AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_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 Rv0347 300 hypothetical protein Rv0347 #2 dnaK 226 dnaK #3 dnaJ 35 dnaJ #4 dnaJ2 74 dnaJ2 #5 hrcA 171 hrcA Motif number 1 AGATGGGGCACACCCAACGGACTGGCTG 1 9 1 CACACCCAAC 0.483423 -292 CCAACGGACTGGCTGTCAGGCTATCCCACG 1 24 1 GGCTGTCAGG 0.895266 -277 AGCGGCACCTCGCAGCCGCGTGGGATAGCC 1 42 0 CGCAGCCGCG 0.503636 -259 GCTGCGAGGTGCCGCTTGGCAACCAATCGG 1 56 1 GCCGCTTGGC 0.759338 -245 GACAACAAAGCACCGTTGACCGATCGATTG 1 89 0 CACCGTTGAC 0.433343 -212 TTGTCGTGCCGACCGTCGCGGGTGGCCGCG 1 114 1 GACCGTCGCG 0.949138 -187 CGACTGTCAACGCGGCCACCCGCGACGGTC 1 124 0 CGCGGCCACC 0.510576 -177 TGCGGTCACAGGCTGACGCGCCTGGCCAGC 1 158 1 GGCTGACGCG 0.930576 -143 CGAGCGTCTGGCTGGCCAGGCGCGTCAGCC 1 168 0 GCTGGCCAGG 0.513597 -133 TGGCCAGCCAGACGCTCGCGAAGTGCGGGT 1 180 1 GACGCTCGCG 0.959976 -121 ACGACACCCTCGCGGCCAGGACGGACCCGC 1 204 0 CGCGGCCAGG 0.508032 -97 ACACTACGACCGCGGCTACGACACCCTCGC 1 221 0 CGCGGCTACG 0.534105 -80 TGGGAGAGGCCCCGGTCAAGCCCGGAGAGC 2 16 0 CCCGGTCAAG 0.973998 -211 CGGGGCCTCTCCCAGCTACGCCCCGAGCGT 2 32 1 CCCAGCTACG 0.63191 -195 CGGCAGGGCACACGCTCGGGGCGTAGCTGG 2 43 0 CACGCTCGGG 0.941401 -184 CGAGCGTGTGCCCTGCCGACACGCGGGAAC 2 55 1 CCCTGCCGAC 0.92373 -172 GGGAACAAGACCCGCACGACCAGCGTTAGC 2 79 1 CCCGCACGAC 0.922929 -148 GACAGCACACCGCCGTCGAGGCAAGCTTGA 2 149 1 CGCCGTCGAG 0.969428 -78 ATGAGTGCACCCCGCTCAAGCTTGCCTCGA 2 164 0 CCCGCTCAAG 0.960621 -63 TCGCGTCACCCCCTCTCGCCTTCCTCTTTT 3 15 0 CCCTCTCGCC 0.903223 -21 TTTGTGGATAGCCGCTTGAGAAGCGGCATA 4 30 1 GCCGCTTGAG 0.874981 -45 GGCGGATCTTCCCTACCGAGTGGCTGAAGC 5 12 1 CCCTACCGAG 0.574924 -160 AGTGGCTGAAGCCCGACGAGATCATGCTGG 5 30 1 GCCCGACGAG 0.949579 -142 ACGAGATCATGCTGGACACGTTAGTCGGGG 5 45 1 GCTGGACACG 0.72626 -127 CGTTAGTCGGGGCACACGCCCCCTGACCAT 5 63 1 GGCACACGCC 0.761317 -109 GGCGTCTGCCGATGGTCAGGGGGCGTGTGC 5 74 0 GATGGTCAGG 0.528001 -98 CCTGACCATCGGCAGACGCCTGCTAGATGA 5 84 1 GGCAGACGCC 0.797114 -88 GACGGTCAGTGGCCGCCGAGAACGTAAAAT 5 112 1 GGCCGCCGAG 0.963112 -60 GTAAAATGAAGCCGGTCAGGCAGCGTAAGA 5 135 1 GCCGGTCAGG 0.829713 -37 ********** Masking position 3 Map Score: 40.0262 Number of sites scoring better than the average of aligned sites = 92566 Number in coding regions = 86366 Number in noncoding regions = 6200 Number of orfs with sites within 600 bp upstream = 1668 Fraction of orfs with sites within 600 bp upstream = 0.267909 Motif number 2 GGGATAGCCTGACAGCCAGTCCGTTGGGTG 1 21 0 GACAGCCAGT 0.574669 -280 GCACCTCGCAGCCGCGTGGGATAGCCTGAC 1 38 0 GCCGCGTGGG 0.643942 -263 GCTGCGAGGTGCCGCTTGGCAACCAATCGG 1 56 1 GCCGCTTGGC 0.663483 -245 TGTCAACGCGGCCACCCGCGACGGTCGGCA 1 120 0 GCCACCCGCG 0.990817 -181 TGGCCGCGTTGACAGTCGATATTGCGGTCA 1 136 1 GACAGTCGAT 0.703259 -165 CGTCTGGCTGGCCAGGCGCGTCAGCCTGTG 1 164 0 GCCAGGCGCG 0.977814 -137 TGGCCAGCCAGACGCTCGCGAAGTGCGGGT 1 180 1 GACGCTCGCG 0.990646 -121 CCGCGGCTACGACACCCTCGCGGCCAGGAC 1 212 0 GACACCCTCG 0.967242 -89 GGGTGTCGTAGCCGCGGTCGTAGTGTGAGA 1 225 1 GCCGCGGTCG 0.865098 -76 GTGAGACTCCGACACCTGATCCGCCAGCGC 1 249 1 GACACCTGAT 0.788241 -52 GTCGGCAGGGCACACGCTCGGGGCGTAGCT 2 45 0 CACACGCTCG 0.738998 -182 GTGCCCTGCCGACACGCGGGAACAAGACCC 2 62 1 GACACGCGGG 0.979052 -165 GCGGGAACAAGACCCGCACGACCAGCGTTA 2 77 1 GACCCGCACG 0.855408 -150 TTTGTGGATAGCCGCTTGAGAAGCGGCATA 4 30 1 GCCGCTTGAG 0.9384 -45 TCGGGCTTCAGCCACTCGGTAGGGAAGATC 5 16 0 GCCACTCGGT 0.959668 -156 GATCATGCTGGACACGTTAGTCGGGGCACA 5 49 1 GACACGTTAG 0.820141 -123 ACCATCGGCAGACGCCTGCTAGATGACGGT 5 88 1 GACGCCTGCT 0.929204 -84 GTAAAATGAAGCCGGTCAGGCAGCGTAAGA 5 135 1 GCCGGTCAGG 0.84748 -37 ********** Masking position 3 Map Score: 23.8274 Number of sites scoring better than the average of aligned sites = 24660 Number in coding regions = 22802 Number in noncoding regions = 1858 Number of orfs with sites within 600 bp upstream = 1012 Fraction of orfs with sites within 600 bp upstream = 0.162544 Motif number 3 TATCCCACGCGGCTGCGAGGTGCCGCTTGGCA 1 45 1 GGCTGGAGTG 0.848078 -256 GTTTCCGATTGGTTGCCAAGCGGCACCTCGCA 1 58 0 GGTTGCAGCG 0.959953 -243 CGAGCGTCTGGCTGGCCAGGCGCGTCAGCCTG 1 166 0 GCTGGCAGCG 0.928637 -135 CCAGCCAGACGCTCGCGAAGTGCGGGTCCGTC 1 183 1 GCTCGGAGTG 0.980923 -118 TCGTAGCCGCGGTCGTAGTGTGAGACTCCGAC 1 230 1 GGTCGAGGTG 0.923677 -71 TCCGACACCTGATCCGCCAGCGCAGAGATGTG 1 256 1 GATCCCCGCG 0.816241 -45 TGAGATCAACGGACGGAAGGCGACG 1 286 1 GGACGAAGCG 0.938238 -15 CCCCGGTCAAGCCCGGAGAGCAGTGC 2 5 0 GCCCGAGGCA 0.855192 -222 CAGGGCACACGCTCGGGGCGTAGCTGGGAGAG 2 38 0 GCTCGGGGTA 0.895486 -189 AACAAGACCCGCACGACCAGCGTTAGCATGCT 2 82 1 GCACGCCGCG 0.982835 -145 GCTCAAGCTTGCCTCGACGGCGGTGTGCTGTC 2 149 0 GCCTCACGCG 0.837262 -78 GTCGAGGCAAGCTTGAGCGGGGTGCACTCATC 2 163 1 GCTTGGCGGG 0.922121 -64 ACGCGCACCTGCTGCAGGGTTTGTGG 4 5 1 GCACCGCGCA 0.83072 -70 GTGGATAGCCGCTTGAGAAGCGGCATAAAGAC 4 33 1 GCTTGGAGCG 0.985829 -42 GTCTGCCGATGGTCAGGGGGCGTGTGCCCCGA 5 69 0 GGTCAGGGCG 0.952629 -103 AAATGAAGCCGGTCAGGCAGCGTAAGAAGTGA 5 138 1 GGTCAGCGCG 0.967436 -34 ***** ** *** Masking position 10 Map Score: 18.3722 Number of sites scoring better than the average of aligned sites = 20946 Number in coding regions = 19381 Number in noncoding regions = 1565 Number of orfs with sites within 600 bp upstream = 879 Fraction of orfs with sites within 600 bp upstream = 0.141182 Motif number 4 GCCTGACAGCCAGTCCGTTGGGTGTGCCCC 1 15 0 CAGTCCGTTG 0.993879 -286 GATCGGTCAACGGTGCTTTGTTGTCGTGCC 1 94 1 CGGTGCTTTG 0.916731 -207 TGTTGTCGTGCCGACCGTCGCGGGTGGCCG 1 112 1 CCGACCGTCG 0.965429 -189 CGTCGCCTTCCGTCCGTTGATCTCACATC 1 282 0 CCGTCCGTTG 0.996035 -19 TTAGCATGCTCAGTAAGTTGAGTGCATCAG 2 104 1 CAGTAAGTTG 0.913228 -123 TGCTAGATGACGGTCAGTGGCCGCCGAGAA 5 104 1 CGGTCAGTGG 0.974535 -68 ********** Masking position 8 Map Score: 4.31088 Number of sites scoring better than the average of aligned sites = 844 Number in coding regions = 779 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 GCACACCCAACGGACTGGCTGTCAGGCTAT 1 18 1 CGGACTGGCT 0.752069 -283 AGCGGCACCTCGCAGCCGCGTGGGATAGCC 1 42 0 CGCAGCCGCG 0.763333 -259 CGGTCACAGGCTGACGCGCCTGGCCAGCCA 1 160 1 CTGACGCGCC 0.904308 -141 GCGGCCAGGACGGACCCGCACTTCGCGAGC 1 193 0 CGGACCCGCA 0.981136 -108 GCGAGGGTGTCGTAGCCGCGGTCGTAGTGT 1 221 1 CGTAGCCGCG 0.778194 -80 GATCAGGTGTCGGAGTCTCACACTACGACC 1 240 0 CGGAGTCTCA 0.87302 -61 ACTCCGACACCTGATCCGCCAGCGCAGAGA 1 254 1 CTGATCCGCC 0.976366 -47 CGGGCTTGACCGGGGCCTCTCCCAGCTACG 2 22 1 CGGGGCCTCT 0.887857 -205 CATGCTAACGCTGGTCGTGCGGGTCTTGTT 2 82 0 CTGGTCGTGC 0.474432 -145 ACTCAACTTACTGAGCATGCTAACGCTGGT 2 97 0 CTGAGCATGC 0.741099 -130 CAATTCAGAGCTGAGCCTGATGCACTCAAC 2 120 0 CTGAGCCTGA 0.888009 -107 GCTTGATTCTCCTATGCCGCGT 4 63 0 TTGATTCTCC 0.223849 -12 TGGCGGATCTTCCCTACCGAGTG 5 4 1 CGGATCTTCC 0.783047 -168 CACACGCCCCCTGACCATCGGCAGACGCCT 5 75 1 CTGACCATCG 0.859146 -97 TCGGCGGCCACTGACCGTCATCTAGCAGGC 5 101 0 CTGACCGTCA 0.937297 -71 CTTACGCTGCCTGACCGGCTTCATTTTACG 5 134 0 CTGACCGGCT 0.935339 -38 ********** Masking position 1 Map Score: 10.3558 Number of sites scoring better than the average of aligned sites = 20741 Number in coding regions = 19240 Number in noncoding regions = 1501 Number of orfs with sites within 600 bp upstream = 922 Fraction of orfs with sites within 600 bp upstream = 0.148089 Motif number 6 ********** No masking Map Score: -1.16286e-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: -1.16286e-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: -1.16286e-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