AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i314_aful_mthe_100.orf -o314_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 RAG50267 46 Archaeoglobus_fulgidus #2 RAG23554 37 Archaeoglobus_fulgidus #3 RAG23596 126 Archaeoglobus_fulgidus #4 RAG49167 48 Archaeoglobus_fulgidus #5 RTH01966 139 M.thermo #6 RTH00914 96 M.thermo #7 RTH00954 31 M.thermo #8 RTH00250 30 M.thermo #9 RTH00057 21 M.thermo #10 RTH01659 205 M.thermo Motif number 1 CCTGAAAAGGTTTTAAAGCTGACGACAATT 3 18 0 TTTTAAAGCT 0.703931 -109 ATCGTGAAGAAGTTATAGATAATGTTGTTT 3 65 0 AGTTATAGAT 0.915627 -62 TACTTTAGTTAGTTATTTATTACACTTTTC 4 17 1 AGTTATTTAT 0.60895 -32 AACACTAAAATCTTAAATACATTGCTGGTG 5 50 0 TCTTAAATAC 0.708394 -90 AAGATTTTAGTGTTCAATATTGTTAGGACC 5 66 1 TGTTCAATAT 0.796536 -74 GAAGGGAGATAGTTATAGCCGTGATAAC 6 9 0 AGTTATAGCC 0.881709 -88 AACTGTGCTCTGTTATATATCTGAGACATG 6 64 0 TGTTATATAT 0.93072 -33 ATAAGGGAGTATTTAAATCTTGACATGGTG 10 58 0 ATTTAAATCT 0.74269 -148 CATGATTTAGAGTTACATACACCGCCAGTA 10 107 0 AGTTACATAC 0.832856 -99 ATGGTTAACCAGTTAAATATGAATTTTTTG 10 134 1 AGTTAAATAT 0.95795 -72 TTTGAATTTATGTTAAATCCAGCTGTTTTT 10 160 1 TGTTAAATCC 0.939149 -46 GTTTTTACGGTGTTAAAGATTAAGGTGATA 10 184 1 TGTTAAAGAT 0.949393 -22 ********** Masking position 4 Map Score: 8.38431 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 151 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 ATGAAGGCATCAGAAAAAGTTGATTTGAAT 1 25 0 CAGAAAAAGT 0.934666 -22 ATTTGACATGCTGAGGTGGTGGGGAAC 2 21 1 CTGAGGTGGT 0.939204 -17 AAATTCTCACCTGAAAAGGTTTTAAAGCTG 3 27 0 CTGAAAAGGT 0.961172 -100 TCTCGCTATCGTGAAGAAGTTATAGATAAT 3 72 0 GTGAAGAAGT 0.947694 -55 TCACGATAGCGAGAAAAAGTTAATATTCTT 3 88 1 GAGAAAAAGT 0.949471 -39 TGTTCATTGTGGGAGATGGTTAA 5 4 0 GGGAGATGGT 0.970195 -136 TATTCATGAAGGGAGATAGTTATAGCCGTG 6 16 0 GGGAGATAGT 0.964229 -81 ********** Masking position 4 Map Score: 4.57476 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 563 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TTTTTTGATTCAAATCAACTTTTTCTGATGCCT 1 18 1 CAAATAATTT 0.970733 -29 CTCAGCATGTCAAATAAAGGTTTCG 2 3 0 CAAATAATTT 0.970703 -35 ACTCTGAAAGAATATTAACTTTTTCTCGCTATC 3 92 0 AATATAATTT 0.943488 -35 ATATCTGAGACATGTAATAATTTTTATCTATAT 6 45 0 CATGTATTTT 0.914255 -52 CCCAAACCACCATGTCAAGATTTAAATACTCCC 10 51 1 CATGTAATTT 0.980903 -155 TAACCAGTTAAATATGAATTTTTTGAATTTATG 10 139 1 AATATAATTT 0.944107 -67 TATATCACCTTAATCTTTAACACCGTAA 10 188 0 CACCTAATTT 0.926303 -18 ***** ** *** Masking position 7 Map Score: 3.01697 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 42 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 AAATATTACTCAAGATGTTCATTGTGGGAGAT 5 17 0 CAAGTGTCAT 0.969447 -123 GACTGAACTGGAGTCTGGTCCTAACAATATTG 5 80 0 GAGTTGTCCT 0.941145 -60 ATTATAACTTGAGGCTGATCCTGACTGAACTG 5 102 0 GAGGTGTCCT 0.970611 -38 TAATTTTTATCTATATATTCATGAAGGGAGAT 6 29 0 CTATTATCAT 0.845129 -68 CCCGCATAACTGGCTGTTCATATTCATGACC 10 10 1 CTGGTGTCAT 0.993403 -196 GTTTGGGGTGCTGTGTGGTCATGAATATGAAC 10 26 0 CTGTTGTCAT 0.986541 -180 TCATATTTAACTGGTTAACCATGATTTAGAGT 10 124 0 CTGGTACCAT 0.9095 -82 **** ** **** Masking position 6 Map Score: 2.83126 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 174 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 CATGCTGAGGTGGTGGGGAAC 2 27 1 TGGTGGGGAA 0.987049 -11 TCATTGTGGGAGATGGTTAA 5 1 0 AGATGGTTAA 0.857231 -139 TTAAATACATTGCTGGTGAAAATATTACTC 5 38 0 TGCTGGTGAA 0.963111 -102 AAATCTAGGAAGGTGGGTTAATC 8 18 1 AGGTGGGTTA 0.962932 -13 AATCTTGACATGGTGGTTTGGGGTGCTGTG 10 43 0 TGGTGGTTTG 0.955311 -163 TATTCCATACTGGCGGTGTATGTAACTCTA 10 100 1 TGGCGGTGTA 0.971109 -106 ********** Masking position 5 Map Score: 1.95026 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 295 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TGAACTTCAAAAACTCTGAAAGAATATTAAC 3 106 0 CTAAACTGAA 0.885248 -21 TAATAAATAACTAACTAAAGTAAGCTCG 4 2 0 CTTAAGTGTC 0.984371 -47 GGCAAAACCTCGGAAAAGTGTAATAAATAACTAAC 4 24 0 CTAAAGTATA 0.864658 -25 GAGGCTGATCCTGACTGAACTGGAGTCTGGTCCTAAC 5 87 0 CTTAACTATC 0.986352 -53 TAACGGTTTTCTATTATAACTTGAGGCTGATCCTGAC 5 109 0 CTAAACTAGC 0.953038 -31 GTACTCCTCTTTTAACTGTGCTCTGTTATATAT 6 74 0 CTTAACTGTC 0.993345 -23 ACAATCTCGGTTAACTCAGGTCACTGGAGAG 7 10 0 CTTAACTGTC 0.993345 -22 ** * **** * ** Masking position 9 Map Score: 2.26761 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 62 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 ********** No masking Map Score: -1.51102e-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 8 ********** No masking Map Score: -1.51102e-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 9 ********** No masking Map Score: -1.51102e-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