AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_ecoli_reg_100.orf -o00290_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 b0024 102 orf, hypothetical protein #2 ileS 42 isoleucine tRNA synthetase #3 leuA 92 2-isopropylmalate synthase #4 leuL 300 leu operon leader peptide #5 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #6 aceE 160 pyruvate dehydrogenase (decarboxylase component) #7 leuS 234 leucine tRNA synthetase #8 avtA 177 alanine-alpha-ketoisovalerate (or valine-pyruvate) transaminase, transaminase C #9 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #10 ilvG_1 139 acetolactate synthase II, large subunit, cryptic, interrupted #11 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #12 ilvD 95 dihydroxyacid dehydratase #13 ilvC 149 ketol-acid reductoisomerase #14 holC 52 DNA polymerase III, chi subunit #15 BIME233 22 BIME #16 pepA 266 aminopeptidase A/I Motif number 1 GGATTTGTGCAAATAAGCGCCGTTA 1 88 1 AAAAAGCGCC 0.813101 -15 GTCAAACAAAAAACCCGCGCCATTGCGCGGG 3 22 1 AAACCGCGCC 0.987749 -71 GGGCATAAAAAAACCCGCGCAATGGCGCGGG 3 35 0 AAACCGCGCA 0.97783 -58 TCGCTTACTTTAACCACCGCAGCACAATTAG 4 163 1 TAACACCGCA 0.976473 -138 TAAATCAGCTCCAGATGAATGC 4 289 0 AAACAGCTCC 0.926789 -12 CGGATCTGAAAAACCACCTCAACGCTACATT 7 180 1 AAACACCTCA 0.931492 -55 GTTGCAGGATAAAGCACCGCTCACTCTTCAA 8 82 1 AAACACCGCT 0.940626 -96 ACACGATTCCAAAACCCCGCCGGCGCAAACC 9 24 1 AAACCCCGCC 0.993723 -82 GCTTAAACGAAAAACCCCGCCCGGTTTGCGC 9 46 0 AAACCCCGCC 0.993723 -60 GTTTTTCGTTTAAGCACCTCCCGGAAAGTCG 9 62 1 TAACACCTCC 0.921069 -44 TAACGAACTAAGACCCCCGCACCGAAAGGTC 10 22 1 AGACCCCGCA 0.916542 -118 AGGTCAAAAAAAACCCCCGGACCTTTCGGTG 10 41 0 AAACCCCGGA 0.871533 -99 TTCCTCATGTTAGCCAGCGCCTTCGGCATCC 11 117 1 TAGCAGCGCC 0.942324 -184 ACGCATCAGGTATACACCGCAGC 14 3 0 TATCACCGCA 0.81539 -50 GATTAACACGAAGTCATCGCAACAGCGGACA 16 177 1 AAGCATCGCA 0.746518 -90 ATTCTATCTGTAGCCACCGCCGTTGTCTTTA 16 227 1 TAGCACCGCC 0.969769 -40 *** ******* Masking position 8 Map Score: 23.85 Number of sites scoring better than the average of aligned sites = 1442 Number in coding regions = 1314 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 ACGCAGTCAAACAAAAAACCCGCGCCATTGC 3 17 1 AAAAAAACCC 0.916147 -76 CGCTTCGGGCATAAAAAAACCCGCGCAATGG 3 41 0 AAAAAAAACC 0.823402 -52 ATAAAAAATGCAGAATAAACCAGACATTCAT 5 33 0 CGAATAAACC 0.926953 -195 GGGGTAATAAGAATAAACAGGAGGAAAGG 5 209 0 AGAATAAACA 0.832174 -19 TAATTTTTACCAGAAAAATCA 6 1 0 CGAAAAATCA 0.855819 -160 TAGATAGATAAGGAATAACCC 6 150 1 AGAATAACCC 0.962504 -11 AAATTAATGTATGAATAATCCGGGCATCATT 7 94 1 AGAATAATCC 0.854467 -141 CTATGCGGATCTGAAAAACCACCTCAACGCT 7 175 1 CGAAAAACCA 0.962896 -60 AGGTGCTTAAACGAAAAACCCCGCCCGGTTT 9 50 0 AGAAAAACCC 0.980195 -56 TTTTAAGGTCAAAAAAAACCCCCGGACCTTT 10 46 0 AAAAAAACCC 0.916147 -94 TGTATCGTTCCTGAAAAAACAGTTGCTGCCA 11 57 0 CGAAAAAACA 0.917183 -244 ACACATCACCCGGAAAGACCAGGTTGAAGCG 11 155 1 CGAAAGACCA 0.816683 -146 * ********* Masking position 5 Map Score: 11.0984 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 429 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 AAAACCCGCGCAATGGCGCGGGTTTTTTGT 3 27 0 CAATGGCGCG 0.946123 -66 CAACGAGGAAAAAGGGGACAAAATGCACGC 4 62 0 AAAGGGGACA 0.821327 -239 GGCGAGAGTTCAATGGGACAGGTTCCAGAA 6 107 1 CAATGGGACA 0.941956 -54 ATACGGCTACAAATGTAGCGTTGAGGTGGT 7 192 0 AAATGTAGCG 0.892491 -43 GCACCCCAGCAAATGTAGCGTTATTGTTAC 8 124 1 AAATGTAGCG 0.892491 -54 ATACAAAAAATGGGACGGCACGCACCG 12 8 1 AAATGGGACG 0.988508 -88 TCTGTCTCGTAAATGGGACGGTGCGTGCCG 12 26 0 AAATGGGACG 0.988508 -70 GCAAAAATTGCAATGTGACGTTGTGAATAT 13 36 1 CAATGTGACG 0.958769 -114 AAATGGGGCTTCTTGTGGTG 14 43 0 AAATGGGGCT 0.934915 -10 ********** Masking position 3 Map Score: 7.52665 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 325 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 TGACATATTTCAGCATAAATTTTTGCATCTAA 4 93 0 CAGAAAATTT 0.854921 -208 ATTCTACATTCAATAAAAAATGCAGAATAAAC 5 44 0 CAAAAAAATG 0.883487 -184 CCCACACATTCAGAATAAAATTCTACATTCAA 5 63 0 CAGAAAAATT 0.970486 -165 TAAGAATAAACAGGAGGAAAGGTGAAAAGAAA 5 199 0 CAGAGAAAGG 0.910831 -29 AGCCGCCAACCAGGATAAAATGTCAGCCCTAA 8 45 1 CAGAAAAATG 0.985485 -133 AAAGTCGGCCCAGAAGAAAAGGACTGGAGC 9 86 1 CAGAAAAAGG 0.974656 -20 CAATGAATAACAGCACAAAATTCTGTTTCTCA 10 95 1 CAGAAAAATT 0.970486 -45 ATTGGCACGTCAGAACAAAATCTGAGAGGTGA 16 129 0 CAGAAAAATC 0.950711 -138 *** * ****** Masking position 5 Map Score: 5.34088 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 106 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 CCAGACATTCATGTCTGACCTATTCTGCAATCA 5 12 0 AGTTGACCAT 0.97035 -216 TTTATTCTGAATGTGTGGGCTCTCTATTTTAGG 5 76 1 AGTTGGGCCT 0.99067 -152 TTTGACGCGGACGTTTGGGCTATGCTATGCGGA 7 151 1 AGTTGGGCAT 0.993704 -84 TTTCCGGGTGATGTGTTGGCCATGGATGCCGAA 11 138 0 AGTTTGGCAT 0.960422 -163 GACATGAAGCAGGTATGGCCCATCACTGTTCAG 11 201 0 AGTTGGCCAT 0.991744 -100 GAACTTGAGAACGTCTGGCCGCTGGTGCCGCCT 11 243 1 AGTTGGCCCT 0.987783 -58 AGAATAAATGACGTTTAAGCCATGAAACAAGCT 16 51 0 AGTTAAGCAT 0.869442 -216 * ** ***** ** Masking position 1 Map Score: 5.30902 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 31 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 AGATAGATAAGGAATAACCC 6 151 1 GGAATAACCC 0.720033 -10 GGACTGGAACAACACACGATTCCAA 9 6 1 GGAACAACAC 0.868975 -100 CCAACGGTTAGGGATGGTTCGACAATGGCA 11 32 1 GGGATGGTTC 0.832384 -269 TGTTTTTTCAGGAACGATACAGCGAAACCA 11 67 1 GGAACGATAC 0.911027 -234 ACATGAAGCAGGTATGGCCCATCACTGTTC 11 203 0 GGTATGGCCC 0.880395 -98 TACAAAAAATGGGACGGCACGCACCGTCCC 12 12 1 GGGACGGCAC 0.987455 -84 TCTCGTAAATGGGACGGTGCGTGCCGTCCC 12 22 0 GGGACGGTGC 0.955987 -74 TGGTGGTGGCGGAACGGTACTTAGGCATAC 12 73 0 GGAACGGTAC 0.968478 -23 AGGGACAGCCCTCGATGTTGA 13 2 1 GGGACAGCCC 0.939069 -148 ********** Masking position 4 Map Score: 5.614 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 343 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 AAAATGCACGCGTTGCAAAACCTATCCTGA 4 43 0 CGTTGCAAAA 0.951013 -258 CTCGTTGATTAGATGCAAAAATTTATGCTG 4 85 1 AGATGCAAAA 0.826579 -216 CTAATTTTACGGATGCAGAACTCACGCTGG 4 194 1 GGATGCAGAA 0.97874 -107 TAGAGTTACTGGATACAAAAACGGATGTCA 4 249 0 GGATACAAAA 0.671367 -52 CTGATTGCAGAATAGGTCAGAC 5 3 1 GATTGCAGAA 0.933292 -225 ATTCAATAAAAAATGCAGAATAAACCAGAC 5 39 0 AAATGCAGAA 0.699203 -189 CAATGGGACAGGTTCCAGAAAACTCAACGT 6 117 1 GGTTCCAGAA 0.961068 -44 CCCTAATCAGCGTTGCAGGATAAAGCACCG 8 71 1 CGTTGCAGGA 0.880449 -107 AACAACACACGATTCCAAAACCCCGCCGGC 9 18 1 GATTCCAAAA 0.711535 -88 TTCGCTGTATCGTTCCTGAAAAAACAGTTG 11 63 0 CGTTCCTGAA 0.679809 -238 TGTTGGCCATGGATGCCGAAGGCGCTGGCT 11 128 0 GGATGCCGAA 0.896585 -173 TCGATGTTGACGTTGCAAAAATTGCAATGT 13 22 1 CGTTGCAAAA 0.951013 -128 ********** Masking position 10 Map Score: 7.26489 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 1015 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 8 TTATGCCCGAAGCGAGGCGCTCTAAAAGAGACAAGG 3 58 1 ACGGGCGCAA 0.99202 -35 ACGGATGTCAACCCTGACGCAATAAAAACGTCCCGC 4 223 0 ACCGACGCAA 0.984441 -78 AGTTTTCTGGAACCTGTCCCATTGAACTCTCGCCGG 6 105 0 ACCGTCCCAA 0.871859 -56 GGTACTGACGAACGGGAAGCCGGAAAAG 8 3 0 ACGGAAGCAA 0.984825 -175 TCGTCAGTACCTCGGGAAGCCGCCAACCAGGATAAA 8 28 1 CCGGAAGCAA 0.973507 -150 TAAAAACATAACCGAGGAGCAGACAATGAATAACAG 10 72 1 ACGGGAGCAA 0.987401 -68 CCGCTGGTGCCGCCTGGCGCCAGTAATTCAGAAATG 11 261 1 CCCGGCGCAA 0.977291 -40 CAATCTCGCAAACGCGAACCGAACAATAAGAAGCAC 13 105 1 ACGGAACCAA 0.958266 -45 * ** ***** ** Masking position 15 Map Score: 4.35661 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 151 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 TAAAAAAACCCGCGCAATGGCGCGGGTTTTTT 3 29 0 CCGCAAGGCG 0.950029 -64 GCCTTTCGCGCACTCGACGTTGAAATGATGCC 7 116 0 CCTCGAGTTG 0.936775 -119 ACGTCGAGTGCGCGAAAGGCTGTTTTGACGCG 7 128 1 CCGAAAGCTG 0.919357 -107 GGTACTGACGAACGGGAAGCCGGAAAAG 8 7 0 ACGGGAGCCG 0.92287 -171 TCGTCAGTACCTCGGGAAGCCGCCAACCAGGA 8 28 1 CCGGGAGCCG 0.993458 -150 GGTGCTTTATCCTGCAACGCTGATTAGGGCTG 8 68 0 CTGCAAGCTG 0.878413 -110 TTAAGCACCTCCCGGAAAGTCGGCCCAGAAGA 9 71 1 CCGGAAGTCG 0.971487 -35 GATGTGTTGGCCATGGATGCCGAAGGCGCTGG 11 130 0 CATGGAGCCG 0.786671 -171 AGGGACAGCCCTCGATGTTGACGTTGCAAA 13 9 1 CCTCGAGTTG 0.936775 -141 GGTGATTCCTCGTGATGTTGTGCTTCTTAT 13 130 0 CCGTGAGTTG 0.902473 -20 TTGCGTCAGGCAAGGCTGTTAT 15 7 1 CGGCAAGCTG 0.914579 -16 * ***** **** Masking position 7 Map Score: 5.41529 Number of sites scoring better than the average of aligned sites = 1434 Number in coding regions = 1369 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 TTTTTTTATGCCCGAAGCGAGGCGCTCTAA 3 53 1 CCCGAAGCGA 0.789583 -40 CAGAACTCACGCTGGCGGGACGTTTTTATT 4 209 1 GCTGGCGGGA 0.966128 -92 GGATGTCAACCCTGACGCAATAAAAACGTC 4 227 0 CCTGACGCAA 0.981081 -74 CCAAAACCCCGCCGGCGCAAACCGGGCGGG 9 32 1 GCCGGCGCAA 0.982101 -74 GCTGGTGCCGCCTGGCGCCAGTAATTCAGA 11 263 1 CCTGGCGCCA 0.979695 -38 GAGTGGTGGTGGCGGAACGGTACTTAG 12 79 0 GGTGGCGGAA 0.868676 -17 AACAGCCTTGCCTGACGCAA 15 1 0 CCTGACGCAA 0.981081 -22 ********** Masking position 10 Map Score: 2.76004 Number of sites scoring better than the average of aligned sites = 1247 Number in coding regions = 1189 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 11 ACGCTTTTCATCGGTTGACATATTTCAGCATAAATTT 4 103 0 TGTGAATTTA 0.769755 -198 GCATTTTTTATTGAATGTAGAATTTTATTCTGAATGT 5 53 1 TGTGGATTTA 0.967435 -175 TTTAATCCTCTGTAATGGAGGATTTTATCGTTTCTTT 5 169 1 TTTGGATTTA 0.981378 -59 AGAAACAGAATTTTGTGCTGTTATTCATTGTCTGCTC 10 88 0 TTTGGTATTA 0.776212 -52 TGACAGGAAATTTATTGCGGAAATTGATATATTCACA 13 57 0 TTTGGAATTA 0.95009 -93 AAATGGGGCTTCTTGTGGTGGATTTAAATACGCATCA 14 26 0 TTTGGATTTA 0.981437 -27 AAGACGAGTTTTTACGGGCGTATTTAAA 16 2 0 TTGGGATTTA 0.933521 -265 TAAAAACTCGTCTTTTGCAGGATTTTAGCTTGTTTCA 16 25 1 TTTGGATTTA 0.981407 -242 * * ** * **** * Masking position 17 Map Score: 2.84631 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 41 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TCGGTTGACATATTTCAGCATAAATTTTTGCATCT 4 95 0 TATTCGCAAT 0.578913 -206 AGAAACGATAAAATCCTCCATTACAGAGGATTAAA 5 169 0 AAATCCCAAA 0.974672 -59 TTTCTGGTAAAAATTATCCAGAAGATGTTGTAAAT 6 16 1 AAATACCAAA 0.770751 -145 CTTGCTTTGCTAATACGCCCACAAACTCTGTAAAT 7 63 1 TAATCCCCAA 0.821416 -172 GCAGACAATGAATAACAGCACAAAATTCTGTTTCT 10 90 1 AATACGCAAA 0.714573 -50 GATAATTTCTCCAACATTTCTGAATTAC 11 283 0 AATTCCCAAT 0.879613 -18 TGAATATATCAATTTCCGCAATAAATTTCCTGTCA 13 59 1 AATTCGCAAA 0.946786 -91 ATGCGTATTTAAATCCACCACAAGAAGCCCCATTT 14 28 1 AAATCCCAAA 0.974672 -25 TTTAAATACGCCCGTAAAAACTCGTCTT 16 4 1 AAATCCCCAA 0.943009 -263 AAACAAGCTAAAATCCTGCAAAAGACGAGTTTTTA 16 25 0 AAATCGCAAA 0.963029 -242 **** * *** * * Masking position 13 Map Score: 3.06855 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 136 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 TTTCAGCATAAATTTTTGCATCTAATCAAC 4 88 0 AATTTTTGCA 0.805614 -213 AAGCGATATTAATTTCTGCTTAACTACCGA 4 139 0 AATTTCTGCT 0.857699 -162 ATTCAGAATAAAATTCTACATTCAATAAAA 5 58 0 AAATTCTACA 0.777251 -170 AACTTACAGCAATTTCTCTATTTTTTTAAT 5 113 0 AATTTCTCTA 0.758095 -115 AGAAACGATAAAATCCTCCATTACAGAGGA 5 174 0 AAATCCTCCA 0.926522 -54 TTTCTGGTAAAAATTATCCAGAAGATGTTG 6 16 1 AAATTATCCA 0.663367 -145 TAACAGCACAAAATTCTGTTTCTCAAGATT 10 102 1 AAATTCTGTT 0.455766 -38 GATAATTTCTCCAACATTTCTGA 11 288 0 AATTTCTCCA 0.957547 -13 GTCACATTGCAATTTTTGCAACGTCAACAT 13 25 0 AATTTTTGCA 0.805614 -125 TGAATATATCAATTTCCGCAATAAATTTCC 13 59 1 AATTTCCGCA 0.835148 -91 ATGCGTATTTAAATCCACCACAAGAAGCCC 14 28 1 AAATCCACCA 0.615707 -25 AAACAAGCTAAAATCCTGCAAAAGACGAGT 16 30 0 AAATCCTGCA 0.937652 -237 ********** Masking position 2 Map Score: 4.01334 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 718 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 14 GGTCCAACTCCCAAATGTGTTC 1 1 1 GTCCAACTCC 0.94913 -102 GGTTTGGGTCCTTGTCTCTTTTAGAGCG 3 75 0 GTCCTTGTCC 0.957528 -18 GGATTTTATCGTTTCTTTTCACCTTTCCTCCT 5 188 1 GTTCTTTTCC 0.909001 -40 CGTTTCATCTCCCGGGTCGTTAA 7 2 1 GTTCATCTCC 0.986668 -233 GGCCATACCTGCTTCATGTCTCAATCGACGAA 11 214 1 GTTCATGTCC 0.980443 -87 ATACTCAACGGATTCACCTCTCAGATTTTGTT 16 116 1 GTTCACCTCC 0.970895 -151 * ******** * Masking position 9 Map Score: 0.280308 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 48 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 ********** No masking Map Score: 2.17669e-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