AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 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 grpE 122 phage lambda replication; host DNA synthesis; heat shock protein; protein repair #8 HI0071 63 heat shock protein (grpE) #9 HI0374 50 H. influenzae predicted coding region HI0374 #10 HI0376 56 conserved hypothetical protein #11 HI0377 59 iscU protein (iscU) #12 HI0378 60 nifS protein (nifS) #13 HI0379 52 conserved hypothetical protein #14 HI0380 300 conserved hypothetical protein #15 HI1237 265 heat shock protein 70 (dnaK) #16 HI1238 50 heat shock protein (dnaJ) Motif number 1 GACGTGGTTTACGACCCCATTTAGTAGTCA 1 167 1 ACGACCCCAT 0.92075 -134 CATTTAGTAGTCAACCGCAGTGAGTGAGTC 1 184 1 TCAACCGCAG 0.677075 -117 ACCAGACGTTTCGCCCCTATTACAGACTCA 1 242 1 TCGCCCCTAT 0.943706 -59 AAATTCCCCTTCGCCCGTGTCAGTATAATT 2 28 0 TCGCCCGTGT 0.917026 -61 AATTTCCTCTCCGCCCGTGCATTCATCTAG 2 53 1 CCGCCCGTGC 0.867096 -36 CTTTTTTAAATTGCCCCTAGATGAATGCAC 2 69 0 TTGCCCCTAG 0.875065 -20 GCGCATACCGATAACCCCACCGTGGTCGCC 3 12 1 ATAACCCCAC 0.821984 -84 CCCACCGTGGTCGCCTGCGCGTGGGGTTTG 3 27 1 TCGCCTGCGC 0.780298 -69 GGCTGGATGTACGACCGTGTTTACGGAGTA 5 45 0 ACGACCGTGT 0.792925 -43 AATGTCAGACTTGACCCTGCTATGCAATAC 6 102 1 TTGACCCTGC 0.948001 -76 CTGCTATGCAATACCCCCACTTTTACAATA 6 118 1 ATACCCCCAC 0.881469 -60 CACCTCAAACTCGCCCCTGCCCGGGGTTTT 6 149 0 TCGCCCCTGC 0.979291 -29 CAAATTACATTTGCCCCCACAT 9 3 0 TTGCCCCCAC 0.986226 -48 CAAATGTAATTTGCCCCTACGAGATGTGAA 9 20 1 TTGCCCCTAC 0.972818 -31 GCGGTCAAAATTGACCGCACTTTTTCACAT 10 13 0 TTGACCGCAC 0.972776 -44 GCGGTCAATTTTGACCGCATTTTTAGCGGT 10 25 1 TTGACCGCAT 0.912221 -32 TATGCTAAATATAACCGCACTTTTTTATTA 12 33 0 ATAACCGCAC 0.787739 -28 GACTGAGCTAACGACCCCACTGTATTAAAT 14 13 0 ACGACCCCAC 0.975579 -288 ********** Masking position 5 Map Score: 24.85 Number of sites scoring better than the average of aligned sites = 2494 Number in coding regions = 2320 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 2 AATTACCCGTTTATAGGGCGA 2 2 0 TTATAGGGCG 0.808571 -87 TTTTTTATTGTAAAAGTGGGGGTATTGCAT 6 123 0 TAAAAGTGGG 0.9391 -55 TCATGTGAAAAAGTGCGGTCAATTTTG 10 8 1 AAAAAGTGCG 0.984244 -49 CCAACACCGCTAAAAATGCGGTCAAAATTG 10 30 0 TAAAAATGCG 0.912313 -27 TTTTTTAATAAAAAAGTGCGGTTATATTTA 12 28 1 AAAAAGTGCG 0.984244 -33 ACCAACGGATTAAAAGTCCGCTGCTCTACC 14 43 0 TAAAAGTCCG 0.969553 -258 ACTGACGGATTAAGAGTCCGCTACTCTACC 14 142 0 TAAGAGTCCG 0.881518 -159 TTTTTATTTCTTAAAGTGCGGTAATTTCCG 15 135 0 TTAAAGTGCG 0.974115 -131 CTTAGCATAAACAAAGGGCGTGGAAACACG 16 23 1 ACAAAGGGCG 0.921958 -28 CAAAAGGGCGTGTTTCCACG 16 41 0 CAAAAGGGCG 0.963086 -10 ********** Masking position 5 Map Score: 10.7446 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 203 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 GGCATTCATCAAAAAATTGTAATAAAAAGA 1 21 0 AAAAAATTGT 0.900326 -280 GCAAAAGCACAAAAAATTTTTGCATCTCCC 1 130 1 AAAAAATTTT 0.891262 -171 GGATGAATAATAAAAATGGTGGGTTGTGAG 14 187 0 TAAAAATGGT 0.884177 -114 CAATAACCGCTAAAAATAGTCAAGAATTTA 14 245 0 TAAAAATAGT 0.837416 -56 TATTTTAAAGTAAAAATTTTCGCCAAATTT 15 23 1 TAAAAATTTT 0.961532 -243 TTTTCTTGCCTGAAAATTTTGTTTTCCCCT 15 66 1 TGAAAATTTT 0.870491 -200 GAGAAAATTTTAAAAATTTTTTATTTCTTA 15 152 0 TAAAAATTTT 0.961532 -114 GTACTCCTAGTAAAAATTTTAAAATTCGGG 15 243 0 TAAAAATTTT 0.961532 -23 ********** Masking position 5 Map Score: 7.59352 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 17 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TTACGTCTTGTCCTGCCATATCGCGAAATTTCTGCGC 1 95 1 TCGCAGCGAA 0.977147 -206 GAATTCAGAATCAGGCCGGAGTGCTAAATACTCCGTA 5 17 1 TCGCAGCTAA 0.986861 -71 CTGAAACTGATCCCCATAATAAGCGAAGTTAGCGAGA 7 68 1 TCCATGCGAA 0.964481 -55 CTATCCCCCAACACCGCTAAAAATGCGGTC 10 37 0 TCCCAGCTAA 0.991875 -20 AGTCCGCTGCTCTACCGACTGAGCTAACGACCCCACT 14 22 0 TCCCTGCTAA 0.991921 -279 AGTCCGCTACTCTACCAACTGAGCTAACAACCCAACT 14 121 0 TCCCTGCTAA 0.991921 -180 CTAAAAATAGTCAAGAATTTAAGCTAATTAAAGAAAT 14 229 0 TCGATGCTAA 0.967229 -72 AGGGTATTCTACCACAATAACCGCTAAAAATAGTCAA 14 252 0 ACCAAGCTAA 0.895895 -49 ** ** * ***** Masking position 16 Map Score: 7.49149 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 77 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 ATGTGGTTGTGAGTCTGTAATAGGGGCGAAACGTCTGGTT 1 241 0 GTGAGGCGAA 0.855377 -60 TTTTACCTGATTCGCCGTTATCGCGGCGGATCGCAGCCCT 3 57 1 TGGAGGCGGA 0.536995 -39 TTTTCCGAGGTCCTTGTTGCGAAGATTGATGAC 7 4 1 TGGCGGCGAA 0.84775 -119 GCGAGATGAATGCGAAAAAAACGCGGAGAAATTC 7 99 1 TGAAGGAGAA 0.908381 -24 GGTCGTTAGCTCAGTCGGTAGAGCAGCGGACTTTTAATCC 14 27 1 TGGAGGCGGA 0.9947 -274 CAGAGAGTGGTGGGTCGTGAAGGATTCGAACCTTCGACCA 14 69 0 TGGAGTCGAA 0.980712 -232 GGTTGTTAGCTCAGTTGGTAGAGTAGCGGACTCTTAATCC 14 126 1 TGGAGGCGGA 0.995203 -175 ATAAAAATGGTGGGTTGTGAGAGACTAGAACTCTCGACTG 14 168 0 TGGAGTAGAA 0.909194 -133 GAAAAAGGGATTTGTGATAAATTTGGCGAAAATTTTTACT 15 31 0 TGAATGCGAA 0.832889 -235 * * * * * ***** Masking position 20 Map Score: 6.95558 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 428 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 TTACGACCCCATTTAGTAGTCAACCGCAGTG 1 175 1 ATTTAGTAGC 0.944998 -126 TACTTGACTGATTTAGTCGGGTATTTAACCT 6 48 0 ATTTAGTCGG 0.981122 -130 TTGGTCAACTATTTACTTGACTGATTTAGTC 6 61 0 ATTTACTTGC 0.948234 -117 TAGTTGACCAATTTACTCGGGAATGTCAGAC 6 81 1 ATTTACTCGG 0.956389 -97 TATTTAGTTGCCATTATCTGAC 11 2 1 ATTTAGTTGC 0.977484 -58 CCACTCTCTGATTTAGTTGTCCAGTTGGGTT 14 99 1 ATTTAGTTGC 0.977484 -202 TACCCTTAAATTTTAGTCGGGTATCATT 14 283 1 TTTTAGTCGG 0.915179 -18 ********* * Masking position 5 Map Score: 6.54267 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 10 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 7 CTGCGGTTGACTACTAAATGGGGTCGTAAA 1 174 0 CTACTAAATG 0.600351 -127 AACATTCTCAGGGCTGCGATCCGCCG 3 80 0 CTCAGGGCTG 0.860283 -16 GTATTTAGCACTCCGGCCTGATTCTGAATT 5 18 0 CTCCGGCCTG 0.970225 -70 AGGAATCAGGCTACCGGCTGGATGTACGAC 5 60 0 CTACCGGCTG 0.977645 -28 GACCAATTTACTCGGGAATGTCAGACTTGA 6 86 1 CTCGGGAATG 0.915942 -92 TCACCTCAAACTCGCCCCTGCCCGGGGTTT 6 150 0 CTCGCCCCTG 0.774921 -28 TAATTTGCCCCTACGAGATGTGAATAAATA 9 26 1 CTACGAGATG 0.785726 -25 TTTTTCAATTCTAGTGAATGCCATTGTCAG 11 28 0 CTAGTGAATG 0.732883 -32 GTCCGCTGCTCTACCGACTGAGCTAACGAC 14 28 0 CTACCGACTG 0.981517 -273 GTCCGCTACTCTACCAACTGAGCTAACAAC 14 127 0 CTACCAACTG 0.937453 -174 GAGACTAGAACTCTCGACTGACGGATTAAG 14 158 0 CTCTCGACTG 0.9024 -143 ********** Masking position 2 Map Score: 5.75634 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 893 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 8 GCGATAACGGCGAATCAGGTAAAACAAACC 3 51 0 CGAATCAGGT 0.956099 -45 TCGGTATCGGAATCAGGAGAATTTATA 4 9 1 GGAATCAGGA 0.983159 -19 AAAAGAATTCAGAATCAGGCCGGAGTGCTA 5 13 1 AGAATCAGGC 0.983159 -75 TCAATGCAAGGAATCAGGCTACCGGCTGG 5 69 0 GGAATCAGGC 0.995707 -19 CAAAGGGCGTGGAAACACGCCCTTTTG 16 34 1 GGAAACACGC 0.952432 -17 ********** Masking position 4 Map Score: 2.98285 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 82 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 TGGTTTCAACTGCCCAATTTCATTTTTTTG 1 216 0 TGCCCAATTT 0.920711 -85 ACTATTTACTTGACTGATTTAGTCGGGTAT 6 55 0 TGACTGATTT 0.933677 -123 AGTAAATAGTTGACCAATTTACTCGGGAAT 6 75 1 TGACCAATTT 0.974185 -103 CTTACATATCTGACTAATTTAG 13 3 0 TGACTAATTT 0.968992 -50 CTTAAATTCTTGACTATTTTTAGCGGTTAT 14 243 1 TGACTATTTT 0.86645 -58 TCATCATTTGAGACTTATTTTGAAAAACAA 15 102 1 AGACTTATTT 0.879319 -164 TAGGGCTTTTAGACCTATTTATTACGAATT 15 212 0 AGACCTATTT 0.897949 -54 ********** Masking position 8 Map Score: 4.4516 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 64 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 CATCAAGGGGGAGATGCAAAAATTTTTTGTG 1 137 0 GAGATGAAAA 0.80054 -164 TCATCTAGGGGCAATTTAAAAAAG 2 75 1 GCAATTAAAA 0.895469 -14 GCATTCACTAGAATTGAAAAAAGGAAAGTTA 11 37 1 GAATTGAAAA 0.954881 -23 GCTAATTAAAGAAATTTAAAATATTAGGGAT 14 213 0 GAAATTAAAA 0.94602 -88 CGCACTTTAAGAAATAAAAAATTTTTAAAAT 15 145 1 GAAATAAAAA 0.812158 -121 TTTCAAGAGAAAATTTTAAAAATTTTTTATT 15 157 0 AAATTTAAAA 0.679152 -109 ATATTCTTTCGCATTTCAAGAGAAAATTTTA 15 170 0 GCATTTAAGA 0.837633 -96 TATTTATTACGAATTGTAAGATGTGGATATT 15 196 0 GAATTGAAGA 0.911855 -70 GCCCTACCCCGAATTTTAAAATTTTTACTAG 15 236 1 GAATTTAAAA 0.955736 -30 ****** **** Masking position 5 Map Score: 2.86098 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 137 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 11 CGCAGCCAAGGCATTCATCAAAAAATTGTA 1 30 0 GCATTCATCA 0.986902 -271 CTCCGCCCGTGCATTCATCTAGGGGCAATT 2 61 1 GCATTCATCT 0.986902 -28 CGTTTTTTTCGCATTCATCTCGCTAACTTC 7 92 0 GCATTCATCT 0.986902 -31 TCTGACAATGGCATTCACTAGAATTGAAAA 11 27 1 GCATTCACTA 0.917544 -33 ********** Masking position 5 Map Score: 2.1157 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 24 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 TCGCCTGCGCGTGGGGTTTGTTTTACCTGA 3 37 1 GTGGGGTTTG 0.990256 -59 TTTTTTTATCGTGGCGTTTGTACCTGTT 6 9 0 GTGGCGTTTG 0.966512 -169 TTGTAAAAGTGGGGGTATTGCATAGCAGGG 6 116 0 GGGGGTATTG 0.943768 -62 TCAGAGAGTGGTGGGTCGTGAAGGATTCGA 14 80 0 GTGGGTCGTG 0.983501 -221 AATAAAAATGGTGGGTTGTGAGAGACTAGA 14 179 0 GTGGGTTGTG 0.990256 -122 ********** Masking position 9 Map Score: 1.73622 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 63 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 ATTTAGTAGTCAACCGCAGTGAGTGAGTCT 1 185 1 CAACCGCAGT 0.821187 -116 CGTCTGGTTTCAACTGCCCAATTTCATTTT 1 220 0 CAACTGCCCA 0.864054 -81 CTATCCCCCAACACCGCTAAAAATGCGG 10 39 0 CAACACCGCT 0.847451 -18 ATGCTAAATATAACCGCACTTTTTTATTAA 12 32 0 TAACCGCACT 0.756012 -29 ACTGAGCTAACGACCCCACTGTATTAAATG 14 12 0 CGACCCCACT 0.961907 -289 GCTGCTCTACCGACTGAGCTAACGACCCCA 14 24 0 CGACTGAGCT 0.862392 -277 GAATCCTTCACGACCCACCACTCTCTGATT 14 82 1 CGACCCACCA 0.896465 -219 ACTGAGCTAACAACCCAACTGGACAACTAA 14 111 0 CAACCCAACT 0.95697 -190 GCTACTCTACCAACTGAGCTAACAACCCAA 14 123 0 CAACTGAGCT 0.89798 -178 TAGTCTCTCACAACCCACCATTTTTATTAT 14 181 1 CAACCCACCA 0.924017 -120 ********** Masking position 3 Map Score: 4.29762 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 754 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 14 GTAAACCACGTCATCAAGGGGGAGATGCAAA 1 148 0 TCATCAGGGG 0.991686 -153 ATATATTCGGTCATCATGTGGTTGTGAGTCT 1 265 0 TCATCAGTGG 0.948594 -36 GCCCGTGCATTCATCTAGGGGCAATTTAAAA 2 65 1 TCATCTGGGG 0.979256 -24 TGATTCGCCGTTATCGCGGCGGATCGCAGCC 3 64 1 TTATCGGGCG 0.974568 -32 TGCCATTTTTTTATCGTGGCGTTTGTACCTG 6 13 0 TTATCGGGCG 0.974568 -165 CTAACTTCGCTTATTATGGGGATCAGTTTCA 7 69 0 TTATTAGGGG 0.940316 -54 TAAGTTAATATCATTGCGAGGCTTACCTACA 8 14 1 TCATTGGAGG 0.887835 -50 ****** **** Masking position 3 Map Score: 4.6272 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 114 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 CGTAATCTTTTCTTTTTATTACAATT 1 7 1 CTTTTCTTTT 0.969151 -294 TTTAACTTTCCTTTTTTCAATTCTA 11 45 0 CTTTCCTTTT 0.971358 -15 AAATATACTGCTTATCTTTT 12 1 0 CTTATCTTTT 0.905202 -60 TATAACCGCACTTTTTTATTAAAAAATATA 12 24 0 CTTTTTTATT 0.807742 -37 TTATTTCTTTCCTATTTTAAAGTAAA 15 7 1 CTTTCCTATT 0.959462 -259 ********** Masking position 7 Map Score: 1.11218 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 23 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863