AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_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 rplY 216 rplY #2 prsA 91 prsA #3 glmU 254 glmU #4 Rv1112 131 hypothetical protein Rv1112 #5 mrsA 124 mrsA #6 ftsH 66 ftsH #7 Rv3627c 137 hypothetical protein Rv3627c Motif number 1 GCCGTGACGCCCGGCTAGGCTAACCCATGG 1 78 0 CCGGCTAGGC 0.985048 -139 GCCGGGCGTCACGGCGAGGGTGGTCGGCGG 1 93 1 ACGGCGAGGG 0.906992 -124 CTGCTGTAGACCGCCGACCACCCTCGCCGT 1 103 0 CCGCCGACCA 0.86533 -114 CGGTGTTCTGCCGGCCTGCTGTAGACCGCC 1 118 0 CCGGCCTGCT 0.954033 -99 CGACAGCTTGTCGGCCTCCGTCGATAACGG 1 145 0 TCGGCCTCCG 0.714235 -72 GTTTGGGGGCACGGCCAGGGTCGCGACAGC 1 168 0 ACGGCCAGGG 0.973088 -49 AGTCGCATCCCGGCTACCCGGCGACAAAT 2 10 1 CCGGCTACCC 0.981068 -82 TCGATCCCAAACGGCGAGGGCAGCGCG 2 75 1 ACGGCGAGGG 0.906992 -17 CCTGGCGCGCGTCACCCGCGT 3 2 1 CTGGCGCGCG 0.927951 -253 GCCGGAAAACCCGACGCGGGTGACGCGCGC 3 15 0 CCGACGCGGG 0.638715 -240 AGGGCCGGATAAGGCGCCGGAAAACCCGAC 3 30 0 AAGGCGCCGG 0.489843 -225 GGCCCTTTATCCGGTCCGGCCACATCAACA 3 54 1 CCGGTCCGGC 0.953735 -201 CGTCTACCCACCGGCCCCACGCAAACCGAT 3 89 0 CCGGCCCCAC 0.970692 -166 CGGTGGGTAGACGGCGACAGCGTTGACTGT 3 106 1 ACGGCGACAG 0.656232 -149 GACGGTGTCAACGCCGTCAGCACAGTCAAC 3 127 0 ACGCCGTCAG 0.748941 -128 GATGTGCAATCCGTCGTGGTGTAATCGGCA 3 169 1 CCGTCGTGGT 0.828641 -86 GGTTCGAGTCCTGGCGACGGAGCTTCAAGG 3 228 1 CTGGCGACGG 0.50548 -27 CTTGCCTGTACCGCCGACCTCGCCCGCTGC 4 42 1 CCGCCGACCT 0.959954 -90 CCGACCTCGCCCGCTGCGCTGACACACGTC 4 55 1 CCGCTGCGCT 0.849388 -77 GCGCTGACACACGTCGACCGTACCGGCAAT 4 70 1 ACGTCGACCG 0.654163 -62 CGAGGCGGTGCCGCCTTCGGCGCCATTGCC 4 94 0 CCGCCTTCGG 0.929648 -38 GAAGGCGGCACCGCCTCGCCTTAAACTTGG 4 106 1 CCGCCTCGCC 0.959669 -26 CACCGACACGCCGACGAGCGCACACAAACA 5 37 0 CCGACGAGCG 0.957477 -88 ATCGGCCGTGCCGGCCAGGTCCTTCCCGAT 6 42 0 CCGGCCAGGT 0.980451 -25 TTGGACCTGCCCGTTGTCCCATGCACTCTG 7 29 0 CCGTTGTCCC 0.608869 -109 TGCCACGGTACCGGCTCGACTAGGGTGTCC 7 68 0 CCGGCTCGAC 0.953121 -70 CCGAACCGGCCGGGCGACGCTGCCACGGTA 7 88 0 CGGGCGACGC 0.724575 -50 CGTCGCCCGGCCGGTTCGGCAGAATGGGAC 7 99 1 CCGGTTCGGC 0.917278 -39 TCCTGCCTTTCCGGTCCCATTCTGCCGAAC 7 112 0 CCGGTCCCAT 0.666299 -26 ********** Masking position 3 Map Score: 46.7418 Number of sites scoring better than the average of aligned sites = 66245 Number in coding regions = 62051 Number in noncoding regions = 4194 Number of orfs with sites within 600 bp upstream = 1478 Fraction of orfs with sites within 600 bp upstream = 0.237392 Motif number 2 TTGTCCGCACGGTTGGGGCACAGCTATCC 1 7 1 GCCGGTGGGC 0.834077 -210 CTTGTGAGCTGCTCGGATAGCTGTGCCCCAACC 1 21 0 GCCGGTACTG 0.957279 -196 GTGACGCCCGGCTAGGCTAACCCATGGCTACTG 1 72 0 GCAGGTACCC 0.984782 -145 GGGCGTCACGGCGAGGGTGGTCGGCGGTCTACA 1 96 1 GCAGGTGTCG 0.941316 -121 GGCCGGCAGAACACCGTTATCGACGGAGGCCGA 1 132 1 ACCCGTACGA 0.722205 -85 TGGGGGCACGGCCAGGGTCGCGACAGCTTGTCG 1 162 0 GCAGGTCCGA 0.928221 -55 CTCCTGGGTGGCTCGGTTACCTCGTTTGGGGGC 1 188 0 GCCGGTACTC 0.964644 -29 AGTCGCATCCCGGCTACCCGGCGACAAATC 2 8 1 TCCGGTACCG 0.898551 -84 ATCCCAAACGGCGAGGGCAGCGCG 2 78 1 GCAGGCACGC 0.704837 -14 GGAAAACCCGACGCGGGTGACGCGCGCCAGG 3 9 0 ACCGGTGCGC 0.984264 -246 GGCCACATCAACAAGGGTATCGGTTTGCGTGGG 3 71 1 ACAGGTACGG 0.938393 -184 GTCAGCACAGTCAACGCTGTCGCCGTCTACCCA 3 109 0 TCACGTGCGC 0.810616 -146 CCTCCTTGAAGCTCCGTCGCCAGGACTCGAACC 3 228 0 GCCCGCGCAG 0.809032 -27 GCAAGTCACCGCTCGATTCACCCCCACATCCCA 4 14 0 GCCGATCCCC 0.775233 -118 AGCGCAGCGGGCGAGGTCGGCGGTACAGGCAAG 4 42 0 GCAGGCGCGG 0.837093 -90 GCCGCCTTCGGCGCCATTGCCGGTACGGTCGAC 4 82 0 GCCCATGCGG 0.880446 -50 ACACAAACATGCACGCTTGTCGCCCGAAAGTGA 5 13 0 GCCGCTGCGC 0.956342 -112 TTGGTTCACCGACACGCCGACGAGCGCACACAA 5 40 0 GAACGCGCGA 0.519311 -85 CGTCAACTGTGAAAGGTTGTCCGT 5 111 1 GAAGGTGCCG 0.882356 -14 AGCTGGAAAGTCCAGGTTACCGCTC 6 3 0 TCAGGTACGC 0.934389 -64 GGCCGTGCCGGCCAGGTCCTTCCCGATACACGC 6 36 0 GCAGGCCTCC 0.736223 -31 GACCTGGCCGGCACGGCCGATGATCG 6 51 1 GCCGGCGTGA 0.91039 -16 TACCGGCTCGACTAGGGTGTCCACGGACGCATT 7 57 0 ACAGGTGCCA 0.863351 -81 GGGCGACGCTGCCACGGTACCGGCTCGACTAGG 7 74 0 GCACGTACGG 0.97129 -64 TGGCAGCGTCGCCCGGCCGGTTCGGCAGAATGG 7 93 1 GCCGGCGTTC 0.78409 -45 ** *** ** *** Masking position 2 Map Score: 39.7318 Number of sites scoring better than the average of aligned sites = 32009 Number in coding regions = 29833 Number in noncoding regions = 2176 Number of orfs with sites within 600 bp upstream = 1152 Fraction of orfs with sites within 600 bp upstream = 0.185031 Motif number 3 TTGTCCGCACGGTTGGGGCACAGCTATCCG 1 11 1 GGTTGGGGCA 0.560934 -206 ACAGCTATCCGAGCAGCTCACAAGGATCGA 1 30 1 GAGCAGCTCA 0.410474 -187 TAGCCTAGCCGGGCGTCACGGCGAGGGTGG 1 86 1 GGGCGTCACG 0.909465 -131 TACAGCAGGCCGGCAGAACACCGTTATCGA 1 125 1 CGGCAGAACA 0.593963 -92 CCTCGTTTGGGGGCACGGCCAGGGTCGCGA 1 172 0 GGGCACGGCC 0.524688 -45 TGTCGCTCCTGGGTGGCTCGGTTACCTCGT 1 196 0 GGGTGGCTCG 0.918113 -21 CCCGGCTACCCGGCGACAAATCCGGGCGGT 2 19 1 CGGCGACAAA 0.677839 -73 CGACAAATCCGGGCGGTGCGCTACGTACCA 2 32 1 GGGCGGTGCG 0.965645 -60 CAAACGGCGAGGGCAGCGCG 2 82 1 GGGCAGCGCG 0.993061 -10 AACCCGACGCGGGTGACGCGCGCCAGG 3 8 0 GGGTGACGCG 0.914423 -247 GTGTCAACGCCGTCAGCACAGTCAACGCTG 3 123 0 CGTCAGCACA 0.901109 -132 GTGCTGACGGCGTTGACACCGTCTAAAGTC 3 134 1 CGTTGACACC 0.424612 -121 GTGGTGTAATCGGCAGCACCTCTGATTTTG 3 184 1 CGGCAGCACC 0.97431 -71 CGGGCGAGGTCGGCGGTACAGGCAAGTCAC 4 38 0 CGGCGGTACA 0.872883 -94 GGTCGACGTGTGTCAGCGCAGCGGGCGAGG 4 59 0 TGTCAGCGCA 0.713141 -73 TTGCCGGTACGGTCGACGTGTGTCAGCGCA 4 69 0 GGTCGACGTG 0.610376 -63 ATGGCGCCGAAGGCGGCACCGCCTCGCCTT 4 98 1 AGGCGGCACC 0.898178 -34 CATCACTTTCGGGCGACAAGCGTGCATGTT 5 11 1 GGGCGACAAG 0.829456 -114 TGTGTGCGCTCGTCGGCGTGTCGGTGAACC 5 41 1 CGTCGGCGTG 0.829104 -84 TATCCACTCTTGGCAGCGAATATGCCTGTT 5 71 0 TGGCAGCGAA 0.489386 -54 TCACAGTTGACGGCTGCGCACATATCCACT 5 93 0 CGGCTGCGCA 0.897033 -32 GGAAGGACCTGGCCGGCACGGCCGATGATC 6 46 1 GGCCGGCACG 0.937025 -21 GCGTCGGCTCCTTCAGATCAG 7 2 1 CGTCGGCTCC 0.91667 -136 ATGGGACAACGGGCAGGTCCAATGCGTCCG 7 37 1 GGGCAGGTCC 0.790916 -101 CGAACCGGCCGGGCGACGCTGCCACGGTAC 7 87 0 GGGCGACGCT 0.882195 -51 ********** Masking position 2 Map Score: 26.8199 Number of sites scoring better than the average of aligned sites = 50254 Number in coding regions = 47025 Number in noncoding regions = 3229 Number of orfs with sites within 600 bp upstream = 1354 Fraction of orfs with sites within 600 bp upstream = 0.217475 Motif number 4 CGCACGGTTGGGGCACAGCTATCCGAGCAG 1 16 1 GGGCACAGCT 0.86968 -201 GCTAACCCATGGCTACTGCATTGGGGAAAT 1 60 0 GGCTACTGCA 0.980704 -157 GTGGTCGGCGGTCTACAGCAGGCCGGCAGA 1 112 1 GTCTACAGCA 0.954554 -105 TATCCGGTCCGGCCACATCAACAAGGGTAT 3 61 1 GGCCACATCA 0.971911 -194 GTGGGTAGACGGCGACAGCGTTGACTGTGC 3 108 1 GGCGACAGCG 0.942156 -147 GCGTCGGCTCCTTCAGATCAGAGTG 7 6 1 GGCTCCTTCA 0.932179 -132 CCTGCCCGTTGTCCCATGCACTCTGATCTG 7 24 0 GTCCCATGCA 0.947082 -114 CAACGGGCAGGTCCAATGCGTCCGTGGACA 7 43 1 GTCCAATGCG 0.935901 -95 TGCCTTTCCGGTCCCATTCTGCCGAACCGG 7 109 0 GTCCCATTCT 0.718447 -29 ********** Masking position 9 Map Score: 4.35978 Number of sites scoring better than the average of aligned sites = 5759 Number in coding regions = 5362 Number in noncoding regions = 397 Number of orfs with sites within 600 bp upstream = 342 Fraction of orfs with sites within 600 bp upstream = 0.0549309 Motif number 5 GTCACGGCGAGGGTGGTCGGCGGTCTACAG 1 100 1 GGGTGGTCGG 0.986759 -117 GGGTCGCGACAGCTTGTCGGCCTCCGTCGA 1 151 0 AGCTTGTCGG 0.954966 -66 ATTTGTCGCCGGGTAGCCGGGATGCGACT 2 10 0 GGGTAGCCGG 0.971831 -82 TACGTACCATGGGTAATCCAATTCGATCCC 2 53 1 GGGTAATCCA 0.807313 -39 CACCCGCGTCGGGTTTTCCGGCGCCTTATC 3 23 1 GGGTTTTCCG 0.940266 -232 CACATCAACAAGGGTATCGGTTTGCGTGGG 3 74 1 AGGGTATCGG 0.940209 -181 TGGGGCCGGTGGGTAGACGGCGACAGCGTT 3 100 1 GGGTAGACGG 0.95881 -155 ATCCGTCGTGGTGTAATCGGCAGCACCTCT 3 177 1 GTGTAATCGG 0.786232 -78 TGCGCTCGTCGGCGTGTCGGTGAACCAACA 5 45 1 GGCGTGTCGG 0.973082 -80 CAACTGTGAAAGGTTGTCCGT 5 114 1 AGGTTGTCCG 0.981075 -11 CGGCTCGACTAGGGTGTCCACGGACGCATT 7 57 0 AGGGTGTCCA 0.833429 -81 ********** Masking position 8 Map Score: 13.2043 Number of sites scoring better than the average of aligned sites = 4569 Number in coding regions = 4206 Number in noncoding regions = 363 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 6 CAGCTCACAAGGATCGAATTTCCCCAATGC 1 43 1 GGATCGAATT 0.983232 -174 GAGCCACCCAGGAGCGACAT 1 207 1 GGAGCGACAT 0.928302 -10 TCGCCGTTTGGGATCGAATTGGATTACCCA 2 62 0 GGATCGAATT 0.983232 -30 TGATGTGGCCGGACCGGATAAAGGGCCGGA 3 51 0 GGACCGGATA 0.926349 -204 TCCACTCTTGGCAGCGAATATGCCTGTTGG 5 69 0 GCAGCGAATA 0.935545 -56 CCACGGTACCGGCTCGACTAGGGTGTCCAC 7 66 0 GGCTCGACTA 0.94674 -72 ********** Masking position 5 Map Score: 1.80348 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 147 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 ********** No masking Map Score: -1.07759e-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 8 ********** No masking Map Score: -1.07759e-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: -1.07759e-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