AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR6_ecoli_bsub_300.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 dgt 83 deoxyguanosine triphosphate triphosphohydrolase #2 htrA 129 periplasmic serine protease Do; heat shock protein HtrA #3 tig 300 trigger factor; a molecular chaperone involved in cell division #4 clpP 245 ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 #5 clpX 125 ATP-dependent specificity component of clpP serine protease, chaperone #6 lon 187 DNA-binding, ATP-dependent protease La; heat shock K-protein #7 hupB 208 DNA-binding protein HU-beta, NS1 (HU-1) #8 ybaU 191 putative protease maturation protein #9 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #10 yihD 69 orf, hypothetical protein #11 yihE 77 orf, hypothetical protein #12 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #13 spoIIE 300 serine phosphatase #14 yabS 84 similar to hypothetical proteins #15 yabT 88 yabT #16 yacA 103 similar to cell-cycle protein #17 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #18 yacB 194 similar to hypothetical proteins #19 yacC 85 similar to hypothetical proteins #20 yacD 46 similar to protein secretion PrsA homolog #21 ybcO 300 ybcO #22 ybcP 66 ybcP #23 ybcQ 43 similar to hypothetical proteins #24 ybdB 64 similar to ABC transporter (permease) #25 ybdD 46 ybdD #26 ybdE 105 similar to hypothetical proteins #27 yczA 300 yczA #28 ycbL 96 similar to two-component response regulator [YcbM] #29 yclJ 212 similar to two-component response regulator [YclK] #30 yerE 264 similar to hypothetical proteins #31 yerF 61 similar to ATP-dependent DNA helicase #32 yerG 23 similar to DNA ligase #33 yerI 161 yerI #34 htrA 168 serine protease Do (heat-shock protein) #35 ykoG 300 similar to two-component response regulator [YkoH] #36 resD 80 two-component response regulator #37 resC 135 essential protein similar to cytochrome c biogenesis protein #38 resA 131 essential protein similar to cytochrome c biogenesis protein #39 ypuL 91 similar to hypothetical proteins #40 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #41 ypuI 54 similar to hypothetical proteins from B. subtilis #42 ypuG 280 similar to hypothetical proteins #43 ppiB 253 peptidyl-prolyl isomerase #44 yrkP 267 similar to two-component response regulator [YrkQ] #45 phoP 211 two-component response regulator #46 citH 43 malate dehydrogenase #47 citC 163 isocitrate dehydrogenase #48 citZ 300 citrate synthase II #49 yvqA 277 similar to two-component response regulator [YvqB] #50 yvrI 300 yvrI #51 yyxA 68 alternate gene name: yycK; similar to serine protease Do #52 yycJ 21 yycJ #53 yycF 300 similar to two-component response regulator [YycG] Motif number 1 CATGACAAAAAAAAGCCCACCACCTGGCGGTGAC 4 49 0 AAAACCCCCC 0.608261 -197 AAGGGGAGATAAAATCCCCCCTTTTTGGTTAACT 6 31 0 AAAACCCCTT 0.934664 -157 CTTGAACTTCGTCACATCCCCACTGGGGACAACG 8 12 0 GTCAACCCCT 0.771596 -180 GGTGTAACAACACTCCGCTGTAGATGACT 8 173 0 AACACCCCCT 0.894311 -19 TCAAGCGGTTAAGACACCGCCCTTTCACGGCGGT 13 50 1 AAGAACCCTT 0.812321 -251 AGGATAATATACAAAATCCCCCTTACTTCGACAA 21 201 1 ACAAACCCTT 0.802484 -100 ATAAAATCCCCCTTAAGAGAAAAT 22 53 0 ATAAACCCTT 0.938638 -14 GACCTTGACTTACAAAACGCCTTTTTGACTGAAG 24 30 0 TACAACCCTT 0.789834 -35 AAAAGAGCCCCTCTCCTCGTTTTA 25 33 0 AAAAACCCCT 0.958556 -14 TAAGAAACACAAAAAACCCCCGTCCTATGCAAAG 27 208 0 AAAAACCCTC 0.84535 -93 ATTTTTATTGATAAGACCGCCTCTGGGGCGCGTC 29 31 1 ATAAACCCCT 0.912023 -182 GCTTTTTTATATAATAGCACCATTTTAAACAGAA 29 167 0 ATAAACCCTT 0.938638 -46 TGAAAAAAGAATCAAAACACCTTTTTCAGTGAAT 30 151 1 ATCAACCCTT 0.930318 -114 TTCCAGCATCAACATACCTCCCCTTGATTTGTGT 33 95 0 AACAACCCCT 0.952803 -67 AAGCGCACAAAAAAATACACCATTCGGTCAACCT 35 75 1 AAAATCCCTT 0.900189 -226 TATCTCAGCCAAAACAGCACCCCTAGTGCTTTCC 35 176 1 AAAAACCCCT 0.958558 -125 GCTCTGCCATGACATCACTCCCTTTTCGC 37 6 0 GACACCCCTT 0.823377 -130 GCCAAATCTAAAAAAAACGCCGTTT 39 2 0 AAAAACCCTT 0.971534 -90 ATCAATACTCCTTTCCCATTTATC 44 1 1 ATCATCCCTT 0.779155 -267 AGGACATTCCGACAATTCGCCTTTTACATCATTT 45 98 0 GACATCCCTT 0.746131 -114 TGATTTCCCCGAAAAAACGCCTTTATTTGCGGGT 48 16 0 GAAAACCCTT 0.927235 -285 TCCTTTTCAATAAATTTCCCCTTTAAGAGTGTTG 48 267 0 TAAATCCCTT 0.532237 -34 ATATAACATCTCCTTTTCAATAAATT 48 285 0 ATAAACCCTT 0.938638 -16 GATCCATAGGAAAATACCTCCCTTCTTTTTCTGC 50 149 1 AAAAACCCTT 0.971534 -152 **** * * ** ** Masking position 4 Map Score: 24.6645 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 201 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 AATGCTGGGCAAAAAGCGCAAAATCCAGACA 3 48 0 AAAAAGGCAA 0.751906 -253 TTAGTTAACCAAAAAGGGGGGATTTTATCTC 6 29 1 AAAAAGGGGG 0.872046 -159 CAGAGCAGAAAAAAAGCAAGTGAAGAGATTC 9 233 0 AAAAAGAAGT 0.556489 -38 CAGTTTTTTTAGAAAGAAAGCGAA 18 4 0 AGAAAGAAGC 0.780544 -191 GAATGTTTGTAAAAAGTAAAGTAGAGAAACT 18 153 1 AAAAAGAAAG 0.672849 -42 CAGATGAGTTAGAAAGGAGGATATCAA 27 284 1 AGAAAGAGGA 0.726453 -17 ATGGTTACATAAAAAGGGAGGCTGAGAG 30 8 0 AAAAAGGAGG 0.929918 -257 TTTTTCATAAAAAAAGAGAGCATATGGCAGT 30 127 0 AAAAAGGAGC 0.917529 -138 GGAAATTGTGAAAAAGTGCGGAAAACGGTAC 34 42 0 AAAAAGGCGG 0.921229 -127 GAATAAAGATAAAAAGGGCAGGCCAAACCG 37 116 1 AAAAAGGCAG 0.713179 -20 CATAACCTTCAAAAAGTAAGAAATGTGAAAT 38 61 1 AAAAAGAAGA 0.921818 -71 TTAAGGTTGAAAAAAGTAAGATAATACTTGA 39 61 1 AAAAAGAAGA 0.921818 -31 ACTCTCCCTGAAAAAGGGAGAGTAAACG 40 8 0 AAAAAGGAGA 0.94177 -115 TATGATGATGAAAAAGCGCGATTCATTAAAC 41 13 0 AAAAAGGCGA 0.934446 -42 GATAAAAGGAAAAAAGAACGCCCGGCCTCTA 42 53 1 AAAAAGACGC 0.877278 -228 AGTGCTTCTTAGAAAGGAAAACCAGAAGCAA 42 83 1 AGAAAGAAAA 0.523654 -198 ATTAAAATAAAGAAAGTAGGCATACAA 43 237 1 AGAAAGAGGC 0.646245 -17 TAAAAAGAGAGAAAGGCTTGCT 45 2 1 AAAAAGGAGA 0.94177 -210 CATTTATAGTAAAAAGAGAAAGGCTGTATTA 45 33 0 AAAAAGGAAA 0.774706 -179 AGGCTTACTTAAAAAGCACGATGCAAGTATT 48 226 0 AAAAAGACGA 0.912219 -75 AAAGGAAGAGAAAAAGAGCGAGGAAGATGTA 49 132 0 AAAAAGGCGA 0.934446 -146 GGTTAAGGGAAGAAAGGAAGAGAAAAAGAGC 49 144 0 AGAAAGAAGA 0.837939 -134 ATGACTGCAGAAAAAGAAGGGAGGTATTTTC 50 158 0 AAAAAGAGGG 0.832453 -143 GGAAAGCAAAAAAAAGTAAACTACTACTTTC 50 254 0 AAAAAGAAAC 0.632951 -47 ****** **** Masking position 5 Map Score: 23.169 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 305 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 3 ACAGCAGGTTTTTTCAATTTTATCCAGGAGA 4 220 1 TTTTCATTTT 0.777515 -26 CCGCTATGCCATTTTATTTTTGAACGCAGGC 9 16 0 ATTTTTTTTT 0.844462 -255 AAGCCGATTTTTTTCATTTTTAGACAACATT 13 138 1 TTTTCTTTTT 0.854757 -163 GCTTGTCAGCTTTTCTATTTTTAAAGGGTTA 21 136 1 TTTTCATTTT 0.777515 -165 TATCATTTCTTTTTTATGGCTTCAG 24 5 1 ATTTCTTTTT 0.816541 -60 ACGTGTGTGTTTTTTGATTTTGTAAAGGTTA 28 55 1 TTTTTATTTT 0.809993 -42 AGTGAAAATATTTTCCCTTTTCCTGTTAATT 33 55 0 TTTTCCTTTT 0.630753 -107 TCCCATAATCTTTTCATTTTTATCCCACAGT 34 70 1 TTTTCTTTTT 0.854757 -99 TATCCCACAGTTTTTGTTTATGATAAACTCA 34 90 1 TTTTTTTTAT 0.564792 -79 GGATATGCAGTTTTTTATTTTACCAAAAAAA 35 16 0 TTTTTATTTT 0.809993 -285 CCGTATACAATTTTTTATTTTAACATCATAA 35 208 1 TTTTTATTTT 0.809993 -93 CTGAGCGGAAATTTTCTTTATGCGGCCTTTC 37 39 1 ATTTTTTTAT 0.495327 -97 CGGGCGTTCTTTTTTCCTTTTATCCCTTCTA 42 46 0 TTTTTCTTTT 0.675719 -235 TCAGGTTTCATTTTTATTTTTTAGTAAAGCT 43 118 1 TTTTTTTTTT 0.877733 -136 TACTTTCTTTATTTTAATTTTCAAAGGAGAT 43 224 0 ATTTTATTTT 0.763261 -30 TTTAGAAAACATTTTATTTTTCTTATATAGA 47 114 0 ATTTTTTTTT 0.844462 -50 TTTACCTATAATTTTTTTTTTCCATTCTGTG 48 48 0 ATTTTTTTTT 0.844462 -253 AAATGTAAGCATTTTCTTTTTGGGGGAGAGA 48 195 1 ATTTTTTTTT 0.844462 -106 TCACATATTCTTTTCATTTTTATCCCACAAT 49 190 0 TTTTCTTTTT 0.854757 -88 CTAAACCTTTATTTTTTTTATCTTTTGACCT 53 173 1 ATTTTTTTAT 0.495327 -128 CATTTTGATTTTCCTCCTGCCG 53 289 0 ATTTTATTTT 0.763261 -12 ***** ***** Masking position 4 Map Score: 17.8207 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 161 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 CCTCTCCCGCGTGAGAAATACGCTTCCCCGT 1 61 0 GTGAGAATAC 0.708915 -23 TATTTCTCACGCGGGAGAGGAC 1 72 1 GCGGGAAGGA 0.780601 -12 ACCTGTGCTTGCGGGGTAAGAGTTGACCGAG 3 255 1 GCGGGGAAGA 0.889126 -46 GCATGGAACCGTGCGAAAAGCCTCTTTCGGT 4 89 1 GTGCGAAAGC 0.886734 -157 GGCGTTGAATGTGGGGGAAACATCCCCATAT 6 84 1 GTGGGGAAAC 0.943443 -104 ATCTAACTTAGCGAGACAAAAAAAGGCTGGC 7 66 0 GCGAGAAAAA 0.849645 -143 AAGGATTCAAGTGCGATATAAATTATAAAGA 7 177 1 GTGCGAATAA 0.761053 -32 AAATGGCATAGCGGGATATGCCGCGAGCGGG 9 33 1 GCGGGAATGC 0.81078 -238 AATATAACAGGTGGGAGATGAGAGGA 13 285 1 GTGGGAATGA 0.71377 -16 AATTCACATAGCGCGGAAAAACGGAAAAAGC 30 198 0 GCGCGGAAAA 0.911051 -67 TTGTGAAAAAGTGCGGAAAACGGTACACTTC 34 37 0 GTGCGGAAAC 0.926513 -132 AACAAAAACTGTGGGATAAAAATGAAAAGAT 34 77 0 GTGGGAAAAA 0.92329 -92 CTGAGATAAAGCGCGGAAGAAACGCGCTTTG 35 153 0 GCGCGGAGAA 0.812402 -148 GAGCGCAGAAGCGGGAGAAAAAGCCTTTGCT 42 109 0 GCGGGAAAAA 0.934299 -172 GAATCATGAGGTGAGAGAGAC 44 257 1 GTGAGAAGAC 0.746258 -11 AACAAACATTGTGGGATAAAAATGAAAAGAA 49 183 1 GTGGGAAAAA 0.92329 -95 ATTGCAATCAGCGCGGGAAACCCCAAATTGC 50 85 1 GCGCGGAAAC 0.937091 -216 ATGTATGTAAGTGAGGAAAACCGATAAAACG 50 187 1 GTGAGGAAAC 0.868918 -114 AAATAATGGAGTGAGACAAAC 52 11 1 GTGAGAAAAC 0.874308 -11 ****** **** Masking position 8 Map Score: 14.5354 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 542 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 5 GCAGGCCGTTTTTCATAAAATCT 3 4 0 TTTCATAAAA 0.903423 -297 CGGAAATTCTTTTCATAAACGAATATCAAG 13 170 1 TTTCATAAAC 0.955149 -131 AGCCAATCATTTACATAAAAAAACTGCCAG 18 45 0 TTACATAAAA 0.738357 -150 ACGCGGTTTCTTTCATAAATCAATTCCAGC 19 42 0 TTTCATAAAT 0.807623 -44 TTAGTTTTTATTTCATCAACTAGAAATAGA 29 117 0 TTTCATCAAC 0.756702 -96 GTGGAAATGGTTACATAAAAAGGGAGGCTG 30 15 0 TTACATAAAA 0.738357 -250 TTGATTCTTTTTTCATAAAAAAAGAGAGCA 30 136 0 TTTCATAAAA 0.903423 -129 ACATACGTTCTATCATAAACCAAATCCGTA 31 18 0 TATCATAAAC 0.924033 -44 CTGTTAATTGTAACATAAAAACCCTTGTGC 33 34 0 TAACATAAAA 0.617055 -128 GACTCAGTCCTTTCATATACAATATGAAGT 34 12 1 TTTCATATAC 0.677306 -157 GACTTGAGTTTATCATAAACAAAAACTGTG 34 95 0 TATCATAAAC 0.924033 -74 GAGCATCAGCTTTCATAAATTGGTAAGATT 44 156 1 TTTCATAAAT 0.807623 -112 ATGAAAGCGCTATCATAAACGTCTTTATTT 45 61 1 TATCATAAAC 0.924033 -151 CCCTTAACCATATCATAAACAAACATTGTG 49 166 1 TATCATAAAC 0.924033 -112 ********** Masking position 5 Map Score: 10.2825 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 35 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 GCGAGACAAAAAAAGGCTGGCAAGCCCGAA 7 57 0 AAAAGGCTGG 0.745151 -152 GGGGTGTTGTAAGGGGATGGCTGGCCTGAT 7 122 1 AAGGGGATGG 0.86112 -87 AAAATTAGGTAAAGGGATGGCCTTGTTCTT 9 191 1 AAAGGGATGG 0.831104 -80 TACCGCCGTGAAAGGGCGGTGTCTTAACCG 13 55 0 AAAGGGCGGT 0.845231 -246 TGCTTACTGTGGGAGGAGGTAAGGA 17 83 1 GGGAGGAGGT 0.827554 -15 CTTAACCCTAAAAGGGCTGGAATTGATTTA 19 27 1 AAAGGGCTGG 0.786519 -59 TGCAAAAATTGAGAGGAGGTTTACTT 21 285 1 GAGAGGAGGT 0.950542 -16 AGATGAGTTAGAAAGGAGGATATCAA 27 285 1 GAAAGGAGGA 0.682154 -16 AACACAAATCAAGGGGAGGTATGTTGATGC 33 94 1 AAGGGGAGGT 0.901875 -68 ATAGGGACGGGAGAGGATGGTCAAAT 35 285 1 GAGAGGATGG 0.928395 -16 AGTAAAAAGAGAAAGGCTGTATTAAGCAAG 45 27 0 GAAAGGCTGT 0.87657 -185 TAATGACGTTGAAAGGATGTGAAGAGCC 49 260 1 GAAAGGATGT 0.904629 -18 TGCAGAAAAAGAAGGGAGGTATTTTCCTAT 50 154 0 GAAGGGAGGT 0.950542 -147 TAATTTAGTAGGGAGGCGGT 50 291 1 GGGAGGCGGT 0.782277 -10 AACGTTCTTGGAAAGGATGGAAT 51 56 1 GAAAGGATGG 0.911424 -13 GCACTCCGGTGAGGGGAGGTTTCAATAAAG 53 65 1 GAGGGGAGGT 0.960344 -236 ********** Masking position 5 Map Score: 11.7359 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 185 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 CACAAAGAACAAAGAAGAGGTTTTGACCC 5 107 1 AAAGAAGAGG 0.836899 -19 TATAAATTATAAAGAGGAAGAGAAGA 7 193 1 AAAGAGGAAG 0.962238 -16 CCCTCCAAGCAAAGAAGAAGCATAGGCTCT 16 25 0 AAAGAAGAAG 0.964598 -79 TTGAAGAGGAAAGGAAGAAGCAG 32 11 1 AAGGAAGAAG 0.962238 -13 CATAAGATATAAGGAAGAAGCTATC 41 40 1 AAGGAAGAAG 0.962238 -15 AAGCACATTAAAGGAGGAAGCACC 42 5 0 AAGGAGGAAG 0.959727 -276 TTTATAGTAAAAAGAGAAAGGCTGTATTAA 45 32 0 AAAGAGAAAG 0.796981 -180 GCAAGGAAAAAGCCTAAAACTA 46 3 1 AAGGAAAAAG 0.796981 -41 AACTAGCCATAAAGGAGAAGAGAGAC 46 28 1 AAAGGAGAAG 0.836899 -16 TCAGGTTTTTATAGAGGAAGTCGTAAAACA 50 121 0 ATAGAGGAAG 0.764023 -180 CGGCCGGTTCAAAGAAGAAGACGTCATTGA 53 28 1 AAAGAAGAAG 0.964598 -273 ********** Masking position 8 Map Score: 11.3757 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 57 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 CAATCACATTCCCTGTTACCAGAATCATCCC 3 190 0 CCCTGTACCA 0.81655 -111 CATCCCGGTTCCGCGAAGCCAACAACCTGTG 3 231 1 CCGCGAGCCA 0.858472 -70 TTGAAAAAACCTGCTGTACCGATTGTAACCT 4 206 0 CTGCTTACCG 0.600937 -40 GCGGCATATCCCGCTATGCCATTTTATTTTT 9 26 0 CCGCTTGCCA 0.964909 -245 GATCCCCTCCGCCGCTACCATATT 13 4 1 CCCCTCGCCG 0.848408 -297 GGTGTCTTAACCGCTTGACCAACGGGCCAAA 13 37 0 CCGCTGACCA 0.716895 -264 GGATTCGAACCCGTGTTACCGCCGTGAAAGG 13 70 0 CCGTGTACCG 0.787712 -231 ATTCCATTGGCCCCTTTACCAAGCTGTTTAC 15 67 0 CCCCTTACCA 0.915643 -22 GTAAAAGCCGCAGCTGAGCCAATCATTTACA 18 60 0 CAGCTAGCCA 0.551664 -135 TTCCTAATGCCTCTTCAGCCGCAAACGGAGC 26 43 0 CTCTTAGCCG 0.442497 -63 ACCGATCCTCCCCTGATGCCGAATGGGCTTC 27 33 1 CCCTGTGCCG 0.935699 -268 GGGTTTCTCTCCCCGTTACCAAGAGAGGAGT 27 99 1 CCCCGTACCA 0.899043 -202 TCTAACTCATCTGCTATGCCACCACCAGCCA 27 266 0 CTGCTTGCCA 0.820669 -35 TAGAAAACCCTTGTGCCATATTGGCACA 33 8 1 CCCTTTGCCA 0.944753 -154 AACATAAAAACCCTTGTGCCAATATGGCACA 33 22 0 CCCTTTGCCA 0.944753 -140 AAAATATTTTCACTTCTGCCGAAACACAAAT 33 72 1 CACTTTGCCG 0.746955 -90 AATTTCCGCTCAGCTCTGCCATGACATCACT 37 21 0 CAGCTTGCCA 0.820669 -115 GGAGAACCGGCCCTGCGGCCGGTTCAAAGAA 53 13 1 CCCTGGGCCG 0.808573 -288 ***** ***** Masking position 9 Map Score: 11.8143 Number of sites scoring better than the average of aligned sites = 1387 Number in coding regions = 1337 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 GATTTTATGAAAAACGGCCTGCGGGCCGTTT 3 12 1 AAAACGGCCG 0.979082 -289 CAGACAAAACAAAACGGCCCGCAGGCCGTTT 3 23 0 AAAACGGCCG 0.979082 -278 CATTCAGACGAAAATTGCCCGGGAATTGTGA 3 75 1 AAAATTGCCG 0.964709 -226 AAAATCACCTAAAATCGCCCGCTCGCGGCAT 9 50 0 AAAATCGCCG 0.924893 -221 TCTTTCTAAAAAAACTGCCGGCTGACGCTGG 18 18 1 AAAACTGCCG 0.982596 -177 TTTACATAAAAAAACTGCCAGCGTCAGCCGG 18 35 0 AAAACTGCCG 0.982596 -160 TGAAATTATGAAAATTGCCTGCCGTATGTTA 49 218 1 AAAATTGCCG 0.964709 -60 ********* * Masking position 4 Map Score: 8.2355 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 51 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TAGTTAACCAAAAAGGGGGGATTTTATCTCC 6 30 1 AAAGGGGGGA 0.723099 -158 GAGGAAAAATTAAAGGGGAGATAAAATCCCC 6 46 0 TAAGGGGAGA 0.925247 -142 CTTGCCCTTATTAAGGGGTGTTGTAAGGGGA 7 108 1 TTAGGGGTGT 0.577368 -101 AAATTGCATTTTAAGAGGTGATTTTGATCAC 9 117 1 TTAGAGGTGA 0.514355 -154 CAAACATGCGTCAGGGGGTGTAAAACAACGT 12 68 1 TCAGGGGTGT 0.833552 -79 AATTGTTTTAAAACGAGGAGAGGGGCTCTTT 25 25 1 AAAGAGGAGA 0.804226 -22 CCTCTCTTGGTAACGGGGAGAGAAACCCGGC 27 96 0 TAAGGGGAGA 0.925247 -205 TGTGTTTCTTAAAGGAGGTGACGGCCAATGT 27 231 1 AAAGAGGTGA 0.835974 -70 GAAAATAGAGAAACGGAGTGAACATG 34 153 1 AAAGGAGTGA 0.863231 -16 GCGAAAAGGGAGTGATGTCATGGCA 37 5 1 AAAGGAGTGA 0.863231 -131 TCTCCCTGAAAAAGGGAGAGTAAACG 40 6 0 AAAGGAGAGT 0.706895 -117 TCTCCCTTTTTCAGGGAGAGTTTTTTTATGT 40 18 1 TCAGGAGAGT 0.647541 -105 TATTCAAAACACAAGAGGTGTTTGCTCGGAG 42 137 0 ACAGAGGTGT 0.624353 -144 AATAGCCGCGACAAGGAGAGACAGGCTATAA 43 183 1 ACAGGAGAGA 0.77775 -71 ACAACAAGAATCATGAGGTGAGAGAGAC 44 250 1 TCAGAGGTGA 0.795185 -18 GAATAACCGTTAAAGGAGTGTAAGAAC 49 7 0 TAAGGAGTGT 0.768175 -271 ATTGTCCCAATAATGAGGAGAAAAGCAAAGC 49 74 1 TAAGAGGAGA 0.819793 -204 TTAAGGGAAGAAAGGAAGAGAAAAAGAGCGA 49 142 0 AAAGAAGAGA 0.651539 -136 AAATAATGGAGTGAGACAAAC 52 4 1 TAAGGAGTGA 0.874836 -18 *** ******* Masking position 3 Map Score: 12.6434 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 219 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 AATCGGTACAGCAGGTTTTTTCAATTTTAT 4 213 1 GCAGGTTTTT 0.955271 -33 AACCAAAAAGGGGGGATTTTATCTCCCCTT 6 35 1 GGGGGATTTT 0.766653 -153 TTTCTGCCTCGGAGGTATTTAAACA 12 132 1 GGAGGTATTT 0.822537 -15 TCTTGCAGAAGCCGATTTTTTTCATTTTTA 13 130 1 GCCGATTTTT 0.384645 -171 CTCACAATGAGCAGGTATTTTAAAGATATT 16 75 0 GCAGGTATTT 0.849481 -29 AGCGTCAGCCGGCAGTTTTTTTAGAAAGAA 18 17 0 GGCAGTTTTT 0.72733 -178 GGCTGACGCTGGCAGTTTTTTTATGTAAAT 18 37 1 GGCAGTTTTT 0.72733 -158 GCTCTTTAGCGGGTTTTTAATTTGAGAA 20 9 1 GCGGGTTTTT 0.954381 -38 GTCGAAGTAAGGGGGATTTTGTATATTATC 21 203 0 GGGGGATTTT 0.766653 -98 TTTCTCTTAAGGGGGATTTTAT 22 55 1 GGGGGATTTT 0.766653 -12 TGCATAGGACGGGGGTTTTTTGTGTTTCTT 27 211 1 GGGGGTTTTT 0.945 -90 CTTAGGATATGCAGTTTTTTATTTTACCAA 35 21 0 GCAGTTTTTT 0.485251 -280 CTATAGGGTAGCCAGTTTTTCCGGCAATGA 42 235 1 GCCAGTTTTT 0.764592 -46 ATTGTAAGGCTCAAGTTTTTCAGATCCGCA 44 49 0 TCAAGTTTTT 0.366319 -219 TTACATACTGGGAGGTTTTTATT 47 151 1 GGAGGTTTTT 0.946062 -13 GCCTTTATTTGCGGGTTTTTG 48 2 0 GCGGGTTTTT 0.954381 -299 AAAGCACGATGCAAGTATTTCTCTCCCCCA 48 215 0 GCAAGTATTT 0.564156 -86 TAAGTAAGCCTCATGTTTTTACAACACTCT 48 246 1 TCATGTTTTT 0.124815 -55 TTCCTATGGATCAGGTTTTTATAGAGGAAG 50 131 0 TCAGGTTTTT 0.715948 -170 GAAAAAGAAGGGAGGTATTTTCCTATGGAT 50 150 0 GGAGGTATTT 0.822537 -151 ********** Masking position 8 Map Score: 15.1956 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 535 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 12 CGGCATTATAGCGGCATCACTTTTATGAGTC 3 139 0 GCGGCATCCT 0.854146 -162 GCACAAAGGCCCGTCACCGCCAGGTGGTGGG 4 37 1 CCGTCACCCC 0.946726 -209 TGTTATGGGTACGGCATCACCATATTTCAAG 4 148 0 ACGGCATCCC 0.901128 -98 GCGTTGTCCCCAGTGGGGATG 8 1 1 GCGTTGTCCC 0.825989 -191 TCGCCCGCTCGCGGCATATCCCGCTATGCCA 9 36 0 GCGGCATACC 0.854146 -235 AAGCTTGTAAGCGGCGCCACCAAAATCATCG 11 11 1 GCGGCGCCCC 0.981432 -67 GGAGAGAAACCCGGCATCGCCTACTATCCGT 27 80 0 CCGGCATCCC 0.979408 -221 CGAGGGTCTCGCGGTACCACCTTTATTAACA 27 175 0 GCGGTACCCC 0.968248 -126 CGTACATTGGCCGTCACCTCCTTTAAGAAAC 27 234 0 CCGTCACCCC 0.946726 -67 TATGCGCTGCATCTCCTCACCTAACC 28 81 0 GCTGCATCCC 0.947416 -16 GCTGTGCCTCCAGTATTATAA 45 201 0 GCTGTGCCCC 0.790064 -11 ACATGTTTCACCTTTATCGCCAGTTGTTTAT 53 133 0 CCTTTATCCC 0.522056 -168 ******** ** Masking position 2 Map Score: 8.3037 Number of sites scoring better than the average of aligned sites = 1074 Number in coding regions = 1032 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 13 TCGTCTTTACAAAAGCCTGG 2 1 0 AAAAGCCTGG 0.564777 -129 GAACCGTGCGAAAAGCCTCTTTCGGTGTTA 4 94 1 AAAAGCCTCT 0.891495 -152 TCTCAAATTAAAAACCCGCTAAAGAGC 20 8 0 AAAACCCGCT 0.687931 -39 TTGACTTACAAAACGCCTTTTTGACTGAAG 24 30 0 AAACGCCTTT 0.943993 -35 AAAAGAATCAAAACACCTTTTTCAGTGAAT 30 155 1 AAACACCTTT 0.769913 -110 GAAAAACGGAAAAAGCCGTTAATCTCGTTA 30 184 0 AAAAGCCGTT 0.883033 -81 TAGAAAACCCTTGTGCCATATTG 33 4 1 AAAACCCTTG 0.827285 -158 TTGTAACATAAAAACCCTTGTGCCAATATG 33 27 0 AAAACCCTTG 0.827285 -135 GATCACGGTAAAAACGCTTTCTAAATTTCA 38 31 1 AAAACGCTTT 0.505265 -101 AATCTAAAAAAAACGCCGTTT 39 2 0 AAACGCCGTT 0.891172 -90 AAGCGGGAGAAAAAGCCTTTGCTTCTGGTT 42 102 0 AAAAGCCTTT 0.940085 -179 CGCTCCGAGCAAACACCTCTTGTGTTTTGA 42 135 1 AAACACCTCT 0.606744 -146 GCGCTATCATAAACGTCTTTATTTCTTTTA 45 67 1 AAACGTCTTT 0.540716 -145 TTCCCCGAAAAAACGCCTTTATTTGCGGGT 48 16 0 AAACGCCTTT 0.943993 -285 TGCTGGAACTAAAACCCTTTGCTTTTGAAA 48 158 0 AAAACCCTTT 0.918279 -143 ********** Masking position 3 Map Score: 6.659 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 207 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 TTGTCTGGATTTTGCGCTTTTTGCCCAGCATTCAGACGA 3 47 1 TGGCTTTGGC 0.73688 -254 CAAAGGCCCGTCACCGCCAGGTGGTGGGCTTTTTTTTGT 4 40 1 TCGCAGTGGC 0.976939 -206 CGCAAGCCGCTTACAGCGTTGTGCCGCCCTGGATAAGTA 5 36 0 TCGCTGTGCC 0.98852 -90 AGAATGGCATTTGCGTCGTCGTGTGCGGCACAAAGAACA 5 79 1 TCTCTGTGGC 0.895393 -47 ATTCGGTGACTTTCTGCGTCTTGTGGGCTGACAATTGCC 8 78 1 TCGCTTTGCT 0.725362 -114 ACTATTAATTTATCAGCAAGGGGACGCGCCCCAGAGGCG 29 48 0 TCGCAGGGGC 0.959527 -165 CATATGGCAGTACCTGCATGGTGAGTCCTGTATCGGCAG 30 99 0 TCGCTGTGCT 0.922865 -166 ATCTGGATAATACCAGCGTGGGGAAGTGCAGGTTGACCG 35 99 0 TCGCTGGGGC 0.985227 -202 TTTATCTTTATTCCCGCGTATGGCCCCGCCGAAGATTGG 37 90 0 TCGCTTGGGC 0.936396 -46 CAGCTGGATAGTGCTGCTTTGTGAGGACCTGAATCATGA 43 40 1 GCGCTGTGCC 0.936638 -214 TTCCCATTTATCACGGCAATGTGTAGTGCGGATCTGAAA 44 23 1 TCGCAGTGGC 0.976919 -245 AAACTACTACTTTCCGCCTAGTGTCTTCCAAAATACTTT 50 229 0 TCGCTGTGCC 0.98852 -72 * * ** * *** ** Masking position 7 Map Score: 8.362 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 384 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 15 CCTATTTGAATGCTTTCGGGATGATTCTGGTAACAGGG 3 173 1 TGCTTCATTT 0.965105 -128 AAGATTGTTATGCTTGAAATATGGTGATGCCGTACCCA 4 136 1 TGCTTAATTT 0.720502 -110 GACACGACTGTGCTTCACGCCATCTATTAACATGTACG 6 120 0 TGCTTACATT 0.363516 -68 TTGCTCCCAAAATCTTTCTGTCGCGATTC 12 2 1 TGCTCCATTT 0.909579 -145 ATCCTATCTGTGCTTTCGCTATAATGACAGGCAACGAA 13 249 1 TGCTTCATTC 0.789586 -52 TCGGCAGCCTGCTTCCGAGATGGTTATTGTTTGTATT 17 10 1 TGCTTCATTT 0.965105 -88 GCACCCCTAGTGCTTTCCGTATACAATTTTTTATTTTA 35 192 1 TGCTTCATAT 0.689576 -109 ATGATTTCGTTGTTTACAAAATGATTCTTATCATCTAT 35 238 0 TGTTTCATTT 0.578343 -63 GTTTTCCCCCTGCTTTCCTTCTGTTACTTTCATTTTAT 36 53 0 TGCTTCCTTT 0.934234 -28 TTTTTATGTTTGCTTCCAGAAATATAATTGTTATTCAT 40 40 1 TGCTTCAATT 0.922661 -83 GTTTGCTCACGTCCTTGTGGTGGTTTGTACA 40 102 0 TGCTCCCTTT 0.837839 -21 TTGTATGCCTACTTTCTTTATTTTAATTTTCAAAGGA 43 227 0 TACTTCATTT 0.578343 -27 TGAAAGCTGATGCTCGCCACAAATTTGTCACATTTTCT 44 133 0 TGCTCCAATT 0.812705 -135 CGGAATGTCCTGCTTTCGCTAAAATAAAATCATGAAAC 45 121 1 TGCTTCAATA 0.658217 -91 GCTGTGCCTCCAGTATTATAATTCCCCGACAT 45 190 0 TGCCTCATTT 0.865859 -22 TTATGAAAATTGCCTGCCGTATGTTAAAACTAGTTTAT 49 223 1 TGCCTCATTA 0.510279 -55 TACTTTTTTTTGCTTTCCTTCATTTAATTTAGTAGGGA 50 267 1 TGCTTCCATT 0.8597 -34 ***** * ** * * Masking position 1 Map Score: 5.69271 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 159 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467