AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i324_mixed9_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 yvdH 39 similar to maltodextrin transport system permease #2 yvdG 95 similar to maltose/maltodextrin-binding protein #3 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase #4 yvdE 205 similar to transcriptional regulator (LacI family) #5 yvdD 116 similar to hypothetical proteins Motif number 1 CTCTATTCTTCCGGACGCTATCCCGCCGTT 1 10 0 CCGGACGCTT 0.919041 -30 TTTTCCGCCCTCTATTCTTCCGGAC 1 25 0 CCGCCCTCTT 0.995673 -15 GTTGTTGTAACCGCTTTCTATAGGACAATAC 2 38 1 CCGCTTTCTT 0.984108 -58 CTCTTTTCCTCCTTCTATTTACGAAACT 2 78 0 CCTCCTTCTT 0.995089 -18 GCGCCTTATTCTGTTATCGGTAAC 3 4 1 CCTTATTCTT 0.946164 -109 AAACTATGAGCCGGCTTCAATAAAACGGAAA 3 78 1 CCGGCTTCAT 0.932656 -35 TAGGTGGCAGACTCATTCTCTCCACTTCCAT 4 26 0 ACTCATTCTT 0.932209 -180 CTTAAGGAAACCTCACTTTGTTAAAAACACT 4 80 0 CCTCACTTTT 0.916572 -126 TTTCATCCCCTCCTTATCTGTGCTTATTA 4 187 0 CCTCCTTATT 0.952074 -19 CTCATCACTCCTGCATTCTTTATGTATTTCA 5 12 1 CTGCATTCTT 0.956388 -105 ********* * Masking position 11 Map Score: 12.9343 Number of sites scoring better than the average of aligned sites = 1012 Number in coding regions = 842 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 2 TTTTCCGCCCTCTATTCTTCCGGA 1 26 0 TTTCCCCCTA 0.990219 -14 CTCTTTTCCTCCTTCTATTTACGAAAC 2 79 0 TTTCCCCTTA 0.989412 -17 GAACAATCCTTTTCACCCTGTTACCGATAACAG 3 21 0 TTTCACCTTA 0.988534 -92 GTTCCCACAATTTCATCATGATACTTTCAAACT 3 50 1 TTTCACATTA 0.91736 -63 ATCATGATACTTTCAAACTATGAGCCGGCTTCA 3 64 1 TTTCAACTGA 0.94245 -49 GTTTCCCCCTTTGATTTCCGTTTT 3 99 0 TTTCCCCTGA 0.984346 -14 TTTCATCCCCTCCTTATCTGTGC 4 193 0 TTTCACCCCC 0.950253 -13 TCTTTATGTATTTCATATTGATATTATCACATG 5 28 1 TTTCAATTTA 0.888022 -89 CACTATATATTGTCCCATCTTCATGTGATAATA 5 49 0 TGTCCATCCA 0.797807 -68 CTTGTCATCTCCGCATCTATATATC 5 102 0 TGTCACTCCA 0.928094 -15 ***** *** ** Masking position 3 Map Score: 8.93915 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 698 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 3 AACGGCGGGATAGCGTCCGGAAGAATAGAG 1 11 1 TAGCGTCCGG 0.964964 -29 TCCGGAAGAATAGAGGGCGGAAAA 1 26 1 TAGAGGGCGG 0.997182 -14 TATTGTCCTATAGAAAGCGGTTACAACAAC 2 38 0 TAGAAAGCGG 0.988025 -58 GTTTCGTAAATAGAAGGAGGAAAAGAG 2 79 1 TAGAAGGAGG 0.984332 -17 TTCCGTTTTATTGAAGCCGGCTCATAGTTT 3 78 0 TTGAAGCCGG 0.985593 -35 ********** Masking position 1 Map Score: 5.00178 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 179 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 AAGCGGTTACAACAACTTTCGATTTGTTACCGAT 2 20 0 AAAACTTCTT 0.929097 -76 ATGAAATTGTGGGAACAATCCTTTTCACCCTGTT 3 32 0 GGAACATCTT 0.969847 -81 CACTTCCATCAGAAAATCTCTTTT 4 1 0 AGAAACTCTT 0.991681 -205 TCACTTTGTTAAAAACACTCGATTTTTCATGGAT 4 65 0 AAAACCTCTT 0.985563 -141 ATTTCCCTTAAGGAAACCTCACTTTGTTAAAAAC 4 83 0 AGAAACTCTT 0.992286 -123 GTTTCCTTAAGGGAAATCTCTTTTTTATTTCTCT 4 100 1 GGAAACTCTT 0.990689 -106 ** *** *** ** Masking position 9 Map Score: 4.60884 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 66 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 CATTCTGTTATCGGTAACAAATCGAAAGT 2 10 1 ATCGGTAACA 0.994615 -86 TCCTATAGAAAGCGGTTACAACAACTTTCG 2 33 0 AGCGGTTACA 0.991233 -63 TTATTCTGTTATCGGTAACAGGGTGAAAAG 3 16 1 ATCGGTAACA 0.994615 -97 TCGTATATTTAGCAGTAATAGAGGACTTTA 4 144 1 AGCAGTAATA 0.947639 -62 ********** Masking position 6 Map Score: 4.47343 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 40 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GCTTCAATAAAACGGAAATCAAAGGGGGAA 3 91 1 AACGGAAATC 0.979968 -22 GTATGAATCCATGAAAAATCGAGTGTTTTT 4 59 1 ATGAAAAATC 0.894126 -147 AGGTTTCCTTAAGGGAAATCTCTTTTTTAT 4 98 1 AAGGGAAATC 0.992432 -108 ATGCAGGCCAAAGAGAAATAAAAAAGAGAT 4 115 0 AAGAGAAATA 0.955234 -91 ********** Masking position 6 Map Score: 0.370378 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 199 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 ********** No masking Map Score: -1.11312e-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: -1.11312e-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: -1.11312e-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