AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i041_Ribose_Metabolism_1_bsub_reg_100.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 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #2 rbsR 300 transcriptional regulator (LacI family) Motif number 1 GTACACTTTAAAACGTTGATTTTATTTACGAAAGGGGT 1 19 0 AAAGGATTTA 0.92042 -105 TATTATAAGGAAATGGAGGTACACTTTAAAACGTTGAT 1 37 0 AAAGGGAATA 0.986175 -87 CTTATAATAAAAAGGGATAGAAACGATACTTCTTGTAA 1 66 1 AAAGTAAATA 0.978546 -58 ATCCGACTTAAAAAGGAGGATGATTCAA 1 106 1 AAAGGGTAAA 0.974527 -18 TCATCCCAGAAAATGTTTAATTATGTTAGAGAATTCGG 2 18 0 AAAGTATATA 0.966025 -283 TTAGACCTGTAAATGGGGAGAAACAGAAAAGACTATCA 2 53 0 AAAGGAAAAA 0.979454 -248 TTACAGGTCTAAACGCATGACTTTGAAACAATTTTAAT 2 79 1 AAAGTGCTAA 0.846349 -222 CTTTGTCAAAAAAAGAGTGAAAACCTTAAATTTTTCAA 2 163 1 AAAGTGAATA 0.982343 -138 CTATCTATGTAAACGGTTACATAAACAAGGAGGAGCTG 2 271 1 AAAGTAAAAA 0.973703 -30 *** * ** * * ** Masking position 3 Map Score: 9.021 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 395 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 2 ACCCCTTTCGTAAATAAAATCAACGTTTTA 1 19 1 TAAATAAAAT 0.667074 -105 GAAACGATACTTCTTGTAAAAATCCGACTT 1 85 1 TTCTTGTAAA 0.884634 -39 GTAAAAATCCGACTTAAAAAGGAGGATGAT 1 100 1 GACTTAAAAA 0.841107 -24 TTCTCTAACATAATTAAACATTTTCTGGGA 2 23 1 TAATTAAACA 0.918682 -278 ATATTAAGTTTTATTAAAATTGTTTCAAAG 2 99 0 TTATTAAAAT 0.749198 -202 GGATGAAGATTTCTTGAACAAATATTAAGT 2 120 0 TTCTTGAACA 0.951624 -181 ATTGTATATATAATTGAAAAATTTAAGGTT 2 184 0 TAATTGAAAA 0.961995 -117 AAAAGAAATCTAATTGTAAATTGTATATAT 2 203 0 TAATTGTAAA 0.875845 -98 CTTCGGATTGTTCATGATAATCTATCTATG 2 250 1 TTCATGATAA 0.636021 -51 TGTAAACGGTTACATAAACAAGGAGGAGCT 2 278 1 TACATAAACA 0.891112 -23 ********** Masking position 5 Map Score: 5.18871 Number of sites scoring better than the average of aligned sites = 2039 Number in coding regions = 1666 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 395 Fraction of orfs with sites within 600 bp upstream = 0.0634436 Motif number 3 CGTGTCTAACCCCTTTCGTAA 1 2 1 GTGTCTAACC 0.981494 -122 ACGTTTTAAAGTGTACCTCCATTTCCTTAT 1 41 1 GTGTACCTCC 0.968001 -83 AAGAAGTATCGTTTCTATCCCTTTTTATTA 1 70 0 GTTTCTATCC 0.988009 -54 AGTCTTTTCTGTTTCTCCCCATTTACAGGT 2 57 1 GTTTCTCCCC 0.990722 -244 ********** Masking position 4 Map Score: 1.41004 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 66 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 GATTTTTACAAGAAGTATCGTTTCTATCCCT 1 78 0 AGAAGTATGT 0.879063 -46 CTCCCCATTTACAGGTCTAAACGCATGACTT 2 71 1 ACAGGTCTAA 0.88284 -230 GATTTCTTGAACAAATATTAAGTTTTATTAA 2 112 0 ACAAATATAA 0.96788 -189 TATTTGTTCAAGAAATCTTCATCCATATTTG 2 126 1 AGAAATCTCA 0.942027 -175 CAAAGTCTTCACAAATATGGATGAAGATTTC 2 137 0 ACAAATATGA 0.961513 -164 AAATATCAAAAGAAATCTAATTGTAAATTGT 2 209 0 AGAAATCTAT 0.940562 -92 AGTTAGCAATAAAAATATCAAAAGAAATCTA 2 221 0 AAAAATATAA 0.883523 -80 ******** ** Masking position 3 Map Score: 0.758378 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 283 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 ********** No masking Map Score: -5.51791e-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: -5.51791e-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: -5.51791e-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