AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i044_aful_mthe_300.orf -o044_aful_mthe_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 RTH01594 70 M.thermo #2 RTH00410 159 M.thermo #3 RTH00566 28 M.thermo #4 RTH00282 154 M.thermo Motif number 1 TGTAATTGCATATTCGCTGGAAAAAAATAC 1 26 1 TATTCGCTGG 0.95904 -45 CTGCCATACCCATCAGCAGCGACCTTCGAT 2 16 1 CATCAGCAGC 0.984323 -144 AGAGTGGGGATATTAGGTGCAATAATTCAC 2 46 0 TATTAGGTGC 0.936667 -114 AATCTGGGAGTAACCGCTTCAACAGAGAAT 2 87 1 TAACCGCTTC 0.829327 -73 ACCTGATTTTAACCGGAGGAAATTTCAG 3 10 1 TAACCGGAGG 0.858011 -19 ATGGTTAATCTATCAGGAAGAGTAAAAAAA 4 12 1 TATCAGGAAG 0.892958 -143 GTGGTTAATCCATCAGGAGCCGGGAAAAGA 4 61 1 CATCAGGAGC 0.979801 -94 AAGATCTTCTCCTCCGCTGGAGGACATAAC 4 87 1 CCTCCGCTGG 0.78441 -68 ********** Masking position 6 Map Score: 5.80612 Number of sites scoring better than the average of aligned sites = 1046 Number in coding regions = 1000 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 CGAACTAATAAGTATTTTTTTCCAGCGAAT 1 37 0 AGTATTTTTT 0.965742 -34 TCGGTAGGGGAAGATTTTTTTACTCTTCCT 4 26 0 AAGATTTTTT 0.977377 -129 AGCGGAGGAGAAGATCTTTTCCCGGCTCCT 4 75 0 AAGATCTTTT 0.954534 -80 CTTCAGACACAGAATTATTTAGGATTATTT 4 126 1 AGAATTATTT 0.951699 -29 AGAATTATTTAGGATTATTTTAGTGATAA 4 136 1 AGGATTATTT 0.987423 -19 ********** Masking position 5 Map Score: 4.6526 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 37 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 GCAATTACATTATAATAACCAGAA 1 5 0 TATAATAACC 0.945836 -66 AGTAAAATCTGGGAGTAACCGCTTCAACAG 2 82 1 GGGAGTAACC 0.984406 -78 ACCTGATTTTAACCGGAGGAAATT 3 5 1 GATTTTAACC 0.923783 -24 CTCTTCCTGATAGATTAACCATC 4 4 0 TAGATTAACC 0.990128 -151 CGGCTCCTGATGGATTAACCACGATCCTCG 4 53 0 TGGATTAACC 0.990805 -102 ********** Masking position 6 Map Score: 4.53805 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 39 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 CTTATTAGTTCGGTATGACATAAATA 1 55 1 CGGTATGACA 0.991212 -16 CGCTGCTGATGGGTATGGCAGTTATA 2 7 0 GGGTATGGCA 0.971902 -153 CTGATTTTAACCGGAGGAAATTTCAG 3 13 1 CCGGAGGAAA 0.962642 -16 CCACGATCCTCGGTAGGGGAAGATTTTTTT 4 35 0 CGGTAGGGGA 0.990327 -120 TTCTCCTCCGCTGGAGGACATAACTTTATA 4 93 1 CTGGAGGACA 0.98573 -62 ********** Masking position 5 Map Score: 2.47945 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 215 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 ATTAGGTGCAATAATTCACATCGAAGGTCG 2 35 0 ATAATTCACA 0.929319 -125 CTCCCAGATTTTACTTCAGAAAGAGTGGGG 2 67 0 TTACTTCAGA 0.981988 -93 TGGATATATATGGATTCAGAGTGCGTGTGG 2 122 0 TGGATTCAGA 0.969678 -38 TAACTTTATAATGCTTCAGACACAGAATTA 4 113 1 ATGCTTCAGA 0.988281 -42 ********** Masking position 5 Map Score: 0.601362 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 80 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 CATATTCGCTGGAAAAAAATACTTATTAGT 1 34 1 GGAAAAAAAT 0.921039 -37 TAGTTCGGTATGACATAAATA 1 60 1 TGACATAAAT 0.887579 -11 AAATTTCCCTGGATATATATGGATTCAGAG 2 131 0 GGATATATAT 0.948308 -29 ATATATCCAGGGAAATTTATAGTTGGG 2 143 1 GGAAATTTAT 0.960715 -17 TTTAACCGGAGGAAATTTCAG 3 18 1 GGAAATTTCA 0.725947 -11 CTCCGCTGGAGGACATAACTTTATAATGCT 4 98 1 GGACATAACT 0.976799 -57 ********** Masking position 5 Map Score: 1.89295 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 79 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 ********** No masking Map Score: 7.34864e-14 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: 7.34864e-14 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 9 ********** No masking Map Score: 7.34864e-14 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