AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoH_ecoli_hinf_100.orf -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 clpP 245 ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 #4 clpX 125 ATP-dependent specificity component of clpP serine protease, chaperone #5 lon 187 DNA-binding, ATP-dependent protease La; heat shock K-protein #6 htpG 109 chaperone Hsp90, heat shock protein C 62.5 #7 gapA 300 glyceraldehyde-3-phosphate dehydrogenase A #8 clpB 129 heat shock protein #9 grpE 122 phage lambda replication; host DNA synthesis; heat shock protein; protein repair #10 rpsU 237 30S ribosomal subunit protein S21 #11 dnaG 110 DNA biosynthesis; DNA primase #12 rpoD 194 RNA polymerase, sigma(70) factor; regulation of proteins induced at high temperatures #13 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #14 ftsJ 125 cell division protein #15 ibpA 230 heat shock protein #16 hslV 92 heat shock protein hslVU, proteasome-related peptidase subunit #17 ftsN 91 essential cell division protein #18 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #19 mopB 275 GroES, 10 Kd chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity #20 mopA 43 GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein #21 HI0071 63 heat shock protein (grpE) #22 HI0104 216 heat shock protein (htpG) #23 HI0462 192 ATP-dependent proteinase (lon) #24 HI0496 218 heat shock protein (hslV) #25 HI0531 231 ribosomal protein S21 (rpS21) #26 HI0532 133 DNA primase (dnaG) #27 HI0533 69 RNA polymerase sigma-70 factor (rpoD) #28 HI0542 162 chaperonin (groES) #29 HI0543 22 heat shock protein (groEL) #30 HI0714 122 ATP-dependent Clp protease, proteolytic subunit (clpP) #31 HI0859 127 ATP-dependent Clp protease, ATPase subunit (clpB) #32 HI1237 265 heat shock protein 70 (dnaK) #33 HI1238 50 heat shock protein (dnaJ) #34 HI1334 126 cell division protein (ftsJ) #35 HI1335 90 cell division protein (ftsH) Motif number 1 CTTAAGTGCCGAAGAGCGATCGGGAAGCCC 12 19 1 GAAGAGCGAT 0.884906 -176 ACGAAACGTTAAAGTGCGATAGCCGCCACA 15 21 0 AAAGTGCGAT 0.985735 -210 ATTTTCATGAAAAGTGTGATGAATATTGAA 18 41 0 AAAGTGTGAT 0.819864 -115 GGCGATGAAGAAATTGCGATGAAATGTGAG 19 90 1 AAATTGCGAT 0.832162 -186 TATTTCATTTAAAGTGCGGTTTAAATTCCT 22 109 1 AAAGTGCGGT 0.994282 -108 TTTAAGAGGAAAAGTGCGGTAAAAAAACAC 22 140 0 AAAGTGCGGT 0.994282 -77 TCGTGGTGTGAAAGTGCGGTCGTTTTTGGC 26 98 0 AAAGTGCGGT 0.994282 -36 TAATAATTTGTAAGTGCGGTTTCTATATAA 28 128 0 TAAGTGCGGT 0.956701 -35 TGATTGAATAAAAGTGCGGTCGCTCTTTTT 30 26 1 AAAGTGCGGT 0.994282 -97 CCCACAAATAAAAATGCGATCGCTTTTATT 30 56 0 AAAATGCGAT 0.832162 -67 TTTATTTCTTAAAGTGCGGTAATTTCCGTT 32 133 0 AAAGTGCGGT 0.994282 -133 TTTATGCTAAGAAGAGCGGTGAA 33 4 0 GAAGAGCGGT 0.950856 -47 TCCTAATAAAAAAGAGCGGTTGATTTTCTC 34 17 1 AAAGAGCGGT 0.982403 -110 ********** Masking position 3 Map Score: 29.5134 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 60 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 2 AACCACGTCATCAAGGGGGAGATGCAAAAA 1 146 0 TCAAGGGGGA 0.98904 -155 GAGAATAATTTCAAGCGAGAGCAGGTGATC 6 25 0 TCAAGCGAGA 0.966335 -85 AGAGATGGGGACAAGGGAGAATAATTTCAA 6 41 0 ACAAGGGAGA 0.827636 -69 TTACGCAGCGTCAAGCGGAATCGTGTCAAT 7 224 0 TCAAGCGGAA 0.973431 -77 TTTCAGGGTTTCAAGGGAAGCACTCACATT 9 44 0 TCAAGGGAAG 0.849577 -79 CTTCGCCCCTTCAAGGGGGAAAAAGAAAAA 19 162 0 TCAAGGGGGA 0.98904 -114 ACGGACTTTCTCAAAGGAGAGTTATCA 19 259 1 TCAAAGGAGA 0.74787 -17 TTTATAGCGATCAAGGGGGATAAGAAATTT 22 77 1 TCAAGGGGGA 0.98904 -140 AAGAAAGATTTCAAGAGGAATTTAAGAGGA 22 160 0 TCAAGAGGAA 0.958504 -57 AAAAAGGAATTCAAGGAAAAGATTATAACA 23 118 0 TCAAGGAAAA 0.827003 -75 TTGATTAAATTCAAGAGGGAAATTTATATT 24 151 0 TCAAGAGGGA 0.966783 -68 CTCAATCACATCAAGCAAAACGAGTATAAA 27 49 1 TCAAGCAAAA 0.70978 -21 TGAATAAATTTCAAGAGAAAAAATGAAATA 31 50 0 TCAAGAGAAA 0.934915 -78 ATGATGAACTTCAAGGGGAAAACAAAATTT 32 79 0 TCAAGGGGAA 0.986229 -187 CTTTCGCATTTCAAGAGAAAATTTTAAAAA 32 166 0 TCAAGAGAAA 0.934915 -100 TCTGTCAAATTCAAGCCGAAGCTAATTGAA 34 63 0 TCAAGCCGAA 0.767737 -64 ********** Masking position 4 Map Score: 24.5397 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 50 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 AAGGCATTCATCAAAAAATTGTAATAAAAA 1 23 0 TCAAAAAATT 0.801245 -278 GCGCAAAAGCACAAAAAATTTTTGCATCTC 1 128 1 ACAAAAAATT 0.909949 -173 TAGCGTAACAACAAAAGATTGTTATGCTTG 3 122 1 ACAAAAGATT 0.728549 -124 GATTCTAACAAAACATTAACACCAACT 7 8 1 ACAAAACATT 0.728549 -293 CAAGTTTAGGACAAAATTTTGCCAGTTGGT 7 31 0 ACAAAATTTT 0.89268 -270 TTTAAATGAAATAAAAAATTTCTTATCCCC 22 92 0 ATAAAAAATT 0.834729 -125 ATTAAATTTCACAAAATATTGAGTT 23 6 0 ACAAAATATT 0.927899 -187 GTGAAATTTAATAAAATTTTTCATTATTTT 23 24 1 ATAAAATTTT 0.806108 -169 TTTGGCAAAAATAAAATTTTAAATTGCAAT 25 183 1 ATAAAATTTT 0.806108 -49 AAAAATTCTGACAAAATATTTTTCCTATTT 28 67 0 ACAAAATATT 0.927899 -96 CAAGGGGCTTACAAAAAATTCTGACAAAAT 28 80 0 ACAAAAAATT 0.909949 -83 TTATCTATCAATAAAAATTTGATGATAGGT 31 12 0 ATAAAAATTT 0.7655 -116 ATAGATAAAATCAAAATATTTCATTTTTTC 31 34 1 TCAAAATATT 0.836981 -94 CAAGGGGAAAACAAAATTTTCAGGCAAGAA 32 68 0 ACAAAATTTT 0.89268 -198 ACTTTAAGAAATAAAAAATTTTTAAAATTT 32 148 1 ATAAAAAATT 0.834729 -118 TAAAAAATTTTTAAAATTTTCTCTTGAAAT 32 159 1 TTAAAATTTT 0.623868 -107 ACCCCGAATTTTAAAATTTTTACTAGGAGT 32 241 1 TTAAAATTTT 0.623868 -25 CTTTCCTAAGTTAAAAAATTTCGTCACAAG 35 50 0 TTAAAAAATT 0.66832 -41 ********** Masking position 9 Map Score: 16.0927 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 97 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 GTGGGCTTTTTTTTGTCATGAATTTTGCATGGAACCG 3 63 1 TTTTCTAATG 0.979768 -183 CACATCCTGTTTTTAACCTTAAAATGGCATTATTGAG 6 73 1 TTTTCTAATG 0.979768 -37 ACTGGCAAAATTTTGTCCTAAACTTGATCTCGACGAA 7 35 1 TTTTCTAATA 0.859694 -266 CGTGATTTTCTTTTCACATTAATCTGGTCAATAACCT 8 38 1 TTTTCTAATG 0.979768 -92 CTCCGCGTTTTTTTCGCATTCATCTCGCTAACTTCGC 9 90 0 TTTTCTCATG 0.938649 -33 TATCTTTATTCCTTAAATTCGTATGTTCAGT 20 23 0 TTTACTAATG 0.837492 -21 TATCCTTTACTTTTTCCCTAAAAATAGATTAGAATTG 25 110 1 TTTTCTAATG 0.979768 -122 TATTTTAGATTTTTTACGTAAAATTCGCTGACTTTCG 28 35 0 TTTTCTAATG 0.979768 -128 AAGGAGGATTTTTTTTCTTTCAAGGGGCTTACAAAAA 28 93 0 TTTTCTCAGG 0.885369 -70 ATATTTCATTTTTTCTCTTGAAATTTATTCAACCGAG 31 49 1 TTTTCTAATA 0.859694 -79 TTGGCGAAAATTTTTACTTTAAAATAGGAAAGAAATA 32 12 0 TTTTCTAATG 0.979768 -254 TAAAAATTTTTTATTTCTTAAAGTGCGGTAATTTCCG 32 135 0 TTATCTAAGG 0.722348 -131 ATTTTTAAAATTTTCTCTTGAAATGCGAAAGAATATC 32 165 1 TTTTCTAAGG 0.960703 -101 **** * * ** * * Masking position 12 Map Score: 18.7548 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 36 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 GTCTTGTCCTGCCATATCGCGAAATTTCTGCGCA 1 99 1 GAATCGCGAA 0.723626 -202 GCGGTTGACTACTAAATGGGGTCGTAAACCACGT 1 168 0 AAATGGGGTG 0.920912 -133 AAAAAAGCCCACCACCTGGCGGTGACGGGCCTTT 3 41 0 AACTGGCGGG 0.90327 -205 TGTTATGCTTGAAATATGGTGATGCCGTACCCAT 3 141 1 GAATGGTGAG 0.726278 -105 CATGTACGTCAGTATATGGGGATGTTTCCCCCAC 5 94 0 AAATGGGGAG 0.930984 -94 CGTACATGTTAATAGATGGCGTGAAGCACAGTCG 5 120 1 AAATGGCGTA 0.909756 -68 GTGTCATCTGATTACCTGGCGGAAATTAAACTAA 5 153 1 AACTGGCGGA 0.87812 -35 CAGGATGTGGGAGAGATGGGGACAAGGGAGAATA 6 48 0 GAATGGGGAA 0.922133 -62 TGGGCTTGAGACCACATGGGGTCGGCGCCCCGAA 7 129 0 AAATGGGGTG 0.920912 -172 TTCACTAACAAATAGCTGGTGGAATAT 7 284 1 AACTGGTGGA 0.526059 -17 CCATTTTGAAATAAGCTGGCGTTGATGCCAGCGG 10 184 1 AACTGGCGTG 0.853678 -54 TAACGGCTGAAGGACATCGGGTCAATCGCCCAAC 12 137 1 AAATCGGGTA 0.639013 -58 GGTGATATATGGGAGATGGCGGTAGAATGACCCG 14 41 0 GAATGGCGGA 0.948345 -85 ATAATGCAATTATAGATGGGGGGGATTTTGAGGG 16 13 0 TAATGGGGGG 0.80679 -80 CGCCGCTTAAGTAACATGGCGGGCTGACGAACGA 17 48 1 GAATGGCGGC 0.775654 -44 TCTGATCAGCACAAAATCGGGTGAAAACCCTGAT 19 124 0 AAATCGGGTA 0.639013 -152 CTGGTGACCAGAGAAATGGGGATGAGGCTTCGCC 19 185 0 GAATGGGGAG 0.938833 -91 AAAGTTGTTCGTTATATGGCGACAAATTGATTAA 24 173 0 GAATGGCGAA 0.930013 -46 ACTTAGTTTATGCAAATGGCGAAAGCCGAAATCA 31 89 1 TAATGGCGAA 0.723502 -39 * * ******* * Masking position 7 Map Score: 13.3436 Number of sites scoring better than the average of aligned sites = 1143 Number in coding regions = 1074 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 GATGCAAAAATTTTTTGTGCTTTTGCGCAGA 1 125 0 TTTTTTTGCT 0.366 -176 GAAAATCACATTTTTATCGTAATTGCCCTTT 7 94 1 TTTTTACGTA 0.853587 -207 TTTCTCCGCGTTTTTTTCGCATTCATCTCGC 9 99 0 TTTTTTCGCA 0.87233 -24 CGTATTTTTTGCTTACGTTGGGATT 14 5 1 TTTTTTCTTA 0.915808 -121 ATCAGCGGACTTTTTTTTGCAGTTTATGGTC 15 75 0 TTTTTTTGCA 0.710352 -156 TGATCAGAATTTTTTTTCTTTTTCCCCCTTG 19 150 1 TTTTTTCTTT 0.719139 -126 TATCTTTATTCCTTAAATTCGTATG 20 29 0 TTTATTCTTA 0.769416 -15 GATAAGAAATTTTTTATTTCATTTAAAGTGC 22 95 1 TTTTTATTCA 0.691242 -122 TCCTTGTGTTTTTTTACCGCACTTTTCCTCT 22 135 1 TTTTTACGCA 0.826969 -82 TGACGTTCAATTTTTATCTTT 22 206 1 TTTTTACTTT 0.641705 -11 GCCAAAATTCTTTTTTGTTTAAAACCCACTT 23 73 1 TTTTTTTTTA 0.796098 -120 TAAAACCCACTTTATAACTCAGATTTTGTTA 23 92 1 TTTATACTCA 0.656755 -101 GATCATACATTTTTTAGCTTATATTCAATAA 24 48 1 TTTTTACTTA 0.883837 -171 CAACTTCACATTTTTTATTTATGAGTGAAGA 24 110 1 TTTTTTTTTA 0.796098 -109 ATATTGTAGATTTATTCTTCACTCATAAATA 24 125 0 TTTATTTTCA 0.495417 -94 AAGAGGGAAATTTATATTGTAGATTTATTCT 24 138 0 TTTATATGTA 0.390954 -81 CTATTTTAGATTTTTTACGTAAAATTCGCTG 28 42 0 TTTTTTCGTA 0.892874 -121 TAAGGAGGATTTTTTTTCTTTCAAGGGGCTT 28 100 0 TTTTTTCTTT 0.719139 -63 TTGGCGAAAATTTTTACTTTAAAATAGGAAA 32 18 0 TTTTTATTTA 0.731973 -248 TTAAAAATTTTTTATTTCTTAAAGTGCGGTA 32 142 0 TTTATTCTTA 0.769416 -124 TTTCTCAATGTTTTTTACTGATTTCAATTAG 34 41 1 TTTTTTCTGA 0.596102 -86 GTGACGAAATTTTTTAACTTAGGAAAGGTAG 35 53 1 TTTTTACTTA 0.883837 -38 ****** **** Masking position 5 Map Score: 12.7934 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 243 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 7 ACGTCATCAAGGGGGAGATGCAAAAATTTTTTG 1 139 0 GGGGGAGAAA 0.978888 -162 TGAATGCACGGGCGGAGAGGAAATTCCCCTTCG 2 45 0 GGCGGAGAAA 0.89282 -44 GCATTCATCTAGGGGCAATTTAAAAAAG 2 71 1 AGGGGCAAAA 0.937816 -18 GAAAAATTAAAGGGGAGATAAAATCCCCCCTTT 5 41 0 AGGGGAGAAA 0.974458 -147 GCCGAGAATAGAGGAAAAATTAAAGGGGAGATA 5 54 0 GAGGAAAAAA 0.591578 -134 CTGATTACCTGGCGGAAATTAAACTAAGAGAGA 5 160 1 GGCGGAAAAA 0.918991 -28 GGCTTTCTCCAGGGGCGAACAAAGTTTTACATC 10 62 0 AGGGGCGAAA 0.917178 -176 AGTTATCCCCATGGGAAAGTTAA 14 113 1 ATGGGAAAAA 0.788494 -13 GCCCCTTCAAGGGGGAAAAAGAAAAAAAATTCT 19 155 0 GGGGGAAAAA 0.98441 -121 TAGCGATCAAGGGGGATAAGAAATTTTTTATTT 22 81 1 GGGGGATAAA 0.898837 -136 ATATTGGGGTAGGGAAAAAGGAATTCAAGGAAA 23 129 0 AGGGAAAAAA 0.904027 -64 ATCTATTTTTAGGGAAAAAGTAAAGGATAGAAT 25 106 0 AGGGAAAAAA 0.904027 -126 TTATTAAATAAGGGAAAAGAAA 29 10 1 AAGGGAAAAA 0.867966 -13 ATGAACTTCAAGGGGAAAACAAAATTTTCAGGC 32 73 0 AGGGGAAAAA 0.981117 -193 ******** ** Masking position 8 Map Score: 15.4079 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 92 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ACTAAATGGGGTCGTAAACCACGTCATCAAGGGG 1 158 0 GTAAACCCGT 0.839484 -143 CGCTAAATTCGCACAAAGGCCCGTCACCGCCAGG 3 27 1 GCAAGGCCGT 0.908512 -219 ATGGAACCGTGCGAAAAGCCTCTTTCGGTGTTAG 3 91 1 GCAAGCCCTT 0.958276 -155 GCCATTCTCAGGCGCAAGCCGCTTACAGCGTTGT 4 53 0 GGAAGCCCTT 0.97821 -73 GGGTCAAAACCTCTTCTTTGTTCTT 4 111 0 GGAAACCCTT 0.960235 -15 GTTCGCCCCTGGAGAAAGCCTCGTGTATACTCCT 10 75 1 GGAAGCCCGT 0.990018 -163 GTCACTCAAGGGATTAACCTCTTATTACAACTG 13 77 0 GGTAACCCTT 0.719865 -23 ATCTATAATTGCATTATGCCCCGTACTTTTGTAC 16 30 1 GCATGCCCGT 0.843741 -63 ACGAATACAGAGTACAAACCCCGTACAAAAGTAC 16 52 0 AGAAACCCGT 0.792865 -41 TGCCGTGACTGGTCAAAGGCCCGCCGCTTAAGTA 17 27 1 GGAAGGCCGC 0.753785 -65 CCCCTTGAAGGGGCGAAGCCTCATCCCCATTTCT 19 174 1 GGAAGCCCAT 0.917186 -102 TGGTCACCAGCCGGGAAACCACGTAAGCTCCGGC 19 209 1 CCAAACCCGT 0.743749 -67 GGTTTCAACTGGTTAAAACCGCTTAAACAGGGTA 25 50 0 GGAAACCCTT 0.960235 -182 ** ***** *** Masking position 10 Map Score: 9.15593 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 246 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CCATATCGCGAAATTTCTGCGCAAAAGCACA 1 110 1 AAATTTTGCG 0.794736 -191 TGTGAGTCTGTAATAGGGGCGAAACGTCTGG 1 243 0 TAATAGGGCG 0.701343 -58 TTAGTTAACCAAAAAGGGGGGATTTTATCTC 5 29 1 AAAAAGGGGG 0.912397 -159 ATTGCCCTTTAAAATTCGGGGCGCCGACCCC 7 115 1 AAAATTGGGG 0.945737 -186 AGCTTATTTCAAAATGGTGCGGAATTTTACT 10 170 0 AAAATGTGCG 0.814294 -68 ATGAATTGCTAAAAATCGGGGCCT 11 97 1 AAAAATGGGG 0.926795 -14 CAGTTGCCCAAAATTTGGGCGCAATCGGACA 19 18 0 AAATTTGGCG 0.94606 -258 TAATTTGGGTAAATATTGGGGTAGGGAAAAA 23 143 0 AAATATGGGG 0.901927 -50 TTTATTACCTAAAATGTTGCGCGATTTTACC 25 23 1 AAAATGTGCG 0.814294 -209 GGATTTGTGATAAATTTGGCGAAAATTTTTA 32 33 0 TAAATTGGCG 0.843989 -233 TAAAAATTTTAAAATTCGGGGTAGGGCTTTT 32 232 0 AAAATTGGGG 0.945737 -34 GATTGTACCCAAATATAGGCGAAACGACTAC 34 91 1 AAATATGGCG 0.927222 -36 ****** **** Masking position 3 Map Score: 8.0586 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 230 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 10 GTCTGTAATAGGGGCGAAACGTCTGGTTTCA 1 238 0 GGGGCGAACG 0.983266 -63 TTTACGCAGCATAACGCGCTAAATTC 3 6 1 GCAGCAAACG 0.781289 -240 TGCCAGAGGCGCAACTGTGCCGCTAT 4 6 1 GAGGCGAACT 0.824163 -120 CTTATCCAGGGCGGCACAACGCTGTAAGCGG 4 38 1 GCGGCAAACG 0.981896 -88 GTCGTCGTGTGCGGCACAAAGAACAAAGAAG 4 93 1 GCGGCAAAAG 0.795563 -33 CCACATGGGGTCGGCGCCCCGAATTTTAAAG 7 121 0 TCGGCGCCCG 0.79272 -180 GTTGATGCCAGCGGCAAACCGAATTAATCAA 10 204 1 GCGGCAACCG 0.978078 -34 GCGGCTGTCGGGGGCTTCCCGATCGCTCTTC 12 29 0 GGGGCTCCCG 0.869333 -166 ATAGACTGAGGGGGCAGCACGAAACGTTAAA 15 38 0 GGGGCACACG 0.956689 -193 ACAAAAGTACGGGGCATAATGCAATTATAGA 16 31 0 GGGGCAAATG 0.758552 -62 CTCACGATGCGAGGCGGATCGAAAAATTCAA 18 15 1 GAGGCGATCG 0.853798 -141 ATATCATTGCGAGGCTTACCTACAAGAGCAA 21 21 1 GAGGCTACCT 0.512639 -43 TACCCAAATATAGGCGAAACGACTACAAAAA 34 96 1 TAGGCGAACG 0.824163 -31 ****** **** Masking position 5 Map Score: 6.33366 Number of sites scoring better than the average of aligned sites = 1208 Number in coding regions = 1126 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 11 GACTCACTCACTGCGGTTGACTACTAAATGG 1 183 0 CTGCGGTTGC 0.868322 -118 TTGTAAAGCACCGCGGCCTTTTTTGAAAGGG 10 124 0 CCGCGGCCTT 0.708328 -114 CGAAAGGAATGCGCGGCTTATTTTCGTTTAT 11 68 1 GCGCGGCTTT 0.927302 -43 CTGCCTCTCAGTGCGGCTGTCGGGGGCTTCC 12 41 0 GTGCGGCTGC 0.946117 -154 TTCATTTAAAGTGCGGTTTAAATTCCTTGTG 22 112 1 GTGCGGTTTA 0.850064 -105 TGTATGATCTGAGCGGTTTTTAAATCAGCGT 24 26 0 GAGCGGTTTT 0.92052 -193 TGGTGTGAAAGTGCGGTCGTTTTTGGCGTAG 26 94 0 GTGCGGTCGT 0.972916 -40 TAATTTGTAAGTGCGGTTTCTATATAAGGAG 28 124 0 GTGCGGTTTT 0.96936 -39 TTGAATAAAAGTGCGGTCGCTCTTTTTAATA 30 29 1 GTGCGGTCGT 0.972916 -94 TAATAAAAAAGAGCGGTTGATTTTCTCAATG 34 20 1 GAGCGGTTGT 0.948638 -107 ********* * Masking position 4 Map Score: 5.47074 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 390 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 CTGCCATATCGCGAAATTTCTGCGCAAAAG 1 107 1 GCGAAATTTC 0.441553 -194 CACGGGCGAAGGGGAATTTCCTCTCCGCCC 2 39 1 GGGGAATTTC 0.830488 -50 CCGCCAGGTGGTGGGCTTTTTTTTGTCATG 3 53 1 GTGGGCTTTT 0.752021 -193 AACCAAAAAGGGGGGATTTTATCTCCCCTT 5 35 1 GGGGGATTTT 0.962554 -153 GATCCGGTACGCGTGATTTTCTTTTCACAT 8 27 1 GCGTGATTTT 0.701722 -103 GTAAAGCACCGCGGCCTTTTTTGAAAGGGA 10 123 0 GCGGCCTTTT 0.77859 -115 TCAAAATGGTGCGGAATTTTACTGCAATTG 10 163 0 GCGGAATTTT 0.895642 -75 TGCGGCTGTCGGGGGCTTCCCGATCGCTCT 12 31 0 GGGGGCTTCC 0.693344 -164 CCGGGAGATTTCAGACGAAAGT 13 3 1 GGGAGATTTC 0.703101 -97 AGCCTTATCAGCGGACTTTTTTTTGCAGTT 15 82 0 GCGGACTTTT 0.886442 -149 TTATAGATGGGGGGGATTTTGAGGGTT 16 8 0 GGGGGATTTT 0.962554 -85 TACTTAAGCGGCGGGCCTTTGACCAGTCAC 17 31 0 GCGGGCCTTT 0.798447 -61 CTAAAATGTTGCGCGATTTTACCCTGTTTA 25 31 1 GCGCGATTTT 0.777124 -201 TTCTATATAAGGAGGATTTTTTTTCTTTCA 28 108 0 GGAGGATTTT 0.610093 -55 ********** Masking position 8 Map Score: 6.32791 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 596 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 13 CAGCGTTGTGCCGCCCTGGATAAGTATAGCG 4 31 0 CCGCCTGGAT 0.91817 -95 GTTCTTTGTGCCGCACACGACGACGCAAATG 4 86 0 CCGCCACGAC 0.992924 -40 CGGTTGTTTACCGCCAACGATAATTACGAGG 12 92 0 CCGCAACGAT 0.961401 -103 ACCGCTCACGATGCGAGGCGGA 18 2 1 CCGCCACGAT 0.992365 -154 TCCGCGCACGACACTGAACATA 20 2 1 CCGCCACGAC 0.992924 -42 **** ****** Masking position 10 Map Score: 2.71648 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 17 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 GGTTTTTTCAATTTTATCCAGGAGACGGAA 3 226 1 ATTTTATCCA 0.5999 -20 TCTTAGTTTAATTTCCGCCAGGTAATCAGA 5 159 0 ATTTCCGCCA 0.877782 -29 ATTGTCATCAATCTTCGCAACAAGGACCTC 9 17 0 ATCTTCGCAA 0.910093 -106 GCGCGTAAAAATTTACGCAATTGGTTACGA 14 81 1 ATTTACGCAA 0.81794 -45 ATTTTTCATTATTTTAGCCATTATCACTTC 23 39 1 ATTTTAGCCA 0.858217 -154 ACAAAAAAGAATTTTGGCAAATGAAGTGAT 23 61 0 ATTTTGGCAA 0.727886 -132 TTAAAATTTTATTTTTGCCAAAGCACCTGT 25 175 0 ATTTTTGCCA 0.774403 -57 CACAACAAAAATCTACGCCAAAAACGACCG 26 82 1 ATCTACGCCA 0.842567 -52 AAAAAATCTTATCTTCTCAATCACATCAAG 27 34 1 ATCTTCTCAA 0.714891 -36 TAAAGTAAAAATTTTCGCCAAATTTATCAC 32 28 1 ATTTTCGCCA 0.968494 -238 AGAGCGGTTGATTTTCTCAATGTTTTTTAC 34 29 1 ATTTTCTCAA 0.800136 -98 ********** Masking position 1 Map Score: 3.36583 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 531 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 15 ATAATAAGCGAAGTTAGCGAGATGAATGCG 9 83 1 AAGTTAGCGA 0.698029 -40 AACTGTGTTAAAAACAGCGTCAGGATACTC 13 52 0 AAAACAGCGT 0.90619 -48 ATAGCTCCTGAAATCAGCGAGAATGTAAGA 15 206 0 AAATCAGCGA 0.956906 -25 CGAACGAATAAATACAGCGAAACGATA 17 75 1 AATACAGCGA 0.845634 -17 AGCGGTTTTTAAATCAGCGTTTGTGAGGAA 24 16 0 AAATCAGCGT 0.90619 -203 TATTATACGAAAGTCAGCGAATTTTACGTA 28 28 1 AAGTCAGCGA 0.937273 -135 GCTTTTATTAAAAAGAGCGACCGCACTTTT 30 35 0 AAAAGAGCGA 0.903566 -88 TTCCTAATAAAAAAGAGCGGTTGATTTTCT 34 16 1 AAAAGAGCGG 0.774064 -111 ********** Masking position 6 Map Score: 1.16979 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 331 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899