AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -irpoN_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 0.914137 -112 CTGCAGCAGCTAAAAAATTATACTTCCTGTG 1 60 0 TAAAAATTAT 0.947619 -60 AAATTATTATATATTTTTTCTTCTCATA 1 102 0 TATAATTTTT 0.945935 -18 ATTTTCTTTGTATTTATTTTTTGTACTGGAT 2 16 0 TATTATTTTT 0.813298 -149 TACTAAATGTTATACAATTTTCTTTGTATTT 2 32 0 TATAAATTTT 0.957097 -133 AAAGCGAATATAAAGCTTTTTAAGCAGAAAA 2 65 0 TAAACTTTTT 0.815697 -100 ACATAAGTACTATACAATTAAACGTTACATT 2 108 1 TATAAATTAA 0.813081 -57 TACACAAACTTAAAACATTATTTTT 2 150 1 TAAACATTAT 0.923112 -15 TCAGTATTCTTATTATTTTATGTCACAAACA 3 24 1 TATTTTTTAT 0.675205 -277 GTTATAAATATAATGAATTATGTGGATACTG 3 78 0 TAATAATTAT 0.818287 -223 TCATTATATTTATAACACTATAAACTGCAAA 3 93 1 TATACACTAT 0.79983 -208 ATTAAAATCTTATAGATTTATAAAAACAACT 3 136 1 TATAATTTAT 0.973897 -165 AGAAGTCTTATATAAATTTATTAGTTGTTTT 3 158 0 TATAATTTAT 0.973896 -143 CTTCTCACTCTACATAATTATGGACAAAAAA 3 184 1 TACAAATTAT 0.890797 -117 AACATTTTTTTATAACATTTTTGTCACAATA 3 215 0 TATACATTTT 0.936674 -86 AGCATTAACCTATACATTTAGGTTTTTAATA 3 262 1 TATAATTTAG 0.835043 -39 **** ****** Masking position 9 Map Score: 22.5112 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 647 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 2 AATAAAATAATACTATATAATTAA 1 4 0 TACTATAAAT 0.932497 -116 TTAAGCTCAGTGATATAAATAAAATAATACT 1 21 0 TGATATAATA 0.828626 -99 AAATTATTATATATTTTTTCTTCTC 1 105 0 TATTATAATT 0.95312 -15 ATATACTAAATGTTATACAATTTTCTTTGTA 2 35 0 TGTTATAAAT 0.974219 -130 CTGCTTAAAAAGCTTTATATTCGCTTTTTGT 2 69 1 AGCTTTAATT 0.709496 -96 ATCACATAAGTACTATACAATTAAACGTTAC 2 105 1 TACTATAAAT 0.932497 -60 CAGTTTATAGTGTTATAAATATAATGAATTA 3 89 0 TGTTATAATA 0.964201 -212 AAAATTAAAATCTTATAGATTTATAAAAACA 3 133 1 TCTTATAATT 0.976743 -168 GAGTGAGAAGTCTTATATAAATTTATTAGTT 3 163 0 TCTTATAAAA 0.940557 -138 GTGACAAAAATGTTATAAAAAAATGTTGCTT 3 219 1 TGTTATAAAA 0.951449 -82 AATGTTGCTTTCTTTTACATTCAGCATTAAC 3 240 1 TCTTTTAATT 0.903925 -61 TTCAGCATTAACCTATACATTTAGGTTTTTA 3 259 1 ACCTATAATT 0.897961 -42 ******* *** Masking position 7 Map Score: 13.2168 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 282 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 TTCTCATAATCTGGATTAACTGCAGCAGCT 1 80 0 CTGGATTAAC 0.995334 -40 ATTTTTTGTACTGGATTAACA 2 2 0 CTGGATTAAC 0.995334 -163 CTTTTACATTCAGCATTAACCTATACATTT 3 251 1 CAGCATTAAC 0.98512 -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 CAGTGATATAAATAAAATAATACTATATAAT 1 14 0 AATAAATAAT 0.721666 -106 GCTTAACAACAATACACAGGAAGTATAATTT 1 46 1 AATAACAGGA 0.76964 -74 TGTTAATCCAGTACAAAAAATAAATACAAA 2 10 1 AGTAAAAAAA 0.820383 -155 ACAAAAAATAAATACAAAGAAAATTGTATAA 2 23 1 AATAAAAGAA 0.957773 -142 TTAAGCAGAAAATATACTAAATGTTATACAA 2 46 0 AATAACTAAA 0.886754 -119 TGTGACATAAAATAATAAGAATACTGATAAT 3 20 0 AATATAAGAA 0.930426 -281 TAGTGTTATAAATATAATGAATTATGTGGAT 3 82 0 AATAAATGAA 0.950209 -219 TTATATTTATAACACTATAAACTGCAAATCA 3 96 1 AACATATAAA 0.69383 -205 TTGTGACAAAAATGTTATAAAAAAATGTTGC 3 217 1 AATGTATAAA 0.822013 -84 GTTAATGCTGAATGTAAAAGAAAGCAACATT 3 240 0 AATGAAAAGA 0.781303 -61 TTACCTTAAAAATATTAAAAACCTAAATGTA 3 274 0 AATATAAAAA 0.934638 -27 **** ****** Masking position 1 Map Score: 6.7927 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 750 Number in noncoding regions = 404 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 5 TTAATTGTATAGTACTTATGTGATTCCTAACAA 2 96 0 AGTTTTGTGA 0.993312 -69 TAATGTTTTAAGTTTGTGTATGAACTATTACAA 2 137 0 AGTGTTATGA 0.983 -28 TTGTGTAACTAGTGTGTTTGTGACATAAAATAA 3 36 0 AGTGTTGTGA 0.995666 -265 ATACTGTAGTAGTCATTGTGTAACTAGTGTGTT 3 51 0 AGTTTTGTAA 0.973946 -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