCAAGCGATATTAAATTATATAATTTTCTATT 2 226 0 TTATTATATA 0.97888 -75 GTTTATAACATTTCTTTAGATACTTCAAGCGA 2 250 0 TTTTTAGATA 0.969158 -51 ** ******** Masking position 6 Map Score: 22.1017 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 460 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 2 TTTGAAAAATTTGTATCGTTGTTTT 1 5 1 AAAAATTTTA 0.957168 -245 ATCGTTGTTTTATATTTTTTAGTTTTTAAGT 1 25 1 TATATTTTTA 0.769897 -225 AAAAGAGCTAAATGTTTTATATTTCTTAACT 1 71 0 AATGTTTTTA 0.972428 -179 CCTTTACTGAAAAAATATATAGAATTTAGTA 1 112 0 AAAAATATTA 0.932956 -138 AAGTGTTGATAAAGTTCTTTAAATGCTGAGG 1 151 1 AAAGTTCTTA 0.862288 -99 CCTTTTTTGGAATAATTTATACCTTAAAATA 1 207 1 AATAATTTTA 0.965863 -43 TTTCCGTCATATTATTTTATATATGGTAATT 2 36 1 ATTATTTTTA 0.792428 -265 AAGACAATCAAATGTTTTGTATTAGATAATT 2 68 1 AATGTTTTTA 0.972447 -233 TAATACTAAGAAAATTATCTAATACAAAACA 2 80 0 AAAATTATTA 0.949525 -221 GGAATAGCAAAATGATATATAAATTAACTAT 2 157 0 AATGATATTA 0.944787 -144 TTATTTAATTAAAAATTTTTAAATACAAAGG 2 186 0 AAAAATTTTA 0.956229 -115 TTTTTAATTAAATAATTAATATATAATAGAA 2 202 1 AATAATTATA 0.743556 -99 TATATAATAGAAAATTATATAATTTAATATC 2 221 1 AAAATTATTA 0.948481 -80 TATCTAAAGAAATGTTATAAACTCAAAAAGT 2 260 1 AATGTTATAA 0.689407 -41 ******** ** Masking position 11 Map Score: 21.0366 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 539 Number in noncoding regions = 379 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 3 ATCGTTGTTTTATATTTTTTAGTTTTTAAG 1 25 1 TATATTTTTT 0.967151 -225 CTAAATGTTTTATATTTCTTAACTGCAATA 1 65 0 TATATTTCTT 0.822784 -185 ATAAAACATTTAGCTCTTTTAAAGATCATC 1 82 1 TAGCTCTTTT 0.78021 -168 CTAAATTCTATATATTTTTTCAGTAAAGGT 1 114 1 TATATTTTTT 0.967151 -136 ATGCTGAGGTTATCTCATTTTACCATAGAT 1 173 1 TATCTCATTT 0.955441 -77 ACTTCTATTCTTTTTTAGTACTTAA 2 6 1 TATTCTTTTT 0.541724 -295 TAATTTCCGTCATATTATTTTATATATGGT 2 33 1 CATATTATTT 0.882787 -268 TGTTTTGTATTAGATAATTTTCTTAGTATT 2 80 1 TAGATAATTT 0.806416 -221 TTCTTAGTATTATCCTATTTGAAGCATATT 2 99 1 TATCCTATTT 0.89171 -202 TAGCTATAATTATATTATTAATTAATAGTT 2 133 1 TATATTATTA 0.835542 -168 AGTTAATTTATATATCATTTTGCTATTCCT 2 159 1 TATATCATTT 0.976998 -142 TTTTCTATTATATATTAATTATTTAATTAA 2 205 0 TATATTAATT 0.845996 -96 GATATTAAATTATATAATTTTCTATTATAT 2 222 0 TATATAATTT 0.934856 -79 TTTTTGAGTTTATAACATTTCTTTAGATAC 2 259 0 TATAACATTT 0.831071 -42 ********** Masking position 2 Map Score: 16.4181 Number of sites scoring better than the average of aligned sites = 1011 Number in coding regions = 688 Number in noncoding regions = 323 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 4 TTTGAAAAATTTGTATCGTTGTTT 1 5 1 AAAAATTTGT 0.743844 -245 CCTTTACTGAAAAAATATATAGAATTTAGT 1 113 0 AAAAATATAT 0.742085 -137 CAGCATTTAAAGAACTTTATCAACACTTGA 1 149 0 AGAACTTTAT 0.906808 -101 CCTTTTTTGGAATAATTTATACCTTAAAAT 1 207 1 AATAATTTAT 0.701366 -43 ATTCTTTTTTAGTACTTAATTTCCGTCATA 2 17 1 AGTACTTAAT 0.777828 -284 ATTACCATATATAAAATAATATGACGGAAA 2 36 0 ATAAAATAAT 0.60012 -265 GATAATACTAAGAAAATTATCTAATACAAA 2 83 0 AGAAAATTAT 0.920253 -218 ATTATTAATTAATAGTTAATTTATATATCA 2 146 1 AATAGTTAAT 0.78204 -155 TTATTTAATTAAAAATTTTTAAATACAAAG 2 187 0 AAAAATTTTT 0.474785 -114 TTTTTAATTAAATAATTAATATATAATAGA 2 202 1 AATAATTAAT 0.721488 -99 AATATATAATAGAAAATTATATAATTTAAT 2 219 1 AGAAAATTAT 0.920253 -82 TTCAAGCGATATTAAATTATATAATTTTCT 2 229 0 ATTAAATTAT 0.649399 -72 TATAAACTCAAAAAGTTCATAAGAATTTGA 2 275 1 AAAAGTTCAT 0.72678 -26 ********** Masking position 4 Map Score: 8.71044 Number of sites scoring better than the average of aligned sites = 1770 Number in coding regions = 1167 Number in noncoding regions = 603 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 5 TACTTAAAAACTAAAAAATATAAAACAACG 1 27 0 CTAAAAAATA 0.94514 -223 AGTAGATGATCTTTAAAAGAGCTAAATGTT 1 86 0 CTTTAAAAGA 0.964651 -164 ATAACCTCAGCATTTAAAGAACTTTATCAA 1 156 0 CATTTAAAGA 0.711637 -94 ATAAATTATTCCAAAAAAGGTGAAATCTAT 1 197 0 CCAAAAAAGG 0.857445 -53 ATAATTTATACCTTAAAATAGAACCAATAA 1 218 1 CCTTAAAATA 0.933926 -32 AAAATAGAACCAATAAAATAAAAATAAA 1 232 1 CAATAAAATA 0.936745 -18 AAATTAAGTACTAAAAAAGAATAGAAGT 2 9 0 CTAAAAAAGA 0.964697 -292 GAATTACCATATATAAAATAATATGACGGA 2 38 0 ATATAAAATA 0.75528 -263 ********** Masking position 6 Map Score: 4.98298 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 384 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 ********** No masking Map Score: 1.81432e-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 7 ********** No masking Map Score: 1.81432e-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 8 ********** No masking Map Score: 1.81432e-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