AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -inagC_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 CT016 208 hypothetical protein #2 CT017 185 hypothetical protein #3 mrsA 245 Phosphoglucomutase Motif number 1 AAAGACATGTTTTAATTTTTCTGGATATGA 1 65 0 TTTAATTTTT 0.909777 -144 ACAGTCGCAGTTGACTTTTTCCTTTAAGTC 2 54 1 TTGACTTTTT 0.981563 -132 CGTGCGAACGTTGTCTATTTCT 2 174 1 TTGTCTATTT 0.833463 -12 AACTAAATGATTTATTTTTTTTGTTTTT 3 9 0 TTTATTTTTT 0.851155 -237 TAATTATTTTCTTACTTCTTATTTAAAAAG 3 44 1 CTTACTTCTT 0.834297 -202 CAAACGGCCATTCACTTTTTAAATAAGAAG 3 58 0 TTCACTTTTT 0.973368 -188 GAATGGCCGTTTGAATTTTTGTTTGGTTAT 3 75 1 TTGAATTTTT 0.924109 -171 GTATCAATAGCTTACTATTTATAACCAAAC 3 95 0 CTTACTATTT 0.918726 -151 GAGATAAATATTCCCTATTTTTATCAAAAT 3 171 0 TTCCCTATTT 0.835858 -75 ********** Masking position 6 Map Score: 6.47018 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 244 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 ACACAATCAAAGTACTATCTCCCCCTTACACTT 1 31 0 AGACTTTCCC 0.966836 -178 TTGATTGCTAAAAACCCTCTCTCCCGACTTCTC 1 101 0 AAACCTTCTC 0.954433 -108 GAGGGTTTTTAGCAATCAACCTCCGCGTGTGCT 1 115 1 AGAATACCTC 0.965564 -94 TCTGTTTGTCAAAAATGTACCCCTTAACTACAA 1 150 1 AAAATTCCCC 0.957911 -59 CTCCAACAGAAGGACTCACTTTCCTCGGCATTG 1 180 0 AGACTATTTC 0.809467 -29 CCTTTAAGTCAATAATAATTCCCTCTCTAGAGG 2 74 1 AAAATATCCC 0.934307 -112 GCAGCTCTAGAAGACTCATCCTCTAGAGAGGGA 2 93 0 AAACTACCTC 0.990011 -93 CAATTCGCTAAAATCTGAGCCTCCAATGAGGCA 2 129 0 AATCTACCTC 0.942358 -57 TCGCCTTCTTAAGACCTTTCCTCAAACATCAAT 3 129 0 AAACCTCCTC 0.976275 -117 ** *** * **** Masking position 1 Map Score: 6.69166 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 157 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 TCAAAGTACTATCTCCCCCTTACACTTGAGTCAT 1 24 0 ATCTCCCTAA 0.965069 -185 CTCTCTCCCGACTTCTCTCTAACAAAGACATGTT 1 84 0 ACTTCTCTAA 0.976223 -125 TTTGTCAAAAATGTACCCCTTAACTACAATGCCG 1 154 1 ATGTCCCTAC 0.894749 -55 ACTGTTCGATCCTTTACTCTGAAAACGCCAGTCT 2 25 0 CCTTCTCTAA 0.984877 -161 CTTCTTAAGACCTTTCCTCAAACATCAATCTGGG 3 124 0 CCTTCTCAAA 0.959743 -122 AATAGGGAATATTTATCTCTGAAAATCAAGGATC 3 182 1 ATTTCTCTAA 0.976683 -64 TAAGAATATCCTTTGGCTCAAAACTAACTGATCC 3 211 0 CTTTCTCAAC 0.932301 -35 TGCTCTATCCCTAAGAATATCCTTTG 3 230 0 CTCTCCCTAA 0.977689 -16 **** **** * * Masking position 12 Map Score: 4.68554 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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 TTCTAGAGCTGCGAATGCCTCATTGGAGGC 2 114 1 GCGAATGCCT 0.984758 -72 TCAGATTTTAGCGAATTGCAGGAGTTTTTG 2 144 1 GCGAATTGCA 0.994792 -42 TATTTAAAAAGTGAATGGCCGTTTGAATTT 3 63 1 GTGAATGGCC 0.984758 -183 TCTTAAGAAGGCGAATTGCAAAGATTTTGA 3 148 1 GCGAATTGCA 0.994792 -98 ********** Masking position 5 Map Score: 3.10794 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 5 CTCAAGTGTAAGGGGGAGATAGTACTTTGA 1 28 1 AGGGGGAGAT 0.976873 -181 TGTCTTTGTTAGAGAGAAGTCGGGAGAGAG 1 88 1 AGAGAGAAGT 0.824517 -121 AGAGAAGTCGGGAGAGAGGGTTTTTAGCAA 1 100 1 GGAGAGAGGG 0.879047 -109 TAGCACACGCGGAGGTTGATTGCTAAAAAC 1 119 0 GGAGGTTGAT 0.936932 -90 ATTGTAGTTAAGGGGTACATTTTTGACAAA 1 154 0 AGGGGTACAT 0.86315 -55 TCCTTCTGTTGGAGGTTGTT 1 199 1 GGAGGTTGTT 0.844684 -10 CATCCTCTAGAGAGGGAATTATTATTGACT 2 80 0 AGAGGGAATT 0.876814 -106 TTCCCTCTCTAGAGGATGAGTCTTCTAGAG 2 92 1 AGAGGATGAG 0.785638 -94 CTTGATTTTCAGAGATAAATATTCCCTATT 3 182 0 AGAGATAAAT 0.865679 -64 GGATATTCTTAGGGATAGAGCA 3 234 1 AGGGATAGAG 0.908833 -12 ********** Masking position 4 Map Score: 3.20507 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 615 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 GAGTCATTTAGGAATTTGTA 1 1 0 GGAATTTGTA 0.97614 -208 AGTGTAAGGGGGAGATAGTACTTTGATTGT 1 32 1 GGAGATAGTA 0.817687 -177 CTCTAGAGAGGGAATTATTATTGACTTAAA 2 76 0 GGAATTATTA 0.963568 -110 GCGAATTGCAGGAGTTTTTGCGTGCGAACG 2 154 1 GGAGTTTTTG 0.971362 -32 AATGGCCGTTTGAATTTTTGTTTGGTTATA 3 76 1 TGAATTTTTG 0.863424 -170 ATAAAAATAGGGAATATTTATCTCTGAAAA 3 177 1 GGAATATTTA 0.923912 -69 ********** Masking position 3 Map Score: 2.03044 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 76 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 7 ********** No masking Map Score: -1.11255e-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: -1.11255e-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 9 ********** No masking Map Score: -1.11255e-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