AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_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 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 Motif number 1 ACCACGTCATCAAGGGGGAGATGCAAAAAT 1 145 0 CAAGGGGGAG 0.965624 -156 GAGTCTGTAATAGGGGCGAAACGTCTGGTT 1 241 0 TAGGGGCGAA 0.924927 -60 ATTATACTGACACGGGCGAAGGGGAATTTC 2 29 1 CACGGGCGAA 0.983146 -60 TAGATGAATGCACGGGCGGAGAGGAAATTC 2 52 0 CACGGGCGGA 0.981961 -37 CGCAGGCGACCACGGTGGGGTTATCGGTAT 3 16 0 CACGGTGGGG 0.979858 -80 AAACAAACCCCACGCGCAGGCGACCACGGT 3 30 0 CACGCGCAGG 0.917482 -66 AATTCAGAATCAGGCCGGAGTGCTAAATAC 5 18 1 CAGGCCGGAG 0.882039 -70 ACTCCGTAAACACGGTCGTACATCCAGCCG 5 46 1 CACGGTCGTA 0.893886 -42 TATTGCATAGCAGGGTCAAGTCTGACATTC 6 101 0 CAGGGTCAAG 0.949358 -77 AAACCCCGGGCAGGGGCGAGTTTGAGGTGA 6 150 1 CAGGGGCGAG 0.993963 -28 ********** Masking position 2 Map Score: 14.1189 Number of sites scoring better than the average of aligned sites = 920 Number in coding regions = 850 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 CGTCATCAAGGGGGAGATGCAAAAATTTTT 1 141 0 GGGGAGATGC 0.904801 -160 AAATGAAATTGGGCAGTTGAAACCAGACGT 1 221 1 GGGCAGTTGA 0.809058 -80 GCCCTATAAACGGGTAATTATACTGACACG 2 13 1 CGGGTAATTA 0.871236 -76 CACGGGCGAAGGGGAATTTCCTCTCCGCCC 2 39 1 GGGGAATTTC 0.990026 -50 ATTCATCTAGGGGCAATTTAAAAAAG 2 73 1 GGGCAATTTA 0.946314 -16 ATCGGAATCAGGAGAATTTATA 4 16 1 GGAGAATTTA 0.948247 -12 CCGTGTTTACGGAGTATTTAGCACTCCGGC 5 31 0 GGAGTATTTA 0.915276 -57 CTGATTTAGTCGGGTATTTAACCTTCAGTG 6 42 0 CGGGTATTTA 0.944404 -136 CCAATTTACTCGGGAATGTCAGACTTGACC 6 88 1 CGGGAATGTC 0.879243 -90 TGTAAAAGTGGGGGTATTGCATAGCAGGGT 6 115 0 GGGGTATTGC 0.973444 -63 AAAAAAACGCGGAGAAATTC 8 113 1 GGAGAAATTC 0.907355 -10 ********** Masking position 2 Map Score: 12.3299 Number of sites scoring better than the average of aligned sites = 885 Number in coding regions = 758 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 3 ATAAAGAATGAATCGCAGCCAAGGCATTCA 1 43 0 AATCGCAGCC 0.966809 -258 GTGAGTCTGTAATAGGGGCGAAACGTCTGG 1 243 0 AATAGGGGCG 0.949692 -58 TGACCGAATATATAGTGGAGACGTTTAG 1 283 1 TATAGTGGAG 0.869946 -18 GATTCGCCGTTATCGCGGCGGATCGCAGCC 3 65 1 TATCGCGGCG 0.996366 -31 TATCGCGGCGGATCGCAGCCCTGAGAATGT 3 75 1 GATCGCAGCC 0.944708 -21 GCCATTTTTTTATCGTGGCGTTTGTACCTG 6 13 0 TATCGTGGCG 0.98681 -165 CGGCGCAGAGTATAGCAGCGAGATCGGCAT 7 46 1 TATAGCAGCG 0.976693 -73 AATGCGAAAAAAACGCGGAGAAATTC 8 107 1 AAACGCGGAG 0.896194 -16 ********** Masking position 2 Map Score: 8.01208 Number of sites scoring better than the average of aligned sites = 1643 Number in coding regions = 1562 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 TGCGCATACCGATAACCCCACCGTGG 3 3 1 CGAACGATAC 0.992143 -93 ATAAATTCTCCTGATTCCGATACCGA 4 3 0 CTATCGATCC 0.97565 -25 ACATCCAGCCGGTAGCCTGATTCCTTGCATTGA 5 65 1 GGACCGATCC 0.913473 -23 TATCATAAAACGAAGACAGATGCCGATCTCGCTG 7 61 0 CGAACGATCC 0.9972 -58 GTCCTTGTTGCGAAGATTGATGACAATGTGAGTG 8 20 1 CGAATGATAC 0.954111 -103 CCTTGAAACCCTGAAACTGATCCCCATAATAAGC 8 58 1 CTAACGATCC 0.992595 -65 ** * ** *** ** Masking position 10 Map Score: 4.17672 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 148 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CGCAGCCAAGGCATTCATCAAAAAATTGTA 1 30 0 GCATTCATCA 0.990531 -271 CTCCGCCCGTGCATTCATCTAGGGGCAATT 2 61 1 GCATTCATCT 0.994595 -28 CGTTTTTTTCGCATTCATCTCGCTAACTTC 8 92 0 GCATTCATCT 0.994595 -31 ********** Masking position 7 Map Score: 3.68375 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 7 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TGCAGACTCACTCACTGCGGTTGACTACTAAATG 1 184 0 CTACTGCTTA 0.966914 -117 TATAAATTCTCCTGATTCCGATACC 4 13 0 ATAATTCCTA 0.802324 -15 CGGCCTGATTCTGAATTCTTTTTA 5 1 0 CTAATTCTTA 0.962842 -87 GTCTTACTTCACCTCAAACTCGCCCC 6 162 0 CTACTTCCTA 0.991357 -16 AGATCGGCATCTGTCTTCGTTTTATGATAAGATG 7 66 1 CTTCTTCTTA 0.976372 -53 TGTCTTTCTTCATCTAAAGATTATTCA 7 102 0 CTTCTTCCTA 0.980354 -17 ATTCATCTCGCTAACTTCGCTTATTATGGGGATC 8 76 0 CTACTTCTTT 0.95173 -47 ** ***** ** * Masking position 6 Map Score: 3.57428 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 72 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 AGGCATTCATCAAAAAATTGTAATAAAAAG 1 22 0 CAAAAAATTG 0.982899 -279 TCTTTATATGAATAAAATTGCTGTCAATTT 1 66 1 AATAAAATTG 0.913939 -235 CAGGACAAGACGTAAAATTGACAGCAATTT 1 80 0 CGTAAAATTG 0.919953 -221 CGCAAAAGCACAAAAAATTTTTGCATCTCC 1 129 1 CAAAAAATTT 0.90062 -172 AGTGAGTCTGCAAAAAAATGAAATTGGGCA 1 206 1 CAAAAAAATG 0.935182 -95 ACGCCACGATAAAAAAATGGCACTGAAGGT 6 22 1 AAAAAAATGG 0.878727 -156 ********** Masking position 5 Map Score: 2.51678 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 268 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 8 AAAGAATGAATCGCAGCCAAGGCATTCATCA 1 40 0 TCGCAGCCAG 0.993026 -261 AATTGGGCAGTTGAAACCAGACGTTTCGCCC 1 227 1 TTGAAACCAA 0.84179 -74 TATTACAGACTCACAACCACATGATGACCGA 1 259 1 TCACAACCAA 0.882177 -42 TCGCGGCGGATCGCAGCCCTGAGAATGTT 3 77 1 TCGCAGCCCG 0.989671 -19 TCGGTATCGGAATCAGGAGAATTTATA 4 7 1 TCGGAATCAG 0.886204 -21 TCATCAATCTTCGCAACAAGGACCTCGGAAA 8 12 0 TCGCAACAAG 0.964846 -111 AGTGCTTCCCTTGAAACCCTGAAACTGATCC 8 50 1 TTGAAACCCG 0.929203 -73 ********* * Masking position 5 Map Score: 1.28657 Number of sites scoring better than the average of aligned sites = 856 Number in coding regions = 807 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 9 CAAAAAATTGTAATAAAAAGAAAAGATTACG 1 11 0 TAATAAAAGA 0.924724 -290 GCCAAGGCATTCATCAAAAAATTGTAATAAA 1 25 0 TCATCAAAAA 0.929875 -276 GCAATTTTATTCATATAAAGAATGAATCGCA 1 56 0 TCATAAAAGA 0.983208 -245 ACGCATCTTATCATAAAACGAAGACAGATGC 7 72 0 TCATAAACGA 0.965141 -47 TGTCTTTCTTCATCTAAAGATTATTCACGC 7 99 0 TCATCAAAGA 0.98432 -20 ***** ***** Masking position 7 Map Score: 2.41664 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ********** No masking Map Score: 9.48026e-14 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 11 ********** No masking Map Score: 9.48026e-14 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 12 CATTTTTTTGCAGACTCACTCACTGCGGTTG 1 195 0 CGACTCACTC 0.936096 -106 TTGAAACCAGACGTTTCGCCCCTATTACAGA 1 237 1 AGTTTCGCCC 0.924721 -64 AGAGGAAATTCCCCTTCGCCCGTGTCAGTAT 2 32 0 CCCTTCGCCC 0.940394 -57 TTTGTTTTACCTGATTCGCCGTTATCGCGGC 3 53 1 CGATTCGCCG 0.97557 -43 TACTTCACCTCAAACTCGCCCCTGCCCGGGG 6 153 0 CAACTCGCCC 0.985095 -25 CGGTCTCTCTCACTGGATGTT 7 1 1 CGTCTCTCTC 0.936086 -118 AGACAGATGCCGATCTCGCTGCTATACTCTG 7 51 0 CATCTCGCTG 0.931039 -68 * ********* Masking position 6 Map Score: 0.331728 Number of sites scoring better than the average of aligned sites = 1049 Number in coding regions = 981 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 13 ********** No masking Map Score: 9.48026e-14 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: 9.48026e-14 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: 9.48026e-14 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