AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__aful_reg_300.orf -o056_aful_300.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 0.872952 -17 TTGGTTTGAAAGAGGAGGAGTACACAAACA 3 27 0 AGAGGAGGAG 0.854007 -54 GGAGGGAGAGTGAGGGAAGG 4 1 1 GGAGGGAGAG 0.988736 -173 GCAAAAATTAGGAGGGATAGTAGGCTGAAA 4 64 0 GGAGGGATAG 0.895891 -110 ATACCATCATGGTGGGGCAGCAAAAATTAG 4 83 0 GGTGGGGCAG 0.974151 -91 TGCCGGTACGGGTGGTGGAGTTCTTTTTAC 5 72 0 GGTGGTGGAG 0.980099 -229 AGCGCATGCTGGTGGTGGGAGTGATGAAAA 6 92 1 GGTGGTGGGA 0.849149 -91 CTTTTCTAAAGGAGTTAGAGGTGGTTTTAA 6 163 1 GGAGTTAGAG 0.861257 -20 TTCAAATCCGGGAGGCGGGACTTGAATGCT 8 120 0 GGAGGCGGGA 0.929208 -178 CCACTCCGCGGCAGGCGGAGATCCCATGGT 8 156 0 GCAGGCGGAG 0.930607 -142 CGCCTGCCGCGGAGTGGCGGACTACAGTCC 8 169 1 GGAGTGGCGG 0.923758 -129 GCCTTAGCTCAGAGGTAGAGCGTGGGACTG 8 193 0 AGAGGTAGAG 0.861257 -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 TAAAGCCACCGATTTAAAAACCTTTTTTCAAATAG 1 24 1 GTTAAAAATT 0.980344 -169 AGTAGGGGCGGAATTAAAAAAGGTT 2 1 0 GATAAAAAGT 0.917681 -31 ACAGCCGGTGGATTAAAAAAGTTATCAGCTTTCCT 4 140 0 GTTAAAAATT 0.980344 -34 CCATAAACAGGAAGTAAAAAGAACTCCACCACCCG 5 59 1 GAGAAAAAAT 0.879431 -242 TGCAAGCTAAGTTTTAAAAACTACTTACCTTTGTA 6 16 0 GTTAAAAAAT 0.957598 -167 ACCAGCATGCGCTTTAAAAAGTTTTGGTTCGCCCA 6 70 0 GTTAAAAATT 0.980344 -113 GTGGTGGGAGTGATGAAAAAGTTCTCTGGAAAAGA 6 103 1 TATAAAAATT 0.767824 -80 ATCATTAAATGAATGAAAAAATTTTAAACTTAACG 7 14 1 GATAAAAATT 0.976729 -51 CGATTTTAGAGTATAAAAAATGAGTAGGGATATAA 8 80 1 GATAAAAAAT 0.950012 -218 GAGCGAATCTGCTTAAAAATCTTGTGCCTACCAGC 8 240 1 GTTAAAATTT 0.86371 -58 CAAAATTGGGGGTGATAAAAACTTTGCTGGTAGGC 8 265 0 GTGTAAAATT 0.708644 -33 * ** ***** * * Masking position 8 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 AAATCCCTCCAATTTTTGTTTGTGTACTCCT 3 11 1 AATTTTGTTT 0.941179 -70 TATCCCTCCTAATTTTTGCTGCCCCACCATG 4 75 1 AATTTTGCTG 0.95859 -99 AAACAAATAAATGTTTTGTTTTTTGTCAAAA 5 205 1 ATTTTTGTTT 0.834895 -96 ATTATTTTTTAAGTTTTGGTTGGATGGTGTG 5 263 0 AATTTTGGTT 0.972858 -38 GTAGTTTTTAAAACTTAGCTTGCAGCAGTGC 6 27 1 AACTTAGCTT 0.81604 -156 GCGCTTTAAAAAGTTTTGGTTCGCCCAGGCA 6 66 0 AATTTTGGTT 0.972858 -117 CGGGACTTGAATGCTTTGGTTTATATCCCTA 8 104 0 ATCTTTGGTT 0.903595 -194 GGGGTGATAAAAACTTTGCTGGTAGGCACAA 8 261 0 AACTTTGCTG 0.950152 -37 TATCACCCCCAATTTTGGCTTTAAC 8 283 1 AATTTGGCTT 0.926349 -15 ** ******** Masking position 6 Map Score: 7.02863 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 73 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 GAAAACGATTTACAGCTTAGCCTAATGTCAGCAG 1 167 1 TCAGCTGCTA 0.959919 -26 ACCCTTATTTTTCAGCCTACTATCCCTCCTAATT 4 55 1 TCAGCTCATC 0.931421 -119 TAAAAAAGTTATCAGCTTTCCTTTCCGGAATTTT 4 128 0 ACAGCTCTTT 0.968885 -46 TGCAATGTCCTTCAGCATAGGCTTTGTAGCTATT 5 104 0 TCAGCTGCTT 0.98216 -197 CACTCCCACCACCAGCATGCGCTTTAAAAAGTTT 6 81 0 ACAGCTCCTT 0.98388 -102 TTCATTGTAGTACAGCTTTTACTTCTTTTCTAAA 6 139 1 TCAGCTTCTT 0.960682 -44 TCTCCTCAAGCAGCCTCTTTTCGCCTTTCAGC 8 9 1 ACAGCTTTTC 0.892775 -289 CTTTTCGCCTTTCAGCGAACCCTCTTCAAATTCC 8 27 1 TCAGCACCTC 0.960637 -271 TCTTGTGCCTACCAGCAAAGTTTTTATCACCCCC 8 259 1 ACAGCAGTTT 0.841781 -39 GCTCCGTGTTGCAGCGTCCGTTAAATATATATT 9 23 0 TCAGCTCTTA 0.951998 -23 * **** * * *** Masking position 4 Map Score: 8.58128 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 349 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 AACAAGAATACGTATTTGATTTGTAGCAGT 1 92 1 CGTATTTGAT 0.737369 -101 TAAGTAGGGGCGGAATTAAAAAAGGTT 2 8 0 CGGAATTAAA 0.733174 -24 CCACCATGATGGTATATGCTTTTGCATGTC 4 98 1 GGTATATGCT 0.655746 -76 TCCTGTTTATGGGATTTACATCAATACATC 5 41 0 GGGATTTACA 0.954969 -260 TAAACGTGACGGGATTTGCATCATTACCAG 5 160 0 GGGATTTGCA 0.986881 -141 GCCCAGGCAAGGTAATTGCACTGCTGCAAG 6 45 0 GGTAATTGCA 0.886105 -138 TGAGGTTTGTGGAATTTGAAGAGGGTTCGC 8 41 0 GGAATTTGAA 0.900097 -257 AAAATGAGTAGGGATATAAACCAAAGCATT 8 96 1 GGGATATAAA 0.844911 -202 TCCGGGAGGCGGGACTTGAATGCTTTGGTT 8 114 0 GGGACTTGAA 0.948584 -184 TCCCGCCTCCCGGATTTGAACCGGGGACCA 8 130 1 CGGATTTGAA 0.968571 -168 ********** Masking position 4 Map Score: 6.46431 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 413 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TTTCAAATAGAACTGCAAGAATACGTAAAAT 1 49 1 AACTGCAAAA 0.957317 -144 AAATCCAAGTAATTGCAACAAGAATACGTAT 1 76 1 AATTGCAAAA 0.863543 -117 AATTCTCGGCAACTGCTACAAATCAAATACG 1 102 0 AACTGCTAAA 0.970446 -91 CACTGCTGACATTAGGCTAAG 1 182 0 CACTGCTGCA 0.873412 -11 TACCGGCAATAATAGCTACAAAGCCTATGCT 5 94 1 AATAGCTAAA 0.565906 -207 TGCTGAAGGACATTGCAAAAACAGTTATAAG 5 121 1 CATTGCAAAA 0.936824 -180 AATAATGAAGCACTTCTAAAACC 5 288 1 CACTTCTAAA 0.930076 -13 AAGGTAATTGCACTGCTGCAAGCTAAGTTTT 6 36 0 CACTGCTGAA 0.970661 -147 TTAAACTTAACGCTTCTAAAATAACCATGCT 7 37 1 CGCTTCTAAA 0.851174 -28 ATTTAACGGACGCTGCAACACGGAGC 9 30 1 CGCTGCAAAC 0.824953 -16 ******** ** Masking position 6 Map Score: 5.20939 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 405 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 GGTTTTTAAATCGGTGGCTTTAGCCTTAAA 1 16 0 TCGGTGGCTT 0.991023 -177 TAAATCGTTTTCGGTGCCTTAGATAACAAT 1 149 0 TCGGTGCCTT 0.982961 -44 ACCTGAACAGCCGGTGGATTAAAAAAGTTA 4 151 0 CCGGTGGATT 0.970816 -23 GAAAGAAGTCCGGTTGCTCTTATTTGTCC 5 10 1 CCGGTTGCTC 0.924032 -291 CAAAATCTTCCCGATGCTTTCTTATTGTTC 5 231 1 CCGATGCTTT 0.854547 -70 TAAGGCGGGTTCGATAGCTTACTGAGCGAA 8 217 1 TCGATAGCTT 0.877277 -81 ********** Masking position 5 Map Score: 1.58041 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 103 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 8 AGTTCTATTTGAAAAAAGGTTTTTAAATCG 1 33 0 GAAAAAAGGT 0.968903 -160 GGGGCGGAATTAAAAAAGGTT 2 2 0 TAAAAAAGGT 0.859853 -30 TCCGTCAAGGGAAGAGATTTT 3 70 1 GAAGAGATTT 0.841672 -11 GCCGGTGGATTAAAAAAGTTATCAGCTTTC 4 142 0 TAAAAAAGTT 0.826556 -32 AAGTTCTCTGGAAAAGAGTTCATTGTAGTA 6 121 1 GAAAAGAGTT 0.979402 -62 AACTCCTTTAGAAAAGAAGTAAAAGCTGTA 6 149 0 GAAAAGAAGT 0.888147 -34 TTAAATGAATGAAAAAATTTTAAACTTAAC 7 18 1 GAAAAAATTT 0.846988 -47 GCTGAAAGGCGAAAAGAGGCTGCTTGAGGA 8 13 0 GAAAAGAGGC 0.934652 -285 TGTGGAATTTGAAGAGGGTTCGCTGAAAGG 8 34 0 GAAGAGGGTT 0.844487 -264 ********** Masking position 5 Map Score: 5.44561 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 482 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 AGGAGTACACAAACAAAAATTGGAGGGATT 3 12 0 AAACAAAAAT 0.593004 -69 TCCTCTTTCAAACCAAAAAGCTTATTATTT 3 41 1 AACCAAAAAG 0.840113 -40 CCCTTGACGGAAATAATAAGCTTTTTGGTT 3 51 0 AAATAATAAG 0.835358 -30 ATAGTAGGCTGAAAAATAAGGGTTTACATG 4 48 0 GAAAAATAAG 0.944333 -126 AATACATCCGGACAAATAAGAGCAACCGGA 5 19 0 GACAAATAAG 0.9333 -282 TTGTGATTAAAACAAATAAATGTTTTGTTT 5 196 1 AACAAATAAA 0.687537 -105 ATGGTGTGAAGAACAATAAGAAAGCATCGG 5 241 0 GAACAATAAG 0.943271 -60 ACCAAAACTTAAAAAATAATGAAGCACTTC 5 274 1 AAAAAATAAT 0.824685 -27 TTTAGAGTATAAAAAATGAGTAGGGATATA 8 84 1 AAAAAATGAG 0.82774 -214 ********** Masking position 5 Map Score: 2.22288 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 48 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 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 Motif number 12 ********** 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