AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i041_bsub_mtub_300.orf -o041_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #2 rbsR 300 transcriptional regulator (LacI family) #3 rbsK 300 rbsK Motif number 1 ATTGGTTCTGGGTGGTCCGTAATCGAGGTGA 3 17 1 GGTGGCCGTA 0.994713 -284 AGCCAGGATAGCTCGGCCGTATCGCAATGTT 3 47 1 GCTCGCCGTA 0.945813 -254 AGCGGTTGCCGGTGCCGGGGCATGTGTTGAT 3 92 0 GGTGCGGGGC 0.977289 -209 CGATGGTCTGAGTGCGTCGTCGTTTGATGCG 3 136 0 AGTGCTCGTC 0.844815 -165 CGATGCTGTCGGTCGATGGTCTGAGTGCGTC 3 149 0 GGTCGTGGTC 0.967086 -152 TGGTCGGGATGCTGGACCGGCTCGATGCTGT 3 171 0 GCTGGCCGGC 0.910753 -130 GATCGGGACGGGTGGTCGGGATGCTGGACCG 3 183 0 GGTGGCGGGA 0.989607 -118 GTGTCCTGTCGGTGGCGCGTCCCAGTATTCG 3 226 0 GGTGGGCGTC 0.995717 -75 GGTATCAGTGGGTGTCCTGTCGGTGGCGCGT 3 237 0 GGTGTCTGTC 0.920289 -64 ***** ***** Masking position 3 Map Score: 9.78001 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 317 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 TTATTTACGAAAGGGGTTAGACACG 1 2 0 AAGGGTAAAC 0.95872 -122 TATTATAAGGAAATGGAGGTACACTTTAAAACGT 1 41 0 AAAGGGGAAC 0.993967 -83 CTTATAATAAAAAGGGATAGAAACGATACTTCTT 1 66 1 AAAGGTAAAC 0.99004 -58 ATCCGACTTAAAAAGGAGGATGATTCAA 1 106 1 AAAGGGGTAT 0.871024 -18 TTAGACCTGTAAATGGGGAGAAACAGAAAAGACT 2 57 0 AAAGGGAAAC 0.992247 -244 GTCTTCACAAATATGGATGAAGATTTCTTGAACA 2 130 0 ATAGGTGAAT 0.821881 -171 CTTTGTCAAAAAAAGAGTGAAAACCTTAAATTTT 2 163 1 AAAGATGAAC 0.961832 -138 CTATCTATGTAAACGGTTACATAAACAAGGAGGA 2 271 1 AAAGGTAAAA 0.928024 -30 TCAACGCATCAAACGACGACGCACTCAGACCATC 3 132 1 AAAGAGAGAC 0.870016 -169 *** ** ** * ** Masking position 13 Map Score: 6.29054 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 521 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 TTTTATTTACGAAAGGGGTTAGACACG 1 7 0 GAAAGGGGTA 0.948426 -117 TATTATAAGGAAATGGAGGTACACTTTAAAA 1 44 0 AAATGGAGTA 0.876429 -80 TCCTTATAATAAAAAGGGATAGAAACGATAC 1 64 1 AAAAAGGGTA 0.980194 -60 AATCCGACTTAAAAAGGAGGATGATTCAA 1 105 1 AAAAAGGAGA 0.965379 -19 TTAGACCTGTAAATGGGGAGAAACAGAAAAG 2 60 0 AAATGGGGGA 0.981718 -241 ACTTTGTCAAAAAAAGAGTGAAAACCTTAAA 2 162 1 AAAAAGAGGA 0.965379 -139 CGGTTACATAAACAAGGAGGAGCTGTT 2 284 1 AACAAGGAGA 0.895614 -17 ******** ** Masking position 2 Map Score: 3.88943 Number of sites scoring better than the average of aligned sites = 868 Number in coding regions = 577 Number in noncoding regions = 291 Number of orfs with sites within 600 bp upstream = 314 Fraction of orfs with sites within 600 bp upstream = 0.0504337 Motif number 4 CCTTTTTAAGTCGGATTTTTACAAGAAGTAT 1 91 0 TCGGATTTTA 0.921334 -33 GTTAGAGAATTCGGACTCGTA 2 1 0 TCGGATCGTA 0.964573 -300 ATTGCTAACTTCGGATTGTTCATGATAATCT 2 242 1 TCGGATGTTC 0.994495 -59 AGCGATTGGTTCTGGGTGGTCCGTAATCGAG 3 13 1 TCTGGTGGTC 0.941484 -288 CTCGGCCGTATCGCAATGTTCAGCGAGTCGA 3 58 1 TCGCATGTTC 0.976431 -243 GGCAACCGCTGCGGAGTGGTCAACGCATCAA 3 113 1 GCGGATGGTC 0.990454 -188 ***** ***** Masking position 7 Map Score: 2.41483 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 279 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GACCGGCTCGATGCTGTCGGTCGATGGTCT 3 158 0 ATGCTGTCGG 0.996087 -143 GTATTCGAACATGCTTGCGGATCGGGACGG 3 203 0 ATGCTTGCGG 0.974071 -98 ATCAGTGGGTGTCCTGTCGGTGGCGCGTCC 3 235 0 GTCCTGTCGG 0.987627 -66 GCTTGCTGTTGGCTGAAATCAC 3 289 0 TTGCTGTTGG 0.973216 -12 ********** Masking position 5 Map Score: 1.21534 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 230 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 GTAAATAAAATCAACGTTTTAAAGTGTACCT 1 28 1 TCAACGTTTA 0.9396 -96 CTAACATAATTAAACATTTTCTGGGATGATA 2 27 1 TAAACATTTC 0.873977 -274 TTTACAGGTCTAAACGCATGACTTTGAAACA 2 78 1 TAAACGCATA 0.96616 -223 TCTATCTATGTAAACGGTTACATAAACAAGG 2 270 1 TAAACGGTTC 0.94335 -31 AGTCGATGGATCAACACATGCCCCGGCACCG 3 83 1 TCAACACATC 0.961061 -218 TGCGGAGTGGTCAACGCATCAAACGACGACG 3 122 1 TCAACGCATA 0.978888 -179 ********* * Masking position 4 Map Score: 0.958072 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 315 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TACGAGTCCGAATTCTCTAACATAA 2 6 1 GTCCGAATTC 0.978273 -295 GTTCTGGGTGGTCCGTAATCGAGGTGAGCC 3 21 1 GTCCGTAATC 0.920021 -280 AGGATAGCTCGGCCGTATCGCAATGTTCAG 3 51 1 GGCCGTATCG 0.84622 -250 TCGGTCGATGGTCTGAGTGCGTCGTCGTTT 3 142 0 GTCTGAGTGC 0.901036 -159 ATGCTGGACCGGCTCGATGCTGTCGGTCGA 3 164 0 GGCTCGATGC 0.948393 -137 GGGACGGGTGGTCGGGATGCTGGACCGGCT 3 180 0 GTCGGGATGC 0.969341 -121 CCGACCACCCGTCCCGATCCGCAAGCATGT 3 195 1 GTCCCGATCC 0.964011 -106 GCTTGCTGTTGGCTGAAATCACTTGTGTCA 3 281 0 GGCTGAAATC 0.88665 -20 ********** Masking position 3 Map Score: 1.59458 Number of sites scoring better than the average of aligned sites = 1281 Number in coding regions = 1213 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 ********** No masking Map Score: 9.26138e-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 9 ********** No masking Map Score: 9.26138e-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 10 ********** No masking Map Score: 9.26138e-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