AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_ecoli_bsub_300.orf -o255_ecoli_bsub_300.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 dnaK 300 chaperone Hsp70; DNA biosynthesis; autoregulated heat shock proteins #2 dnaJ 88 chaperone with DnaK; heat shock protein #3 yfhE 95 orf, hypothetical protein #4 b2529 27 orf, hypothetical protein #5 yfhO 87 putative aminotransferase #6 b2531 177 orf, hypothetical protein #7 b2532 118 putative ATP synthase beta subunit #8 grpE 122 phage lambda replication; host DNA synthesis; heat shock protein; protein repair #9 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #10 ynbA 220 similar to GTP-binding protein protease modulator #11 ynbB 187 similar to hypothetical proteins #12 glnR 110 transcriptional regulator #13 dnaJ 199 heat-shock protein #14 dnaK 23 class I heat-shock protein (chaperonin) #15 grpE 71 heat-shock protein #16 hrcA 119 transcriptional regulator #17 hemN 52 coproporphyrinogen III oxidase #18 lepA 133 GTP-binding protein #19 spoIIP 62 spoIIP #20 gpr 203 spore protease Motif number 1 CGTAATCTTTTCTTTTTATTACAATTTTTT 1 9 1 TTTCTTTTAT 0.761903 -292 GATGCAAAAATTTTTTGTGCTTTTGCGCAGAA 1 124 0 TTTTTTTGCT 0.784059 -177 TCTGCGCCGTTTTCCCGTTCTTTAACATCCAG 7 23 0 TTTCCCTTCT 0.868924 -96 TCCGCGTTTTTTTCGCATTCATCTCGCTAACT 8 94 0 TTTCGCTTCT 0.868924 -29 TTTCTCATTATTTCTTTTTCATACAACGGGCT 9 64 0 TTTCTTTTCT 0.954067 -237 TGGATGTTCCTTTCTTTTGCATATTGGGCAGT 10 111 0 TTTCTTTGCT 0.966327 -110 TCCTGAATCGTTTCTTGTTCGTTCAAATGGAT 10 138 0 TTTCTTTTCT 0.954067 -83 CTAAAATGGCTTTCTCCTGAATCGTTTCTTGT 10 152 0 TTTCTCTGAT 0.891532 -69 TTTTTAAAAATTTCTCCTGGATTTGATGTTAA 12 13 1 TTTCTCTGGT 0.927081 -98 GCTTTGACTTTTTTTCTTGCCCGGGATAAAAG 13 109 1 TTTTTCTGCC 0.680777 -91 AATTGACATTTTTCTTGTGGTTTGATACTTTT 16 48 1 TTTCTTTGGT 0.872426 -72 CTGGGTTGCTTTTCTCTTTCACGTAC 18 5 0 TTTCTCTTCC 0.924242 -129 ATAGGGAACTTTTCTCTTTCTTGTTTTACATT 18 42 1 TTTCTCTTCT 0.974758 -92 ****** *** * Masking position 8 Map Score: 12.2842 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 252 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 ATTACAATTTTTTGATGAATGCCTTGGCTGCGATTCATTC 1 28 1 TTGAACCGCG 0.943317 -273 GATTCATTCTTTATATGAATAAAATTGCTGTCAATTTTAC 1 59 1 TTGAAAAGCG 0.931575 -242 TTTACGACCCCATTTAGTAGTCAACCGCAGTGAGTGAGTC 1 174 1 CAGTACAGCG 0.959618 -127 TAAATTGCCCCTAGATGAATGCACGGGCGGAGAGGAAATT 2 53 0 CTGAACAGCG 0.97136 -36 TAAAAAGAATTCAGAATCAGGCCGGAGTGC 5 1 1 TAGAACATCG 0.892176 -87 CATCTTATCATAAAACGAAGACAGATGCCGATCTCGCTGC 7 60 0 TAGAACAGCG 0.990567 -59 AAGCAATCGATTTGTGGTATACACATGCAGGGTTTGGTAT 10 62 1 TTGTACAGCG 0.981169 -159 AAAGCCATTTTAGTCGGATGTCAGCTGCCGCATATCACGG 10 171 1 TAGATCAGCG 0.96304 -50 ATTCACCTTCTTTACAGAAAGAAGCCGCAGTACAAGACTG 17 20 0 TTGAAAAGCG 0.931575 -33 GTTCATAGAGTAATTACTAGACAAGCGCTGGAGGGATTCA 19 33 1 TACTACAGCG 0.878503 -30 ATTAAGTACCTATATTGTTGCCATTTGCTGAATAAATCAT 20 157 0 TAGTTCAGCG 0.938886 -47 ** *** ** ** * Masking position 18 Map Score: 8.89624 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 248 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 GAGATGAATGCGAAAAAAACGCGGAGAAAT 8 101 1 CGAAAAAAAC 0.885136 -22 AGAAATAATGAGAAAGAAGCTCACTATAAT 9 81 1 AGAAAGAAGC 0.943711 -220 TGCGCTTTCCCGAGAAATACTTTATTTCTT 9 175 0 CGAGAAATAC 0.615946 -126 TTATTGTTCCCGAAAAAAGCAATTGTTTCG 9 212 1 CGAAAAAAGC 0.96404 -89 AATATGCAAAAGAAAGGAACATCCATTTGA 10 118 1 AGAAAGGAAC 0.77967 -103 ATTTGATTCTGGAAAGGAGCTTCCCTTCAC 11 38 0 GGAAAGGAGC 0.818227 -150 CGGCTATGTCCAAGAAGAGCAAAGTATCAT 11 126 1 CAAGAAGAGC 0.799744 -62 CGGAGCTGACCGAAAAGAACACATTTCATA 13 37 1 CGAAAAGAAC 0.849815 -163 AAGTCAAAGCCAAGAGATGCCTGACTTTGA 13 89 0 CAAGAGATGC 0.605476 -111 GAAATTCGGGAGAGTGAAGCGAG 13 187 1 AGAGTGAAGC 0.645141 -13 ATAACTCACCCAAAAAAAGCGCCAAAAACT 16 18 0 CAAAAAAAGC 0.842203 -102 CCTTCTTTACAGAAAGAAGCCGCAGTACAA 17 25 0 AGAAAGAAGC 0.943711 -28 GTACGTGAAAGAGAAAAGCAACCCAGATA 18 10 1 AGAGAAAAGC 0.925179 -124 ********** Masking position 3 Map Score: 7.98882 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 867 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 4 AAAATGGCACTGAAGGTTAAATACCCGACT 6 35 1 TGAAGGTTAA 0.905445 -143 AGGGGCGAGTTTGAGGTGAAGTAAGAC 6 161 1 TTGAGGTGAA 0.954878 -17 TCTCTCTCACTGGATGTTAAAGAACGGGAA 7 14 1 TGGATGTTAA 0.865934 -105 AGAGAGAACAGAGAGGTGAAG 9 290 1 GAGAGGTGAA 0.784614 -11 TCTCCTGGATTTGATGTTAAGAATCCTTAC 12 25 1 TTGATGTTAA 0.733724 -86 TTACATAGCAGGAGGTTATTCAA 14 10 1 AGGAGGTTAT 0.634771 -14 TACACTTTGAGGGAGGTGAACACA 15 58 1 GGGAGGTGAA 0.965617 -14 CTTTCTGTAAAGAAGGTGAATCCG 17 39 1 AGAAGGTGAA 0.905288 -14 GTTGTATCTTAGGAGGTGAAACAC 20 5 0 AGGAGGTGAA 0.962985 -199 GCACAGTGTCTTAAGGTTAAATCTTCTTCA 20 40 1 TTAAGGTTAA 0.802187 -164 ATATAGGTACTTAATGTGAAGGAGGCCCCT 20 182 1 TTAATGTGAA 0.658182 -22 ********** Masking position 4 Map Score: 7.12947 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 448 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 AGTGGGGGTATTGCATAGCAGGGTCAAGTCTG 6 107 0 TTGCATGAGG 0.989349 -71 TTCCTTTCTTTTGCATATTGGGCAGTAGTATT 10 105 0 TTGCATTGGG 0.870641 -116 CTTAACTTAGTTTCATTATAGGTGATGTTATA 12 72 0 TTTCATAAGG 0.92248 -39 TTACATAGCAGGAGGTTATTCA 14 1 1 TTACATGAGG 0.958983 -23 TTTTGGCAAATTTTATCGAAGGGCAGCACCTG 15 16 1 TTTTATGAGG 0.954512 -56 GTATTTTGCGTTTAATAGTAGGAGTGATAGAT 18 111 1 TTTAATGAGG 0.92248 -23 GTGCTACAGGTTGTATCTTAGGAGGTGAAACA 20 12 0 TTGTATTAGG 0.87362 -192 GTAAAGTATTTTTCATTGAAGGTTCTCTTTTT 20 122 1 TTTCATGAGG 0.987167 -82 ****** * *** Masking position 5 Map Score: 3.73037 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 36 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 ACGTCTTGTCCTGCCATATCGCGAAATTTCTGC 1 97 1 CTGCCTACCG 0.856703 -204 TCGCCCTATAAACGGGTAATTATA 2 2 1 CGCCCATACG 0.664147 -87 AATTCCCCTTCGCCCGTGTCAGTATAATTACCC 2 24 0 CGCCCTGCGT 0.73104 -65 TTACCTGATTCGCCGTTATCGCGGCGGATCGCA 3 59 1 CGCCGTACCG 0.990966 -37 GTGCTAAATACTCCGTAAACACGGTCGTACATC 5 37 1 CTCCGAACCG 0.962099 -51 TCGTACATCCAGCCGGTAGCCTGATTCCTTGCA 5 61 1 AGCCGTACTG 0.678654 -27 ACCTCAAACTCGCCCCTGCCCGGGGTTTTTTAT 6 145 0 CGCCCTGCGG 0.971696 -33 CTATACTCTGCGCCGTTTTCCCGTTCTTTAACA 7 28 0 CGCCGTTCCG 0.986359 -91 ATAAGGAATCCTGCGCTTTCCCGAGAAATACTT 9 183 0 CTGCGTTCCG 0.86478 -118 TTTCGGTCAGCTCCGGAAGCGGGGCTGACACTA 13 19 0 CTCCGAACGG 0.928986 -181 AAGCCGCCGCAGTCTTGTACTGCGGCT 17 5 1 CGCCGAGCTG 0.939357 -48 ***** ** * ** Masking position 4 Map Score: 3.84868 Number of sites scoring better than the average of aligned sites = 2202 Number in coding regions = 2030 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 AATCAGGTAAAACAAACCCCACGCGCAGGC 3 39 0 AACAAACCCC 0.965086 -57 AACAGGTACAAACGCCACGATAAAAA 6 7 1 TACAAACGCC 0.952177 -171 CTTTTACAATAAAAAACCCCGGGCAGGGGC 6 137 1 AAAAAACCCC 0.930476 -41 ATGAATGCGAAAAAAACGCGGAGAAATTC 8 104 1 AAAAAACGCG 0.879115 -19 TGCCGATTGTGACAAACGCCTATCATGTGT 9 242 0 GACAAACGCC 0.981919 -59 ACTCACCCAAAAAAAGCGCCAAAAACTTCA 16 15 0 AAAAAGCGCC 0.955243 -105 GTAATTACTAGACAAGCGCTGGAGGGATTC 19 42 1 GACAAGCGCT 0.849703 -21 ********** Masking position 5 Map Score: 2.61272 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 312 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 TGCGATTCATTCTTTATATGAATAAAATTGC 1 56 1 TCTTATATGA 0.857793 -245 TTTGCATCTCCCCCTTGATGACGTGGTTTAC 1 148 1 CCCTTGATGA 0.973276 -153 AGACTCACAACCACATGATGACCGAATATAT 1 265 1 CCCATGATGA 0.836536 -36 TTTTAAATTGCCCCTAGATGAATGCACGGGC 2 65 0 CCCTAGATGA 0.973276 -24 CGGTCTCTCTCACTGGATGTTAAAGAACGG 7 10 1 TCCTGGATGT 0.727082 -109 GCATCTGTCTTCGTTTTATGATAAGATGCGT 7 72 1 TCTTTTATGA 0.857793 -47 GCGTGAATAATCTTTAGATGAAGAAAGACA 7 99 1 TCTTAGATGA 0.93432 -20 AAAAATCAGCCCGTTGTATGAAAAAGAAATA 9 57 1 CCTTGTATGA 0.889864 -244 CTCTCTGTTCTCTCTATATGATATTCAAGCG 9 274 0 TCCTATATGA 0.906888 -27 TATATTGTTGCCATTTGCTGAATAAATCATG 20 156 0 CCTTTGCTGA 0.82645 -48 ** ******** Masking position 9 Map Score: 3.43374 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 188 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 CCATATCGCGAAATTTCTGCGCAAAAGCAC 1 110 1 AAATTTCTGC 0.780847 -191 GGGCGGAGAGGAAATTCCCCTTCGCCCGTG 2 39 0 GAAATTCCCC 0.921562 -50 CTTTTTTAAATTGCCCCTAGATGAATG 2 72 0 AAATTGCCCC 0.87159 -17 TATAAATTCTCCTGATTCCGAT 4 16 0 TAAATTCTCC 0.914294 -12 GCCGGAGTGCTAAATACTCCGTAAACACGG 5 31 1 TAAATACTCC 0.688929 -57 GAATTTCTCCGCGTTTTTTT 8 113 0 GAATTTCTCC 0.967334 -10 AGAATTTTCAAAATGCTCATCCGTGATAT 10 202 0 AAAATGCTCA 0.689384 -19 ATTTTTTAAAAATTTCTCCTGGATTTGAT 12 10 1 AAATTTCTCC 0.960818 -101 TCACTCTCCCGAATTTCTCACATAAATTAG 13 174 0 GAATTTCTCA 0.853611 -26 ********** Masking position 5 Map Score: 1.86289 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 257 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 CCGGTAGCCTGATTCCTTGCATTGA 5 73 1 GATTCCTTCA 0.96956 -15 CAATGTGAGTGCTTCCCTTGAAACCCTGAAA 8 43 1 GCTTCCCTGA 0.904948 -80 CTGGAAAGGAGCTTCCCTTCACTTGCCGGCA 11 29 0 GCTTCCCTCA 0.976483 -159 TTGATGTTAAGAATCCTTACATCGTATTGAC 12 35 1 GAATCCTTCA 0.96956 -76 GTTTTACATTGAATCTTTACAATCCTATTGA 18 64 1 GAATCTTTCA 0.831297 -70 TGAATCCCTCCAGCGCTTGTCT 19 51 0 GAATCCCTCA 0.980425 -12 ******** ** Masking position 4 Map Score: 1.48097 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 39 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 11 AGTTTGAGGTGAAGTAAGAC 6 168 1 GAAGTAAGAC 0.950833 -10 ATCTTTAGATGAAGAAAGACA 7 108 1 GAAGAAAGAC 0.96517 -11 AAACGATTCAGGAGAAAGCCATTTTAGTCG 10 157 1 GGAGAAAGCC 0.957477 -64 CAAAGTGTAAGGAGAAGGACAGGTGCTGCC 15 37 0 GGAGAAGGAC 0.957479 -35 CTTCTTTACAGAAAGAAGCCGCAGTACAAG 17 24 0 GAAAGAAGCC 0.824117 -29 CAAGCTAGAGGAAGTAGAACTGT 19 4 0 GAAGTAGAAC 0.75181 -59 TACTTAATGTGAAGGAGGCCCCTGT 20 189 1 GAAGGAGGCC 0.97759 -15 ********** Masking position 6 Map Score: 1.80652 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 146 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 TTTCTTTTTATTACAATTTTTTGATGAATGCCT 1 19 1 TTAATTTTTG 0.635296 -282 AACTGCCCAATTTCATTTTTTTGCAGACTCACT 1 206 0 TTATTTTTTG 0.932017 -95 AGATTTTGTTTTTAATCATTTTGTCAGAGTATT 9 108 0 TTATCTTTTG 0.95626 -193 GAGAAATACTTTATTTCTTATTGTATTCACGGA 9 161 0 TTTTCTATTG 0.879926 -140 CAAATGGATGTTCCTTTCTTTTGCATATTGGGC 10 114 0 TTTTTTTTTG 0.845218 -107 GGTAGACCGCTTCTATTTTAATGAAGAAAATGA 11 78 1 TTATTTAATG 0.594466 -110 TTAAGAATCCTTACATCGTATTGACACATAATA 12 41 1 TTATCTATTG 0.948448 -70 ATAAATTAGATTGTATCATTTTGAATTATGATT 13 150 0 TTATCTTTTG 0.956261 -50 TTTCTTGTGGTTTGATACTTTTGTTATAGAATT 16 58 1 TTATATTTTG 0.771804 -62 ATTGAATCTTTACAATCCTATTGATATAATCTA 18 71 1 TAATCTATTG 0.820302 -63 AAAAATACTTTACATTTATATTGCAATCTAAAG 20 102 0 TATTTTATTG 0.532751 -102 ** *** ***** Masking position 9 Map Score: 3.22325 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 91 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 13 TGAATGCCTTGGCTGCGATTCATTCTTTAT 1 43 1 GGCTGCGATT 0.794801 -258 CCAGACGTTTCGCCCCTATTACAGACTCAC 1 243 1 CGCCCCTATT 0.927821 -58 CTAAACGTCTCCACTATATATTCGGTCA 1 283 0 CTCCACTATA 0.720909 -18 GGCTGCGATCCGCCGCGATAACGGCGAATC 3 65 0 CGCCGCGATA 0.981879 -31 CAGGTACAAACGCCACGATAAAAAAATGGC 6 13 1 CGCCACGATA 0.960077 -165 ATGCCGATCTCGCTGCTATACTCTGCGCCG 7 46 0 CGCTGCTATA 0.955995 -73 GATGGTAGACCGCTTCTATTTTAATGAAGA 11 75 1 CGCTTCTATT 0.807667 -113 ********** Masking position 8 Map Score: 0.236972 Number of sites scoring better than the average of aligned sites = 598 Number in coding regions = 558 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 14 ********** No masking Map Score: -6.0585e-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: -6.0585e-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