AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 leuA 92 2-isopropylmalate synthase #2 leuL_leuO 482 leuL: leu operon leader peptide, leuO: probable transcriptional activator for leuABCD operon #3 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #4 acnB 300 aconitate hydrase B #5 yeaU 81 putative tartrate dehydrogenase #6 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #7 ivbL 300 ilvB operon leader peptide #8 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #9 ilvD 95 dihydroxyacid dehydratase #10 ilvC 149 ketol-acid reductoisomerase Motif number 1 GTCAAACAAAAAACCCGCGCCATTGCGCGGG 1 22 1 AAACCGCGCC 0.995562 -71 GGGCATAAAAAAACCCGCGCAATGGCGCGGG 1 35 0 AAACCGCGCA 0.965968 -58 TCGCTTACTTTAACCACCGCAGCACAATTAG 2 345 1 TAACACCGCA 0.807921 -138 ACGCAATAAAAACGTCCCGCCAGCGTGAGTT 2 394 0 AACTCCCGCC 0.962907 -89 TAAATCAGCTCCAGATGAATGC 2 471 0 AAACAGCTCC 0.946662 -12 GTCAAAATTTAAACTACCGCCTCTTTATACT 4 20 0 AAATACCGCC 0.967495 -281 ACACGATTCCAAAACCCCGCCGGCGCAAACC 6 24 1 AAACCCCGCC 0.996177 -82 GCTTAAACGAAAAACCCCGCCCGGTTTGCGC 6 46 0 AAACCCCGCC 0.996177 -60 GTTTTTCGTTTAAGCACCTCCCGGAAAGTCG 6 62 1 TAACACCTCC 0.868741 -44 AAATACGTCAAAATTCGTGCCGAAATTGCGC 7 47 1 AAATCGTGCC 0.809428 -254 CGACTGACGAAACCTCGCTCCGGCGGGGTTT 7 148 1 AACTCGCTCC 0.816493 -153 CAGATAACAAAAAACCCCGCCGGAGCGAGGT 7 159 0 AAACCCCGCC 0.996177 -142 TTCCTCATGTTAGCCAGCGCCTTCGGCATCC 8 117 1 TAGCAGCGCC 0.843501 -184 *** ******* Masking position 2 Map Score: 22.6145 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1052 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 GTTTTTTTATGCCCGAAGCGAGGCGCTCTA 1 52 1 GCCCGAAGCG 0.854605 -41 ATAAAAACGTCCCGCCAGCGTGAGTTCTGC 2 390 0 CCCGCCAGCG 0.980576 -93 TTGTCATAGTGCGGCAGGCGATTCTCTTCA 4 261 0 GCGGCAGGCG 0.995267 -40 ATTCCAAAACCCCGCCGGCGCAAACCGGGC 6 29 1 CCCGCCGGCG 0.996868 -77 CCGGCGCAAACCGGGCGGGGTTTTTCGTTT 6 43 1 CCGGGCGGGG 0.931586 -63 GGCCGACTTTCCGGGAGGTGCTTAAACGAA 6 66 0 CCGGGAGGTG 0.939041 -40 GCGGTTACCAGCCGCAGGCGACTGACGAAA 7 130 1 GCCGCAGGCG 0.997237 -171 AACAAAAAACCCCGCCGGAGCGAGGTTTCG 7 155 0 CCCGCCGGAG 0.97332 -146 GGCCATGGATGCCGAAGGCGCTGGCTAACA 8 124 0 GCCGAAGGCG 0.975786 -177 AGAACGTCTGGCCGCTGGTGCCGCCTGGCG 8 250 1 GCCGCTGGTG 0.93652 -51 TGAATTACTGGCGCCAGGCGGCACCAGCGG 8 261 0 GCGCCAGGCG 0.980437 -40 ********** Masking position 2 Map Score: 19.9627 Number of sites scoring better than the average of aligned sites = 1806 Number in coding regions = 1712 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 TAAATGTGCTTATTTAATAATTAATTTATATATTT 2 100 1 TATTATAAAT 0.88789 -383 TGATCAATTAATGTTAAGAATTAATGCATTAAATA 2 130 0 ATTTAGAAAT 0.718064 -353 TTCTTAACATTAATTGATCAATAATATTCACCAAA 2 145 1 TATTATAAAT 0.88789 -338 GCAAAACATATAATTCAATACAAATCATCAGGATA 2 198 1 TATTAAAAAT 0.758129 -285 TCGGTTGACATATTTCAGCATAAATTTTTGCATCT 2 277 0 TATTAGAAAT 0.969672 -206 AAAGCGTCGGTAGTTAAGCAGAAATTAATATCGCT 2 315 1 TATTAGAAAT 0.969672 -168 GTGGGCTCTCTATTTTAGGATTAATTAAAAAAATA 3 90 1 TATTAGAAAT 0.969672 -138 ACAGAGGATTAAATTGATAATAAATCGGCTGAATC 3 147 0 AATTATAAAT 0.737929 -81 ATTTAGTGCATAGTTGAGTATCGATCACAGTTTGC 7 16 0 TATTAGAGAT 0.947018 -285 CAGAACGCGCAATTTCGGCACGAATTTTGACGTAT 7 49 0 AATTGGAAAT 0.66118 -252 CAGCAACTGTTTTTTCAGGAACGATACAGCGAAAC 8 60 1 TTTTAGAGAT 0.800193 -241 CTGGCGCCAGTAATTCAGAAATGTTGGAGAAATTA 8 274 1 TATTAGAGTT 0.674301 -27 ** ** ** * *** Masking position 10 Map Score: 7.57637 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 28 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TTACCACAGCATAATAATCCATAATGTT 2 5 1 CACACTAAAT 0.892352 -478 CAATAATATTCACCAAATCAATATCAAAAAAAAT 2 163 1 CACCATCAAT 0.960586 -320 TAATTCAATACAAATCATCAGGATAGGTTTTGCA 2 208 1 CAAACTCAAT 0.963044 -275 TTACTTTAACCACCGCAGCACAATTAGCTAATTT 2 349 1 CACCCGCAAT 0.974201 -134 ATAGAGAGCCCACACATTCAGAATAAAATTCTAC 3 69 0 CACAATCAAT 0.963045 -159 AATCTGTTTACAAAAAAGCAACATAAAAAAGTGG 4 148 0 CAAAAGCAAT 0.712439 -153 AACAGATTAACACCTCGTCAAAATCCTGCTATTC 4 174 1 CACCCTCAAT 0.989939 -127 CATCAAAATTGACAACATCACCATCCTATAATTG 5 39 0 GACACTCAAT 0.924734 -43 AAAACGTGATCAACCCCTCAATTTTCCCTTGCTG 7 201 1 CAACCTCATT 0.858097 -100 TTGATATATTCACAACGTCACATTGCAATTTTTG 10 37 0 CACACTCATT 0.963105 -113 CAATAAGAAGCACAACATCACGAGGAATCACC 10 128 1 CACACTCAAG 0.951952 -22 **** * *** ** Masking position 10 Map Score: 9.66694 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 481 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 GATTAGATTGTTTTCGCAACAAAAACATTA 2 32 0 TTTTCGCAAC 0.917404 -451 ATCAGGATAGGTTTTGCAACGCGTGCATTT 2 224 1 GTTTTGCAAC 0.936023 -259 TCAGCATAAATTTTTGCATCTAATCAACGA 2 268 0 TTTTTGCATC 0.828134 -215 GCCAGCGTGAGTTCTGCATCCGTAAAATTA 2 377 0 GTTCTGCATC 0.941786 -106 TGTCTGACCTATTCTGCAATCAG 3 4 0 ATTCTGCAAT 0.832237 -224 TGTCTGGTTTATTCTGCATTTTTTATTGAA 3 38 1 ATTCTGCATT 0.638202 -190 TAAATGCCCAGTACCGCAACGGGCAGAATA 4 203 0 GTACCGCAAC 0.812356 -98 GGTTTTTTGTTATCTGCAATTCAGTACAAA 7 174 1 TATCTGCAAT 0.610864 -127 GATAATTTCTCCAACATTTCTGAAT 8 286 0 TTTCTCCAAC 0.817136 -15 CCTAAGTACCGTTCCGCCACCACCACTC 9 78 1 GTTCCGCCAC 0.865075 -18 CACATTGCAATTTTTGCAACGTCAACATCG 10 23 0 TTTTTGCAAC 0.931281 -127 AATATATCAATTTCCGCAATAAATTTCCTG 10 61 1 TTTCCGCAAT 0.917595 -89 ********** Masking position 7 Map Score: 8.20367 Number of sites scoring better than the average of aligned sites = 1413 Number in coding regions = 1307 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 AAACAAAAAACCCGCGCCATTGCGCGGGTTTT 1 25 1 CCGCGCCTTG 0.947464 -68 CAATAAAAACGTCCCGCCAGCGTGAGTTCTGC 2 390 0 GTCCGCCGCG 0.940383 -93 CGATTCTCTTCACGCTCCTGTGAGACAGCAGT 4 241 0 CAGCTCCGTG 0.922691 -60 AGCGTGAAGAGAATCGCCTGCCGCACTATGAC 4 257 1 GATCGCCGCC 0.833851 -44 CCCCGCCCGGTTTGCGCCGGCGGGGTTTTGGA 6 31 0 TTGCGCCGCG 0.964698 -75 GAGGTTTCGTCAGTCGCCTGCGGCTGGTAACC 7 132 0 CATCGCCGCG 0.976906 -169 CTGACGAAACCTCGCTCCGGCGGGGTTTTTTG 7 151 1 CTGCTCCGCG 0.979669 -150 CTCATGTTAGCCAGCGCCTTCGGCATCCATGG 8 120 1 CCGCGCCTCG 0.986522 -181 CTGGCGCCAGGCGGCACCAGCGGCCAGACGTT 8 252 0 GCGCACCGCG 0.962711 -49 CTGGTGCCGCCTGGCGCCAGTAATTCAGAAAT 8 264 1 CTGCGCCGTA 0.855959 -37 AATGGGACGGCACGCACCGTCCCATTTACGAG 9 19 1 CAGCACCTCC 0.761433 -77 ** ***** *** Masking position 7 Map Score: 8.05913 Number of sites scoring better than the average of aligned sites = 3114 Number in coding regions = 2991 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 TCTTTTAGAGCGCCTCGCTTCGGGCATAAAAA 1 55 0 CGCTCGCTCG 0.946853 -38 CATTTTGTCCCCTTTTTCCTCGTTGATTAGAT 2 249 1 CCTTTTCTCG 0.973165 -234 TAACTACCGACGCTTTTCATCGGTTGACATAT 2 299 0 CGTTTTCTCG 0.985981 -184 AGGATTTTATCGTTTCTTTTCACCTTTCCTCC 3 187 1 CGTTCTTTCA 0.816247 -41 GTGATAATCACCTTTCTCAACGAATCCCAAGA 4 54 0 CCTTCTCACG 0.927363 -247 GTGCGGCAGGCGATTCTCTTCACGCTCCTGTG 4 251 0 CGTTCTCTCA 0.9784 -50 GACGGTTCTCCTCGCTCTCATTGT 4 287 0 CGTTCTCTCG 0.992798 -14 AAACCCCGCCCGGTTTGCGCCGGCGGGGTTTT 6 34 0 CGTTTGCCCG 0.901054 -72 ACTGATAACCCCGATTTCCTCATGTTAGCCAG 8 102 1 CCATTTCTCA 0.680505 -199 ** ***** *** Masking position 5 Map Score: 4.89364 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 473 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 GCCGCACTATGACAATGAGAGCGAGGAGAAC 4 276 1 GACAATGAAG 0.976924 -25 GTATTATGTCAACACTGAAAGTATACGTGTT 7 89 0 AACACTGAAG 0.897515 -212 TTACAGGGGAGACAATGGAAAATTTTTCAGC 7 231 0 GACAATGGAA 0.948129 -70 GGGATGGTTCGACAATGGCAGCAACTGTTTT 8 42 1 GACAATGGAG 0.989625 -259 TTACGAGACAGACACTGGGAGTAAATAAAGT 9 44 1 GACACTGGAG 0.990382 -52 ******** ** Masking position 6 Map Score: 1.89754 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 36 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TCAGGGTTGACATCCGTTTTTGTATCCAGTAACTC 2 424 1 CTCCTTTGTT 0.955612 -59 TTGTGGGATTCAGCCGATTTATTATCAATTTAATC 3 141 1 CGCCTTTTTT 0.993127 -87 TTTCACCTTTCCTCCTGTTTATTCTTATTACCCC 3 204 1 CTCCTTTTTT 0.985909 -24 ATTTAAACTACCGCCTCTTTATACTCGGATTCAC 4 10 0 CGCCTTTTAT 0.967742 -291 CTTAACGATTCAGCCACTTTTTTATGTTGCTTTTT 4 135 1 CGCCTTTTTT 0.993127 -166 GCTCCAGTCCTTTTCTTCTGGGCCGACTT 6 87 0 CGTCTTTTTT 0.949351 -19 CGGTGCGTGCCGTCCCATTTTTTGTAT 9 3 0 CTCCTTTTTT 0.985909 -93 * *** *** ** * Masking position 8 Map Score: 7.31655 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 37 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 CGAGTATAAAGAGGCGGTAGTTTAAATTTT 4 18 1 GAGGCGGTAG 0.859798 -283 ACGCTCCTGTGAGACAGCAGTTTGTAGGGT 4 232 0 GAGACAGCAG 0.850638 -69 GGACTGGAACAACACACGATTCCAA 6 6 1 GGAACAACAC 0.786402 -100 TGTTTTTTCAGGAACGATACAGCGAAACCA 8 67 1 GGAACGATAC 0.847571 -234 AGACCAGGTTGAAGCGGCACTCGACACCAT 8 170 1 GAAGCGGCAC 0.95814 -131 TTACTGGCGCCAGGCGGCACCAGCGGCCAG 8 257 0 CAGGCGGCAC 0.874315 -44 TACAAAAAATGGGACGGCACGCACCGTCCC 9 12 1 GGGACGGCAC 0.99314 -84 TCTCGTAAATGGGACGGTGCGTGCCGTCCC 9 22 0 GGGACGGTGC 0.945838 -74 TGGTGGTGGCGGAACGGTACTTAGGCATAC 9 73 0 GGAACGGTAC 0.969671 -23 AGGGACAGCCCTCGATGTTGA 10 2 1 GGGACAGCCC 0.920318 -148 ********** Masking position 5 Map Score: 6.22067 Number of sites scoring better than the average of aligned sites = 1047 Number in coding regions = 981 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 11 GAAAAGAAACGATAAAATCCTCCATTACAGAG 3 176 0 GATAAACCTC 0.967052 -52 TTCGCATGGTGATAATCACCTTTCTCAACGAA 4 62 0 GATATCCCTT 0.928195 -239 TTTGTAAACAGATTAACACCTCGTCAAAATCC 4 168 1 GATAACCCTC 0.993588 -133 CAGTTACGGGGATTAATTCCTTTTCAGTCAAT 5 11 1 GATAATCCTT 0.90938 -71 GTGCTTAAACGAAAAACCCCGCCCGGTTTGCG 6 47 0 GAAAACCCGC 0.93328 -59 TACAAAACGTGATCAACCCCTCAATTTTCCCT 7 198 1 GATAACCCTC 0.993588 -103 *** *** **** Masking position 5 Map Score: 1.66943 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 107 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 GCACGCAGTCAAACAAAAAACCCGCGCCATTGCGC 1 15 1 AACAAAACGC 0.874328 -78 TATCAAAAAAAATCGCAAAACATATAATTCAATAC 2 184 1 AACCAAACAT 0.950068 -299 AAATCGGCTGAATCCCACAACTTACAGCAATTTCT 3 126 0 AACCACACAC 0.978248 -102 TGCGGCTGGTAACCGCAAAGCACACTGTATTATGT 7 111 0 AACCAAACAC 0.991935 -190 AAATATTGTTAAACACAAAACCAACAAGGTCCCCA 7 276 1 AACCAAACAC 0.991935 -25 TCAATCTCGCAAACGCGAACCGAACAATAAGAAGC 10 104 1 AACCGAACAC 0.978248 -46 ** * **** * ** Masking position 9 Map Score: 0.941502 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 36 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 AAACGGATGTCAACCCTGACGCAATAAAAA 2 413 0 CAACCCTGAC 0.965221 -70 ACGATAAAATCCTCCATTACAGAGGATTAA 3 170 0 CCTCCATTAC 0.924911 -58 ATCTCTAGACCATCCTTAACGATTCAGCCA 4 121 1 CATCCTTAAC 0.893908 -180 ATTGTCGAACCATCCCTAACCGTTGGTTAT 8 28 0 CATCCCTAAC 0.970995 -273 TACAGCGAAACCACCCTTACTGATAACCCC 8 84 1 CCACCCTTAC 0.937006 -217 GCGCCTTCGGCATCCATGGCCAACACATCA 8 133 1 CATCCATGGC 0.893655 -168 ********** Masking position 7 Map Score: 0.434989 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 84 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 GGTCAGACATGAATGTCTGGTTTATTCTGC 3 25 1 GAATGTCTGG 0.982337 -203 ATTTTATTCTGAATGTGTGGGCTCTCTATT 3 74 1 GAATGTGTGG 0.940461 -154 AATCGTTAAGGATGGTCTAGAGATTGTTTC 4 115 0 GATGGTCTAG 0.920031 -186 TGTCAATTTTGATGGTCAGGAAGTGAGAAC 5 59 1 GATGGTCAGG 0.948048 -23 ACGAACTTGAGAACGTCTGGCCGCTGGTGC 8 241 1 GAACGTCTGG 0.979056 -60 ********** Masking position 6 Map Score: 0.343486 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 272 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 AAATAAGCACATTTAATCCATTTTGTAGATGA 2 83 0 ATTTAATCAT 0.966075 -400 TAATTTATATATTTAATGCATTAATTCTTAAC 2 121 1 ATTTAATCAT 0.966075 -362 ATCGCAAAACATATAATTCAATACAAATCATC 2 195 1 ATATAATCAT 0.874802 -288 TTTATTATCAATTTAATCCTCTGTAATGGAGG 3 158 1 ATTTAATCTT 0.877989 -70 TTCAGTGTTGACATAATACAGTGTGCTTTGCG 7 101 1 ACATAATCAT 0.850394 -200 CGTTTGCGAGATTGAATTCACTATATGACAGG 10 87 0 ATTGAATCAT 0.666928 -63 ******* ** * Masking position 6 Map Score: 0.157133 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 11 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467