AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i041_Ribose_Metabolism_1_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 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #2 rbsR 300 transcriptional regulator (LacI family) Motif number 1 CGTGTCTAACCCCTTTCGTAAATAA 1 2 1 GTTTACCCTT 0.979707 -122 ACGTTTTAAAGTGTACCTCCATTTCCTTATAATA 1 41 1 GTTCCCCTTT 0.996474 -83 AAGAAGTATCGTTTCTATCCCTTTTTATTATAAG 1 66 0 GTTTACCTTT 0.994529 -58 TTGAATCATCCTCCTTTTTAAGTCGGAT 1 106 0 ATACCCCTTT 0.932502 -18 AGTCTTTTCTGTTTCTCCCCATTTACAGGTCTAA 2 57 1 GTTTCCCTTT 0.994419 -244 TGTTCAAGAAATCTTCATCCATATTTGTGAAGAC 2 130 1 ATTCACCTAT 0.933736 -171 AAAATTTAAGGTTTTCACTCTTTTTTTGACAAAG 2 163 0 GTTCATCTTT 0.969876 -138 TCCTCCTTGTTTATGTAACCGTTTACATAGATAG 2 271 0 TTTTACCTTT 0.965659 -30 ** * ** ** *** Masking position 2 Map Score: 10.08 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 462 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 TTTTATTTACGAAAGGGGTTAGACACG 1 7 0 GAAAGGGGTA 0.969286 -117 TATTATAAGGAAATGGAGGTACACTTTAAAA 1 44 0 AAATGGAGTA 0.924079 -80 TCCTTATAATAAAAAGGGATAGAAACGATAC 1 64 1 AAAAAGGGTA 0.988363 -60 AATCCGACTTAAAAAGGAGGATGATTCAA 1 105 1 AAAAAGGAGA 0.97953 -19 TTAGACCTGTAAATGGGGAGAAACAGAAAAG 2 60 0 AAATGGGGGA 0.989265 -241 ACTTTGTCAAAAAAAGAGTGAAAACCTTAAA 2 162 1 AAAAAGAGGA 0.97953 -139 CGGTTACATAAACAAGGAGGAGCTGTT 2 284 1 AACAAGGAGA 0.936403 -17 ******** ** Masking position 2 Map Score: 7.74917 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 3 CAGAAAATGTTTAATTATGTTAGAGAATTCGGACTCGTA 2 11 0 TATATGAATT 0.979093 -290 TGAAACAATTTTAATAAAACTTAATATTTGTTCAAGAAA 2 102 1 TATATAAATT 0.982605 -199 GAAATCTTCATCCATATTTGTGAAGACTTTGTCAAAAAA 2 137 1 TATTTAAATT 0.990601 -164 TTGTAAATTGTATATATAATTGAAAAATTTAAGGTTTTC 2 181 0 TATTTAAATT 0.990566 -120 AATTTACAATTAGATTTCTTTTGATATTTTTATTGCTAA 2 211 1 TATTTGAATT 0.988685 -90 TTCATGATAATCTATCTATGTAAACGGTTACATAAACAA 2 260 1 TATTTAAGTT 0.974708 -41 * ** * * ** * ** Masking position 11 Map Score: 3.72627 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 62 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 TTATAAGGAAATGGAGGTACACTTTAAAAC 1 43 0 ATGGAGGTAC 0.980485 -81 CCGACTTAAAAAGGAGGATGATTCAA 1 108 1 AAGGAGGATG 0.9863 -16 CTTCACAAATATGGATGAAGATTTCTTGAA 2 132 0 ATGGATGAAG 0.969651 -169 TTACATAAACAAGGAGGAGCTGTT 2 287 1 AAGGAGGAGC 0.990715 -14 ********** Masking position 5 Map Score: 1.41004 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 125 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 TTCTTGTAAAAATCCGACTTAAAAAGGAGG 1 95 1 AATCCGACTT 0.9288 -29 TACGAGTCCGAATTCTCTAACATA 2 5 1 AGTCCGAATT 0.906342 -296 TATCATGAACAATCCGAAGTTAGCAATAAA 2 239 0 AATCCGAAGT 0.906342 -62 ********** Masking position 7 Map Score: 1.40557 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 26 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TAAGTCGGATTTTTACAAGAAGTATCGTTT 1 86 0 TTTTACAAGA 0.927359 -38 AACTTAATATTTGTTCAAGAAATCTTCATC 2 119 1 TTGTTCAAGA 0.987244 -182 TTCATCCATATTTGTGAAGACTTTGTCAAA 2 143 1 TTTGTGAAGA 0.90842 -158 TTGTGAAGACTTTGTCAAAAAAAGAGTGAA 2 154 1 TTTGTCAAAA 0.869387 -147 AAACCTTAAATTTTTCAATTATATATACAA 2 183 1 TTTTTCAATT 0.812296 -118 TAACTTCGGATTGTTCATGATAATCTATCT 2 247 1 TTGTTCATGA 0.97125 -54 CAGCTCCTCCTTGTTTATGTAACCGTTTAC 2 279 0 TTGTTTATGT 0.694545 -22 ********** Masking position 7 Map Score: 2.68321 Number of sites scoring better than the average of aligned sites = 1491 Number in coding regions = 1286 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 7 CGTGTCTAACCCCTTTCGTAAATAA 1 5 1 TCTAACCCTT 0.978031 -119 AAGTATCGTTTCTATCCCTTTTTATTATAAG 1 66 0 TCTATCCTTT 0.973689 -58 TCTAACATAATTAAACATTTTCTGGGATGAT 2 26 1 TTAAACATTT 0.847327 -275 CTTTTCTGTTTCTCCCCATTTACAGGTCTAA 2 60 1 TCTCCCCTTT 0.952506 -241 CGCATGACTTTGAAACAATTTTAATAAAACT 2 92 1 TGAAACATTT 0.938035 -209 TCCTTGTTTATGTAACCGTTTACATAGATAG 2 271 0 TGTAACCTTT 0.988178 -30 ******* *** Masking position 10 Map Score: 0.987928 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 357 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 8 ********** 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 9 ********** 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 10 ********** 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