AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i170_Urease_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv1847 277 hypothetical protein Rv1847 #2 ureA 48 ureA Motif number 1 GCTTACTACTCGCTGTCGTATCCAAACCGGCG 1 51 1 CGCTGTCGTC 0.899192 -227 GGTACGGCCGCCCGCCGGTTTGGATACGACAG 1 63 0 CCCGCCGGTG 0.936941 -215 GGTGCATAGGCCCGGTACGGCCGCCCGCCGGT 1 76 0 CCCGGTACGC 0.983591 -202 GTAATGTTTGCGAGCCGGGTGCATAGGCCCGG 1 93 0 CGAGCCGGGC 0.995261 -185 ATTACTTCGTCGAGCCACAACGACCGCGGCCG 1 163 1 CGAGCCACAG 0.916147 -115 CCACAACGACCGCGGCCGAGTCCTGAGGGCTG 1 177 1 CGCGGCCGAC 0.99861 -101 TGCAGTGACCCCCGGTCGACTCGATCGGCGAG 1 207 1 CCCGGTCGAC 0.991643 -71 ACTCGATCGGCGAGCCCCGTGCCTTGGTGCAC 1 225 1 CGAGCCCCGC 0.996848 -53 CACCAACGGGCGAGCCCCGTGCACCAAGGCAC 1 243 0 CGAGCCCCGC 0.996848 -35 CCCGCTCGAAACCGTTGAACCT 2 1 1 CCCGCTCGAC 0.991643 -48 CCTGCCACGCCGCGGCAGGTTCAACGGTTTCG 2 17 0 CGCGGCAGGC 0.99861 -32 CCTGCCGCGGCGTGGCAGGATCGCAGAGC 2 30 1 CGTGGCAGGC 0.9877 -19 ********* * Masking position 1 Map Score: 26.8412 Number of sites scoring better than the average of aligned sites = 18686 Number in coding regions = 17248 Number in noncoding regions = 1438 Number of orfs with sites within 600 bp upstream = 844 Fraction of orfs with sites within 600 bp upstream = 0.135561 Motif number 2 ACGCTGGTTTCAACCCGCAGGAGATGAACGA 1 14 0 CACCCGCAGG 0.923837 -264 TAGTAAGCCGGAGTACGCTGGTTTCAACCCG 1 28 0 GATACGCTGG 0.843247 -250 CGCCGGTTTGGATACGACAGCGAGTAGTAAG 1 52 0 GAACGACAGC 0.954217 -226 CTGTCGTATCCAAACCGGCGGGCGGCCGTAC 1 63 1 CAACCGGCGG 0.920056 -215 GCATAGGCCCGGTACGGCCGCCCGCCGGTTT 1 74 0 GGACGGCCGC 0.991511 -204 TAATGTTTGCGAGCCGGGTGCATAGGCCCGG 1 93 0 GACCGGGTGC 0.914433 -185 AGTAATGATAGGCAAGGCTGCCCTAATTTAG 1 138 0 GGAAGGCTGC 0.850641 -140 CAGCCCTCAGGACTCGGCCGCGGTCGTTGTG 1 178 0 GATCGGCCGC 0.996688 -100 TCGACCGGGGGTCACTGCAGCCCTCAGGACT 1 195 0 GTACTGCAGC 0.857815 -83 CTCGCCGATCGAGTCGACCGGGGGTCACTGC 1 208 0 GATCGACCGG 0.968291 -70 CTCGATCGGCGAGCCCCGTGCCTTGGTGCAC 1 226 1 GACCCCGTGC 0.960068 -52 ACCAACGGGCGAGCCCCGTGCACCAAGGCAC 1 243 0 GACCCCGTGC 0.960068 -35 AGGTTCAACGGTTTCGAGCGGG 2 2 0 GTTCGAGCGG 0.760568 -47 CGAAACCGTTGAACCTGCCGCGGCGTGGCAG 2 17 1 GACCTGCCGC 0.994955 -32 GCTCTGCGATCCTGCCACGCCGCGGCAG 2 31 0 GACCTGCCAC 0.91827 -18 ** ******** Masking position 10 Map Score: 24.6564 Number of sites scoring better than the average of aligned sites = 34361 Number in coding regions = 32224 Number in noncoding regions = 2137 Number of orfs with sites within 600 bp upstream = 1112 Fraction of orfs with sites within 600 bp upstream = 0.178606 Motif number 3 GGAGTACGCTGGTTTCAACCCGCAGGAGAT 1 20 0 GGTTTCAACC 0.926379 -258 CCGCCGGTTTGGATACGACAGCGAGTAGTA 1 54 0 GGATACGACA 0.955083 -224 TGCATAGGCCCGGTACGGCCGCCCGCCGGT 1 76 0 CGGTACGGCC 0.98651 -202 GCAGCCCTCAGGACTCGGCCGCGGTCGTTG 1 180 0 GGACTCGGCC 0.995249 -98 GTCGACCGGGGGTCACTGCAGCCCTCAGGA 1 197 0 GGTCACTGCA 0.853192 -81 GCTCGCCGATCGAGTCGACCGGGGGTCACT 1 210 0 CGAGTCGACC 0.970296 -68 TTGGTGCACGGGGCTCGCCCGTTGGTGTAG 1 248 1 GGGCTCGCCC 0.919154 -30 CAGGTTCAACGGTTTCGAGCGGG 2 4 0 GGTTTCGAGC 0.950457 -45 GCTCTGCGATCCTGCCACGCCGCGGC 2 33 0 CGATCCTGCC 0.922205 -16 ********** Masking position 6 Map Score: 9.44356 Number of sites scoring better than the average of aligned sites = 10688 Number in coding regions = 9971 Number in noncoding regions = 717 Number of orfs with sites within 600 bp upstream = 567 Fraction of orfs with sites within 600 bp upstream = 0.0910697 Motif number 4 TGAAACCAGCGTACTCCGGCTTACTACTCG 1 33 1 GTACTCCGGC 0.953322 -245 GCCGGTTTGGATACGACAGCGAGTAGTAAG 1 52 0 ATACGACAGC 0.886348 -226 GCTGTCGTATCCAAACCGGCGGGCGGCCGT 1 62 1 CCAAACCGGC 0.977856 -216 CTTCGTCGAGCCACAACGACCGCGGCCGAG 1 167 1 CCACAACGAC 0.991412 -111 GTCCTTGTGTCTACACCAACGGGCGAGCCC 1 258 0 CTACACCAAC 0.975006 -20 GTTGGTGTAGACACAAGGAC 1 268 1 ACACAAGGAC 0.921542 -10 ********** Masking position 3 Map Score: 1.29953 Number of sites scoring better than the average of aligned sites = 9799 Number in coding regions = 9185 Number in noncoding regions = 614 Number of orfs with sites within 600 bp upstream = 492 Fraction of orfs with sites within 600 bp upstream = 0.0790235 Motif number 5 ********** No masking Map Score: 6.91659e-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 6 ********** No masking Map Score: 6.91659e-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: 6.91659e-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