AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i115_Glycine_Transport_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 = 0.5 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 0.967809 -181 TAACAATTCAGCGAGTGAATATTTTGAAAA 3 65 1 GCGAGTGAAT 0.837022 -131 AAGCATGATGGAGAGAGAAAAAGAATGCTC 3 110 0 GAGAGAGAAA 0.958187 -86 TGCCCGACGTGGCAGCGAAAATGGTGCAAA 3 156 0 GGCAGCGAAA 0.969229 -40 GGGCAACAAAGGAAGAAAAATCCAT 3 181 1 GGAAGAAAAA 0.813701 -15 TTTTGTCAAAGATAGCGAAAAAACGCCTGA 4 90 0 GATAGCGAAA 0.977818 -211 TATAAGGGCTGAGAGCAAATCGAGAAAGTT 4 126 0 GAGAGCAAAT 0.967689 -175 GAATATTGATGCGAGCAAATCGCCGGAATT 4 164 0 GCGAGCAAAT 0.961283 -137 GGCAACCCCTGATGGCAAATGTGGCATGAA 4 191 0 GATGGCAAAT 0.890335 -110 AGTATGTTAGGGTAGAAAAAAGTGACTATT 4 231 1 GGTAGAAAAA 0.934939 -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 CATATTCGGTCCGGCGTTTCCT 1 2 0 CCGGGTTTCC 0.997983 -142 GTTGATAATGGCGGGGTTAGCTTGAGCGGAA 1 69 0 GCGGGTTAGC 0.979702 -75 TAGTAAGGGCGCGACGTTTGCGCCCTTT 2 16 1 GCGAGTTTGC 0.968122 -18 GGTGCAAAAACCGTAGTTTGCCATAAGCATG 3 133 0 CCGTGTTTGC 0.992201 -63 GATTTTTCTTCCTTTGTTGCCCGACGTGGCA 3 172 0 CCTTGTTGCC 0.947299 -24 GAGCAAATCGCCGGAATTTCCCGTGATATAA 4 151 0 CCGGATTTCC 0.984654 -150 CATTTGCCATCAGGGGTTGCCTCAGATTCTC 4 200 1 CAGGGTTGCC 0.981548 -101 **** ****** Masking position 7 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 GATTCTGCAACTGAATCCTTCCGCTCAAGC 1 51 1 CTGAATCCTT 0.826933 -93 CTCAAGCTAACCCCGCCATTATCAACTATG 1 74 1 CCCCGCCATT 0.975374 -70 GGCGCAAACGTCGCGCCCTTACTAAAGCA 2 10 0 TCGCGCCCTT 0.993033 -24 GGCGCGACGTTTGCGCCCTTT 2 23 1 TTGCGCCCTT 0.994217 -11 ACTACGGTTTTTGCACCATTTTCGCTGCCA 3 147 1 TTGCACCATT 0.951555 -49 TCGATTTGCTCTCAGCCCTTATATCACGGG 4 133 1 CTCAGCCCTT 0.979497 -168 ********** Masking position 9 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 0.957281 -52 CTTTTACTGTTGTTTTCAGCGAATTAAGAG 1 109 0 TGTTTTCAGC 0.957281 -35 GATGCTTTCCTCATTCTTTTAC 1 132 0 TGCTTTCCTC 0.991521 -12 TTTCTCGATTTGCTCTCAGCCCTTATATCA 4 129 1 TGCTCTCAGC 0.992141 -172 TCCGGCGATTTGCTCGCATCAATATTCATG 4 167 1 TGCTCGCATC 0.981371 -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 AGGAAACGCCGGACCGAATATGCC 1 5 1 AACGCCGGAC 0.95684 -139 TTTTCTCTTAATTCGCTGAAAACAACAGTA 1 105 1 ATTCGCTGAA 0.94265 -39 CAAAATATTCACTCGCTGAATTGTTATACA 3 61 0 ACTCGCTGAA 0.883263 -135 TGCTCAGTTTATTGTCTGAATTTTCAAAAT 3 85 0 ATTGTCTGAA 0.909274 -111 TGTTGCATTATTCGCCTGAAACCACAATAT 4 60 1 TTCGCCTGAA 0.966923 -241 ATAGCGAAAAAACGCCTGAATATTGTGGTT 4 79 0 AACGCCTGAA 0.992201 -222 ATGCGAGCAAATCGCCGGAATTTCCCGTGA 4 156 0 ATCGCCGGAA 0.98766 -145 AATCTGAGGCAACCCCTGATGGCAAATGTG 4 198 0 AACCCCTGAT 0.941757 -103 ********** Masking position 9 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 CATTCTTTTTCTCTCTCCATCATGCTTATG 3 113 1 CTCTCTCCAT 0.98645 -83 AAAATATCAACTTTCTCGATTTGCTCTCAG 4 118 1 CTTTCTCGAT 0.980049 -183 AAAAAAGTGACTATTTCCATTGGGTAATAT 4 246 1 CTATTTCCAT 0.969473 -55 CTTTATTTGTCTATGTCGATATATTACCCA 4 266 0 CTATGTCGAT 0.979196 -35 ********** Masking position 6 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 0.981012 -179 GAATGCTCAGTTTATTGTCTGAATTTTCAA 3 88 0 TTTATTGTCT 0.848478 -108 TCACCACAAATTATTTGCGTGATAAAAAGC 4 15 0 TTATTTGCGT 0.907489 -286 CTCTGTTGCATTATTCGCCTGAAACCACAA 4 57 1 TTATTCGCCT 0.981012 -244 ATTCAGGCGTTTTTTCGCTATCTTTGACAA 4 88 1 TTTTTCGCTA 0.888796 -213 AAAGTTGATATTTTTTGTCAAAGATAGCGA 4 102 0 TTTTTTGTCA 0.953948 -199 AAAGATTCCTTTATTTGTCTATGTCGATAT 4 274 0 TTATTTGTCT 0.953948 -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 AAACAACAGTAAAAGAATGAGGAAAGCATC 1 124 1 AAAAGAATGA 0.966579 -20 TGGAGAGAGAAAAAGAATGCTCAGTTTATT 3 102 0 AAAAGAATGC 0.968964 -94 CGTCGGGCAACAAAGGAAGAAAAATCCAT 3 177 1 CAAAGGAAGA 0.952725 -19 TATTTTTTGTCAAAGATAGCGAAAAAACGC 4 94 0 CAAAGATAGC 0.936218 -207 GCAATAGAAAGATTCCTTTATT 4 289 0 AATAGAAAGA 0.926449 -12 ********** Masking position 4 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