AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i115_Glycine_Transport_ecoli_hinf_reg_300.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 yehZ 143 putative transport system permease protein #2 BIME97 33 BIME #3 bglX 195 beta-D-glucoside glucohydrolase, periplasmic #4 proV 300 ATP-binding component of transport system for glycine, betaine and proline Motif number 1 CACTCCTTGTGGTGGCGAAAAAATATCACA 3 15 1 GGTGGCGAAA 0.972991 -181 TAACAATTCAGCGAGTGAATATTTTGAAAA 3 65 1 GCGAGTGAAT 0.860216 -131 AAGCATGATGGAGAGAGAAAAAGAATGCTC 3 110 0 GAGAGAGAAA 0.964862 -86 TGCCCGACGTGGCAGCGAAAATGGTGCAAA 3 156 0 GGCAGCGAAA 0.974189 -40 GGGCAACAAAGGAAGAAAAATCCAT 3 181 1 GGAAGAAAAA 0.839578 -15 TTTTGTCAAAGATAGCGAAAAAACGCCTGA 4 90 0 GATAGCGAAA 0.98142 -211 TATAAGGGCTGAGAGCAAATCGAGAAAGTT 4 126 0 GAGAGCAAAT 0.972889 -175 GAATATTGATGCGAGCAAATCGCCGGAATT 4 164 0 GCGAGCAAAT 0.96748 -137 GGCAACCCCTGATGGCAAATGTGGCATGAA 4 191 0 GATGGCAAAT 0.906787 -110 AGTATGTTAGGGTAGAAAAAAGTGACTATT 4 231 1 GGTAGAAAAA 0.945112 -70 ********** Masking position 8 Map Score: 10.9072 Number of sites scoring better than the average of aligned sites = 1270 Number in coding regions = 1153 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 2 AGGAAACGCCGGACCGAATATG 1 2 1 GGAAACCCGG 0.998073 -142 TTCCGCTCAAGCTAACCCCGCCATTATCAAC 1 69 1 GCTAACCCGC 0.98059 -75 AAAGGGCGCAAACGTCGCGCCCTTACTA 2 16 0 GCAAACTCGC 0.969496 -18 CATGCTTATGGCAAACTACGGTTTTTGCACC 3 133 1 GCAAACACGG 0.992547 -63 TGCCACGTCGGGCAACAAAGGAAGAAAAATC 3 172 1 GGCAACAAGG 0.949535 -24 TTATATCACGGGAAATTCCGGCGATTTGCTC 4 151 1 GGAAATCCGG 0.98533 -150 GAGAATCTGAGGCAACCCCTGATGGCAAATG 4 200 0 GGCAACCCTG 0.982358 -101 ****** **** Masking position 5 Map Score: 8.26989 Number of sites scoring better than the average of aligned sites = 719 Number in coding regions = 681 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 GCTTGAGCGGAAGGATTCAGTTGCAGAATC 1 51 0 AAGGATTCAG 0.823212 -93 CATAGTTGATAATGGCGGGGTTAGCTTGAG 1 74 0 AATGGCGGGG 0.974747 -70 TGCTTTAGTAAGGGCGCGACGTTTGCGCC 2 10 1 AAGGGCGCGA 0.992853 -24 AAAGGGCGCAAACGTCGCGCC 2 23 0 AAGGGCGCAA 0.994067 -11 TGGCAGCGAAAATGGTGCAAAAACCGTAGT 3 147 0 AATGGTGCAA 0.950353 -49 CCCGTGATATAAGGGCTGAGAGCAAATCGA 4 133 0 AAGGGCTGAG 0.978973 -168 ********** Masking position 2 Map Score: 4.61987 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 751 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 4 TTATCAACTATGCTTTTCTCTTAATTCGCT 1 92 1 TGCTTTTCTC 0.958994 -52 CTTTTACTGTTGTTTTCAGCGAATTAAGAG 1 109 0 TGTTTTCAGC 0.958994 -35 GATGCTTTCCTCATTCTTTTAC 1 132 0 TGCTTTCCTC 0.991873 -12 TTTCTCGATTTGCTCTCAGCCCTTATATCA 4 129 1 TGCTCTCAGC 0.992467 -172 TCCGGCGATTTGCTCGCATCAATATTCATG 4 167 1 TGCTCGCATC 0.982136 -134 ********** Masking position 4 Map Score: 3.72113 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 189 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 GGCATATTCGGTCCGGCGTTTCCT 1 5 0 GTCCGGCGTT 0.950871 -139 TACTGTTGTTTTCAGCGAATTAAGAGAAAA 1 105 0 TTCAGCGAAT 0.935154 -39 TGTATAACAATTCAGCGAGTGAATATTTTG 3 61 1 TTCAGCGAGT 0.868515 -135 ATTTTGAAAATTCAGACAATAAACTGAGCA 3 85 1 TTCAGACAAT 0.897423 -111 ATATTGTGGTTTCAGGCGAATAATGCAACA 4 60 0 TTCAGGCGAA 0.962424 -241 AACCACAATATTCAGGCGTTTTTTCGCTAT 4 79 1 TTCAGGCGTT 0.991077 -222 TCACGGGAAATTCCGGCGATTTGCTCGCAT 4 156 1 TTCCGGCGAT 0.986374 -145 CACATTTGCCATCAGGGGTTGCCTCAGATT 4 198 1 ATCAGGGGTT 0.933904 -103 ********** Masking position 2 Map Score: 6.56544 Number of sites scoring better than the average of aligned sites = 1677 Number in coding regions = 1510 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 6 CATAAGCATGATGGAGAGAGAAAAAGAATG 3 113 0 ATGGAGAGAG 0.987539 -83 CTGAGAGCAAATCGAGAAAGTTGATATTTT 4 118 0 ATCGAGAAAG 0.981642 -183 ATATTACCCAATGGAAATAGTCACTTTTTT 4 246 0 ATGGAAATAG 0.971887 -55 TGGGTAATATATCGACATAGACAAATAAAG 4 266 1 ATCGACATAG 0.980856 -35 ********** Masking position 5 Map Score: 1.1567 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 48 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 TTTGTGATATTTTTTCGCCACCACAAGGAG 3 17 0 TTTTTCGCCA 0.980893 -179 GAATGCTCAGTTTATTGTCTGAATTTTCAA 3 88 0 TTTATTGTCT 0.84766 -108 TCACCACAAATTATTTGCGTGATAAAAAGC 4 15 0 TTATTTGCGT 0.906955 -286 CTCTGTTGCATTATTCGCCTGAAACCACAA 4 57 1 TTATTCGCCT 0.980893 -244 ATTCAGGCGTTTTTTCGCTATCTTTGACAA 4 88 1 TTTTTCGCTA 0.888168 -213 AAAGTTGATATTTTTTGTCAAAGATAGCGA 4 102 0 TTTTTTGTCA 0.953668 -199 AAAGATTCCTTTATTTGTCTATGTCGATAT 4 274 0 TTATTTGTCT 0.953668 -27 ********** Masking position 5 Map Score: 5.28783 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 736 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 8 GATGCTTTCCTCATTCTTTTACTGTTGTTT 1 124 0 TCATTCTTTT 0.966374 -20 AATAAACTGAGCATTCTTTTTCTCTCTCCA 3 102 1 GCATTCTTTT 0.968773 -94 ATGGATTTTTCTTCCTTTGTTGCCCGACG 3 177 0 TCTTCCTTTG 0.952439 -19 GCGTTTTTTCGCTATCTTTGACAAAAAATA 4 94 1 GCTATCTTTG 0.935838 -207 AATAAAGGAATCTTTCTATTGC 4 289 1 TCTTTCTATT 0.926015 -12 ********** Masking position 7 Map Score: 0.763063 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 89 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 ********** No masking Map Score: -7.93376e-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 10 ********** No masking Map Score: -7.93376e-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 11 ********** No masking Map Score: -7.93376e-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