AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i292_3_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 ycsF 204 similar to lactam utilization protein #2 ycsG 203 alternate gene name: ycsH; similar to branched chain amino acids transporter #3 ycsI 23 similar to hypothetical proteins #4 ycsJ 43 similar to allophanate hydrolase Motif number 1 AAAAAGAGAGTCCTAAGATGGACT 1 2 1 AAAAAGAGCT 0.943582 -203 TGCCAAACTAAAAAGAGAGTCCATCTTAGGACT 1 19 0 AAAAAGAGCA 0.99246 -186 TGGTCCCAGAATAAAACCTGCCAAACTAAAAAG 1 37 0 ATAAACCTCA 0.848955 -168 TACTTTTGTCAGAAAACCTACCATGGTCCCAGA 1 60 0 AGAAACCTCA 0.957138 -145 CACTTATAATGAAATAAAGTTCAAAAATTCGGA 1 113 1 GAAAAAAGCA 0.949639 -92 GAATTTCGGGACAATAAATGACATAAAGCATAT 1 157 1 ACAAAAATCA 0.798119 -48 GCAAAAAATCAGAAAACAGCTCAAAGCGGCTGG 2 74 1 AGAAACAGCA 0.982435 -130 CCTCTGTTCTGAAATAGCTGTCACTTCAATTCC 2 105 0 GAAAAGCTCA 0.970504 -99 CAGCTATTTCAGAACAGAGGTCAACATAAAGGA 2 118 1 AGAAAGAGCA 0.990865 -86 TGGAGCAGCAGAAAAAGACAGCAGGAAAAAAGC 2 162 1 GAAAAGACCA 0.94065 -42 AGACAGCAGGAAAAAAGCGGGCAGCTGGTCATT 2 177 1 AAAAAGCGCA 0.991942 -27 **** **** ** Masking position 6 Map Score: 14.3158 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 652 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 AGAATCCCTCCTGCCAAAGCAAAC 1 191 0 TCCCTCCTGC 0.981041 -14 TTCCAGCCGCTTTGAGCTGTTTTCTGATTT 2 79 0 TTTGAGCTGT 0.867378 -125 GTCACTTCAATTCCAGCCGCTTTGAGCTGT 2 89 0 TTCCAGCCGC 0.98754 -115 CCATCTATTGTTCCTCCTTTATGTTGACCT 2 135 0 TTCCTCCTTT 0.898866 -69 CTGCTGTCTTTTTCTGCTGCTCCATCTATT 2 156 0 TTTCTGCTGC 0.989188 -48 GCCCGCTTTTTTCCTGCTGTCTTTTTCTGC 2 169 0 TTCCTGCTGT 0.99388 -35 CAGCAATGACCAGCTGCCCGCTTTTTT 2 187 0 GACCAGCTGC 0.951343 -17 ********** Masking position 7 Map Score: 5.88382 Number of sites scoring better than the average of aligned sites = 1902 Number in coding regions = 1769 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 AAGAGAGTCCATCTTAGGACTCTCTTTTT 1 10 0 ATCTTAGGAC 0.974147 -195 GGCAGGTTTTATTCTGGGACCATGGTAGGT 1 48 1 ATTCTGGGAC 0.966594 -157 ACTATTCCGAATTTTTGAACTTTATTTCAT 1 121 0 ATTTTTGAAC 0.956881 -84 GTCGTTCCGAATTTCGGGACAATAAATGAC 1 149 1 ATTTCGGGAC 0.992242 -56 AGTGACAGCTATTTCAGAACAGAGGTCAAC 2 113 1 ATTTCAGAAC 0.974861 -91 ********** Masking position 2 Map Score: 4.11609 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 102 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 AAACTGATATGATTCACTTATAATGAAATA 1 99 1 GATTCACTTA 0.918684 -106 CAGCGCATGGGCTCCATCTCCATAAATGAA 2 36 0 GCTCCATCTC 0.990531 -168 TTTTTCTGCTGCTCCATCTATTGTTCCTCC 2 148 0 GCTCCATCTA 0.994424 -56 TTGTTTAATTGCTCCACTTATA 3 3 0 GCTCCACTTA 0.994424 -21 ********** Masking position 6 Map Score: 2.65539 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 64 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 AAAACCTGCCAAACTAAAAAGAGAGTCCATC 1 27 0 AAACTAAAAG 0.964579 -178 AGTATTTCACAAACTGATATGATTCACTTAT 1 89 1 AAACTGATAG 0.949108 -116 CCATAAATGAAAACTGAACCGCTTTTAAATG 2 16 0 AAACTGAACG 0.980978 -188 AAAGCGGCTGGAATTGAAGTGACAGCTATTT 2 96 1 GAATTGAAGG 0.978439 -108 TGATGAACGAGAATTAAAGAGGTGAGAAAG 4 24 1 GAATTAAAGG 0.952788 -20 ********* * Masking position 5 Map Score: 0.124917 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 206 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CGATATGCTTTATGTCATTTATTGTCCCGA 1 162 0 TATGTCATTT 0.956984 -43 TGTGTCATTTAAAAGCGGTT 2 1 1 TGTGTCATTT 0.970565 -203 AAGCGGTTCAGTTTTCATTTATGGAGATGG 2 23 1 GTTTTCATTT 0.910597 -181 GAGCCCATGCGCTGACATTTGCGCAAAAAA 2 52 1 GCTGACATTT 0.984741 -152 TTCTGAAATAGCTGTCACTTCAATTCCAGC 2 102 0 GCTGTCACTT 0.989653 -102 CTTTTTTCCTGCTGTCTTTTTCTGCTGCTC 2 164 0 GCTGTCTTTT 0.984741 -40 ********** Masking position 3 Map Score: 6.42084 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 591 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 ********** No masking Map Score: -8.85746e-13 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: -8.85746e-13 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: -8.85746e-13 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