AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i196_bsub_mtub_100.orf -o196_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 sucC 172 succinyl-CoA synthetase (beta subunit) #2 sucD 28 succinyl-CoA synthetase (alpha subunit) #3 smf 60 DNA processing Smf protein homolog #4 topA 187 DNA topoisomerase I #5 gid 75 glucose-inhibited division protein #6 codV 67 integrase/recombinase #7 xerC 90 xerC #8 viuB 32 viuB #9 Rv2898c 247 hypothetical protein Rv2898c #10 topA 300 topA Motif number 1 CGGGGTGAGATCTTTCGGCCTGGGATAGCCGAC 7 10 0 TCCGGCCGGG 0.954962 -81 CGAAAGATCTCACCCCGGACACGGTGCGGCGCGT 7 27 1 CACGGACCGG 0.982197 -64 CATGACGTCTCGAGCCCGAGTCGACGCGCCGCAC 7 50 0 CGCCGAGCGA 0.982742 -41 CTCGAGACGTCATGCCTGCGACTGTGGGGGA 7 70 1 CACTGCGCTG 0.894256 -21 CTGTCCAGACCCGACCCGCGTCGA 8 1 0 CCCCGCGCGA 0.980947 -32 CGGGACTCTTCCGGCGCCGAACATGATGTT 9 7 1 TCCGGCGCGA 0.987751 -241 ATGATGTTGCTGGATCGGCGTGTGCCGCCTGCGG 9 33 1 TGCGGCGGTG 0.948391 -215 CTACTCGCAACGCACCGCAGGCGGCACACGCCGA 9 47 0 CGCGCAGCGG 0.967924 -201 GAAGTTGCTATGTGACGGAGACGATGATGACAAG 9 92 1 TGCGGAGCGA 0.979108 -156 GAGACGATGATGACAAGGACGCGGTGTCGTGATC 9 109 1 TGAGGACCGG 0.819828 -139 TCCACAGCCCCAGTACTGCGCGGGATCACGACAC 9 132 0 CACTGCGGGG 0.946182 -116 GGGCTGTGGACAGGGCCGCGACTGGGGATAACTG 9 156 1 CACCGCGCTG 0.971874 -92 CGCGTCTCACCGATGCCGCGACGACCAGTTATCC 9 181 0 CGCCGCGCGA 0.995823 -67 GGCCAACCTGCACGCTGGCCCCGACATCACCTGC 9 222 0 CATGGCCCGA 0.830175 -26 CCTAGCTCGGCGACGATGCGGTCCCG 10 3 1 TACGGCGCGA 0.989904 -298 GGCGACGATGCGGTCCCGCTGGGGTCCGCTGAGG 10 19 1 CGCCGCTGGG 0.89022 -282 CGCTGGGGTCCGCTGAGGAGCCGGGCAGTCGGAC 10 35 1 CGAGGAGCGG 0.968842 -266 CAGTCGGACCTAGTTCGGCGACGATGCGGATCTC 10 60 1 TACGGCGCGA 0.989904 -241 TTGTCAGTTGCCCACAGGCGAGGGAACGCCGGCG 10 180 1 CCAGGCGGGG 0.940961 -121 AGGTGAATTCCGGTACGCCGGCGTTCCCTCGCCT 10 195 0 CGCGCCGCGT 0.892962 -106 CGGCCCCTATCGAGACCGCCCCGGTAGGTAGAGG 10 251 0 CGCCGCCCGG 0.995205 -50 CTCCATCTCTTATCCCGGCCCCTATCGAGACCGC 10 266 0 TACGGCCCTA 0.853009 -35 ** ***** *** Masking position 8 Map Score: 39.7737 Number of sites scoring better than the average of aligned sites = 2235 Number in coding regions = 2076 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 GTGAGCAAGACCCTGCTCACCG 5 1 0 CCCGCCACCG 0.947485 -75 CCCGAGTCGACGCGCCGCACCGTGTCCGGGGT 7 38 0 CGCCCCACCG 0.574361 -53 ATGTCCTCCTGTCCAGACCCGACCCGCGTC 8 13 0 CTGCCGACCC 0.972901 -20 GCACCGCAGGCGGCACACGCCGATCCAGCAAC 9 38 0 CGGACCGCCG 0.84543 -210 CCCGGCTACTCGCAACGCACCGCAGGCGGCAC 9 54 0 CGCACCACCG 0.87616 -194 AGTCGCGGCCCTGTCCACAGCCCCAGTACTGC 9 147 0 CTGCCCAGCC 0.858538 -101 TGCCACGAATCGCGTCTCACCGATGCCGCGAC 9 193 0 CGCTCCACCG 0.968853 -55 TGCCCGGCTCCTCAGCGGACCCCAGCGGGACC 10 30 0 CTCGCGACCC 0.981618 -271 TCCGAGCGTCCTGAGCGGCCCGTTTGAGCCTT 10 92 1 CTGGCGCCCG 0.886555 -209 TAGGGCGGGCCTGCGCAAACCGGCTGCAAACA 10 138 0 CTGGCAACCG 0.960318 -163 AGGTAGAGGACGCGGCCGACTGCCGAATCCCA 10 228 0 CGCGCGACTG 0.921185 -73 CGGCCGCGTCCTCTACCTACCGGGGCGGTCTC 10 242 1 CTCACTACCG 0.934964 -59 TCTCTTATCCCGGCCCCTATCGAGACCGCCCC 10 263 0 CGGCCTATCG 0.728713 -38 CTGCGCCCACGCTCCATCTCTT 10 289 0 CTGGCCACGC 0.899956 -12 *** ** ***** Masking position 6 Map Score: 16.9686 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 458 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 TAATACCTCCCCAGGAAGGGCTTTTAAATGG 6 44 0 CCAGGAGGGC 0.898589 -24 CTCACCCCGGACACGGTGCGGCGCGTCGACT 7 35 1 ACACGGGCGG 0.946498 -56 CGGTGCGGCGCGTCGACTCGGGCTCGAGACG 7 48 1 CGTCGATCGG 0.790503 -43 GTCATGCCTGCGACTGTGGGGGA 7 78 1 CGACTGGGGG 0.922907 -13 TCGACGCGGGTCGGGTCTGGACAGG 8 5 1 CGCGGGCGGG 0.910643 -28 CGGTGCGTTGCGAGTAGCCGGGACCCGAGAA 9 64 1 CGAGTACCGG 0.944389 -184 ACGATGATGACAAGGACGCGGTGTCGTGATC 9 112 1 CAAGGAGCGG 0.963252 -136 ACATCACCTGCCACGAATCGCGTCTCACCGA 9 202 0 CCACGATCGC 0.787949 -46 CCTAGCTCGGCGACGATGCGGTCCCGCTGGG 10 11 1 CGACGAGCGG 0.993452 -290 TGCGGTCCCGCTGGGGTCCGCTGAGGAGCCG 10 27 1 CTGGGGCCGC 0.777256 -274 GAACTAGGTCCGACTGCCCGGCTCCTCAGCG 10 45 0 CGACTGCCGG 0.964631 -256 CCTAGTTCGGCGACGATGCGGATCTCCGAGC 10 68 1 CGACGAGCGG 0.993452 -233 CCAAAGGCTCAAACGGGCCGCTCAGGACGCT 10 96 0 AAACGGCCGC 0.728667 -205 ATCTCGCACTCTAGGGCGGGCCTGCGCAAAC 10 150 0 CTAGGGGGGC 0.91853 -151 TGCCCACAGGCGAGGGAACGCCGGCGTACCG 10 188 1 CGAGGGACGC 0.943681 -113 CCCGGTAGGTAGAGGACGCGGCCGACTGCCG 10 235 0 AGAGGAGCGG 0.972332 -66 GGCGGTCTCGATAGGGGCCGGGATAAGAGAT 10 265 1 ATAGGGCCGG 0.90411 -36 AGAGATGGAGCGTGGGCGCAG 10 290 1 CGTGGGGCAG 0.740095 -11 ****** **** Masking position 10 Map Score: 21.834 Number of sites scoring better than the average of aligned sites = 1505 Number in coding regions = 1377 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TAAAATATTCCCCATCCTTCTTTGAAATTTATG 1 12 1 CCCCTTCTTT 0.995443 -161 AATAGACTGCGCTTTCATTCTATAATAATACTG 1 117 0 GCCATTCTAT 0.844078 -56 TGGTCCCCTGCCTTTCATTCTTTC 2 2 0 CCCATTCTTT 0.988424 -27 GCCTTGACGGCTGTCCCTTTTTTA 3 2 0 CTCCTTTTTT 0.8918 -59 GCCGTCAAGGCTGTTCCTGCTTTTTCTAACAAA 3 24 1 CTCCTGCTTT 0.951466 -37 TGGCTTTCAACATTTCATTCTTTATCATGAACG 4 93 0 CACATTCTTT 0.9665 -95 GCAGGGTCTTGCTCACCTTCTTTGTGTGTTAAA 5 17 1 GCCCTTCTTT 0.987225 -59 GTTTATTATTCAAGGCCTTCTTTTAACACACAA 5 38 0 CACCTTCTTT 0.986632 -38 ** ******** Masking position 8 Map Score: 7.47526 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 332 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 TAAAAAAGGGACAGCCGTCAAGGCTGT 3 8 1 GGGACAGCCG 0.990663 -53 CAATTTTATTTTTGCAGCTGTCTTTATTTG 4 124 0 TTTGCAGCTG 0.771209 -64 CTTTCGGCCTGGGATAGCCGAC 7 3 0 GGGATAGCCG 0.948285 -88 GGGTCGGGTCTGGACAGGAGGACAT 8 18 1 TGGACAGGAG 0.793815 -15 GCCGCGACTGGGGATAACTGGTCGTCGCGG 9 170 1 GGGATAACTG 0.800806 -78 GACGCGATTCGTGGCAGGTGATGTCGGGGC 9 209 1 GTGGCAGGTG 0.95299 -39 AGGTGATGTCGGGGCCAGCGTGCAGGTTGG 9 224 1 GGGGCCAGCG 0.918181 -24 GGTCCCGCTGGGGTCCGCTGAGGAGCCGGG 10 30 1 GGGTCCGCTG 0.915052 -271 GGGTAATCTGTTTGCAGCCGGTTTGCGCAG 10 130 1 TTTGCAGCCG 0.812724 -171 CCCTCGCCTGTGGGCAACTGACAATCTCGC 10 174 0 TGGGCAACTG 0.951217 -127 ********** Masking position 10 Map Score: 4.93386 Number of sites scoring better than the average of aligned sites = 2172 Number in coding regions = 2023 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 ********** No masking Map Score: -3.63555e-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 TTATTAAAAACATAAATTTCAAAGAAGGATGGGGA 1 20 0 CAATTTAAGA 0.946633 -153 ACAATTCTTCCAGTATTATTATAGAATGAAAGCGC 1 107 1 CAATATAAGA 0.976062 -66 ACTTATGTAACAAAACTAAAATAGACTGCGCTTTC 1 134 0 CAATAAAAGA 0.981513 -39 TTTAAATCCTCACTATTATTAAATATTACAATACC 4 28 0 CAATATAATA 0.84099 -160 TCATGAACGTCATTAATTAAATAGAAAACAATATG 4 67 0 CAATTAAAGA 0.958501 -121 TAATGACGTTCATGATAAAGAATGAAATGTTGAAA 4 87 1 CAAAAAATGA 0.827442 -101 AAGACAGCTGCAAAAATAAAATTGAAATATCTTGA 4 130 1 CAATAAATGA 0.958501 -58 ** * *** * *** Masking position 5 Map Score: 1.60514 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 114 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 GAGAGAGAACACCTCTTGAGGGGGATGAAA 4 168 1 ACCTCTTGAG 0.883749 -20 GTATTGATTGCAACCTGAGCGCGATTTGT 6 10 1 GCAACCTGAG 0.853115 -58 GCCTAATACCTCCCCAGGAAGGGCTTT 6 51 0 ACCTCCCCAG 0.979977 -17 CGCAGGCATGACGTCTCGAGCCCGAGTCGA 7 60 0 ACGTCTCGAG 0.881676 -31 GGCGGCACACGCCGATCCAGCAACATCATG 9 32 0 GCCGATCCAG 0.700508 -216 ATCGGCGTGTGCCGCCTGCGGTGCGTTGCG 9 46 1 GCCGCCTGCG 0.94002 -202 GCGAGTAGCCGGGACCCGAGAAGTTGCTAT 9 73 1 GGGACCCGAG 0.855727 -175 GGCCCTGTCCACAGCCCCAGTACTGCGCGG 9 143 0 ACAGCCCCAG 0.935114 -105 CCGACTGCCCGGCTCCTCAGCGGACCCCAG 10 37 0 GGCTCCTCAG 0.921029 -264 GGATCTCCGAGCGTCCTGAGCGGCCCGTTT 10 87 1 GCGTCCTGAG 0.967827 -214 CCCTATCGAGACCGCCCCGGTAGGTAGAGG 10 251 0 ACCGCCCCGG 0.929278 -50 ********** Masking position 10 Map Score: 6.86179 Number of sites scoring better than the average of aligned sites = 954 Number in coding regions = 864 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 ********** No masking Map Score: -3.63555e-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: -3.63555e-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: -3.63555e-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