AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i087_bsub_mtub_100.orf -o087_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 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #2 mtlD 52 mannitol-1-phosphate dehydrogenase #3 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #4 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #5 fruR 279 transcriptional regulator (DeoR family) #6 crh 23 catabolite repression HPr-like protein #7 yvcL 22 similar to hypothetical proteins #8 yvcJ 24 similar to hypothetical proteins #9 yvcI 300 similar to mutator MutT protein Motif number 1 CAATTTTTTAAAAATAAAAAGGCTCCTGGTT 1 10 0 AAAAAAAAGG 0.930069 -163 TATACAATTGAAAGTAAAGAGGACTTTGGCAC 1 52 0 AAAGAAGAGG 0.961339 -121 AGCGACAAACAAAACAGGGAGGGTTTATAT 1 153 1 AAAAAGGAGG 0.917829 -20 TGATTGAGGGAAAAAAACGGGAAGTTCATTCT 3 67 1 AAAAAAGGGA 0.967255 -172 TTGGGTGCGCAAAAGAACGAGAATGAACTTCC 3 86 0 AAAAAAGAGA 0.984084 -153 GCCCTTTTACACAACAAAAAGGCATGAGCAAA 3 119 0 ACAAAAAAGG 0.880754 -120 CTTACAGCTAAAAATCATGACAACGAATTCAC 3 185 0 AAAACAGACA 0.877141 -54 TCAGACTAGTAAAAAGAGGAGGTCAATTCTT 3 218 1 AAAAGAGAGG 0.963943 -21 TTGTCATCTGACAAGCACGGCGTACTAACACC 4 12 0 ACAACAGGCG 0.753123 -86 CCTCATGCAACATGCATGAGGTTTTTTTATG 5 10 1 ACATCAGAGG 0.77733 -270 TTTTTTCATTAAAATAAGAAGAAAATGTCGTA 5 73 1 AAAAAAAAGA 0.891985 -207 AAATTCGACAAAAATAAGGACAATTGTACGAC 5 99 0 AAAAAAGACA 0.948072 -181 CCGTAAAGAAAAGGGGAGATCTT 6 5 1 AAAGAAGGGG 0.922354 -19 TGTATTCATTATAAAAAGGGGGTCAATTACTT 9 82 0 ATAAAAGGGG 0.899268 -219 ATTTATGGACAAAAAAAGGACACGGATAACTG 9 134 0 AAAAAAGACA 0.948072 -167 TTTTGTCCATAAATAAAAGAGAATTCCAGTTA 9 152 1 AAATAAGAGA 0.908936 -149 GATGCCTCCCACAATGAAGAGACATTGACAAT 9 236 0 ACAAGAGAGA 0.902136 -65 TTGAAGCGGTATAATAAAGAGACGATGACAGG 9 268 1 ATAAAAGAGA 0.920653 -33 **** ** **** Masking position 3 Map Score: 24.2908 Number of sites scoring better than the average of aligned sites = 1620 Number in coding regions = 1161 Number in noncoding regions = 459 Number of orfs with sites within 600 bp upstream = 473 Fraction of orfs with sites within 600 bp upstream = 0.0759717 Motif number 2 TGGCACATGACTGTGACAATTTTTTAAAAATAAAA 1 23 0 CTTGACTTTT 0.970396 -150 TGATGCTTCCCTTTGACTCTATGTTAAAACGCTTA 1 91 0 CTTGACTTTT 0.970396 -82 AAGCATCATTCTCTGAACATATTTTTGTATCTTAC 1 118 1 CTTGAATTTT 0.928701 -55 AGACTTACGCCTGTGAATTCGTTGTCATGATTTTT 3 173 1 CTTGAACTGT 0.739474 -66 AAGAATTGACCTCCTCTTTTTACTAGTC 3 221 0 AATGACCTTT 0.97335 -18 AATTGTACGACATTTTCTTCTTATTTTAATGAAAA 5 75 0 CATTTCCTTT 0.667677 -205 AATGTCGTACAATTGTCCTTATTTTTGTCGAATTT 5 96 1 AATGTCTTTT 0.86074 -184 ATAGCGTTTACAATGAAATTGTATTCAAAATGAAT 5 232 1 CATGAATTTT 0.953235 -48 ATTGTATTCAAAATGAATACGTTTTCATTAGGAGG 5 249 1 AATGAACTTT 0.938074 -31 TTAATAAAGTAATTGACCCCCTTTTTATAATGAAT 9 76 1 AATGACCTTT 0.974375 -225 ATTTTGCTGTAACTGGAATTCTCTTTTATTTATGG 9 158 0 AATGGATTTT 0.668295 -143 CTTTTCTTCTATTTTACAGCATATTCATTCCTTAA 9 201 0 ATTTACCTTT 0.755018 -100 AATGAAGAGACATTGACAATCTTTTCTTCTATTTT 9 221 0 CATGACTTTT 0.980871 -80 ** **** * * ** Masking position 4 Map Score: 11.8386 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 745 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 CTGTTTTGTTTGTCGCTGTAAGATACAAAAAT 1 138 0 TCGCTGTAAG 0.994837 -35 TGTCATGATTTTTAGCTGTAAGGTCAGACTAG 3 195 1 TAGCTGTAAG 0.988442 -44 TGTGAAGTAATAAAGCTTTAAGTTAAAAGGAG 4 66 1 TAGCTTTAAG 0.966552 -32 TGGGTTTTAATTCCGCTGTAACACATGTGTAA 9 28 1 TCGCTGTAAC 0.990168 -273 ATTCAGATGATTTTGCTGTAACTGGAATTCTC 9 170 0 TTGCTGTAAC 0.962048 -131 CTCTTTATTATACCGCTTCAAGATGCCTCCCA 9 257 0 TCGCTTCAAG 0.959689 -44 * ********* Masking position 7 Map Score: 5.03285 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 46 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TAAATTCAGTTTATCCTTATAACGTGTTAC 3 18 1 TTATCCTTAT 0.784443 -221 GAGAATGAACTTCCCGTTTTTTTCCCTCAA 3 70 0 TTCCCGTTTT 0.920265 -169 GGGAAGTTCATTCTCGTTCTTTTGCGCACC 3 85 1 TTCTCGTTCT 0.785975 -154 CCGTTTACATTTGCCCTTTTACACAACAAA 3 133 0 TTGCCCTTTT 0.953424 -106 AAGAATTGACCTCCTCTTTTTACTAGTCTG 3 219 0 CTCCTCTTTT 0.802723 -20 TTTTATCATTCTCCTTTTAACTTAAAGC 4 80 0 TTCTCCTTTT 0.987702 -18 GTACGACATTTTCTTCTTATTTTAATGAAA 5 76 0 TTCTTCTTAT 0.892389 -204 TGTCGTACAATTGTCCTTATTTTTGTCGAA 5 98 1 TTGTCCTTAT 0.935311 -182 TCTTTCACGTTTCTCCATATTAACGTATGT 5 151 0 TTCTCCATAT 0.89482 -129 AAGATCTCCCCTTTTCTTTACGG 6 9 0 CTCCCCTTTT 0.953354 -15 TTGGCACGGATTCTCCAGTTATCCGTGTCC 9 119 1 TTCTCCAGTT 0.737939 -182 CCAGTTATCCGTGTCCTTTTTTTGTCCATA 9 133 1 GTGTCCTTTT 0.839996 -168 TGACAATCTTTTCTTCTATTTTACAGCATA 9 213 0 TTCTTCTATT 0.649364 -88 ********** Masking position 2 Map Score: 10.2607 Number of sites scoring better than the average of aligned sites = 1996 Number in coding regions = 1539 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 515 Fraction of orfs with sites within 600 bp upstream = 0.0827176 Motif number 5 TTACGCCTGTGAATTCGTTGTCATGATTTTT 3 177 1 GAATTCTTGT 0.944178 -62 TATTTTTGTCGAATTTACAGTTTACAAACCC 5 115 1 GAATTTCAGT 0.81285 -165 TATTCATTTTGAATACAATTTCATTGTAAAC 5 237 0 GAATACATTT 0.857939 -43 TATTCAAAATGAATACGTTTTCATTAGGAGG 5 253 1 GAATACTTTT 0.914263 -27 TTTTTATAATGAATACACTTTTTTGGCACGG 9 97 1 GAATACCTTT 0.975049 -204 GCTGTAACTGGAATTCTCTTTTATTTATGGA 9 157 0 GAATTCCTTT 0.975049 -144 TAATTCAGATGATTTTGCTGTAACTGGAATT 9 173 0 GATTTTCTGT 0.81285 -128 ATTAAGGAATGAATATGCTGTAAAATAGAAG 9 200 1 GAATATCTGT 0.960375 -101 ****** **** Masking position 2 Map Score: 4.41949 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 285 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 TACAATTGAAAGTAAAGAGGACTTTGGCACA 1 51 0 AGTAAAAGGA 0.716445 -122 CAGTTCACCTCGTTGAAATGGCGATCAAATC 2 30 0 CGTTGAATGG 0.972122 -23 ATCAGTAACACGTTATAAGGATAAACTGAAT 3 21 0 CGTTATAGGA 0.957566 -218 CCTGTGAATTCGTTGTCATGATTTTTAGCTG 3 182 1 CGTTGTATGA 0.957516 -57 TAAAGCTTTAAGTTAAAAGGAGAATGATAAA 4 76 1 AGTTAAAGGA 0.933771 -22 TATAGACATACGTTAATATGGAGAAACGTGA 5 146 1 CGTTAAATGG 0.956154 -134 AGCCTTGAAATGAGGTGGCTAT 7 3 1 CCTTGAATGA 0.910698 -20 AATAAAGAGACGATGACAGGACGAAGGTTAG 9 280 1 CGATGAAGGA 0.945949 -21 ****** **** Masking position 8 Map Score: 3.27915 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 277 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 TCTATGTTAAAACGCTTACAGTCCCTATAC 1 79 0 AACGCTTACA 0.934177 -94 TTTACATTTGCCCTTTTACACAACAAAAAG 3 130 0 CCCTTTTACA 0.915291 -109 TTCCAGTTTAACCGTTTACATTTGCCCTTT 3 144 0 ACCGTTTACA 0.992074 -95 TGTCGAATTTACAGTTTACAAACCCTATAG 5 121 1 ACAGTTTACA 0.959977 -159 AACCGAAAATAGCGTTTACAATGAAATTGT 5 224 1 AGCGTTTACA 0.979033 -56 ********** Masking position 6 Map Score: 1.77768 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 104 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TCACAGGCGTAAGTCTTCCAGTTTAACCGT 3 159 0 AAGTCTTCCA 0.964561 -80 TTAATGAAAAAAGTCTTTTATATTCATAGT 5 55 0 AAGTCTTTTA 0.920493 -225 ATAACTATCAAAATCTTTCACGTTTCTCCA 5 164 0 AAATCTTTCA 0.975037 -116 AAATCATTCAAATTCATTCAATAACTATCA 5 184 0 AATTCATTCA 0.939241 -96 TAGGCAACTAAAATCATTCAAATTCATTCA 5 194 0 AAATCATTCA 0.964613 -86 ********** Masking position 4 Map Score: 1.19716 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 135 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 AACCAGGAGCCTTTTTATTTTTAAAAAA 1 9 1 GCCTTTTTAT 0.983945 -164 TTTTGCTCATGCCTTTTTGTTGTGTAAAAG 3 118 1 GCCTTTTTGT 0.957281 -121 CATGCATGAGGTTTTTTTATGTTTAGTGAT 5 21 1 GTTTTTTTAT 0.857744 -259 GTAATTGACCCCCTTTTTATAATGAATACA 9 84 1 CCCTTTTTAT 0.933564 -217 GATTGTCAATGTCTCTTCATTGTGGGAGGC 9 235 1 GTCTCTTCAT 0.921965 -66 TCCTGTCATCGTCTCTTTATTATACCGCTT 9 271 0 GTCTCTTTAT 0.969981 -30 ********** Masking position 6 Map Score: 2.76188 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 189 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 ********** No masking Map Score: 3.48409e-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: 3.48409e-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 12 ********** No masking Map Score: 3.48409e-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