AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i122_ecoli_mtub_100.orf -o122_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 arsR 300 transcriptional repressor of chromosomal ars operon #2 Rv2642 135 hypothetical protein Rv2642 Motif number 1 CTCTCTCACTCCAGCCAGAGCCACCAACTCAGGG 1 88 1 CGCGAGCCAC 0.977623 -213 CCAGAGCCACCAACTCAGGGCTGGAAAGTAAAAA 1 102 1 CCCGGGCTGG 0.995825 -199 AGTAAAAAACCGACGCAAAGTCGGTTTTTTTACG 1 128 1 CCCAAGTCGG 0.981879 -173 CTTGGAGACGCACCCCGGGGTCAGGCCTACAG 2 9 0 CCCGGGTCAG 0.99561 -127 CCCCGGGGTGCGTCTCCAAGCCGCGGAGCCCACC 2 23 1 CCCAAGCCGC 0.995141 -113 GCCGCGGAGCCCACCCCGGGCCACTCAATGCCCC 2 42 1 CCCGGGCCAC 0.974315 -94 GTGAACGGCGCTACGCGGGTTAGGGGGCATTGAG 2 65 0 CCCGGTTAGG 0.940604 -71 TAGCGCCGTTCACCGCGTGGCCGCTTGCGGACCT 2 86 1 CCCTGGCCGC 0.997186 -50 TGACAAATATCGAATCAGGTCCGCAAGCGGCCAC 2 102 0 CACGGTCCGC 0.983599 -34 * * * ******* Masking position 6 Map Score: 15.6573 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 901 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 GTTTTTTACTTTCCAGCCCTGAGTTGGTGG 1 108 0 TTCCAGCCCT 0.976295 -193 TTACGTCCTGATTCAGACCTCCTTTCAAAT 1 157 1 ATTCAGACCT 0.983136 -144 CCAACTCAAAATTCACACCTATTACCTTCC 1 193 1 ATTCACACCT 0.975622 -108 ATTGCGCTCCTGATTGTTGCA 1 290 0 TTGCGCTCCT 0.974265 -11 GCGTGGCCGCTTGCGGACCTGATTCGATAT 2 100 1 TTGCGGACCT 0.99288 -36 ********** Masking position 2 Map Score: 3.19717 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 146 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 CAGGGCTGGAAAGTAAAAAACCGACGCAAA 1 117 1 AAGTAAAAAA 0.977898 -184 CTGAATCAGGACGTAAAAAAACCGACTTTG 1 143 0 ACGTAAAAAA 0.952226 -158 ATGAATAGCCAACTCAAAATTCACACCTAT 1 185 1 AACTCAAAAT 0.895889 -116 CACATTCGTTAAGTCATATATGTTTTTGAC 1 233 1 AAGTCATATA 0.902053 -68 CGAAGCGGATAAGTCAAAAACATATATGAC 1 245 0 AAGTCAAAAA 0.990068 -56 ********** Masking position 6 Map Score: 2.59342 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 130 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 CTTGCAATGTTAGCCACTGGCTAATAGTATTG 1 40 1 TAGCCACTCT 0.994502 -261 ACTCCAGCCAGAGCCACCAACTCAGGGCTGGA 1 95 1 GAGCCACCCT 0.994583 -206 GCTTCGAAGAGAGACACTACCTGCAACAATCA 1 269 1 GAGACACTCT 0.987358 -32 AGCCCACCCCGGGCCACTCAATGCCCCCTAAC 2 49 1 GGGCCACTAT 0.988279 -87 GTTCACCGCGTGGCCGCTTGCGGACCTGATTC 2 93 1 TGGCCGCTCG 0.975372 -43 ******** ** Masking position 7 Map Score: 2.18353 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 150 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TAACATTGCAAGAATTAGCGATTTCTTCAGC 1 21 0 AAATTAGCGA 0.983123 -280 TAATTCTTGCAATGTTAGCCACTGGCTAATA 1 35 1 ATGTTAGCCA 0.974516 -266 ACAGCTCAATACTATTAGCCAGTGGCTAACA 1 47 0 ATATTAGCCA 0.988352 -254 CTCCTTTCAAATGAATAGCCAACTCAAAATT 1 175 1 AGAATAGCCA 0.980312 -126 ATCAATATTGACAAATATCGAATCAGGTCCG 2 113 0 AAAATATCGA 0.886276 -23 * ********* Masking position 6 Map Score: 1.32768 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 132 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 ACGTCCTGATTCAGACCTCCTTTCAAATGA 1 159 1 TCAGACCTCC 0.993572 -142 AACTCAAAATTCACACCTATTACCTTCCTC 1 195 1 TCACACCTAT 0.976077 -106 CACCCCGGGGTCAGGCCTACAG 2 3 0 TCAGGCCTAC 0.983344 -133 ********** Masking position 3 Map Score: 0.0946658 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 29 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 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