AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i040_Rhamnose_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 yulE 25 similar to L-rhamnose isomerase #2 yulB 56 similar to transcriptional regulator (DeoR family) #3 yuxG 137 alternate gene name: yulA; similar to sorbitol-6-phosphate 2-dehydrogenase #4 tlpB 113 methyl-accepting chemotaxis protein #5 mcpA 125 methyl-accepting chemotaxis protein #6 tlpA 176 methyl-accepting chemotaxis protein #7 mcpB 157 methyl-accepting chemotaxis protein Motif number 1 TCGTAGTCCGTCTTATATTTTTATCATAGCAT 2 15 0 TCTTTTTTTT 0.926956 -42 CATATCTGCTGCTTTCTTTTTTTGTTAAAAAG 3 27 1 GCTTCTTTTT 0.958664 -111 TTTTTGTTTATTTTTGCTTTTTAACAAAAAAA 3 43 0 TTTTGTTTTT 0.959021 -95 TATATATGATTTCTGTTTGTTTTTGAATCGTT 3 73 0 TTCTTTGTTT 0.8538 -65 AGCTTGTTGCGCTTGGGTGTTTTTTTTAGTTT 4 27 1 GCTTGTGTTT 0.845206 -87 TGGGTGTTTTTTTTAGTTTTTTTATTAAACCT 4 40 1 TTTTGTTTTT 0.959021 -74 TTTGTTAAATTTCTTCTTTTTTGCTGTATATA 5 51 1 TTCTCTTTTT 0.986561 -75 CATTCATTTCTCCTTTTTTATGCTACCCT 5 107 0 TTCTCTTTTT 0.986561 -19 TTTAGAACTATTTTTCATTTTTTCCTCCATTT 6 88 1 TTTTCTTTTT 0.978607 -89 TTTCATTTTTTCCTCCATTTTCAATGTAATTT 6 100 1 TCCTCTTTTC 0.94501 -77 GTTTAGCCCCCCTTGTTTTTTATAAGATATG 7 10 1 CCCTGTTTTT 0.911868 -148 TTTGGCTGTCTTCTGCCTTTTTAACTTTCATT 7 56 0 TTCTCTTTTT 0.986561 -102 AAAAAGAACTTCTTCCATTTTTTATTTTAAAA 7 85 1 TCTTCTTTTT 0.986561 -73 GTCACTTGCTCCTTCAGGTTTGATACAGTAT 7 137 0 TCCTCGGTTT 0.887746 -21 **** * ***** Masking position 4 Map Score: 22.8227 Number of sites scoring better than the average of aligned sites = 1545 Number in coding regions = 1194 Number in noncoding regions = 351 Number of orfs with sites within 600 bp upstream = 363 Fraction of orfs with sites within 600 bp upstream = 0.0583039 Motif number 2 CGGCTCTCTCCCTTTATCAGTTTT 1 2 0 CCTTTATATT 0.860333 -24 TCTGCTGCTTTCTTTTTTTGTTAAAAAGCAAAA 3 31 1 TCTTTTTTTA 0.773443 -107 GTTTTTGAATCGTTTTTGTTTATTTTTGCTTTT 3 54 0 CGTTTTTTTT 0.952539 -84 ATATATGATTTCTGTTTGTTTTTGAATCGTTTT 3 71 0 TCTGTTTTTT 0.834978 -67 TTATTTGTATCCGTTTTCATTATATATGATTTC 3 92 0 CCGTTTTATT 0.917949 -46 TTCCTCCATACCCTTTTATTTGTATCCGTTTTC 3 107 0 CCCTTTTTTT 0.917949 -31 CGCTTGGGTGTTTTTTTTAGTTTTTTTATTAAA 4 36 1 TTTTTTTATT 0.736813 -78 TTAAATTTCTTCTTTTTTGCTGTATATATTTAC 5 55 1 TCTTTTTGTT 0.968013 -71 ATTCATTTCTCCTTTTTTATGCTACCCTTCATA 5 102 0 CCTTTTTAGT 0.90128 -24 TTGATAGCGCTGTTTTTCGGTTT 6 1 0 TGTTTTTGTT 0.887887 -176 ATCAAAGCGCTGTTTTTTTATATGGTAAACAAT 6 29 1 TGTTTTTTTT 0.917512 -148 AATTTAGAACTATTTTTCATTTTTTCCTCCATT 6 86 1 TATTTTTATT 0.736813 -91 ATTTTTTCCTCCATTTTCAATGTAATTTAAAGG 6 104 1 CCATTTTATT 0.930119 -73 GTTTAGCCCCCCTTGTTTTTTATAAGATATGCA 7 11 1 CCTTGTTTTT 0.90128 -147 CTGTCTTCTGCCTTTTTAACTTTCATTGCCCAA 7 50 0 CCTTTTTATT 0.987129 -108 TGGAAGAAGTTCTTTTTGGCTGTCTTCTGCCTT 7 69 0 TCTTTTTGTT 0.968013 -89 AGAACTTCTTCCATTTTTTATTTTAAAACTTTT 7 89 1 CCATTTTTTT 0.93012 -69 ******* * * * Masking position 7 Map Score: 21.2037 Number of sites scoring better than the average of aligned sites = 2053 Number in coding regions = 1544 Number in noncoding regions = 509 Number of orfs with sites within 600 bp upstream = 503 Fraction of orfs with sites within 600 bp upstream = 0.0807902 Motif number 3 ATATATGCTATGATAAAAAT 2 1 1 ATATATGCTA 0.844456 -56 AGAAAGCGGCATATCTGCTGCTTTCTTTTT 3 18 1 ATATCTGCTG 0.993282 -120 GCTACCCTTCATATCGGCTGGAAATGGGTA 5 85 0 ATATCGGCTG 0.997007 -41 TTTACAAATTATATCGGCGGATCTTCCTTT 6 132 0 ATATCGGCGG 0.99338 -45 GATACAGTATATATCGGCTGCTTAAAAAAG 7 117 0 ATATCGGCTG 0.997007 -41 ********** Masking position 4 Map Score: 9.81025 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 55 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 ATATGCCGCTTTCTCGTTTCA 3 1 0 TTCTCGTTTA 0.966552 -137 AAACCTTTTATCCTAGTTTGACGATATTAGA 4 66 1 TCCTAGTTTA 0.960046 -48 TCTCGTTGACTCCTCCTTTAAGATAAATCTA 4 93 0 TCCTCCTTTA 0.994189 -21 TTTGTTAAATTTCTTCTTTTTTGCTGTATAT 5 51 1 TTCTTCTTTT 0.889185 -75 CATTCATTTCTCCTTTTTTATGCTACCC 5 108 0 TTCTCCTTTT 0.967121 -18 AATAATAAAGTCCTAGTTTAACAGGTGAATT 6 59 1 TCCTAGTTTA 0.960072 -118 TTTCATTTTTTCCTCCATTTTCAATGTAATT 6 100 1 TCCTCCATTT 0.933985 -77 TATCGGCGGATCTTCCTTTAAATTACATTGA 6 120 0 TCTTCCTTTA 0.943734 -57 TTCCTTTTGAACCTTCTTTCAATAATTTACA 6 156 0 ACCTTCTTTA 0.880349 -21 ********* * Masking position 4 Map Score: 10.6075 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 482 Number in noncoding regions = 328 Number of orfs with sites within 600 bp upstream = 392 Fraction of orfs with sites within 600 bp upstream = 0.0629618 Motif number 5 TTCTGTTTGTTTTTGAATCGTTTTTGTTTATTTT 3 61 0 TTTTATCTTT 0.974577 -77 ATACCCTTTTATTTGTATCCGTTTTCATTATATA 3 99 0 ATTTATCTTT 0.959832 -39 TTTAGTTTTTTTATTAAACCTTTTATCCTAGTTT 4 51 1 TTATAACTTT 0.933482 -63 TTTGCTGTATATATTTACCCATTTCCAGCCGATA 5 70 1 ATATACCTTT 0.904234 -56 TAACAGGTGAATTTAGAACTATTTTTCATTTTTT 6 77 1 ATTTAACTTT 0.959811 -100 TATTTTTCATTTTTTCCTCCATTTTCAATGTAAT 6 96 1 TTTTCTCTTT 0.910568 -81 TTCCTTTTGAACCTTCTTTCAATAATTT 6 159 0 TTTTACCCTT 0.916605 -18 CCATTTTTTATTTTAAAACTTTTTTAAGCAGCCG 7 99 1 TTTTAACTTT 0.974577 -59 **** *** *** Masking position 4 Map Score: 5.21084 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 465 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 GCGCTTTGATAGCGCTGTTTTTCGGTTT 6 9 0 AGCGCTGTTT 0.996305 -168 GCGCTATCAAAGCGCTGTTTTTTTATATGG 6 24 1 AGCGCTGTTT 0.996305 -153 ********** Masking position 6 Map Score: 0.479474 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 27 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ********** No masking Map Score: -1.34049e-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: -1.34049e-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: -1.34049e-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