AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i003_ecoli_bsub_100.orf -o003_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 guaA 68 GMP synthetase (glutamine-hydrolyzing) #2 guaB 161 IMP dehydrogenase #3 guaB 120 inositol-monophosphate dehydrogenase #4 guaA 232 GMP synthetase Motif number 1 ACAGATAATATAAATCGCCCGACATGAAGT 1 24 0 TAAATCGCCC 0.978613 -45 TTTAGAATTTGATCTCGCTCAC 2 3 0 GATCTCGCTC 0.956931 -159 CAGTCGATAGTAACCCGCCCTTCGGGGATA 2 46 1 TAACCCGCCC 0.982436 -116 TAACCGATTGCATCTACCCCTTTTTGCAAA 2 86 0 CATCTACCCC 0.89042 -76 GGGCAATATCTCGACCAGAGTGGTTA 2 146 0 TATCTCGACC 0.921557 -16 CTAAATATTTCAACTCTTTCCCGCTTCCTT 3 37 1 CAACTCTTTC 0.775694 -84 TGTAGATTATCAACTAGCCAAGAGCATGTC 3 67 0 CAACTAGCCA 0.822534 -54 TAGTAAATCCCCCTCTTTTCGGC 3 108 0 TAAATCCCCC 0.933062 -13 AATTTTCCCATAACTCTCTCGAATCATTCC 4 28 0 TAACTCTCTC 0.968436 -205 GGAGTCAGGCCAACTCGCTCCCAGACTCCG 4 119 0 CAACTCGCTC 0.994937 -114 GACAGATATGAAGCTCGCTCCGCCCTCTTT 4 165 0 AAGCTCGCTC 0.909794 -68 ********** Masking position 2 Map Score: 11.6157 Number of sites scoring better than the average of aligned sites = 1551 Number in coding regions = 1409 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 TTCTCTTCGCCCGACTTCATG 1 1 1 TTCCTTCGCC 0.924972 -68 TTCGCCCGACTTCATGTCGGGCGATTTATAT 1 16 1 TTCTGTCGGG 0.868508 -53 TGACGCTTATTCCGAGGCAAGTGAAA 1 53 0 CTTTTCCGAG 0.856076 -16 GATAGTAACCCGCCCTTCGGGGATAGCAAGC 2 51 1 CGCCTTCGGG 0.983867 -111 TTATTAACCACTCTGGTCGAGATATTGCCC 2 142 1 CTCGGTCGAG 0.886403 -20 AATATTTCAACTCTTTCCCGCTTCCTTGACA 3 40 1 CTCTTCCCGC 0.974379 -81 GTAAATCCCCCTCTTTTCGGCAAAATATTAT 3 98 0 CTCTTTCGGC 0.991661 -23 TGGTCTTGACCGCTTATCGACGTGTTGTTAG 4 72 1 CGCTATCGAC 0.785473 -161 GTCAGGCCAACTCGCTCCCAGACTCCGATAA 4 115 0 CTCCTCCCAG 0.945538 -118 GCGAGTTGGCCTGACTCCGGCAAACGGCCTT 4 131 1 CTGCTCCGGC 0.970549 -102 AGATATGAAGCTCGCTCCGCCCTCTTTGGCA 4 161 0 CTCCTCCGCC 0.989647 -72 *** ******* Masking position 8 Map Score: 10.1015 Number of sites scoring better than the average of aligned sites = 2136 Number in coding regions = 1942 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 3 ATTGCATCTACCCCTTTTTGCAAAAAATGC 2 80 0 CCCCTTTTTG 0.979051 -82 TAGTAAATCCCCCTCTTTTCGGCAAAATA 3 102 0 CCCCTCTTTT 0.990846 -19 AGCTCGCTCCGCCCTCTTTGGCAAGGCCGT 4 154 0 GCCCTCTTTG 0.994063 -79 CTTCATATCTGTCCTCGTTTTTTTCTGTGT 4 182 1 GTCCTCGTTT 0.93694 -51 GTCACCTAATCTCCTCTAAGTTTTTTGACA 4 209 0 CTCCTCTAAG 0.909087 -24 ********** Masking position 5 Map Score: 2.28434 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 152 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 4 CGGGCGATTTATATTATCTGTTTCACTTGC 1 33 1 ATATTATCTG 0.98935 -36 TTTCGGCAAAATATTATATGTAGATTATCA 3 85 0 ATATTATATG 0.971477 -36 GAATTAGTGAATATTATCGGAGTCTGGGAG 4 102 1 ATATTATCGG 0.987355 -131 ********** Masking position 6 Map Score: 1.24115 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 26 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GATAGCAAGCATTTTTTGCAAAAAGGGGTA 2 72 1 ATTTTTTGCA 0.808839 -90 AGTGGTTAATAAATATTGCCGCGGCATTAT 2 124 0 AAATATTGCC 0.986437 -38 ACTCTGGTCGAGATATTGCCC 2 151 1 AGATATTGCC 0.977094 -11 TCCGTTATCTAAATATTTCAACTCTTTCCC 3 29 1 AAATATTTCA 0.824845 -92 TCTACATATAATATTTTGCCGAAAAGAGGG 3 91 1 ATATTTTGCC 0.980679 -30 TCTTTTAATTAAATTTTCCCATAACTCTCT 4 39 0 AAATTTTCCC 0.953823 -194 ********** Masking position 6 Map Score: 3.87988 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 280 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 TTCTCTTCGCCCGACTTCAT 1 1 1 TTCTCTTCGC 0.929721 -68 TATTATCTGTTTCACTTGCCTCGGAATAAG 1 44 1 TTCACTTGCC 0.95797 -25 CTCTTTCCCGCTTCCTTGACATGCTCTTGG 3 50 1 CTTCCTTGAC 0.893639 -71 TTCCTTGACATGCTCTTGGCTAGTTGATAA 3 61 1 TGCTCTTGGC 0.989097 -60 TAAAAGAAGATGGTCTTGACCGCTTATCGA 4 62 1 TGGTCTTGAC 0.975766 -171 CTCCGGCAAACGGCCTTGCCAAAGAGGGCG 4 145 1 CGGCCTTGCC 0.982375 -88 ********** Masking position 6 Map Score: 1.00196 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 387 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ********** No masking Map Score: 1.04693e-12 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: 1.04693e-12 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: 1.04693e-12 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