AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -inagC_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 CT017 185 hypothetical protein #2 mrsA 245 Phosphoglucomutase Motif number 1 GACTTAAAGGAAAAAGTCAACTGCGACTGTT 1 53 0 AAAAAGTAAC 0.979611 -133 AGAAATAGACAACGTTCGCACGC 1 173 0 AAATAGAAAC 0.950039 -13 AAAAACAAAAAAAATAAATCATTTAGTTT 2 9 1 AAAAAATAAT 0.922101 -237 AGAAGTAAGAAAATAATTATCGAAAACTAAA 2 32 0 AAATAATATC 0.881405 -214 TTCACTTTTTAAATAAGAAGTAAGAAAATAA 2 47 0 AAATAAGAGT 0.895845 -199 CTTCTTATTTAAAAAGTGAATGGCCGTTTGA 2 58 1 AAAAAGTAAT 0.968041 -188 GTTTGGTTATAAATAGTAAGCTATTGATACC 2 95 1 AAATAGTAGC 0.981084 -151 ATTTTGATAAAAATAGGGAATATTTATCTCT 2 171 1 AAATAGGAAT 0.970326 -75 ******* *** Masking position 5 Map Score: 7.45026 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 113 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 TTCTAGAGCTGCGAATGCCTCATTGGAGGC 1 114 1 GCGAATGCCT 0.98924 -72 TCAGATTTTAGCGAATTGCAGGAGTTTTTG 1 144 1 GCGAATTGCA 0.996201 -42 TATTTAAAAAGTGAATGGCCGTTTGAATTT 2 63 1 GTGAATGGCC 0.98924 -183 TCTTAAGAAGGCGAATTGCAAAGATTTTGA 2 148 1 GCGAATTGCA 0.996201 -98 ********** Masking position 5 Map Score: 4.71159 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 9 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 3 GAATAGTCCGAAGAAGACTGGCGTTT 1 6 1 GTCCGAAGAG 0.989888 -180 CGATCCTTTACTCTGAAAACGCCAGTCTTCT 1 22 0 CTCTGAAAAG 0.987135 -164 AAGACTCATCCTCTAGAGAGGGAATTATTAT 1 85 0 CTCTAGAGAG 0.973574 -101 AAATCTGAGCCTCCAATGAGGCATTCGCAGC 1 121 0 CTCCAATGAG 0.953664 -65 TTGAGGAAAGGTCTTAAGAAGGCGAATTGCA 2 137 1 GTCTTAAGAG 0.967309 -109 GAATATTTATCTCTGAAAATCAAGGATCAGT 2 188 1 CTCTGAAAAC 0.946234 -58 ********* * Masking position 9 Map Score: 2.90216 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 225 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 4 ACTGGCGTTTTCAGAGTAAAGGATCGAACAG 1 27 1 TCAGAGAAAG 0.979689 -159 TATTATTGACTTAAAGGAAAAAGTCAACTGC 1 60 0 TTAAAGAAAA 0.915615 -126 CAGATTGATGTTTGAGGAAAGGTCTTAAGAA 2 126 1 TTTGAGAAAG 0.983006 -120 TTGCAAAGATTTTGATAAAAATAGGGAATAT 2 163 1 TTTGATAAAA 0.91378 -83 TCCTTGATTTTCAGAGATAAATATTCCCTAT 2 183 0 TCAGAGTAAA 0.946469 -63 ATCAGTTAGTTTTGAGCCAAAGGATATTCTT 2 213 1 TTTGAGCAAA 0.919926 -33 ****** **** Masking position 5 Map Score: 2.44919 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 162 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 5 TGATTTATTTTTTTTGTTTTT 2 2 0 TTTTTGTTTT 0.976575 -244 AAAATAAATCATTTAGTTTTCGATAATTAT 2 21 1 ATTTAGTTTT 0.976575 -225 GCCGTTTGAATTTTTGTTTGGTTATAAATA 2 80 1 TTTTTGTTTG 0.960714 -166 ATCAAGGATCAGTTAGTTTTGAGCCAAAGG 2 206 1 AGTTAGTTTT 0.960714 -40 ********** Masking position 4 Map Score: 1.53538 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 97 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 GTTTTCAGAGTAAAGGATCGAACAGTCGCAG 1 33 1 TAAGGATCGA 0.965258 -153 ATTATTGACTTAAAGGAAAAAGTCAACTGCG 1 59 0 TAAGGAAAAA 0.888764 -127 ATTCCCTCTCTAGAGGATGAGTCTTCTAGAG 1 91 1 TGAGGATGAG 0.983135 -95 AATGCCTCATTGGAGGCTCAGATTTTAGCGA 1 127 1 TGAGGCTCAG 0.980754 -59 AGATTGATGTTTGAGGAAAGGTCTTAAGAAG 2 127 1 TGAGGAAAGG 0.968575 -119 TCTCTGAAAATCAAGGATCAGTTAGTTTTGA 2 197 1 TAAGGATCAG 0.989997 -49 * ********* Masking position 4 Map Score: 3.81292 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 111 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 CTTTAAGTCAATAATAATTCCCTCTCTAGAGG 1 75 1 ATAAATTCCC 0.986619 -111 TTAGTTTTCGATAATTATTTTCTTACTTCTTA 2 33 1 ATAAATTTTC 0.835048 -213 CAATAGCTTACTATTTATAACCAAACAAAAAT 2 89 0 CTATATAACC 0.939905 -157 AAATAGTAAGCTATTGATACCCAGATTGATGT 2 105 1 CTATATACCC 0.984162 -141 ATTTTCAGAGATAAATATTCCCTATTTTTATC 2 176 0 ATAAATTCCC 0.986611 -70 TGCTCTATCCCTAAGAATATCCTTTGGCTCAA 2 224 0 CTAAATATCC 0.980937 -22 **** ****** Masking position 7 Map Score: 3.76298 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 48 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 CCTCTCTAGAGGATGAGTCTTCTAGAGCTGC 1 95 1 GGAGAGTCTT 0.964162 -91 CTCATTGGAGGCTCAGATTTTAGCGAATTGC 1 132 1 GCTAGATTTT 0.94156 -54 TTAGCGAATTGCAGGAGTTTTTGCGTGCGAA 1 151 1 GCAGAGTTTT 0.979283 -35 GTGAATGGCCGTTTGAATTTTTGTTTGGTTA 2 73 1 GTTGAATTTT 0.802183 -173 TGATGTTTGAGGAAAGGTCTTAAGAAGGCGA 2 131 1 GGAAGGTCTT 0.964162 -115 AAGGCGAATTGCAAAGATTTTGATAAAAATA 2 155 1 GCAAGATTTT 0.967805 -91 *** ******* Masking position 8 Map Score: 0.462838 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 187 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ********** No masking Map Score: 9.48026e-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 10 ********** No masking Map Score: 9.48026e-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 11 ********** No masking Map Score: 9.48026e-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