AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i240_sensory_cassete6_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yehU 221 putative 2-component sensor protein #2 b2380 300 putative sensor protein Motif number 1 CTCGCGAGGTCCCGGTTTAACTTTAGACGC 1 24 1 CCCGGTTTAA 0.960245 -198 TAACTTTAGACGCAGTTTTGCGAACCAGGT 1 41 1 CGCAGTTTTG 0.866965 -181 TTGCGAACCAGGTAGTTTTGCCCGTTTTTT 1 58 1 GGTAGTTTTG 0.601454 -164 GGTAGTTTTGCCCGTTTTTTGTGCATCTAT 1 68 1 CCCGTTTTTT 0.891453 -154 GCATCTATAGGGTGATTTTATTTTTGCCAG 1 90 1 GGTGATTTTA 0.861889 -132 ATTTTTGCCAGGCGATTTTGAGTGATCGTA 1 109 1 GGCGATTTTG 0.947895 -113 ATGTATGTTACGCGTTTTAAAGGGAAGTGT 1 191 1 CGCGTTTTAA 0.961847 -31 CTGTCTGTCCAGCGTTTTAGAACATTTTAT 2 22 1 AGCGTTTTAG 0.851865 -279 AAGCAGAGTTCCTCATTTAACGTCATTAAT 2 50 0 CCTCATTTAA 0.755849 -251 AGATAAATTTCCTGTTTTTAAAGCAGAGTT 2 70 0 CCTGTTTTTA 0.947946 -231 GAAAATTACCACTCATTTTATTAACATAAT 2 110 1 ACTCATTTTA 0.488235 -191 ATCTATCAATCCCCTTTTAAAATTGTGGTT 2 203 1 CCCCTTTTAA 0.919393 -98 TGACCAGCAGGCCGTTTTTGAGGAAAAACC 2 229 0 GCCGTTTTTG 0.968688 -72 ********** Masking position 6 Map Score: 10.6942 Number of sites scoring better than the average of aligned sites = 3485 Number in coding regions = 3040 Number in noncoding regions = 445 Number of orfs with sites within 600 bp upstream = 412 Fraction of orfs with sites within 600 bp upstream = 0.0661741 Motif number 2 ACCGGGACCTCGCGAGCAAGGGTGAGACG 1 9 0 CGCAGCAAGG 0.988944 -213 GACGCAGTTTTGCGAACCAGGTAGTTTTGCC 1 49 1 TGCAACCAGG 0.976721 -173 CCTATAGATGCACAAAAAACGGGCAAAACTA 1 70 0 CACAAAAACG 0.747057 -152 GAAAGTTAAACGCAGGCAATGTATGTTACGC 1 173 1 CGCGGCAATG 0.932508 -49 CCCTTTAAAACGCGTAACATACATTGCCTGC 1 184 0 CGCTAACATA 0.754418 -38 ACCCGCAAACCACACTTCCCTTTA 1 208 0 CGCAACCACA 0.985883 -14 TGTTCTAAAACGCTGGACAGACAGAAATTAA 2 15 0 CGCGGACAGA 0.962028 -286 AATTTATCTGCGCTAACAAGAAAATTACCAC 2 91 1 CGCAACAAGA 0.988268 -210 TCAATAAATTTACTAACCAGAAGTGCATTAT 2 144 1 TACAACCAGA 0.865185 -157 *** ******* Masking position 9 Map Score: 6.21843 Number of sites scoring better than the average of aligned sites = 4024 Number in coding regions = 3851 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 CGGTTTAACTTTAGACGCAGTTTTGCGAAC 1 36 1 TTAGACGCAG 0.987893 -186 TCAAAGAAAGTTAAACGCAGGCAATGTATG 1 168 1 TTAAACGCAG 0.994509 -54 TAAAATGTTCTAAAACGCTGGACAGACAGA 2 21 0 TAAAACGCTG 0.943609 -280 ATTTCCTGTTTTTAAAGCAGAGTTCCTCAT 2 64 0 TTTAAAGCAG 0.960353 -237 TAATTTTCTTGTTAGCGCAGATAAATTTCC 2 88 0 GTTAGCGCAG 0.962478 -213 ********** Masking position 7 Map Score: 3.40696 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 312 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 CACGAATTCTCATTTTTCTGCAAGAGTTCA 1 141 1 CATTTTTCTG 0.96414 -81 GACAGACAGAAATTAATCAG 2 1 0 AATTAATCAG 0.945516 -300 CATTTAACGTCATTAATAAAATGTTCTAAA 2 37 0 CATTAATAAA 0.798745 -264 AAAAACAGGAAATTTATCTGCGCTAACAAG 2 81 1 AATTTATCTG 0.915364 -220 AATTTATTGAAATTATTATGTTAATAAAAT 2 124 0 AATTATTATG 0.870791 -177 ACCAGAAGTGCATTATCAAGAGATGCATTG 2 159 1 CATTATCAAG 0.820773 -142 GCTAATACACCATTTATCTATCAATCCCCT 2 188 1 CATTTATCTA 0.863553 -113 GAGGTTTAATCCTTATTCAGAGTCACCC 2 283 1 CCTTATTCAG 0.921824 -18 ********** Masking position 4 Map Score: 2.56341 Number of sites scoring better than the average of aligned sites = 1519 Number in coding regions = 1295 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 5 ********** No masking Map Score: 1.50878e-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 6 ********** No masking Map Score: 1.50878e-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 7 ********** No masking Map Score: 1.50878e-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