AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i045_Trehalose_Utilization_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 treC 49 trehalase 6-P hydrolase #2 treB 118 PTS system enzyme II, trehalose specific #3 treR 300 repressor of treA,B,C Motif number 1 TCGTTTCCTGAACGATAAAT 2 1 1 TCGTTTCCTG 0.95316 -118 GATCTTCGCTGCGTTTCGGGAACGTTCCCG 2 34 1 GCGTTTCGGG 0.975072 -85 CGTTTCGGGAACGTTCCCGTTTTTAAATTT 2 45 1 ACGTTCCCGT 0.937588 -74 TCTTTTCACGGCGTTACCGGATGCGTAAGG 3 38 0 GCGTTACCGG 0.99479 -263 GGTAAGCCCGTCTTTTCACGGCGTTACCGG 3 48 0 TCTTTTCACG 0.858373 -253 GGAGATTAAAACTTTTCCGGTAAGCCCGTC 3 66 0 ACTTTTCCGG 0.99 -235 GATAAACCAGACTTTACCCATTGCTGAATG 3 229 1 ACTTTACCCA 0.871785 -72 TTTGAGCCTAACGTTACCCGTGCATTCAGC 3 251 0 ACGTTACCCG 0.99462 -50 ATTAAACAACACGTTACAGGACAACAGG 3 283 1 ACGTTACAGG 0.985309 -18 ********** Masking position 5 Map Score: 13.9251 Number of sites scoring better than the average of aligned sites = 1415 Number in coding regions = 1321 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GGCGCAATTGCGCCCCGAAGAAAA 1 1 0 CGCCCAAAAA 0.984129 -49 GTTCCCGAAACGCAGCGAAGATCACAATTTATCG 2 23 0 CGCGCAAATA 0.995208 -96 GAATATATTGCGCGGAAAAATTTAAAAACGGGAA 2 58 0 CGCGAAATTA 0.968119 -61 CAATATATTCTGCAGCCAACCAAAAATGTCATCT 2 82 1 TGCGCAACAA 0.98333 -37 GTGAAAAAAGCGCCGCAAATAATAAGGAGAATCC 3 141 1 CGCGCAAAAA 0.996316 -160 TCGCCATAGATGCTACGAATATTATTGGATTCTC 3 167 0 TGCACAAATA 0.939602 -134 ATATAATACCTGCTGACAACTAAACCAACGATAA 3 200 1 TGCGAAATAA 0.950359 -101 *** ** ** ** * Masking position 8 Map Score: 7.11568 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 410 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 CCTCGCATTCGCAGGAATAACGTA 1 36 1 GCAGGAATAA 0.894218 -14 TCGTTTCCTGAACGATAAATTGTGATCTT 2 10 1 GAACGATAAA 0.749707 -109 TTGGTTGGCTGCAGAATATATTGCGCGGAA 2 75 0 GCAGAATATA 0.935401 -44 CTGAGCAGGGACGTTAAAACGTCACGGC 3 9 1 GGACGTTAAA 0.950227 -292 CTCCCTCGACGGAGATTAAAACTTTTCCGG 3 76 0 GGAGATTAAA 0.946482 -225 TTCACTTACCGGAGGTTATATGGAACCTGA 3 116 0 GGAGGTTATA 0.978376 -185 AAAAAGCGCCGCAAATAATAAGGAGAATCC 3 145 1 GCAAATAATA 0.691367 -156 TTAGTTGTCAGCAGGTATTATATCGCCATA 3 193 0 GCAGGTATTA 0.931325 -108 ********** Masking position 3 Map Score: 3.4828 Number of sites scoring better than the average of aligned sites = 1296 Number in coding regions = 1145 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 4 TTTTCTTCGGGGCGCAATTGCGCCCCCT 1 9 1 GGGGCGCAAT 0.979807 -41 CAATTGCGCCCCCTCGCATTCGCAGGAATA 1 25 1 CCCTCGCATT 0.985598 -25 TTTAAATTTTTCCGCGCAATATATTCTGCA 2 66 1 TCCGCGCAAT 0.989143 -53 CTTATTATTTGCGGCGCTTTTTTCACTTAC 3 137 0 GCGGCGCTTT 0.986727 -164 CCTAACGTTACCCGTGCATTCAGCAATGGG 3 245 0 CCCGTGCATT 0.985598 -56 ********** Masking position 10 Map Score: 3.05732 Number of sites scoring better than the average of aligned sites = 1158 Number in coding regions = 1085 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 GCGCAATTGCGCCCCCTCGCATTCGCAGGA 1 22 1 GCCCCCTCGC 0.998529 -28 AAAGCCCCATGGCAGATGACATT 2 106 0 GCCCCATGGC 0.990198 -13 ATCCCACGCCTCTCCCTCGACGGAGATTAA 3 87 0 TCTCCCTCGA 0.964722 -214 TATGGAACCTGATCCCACGCCTCTCCCTCG 3 98 0 GATCCCACGC 0.977465 -203 AACCAGACTTTACCCATTGCTGAATGCACG 3 233 1 TACCCATTGC 0.940976 -68 ********** Masking position 5 Map Score: 3.088 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 308 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 CTGAGCAGGGACGTTAAAACGTCA 3 5 1 GCAGGGACGT 0.981381 -296 TACCGGATGCGTAAGGCCGTGACGTTTTAA 3 24 0 GTAAGGCCGT 0.998363 -277 TACGCATCCGGTAACGCCGTGAAAAGACGG 3 41 1 GTAACGCCGT 0.995624 -260 AACTTTTCCGGTAAGCCCGTCTTTTCACGG 3 57 0 GTAAGCCCGT 0.995624 -244 ********** Masking position 3 Map Score: 5.08695 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 56 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: -2.24942e-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: -2.24942e-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: -2.24942e-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