AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icarP_mjan_opreg_100.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ1019 132 carbamoyl-phosphate synthase, small (or glutamine) subunit (carA) #2 MJ1378 184 carbamoyl-phosphate synthase, medium subunit (carB1) #3 MJ1381 124 carbamoyl-phosphate synthase, large subunit (carB2) Motif number 1 GTCTATTCACCATTTCATCAATTATTAACAACCAT 1 2 1 TTAACATAAT 0.958696 -131 TAATCATCTATCTACTGCTTTTAGAGGACATTATGCATTTTATA 1 50 0 TTACTTTAAT 0.967324 -83 AACTATCACATATATATATGATTGGGATAATCATCTATCTACTG 1 77 0 TTAATATAAT 0.986619 -56 TATGTGATAGTTTATAGGTATTTTGGTGAAATAT 1 109 1 TTAGTTTAAT 0.941429 -24 ATTATCACCATTTACCTACCATTAACTTTAAAAACCTTAACTGA 2 11 1 TTAACATAAA 0.915128 -174 TTTAAAAACCTTAACTGATTATTAGGAAAAGGATACTTAAAGTT 2 37 1 TAAATATAAT 0.959469 -148 ATTGCATAACTATATTTATGTTACTTAACTTTAAGTATCCTTTT 2 63 0 TTAATTTTAA 0.807989 -122 TTATGCAATTTTAAAAGCTCATCCTCAATATTAAGATAATCTGA 2 98 1 TAACTATAAA 0.791582 -87 TATTTATATATTTAACTATTATTATTCAGATTATCTTAATATTG 2 123 0 TTAATATAAT 0.986615 -62 AATAGTTAAATATATAAATATTGTAAAATATTATTGTGGTGGAT 2 147 1 TTAATTTAAT 0.988424 -38 TTCATAAATATTTTGGGATTGATTATATCCTTCTTT 3 3 1 CTAATTTAAT 0.930905 -122 GAACGTCTTCTTTAACTATCTTCCAAAGAAGGATATAATCAATC 3 27 0 TTAATTTAAT 0.988429 -98 TGAGATAGTTTTAAAAGATATTGAAAATAAAAAATAGGTGATTA 3 90 1 TAAATTTAAA 0.926921 -35 * ** ** ** * ** Masking position 4 Map Score: 16.6144 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 450 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 2 ACAACCATAAATTATAAAATGCATAATGTCCTCTAAA 1 38 1 ATATAATAAT 0.693362 -95 ACATATATATATGATTGGGATAATCATCTATCTACTG 1 77 0 ATATGGAAAT 0.977966 -56 TAGTTTATAGGTATTTTGGTGAAATAT 1 116 1 GTTTGGTAAT 0.874897 -17 ACCTTAACTGATTATTAGGAAAAGGATACTTAAAGTT 2 44 1 ATATGGAAAT 0.980712 -141 GATTATCTTAATATTGAGGATGAGCTTTTAAAATTGC 2 102 0 ATTTGGAATT 0.913743 -83 CAATATTAAGATAATCTGAATAATAATAGTTAAATAT 2 123 1 ATATGAAAAT 0.976413 -62 AAATATATAAATATTGTAAAATATTATTGTGGTGGAT 2 154 1 ATTTAAAAAT 0.937965 -31 TTCATAAATATTTTGGGATTGATTATATCCTTCTTT 3 10 1 ATTTGATAAT 0.931526 -115 TTCTTTAACTATCTTCCAAAGAAGGATATAATCAATC 3 27 0 ATTTAAAAAT 0.965137 -98 GTTTTAAAAGATATTGAAAATAAAAAATAGGTGATTA 3 97 1 ATTTAAAAAA 0.805419 -28 ** ** *** * ** Masking position 5 Map Score: 9.84493 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 357 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 CTGCTTTTAGAGGACATTATGCATTTTATA 1 50 0 AGGACATTAT 0.832738 -83 AGCAGTAGATAGATGATTATCCCAATCATA 1 75 1 AGATGATTAT 0.927733 -58 TCATATATATATGTGATAGTTTATAGGTAT 1 100 1 ATGTGATAGT 0.953218 -33 GGTAGGTAAATGGTGATAAT 2 1 0 TGGTGATAAT 0.958536 -184 ATCCTCAATATTAAGATAATCTGAATAATA 2 118 1 TTAAGATAAT 0.80801 -67 ATATTGTAAAATATTATTGTGGTGGATATT 2 164 1 ATATTATTGT 0.537822 -21 CTTCCAAAGAAGGATATAATCAATCCCAAA 3 22 0 AGGATATAAT 0.896426 -103 ATCCTTCTTTGGAAGATAGTTAAAGAAGAC 3 37 1 GGAAGATAGT 0.86244 -88 AAGAAAGAAGTTGAGATAGTTTTAAAAGAT 3 79 1 TTGAGATAGT 0.914445 -46 AATAAAAAATAGGTGATTAT 3 115 1 AGGTGATTAT 0.967844 -10 ********** Masking position 6 Map Score: 7.45239 Number of sites scoring better than the average of aligned sites = 1207 Number in coding regions = 1066 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 4 ATTTTATAATTTATGGTTGTTAATAATTGAT 1 27 0 TTATGTTGTT 0.933444 -106 TTAGAGGACATTATGCATTTTATAATTTATG 1 43 0 TTATGATTTT 0.974929 -90 TCAGTTAAGGTTTTTAAAGTTAATGGTAGGT 2 24 0 TTTTTAAGTT 0.865318 -161 ATAACTATATTTATGTTACTTAACTTTAAGT 2 71 0 TTATGTACTT 0.854071 -114 ATAAATATAGTTATGCAATTTTAAAAGCTCA 2 88 1 TTATGAATTT 0.967598 -97 CTCAACTTCTTTCTTTATTTTAGGAACGTCT 3 63 0 TTCTTATTTT 0.894534 -62 TAATCACCTATTTTTTATTTTCAATATCTTT 3 103 0 TTTTTATTTT 0.909839 -22 ***** ***** Masking position 4 Map Score: 1.78429 Number of sites scoring better than the average of aligned sites = 821 Number in coding regions = 674 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 ********** No masking Map Score: 1.01908e-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 6 ********** No masking Map Score: 1.01908e-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 7 ********** No masking Map Score: 1.01908e-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