AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__aful_reg_100.orf -o056_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 Input sequences: #1 RAG48429 192 Archaeoglobus_fulgidus #2 RAG21207 31 Archaeoglobus_fulgidus #3 RAG50420 80 Archaeoglobus_fulgidus #4 RAG21288 173 Archaeoglobus_fulgidus #5 RAG22420 300 Archaeoglobus_fulgidus #6 RAG45771 182 Archaeoglobus_fulgidus #7 RAG45588 64 Archaeoglobus_fulgidus #8 RAG35664 297 Archaeoglobus_fulgidus #9 RAG49289 45 Archaeoglobus_fulgidus Motif number 1 GAGCTAAGTAGGGGCGGAATTAAAAAA 2 15 0 GTAGGGGCGG 0.900697 -17 TTGGTTTGAAAGAGGAGGAGTACACAAACA 3 27 0 AGAGGAGGAG 0.885346 -54 GGAGGGAGAGTGAGGGAAGG 4 1 1 GGAGGGAGAG 0.991444 -173 GCAAAAATTAGGAGGGATAGTAGGCTGAAA 4 64 0 GGAGGGATAG 0.919091 -110 ATACCATCATGGTGGGGCAGCAAAAATTAG 4 83 0 GGTGGGGCAG 0.980295 -91 TGCCGGTACGGGTGGTGGAGTTCTTTTTAC 5 72 0 GGTGGTGGAG 0.984851 -229 AGCGCATGCTGGTGGTGGGAGTGATGAAAA 6 92 1 GGTGGTGGGA 0.881386 -91 CTTTTCTAAAGGAGTTAGAGGTGGTTTTAA 6 163 1 GGAGTTAGAG 0.891237 -20 TTCAAATCCGGGAGGCGGGACTTGAATGCT 8 120 0 GGAGGCGGGA 0.945436 -178 CCACTCCGCGGCAGGCGGAGATCCCATGGT 8 156 0 GCAGGCGGAG 0.946533 -142 CGCCTGCCGCGGAGTGGCGGACTACAGTCC 8 169 1 GGAGTGGCGG 0.941155 -129 GCCTTAGCTCAGAGGTAGAGCGTGGGACTG 8 193 0 AGAGGTAGAG 0.891237 -105 ********** Masking position 4 Map Score: 12.4268 Number of sites scoring better than the average of aligned sites = 2667 Number in coding regions = 2548 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 2 CTATTTGAAAAAAGGTTTTTAAATCGGTGGCTTTA 1 24 0 AATTTTTAAC 0.98298 -169 AACCTTTTTTAATTCCGCCCCTACT 2 1 1 ACTTTTTATC 0.928105 -31 AGGAAAGCTGATAACTTTTTTAATCCACCGGCTGT 4 140 1 AATTTTTAAC 0.98298 -34 CGGGTGGTGGAGTTCTTTTTACTTCCTGTTTATGG 5 59 0 ATTTTTTCTC 0.894139 -242 TACAAAGGTAAGTAGTTTTTAAAACTTAGCTTGCA 6 16 1 ATTTTTTAAC 0.96317 -167 TGGGCGAACCAAAACTTTTTAAAGCGCATGCTGGT 6 70 1 AATTTTTAAC 0.98298 -113 TCTTTTCCAGAGAACTTTTTCATCACTCCCACCAC 6 103 0 AATTTTTATA 0.792941 -80 CGTTAAGTTTAAAATTTTTTCATTCATTTAATGAT 7 14 0 AATTTTTATC 0.97984 -51 TTATATCCCTACTCATTTTTTATACTCTAAAATCG 8 80 0 ATTTTTTATC 0.956536 -218 GCTGGTAGGCACAAGATTTTTAAGCAGATTCGCTC 8 240 0 AAATTTTAAC 0.880074 -58 GCCTACCAGCAAAGTTTTTATCACCCCCAATTTTG 8 265 1 AATTTTACAC 0.737979 -33 * * ***** ** * Masking position 1 Map Score: 10.9989 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 78 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 TGAAAAAAGGTTTTTAAATCGGTGGCTTTA 1 24 0 TTTTTAAATC 0.939725 -169 AACCTTTTTTAATTCCGCCCCTACT 2 6 1 TTTTTAATTC 0.922156 -26 GTAAACCCTTATTTTTCAGCCTACTATCCC 4 51 1 ATTTTTCAGC 0.723415 -123 TCCCTCCTAATTTTTGCTGCCCCACCATGA 4 77 1 TTTTTGCTGC 0.731721 -97 AGCTGATAACTTTTTTAATCCACCGGCTGT 4 145 1 TTTTTTAATC 0.939763 -29 GGTGGAGTTCTTTTTACTTCCTGTTTATGG 5 59 0 TTTTTACTTC 0.915073 -242 AACATTTATTTGTTTTAATCACAAAAATCG 5 190 0 TGTTTTAATC 0.694731 -111 AGGTAAGTAGTTTTTAAAACTTAGCTTGCA 6 21 1 TTTTTAAAAC 0.811208 -162 GAACCAAAACTTTTTAAAGCGCATGCTGGT 6 75 1 TTTTTAAAGC 0.927679 -108 TTCCAGAGAACTTTTTCATCACTCCCACCA 6 104 0 CTTTTTCATC 0.83102 -79 TGTAGTACAGCTTTTACTTCTTTTCTAAAG 6 144 1 CTTTTACTTC 0.788774 -39 AGTTTAAAATTTTTTCATTCATTTAATGAT 7 14 0 TTTTTCATTC 0.78472 -51 TCCCTACTCATTTTTTATACTCTAAAATCG 8 80 0 TTTTTTATAC 0.767064 -218 TAGGCACAAGATTTTTAAGCAGATTCGCTC 8 240 0 ATTTTTAAGC 0.741977 -58 ********** Masking position 5 Map Score: 10.633 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 263 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 CTCGGCAACTGCTACAAATCAAATACGTAT 1 99 0 GCTACAAATC 0.967493 -94 ATTAGGCTAAGCTGTAAATCGTTTTCGGTG 1 163 0 GCTGTAAATC 0.946662 -30 CTTTAATTGTCATGTAAACCCTTATTTTTC 4 38 1 CATGTAAACC 0.875969 -136 CGGATGTATTGATGTAAATCCCATAAACAG 5 39 1 GATGTAAATC 0.906795 -262 GGCAATAATAGCTACAAAGCCTATGCTGAA 5 98 1 GCTACAAAGC 0.932001 -203 AACTGGTAATGATGCAAATCCCGTCACGTT 5 158 1 GATGCAAATC 0.978152 -143 AATGAGTAGGGATATAAACCAAAGCATTCA 8 98 1 GATATAAACC 0.9411 -200 ********** Masking position 6 Map Score: 5.85051 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 148 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 TGCTGACATTAGGCTAAGCTGTAAATCGTTT 1 169 0 AGGCAAGCTG 0.981293 -24 AAATTCCGGAAAGGAAAGCTGATAACTTTTT 4 129 1 AAGGAAGCTG 0.964961 -45 ATAGCTACAAAGCCTATGCTGAAGGACATTG 5 105 1 AGCCATGCTG 0.973604 -196 AACTTTTTAAAGCGCATGCTGGTGGTGGGAG 6 82 1 AGCGATGCTG 0.986029 -101 TTAGAAAAGAAGTAAAAGCTGTACTACAATG 6 141 0 AGTAAAGCTG 0.829863 -42 GAATTTGAAGAGGGTTCGCTGAAAGGCGAAA 8 29 0 AGGGTCGCTG 0.957726 -269 ATATATATTTAACGGACGCTGCAACACGGAG 9 24 1 AACGACGCTG 0.967511 -22 **** ****** Masking position 1 Map Score: 4.31119 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 160 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 TTTAAGGCTAAAGCCACCGATTTAAAAACC 1 16 1 AAGCCACCGA 0.992303 -177 ATTGTTATCTAAGGCACCGAAAACGATTTA 1 149 1 AAGGCACCGA 0.985371 -44 TAACTTTTTTAATCCACCGGCTGTTCAGGT 4 151 1 AATCCACCGG 0.974903 -23 GGACAAATAAGAGCAACCGGACTTCTTTC 5 10 0 GAGCAACCGG 0.934226 -291 GAACAATAAGAAAGCATCGGGAAGATTTTG 5 231 0 AAAGCATCGG 0.872783 -70 TTCGCTCAGTAAGCTATCGAACCCGCCTTA 8 217 0 AAGCTATCGA 0.89302 -81 ********** Masking position 6 Map Score: 1.58041 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 107 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ACTTGGATTTTACGTATTCTTGCAGTTCTATT 1 54 0 TCGATTCTTG 0.952708 -139 ACAAATCAAATACGTATTCTTGTTGCAATTAC 1 84 0 TCGATTCTTG 0.952708 -109 AAATCCCTCCAATTTTTGTTTGTGTACT 3 7 1 CCCATTTTTG 0.970411 -74 CTACTATCCCTCCTAATTTTTGCTGCCCCACC 4 71 1 TCTATTTTTG 0.912157 -103 AGCTTTCCTTTCCGGAATTTTGACATGCAAAA 4 117 0 TCGAATTTTG 0.928761 -57 TTCTTTTTACTTCCTGTTTATGGGATTTACAT 5 50 0 TCCGTTTATG 0.837983 -251 GAGTTCCTTATAACTGTTTTTGCAATGTCCTT 5 126 0 TACGTTTTTG 0.865964 -175 CCCGTCACGTTTACGATTTTTGTGATTAAAAC 5 177 1 TACATTTTTG 0.929663 -124 GTTTTTATCACCCCCAATTTTGGCTTTAAC 8 278 1 CCCAATTTTG 0.912034 -20 * ** ******* Masking position 8 Map Score: 3.92319 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 132 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 AACCTTTTTTAATTCCGCCCCTACTTAGCTC 2 11 1 ATTCCGCCCC 0.905029 -21 AAAATCTCTTCCCTTGACGGAAA 3 68 0 ATCTCTTCCC 0.960809 -13 ATTAAAGTTTAATACCTTCCCTCACTCTCCC 4 14 0 ATACCTTCCC 0.986741 -160 TAATGATGCAAATCCCGTCACGTTTACGATT 5 164 1 ATCCCGTCAC 0.940892 -137 GTTTTTTGTCAAAATCTTCCCGATGCTTTCT 5 222 1 AAATCTTCCC 0.784398 -79 CAGCAGTGCAATTACCTTGCCTGGGCGAACC 6 49 1 ATACCTTGCC 0.924909 -134 AAACCAAAGCATTCAAGTCCCGCCTCCCGGA 8 113 1 ATCAAGTCCC 0.834544 -185 GGAGTGGCGGACTACAGTCCCACGCTCTACC 8 179 1 ATACAGTCCC 0.964285 -119 * ********* Masking position 1 Map Score: 2.16048 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 396 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 ********** No masking Map Score: -2.76868e-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 10 ********** No masking Map Score: -2.76868e-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: -2.76868e-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