AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i053_Altronate_Metabolism_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 yjlC 300 yjlC #2 yjlD 39 similar to NADH dehydrogenase #3 yjmA 197 similar to glucuronate isomerase #4 yjmB 67 similar to Na+:galactoside symporter #5 yjmC 104 similar to malate dehydrogenase #6 yjmE 24 similar to D-mannonate hydrolase #7 yjmG 47 similar to hexuronate transporter #8 yjmH 87 similar to transcriptional regulator (LacI family) #9 yjmI 76 similar to tagaturonate reductase Motif number 1 ATTCACGTTCAAATTTTGTTCAAAAA 1 7 1 GTTCAAATTT 0.877545 -294 TTCAAAAAGTGTTATCATATAGAAGGTAAT 1 29 1 GTTATCATAT 0.885569 -272 AAACTGGGTAGTAAACATTTATTTTTGTAA 1 165 1 GTAAACATTT 0.973874 -136 TTATGACAGCGTTAACATTTCATTTTCAAA 3 83 1 GTTAACATTT 0.994461 -115 AAATGTTAACGTTAACATTTTGATTTGTTT 3 151 0 GTTAACATTT 0.994461 -47 AAATGTTAACGTTAACATTTTGAAATAGAA 3 161 1 GTTAACATTT 0.994461 -37 TTATGCACACGTTAACATTTTTCTGTATAA 9 36 0 GTTAACATTT 0.994461 -41 ********** Masking position 7 Map Score: 15.4408 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 4 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 CTTTACTCTCTCTGAAAATAGCAAACACAA 1 73 0 TCTGAAAATA 0.914947 -228 TAATACTGAATATGGCAAGATGAAAAACTG 1 141 1 TATGGCAAGA 0.726463 -160 AACATTTATTTTTGTAAATGATTGTGCATG 1 178 1 TTTGTAAATG 0.954183 -123 TGCTGATTTTTTTGGAAAGGGTAGTGCCTC 1 253 0 TTTGGAAAGG 0.975076 -48 AAGGAATGCTTTTGGCAATGCCAGATTCAT 3 19 0 TTTGGCAATG 0.984787 -179 CCGAGTGCTTTCTGGCAATGTCTTTTTTTA 3 50 1 TCTGGCAATG 0.981365 -148 CAATCTCTTTTTTGAAAATGAAATGTTAAC 3 93 0 TTTGAAAATG 0.954191 -105 AACGTTAACATTTTGAAATAGAATGAAAGA 3 168 1 TTTTGAAATA 0.827864 -30 TTTAAAATAATTTGTAAATAAAATGTGTTT 5 30 1 TTTGTAAATA 0.928639 -75 TCTGGAAATATAGTGGGAGA 8 1 1 TCTGGAAATA 0.977086 -87 ********** Masking position 7 Map Score: 12.8147 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 462 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 AAGGGTAGTGCCTCTCCCTGTCTCACGCTTT 1 236 0 CCTCTCCCTT 0.994898 -65 CAAAAGCATTCCTTTCCGAGTGCTTTCTGGC 3 35 1 CCTTTCCGAT 0.963716 -163 GTCCTCACCGTCTTTCATTCTAT 3 185 0 CCTCACCGTT 0.982718 -13 CAAAGTGTCCGCTCAGTATCGCTGAGCGG 4 9 1 CCGCTCAGTT 0.976075 -59 GTTCCACCTCTGTGTCTTAAGAATTTT 4 51 0 CCTCTGTGTT 0.909605 -17 TGCCTCCTTCCTTTTCAGTTTTTTGGGCACT 5 79 0 CTTTTCAGTT 0.796917 -26 AAACATACCGCCTCTCCCACTATATTTCCAG 8 12 0 CCTCTCCCAT 0.986187 -76 TTATTGCCTCCCTCTCACTTTATGCACACGT 9 54 0 CCTCTCACTT 0.989521 -23 ********* * Masking position 11 Map Score: 8.5213 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 228 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 AAAATCCTTTACTCTCTCTGAAAATAGCAA 1 79 0 ACTCTCTCTG 0.840624 -222 AAGGGTAGTGCCTCTCCCTGTCTCACGCTT 1 237 0 CCTCTCCCTG 0.985769 -64 CGTATATCCTCCGTCCTTTATATCAAT 2 23 0 CCTCCGTCCT 0.954278 -17 GTCCTCACCGTCTTTCATTCTA 3 186 0 CCTCACCGTC 0.95582 -12 GTTCCACCTCTGTGTCTTAAGAATTT 4 52 0 CCTCTGTGTC 0.917306 -16 GCAAGTGCCTCCTTCCTTTTCAGTTTT 5 88 0 CCTCCTTCCT 0.884419 -17 CTCAACCTCACCCCTATGTTGGTTC 7 33 0 CCTCACCCCT 0.971189 -15 AAACATACCGCCTCTCCCACTATATTTCCA 8 13 0 CCTCTCCCAC 0.970321 -75 CCTTATTGCCTCCCTCTCACTTTATGCA 9 59 0 CCTCCCTCTC 0.99202 -18 ********** Masking position 3 Map Score: 7.31258 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 424 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 5 CTGAAAATAGCAAACACAAAAAACTCCAAT 1 62 0 CAAACACAAA 0.902893 -239 TATTTTTATCTAAAAATAAACAATTGAATA 1 113 0 TAAAAATAAA 0.968268 -188 TATTTTTAGATAAAAATAATACTGAATATG 1 125 1 TAAAAATAAT 0.929947 -176 CAATCATTTACAAAAATAAATGTTTACTAC 1 172 0 CAAAAATAAA 0.953562 -129 AACGCTGTCATAAACATAAAAAAAGACATT 3 66 0 TAAACATAAA 0.95356 -132 AAAGGTAAAATAAAAACAAATCAAAATGTT 3 138 1 TAAAAACAAA 0.953562 -60 TAAAGAATATTTAAAATAATTTGTAAATAA 5 21 1 TTAAAATAAT 0.733756 -84 ********** Masking position 6 Map Score: 6.13204 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 278 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 6 AATTCGATTACCTTCTATATGATAACACTT 1 35 0 CCTTCTATAT 0.892905 -266 CATGAATTCACAATCCTTATTCTTATGCCT 1 204 1 CAATCCTTAT 0.908315 -97 TTGCCAAAAGCATTCCTTTCCGAGTGCTTT 3 31 1 CATTCCTTTC 0.931264 -167 TTTACCTTTATATTCCTTTGGGATCAATCT 3 117 0 TATTCCTTTG 0.727363 -81 CACCGTCTTTCATTCTATTTCAAAATGTTA 3 173 0 CATTCTATTT 0.891357 -25 TTATTTTAAATATTCTTTATATTATATTG 5 10 0 TATTCTTTAT 0.862988 -95 GCAAGTGCCTCCTTCCTTTTCAGTTTTTTG 5 85 0 CCTTCCTTTT 0.976785 -20 CTAATTCCCTTCCTTATCATACCGGCT 8 71 0 CCTTCCTTAT 0.981074 -17 TTTCAGCGGGCATTCTTTATACAGAAAAAT 9 20 1 CATTCTTTAT 0.969685 -57 ********** Masking position 4 Map Score: 8.49741 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 665 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 7 AAAATAAACAATTGAATAAGTCAAAATCCT 1 101 0 ATTGAATAAG 0.831594 -200 TAAAAATAATACTGAATATGGCAAGATGAA 1 135 1 ACTGAATATG 0.976382 -166 TTTATATCAATTTGAATCTGAGA 2 4 0 TTTGAATCTG 0.920777 -36 TCCTTTTAATGAATCTGGCATTGCCAA 3 8 1 AATGAATCTG 0.926281 -190 CAATCTCTTTTTTGAAAATGAAATGTTAAC 3 93 0 TTTGAAAATG 0.820391 -105 TGCCCAAAAAACTGAAAAGGAAGGAGGCAC 5 81 1 ACTGAAAAGG 0.904053 -24 ATGACTGAATCCGGAGGTGCGAG 6 4 1 ACTGAATCCG 0.959962 -21 AAGCGGTGCAACAGAAACTGAACCAACATA 7 14 1 ACAGAAACTG 0.879879 -34 ********** Masking position 5 Map Score: 4.29497 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 423 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 ********** No masking Map Score: -1.58208e-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: -1.58208e-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 10 ********** No masking Map Score: -1.58208e-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