AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i090_Sugar_Transport_2_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 malZ 155 maltodextrin glucosidase #2 malE 300 periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis Motif number 1 TTCCGAAAGTTATCCGCCCCCGTCCTCCTC 1 58 1 TATCCGCCCC 0.980286 -98 CCGCCCCCGTCCTCCTCCCCCAAATATCCT 1 71 1 CCTCCTCCCC 0.999559 -85 GAAAATCTGATCACCTTGCCATAGCCTAAT 1 122 0 TCACCTTGCC 0.875274 -34 TGGCTTAAATCCTCCACCCCCTGGCTTTTT 2 20 1 CCTCCACCCC 0.997878 -281 CATCCTCCCGCCTCCTCCCCCATAAAAAAG 2 44 0 CCTCCTCCCC 0.999559 -257 GCCGTGTTCTCATCCTCCCGCCTCCTCCCC 2 54 0 CATCCTCCCG 0.986632 -247 CCTCCTTGCCCCTACGCCCCACCGTCGCTT 2 200 0 CCTACGCCCC 0.992109 -101 CTCTTTCCATCCTCCTTGCCCCTACGCCCC 2 210 0 CCTCCTTGCC 0.995596 -91 TATACGGCAACCTCTTTCCATCCTCCTTGC 2 221 0 CCTCTTTCCA 0.890415 -80 ********** Masking position 9 Map Score: 22.8207 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 213 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 CGTTCTGTAAGCCGGTTCAGGAGGAAATCC 1 17 1 GCCGGTTCAG 0.931238 -139 TTTCGGAATAGCCGGATCAGGATTTCCTCC 1 36 0 GCCGGATCAG 0.989717 -120 GGAGGACGGGGGCGGATAACTTTCGGAATA 1 56 0 GGCGGATAAC 0.971065 -100 GATATTTGGGGGAGGAGGACGGGGGCGGAT 1 69 0 GGAGGAGGAC 0.994373 -87 ATAGCCTAATGCAGGATCACTCATCATCTG 1 102 0 GCAGGATCAC 0.973888 -54 AAAGCCAGGGGGTGGAGGATTTAAGCCATC 2 18 0 GGTGGAGGAT 0.931128 -283 GCTTTTTTATGGGGGAGGAGGCGGGAGGAT 2 43 1 GGGGGAGGAG 0.992339 -258 GGAGGAGGCGGGAGGATGAGAACACGGCTT 2 56 1 GGAGGATGAG 0.996246 -245 GCGACGGTGGGGCGTAGGGGCAAGGAGGAT 2 202 1 GGCGTAGGGG 0.944844 -99 GTAGGGGCAAGGAGGATGGAAAGAGGTTGC 2 215 1 GGAGGATGGA 0.94639 -86 ********** Masking position 4 Map Score: 15.9872 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 1018 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 3 CTGAACCGGCTTACAGAACGCAAGGA 1 2 0 TACAAACAGG 0.995445 -154 CTCCTCCCCCATAAAAAAGCCAGGGGGTGGAGGAT 2 28 0 AAAAAACAGG 0.892931 -273 TCGGTTTAGTTCACAGAAGCCGTGTTCTCATCCTC 2 67 0 TACAAACGGT 0.990078 -234 GTGATGTTGCTTGCAAAAATCGTGGCGATTTTATG 2 120 1 TGCAAACGGG 0.995788 -181 GTGATCTCTGTTACAGAATTGGCGGTAATGTGGAG 2 162 0 TACAAAGGGG 0.993299 -139 GTAACAGAGATCACACAAAGCGACGGTGGGGCGTA 2 183 1 TACAAACGCG 0.993301 -118 * *** ** ** ** Masking position 8 Map Score: 3.75285 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 136 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 CAAATATCCTTCAGATGATGAGTGATCCTG 1 91 1 TCAGATGATG 0.951514 -65 ATCAGGAGATGGCTTAAATCC 2 2 1 TCAGGAGATG 0.984934 -299 CATAAAAAAGCCAGGGGGTGGAGGATTTAA 2 24 0 CCAGGGGGTG 0.959889 -277 TTTTTATGGGGGAGGAGGCGGGAGGATGAG 2 46 1 GGAGGAGGCG 0.948072 -255 GGCGGGAGGATGAGAACACGGCTTCTGTGA 2 62 1 TGAGAACACG 0.891463 -239 TGAACTAAACCGAGGTCATGTAAGGAATTT 2 89 1 CGAGGTCATG 0.96983 -212 TAAGGAATTTCGTGATGTTGCTTGCAAAAA 2 109 1 CGTGATGTTG 0.771879 -192 TTGGCGGTAATGTGGAGATGCGCACATAAA 2 149 0 TGTGGAGATG 0.97496 -152 ********** Masking position 4 Map Score: 2.96861 Number of sites scoring better than the average of aligned sites = 1986 Number in coding regions = 1853 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 5 ********** 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 6 ********** 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 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