AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i202_exonuclease_sbcc_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 addB 183 ATP-dependent deoxyribonuclease (subunit B) #2 sbcD 71 exonuclease SbcD homolog #3 yirY 300 similar to DNA exonuclease Motif number 1 GATTATCTCCGCACATCTCTCCCTGCCCAACATAT 1 54 0 GCCTCCCCTG 0.973511 -130 GAGATGTGCGGAGATAATCAGCTTTTTATATGTGA 1 70 1 GAATCGCTTT 0.722695 -114 CTGATCTATTGGTAAAAACGGCCTTTTCACATATA 1 96 0 GGAACGCCTT 0.942323 -88 ATTAGAAGACCCCTCTCTTTTTATCTCTC 1 165 0 GACCCCTCTT 0.829831 -19 TAGAAAACGAGACCCGCTCCGCCTGAAATTCCGGA 2 25 0 GACTCGCCTG 0.975827 -47 ATGCTTTCACCTCTCTTTTATATAGAA 2 55 0 GCACCCTCTT 0.90273 -17 ATCCAAGCATTCTGATCTCTGCCTTCATCCAGCCA 3 15 0 TCCTCGCCTT 0.980125 -286 GAAATCCGTGTCGCGGACCAGCTGTCACTTGAAGA 3 57 1 TCACCGCTGT 0.615186 -244 GTCACTTGAAGAGATTCACAGGCTGCGGAAGGCGC 3 80 1 GACACGGCTG 0.919183 -221 GGCTGCGGAAGGCGCACCCGGGCTTTATCCATATC 3 100 1 GGCCCGGCTT 0.960462 -201 GTTCTGTTCTTCAAAAACCGGCCTGATATGGATAA 3 124 0 TCACCGCCTG 0.979022 -177 TTAACCTCGATCCGTTCCCGGTCTTTGTTCTGTTC 3 150 0 TCCCCGTCTT 0.953928 -151 TCTTCATCCGGCACCGCACCGCCAGTTTGTTTTTC 3 222 0 GCCACGCCAG 0.923842 -79 TGATGCAAGCTCTAAAAACAGCCTCACCATTTCTT 3 253 0 TCAACGCCTC 0.820355 -48 TGTTTTTAGAGCTTGCATCAGGCGTTGAAGAGGAG 3 268 1 GCATCGGCGT 0.894853 -33 ** *** ***** Masking position 9 Map Score: 13.2387 Number of sites scoring better than the average of aligned sites = 3399 Number in coding regions = 3117 Number in noncoding regions = 282 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 AGATTGGTCATTTTCGTCAACATTCGATAA 1 129 1 TTTTCGTCAA 0.968163 -55 CAGCCTGTGAATCTCTTCAAGTGACAGCTG 3 75 0 ATCTCTTCAA 0.977886 -226 GTCTTTGTTCTGTTCTTCAAAAACCGGCCT 3 135 0 TGTTCTTCAA 0.969029 -166 TTTTCATAAAATTTCTTAAAGCGGTCCTCG 3 197 0 ATTTCTTAAA 0.947087 -104 GCCAGTTTGTTTTTCATAAAATTTCTTAAA 3 207 0 TTTTCATAAA 0.851703 -94 CAGCCTCACCATTTCTTCATCCGGCACCGC 3 240 0 ATTTCTTCAT 0.931707 -61 TTCGCATCCTCCTCTTCAACGCCTGATGC 3 282 0 TCCTCTTCAA 0.954658 -19 ********** Masking position 9 Map Score: 5.32435 Number of sites scoring better than the average of aligned sites = 1219 Number in coding regions = 1117 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 TCCGGAGCTTATGGATCTCG 2 1 0 ATGGATCTCG 0.916216 -71 TTCAGGCGGAGCGGGTCTCGTTTTCTATAT 2 33 1 GCGGGTCTCG 0.993692 -39 ACTTGGAAATCCGTGTCGCGGACCAGCTGT 3 52 1 CCGTGTCGCG 0.956648 -249 TTCACAGGCTGCGGAAGGCGCACCCGGGCT 3 94 1 GCGGAAGGCG 0.968867 -207 AAGACCGGGAACGGATCGAGGTTAAACATG 3 160 1 ACGGATCGAG 0.973075 -141 ATTTCTTAAAGCGGTCCTCGATTGAGACAT 3 187 0 GCGGTCCTCG 0.954808 -114 CGGTGCGGTGCCGGATGAAGAAATGGTGAG 3 236 1 CCGGATGAAG 0.855994 -65 ********** Masking position 3 Map Score: 2.07122 Number of sites scoring better than the average of aligned sites = 804 Number in coding regions = 741 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 CGAAAATGACCAATCTGATCTATTGGTAAA 1 115 0 CAATCTGATC 0.961744 -69 TCAGATTGGTCATTTTCGTCAACATTCGAT 1 127 1 CATTTTCGTC 0.931819 -57 TCAATCCAAGCATTCTGATCTCTGCCTTCA 3 23 0 CATTCTGATC 0.961749 -278 CGCAGCCTGTGAATCTCTTCAAGTGACAGC 3 77 0 GAATCTCTTC 0.940424 -224 AACAGCCTCACCATTTCTTCATCCGGCACC 3 242 0 CCATTTCTTC 0.950777 -59 TTCGCATCCTCCTCTTCAACGCCTGAT 3 284 0 CCTCCTCTTC 0.954341 -17 ********** Masking position 6 Map Score: 1.18403 Number of sites scoring better than the average of aligned sites = 1172 Number in coding regions = 1079 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 GCCTTTTCACATATAAAAAGCTGATTATCT 1 81 0 ATATAAAAAG 0.968777 -103 ATTCGATAAAATATAGAGAGATAAAAAGAG 1 150 1 ATATAGAGAG 0.986702 -34 ATATAGAGAGATAAAAAGAGAGGGGTCTTC 1 160 1 ATAAAAAGAG 0.950004 -24 CCTCTCTTTTATATAGAAAACGAGACCCGC 2 43 0 ATATAGAAAA 0.923562 -29 ********** Masking position 5 Map Score: 0.866649 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 103 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 ********** No masking Map Score: 7.69818e-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 7 ********** No masking Map Score: 7.69818e-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 8 ********** No masking Map Score: 7.69818e-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