AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_aful_reg_100.orf -o054_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: RAG47711 27 Archaeoglobus_fulgidus RAG47320 27 Archaeoglobus_fulgidus Input sequences: #1 RAG47710 69 Archaeoglobus_fulgidus #2 RAG09686 71 Archaeoglobus_fulgidus #3 RAG48909 68 Archaeoglobus_fulgidus #4 RAG02411 38 Archaeoglobus_fulgidus #5 RAG47340 36 Archaeoglobus_fulgidus #6 RAG02631 207 Archaeoglobus_fulgidus #7 RAG47453 272 Archaeoglobus_fulgidus #8 RAG17481 39 Archaeoglobus_fulgidus #9 RAG46689 78 Archaeoglobus_fulgidus Motif number 1 GGTTACCGTAAAAAATTTTAAGGTATAAGTTAATT 1 38 1 AAATTTTATA 0.956587 -32 TTCTTACCGCAAATGTATTTATGTTTTGGAGATGA 2 20 0 AAATATTATT 0.933324 -52 AAAATTTTCAGAAAGTTTTTAATTTCACCTTCCGA 3 20 0 GAATTTTATT 0.984431 -49 AAAACTTTCTGAAAATTTTAATTTACCTGCTCAGA 3 36 1 GAATTTTATA 0.940079 -33 CAAAAGTTTTTAGCTTGCCGTCATTT 5 2 1 AAATTTTATT 0.988865 -35 CAGCTAAAAGAATTCTTTTCAAATTGATGCCGTTA 6 107 1 AATTTTTATT 0.918592 -101 CAATCAACCGCAATCTTTTAAGCTTTTTCCGTGTC 6 176 0 CAATTTTATT 0.959329 -32 AGTAGCCTTGAAAAATCTTTAGATTGGAGCGGACC 7 109 0 AAATCTTATT 0.974479 -164 CTCAGAAAACTCTTTATTTTGCCTCTTAAC 8 6 1 AAATCTTATT 0.974473 -34 GAAAACCCAGGAAGTTTTTTAACTTTTGTTTAATC 9 18 1 GAATTTTATT 0.984431 -61 GGAGAGGTTTAAATCTTTTGAGATTAAACAAAAGT 9 39 0 AAATTTTATT 0.988864 -40 *** **** * ** Masking position 11 Map Score: 19.4341 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 39 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 TTAAAATTTTCAGAAAGTTTTTAATTTCACCT 3 25 0 CAGAAAGTTT 0.966187 -44 ACTTTCAAAGCTGGCAGATCTTTAATT 6 6 0 CTGGCAGTTT 0.961839 -202 TTTCCCTAGACAGGACGATCTTAGAGAAAGGA 6 59 1 CAGGACGTTT 0.991551 -149 CTGAGCCATCCACGCCGATTTTGGGAATCCAG 7 180 1 CACGCCGTTT 0.948799 -93 TTTGGGAATCCAGGCAGTTTTTAACACTTGCC 7 199 1 CAGGCAGTTT 0.994448 -74 CGCATTGCTGGAGGCAAGTGTTAAAAACTGCC 7 211 0 GAGGCAATTT 0.931105 -62 CTCAGAAAACTCTTTATTTTGCCT 8 3 1 CAGAAAATTT 0.889679 -37 GAGGAAAAGGTTAAGAGGCAAA 8 28 0 GAGGAAAGTT 0.84286 -12 TCTGAAAACCCAGGAAGTTTTTTAACTTTTGT 9 15 1 CAGGAAGTTT 0.993988 -64 AACCTCTCCGCATGACGGGATTGT 9 65 1 CATGACGGTT 0.832272 -14 ******* * ** Masking position 11 Map Score: 11.4274 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 480 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 CACTTCAATTCGGAAGGTGAAAT 3 2 1 ACTCAATCGG 0.870087 -67 AAAACCTAAACTTTCAAAGCTGGCAGATCTTT 6 15 0 CTTCAAGCTG 0.982631 -193 AGAGTGCAGAACATCAACGCTGCCGACACGGA 6 152 1 ACTCAAGCTG 0.982631 -56 GGCCGTCGCTCTATCCATGCTGAGCCACGGGC 7 42 0 CTTCCAGCTG 0.982286 -231 AGAGCGACGGCCTTCTAAGCCGTAGATCGCGG 7 62 1 CCTCTAGCCG 0.972448 -211 CTGCTGAGCAATTGTAAAGCTGCTGAATGGTA 7 143 0 ATGTAAGCTG 0.750716 -130 ATTGCCTGAGCCATCCACGCCGATTTTGGGAA 7 175 1 CCTCCAGCCG 0.992921 -98 ACACTTGCCTCCAGCAATGCGGTCTGATAATC 7 222 1 CCGCAAGCGG 0.994216 -51 ACAATCCCGTCATGCGGAGAGGTTTAA 9 62 0 CCGTCAGCGG 0.970747 -17 ** **** **** Masking position 7 Map Score: 10.6073 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 497 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 GTATTTATGTTTTGGAGATGATGGCAGAGC 2 9 0 TTTGGAGAGT 0.973768 -63 GCACTCAGTTTGTGCAGAGGTTATTAATTCTT 2 50 0 TGTGCAGAGT 0.9833 -22 TAAATTAAAATTTTCAGAAAGTTTTTAATTTC 3 29 0 TTTTCAGAAT 0.839672 -40 GAACCAATTCTGAGCAGGTAAATTAAAAT 3 50 0 TTCTGAGCGT 0.961504 -19 GCTTTACAATTGCTCAGCAGATTGCCTGAGCC 7 155 1 TGCTCAGCGT 0.975378 -118 ACTTCCTGGGTTTTCAGAGGTT 9 1 0 TTTTCAGAGT 0.975832 -78 AATCCCGTCATGCGGAGAGGTTTAAATCTTTT 9 55 0 TGCGGAGAGT 0.981862 -24 ******** * * Masking position 6 Map Score: 4.82271 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 305 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 GCTACCCCCTTTTCCCTTCATTTTGAAT 4 21 0 CTTTTCCCTT 0.984477 -18 AGCTTGCCGTCATTTTTCTTCTGTA 5 22 1 CATTTTTCTT 0.843596 -15 TCTTTTTTTACTTTTCCCTAGACAGGACGA 6 47 1 CTTTTCCCTA 0.977905 -161 TGGTCTGATTCCTTTCTCTAAGATCGTCCT 6 70 0 CCTTTCTCTA 0.941672 -138 ATCTTTTAAGCTTTTTCCGTGTCGGCAGCG 6 169 0 CTTTTTCCGT 0.936497 -39 TGCCTCTTAACCTTTTCCTC 8 30 1 CCTTTTCCTC 0.96232 -10 ********** Masking position 5 Map Score: 2.793 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 340 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 AAGGTTACCGTAAAAAATTTTAAGGTATAA 1 36 1 TAAAAAATTT 0.936125 -34 ATTCTTACCGCAAATGTATTTATGTTTTGG 2 26 0 CAAATGTATT 0.464598 -46 AAGGTGAAATTAAAAACTTTCTGAAAATTT 3 24 1 TAAAAACTTT 0.818502 -45 AGCAGGTAAATTAAAATTTTCAGAAAGTTT 3 37 0 TTAAAATTTT 0.68124 -32 CAAAAGTTTTTAGCTTGCCG 5 1 1 CAAAAGTTTT 0.951084 -36 CCCCACCAGCTAAAAGAATTCTTTTCAAAT 6 101 1 TAAAAGAATT 0.915633 -107 GGAAAAAGCTTAAAAGATTGCGGTTGATTG 6 181 1 TAAAAGATTG 0.87747 -27 CCGCTCCAATCTAAAGATTTTTCAAGGCTA 7 112 1 CTAAAGATTT 0.911842 -161 AAACAAAAGTTAAAAAACTTCCTGGGTTTT 9 19 0 TAAAAAACTT 0.795621 -60 TGTTTAATCTCAAAAGATTTAAACCTCTCC 9 44 1 CAAAAGATTT 0.973823 -35 ********** Masking position 4 Map Score: 5.17446 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 175 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 7 CAATTAGTACCACCGACACTCAAAAAGGTT 1 12 1 CACCGACACT 0.902483 -58 GTTTTTAGCTTGCCGTCATTTTTCTTCTGT 5 16 1 TGCCGTCATT 0.985421 -21 TTCAAATTGATGCCGTTACTAGCACTAAAG 6 124 1 TGCCGTTACT 0.968696 -84 ACATCAACGCTGCCGACACGGAAAAAGCTT 6 162 1 TGCCGACACG 0.988874 -46 CGGCTTAGAAGGCCGTCGCTCTATCCATGC 7 54 0 GGCCGTCGCT 0.970543 -219 ACAATCCCGTCATGCGGAGAGGTT 9 65 0 TCCCGTCATG 0.940879 -14 ********** Masking position 5 Map Score: 2.54061 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 123 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GTTTTGGAGATGATGGCAGAGC 2 3 0 TGATGGCAGA 0.846646 -69 AAAAGTTTTTAGCTTGCCGTCATTTTTCTT 5 12 1 AGCTTGCCGT 0.950064 -25 AAACTTTCAAAGCTGGCAGATCTTTAATT 6 10 0 AGCTGGCAGA 0.978302 -198 GAATTCTTTTAGCTGGTGGGGCTGGTCTGA 6 92 0 AGCTGGTGGG 0.934875 -116 CTAGCACTAAAGAGTGCAGAACATCAACGC 6 142 1 AGAGTGCAGA 0.808144 -66 AAAGCTTAAAAGATTGCGGTTGATTGCTTA 6 185 1 AGATTGCGGT 0.965839 -23 TCTACGGCTTAGAAGGCCGTCGCTCTATCC 7 58 0 AGAAGGCCGT 0.88699 -215 TCTAAGCCGTAGATCGCGGGTTCAAATCCC 7 75 1 AGATCGCGGG 0.963069 -198 ATTGGAGCGGACCCGGCGGGATTTGAACCC 7 92 0 ACCCGGCGGG 0.867475 -181 ********** Masking position 6 Map Score: 3.02415 Number of sites scoring better than the average of aligned sites = 1045 Number in coding regions = 996 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 ACCTCTGCACAAACTGAGTGC 2 61 1 AAACTGAGTG 0.915113 -11 GTGAAATTAAAAACTTTCTGAAAATTTTAA 3 27 1 AAACTTTCTG 0.896187 -42 TGAAAATTTTAATTTACCTGCTCAGAATTG 3 45 1 AATTTACCTG 0.789716 -24 ATTGCTCAGCAGATTGCCTGAGCCATCCAC 7 163 1 AGATTGCCTG 0.932714 -110 GGATTCCCAAAATCGGCGTGGATGGCTCAG 7 180 0 AATCGGCGTG 0.903175 -93 CAAGTGTTAAAAACTGCCTGGATTCCCAAA 7 199 0 AAACTGCCTG 0.993981 -74 AAAAGTTAAAAAACTTCCTGGGTTTTCAGA 9 15 0 AAACTTCCTG 0.982395 -64 ********** Masking position 1 Map Score: 3.57759 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 307 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 ********** No masking Map Score: 1.12509e-12 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: 1.12509e-12 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: 1.12509e-12 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