AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i092_Sugar_Utilization_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 licT 95 transcriptional antiterminator (BglG family) #2 yxiP 206 yxiP #3 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component Motif number 1 CCAGCTTCCGTCTTTCCCTG 1 1 1 CCAGCTTCCG 0.975344 -95 GCTCTGTCTCCTCTCTGCTGAATCCC 2 191 0 TCTCCTCTCT 0.941175 -16 TTAGGTTTTGCCTGCTTTCGCAGTAACAAT 3 128 0 CCTGCTTTCG 0.979575 -173 ATTGCGAGAGTCTCCTCCTGCACCTGCACC 3 160 0 TCTCCTCCTG 0.913511 -141 AAATGCTGCATCACCTCCTAAAAGAGAATA 3 210 0 TCACCTCCTA 0.870418 -91 CCGCCTTTCACCAGCTTTTTTTGTATCAAA 3 237 0 CCAGCTTTTT 0.939483 -64 TGAAAGGTGGCCGCCTTTCACCAGCTTTTT 3 247 0 CCGCCTTTCA 0.963849 -54 TGAAAGGCGGCCACCTTTCATCCAGCAGTC 3 257 1 CCACCTTTCA 0.983385 -44 GTGTATACCTCCTTTTTATGGGGGGAC 3 284 0 CCTCCTTTTT 0.967871 -17 ********** Masking position 6 Map Score: 8.72025 Number of sites scoring better than the average of aligned sites = 1107 Number in coding regions = 740 Number in noncoding regions = 367 Number of orfs with sites within 600 bp upstream = 382 Fraction of orfs with sites within 600 bp upstream = 0.0613556 Motif number 2 TGTACTAGGTCAATATCATCAGGGAAAGACG 1 19 0 CAAATCATCA 0.559344 -77 TGATATTGACCTAGTACAAAAAGAATGTACA 1 32 1 CTATACAAAA 0.744516 -64 ATTTGAAGCGAAAAAACATAAATATTTTGTA 2 87 0 AAAAACATAA 0.920291 -120 AACCCCAGCAATAAATCAAAAGTATGATTTG 2 113 0 ATAATCAAAA 0.881443 -94 CCCTTCTGGAAAATACCATAAAATATAGTTA 2 163 0 AAAACCATAA 0.936966 -44 ACTATCGTTTCTAGAACAAAAGTAATCATAA 3 16 0 CTAAACAAAA 0.95822 -285 AAACGATAGTCAACACCAAAAATGAAAGCGT 3 37 1 CAAACCAAAA 0.980423 -264 GTATACCTACAAACAAATAAAACGACCCGTC 3 94 1 AAAAAATAAA 0.640122 -207 CGAAAGCAGGCAAAACCTAAATGGTGCAGGT 3 138 1 CAAACCTAAA 0.952262 -163 AAGAGAATAAAAAAACCTAAATGACACAGAT 3 188 0 AAAACCTAAA 0.936966 -113 GCAGCATTTGATACAAAAAAAGCTGGTGAAA 3 231 1 ATAAAAAAAA 0.72474 -70 *** ******* Masking position 3 Map Score: 7.15731 Number of sites scoring better than the average of aligned sites = 1858 Number in coding regions = 1534 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 309 Fraction of orfs with sites within 600 bp upstream = 0.0496306 Motif number 3 ATTGACCTAGTACAAAAAGAATGTACAATC 1 36 1 TACAAAAAGA 0.866097 -60 GAAGCGAAAAAACATAAATATTTTGTAAAA 2 84 0 AACATAAATA 0.967033 -123 CCAGCAATAAATCAAAAGTATGATTTGAAG 2 110 0 ATCAAAAGTA 0.866097 -97 AACAAAAGTAATCATAAAGATT 3 3 0 ATCATAAAGA 0.858798 -298 TCGTTTCTAGAACAAAAGTAATCATAAAGA 3 13 0 AACAAAAGTA 0.946424 -288 GATAGTCAACACCAAAAATGAAAGCGTTGA 3 41 1 ACCAAAAATG 0.90171 -260 AAGCAGGCAAAACCTAAATGGTGCAGGTGC 3 141 1 AACCTAAATG 0.922051 -160 AGAATAAAAAAACCTAAATGACACAGATTG 3 186 0 AACCTAAATG 0.922051 -115 CAGCATTTGATACAAAAAAAGCTGGTGAAA 3 232 1 TACAAAAAAA 0.703384 -69 ********** Masking position 6 Map Score: 4.11275 Number of sites scoring better than the average of aligned sites = 1342 Number in coding regions = 1013 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 332 Fraction of orfs with sites within 600 bp upstream = 0.0533248 Motif number 4 GCTGGGGTTAGGTGCATCTGGTACCATTTA 2 135 1 GGTGCATCTG 0.917423 -72 TTCCAGAAGGGATTCAGCAGAGAGGAGACA 2 183 1 GATTCAGCAG 0.986468 -24 TTTAGCACTAGATTCGTGAGATGTCAACGC 3 64 0 GATTCGTGAG 0.909273 -237 CAAATAAAACGACCCGTCAGGATTGTTACT 3 107 1 GACCCGTCAG 0.918719 -194 AAATGGTGCAGGTGCAGGAGGAGACTCTCG 3 156 1 GGTGCAGGAG 0.979008 -145 TTTAGGAGGTGATGCAGCATTTGATACAAA 3 218 1 GATGCAGCAT 0.955166 -83 GGCCACCTTTCATCCAGCAGTCCCCCCATA 3 265 1 CATCCAGCAG 0.955896 -36 ********** Masking position 5 Map Score: 2.71304 Number of sites scoring better than the average of aligned sites = 1619 Number in coding regions = 1492 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 ********** No masking Map Score: 7.91135e-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 6 ********** No masking Map Score: 7.91135e-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: 7.91135e-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