AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -idnaA_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 RP029 300 RECF PROTEIN (recF) #2 RP303 89 RNA POLYMERASE SIGMA-32 FACTOR (rpoH) #3 RP415 300 DIAMINOPIMELATE EPIMERASE (dapF) #4 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #5 RP512 164 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE BETA CHAIN (nrdB) #6 RP513 300 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE ALPHA CHAIN (nrdA) #7 RP600 195 unknown Motif number 1 TTTTAGAGCATTTAATGTTTATTATCACTCCTGA 1 25 1 TTATTTATTA 0.799921 -276 TATGGAGTTCTATAAAATTTTTGTAATACTTGAA 1 76 0 TAAATTTTGT 0.833206 -225 TATAGGACTTTACAATTTTTCATTGTTCATAGTA 1 111 1 TAATTTCATT 0.721037 -190 TCAATAATTATACTATTATTCTTTCATAAA 1 281 1 TAATTTCTTT 0.957841 -20 AATAAACTTTTTCTATAATTTTTTTAAATAAAAT 2 17 0 TTATTTTTTT 0.963369 -73 ATATCAATCTTAGGATACTTATTTATATATCAAT 3 92 1 TAATTTATTT 0.960465 -209 TATATATCAATTAAAATGTTATTTAGCAATGATT 3 115 1 TTAATTATTT 0.926515 -186 TAGCAATGATTATTATCTTTATTTTTGTCTTACT 3 138 1 TAATTTATTT 0.960386 -163 ATTATACTAATTTCATGCTTCTTATTACTTCACA 3 197 0 TTATTTCTTA 0.789114 -104 ATTTGTATTATAGCAAATTTCTTTAAATTTACTA 3 258 0 TAAATTCTTT 0.944983 -43 CTGGACTATTTAGCAAAGTTATGTTGTAACAATG 4 52 1 TAAATTATGT 0.763786 -55 AGAGAAATTATAGAATAATTTTTTGCATGTAATC 5 94 0 TAATTTTTTT 0.974074 -71 TATTACATTGTTTAAAGGTTTTTTATCGTGAGCT 5 128 0 TTAATTTTTT 0.951977 -37 CTTTTGTATTATTTTTTTCAACAATAA 6 4 1 TTATTTTTTT 0.963369 -297 AATGCGATACTTAAACAGTTTTTTTAAAAAATTT 6 36 1 TTACTTTTTT 0.805738 -265 AGATACGAGATATCAAAATTTTTTAAAAAAACTG 6 51 0 TAAATTTTTT 0.965748 -250 AATATAAATATTTTATTTTTTTTTAGATTTTTGA 6 168 0 TTATTTTTTT 0.963368 -133 TAGTCGTTATTATAATGCTTTTTTGCAAAAATGA 6 258 0 TAATTTTTTT 0.97395 -43 CTATAACATCTTGCAAAATTTTTTTATAATAATA 7 11 1 TTAATTTTTT 0.952131 -185 AATTTTTTTATAATAATATTATTAAAATAATAAG 7 27 1 TAAATTATTA 0.482375 -169 TTTCCCAATGTAGAATGGTTATTAGAGTGCTTAA 7 129 0 TAATTTATTA 0.849994 -67 GGGAAAGTTCTATTAACTTTTATTATCAATAATA 7 157 1 TAAATTTATT 0.758689 -39 ** ** ****** Masking position 9 Map Score: 30.843 Number of sites scoring better than the average of aligned sites = 1042 Number in coding regions = 666 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 TATAAAATTTTTGTAATACTTGAATTTTAGAGTCTG 1 64 0 TTTAATTATT 0.801804 -237 TGTCATGCAATTGATATACTGTACTATGAACAATGA 1 130 0 TTAAATGATA 0.975143 -171 ATATTTGTTCTTTTGAGTTTGAATTATTAATCAAAT 1 179 0 TTTATTGATA 0.879488 -122 ATTTATTCTGTATAGAAATTGCAATAGTAGTTCTGC 1 237 0 TAAAATGATA 0.942738 -64 AGTATAATTATTGATATATTGCATTTATTCTGTATA 1 259 0 TTAAATGATT 0.944204 -42 AAAAAAATTATAGAAAAAGTTTATTTTAGATCATAT 2 26 1 TAAAATTATT 0.801776 -64 TATTGGTGTTTTATTAGACTTTATTATATCAATCTT 3 67 1 TTTAATTATA 0.903618 -234 ACTAGTATTTTAAAAAATTTGCAGTAAGACAAAAAT 3 158 0 TAAATTGATA 0.878147 -143 TTTAAAATACTAGTTATTGTGAAGTAATAAGAAGCA 3 180 1 TATATTGATA 0.758933 -121 TATAGCAAATTTCTTTAAATTTACTATAATGAATTG 3 248 0 TTTTATTATA 0.58525 -53 GTTTTACATATTAAAAATTTGTATTATAGCAAATTT 3 272 0 TTAATTGATA 0.944177 -29 CAATATTGTATTGATTCACTGGACTATTTAGCAAAG 4 34 1 TTATATGATA 0.855474 -73 ATAAAAAACCTTTAAACAATGTAATATTAGTAATAA 5 136 1 TTAAATGATA 0.975143 -29 AACAGTTTTTTTAAAAAATTTTGATATCTCGTATCT 6 49 1 TTAAATTGTA 0.721252 -252 TTTATTTTTTTTTAGATTTTTGACTTGACAAAAATA 6 155 0 TTAATTTATT 0.801804 -146 ATTTATTCAATATAAATATTTTATTTTTTTTTAGAT 6 174 0 TAAAATTATT 0.801784 -127 CGAAATCATTTTAAAATACTTGAATAATTAAGCACT 7 102 1 TTAAATTATA 0.956028 -94 ** * * * ** * ** Masking position 10 Map Score: 15.1556 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 432 Number in noncoding regions = 274 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 TCAATGTACAATTTTTAGAGCATTTAATGTTTA 1 13 1 ATTTTAACAT 0.569031 -288 TTTGAGTTTGAATTATTAATCAAATTTGCACAT 1 171 0 AATATTACAA 0.862019 -130 TCAAAAGAACAAATATATATCAAGACACAGTAA 1 199 1 AAAATAACAA 0.698462 -102 GAATAAATGCAATATATCAATAATTATACTATT 1 265 1 AATTATATAA 0.479624 -36 TTATACTATTATTCTTTCATAAA 1 288 1 ATTTTTAAAA 0.610184 -13 TATTTAAAAAAATTATAGAAAAAGTTTATTTTA 2 21 1 AATATAAAAA 0.899541 -69 AATAAAGTCTAATAAAACACCAATACTTAAAAA 3 59 0 AATAAAACAA 0.887375 -242 GTATCCTAAGATTGATATAATAAAGTCTAATAA 3 77 0 ATTATAATAA 0.756432 -224 TAGGATACTTATTTATATATCAATTAAAATGTT 3 102 1 ATTATAACAA 0.90675 -199 TCATTATAGTAAATTTAAAGAAATTTGCTATAA 3 252 1 AAATTAAAAA 0.548724 -49 TTATCTCAACATTGTTACAACATAACTTTGCTA 4 62 0 ATTTTAACAT 0.569031 -45 GTTGAGATAAAATCTAAAAACAAAAAATAATT 4 85 1 AATTAAACAA 0.903915 -22 TAGTTACATAAATCATATACCAAATCGTAATTT 5 16 1 AATATAACAA 0.953196 -149 TTTTGCATGTAATCTTACACCAAATTTTTGAGT 5 75 0 AATTTAACAA 0.9605 -90 GAGCTAGAGAAATTATAGAATAATTTTTTGCAT 5 100 0 AATATAATAA 0.866746 -65 AATTTATTACTAATATTACATTG 5 152 0 AATTATATAA 0.479621 -13 GAGATATCAAAATTTTTTAAAAAAACTGTTTAA 6 46 0 AATTTTAAAA 0.766304 -255 ATCTAGATCTAATAAAATACCAATCTTTATGGA 6 81 1 AATAAAACAA 0.887375 -220 TCAAGTCAAAAATCTAAAAAAAAATAAAATATT 6 163 1 AATTAAAAAA 0.805278 -138 TTTTAATAATATTATTATAAAAAAATTTTGCAA 7 21 0 ATTTTAAAAA 0.835394 -175 TTATAATAATATTATTAAAATAATAAGGTTCTA 7 34 1 ATTTTAATAA 0.787379 -162 TTTTATTATCAATAATAGAAAAAAACGTAAAT 7 174 1 AATATAAAAA 0.899541 -22 *** *** * *** Masking position 9 Map Score: 23.2222 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 675 Number in noncoding regions = 348 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 4 TATTACAAAAATTTTATAGAACTCCATATTA 1 82 1 ATTTTATAGA 0.861658 -219 TGTTTGATTTTATTTAAAAAAATTATA 2 7 1 ATTTTATTTA 0.950191 -83 GAAAAAGTTTATTTTAGATCATATATATGTT 2 38 1 ATTTTAGATA 0.90072 -52 CTGAAAAACTATTTTCGTTTATACTAACATA 2 63 0 ATTTTCGTTA 0.805481 -27 TGAATTGATTTTATTTCATGTTGTTAGT 3 8 1 ATTTTATTTA 0.950191 -293 GCTAAATAACATTTTAATTGATATATAAATA 3 111 0 ATTTTAATTA 0.908208 -190 AATAACTAGTATTTTAAAAAATTTGCAGTAA 3 167 0 ATTTTAAAAA 0.827084 -134 TTGTTTTTAGATTTTATCTCAACATTGTTAC 4 77 0 ATTTTATCTA 0.816754 -30 AGATATCAAAATTTTTTAAAAAAACTGTTTA 6 47 0 ATTTTTTAAA 0.748184 -254 AAAGATTGGTATTTTATTAGATCTAGATACG 6 78 0 ATTTTATTAA 0.924184 -223 TAAATATTTTATTTTTTTTTAGATTTTTGAC 6 167 0 ATTTTTTTTA 0.85964 -134 AAATGACACCATTTTAGTGTATAGAACTTCA 6 233 0 ATTTTAGTGA 0.837067 -68 ATCTTGCAAAATTTTTTTATAATAATATTAT 7 18 1 ATTTTTTTAA 0.796479 -178 TATGAACATCATTTTCAATGATATAGAGCCT 7 65 1 ATTTTCAATA 0.722512 -131 TACCGAAATCATTTTAAAATACTTGAATAAT 7 99 1 ATTTTAAAAA 0.827595 -97 ********* * Masking position 1 Map Score: 12.6551 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 480 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 TTACAAAAATTTTATAGAACTCCATATTAT 1 84 1 TTTATAGAAC 0.97204 -217 AGAACTCCATATTATAGGACTTTACAATTT 1 99 1 ATTATAGGAC 0.847545 -202 TTTTTCATTGTTCATAGTACAGTATATCAA 1 126 1 TTCATAGTAC 0.812238 -175 GCATTTATTCTGTATAGAAATTGCAATAGT 1 245 0 TGTATAGAAA 0.92108 -56 ATTTAAAAAAATTATAGAAAAAGTTTATTT 2 22 1 ATTATAGAAA 0.949478 -68 TCCTCAATTCATTATAGTAAATTTAAAGAA 3 244 1 ATTATAGTAA 0.872525 -57 TTATAGTAAATTTAAAGAAATTTGCTATAA 3 255 1 TTTAAAGAAA 0.714269 -46 AAAAATTTGTATTATAGCAAATTTCTTTAA 3 266 0 ATTATAGCAA 0.800934 -35 AGCTAGAGAAATTATAGAATAATTTTTTGC 5 102 0 ATTATAGAAT 0.774912 -63 TAATTACCAATGTATAGTAACTAAATCTTA 6 127 1 TGTATAGTAA 0.806092 -174 ACCATTTTAGTGTATAGAACTTCAATTAAG 6 227 0 TGTATAGAAC 0.94171 -74 GAAAATGATGTTCATAGAACCTTATTATTT 7 51 0 TTCATAGAAC 0.924007 -145 ATAATAAAAGTTAATAGAACTTTCCCAATG 7 153 0 TTAATAGAAC 0.887131 -43 TTTATTATCAATAATAGAAAAAAACGTAAA 7 175 1 ATAATAGAAA 0.811772 -21 ********** Masking position 6 Map Score: 13.9064 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 159 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TTTTAGAGTCTGTTATCTCAGGAGTGATAA 1 46 0 TGTTATCTCA 0.742467 -255 TGTTTGATTTTATTTAAAAAAATTATA 2 8 1 TTTTATTTAA 0.703408 -82 TGAATTGATTTTATTTCATGTTGTTAGT 3 9 1 TTTTATTTCA 0.904027 -292 AGTATTGGTGTTTTATTAGACTTTATTATA 3 65 1 TTTTATTAGA 0.94805 -236 CTAAATAACATTTTAATTGATATATAAATA 3 111 0 TTTTAATTGA 0.720157 -190 TGTTTTTAGATTTTATCTCAACATTGTTAC 4 77 0 TTTTATCTCA 0.80204 -30 AATTATTTTTTGTTTTTAGATTTTATCTCA 4 87 0 TGTTTTTAGA 0.783491 -20 AAGATTGGTATTTTATTAGATCTAGATACG 6 78 0 TTTTATTAGA 0.94805 -223 ATATTTTATTTTTTTTTAGATTTTTGACTT 6 165 0 TTTTTTTAGA 0.835621 -136 AATGTAGAATGGTTATTAGAGTGCTTAATT 7 127 0 GGTTATTAGA 0.730861 -69 ********** Masking position 4 Map Score: 3.92352 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 187 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TAATAGTATAATTATTGATATATTGCATTTA 1 268 0 ATTTTGATAT 0.728761 -33 ATTTAAAAAAATTATAGAAAAAGTTTATTTT 2 22 1 ATTTAGAAAA 0.921393 -68 AAAGATAATAATCATTGCTAAATAACATTTT 3 127 0 ATCTTGCTAA 0.853926 -174 CTTACTGCAAATTTTTTAAAATACTAGTTAT 3 166 1 ATTTTTAAAA 0.879341 -135 AAAAATTTGTATTATAGCAAATTTCTTTAAA 3 265 0 ATTTAGCAAA 0.893001 -36 GTATCGCATTATTGTTGAAAAAAATAATACA 6 15 0 ATTTTGAAAA 0.976812 -286 AGATATCAAAATTTTTTAAAAAAACTGTTTA 6 47 0 ATTTTTAAAA 0.879341 -254 AAATGGTGTCATTTTTGCAAAAAAGCATTAT 6 250 1 ATTTTGCAAA 0.967735 -51 TAGGCTCTATATCATTGAAAATGATGTTCAT 7 66 0 ATCTTGAAAA 0.947733 -130 GTTTTTTTCTATTATTGATAATAAAAGTTAA 7 169 0 ATTTTGATAA 0.950236 -27 *** ******* Masking position 5 Map Score: 10.3122 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 170 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 TAATACTTGAATTTTAGAGTCTGTTATCTC 1 57 0 ATTTTAGAGT 0.889633 -244 AAATTTGCACATTCTTGTGTCATGCAATTG 1 153 0 ATTCTTGTGT 0.945295 -148 CTGAAAAACTATTTTCGTTTATACTAACAT 2 64 0 ATTTTCGTTT 0.786346 -26 TATTATCTTTATTTTTGTCTTACTGCAAAT 3 148 1 ATTTTTGTCT 0.956006 -153 CTTACACCAAATTTTTGAGTTTAACATGCA 5 65 0 ATTTTTGAGT 0.948835 -100 ACTAAATCTTATTTTTGTCAAGTCAAAAAT 6 146 1 ATTTTTGTCA 0.774044 -155 TTTTTTTTAGATTTTTGACTTGACAAAAAT 6 156 0 ATTTTTGACT 0.919346 -145 ATAAATTATTATTCTCGTGTCTACTTAATT 6 204 1 ATTCTCGTGT 0.920812 -97 AAATGACACCATTTTAGTGTATAGAACTTC 6 234 0 ATTTTAGTGT 0.938948 -67 ********** Masking position 5 Map Score: 8.39328 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 52 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 ********** No masking Map Score: 3.36387e-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 10 ********** No masking Map Score: 3.36387e-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 11 ********** No masking Map Score: 3.36387e-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