AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -intrC_rpxx_opreg_100.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 RP129 119 PUTATIVE GLUTAMINE TRANSPORT SYSTEM PERMEASE PROTEIN GLNP (glnP) #2 RP150 164 AMINO-ACID ABC TRANSPORTER BINDING PROTEIN (yqiX) #3 RP562 300 NITROGEN ASSIMILATION REGULATORY PROTEIN NTRX (ntrX) Motif number 1 TTAATTATATAGTATTATTTTATTTATA 1 8 1 TATATATTAT 0.948402 -112 CTGCAGCAGCTAAAAAATTATACTTCCTGTG 1 60 0 TAAAAATTAT 0.956083 -60 AAATTATTATATATTTTTTCTTCTCATA 1 102 0 TATAATTTTT 0.959319 -18 ATTTTCTTTGTATTTATTTTTTGTACTGGAT 2 16 0 TATTATTTTT 0.854653 -149 TACTAAATGTTATACAATTTTCTTTGTATTT 2 32 0 TATAAATTTT 0.964107 -133 AAAGCGAATATAAAGCTTTTTAAGCAGAAAA 2 65 0 TAAACTTTTT 0.819763 -100 ACATAAGTACTATACAATTAAACGTTACATT 2 108 1 TATAAATTAA 0.83975 -57 TACACAAACTTAAAACATTATTTTT 2 150 1 TAAACATTAT 0.916756 -15 TCAGTATTCTTATTATTTTATGTCACAAACA 3 24 1 TATTTTTTAT 0.800833 -277 GTTATAAATATAATGAATTATGTGGATACTG 3 78 0 TAATAATTAT 0.844375 -223 ATTTGCAGTTTATAGTGTTATAAATATAATG 3 94 0 TATATGTTAT 0.811125 -207 ATTAAAATCTTATAGATTTATAAAAACAACT 3 136 1 TATAATTTAT 0.98053 -165 AGAAGTCTTATATAAATTTATTAGTTGTTTT 3 158 0 TATAATTTAT 0.980529 -143 CTTCTCACTCTACATAATTATGGACAAAAAA 3 184 1 TACAAATTAT 0.907648 -117 AACATTTTTTTATAACATTTTTGTCACAATA 3 215 0 TATACATTTT 0.931355 -86 AGCATTAACCTATACATTTAGGTTTTTAATA 3 262 1 TATAATTTAG 0.872337 -39 **** ****** Masking position 8 Map Score: 22.3099 Number of sites scoring better than the average of aligned sites = 914 Number in coding regions = 555 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 ATAAATAAAATAATACTATATAATTAA 1 6 0 TAATCTATAA 0.685028 -114 AAATTATTATATATTTTTTCTTC 1 107 0 AATTTTATAA 0.824225 -13 TACAAAAAATAAATACAAAGAAAATTGTATAA 2 22 1 AAATCAAAGA 0.802885 -143 AAAATATACTAAATGTTATACAATTTTCTTTG 2 37 0 AAATTTATAA 0.975894 -128 GGAATCACATAAGTACTATACAATTAAACGTT 2 102 1 AAGTCTATAA 0.865893 -63 GTTCATACACAAACTTAAAACATTATTTTT 2 145 1 AAACTAAAAA 0.718912 -20 TTGTGACATAAAATAATAAGAATACTGATAAT 3 20 0 AAATATAAGA 0.642534 -281 ATAGTGTTATAAATATAATGAATTATGTGGAT 3 82 0 AAATTAATGA 0.913985 -219 ACTGCAAATCAAATTTAAAAATTAAAATCTTA 3 116 1 AAATTAAAAT 0.633038 -185 TTAAAAATTAAAATCTTATAGATTTATAAAAA 3 130 1 AAATTTATAA 0.975894 -171 GTAGAGTGAGAAGTCTTATATAAATTTATTAG 3 165 0 AAGTTTATAA 0.927484 -136 ATTGTGACAAAAATGTTATAAAAAAATGTTGC 3 216 1 AAATTTATAA 0.975894 -85 GGTTAATGCTGAATGTAAAAGAAAGCAACATT 3 240 0 GAATTAAAAA 0.734422 -61 TTTACCTTAAAAATATTAAAAACCTAAATGTA 3 274 0 AAATTTAAAA 0.968495 -27 **** ***** * Masking position 8 Map Score: 13.7076 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 591 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 3 TTCTCATAATCTGGATTAACTGCAGCAGCT 1 80 0 CTGGATTAAC 0.995739 -40 ATTTTTTGTACTGGATTAACA 2 2 0 CTGGATTAAC 0.995739 -163 CTTTTACATTCAGCATTAACCTATACATTT 3 251 1 CAGCATTAAC 0.986421 -50 ********** Masking position 5 Map Score: 2.83963 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 ATAGTATTATTTTATTTATATCACTGAGCT 1 19 1 TTTATTTATA 0.715145 -101 ACACAGGAAGTATAATTTTTTAGCTGCTGC 1 59 1 TATAATTTTT 0.682189 -61 AAATTATTATATATTTTTTCTTCTCATAA 1 101 0 TATATTTTTT 0.967045 -19 TTTCTTTGTATTTATTTTTTGTACTGGATT 2 15 0 TTTATTTTTT 0.903901 -150 TAACATTTAGTATATTTTCTGCTTAAAAAG 2 51 1 TATATTTTCT 0.824236 -114 ACAAACTTAAAACATTATTTTT 2 153 1 AACATTATTT 0.530684 -12 CATAATTCATTATATTTATAACACTATAAA 3 87 1 TATATTTATA 0.879942 -214 CTATAAGATTTTAATTTTTAAATTTGATTT 3 121 0 TTAATTTTTA 0.625558 -180 TAAAATCTTATAGATTTATAAAAACAACTA 3 138 1 TAGATTTATA 0.666597 -163 AAGTCTTATATAAATTTATTAGTTGTTTTT 3 157 0 TAAATTTATT 0.770256 -144 TTTTTGTCACAATATTTTTTGTCCATAATT 3 199 0 AATATTTTTT 0.944033 -102 ATTTTTTTATAACATTTTTGTCACAATATT 3 213 0 AACATTTTTG 0.728568 -88 AAAAGAAAGCAACATTTTTTTATAACATTT 3 226 0 AACATTTTTT 0.919629 -75 TTAGGTTTTTAATATTTTTAAGGTAAATTG 3 279 1 AATATTTTTA 0.91417 -22 ********** Masking position 4 Map Score: 12.6 Number of sites scoring better than the average of aligned sites = 1751 Number in coding regions = 1170 Number in noncoding regions = 581 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 5 TTGTTAGGAATCACATAAGTACTATACAATTAA 2 96 1 TCACAAAACT 0.99236 -69 TTGTAATAGTTCATACACAAACTTAAAACATTA 2 137 1 TCATAACACT 0.980608 -28 TTATTTTATGTCACAAACACACTAGTTACACAA 3 36 1 TCACAACACT 0.995047 -265 AACACACTAGTTACACAATGACTACTACAGTAT 3 51 1 TTACAAAACT 0.970319 -250 ***** ** *** Masking position 7 Map Score: 0.263166 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 2 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ********** No masking Map Score: 2.65333e-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: 2.65333e-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: 2.65333e-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