AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_aful_reg_300.orf -o020_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 RAG48032 19 Archaeoglobus_fulgidus #2 RAG50014 300 Archaeoglobus_fulgidus #3 RAG46888 145 Archaeoglobus_fulgidus Motif number 1 TCACTGACGATATTTAAATTTTTCTTTAAG 2 13 1 TATTTAAATT 0.757055 -288 TTTAAATTTTTCTTTAAGATAAAAACTTAA 2 25 1 TCTTTAAGAT 0.9748 -276 AAGCAAATTAGTTTTAAGTTTTTATCTTAA 2 38 0 GTTTTAAGTT 0.966604 -263 ACTAATTTGCTTTTTAAGTTTGTAGCTTGA 2 56 1 TTTTTAAGTT 0.972279 -245 TAAGTTTGTAGCTTGAATTTTTCTGTACGT 2 70 1 GCTTGAATTT 0.82472 -231 TTTCTCTCTTTCTTTTAGGTAATATCATTG 2 135 0 TCTTTTAGGT 0.905131 -166 TTCCAGAAGATTTTTAAGGTGGTCAGAAAC 2 239 0 TTTTTAAGGT 0.95899 -62 CGCTTGAAGTTTAGGTTTGTT 3 2 1 GCTTGAAGTT 0.973168 -144 CTGTTGCCTCTCTTTAAAATTCACTTCGTA 3 75 0 TCTTTAAAAT 0.891703 -71 ********** Masking position 4 Map Score: 9.50324 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 225 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 TTTATCTTAAAGAAAAATTTAAATATCGTC 2 18 0 AGAAAAATTT 0.945436 -283 TTCCGACGTACAGAAAAATTCAAGCTACAA 2 75 0 CAGAAAAATT 0.888525 -226 TTCTGTACGTCGGAAAATTTATATTGCAAT 2 90 1 CGGAAAATTT 0.977576 -211 TCTAAGATTGCAAGAAATTTCAGAGTTGGT 2 194 0 CAAGAAATTT 0.881607 -107 ATCTTTCTTCCAGAAGATTTTTAAGGTGGT 2 246 0 CAGAAGATTT 0.986017 -55 ATCTTCTGGAAGAAAGATTGATTGAAAAAA 2 258 1 AGAAAGATTG 0.879493 -43 AAAAAAATGGAAGACGATTTGCCATCACC 2 282 1 AAGACGATTT 0.921497 -19 ACGCACGAGAAAAAAGATTTTATATAACAA 3 27 0 AAAAAGATTT 0.965051 -119 ********** Masking position 7 Map Score: 6.40208 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 291 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 TTTTCTTTAAGATAAAAACTTAAAACTAAT 2 32 1 GATAAAAACT 0.948359 -269 AAAAATTCAAGCTACAAACTTAAAAAGCAA 2 62 0 GCTACAAACT 0.983956 -239 GATGTTACTTGCCAAAAACTCACTTACCAA 2 169 1 GCCAAAAACT 0.991217 -132 ATCTAAGATTGCAAGAAATTTCAGAGTTGG 2 195 0 GCAAGAAATT 0.924612 -106 TTTTAAGGTGGTCAGAAACTGCTGCTGGAC 2 228 0 GTCAGAAACT 0.977748 -73 ********** Masking position 6 Map Score: 2.83726 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 90 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 TTTAAATATCGTCAGTGAGA 2 1 0 GTCAGTGAGA 0.971986 -300 GAATTTTTCTGTACGTCGGAAAATTTATAT 2 84 1 GTACGTCGGA 0.795442 -217 ATCATTGTGAGCAAGTGGCAATATTGCAAT 2 112 0 GCAAGTGGCA 0.962621 -189 TTACCTAAAAGAAAGAGAGAAATCCTGATG 2 143 1 GAAAGAGAGA 0.945979 -158 TGAGTTTTTGGCAAGTAACATCAGGATTTC 2 161 0 GCAAGTAACA 0.953691 -140 TTCAGAGTTGGTAAGTGAGTTTTTGGCAAG 2 176 0 GTAAGTGAGT 0.957321 -125 TTTTAAGGTGGTCAGAAACTGCTGCTGGAC 2 228 0 GTCAGAAACT 0.681338 -73 AAAATCTTCTGGAAGAAAGATTGATTGAAA 2 255 1 GGAAGAAAGA 0.910275 -46 TGATTAGTACGCACGAGAAAAAAGATTTTA 3 35 0 GCACGAGAAA 0.840284 -111 ********** Masking position 5 Map Score: 2.41217 Number of sites scoring better than the average of aligned sites = 867 Number in coding regions = 804 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 GTTTTAAGTTTTTATCTTAAAGAAAAATTT 2 28 0 TTTATCTTAA 0.856646 -273 CGTCGGAAAATTTATATTGCAATATTGCCA 2 97 1 TTTATATTGC 0.97567 -204 GAAAAAAGATTTTATATAACAAACCTAAAC 3 19 0 TTTATATAAC 0.658829 -127 CTTCGTATGCTTTGTATTGATTAGTACGCA 3 52 0 TTTGTATTGA 0.946794 -94 TAGTATAATGTTTATATAGAGGGATTAATA 3 106 1 TTTATATAGA 0.679578 -40 ********** Masking position 5 Map Score: 2.24383 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 26 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ********** No masking Map Score: -8.85746e-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 7 ********** No masking Map Score: -8.85746e-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 8 ********** No masking Map Score: -8.85746e-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