AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00600_rpxx_reg_300.orf -o00600_rpxx_300.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 RP046 198 PROLIPOPROTEIN DIACYLGLYCERYL TRANSFERASE (lgt) #2 RP407 300 unknown #3 RP408 148 LIPOPROTEIN SIGNAL PEPTIDASE (lspA) #4 RP409 21 unknown #5 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #6 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #7 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 ATTATTATTATTATAAAATACAAATCATTTT 1 20 1 TTATAAATAC 0.841917 -179 TTCTTAGTAATAATAAAAAAATGATTTGTAT 1 37 0 TAATAAAAAA 0.819403 -162 TTGGTATTACTAAGCAAATATAAATACTGTC 1 103 1 TAAGAAATAT 0.875587 -96 TTGCATCAATCTATAAAAAACTGTATTAATT 1 154 1 CTATAAAAAC 0.698443 -45 AATAATTATATTCACCATTTACA 2 3 1 TAATATATTC 0.615643 -298 TAATATTTTTTAAATAAATATTGTAATGTAA 2 29 0 TAAAAAATAT 0.826038 -272 TTATTTATATTAATGAAAATTAACTTATATT 2 145 1 TAATAAAATT 0.932819 -156 GATTTAAAATTAATTAAATATAAGTTAATTT 2 161 0 TAATAAATAT 0.984227 -140 AATTTTAAATCAATAAAAAACTCATAACCCA 2 181 1 CAATAAAAAC 0.945522 -120 CATAACCCAGCAATCAAAATTTTACAATTTT 2 203 1 CAATAAAATT 0.891499 -98 AAAGAAATTACAATAAAAAATTGTAAAATTT 2 219 0 CAATAAAAAT 0.96464 -82 ATATTATTCATAATCAAAAATTGATTCAAAT 2 261 1 TAATAAAAAT 0.978769 -40 AGTACCAATCTAATCAAATATTCTGAGATTC 6 23 0 TAATAAATAT 0.984311 -52 TTATTAAGATTAATTAAATCTGTAATATAAA 7 124 0 TAATAAATCT 0.894872 -177 AATTTAACACCAATGAAATATATTAATTTTG 7 161 1 CAATAAATAT 0.973773 -140 TTCATATGACTAATAAAATATTAATGAAATA 7 206 1 TAATAAATAT 0.984301 -95 AATAAAATATTAATGAAATACCACACTTTAA 7 217 1 TAATAAATAC 0.97556 -84 TAATGATCAGTAATAATAAATATTAAATTTA 7 269 1 TAATATAAAT 0.860182 -32 AGTAACATAATTAAATTTAATATTTATT 7 283 0 TAATAAATTT 0.94913 -18 **** ****** Masking position 6 Map Score: 27.6226 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 357 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 2 TCTATAAAAAACTGTATTAATTACTTTGTAAT 1 163 1 ATTATTAATT 0.961001 -36 TGTATTAATTACTTTGTAATTTCCAGCAACTT 1 175 1 ATTGTAATTT 0.645755 -24 GTAAATGGTGAATATAATTATT 2 1 0 ATTAATTATT 0.813977 -300 ATTAACTTATATTTAATTAATTTTAAATCAAT 2 163 1 ATAATTAATT 0.727339 -138 ACAATAAAAAATTGTAAAATTTTGATTGCTGG 2 209 0 ATTAAAATTT 0.885375 -92 TCAATTTTATAAATTGATGTTTTGT 3 4 1 ATTATAAATT 0.721032 -145 GACAATAGTAAGTCTAATCATTCCAAAAAGGA 3 75 0 ATTAATCATT 0.924843 -74 ACTATTGTCCATTTTGATAATTAACATTCCTT 3 98 1 ATTGATAATT 0.919215 -51 TGTATTTATAAATATATTAATTATCT 3 133 1 ATTATTAATT 0.813886 -16 TATTTGATGCACTTTAAAAATTTGCTAATTAA 5 13 1 ATTAAAAATT 0.955129 -137 TTTTATCTTCACTGTATTAATTTCATATTCTT 5 78 1 ATTATTAATT 0.961001 -72 TTAAATCTGTAATATAAAAATTAACAAGTTAG 7 110 0 ATTAAAAATT 0.912666 -191 ACACCAATGAAATATATTAATTTTGCTCTAAT 7 167 1 ATTATTAATT 0.813886 -134 GAAATACCACACTTTAAACATTAAGGTACATG 7 231 1 ATTAAACATT 0.882586 -70 AACATAATTAAATTTAATATTTATTATTACTG 7 276 0 ATTAATATTT 0.918375 -25 * * ******** Masking position 1 Map Score: 22.8549 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 180 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 CTTTTGAGTTAAAATTATTGATAAAAATAA 1 70 0 AAAATTATTG 0.615235 -129 CAGTTTTTTATAGATTGATGCAATGGCTTA 1 147 0 TAGATTGATG 0.731902 -52 TATAAAAAACTGTATTAATTACTTTGTAAT 1 165 1 TGTATTAATT 0.877665 -34 TTTACATTACAATATTTATTTAAAAAATAT 2 28 1 AATATTTATT 0.705127 -273 AAATCTTATTTATATTAATGAAAATTAACT 2 140 1 TATATTAATG 0.930681 -161 TAATTAAATATAAGTTAATTTTCATTAATA 2 152 0 TAAGTTAATT 0.758075 -149 TTATTGATTTAAAATTAATTAAATATAAGT 2 167 0 AAAATTAATT 0.946652 -134 TTCATAATCAAAAATTGATTCAAATAATCT 2 267 1 AAAATTGATT 0.865848 -34 AATTGCTCCGAAGATTATTTGAATCAATTT 2 278 0 AAGATTATTT 0.674595 -23 TCAATTTTATAAATTGATGTTTTGTTGCA 3 10 1 TAAATTGATG 0.767966 -139 ACAAAAAAGGAATGTTAATTATCAAAATGG 3 106 0 AATGTTAATT 0.851541 -43 TATTTATAAATATATTAATTATCT 3 135 1 TATATTAATT 0.954758 -14 CAGTTCTTATAGAATTAATTAGCAAATTTT 5 29 0 AGAATTAATT 0.857808 -121 TTATCTTCACTGTATTAATTTCATATTCTT 5 80 1 TGTATTAATT 0.877665 -70 TTCTCTTATTAAGATTAATTAAATCTGTAA 7 130 0 AAGATTAATT 0.93605 -171 ACCAATGAAATATATTAATTTTGCTCTAAT 7 169 1 TATATTAATT 0.954758 -132 TGACTAATAAAATATTAATGAAATACCACA 7 212 1 AATATTAATG 0.943366 -89 AGTAATAATAAATATTAAATTTAATTATGT 7 277 1 AATATTAAAT 0.664594 -24 ********** Masking position 5 Map Score: 18.7254 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 408 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 4 TTGTATTTTATAATAATAATAATAGGTAAAA 1 12 0 TAAAATAATA 0.782734 -187 TTAGTAATAATAAAAAAATGATTTGTATTTT 1 34 0 TAAAAAATGA 0.591534 -165 ATTTTTTTATTATTACTAAGAATTTTATTTT 1 46 1 TATACTAAGA 0.889037 -153 AAATTATTGATAAAAATAAAATTCTTAGTAA 1 58 0 TAAAATAAAA 0.666084 -141 AAGCATTTGGTATTACTAAGCAAATATAAAT 1 97 1 TATACTAAGC 0.858659 -102 TATATGTAACTAAGAATAATATGTTCTAAAA 2 82 0 TAAAATAATA 0.929837 -219 AAATAAGATTTATAACTATGCTTTTTGTATT 2 120 0 TATACTATGC 0.682778 -181 TTTTCATTAATATAAATAAGATTTATAACTA 2 133 0 TATAATAAGA 0.960127 -168 AATTTTTGATTATGAATAATATGAACTATAT 2 252 0 TATAATAATA 0.946267 -49 GTTTAGTATCTAAGACAAATAGATAGAGATG 5 118 0 TAAACAAATA 0.788742 -32 TGATAGACGATAATAACAATACTTGAAGTAG 7 63 0 TAAAACAATA 0.687867 -238 TATTATCGTCTATCACTAATAAAGACGTAAA 7 79 1 TATACTAATA 0.945452 -222 AAATCTGTAATATAAAAATTAACAAGTTAGT 7 109 0 TATAAAATTA 0.685555 -192 ATTTAATTAATCTTAATAAGAGAAGAATTTA 7 136 1 TCTAATAAGA 0.701482 -165 GTCATATGAATATCAATATTAGAGCAAAATT 7 185 0 TATAATATTA 0.883165 -116 TTGATATTCATATGACTAATAAAATATTAAT 7 200 1 TATACTAATA 0.945452 -101 *** ******* Masking position 5 Map Score: 16.3187 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 471 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 5 TAAAAAAATGATTTGTATTTTATAATAATA 1 25 0 ATTTGTATTT 0.686868 -174 GGCTTAGTTGTTTTGTAATGACAGTATTTA 1 123 0 TTTTGTAATG 0.966368 -76 GTATTAATTACTTTGTAATTTCCAGCAACT 1 176 1 CTTTGTAATT 0.929596 -23 TTTAAATAAATATTGTAATGTAAATGGTGA 2 22 0 TATTGTAATG 0.960063 -279 TAACTATGCTTTTTGTATTTTCAATATATA 2 109 0 TTTTGTATTT 0.932953 -192 TACAATTTTTTATTGTAATTTCTTTATATA 2 225 1 TATTGTAATT 0.962686 -76 TTTTTCTCCTTTTTGGAATGATTAGACTTA 3 69 1 TTTTGGAATG 0.844042 -80 AACATTCCTTTTTTGTATTTATAAATATAT 3 120 1 TTTTGTATTT 0.932953 -29 TAGTCATTGTAGTTTAGTATCTAA 5 136 0 CATTGTAGTT 0.747012 -14 CTACTTCAAGTATTGTTATTATCGTCTATC 7 63 1 TATTGTTATT 0.766674 -238 AGGTACATGATAATGTAATGATCAGTAATA 7 254 1 TAATGTAATG 0.754396 -47 ********** Masking position 4 Map Score: 10.1341 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 191 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 ATTTTACCTATTATTATTATTATA 1 5 1 TACCTATTAT 0.759817 -194 TGCTTTTGAGTTAAAATTATTGATAAAAAT 1 72 0 TTAAAATTAT 0.565766 -127 ATTTTTTAAATAAATATTGTAATGTAAATG 2 26 0 TAAATATTGT 0.817853 -275 ATTTATTTAAAAAATATTATCATAATATTC 2 41 1 AAAATATTAT 0.62929 -260 AAATATTATCATAATATTCTATTTATGATG 2 52 1 ATAATATTCT 0.617813 -249 GATGTTTTAGAACATATTATTCTTAGTTAC 2 78 1 AACATATTAT 0.863119 -223 AGCATAGTTATAAATCTTATTTATATTAAT 2 129 1 TAAATCTTAT 0.754973 -172 TTATATATAGTTCATATTATTCATAATCAA 2 248 1 TTCATATTAT 0.917582 -53 CTGTATTAATTTCATATTCTTTTTGAAGTC 5 89 1 TTCATATTCT 0.888665 -61 CCAATCTAATCAAATATTCTGAGATTCCTT 6 20 0 CAAATATTCT 0.719254 -55 ATTACATATTATTTCAAGCAAT 6 63 0 TACATATTAT 0.950859 -12 TGGTATTTCATTAATATTTTATTAGTCATA 7 210 0 TTAATATTTT 0.491963 -91 TCAGTAATAATAAATATTAAATTTAATTAT 7 275 1 TAAATATTAA 0.583092 -26 ********** Masking position 7 Map Score: 6.45934 Number of sites scoring better than the average of aligned sites = 891 Number in coding regions = 597 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 7 ATAATATTCTATTTATGATGTTTTAGAACA 2 62 1 ATTTATGATG 0.880647 -239 AATATGAACTATATATAAAGAAATTACAAT 2 236 0 ATATATAAAG 0.785086 -65 ATTTGAATCAATTTTTGATTATGAATAATA 2 262 0 ATTTTTGATT 0.823273 -39 CCTTTTTTGTATTTATAAATATATTAATTA 3 126 1 ATTTATAAAT 0.407085 -23 TATATTTGATGCACTTTAAAA 5 2 1 ATATTTGATG 0.930649 -148 TAATTAGCAAATTTTTAAAGTGCATCAAAT 5 14 0 ATTTTTAAAG 0.904321 -136 ATTTCATATTCTTTTTGAAGTCATCTCTAT 5 97 1 CTTTTTGAAG 0.829618 -53 GAATCTCAGAATATTTGATTAGATTGGTAC 6 23 1 ATATTTGATT 0.791072 -52 GATAATAACAATACTTGAAGTAGTTCATAA 7 56 0 ATACTTGAAG 0.803722 -245 ATGTACCTTAATGTTTAAAGTGTGGTATTT 7 232 0 ATGTTTAAAG 0.790469 -69 ********** Masking position 6 Map Score: 3.45824 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 342 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 ********** No masking Map Score: 2.27617e-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 9 ********** No masking Map Score: 2.27617e-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 10 ********** No masking Map Score: 2.27617e-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