AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i315_mixed29_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pksF 300 pksF #2 pksG 224 pksG Motif number 1 GGACACAGATTTGAGCCTGAAGATCAGTTAGT 1 151 1 TTGAGCCGAG 0.997652 -150 GATCAGTTAGTTGAGCTAGGAGCTGACTCTGT 1 172 1 TTGAGCTGAG 0.985015 -129 GAGCTAGGAGCTGACTCTGTAGACAGAGCTGA 1 184 1 CTGACTCGAG 0.981308 -117 ACCGATGTTTTTCACCCCGGATAGCTCAATGC 1 260 0 TTCACCCGAT 0.986849 -41 ATGGTTTCAGCCGGAATAGAAGCGATG 2 6 1 TTCAGCCGAT 0.98685 -219 CTTAGCTGCATTGACTCCGAAGTCACGGGATC 2 158 0 TTGACTCGAG 0.993083 -67 ******* * ** Masking position 4 Map Score: 6.62198 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 141 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 2 ATATACCTATAAAAATCATTAAAATAATCC 1 36 1 AAAAATCATT 0.860799 -265 AAATCATTAAAATAATCCCTTGAGGAGAGA 1 48 1 AATAATCCCT 0.936247 -253 CTGTTTATCCATAATGCGCTCTCTCCTCAA 1 67 0 ATAATGCGCT 0.730758 -234 TCTTTGAAGTATTAATCACCAATATTTGCG 1 101 1 ATTAATCACC 0.880252 -200 ATTTTTAACGATAAATCCTCTAGCACCATC 1 225 0 ATAAATCCTC 0.884567 -76 ATTTATCGTTAAAAATCCCTCGCATTGAGC 1 239 1 AAAAATCCCT 0.961405 -62 CCGGGGTGAAAAACATCGGTGAATTAGCTG 1 272 1 AAACATCGGT 0.905307 -29 CGCCAAAGACATTCATCGCTTCTATTCCGG 2 21 0 ATTCATCGCT 0.885289 -204 TTAATGAAAGAAAAAGCGGTAGCACTGCCT 2 122 1 AAAAAGCGGT 0.939766 -103 ATAAAGCATCAATAATCGGCTTAGCTGCAT 2 179 0 AATAATCGGC 0.932136 -46 TCTGCTTCAGATAAAGCATCAATAATCGGC 2 189 0 ATAAAGCATC 0.753227 -36 ********** Masking position 1 Map Score: 6.32946 Number of sites scoring better than the average of aligned sites = 2590 Number in coding regions = 2219 Number in noncoding regions = 371 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 3 CTAATTCAGGAAGCACCTCGCAAATATTGG 1 119 0 AAGCACCTCG 0.821549 -182 TCTACAGAGTCAGCTCCTAGCTCAACTAAC 1 177 0 CAGCTCCTAG 0.93455 -124 GTGATAATTTCAGCTCTGTCTACAGAGTCA 1 195 0 CAGCTCTGTC 0.974419 -106 ATAAATCCTCTAGCACCATCGTGATAATTT 1 215 0 TAGCACCATC 0.936306 -86 TCACCCCGGATAGCTCAATGCGAGGGATTT 1 251 0 TAGCTCAATG 0.916346 -50 AAAGCACCTCAGCTAATTCACCGATGTTT 1 282 0 CAGCTAATTC 0.87237 -19 TGTATTTGGCCAGCTCCATGACATCAAGGT 2 60 0 CAGCTCCATG 0.983015 -165 GAAAAAGCGGTAGCACTGCCTTATGAAGAT 2 131 1 TAGCACTGCC 0.884469 -94 GGAGTCAATGCAGCTAAGCCGATTATTGAT 2 172 1 CAGCTAAGCC 0.913305 -53 ********** Masking position 2 Map Score: 5.17969 Number of sites scoring better than the average of aligned sites = 2406 Number in coding regions = 2212 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 4 TCATTAAAATAATCCCTTGAGGAGAGAGCG 1 51 1 AATCCCTTGA 0.984334 -250 TATCGTTAAAAATCCCTCGCATTGAGCTAT 1 242 1 AATCCCTCGC 0.968309 -59 GGCGGAACGGCATACCTTGATGTCATGGAG 2 47 1 CATACCTTGA 0.959081 -178 CAGACACTTAGATACTGCGAGATTTGAAAA 2 88 1 GATACTGCGA 0.905946 -137 GCCTTATGAAGATCCCGTGACTTCGGAGTC 2 148 1 GATCCCGTGA 0.990558 -77 ********** Masking position 3 Map Score: 1.48613 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 124 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 CCATAATGCGCTCTCTCCTCAAGGGATTATTTTA 1 55 0 CTTCCCAAGG 0.760848 -246 ATAATTTCAGCTCTGTCTACAGAGTCAGCTCCTA 1 188 0 CTTGCCAGAG 0.543265 -113 TCAAGGTATGCCGTTCCGCCAAAGACATTCATCG 2 33 0 CCTTCCAAAG 0.749387 -192 TTGGCCAGCTCCATGACATCAAGGTATGCCGTTC 2 51 0 CCTGCCAAGG 0.659769 -174 TATGAAGATCCCGTGACTTCGGAGTCAATGCAGC 2 152 1 CCTGCCGGAG 0.967233 -73 ** ** * ***** Masking position 4 Map Score: 1.20311 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 105 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ********** No masking Map Score: 1.74326e-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 7 ********** No masking Map Score: 1.74326e-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: 1.74326e-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