AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icarP_ecoli_bsub_100.orf -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 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #3 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #4 pyrB 145 aspartate carbamoyltransferase Motif number 1 GAAATAAAAACGAGCAGAAAAAAGTGGACCAA 1 27 0 CAGCAAAAAA 0.962742 -274 AAGAAGATTGCATGAAATAAAAACGAGCAGAA 1 40 0 CTGAATAAAA 0.915752 -261 CCGCATTTCAGCCGCATAAAAAAACAGGCTGA 2 16 0 GCGCAAAAAA 0.967746 -191 CAGCACGACTCCAGCACAAAAACGTTGATGCG 2 51 0 CAGCAAAAAA 0.962742 -156 ATGGGAATTCCGCTCAAAAAAAATCAGCACGA 2 75 0 CCTCAAAAAA 0.91346 -132 CGGAATTCCCATTGAACAGAAAATTTATAAAT 2 95 1 ATGAAAGAAA 0.898374 -112 AAAATTTATAAATGAATAAAAATATTAAATAT 2 114 1 ATGAAAAAAA 0.968209 -93 AACATTATAACATGAATAAAAATTAATTCAAT 2 149 0 CTGAAAAAAA 0.983029 -58 ATGTTAAATAATTTCACAAAGACCAAGAGGGT 2 176 1 ATTCAAAAGA 0.720041 -31 ATGCCTTTATATCGAAAAAAAA 3 1 0 ACGAAAAAAA 0.950186 -70 TTTCGATATAAAGGCATAAAAATTCATTTTTA 3 16 1 AGGCAAAAAA 0.919479 -55 CCTCTCTGGACTTTCATTAAAAGGTT 4 5 0 CTTCATAAAA 0.759625 -141 TCAACTTAAGGCTGAAAAAAAACCCCGGTCTA 4 106 0 GTGAAAAAAA 0.967586 -40 TCAGCCTTAAGTTGAAAAGAGAGGGGAAAGAA 4 123 1 GTGAAAGAGA 0.715512 -23 * **** ***** Masking position 6 Map Score: 15.7683 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 993 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 2 CCAGAGAATATTCACTCACTTTATTTGCATA 1 272 0 TCACTCACTT 0.962842 -29 AACAAGTTCACCCTCTTGGTCTTTGTG 2 190 0 TCACCCTCTT 0.988646 -17 CTAACAGCCCACCTCTTGATGAATAAT 3 54 0 GCCACCTCTT 0.947523 -17 GCATTGAAGCTTCCTTCTCTTCATAACCCTT 4 42 0 TCCTTCTCTT 0.983489 -104 GCTTCAATGCTGCCCTCTATTTAACCATACC 4 63 1 TCCCTCTATT 0.979628 -83 GTTCTTTCCCCTCTCTTTTCAACTTAA 4 129 0 TCCCTCTCTT 0.996793 -17 * ********* Masking position 10 Map Score: 5.75194 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 111 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 CAACTTAATGGCGGGATTTTTTATATTATT 1 149 0 GCGGGATTTT 0.972681 -152 CTGGCAAACGGCGGCATTCTGGAGATATGG 1 190 0 GCGGCATTCT 0.986059 -111 TCTGCTTACCGACGAATTTCTGGCAAACGG 1 209 0 GACGAATTTC 0.92623 -92 TTGATGCGGTGCCGCATTTCAGCCGCATAA 2 29 0 GCCGCATTTC 0.99023 -178 TTTTTTTTGAGCGGAATTCCCATTGAACAG 2 84 1 GCGGAATTCC 0.990387 -123 ********** Masking position 6 Map Score: 3.41098 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 362 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 TTGACCATTTGGTCCACTTTTTTCTGCTCGTT 1 19 1 GGTCCCTTTT 0.986412 -282 GAACAGGTTAGATGATCTTTTTGTCGCTTAAT 1 91 1 GATGACTTTT 0.958144 -210 TTTTGTGGCTCATGCATGTTTTACAGGCATTA 1 119 0 CATGCTTTTT 0.755272 -182 CATTGATTTACGTCATCATTGTGAATTAATAT 1 243 1 CGTCACTTGT 0.914062 -58 CGCGGTCAGCCTGTTTTTTTATGCG 2 4 1 GGTCACTGTT 0.964989 -203 ACGTTGATGCGGTGCCGCATTTCAGCCGCATA 2 30 0 GGTGCGATTT 0.833756 -177 TGCGGCACCGCATCAACGTTTTTGTGCTGGAG 2 43 1 CATCACTTTT 0.937185 -164 GTGCTGGAGTCGTGCTGATTTTTTTTGAGCGG 2 66 1 CGTGCGTTTT 0.962525 -141 AGACCAAGAGGGTGAACTTGTT 2 195 1 GGTGACTGTT 0.971543 -12 ***** * **** Masking position 3 Map Score: 4.19066 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 744 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 GTCATCATTGTGAATTAATATGCAAATAAA 1 254 1 TGAATTAATA 0.80088 -47 ATAAAGTGAGTGAATATTCTCTGGAGGGTG 1 279 1 TGAATATTCT 0.788764 -22 GGAGTCGTGCTGATTTTTTTTGAGCGGAAT 2 71 1 TGATTTTTTT 0.824069 -136 TATTCATTTATAAATTTTCTGTTCAATGGG 2 102 0 TAAATTTTCT 0.759384 -105 AATCGTATATTTAATATTTTTATTCATTTA 2 122 0 TTAATATTTT 0.75601 -85 AATATACGATTGAATTAATTTTTATTCATG 2 141 1 TGAATTAATT 0.884747 -66 GTTATAATGTTAAATAATTTCACAAAGACC 2 170 1 TAAATAATTT 0.806407 -37 ATTATAAAAATGAATTTTTATGCCTTTATA 3 22 0 TGAATTTTTA 0.899498 -49 CACCTCTTGATGAATAATTAATTATAAAAA 3 42 0 TGAATAATTA 0.772611 -29 ********** Masking position 5 Map Score: 2.71847 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 563 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 6 CTAACCTGTTCTGGAAAACGCTTGCGCAGC 1 72 0 CTGGAAAACG 0.992229 -229 CGCTTAATGCCTGTAAAACATGCATGAGCC 1 115 1 CTGTAAAACA 0.954083 -186 CGACGAATTTCTGGCAAACGGCGGCATTCT 1 200 0 CTGGCAAACG 0.982913 -101 TTTTATGCGGCTGAAATGCGGCACCGCATC 2 27 1 CTGAAATGCG 0.918719 -180 CAACTTAAGGCTGAAAAAAAACCCCGGTCT 4 107 0 CTGAAAAAAA 0.875326 -39 ********** Masking position 6 Map Score: 1.01608 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 674 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ********** No masking Map Score: -2.95996e-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: -2.95996e-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: -2.95996e-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