AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i090_Sugar_Transport_2_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 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 0.872069 -14 ATTCCTACCGAAAGGGTGACAATCA 2 126 1 AAGGGTGACA 0.932211 -15 ATCATTCGGAACCGGCGGAATTGCCCGGGAA 3 20 0 ACGGCGGAAT 0.961201 -160 TTACATGGCAGCCAGAGGGCTTTGTGCACTT 3 90 1 GCAGAGGGCT 0.626731 -90 CTAAAACAATGCGAGCTGAATAATGGAGGCA 3 153 1 GCAGCTGAAT 0.85936 -27 CCTACAAGTTACGGGGTGAATTGCATTGAAA 4 92 1 ACGGGTGAAT 0.949431 -209 GCGAATTGAAGCCGGGGGATAAACTGGACTC 4 192 1 GCGGGGGATA 0.885713 -109 CGAACCGCTGAACGGCTGACTTGAAAGCTCT 4 240 0 AAGGCTGACT 0.897245 -61 AACGGCGGGATAGCGTCCGGA 5 1 1 AAGGCGGGAT 0.881233 -39 CGGAAGAATAGAGGGCGGAAAA 5 28 1 GAGGCGGAAA 0.96571 -12 TTCGTAAATAGAAGGAGGAAAAGAG 6 81 1 GAGGAGGAAA 0.916726 -15 GTTATCGGTAACAGGGTGAAAAGGATTGTTC 7 23 1 ACGGGTGAAA 0.955244 -90 AACGGAAATCAAAGGGGGAAAC 7 101 1 AAGGGGGAAA 0.965081 -12 GGATTCATACGCTAGGTGGCAGACTCATTCT 8 38 0 GCAGGTGGCA 0.787263 -168 ATTTAGCAGTAATAGAGGACTTTATCACTAG 8 150 1 AAAGAGGACT 0.665856 -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 CGGTAGGAATGAAAGCGCTTTAAAGATAAT 2 106 0 GAAAGCGCTT 0.9918 -35 CGGCTGACTTGAAAGCTCTCAGCAAGCGCC 4 229 0 GAAAGCTCTC 0.925984 -72 TTTTAGCGCAGAAAGTGCTTCGCGAACCGC 4 263 0 GAAAGTGCTT 0.971522 -38 GTAACAAATCGAAAGTTGTTGTAACCGCTT 6 24 1 GAAAGTTGTT 0.922412 -72 TTGTCCTATAGAAAGCGGTTACAACAACTT 6 36 0 GAAAGCGGTT 0.981141 -60 CTTCCATCAGAAAATCTCTTTT 8 3 0 AAAATCTCTT 0.785067 -203 TTCCTTAAGGGAAATCTCTTTTTTATTTCT 8 102 1 GAAATCTCTT 0.965597 -104 ********** Masking position 4 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 ACTATTTACTTCATAGAGTAAATTTTTTTACCTAAATAAAAA 2 35 0 TTATAATTTC 0.860426 -106 AGTAAATAGTTTGTTTACACATTTTCTCAGGCATGCTATATT 2 67 1 TTAACATTTC 0.831513 -74 TTCTCAGGCATGCTATATTATCTTTAAAGCGCTTTCATTCCT 2 90 1 TTATATTTTC 0.951239 -51 GAGCCGCAAATGGTTCAGTCTTTTTACATGGCAGCCAGAGGG 3 67 1 TTATCTTTTC 0.990007 -113 TAGTAAAATATTTTACTTTCTTTTTCACAAATGTCAAGTGCA 3 114 0 TTTTCTTTTT 0.754246 -66 GTTTACGATCTATTATACTCTGTTTTGTGGGCCGCCAAAAGA 4 43 0 TTATCTTTTC 0.990007 -258 TATATTTTTTTGTTTTAATCTGTTTATATTTCAATGCAATTC 4 109 0 TTATCTTTTC 0.990007 -192 GGAAATCTCTTTTTTATTTCTCTTTGGCCTGCATCGTATATT 8 111 1 TTTTCTTTTC 0.969046 -95 CCTCATCACTCCTGCATTCTTTATGTATTTCATATTGATAT 9 10 1 TTATCTTATC 0.939822 -107 * * * *** *** * Masking position 13 Map Score: 5.86091 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 274 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 GGATGACTTAGGACACTAAGTCATTTTT 2 8 1 TTGGACACTA 0.942831 -133 GTACAAGACTTTTTGACAAAATAGTCAAAAT 4 13 1 TTTGACAAAA 0.714978 -288 AATTCGCCATTTTTGATCATATCTAATAGGG 4 168 0 TTTGATCATA 0.794499 -133 ACCGCTTTCTATAGGACAATACAATTGTTAT 6 47 1 ATGGACAATA 0.976335 -49 TTATCACTAGTTTGGATAATAAGCACAGATA 8 171 1 TTGGATAATA 0.962911 -35 TCCCATCTTCATGTGATAATATCAATATGAA 9 39 0 ATTGATAATA 0.906315 -78 TCACATGAAGATGGGACAATATATAGTGTGT 9 54 1 ATGGACAATA 0.976303 -63 ** ******** Masking position 6 Map Score: 2.55511 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 84 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 ATAGTCAAAATCTTTTGGCGGCCCACAAAAC 4 33 1 TCTTTTGCGG 0.96275 -268 TGTAGGTCTGGCTGTTTACGATCTATTATAC 4 67 0 GCTGTTACGA 0.974056 -234 TAAACTGGACTCTGTTCAGGCGCTTGCTGAG 4 211 1 TCTGTTAGGC 0.872552 -90 CAGCCGTTCAGCGGTTCGCGAAGCACTTTCT 4 253 1 GCGGTTGCGA 0.940023 -48 AAGCCCCATCGCTTTTAGCGCAGAAAGTGCT 4 274 0 GCTTTTGCGC 0.945262 -27 CATTCTGTTATCGGTAACAAATCG 6 4 1 TCTGTTTCGG 0.976763 -92 TTTTCCTCCTTCTATTTACGAAACTATAACA 6 72 0 TCTATTACGA 0.8556 -24 GCGCCTTATTCTGTTATCGGTAACAGGGTG 7 10 1 TCTGTTTCGG 0.976763 -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 CAAAGCCCTCTGGCTGCCATGTAAAAAGAC 3 84 0 TGGCTGCCAT 0.957586 -96 TGTATCTGCCTCCATTATTCAGCTC 3 165 0 CTGCCTCCAT 0.946912 -15 GAAGAAGTAGCGGATGCCCTATTAGATATG 4 152 1 CGGATGCCCT 0.857077 -149 GTTTATCCCCCGGCTTCAATTCGCCATTTT 4 186 0 CGGCTTCAAT 0.971453 -115 TCTATTCTTCCGGACGCTATCCCGCCGTT 5 10 0 CGGACGCTAT 0.92367 -30 TTTTCCGCCCTCTATTCTTCCGGAC 5 25 0 CGCCCTCTAT 0.899331 -15 AACTATGAGCCGGCTTCAATAAAACGGAAA 7 79 1 CGGCTTCAAT 0.971453 -34 TATTTCTCTTTGGCCTGCATCGTATATTTA 8 125 1 TGGCCTGCAT 0.858063 -81 ********** Masking position 10 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 TTTTTTACCTAAATAAAAAATGACTTAGTG 2 24 0 AAATAAAAAA 0.959126 -117 TTTTTTATTTAGGTAAAAAAATTTACTCTA 2 34 1 AGGTAAAAAA 0.919428 -107 GTGAAAAAGAAAGTAAAATATTTTACTAAA 3 128 1 AAGTAAAATA 0.885047 -52 AAACAGATTAAAACAAAAAAATATATGAAG 4 126 1 AAACAAAAAA 0.913576 -175 GGCCAAAGAGAAATAAAAAAGAGATTTCCC 8 110 0 AAATAAAAAA 0.959126 -96 ********** Masking position 5 Map Score: 1.0267 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 181 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 8 ACCTCTCTTACAATACAAATCTAGCTTTCTC 1 12 0 CAATCAAATC 0.958127 -28 CCAACTCATTTCCCGGGCAATT 3 2 1 CAACCATTTC 0.959751 -178 GTTTATATTTCAATGCAATTCACCCCGTAAC 4 99 0 CAATCAATTC 0.984999 -202 TTCTATAGGACAATACAATTGTTATAGTTTC 6 53 1 CAATCAATTG 0.801624 -43 ATTGTGGGAACAATCCTTTTCACCCTGTTAC 7 30 0 CAATCTTTTC 0.941608 -83 **** ****** Masking position 3 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 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