AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_aful_mthe_100.orf -o164_aful_mthe_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 RAG04733 300 Archaeoglobus_fulgidus #2 RAG12654 142 Archaeoglobus_fulgidus #3 RAG07415 102 Archaeoglobus_fulgidus #4 RTH01812 104 M.thermo #5 RTH00789 78 M.thermo #6 RTH00588 38 M.thermo #7 RTH00837 72 M.thermo #8 RTH01538 300 M.thermo Motif number 1 GTTCAGAACGTTTCATAAGCTGACGATACGT 1 24 1 TTTCTAAGCT 0.916057 -277 GCGTAGAGCCTTTCGGGAGTGTCGATACCGC 2 106 0 TTTCGGAGTG 0.989226 -37 CGAAGCAATTTTTCCTGAGTGTTAATAAGGT 3 11 1 TTTCTGAGTG 0.986172 -92 TTCGTGAGTTTTCCTGGAGTGTAAGGATTGC 3 50 0 TTCCGGAGTG 0.955462 -53 CTATTTAATGTTTCGTGAGTTTTCCTGGAGT 3 61 0 TTTCTGAGTT 0.988567 -42 TGGTTAACGCTTTCCTGAGCTATTTAATGTT 3 80 0 TTTCTGAGCT 0.991097 -23 TACACTTCAATTTACTGACTTTTCAATCCCA 4 62 1 TTTATGACTT 0.838342 -43 GTTCATACTGTTTATGGACCTGTTTTTCTCT 5 31 0 TTTAGGACCT 0.895786 -48 ACTTATTAGTTTTCAGGAGCTCACCAAGTCT 8 52 0 TTTCGGAGCT 0.993071 -249 **** ****** Masking position 8 Map Score: 11.0153 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 345 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 TCATCTCCAAAATCAATCGTTTTATCTGCAA 1 56 1 AATCAATCTT 0.616324 -245 CGCTTCCCAGAAGAAGGTATTGTCCTAAAAT 1 102 1 AAGAAGGTTT 0.720397 -199 CTCTCGTGGCAGGTAATTATTTTTCATTTTG 1 214 1 AGGTAATTTT 0.931819 -87 ACTCCCTATGTGGAAACTATTTTTTTTCCCG 1 245 1 TGGAAACTTT 0.655 -56 AACATTGTTAAGGTAACTATTTAAAAGTTTC 1 275 0 AGGTAACTTT 0.884833 -26 CAATTCCTGCAGGAAATTGTTGCATAATAAA 2 18 1 AGGAAATTTT 0.97086 -125 CGAAGCAATTTTTCCTGAGTGTT 3 3 1 AAGCAATTTT 0.929695 -100 AGGTTGACTGAGGCAATCCTTACACTCCAGG 3 38 1 AGGCAATCTT 0.908587 -65 TAAATAGCTCAGGAAAGCGTTAACCATT 3 85 1 AGGAAAGCTT 0.859042 -18 TAAAAAAATAAATAAATTTTTCTGGGATTTT 4 18 0 AATAAATTTT 0.812131 -87 TTTTTTATCCAAGTAATTTTTACACTTCAAT 4 42 1 AAGTAATTTT 0.894309 -63 GATTGGCATAGGAATCTATTTATTGTATCC 7 10 1 AGGAATCTTT 0.689021 -63 TCTTCCTTTTAATAAATTATTCGTAGGATAC 7 35 0 AATAAATTTT 0.620467 -38 CCTGAAAACTAATAAGTTATTACTATATATT 8 66 1 AATAAGTTTT 0.567823 -235 ******** ** Masking position 5 Map Score: 9.60498 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 342 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 GTCAGCTTATGAAACGTTCTGAACCATCTGGCAG 1 14 0 GAACTTTAAC 0.962976 -287 ATCTCCAAAATCAATCGTTTTATCTGCAACTATT 1 58 1 TAATGTTATC 0.880077 -243 TCCTACTTTATCAACATTTTCATCCAGCCTGCCG 1 139 1 TAACTTTATC 0.983737 -162 AACTTAACATTGTTAAGGTAACTATTT 1 284 0 TAACTTTAAG 0.941775 -17 ATTGCCTCAGTCAACCTTATTAACACTCAGGAAA 3 21 0 TAACTTTAAC 0.983737 -82 GAAAAATTTATTTATTTTTTTATCCAAGTAATTT 4 27 1 TTATTTTATC 0.706015 -78 AACAGGTCCATAAACAGTATGAACCATATAACAG 5 38 1 TAACGTTAAC 0.962976 -41 ACTATATATTTAAATCTTATTATCAAAGTATTTA 8 87 1 TAATTTTATC 0.944652 -214 TAGAGCCTCTTTAACCTTCTGATGTCCCCATATG 8 198 0 TAACTTTATG 0.941775 -103 CCACTTGCTGGAACCTTTATGAACCCTTCAATTA 8 255 1 GACCTTTAAC 0.844338 -46 * *** ** * *** Masking position 8 Map Score: 7.64404 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 81 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 GGCGAGTATGAATGGGGCGTAGAGCCTTTC 2 123 0 TATGGGGCGT 0.995175 -20 CTGCTGTTCTTTGATGGGGCCT 5 1 0 TATGGGGCCT 0.995175 -78 AAGTCTTTTATAGACGGGGCGTGATATTATTA 8 26 0 TACGGGGCGT 0.989352 -275 TATCAAAGTATTTATAGGGCCGGGTGAAAATA 8 107 1 TATAGGGCCG 0.977099 -194 CAGCAAGTGGTCCATGGGGCAGTCTGTGAAAA 8 233 0 TATGGGGCAG 0.987898 -68 * ********* Masking position 4 Map Score: 3.77007 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 12 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 GTCCTAAAATCTGAAATCCTACTTTATCAACATTTT 1 123 1 CTGTCCACTA 0.930241 -178 TTTAATGTTTCGTGAGTTTTCCTGGAGTGTAAGGAT 3 53 0 CGTTTTCCTA 0.823514 -50 ATAAATTTTTCTGGGATTTTCCTAGGT 4 2 0 CTGTTTCCTG 0.977525 -103 TTTCTGCTCTTTCCCTTAAGTTCATGCGT 6 20 0 CTGTTTCCTA 0.987148 -19 AAAAACTCGTCTGAATTTTACATCTATATTTTCACC 8 129 0 CTGTTTCATA 0.946143 -172 CACTGGATAACTGTCTTTCGCCTTCATACTGAAAAA 8 160 0 CTGTTCCCTA 0.991859 -141 CTTTAACCTTCTGATGTCCCCATATGTTCACTGGAT 8 188 0 CTGTCCCATG 0.939257 -113 CTTCTATCCTCCTTTAGCAGAATAAT 8 285 0 CTTTCCCCTA 0.964681 -16 *** *** *** * Masking position 7 Map Score: 3.41568 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 314 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 AGTTTCGGGAAAAAAAATAGTTTCCACATA 1 251 0 AAAAAAATAG 0.923871 -50 ACTCACGAAACATTAAATAGCTCAGGAAAG 3 72 1 CATTAAATAG 0.835351 -31 TTGGATAAAAAAATAAATAAATTTTTCTGG 4 24 0 AAATAAATAA 0.745999 -81 TCGTAGGATACAATAAATAGATTCCTATGC 7 16 0 CAATAAATAG 0.959919 -57 TTATTAAAAGGAAGAAATAGGTGGTGGTTT 7 51 1 GAAGAAATAG 0.916744 -22 AATAAGATTTAAATATATAGTAATAACTTA 8 78 0 AAATATATAG 0.907305 -223 AGGGCCGGGTGAAAATATAGATGTAAAATT 8 122 1 GAAAATATAG 0.850706 -179 ********** Masking position 5 Map Score: 1.6534 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 35 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 GACAATACCTTCTTCTGGGAAGCGTATTTA 1 96 0 TCTTCTGGGA 0.919628 -205 GCAACAATTTCCTGCAGGAATTGTCCTTCC 2 11 0 CCTGCAGGAA 0.968525 -132 TAAGCGAACTCTCGCAGGGAGACGAGCGGT 2 81 1 CTCGCAGGGA 0.967901 -62 ACCTTATTAACACTCAGGAAAAATTGCTTC 3 12 0 CACTCAGGAA 0.862759 -91 ATAAATAAATTTTTCTGGGATTTTCCTAGG 4 12 0 TTTTCTGGGA 0.93244 -93 AACTTATTAGTTTTCAGGAGCTCACCAAGT 8 54 0 TTTTCAGGAG 0.820761 -247 CCATGGACCACTTGCTGGAACCTTTATGAA 8 248 1 CTTGCTGGAA 0.966108 -53 ********** Masking position 5 Map Score: 1.26564 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 454 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 CCAAAGCAAGCCCTTTAATAAATCCAGGTA 1 176 0 CCCTTTAATA 0.97059 -125 GTAATTTTTACACTTCAATTTACTGACTTT 4 54 1 CACTTCAATT 0.933336 -51 TCTGCTCTTTCCCTTAAGTTCATGCGTTCC 6 17 0 CCCTTAAGTT 0.923137 -22 CCTATTTCTTCCTTTTAATAAATTATTCGT 7 42 0 CCTTTTAATA 0.863474 -31 CCTTTATGAACCCTTCAATTATTCTGCTAA 8 268 1 CCCTTCAATT 0.986511 -33 ********** Masking position 5 Map Score: 0.132756 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 54 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ********** No masking Map Score: 1.36667e-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: 1.36667e-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: 1.36667e-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