AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_aful_reg_300.orf -o060_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 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 #12 RAG05969 220 Archaeoglobus_fulgidus Motif number 1 TTTCCTGCCCTAAGCAAGAAATATAAATCT 1 18 0 TAAGCAAGAA 0.945888 -24 ATCGGGGCAAAAAGCAAGACTGGGATGAAC 2 137 0 AAAGCAAGAC 0.83536 -164 TTGAGGGGCTAAAGCGGGTACGATGAAAGT 2 252 1 AAAGCGGGTA 0.909622 -49 AAAAGGAGGTTAAGCGGGAAG 6 2 0 TAAGCGGGAA 0.987526 -143 AATGATGATGTAACCGAAAATTTAAAATTT 6 51 0 TAACCGAAAA 0.869175 -94 TTGCCTATGCAAAGCAGGGAATGATGATGT 6 70 0 AAAGCAGGGA 0.906734 -75 GATGTGATTGTAAGCGAGGCTAAAGATAAA 8 41 0 TAAGCGAGGC 0.832369 -22 CTGTTGAATCTTACCGGAAAATTACTTCTG 11 133 1 TTACCGGAAA 0.665364 -161 AATTTCCAAAAAAGCAAGCATAAAAACTCA 11 166 1 AAAGCAAGCA 0.767 -128 AAAGGCGTTTTTAGCGAGAAATAATCCCCA 12 80 0 TTAGCGAGAA 0.902554 -141 GAAAACTACTTAAGCAAAAAACTACTGTGG 12 127 0 TAAGCAAAAA 0.891942 -94 ATAAGTTTGAAAACCGGAAATCGCTTAAGA 12 155 0 AAACCGGAAA 0.914254 -66 CAAACTTATAAAAGCGGAAAAAGGCTTTTA 12 176 1 AAAGCGGAAA 0.973962 -45 ATTATAAGCCAAAGTGGAAATC 12 209 1 AAAGTGGAAA 0.694835 -12 ********** Masking position 3 Map Score: 11.9874 Number of sites scoring better than the average of aligned sites = 877 Number in coding regions = 807 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 CCTAAGCAAGAAATATAAATCTTGCTGAG 1 7 0 AAATAAACTT 0.984997 -35 CAAGCTTGCTAAATTCAAATATTTAATCTTTAC 2 44 0 AAATAAAATT 0.970355 -257 TTTTGAAAGAAAATTTTAAGATTAATTTGCGGA 5 20 1 AAATTAAATT 0.811722 -32 ATGTAACCGAAAATTTAAAATTTTGCATATACC 6 41 0 AAATAAATTT 0.544372 -104 AAGCGAGGCTAAAGATAAATCTTCTGGTTGTTT 8 27 0 AAAGAAACTT 0.974425 -36 AATTTTTAATAAATGGAAAGATTTATCATTACT 9 22 1 AAATAAAATT 0.971176 -40 CGACTGCACCAAAATCAAAGCTTTATTATTCTC 10 34 1 AAAAAAACTT 0.935087 -38 ATCAAAAAAGAAAGGAAAACTTTAAATAGTAAT 11 218 1 AAAGAAATTT 0.928004 -76 ACATAATCCCAAATAAAAAGCTTTATAAAAACA 12 43 0 AAATAAACTT 0.98583 -178 **** *** *** Masking position 8 Map Score: 10.6639 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 39 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 AGCAATGATAGGAGTGCTGATACCTCTGCT 2 77 1 GGAGTGCTGA 0.848606 -224 TACGGAATTGGCCGTGAGCCTCATAGGATT 2 200 1 GCCGTGAGCC 0.948733 -101 GGCGTGATGCCAACCATACA 4 15 0 GGCGTGATGC 0.986218 -10 ACTGGGAGTTCCGCAAATTAATCT 5 38 0 GGAGTTCCGC 0.944762 -14 CCGGCTATGAGGCGTTAGGCCGGGGTTGCC 11 19 1 GGCGTTAGGC 0.987563 -275 ACGCTCTCCAGGCGTGCGCCTTACCGCTCG 11 48 0 GGCGTGCGCC 0.70872 -246 AGAGCGTGTGGGCGTTCGCCCGCGTGGGTT 11 71 1 GGCGTTCGCC 0.706869 -223 ********** Masking position 5 Map Score: 8.03755 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 4 TCGTCTCGTTCATCCCAGTCTTGCTTTTTG 2 130 1 CATCCCAGTC 0.948991 -171 GTTACATCATCATTCCCTGCTTTGCATAGG 6 67 1 CATTCCCTGC 0.948991 -78 ATTCAGCCCCGGCTATGAGGCGT 11 4 1 CAGCCCCGGC 0.996668 -290 TACCGCTCGGCAACCCCGGCCTAACGCCTC 11 27 0 CAACCCCGGC 0.99507 -267 CGCCCACACGCTCTCCAGGCGTGCGCCTTA 11 55 0 CTCTCCAGGC 0.93942 -239 GTTCGAATCCCACCCCCGGCGCTGTTGTAT 11 98 1 CACCCCCGGC 0.998187 -196 ********** Masking position 5 Map Score: 7.64555 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 5 TAATTTCTTTTTTGAAAGAAAATTTTAA 5 8 1 TTTTTGAAAG 0.974001 -44 ATATACCCACTTCTTAAAAAGGAGGTTAAGC 6 17 0 TTCTTAAAAG 0.819838 -128 CTTTTTTAAATTGCCCCCTGTC 7 2 1 TTTTTAAATT 0.892761 -29 TTTTTCGTATTAATTTTTAAT 9 1 1 TTTTTGTATT 0.698377 -61 ATCTTTCCATTTATTAAAAATTAATACGAAA 9 13 0 TTATTAAAAT 0.65707 -49 CTTTTTTCGAATTATTTTCTAAA 10 3 1 TTTTTGAATT 0.942692 -69 TATGCTTGCTTTTTTGGAAATTCCACAGAAG 11 157 0 TTTTTGAAAT 0.959525 -137 TTTTCCTTTCTTTTTTGATTGATTATTATAC 11 206 0 TTTTTGATTG 0.786886 -88 CGACTGTTTGTTTTTATAAAGCTTTTTATTT 12 35 1 TTTTTTAAAG 0.855425 -186 AAAAACGCCTTTTTTTAAAAGTATAAACTCC 12 98 1 TTTTTAAAAG 0.931737 -123 ***** ***** Masking position 5 Map Score: 5.0616 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 136 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 TCGTTTCGCAAAGTTCTACGGAATTGGCCGTGAGC 2 184 1 AATTACGATT 0.980828 -117 AACCTCAGTAAATTTTAGCGGCATTTATAACTTTC 2 276 0 AATTGCGATT 0.976963 -25 AAATAAAATTGAGCTGGAGTATATAAAATG 3 12 0 AATTGCGAGT 0.985233 -20 GACGTCATCAAAGCTAAACCGCATTGCCTATGCAA 6 88 0 AACTACGATT 0.976975 -57 GCTTTTTTGGAAATTCCACAGAAGTAATTTTCCGG 11 146 0 AATTACGAGT 0.987727 -148 TTAAAAGTATAAACTCCACAGTAGTTTTTTGCTTA 12 112 1 AACTACGAGT 0.985234 -109 ** ** ** * *** Masking position 5 Map Score: 4.08022 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 AAAGTTCTACGGAATTGGCCGTGAGCCTCAT 2 193 1 GAATTGGCCG 0.957533 -108 AATTTTAAGATTAATTTGCGGAACTCCCAGT 5 31 1 TAATTTGCGG 0.961691 -21 TGCAAAATTTTAAATTTTCGGTTACATCATC 6 47 1 TAATTTTCGG 0.941959 -98 CTTTTTTAAATTGCCCCCTGTCCTTCA 7 7 1 TAATTGCCCC 0.90586 -24 TTCCACAGAAGTAATTTTCCGGTAAGATTCA 11 137 0 GAATTTTCCG 0.962606 -157 TTCCGCATCATGAATTTCCCGATAAATAATT 11 248 0 TAATTTCCCG 0.979604 -46 AGACCGAGCAGCAATTTCCGCATCATGAATT 11 263 0 GAATTTCCGC 0.964226 -31 GTTTTCTTAAGCGATTTCCGGTTTTCAAACT 12 151 1 GGATTTCCGG 0.952906 -70 * ********* Masking position 4 Map Score: 5.60782 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 99 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ACTTCTTAAAAAGGAGGTTAAGCGGGAAG 6 10 0 AAGGAGGTTA 0.889848 -135 TTGCATAGGCAATGCGGTTTAGCTTTGATG 6 88 1 AATGCGGTTT 0.796048 -57 GATTTTGGTGCAGTCGTTTAGAAAATAATT 10 20 0 CAGTCGTTTA 0.899323 -52 AATTCCACAGAAGTAATTTTCCGGTAAGAT 11 140 0 AAGTAATTTT 0.641669 -154 ACGAATAAAACATGAGTTTTTATGCTTGCT 11 178 0 CATGAGTTTT 0.836527 -116 CTTTTAAAAAAAGGCGTTTTTAGCGAGAAA 12 89 0 AAGGCGTTTT 0.975885 -132 ATAAACTCCACAGTAGTTTTTTGCTTAAGT 12 120 1 CAGTAGTTTT 0.929711 -101 TTTTTTGCTTAAGTAGTTTTCTTAAGCGAT 12 136 1 AAGTAGTTTT 0.941295 -85 AAAGCGGAAAAAGGCTTTTATATATTATAA 12 186 1 AAGGCTTTTA 0.703792 -35 ********** Masking position 8 Map Score: 3.32597 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 541 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 AGAAGGTACATCGGGGCAAAAAGCAAGACT 2 146 0 TCGGGGCAAA 0.940855 -155 CATAGGATTCGTGGGGCTGATGTACTACTT 2 221 1 GTGGGGCTGA 0.985958 -80 ACTACTTTTTGAGGGGCTAAAGCGGGTACG 2 244 1 GAGGGGCTAA 0.993351 -57 TTGATTATACGAGGGGTTAAAAACCTTTGA 6 121 0 GAGGGGTTAA 0.958528 -24 GTGATTGTAAGCGAGGCTAAAGATAAATCT 8 38 0 GCGAGGCTAA 0.981159 -25 CGCCTCATAGCCGGGGCTGAAT 11 3 0 CCGGGGCTGA 0.987536 -291 ********** Masking position 10 Map Score: 5.54985 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 160 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 10 TCTTTACTGACCTCATGAGCATTATCATAA 2 21 0 CCTCATGAGC 0.915694 -280 CTCTGCTGCTCCCCATAGCCCTCTTAGAAC 2 100 1 CCCCATAGCC 0.97533 -201 TGGCCGTGAGCCTCATAGGATTCGTGGGGC 2 208 1 CCTCATAGGA 0.882655 -93 TTCATCGTACCCGCTTTAGCCCCTCAAAAA 2 249 0 CCGCTTTAGC 0.952007 -52 CTTCCCGCTTAACCTCCTTTTTAA 6 5 1 CCGCTTAACC 0.962727 -140 CAAAGCTAAACCGCATTGCCTATGCAAAGC 6 85 0 CCGCATTGCC 0.987865 -60 CGGCCTAACGCCTCATAGCCGGGGCTGAAT 11 11 0 CCTCATAGCC 0.985381 -283 GATTTCCACTTTGGCTTATAATATA 12 206 0 CCACTTTGGC 0.927393 -15 ********** Masking position 6 Map Score: 7.49755 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 308 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 TGGGGAGCAGCAGAGGTATCAGCACTCCTATCA 2 82 0 CAGATACAGC 0.984506 -219 CGACACTTCCCAGAAGGTACATCGGGGCAAAAA 2 154 0 CAGAGTCATC 0.909865 -147 TTCAACAGCCAAGATACAACAGCGCCGGGGGTG 11 108 0 AAGACACAGC 0.987167 -186 ATTTTCCGGTAAGATTCAACAGCCAAGATACAA 11 122 0 AAGACACAGC 0.987167 -172 CAACACCAACAGACCGAGCAGCAATTTCCGCA 11 272 0 CAGAGACAGC 0.994263 -22 **** ** **** Masking position 4 Map Score: 0.548559 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 65 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 CTCAGCAAGATTTATATTTCTTGC 1 5 1 GCAAGATTTA 0.895051 -37 CCTGCCCTAAGCAAGAAATATAAATCTTGC 1 15 0 GCAAGAAATA 0.986091 -27 CTTGCTTAGGGCAGGAAATAGG 1 30 1 GCAGGAAATA 0.96964 -12 ATAAACTGTAGGAAGAAGTAATGATAAATC 9 41 0 GGAAGAAGTA 0.921943 -21 GGCGTTTTTAGCGAGAAATAATCCCCAAAC 12 77 0 GCGAGAAATA 0.96964 -144 ********** Masking position 6 Map Score: 1.00545 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 26 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 ********** No masking Map Score: -1.19128e-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 14 ********** No masking Map Score: -1.19128e-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 15 ********** No masking Map Score: -1.19128e-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