AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00900_mtub_reg_100.orf -o00900_mtub_100.ace -a/home/amcguire/genomes/ORF_mtub.txt -z/home/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 GCCCCATTGGCGGCCATGGAAGTACTCGTT 1 18 0 CGGCCATGGA 0.893546 -283 TTGCGCGACGCGGCGCGGCCCACCGGTGGC 1 46 0 CGGCGCGGCC 0.739437 -255 TTGGCTGGTCCGGCCCGGCCCAGGATGGCG 1 78 0 CGGCCCGGCC 0.971617 -223 CTGTCTTCAGCGCCCTTGGGTTGGCTGGTC 1 98 0 CGCCCTTGGG 0.842077 -203 TGTGTGGTTTCCGCGAGCCCACCCGCCGAA 1 163 1 CCGCGAGCCC 0.928408 -138 TATTCCGCGCCGGCGCGAGTGGCCGCTATC 1 198 0 CGGCGCGAGT 0.911125 -103 AGGCTCAGCGCGGCGCCCCTTTCTCATTTG 1 250 0 CGGCGCCCCT 0.92576 -51 AGGGGCGCCGCGCTGAGCCTGAATGCACCG 1 260 1 CGCTGAGCCT 0.90338 -41 GGACCGCTGCCGGTGCTGCCGGTGCATTCA 1 279 0 CGGTGCTGCC 0.892196 -22 GTGATGATCCCGGCGATGGTGACATACTGC 2 14 1 CGGCGATGGT 0.990539 -287 CGGACGCAGGCGGCCAGCAGTATGTCACCA 2 30 0 CGGCCAGCAG 0.920548 -271 CGGAGTCAGCCCGCGACCGGACGCAGGCGG 2 47 0 CCGCGACCGG 0.90041 -254 GCCAGCGGCACGCTCCTGGTGACCGGAGTC 2 70 0 CGCTCCTGGT 0.903086 -231 CGGGGAGATCTGGCCAGCGGCACGCTCCTG 2 82 0 TGGCCAGCGG 0.814341 -219 TTATCCCGCGCGGCCCGCGGGGAGATCTGG 2 99 0 CGGCCCGCGG 0.74957 -202 GTATTTCTTGCTCCGCGGCTTATCCCGCGC 2 118 0 CTCCGCGGCT 0.737175 -183 ACCGCTAGGACCGCGATCAGTATGAGTAGC 2 146 1 CCGCGATCAG 0.730034 -155 GCACGCCAAACTCCCATCCCACCCGGCCAT 2 174 1 CTCCCATCCC 0.580013 -127 CCATCCCACCCGGCCATGGTAGGACTGCTG 2 187 1 CGGCCATGGT 0.986388 -114 GCCGTTATTACGCCGAGCGTGAACTCAGTG 2 223 1 CGCCGAGCGT 0.988489 -78 ACCATCCTTTCGCCGAGCGTGTACCCAGTG 2 275 0 CGCCGAGCGT 0.988489 -26 ACGGCAGCCTCGGTCATCGGGGTGATAGCG 3 60 0 CGGTCATCGG 0.941875 -20 AACCTACCCGCCGTGATGGGAAGTATAGGT 4 57 1 CCGTGATGGG 0.866822 -244 AAGTATAGGTCGCCGCAGGGTATGCGTGTC 4 77 1 CGCCGCAGGG 0.528856 -224 GTTGTCCAGACGCCCCGGGTCATCCACTAC 4 112 0 CGCCCCGGGT 0.985446 -189 TTGCTAACAACCCTGATGGTCGTGTTGGTC 4 158 1 CCCTGATGGT 0.772722 -143 GAAGCAATATCGCCGATTGCTCGTTCGCTG 4 244 1 CGCCGATTGC 0.797536 -57 ********** Masking position 1 Map Score: 41.4512 Number of sites scoring better than the average of aligned sites = 62438 Number in coding regions = 58289 Number in noncoding regions = 4149 Number of orfs with sites within 600 bp upstream = 1459 Fraction of orfs with sites within 600 bp upstream = 0.23434 Motif number 2 CCCCATTGGCGGCCATGGAAGTACTCGTTTG 1 16 0 GGCCATGGAG 0.872585 -285 CCGCCAATGGGGCCACCGGTGGGCCGCGCCG 1 35 1 GGCCACCGGG 0.975805 -266 CCACCGGTGGGCCGCGCCGCGTCGCGCAAAT 1 47 1 GCCGCGCCGG 0.913569 -254 GTCCGGCCCGGCCCAGGATGGCGATTTGCGC 1 70 0 GCCCAGGATG 0.85683 -231 CCAACCCAAGGGCGCTGAAGACAGCATAAAC 1 104 1 GGCGCTGAAA 0.603667 -197 TCGGCGGGTGGGCTCGCGGAAACCACACAAG 1 161 0 GGCTCGCGGA 0.923967 -140 ATTCCGCGCCGGCGCGAGTGGCCGCTATCGA 1 196 0 GGCGCGAGTG 0.914599 -105 CACTCGCGCCGGCGCGGAATACACTGTCGGG 1 207 1 GGCGCGGAAA 0.838572 -94 TACACTGTCGGGCCATAGGCACGCCAAATGA 1 226 1 GGCCATAGGA 0.820806 -75 AGAAAGGGGCGCCGCGCTGAGCCTGAATGCA 1 256 1 GCCGCGCTGG 0.877037 -45 TGATGATCCCGGCGATGGTGACATACTGCTG 2 15 1 GGCGATGGTA 0.930538 -286 GGACGCAGGCGGCCAGCAGTATGTCACCATC 2 28 0 GGCCAGCAGA 0.961271 -273 GCACGCTCCTGGTGACCGGAGTCAGCCCGCG 2 62 0 GGTGACCGGG 0.763235 -239 GGGGAGATCTGGCCAGCGGCACGCTCCTGGT 2 80 0 GGCCAGCGGA 0.991964 -221 TATCCCGCGCGGCCCGCGGGGAGATCTGGCC 2 97 0 GGCCCGCGGG 0.995147 -204 CGCGGGATAAGCCGCGGAGCAAGAAATACCG 2 119 1 GCCGCGGAGA 0.951165 -182 CATCCCACCCGGCCATGGTAGGACTGCTGGC 2 188 1 GGCCATGGTG 0.937982 -113 CCGTTATTACGCCGAGCGTGAACTCAGTGCA 2 224 1 GCCGAGCGTA 0.96662 -77 CCATCCTTTCGCCGAGCGTGTACCCAGTGCG 2 273 0 GCCGAGCGTT 0.754999 -28 CGGCAGCCTCGGTCATCGGGGTGATAGCGGA 3 58 0 GGTCATCGGG 0.765641 -22 AGTATAGGTCGCCGCAGGGTATGCGTGTCTT 4 78 1 GCCGCAGGGA 0.855127 -223 TTGTCCAGACGCCCCGGGTCATCCACTACAG 4 110 0 GCCCCGGGTA 0.964895 -191 GGTCGTGTTGGTCGACGGGCATAGGTACATG 4 175 1 GTCGACGGGA 0.647941 -126 ********* * Masking position 1 Map Score: 31.539 Number of sites scoring better than the average of aligned sites = 26078 Number in coding regions = 24075 Number in noncoding regions = 2003 Number of orfs with sites within 600 bp upstream = 1045 Fraction of orfs with sites within 600 bp upstream = 0.167845 Motif number 3 CGCCAATGGGGCCACCGGTGGGCCGCGCCG 1 36 1 GCCACCGGTG 0.982414 -265 CGGCGGGTGGGCTCGCGGAAACCACACAAG 1 161 0 GCTCGCGGAA 0.826398 -140 CCGAATCATCGATAGCGGCCACTCGCGCCG 1 188 1 GATAGCGGCC 0.946915 -113 CGCTGCCGGTGCTGCCGGTGCATTCAGGCT 1 275 0 GCTGCCGGTG 0.853679 -26 CGGCAGCACCGGCAGCGGTCCAG 1 288 1 GGCAGCGGTC 0.7861 -13 CCAGTGATGATCCCGGCGATGGTGACAT 2 9 1 GATCCCGGCG 0.774731 -292 GACGCAGGCGGCCAGCAGTATGTCACCATC 2 28 0 GCCAGCAGTA 0.897514 -273 CTGGCCGCCTGCGTCCGGTCGCGGGCTGAC 2 43 1 GCGTCCGGTC 0.955321 -258 GTCGCGGGCTGACTCCGGTCACCAGGAGCG 2 60 1 GACTCCGGTC 0.685885 -241 GGGAGATCTGGCCAGCGGCACGCTCCTGGT 2 80 0 GCCAGCGGCA 0.979597 -221 GCGGCTTATCCCGCGCGGCCCGCGGGGAGA 2 104 0 CCGCGCGGCC 0.899219 -197 TGATCGCGGTCCTAGCGGTATTTCTTGCTC 2 135 0 CCTAGCGGTA 0.88288 -166 CGCTAGGACCGCGATCAGTATGAGTAGCAC 2 148 1 GCGATCAGTA 0.22798 -153 AACGGCTCATGCCAGCAGTCCTACCATGGC 2 199 0 GCCAGCAGTC 0.955443 -102 GCGATTTTTCGCGTGCGTTCTTGCACTGAG 2 246 0 GCGTGCGTTC 0.650857 -55 TCCGGAGTAAGATAGGGGTGCTTGTTAAGT 3 14 0 GATAGGGGTG 0.657025 -66 TCATCGGGGTGATAGCGGACCACCCTATCT 3 47 0 GATAGCGGAC 0.8332 -33 GACACGCATACCCTGCGGCGACCTATACTT 4 77 0 CCCTGCGGCG 0.859824 -224 TTGTCCAGACGCCCCGGGTCATCCACTACA 4 111 0 GCCCCGGGTC 0.852061 -190 ********** Masking position 8 Map Score: 20.0318 Number of sites scoring better than the average of aligned sites = 29465 Number in coding regions = 27568 Number in noncoding regions = 1897 Number of orfs with sites within 600 bp upstream = 1010 Fraction of orfs with sites within 600 bp upstream = 0.162223 Motif number 4 AGCCCACCCGCCGAATCATCGATAGCGGCCACTCG 1 178 1 CGATACGTAG 0.974848 -123 CGCGCCGGCGCGGAATACACTGTCGGGCCATAGGC 1 211 1 CGATCCTTCG 0.99301 -90 TCCTGGTGACCGGAGTCAGCCCGCGACCGGACGCA 2 52 0 CGATACCGCG 0.962978 -249 CGTTCTTGCACTGAGTTCACGCTCGGCGTAATAAC 2 226 0 CGATCCGTCG 0.998652 -75 AAAAATCGCACTGGGTACACGCTCGGCGAAAGGAT 2 267 1 CGGTCCGTCG 0.996324 -34 AGCAATATCGCCGATTGCTCGTTCGCTGAAAATAG 4 246 1 CGATCCGTCG 0.998653 -55 * ** * * ** *** Masking position 6 Map Score: 6.95091 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 253 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 CGGTGGCCCCATTGGCGGCCATGGAAGTAC 1 23 0 ATTGGCGGCC 0.866361 -278 CTTGTGTGGTTTCCGCGAGCCCACCCGCCG 1 161 1 TTCCGCGAGC 0.985365 -140 CTATCGATGATTCGGCGGGTGGGCTCGCGG 1 173 0 TTCGGCGGGT 0.959496 -128 CCCTTTCTCATTTGGCGTGCCTATGGCCCG 1 234 0 TTTGGCGTGC 0.995082 -67 CGCGGGGAGATCTGGCCAGCGGCACGCTCC 2 84 0 TCTGGCCAGC 0.890253 -217 GGGATGGGAGTTTGGCGTGCTACTCATACT 2 164 0 TTTGGCGTGC 0.995082 -137 CAGTGCGATTTTTCGCGTGCGTTCTTGCAC 2 250 0 TTTCGCGTGC 0.986206 -51 GCACCATCCTTTCGCCGAGCGTGTACCCAG 2 277 0 TTCGCCGAGC 0.970466 -24 ********** Masking position 6 Map Score: 10.3856 Number of sites scoring better than the average of aligned sites = 2196 Number in coding regions = 2015 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 6 AGCGCGGCGCCCCTTTCTCATTTGGCGTGC 1 244 0 CCCTTTCTCA 0.991005 -57 TAACAAGCACCCCTATCTTACTCCGGAGTA 3 17 1 CCCTATCTTA 0.986154 -63 TAGCGGACCACCCTATCTTACTCCGGAGTA 3 35 0 CCCTATCTTA 0.986154 -45 CAATTGCCTGGCCTTTCTCGGAG 4 4 0 GCCTTTCTCG 0.960171 -297 ********** Masking position 6 Map Score: 1.90852 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TTTCGTGTTTATGCTGTCTTCAGCGCCCTT 1 111 0 ATGCTGTCTT 0.86888 -190 CCGATGACCGAGGCTGCCGT 3 70 1 AGGCTGCCGT 0.990634 -10 AGGCAATTGAATGTTGCAGTATTGTCGAAG 4 25 1 ATGTTGCAGT 0.939649 -276 CACGGCGGGTAGGTTGCCTTCGACAATACT 4 42 0 AGGTTGCCTT 0.987829 -259 TGGGAAGTATAGGTCGCCGCAGGGTATGCG 4 73 1 AGGTCGCCGC 0.944675 -228 GCATAGGTACATGTTGCGTTGATATTTGAA 4 193 1 ATGTTGCGTT 0.936207 -108 ********** Masking position 1 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 TAGCGGCCACTCGCGCCGGCGCGGAATACAC 1 200 1 TCGCGCCGGG 0.989364 -101 GCATTCAGGCTCAGCGCGGCGCCCCTTTCTC 1 255 0 TCAGCGCGGG 0.909608 -46 CCAGTGATGATCCCGGCGATGGTGACAT 2 8 1 TGATCCCGGG 0.896674 -293 GGTCGCGGGCTGACTCCGGTCACCAGGAGCG 2 59 1 TGACTCCGGC 0.871175 -242 GCTGGCCAGATCTCCCCGCGGGCCGCGCGGG 2 94 1 TCTCCCCGCG 0.947045 -207 GCGGTATTTCTTGCTCCGCGGCTTATCCCGC 2 120 0 TTGCTCCGCG 0.944878 -181 CACCCCTATCTTACTCCGGAGTAAGATAGGG 3 24 1 TTACTCCGGG 0.981699 -56 TGGTCCGCTATCACCCCGATGACCGAGGCTG 3 55 1 TCACCCCGAG 0.969317 -25 GAAGTATAGGTCGCCGCAGGGTATGCGTGTC 4 76 1 TCGCCGCAGG 0.89244 -225 AGTTGTCCAGACGCCCCGGGTCATCCACTAC 4 112 0 ACGCCCCGGT 0.815768 -189 CGATATTGCTTCACTTCGGAGATACCCAAAT 4 225 0 TCACTTCGGG 0.943214 -76 CGACTCACTGTTGCTCCGGTGAGGTTAAGA 4 281 1 TTGCTCCGGG 0.986299 -20 ********* * Masking position 7 Map Score: 13.1016 Number of sites scoring better than the average of aligned sites = 6113 Number in coding regions = 5648 Number in noncoding regions = 465 Number of orfs with sites within 600 bp upstream = 340 Fraction of orfs with sites within 600 bp upstream = 0.0546097 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