AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_rpxx_reg_100.orf -o00710_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP091 174 ASPARTATE AMINOTRANSFERASE A (aatA) #2 RP299 223 GALACTOSE-6-PHOSPHATE ISOMERASE LACB SUBUNIT (lacA) #3 RP376 300 MALATE DEHYDROGENASE (mdh) #4 RP492 300 PYRUVATE,PHOSPHATE DIKINASE PRECURSOR (ppdK) Motif number 1 ATAATATGAATTTAGTAATTAAACT 1 3 0 TTAAATTAAA 0.859766 -172 AAGCATATCTTAATAAATTTTTAAATAAAATAA 1 49 1 TATATTTTTA 0.884624 -126 AATTTTTAAATAAAATAATTTTATTGAGATTAA 1 64 1 TAAAATTTTA 0.73188 -111 TAAACGATAATACAGCAATTTTAATCTCAATAA 1 84 0 TAAAATTTTA 0.971359 -91 AGAATCCGAATTCAGTATTTTAAGATTCTCAAA 1 143 1 TTAATTTTAA 0.931856 -32 TATTTATTCTTTATTTATTTTTACAGAGCACTT 2 52 0 TTTATTTTTA 0.836037 -172 ATAAATACATTAAAAAAATGTTAATATGAAAAT 2 78 1 TAAAATGTTA 0.821172 -146 TTAGAAATCTTTAATTATTTTCATATTAACATT 2 94 0 TTAATTTTCA 0.92743 -130 TTTGCTATAATTATAAATTTTTAGAAATCTTTA 2 114 0 TTTATTTTTA 0.831872 -110 CGCTTAGCTGTAAATAAATTTTAAAGTTAATAA 2 152 0 TAAAATTTTA 0.96509 -72 GCTTACATAGTATATAATTTTTATCATAATTTT 2 184 1 TAAATTTTTA 0.966074 -40 TATTGATGATTACTTCATTTTTATATACAAATT 3 91 1 TATATTTTTA 0.89096 -210 TTCATTTTTATATACAAATTAAATATTCATGAA 3 104 1 TAAAATTAAA 0.906835 -197 AAATTAAATATTCATGAATTTAAAAAGTGTATT 3 119 1 TTAAATTTAA 0.937558 -182 GATTTATGTATTTACAATTTAAAAATTCTTTTT 3 218 1 TTAATTTAAA 0.848418 -83 TAACATATTATTGACTAATTTAAGAAAAGCTAC 4 73 0 TTAAATTTAA 0.9375 -228 AATAATATGTTAAAAGAATTTCAATTAGCTTGT 4 94 1 TAAAATTTCA 0.95713 -207 ATATTGTGTGTACAATAATTACAATAAATTTTC 4 140 0 TAAAATTACA 0.902418 -161 TATCTTTCTTTAAAGAATTGACATTATGGAATT 4 192 0 TAAATTGACA 0.609919 -109 TAAAGAAAGATATCTTAATTTAACATTGCTACT 4 213 1 TACAATTTAA 0.740878 -88 TTTTAAGTACTACATTATTTATACATTAGGAAA 4 251 0 TAAATTTATA 0.927106 -50 ** * ******* Masking position 9 Map Score: 28.9586 Number of sites scoring better than the average of aligned sites = 1296 Number in coding regions = 833 Number in noncoding regions = 463 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 2 TTACTAAATTCATATTATTTACACTATAATA 1 18 1 CATATTATTA 0.882876 -157 TCAATAAAATTATTTTATTTAAAAATTTATT 1 60 0 TATTTTATTA 0.950036 -115 TGTATTATCGTTTATTATTAATGTTATTCTA 1 103 1 TTTATTATTA 0.966015 -72 TTCGGATTCTTATATACTTTAGAATAACATT 1 122 0 TATATACTTA 0.820091 -53 TTTTAATGTATTTATTCTTTATTTATTTTTA 2 62 0 TTTATTCTTA 0.950672 -162 AATTATTAACTTTAAAATTTATTTACAGCTA 2 150 1 TTTAAAATTA 0.697572 -74 ATTCTGTGATTTTTTTATTAAAAGATAGACT 3 39 0 TTTTTTATTA 0.955765 -262 GAAATGGTTTTATATTATTGATGATTACTTC 3 76 1 TATATTATTA 0.965494 -225 AAAATACACTTTTTAAATTCATGAATATTTA 3 123 0 TTTTAAATTA 0.610146 -178 AAAAGTGTATTTTTATATTTATCGTGGTACT 3 141 1 TTTTATATTA 0.853382 -160 TTAAAAATTCTTTTTTCTTAAAGCCATTTGT 3 236 1 TTTTTTCTTA 0.928997 -65 CCCTCTATAATATATTATTTAATACGCATAA 3 276 0 TATATTATTA 0.962451 -25 ATTCTTTTAACATATTATTGACTAATTTAAG 4 82 0 CATATTATTA 0.882933 -219 TTGCTACTATTTTTTTCCTAATGTATAAATA 4 238 1 TTTTTTCCTA 0.639676 -63 TTTTAAGTACTACATTATTTATACATTAGGA 4 253 0 TACATTATTA 0.789577 -48 ********* * Masking position 11 Map Score: 16.7633 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 515 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TTAATTACTAAATTCATATTATTTACACTATA 1 14 1 AATATATTAT 0.921697 -161 TTATTAAGATATGCTTTATTATAGTGTAAATA 1 33 0 ATCTTATTAT 0.740169 -142 ATAAATTTTTAAATAAAATAATTTTATTGAGA 1 61 1 AATAAATAAT 0.681311 -114 TTGCTGTATTATCGTTTATTATTAATGTTATT 1 99 1 ATGTTATTAT 0.88338 -76 CAAAATTATTATTTGATATAATACAACTATTA 2 19 1 ATTATATAAT 0.862891 -205 ATTTTTAGAAATCTTTAATTATTTTCATATTA 2 99 0 ATTTAATTAT 0.928187 -125 ATTTCTAAAAATTTATAATTATAGCAAAAAAA 2 119 1 ATTTAATTAT 0.928966 -105 TAATTATAGCAAAAAAAATTATTAACTTTAAA 2 134 1 AAAAAATTAT 0.653008 -90 AAGCGCTTACATAGTATATAATTTTTATCATA 2 180 1 ATGATATAAT 0.683737 -44 TAATTTTTTGATGGAAAATTATGATAAAAATT 2 199 0 ATGAAATTAT 0.907905 -25 ATCTGAAATGGTTTTATATTATTGATGATTAC 3 72 1 GTTATATTAT 0.7643 -229 GCCATTTGTAATATAGTATTATGCGTATTAAA 3 258 1 ATTGTATTAT 0.836805 -43 TGCGTATTAAATAATATATTATAGAGGGCATA 3 279 1 ATAATATTAT 0.48843 -22 TTGTTATTATAATTGTAATTATATTGTGTGTA 4 161 0 AATTAATTAT 0.84978 -140 ACATTATGGAATTTGTTATTATAATTGTAATT 4 173 0 ATTTTATTAT 0.943205 -128 TTCTTTAAAGAATTGACATTATGGAATTTGTT 4 188 0 AATACATTAT 0.710565 -113 AATAGTAGCAATGTTAAATTAAGATATCTTTC 4 217 0 ATTAAATTAA 0.632481 -84 ** * ******* Masking position 8 Map Score: 12.8395 Number of sites scoring better than the average of aligned sites = 1129 Number in coding regions = 708 Number in noncoding regions = 421 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 4 AAAATTATTTTATTTAAAAATTTATTAAGA 1 56 0 TATTTAAAAA 0.696312 -119 AGAATAACATTAATAATAAACGATAATACA 1 103 0 TAATAATAAA 0.646692 -72 AGTTGTATTATATCAAATAATAATTTTGTT 2 17 0 TATCAAATAA 0.759817 -207 AGAATAAATACATTAAAAAAATGTTAATAT 2 75 1 CATTAAAAAA 0.872969 -149 AAAATGTTAATATGAAAATAATTAAAGATT 2 92 1 TATGAAAATA 0.68091 -132 TTTATAATTATAGCAAAAAAAATTATTAAC 2 130 1 TAGCAAAAAA 0.891786 -94 GATGGAAAATTATGATAAAAATTATATACT 2 192 0 TATGATAAAA 0.804831 -32 CATAATTTTCCATCAAAAAATTAACT 2 208 1 CATCAAAAAA 0.830327 -16 GTCTATCTTTTAATAAAAAAATCACAGAAT 3 40 1 TAATAAAAAA 0.944891 -261 TAATCATCAATAATATAAAACCATTTCAGA 3 73 0 TAATATAAAA 0.762113 -228 CAAATGGCTTTAAGAAAAAAGAATTTTTAA 3 236 0 TAAGAAAAAA 0.941446 -65 GTATTATGCGTATTAAATAATATATTATAG 3 273 1 TATTAAATAA 0.81574 -28 ATTACAATTATAATAACAAATTCCATAATG 4 174 1 TAATAACAAA 0.730551 -127 ATTTATACATTAGGAAAAAAATAGTAGCAA 4 238 0 TAGGAAAAAA 0.915425 -63 ********** Masking position 2 Map Score: 10.5292 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 498 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 5 ACTATAATAAAGCATATCTTAATAAATTTTTA 1 40 1 AGATATCTAA 0.965493 -135 ATTTTTACAGAGCACTTCTAATAGTTGTATTA 2 37 0 AGACTTCTAT 0.924413 -187 AAAATAATTAAAGATTTCTAAAAATTTATAAT 2 106 1 AAATTTCTAA 0.945756 -118 CTGAATAGTGAGAACTTGTAAAGATGTGAG 3 9 0 AGACTTGTAA 0.930559 -292 AAAATCACAGAATATATCTGAAATGGTTTTAT 3 57 1 AAATATCTAA 0.887574 -244 TATTTATCGTGGTACTTCTGAATAGGCCTAGT 3 156 1 GGACTTCTAA 0.949794 -145 TTAAGAAAAAAGAATTTTTAAATTGTAAATAC 3 225 0 AGATTTTTAA 0.873423 -76 AGATTATGGTAGCTTTTCTTAAATTAGTCAAT 4 65 1 AGTTTTCTAA 0.896852 -236 TTGACATTATGGAATTTGTTATTATAATTGTA 4 176 0 GGATTTGTAT 0.692274 -125 TCTTTAAAGAAAGATATCTTAATTTAACATTG 4 209 1 AAATATCTAA 0.887574 -92 ** ****** ** Masking position 7 Map Score: 5.50289 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 135 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TCTCAATAAAATTATTTTATTTAAAAATTT 1 63 0 ATTATTTTAT 0.916696 -112 CTGAATTCGGATTCTTATATACTTTAGAAT 1 128 0 ATTCTTATAT 0.928399 -47 ATTCAACAAAATTATTATTTGATATAATAC 2 13 1 ATTATTATTT 0.724099 -211 TAATGTATTTATTCTTTATTTATTTTTACA 2 60 0 ATTCTTTATT 0.65999 -164 TCATATTAACATTTTTTTAATGTATTTATT 2 77 0 ATTTTTTTAA 0.8202 -147 ATCTTTAATTATTTTCATATTAACATTTTT 2 91 0 ATTTTCATAT 0.669133 -133 TAAAGTTAATAATTTTTTTTGCTATAATTA 2 134 0 AATTTTTTTT 0.500052 -90 AGTTAATTTTTTGATGGAAAATTAT 2 209 0 ATTTTTTGAT 0.806685 -15 ATATTCTGTGATTTTTTTATTAAAAGATAG 3 42 0 ATTTTTTTAT 0.960476 -259 TGATTACTTCATTTTTATATACAAATTAAA 3 97 1 ATTTTTATAT 0.932699 -204 TAAAAAGTGTATTTTTATATTTATCGTGGT 3 139 1 ATTTTTATAT 0.932699 -162 CAATTTAAAAATTCTTTTTTCTTAAAGCCA 3 232 1 ATTCTTTTTT 0.904797 -69 TCTATAATATATTATTTAATACGCATAATA 3 274 0 ATTATTTAAT 0.691356 -27 GCTAATTGAAATTCTTTTAACATATTATTG 4 93 0 ATTCTTTTAA 0.810108 -208 ********** Masking position 1 Map Score: 15.0403 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 462 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 7 ********** No masking Map Score: -2.59896e-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: -2.59896e-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 9 ********** No masking Map Score: -2.59896e-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