AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_ecoli_reg_300.orf -o00240_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: BIME6 21 BIME Input sequences: #1 polB 74 DNA polymerase II #2 araB 300 L-ribulokinase #3 rpsB 300 30S ribosomal subunit protein S2 #4 tsf 257 protein chain elongation factor EF-Ts #5 pyrH 146 uridylate kinase #6 frr 291 ribosome releasing factor #7 yaeM 91 putative ATP-binding component of a transport system #8 yaeS 185 orf, hypothetical protein #9 cdsA 120 CDP-diglyceride synthetase #10 yaeT 29 orf, hypothetical protein #11 hlpA 121 histone-like protein, located in outer membrane or nucleoid #12 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #13 dnaE 36 DNA polymerase III, alpha subunit #14 dnaQ 64 DNA polymerase III, epsilon subunit #15 prpC 41 putative citrate synthase; propionate metabolism? #16 prpD 33 orf, hypothetical protein #17 prpE 39 putative propionyl-CoA synthetase #18 BIME21 47 BIME #19 codB 152 cytosine permease/transport #20 ybaN 69 putative gene 58 #21 apt 152 adenine phosphoribosyltransferase #22 dnaX 128 DNA polymerase III, tau and gamma subunits; DNA elongation factor III #23 ushA 217 UDP-sugar hydrolase (5'-nucleotidase) #24 leuS 234 leucine tRNA synthetase #25 trxB 300 thioredoxin reductase #26 ycaP 120 orf, hypothetical protein #27 serC 198 3-phosphoserine aminotransferase #28 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #29 ycaL 144 putative heat shock protein #30 cmk 172 cytidylate kinase #31 ycbQ 300 putative fimbrial-like protein #32 ycbR 82 putative chaperone #33 ycbS 24 putative outer membrane protein #34 pyrD 110 dihydro-orotate dehydrogenase #35 pyrC 105 dihydro-orotase #36 yceB 133 orf, hypothetical protein #37 grxB 63 glutaredoxin 2 #38 yceL 205 orf, hypothetical protein #39 yceD 159 orf, hypothetical protein #40 rpmF 51 50S ribosomal subunit protein L32 #41 plsX 110 glycerolphosphate auxotrophy in plsB background #42 fabH 67 3-oxoacyl-[acyl-carrier-protein] synthase III; acetylCoA ACP transacylase #43 acpP 210 acyl carrier protein #44 fabF 87 3-oxoacyl-[acyl-carrier-protein] synthase II #45 pabC 119 4-amino-4-deoxychorismate lyase #46 tdk 300 thymidine kinase #47 pgpB 169 non-essential phosphatidylglycerophosphate phosphatase, membrane bound #48 yciS 148 orf, hypothetical protein #49 pyrF 193 orotidine-5'-phosphate decarboxylase #50 holE 138 DNA polymerase III, theta subunit #51 dcd 91 2'-deoxycytidine 5'-triphosphate deaminase #52 udk 263 uridine/cytidine kinase #53 yohJ 238 orf, hypothetical protein #54 cdd 129 cytidine/deoxycytidine deaminase #55 rsuA 148 16S pseudouridylate 516 synthase #56 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #57 nrdB 21 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #58 usg 65 putative PTS system enzyme II A component #59 pdxB 98 erythronate-4-phosphate dehyrogenase #60 upp 297 uracil phosphoribosyltransferase #61 ndk 148 nucleoside diphosphate kinase #62 b2520 47 orf, hypothetical protein #63 ygaM 139 orf, hypothetical protein #64 nrdH 247 glutaredoxin-like protein; hydrogen donor #65 pyrG 227 CTP synthetase #66 mazG 70 orf, hypothetical protein #67 chpR 77 suppressor of inhibitory function of ChpA, PemI-like, autoregulated #68 relA 47 (p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor #69 ygcA 56 putative enzyme #70 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #71 ygdP 300 putative invasion protein #72 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #73 rpsO 148 30S ribosomal subunit protein S15 #74 rbfA 74 ribosome-binding factor A #75 infB 24 protein chain initiation factor IF-2 #76 nusA 27 transcription pausing; L factor #77 yhbC 200 orf, hypothetical protein #78 metY 300 tRNA #79 rpoA 25 RNA polymerase, alpha subunit #80 rpsD 33 30S ribosomal subunit protein S4 #81 rpsM 146 30S ribosomal subunit protein S13 #82 rpmJ 31 50S ribosomal subunit protein L36 #83 rpsH 33 30S ribosomal subunit protein S8, and regulator #84 rplN 164 50S ribosomal subunit protein L14 #85 rplC 32 50S ribosomal subunit protein L3 #86 rpsJ 237 30S ribosomal subunit protein S10 #87 yheD 179 putative export protein A for general secretion pathway (GSP) #88 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #89 ftsY 149 cell division membrane protein #90 dfp 93 flavoprotein affecting synthesis of DNA and pantothenate metabolism #91 pyrE 94 orotate phosphoribosyltransferase #92 rph 126 RNase PH #93 gmk 251 guanylate kinase #94 rpoZ 54 RNA polymerase, omega subunit #95 dnaA 300 DNA biosynthesis; initiation of chromosome replication; can be transcription regulator #96 udp 298 uridine phosphorylase #97 polA 300 DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3' --> 5' exonuclease #98 rpoB 300 RNA polymerase, beta subunit #99 rpoC 76 RNA polymerase, beta prime subunit #100 cpdB 189 2':3'-cyclic-nucleotide 2'-phosphodiesterase #101 nrdD 300 anaerobic ribonucleoside-triphosphate reductase #102 holC 52 DNA polymerase III, chi subunit #103 BIME233 22 BIME #104 pepA 266 aminopeptidase A/I #105 holD 102 DNA polymerase III, psi subunit #106 deoC 257 2-deoxyribose-5-phosphate aldolase #107 deoA 83 thymidine phosphorylase #108 deoB 51 phosphopentomutase #109 deoD 56 purine-nucleoside phosphorylase Motif number 1 TAACGCATCTGCGGCGCGAAATATGAAGGG 4 117 1 GCGGCGCGAA 0.971512 -141 CGCTCCGGTTGCTGCGCGCTGGCCGTGACC 6 101 0 GCTGCGCGCT 0.444192 -191 GTACGTGAGGATGGCGAGCACTGCCCGGGG 6 138 1 ATGGCGAGCA 0.422145 -154 TGCCGGATGCACCGCGCGACGCATCCGACA 18 16 0 ACCGCGCGAC 0.750561 -32 CCCCGTCAGAACGGCGAGGCTGAATGCACA 22 54 0 ACGGCGAGGC 0.755195 -75 TTCAACGTCGAGTGCGCGAAAGGCTGTTTT 24 124 1 AGTGCGCGAA 0.70906 -111 CGTTAACATAACCGCGCGCATTATACGCGC 30 128 0 ACCGCGCGCA 0.934149 -45 CGAAAAATAAAGGGCGCGAATGCGCCCTCG 35 14 0 AGGGCGCGAA 0.937279 -92 AGGGCGCGCATATTAACTTT 39 150 0 AGGGCGCGCA 0.955884 -10 AACCACGCAGACTGCGCGCAACATGAGCAT 43 27 0 ACTGCGCGCA 0.887917 -184 CATTTCGCAGACGGCGCGAAAATGGTACTT 48 66 1 ACGGCGCGAA 0.971124 -83 TCCGGCAACGACGGCGCAGAAAAAGCCTGC 49 69 1 ACGGCGCAGA 0.691514 -125 AAACAGGTAAACGGCGAGCATTCTACCCGT 49 135 0 ACGGCGAGCA 0.853584 -59 GGCACCGGAAGTGGCGCGAAACAGGTAAAC 49 153 0 GTGGCGCGAA 0.811233 -41 ATTAACTCTGAGCGCGCGGCAACGCTATTC 52 204 1 AGCGCGCGGC 0.503937 -60 AATTTGCGATGCGTCGCGCATTTTTGATGT 54 11 1 GCGTCGCGCA 0.614029 -119 TCTGACCTAAGGTGCGCGAAAGCCACTTTT 56 108 1 GGTGCGCGAA 0.711989 -193 GTCTTCTTTCGCCGCGCGCCTGGGGAAAAG 60 118 0 GCCGCGCGCC 0.524624 -180 AGCGTACGAGATGGCGCGGATTATAATGAG 61 92 0 ATGGCGCGGA 0.827409 -57 AAATGAAGATACGGCGCGATGATACGCGTC 64 210 0 ACGGCGCGAT 0.816408 -38 CCTGAAACCTGCGGCGCGCATTTCAATCGC 70 91 1 GCGGCGCGCA 0.979718 -60 CCTCTCATTAGCCGCGCGAACCTCTGCAAC 72 113 0 GCCGCGCGAA 0.908256 -65 CCCCATATCGAGGGCGCGGCATTATAACAC 84 87 0 AGGGCGCGGC 0.902531 -78 CTTATTATACACGGCGCGGCCATGTGACGT 93 187 0 ACGGCGCGGC 0.948311 -65 AAACGATCCTGCCGCGAGGCGGGCACGATT 95 37 0 GCCGCGAGGC 0.454289 -264 CCTGTTGTCAGGGGCGCAAATATAGCAAAT 105 72 0 GGGGCGCAAA 0.471473 -31 ********** Masking position 5 Map Score: 28.8761 Number of sites scoring better than the average of aligned sites = 2016 Number in coding regions = 1908 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 GATATAAAAGTGAAAAAGGGGGCCATATGCAG 4 191 0 TGAAAAAGGG 0.665753 -67 TTATCAAAAAGGAGCCGCCTGAGGG 5 4 1 TCAAAAAGGC 0.765775 -143 AGAATAAAAAGCAAAACGCCGCCAGCCGATCC 7 50 0 GCAAAACGGC 0.952979 -42 ATGAATGAGTGCAAAAAGGTGGGGGAAAAATT 19 30 0 GCAAAAAGGG 0.914104 -123 GTTTCAAACAGCAAAAAGGGGGAATTTC 19 135 1 GCAAAAAGGG 0.914104 -18 ATCGCAACCCTGAAAAAGTGACTTTCCT 23 7 0 TGAAAAAGAC 0.44795 -211 TCTTTCTTTATCAAAACGTCGGCACATTGTCG 29 38 1 TCAAAACGGG 0.817563 -107 AACAGGTTCGGAAAACGTTTGCGTTTTTTTT 34 10 1 GGAAAACGTG 0.782185 -101 TTCGTGCAAAGGAAAACGTTTCCGCTTATCCT 35 40 1 GGAAAACGTC 0.808901 -66 CAGAAAAAACTGAAAACGGCGGCAACCCGCGA 36 37 0 TGAAAACGGG 0.762926 -97 TATTTTTTTATCAAAACGTCGCTTTGATAGAG 38 135 0 TCAAAACGGC 0.840822 -71 ACATCAACCTGCAAAACGAAGCGCATAGTTTA 39 13 0 GCAAAACGGC 0.952979 -147 CAATCATAACTGAAAACGCCAGTTCCAGGAAA 47 123 0 TGAAAACGAG 0.526564 -47 ATCCCTCAAGGGAAAAAGATCCATGGCATACT 55 41 0 GGAAAAAGCC 0.638068 -108 AACTCAGGAAGGAAAAAGTGGCTTTCGCGCAC 56 119 0 GGAAAAAGGC 0.90008 -182 GAAAAGACGTGCAAAAAGGTTGTGTAAAGCAG 60 92 0 GCAAAAAGTG 0.755807 -206 GATTCACCAGGCAAAAAGAAACCCCGAAGACA 64 52 0 GCAAAAAGAC 0.812572 -196 CAACAAACCTGGAAAACGAGGCG 80 2 0 GGAAAACGGC 0.935708 -32 AAGCAGCTACGCAAAACGCAACAACTTTGCGC 93 135 1 GCAAAACGAC 0.875071 -117 ACAACTTTGCGCAAAAAGTGTGAGCAAGGGCT 93 155 1 GCAAAAAGTG 0.755807 -97 TCAAGATCCTGCAAAACGATCGGGACCGCGGA 95 153 0 GCAAAACGCG 0.770906 -148 GTCAGAAGAAGCAAAAAGACACTTTACCGAAG 96 251 0 GCAAAAAGAC 0.812572 -48 GCCTTACAGCGCAAAAAGGCTGGTGACTAAAA 98 42 0 GCAAAAAGTG 0.755807 -259 GGAAAGCACCGGAAAACGAAACGAAAAAACCG 101 223 1 GGAAAACGAC 0.834164 -78 ******** ** Masking position 6 Map Score: 22.5006 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 579 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 ATATTTCGCGCCGCAGATGCGTTATCTTCG 4 111 0 CCGCAGATGC 0.956112 -147 TGGGGGTCGCTTTTGCTGAAGTATCG 9 7 1 TCGCTTTTGC 0.850189 -114 CTCCTTACCATCCCATTTGCACCGGAGGGT 11 96 0 TCCCATTTGC 0.774295 -26 AGCACAACAATCGCAGTTGCAATTATTGCG 21 11 1 TCGCAGTTGC 0.980194 -142 AAGCTTCATCACGCAGATGCGTGA 41 5 0 ACGCAGATGC 0.894909 -106 TTTGGTCTTTCCCCAGTTGCCTGGGGAAAA 41 43 0 CCCCAGTTGC 0.954331 -68 AAAATGTTAAACGCAGTTGCGCAAATTATC 52 119 0 ACGCAGTTGC 0.974363 -145 GTGCTCCAGACCGCAGTTGCGGTTATAGGG 77 91 1 CCGCAGTTGC 0.98982 -110 ACTACACTCCTCGCTGTTGCTTCATGGCAC 89 125 0 TCGCTGTTGC 0.946222 -25 GTAGCTGCTTCCGCATTTGCCTGTCATTCA 93 115 0 CCGCATTTGC 0.969099 -137 AATTTATGCAACGCATTTGCGTCATGGTGA 96 195 1 ACGCATTTGC 0.924578 -104 TAACTCATGTCCGCTGTTGCGATGACTTCG 104 185 0 CCGCTGTTGC 0.971886 -82 ********** Masking position 8 Map Score: 13.793 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 312 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 GGGGCCATATGCAGGCCCCCTAACCAAACG 4 175 0 GCAGGCCCCC 0.901765 -83 GTTGCTGCGCGCTGGCCGTGACCAAACTGC 6 94 0 GCTGGCCGTG 0.91827 -198 TTGCGGATCGGCTGGCGGCGTTTTGCTTTT 7 46 1 GCTGGCGGCG 0.937089 -46 TACGATTGCGGCAGGCCGTGTTATTATTGT 12 55 1 GCAGGCCGTG 0.943322 -50 GAGCACAGGCGCAGGCGGTCAAAGGTTAAA 21 67 1 GCAGGCGGTC 0.952976 -86 TGGCAGGCTCTGAAACGCTGGA 22 117 0 GCAGGCTCTG 0.720205 -12 AAACAGGACCACTGGCTGCC 24 225 1 ACTGGCTGCC 0.775526 -10 AACCCCACAGGCTGGCTGTGGGGATTAAGC 28 23 0 GCTGGCTGTG 0.83568 -48 ACCCGCGAATACAGGCTGCCGCGGCGGGTC 36 15 0 ACAGGCTGCC 0.836544 -119 AAAGGCAACCACAGGCTGCCTTTTTCTTTG 39 105 1 ACAGGCTGCC 0.836544 -55 CTGCGAGTTCGCTGGCAGCGTCCTG 42 6 0 GCTGGCAGCG 0.624535 -62 GTGAACATCTCCAGGCGGTCGTTCGACCGC 44 11 1 CCAGGCGGTC 0.828455 -77 AAGATAAAACTCAGGCGGTCGAACGACCGC 44 25 0 TCAGGCGGTC 0.817308 -63 CAGCCACAGGCCCTCAATGATATGA 46 286 0 ACAGGCCCTC 0.744502 -15 CGCAAGTATGCCTGGCCGCGAGATTATGGC 59 36 1 CCTGGCCGCG 0.780201 -63 GCCGCAGGTTTCAGGCGCTCCAAAGGTGCG 70 76 0 TCAGGCGCTC 0.604515 -75 AAGGGGCCACTCAGGCCCCCTTTTCTGAAA 72 21 0 TCAGGCCCCC 0.669581 -157 ACACATACTTGCAGGCGGTGATGTGAATTA 89 36 1 GCAGGCGGTG 0.943322 -114 AGGATTGAAAACTGGCCGTCGATTTAACGA 90 46 0 ACTGGCCGTC 0.85201 -48 CTCAATTGATACTGGCGGCGATTATAGCCA 105 20 1 ACTGGCGGCG 0.862419 -83 ********** Masking position 5 Map Score: 16.6455 Number of sites scoring better than the average of aligned sites = 1985 Number in coding regions = 1909 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 GCCTGAGGGCGGCTTCTTTTTGTGCCCATCTTG 5 27 1 GGCTTTTTGT 0.84482 -120 TGGATTATTAGGCTATTTTATTTGCCATTTTGG 6 168 0 GGCTTTATTT 0.736905 -124 GATCTACTGAGCGGCGTTTTTGTCGTTCAAGAA 7 12 0 GCGTTTTTGT 0.84482 -80 GGTTTTACACGGCTTTTTTTTGTATAGGCTTCA 8 120 1 GGCTTTTTGT 0.84482 -66 GCGTTTTTTATTCCCTGACAGGG 8 173 0 GCGTTTATTC 0.773328 -13 TTCATTAACAGGGGCGTTTATTCATCATTTAAT 25 105 1 GGGTTTATTC 0.756499 -196 TGTGATGCAAGCCACATTTTTGCCCTCAACGGT 27 57 1 GCCTTTTTGC 0.879255 -142 GCCAGCCTGTGGGGTTTTTATTTCTGTTGTAGA 28 37 1 GGGTTTATTT 0.718358 -34 GCACATTGTCGGCGTTTTTTTTCGGACCTTGTG 29 59 1 GGCTTTTTTC 0.818545 -86 GAAAACGTTTGCGTTTTTTTTGCCGCAGGTCAA 34 21 1 GCGTTTTTGC 0.868959 -90 GGGCGCATTCGCGCCCTTTATTTTTCGTGCAAA 35 17 1 GCGTTTATTT 0.736905 -89 TCCGGCTGAAGGGATGTTTTTGCCGGACACAAA 35 71 0 GGGTTTTTGC 0.857926 -35 ATAAACTCCAGCCAACTTTATTTCATATCATTG 46 264 1 GCCTTTATTT 0.754648 -37 CTAACATAGCGCCTCATTTTTTTGCGGGTGATG 53 13 0 GCCTTTTTTT 0.802641 -226 TGACGGGGTAGGGGGATTTTTGTGATTCACCAG 64 74 0 GGGTTTTTGT 0.832147 -174 GGGGTGGATAGCCGTTTTTATTCACCTTTTCTG 71 138 0 GCCTTTATTC 0.789316 -163 GGGCCTGAGTGGCCCCTTTTTTCAAGCTGACGG 72 33 1 GGCTTTTTTC 0.818545 -145 GGGGCTAACAGCCCCTTTTTTGTCAGGAGAATT 74 48 1 GCCTTTTTGT 0.8567 -27 CACATTTTGTGCGTAATTTATTCACAAGCTTGC 88 99 1 GCGTTTATTC 0.773327 -146 CTGATGAGTCGCCTTTTTTTTGTCTGTAGAAAA 91 52 1 GCCTTTTTGT 0.8567 -43 GCAGAATGAAGGGTGATTTATGTGATTTGCATC 96 148 1 GGGTTTATGT 0.789448 -151 *** ******* Masking position 7 Map Score: 16.3171 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 404 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 GTGGTATAAAGCGCGCCGGACTTCCGATCCATT 3 133 1 GCGCCGGCTT 0.934549 -168 ACCCCAAAGGGCACCCCGGAATATGTGCCGATA 3 222 0 GCCCCGGATA 0.927528 -79 ACTGATGTAAGCTCCCGGGAATTCTCGAGCTTG 4 58 0 GCCCGGGATT 0.968819 -200 GGAGATGTGATCTGCCCGGCATTAAACCGCACA 4 223 0 TCCCCGGATT 0.887835 -35 AGGTATCGTCGCCGCCCGGTTTGGTCTTTCCCC 41 59 0 GCCCCGGTTG 0.792745 -52 TCGTGGTAAGACCTGCCGGGATTTAGTTGCAAA 43 122 1 ACGCCGGATT 0.627182 -89 TAAAAGGTCCGCTTGCGGGCCTTTTTTCTTAGC 45 31 1 GCGCGGGCTT 0.866845 -89 AGCCAGGATGGCAAGCCGGAATTGATGATCCTC 50 73 0 GCGCCGGATT 0.962322 -66 ACGAATACTGGCGACCAGGTCTTGCGGATAAAG 52 16 0 GCCCAGGCTT 0.85454 -248 AACGTAATTTGCCCCCGGGAATTCTTTGTCAAC 52 170 1 GCCCGGGATT 0.968846 -94 TTATTTTTTCGCTCCCCGGCATTACGCAATGCG 53 136 0 GCCCCGGATT 0.985539 -103 CCATAATCTCGCGGCCAGGCATACTTGCGAAGA 59 32 0 GCCCAGGATA 0.66352 -67 CCCCGTTGTCTCTTCCCGGTATTTCATCTCTAT 88 64 1 TCCCCGGATT 0.887835 -181 CTCCGTTTTTGCCACTCGGCTTTGCTTTCATCA 93 44 0 GCCTCGGTTT 0.578448 -208 AGCACAATCCGCTGCCGGGTTTTAACCCGACAG 99 33 0 GCCCGGGTTT 0.917033 -44 ** ***** *** Masking position 12 Map Score: 11.4403 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 240 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 ACATTGTACGTCGCTTTTCAGCGCAGCCCCACAAGGG 5 73 0 TCTCACGCGC 0.9372 -74 TGTGTTAATACCCGTCGTCATCGCGGCGTTGTTTCTG 9 52 1 CCTCACGCGC 0.985687 -69 AGAATTTGACCTGCTTATCGATGCTGCCGATTGCACA 25 185 1 CTTCGTGCGC 0.737025 -116 TAGTCAACAGTTCATCGGCATGGCGGCGGTGATAGCG 26 58 0 TTTCAGGCGC 0.840401 -63 TCCTGACCCGCCGCGGCAGCCTGTATT 36 1 1 TCGCGCGCGC 0.825303 -133 TGCGTCAATATCCTGACACAACGCAGCATGTGTCACC 36 86 0 TCGCACGCGC 0.917854 -48 TTTCTATTCTGCATTGCCGCTAAGACTTTT 38 186 0 CTTCATGCGC 0.868916 -20 TTAGACGTGTCAAGGTATCGTCGCCGCCCGGTTTGGT 41 67 0 CAGCGCGCGC 0.902944 -44 GAAATCTTCGCAAGTATGCCTGGCCGCGAGATTATGG 59 28 1 CATCCGGCGC 0.723589 -71 GATTATACCTCCTTTCTTCAAGGCGGCAATATTCTTT 60 257 0 CCTCAGGCGC 0.974932 -41 ATTTTCTTAACTGAGGTTCATCGCGGCTTTATGGACT 63 80 0 CTGCACGCGC 0.969893 -60 CCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTC 91 12 0 CATCACGCGC 0.967094 -83 TGAGCAAGGGCTACGTCACATGGCCGCGCCGTGTATA 93 175 1 CTGCAGGCGC 0.947898 -77 TCGCCATCCGCTTATCCACAACGCCGCACCTTTTTCG 101 182 0 CTTCACGCGC 0.977287 -119 AAATACGCATCAGGTATACACCGCAGC 102 1 0 CATCACGCGC 0.967094 -52 GCGAATCGCTCCTGTTGTCAGGGGCGCAAATATAGCA 105 75 0 CCTCAGGGGC 0.752894 -28 ** * ** *** ** Masking position 9 Map Score: 12.66 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 550 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 CCATAGCATTTTTATCCATAAGATTAGCGG 2 209 1 TTTATCCATA 0.79787 -92 CTTACCCTTATTTATCCATCACGGGAA 6 8 0 TTTATCCATC 0.606849 -284 TACCGCTTTATCCGCAAGACCTGGTC 52 7 1 TTTATCCGCA 0.697887 -257 TCCTTCCTGAGTTATCCACAAAGTTATGCA 56 138 1 GTTATCCACA 0.916737 -163 TCTTCACAACTCTATCCACAGAAAAGGTGA 71 120 1 TCTATCCACA 0.910038 -181 AATAAAAACGGCTATCCACCCCTTCCTCTG 71 149 1 GCTATCCACC 0.705102 -152 AATGAGAGGCTTTACCCACATAGAGCTGGG 72 134 1 TTTACCCACA 0.910038 -44 GTTTATTTTTTCTACCCATATCCTTGAAGC 84 56 1 TCTACCCATA 0.549019 -109 AGACCGTGATTTTATCCACAAGTTCAATGC 88 130 0 TTTATCCACA 0.947958 -115 ATTTTCCCGATTTATCCACAGGACTTTCCA 95 82 0 TTTATCCACA 0.947958 -219 GTTGCATAAATTTACCCACCAAAAGTGATG 96 177 0 TTTACCCACC 0.798211 -122 ATAATTCATATCTATCCACATTAGAAAAAA 97 27 1 TCTATCCACA 0.910038 -274 TATGCACAAAGTTATCCACATGACGATTTG 97 168 1 GTTATCCACA 0.916737 -133 TGTGGCATCCTTTACCCATAATCTGATAAA 97 267 1 TTTACCCATA 0.686729 -34 TCGCCATCCGCTTATCCACAACGCCGCACC 101 189 0 CTTATCCACA 0.757693 -112 TTAAGAACAGGTTATCCACAGAAATTGGGA 101 266 0 GTTATCCACA 0.916737 -35 ********** Masking position 4 Map Score: 10.7769 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 67 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 GTCCATATTGCATCAGACATTGCCGTCAC 2 10 1 GCATCAGACA 0.876969 -291 GCGATAAAAAGCGTCAGGTAGGATCCGCTA 2 233 0 GCGTCAGGTA 0.783794 -68 GCTGTGTACAGCATCAGACGTCGAATTTTC 3 72 0 GCATCAGACG 0.782533 -229 ACCGCGCGACGCATCCGACAATAAC 18 6 0 GCATCCGACA 0.907818 -42 GTCGCGCGGTGCATCCGGCACTGTGTGCCG 18 26 1 GCATCCGGCA 0.97164 -22 AGACAAGTCTGCGTCCGGTGAAGATAAATC 23 142 0 GCGTCCGGTG 0.71659 -76 CTTATCCTTTGTGTCCGGCAAAAACATCCC 35 64 1 GTGTCCGGCA 0.833572 -42 TATTCGACTGGTATCAGACGGATGAAATCC 52 229 1 GTATCAGACG 0.417385 -35 TCTTTTAACGGTATCCGGCAACCAGCCAGG 70 28 1 GTATCCGGCA 0.872138 -123 AAGCGTGATAGCAACAGGCATTGCGGAAAG 98 191 1 GCAACAGGCA 0.725195 -110 ATTTAAATACGCATCAGGTATACACCGCAG 102 12 0 GCATCAGGTA 0.831564 -41 TTGCGTCAGGCAAGGCTGTTAT 103 3 1 GCGTCAGGCA 0.947941 -20 AGGCGTAGACGCATCCGGCAAAAGCCGCCT 107 38 1 GCATCCGGCA 0.97164 -46 ********** Masking position 5 Map Score: 8.97901 Number of sites scoring better than the average of aligned sites = 1359 Number in coding regions = 756 Number in noncoding regions = 603 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 10 AAAGAAGCCGCCCTCAGGCGGCTCCTTTTTG 5 15 0 CCCTCAGGCG 0.945902 -132 AAAGCAAAACGCCGCCAGCCGATCCGCAAGG 7 44 0 GCCGCCAGCG 0.901044 -48 AATGGCGAACCCCACCGGCGGCAACAGAAAC 9 82 0 CCCACCGGCG 0.951293 -39 AAATAAAAACCCCACAGGCTGGCTGTGGGGA 28 29 0 CCCACAGGCG 0.924257 -42 GCAAAAACATCCCTTCAGCCGGAGCATAGAG 35 81 1 CCCTTCAGCG 0.826306 -25 CAGCGATAAACTCGCCAGCAGAAAAAACTGA 36 56 0 CTCGCCAGCG 0.860014 -78 AGAAAAAAGGCCCGCAAGCGGACCTTTTATA 45 29 0 CCCGCAAGCG 0.98165 -91 CCCGAAGGCTGTTTACTTTAC 86 1 1 CCCGAAGGCG 0.924257 -237 TCGTGCGTCACCCTCAAGCAGGGTCTTTTCG 95 212 1 CCCTCAAGCG 0.937866 -89 CGGGTTTTAACCCGACAGCAGTGACCTGTTT 99 20 0 CCCGACAGCG 0.94401 -57 CGGGTTAAAACCCGGCAGCGGATTGTGCTAA 99 37 1 CCCGGCAGCG 0.934086 -40 GACGTATCTACCCGTAGGCCGGATAAGGCGT 107 13 1 CCCGTAGGCG 0.924257 -71 ********* * Masking position 3 Map Score: 10.1547 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 483 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 GAAGTCCGGCGCGCTTTATACCACAAATAC 3 127 0 GCGCTTTATA 0.894854 -174 TGAATAATCCGGGCATCATTTCAACGTCGA 24 105 1 GGGCATCATT 0.447419 -130 CTTAAATTTCCCGCTTTATAAGCCGATTAA 25 133 0 CCGCTTTATA 0.56775 -168 ACATAACCGCGCGCATTATACGCGCCGACG 30 123 0 GCGCATTATA 0.932911 -50 ACTAAAGAAAGGGCTTTATATATCACGCAT 31 83 1 GGGCTTTATA 0.797869 -218 ACGAGATGGCGCGGATTATAATGAGCAACA 61 87 0 GCGGATTATA 0.826981 -62 AGGTAGGCCCGCGGTTGATAATAACGAGGA 63 17 0 GCGGTTGATA 0.596248 -123 TAAATGACAAGCGCTTGATTTGCGTCAAAA 65 48 1 GCGCTTGATT 0.516544 -180 CGCGGATCATATACATATCTT 70 2 1 GCGGATCATA 0.706995 -149 CGATAAATCGGGGCTTTATATAACTGAACC 77 119 0 GGGCTTTATA 0.797869 -82 TCTCCCTTAAGCGCATTATTTTACAAAAAA 78 88 0 GCGCATTATT 0.77569 -213 ATCGAGGGCGCGGCATTATAACACCGCTTC 84 81 0 CGGCATTATA 0.498843 -84 CGACAAGCCCGCGCATTATACATACTTAAC 86 55 0 GCGCATTATA 0.932911 -183 AAATGTGGCTGCGCATTATACGGACTTCCG 92 85 0 GCGCATTATA 0.932911 -42 AGAAATGACTGGGCATGATACTGAAATCAG 94 13 0 GGGCATGATA 0.765031 -42 GATCGGGACCGCGGATCATAGCCTAAACTG 95 138 0 GCGGATCATA 0.706995 -163 ********** Masking position 6 Map Score: 7.39257 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 212 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 12 GTGTGTGTTGTTACACAAAGTGAGATTGTC 3 191 0 TTACACAAAG 0.505853 -110 ATAGTTCGAGTTGCAGAAAGGCGGCAAGCT 4 34 1 TTGCAGAAAG 0.856581 -224 TAAAGGGCTATTGCGGTAAGTTGACCATAA 48 96 1 TTGCGGTAAG 0.761478 -53 TTAAACGCAGTTGCGCAAATTATCCGCCTT 52 113 0 TTGCGCAAAT 0.629784 -151 CTCCCCGGCATTACGCAATGCGCAGCGAAC 53 128 0 TTACGCAATG 0.512243 -111 CATGAAACTATTGCGGAAAGAATTCCAAAA 56 266 1 TTGCGGAAAG 0.967742 -35 TATTGCCGCCTTGAAGAAAGGAGGTATAAT 60 263 1 TTGAAGAAAG 0.430418 -35 TGATAGCGGTTTGAGGAAAGGGTT 67 64 1 TTGAGGAAAG 0.791479 -14 CCAGTGTACGTTACGCAAAGTGTTAAACAA 73 74 0 TTACGCAAAG 0.837184 -75 CTCACACTTTTTGCGCAAAGTTGTTGCGTT 93 149 0 TTGCGCAAAG 0.962724 -103 TATAAAAATGTTGCGCAATGTTAACTATAG 96 65 1 TTGCGCAATG 0.840639 -234 GCAACAGGCATTGCGGAAAGTGTTCCATTT 98 201 1 TTGCGGAAAG 0.967742 -100 CGGATGGCGATTGCGGAAAGCACCGGAAAA 101 209 1 TTGCGGAAAG 0.967742 -92 ********** Masking position 8 Map Score: 7.6505 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 301 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 13 AATTGTTGGCGCTGTGTACAGCATCAGACGTCG 3 79 0 GCTGTCAGCA 0.828248 -222 GTACATTCTGGCGTTTTCGAGCACAGGCGCAGG 21 49 1 GCTTTGAGCA 0.748784 -104 AGTCCAAAATGCCATTTTCTGCATTATTCACAT 38 88 1 GCTTTCTGCA 0.76491 -118 AACTGAAAACGCCAGTTCCAGGAAAAATTGACA 47 115 0 GCGTTCAGGA 0.905135 -55 GAGAGGGATTGCAGTTTGCAGCAATCCCTCTTT 53 75 0 GCTTTCAGCA 0.972634 -164 TGACAGACCCGCAATTTTCAGGACAATTCA 66 51 1 GCTTTCAGGA 0.972634 -20 TTCTTGCGAGTTTCAGAAAAGGGGGCCT 72 6 1 GCGTTCAGAA 0.757702 -172 GCGGTCTGGAGCACTTTCCAGAAGGATTTTTTC 77 72 0 GCTTTCAGAA 0.92094 -129 TCCTGAAAACGGGCTTTTCAGCATGGAACGTAC 81 101 1 GGTTTCAGCA 0.864597 -46 ACTTTGCGAGGCGCTTTCCAGGATTGAAAACTG 90 62 0 GCTTTCAGGA 0.972634 -32 TGCAATAAAGACGATTTTCAGGAAGCGTCCTCG 93 81 0 ACTTTCAGGA 0.683897 -171 TTTATCCACAGGACTTTCCAGAACTCGCTAAGT 95 69 0 GGTTTCAGAA 0.676662 -232 GCGGTCCCGATCGTTTTGCAGGATCTTGACTCG 95 156 1 TCTTTCAGGA 0.683897 -145 TTATTATCATGCTTTTTACAGCATGATGTTTGT 97 113 0 GCTTTCAGCA 0.972634 -188 GTAAAAACTCGTCTTTTGCAGGATTTTAGCTTG 104 24 1 GTTTTCAGGA 0.70069 -243 ** *** ***** Masking position 13 Map Score: 7.95149 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 212 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 TAATCAATGTGGACTTTTCTGCCGTGATTAT 2 152 0 GGACTTTCTG 0.767984 -149 AGGATTGTAGGGAATTTACAGACGTAAAAAA 25 248 0 GGAATTTCAG 0.742558 -53 ATGGCATTTTGGACTTTTCACAGGGTCTGGT 38 72 0 GGACTTTCAC 0.912385 -134 GGACCTTACTCCTCAATTACG 40 41 0 GGACCTTCTC 0.410106 -11 CCGCGATTTGCACAAAATGCTCA 43 3 1 GCGATTTCAC 0.687919 -208 GCGGCTTTATGGACTTTTCTGAAAGCGTTGT 63 64 0 GGACTTTCTG 0.767984 -76 TGACAGACCCGCAATTTTCAGGACAATTCA 66 51 1 GCAATTTCAG 0.636645 -20 ACTCTCTGCAGGGCATTACACACTAATAACA 71 214 0 GGGCATTCAC 0.62237 -87 TCAGGTGGAAGGGCTGTTCACG 74 2 0 GGGCTGTCAC 0.679855 -73 CGCGGGCTTTTCACCTCATCCAGA 76 14 0 GGGCTTTCAC 0.943646 -14 GCGGTCTGGAGCACTTTCCAGAAGGATTTTT 77 74 0 GCACTTTCAG 0.889933 -127 TCCTGAAAACGGGCTTTTCAGCATGGAACGT 81 101 1 GGGCTTTCAG 0.955363 -46 ACTTTGCGAGGCGCTTTCCAGGATTGAAAAC 90 64 0 GCGCTTTCAG 0.928579 -30 TTTATCCACAGGACTTTCCAGAACTCGCTAA 95 71 0 GGACTTTCAG 0.93012 -230 AACGCTACTGGCGCCTTACAGCGCAAAAAGG 98 55 0 GCGCCTTCAG 0.777299 -246 CCATTTCATTGCGATTTACACAGAACGGACG 98 157 0 GCGATTTCAC 0.687919 -144 ******* *** Masking position 7 Map Score: 7.94999 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 232 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 15 TGTAACAAAGCGGGACCAAAGCCATGACAA 2 101 1 CGGGACCAAA 0.891814 -200 CGAGAATTCCCGGGAGCTTACATCAGTAAG 4 64 1 CGGGAGCTTA 0.73777 -194 AAGTGAAAAAGGGGGCCATATGCAGGCCCC 4 186 0 GGGGGCCATA 0.643449 -72 GTAAGTATCGCGGGGGCGTAAGTCTGGTTA 6 45 1 CGGGGGCGTA 0.959286 -247 CGCGCAGCAACCGGAGCGTACAAAAGTACG 6 113 1 CCGGAGCGTA 0.725103 -179 GAGCACTGCCCGGGGCCAAAATGGCAAATA 6 153 1 CGGGGCCAAA 0.929721 -139 GTGTGCAAACCGGGGGCGTATTATGTGCGA 34 72 0 CGGGGGCGTA 0.959286 -39 ATCCCTTCAGCCGGAGCATAGAGATTA 35 89 1 CCGGAGCATA 0.782238 -17 CCTCATCATTCGCGGGCAAAAGTTACTAAG 50 110 0 CGCGGGCAAA 0.792208 -29 AAAGAATTCCCGGGGGCAAATTACGTTGAT 52 167 0 CGGGGGCAAA 0.976883 -97 GCGTAATGCCGGGGAGCGAAAAAATAAGCG 53 142 1 GGGGAGCGAA 0.776475 -97 AGACAGGCTTCGGGGTCAAAGACGCGTATT 64 27 0 CGGGGTCAAA 0.769034 -221 AATTGAATCACGGGAGTAAAGACAG 83 19 1 CGGGAGTAAA 0.615813 -15 CTAACTCCGACGGGAGCAAATCC 99 64 1 CGGGAGCAAA 0.963413 -13 ********** Masking position 10 Map Score: 6.06783 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 203 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035