AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_mjan_pyro_300.orf -o308_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -x5 -e 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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ07595 300 M_jannaschii_chromosome #2 RPH00031 35 Pyrococcus_OT3 #3 RPH00029 65 Pyrococcus_OT3 Motif number 1 ATGCCTTTTTTTATTACAAAATTTTTTACA 1 19 1 TTATTACAAA 0.942133 -282 TCATAGTTTCTTGTAAAAAATTTTGTAATA 1 30 0 TTGTAAAAAA 0.943576 -271 AACTATGAGCTTATTAAAAATTTATTAATG 1 52 1 TTATTAAAAA 0.819969 -249 TATTAAAAATTTATTAATGAGATAAACTAT 1 63 1 TTATTAATGA 0.699414 -238 TATATTGCAATTGTTACAATAGTTTATCTC 1 81 0 TTGTTACAAT 0.880829 -220 GGTTTCGAAGTTATTGAAGACTAAAATATT 1 116 0 TTATTGAAGA 0.942342 -185 AAACGCTTGTTTATAAAGATGAGTCTTTTA 1 155 1 TTATAAAGAT 0.896029 -146 CTAAGTCAATTTATAAAAGACTCATCTTTA 1 168 0 TTATAAAAGA 0.945207 -133 AATCTTGTCCTTATTAAAAAAGAAAATAGA 1 200 0 TTATTAAAAA 0.819969 -101 TTAAAATATATTATGGAAATTCAATATATA 1 230 0 TTATGGAAAT 0.849984 -71 AAATTTTAAATTGTTAAAATATATTATGGA 1 243 0 TTGTTAAAAT 0.953827 -58 TAAGGAGGGTTTATAGAGATTT 2 3 0 TTATAGAGAT 0.828393 -33 ********** Masking position 4 Map Score: 16.1565 Number of sites scoring better than the average of aligned sites = 1718 Number in coding regions = 1370 Number in noncoding regions = 348 Number of orfs with sites within 600 bp upstream = 282 Fraction of orfs with sites within 600 bp upstream = 0.0452939 Motif number 2 TTTCTTGTAAAAAATTTTGTAATAAAAAAAG 1 23 0 AAAATTTTGA 0.972611 -278 ATCTCATTAATAAATTTTTAATAAGCTCATA 1 55 0 TAAATTTTTA 0.906565 -246 TTAATGAGATAAACTATTGTAACAATTGCAA 1 76 1 AAACTATTGA 0.955368 -225 AAATATTCAATATATATTGCAATTGTTACAA 1 92 0 TATATATTGA 0.966489 -209 ATTGAAGACTAAAATATTCAATATATATTGC 1 103 0 AAAATATTCA 0.958139 -198 GGACAAGATTTATATATTGAATTTCCATAAT 1 220 1 TATATATTGA 0.966489 -81 GAATTTCCATAATATATTTTAACAATTTAAA 1 238 1 AATATATTTA 0.922952 -63 ATTTAATTTTTAAATTTTAAATTGTTAAAAT 1 253 0 TAAATTTTAA 0.846522 -48 TATAGCAAAAAATCTTTTCCATTCACGGTGA 3 16 0 AATCTTTTCA 0.88054 -50 ********* * Masking position 5 Map Score: 9.42473 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 458 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 TTCATTTATGCCTTTTTTTATTACAAAATT 1 12 1 CCTTTTTTTA 0.965717 -289 ATAAAAGACTCATCTTTATAAACAAGCGTT 1 156 0 CATCTTTATA 0.831805 -145 TAAATCTTGTCCTTATTAAAAAAGAAAATA 1 202 0 CCTTATTAAA 0.849664 -99 TATTGAATTTCCATAATATATTTTAACAAT 1 234 1 CCATAATATA 0.803201 -67 AATTCTATCTCCCCCATTTAATTTTTAAAT 1 269 0 CCCCCATTTA 0.89279 -32 TGCCCTTCTTTTAATTCTATCTC 1 288 0 CCTTCTTTTA 0.977922 -13 CTCTATAAACCCTCCTTATGATATGCCTTT 2 15 1 CCTCCTTATG 0.948712 -21 AGGAAAGAACCCTTTATATAGCAAAAAATC 3 33 0 CCTTTATATA 0.965716 -33 ********** Masking position 7 Map Score: 4.73419 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 418 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 ********** No masking Map Score: -4.02005e-14 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 5 ********** No masking Map Score: -4.02005e-14 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 TGTAATAAAAAAAGGCATAAATGAAT 1 7 0 AAAGGCATAA 0.916609 -294 CATATTTCTTAAACGCTTGTTTATAAAGAT 1 145 1 AAACGCTTGT 0.961073 -156 TCAATTTATAAAAGACTCATCTTTATAAAC 1 163 0 AAAGACTCAT 0.929654 -138 AAATCTCTATAAACCCTCCTTATGATATGC 2 11 1 AAACCCTCCT 0.917012 -25 CAAAGGCATATCATAAGGAGG 2 25 0 AAAGGCATAT 0.976846 -11 TTTGCTATATAAAGGGTTCTTTCCTATGGG 3 38 1 AAAGGGTTCT 0.953346 -28 ********** Masking position 3 Map Score: 0.401153 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 184 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: -4.02005e-14 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: -4.02005e-14 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: -4.02005e-14 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