AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i196_mixed_replication_rec__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 xerC 90 xerC #2 viuB 32 viuB #3 Rv2898c 247 hypothetical protein Rv2898c #4 topA 300 topA Motif number 1 GGTGAGATCTTTCGGCCTGGGATAGCCGAC 1 11 0 TTCGGCCTGG 0.877745 -80 AAGATCTCACCCCGGACACGGTGCGGCGCG 1 30 1 CCCGGACACG 0.987375 -61 CCGGACACGGTGCGGCGCGTCGACTCGGGC 1 41 1 TGCGGCGCGT 0.795585 -50 GACGTCTCGAGCCCGAGTCGACGCGCCGCA 1 51 0 GCCCGAGTCG 0.947913 -40 TCCCCCACAGTCGCAGGCATGAC 1 78 0 CCCACAGTCG 0.753234 -13 TCCAGACCCGACCCGCGTCGA 2 2 0 ACCCGCGTCG 0.779024 -31 TGTCCTCCTGTCCAGACCCGACCCGCGTCG 2 12 0 TCCAGACCCG 0.899481 -21 CGGGACTCTTCCGGCGCCGAACATGATGT 3 10 1 TCCGGCGCCG 0.996033 -238 CGCACCGCAGGCGGCACACGCCGATCCAGC 3 41 0 GCGGCACACG 0.855635 -207 GTGTGCCGCCTGCGGTGCGTTGCGAGTAGC 3 52 1 TGCGGTGCGT 0.552653 -196 TTGCGAGTAGCCGGGACCCGAGAAGTTGCT 3 71 1 CCGGGACCCG 0.903411 -177 GTTGCTATGTGACGGAGACGATGATGACAA 3 95 1 GACGGAGACG 0.787647 -153 ATGACAAGGACGCGGTGTCGTGATCCCGCG 3 118 1 CGCGGTGTCG 0.964139 -130 GGTGTCGTGATCCCGCGCAGTACTGGGGCT 3 131 1 TCCCGCGCAG 0.81874 -117 GTACTGGGGCTGTGGACAGGGCCGCGACTG 3 150 1 TGTGGACAGG 0.629948 -98 CGACCAGTTATCCCCAGTCGCGGCCCTGTC 3 164 0 TCCCCAGTCG 0.94216 -84 GTCTCACCGATGCCGCGACGACCAGTTATC 3 182 0 TGCCGCGACG 0.967702 -66 CAACCTGCACGCTGGCCCCGACATCACCTG 3 223 0 GCTGGCCCCG 0.893998 -25 CCTAGCTCGGCGACGATGCGGTCCC 4 6 1 CTCGGCGACG 0.957332 -295 TCGGCGACGATGCGGTCCCGCTGGGGTCCG 4 17 1 TGCGGTCCCG 0.977623 -284 CCCGCTGGGGTCCGCTGAGGAGCCGGGCAG 4 33 1 TCCGCTGAGG 0.911373 -268 GCTGAGGAGCCGGGCAGTCGGACCTAGTTC 4 46 1 CGGGCAGTCG 0.844947 -255 TCGGACCTAGTTCGGCGACGATGCGGATCT 4 63 1 TTCGGCGACG 0.967139 -238 GCTCAAACGGGCCGCTCAGGACGCTCGGAG 4 91 0 GCCGCTCAGG 0.840161 -210 GGGTAATCTGTTTGCAGCCGGTTTGCGCAG 4 130 1 TTTGCAGCCG 0.573848 -171 TTTGCGCAGGCCCGCCCTAGAGTGCGAGAT 4 151 1 CCCGCCCTAG 0.797342 -150 GATTGTCAGTTGCCCACAGGCGAGGGAACG 4 178 1 TGCCCACAGG 0.750509 -123 CACCTGGGATTCGGCAGTCGGCCGCGTCCT 4 224 1 TCGGCAGTCG 0.913571 -77 TACCTACCGGGGCGGTCTCGATAGGGGCCG 4 255 1 GGCGGTCTCG 0.943798 -46 CATCTCTTATCCCGGCCCCTATCGAGACCG 4 267 0 CCCGGCCCCT 0.917625 -34 CTGCGCCCACGCTCCATCTCT 4 290 0 TGCGCCCACG 0.981104 -11 ********** Masking position 10 Map Score: 45.1773 Number of sites scoring better than the average of aligned sites = 102048 Number in coding regions = 95881 Number in noncoding regions = 6167 Number of orfs with sites within 600 bp upstream = 1629 Fraction of orfs with sites within 600 bp upstream = 0.261645 Motif number 2 TCGGCTATCCCAGGCCGAAAGATCTCACCC 1 12 1 CAGGCCGAAA 0.824161 -79 CGAAAGATCTCACCCCGGACACGGTGCGGC 1 27 1 CACCCCGGAC 0.945335 -64 CCCGAGTCGACGCGCCGCACCGTGTCCGGG 1 40 0 CGCGCCGCAC 0.990126 -51 ATGACGTCTCGAGCCCGAGTCGACGCGCCG 1 53 0 GAGCCCGAGT 0.890406 -38 TCGACGCGGGTCGGGTCTGGAC 2 3 1 GACGCGGGTC 0.798326 -30 GGACTCTTCCGGCGCCGAACATGATGTTGC 3 13 1 GGCGCCGAAC 0.990007 -235 CAACGCACCGCAGGCGGCACACGCCGATCC 3 44 0 CAGGCGGCAC 0.897596 -204 CAACTTCTCGGGTCCCGGCTACTCGCAACG 3 69 0 GGTCCCGGCT 0.792468 -179 GCGGGATCACGACACCGCGTCCTTGTCATC 3 117 0 GACACCGCGT 0.911121 -131 GCGGTGTCGTGATCCCGCGCAGTACTGGGG 3 129 1 GATCCCGCGC 0.971472 -119 GTTATCCCCAGTCGCGGCCCTGTCCACAGC 3 158 0 GTCGCGGCCC 0.805169 -90 GCGTCTCACCGATGCCGCGACGACCAGTTA 3 184 0 GATGCCGCGA 0.94367 -64 CCTGCACGCTGGCCCCGACATCACCTGCCA 3 220 0 GGCCCCGACA 0.910898 -28 GGACCGCATCGTCGCCGAGCTAGG 4 5 0 GTCGCCGAGC 0.969574 -296 GGACCCCAGCGGGACCGCATCGTCGCCGAG 4 16 0 GGGACCGCAT 0.910278 -285 GGTCCGCTGAGGAGCCGGGCAGTCGGACCT 4 41 1 GGAGCCGGGC 0.95724 -260 GATCCGCATCGTCGCCGAACTAGGTCCGAC 4 62 0 GTCGCCGAAC 0.951915 -239 AAGGCTCAAACGGGCCGCTCAGGACGCTCG 4 94 0 CGGGCCGCTC 0.961299 -207 ACTCTAGGGCGGGCCTGCGCAAACCGGCTG 4 144 0 GGGCCTGCGC 0.891477 -157 GGAACGCCGGCGTACCGGAATTCACCTGGG 4 202 1 CGTACCGGAA 0.483571 -99 GGCCCCTATCGAGACCGCCCCGGTAGGTAG 4 254 0 GAGACCGCCC 0.958504 -47 GGTCTCGATAGGGGCCGGGATAAGAGATGG 4 268 1 GGGGCCGGGA 0.982561 -33 ********** Masking position 5 Map Score: 33.1829 Number of sites scoring better than the average of aligned sites = 43666 Number in coding regions = 40595 Number in noncoding regions = 3071 Number of orfs with sites within 600 bp upstream = 1309 Fraction of orfs with sites within 600 bp upstream = 0.210247 Motif number 3 CATGACGTCTCGAGCCCGAGTCGACGCGCC 1 54 0 CGAGCCCGAG 0.832031 -37 ATGTCCTCCTGTCCAGACCCGACCCGCG 2 15 0 CTGTCCAGAC 0.963251 -18 AGTCGCGGCCCTGTCCACAGCCCCAGTACT 3 149 0 CTGTCCACAG 0.815723 -99 CGACGACCAGTTATCCCCAGTCGCGGCCCT 3 167 0 TTATCCCCAG 0.907442 -81 ACCTGCACGCTGGCCCCGACATCACCTGCC 3 221 0 TGGCCCCGAC 0.970305 -27 GGCTCCTCAGCGGACCCCAGCGGGACCGCA 4 27 0 CGGACCCCAG 0.958056 -274 TGCAAACAGATTACCCACACCAAAGGCTCA 4 116 0 TTACCCACAC 0.940321 -185 TAGGGCGGGCCTGCGCAAACCGGCTGCAAA 4 140 0 CTGCGCAAAC 0.81892 -161 AGATTGTCAGTTGCCCACAGGCGAGGGAAC 4 177 1 TTGCCCACAG 0.981873 -124 CTGCGCCCACGCTCCATCTC 4 291 0 CTGCGCCCAC 0.968669 -10 ********** Masking position 9 Map Score: 10.0943 Number of sites scoring better than the average of aligned sites = 3807 Number in coding regions = 3469 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 4 TCTTTCGGCCTGGGATAGCCGAC 1 3 0 TGGGTAGCCG 0.773961 -88 CCGAGTCGACGCGCCGCACCGTGTCCGGGGT 1 38 0 GCGCGCACCG 0.752876 -53 CTGGATCGGCGTGTGCCGCCTGCGGTGCGTT 3 42 1 GTGTCCGCCT 0.854254 -206 GCGGTGCGTTGCGAGTAGCCGGGACCCGAGA 3 63 1 GCGATAGCCG 0.905521 -185 GGCCGCGACTGGGGATAACTGGTCGTCGCGG 3 169 1 GGGGTAACTG 0.893974 -79 GCCACGAATCGCGTCTCACCGATGCCGCGAC 3 193 0 GCGTTCACCG 0.944266 -55 AGGTGATGTCGGGGCCAGCGTGCAGGTTGGC 3 224 1 GGGGCAGCGT 0.80435 -24 GCGGCCAACCTGCACGCTGGC 3 237 0 GCGGCAACCT 0.980366 -11 CGGTCCCGCTGGGGTCCGCTGAGGAGCCGGG 4 29 1 GGGGCCGCTG 0.984938 -272 CGCTGAGGAGCCGGGCAGTCGGACCTAGTTC 4 45 1 CCGGCAGTCG 0.895346 -256 CGGCGACGATGCGGATCTCCGAGCGTCCTGA 4 75 1 GCGGTCTCCG 0.972095 -226 AGCGTCCTGAGCGGCCCGTTTGAGCCTTTGG 4 96 1 GCGGCCGTTT 0.84874 -205 AGCCTTTGGTGTGGGTAATCTGTTTGCAGCC 4 118 1 GTGGTAATCT 0.412582 -183 TGGGTAATCTGTTTGCAGCCGGTTTGCGCAG 4 129 1 GTTTCAGCCG 0.435999 -172 GCACTCTAGGGCGGGCCTGCGCAAACCGGCT 4 145 0 GCGGCCTGCG 0.885023 -156 TCCCTCGCCTGTGGGCAACTGACAATCTCGC 4 174 0 GTGGCAACTG 0.933361 -127 CAGGTGAATTCCGGTACGCCGGCGTTCCCTC 4 199 0 CCGGACGCCG 0.869792 -102 GGTAGAGGACGCGGCCGACTGCCGAATCCCA 4 228 0 GCGGCGACTG 0.918484 -73 **** ****** Masking position 3 Map Score: 15.6861 Number of sites scoring better than the average of aligned sites = 37833 Number in coding regions = 35069 Number in noncoding regions = 2764 Number of orfs with sites within 600 bp upstream = 1192 Fraction of orfs with sites within 600 bp upstream = 0.191455 Motif number 5 ********** No masking Map Score: -1.78814e-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 6 ********** No masking Map Score: -1.78814e-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: -1.78814e-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