AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i035_Sugars_Metabolism_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 yckG 231 similar to D-arabino 3-hexulose 6-phosphate formaldehyde lyase #2 araA 207 L-arabinose isomerase Motif number 1 ACTTTTTTGCAGACTCTTTTTTCATTATACTCACTC 1 67 1 AGTTTTTTTT 0.905891 -165 AGATTTCTTTCGCTTGATTTTATGAGTGAGTATAAT 1 90 0 CGTATTTTAG 0.989547 -142 ACTCCCTTTTCGAATTATTGTTCATTCTATAGGTTC 1 197 0 CGTATTGTTT 0.941164 -35 GGGCAGAGCCCGGCTTTTTATTCAATAGGACGGCCA 2 25 0 CGTTTTATAT 0.943504 -183 GCTCTGCCCCCGGCTTTTTTTAAAAGAAAAGATTGA 2 52 1 CGTTTTTTAG 0.987157 -156 ATATTTTGTACGAACAATTTTATTATAGTAATTGAC 2 98 0 CGCATTTTAT 0.964041 -110 ATTTATTTATAGGTTTATTTTCCTATCATTAGTACG 2 132 1 AGTATTTTAT 0.957642 -76 ATCATTAGTACGTATCTTTTGTATTTGAAAGCGTTT 2 156 1 CGTTTTTGTT 0.919494 -52 TATTTGAAAGCGTTTTATTTTATGAGAAAGGGGCAG 2 177 1 CGTATTTTAG 0.989547 -31 ** * ***** ** Masking position 8 Map Score: 7.75536 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 559 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 CCTTAGTAACCTTTTTGTATGTTAGATACG 1 22 1 CTTTTTGTAT 0.968271 -210 CGAAAGAAATCTGATTGTCTCTCCTCACAG 1 114 1 CTGATTGTCT 0.863361 -118 CTCCAAGTAACTTGTTGACTTCAAAGTGCC 1 148 1 CTTGTTGACT 0.940064 -84 AAAGAAGGAACCTATAGAATGAACAATAAT 1 190 1 CCTATAGAAT 0.922105 -42 GATCCACTCCCTTTTCGAATTATTGTTCAT 1 208 0 CTTTTCGAAT 0.935604 -24 GGCTGGCCGTCCTATTGAATAAAAAGCCGG 2 22 1 CCTATTGAAT 0.979586 -186 TTAGTACGTATCTTTTGTATTTGAAAGCGT 2 160 1 TCTTTTGTAT 0.82699 -48 ********** Masking position 5 Map Score: 3.05207 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 529 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 3 TAAGTAAGTGATGATACGTATCTAACATAC 1 38 0 ATGATACGTA 0.973317 -194 CTCTTTTTTCATTATACTCACTCATAAAAT 1 80 1 ATTATACTCA 0.923808 -152 AGAATGAACAATAATTCGAAAAGGGAGTGG 1 205 1 ATAATTCGAA 0.82806 -27 GATTGACAGTATAATAGTCAATTACTATAA 2 82 1 ATAATAGTCA 0.902256 -126 GAACAATTTTATTATAGTAATTGACTATTA 2 93 0 ATTATAGTAA 0.895297 -115 ATACGTACTAATGATAGGAAAATAAACCTA 2 141 0 ATGATAGGAA 0.975485 -67 TCAAATACAAAAGATACGTACTAATGATAG 2 154 0 AAGATACGTA 0.883352 -54 ********** Masking position 4 Map Score: 3.28323 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 245 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 GAGTCTGCAAAAAAGTAAGTAAGTGATGATA 1 52 0 AAAAGTAAGA 0.96331 -180 GCTTGATTTTATGAGTGAGTATAATGAAAAA 1 84 0 ATGAGTGAGA 0.923835 -148 TCATAAAATCAAGCGAAAGAAATCTGATTGT 1 101 1 AAGCGAAAGA 0.926846 -131 GGATACTGTGAGGAGAGACAATCAGATTTCT 1 118 0 AGGAGAGACA 0.832818 -114 TCTTTTGTTGAGAAGTAGGCACTTTGAAGTC 1 164 0 AGAAGTAGGA 0.896223 -68 ACTTCTCAACAAAAGAAGGAACCTATAGAAT 1 179 1 AAAAGAAGGA 0.953679 -53 CAATAATTCGAAAAGGGAGTGGATCAACA 1 213 1 AAAAGGGAGG 0.861293 -19 GGCTTTTTTTAAAAGAAAAGATTGACAGTAT 2 63 1 AAAAGAAAAA 0.82467 -145 GTTTTATTTTATGAGAAAGGGGCAGTTTAC 2 188 1 ATGAGAAAGG 0.920198 -20 ********* * Masking position 1 Map Score: 1.8247 Number of sites scoring better than the average of aligned sites = 2033 Number in coding regions = 1557 Number in noncoding regions = 476 Number of orfs with sites within 600 bp upstream = 444 Fraction of orfs with sites within 600 bp upstream = 0.0713138 Motif number 5 AAAAGGTTACTAAGGGGGGATTCTAT 1 7 0 TAAGGGGGGA 0.981962 -225 CTTTTGTTGAGAAGTAGGCACTTTGAAGTC 1 164 0 GAAGTAGGCA 0.973498 -68 TTTAAAAAAAGCCGGGGGCAGAGCCCGGCT 2 46 0 GCCGGGGGCA 0.995011 -162 TATTTTATGAGAAAGGGGCAGTTTAC 2 192 1 GAAAGGGGCA 0.993195 -16 ********** Masking position 10 Map Score: 0.917574 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 218 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 CGGGGGCAGAGCCCGGCTTTTTATTCAATA 2 34 0 GCCCGGCTTT 0.998158 -174 CGGGCTCTGCCCCCGGCTTTTTTTAAAAGA 2 49 1 CCCCGGCTTT 0.998158 -159 ********** Masking position 8 Map Score: 0.543252 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: 7.2008e-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 8 ********** No masking Map Score: 7.2008e-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: 7.2008e-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