AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_bsub_mtub_100.orf -o146_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yufT 300 similar to NADH dehydrogenase #2 Rv0079 300 hypothetical protein Rv0079 #3 Rv0081 94 hypothetical protein Rv0081 #4 nuoA 300 nuoA #5 nuoH 115 nuoH Motif number 1 TGGGCCGTTCACGACCCAGCCTCATGCGCTG 2 12 1 ACGACCCACC 0.774151 -289 AACCTCGTACATGTCCAGAGCGAGCCTCAGC 2 55 1 ATGTCCAGGC 0.522825 -246 CTGCGCAGCGACGGAAACTGCCACACTCAAA 2 88 1 ACGGAAACGC 0.740093 -213 TCGACTCGTTGCCACACGTGCGCCCAGTAGG 2 120 0 GCCACACGGC 0.876879 -181 CGGCTAGTCCGCGGCCCAACGGCGGCATTTC 2 158 0 GCGGCCCACG 0.976725 -143 TGTGGGCTGTGTCACCACCCGGAAAATTCGG 2 186 0 GTCACCACCG 0.696692 -115 CGACACGGACGCGGACAGGGCCGAAAGTCCC 2 225 0 GCGGACAGGC 0.986689 -76 AGCTTGTCTGGCCGACACGGACGCGGACAGG 2 237 0 GCCGACACGA 0.722047 -64 TGGCCCGATTGTGGCCAATGCCCAAAGCTTG 2 262 0 GTGGCCAAGC 0.869914 -39 ATGCGTGCGGGCCGCCCGCGGCCAATCGG 3 9 0 GCCGCCCGGG 0.995372 -86 TGGGGATTGCGCGTCCCGGCGAATTGTATGA 4 67 0 GCGTCCCGCG 0.952922 -234 GCGACCGACGCCGGACCCAGCCACGGGTTCT 4 111 1 CCGGACCCGC 0.956218 -190 ATGCACCAGCCTGACCCCGGGAATGTGGGGT 4 160 1 CTGACCCCGG 0.646131 -141 TAGTCGCGCAACGGCCACCCCACATTCCCGG 4 176 0 ACGGCCACCC 0.981161 -125 GGTCACTGTGACGGCCCGAAGCCCCGGTTCG 4 214 1 ACGGCCCGAG 0.87292 -87 GGCTGCCGTGACGAACCGGGGCTTCGGGCCG 4 225 0 ACGAACCGGG 0.862588 -76 CAGCCCGGTCACCGCCCGGCCGCCGCGCTGG 4 251 1 ACCGCCCGCC 0.983848 -50 GTCGTACGGGGCCGCCAGCGCGGCGGCCGGG 4 265 0 GCCGCCAGGC 0.994263 -36 ACGCGCGCTCGCGGCAAGGGGAGACGC 5 7 0 GCGGCAAGGG 0.968586 -109 CGCGTGTTCCCCCGCAAGCGGGAGGTGCCCC 5 33 1 CCCGCAAGGG 0.828459 -83 CCCCCAGTACGCCGACACACCGATTTTGATG 5 60 1 GCCGACACCC 0.964887 -56 ATGTACCAGTGCGGACCCTCGCGCAAGGAGT 5 88 1 GCGGACCCCG 0.981345 -28 GGCCGCCACTCCTTGCGCGAGG 5 104 0 GCCGCCACCC 0.99003 -12 ******** ** Masking position 6 Map Score: 32.6746 Number of sites scoring better than the average of aligned sites = 4141 Number in coding regions = 3892 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 CAGCCTCATGCGCTGCATCTGCTCGCCAACC 2 28 1 CGCTGCACTG 0.959256 -273 CAGAGCGAGCCTCAGCTTCTGCGCAGCGACG 2 70 1 CTCAGCTCTG 0.957252 -231 TCAGCTTCTGCGCAGCGACGGAAACTGCCAC 2 81 1 CGCAGCGCGG 0.981482 -220 CTGCTCGGCTTTCGATTGTGGCCC 2 287 0 CTCGGCTTCG 0.961635 -14 AATTCTTCAACTCGTCAACCGATGTAACGCT 3 55 1 CTCGTCACCG 0.958075 -40 CGCGTCTCCTGAGAGCTTCAG 3 84 0 CGCGTCTCTG 0.978726 -11 TGTTGTTAATCTCGGCATTTGCC 4 3 0 CTCGGCATTG 0.939977 -298 CCCTGATAAGCGCAGCATTTGTTGTTAATCT 4 22 0 CGCAGCATTG 0.933844 -279 AGTTTTGCTTCGCAGCGACCGACGCCGGACC 4 97 1 CGCAGCGCCG 0.990328 -204 CGGACCCAGCCACGGGTTCTGCTTCGACTCG 4 122 1 CACGGGTCTG 0.884812 -179 CGTGACGAACCGGGGCTTCGGGCCGTCACAG 4 219 0 CGGGGCTCGG 0.954076 -82 CCCGGTTCGTCACGGCAGCCCGGTCACCGCC 4 236 1 CACGGCACCC 0.92483 -65 GGGCCGCCAGCGCGGCGGCCGGGCGGTGACC 4 257 0 CGCGGCGCCG 0.997476 -44 CACGCGCGCTCGCGGCAAGGGGAGACGC 5 8 0 CGCGGCAGGG 0.963342 -108 GCCGCGAGCGCGCGTGTTCCCCCGCAAGCGG 5 23 1 CGCGTGTCCC 0.688007 -93 ******* *** Masking position 1 Map Score: 23.5104 Number of sites scoring better than the average of aligned sites = 1608 Number in coding regions = 1520 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 GAGGCTGGGTCGTGAACGGCCCAA 2 5 0 CGTGAACGGC 0.86937 -296 GACCCAGCCTCATGCGCTGCATCTGCTCGC 2 24 1 CATGCGCTGC 0.795835 -277 GTGGCAGTTTCCGTCGCTGCGCAGAAGCTG 2 82 0 CCGTCGCTGC 0.942877 -219 CGTTGCCACACGTGCGCCCAGTAGGCTTTG 2 115 0 CGTGCGCCCA 0.929296 -186 AAATTCGGCTAGTCCGCGGCCCAACGGCGG 2 164 0 AGTCCGCGGC 0.890363 -137 CTGGCCGACACGGACGCGGACAGGGCCGAA 2 231 0 CGGACGCGGA 0.956131 -70 CGATTGGCCGCGGGCGGCCCGCACGCATCC 3 12 1 CGGGCGGCCC 0.960583 -83 TTCTTCAACTCGTCAACCGATGTAACGCTG 3 57 1 CGTCAACCGA 0.632123 -38 TACAATTCGCCGGGACGCGCAATCCCCAGT 4 70 1 CGGGACGCGC 0.74802 -231 GGTCCGGCGTCGGTCGCTGCGAAGCAAAAC 4 98 0 CGGTCGCTGC 0.987436 -203 AGTCGCGCAACGGCCACCCCACATTCCCGG 4 176 0 CGGCCACCCC 0.975125 -125 CTGTGACGGCCCGAAGCCCCGGTTCGTCAC 4 219 1 CCGAAGCCCC 0.796327 -82 CACGGCAGCCCGGTCACCGCCCGGCCGCCG 4 246 1 CGGTCACCGC 0.982067 -55 GGTCACCGCCCGGCCGCCGCGCTGGCGGCC 4 257 1 CGGCCGCCGC 0.996197 -44 CATGATCCGTCGTACGGGGCCGCCAGCGCG 4 274 0 CGTACGGGGC 0.932631 -27 GGAACACGCGCGCTCGCGGCAAGGGGAGAC 5 13 0 CGCTCGCGGC 0.930213 -103 CCCCCGCAAGCGGGAGGTGCCCCCAGTACG 5 41 1 CGGGAGGTGC 0.920963 -75 AGGTGCCCCCAGTACGCCGACACACCGATT 5 55 1 AGTACGCCGA 0.560027 -61 GGCCGCCACTCCTTGCGCGAGG 5 104 0 CCGCCACTCC 0.745337 -12 ********** Masking position 1 Map Score: 23.1124 Number of sites scoring better than the average of aligned sites = 4300 Number in coding regions = 4018 Number in noncoding regions = 282 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 4 ACAGCAGTTCGAAGCGTGGCAGCTTGCAGA 1 108 1 GAAGCGTGGC 0.762865 -193 GCAGATGCAGCGCATGAGGCTGGGTCGTGA 2 20 0 CGCATGAGGC 0.923692 -281 TGGACATGTACGAGGTTGGCGAGCAGATGC 2 42 0 CGAGGTTGGC 0.728059 -259 CAGTAGGCTTTGAGTGTGGCAGTTTCCGTC 2 97 0 TGAGTGTGGC 0.971633 -204 CTACTGGGCGCACGTGTGGCAACGAGTCGA 2 121 1 CACGTGTGGC 0.972767 -180 AGTCCCATGCCAAATGTGGGCTGTGTCACC 2 201 0 CAAATGTGGG 0.962107 -100 GATTGTGGCCCGATTGTGGCCAATGCCCAA 2 268 0 CGATTGTGGC 0.989683 -33 GCTCGGCTTTCGATTGTGGCCCGATTGTGG 2 279 0 CGATTGTGGC 0.989683 -22 AGATTAACAACAAATGCTGCGCTTATCAGG 4 22 1 CAAATGCTGC 0.725799 -279 GCGAATTGTATGAATGTTGGTCTAACCCCC 4 50 0 TGAATGTTGG 0.654111 -251 CCTGACCCCGGGAATGTGGGGTGGCCGTTG 4 169 1 GGAATGTGGG 0.954643 -132 GGGCACCTCCCGCTTGCGGGGGAACACGCG 5 33 0 CGCTTGCGGG 0.913265 -83 ********** Masking position 9 Map Score: 10.1461 Number of sites scoring better than the average of aligned sites = 804 Number in coding regions = 742 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TCGTTCTCAATTGAAAAATGCGCTATGTATA 1 181 0 TTGAAAATGC 0.680245 -120 TCAATTGAGAACGAGAAAAGGAGGTCTTATC 1 198 1 ACGAAAAAGG 0.822287 -103 ATAAAAGCAAATAAAAAAGGCGATAAAATAG 1 249 0 ATAAAAAGGC 0.692236 -52 CAAGAAGGGAATGATAAAAGCAAATAAAAAA 1 262 0 ATGAAAAAGC 0.94364 -39 TTGGCAAAATACGCAAAAAGA 1 290 1 ACGCAAAAGA 0.855861 -11 GGAAACTGCCACACTCAAAGCCTACTGGGCG 2 100 1 ACACCAAAGC 0.933054 -201 GAGTCGATCCACACGAAATGCCGCCGTTGGG 2 144 1 ACACAAATGC 0.956994 -157 CGAAAGTCCCATGCCAAATGTGGGCTGTGTC 2 204 0 ATGCAAATGT 0.757394 -97 ATTGTGGCCAATGCCCAAAGCTTGTCTGGCC 2 255 0 ATGCCAAAGC 0.952256 -46 GCCGAGATTAACAACAAATGCTGCGCTTATC 4 18 1 ACAAAAATGC 0.921259 -283 ATTCGCCGGGACGCGCAATCCCCAGTTTTGC 4 74 1 ACGCCAATCC 0.815842 -227 **** ****** Masking position 7 Map Score: 4.1028 Number of sites scoring better than the average of aligned sites = 1518 Number in coding regions = 1375 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 CAAGCTGCCACGCTTCGAACTGCTGTAATG 1 104 0 CGCTTCGAAC 0.833192 -197 AGCTGAGGCTCGCTCTGGACATGTACGAGG 2 57 0 CGCTCTGGAC 0.810893 -244 CAGTTTCCGTCGCTGCGCAGAAGCTGAGGC 2 78 0 CGCTGCGCAG 0.917833 -223 GGCAACGAGTCGATCCACACGAAATGCCGC 2 138 1 CGATCCACAC 0.824445 -163 GCCGCCGTTGGGCCGCGGACTAGCCGAATT 2 163 1 GGCCGCGGAC 0.958367 -138 CTTGTCTGGCCGACACGGACGCGGACAGGG 2 236 0 CGACACGGAC 0.876586 -65 TGGCCGCGGGCGGCCCGCACGCATCCGCAC 3 16 1 CGGCCCGCAC 0.993758 -79 CGGCCCGCACGCATCCGCACTATCTGATAA 3 26 1 GCATCCGCAC 0.886716 -69 CAATTCGCCGGGACGCGCAATCCCCAGTTT 4 72 1 GGACGCGCAA 0.7205 -229 GGTTCTGCTTCGACTCGCACAGGTATGCAC 4 136 1 CGACTCGCAC 0.965775 -165 GTCACTGTGACGGCCCGAAGCCCCGGTTCG 4 215 1 CGGCCCGAAG 0.860555 -86 CCGCGCTGGCGGCCCCGTACGACGGATCAT 4 273 1 GGCCCCGTAC 0.971794 -28 GCGGGAGGTGCCCCCAGTACGCCGACACAC 5 50 1 CCCCCAGTAC 0.41997 -66 CCTTGCGCGAGGGTCCGCACTGGTACATCA 5 86 0 GGGTCCGCAC 0.977109 -30 ********** Masking position 9 Map Score: 12.7291 Number of sites scoring better than the average of aligned sites = 1126 Number in coding regions = 1032 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 CAATCCTGATCAAGCTGAAGGAAAG 1 4 0 CAAGCGAGGA 0.95389 -297 ACGAGGTTGGCGAGCAGATGCAGCGCATGAGG 2 31 0 CGAGCGAGCA 0.995273 -270 TCGCTGCGCAGAAGCTGAGGCTCGCTCTGGAC 2 67 0 GAAGCGAGCT 0.782544 -234 CGTGTGGCAACGAGTCGATCCACACGAAATGC 2 133 1 CGAGTGACCA 0.91825 -168 CCGAATTTTCCGGGTGGTGACACAGCCCACAT 2 186 1 CGGGTGTACA 0.754087 -115 CATCGGTTGACGAGTTGAAGAATTTATCAGAT 3 47 0 CGAGTGAGAA 0.883509 -48 CATACCTGTGCGAGTCGAAGCAGAACCCGTGG 4 131 0 CGAGTGAGCA 0.987238 -170 TTCCCGGGGTCAGGCTGGTGCATACCTGTGCG 4 151 0 CAGGCGGGCA 0.97559 -150 ACCGGGGCTTCGGGCCGTCACAGTGACCTTCA 4 210 0 CGGGCGTACA 0.892991 -91 GCTGCCGTGACGAACCGGGGCTTCGGGCCGTC 4 223 0 CGAACGGGCT 0.844986 -78 TGTTCCCCCGCAAGCGGGAGGTGCCCCCAGTA 5 37 1 CAAGCGGGGT 0.87174 -79 ***** ** *** Masking position 7 Map Score: 7.39463 Number of sites scoring better than the average of aligned sites = 1254 Number in coding regions = 1185 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 ********** No masking Map Score: 1.36667e-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: 1.36667e-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: 1.36667e-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