AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_ecoli_bsub_100.orf -o056_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 leuA 92 2-isopropylmalate synthase #2 leuL 300 leu operon leader peptide #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 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #8 ilvD 95 dihydroxyacid dehydratase #9 ilvC 149 ketol-acid reductoisomerase #10 ycsA 107 similar to 3-isopropylmalate dehydrogenase #11 ilvD 288 dihydroxy-acid dehydratase #12 leuC 49 3-isopropylmalate dehydratase (large subunit) #13 ilvB 300 acetolactate synthase (acetohydroxy-acid synthase) (large subunit) #14 alsS 154 alpha-acetolactate synthase (pH6) Motif number 1 CAGTCAAACAAAAAACCCGCGCCATTGCGC 1 20 1 AAAAACCCGC 0.984068 -73 TCGGGCATAAAAAAACCCGCGCAATGGCGC 1 38 0 AAAAACCCGC 0.984068 -55 CTGACGCAATAAAAACGTCCCGCCAGCGTG 2 216 0 AAAAACGTCC 0.952788 -85 AAGAAACGATAAAATCCTCCATTACAGAGG 3 175 0 AAAATCCTCC 0.864448 -53 ACACCTCGTCAAAATCCTGCTATTCTGCCC 4 183 1 AAAATCCTGC 0.89832 -118 ACACGATTCCAAAACCCCGCCGGCGCAAAC 6 24 1 AAAACCCCGC 0.977766 -82 GCTTAAACGAAAAACCCCGCCCGGTTTGCG 6 47 0 AAAACCCCGC 0.977766 -59 CGAGATAGTAAAAAAAGCCCGTGACATTGT 10 43 0 AAAAAAGCCC 0.926361 -65 AGATAAAAAAGGTGCAGATCATGCA 11 6 1 AAAAAGGTGC 0.89491 -283 AATTCACATAAAAAAGGTGCATGATCTGCA 11 23 0 AAAAAGGTGC 0.89491 -266 CTTATTTGCAAAAACAGCCCATAAATAAAC 11 212 1 AAAACAGCCC 0.899567 -77 TTATTCAATAAAAAAAGCCCTTCCGCCCAC 13 218 0 AAAAAAGCCC 0.926361 -83 ********** Masking position 4 Map Score: 16.3879 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 522 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 AATTTCTGCTTAACTACCGACGCTTTTCATCGG 2 126 0 TAACCCGCGC 0.943155 -175 TCGCTTACTTTAACCACCGCAGCACAATTAGCT 2 163 1 TAACCCGAGC 0.842556 -138 AGCATATCGCATTCATCTGGAGCTGATTTA 2 281 1 ATTCCTGAGC 0.770792 -20 ATTGATAATAAATCGGCTGAATCCCACAACTTA 3 137 0 AATCCTGATC 0.947752 -91 GTCAAAATTTAAACTACCGCCTCTTTATACTCG 4 18 0 AAACCCGCTC 0.978843 -283 GCATGGTGATAATCACCTTTCTCAACGAATCCC 4 58 0 AATCCTTCTC 0.925457 -243 TTTACCCTACAAACTGCTGTCTCACAGGAGCGT 4 229 1 AAACCTGCTC 0.98253 -72 GCGTGAAGAGAATCGCCTGCCGCACTATGACAA 4 258 1 AATCCTGCGC 0.989013 -43 GCCCAGAAGAAAAGGACTGGAGC 6 93 1 AAAGCTGAGC 0.861874 -13 GAAAATCGTCTTACTCGATAACCAAC 7 4 1 AATCCTTCTC 0.925457 -297 ACGGCCTGTTAATCGGCCGTCTCATGGATATTT 13 112 0 AATCCCGCTC 0.978843 -189 TTCAATAAAAAAAGCCCTTCCGCCCACAATCAG 13 212 0 AAAGCTTCGC 0.810268 -89 **** *** *** Masking position 7 Map Score: 10.4331 Number of sites scoring better than the average of aligned sites = 1156 Number in coding regions = 1101 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 AACAAAAAACCCGCGCCATTGCGCGGGTTT 1 26 1 CCGCGCCATT 0.949435 -67 TGCAGAATAAACCAGACATTCATGTCTGAC 3 26 0 ACCAGACATT 0.762137 -202 AAATAGAGAGCCCACACATTCAGAATAAAA 3 75 0 CCCACACATT 0.957968 -153 ACGGTGCGTGCCGTCCCATTTTTTGTAT 8 9 0 CCGTCCCATT 0.988172 -87 ACGGCACGCACCGTCCCATTTACGAGACAG 8 25 1 CCGTCCCATT 0.988172 -71 TATATTCACAACGTCACATTGCAATTTTTG 9 37 0 ACGTCACATT 0.95121 -113 TAAAAAAAGCCCGTGACATTGTGTCACGGG 10 35 0 CCGTGACATT 0.98127 -73 ATACAGGCCGCCCTCACCTTGTTTTGTTCT 11 178 0 CCCTCACCTT 0.932954 -111 ********** Masking position 9 Map Score: 5.92045 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 108 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 GCATCTAATCAACGAGGAAAAAGGGGACAA 2 71 0 AACGAGGAAA 0.978778 -230 AAATATGTCAACCGATGAAAAGCGTCGGTA 2 115 1 ACCGATGAAA 0.854244 -186 TAAGAATAAACAGGAGGAAAGGTGAAAAGA 3 201 0 CAGGAGGAAA 0.96654 -27 CGAAGTTTTTACGGAGGGAAACAATCTCTA 4 98 1 ACGGAGGGAA 0.877513 -203 TGACAATGAGAGCGAGGAGAACCGTC 4 285 1 AGCGAGGAGA 0.831033 -16 CGCTGGCTAACATGAGGAAATCGGGGTTAT 7 106 0 CATGAGGAAA 0.817144 -195 AGCACAACATCACGAGGAATCACC 9 136 1 CACGAGGAAT 0.80255 -14 CTCTAGGTAGAGGGAGGAAATAAAAG 12 34 1 AGGGAGGAAA 0.963122 -16 CAAGGGTGGTACCGCGGAAAGAAAAGCCTT 13 148 1 ACCGCGGAAA 0.877513 -153 ATGATCTTTAAAGGATGAAAATCCAAAAGG 13 271 1 AAGGATGAAA 0.876624 -30 GAAAATCCAAAAGGAGGAACTAAA 13 287 1 AAGGAGGAAC 0.905824 -14 ********** Masking position 4 Map Score: 6.51241 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 162 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 ACTTCGTTAATTCGCATGGTGATAATCACC 4 74 0 TTCGCATGGT 0.797703 -227 GCTGAATCGTTAAGGATGGTCTAGAGATTG 4 119 0 TAAGGATGGT 0.96341 -182 TCAGTCAATTATAGGATGGTGATGTTGTCA 5 34 1 ATAGGATGGT 0.672418 -48 GGGCCGACTTTCCGGGAGGTGCTTAAACGA 6 67 0 TCCGGGAGGT 0.881734 -39 AACCAACGGTTAGGGATGGTTCGACAATGG 7 30 1 TAGGGATGGT 0.905904 -271 GGGTTATCAGTAAGGGTGGTTTCGCTGTAT 7 83 0 TAAGGGTGGT 0.976738 -218 ACCTGGTCTTTCCGGGTGATGTGTTGGCCA 7 149 0 TCCGGGTGAT 0.822355 -152 CCATCACTGTTCAGCATGGTGTCGAGTGCC 7 185 0 TCAGCATGGT 0.873434 -116 GACATTGTGTCACGGGTGGTCGGTTATTGA 10 21 0 CACGGGTGGT 0.963535 -87 AGGCCGTAAACAAGGGTGGTACCGCGGAAA 13 138 1 CAAGGGTGGT 0.95354 -163 ********** Masking position 10 Map Score: 5.68014 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 406 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TTGGAATCGTGTGTTGTTCCAGTCC 6 6 0 GTGTTGTTCC 0.936869 -100 TGGTTTCGCTGTATCGTTCCTGAAAAAACA 7 67 0 GTATCGTTCC 0.963049 -234 GGGACGGTGCGTGCCGTCCCATTTTTTGTA 8 12 0 GTGCCGTCCC 0.988941 -84 GGGACGGCACGCACCGTCCCATTTACGAGA 8 22 1 GCACCGTCCC 0.979327 -74 GTATGCCTAAGTACCGTTCCGCCACCACCA 8 73 1 GTACCGTTCC 0.985562 -23 TCAACATCGAGGGCTGTCCCT 9 2 0 GGGCTGTCCC 0.962881 -148 ********** Masking position 7 Map Score: 3.9658 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 86 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 AATCTCTAGACCATCCTTAACGATTCAGCCA 4 120 1 CCATCCTAAC 0.906812 -181 CATTGTCGAACCATCCCTAACCGTTGGTTAT 7 28 0 CCATCCTAAC 0.906812 -273 TACAGCGAAACCACCCTTACTGATAACCCCG 7 84 1 CCACCCTACT 0.96102 -217 AAGTACCGTTCCGCCACCACCACTC 8 81 1 CCGCCACACC 0.887272 -15 AGGGACAGCCCTCGATGTTGACGTTG 9 6 1 CAGCCCCGAT 0.771232 -144 CAATAACCGACCACCCGTGACACAATGTCAC 10 22 1 CCACCCTGAC 0.976055 -86 TAAATACAGGCCGCCCTCACCTTGTTTTGTT 11 180 0 CCGCCCCACC 0.987698 -109 TTCCGCGGTACCACCCTTGTTTACGGCCTGT 13 136 0 CCACCCTGTT 0.836558 -165 AAAAGCCCTTCCGCCCACAATCAGCCGCGCA 13 205 0 CCGCCCCAAT 0.976576 -96 ****** **** Masking position 5 Map Score: 3.13595 Number of sites scoring better than the average of aligned sites = 809 Number in coding regions = 752 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 AAAATGCACGCGTTGCAAAACCTATCCTGA 2 43 0 CGTTGCAAAA 0.887282 -258 CTCGTTGATTAGATGCAAAAATTTATGCTG 2 85 1 AGATGCAAAA 0.906569 -216 CTAATTTTACGGATGCAGAACTCACGCTGG 2 194 1 GGATGCAGAA 0.985892 -107 TAGAGTTACTGGATACAAAAACGGATGTCA 2 249 0 GGATACAAAA 0.777137 -52 CTGATTGCAGAATAGGTCAGAC 3 3 1 GATTGCAGAA 0.923161 -225 ATTCAATAAAAAATGCAGAATAAACCAGAC 3 39 0 AAATGCAGAA 0.862032 -189 ATTTTTTATTGAATGTAGAATTTTATTCTG 3 55 1 GAATGTAGAA 0.691869 -173 TGTTGGCCATGGATGCCGAAGGCGCTGGCT 7 128 0 GGATGCCGAA 0.94229 -173 TCGATGTTGACGTTGCAAAAATTGCAATGT 9 22 1 CGTTGCAAAA 0.887282 -128 ********** Masking position 4 Map Score: 3.57631 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 562 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 TTGACATATTTCAGCATAAATTTTTGCATC 2 96 0 TCAGCATAAA 0.958748 -205 CGTCGGTAGTTAAGCAGAAATTAATATCGC 2 137 1 TAAGCAGAAA 0.750635 -164 AATAAAAAATGCAGAATAAACCAGACATTC 3 35 0 GCAGAATAAA 0.941022 -193 GCCCACACATTCAGAATAAAATTCTACATT 3 66 0 TCAGAATAAA 0.959532 -162 GGGGTAATAAGAATAAACAGGAGGAAA 3 211 0 TAAGAATAAA 0.844317 -17 TTACAAAAAAGCAACATAAAAAAGTGGCTG 4 145 0 GCAACATAAA 0.78152 -156 GAAAGTCGGCCCAGAAGAAAAGGACTGGAG 6 85 1 CCAGAAGAAA 0.83078 -21 CTGAAAATTGTCAAAATAAAATCCAATCAA 11 241 1 TCAAAATAAA 0.844317 -48 ********** Masking position 6 Map Score: 2.28896 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 317 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 TTATGCCCGAAGCGAGGCGCTCTAAAAGAG 1 58 1 AGCGAGGCGC 0.905122 -35 TGCAGAACTCACGCTGGCGGGACGTTTTTA 2 207 1 ACGCTGGCGG 0.876104 -94 ACGGATGTCAACCCTGACGCAATAAAAACG 2 229 0 ACCCTGACGC 0.856801 -72 TGAAGAGAATCGCCTGCCGCACTATGACAA 4 261 1 CGCCTGCCGC 0.956225 -40 TTCCAAAACCCCGCCGGCGCAAACCGGGCG 6 30 1 CCGCCGGCGC 0.790971 -76 GCCGACTTTCCGGGAGGTGCTTAAACGAAA 6 65 0 CGGGAGGTGC 0.876538 -41 GCCATGGATGCCGAAGGCGCTGGCTAACAT 7 123 0 CCGAAGGCGC 0.942271 -178 GAACGTCTGGCCGCTGGTGCCGCCTGGCGC 7 251 1 CCGCTGGTGC 0.975292 -50 CCGCTGGTGCCGCCTGGCGCCAGTAATTCA 7 261 1 CGCCTGGCGC 0.992477 -40 ********** Masking position 6 Map Score: 5.00991 Number of sites scoring better than the average of aligned sites = 2898 Number in coding regions = 2749 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 11 GACATCCGTTTTTGTATCCAGTAACTCTAA 2 250 1 TTTGTATCCA 0.753944 -51 GATTTTATCGTTTCTTTTCACCTTTCCTCC 3 189 1 TTTCTTTTCA 0.909047 -39 CGGGGATTAATTCCTTTTCAGTCAATTATA 5 17 1 TTCCTTTTCA 0.870559 -65 TTTATATAGCTTTCTTTCGATTTGAACCCT 11 134 0 TTTCTTTCGA 0.875676 -155 CTCATGGATATTTCTATCCGCTTTAGTAAC 13 95 0 TTTCTATCCG 0.914714 -206 CGAAAAGGCTTTTCTTTCCGCGGTACCACC 13 152 0 TTTCTTTCCG 0.96102 -149 TCAATATGCATTCCTTTCCATAGGTTAATA 14 11 1 TTCCTTTCCA 0.96102 -144 ********** Masking position 5 Map Score: 1.59792 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 98 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 CTGCGGTGGTTAAAGTAAGCGATATTAATT 2 155 0 TAAAGTAAGC 0.972214 -146 TGGGAGTAAATAAAGTATGCCTAAGTACCG 8 59 1 TAAAGTATGC 0.91405 -37 CTTCCCCTGTTATCGTAAGCGCTTTCTATT 10 84 0 TATCGTAAGC 0.96345 -24 GAAAACTATTTATAGTAAGTAACAATATTA 11 96 1 TATAGTAAGT 0.823915 -193 TAAGACCGCTTAACGTAAGCTG 12 3 0 TAACGTAAGC 0.974207 -47 ********** Masking position 6 Map Score: 1.10111 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 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 13 TGCATTTTGTCCCCTTTTTCCTCGTTGATTAG 2 65 1 CCCCTTTTCT 0.984072 -236 GAAAAACCCCGCCCGGTTTGCGCCGGCGGGGT 6 37 0 GCCCGTTTCG 0.952345 -69 TTACTGATAACCCCGATTTCCTCATGTTAGCC 7 100 1 CCCCGTTTCT 0.980755 -201 TCTCCTTCCCCTGTTATCGTAAGCGCTTT 10 89 0 CCCCTTTACG 0.976595 -19 GCATGATCTGCACCTTTTTTATCT 11 3 0 CACCTTTTAT 0.799489 -286 GCAGATCATGCACCTTTTTTATGTGAATTCAC 11 24 1 CACCTTTTAT 0.799489 -265 CTAGAGCTAAGACCGCTTAACGTAAGCTG 12 8 0 GACCGTTACG 0.774555 -42 CGCGGTACCACCCTTGTTTACGGCCTGTTAAT 13 132 0 CCCTTTTTCG 0.886337 -169 AGCCTTTTCGCCCCTTTTAGCTATCGCAGTTA 13 172 1 CCCCTTTACT 0.970068 -129 ***** *** ** Masking position 7 Map Score: 4.30536 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 279 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 GTTTTTGTATCCAGTAACTCTAAAAGCATA 2 257 1 CCAGTAACTC 0.978959 -44 GGAATTAATCCCCGTAACTG 5 1 0 CCCGTAACTG 0.968287 -81 TTCGACAATGGCAGCAACTGTTTTTTCAGG 7 49 1 GCAGCAACTG 0.954467 -252 CCGCCTGGCGCCAGTAATTCAGAAATGTTG 7 270 1 CCAGTAATTC 0.899123 -31 AATCAGCCGCGCAGTAACTGCGATAGCTAA 13 188 0 GCAGTAACTG 0.978959 -113 ********** Masking position 6 Map Score: 0.521814 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 121 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 TTGTATTGAATTATATGTTTTGCGATTT 2 2 0 TTTGTTTGTT 0.83109 -299 AATGTGTGGGCTCTCTATTTTAGGATTAATTAAAAAA 3 85 1 CTTATTTGTT 0.968468 -143 AGAGAAATTGCTGTAAGTTGTGGGATTCAGCCGATTT 3 124 1 CTAGTTTGTT 0.92416 -104 AAACTACCGCCTCTTTATACTCGGATTCAC 4 4 0 CTTATATGTT 0.828817 -297 TGATGTTGTGCTTCTTATTGTTCGGTTCGCGTTTGCG 9 111 0 CTTATTTGTT 0.968468 -39 GGATTTTATTTTGACAATTTTCAGTTTATTTATGGGC 11 228 0 TTAATTTGTT 0.890953 -61 CTCCTAAATTCTTTCAATTGTTTGATTGGATTTTATT 11 255 0 CTAATTTGTT 0.961434 -34 TCACAAGATATTTAAAATTTTACGTTTAAAATGCATA 14 115 1 TTAATTTGTT 0.890953 -40 CCTCACTCCTTATTATGCATTTTAAACGTAAA 14 133 0 CTTATTTATT 0.750684 -22 ** **** * * ** Masking position 8 Map Score: 2.25353 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 39 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987