AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i090_Sugar_Transport_2_bsub_reg_100.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 yvdH 39 similar to maltodextrin transport system permease #4 yvdG 95 similar to maltose/maltodextrin-binding protein #5 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase Motif number 1 CGTTTTCACCTCTCTTACAATAC 1 27 0 TTTCACCTCT 0.972204 -13 TTTAAAGCGCTTTCATTCCTACCGAAAGGG 2 112 1 TTTCATTCCT 0.935812 -29 TGATTGTCACCCTTTCGGTAGGAA 2 127 0 TGTCACCCTT 0.977434 -14 TTTTCCGCCCTCTATTCTTCC 3 29 0 TTTCCGCCCT 0.990375 -11 CTCTTTTCCTCCTTCTATTTACGA 4 82 0 TTTCCTCCTT 0.991421 -14 GAACAATCCTTTTCACCCTGTTACCGATAA 5 24 0 TTTCACCCTG 0.989085 -89 GTTCCCACAATTTCATCATGATACTTTCAA 5 50 1 TTTCATCATG 0.850549 -63 CCCCCTTTGATTTCCGTTTTATTGAAGCCG 5 89 0 TTTCCGTTTT 0.848912 -24 GTTTCCCCCTTTGATTTCCGT 5 102 0 TTTCCCCCTT 0.995828 -11 ********** Masking position 3 Map Score: 14.6564 Number of sites scoring better than the average of aligned sites = 1026 Number in coding regions = 740 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 2 CGTCCGGAAGAATAGAGGGCGGAAAA 3 24 1 AATGAGGGGG 0.995705 -16 ATCGGTAACAAATCGAAAGTTGTTGTAACCGC 4 20 1 AATGAAAGTG 0.97071 -76 TGTATTGTCCTATAGAAAGCGGTTACAACAAC 4 38 0 TATGAAAGGG 0.991366 -58 TAGTTTCGTAAATAGAAGGAGGAAAAGAG 4 77 1 AATGAAGGGG 0.998425 -19 ATTTCCGTTTTATTGAAGCCGGCTCATAGTTT 5 78 0 TATGAAGCGG 0.987328 -35 ATAAAACGGAAATCAAAGGGGGAAAC 5 97 1 AATAAAGGGG 0.989907 -16 *** ***** ** Masking position 6 Map Score: 10.1017 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 141 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 CATAGAGTAAATTTTTTTACCTAAATAAAAA 2 35 0 ATTTTTTACC 0.958615 -106 TGAAGTAAATAGTTTGTTTACACATTTTCTC 2 64 1 ATTTGTTTAC 0.902888 -77 CATTCTGTTATCGGTAACAAAT 4 2 1 ATCTGTTATC 0.990521 -94 AACAACTTTCGATTTGTTACCGATAACAGAA 4 13 0 GTTTGTTACC 0.982053 -83 GCGCCTTATTCTGTTATCGGTAACAGGG 5 8 1 ATCTGTTATC 0.990521 -105 AATCCTTTTCACCCTGTTACCGATAACAGAA 5 19 0 ACCTGTTACC 0.988517 -94 * ********* Masking position 5 Map Score: 5.79073 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 103 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 GGATGACTTAGGACACTAAGTCATTT 2 7 1 CTTAGGACAC 0.926479 -134 TCATTTTTTATTTAGGTAAAAAAATTTACT 2 31 1 TTTAGGTAAA 0.886958 -110 ATTGTCACCCTTTCGGTAGGAATGAAAGCG 2 119 0 TTTCGGTAGG 0.908785 -22 CCCTCTATTCTTCCGGACGCTATCCCGCCG 3 13 0 TTCCGGACGC 0.918828 -27 CATTCTGTTATCGGTAACAAATCGAAAG 4 9 1 TATCGGTAAC 0.979527 -87 AACCGCTTTCTATAGGACAATACAATTGTT 4 46 1 TATAGGACAA 0.889721 -50 CCTCCTTCTATTTACGAAACTATAACAATT 4 69 0 TTTACGAAAC 0.883191 -27 CTTATTCTGTTATCGGTAACAGGGTGAAAA 5 15 1 TATCGGTAAC 0.979527 -98 ********** Masking position 6 Map Score: 4.07051 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 855 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 ACTTAGTGTCCTAAGTCATCC 2 2 0 CTAAGTCATC 0.990821 -139 ACTTAGGACACTAAGTCATTTTTTATTTAG 2 16 1 CTAAGTCATT 0.986456 -125 TACACATTTTCTCAGGCATGCTATATTATC 2 82 1 CTCAGGCATG 0.987056 -59 ********** Masking position 4 Map Score: 0.159694 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 19 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ********** No masking Map Score: 2.43208e-15 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 7 ********** No masking Map Score: 2.43208e-15 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: 2.43208e-15 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