AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00770_ecoli_reg_100.orf -o00770_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #2 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #3 panB 113 3-methyl-2-oxobutanoate hydroxymethyltransferase #4 rnc 271 RNase III, ds RNA #5 agaZ 248 putative tagatose 6-phosphate kinase 2 #6 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #7 ilvG_1 139 acetolactate synthase II, large subunit, cryptic, interrupted #8 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #9 ilvD 95 dihydroxyacid dehydratase #10 ilvC 149 ketol-acid reductoisomerase #11 coaA 186 pantothenate kinase Motif number 1 TAACGTAGCAGCACTGTCACCTTC 3 4 1 CGAGCAGCAC 0.987197 -110 ATGATTTATCCGTAGCAGCACTGCCAGAAGG 3 30 0 CGAGCAGCAC 0.987197 -84 TGATAAAATGCCAGACAGCACAACATCAATT 3 79 1 CCGACAGCAC 0.9342 -35 ACCTCCAGGTTGCCACGGCACACGAAACAGC 4 138 1 TGCACGGCAC 0.971313 -134 GGACTGGAACAACACACGATTCCAA 6 5 1 TGAACAACAC 0.746393 -101 GCAGACAATGAATAACAGCACAAAATTCTGT 7 90 1 AAAACAGCAC 0.7283 -50 CATCCATGGCCAACACATCACCCGGAAAGAC 8 143 1 CACACATCAC 0.831154 -158 AAGACCAGGTTGAAGCGGCACTCGACACCAT 8 169 1 TGAGCGGCAC 0.980068 -132 ATTACTGGCGCCAGGCGGCACCAGCGGCCAG 8 257 0 CCGGCGGCAC 0.953966 -44 ATACAAAAAATGGGACGGCACGCACCGTCCC 9 11 1 TGGACGGCAC 0.971313 -85 GTGGTGGTGGCGGAACGGTACTTAGGCATAC 9 73 0 CGAACGGTAC 0.892255 -23 TTGATATATTCACAACGTCACATTGCAATTT 10 40 0 CAAACGTCAC 0.92654 -110 CAATAAGAAGCACAACATCACGAGGAATCAC 10 128 1 CAAACATCAC 0.887127 -22 ATATTTGCCATGGCGCGTCACAGTTCTGTTG 11 127 0 TGCGCGTCAC 0.8985 -60 ** ******** Masking position 10 Map Score: 16.4293 Number of sites scoring better than the average of aligned sites = 1598 Number in coding regions = 1508 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GAATAAACAGGAGGAAAGGTGAAAAGAAACGA 1 196 0 GAGAAAGTGA 0.802028 -32 CGCCATAACGGCGACAACGTGAACGAAGATGG 4 14 0 GCGCAAGTGA 0.993951 -258 CGCCGTTATGGCGACAACGTGAATTATTTATG 4 33 1 GCGCAAGTGA 0.993951 -239 AGAGTAGCTTGCGTCAATGGGCAAGGTGGGCT 5 82 0 GCGCAAGGGC 0.976375 -167 AGTTGATACTGCGTCATGGTGAGATAAAAATA 5 178 0 GCGCATGTGA 0.976915 -71 TAGGGATGGTTCGACAATGGCAGCAACTGTTT 8 40 1 TCGCAAGGCA 0.924844 -261 AGTGTCTGTCTCGTAAATGGGACGGTGCGTGC 9 28 0 TCGAAAGGGA 0.959768 -68 GAATTCAATCTCGCAAACGCGAACCGAACAAT 10 100 1 TCGAAAGCGA 0.94254 -50 GAACTGTGACGCGCCATGGCAAATATCGCTTT 11 132 1 GCGCATGCAA 0.773835 -55 CATAGCTCTATCGGCAAAGCGATATTTGCCAT 11 147 0 TCGCAAGCGA 0.987986 -40 *** *** **** Masking position 6 Map Score: 11.4816 Number of sites scoring better than the average of aligned sites = 726 Number in coding regions = 689 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 ACTATACATTCGGCGGGCCAGTTTAGCACAAAGA 2 39 0 CGGCGGATTT 0.95706 -62 GTCACATTGGTGGGGGCAATGATTTATCCGTAGC 3 45 0 TGGGGGTATT 0.913689 -69 TCGTTAGCCACGGGAGATTTATCTCATAAATAAT 4 55 0 CGGGAGTTCT 0.962031 -217 TACACAACGACGGGGGATGTCGTTAGCCACGGGA 4 74 0 CGGGGGTGTT 0.993336 -198 CCTTAAACTTCGGGGGAATATTCTATACACAACG 4 99 0 CGGGGGATCT 0.972802 -173 CGGCGCAAACCGGGCGGGGTTTTTCGTTTAAGCA 6 44 1 CGGGCGTTTT 0.967648 -62 CCTTTCGGTGCGGGGGTCTTAGTTCGTTAAGGCT 7 17 0 CGGGGGTGTT 0.993336 -123 CCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAA 7 43 1 CGGGGGTTTT 0.994497 -97 GATAGCTTCCTGGCAGAGATTTTTTCTTATTATT 11 53 1 TGGCAGTTTT 0.816675 -134 AGCATGTTTCTGGCGGTCATAGCTCTATCGGCAA 11 162 0 TGGCGGTGCT 0.930003 -25 ****** * *** Masking position 14 Map Score: 11.8621 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 260 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 TTTGTGCTAAACTGGCCCGCCGAATGTATAGT 2 41 1 ATGCCCGCCG 0.962246 -60 CGGATAAATCATTGCCCCCACCAATGTGACTG 3 49 1 ATCCCCCACC 0.914292 -65 TGGCTAACGACATCCCCCGTCGTTGTGTATAG 4 79 1 CTCCCCGTCG 0.932653 -193 TGTATAGAATATTCCCCCGAAGTTTAAGGTTG 4 104 1 ATCCCCGAAG 0.951042 -168 ACACGATTCCAAAACCCCGCCGGCGCAAACCG 6 24 1 AACCCCGCCG 0.993025 -82 GCTTAAACGAAAAACCCCGCCCGGTTTGCGCC 6 45 0 AACCCCGCCC 0.994362 -61 TAACGAACTAAGACCCCCGCACCGAAAGGTCC 7 22 1 AACCCCGCAC 0.982993 -118 AGGTCAAAAAAAACCCCCGGACCTTTCGGTGC 7 40 0 AACCCCGGAC 0.94258 -100 AGTTAGTTCCCCGTCCTGAATCTTGA 7 124 0 ATCCCCGTCC 0.986562 -16 * * ******** Masking position 6 Map Score: 10.5974 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 247 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 GATTTTATCGTTTCTTTTCACCTTTCCTCC 1 189 1 TTTCTTTTCA 0.910791 -39 TGACTGGAATTTGGGTTTCGAGGCTCTTTG 2 15 1 TTGGGTTTCG 0.752315 -86 TTCGTAAAACTTTCGTTTCATTTCGTTTTG 5 21 1 TTTCGTTTCA 0.981078 -228 TTTCGTTTCATTTCGTTTTGCCTATTAACG 5 31 1 TTTCGTTTTG 0.943557 -218 CGCAAGCTACTCTCGTTTCAGTGACTTTCA 5 101 1 TCTCGTTTCA 0.923745 -148 AACCATTATCTTTCGTTTTATTTTTATCTC 5 160 1 TTTCGTTTTA 0.952978 -89 GATATTAATCTTTCGTTTTGTTTCAGTTGA 5 204 0 TTTCGTTTTG 0.943557 -45 GGGCGGGGTTTTTCGTTTAAGCACCTCCCG 6 55 1 TTTCGTTTAA 0.889148 -51 ATCTGTCACATTGCTTTTCAACGATAGCTT 11 31 1 TTGCTTTTCA 0.833069 -156 ********** Masking position 6 Map Score: 8.82726 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 142 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 TAACGTAGCAGCACTGTCACC 3 2 1 AACGTAGCAG 0.951753 -112 GCACTGCCAGAAGGTGACAGTGCTGCTACG 3 14 0 AAGGTGACAG 0.773856 -100 TGCCACGGCACACGAAACAGCGTTGGTCCC 4 148 1 CACGAAACAG 0.982774 -124 CTGAAACTGCAGCGAAGCAGTTAGCAGAAC 4 192 1 AGCGAAGCAG 0.927751 -80 CAATTCAGCACACGAAACAGACCTGATATA 4 226 0 CACGAAACAG 0.982774 -46 TTTATCTCACCATGACGCAGTATCAACTGA 5 182 1 CATGACGCAG 0.910156 -67 TTTTTTCAGGAACGATACAGCGAAACCACC 8 69 1 AACGATACAG 0.898231 -232 TCGATTGAGACATGAAGCAGGTATGGCCCA 8 212 0 CATGAAGCAG 0.937713 -89 CCGTCCCATTTACGAGACAGACACTGGGAG 9 35 1 TACGAGACAG 0.896386 -61 GTTGAAAAGCAATGTGACAGATATTCCATC 11 23 0 AATGTGACAG 0.853668 -164 TTTGCCATGGCGCGTCACAGTTCTGTTGAA 11 125 0 CGCGTCACAG 0.896774 -62 ********** Masking position 9 Map Score: 8.66042 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 482 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 GTCAGACATGAATGTCTGGTTTATTCTGCA 1 26 1 AATGTCTGGT 0.800807 -202 CAGCACTGTCACCTTCTGGCAGTGCTGCTA 3 19 1 ACCTTCTGGC 0.973935 -95 TTGATGTTGTGCTGTCTGGCATTTTATCAG 3 78 0 GCTGTCTGGC 0.98722 -36 CGAACTTGAGAACGTCTGGCCGCTGGTGCC 8 242 1 AACGTCTGGC 0.973977 -59 GGCCGCTGGTGCCGCCTGGCGCCAGTAATT 8 259 1 GCCGCCTGGC 0.986907 -42 AACATTTCTGAATTACTGGCGCCAGGCGGC 8 269 0 AATTACTGGC 0.820183 -32 TTCAACGATAGCTTCCTGGCAGAGATTTTT 11 47 1 GCTTCCTGGC 0.96877 -140 ********** Masking position 7 Map Score: 4.94193 Number of sites scoring better than the average of aligned sites = 1419 Number in coding regions = 1351 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 8 CATGTCTGACCTATTCTGCAATCAG 1 6 0 CTATTCTGCA 0.976955 -222 AATGTCTGGTTTATTCTGCATTTTTTATTG 1 36 1 TTATTCTGCA 0.953544 -192 ATGTAGAATTTTATTCTGAATGTGTGGGCT 1 67 1 TTATTCTGAA 0.848468 -161 AATGCGTCAACAATTCAGCACACGAAACAG 4 236 0 CAATTCAGCA 0.960022 -36 TAACGCCTTTCTATTAAGCAAATGCAAGCC 5 56 1 CTATTAAGCA 0.877449 -193 TGGCCCATCACTGTTCAGCATGGTGTCGAG 8 189 0 CTGTTCAGCA 0.944398 -112 CTGGCGCCAGTAATTCAGAAATGTTGGAGA 8 274 1 TAATTCAGAA 0.760289 -27 ********** Masking position 10 Map Score: 3.26818 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 227 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 9 TCTCGCCAAATTACCTATCCAACCGAAGTGT 2 73 0 TTACCTACCA 0.951169 -28 CGTATTATCTCGCCAAATTACCTAT 2 86 0 TTATCTCCCA 0.978315 -15 CGTTTTATTTTTATCTCACCATGACGCAGTA 5 173 1 TTATCTCCCA 0.978315 -76 TTTCCTCTCCAGTTCAGATTA 5 238 0 TTTCCTCCCA 0.9861 -11 TTTTCTTATTATTCCTCCCCATCTGGTGTTA 11 74 1 ATTCCTCCCA 0.955678 -113 ******* *** Masking position 6 Map Score: 2.50803 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 47 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 CAGTCACATTGGTGGGGGCAATGATTTATC 3 51 0 GGTGGGGGCA 0.739647 -63 AGTAAGTCCTTTCGTAAAACTTTC 5 5 1 AGTCCTTTCG 0.609871 -244 TGAAACGAGAGTAGCTTGCGTCAATGGGCA 5 91 0 GTAGCTTGCG 0.846136 -158 AAAAACCCCCGGACCTTTCGGTGCGGGGGT 7 34 0 GGACCTTTCG 0.924359 -106 CAACGGTTAGGGATGGTTCGACAATGGCAG 8 33 1 GGATGGTTCG 0.86859 -268 TATCAGTAAGGGTGGTTTCGCTGTATCGTT 8 79 0 GGTGGTTTCG 0.963549 -222 CTCGTAAATGGGACGGTGCGTGCCGTCCCA 9 21 0 GGACGGTGCG 0.968938 -75 GAGTGGTGGTGGCGGAACGGTACT 9 82 0 GGTGGTGGCG 0.967756 -14 GCTTCTTATTGTTCGGTTCGCGTTTGCGAG 10 109 0 GTTCGGTTCG 0.889875 -41 AAGCATGTTTCTGGCGGTCATAGCTC 11 171 0 GTTTCTGGCG 0.659514 -16 ********** Masking position 9 Map Score: 2.12915 Number of sites scoring better than the average of aligned sites = 2571 Number in coding regions = 2434 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 11 TGAATGTCTGGTTTATTCTGCATTTTTTAT 1 34 1 GTTTATTCTG 0.971399 -194 GAATGTAGAATTTTATTCTGAATGTGTGGG 1 65 1 TTTTATTCTG 0.917568 -163 GGATTTTATCGTTTCTTTTCACCTTTCCTC 1 188 1 GTTTCTTTTC 0.800528 -40 CTTTCCTCCTGTTTATTCTTATTACCCC 1 210 1 GTTTATTCTT 0.885954 -18 CTTTCATTATGTTTCTTTTGTGAATCAGAT 5 125 1 GTTTCTTTTG 0.954287 -124 TTATCTTTCGTTTTATTTTTATCTCACCAT 5 165 1 TTTTATTTTT 0.564435 -84 GCTCCAGTCCTTTTCTTCTGGGCCGACTTT 6 86 0 TTTTCTTCTG 0.930758 -20 AGGTCCGGGGGTTTTTTTTGACCTTAAAAA 7 48 1 GTTTTTTTTG 0.902583 -92 GGCAGCAACTGTTTTTTCAGGAACGATACA 8 58 1 GTTTTTTCAG 0.741575 -243 ********** Masking position 6 Map Score: 4.62697 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 290 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 12 AATAGGTCAGACATGAATGTCTGGTTTATT 1 21 1 ACATGAATGT 0.82526 -207 CCCACAACTTACAGCAATTTCTCTATTTTT 1 118 0 ACAGCAATTT 0.973641 -110 GAATTGACTGGAATTTGGGTTTCGAG 2 7 1 ACTGGAATTT 0.89283 -94 AGACAGCACAACATCAATTTATCAGGATAC 3 91 1 ACATCAATTT 0.933762 -23 ACAACGTCACATTGCAATTTTTGCAACGTC 10 30 0 ATTGCAATTT 0.787139 -120 CGTTGTGAATATATCAATTTCCGCAATAAA 10 54 1 ATATCAATTT 0.797797 -96 TCACTATATGACAGGAAATTTATTGCGGAA 10 72 0 ACAGGAAATT 0.803078 -78 CTATCGTTGAAAAGCAATGTGACAGATATT 11 28 0 AAAGCAATGT 0.763801 -159 ********** Masking position 6 Map Score: 0.943847 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 440 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 13 ********** No masking Map Score: -6.60562e-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 14 ********** No masking Map Score: -6.60562e-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 15 ********** No masking Map Score: -6.60562e-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