AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis_+_PPS_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 yqjJ 226 similar to glucose-6-phosphate 1-dehydrogenase (pentose phosphate) #2 pgi 111 glucose-6-phosphate isomerase #3 yugK 103 similar to NADH-dependent butanol dehydrogenase #4 yugJ 229 similar to NADH-dependent butanol dehydrogenase Motif number 1 GTTTCCTTCCTCCTACTAGAACCAG 1 6 1 CTTCCTCCTA 0.933923 -221 AAGATTCACATTTTCCGCTTGATCCTGTAT 1 48 0 TTTTCCGCTT 0.900082 -179 ATTTTTTCAGCATTCTGCTTAAAAAAGGGC 1 113 1 CATTCTGCTT 0.938922 -114 ACCCCGTATATTTCCTTCATTTTAAATCTA 1 168 0 TTTCCTTCAT 0.935699 -59 TCATTCCGCCCTTTCTTCTTGACTTGATTT 2 31 1 CTTTCTTCTT 0.965651 -81 CAAACGGCTATTTCCCCTTTTT 3 3 0 TTTCCCCTTT 0.818139 -101 CGTTTGGCTGCTTCCCTTTTTCTTTTTTGT 3 27 1 CTTCCCTTTT 0.87653 -77 GTTTTGCAACCTCCTCCATGAATTATTAA 4 10 1 CCTCCTCCAT 0.977441 -220 TCTATACATGCATTCTCCATATGAGGGAAG 4 70 1 CATTCTCCAT 0.947829 -160 GGCAGGCCAGCTTCCCTCATATGGAGAATG 4 80 0 CTTCCCTCAT 0.973764 -150 GTGGTGAGGACATTCTGCATAATAAAAAAT 4 194 1 CATTCTGCAT 0.917808 -36 GACATCTCCTCCTTAGATTTTTTA 4 216 0 TCTCCTCCTT 0.950589 -14 ********** Masking position 3 Map Score: 13.3683 Number of sites scoring better than the average of aligned sites = 2323 Number in coding regions = 1813 Number in noncoding regions = 510 Number of orfs with sites within 600 bp upstream = 526 Fraction of orfs with sites within 600 bp upstream = 0.0844844 Motif number 2 AATCCTTTCGTGCTAGAAACATTTTTTCAGC 1 93 1 TGCTGAAACA 0.964827 -134 TTAAGCAGAATGCTGAAAAAATGTTTCTAGC 1 104 0 TGCTAAAAAA 0.989342 -123 TTCAGCATTCTGCTTAAAAAAGGGCTTAAAT 1 118 1 TGCTAAAAAA 0.989237 -109 CTCCAAATGATGCTGGTAAAAAACAGATTTT 3 75 0 TGCTGTAAAA 0.949989 -29 CCCAGCACCTTGCAAAATAAAACCATCTGGT 4 131 1 TGCAAATAAA 0.963868 -99 GAGGACATTCTGCATAATAAAAAATCTAAGG 4 199 1 TGCAAATAAA 0.963845 -31 **** ****** Masking position 9 Map Score: 6.20873 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 257 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 AGGATCAAGCGGAAAATGTGAATCTTGCCT 1 52 1 GGAAAATGTG 0.823222 -175 GAACTTATCTGTGAAATCAAGTCAAGAAGA 2 44 0 GTGAAATCAA 0.778844 -68 TTCATATAAAGTGAAAGATGAAACATTATA 2 71 1 GTGAAAGATG 0.96927 -41 CCGTTATGGAGGGACAGCAGC 2 101 1 GGGACAGCAG 0.980859 -11 ATTTTCCATTGTAACATAAGTTGACAAAAA 3 50 0 GTAACATAAG 0.864647 -54 ATGTTACAATGGAAAATCTGTTTTTTACCA 3 63 1 GGAAAATCTG 0.942518 -41 GTTATAGATTGTGACATATTGGAGAATCTA 4 44 1 GTGACATATT 0.728378 -186 GCAAGGTGCTGGGAAAGAAGCTGATATAAG 4 114 0 GGGAAAGAAG 0.970554 -116 ATGCTGATCGGTGAGAGCTGATTGCTTTAC 4 162 1 GTGAGAGCTG 0.948168 -68 ********** Masking position 6 Map Score: 4.45129 Number of sites scoring better than the average of aligned sites = 1618 Number in coding regions = 1413 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 4 CGTATATTTCCTTCATTTTAAATCTAAAAT 1 164 0 CTTCATTTTA 0.912648 -63 TTATTCGAAGCTTTATTTTAGTACACCCCG 1 192 0 CTTTATTTTA 0.896393 -35 AAGTACCTCACTTTATTCGAAGCTTTATTT 1 204 0 CTTTATTCGA 0.909477 -23 GCCCTTTCTTCTTGACTTGATTTCACAGAT 2 38 1 CTTGACTTGA 0.919785 -74 TCATCTTTCACTTTATATGAACTTATCTGT 2 62 0 CTTTATATGA 0.974244 -50 AGTAAAACCTCCAAATGATGCTGGTAAA 3 86 0 CTCCAAATGA 0.864524 -18 TACATGCATTCTCCATATGAGGGAAGCTGG 4 74 1 CTCCATATGA 0.962779 -156 GAGCTGATTGCTTTACATGTGGTGAGGACA 4 176 1 CTTTACATGT 0.820192 -54 ********** Masking position 5 Map Score: 3.99854 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 551 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 TTTCCTTCCTCCTACTAGAACCAGATACCT 1 12 1 CCTACTAGAA 0.972037 -215 GAACCAGATACCTACAAGAATACAGGATCA 1 29 1 CCTACAAGAA 0.955887 -198 ACAATCCTTTCGTGCTAGAAACATTTTTTC 1 91 1 CGTGCTAGAA 0.929955 -136 TTTTCAGCATTCTGCTTAAAAAAGGGCTTA 1 116 1 TCTGCTTAAA 0.844021 -111 ATATACGGGGTGTACTAAAATAAAGCTTCG 1 187 1 TGTACTAAAA 0.639442 -40 GCTGCTGTCCCTCCATAACGGTATAATGT 2 93 0 CCTCCATAAC 0.850871 -19 TTTGCAACCTCCTCCATGAATTATTAAAAC 4 13 1 CCTCCATGAA 0.971488 -217 GACATCTCCTCCTTAGATTTTTTATTA 4 213 0 CCTCCTTAGA 0.901503 -17 ********** Masking position 3 Map Score: 2.74377 Number of sites scoring better than the average of aligned sites = 990 Number in coding regions = 752 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 6 AAAGCAAACATTTAAGCCCTTTTTTAAGCA 1 128 0 TTTAAGCCCT 0.95097 -99 GAATGACTGGATTCCGCCCTTTGGGT 2 7 0 ATTCCGCCCT 0.996676 -105 GAATCCAGTCATTCCGCCCTTTCTTCTTGA 2 23 1 ATTCCGCCCT 0.996676 -89 CATGTAAAGCAATCAGCTCTCACCGATCAG 4 165 0 AATCAGCTCT 0.950969 -65 ********** Masking position 3 Map Score: 2.60479 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 79 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ********** No masking Map Score: -1.78814e-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 8 ********** No masking Map Score: -1.78814e-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 9 ********** No masking Map Score: -1.78814e-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