AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i007_ecoli_mtub_100.orf -o007_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 nadC 87 quinolinate phosphoribosyltransferase #2 nadA 300 quinolinate synthetase, A protein #3 nadB 300 quinolinate synthetase, B protein #4 nadA 48 nadA Motif number 1 AAATTGAGGATGCCTGAATAGCAAAAAAGCGCCT 2 54 0 TGCTGAGCAA 0.995672 -247 GACATAGAGTTGCTTGCACAGTAAGCTCTGACGA 2 109 0 TGCTGAGTAA 0.988978 -192 TATCTTGTTTAGCATATAAAACAAATTACACCGA 2 216 1 AGCTAAACAA 0.941862 -85 TTTAACGTTAAGCCTGTAAAACGAGATGGTAAG 2 278 1 AGCTGAACGA 0.974703 -23 ATCCGTCTACAGCATGACAAACAAAAACAGATGC 3 19 0 AGCTGAACAA 0.993154 -282 CCCATTTAACTGCCTGAAGAGTAACCCAACGGCC 3 111 1 TGCTGAGTAA 0.989057 -190 GCCCTGCGTCAGCGTGTTTAGCAACTGTAACAAA 3 199 1 AGCTGAGCAA 0.997313 -102 TGCTGACCAAACCATGTTTAGTAAATTAAACAAA 3 273 1 ACCTGAGTAA 0.960017 -28 *** ** ***** Masking position 10 Map Score: 13.4082 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 132 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 CGGTTCAGAGTAGCATGTTTCTACCTTATG 1 42 1 TAGCATGTTT 0.955598 -46 CTGACGATGTCATCAGGTTTACAAAGTGAA 2 86 0 CATCAGGTTT 0.990579 -215 ACCATTCGACTATCTTGTTTAGCATATAAA 2 206 1 TATCTTGTTT 0.932782 -95 CTTACCATCTCGTTTTACAGGCTTA 2 286 0 CATCTCGTTT 0.950117 -15 TCCGTAACGCATCTGTTTTTGTTTGTCAT 3 10 1 CATCTGTTTT 0.868222 -291 CGCCCTGCGTCAGCGTGTTTAGCAACTGTA 3 198 1 CAGCGTGTTT 0.958843 -103 AATATTAAAATAGCAGGTGTTTATCCGCAC 3 231 1 TAGCAGGTGT 0.890014 -70 GTCAGCATAGCATCATGTTGTGCGGATAAA 3 250 0 CATCATGTTG 0.844058 -51 TTCCGCGCTCCAACAGGTTTTCGACTTATA 4 20 0 CAACAGGTTT 0.957095 -29 ********** Masking position 8 Map Score: 8.64061 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 819 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 TAGCGTAATATTCGCTGTTATCGGTGTAATTTGT 2 236 0 TCGCTGACGG 0.99078 -65 CAGCGAATATTACGCTAATGTCGGTTTTAACGTT 2 253 1 TCGCTAGCGG 0.983854 -48 TTTTGTTTGTCATGCTGTAGACGGATCATTATCT 3 27 1 CTGCTGGCGG 0.965735 -274 AGAGAAGTTACTGGCTGGTGGAGGATTAGGTGGT 3 155 0 CGGCTGGAGG 0.991806 -146 AGTTGCTAAACACGCTGACGCAGGGCGGCGAGAA 3 191 0 CCGCTGGAGG 0.9976 -110 CCGCCCCTTCCGCGCTCCAACAGGTTTTCGACTT 4 23 0 CCGCTCAAGG 0.97314 -26 * ***** * *** Masking position 6 Map Score: 6.06261 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 726 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 CAGGATCTCCTTATATGTGGTGCTAATACCC 1 12 1 TTATAGTGGT 0.907198 -76 ATATTCGCTGTTATCGGTGTAATTTGTTTTA 2 232 0 TTATCGTGTA 0.986867 -69 TGATAGATAATGATCCGTCTACAGCATGACA 3 34 0 TGATCGTCTA 0.964886 -267 TTATCTATCATTATAAGTCTACAGAATCTGA 3 55 1 TTATAGTCTA 0.979507 -246 GAACATCGCATTATCTGTGTAGAAATGCCCA 3 84 1 TTATCGTGTA 0.986867 -217 GTTTTCGATTATAAGTCGAAAACCTGTTG 4 9 1 TTATAGTCGA 0.975385 -40 ***** ***** Masking position 4 Map Score: 5.16139 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 26 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TTGGTGGGTCGTGCAGGATGACTCG 2 6 0 GTGCAGGATG 0.996741 -295 ACAAAGTGAAATTGAGGATGCCTGAATAGC 2 66 0 ATTGAGGATG 0.950923 -235 TACGCCTAATGTGCAGGATGCGTCATTTTA 2 157 0 GTGCAGGATG 0.996741 -144 TTACTGGCTGGTGGAGGATTAGGTGGTGAA 3 152 0 GTGGAGGATT 0.987177 -149 ********** Masking position 5 Map Score: 4.51191 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 23 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CACCAATGTAAAAAAGCGCCCTAAAGGCGCTT 2 30 1 AAAAAGGCCT 0.991859 -271 CTGAATAGCAAAAAAGCGCCTTTAGGGCGCTT 2 43 0 AAAAAGGCCT 0.991858 -258 CATCAGGTTTACAAAGTGAAATTGAGGATGCC 2 74 0 ACAAAGGAAT 0.897835 -227 GGCTTAACGTTAAAACCGACATTAGCGTAATA 2 260 0 TAAAACGACT 0.912181 -41 TTCAGGCAGTTAAATGGGCATTTCTACACAGA 3 97 0 TAAATGGCAT 0.903891 -204 GGTGGTGAAATAAAAAGGCCGTTGGGTTACTC 3 129 0 TAAAAAGCCT 0.935377 -172 GGGCGGCGAGAAAAAGAGAAGTTACTGGCTGG 3 171 0 AAAAAGGAAT 0.966171 -130 ****** *** * Masking position 4 Map Score: 3.35747 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 227 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 CTCCAGATAGCTAACGAATCATAAGGTAGA 1 61 0 CTAACGAATC 0.96643 -27 TAGGCGTAAAATGACGCATCCTGCACATTA 2 151 1 ATGACGCATC 0.9712 -150 TCCGTAACGCATCTGTTTTTGTT 3 4 1 GTAACGCATC 0.983173 -297 TGCCTGAAGAGTAACCCAACGGCCTTTTTA 3 121 1 GTAACCCAAC 0.955222 -180 GCTAAACACGCTGACGCAGGGCGGCGAGAA 3 191 0 CTGACGCAGG 0.947419 -110 TGATGCTATGCTGACCAAACCATGTTTAGT 3 265 1 CTGACCAAAC 0.942902 -36 ********** Masking position 4 Map Score: 1.59659 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 753 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 GAACCGGGTATTAGCACCACATATAAGGAGA 1 17 0 TTAGCCCACA 0.951554 -71 TTCGAGTGACTTTTCCCCACCATTCGACTAT 2 188 1 TTTTCCCACC 0.991808 -113 TTAAATGGGCATTTCTACACAGATAATGCGA 3 89 0 ATTTCACACA 0.887749 -212 CGGCCTTTTTATTTCACCACCTAATCCTCCA 3 140 1 ATTTCCCACC 0.984825 -161 ACTTCTCTTTTTCTCGCCGCCCTGCGTCAGC 3 181 1 TTCTCCCGCC 0.962922 -120 TAGCAGGTGTTTATCCGCACAACATGATGCT 3 241 1 TTATCGCACA 0.93849 -60 ***** ***** Masking position 2 Map Score: 1.33013 Number of sites scoring better than the average of aligned sites = 745 Number in coding regions = 695 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 GTGGAATTAGGCGTAAAATGACGCATCCTG 2 144 1 GCGTAAAATG 0.980396 -157 TGCACATTAGGCGTAATTCGAGTGACTTTT 2 172 1 GCGTAATTCG 0.981813 -129 GCTGTTATCGGTGTAATTTGTTTTATATGC 2 227 0 GTGTAATTTG 0.956889 -74 ACCGACATTAGCGTAATATTCGCTGTTATC 2 248 0 GCGTAATATT 0.932119 -53 AACGTTAAGCCTGTAAAACGAGATGGTAAG 2 281 1 CTGTAAAACG 0.871876 -20 ********** Masking position 5 Map Score: 0.606921 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 346 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 10 ********** No masking Map Score: 1.17483e-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 11 ********** No masking Map Score: 1.17483e-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 12 ********** No masking Map Score: 1.17483e-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