AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i090_bsub_mtub_300.orf -o090_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yvfL 39 similar to maltodextrin transport system permease #2 yvfK 140 similar to maltose/maltodextrin-binding protein #3 lacR 179 transcriptional regulator (LacI family) #4 yvfI 300 similar to transcriptional regulator (GntR family) #5 yvdH 39 similar to maltodextrin transport system permease #6 yvdG 95 similar to maltose/maltodextrin-binding protein #7 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase #8 yvdE 205 similar to transcriptional regulator (LacI family) #9 yvdD 116 similar to hypothetical proteins Motif number 1 TGTATTGTAAGAGAGGTGAAAACG 1 26 1 GAAGGTGAAA 0.874716 -14 ATTCCTACCGAAAGGGTGACAATCA 2 126 1 AAGGGTGACA 0.933708 -15 ATCATTCGGAACCGGCGGAATTGCCCGGGAA 3 20 0 ACGGCGGAAT 0.962084 -160 TTACATGGCAGCCAGAGGGCTTTGTGCACTT 3 90 1 GCAGAGGGCT 0.632315 -90 CTAAAACAATGCGAGCTGAATAATGGAGGCA 3 153 1 GCAGCTGAAT 0.862229 -27 CCTACAAGTTACGGGGTGAATTGCATTGAAA 4 92 1 ACGGGTGAAT 0.950568 -209 GCGAATTGAAGCCGGGGGATAAACTGGACTC 4 192 1 GCGGGGGATA 0.888114 -109 CGAACCGCTGAACGGCTGACTTGAAAGCTCT 4 240 0 AAGGCTGACT 0.899431 -61 AACGGCGGGATAGCGTCCGGA 5 1 1 AAGGCGGGAT 0.883716 -39 CGGAAGAATAGAGGGCGGAAAA 5 28 1 GAGGCGGAAA 0.966494 -12 TTCGTAAATAGAAGGAGGAAAAGAG 6 81 1 GAGGAGGAAA 0.918535 -15 GTTATCGGTAACAGGGTGAAAAGGATTGTTC 7 23 1 ACGGGTGAAA 0.956256 -90 AACGGAAATCAAAGGGGGAAAC 7 101 1 AAGGGGGAAA 0.965879 -12 GGATTCATACGCTAGGTGGCAGACTCATTCT 8 38 0 GCAGGTGGCA 0.791245 -168 ATTTAGCAGTAATAGAGGACTTTATCACTAG 8 150 1 AAAGAGGACT 0.671161 -56 ** ******** Masking position 5 Map Score: 14.444 Number of sites scoring better than the average of aligned sites = 2304 Number in coding regions = 1980 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 320 Fraction of orfs with sites within 600 bp upstream = 0.0513974 Motif number 2 ATTATCTTTAAAGCGCTTTCATTCCTACCG 2 106 1 AAGCGCTTTC 0.992177 -35 GGCGCTTGCTGAGAGCTTTCAAGTCAGCCG 4 229 1 GAGAGCTTTC 0.925317 -72 GCGGTTCGCGAAGCACTTTCTGCGCTAAAA 4 263 1 AAGCACTTTC 0.972897 -38 AAGCGGTTACAACAACTTTCGATTTGTTAC 6 24 0 AACAACTTTC 0.925959 -72 AAGTTGTTGTAACCGCTTTCTATAGGACAA 6 36 1 AACCGCTTTC 0.982034 -60 AAAAGAGATTTTCTGATGGAAG 8 3 1 AAGAGATTTT 0.793482 -203 AGAAATAAAAAAGAGATTTCCCTTAAGGAA 8 102 0 AAGAGATTTC 0.967227 -104 ********** Masking position 2 Map Score: 7.96346 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 448 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 ATGAAGTAAATAGTTTGTTTACACATTTTCT 2 63 1 TATTTGTTTA 0.860448 -78 GCAAATGGTTCAGTCTTTTTACATGGCAGCC 3 72 1 CATCTTTTTA 0.668083 -108 TAAAATATTTTACTTTCTTTTTCACAAATGT 3 122 0 TATTTCTTTT 0.822686 -58 CGATCTATTATACTCTGTTTTGTGGGCCGCC 4 49 0 TATCTGTTTT 0.973723 -252 TTTTTTGTTTTAATCTGTTTATATTTCAATG 4 115 0 TATCTGTTTA 0.955811 -186 CATTCTGTTATCGGTAACAAA 6 1 1 CATCTGTTAT 0.924109 -95 GCGCCTTATTCTGTTATCGGTAACAGG 7 7 1 TATCTGTTAT 0.936559 -106 TTCCATCAGAAAATCTCTTTT 8 1 0 AATCTCTTTT 0.857506 -205 AAGGAAACCTCACTTTGTTAAAAACACTCGA 8 77 0 CATTTGTTAA 0.669503 -129 TCCTTAAGGGAAATCTCTTTTTTATTTCTCT 8 103 1 AATCTCTTTT 0.857506 -103 GGACAATATATAGTGTGTTTTTGAATGTTTA 9 67 1 TATGTGTTTT 0.859828 -50 ** ******** Masking position 2 Map Score: 7.6765 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 407 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 CATTTTTTATTTAGGTAAAAAAATTTACTCT 2 32 1 TTAGGAAAAA 0.924978 -109 CCTGAGAAAATGTGTAAACAAACTATTTACT 2 67 0 TGTGTAACAA 0.878663 -74 GCACTTGACATTTGTGAAAAAGAAAGTAAAA 3 115 1 TTTGTAAAAA 0.946429 -65 TCGCATTGTTTTAGTAAAATATTTTACTTTC 3 136 0 TTAGTAAATA 0.834019 -44 TTTTGACTATTTTGTCAAAAAGTCTTGTACT 4 12 0 TTTGTAAAAA 0.946429 -289 ATTGTTATAGTTTCGTAAATAGAAGGAGGAA 6 70 1 TTTCGAAATA 0.748416 -26 ATGATGAAATTGTGGGAACAATCCTTTTCAC 7 38 0 TGTGGAACAA 0.903163 -75 GAAACCTCACTTTGTTAAAAACACTCGATTT 8 74 0 TTTGTAAAAA 0.946429 -132 TTATCACTAGTTTGGATAATAAGCACAGATA 8 171 1 TTTGGTAATA 0.763479 -35 ***** ***** Masking position 8 Map Score: 4.75832 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 438 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 5 ATAGTCAAAATCTTTTGGCGGCCCACAAAAC 4 33 1 TCTTTTGCGG 0.955951 -268 TGTAGGTCTGGCTGTTTACGATCTATTATAC 4 67 0 GCTGTTACGA 0.969258 -234 TAAACTGGACTCTGTTCAGGCGCTTGCTGAG 4 211 1 TCTGTTAGGC 0.851821 -90 CAGCCGTTCAGCGGTTCGCGAAGCACTTTCT 4 253 1 GCGGTTGCGA 0.929395 -48 AAGCCCCATCGCTTTTAGCGCAGAAAGTGCT 4 274 0 GCTTTTGCGC 0.935607 -27 CATTCTGTTATCGGTAACAAATCG 6 4 1 TCTGTTTCGG 0.972451 -92 TTTTCCTCCTTCTATTTACGAAACTATAACA 6 72 0 TCTATTACGA 0.832659 -24 GCGCCTTATTCTGTTATCGGTAACAGGGTG 7 10 1 TCTGTTTCGG 0.972451 -103 ****** **** Masking position 6 Map Score: 3.39137 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 530 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 GTCTTTTTACATGGCAGCCAGAGGGCTTTG 3 84 1 ATGGCAGCCA 0.959746 -96 GAGCTGAATAATGGAGGCAGATACA 3 165 1 ATGGAGGCAG 0.949586 -15 CATATCTAATAGGGCATCCGCTACTTCTTC 4 152 0 AGGGCATCCG 0.863626 -149 AAAATGGCGAATTGAAGCCGGGGGATAAAC 4 186 1 ATTGAAGCCG 0.972927 -115 AACGGCGGGATAGCGTCCGGAAGAATAGA 5 10 1 ATAGCGTCCG 0.927426 -30 GTCCGGAAGAATAGAGGGCGGAAAA 5 25 1 ATAGAGGGCG 0.90416 -15 TTTCCGTTTTATTGAAGCCGGCTCATAGTT 7 79 0 ATTGAAGCCG 0.972927 -34 TAAATATACGATGCAGGCCAAAGAGAAATA 8 125 0 ATGCAGGCCA 0.864571 -81 ********** Masking position 1 Map Score: 3.20981 Number of sites scoring better than the average of aligned sites = 1271 Number in coding regions = 1178 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 GAGAAAGCTAGATTTGTATTGTAAGAGAGGT 1 12 1 GATTTGATTG 0.961117 -28 AATTGCCCGGGAAATGAGTTGG 3 2 0 GAAATGGTTG 0.962675 -178 GTTACGGGGTGAATTGCATTGAAATATAAAC 4 99 1 GAATTGATTG 0.985803 -202 GAAACTATAACAATTGTATTGTCCTATAGAA 6 53 0 CAATTGATTG 0.795908 -43 GTAACAGGGTGAAAAGGATTGTTCCCACAAT 7 30 1 GAAAAGATTG 0.945795 -83 ****** **** Masking position 9 Map Score: 0.613186 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 73 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AGAGAAAGCTAGATTTGTAT 1 1 1 AGAGAAAGCT 0.917336 -39 TTTCGGTAGGAATGAAAGCGCTTTAAAGAT 2 109 0 AATGAAAGCG 0.935492 -32 CATTTGTGAAAAAGAAAGTAAAATATTTTA 3 123 1 AAAGAAAGTA 0.785016 -57 TATTTTACTAAAACAATGCGAGCTGAATAA 3 146 1 AAACAATGCG 0.911608 -34 GTATTGTCCTATAGAAAGCGGTTACAACAA 6 39 0 ATAGAAAGCG 0.955019 -57 ATGGAAGTGGAGAGAATGAGTCTGCCACCT 8 26 1 AGAGAATGAG 0.873101 -180 TGAAATACATAAAGAATGCAGGAGTGATGA 9 13 0 AAAGAATGCA 0.947718 -104 ********** Masking position 5 Map Score: 0.904062 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 822 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 9 ********** No masking Map Score: 2.63855e-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: 2.63855e-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 11 ********** No masking Map Score: 2.63855e-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