AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -idnaA_ctra_opreg_100.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dnaN 129 DNA Pol III (beta chain) #2 dnaA_2 242 Replication Initiation Factor #3 nrdA 300 Ribonucleoside Reductase, Large Chain #4 nrdB 37 Ribonucleoside Reductase, Small Chain Motif number 1 GTTTTTACCTCTTAAAAACTAAGGAGAG 1 9 1 CTCTTAAAAA 0.935272 -121 GCATACGGTTCTTTCAAGAAGAAGCCCTTT 1 47 0 CTTTCAAGAA 0.970796 -83 AGGAAGAATCCTTTTAAGGAGAGAGGGGCA 1 74 0 CTTTTAAGGA 0.97058 -56 GAAGGAGAATCTCTCAAGAAGAGACTTTTT 2 34 0 CTCTCAAGAA 0.967098 -209 TTCAAAAATACGCTTAAGGACAAGAAGTTT 2 117 0 CGCTTAAGGA 0.981277 -126 CAATACATTTCGTTCAAAAATACGCTTAAG 2 129 0 CGTTCAAAAA 0.92192 -114 TTCTCTTTATCGCTTGAGGAATTAAGGATT 2 219 0 CGCTTGAGGA 0.963013 -24 CGAGAGCAAACTTTTAAGCATGATGTCCTA 3 41 0 CTTTTAAGCA 0.915226 -260 TAAAAGTTTGCTCTCGAAAAGAAATTTTTC 3 55 1 CTCTCGAAAA 0.91977 -246 ********** Masking position 4 Map Score: 12.6585 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 183 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 2 CTTAAAAACTAAGGAGAGTATAGCAAAAAGG 1 21 1 AAGGAGAGAT 0.832622 -109 CGGTTCTTTCAAGAAGAAGCCCTTTTTGCTA 1 41 0 AAGAAGAACC 0.974257 -89 GAATCCTTTTAAGGAGAGAGGGGCATACGGT 1 68 0 AAGGAGAGGG 0.949652 -62 TCAATGACAAAGGAAGAATCCTTTTAAGGAG 1 83 0 AGGAAGAACC 0.954868 -47 ATTTCATCCTGGGGAGAAGCAAAAAGTCTCT 2 14 1 GGGGAGAACA 0.803731 -229 AGAATCTCTCAAGAAGAGACTTTTTGCTTCT 2 28 0 AAGAAGAGCT 0.925204 -215 TCAATAATAGAAGGAGAATCTCTCAAGAAGA 2 42 0 AAGGAGAACT 0.97068 -201 TTTTCTCCAGGAGGAGGGTGCATTACCGAAT 2 191 1 GAGGAGGGGC 0.916228 -52 CTCAAGCGATAAAGAGAACGCG 2 231 1 AAAGAGAAGC 0.931829 -12 CGCATACTCAAAGGATAATGCTCTGATTTTT 3 187 1 AAGGATAAGC 0.931829 -114 AAAAAACGGTAGAGAGAGCCCTTATCTTATA 3 222 0 AGAGAGAGCC 0.913476 -79 CTTCAAAATAGAGAATAATGCGTATTCA 3 283 1 GAGAATAAGC 0.711376 -18 ******** ** Masking position 5 Map Score: 9.95843 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 659 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 GAAGAAGCCCTTTTTGCTATACTCTCCTTA 1 30 0 TTTTTGCTAT 0.972151 -100 AAGAAGAGACTTTTTGCTTCTCCCCAGGAT 2 19 0 TTTTTGCTTC 0.99033 -224 GTATTAATAATTTTTGTTTCTGATTTCAGG 2 73 1 TTTTTGTTTC 0.940631 -170 ATCTAGCTTTTTTGTGCTTTTT 3 3 0 TTTGTGCTTT 0.967041 -298 TTCATCGCAGTTTATGCTATTTTTCAATTG 3 82 1 TTTATGCTAT 0.913869 -219 ACTAGAGGCGTCTTTGCTTCAAAATAGAGA 3 267 1 TCTTTGCTTC 0.973991 -34 ********** Masking position 5 Map Score: 6.17241 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 128 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 TTTCAAGAAGAAGCCCTTTTTGCTATACTC 1 36 0 AAGCCCTTTT 0.943378 -94 AAAGAACCGTATGCCCCTCTCTCCTTAAAA 1 63 1 ATGCCCCTCT 0.974893 -67 TTGAGTATGCGAGCCCCTAAAAACCCAAGA 3 168 0 GAGCCCCTAA 0.984839 -133 ACGGTAGAGAGAGCCCTTATCTTATACTTA 3 218 0 GAGCCCTTAT 0.989567 -83 GACGCCTCTAGTCCCCCTATCCGTCAAAAA 3 249 0 GTCCCCCTAT 0.976937 -52 ********** Masking position 8 Map Score: 2.0063 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 64 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 5 CTTTCAAGAAGAAGCCCTTTTTGCTATACTCT 1 35 0 GAACCCTTTT 0.835139 -95 CTGATTTCAGGAAAAATTAATAGAAAAACTTC 2 92 1 GAAAATTATA 0.868988 -151 AAAATTAATAGAAAAACTTCTTGTCCTTAAGC 2 104 1 GAAAACTCTT 0.92557 -139 AATCGCAAATGTAGCATTGCTATTGATAAGCA 2 161 0 GTACATTCTA 0.86284 -82 GTGCATTACCGAATCCTTAATTCCTCAAGCGA 2 208 1 GAACCTTATT 0.957635 -35 AAACTGCGATGAAAAATTTCTTTTCGAGAGCA 3 63 0 GAAAATTCTT 0.956342 -238 TCAATTGCAGGAAACGTTGCTAGCTTCTATAT 3 105 1 GAACGTTCTA 0.966775 -196 AAGAACCGTTAATTTTATTGTTAA 4 24 0 GAACGTTATT 0.957631 -14 *** **** *** Masking position 3 Map Score: 1.58462 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 213 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 TCTTCCTTTGTCATTGATAATAATCCTAATCAGCAAGTA 1 97 1 TCTAAATTAA 0.910046 -33 TGCATTTCATCCTGGGGAGAAGCAAAAAGTCTCTTCTT 2 10 1 TCTGAACAAA 0.796478 -233 TGCACCCTCCTCCTGGAGAAAATCGCAAATGTAGCATTG 2 174 0 TCTAAACAAA 0.943657 -69 AAGCATGATGTCCTACATAAAACATCTAGCTTTTTTGTG 3 17 0 TCTAAAATAG 0.977284 -284 TAGCAACGTTTCCTGCAATTGAAAAATAGCATAAACTGC 3 88 0 TCTATAATAG 0.931486 -213 ACGTCTCGGCTCTTGTATACCATATATAGAAGCTAGCAA 3 121 0 TCTAAAATAG 0.977273 -180 AGAGCCCTTATCTTATACTTAAAAAATCAGAGCATTATC 3 200 0 TCTATAATCA 0.711588 -101 AGTCCCCCTATCCGTCAAAAAAACGGTAGAGAGAGCCCT 3 231 0 TCGAAACTAG 0.940982 -70 TTAATCATATAAATTAACAATAAAATTAACGGT 4 5 1 TCTAAACTAA 0.981452 -33 ** * * * * * *** Masking position 12 Map Score: 1.71103 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 102 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: 1.77168e-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: 1.77168e-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: 1.77168e-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