AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_aful_reg_100.orf -o060_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RAG50337 24 Archaeoglobus_fulgidus Input sequences: #1 RAG01314 41 Archaeoglobus_fulgidus #2 RAG01312 300 Archaeoglobus_fulgidus #3 RAG48606 31 Archaeoglobus_fulgidus #4 RAG28272 24 Archaeoglobus_fulgidus #5 RAG28271 51 Archaeoglobus_fulgidus #6 RAG28270 144 Archaeoglobus_fulgidus #7 RAG47755 30 Archaeoglobus_fulgidus #8 RAG06136 62 Archaeoglobus_fulgidus #9 RAG06282 61 Archaeoglobus_fulgidus #10 RAG06111 71 Archaeoglobus_fulgidus #11 RAG06264 293 Archaeoglobus_fulgidus Motif number 1 CTCAGCAAGATTTATATTTCTTGCTTAGG 1 7 1 AAATTTATTT 0.96399 -35 GCTAAATTCAAATATTTAATCTTTACTGACCTC 2 37 0 AAATTTAATT 0.633879 -264 TTTTGAAAGAAAATTTTAAGATTAATTTGCGGA 5 20 1 AATTTTAATT 0.735928 -32 GATGTAACCGAAAATTTAAAATTTTGCATATAC 6 42 0 AAATTTAATT 0.748068 -103 AAACAACCAGAAGATTTATCTTTAGCCTCGCTT 8 27 1 AAATTTATTT 0.97584 -36 AATAAATGGAAAGATTTATCATTACTTCTTCCT 9 29 1 AAATTTATTT 0.97584 -33 ACCAAAATCAAAGCTTTATTATTCTCAACCAGA 10 41 1 AACTTTATTT 0.897077 -31 ATAAAACATGAGTTTTTATGCTTGCTTTTTTGG 11 171 0 AGTTTTATTT 0.809883 -123 ATAAATAATTACTATTTAAAGTTTTCCTTTCTT 11 225 0 ACATTTAATT 0.891749 -69 ** ****** ** Masking position 7 Map Score: 11.1401 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 12 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 AGCAGAGGTATCAGCACTCCTATCATTGCT 2 77 0 TCAGCACTCC 0.865898 -224 AATCCTATGAGGCTCACGGCCAATTCCGTA 2 200 0 GGCTCACGGC 0.9492 -101 TGTATGGTTGGCATCACGCC 4 15 1 GCATCACGCC 0.987755 -10 AGATTAATTTGCGGAACTCCCAGT 5 38 1 GCGGAACTCC 0.951294 -14 GGCAACCCCGGCCTAACGCCTCATAGCCGG 11 19 0 GCCTAACGCC 0.98822 -275 CGAGCGGTAAGGCGCACGCCTGGAGAGCGT 11 48 1 GGCGCACGCC 0.69192 -246 AACCCACGCGGGCGAACGCCCACACGCTCT 11 71 0 GGCGAACGCC 0.690382 -223 ********** Masking position 6 Map Score: 9.37743 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 70 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 TCGTCTCGTTCATCCCAGTCTTGCTTTTTG 2 130 1 CATCCCAGTC 0.957543 -171 GTTACATCATCATTCCCTGCTTTGCATAGG 6 67 1 CATTCCCTGC 0.957543 -78 ATTCAGCCCCGGCTATGAGGCGT 11 4 1 CAGCCCCGGC 0.99725 -290 TACCGCTCGGCAACCCCGGCCTAACGCCTC 11 27 0 CAACCCCGGC 0.99593 -267 CGCCCACACGCTCTCCAGGCGTGCGCCTTA 11 55 0 CTCTCCAGGC 0.949491 -239 GTTCGAATCCCACCCCCGGCGCTGTTGTAT 11 98 1 CACCCCCGGC 0.998504 -196 ********** Masking position 5 Map Score: 8.79392 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 123 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 ACATCGGGGCAAAAAGCAAGACTGGGATGA 2 139 0 AAAAAGCAAG 0.953899 -162 TTAGCCCCTCAAAAAGTAGTACATCAGCCC 2 234 0 AAAAAGTAGT 0.944609 -67 TTTTCTTTCAAAAAAGAAATTA 5 3 0 AAAAAGAAAT 0.908825 -49 CCCACTTCTTAAAAAGGAGGTTAAGCGGGA 6 13 0 AAAAAGGAGG 0.875651 -132 CCTCCTTTTTAAGAAGTGGGTATATGCAAA 6 23 1 AAGAAGTGGG 0.729682 -122 TCCATTTATTAAAAATTAATACGAAAAA 9 9 0 AAAAATTAAT 0.682074 -53 AAACTGTAGGAAGAAGTAATGATAAATCTT 9 39 0 AAGAAGTAAT 0.944609 -23 GGAAATTCCACAGAAGTAATTTTCCGGTAA 11 143 0 CAGAAGTAAT 0.762557 -151 GGAATTTCCAAAAAAGCAAGCATAAAAACT 11 164 1 AAAAAGCAAG 0.953899 -130 TAATCAATCAAAAAAGAAAGGAAAACTTTA 11 212 1 AAAAAGAAAG 0.930443 -82 GGAAAACTTTAAATAGTAATTATTTATCGG 11 231 1 AAATAGTAAT 0.775767 -63 ********** Masking position 5 Map Score: 8.71997 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 258 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 TCTTTACTGACCTCATGAGCATTATCATAA 2 21 0 CCTCATGAGC 0.935779 -280 CTCTGCTGCTCCCCATAGCCCTCTTAGAAC 2 100 1 CCCCATAGCC 0.985293 -201 TGGCCGTGAGCCTCATAGGATTCGTGGGGC 2 208 1 CCTCATAGGA 0.918408 -93 TTCATCGTACCCGCTTTAGCCCCTCAAAAA 2 249 0 CCGCTTTAGC 0.939206 -52 CTTCCCGCTTAACCTCCTTTTTAA 6 5 1 CCGCTTAACC 0.974268 -140 CAAAGCTAAACCGCATTGCCTATGCAAAGC 6 85 0 CCGCATTGCC 0.989726 -60 CGGCCTAACGCCTCATAGCCGGGGCTGAAT 11 11 0 CCTCATAGCC 0.991322 -283 ********** Masking position 6 Map Score: 7.01444 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 191 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 GCTATGGGGAGCAGCAGAGGTATCAGCACTCCT 2 86 0 GCGCAGGTAT 0.984948 -215 TAGGATTCGTGGGGCTGATGTACTACTTTTTGA 2 223 1 GGGCTGGTAC 0.993321 -78 AAATAAAATTGAGCTGGAGTATATAAAATGT 3 10 0 TGGCTGGTAT 0.98444 -22 CTTTGATTTTGGTGCAGTCGTTTAGAAAATAAT 10 21 0 GGGCAGGTTT 0.985922 -51 TCCCACCCCCGGCGCTGTTGTATCTTGGCTGTT 11 105 1 GGGCTGGTAT 0.99698 -189 ** **** **** Masking position 11 Map Score: 3.23483 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 27 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 AAGAGGGCTATGGGGAGCAGCAGAGGTATC 2 95 0 TGGGGAGCAG 0.8549 -206 TCATAGGATTCGTGGGGCTGATGTACTACT 2 220 1 CGTGGGGCTG 0.952956 -81 TACTACTTTTTGAGGGGCTAAAGCGGGTAC 2 243 1 TGAGGGGCTA 0.982658 -58 ATTGATTATACGAGGGGTTAAAAACCTTTG 6 122 0 CGAGGGGTTA 0.982659 -23 GGTTGAAGGACAGGGGGCAATTTAAAAAAG 7 11 0 CAGGGGGCAA 0.915916 -20 GCCCCGGCTATGAGGCGTTAGGCCGGGGTT 11 16 1 TGAGGCGTTA 0.835508 -278 CCGGGGTTGCCGAGCGGTAAGGCGCACGCC 11 38 1 CGAGCGGTAA 0.952497 -256 ACCAACAGACCGAGCAGCAATTTCCGCATC 11 270 0 CGAGCAGCAA 0.93331 -24 ********** Masking position 4 Map Score: 3.50945 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 469 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 ATTCCGTAGAACTTTGCGAAACGACACTTC 2 178 0 ACTTTGCGAA 0.862377 -123 TTTTAAGATTAATTTGCGGAACTCCCAGT 5 33 1 AATTTGCGGA 0.980664 -19 CAAAATTTTAAATTTTCGGTTACATCATCA 6 49 1 AATTTTCGGT 0.889976 -96 CACAGAAGTAATTTTCCGGTAAGATTCAAC 11 135 0 ATTTTCCGGT 0.912389 -159 ACTTCTGTGGAATTTCCAAAAAAGCAAGCA 11 156 1 AATTTCCAAA 0.83532 -138 CCGCATCATGAATTTCCCGATAAATAATTA 11 247 0 AATTTCCCGA 0.956987 -47 ACCGAGCAGCAATTTCCGCATCATGAATTT 11 262 0 AATTTCCGCA 0.964984 -32 ********** Masking position 1 Map Score: 1.65856 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 210 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 CTCAGCAAGATTTATATTTC 1 1 1 CTCAGCAAGA 0.94975 -41 ATTTCCTGCCCTAAGCAAGAAATATAAATC 1 19 0 CTAAGCAAGA 0.981018 -23 CATCGGGGCAAAAAGCAAGACTGGGATGAA 2 138 0 AAAAGCAAGA 0.811657 -163 AGAAGTGGGTATATGCAAAATTTTAAATTT 6 34 1 ATATGCAAAA 0.917145 -111 ACCGCATTGCCTATGCAAAGCAGGGAATGA 6 76 0 CTATGCAAAG 0.888352 -69 GTGTTCAGCTATGCACAAACAACCAGAA 8 9 1 CTATGCACAA 0.921493 -54 ********** Masking position 7 Map Score: 0.856392 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 71 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TTTTTCGTATTAATTTTTAATA 9 2 1 TTTTCGATTA 0.967671 -60 CTTTTTTCGAATTATTTTCTAAAC 10 4 1 TTTTCGATTA 0.967671 -68 ACAGAAGTAATTTTCCGGTAAGATTCAACAG 11 133 0 TTTTCCGTAA 0.826997 -161 ACTCATGTTTTATTCGTATAATAATCAATCA 11 191 1 TATTCGATAA 0.913595 -103 GCATCATGAATTTCCCGATAAATAATTACTA 11 244 0 TTTCCCATAA 0.91581 -50 CGAGCAGCAATTTCCGCATCATGAATTTCCC 11 259 0 TTTCCGATCA 0.954775 -35 ****** **** Masking position 3 Map Score: 0.505306 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 29 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ********** No masking Map Score: -9.78117e-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 12 ********** No masking Map Score: -9.78117e-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 13 ********** No masking Map Score: -9.78117e-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