AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00900_mtub_reg_300.orf -o00900_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 -e 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 = 1 Input sequences: #1 idsA2 300 idsA2 #2 Rv3137 300 hypothetical protein Rv3137 #3 fadE24 79 fadE24 #4 idsB 300 idsB #5 idsA 22 idsA Motif number 1 TGGCCCCATTGGCGGCCATGGAAGTACTCG 1 20 0 GGCGGCCATG 0.808707 -281 CGGCGCGGCCCACCGGTGGCCCCATTGGCG 1 36 0 CACCGGTGGC 0.869691 -265 GCCACCGGTGGGCCGCGCCGCGTCGCGCAA 1 46 1 GGCCGCGCCG 0.732225 -255 TGGCTGGTCCGGCCCGGCCCAGGATGGCGA 1 77 0 GGCCCGGCCC 0.762663 -224 TCGATGATTCGGCGGGTGGGCTCGCGGAAA 1 170 0 GGCGGGTGGG 0.922496 -131 CGGCGCGAGTGGCCGCTATCGATGATTCGG 1 188 0 GGCCGCTATC 0.970804 -113 AGCGGCCACTCGCGCCGGCGCGGAATACAC 1 201 1 CGCGCCGGCG 0.544863 -100 ATGAGAAAGGGGCGCCGCGCTGAGCCTGAA 1 253 1 GGCGCCGCGC 0.93977 -48 AGCCTGAATGCACCGGCAGCACCGGCAGCG 1 275 1 CACCGGCAGC 0.82951 -26 CTGGACCGCTGCCGGTGCTGCCG 1 288 0 GACCGCTGCC 0.609921 -13 ATGTCACCATCGCCGGGATCATCACTGG 2 9 0 CGCCGGGATC 0.88476 -292 ACCGGACGCAGGCGGCCAGCAGTATGTCAC 2 32 0 GGCGGCCAGC 0.924539 -269 ACCGGAGTCAGCCCGCGACCGGACGCAGGC 2 49 0 GCCCGCGACC 0.574732 -252 GTCGCGGGCTGACTCCGGTCACCAGGAGCG 2 60 1 GACTCCGGTC 0.5864 -241 ACCAGGAGCGTGCCGCTGGCCAGATCTCCC 2 80 1 TGCCGCTGGC 0.954587 -221 GGCCAGATCTCCCCGCGGGCCGCGCGGGAT 2 97 1 CCCCGCGGGC 0.500983 -204 CGCGGGATAAGCCGCGGAGCAAGAAATACC 2 119 1 GCCGCGGAGC 0.912382 -182 ATACCGCTAGGACCGCGATCAGTATGAGTA 2 144 1 GACCGCGATC 0.771765 -157 TCCTACCATGGCCGGGTGGGATGGGAGTTT 2 181 0 GCCGGGTGGG 0.813418 -120 GCCATGGTAGGACTGCTGGCATGAGCCGTT 2 199 1 GACTGCTGGC 0.875285 -102 GAGCCGTTATTACGCCGAGCGTGAACTCAG 2 221 1 TACGCCGAGC 0.897787 -80 GCACCATCCTTTCGCCGAGCGTGTACCCAG 2 277 0 TTCGCCGAGC 0.686046 -24 ACTTAACAAGCACCCCTATCTTACTCCGGA 3 14 1 CACCCCTATC 0.785738 -66 AGATAGGGTGGTCCGCTATCACCCCGATGA 3 47 1 GTCCGCTATC 0.833672 -33 TTCCCATCACGGCGGGTAGGTTGCCTTCGA 4 49 0 GGCGGGTAGG 0.940731 -252 ACGCATACCCTGCGGCGACCTATACTTCCC 4 74 0 TGCGGCGACC 0.939956 -227 TGTAGTGGATGACCCGGGGCGTCTGGACAA 4 111 1 GACCCGGGGC 0.517188 -190 ********** Masking position 3 Map Score: 39.3428 Number of sites scoring better than the average of aligned sites = 72763 Number in coding regions = 68143 Number in noncoding regions = 4620 Number of orfs with sites within 600 bp upstream = 1472 Fraction of orfs with sites within 600 bp upstream = 0.236428 Motif number 2 CCACCGGTGGCCCCATTGGCGGCCATGGAA 1 27 0 CCCCATTGGC 0.622193 -274 TTTGCGCGACGCGGCGCGGCCCACCGGTGG 1 47 0 GCGGCGCGGC 0.827359 -254 GTTGGCTGGTCCGGCCCGGCCCAGGATGGC 1 79 0 CCGGCCCGGC 0.990706 -222 AGCCCACCCGCCGAATCATCGATAGCGGCC 1 178 1 CCGAATCATC 0.7014 -123 ACAGTGTATTCCGCGCCGGCGCGAGTGGCC 1 204 0 CCGCGCCGGC 0.977662 -97 CCGGTGCATTCAGGCTCAGCGCGGCGCCCC 1 261 0 CAGGCTCAGC 0.974525 -40 AATGCACCGGCAGCACCGGCAGCGGTCCAG 1 281 1 CAGCACCGGC 0.966798 -20 TCACCATCGCCGGGATCATCACTGG 2 6 0 CGGGATCATC 0.868831 -295 CGCGACCGGACGCAGGCGGCCAGCAGTATG 2 36 0 CGCAGGCGGC 0.92135 -265 GGAGTCAGCCCGCGACCGGACGCAGGCGGC 2 46 0 CGCGACCGGA 0.788425 -255 TCCTGGTGACCGGAGTCAGCCCGCGACCGG 2 57 0 CGGAGTCAGC 0.819706 -244 CTCCGGTCACCAGGAGCGTGCCGCTGGCCA 2 72 1 CAGGAGCGTG 0.566302 -229 CGCGGCTTATCCCGCGCGGCCCGCGGGGAG 2 105 0 CCCGCGCGGC 0.685026 -196 CCGCTAGGACCGCGATCAGTATGAGTAGCA 2 147 1 CGCGATCAGT 0.657477 -154 AAACTCCCATCCCACCCGGCCATGGTAGGA 2 181 1 CCCACCCGGC 0.960109 -120 GCACTGAGTTCACGCTCGGCGTAATAACGG 2 224 0 CACGCTCGGC 0.891034 -77 GCACTGGGTACACGCTCGGCGAAAGGATGG 2 274 1 CACGCTCGGC 0.891034 -27 ACGGCAGCCTCGGTCATCGGGGTG 3 66 0 CAGCCTCGGT 0.760431 -14 AGTGGATGACCCGGGGCGTCTGGACAACTC 4 114 1 CCGGGGCGTC 0.962124 -187 CGTCGACCAACACGACCATCAGGGTTGTTA 4 162 0 CACGACCATC 0.823136 -139 CTTAACCTCACCGGAGCAACAGTGAGTCGC 4 280 0 CCGGAGCAAC 0.758389 -21 ********** Masking position 7 Map Score: 28.5984 Number of sites scoring better than the average of aligned sites = 54260 Number in coding regions = 50897 Number in noncoding regions = 3363 Number of orfs with sites within 600 bp upstream = 1358 Fraction of orfs with sites within 600 bp upstream = 0.218118 Motif number 3 CTTGTGTGGTTTCCGCGAGCCCACCCGCCG 1 161 1 TTCCGCGAGC 0.983276 -140 CTATCGATGATTCGGCGGGTGGGCTCGCGG 1 173 0 TTCGGCGGGT 0.897048 -128 TAGCGGCCACTCGCGCCGGCGCGGAATACA 1 200 1 TCGCGCCGGC 0.813155 -101 CCCTTTCTCATTTGGCGTGCCTATGGCCCG 1 234 0 TTTGGCGTGC 0.96663 -67 ACCGGACGCAGGCGGCCAGCAGTATGTCAC 2 32 0 GGCGGCCAGC 0.692027 -269 GCCTGCGTCCGGTCGCGGGCTGACTCCGGT 2 49 1 GGTCGCGGGC 0.528906 -252 CGCGGGGAGATCTGGCCAGCGGCACGCTCC 2 84 0 TCTGGCCAGC 0.881972 -217 GGCCAGATCTCCCCGCGGGCCGCGCGGGAT 2 97 1 CCCCGCGGGC 0.743332 -204 GGGATGGGAGTTTGGCGTGCTACTCATACT 2 164 0 TTTGGCGTGC 0.96663 -137 TAATAACGGCTCATGCCAGCAGTCCTACCA 2 203 0 TCATGCCAGC 0.387416 -98 GAGCCGTTATTACGCCGAGCGTGAACTCAG 2 221 1 TACGCCGAGC 0.848663 -80 CAGTGCGATTTTTCGCGTGCGTTCTTGCAC 2 250 0 TTTCGCGTGC 0.947314 -51 GCACCATCCTTTCGCCGAGCGTGTACCCAG 2 277 0 TTCGCCGAGC 0.968995 -24 ACGCATACCCTGCGGCGACCTATACTTCCC 4 74 0 TGCGGCGACC 0.92036 -227 AGTCGCTATTTTCAGCGAACGAGCAATCGG 4 256 0 TTCAGCGAAC 0.529276 -45 ********** Masking position 6 Map Score: 14.3225 Number of sites scoring better than the average of aligned sites = 12667 Number in coding regions = 11734 Number in noncoding regions = 933 Number of orfs with sites within 600 bp upstream = 649 Fraction of orfs with sites within 600 bp upstream = 0.10424 Motif number 4 GCGAGCCCACCCGCCGAATCATCGATAGCGGCCACT 1 175 1 CCCGATACGT 0.975353 -126 ACTCGCGCCGGCGCGGAATACACTGTCGGGCCATAG 1 208 1 GCCGATCCTT 0.990657 -93 GTGCGTTCTTGCACTGAGTTCACGCTCGGCGTAATA 2 228 0 GCCGATCCGT 0.998543 -73 GCGAAAAATCGCACTGGGTACACGCTCGGCGAAAGG 2 264 1 GCCGGTCCGT 0.996027 -37 TTAGCAATGATCTCGGAATTCGAGTTGTCCAGACGC 4 129 0 TCCGATCAGT 0.9792 -172 TGAAGCAATATCGCCGATTGCTCGTTCGCTGAAAAT 4 243 1 TCCGATCCGT 0.996725 -58 ** * ** * * ** * Masking position 9 Map Score: 5.94222 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 161 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ATGGGGCCACCGGTGGGCCGCGCCGCGTCG 1 41 1 CGGTGGGCCG 0.97751 -260 CAGCGCCCTTGGGTTGGCTGGTCCGGCCCG 1 91 0 GGGTTGGCTG 0.991699 -210 GAAGCAACTTGTGTGGTTTCCGCGAGCCCA 1 154 1 GTGTGGTTTC 0.791138 -147 ATGATTCGGCGGGTGGGCTCGCGGAAACCA 1 167 0 GGGTGGGCTC 0.989371 -134 TACCATGGCCGGGTGGGATGGGAGTTTGGC 2 178 0 GGGTGGGATG 0.983213 -123 GAGTAAGATAGGGTGGTCCGCTATCACCCC 3 42 1 GGGTGGTCCG 0.989908 -38 CCATCACGGCGGGTAGGTTGCCTTCGACAA 4 46 0 GGGTAGGTTG 0.967544 -255 ACGACCATCAGGGTTGTTAGCAATGATCTC 4 151 0 GGGTTGTTAG 0.85896 -150 CCTGATGGTCGTGTTGGTCGACGGGCATAG 4 169 1 GTGTTGGTCG 0.935642 -132 ********** Masking position 4 Map Score: 13.4797 Number of sites scoring better than the average of aligned sites = 2052 Number in coding regions = 1865 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 6 GATAAGCCGCGGAGCAAGAAATACCGCTAG 2 124 1 GGAGCAAGAA 0.98627 -177 GTTCACGCTCGGCGTAATAACGGCTCATGC 2 217 0 GGCGTAATAA 0.881146 -84 ATCTTACTCCGGAGTAAGATAGGGGTGCTT 3 21 0 GGAGTAAGAT 0.984953 -59 ATCTTACTCCGGAGTAAGATAGGGTGGTCC 3 31 1 GGAGTAAGAT 0.984953 -49 TCTCCGAAGTGAAGCAATATCGCCGATTGC 4 234 1 GAAGCAATAT 0.876044 -67 TAACCTCACCGGAGCAACAGTGAGTCGCTA 4 278 0 GGAGCAACAG 0.957489 -23 ********** Masking position 6 Map Score: 3.779 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 50 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AAGGGCGCTGAAGACAGCATAAACACGAAA 1 111 1 AAGACAGCAT 0.85814 -190 ACGGCAGCCTCGGTCATCGG 3 70 0 ACGGCAGCCT 0.989751 -10 CTTCGACAATACTGCAACATTCAATTGCCT 4 25 0 ACTGCAACAT 0.934266 -276 AGTATTGTCGAAGGCAACCTACCCGCCGTG 4 42 1 AAGGCAACCT 0.986685 -259 CGCATACCCTGCGGCGACCTATACTTCCCA 4 73 0 GCGGCGACCT 0.939715 -228 TTCAAATATCAACGCAACATGTACCTATGC 4 193 0 AACGCAACAT 0.930539 -108 ********** Masking position 10 Map Score: 1.51767 Number of sites scoring better than the average of aligned sites = 1177 Number in coding regions = 1100 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 8 CCGCCAATGGGGCCACCGGTGGGCCGCGCC 1 35 1 GGCCACCGGT 0.779951 -266 AGCGCCCTTGGGTTGGCTGGTCCGGCCCGG 1 90 0 GGTTGGCTGG 0.907756 -211 TGATTCGGCGGGTGGGCTCGCGGAAACCAC 1 166 0 GGTGGGCTCG 0.93988 -135 AATGAGAAAGGGGCGCCGCGCTGAGCCTGA 1 252 1 GGGCGCCGCG 0.97416 -49 GGCTGACTCCGGTCACCAGGAGCGTGCCGC 2 66 1 GGTCACCAGG 0.953265 -235 CGGCCCGCGGGGAGATCTGGCCAGCGGCAC 2 89 0 GGAGATCTGG 0.796684 -212 GGCCATGGTAGGACTGCTGGCATGAGCCGT 2 198 1 GGACTGCTGG 0.890663 -103 CGGCAGCCTCGGTCATCGGGGTGATAGCGG 3 59 0 GGTCATCGGG 0.978047 -21 GGGAAGTATAGGTCGCCGCAGGGTATGCGT 4 74 1 GGTCGCCGCA 0.914558 -227 CGGGGCGTCTGGACAACTCGAATTCCGAGA 4 125 1 GGACAACTCG 0.895177 -176 TGGTCGTGTTGGTCGACGGGCATAGGTACA 4 174 1 GGTCGACGGG 0.98612 -127 ********** Masking position 7 Map Score: 7.67125 Number of sites scoring better than the average of aligned sites = 12120 Number in coding regions = 11359 Number in noncoding regions = 761 Number of orfs with sites within 600 bp upstream = 587 Fraction of orfs with sites within 600 bp upstream = 0.094282 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 Motif number 10 ********** 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 11 ********** 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