AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_rpxx_reg_100.orf -o00500_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 RP446 300 GLYCOSYL TRANSFERASE (lgtD) #2 RP542 300 PROBABLE REPLICATIVE DNA HELICASE (dnaB) #3 RP593 300 ATP-DEPENDENT DNA HELICASE RECG (recG) Motif number 1 GGTTTTGTAGTTAATTGTTTATTTAAATAGTCT 1 112 1 TTAATTTTAT 0.815978 -189 CAGTGGTACCTTTTTTATTTATTCTTATTTTCA 1 146 1 TTTTTTTTAT 0.954203 -155 AAGTCTTAAATATTAGATTTATTCCTATGAAAA 1 173 0 TATTATTTAT 0.702595 -128 ATTTAAGACTTTTAATAGATAATATTAAAGCAA 1 195 1 TTTAAGATAT 0.836656 -106 AATTTTTTAATTTTTGCTTTAATATTATCTATT 1 208 0 TTTTTTTTAT 0.954196 -93 ATTTTTCAGATTTAAAATATAATTTTTTAATTT 1 228 0 TTTAATATAT 0.919417 -73 AAAATTAGAATTTATAGTATAAATAGTTTTATT 1 256 1 TTTATTATAA 0.488064 -45 TTGCAACTTATTTTTAATATAATTATATTACTA 2 108 1 TTTTTTATAT 0.978005 -193 AAAATTCATCTATATGGTATAATTTCAAATAAT 2 153 1 TATATTATAT 0.957869 -148 ATAAAGATAATTTATTATATACTTCTGTTTCAA 2 188 0 TTTATTATAT 0.985226 -113 TATATCATGATTTATTCTATAGTATCAGAAAGT 2 238 0 TTTATTATAT 0.985485 -63 TTATATTGTATATATTATTTAGTAATAAAATAA 3 17 1 TATATTTTAT 0.911409 -284 ATGGTTTTTATTTAAGTTATATTGATATTATGT 3 82 1 TTTAATATAT 0.956352 -219 TTGAAGATTTTTTATATTATATTACTTGTAGCA 3 150 1 TTTATTATAT 0.953905 -151 CTCGTCTTGTTATTTTTGATAATTTCTTTATTA 3 226 1 TATTTGATAT 0.797841 -75 GATAATTTCTTTATTAGTATATTAACCTTTTTT 3 243 1 TTATTTATAT 0.879342 -58 TAATTGTACTTGTTTAGTATATTAATCTTTAAA 3 273 0 TGTTTTATAT 0.883436 -28 ***** **** * Masking position 10 Map Score: 25.3901 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 396 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 TATGTTACTGAATATTATTTGAATATGCATATCTT 1 20 0 AAAATTTGAA 0.836274 -281 TACATAAACGATAACTATTTATACTAACATCACTA 1 64 0 ATAATTTAAT 0.948787 -237 GGTACCACTGTAGACTATTTAAATAAACAATTAAC 1 121 0 TAAATTTAAA 0.763216 -180 GATTTAAAATATAATTTTTTAATTTTTGCTTTAAT 1 218 0 ATATTTTATT 0.729505 -83 CAATGGTAATAAAACTATTTATACTATAAATTCTA 1 261 0 AAAATTTAAT 0.97977 -40 GATAAAGAATTTACAATGACAATCAAA 2 3 1 TAAATTTAAT 0.948894 -298 ACACTATTGTAAGAATATTTGCTGTATGTAATAAT 2 46 0 AAAATTTGTT 0.918206 -255 AACGCCTCAATACAGTTTTTAAATTACAGACACTA 2 75 0 TAATTTTAAT 0.876198 -226 TTCTGTTTCAAAAATTATTTGAAATTATACCATAT 2 164 0 AAAATTTGAT 0.967111 -137 TCTTTCGATAAAGATAATTTATTATATACTTCTGT 2 193 0 AAAATTTATT 0.939329 -108 AAATTGTTATATCATGATTTATTCTATAGTATCAG 2 243 0 ATAATTTATT 0.876185 -58 AAATCATGATATAACAATTTACAGTTCTAACACAA 2 258 1 ATAATTTAAT 0.948787 -43 TTTATTACTAAATAATATATACAATATAATAATAG 3 11 0 AAAATATAAT 0.816898 -290 GGGATAGACTTAGAAATTTTGTAATGGTTTTTATT 3 59 1 TAATTTTGAT 0.810529 -242 GTCATATTTGAAGATTTTTTATATTATATTACTTG 3 143 1 AAATTTTAAT 0.948859 -158 ** * ***** * * Masking position 4 Map Score: 17.5799 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 301 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 ACTATCTATCATTTATGTTACTGAATATTA 1 38 0 ATTTATGTTA 0.927069 -263 AACGATAACTATTTATACTAACATCACTAT 1 63 0 ATTTATACTA 0.938179 -238 ACTGTAGACTATTTAAATAAACAATTAACT 1 120 0 ATTTAAATAA 0.475804 -181 AATATTTAAGACTTTTAATAGATAATATTA 1 192 1 ACTTTTAATA 0.4386 -109 AATTTTTCAGATTTAAAATATAATTTTTTA 1 232 0 ATTTAAAATA 0.860606 -69 TAATAAAACTATTTATACTATAAATTCTAA 1 260 0 ATTTATACTA 0.938179 -41 TCAATACAGTTTTTAAATTACAGACACTAT 2 74 0 TTTTAAATTA 0.721635 -227 GTTGCAACTTATTTTTAATATAATTATATT 2 107 1 ATTTTTAATA 0.76988 -194 TTTTTAATATAATTATATTACTAATAATGA 2 118 1 AATTATATTA 0.720024 -183 TCAAAAATTATTTGAAATTATACCATATAG 2 162 0 TTTGAAATTA 0.468524 -139 GATAAAGATAATTTATTATATACTTCTGTT 2 192 0 ATTTATTATA 0.806328 -109 TTATATCATGATTTATTCTATAGTATCAGA 2 242 0 ATTTATTCTA 0.803188 -59 CCCTATCTCTACTTATTTTATTACTAAATA 3 32 0 ACTTATTTTA 0.653584 -269 AATGGTTTTTATTTAAGTTATATTGATATT 3 81 1 ATTTAAGTTA 0.835289 -220 TTTAAGTTATATTGATATTATGTCGTATTA 3 92 1 ATTGATATTA 0.910879 -209 TTTGAAGATTTTTTATATTATATTACTTGT 3 149 1 TTTTATATTA 0.866348 -152 AATACAAGATATTGATATTAGGTAATAAAT 3 182 0 ATTGATATTA 0.910879 -119 TCGTCTTGTTATTTTTGATAATTTCTTTAT 3 227 1 ATTTTTGATA 0.585992 -74 ********** Masking position 3 Map Score: 16.7639 Number of sites scoring better than the average of aligned sites = 1336 Number in coding regions = 778 Number in noncoding regions = 558 Number of orfs with sites within 600 bp upstream = 240 Fraction of orfs with sites within 600 bp upstream = 0.038548 Motif number 4 TAAATGATAGATAGTGATGTTAGTATAAATAGTT 1 53 1 ATATATGTTT 0.61844 -248 TAATCTTAAGATTCTGGTTTTGTAGTTAATTGTT 1 97 1 ATTTGTTTTA 0.741399 -204 TTAATTGTTTATTTAAATAGTCTACAGTGGTACC 1 122 1 ATTAATAGTA 0.734313 -179 TTTTTTATTTATTCTTATTTTCATAGGAATAAAT 1 156 1 ATTTATTTTT 0.893073 -145 CATAGGAATAAATCTAATATTTAAGACTTTTAAT 1 177 1 AATTATATTA 0.783348 -124 TCAGATTTAAAATATAATTTTTTAATTTTTGCTT 1 222 0 AATTATTTTA 0.821462 -79 TATACTATAAATTCTAATTTTTCAGATTTAAAAT 1 243 0 ATTTATTTTA 0.960133 -58 TTTTATTACCATTGACATGTTAGAAGTGC 1 282 1 ATTAATGTTA 0.823707 -19 TGCATCTTTGATTGTCATTGTAAATTCTTTATC 2 10 0 ATTTATTGTA 0.930168 -291 TATTAGTAATATAATTATATTAAAAATAAGTTGC 2 110 0 ATATATATTA 0.83117 -191 ATATAGATGAATTTTTATGTTCATTATTAGTAAT 2 134 0 ATTTATGTTT 0.859808 -167 AATTTATTATATACTTCTGTTTCAAAAATTATTT 2 179 0 ATATCTGTTA 0.598601 -122 TTGTTTGTTCAATCTTATTGTGTTAGAACTGTAA 2 276 0 AATTATTGTT 0.469053 -25 CTATTATTATATTGTATATATTATTT 3 3 1 ATTTATATTA 0.949765 -298 CCCTCCAATAATAGTCATATTTGAAGATTTTTTA 3 130 1 ATATATATTA 0.83325 -171 TATTTGAAGATTTTTTATATTATATTACTTGTAG 3 147 1 TTTTATATTA 0.574983 -154 AATATCTTGTATTAAGATAGTATTGATCTCGTCT 3 199 1 ATTAATAGTT 0.488934 -102 TTGATCTCGTCTTGTTATTTTTGATAATTTCTTT 3 221 1 CTTTATTTTA 0.718611 -80 TTATTAGTATATTAACCTTTTTTAAAGATTAATA 3 253 1 ATTACTTTTA 0.670005 -48 TGATATAATTGTACTTGTTTAGTATATTAAT 3 280 0 ATTTCTTGTA 0.809551 -21 *** * ***** * Masking position 8 Map Score: 15.799 Number of sites scoring better than the average of aligned sites = 1617 Number in coding regions = 1040 Number in noncoding regions = 577 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 5 ATAGTTATCGTTTATGTAATCTTAAGATTC 1 81 1 TTTATGTAAT 0.942998 -220 ATTCTGGTTTTGTAGTTAATTGTTTATTTA 1 107 1 TGTAGTTAAT 0.791294 -194 TTAAAATATAATTTTTTAATTTTTGCTTTA 1 220 0 ATTTTTTAAT 0.755689 -81 GAATATTTGCTGTATGTAATAATGCTGCAT 2 39 0 TGTATGTAAT 0.952442 -262 CTTACAATAGTGTCTGTAATTTAAAAACTG 2 68 1 TGTCTGTAAT 0.880263 -233 TTGAAACAGAAGTATATAATAAATTATCTT 2 188 1 AGTATATAAT 0.739683 -113 TGTATATATTATTTAGTAATAAAATAAGTA 3 23 1 ATTTAGTAAT 0.75303 -278 AGACTTAGAAATTTTGTAATGGTTTTTATT 3 64 1 ATTTTGTAAT 0.931943 -237 AGATATTGATATTAGGTAATAAATGCTACA 3 176 0 ATTAGGTAAT 0.913846 -125 GTCTTGTTATTTTTGATAATTTCTTTATTA 3 229 1 TTTTGATAAT 0.739335 -72 ********** Masking position 7 Map Score: 5.4691 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 290 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 ********** No masking Map Score: -6.79689e-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 7 ********** No masking Map Score: -6.79689e-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: -6.79689e-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