AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_ecoli_reg_100.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 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #2 moaA 300 molybdopterin biosynthesis, protein A #3 moaB 21 molybdopterin biosynthesis, protein B #4 moeA 203 molybdopterin biosynthesis Motif number 1 TCGGTCACGCTACCTCTTCTGAAGCCTGTCTGTCA 1 34 1 TCCCTTCGGC 0.973883 -81 GCCTGTCTGTCACTCCCTTCGCAGTGTATCATTCT 1 57 1 CCTCCTTGGT 0.991456 -58 ATAGCGTGCATCGTCCTTTAGAGGTAGA 2 4 0 TGTCTTTGGT 0.947924 -297 CCGCCATTTTCCCTTATTCTGTAGCGAAATAGCAC 2 69 1 CCTATTCGGC 0.895301 -232 TTTTTACCATCCACACTTTCGCTATGTAATCATGT 2 120 0 CACCTTTGAT 0.745971 -181 TCAACTGATACGGTGCTTTGGCCGTGACAATGCTC 2 213 1 CGTCTTTGGT 0.980215 -88 GCGAAGTCATTTCTTCCTTCGCCCTGGTGGCAATC 2 253 0 TCTCCTTGCT 0.861013 -48 CTGATCTCTCCTTTTGACGTT 3 2 0 CCTCTTTGGT 0.994632 -20 AAGGGTGGTTCGCCACTTTTGCTATAAATATCAGA 4 25 1 CCCCTTTGAT 0.967694 -179 ACAGACTGTATGCCACCTCGGGCGTAGCGCTGGGT 4 124 0 TCCCCTCGGT 0.973883 -80 GAAAACACTCCTGCGGAGGCAAAATCGAAT 4 184 0 CCTCTGCGGC 0.953353 -20 * ** **** * ** Masking position 11 Map Score: 10.3717 Number of sites scoring better than the average of aligned sites = 1368 Number in coding regions = 1276 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 2 GTAGCGTGACCGACTTCCCGGTCACGCTAA 1 17 0 CGACTTCCCG 0.677978 -98 CAAGATTTTTCCGTTTAAACAGT 1 102 0 GATTTTTCCG 0.926709 -13 GGACGATGCACGCTATGCCTCCCTGATGAT 2 23 1 CGCTATGCCT 0.846984 -278 GTAAAACCGCCATTTTCCCTTATTCTGTAG 2 63 1 CATTTTCCCT 0.890661 -238 GAAATAGCACGATCATGACGCTATATACAT 2 94 1 GATCATGACG 0.681375 -207 AGTGTTTAGTGGTTATGCCGATACTAGCGT 2 165 0 GGTTATGCCG 0.96449 -136 AGGAAGAAATGACTTCGCCTCCCGTATCTG 2 270 1 GACTTCGCCT 0.92796 -31 CTGATCTCTCCTTTTGACGTT 3 10 0 GATCTCTCCT 0.829143 -12 CGTAGCGCTGGGTCCTGCCTTTACATGCCA 4 107 0 GGTCCTGCCT 0.941 -97 AGGCAAAATCGAATTTGCCTATTATGTCAG 4 168 0 GAATTTGCCT 0.955942 -36 AGGCAAATTCGATTTTGCCTCCGCAGGAGT 4 178 1 GATTTTGCCT 0.985645 -26 ********** Masking position 9 Map Score: 6.68024 Number of sites scoring better than the average of aligned sites = 3573 Number in coding regions = 3319 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 3 TCATTCTTAGCGTGACCGGGAAGTCGG 1 8 1 TAGCGTGACC 0.995855 -107 TCAGAAGAGGTAGCGTGACCGACTTCCCGG 1 26 0 TAGCGTGACC 0.995855 -89 TCATTCTGTTTAACGAGACTGTTTAAACGG 1 85 1 TAACGAGACT 0.900479 -30 CAGGGAGGCATAGCGTGCATCGTCCTTTAG 2 18 0 TAGCGTGCAT 0.975844 -283 ATGCCGATACTAGCGTGTAAATGAGATTTT 2 151 0 TAGCGTGTAA 0.939217 -150 ********** Masking position 2 Map Score: 3.67825 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 89 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TCATTCTTAGCGTGACCGGGAAGTCGGTCA 1 11 1 CGTGACCGGG 0.76243 -104 GAAGAGGTAGCGTGACCGACTTCCCGGTCA 1 23 0 CGTGACCGAC 0.937346 -92 CTGCGAAGGGAGTGACAGACAGGCTTCAGA 1 51 0 AGTGACAGAC 0.921454 -64 ACATCATCAGGGAGGCATAGCGTGCATCGT 2 25 0 GGAGGCATAG 0.942263 -276 GTGCTTTGGCCGTGACAATGCTCGTAAAGA 2 225 1 CGTGACAATG 0.873085 -76 CCTTCGCCCTGGTGGCAATCTTTACGAGCA 2 243 0 GGTGGCAATC 0.969307 -58 TCCAGATACGGGAGGCGAAGTCATTTCTTC 2 272 0 GGAGGCGAAG 0.954901 -29 TTATAGCAAAAGTGGCGAACCACCCTTAAT 4 22 0 AGTGGCGAAC 0.940733 -182 CTACGCCCGAGGTGGCATACAGTCTGTGGC 4 132 1 GGTGGCATAC 0.97775 -72 ACACTCCTGCGGAGGCAAAATCGAATTTGC 4 180 0 GGAGGCAAAA 0.878062 -24 ********** Masking position 6 Map Score: 6.88248 Number of sites scoring better than the average of aligned sites = 2463 Number in coding regions = 2326 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 5 TTCTGTTTAACGAGACTGTTTAAACGGAAAA 1 88 1 CAGACTGTTT 0.990425 -27 TATGCCGATACTAGCGTGTAAATGAGATTTT 2 151 0 CAGCGTGTAA 0.936738 -150 GGTGCAGAGGCTAGAGTGTTTAGTGGTTATG 2 178 0 CAGAGTGTTT 0.992231 -123 GAAAAACGCCACAGACTGTATGCCACCTCGG 4 138 0 AAGACTGTAT 0.930888 -66 TTTGCCTCCGCAGGAGTGTTTTC 4 191 1 CGGAGTGTTT 0.985768 -13 * ********* Masking position 7 Map Score: 1.51568 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 43 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TCGCAGTGTATCATTCTGTTTAACGAGACTG 1 75 1 TCATTCGTTT 0.968046 -40 CAAGATTTTTCCGTTTAAACAGTCTC 1 99 0 TTTTTCGTTT 0.751112 -16 AGCGTCATGATCGTGCTATTTCGCTACAGAA 2 85 0 TCGTGCATTT 0.919902 -216 TACCATCCACACTTTCGCTATGTAATCATGT 2 120 0 ACTTTCCTAT 0.830866 -181 TATGAATTACTCATTCAATTTTTGAATATAG 4 65 1 TCATTCATTT 0.978091 -139 GCCATATCCATCTTTCTATATTCAAAAATTG 4 80 0 TCTTTCATAT 0.95566 -124 TCCTGCCTTTACATGCCATATCCATCTTTCT 4 94 0 ACATGCATAT 0.905789 -110 CATAATAGGCAAATTCGATTTTGCCTCCGCA 4 172 1 AAATTCATTT 0.781269 -32 ****** **** Masking position 4 Map Score: 1.01211 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 390 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 7 ********** No masking Map Score: -1.31207e-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: -1.31207e-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: -1.31207e-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