AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i175_bsub_mtub_100.orf -o175_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 tdh 265 threonine 3-dehydrogenase #2 bioW 251 6-carboxyhexanoate-CoA ligase #3 bioA 247 bioA #4 bioB 300 bioB Motif number 1 CAACCTGTTTGCATTACGCAAACAGGTTGAGAATGC 1 22 0 GCACGCAAGG 0.705384 -244 TTGTCCTTCTGGAAAAGACAGTTCTGTTTACGCTTA 1 185 1 GGAGACTCTG 0.838894 -81 CACCCCCACGGGTACTCACGCTGCGGATAGCGCCCT 3 55 0 GGTCACTCGG 0.963521 -193 TACCCGTGGGGGTGTCCGCTCGTCGGGCTCGTCTAG 3 77 1 GGCCGCGCGG 0.994879 -171 CTCGTCTAGAGCCGACCGGGATTCGGTGCCAGCATC 3 104 1 GCCCGGTCGG 0.989776 -144 ATGCATGCATGGCACCGCCGAATCAGCCTGAAGACA 3 148 0 GGCGCCACAG 0.909165 -100 CAAAACCTCTGCCATCGGGGAGCATGCATGCATGGC 3 171 0 GCCGGGGATG 0.777101 -77 TACTGGGATGGGCCGTGGCGTGGCTGCATTACCCTC 3 215 1 GGTGGCGCTG 0.921706 -33 GCCAACCGGCAATCTGACCAACCGGG 4 1 1 GCCCGGACTG 0.968741 -300 GACCAACCGGGCATAACCCCCGCCGGTGAACCGCAG 4 26 1 GCACCCGCGG 0.957595 -275 GCAACCTCAAGCCGCTCACTAAACTGCGGTTCACCG 4 49 0 GCTCACACTG 0.913014 -252 TTGAGGTTGCGGGATCGACGATTCGGCGTCTGGGCC 4 75 1 GGCGACTCGG 0.989001 -226 GACCCGCCAGGCATCCCACACAGCGGCCCAGACGCC 4 99 0 GCCCACACGG 0.992868 -202 ATCAGCACTCGCACTCGACCCGCCAGGCATCCCACA 4 115 0 GCCGACGCAG 0.972717 -186 ATCGTTGGCAGCGGCCCAGCTATCAGCACTCGCACT 4 136 0 GCCCAGACAG 0.946831 -165 TGAATGAAACGGTGTTCAGGCTACGGTAGCGGTGCG 4 207 0 GGTCAGTCGG 0.944357 -94 TTTCATTCAGGCCGCCGAGCAGGCGGCGGATGGGTT 4 234 1 GCCGAGGCGG 0.991384 -67 GCGGCGGATGGGTTCCGCGCGTGCGGAGATGACGAA 4 256 1 GGCGCGTCGG 0.969962 -45 ** **** * *** Masking position 1 Map Score: 27.4732 Number of sites scoring better than the average of aligned sites = 1750 Number in coding regions = 1645 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 CGGTACATACCACGTCCCAGGGCGCTATCCGCAGC 3 37 1 CACCCGGCGC 0.98827 -211 AGGGCGCTATCCGCAGCGTGAGTACCCGTGGGGGT 3 55 1 CCGCGGATAC 0.68317 -193 CTAGACGAGCCCGACGAGCGGACACCCCCACGGGT 3 78 0 CCGAGGGCAC 0.771096 -170 GATGCTGGCACCGAATCCCGGTCGGCTCTAGACGA 3 105 0 CCGCCGGCGG 0.983981 -143 AGCCTGAAGACACTCAGCCCGATGCTGGCACCGAA 3 125 0 CACGCCGTGC 0.945607 -123 TGTCTTCAGGCTGATTCGGCGGTGCCATGCATGCA 3 148 1 CTGCGCGTGC 0.918826 -100 GCCATGCATGCATGCTCCCCGATGGCAGAGGTTTT 3 171 1 CATCCCGTGG 0.793485 -77 CACGGCCCATCCCAGTAACGGTCGCCAAAACCTCT 3 197 0 CCCAAGGCGC 0.842076 -51 CTGGGATGGGCCGTGGCGTGGCTGCATTACCCTCG 3 217 1 CCGCGGGTGC 0.982633 -31 CCCGGTTGGTCAGATTGCCGGTTGGC 4 2 0 CAGGCGGTGG 0.943358 -299 ACCAACCGGGCATAACCCCCGCCGGTGAACCGCAG 4 27 1 CATCCCGCGG 0.918269 -274 CGGTGAACCGCAGTTTAGTGAGCGGCTTGAGGTTG 4 49 1 CAGAGGACGG 0.600302 -252 GGCCCAGACGCCGAATCGTCGATCCCGCAACCTCA 4 76 0 CCGCGCGTCC 0.937904 -225 CGCCAGGCATCCCACACAGCGGCCCAGACGCCGAA 4 96 0 CCCCACGCCC 0.857119 -205 TCAGCACTCGCACTCGACCCGCCAGGCATCCCACA 4 115 0 CACACCGCAG 0.768098 -186 AGTGCGAGTGCTGATAGCTGGGCCGCTGCCAACGA 4 136 1 CTGGCGGCCG 0.842839 -165 GATCCGTGACCTCCGCCCACGTCGCGTTTGTCCCC 4 169 1 CTCCCCGCGC 0.976686 -132 TCGCGTTTGTCCCCGTGCGCACCGCTACCGTAGCC 4 190 1 CCCGCCACGC 0.951556 -111 CGCACCGCTACCGTAGCCTGAACACCGTTTCATTC 4 207 1 CCGCCGACAC 0.930714 -94 AACCCATCCGCCGCCTGCTCGGCGGCCTGAATGAA 4 235 0 CCGGCCGCGG 0.755877 -66 TTCGTCATCTCCGCACGCGCGGAACCCATCCGCCG 4 257 0 CCGGCCGAAC 0.764819 -44 *** ** ** *** Masking position 1 Map Score: 23.444 Number of sites scoring better than the average of aligned sites = 3057 Number in coding regions = 2866 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 AAAAAAATTTCCGCCCATTTTTCAAGACAGATA 1 149 1 CCGCCCATTC 0.969293 -117 AGCGGACACCCCCACGGGTACTCACGCTGCGGA 3 64 0 CCCACGGGAC 0.900667 -184 CTAGACGAGCCCGACGAGCGGACACCCCCACGG 3 80 0 CCGACGAGGC 0.95694 -168 TCGTCTAGAGCCGACCGGGATTCGGTGCCAGCA 3 105 1 CCGACCGGAC 0.991605 -143 ATGCATGGCACCGCCGAATCAGCCTGAAGACAC 3 147 0 CCGCCGAACC 0.933105 -101 GCCAACCGGCAATCTGACCAACCG 4 2 1 CCAACCGGAC 0.894461 -299 GGCATAACCCCCGCCGGTGAACCGCAGTTTAGT 4 35 1 CCGCCGGTAC 0.980871 -266 CAACCTCAAGCCGCTCACTAAACTGCGGTTCAC 4 51 0 CCGCTCACAC 0.87658 -250 TCCCACACAGCGGCCCAGACGCCGAATCGTCGA 4 89 0 CGGCCCAGCC 0.974733 -212 CGCACTCGACCCGCCAGGCATCCCACACAGCGG 4 109 0 CCGCCAGGAC 0.978672 -192 TCGTTGGCAGCGGCCCAGCTATCAGCACTCGCA 4 138 0 CGGCCCAGTC 0.972779 -163 TCCGTGACCTCCGCCCACGTCGCGTTTGTCCCC 4 171 1 CCGCCCACTC 0.979762 -130 TTCATTCAGGCCGCCGAGCAGGCGGCGGATGGG 4 235 1 CCGCCGAGAC 0.996576 -66 ******** * * Masking position 1 Map Score: 20.4212 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 555 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 AAAATATCACAATAAATGAAAAACAACCTGTTTGCATTACGCA 1 38 0 AAAAAACTTT 0.976129 -228 AATTTCCGCCCATTTTTCAAGACAGATACTTTTGTCCTTCTGG 1 154 1 CAAAGAATTT 0.860182 -112 CATGATATGGAATAAGCGTAAACAGAACTGTCTTTTCCAGAAG 1 190 0 AAAAGACTCT 0.94942 -76 ATCATGGTACAATCCGAATATAACAAGAATTTTTCAAGGAGGA 1 227 1 AAAAAAATTT 0.930519 -39 CTGTAAAAAGAAATCGAAAAAGACCGTTTTGTGTGAAAAC 2 8 1 AAAAGACTTT 0.987706 -244 CAGTTGGTTAAAAGGAAACAAAAAGACCGTTTTCACACAAAAC 2 36 0 AAAAGACTTT 0.987616 -216 CCTTTTAACCAACTGCCATAAATCGATCCTTTCTTCTATTGAC 2 64 1 AAAAGACTTC 0.975168 -188 CTATTGACAGAAACAGGAGAGAATAATATATTCTAATTGTTAA 2 99 1 AAAAAAATTC 0.867462 -153 AAGGGCGAGAAATGATGCAAGAAGAAACTTTTTATAGTGTCAG 2 206 1 AAAAAACTTT 0.976128 -46 ** * * ** * *** Masking position 12 Map Score: 5.25175 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 129 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 GTTTGCATTACGCAAACAGGTTGAGAATGCTTT 1 19 0 CGAAACGGTG 0.737827 -247 TGGTATGTACCGTAGCGATATTGGCAGTATTTC 3 16 0 CGAGCGTATG 0.845313 -232 GGGCGCTATCCGCAGCGTGAGTACCCGTGGGGG 3 56 1 CGAGCGGATA 0.919622 -192 TAGACGAGCCCGACGAGCGGACACCCCCACGGG 3 79 0 CGCGAGGGCA 0.954211 -169 ATGCTGGCACCGAATCCCGGTCGGCTCTAGACG 3 106 0 CGATCCGGCG 0.977554 -142 TGGGATGGGCCGTGGCGTGGCTGCATTACCCTC 3 218 1 CGGGCGGGTG 0.9916 -30 GTTTAGTGAGCGGCTTGAGGTTGCGGGATCGAC 4 61 1 CGCTTGGGTG 0.831389 -240 GGATGCCTGGCGGGTCGAGTGCGAGTGCTGATA 4 119 1 CGGTCGGTCG 0.915476 -182 GCGGAGGTCACGGATCGTTGGCAGCGGCCCAGC 4 152 0 CGATCGTGCA 0.869682 -149 CGGGGACAAACGCGACGTGGGCGGAGGTCACGG 4 172 0 CGGACGGGCG 0.981113 -129 GCACCGCTACCGTAGCCTGAACACCGTTTCATT 4 208 1 CGAGCCGACA 0.897682 -93 TCATTCAGGCCGCCGAGCAGGCGGCGGATGGGT 4 236 1 CGCGAGAGCG 0.834424 -65 ** **** ** ** Masking position 1 Map Score: 6.26102 Number of sites scoring better than the average of aligned sites = 940 Number in coding regions = 870 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 CCAGAAGGACAAAAGTATCTGTCTTGAAAA 1 167 0 AAAAGTATCT 0.911745 -99 AAGCGTAAACAGAACTGTCTTTTCCAGAAG 1 190 0 AGAACTGTCT 0.940885 -76 GTTTTCACACAAAACGGTCTTTTTCGATTT 2 21 0 AAAACGGTCT 0.969812 -231 GTTTTGTGTGAAAACGGTCTTTTTGTTTCC 2 36 1 AAAACGGTCT 0.969812 -216 TGACACTATAAAAAGTTTCTTCTTGCATCA 2 218 0 AAAAGTTTCT 0.910559 -34 ********** Masking position 4 Map Score: 2.07184 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 57 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TTTTTAGCACATAAATGAGCGAATATACAA 1 93 1 ATAAATGAGC 0.96771 -173 ATACAAAATCAGAAATGAGCTAAAACGTTT 1 117 1 AGAAATGAGC 0.991671 -149 ATCTGTCTTGAAAAATGGGCGGAAATTTTT 1 151 0 AAAAATGGGC 0.931037 -115 TGTCAATAGAAGAAAGGATCGATTTATGGC 2 78 0 AGAAAGGATC 0.959688 -174 TGAAAGGGCGAGAAATGATGCAAGAAGAAA 2 203 1 AGAAATGATG 0.937535 -49 ********** Masking position 5 Map Score: 0.861994 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 171 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 TACGCAAACAGGTTGAGAATGCTTTATTTG 1 14 0 GGTTGAGAAT 0.969713 -252 TATATTCAAAGGTTAACAATTAGAATATAT 2 124 0 GGTTAACAAT 0.985936 -128 GAATATAATTGGTTAACAATTTAGGTGAGA 2 147 1 GGTTAACAAT 0.985936 -105 ********** Masking position 6 Map Score: 0.148032 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 ********** No masking Map Score: -1.17707e-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: -1.17707e-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: -1.17707e-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