AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i007_Pyrimidine_Nucleotides_Biosynthesis_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 nadC 87 quinolinate phosphoribosyltransferase #2 nadA 300 quinolinate synthetase, A protein #3 nadB 300 quinolinate synthetase, B protein Motif number 1 AAATTGAGGATGCCTGAATAGCAAAAAAGCGCCT 2 54 0 TGCTGAGCAA 0.995553 -247 GACATAGAGTTGCTTGCACAGTAAGCTCTGACGA 2 109 0 TGCTGAGTAA 0.988678 -192 TATCTTGTTTAGCATATAAAACAAATTACACCGA 2 216 1 AGCTAAACAA 0.940335 -85 TTTAACGTTAAGCCTGTAAAACGAGATGGTAAG 2 278 1 AGCTGAACGA 0.974015 -23 ATCCGTCTACAGCATGACAAACAAAAACAGATGC 3 19 0 AGCTGAACAA 0.992964 -282 CCCATTTAACTGCCTGAAGAGTAACCCAACGGCC 3 111 1 TGCTGAGTAA 0.988755 -190 GCCCTGCGTCAGCGTGTTTAGCAACTGTAACAAA 3 199 1 AGCTGAGCAA 0.997238 -102 TGCTGACCAAACCATGTTTAGTAAATTAAACAAA 3 273 1 ACCTGAGTAA 0.958946 -28 *** ** ***** Masking position 10 Map Score: 13.8347 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 GAATCATAAGGTAGAAACATGCTACTCTGAAC 1 44 0 GTAGAAAAGC 0.983181 -44 ACCCACCAATGTAAAAAAGCGCCCTAAAGGCG 2 27 1 GTAAAAAGGC 0.983182 -274 TGCCTGAATAGCAAAAAAGCGCCTTTAGGGCG 2 46 0 GCAAAAAGGC 0.931753 -255 GGTTTACAAAGTGAAATTGAGGATGCCTGAAT 2 69 0 GTGAAATGGG 0.936551 -232 CTCTATGTCGGTGGAATTAGGCGTAAAATGAC 2 134 1 GTGGAATAGC 0.979108 -167 GGAATTAGGCGTAAAATGACGCATCCTGCACA 2 146 1 GTAAAATAGC 0.973424 -155 GGAAAAGTCACTCGAATTACGCCTAATGTGCA 2 172 0 CTCGAATAGC 0.875472 -129 AAACAAGATAGTCGAATGGTGGGGAAAAGTCA 2 194 0 GTCGAATGGG 0.966667 -107 CATTATCTGTGTAGAAATGCCCATTTAACTGC 3 92 1 GTAGAAAGCC 0.943465 -209 ******* * ** Masking position 6 Map Score: 6.94446 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 667 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 CGAGTCATCCTGCACGACCCACCA 2 5 1 TCATCCTGCA 0.995004 -296 TGCTATTCAGGCATCCTCAATTTCACTTTG 2 65 1 GCATCCTCAA 0.955989 -236 GTAAAATGACGCATCCTGCACATTAGGCGT 2 156 1 GCATCCTGCA 0.99398 -145 GTTTTAACGTTAAGCCTGTAAAACGAGATG 2 276 1 TAAGCCTGTA 0.916115 -25 TTTTTGTTTGTCATGCTGTAGACGGATCAT 3 26 1 TCATGCTGTA 0.952975 -275 TTTCACCACCTAATCCTCCACCAGCCAGTA 3 151 1 TAATCCTCCA 0.972356 -150 ********** Masking position 7 Map Score: 5.03459 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 565 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 CATGCTACTCTGAACCGGGTATTAGCACCAC 1 28 0 TGAACGGGTA 0.933589 -60 ATATTCGCTGTTATCGGTGTAATTTGTTTTA 2 232 0 TTATCGTGTA 0.989576 -69 TGATAGATAATGATCCGTCTACAGCATGACA 3 34 0 TGATCGTCTA 0.985999 -267 TTATCTATCATTATAAGTCTACAGAATCTGA 3 55 1 TTATAGTCTA 0.926124 -246 GAACATCGCATTATCTGTGTAGAAATGCCCA 3 84 1 TTATCGTGTA 0.989576 -217 ***** ***** Masking position 3 Map Score: 2.32065 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 29 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 CGGGTATTAGCACCACATATAAGGAGATCC 1 14 0 CACCACATAT 0.972012 -74 GTTAAAACTCCAGATAGCTAACGAATC 1 71 0 CTCCAGATAG 0.95965 -17 CTTTTTATTTCACCACCTAATCCTCCACCA 3 144 1 CACCACCTAA 0.977962 -157 CCTAATCCTCCACCAGCCAGTAACTTCTCT 3 159 1 CACCAGCCAG 0.987566 -142 TGCGGATAAACACCTGCTATTTTAATATTT 3 230 0 CACCTGCTAT 0.971945 -71 ********** Masking position 9 Map Score: 1.96192 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 298 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 GAACCGGGTATTAGCACCACATATAAGGAGAT 1 16 0 TAGCACACAT 0.989271 -72 TCCGTAACGCATCTGTTTTTGT 3 1 1 TCGTACGCAT 0.97726 -300 CTACAGAATCTGAACATCGCATTATCTGTGTA 3 73 1 TAACACGCAT 0.975496 -228 CAGGTGTTTATCCGCACAACATGATGCTATGC 3 244 1 TCGCAAACAT 0.977865 -57 CATGGTTTGGTCAGCATAGCATCATGTTGTGC 3 257 0 TAGCAAGCAT 0.989271 -44 * **** ***** Masking position 6 Map Score: 1.52598 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 95 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TTACGCCTAATTCCACCGACATAGAGTTGC 2 130 0 TTCCACCGAC 0.957766 -171 TCGAGTGACTTTTCCCCACCATTCGACTAT 2 189 1 TTTCCCCACC 0.98559 -112 GAAATGCCCATTTAACTGCCTGAAGAGTAA 3 105 1 TTTAACTGCC 0.906075 -196 GGCCTTTTTATTTCACCACCTAATCCTCCA 3 141 1 TTTCACCACC 0.991497 -160 CTTCTCTTTTTCTCGCCGCCCTGCGTCAGC 3 182 1 TCTCGCCGCC 0.985799 -119 ********** Masking position 1 Map Score: 1.3106 Number of sites scoring better than the average of aligned sites = 1015 Number in coding regions = 964 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 ATGCGTCATTTTACGCCTAATTCCACCGAC 2 140 0 TTACGCCTAA 0.863703 -161 GTCACTCGAATTACGCCTAATGTGCAGGAT 2 168 0 TTACGCCTAA 0.863703 -133 ATAAAACAAATTACACCGATAACAGCGAAT 2 231 1 TTACACCGAT 0.929488 -70 ACAGCGAATATTACGCTAATGTCGGTTTTA 2 252 1 TTACGCTAAT 0.896787 -49 GGTTTTAACGTTAAGCCTGTAAAACGAGAT 2 275 1 TTAAGCCTGT 0.907929 -26 ********** Masking position 3 Map Score: 1.36944 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 262 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 ********** No masking Map Score: 2.93755e-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: 2.93755e-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: 2.93755e-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