AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i332_aful_mthe_100.orf -o332_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 RAG49593 34 Archaeoglobus_fulgidus #2 RAG50078 24 Archaeoglobus_fulgidus #3 RAG49761 216 Archaeoglobus_fulgidus #4 RTH01043 246 M.thermo Motif number 1 TACTCTGTCACTCAGCTTCAAAGCTTCCCGGATA 3 49 1 CCGCTTCAAC 0.99419 -168 GTCTATTTCACACTCCATCAGGGCTATTCGTTTT 3 83 1 CCCCATCAGC 0.993063 -134 ATTCTGCTGGCAACGCTTCAAGACTTCGTGGATT 3 125 1 CAGCTTCAAC 0.983 -92 AATCAGGCTCCTGAGCTCCAGCTCCCACCAGGAG 4 53 0 CGGCTCCAGC 0.990464 -194 ACTGATGGATCGCGGCTTCAGGGACCTGAATCAG 4 81 0 CCGCTTCAGA 0.99419 -166 ATCAGTTAATCACCTCTTCAGGGCCCCATGACTG 4 109 1 CCTCTTCAGC 0.996058 -138 CCATGACTGGCTGATTTTCAGGTCGGATTTACTG 4 134 1 CGTTTTCAGC 0.936532 -113 TGAGTCCCGGCCAGCCATCAGTAAATCCGACCTG 4 152 0 CACCATCAGA 0.917112 -95 * * ******* * Masking position 10 Map Score: 9.36803 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 379 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 TATGCCTACCTGAATTTGGATTGGAG 1 19 1 TGAATTTGGA 0.988574 -16 AGCCCGCAGTTGAATTTGGACAG 3 4 0 TGAATTTGGA 0.988574 -213 GAATGATATATAAATGTGGATAAAGTTATC 4 13 0 TAAATGTGGA 0.948197 -234 TTCAGGGACCTGAATCAGGCTCCTGAGCTC 4 69 0 TGAATCAGGC 0.975537 -178 GTATCTATTTTTAATCTGTCCATTTAAAAA 4 194 0 TTAATCTGTC 0.917345 -53 GAAATCCACTTTAATCTGGAGGTTTT 4 231 1 TTAATCTGGA 0.988574 -16 ********** Masking position 5 Map Score: 6.4599 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 92 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 AAAACTTTTATGCCTACCTGAATTTGGATTG 1 10 1 ATGTACCTGA 0.973939 -25 CTCAGCTTCAAAGCTTCCCGGATAGTCTATTT 3 59 1 AAGTCCCGGA 0.990261 -158 TGATTAACTGATGGATCGCGGCTTCAGGGACC 4 89 0 ATGTCGCGGC 0.995983 -158 TCAGGGCCCCATGACTGGCTGATTTTCAGGTC 4 126 1 ATGTGGCTGA 0.974376 -121 AAAGATTTACATGAGTCCCGGCCAGCCATCAG 4 165 0 ATGTCCCGGC 0.997239 -82 *** ******* Masking position 6 Map Score: 2.91705 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 52 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 CTCGGAAAATCTCACGATACTCTGTCACTCAG 3 32 1 CTCAGATATC 0.992325 -185 TATTCGTTTTGTCAAGTTATTCTGCTGGCAAC 3 107 1 GTCAGTTATC 0.981348 -110 CAATATCAAACTCATGAAAAACCTTATTAGCC 3 176 1 CTCAGAAAAC 0.964821 -41 CCTTATTAGCCTCTTGTTATTTATTTGCGT 3 197 1 CTCTGTTATT 0.915189 -20 CTGGCCGGGACTCATGTAAATCTTTTTAAATG 4 172 1 CTCAGTAATC 0.992325 -75 **** **** ** Masking position 9 Map Score: 1.12499 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 113 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GATGGAGTGTGAAATAGACTATCCGGGAAG 3 72 0 GAAATAGACT 0.963241 -145 AATAACTTGACAAAACGAATAGCCCTGATG 3 98 0 CAAAACGAAT 0.961698 -119 AGATATTGCAGAAAACGAATCCACGAAGTC 3 146 0 GAAAACGAAT 0.98536 -71 TACAGGTTATGAAATCCACTTTAATCTGGA 4 221 1 GAAATCCACT 0.974898 -26 ********** Masking position 4 Map Score: 0.11069 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 24 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ********** No masking Map Score: 6.63809e-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 7 ********** No masking Map Score: 6.63809e-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: 6.63809e-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