AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i202_exonuclease_sbcc_bsub_reg_100.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 GATTATCTCCGCACATCTCTCCCTGCCCAACATATA 1 53 0 GCCCCCCTGC 0.989229 -131 GAGATGTGCGGAGATAATCAGCTTTTTATATGTGAA 1 70 1 GAACGCTTTT 0.766893 -114 CTGATCTATTGGTAAAAACGGCCTTTTCACATATAA 1 95 0 GGACGCCTTT 0.964151 -89 ATTAGAAGACCCCTCTCTTTTTATCTCTCT 1 164 0 GACCCTCTTT 0.884291 -20 TAGAAAACGAGACCCGCTCCGCCTGAAATTCCGGAG 2 24 0 GACCGCCTGA 0.984013 -48 ATGCTTTCACCTCTCTTTTATATAGAAA 2 54 0 GCACCTCTTT 0.93414 -18 ATCCAAGCATTCTGATCTCTGCCTTCATCCAGCCAG 3 14 0 TCCCGCCTTC 0.9845 -287 GCCCGGGTGCGCCTTCCGCAGCCTGTGAATCTCTTC 3 87 0 GCCCGCCTGT 0.99818 -214 GTTCTGTTCTTCAAAAACCGGCCTGATATGGATAAA 3 123 0 TCACGCCTGA 0.972777 -178 TTAACCTCGATCCGTTCCCGGTCTTTGTTCTGTTCT 3 149 0 TCCCGTCTTT 0.966796 -152 TCTTCATCCGGCACCGCACCGCCAGTTTGTTTTTCA 3 221 0 GCCCGCCAGT 0.984511 -80 TGATGCAAGCTCTAAAAACAGCCTCACCATTTCTTC 3 252 0 TCACGCCTCA 0.892684 -49 ** * * ****** Masking position 9 Map Score: 13.7406 Number of sites scoring better than the average of aligned sites = 1646 Number in coding regions = 1511 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 TTATCGAATGTTGACGAAAATGACCAATCT 1 129 0 TTGACGAAAA 0.967117 -55 CAGCTGTCACTTGAAGAGATTCACAGGCTG 3 75 1 TTGAAGAGAT 0.977111 -226 AGGCCGGTTTTTGAAGAACAGAACAAAGAC 3 135 1 TTGAAGAACA 0.967952 -166 CGAGGACCGCTTTAAGAAATTTTATGAAAA 3 197 1 TTTAAGAAAT 0.945297 -104 TTTAAGAAATTTTATGAAAAACAAACTGGC 3 207 1 TTTATGAAAA 0.847215 -94 GCGGTGCCGGATGAAGAAATGGTGAGGCTG 3 240 1 ATGAAGAAAT 0.929428 -61 GCATCAGGCGTTGAAGAGGAGGATGCGAA 3 282 1 TTGAAGAGGA 0.953106 -19 ********** Masking position 4 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 ATATAGAAAACGAGACCCGCTCCGCCTGAA 2 33 0 CGAGACCCGC 0.924902 -39 TCAAGTGACAGCTGGTCCGCGACACGGATT 3 59 0 GCTGGTCCGC 0.71866 -242 TGGATAAAGCCCGGGTGCGCCTTCCGCAGC 3 101 0 CCGGGTGCGC 0.895672 -200 AGAACAAAGACCGGGAACGGATCGAGGTTA 3 154 1 CCGGGAACGG 0.870572 -147 ATGTCTCAATCGAGGACCGCTTTAAGAAAT 3 187 1 CGAGGACCGC 0.992723 -114 ATTTCTTCATCCGGCACCGCACCGCCAGTT 3 230 0 CCGGCACCGC 0.880428 -71 ********** Masking position 4 Map Score: 4.17588 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 297 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TTTACCAATAGATCAGATTGGTCATTTTCG 1 115 1 GATCAGATTG 0.985877 -69 TGAAGGCAGAGATCAGAATGCTTGGATTGA 3 23 1 GATCAGAATG 0.985877 -278 GGTTTTTGAAGAACAGAACAAAGACCGGGA 3 140 1 GAACAGAACA 0.964517 -161 CAAAGACCGGGAACGGATCGAGGTTAAACA 3 158 1 GAACGGATCG 0.98446 -143 ********** Masking position 7 Map Score: 1.38472 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 169 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 GCCTTTTCACATATAAAAAGCTGATTATCT 1 81 0 ATATAAAAAG 0.968603 -103 ATTCGATAAAATATAGAGAGATAAAAAGAG 1 150 1 ATATAGAGAG 0.986626 -34 ATATAGAGAGATAAAAAGAGAGGGGTCTTC 1 160 1 ATAAAAAGAG 0.949731 -24 CCTCTCTTTTATATAGAAAACGAGACCCGC 2 43 0 ATATAGAAAA 0.923157 -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