AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -ifhlA_mtub_opreg_100.orf -g0.656 -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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0079 300 hypothetical protein Rv0079 #2 Rv0081 94 hypothetical protein Rv0081 #3 Rv0196 112 hypothetical protein Rv0196 #4 PE_PGRS 300 PE_PGRS #5 Rv0748 90 hypothetical protein Rv0748 #6 Rv0749 23 hypothetical protein Rv0749 Motif number 1 GTGGCAGTTTCCGTCGCTGCGCAGAAGCTG 1 82 0 CCGTCGCTGC 0.826394 -219 CGTTGCCACACGTGCGCCCAGTAGGCTTTG 1 115 0 CGTGCGCCCA 0.61632 -186 ATTCGGCTAGTCCGCGGCCCAACGGCGGCA 1 162 0 TCCGCGGCCC 0.949046 -139 TGGCATGGGACTTTCGGCCCTGTCCGCGTC 1 219 1 CTTTCGGCCC 0.841422 -82 TTCGGCCCTGTCCGCGTCCGTGTCGGCCAG 1 231 1 TCCGCGTCCG 0.743163 -70 CGATTGGCCGCGGGCGGCCCGCACGCATCC 2 12 1 CGGGCGGCCC 0.644724 -83 TTGATGGCCGGCGTCCGACGTACGTGC 3 8 1 CCGGCGTCCG 0.540916 -105 GTCCGACGTACGTGCGGCCGGGCCGATCCC 3 23 1 CGTGCGGCCG 0.890457 -90 GCGAAGATCCCCGGCGCTCGAGCGCTTTGT 4 16 1 CCGGCGCTCG 0.506119 -285 TGTCAGAGGCCCGTCGCGGGTCGTCGTGAC 4 43 1 CCGTCGCGGG 0.536634 -258 GACGGCTATCCGGGCGGTGCGGGTTTCGCG 4 73 1 CGGGCGGTGC 0.901445 -228 TGCGGGTTTCGCGGCGCGCCCTGTGCCCGG 4 90 1 GCGGCGCGCC 0.505407 -211 TGCCGACAAACGGGCGGCGGTGCCGGGCAC 4 112 0 CGGGCGGCGG 0.520196 -189 CGGCTCACGGGTCGCGGCGGCGTTGCCGAC 4 135 0 GTCGCGGCGG 0.850141 -166 CGTCCAGCAGCTGGCGCCTGCGAAACGTGT 4 163 1 CTGGCGCCTG 0.762485 -138 ATATCGCGATCCGGCACCGCATGCAGCGCT 4 196 0 CCGGCACCGC 0.547322 -105 CCCTCACGGCCTGGTGCCCGACTACCAGCG 4 266 0 CTGGTGCCCG 0.692272 -35 CCGGCGGGCCTGCGACCGCG 5 1 1 CCGGCGGGCC 0.831912 -90 GGCCTGCGACCGCGCGCGGCGTTGACAGCA 5 17 1 CGCGCGCGGC 0.509866 -74 CATCTGCGGTCGAGCGGCCGAAGCGATGCT 5 43 0 CGAGCGGCCG 0.623437 -48 ********** Masking position 5 Map Score: 40.4218 Number of sites scoring better than the average of aligned sites = 32215 Number in coding regions = 30191 Number in noncoding regions = 2024 Number of orfs with sites within 600 bp upstream = 980 Fraction of orfs with sites within 600 bp upstream = 0.157404 Motif number 2 GGTTGGCGAGCAGATGCAGCGCATGAGGCTGG 1 27 0 CGATGAGCGC 0.981278 -274 GAGCGAGCCTCAGCTTCTGCGCAGCGACGGAA 1 72 1 CGCTTTGCGC 0.740152 -229 GCCACACGTGCGCCCAGTAGGCTTTGAGTGTG 1 109 0 CCCCATAGGC 0.545127 -192 ACACGAAATGCCGCCGTTGGGCCGCGGACTAG 1 154 1 CGCCGTGGGC 0.989298 -147 CCGGAAAATTCGGCTAGTCCGCGGCCCAACGG 1 167 0 CGCTATCCGC 0.914532 -134 CCGACACGGACGCGGACAGGGCCGAAAGTCCC 1 225 0 CCGGAAGGGC 0.788938 -76 CGATTGGCCGCGGGCGGCCCGCACGCATCCGC 2 12 1 CGGCGCCCGC 0.977985 -83 AAGAATTTATCAGATAGTGCGGATGCGTGCGG 2 30 0 CGATATGCGG 0.921282 -65 AACTCGTCAACCGATGTAACGCTGAAGCTCTC 2 63 1 CGATGAACGC 0.819128 -32 TTGATGGCCGGCGTCCGACGTA 3 1 1 TGATGCCGGC 0.355461 -112 TGGCCGGCGTCCGACGTACGTGCGGCCGGGCC 3 15 1 CGACGACGTG 0.59305 -98 ACATATGCCTCGGATGGAGCGGCG 3 99 1 CGATGAGCGG 0.974195 -14 ACAAAGCGCTCGAGCGCCGGGGATCTTCGCCG 4 14 0 CAGCGCGGGG 0.700718 -287 CGACGGGCCTCTGACAAAGCGCTCGAGCGCCG 4 27 0 CGACAAGCGC 0.972498 -274 GTCACGACGACCCGCGACGGGCCTCTGACAAA 4 41 0 CCGCGCGGGC 0.971845 -260 GACGGCTATCCGGGCGGTGCGGGTTTCGCGGC 4 73 1 CGGCGTGCGG 0.985027 -228 GCGGCGGTGCCGGGCACAGGGCGCGCCGCGAA 4 97 0 CGGCAAGGGC 0.973162 -204 GGCGGCGTTGCCGACAAACGGGCGGCGGTGCC 4 118 0 CGACAACGGG 0.909044 -183 CTGGACGGCTCACGGGTCGCGGCGGCGTTGCC 4 138 0 CCGGGCGCGG 0.773841 -163 CAGGCGCCAGCTGCTGGACGGCTCACGGGTCG 4 151 0 CGCTGACGGC 0.967917 -150 GCAGCGCTTCCACACGTTTCGCAGGCGCCAGC 4 172 0 CCACGTTCGC 0.61627 -129 GATCCGGCACCGCATGCAGCGCTTCCACACGT 4 187 0 CCATGAGCGC 0.959057 -114 ACCAGCGACACACCCGTACGGGTAGGAATTAA 4 241 0 CCCCGACGGG 0.931927 -60 GGGTGTGTCGCTGGTAGTCGGGCACCAGGCCG 4 258 1 CGGTATCGGG 0.851245 -43 CCGGCGGGCCTGCGACCGCGCGCGGCGTTGA 5 10 1 CGCGACGCGC 0.902131 -81 TGCGGTCGAGCGGCCGAAGCGATGCTGTCAAC 5 37 0 CGCCGAGCGA 0.863461 -54 CGCTCGACCGCAGATGATGCTGTTGATGCGTT 5 57 1 CGATGTGCTG 0.632514 -34 TGCCGTTCTGCGCCTATTGGGGG 6 2 0 CCCTATGGGG 0.850844 -22 * **** ***** Masking position 1 Map Score: 43.7764 Number of sites scoring better than the average of aligned sites = 44307 Number in coding regions = 41271 Number in noncoding regions = 3036 Number of orfs with sites within 600 bp upstream = 1310 Fraction of orfs with sites within 600 bp upstream = 0.210408 Motif number 3 TCACGACCCAGCCTCATGCGCTGCATCTGC 1 20 1 GCCTCATGCG 0.918117 -281 CCTCGTACATGTCCAGAGCGAGCCTCAGCT 1 57 1 GTCCAGAGCG 0.82679 -244 CCACACGTGCGCCCAGTAGGCTTTGAGTGT 1 110 0 GCCCAGTAGG 0.88374 -191 GCTAGTCCGCGGCCCAACGGCGGCATTTCG 1 157 0 GGCCCAACGG 0.924451 -144 CGGAAAATTCGGCTAGTCCGCGGCCCAACG 1 168 0 GGCTAGTCCG 0.929893 -133 AGGGCCGAAAGTCCCATGCCAAATGTGGGC 1 210 0 GTCCCATGCC 0.921693 -91 GGGACTTTCGGCCCTGTCCGCGTCCGTGTC 1 225 1 GCCCTGTCCG 0.947987 -76 AAGCTTGTCTGGCCGACACGGACGCGGACA 1 239 0 GGCCGACACG 0.952176 -62 GCCCGATTGTGGCCAATGCCCAAAGCTTGT 1 261 0 GGCCAATGCC 0.969828 -40 GGCCGCCCGCGGCCAATCGG 2 1 0 GGCCAATCGG 0.953943 -94 GGCCGCGGGCGGCCCGCACGCATCCGCACT 2 17 1 GGCCCGCACG 0.983977 -78 TTGATGGCCGGCGTCCGACGTACGT 3 6 1 GGCCGGCGTC 0.833767 -107 CGTGCGGCCGGGCCGATCCCAAGCGAGTGG 3 33 1 GGCCGATCCC 0.974197 -80 CGCCGCTCCATCCGAGGCATATGT 3 99 0 GCTCCATCCG 0.682306 -14 CTTTGTCAGAGGCCCGTCGCGGGTCGTCGT 4 40 1 GGCCCGTCGC 0.9811 -261 ACGGCTATCCGGGCGGTGCGGGTTTCGCGG 4 74 1 GGGCGGTGCG 0.918145 -227 TTCGCGGCGCGCCCTGTGCCCGGCACCGCC 4 97 1 GCCCTGTGCC 0.922626 -204 GCTGCTGGACGGCTCACGGGTCGCGGCGGC 4 144 0 GGCTCACGGG 0.894315 -157 CCCGTGAGCCGTCCAGCAGCTGGCGCCTGC 4 154 1 GTCCAGCAGC 0.50476 -147 ACCCCTCACGGCCTGGTGCCCGACTACCAG 4 268 0 GCCTGGTGCC 0.892498 -33 CGCGGTCGCAGGCCCGCCGG 5 1 0 GGCCCGCCGG 0.989016 -90 TGCTGTCAACGCCGCGCGCGGTCGCAGGCC 5 17 0 GCCGCGCGCG 0.873081 -74 GCGGTCGAGCGGCCGAAGCGATGCTGTCAA 5 38 0 GGCCGAAGCG 0.959663 -53 ********** Masking position 1 Map Score: 37.8419 Number of sites scoring better than the average of aligned sites = 31639 Number in coding regions = 29688 Number in noncoding regions = 1951 Number of orfs with sites within 600 bp upstream = 1044 Fraction of orfs with sites within 600 bp upstream = 0.167684 Motif number 4 TCACGACCCAGCCTCATGCGCTGCATCTGC 1 20 1 GCCTCATGCG 0.947151 -281 GCATCTGCTCGCCAACCTCGTACATGTCCA 1 42 1 GCCAACCTCG 0.859813 -259 CACACTCAAAGCCTACTGGGCGCACGTGTG 1 109 1 GCCTACTGGG 0.929642 -192 TCGACTCGTTGCCACACGTGCGCCCAGTAG 1 121 0 GCCACACGTG 0.987033 -180 AAAGTCCCATGCCAAATGTGGGCTGTGTCA 1 203 0 GCCAAATGTG 0.935443 -98 ATGCGTGCGGGCCGCCCGCGGCCAATCGG 2 10 0 GCCGCCCGCG 0.964582 -85 CGCGTCTCCTGAGAGCTTCAG 2 84 0 GCGTCTCCTG 0.82932 -11 CAAGCGAGTGGTGTAACGTGCACGGTAGCC 3 52 1 GTGTAACGTG 0.64331 -61 TATACATAATGGCTACCGTGCACGTTACAC 3 62 0 GGCTACCGTG 0.915312 -51 CGTCGTCACGACGACCCGCGACGGGCCTCT 4 47 0 ACGACCCGCG 0.796715 -254 TCGTGACGACGGCTATCCGGGCGGTGCGGG 4 66 1 GGCTATCCGG 0.443498 -235 AGGGCGCGCCGCGAAACCCGCACCGCCCGG 4 82 0 GCGAAACCCG 0.935767 -219 GTTTCGCGGCGCGCCCTGTGCCCGGCACCG 4 95 1 GCGCCCTGTG 0.780351 -206 CGGCGTTGCCGACAAACGGGCGGCGGTGCC 4 118 0 GACAAACGGG 0.838339 -183 CAACGCCGCCGCGACCCGTGAGCCGTCCAG 4 140 1 GCGACCCGTG 0.985723 -161 GCTGGCGCCTGCGAAACGTGTGGAAGCGCT 4 172 1 GCGAAACGTG 0.974183 -129 GACTACCAGCGACACACCCGTACGGGTAGG 4 247 0 GACACACCCG 0.759286 -54 GCCGTTCTGCGCCTATTGGGGG 6 3 0 GCCTATTGGG 0.788479 -21 ********** Masking position 10 Map Score: 20.8295 Number of sites scoring better than the average of aligned sites = 15792 Number in coding regions = 14499 Number in noncoding regions = 1293 Number of orfs with sites within 600 bp upstream = 796 Fraction of orfs with sites within 600 bp upstream = 0.127851 Motif number 5 AAGCTGAGGCTCGCTCTGGACATGTACGAG 1 58 0 TCGCTCTGGA 0.861682 -243 ACGAAATGCCGCCGTTGGGCCGCGGACTAG 1 156 1 GCCGTTGGGC 0.873147 -145 TGCCAAATGTGGGCTGTGTCACCACCCGGA 1 194 0 GGGCTGTGTC 0.656987 -107 AGCCCACATTTGGCATGGGACTTTCGGCCC 1 209 1 TGGCATGGGA 0.69447 -92 GACAAGCTTTGGGCATTGGCCACAATCGGG 1 260 1 GGGCATTGGC 0.877139 -41 CCGATTGGCCGCGGGCGGCCCGCACG 2 7 1 GGCCGCGGGC 0.744268 -88 CGACGTACGTGCGGCCGGGCCGATCCCAAG 3 26 1 GCGGCCGGGC 0.894982 -87 GTTACACCACTCGCTTGGGATCGGCCCGGC 3 39 0 TCGCTTGGGA 0.9497 -74 AAGCGCTCGAGCGCCGGGGATCTTCGCCGA 4 13 0 GCGCCGGGGA 0.839877 -288 CGGCGCTCGAGCGCTTTGTCAGAGGCCCGT 4 27 1 GCGCTTTGTC 0.905666 -274 CCAGCAGCTGGCGCCTGCGAAACGTGTGGA 4 166 1 GCGCCTGCGA 0.625472 -135 CAACGATATCGCGATCCGGCACCGCATGCA 4 201 0 GCGATCCGGC 0.81514 -100 CAGGCCGTGAGGGGTTGGGAGGCATGCG 4 283 1 GGGGTTGGGA 0.940728 -18 TGTCAACGCCGCGCGCGGTCGCAGGCCCGC 5 14 0 GCGCGCGGTC 0.923086 -77 GTTGACAGCATCGCTTCGGCCGCTCGACCG 5 37 1 TCGCTTCGGC 0.914422 -54 AGCATCATCTGCGGTCGAGCGGCCGAAGCG 5 48 0 GCGGTCGAGC 0.86044 -43 ********** Masking position 3 Map Score: 16.8946 Number of sites scoring better than the average of aligned sites = 20009 Number in coding regions = 18403 Number in noncoding regions = 1606 Number of orfs with sites within 600 bp upstream = 940 Fraction of orfs with sites within 600 bp upstream = 0.15098 Motif number 6 ACATGTCCAGAGCGAGCCTCAGCTTCTGCG 1 63 1 AGCGAGCCTC 0.882991 -238 GGCGGCATTTCGTGTGGATCGACTCGTTGC 1 139 0 CGTGTGGATC 0.891585 -162 GCGGGCGGCCCGCACGCATCCGCACTATCT 2 21 1 CGCACGCATC 0.988517 -74 TAGCAACATACATATGCCTCGGATGGAGCG 3 90 1 CATATGCCTC 0.817505 -23 CCGGGCACAGGGCGCGCCGCGAAACCCGCA 4 90 0 GGCGCGCCGC 0.973013 -211 GATCCGGCACCGCATGCAGCGCTTCCACAC 4 189 0 CGCATGCAGC 0.986395 -112 CGCATGCCTCCCAACCCCTC 4 291 0 CGCATGCCTC 0.992879 -10 GGCCTGCGACCGCGCGCGGCGTTGACAGCA 5 17 1 CGCGCGCGGC 0.984057 -74 GATGCGTTACCGTGTGCATC 5 81 1 CGTGTGCATC 0.98262 -10 ********** Masking position 10 Map Score: 11.9316 Number of sites scoring better than the average of aligned sites = 4228 Number in coding regions = 3898 Number in noncoding regions = 330 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 7 ACGGAAACTGCCACACTCAAAGCCTACTGG 1 98 1 CCACACTCAA 0.795903 -203 ACGAGTCGATCCACACGAAATGCCGCCGTT 1 142 1 CCACACGAAA 0.899391 -159 GGCTGTGTCACCACCCGGAAAATTCGGCTA 1 183 0 CCACCCGGAA 0.981329 -118 CTTGTCTGGCCGACACGGACGCGGACAGGG 1 236 0 CGACACGGAC 0.854624 -65 TGCGTGCGGGCCGCCCGCGGCCAATCGG 2 9 0 CCGCCCGCGG 0.945768 -86 CGCGGGCGGCCCGCACGCATCCGCACTATC 2 20 1 CCGCACGCAT 0.987892 -75 ATCGGCCCGGCCGCACGTACGTCGGACGCC 3 20 0 CCGCACGTAC 0.947197 -93 GCACGTTACACCACTCGCTTGGGATCGGCC 3 43 0 CCACTCGCTT 0.839089 -70 GTGGTGTAACGTGCACGGTAGCCATTATGT 3 59 1 GTGCACGGTA 0.363075 -54 GTCGTCACGACGACCCGCGACGGGCCTCTG 4 46 0 CGACCCGCGA 0.828834 -255 GAAACCCGCACCGCCCGGATAGCCGTCGTC 4 70 0 CCGCCCGGAT 0.984236 -231 CCCGGCACCGCCGCCCGTTTGTCGGCAACG 4 115 1 CCGCCCGTTT 0.93974 -186 TGCAGCGCTTCCACACGTTTCGCAGGCGCC 4 175 0 CCACACGTTT 0.923929 -126 CGATCCGGCACCGCATGCAGCGCTTCCACA 4 190 0 CCGCATGCAG 0.701647 -111 GATGCACACGGTAACGCATCAAC 5 78 0 GCACACGGTA 0.859762 -13 ********** Masking position 4 Map Score: 15.9199 Number of sites scoring better than the average of aligned sites = 8576 Number in coding regions = 7859 Number in noncoding regions = 717 Number of orfs with sites within 600 bp upstream = 504 Fraction of orfs with sites within 600 bp upstream = 0.0809509 Motif number 8 ********** No masking Map Score: -1.29076e-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: -1.29076e-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: -1.29076e-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