AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i035_Sugars_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 yckG 231 similar to D-arabino 3-hexulose 6-phosphate formaldehyde lyase #2 araA 207 L-arabinose isomerase #3 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #4 ysdC 183 similar to endo-1,4-beta-glucanase Motif number 1 TATCTAACATACAAAAAGGTTACTAAGGGGGGAT 1 16 0 AAAAAGTTCT 0.980298 -216 AGTATAATGAAAAAAGAGTCTGCAAAAAAGTAAG 1 64 0 AAAAAGCTCA 0.980846 -168 GTGAGGAGAGACAATCAGATTTCTTTCGCTTGAT 1 108 0 AAATAGTTCT 0.943053 -124 TTCTCATAAAATAAAACGCTTTCAAATACAAAAG 2 171 0 AAAACGTTCA 0.963929 -37 GTACAGACAAAAAAATAGAATCCACCTCAATAGG 3 28 0 AAAAAGATCA 0.983844 -169 CCTTTATTTTAGAAAGCGCTTACAAATTAGATTA 3 160 0 AAAACGTTCA 0.950648 -37 CGAAAAGCATAGAAAAAGGTTTCACTTTTTCTAA 4 53 1 AAAAAGTTCA 0.96916 -131 CATGTTTTGTATAATAAGAATGCAGGACTGATGA 4 145 1 AAATAGATCA 0.957087 -39 * *** ** ** ** Masking position 4 Map Score: 11.5935 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 110 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 ATAGAATCCCCCCTTAGTAACCTTTTTG 1 8 1 CCCCCCTTAT 0.993124 -224 TCTATAGGTTCCTTCTTTTGTTGAGAAGTAG 1 177 0 CCTTCTTTTT 0.861478 -55 GGGGGCAGAGCCCGGCTTTTTATTCAATAGG 2 32 0 CCCGGCTTTT 0.948002 -176 GGGCTCTGCCCCCGGCTTTTTTTAAAAGAAA 2 50 1 CCCGGCTTTT 0.948002 -158 ATTTTCGGTATCCCCTTTATTGTAGTCACTA 3 73 0 TCCCCTTTAT 0.805291 -124 GATTATTTATCCTCCCTTCCTGTCAAATCGA 3 134 0 CCTCCCTTCT 0.99094 -63 TTTTGTTCAACCTCCTTTATTTTAGAAAGCG 3 176 0 CCTCCTTTAT 0.967411 -21 TGTGAAGGCACCTCCCTTATGGTGATGATCT 4 13 1 CCTCCCTTAG 0.949722 -171 CTTCATCAGTCCTGCATTCTTATTATACAAA 4 150 0 CCTGCATTCT 0.897122 -34 GTTCCAAACCCTCCTTCATCAGTCCTGCA 4 165 0 CCCTCCTTCT 0.979417 -19 ********* * Masking position 7 Map Score: 11.3751 Number of sites scoring better than the average of aligned sites = 569 Number in coding regions = 360 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 3 GGTTACTAAGGGGGGATTCTAT 1 3 0 GGGGGATTCT 0.97741 -229 CAAGTTACTTGGAGGATACTGTGAGGAGAG 1 132 0 GGAGGATACT 0.902169 -100 TTGACTTCAAAGTGCCTACTTCTCAACAAA 1 162 1 AGTGCCTACT 0.91176 -70 TCATTCTATAGGTTCCTTCTTTTGTTGAGA 1 182 0 GGTTCCTTCT 0.965856 -50 TTCGAATTATTGTTCATTCTATAGGTTCCT 1 195 0 TGTTCATTCT 0.789199 -37 CACCTCAATAGGCGGATTCTTCCGTATCT 3 10 0 GGCGGATTCT 0.987597 -187 CGCCTATTGAGGTGGATTCTATTTTTTTGT 3 26 1 GGTGGATTCT 0.991617 -171 CTAATTTGTAAGCGCTTTCTAAAATAAAGG 3 164 1 AGCGCTTTCT 0.847692 -33 CCATAAGGGAGGTGCCTTCACACA 4 5 0 GGTGCCTTCA 0.957712 -179 ********** Masking position 7 Map Score: 8.09953 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 402 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 GCCCCCGGCTTTTTTTAAAAGAAAAGATTGACAG 2 57 1 TTTTTAAGAA 0.87158 -151 GTACGAACAATTTTATTATAGTAATTGACTATTA 2 93 0 TTTTTTAGAA 0.958665 -115 TAAATAAATATTTTGTACGAACAATTTTATTATA 2 107 0 TTTTTAAAAA 0.934056 -101 AGTACGTATCTTTTGTATTTGAAAGCGTTTTATT 2 162 1 TTTTTATGAA 0.957999 -46 GAAAGCGTTTTATTTTATGAGAAAGGGGCAGTTT 2 182 1 TATTTAAGAA 0.955161 -26 GTTCAACCTCCTTTATTTTAGAAAGCGCTTACAA 3 169 0 CTTTTTAGAA 0.844261 -28 AGGTTTCACTTTTTCTAAAAGAAAGCTGTAAAAA 4 69 1 TTTTTAAGAA 0.980289 -115 ACCATACGACTATTTCACTTGAAAATCGGGTATA 4 105 0 TATTCATGAA 0.631679 -79 GCGCCATGTTTTGTATAATAAGAATGCAGGACTG 4 141 1 TTGTTAAAAA 0.770253 -43 **** ** ** ** Masking position 4 Map Score: 5.99585 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 379 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 5 TGAGTGAGTATAATGAAAAAAGAGTCTGCAA 1 73 0 TATGAAAAAA 0.676266 -159 ACTCATAAAATCAAGCGAAAGAAATCTGATT 1 99 1 TAAGCGAAAG 0.897953 -133 GAATGAACAATAATTCGAAAAGGGAGTGGAT 1 206 1 TATTCGAAAA 0.770592 -26 GCCGTCCTATTGAATAAAAAGCCGGGCTCTG 2 27 1 TAATAAAAAG 0.518751 -181 CCGGCTTTTTTTAAAAGAAAAGATTGACAGT 2 61 1 TAAAAGAAAA 0.924972 -147 TAGTCAATTACTATAATAAAATTGTTCGTAC 2 96 1 CATAATAAAA 0.621172 -112 TACGTACTAATGATAGGAAAATAAACCTATA 2 139 0 TATAGGAAAA 0.798603 -69 GCGTTTTATTTTATGAGAAAGGGGCAGTTTA 2 186 1 TATGAGAAAG 0.950838 -22 TAAGCGCTTTCTAAAATAAAGGAGGTTGAAC 3 172 1 CAAAATAAAG 0.655998 -25 TGATCTGATGTAATACGAAAAGCATAGAAAA 4 38 1 TATACGAAAA 0.914012 -146 TTCACTTTTTCTAAAAGAAAGCTGTAAAAAC 4 73 1 CAAAAGAAAG 0.916883 -111 ATGTTTTGTATAATAAGAATGCAGGACTGAT 4 146 1 TATAAGAATG 0.758823 -38 * ********* Masking position 8 Map Score: 3.95014 Number of sites scoring better than the average of aligned sites = 1870 Number in coding regions = 1505 Number in noncoding regions = 365 Number of orfs with sites within 600 bp upstream = 376 Fraction of orfs with sites within 600 bp upstream = 0.0603919 Motif number 6 TTTGTATGTTAGATACGTATCATCACTTACTT 1 35 1 AGATACGTAA 0.719877 -197 CAAATACAAAAGATACGTACTAATGATAGGAA 2 151 0 AGATACGTAA 0.986981 -57 AGATACGGAAGAATCCGCCTAT 3 1 1 AGATACGGAA 0.992663 -196 ACAATAAAGGGGATACCGAAAATTTCCTGAAC 3 81 1 GGATACCGAA 0.967928 -116 ********* * Masking position 5 Map Score: 0.613331 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 CTCTTTTTTCATTATACTCACTCATAAAAT 1 80 1 ATTATACTCA 0.973988 -152 GATTGACAGTATAATAGTCAATTACTATAA 2 82 1 ATAATAGTCA 0.943129 -126 GAACAATTTTATTATAGTAATTGACTATTA 2 93 0 ATTATAGTAA 0.960315 -115 TATCCCCTTTATTGTAGTCACTATGCTGTA 3 66 0 ATTGTAGTCA 0.960888 -131 CTGCATTCTTATTATACAAAACATGGCGCT 4 140 0 ATTATACAAA 0.834245 -44 ********** Masking position 5 Map Score: 1.0532 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 23 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 ********** No masking Map Score: -1.62471e-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: -1.62471e-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: -1.62471e-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