AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i174_ecoli_bsub_100.orf -o174_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 accB 300 acetylCoA carboxylase, BCCP subunit; carrier of biotin #2 yngI 43 similar to long-chain acyl-CoA synthetase #3 yngJ 90 similar to butyryl-CoA dehydrogenase #4 ynzE 270 ynzE #5 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) Motif number 1 AACTGCGTCAGGGAGGACGAGGTCGCACATTATAAC 1 32 0 GGGAAGTCGC 0.969458 -269 TTTGCCGGAGGATAGCAGCAGATCGCTGCACAATGT 1 118 1 GACAAGTCGC 0.982472 -183 TGACACTCTGGGGCAAAATAGACCGGCGTCCCGGCC 1 170 1 GGAAAGCCGG 0.991252 -131 CATAGCGATAAATTCCAGCAGGCCGGGACGCCGGTC 1 190 0 AACAAGCCGG 0.984813 -111 ACAATCACACTAAACAAAGAGTACGGAACCCACTC 1 276 1 TAAAAGACGG 0.852888 -25 GAAATGAGAAGGACGGCTTTCTAAGT 4 1 1 GAGAAGACGG 0.968817 -270 GAATGAGGGAAAAAAGCCCGCTAAACAAGCG 5 6 1 AGAAAGCCGC 0.982099 -150 ATATGACAGCAACGCAAAAAGCCCGCTTGTTTAGCG 5 29 0 AAAAAGCCGC 0.985188 -127 TATTAGAGTTGAATTCACAAGTCCGCTCCTGTAAGA 5 62 1 GACAAGCCGC 0.995156 -94 ** ** ** **** Masking position 7 Map Score: 9.83304 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 204 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 GAAATGAGAAGGACGGCTTTCTAAGTCGTC 4 11 1 GGACGGCTTT 0.988534 -260 CGGCTTTCTAAGTCGTCTTTTTTTAAAAAG 4 24 1 AGTCGTCTTT 0.931892 -247 TGAATATGGAGGCGGTGTTTGGACATTTAC 4 119 1 GGCGGTGTTT 0.984867 -152 AACACGTCCTGTACGTGTTTCTCTTCGATT 4 189 0 GTACGTGTTT 0.875798 -82 AACACGTACAGGACGTGTTTTACGTTTTCA 4 200 1 GGACGTGTTT 0.981935 -71 CCGCTTGTTTAGCGGGCTTTTTTCCCTCAT 5 13 0 AGCGGGCTTT 0.980382 -143 CCGCTAAACAAGCGGGCTTTTTGCGTTGCT 5 28 1 AGCGGGCTTT 0.980382 -128 ********** Masking position 8 Map Score: 7.50629 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 251 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 GAAGGTATATTTTGTTTTTTGCCGGAGGAT 1 101 1 TTTGTTTTTT 0.963121 -200 TTCAGTTTTAATTTTCAGACTTTTC 3 6 1 TTTTAATTTT 0.806399 -85 GAATCTCACCTTTGTTTTTTAAAAAATTCA 4 86 0 TTTGTTTTTT 0.963121 -185 TTCTCTTCGATTTTATTTTTATTTAGTACT 4 171 0 TTTTATTTTT 0.944083 -100 TGTTTTACGTTTTCATTTCTAGTCTGGTTA 4 215 1 TTTCATTTCT 0.905206 -56 ATGTATGAAATTTCTTTTTTTATAGGTTAC 5 122 0 TTTCTTTTTT 0.963121 -34 ********** Masking position 7 Map Score: 3.55685 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 142 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 GAAATCGTTATAATGTGCGACCTCGTCCTC 1 26 1 TAATGTGCGA 0.842661 -275 GCGCTGCGGAAAAGGTGACATTGGCGCAAC 1 71 1 AAAGGTGACA 0.943496 -230 TGTTTAGTGTGATTGTGACAGGCGTTTCAC 1 262 0 GATTGTGACA 0.80853 -39 TATCATTAAGAAAGGAGGAACAATGA 2 28 1 AAAGGAGGAA 0.860456 -16 ACAAAGATGTGAAGGAGGAAACGAT 3 76 1 GAAGGAGGAA 0.927195 -15 TTTAAAAAACAAAGGTGAGATTCACATGAA 4 93 1 AAAGGTGAGA 0.956393 -178 ACCATTATTGGAATCTGAGAAACTAGTACT 4 147 1 GAATCTGAGA 0.836394 -124 GCACAAAAAATAATGTGGCACCTAACCAGA 4 237 0 TAATGTGGCA 0.934883 -34 GAATGAGGGAAAAAAGCCCG 5 1 1 GAATGAGGGA 0.966969 -155 ********** Masking position 2 Map Score: 3.32246 Number of sites scoring better than the average of aligned sites = 794 Number in coding regions = 690 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 5 GCAGCGCAAAAACTGCGTCAGGGAGGACGAG 1 47 0 AACTGCGTCG 0.928389 -254 AACAAAATATACCTTCGTTGCGCCAATGTCA 1 86 0 ACCTTCGTTC 0.903488 -215 GGCAAAATAGACCGGCGTCCCGGCCTGCTGG 1 181 1 ACCGGCGTCC 0.995779 -120 CGCTATGCATACAGCTGTCGGGGCATACGCT 1 219 1 ACAGCTGTCG 0.859521 -82 CAGGCGTTTCACCGCCGTCTGTAAAGCGTAT 1 243 0 ACCGCCGTCG 0.994776 -58 TGTGATTGTGACAGGCGTTTCACCGCCGTCT 1 254 0 ACAGGCGTTC 0.962034 -47 GACGACTTAGAAAGCCGTCCTTCTCATTTC 4 10 0 AAAGCCGTCT 0.837359 -261 TCAGCGGTTTACCATCGTTTCCTGTCCCAAA 4 58 0 ACCATCGTTC 0.903487 -213 TAAATGTCCAAACACCGCCTCCATATTCATG 4 117 0 AACACCGCCC 0.866175 -154 ********* * Masking position 1 Map Score: 3.62986 Number of sites scoring better than the average of aligned sites = 2961 Number in coding regions = 2828 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 GAGTTCTATAATCATTCCCTGACAAGAAAA 3 31 0 ATCATTCCCT 0.978228 -60 ATCGTTTCCTCCTTCACATC 3 81 0 ATCGTTTCCT 0.993189 -10 GCGGTTTACCATCGTTTCCTGTCCCAAAAT 4 56 0 ATCGTTTCCT 0.993189 -215 ********** Masking position 1 Map Score: 1.68523 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 11 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 GCTGCCAATTGCTACGAAATCGTTATAA 1 9 1 TTGCTACGAA 0.831266 -292 GTCACCTTTTCCGCAGCGCAAAAACTGCGT 1 60 0 CCGCAGCGCA 0.989568 -241 GGTGACATTGGCGCAACGAAGGTATATTTT 1 84 1 GCGCAACGAA 0.934837 -217 TAGCAGCAGATCGCTGCACAATGTCCGTCA 1 130 1 TCGCTGCACA 0.955416 -171 CTGGAATTTATCGCTATGCATACAGCTGTC 1 208 1 TCGCTATGCA 0.947533 -93 GGAAAAAAGCCCGCTAAACAAGCGGGCTTT 5 18 1 CCGCTAAACA 0.885672 -138 TCTAATATGACAGCAACGCAAAAAGCCCGC 5 39 0 CAGCAACGCA 0.956158 -117 ********** Masking position 10 Map Score: 2.18482 Number of sites scoring better than the average of aligned sites = 1716 Number in coding regions = 1605 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 8 TTAGTGTGATTGTGACAGGCGTTTCACCGC 1 259 0 TGTGACAGGC 0.858653 -42 ATAATCATTCCCTGACAAGAAAAGTCTGAA 3 24 0 CCTGACAAGA 0.95812 -67 ATAGAACTCGCCTAATAGGATGTTACAAAG 3 52 1 CCTAATAGGA 0.846905 -39 AAAGTGATTTTGGGACAGGAAACGATGGTA 4 50 1 TGGGACAGGA 0.955443 -221 GAAGAGAAACACGTACAGGACGTGTTTTAC 4 193 1 ACGTACAGGA 0.861602 -78 TAATGTGGCACCTAACCAGACTAGAAATGA 4 227 0 CCTAACCAGA 0.721918 -44 AGCATCTCCGAACAGCACAAAAAATAA 4 254 0 CCGAACAGCA 0.934123 -17 TCAACTCTAATATGACAGCAACGCAAAAAG 5 44 0 TATGACAGCA 0.74382 -112 ACTATGTTCATCTTACAGGAGCGGACTTGT 5 78 0 TCTTACAGGA 0.960537 -78 ********** Masking position 5 Map Score: 0.692047 Number of sites scoring better than the average of aligned sites = 1505 Number in coding regions = 1321 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 9 AGTTCTATAATCATTCCCTGACAAGAAAAG 3 30 0 TCATTCCCTG 0.978718 -61 ATCGTTTCCTCCTTCACATCT 3 80 0 TCGTTTCCTC 0.987819 -11 CGGTTTACCATCGTTTCCTGTCCCAAAATC 4 55 0 TCGTTTCCTG 0.987819 -216 TTAGCGGGCTTTTTTCCCTCATTC 5 5 0 TTTTTCCCTC 0.920478 -151 ********** Masking position 5 Map Score: 0.452639 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 47 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ********** No masking Map Score: 5.21701e-14 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: 5.21701e-14 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 12 ********** No masking Map Score: 5.21701e-14 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