AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i196_mixed_replication_rec__mtub_reg_300.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 fdhF 57 fdhF #5 Rv2901c 53 hypothetical protein Rv2901c #6 lepB 57 lepB #7 rplS 300 rplS #8 topA 300 topA Motif number 1 CCCGAGTCGACGCGCCGCACCGTGTCCGGGGTGA 1 36 0 CCGCCGCGTG 0.550596 -55 TCCCCCACAGTCGCAGGCATGACGTCT 1 74 0 CCACAGGAGG 0.62894 -17 TCGACGCGGGTCGGGTCTGGACAGGA 2 3 1 GCGCGGCGGT 0.986775 -30 GGACTCTTCCGGCGCCGAACATGATGTTGCTGGA 3 13 1 GCGCCGCTGA 0.962599 -235 GCAGGCGGCACACGCCGATCCAGCAACATCATGT 3 31 0 CCGCCGCAGC 0.966931 -217 CTACTCGCAACGCACCGCAGGCGGCACACGCCGA 3 47 0 CCACCGGCGG 0.952709 -201 GTTGCGAGTAGCCGGGACCCGAGAAGTTGCTATG 3 70 1 GCGGGACAGA 0.642642 -178 GTTGCTATGTGACGGAGACGATGATGACAAGGAC 3 95 1 GCGGAGGTGA 0.650601 -153 TGATGACAAGGACGCGGTGTCGTGATCCCGCGCA 3 116 1 GCGCGGTGTG 0.967285 -132 GTCGTGATCCCGCGCAGTACTGGGGCTGTGGACA 3 134 1 CCGCAGCGGG 0.944662 -114 GTTATCCCCAGTCGCGGCCCTGTCCACAGCCCCA 3 154 0 GCGCGGCGTC 0.935769 -94 ATAACTGGTCGTCGCGGCATCGGTGAGACGCGAT 3 183 1 GCGCGGTGGT 0.96483 -65 GCATCGGTGAGACGCGATTCGTGGCAGGTGATGT 3 199 1 GCGCGACTGG 0.96253 -49 GGCCAACCTGCACGCTGGCCCCGACATCACCTGC 3 222 0 CCGCTGCCGA 0.937341 -26 ATTGACGTGTGACGGCGCTTGGGGCAG 4 4 0 GCGGCGTGGG 0.987428 -54 GGGCACTGAGCGGGGAAGCCGGGGA 5 2 1 GCACTGCGGG 0.94054 -52 GAGCGGGGAAGCCGGGGAACCGGCAGGGAGAAGG 5 18 1 GCGGGGCGGC 0.916183 -36 CCGGGAACGTCTCGGCGATGTTCGAAAGCCGCCA 6 11 1 CCGGCGGTCG 0.791254 -47 ATGTTCGAAAGCCGCCACCTGCGCTGGCTACGCT 6 28 1 GCGCCATCGC 0.8569 -30 TGTTGGGTGTCACGCCAAGCTTCGGGTTTCCACA 7 11 1 CCGCCACTCG 0.742106 -290 GGTTTCCACACGCGCGGTTTGACCCTAGTCATAT 7 35 1 CCGCGGTACC 0.731031 -266 CTTTTCGACGGCCGCGAACCACCGGAGATTTCCT 7 96 1 GCGCGACCCG 0.945955 -205 GCAGTTGTCTGTCGCGGTGGTCGGCCGGGTTGCG 7 167 1 GCGCGGGCGG 0.997072 -134 ATTGGTGCATCTCGCAGCAGGCGGCACGCAACCC 7 193 0 CCGCAGGCGG 0.987314 -108 TGGTCACCAAGCCGGTGGGTTCGGGCTTATTGGT 7 221 0 GCGGTGTCGG 0.937047 -80 TTACCCCCCACACGCAGCGTGCGGTGGTCACCAA 7 245 0 CCGCAGTCGG 0.981668 -56 CATCCTTGGGGTCGCGGCGTGGTTACCCCCCACA 7 267 0 GCGCGGTGTT 0.773237 -34 GGACCGCATCGTCGCCGAGCTAGG 8 1 0 GCGCCGCAGG 0.994333 -300 ACGATGCGGTCCCGCTGGGGTCCGCTGAGGAGCC 8 23 1 CCGCTGGCCG 0.891763 -278 CCGCTGAGGAGCCGGGCAGTCGGACCTAGTTCGG 8 44 1 GCGGGCTGGA 0.578654 -257 GATCCGCATCGTCGCCGAACTAGGTCCGACTGCC 8 58 0 GCGCCGCAGG 0.994334 -243 AAACGGGCCGCTCAGGACGCTCGGAGATCCGCAT 8 83 0 CCAGGACCGG 0.690283 -218 AACTGACAATCTCGCACTCTAGGGCGGGCCTGCG 8 155 0 CCGCACTGGG 0.84069 -146 TTGTCAGTTGCCCACAGGCGAGGGAACGCCGGCG 8 180 1 CCACAGGGGG 0.808572 -121 GCGAGGGAACGCCGGCGTACCGGAATTCACCTGG 8 197 1 GCGGCGCGGA 0.96033 -104 GTAGGTAGAGGACGCGGCCGACTGCCGAATCCCA 8 228 0 GCGCGGGCTG 0.976872 -73 * ***** * *** Masking position 3 Map Score: 62.1081 Number of sites scoring better than the average of aligned sites = 73559 Number in coding regions = 69336 Number in noncoding regions = 4223 Number of orfs with sites within 600 bp upstream = 1427 Fraction of orfs with sites within 600 bp upstream = 0.2292 Motif number 2 AGATCTCACCCCGGACACGGTGCGGCGCGTC 1 31 1 CCGGACCGGT 0.918944 -60 ACATGATGTTGCTGGATCGGCGTGTGCCGCC 3 31 1 GCTGGACGGC 0.912455 -217 TCGCAACGCACCGCAGGCGGCACACGCCGAT 3 46 0 CCGCAGCGGC 0.996059 -202 AGCAACTTCTCGGGTCCCGGCTACTCGCAAC 3 70 0 CGGGTCCGGC 0.922986 -178 GTGGACAGGGCCGCGACTGGGGATAACTGGT 3 161 1 CCGCGATGGG 0.877208 -87 TGACGTGTGACGGCGCTTGGGGCAG 4 5 0 CGGCGCTGGG 0.890454 -53 CGCCGTCACACGTCAATCGGCTGTGTGCGGC 4 21 1 CGTCAACGGC 0.979657 -37 CGGCTGTGTGCGGCAGTCGGTCGGTCGTGG 4 38 1 CGGCAGCGGT 0.971301 -20 CGGGGAAGCCGGGGAACCGGCAGGGAGAAGG 5 21 1 GGGGAACGGC 0.983297 -33 CTGCTCAGACGTCCTTCTCCCTG 5 41 0 GCTCAGCGTC 0.750315 -13 CCGGGAACGTCTCGGCGATGT 6 1 1 CCGGGACGTC 0.766487 -57 AGCGTAGCCAGCGCAGGTGGCGGCTTTCGAA 6 31 0 GCGCAGTGGC 0.9614 -27 ATATGACTAGGGTCAAACCGCGCGTGTGGAA 7 38 0 GGTCAACCGC 0.887403 -263 CGAAAAGCGCCCGCAAATGGTACACATGACT 7 72 0 CCGCAATGGT 0.764999 -229 CTGTCGCGGTGGTCGGCCGGGTTGCGTGCCG 7 175 1 GGTCGGCGGG 0.935177 -126 GTGCATCTCGCAGCAGGCGGCACGCAACCCG 7 192 0 CAGCAGCGGC 0.943474 -109 TTGGTGACCACCGCACGCTGCGTGTGGGGGG 7 245 1 CCGCACCTGC 0.898436 -56 GACCATCCTTGGGGTCGCGGCGTGGTTACCC 7 273 0 GGGGTCCGGC 0.904738 -28 CCTAGCTCGGCGACGATGCGG 8 1 1 CCTAGCCGGC 0.831293 -300 CTGAGGAGCCGGGCAGTCGGACCTAGTTCGG 8 47 1 GGGCAGCGGA 0.913515 -254 TCAGGACGCTCGGAGATCCGCATCGTCGCCG 8 75 0 CGGAGACCGC 0.785149 -226 CACACCAAAGGCTCAAACGGGCCGCTCAGGA 8 100 0 GCTCAACGGG 0.939304 -201 GGGCGGGCCTGCGCAAACCGGCTGCAAACAG 8 137 0 GCGCAACCGG 0.928221 -164 CCACAGGCGAGGGAACGCCGGCGTACCGGAA 8 191 1 GGGAACCCGG 0.649985 -110 ACCTGGGATTCGGCAGTCGGCCGCGTCCTCT 8 225 1 CGGCAGCGGC 0.996065 -76 ****** **** Masking position 10 Map Score: 39.2843 Number of sites scoring better than the average of aligned sites = 45135 Number in coding regions = 42137 Number in noncoding regions = 2998 Number of orfs with sites within 600 bp upstream = 1290 Fraction of orfs with sites within 600 bp upstream = 0.207196 Motif number 3 GTCCTCCTGTCCAGACCCGACCCGCGTCGA 2 9 0 CCGACCGACC 0.990008 -24 CGCACCGCAGGCGGCACACGCCGATCCAGCAA 3 39 0 GCGCACCGCC 0.620001 -209 TGCGAGTAGCCGGGACCCGAGAAGTTGCTATG 3 72 1 CGGACCGAGA 0.618749 -176 GTCCACAGCCCCAGTACTGCGCGGGATCACGA 3 135 0 CCGTACGCGC 0.951564 -113 CAGTCGCGGCCCTGTCCACAGCCCCAGTACTG 3 148 0 CCGTCCCAGC 0.981525 -100 GCCGCGACGACCAGTTATCCCCAGTCGCGGCC 3 169 0 CCGTTACCCC 0.576947 -79 GCACGCTGGCCCCGACATCACCTGCCACGAAT 3 215 0 CCGACACACC 0.944318 -33 CCGACCGACTGCCGCACACAGCCGATTGACGT 4 30 0 GCGCACCAGC 0.855751 -28 CCACGACCGACCGACTGCCGCA 4 46 0 CCCGACGACC 0.602732 -12 CTGCCGGTTCCCCGGCTTCCCCGCTCAGTGCC 5 12 0 CCGGCTCCCC 0.932926 -42 GTTCGAAAGCCGCCACCTGCGCTGGCTACGCT 6 30 1 CGCACCGCGC 0.831088 -28 ACGCAACCCGGCCGACCACCGCGACAGACAAC 7 170 0 GCGACCCCGC 0.943734 -131 CACCAATAAGCCCGAACCCACCGGCTTGGTGA 7 220 1 CCGAACCACC 0.983944 -81 CCACCGGCTTGGTGACCACCGCACGCTGCGTG 7 237 1 GGGACCCCGC 0.79613 -64 CGGCTCCTCAGCGGACCCCAGCGGGACCGCAT 8 26 0 GCGACCCAGC 0.710197 -275 CGGCGACGATGCGGATCTCCGAGCGTCCTGAG 8 75 1 GCGATCCCGA 0.624987 -226 CTCCGAGCGTCCTGAGCGGCCCGTTTGAGCCT 8 91 1 CCGAGCGCCC 0.949115 -210 GCCGGTTTGCGCAGGCCCGCCCTAGAGTGCGA 8 146 1 GCGGCCGCCC 0.980474 -155 CGCCGGCGTACCGGAATTCACCTGGGATTCGG 8 206 1 CCGAATCACC 0.832516 -95 CTGGGATTCGGCAGTCGGCCGCGTCCTCTACC 8 227 1 GCGTCGCCGC 0.79117 -74 CGGCCCCTATCGAGACCGCCCCGGTAGGTAGA 8 253 0 CGGACCCCCC 0.989397 -48 ** **** **** Masking position 12 Map Score: 31.6737 Number of sites scoring better than the average of aligned sites = 21196 Number in coding regions = 19749 Number in noncoding regions = 1447 Number of orfs with sites within 600 bp upstream = 884 Fraction of orfs with sites within 600 bp upstream = 0.141985 Motif number 4 ATCTTTCGGCCTGGGATAGCCGAC 1 4 0 CTGGGATACC 0.593302 -87 TCGACGCGGGTCGGGTCTGGACAGG 2 5 1 CGCGGGTCGG 0.980605 -28 ATAGCAACTTCTCGGGTCCCGGCTACTCGCA 3 72 0 CTCGGGTCCG 0.908211 -176 AGTACTGGGGCTGTGGACAGGGCCGCGACTG 3 149 1 CTGTGGACGG 0.915722 -99 CCAACCTGCACGCTGGCCCCGACATCACCTG 3 223 0 CGCTGGCCCG 0.759972 -25 GCGGGGAAGCCGGGGAACCGGCAGGGAGAAG 5 20 1 CGGGGAACGG 0.911958 -34 TGTTGGGTGTCACGCCAAGCTTCGG 7 5 1 GGGTGTCAGC 0.356717 -296 CAAACCGCGCGTGTGGAAACCCGAAGCTTGG 7 25 0 GTGTGGAACC 0.455455 -276 AGGAAATCTCCGGTGGTTCGCGGCCGTCGAA 7 99 0 CGGTGGTTGC 0.85811 -202 TTGTCTGTCGCGGTGGTCGGCCGGGTTGCGT 7 171 1 CGGTGGTCGC 0.991328 -130 CACCAAGCCGGTGGGTTCGGGCTTATTGGTG 7 220 0 GTGGGTTCGG 0.783004 -81 ACGCAGCGTGCGGTGGTCACCAAGCCGGTGG 7 237 0 CGGTGGTCCC 0.986094 -64 CGCTGCGTGTGGGGGGTAACCACGCCGCGAC 7 260 1 GGGGGGTACC 0.937829 -41 ATGACCATCCTTGGGGTCGCGGCGTGGTTAC 7 275 0 TTGGGGTCCG 0.685165 -26 TGCGGTCCCGCTGGGGTCCGCTGAGGAGCCG 8 27 1 CTGGGGTCGC 0.987972 -274 TCAGGACGCTCGGAGATCCGCATCGTCGCCG 8 75 0 CGGAGATCGC 0.732454 -226 CGCACTCTAGGGCGGGCCTGCGCAAACCGGC 8 146 0 GGCGGGCCGC 0.919714 -155 TGCCCACAGGCGAGGGAACGCCGGCGTACCG 8 188 1 CGAGGGAAGC 0.524506 -113 GAGGGAACGCCGGCGTACCGGAATTCACCTG 8 199 1 CGGCGTACGG 0.765931 -102 ACCTGGGATTCGGCAGTCGGCCGCGTCCTCT 8 225 1 CGGCAGTCGC 0.764132 -76 CTACCTACCGGGGCGGTCTCGATAGGGGCCG 8 254 1 GGGCGGTCCG 0.943278 -47 ******** ** Masking position 5 Map Score: 25.2222 Number of sites scoring better than the average of aligned sites = 27151 Number in coding regions = 25350 Number in noncoding regions = 1801 Number of orfs with sites within 600 bp upstream = 1011 Fraction of orfs with sites within 600 bp upstream = 0.162384 Motif number 5 TCCCCCACAGTCGCAGGCATGACGTCTCG 1 72 0 GTCGCAGGCA 0.917489 -19 CTCGCAACGCACCGCAGGCGGCACACGCCG 3 48 0 ACCGCAGGCG 0.992799 -200 GCGGCCAACCTGCACGCTGGCCCCGACA 3 230 0 CCTGCACGCT 0.798046 -18 CTGCCCCAAGCGCCGTCACACG 4 3 1 GCCCCAAGCG 0.936502 -55 CCGACCGACTGCCGCACACAGCCGATTGAC 4 32 0 GCCGCACACA 0.891006 -26 GAGATCAGCGTAGCCAGCGCAGGTGGCGG 6 39 0 GTAGCCAGCG 0.48936 -19 GCTTCGGGTTTCCACACGCGCGGTTTGACC 7 29 1 TCCACACGCG 0.824585 -272 CTGTGATTTCACTGCATGCGTACCGTCTGG 7 128 1 ACTGCATGCG 0.840856 -173 GGTGCATCTCGCAGCAGGCGGCACGCAACC 7 194 0 GCAGCAGGCG 0.982411 -107 CTTGGTGACCACCGCACGCTGCGTGTGGGG 7 244 1 ACCGCACGCT 0.950598 -57 GCGCAAACCGGCTGCAAACAGATTACCCAC 8 128 0 GCTGCAAACA 0.495061 -173 TTGTCAGTTGCCCACAGGCGAGGGAACGCC 8 180 1 CCCACAGGCG 0.940765 -121 CAGGCGAGGGAACGCCGGCGTACCGGAATT 8 194 1 AACGCCGGCG 0.774381 -107 ********** Masking position 5 Map Score: 9.24856 Number of sites scoring better than the average of aligned sites = 15286 Number in coding regions = 14247 Number in noncoding regions = 1039 Number of orfs with sites within 600 bp upstream = 667 Fraction of orfs with sites within 600 bp upstream = 0.107131 Motif number 6 GGCCGAAAGATCTCACCCCGGACACGGTGCGGCGC 1 24 1 TCTCACCGCC 0.995976 -67 ACCGCGTCCTTGTCATCATCGTCTCCGTCACATAG 3 99 0 TGTCATCGCC 0.962725 -149 CAGTCGCGGCCCTGTCCACAGCCCCAGTACTGCGC 3 145 0 CCTGTCCGCC 0.931157 -103 ACGAATCGCGTCTCACCGATGCCGCGACGACCAGT 3 186 0 TCTCACCGCC 0.995976 -62 CCCAGCGGGACCGCATCGTCGCCGAGCTAGG 8 7 0 CCGCATCGCA 0.974421 -294 GCTCGGAGATCCGCATCGTCGCCGAACTAGGTCCG 8 64 0 CCGCATCGCA 0.974421 -237 AACAGATTACCCACACCAAAGGCTCAAACGGGCCG 8 107 0 CCACACCGCC 0.989781 -194 ACGCTCCATCTCTTATCCCGGCCCCTATCGAGACC 8 268 0 TCTTATCGCC 0.952921 -33 ******* * * * Masking position 7 Map Score: 6.41361 Number of sites scoring better than the average of aligned sites = 1650 Number in coding regions = 1546 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 7 ACGCGGGTCGGGTCTGGACAGGAGGACAT 2 14 1 GGTTGGACAG 0.903244 -19 GCAACATCATGTTCGGCGCCGGAAGAGTCCC 3 12 0 GTTGGCGCCG 0.936128 -236 CAGTACTGGGGCTGTGGACAGGGCCGCGACT 3 148 1 GCTTGGACAG 0.739815 -100 GTGTGACGGCGCTTGGGGCAG 4 1 0 GCTGGGGCAG 0.975179 -57 GGGAGAAGGACGTCTGAGCAG 5 43 1 CGTTGAGCAG 0.951972 -11 CCGTCTGGCACAATTGAGCAGTTGTCTGTCG 7 150 1 CAATGAGCAG 0.681605 -151 AGCGGGACCGCATCGTCGCCGAGCTAGG 8 8 0 CATGTCGCCG 0.835266 -293 CGGAGATCCGCATCGTCGCCGAACTAGGTCC 8 65 0 CATGTCGCCG 0.835266 -236 CTGAGCGGCCCGTTTGAGCCTTTGGTGTGGG 8 102 1 CGTTGAGCCT 0.595615 -199 GTTTGCAGCCGGTTTGCGCAGGCCCGCCCTA 8 139 1 GGTTGCGCAG 0.985378 -162 AATTCACCTGGGATTCGGCAGTCGGCCGCGT 8 220 1 GGATCGGCAG 0.83486 -81 GGTAGGTAGAGGACGCGGCCGACTGCCGAAT 8 232 0 GGAGCGGCCG 0.907907 -69 GGGCGGTCTCGATAGGGGCCGGGATAAGAGA 8 264 1 GATGGGGCCG 0.982934 -37 AGAGATGGAGCGTGGGCGCAG 8 290 1 CGTGGCGCAG 0.9879 -11 *** ******* Masking position 9 Map Score: 13.4722 Number of sites scoring better than the average of aligned sites = 14835 Number in coding regions = 13910 Number in noncoding regions = 925 Number of orfs with sites within 600 bp upstream = 680 Fraction of orfs with sites within 600 bp upstream = 0.109219 Motif number 8 ********** No masking Map Score: 1.36667e-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 9 ********** No masking Map Score: 1.36667e-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 10 ********** No masking Map Score: 1.36667e-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