AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -idnaA_ctra_opreg_300.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 CT273 277 hypothetical protein #3 dnaA_2 242 Replication Initiation Factor #4 nrdA 300 Ribonucleoside Reductase, Large Chain #5 nrdB 37 Ribonucleoside Reductase, Small Chain Motif number 1 GTTTTTACCTCTTAAAAACTAAGGAGAG 1 9 1 CTCTTAAAAA 0.881144 -121 GCATACGGTTCTTTCAAGAAGAAGCCCTTT 1 47 0 CTTTCAAGAA 0.958768 -83 AGGAAGAATCCTTTTAAGGAGAGAGGGGCA 1 74 0 CTTTTAAGGA 0.957054 -56 GAAAGTACAGCTTTCAAAAAATTCCCTTGT 2 71 1 CTTTCAAAAA 0.928591 -207 GATTGTGAGCCTCTCAAGGGAAACTT 2 262 1 CTCTCAAGGG 0.856253 -16 GAAGGAGAATCTCTCAAGAAGAGACTTTTT 3 34 0 CTCTCAAGAA 0.942358 -209 TTCAAAAATACGCTTAAGGACAAGAAGTTT 3 117 0 CGCTTAAGGA 0.963711 -126 CAATACATTTCGTTCAAAAATACGCTTAAG 3 129 0 CGTTCAAAAA 0.901101 -114 TTCTCTTTATCGCTTGAGGAATTAAGGATT 3 219 0 CGCTTGAGGA 0.911426 -24 CGAGAGCAAACTTTTAAGCATGATGTCCTA 4 41 0 CTTTTAAGCA 0.843977 -260 TAAAAGTTTGCTCTCGAAAAGAAATTTTTC 4 55 1 CTCTCGAAAA 0.874749 -246 ********** Masking position 7 Map Score: 15.0662 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 246 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 AAAAACTAAGGAGAGTATAGCAAAAAGGGCTT 1 24 1 GAGAGTTGCA 0.97937 -106 TCCTTTTAAGGAGAGAGGGGCATACGGTTCTT 1 64 0 GAGAGAGGCA 0.967462 -66 GTAGCTAAAGCAGAAGGTTGCAGTGTATCGCA 2 99 1 CAGAAGTGCA 0.961569 -179 TCAAGTATGGTAGAGGGGAGAACGTAAAGCAA 2 203 0 TAGAGGGGAA 0.770481 -75 AGTTTCCCTTGAGAGGCTCACAATCTCAATCA 2 255 0 GAGAGGTACA 0.976568 -23 ATAATAGAAGGAGAATCTCTCAAGAAGAGACT 3 38 0 GAGAATTTCA 0.744791 -205 CCTCCTCCTGGAGAAAATCGCAAATGTAGCAT 3 176 0 GAGAAATGCA 0.967499 -67 TTTTCTCCAGGAGGAGGGTGCATTACCGAATC 3 191 1 GAGGAGGGCA 0.973219 -52 ATACCATATATAGAAGCTAGCAACGTTTCCTG 4 112 0 TAGAAGTGCA 0.977093 -189 TACAAGAGCCGAGACGTTCACAATATCTTGGG 4 143 1 GAGACGTACA 0.905265 -158 CTTGGGTTTTTAGGGGCTCGCATACTCAAAGG 4 169 1 TAGGGGTGCA 0.963109 -132 ****** * *** Masking position 2 Map Score: 11.3927 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 213 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 CTATACTCTCCTTAGTTTTTAAGAGGTAAA 1 14 0 CTTAGTTTTT 0.546251 -116 AAGAAGCCCTTTTTGCTATACTCTCCTTAG 1 29 0 TTTTGCTATA 0.926064 -101 AACCTTCTGCTTTAGCTACAAGGGAATTTT 2 88 0 TTTAGCTACA 0.696639 -190 TATTGAAGAGCTGTGCTTTTAACTAAACAT 2 130 0 CTGTGCTTTT 0.936877 -148 CCTTAAAAACCTTTGCTTTACGTTCTCCCC 2 191 1 CTTTGCTTTA 0.952507 -87 AGAAGAGACTTTTTGCTTCTCCCCAGGATG 3 18 0 TTTTGCTTCT 0.964867 -225 TATTAATAATTTTTGTTTCTGATTTCAGGA 3 74 1 TTTTGTTTCT 0.79235 -169 GGACAAGAAGTTTTTCTATTAATTTTTCCT 3 100 0 TTTTTCTATT 0.635035 -143 GCAAATGTAGCATTGCTATTGATAAGCAAT 3 159 0 CATTGCTATT 0.764892 -84 TCTAGCTTTTTTGTGCTTTTT 4 2 0 TTGTGCTTTT 0.927602 -299 TCATCGCAGTTTATGCTATTTTTCAATTGC 4 83 1 TTATGCTATT 0.773342 -218 CTAGAGGCGTCTTTGCTTCAAAATAGAGAA 4 268 1 CTTTGCTTCA 0.942857 -33 ********** Masking position 7 Map Score: 8.70406 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 595 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 CCACTACTACAATAAGCCGCTTAGCTGCGA 2 43 1 AATAAGCCGC 0.909537 -235 CTAAACATGCGATACACTGCAACCTTCTGC 2 108 0 GATACACTGC 0.916122 -170 ACAGCTCTTCAATACACCTCAAACAGCAAC 2 146 1 AATACACCTC 0.929957 -132 TATTAGATGTAATAAGTTGCTGTTTGAGGT 2 161 0 AATAAGTTGC 0.841449 -117 GGGGAGAAGCAAAAAGTCTCTTCTTGAGAG 3 24 1 AAAAAGTCTC 0.793161 -219 AAAATTAATAGAAAAACTTCTTGTCCTTAA 3 104 1 GAAAAACTTC 0.807163 -139 TTCGTTCAAAAATACGCTTAAGGACAAGAA 3 121 0 AATACGCTTA 0.694898 -122 ATAAGCAATCAATACATTTCGTTCAAAAAT 3 138 0 AATACATTTC 0.875046 -105 TGTCCTACATAAAACATCTAGCTTTTTTGT 4 18 0 AAAACATCTA 0.396251 -283 AAACTGCGATGAAAAATTTCTTTTCGAGAG 4 65 0 GAAAAATTTC 0.689353 -236 TGAAAAATAGCATAAACTGCGATGAAAAAT 4 78 0 CATAAACTGC 0.625269 -223 TCAATTGCAGGAAACGTTGCTAGCTTCTAT 4 105 1 GAAACGTTGC 0.765837 -196 TTTTGAAGCAAAGACGCCTCTAGTCCCCCT 4 261 0 AAGACGCCTC 0.828998 -40 ********** Masking position 4 Map Score: 4.96878 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 676 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 GAAAGAACCGTATGCCCCTCTCTCCTTAAA 1 62 1 TATGCCCCTC 0.847857 -68 TGCGATACACTGCAACCTTCTGCTTTAGCT 2 101 0 TGCAACCTTC 0.942054 -177 TTGCTTTACGTTCTCCCCTCTACCATACTT 2 203 1 TTCTCCCCTC 0.941134 -75 ATACTTGACTTTTTCCCTCCCCCGATTATG 2 227 1 TTTTCCCTCC 0.79432 -51 TGATTGAGATTGTGAGCCTCTCAAGGGAAA 2 255 1 TGTGAGCCTC 0.93315 -23 GATTCGGTAATGCACCCTCCTCCTGGAGAA 3 193 0 TGCACCCTCC 0.961941 -50 CAGGAAACGTTGCTAGCTTCTATATATGGT 4 112 1 TGCTAGCTTC 0.934718 -189 CCTTTGAGTATGCGAGCCCCTAAAAACCCA 4 171 0 TGCGAGCCCC 0.97222 -130 ********** Masking position 1 Map Score: 2.74475 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 150 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 ********** No masking Map Score: 9.90086e-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: 9.90086e-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: 9.90086e-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