AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ioxyR_rpxx_opreg_300.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 TGTATCGTTGTTTTATATTTTTTAGTTTTTAAGT 1 22 1 TTTTTATTTA 0.977555 -228 GAGCTAAATGTTTTATATTTCTTAACTGCAATAC 1 64 0 TTTTTATTTA 0.977637 -186 TGAAAAAATATATAGAATTTAGTAGATGATCTTT 1 102 0 TATAAATTTA 0.681849 -148 TTTATTTTTATTTTATTGGTTCTATTTTAAGGTA 1 226 0 TTTTTTGTTA 0.817349 -24 ACTTCTATTCTTTTTTAGTACTTAATTTCCGTCA 2 11 1 TTTTTATATA 0.984741 -290 ATTTCCGTCATATTATTTTATATATGGTAATTCA 2 35 1 TATTTTTATA 0.883383 -266 CAATCAAATGTTTTGTATTAGATAATTTTCTTAG 2 72 1 TTTTTATATA 0.984711 -229 TATTAGATAATTTTCTTAGTATTATCCTATTTGA 2 87 1 TTTTTTGTTA 0.817349 -214 ATTTGAAGCATATTAATTTAGCTATAATTATATT 2 115 1 TATTATTATA 0.873159 -186 TAGCTATAATTATATTATTAATTAATAGTTAATT 2 133 1 TATATATATA 0.84479 -168 TAATTAAAAATTTTTAAATACAAAGGAATAGCAA 2 178 0 TTTTAATAAA 0.749571 -123 TATTTAAAAATTTTTAATTAAATAATTAATATAT 2 192 1 TTTTAATATA 0.599592 -109 AATTATATAATTTTCTATTATATATTAATTATTT 2 211 0 TTTTTATATA 0.984512 -90 CTTCAAGCGATATTAAATTATATAATTTTCTATT 2 226 0 TATTAATATA 0.570115 -75 TCTTATGAACTTTTTGAGTTTATAACATTTCTTT 2 265 0 TTTTGATTTA 0.901035 -36 **** ** ** ** Masking position 14 Map Score: 21.5026 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 599 Number in noncoding regions = 392 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 2 ACTAGTACTTAAAAACTAAAAAATATAAAACAA 1 29 0 AAAACTAAAA 0.960702 -221 TATTGCAGTTAAGAAATATAAAACATTTAGCTC 1 65 1 AAAAATAAAA 0.938399 -185 AATTTAGTAGATGATCTTTAAAAGAGCTAAATG 1 88 0 ATATCTAAAA 0.932844 -162 TGATTTTAACCTTTACTGAAAAAATATATAGAA 1 119 0 CTTACTAAAA 0.904557 -131 AGTGTTGATAAAGTTCTTTAAATGCTGAGGTTA 1 152 1 AATTCTAAAT 0.800404 -98 TTAAGGTATAAATTATTCCAAAAAAGGTGAAAT 1 201 0 AATATTAAAA 0.801103 -49 AATAGAACCAATAAAATAAAAATAAA 1 234 1 ATAAATAAAT 0.918503 -16 GACGGAAATTAAGTACTAAAAAAGAATAGAAGT 2 11 0 AATACTAAAA 0.973023 -290 TAAGAAAATTATCTAATACAAAACATTTGATTG 2 72 0 ATTAATAAAA 0.977594 -229 AGCTAAATTAATATGCTTCAAATAGGATAATAC 2 105 0 ATTGCTAAAT 0.819878 -196 GAATAGCAAAATGATATATAAATTAACTATTAA 2 154 0 ATATATAAAT 0.767352 -147 TATATTAATTATTTAATTAAAAATTTTTAAATA 2 192 0 ATTAATAAAA 0.97552 -109 AATAATTAATATATAATAGAAAATTATATAATT 2 212 1 ATTAATAAAA 0.977598 -89 ATAGAAAATTATATAATTTAATATCGCTTGAAG 2 227 1 ATTAATAATA 0.799737 -74 AAGAAATGTTATAAACTCAAAAAGTTCATAAGA 2 266 1 ATAACTAAAA 0.979367 -35 ** **** **** Masking position 10 Map Score: 21.2836 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 552 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 AAACAACGATACAAATTTTTCAAA 1 5 0 ACAAATTTTT 0.772607 -245 TATCGTTGTTTTATATTTTTTAGTTTTTAA 1 24 1 TTATATTTTT 0.928177 -226 ACTAAATTCTATATATTTTTTCAGTAAAGG 1 113 1 ATATATTTTT 0.926598 -137 AATGCTGAGGTTATCTCATTTTACCATAGA 1 172 1 TTATCTCATT 0.746221 -78 ATTTTAAGGTATAAATTATTCCAAAAAAGG 1 207 0 ATAAATTATT 0.890756 -43 TTTATTTTTATTTTATTGGTTCTATTT 1 233 0 TTATTTTATT 0.899666 -17 TTAATTTCCGTCATATTATTTTATATATGG 2 32 1 TCATATTATT 0.962126 -269 CTAATACAAAACATTTGATTGTCTTGAATT 2 63 0 ACATTTGATT 0.629746 -238 TTAGCTATAATTATATTATTAATTAATAGT 2 132 1 TTATATTATT 0.965433 -169 TAGTTAATTTATATATCATTTTGCTATTCC 2 158 1 ATATATCATT 0.939807 -143 ATTTTCTATTATATATTAATTATTTAATTA 2 206 0 ATATATTAAT 0.732425 -95 CGATATTAAATTATATAATTTTCTATTATA 2 223 0 TTATATAATT 0.797156 -78 TGAGTTTATAACATTTCTTTAGATACTTCA 2 255 0 ACATTTCTTT 0.678534 -46 ATATCCTCAAATTCTTATGAACTTTT 2 285 0 TCAAATTCTT 0.607914 -16 ********** Masking position 3 Map Score: 12.5645 Number of sites scoring better than the average of aligned sites = 1530 Number in coding regions = 983 Number in noncoding regions = 547 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 4 TATTTTTTAGTTTTTAAGTACTAGTATGTAT 1 37 1 TTTTTAATAC 0.988744 -213 TGTTTTATATTTCTTAACTGCAATACATACT 1 59 0 TTCTTAATGC 0.898339 -191 TTCTATATATTTTTTCAGTAAAGGTTAAAAT 1 119 1 TTTTTCATAA 0.852814 -131 TTGATAAAGTTCTTTAAATGCTGAGGTTATC 1 156 1 TCTTTAATGC 0.964034 -94 ACTTCTATTCTTTTTTAGTACTTAATTTCCG 2 11 1 TTTTTTATAC 0.932641 -290 CATTTGATTGTCTTGAATTACCATATATAAA 2 51 0 TCTTGAATAC 0.928887 -250 TATAATTATATTATTAATTAATAGTTAATTT 2 137 1 TTATTAATAA 0.782274 -164 TAATTAAAAATTTTTAAATACAAAGGAATAG 2 181 0 TTTTTAATAC 0.988209 -120 TATTTAAAAATTTTTAATTAAATAATTAATA 2 192 1 TTTTTAATAA 0.960737 -109 TTATAACATTTCTTTAGATACTTCAAGCGAT 2 249 0 TCTTTAGTAC 0.92888 -52 ******* *** Masking position 4 Map Score: 13.2795 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 232 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 GAAATATAAAACATTTAGCTCTTTTAAAGA 1 77 1 ACATTTAGCT 0.958716 -173 TGAGGTTATCTCATTTTACCATAGATTTCA 1 177 1 TCATTTTACC 0.914243 -73 TGAAGCATATTAATTTAGCTATAATTATAT 2 118 1 TAATTTAGCT 0.971355 -183 AAATGATATATAAATTAACTATTAATTAAT 2 149 0 TAAATTAACT 0.82061 -152 AATTTATATATCATTTTGCTATTCCTTTGT 2 163 1 TCATTTTGCT 0.981591 -138 ********** Masking position 5 Map Score: 0.799637 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 110 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 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