AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i264_bsub_mtub_100.orf -o264_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yvcJ 24 similar to hypothetical proteins #2 yvcI 300 similar to mutator MutT protein #3 Rv1419 179 hypothetical protein Rv1419 #4 uvrC 63 uvrC Motif number 1 CTTTCTCCCCCCTGACTTGTCTTT 1 6 0 CCCCCCTATG 0.899014 -19 GCTTCAAGATGCCTCCCACAATGAAGAGACATT 2 242 0 GCCTCCCCTG 0.964789 -59 CGCCAGCCCCCATGCTCTTCGCGGG 3 3 1 CCAGCCCCGC 0.983013 -177 CCGGTTCAAACCCGCCCGCGAAGAGCATGGGGG 3 17 0 CCCGCCCCAG 0.99396 -163 GCGGGTTTGAACCGGCCAAACGGGGTCAAAGTC 3 35 1 ACCGGCCAGG 0.934901 -145 TTGAGTATGCCCAGGCCGCCGTGACTTTGACCC 3 57 0 CCAGGCCCTG 0.924091 -123 AATGTGTCCCACGGCCCACCATCGGATCCCGAC 3 89 1 ACGGCCCCTC 0.975817 -91 GATCCCGACGACGGCCCACTGTGAACTGCGCCG 3 113 1 ACGGCCCCTG 0.992301 -67 TGTGAACTGCGCCGCTCGTGGTGCATTACCCAG 3 132 1 GCCGCTCTTG 0.836482 -48 GGTGCATTACCCAGACCACGATGAGAGAATGGC 3 151 1 CCAGACCCTG 0.970086 -29 TTCCCCGCCATTCTCTCATCGTGGT 3 165 0 CCCCGCCTTC 0.941692 -15 CCGGCCTGCCCGGCGAACCCCCG 4 1 1 CCGGCCTCGG 0.922538 -63 CCCGGCGAACCCCCGCCTTTCTGGGCGCCGTCG 4 19 1 CCCCGCCTTG 0.980984 -45 ******* * ** Masking position 2 Map Score: 17.7256 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 883 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 2 CAATGTCTCTTCATTGTGGGAGGCATCTTGA 2 241 1 TCATGTGGGA 0.987065 -60 GCCCCCATGCTCTTCGCGGGCGGGTTTGAAC 3 16 1 TCTTGCGGGC 0.994236 -164 GGGGTCAAAGTCACGGCGGCCTGGGCATACT 3 56 1 TCACGCGGCC 0.983807 -124 CGTCGGGATCCGATGGTGGGCCGTGGGACAC 3 92 0 CGATGTGGGC 0.987053 -88 GCGGCGCAGTTCACAGTGGGCCGTCGTCGGG 3 116 0 TCACGTGGGC 0.996598 -64 CGCCATTCTCTCATCGTGGTCTGGGTAATGC 3 154 0 TCATGTGGTC 0.989151 -26 CGAACCCCCGCCTTTCTGGGCGCCGTCGAAG 4 24 1 CCTTCTGGGC 0.970731 -40 **** ****** Masking position 8 Map Score: 9.27741 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 147 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 AAAGACAAGTCAGGGGGGAGAAAG 1 8 1 AGTCAGGGGG 0.986952 -17 TATTCATTATAAAAAGGGGGTCAATTACTT 2 82 0 AAAAAGGGGG 0.987849 -219 GCCCGCGAAGAGCATGGGGGCTGGCG 3 7 0 AGCATGGGGG 0.994275 -173 CCACGATGAGAGAATGGCGGGGAA 3 166 1 AGAATGGCGG 0.995104 -14 GACGGCGCCCAGAAAGGCGGGGGTTCGCCG 4 21 0 AGAAAGGCGG 0.996578 -43 ********** Masking position 1 Map Score: 8.07705 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 53 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 ACATTACGTTACTGGGTTTTAATTCCGCTGTAACAC 2 16 1 AGTTTATTCC 0.980824 -285 ACACATGTGTAATGCTTTTCGGTTATGATTAATAAA 2 48 1 AGTTCGTTAT 0.963766 -253 TTCATTATAAAAAGGGGGTCAATTACTTTATTAATC 2 74 0 AGGTCATTAC 0.951896 -227 CCGTGCCAAAAAAGTGTATTCATTATAAAAAGGGGG 2 92 0 AGTTTATTAT 0.979553 -209 CATAAATAAAAGAGAATTCCAGTTACAGCAAAATCA 2 159 1 AGTCCGTTAC 0.91807 -142 CTTCTATTTTACAGCATATTCATTCCTTAATTCAGA 2 195 0 AGTTTATTCC 0.980823 -106 AAAGATTGTCAATGTCTCTTCATTGTGGGAGGCATC 2 232 1 AGTTTATTGT 0.94601 -69 TCGTCCTGTCATCGTCTCTTTATTATACCGCTTCAA 2 268 0 AGTTTATTAT 0.979559 -33 * * * ** ***** Masking position 1 Map Score: 4.24798 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 146 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 CCCTTTTTATAATGAATACACTTTTTTGGCA 2 94 1 AATGAATAAC 0.98919 -207 TGAATTAAGGAATGAATATGCTGTAAAATAG 2 197 1 AATGAATAGC 0.981711 -104 TGCCTCCCACAATGAAGAGACATTGACAATC 2 235 0 AATGAAGAAC 0.992985 -66 GAAGCGGTATAATAAAGAGACGATGACAGGA 2 270 1 AATAAAGAAC 0.972698 -31 ******** ** Masking position 6 Map Score: 2.50132 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 84 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 ********** No masking Map Score: -8.85746e-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: -8.85746e-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: -8.85746e-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