AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i178_aful_mthe_100.orf -o178_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 RTH00859 82 M.thermo #2 RTH01873 93 M.thermo #3 RTH02110 300 M.thermo #4 RTH01896 16 M.thermo #5 RTH01921 200 M.thermo Motif number 1 TTTTAAAATATTTCAAGTAAAACTTAAAAAAGGAGG 1 35 0 TTTAAAACTA 0.980472 -48 CTTGAAATATTTTAAAATAAACCTGAAAAAGGTGAG 1 54 1 TTTAAAACTA 0.980471 -29 TTAACGGATCTTTCAACAACATCTGATCTTCTGGAT 3 108 1 TTTAACACTA 0.96085 -193 TTATTTTTTCTTTTGAAAAAACTTAAATATCACATT 5 23 1 TTTAAAATTA 0.983837 -178 ATAAATTTTATTTAAATTAAAGTTAATGTGATATTT 5 47 0 TTTAAAATTA 0.982681 -154 ATAATAATTCATTCAAATAAATTTTATTTAAATTAA 5 63 0 ATTAAAATTA 0.905625 -138 ACGCCAATTTTTATTACTACATTTTTTATTACTGAG 5 111 0 TTAAACATTT 0.711026 -90 TTTGTGATAATTAGTATATAAATTAAATTATTACAG 5 160 0 TTAATAATTA 0.830464 -41 TATATACTAATTATCACAAAACTTGAAGGTGGAAG 5 176 1 TTAAAAATTA 0.969634 -25 *** * *** ** * Masking position 6 Map Score: 7.70925 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 45 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 CAAGATTTATATACCTCCTTTTTTAAGTTTTAC 1 22 1 ACCTCCTTTT 0.979529 -61 AAGCTCACCTTTTTCAGGTTTATT 1 69 0 ATCACCTTTT 0.98137 -14 GGACTAGCCCACTTCAGCTGTTTTTTTTTCTAA 2 45 0 ATCAGCTTTT 0.97004 -49 TCTTTCAACAACATCTGATCTTCTGGATTCTTA 3 116 1 ATCTGATTTC 0.920914 -185 TTTCATGGATATCCCTGATTTTCGCGTCGGGTA 3 151 1 ACCTGATTTC 0.868317 -150 TCGACTCATAAATTCTCCAATTCTATCATATGA 3 199 1 ATCTCCATTC 0.968074 -102 AAAACTCTGGACCTCTCCAGTCTCCTCACTGAA 3 243 1 ATCTCCATCT 0.891503 -58 ATCATATCACCTCTTT 4 1 0 ATCACCTTTT 0.98137 -16 * ****** *** Masking position 1 Map Score: 4.43051 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 431 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TATTTCAAGTAAAACTTAAAAAAGGAGGTA 1 33 0 AAAACTTAAA 0.947928 -50 ATTTTAAAATAAACCTGAAAAAGGTGAGCT 1 62 1 AAACCTGAAA 0.847867 -21 AGGCAGAAGCCTCACATAAAATAGAGTGAA 3 27 1 CTCACATAAA 0.687733 -274 AATCAGGGATATCCATGAAAGATAAGAATC 3 141 0 ATCCATGAAA 0.712443 -160 CTCCAGTCTCCTCACTGAAATGATTCAGAT 3 257 1 CTCACTGAAA 0.917649 -44 TTCTTTTGAAAAAACTTAAATATCACATTA 5 30 1 AAAACTTAAA 0.947928 -171 TAAATTTTATTTAAATTAAAGTTAATGTGA 5 52 0 TTAAATTAAA 0.700169 -149 TTACAGTTCCCTAAATTAAACGCCAATTTT 5 136 0 CTAAATTAAA 0.903584 -65 TAATTAGTATATAAATTAAATTATTACAGT 5 159 0 ATAAATTAAA 0.919091 -42 TAATTATCACAAAACTTGAAGGTGGAAG 5 183 1 AAAACTTGAA 0.791511 -18 ********** Masking position 9 Map Score: 4.50899 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 115 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 ACGTTGCATAATCCCATTAAATGGCCTGTT 3 59 0 ATCCCATTAA 0.961599 -242 AGTTTTAGAGATCTCAGTCATATGATAGAA 3 219 0 ATCTCAGTCA 0.982585 -82 AATCTGAATCATTTCAGTGAGGAGACTGGA 3 258 0 ATTTCAGTGA 0.915338 -43 AAACTTAAATATCACATTAACTTTAATTTA 5 41 1 ATCACATTAA 0.94412 -160 CTGGATCCGGATCTCAGTAATAAAAAATGT 5 99 1 ATCTCAGTAA 0.989711 -102 ********** Masking position 6 Map Score: 2.63926 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 35 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 CTTCTGCCTGTGAATTCTTCGAGCC 3 6 0 TGAATTCTTC 0.967074 -295 GCATCACTCTAGGATTCTTAACGGATCTTT 3 91 1 AGGATTCTTA 0.955343 -210 TCTGATCTTCTGGATTCTTATCTTTCATGG 3 129 1 TGGATTCTTA 0.985991 -172 TTTATTTGAATGAATTATTATCTGGATCCG 5 78 1 TGAATTATTA 0.966589 -123 GTATATAAATTAAATTATTACAGTTCCCTA 5 153 0 TAAATTATTA 0.847091 -48 ********** Masking position 5 Map Score: 2.46635 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 36 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 GTTTTTTCAAAAGAAAAAATAATTGGGGAA 5 15 0 AAGAAAAAAT 0.943949 -186 CTTTAATTTAAATAAAATTTATTTGAATGA 5 61 1 AATAAAATTT 0.919052 -140 GGATCTCAGTAATAAAAAATGTAGTAATAA 5 107 1 AATAAAAAAT 0.966291 -94 AAAATGTAGTAATAAAAATTGGCGTTTAAT 5 122 1 AATAAAAATT 0.965603 -79 ********** Masking position 5 Map Score: 1.35892 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 29 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 AGCTGTTTTTTTTTCTAATTCCGTGGACAC 2 33 0 TTTTCTAATT 0.875156 -61 TTTCATGGATATCCCTGATTTTCGCGTCGG 3 151 1 ATCCCTGATT 0.918602 -150 GACTCATAAATTCTCCAATTCTATCATATG 3 201 1 TTCTCCAATT 0.975304 -100 CCCCTTCCCCAATTATTTTTTCTT 5 5 1 TTCCCCAATT 0.988887 -196 ATTATTACAGTTCCCTAAATTAAACGCCAA 5 140 0 TTCCCTAAAT 0.961615 -61 ********** Masking position 8 Map Score: 1.57783 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 95 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AAAGAGGCATCCCTCCTGCGCTGTG 2 4 1 GGGCATCCTC 0.557239 -90 TATTTTATGTGAGGCTTCTGCCTGTGAATTCT 3 18 0 GGGCTTCGCC 0.951023 -283 TAAATGGCCTGTTGGTTCACTCTATTTTATGT 3 40 0 GTGGTTCCTC 0.98675 -261 TTATGCAACGTGGGCATCACTCTAGGATTCTT 3 78 1 TGGCATCCTC 0.985987 -223 TTTATGAGTCGATCCTTCGCTCAGGAGTACCC 3 179 0 GTCCTTCCTC 0.969734 -122 TCTCTAAAACTCTGGACCTCTCCAGTCTCCTC 3 238 1 TTGGACCCTC 0.905685 -63 * ****** *** Masking position 8 Map Score: 0.980816 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 271 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ********** No masking Map Score: 8.47978e-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 10 ********** No masking Map Score: 8.47978e-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 11 ********** No masking Map Score: 8.47978e-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