AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iarcA_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 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #2 gltA_sdhC 600 gltA: citrate synthase, sdhC: succinate dehydrogenase, cytochrome b556 #3 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #4 focA 300 probable formate transporter (formate channel 1) #5 icdA 201 isocitrate dehydrogenase, specific for NADP+ #6 hrpA 257 helicase, ATP-dependent #7 ydcF 271 orf, hypothetical protein #8 aldA 196 aldehyde dehydrogenase, NAD-linked #9 glcD_glcC 250 glcD: glycolate oxidase subunit D, glcC: transcriptional activator for glc operon #10 lldP 300 L-lactate permease #11 sodA 284 superoxide dismutase, manganese #12 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #13 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #14 ycbD 29 similar to aldehyde dehydrogenase #15 ycgA 300 similar to hypothetical proteins #16 ycgB 115 ycgB #17 amyE 148 alpha-amylase #18 lctE 176 L-lactate dehydrogenase #19 lctP 31 L-lactate permease #20 ycgK 192 similar to transcriptional regulator (LysR family) #21 cah 71 cephalosporin C deacetylase #22 ycgL 83 ycgL #23 ycgM 190 similar to proline oxidase #24 yfmT 249 similar to benzaldehyde dehydrogenase #25 yfjN 300 similar to hypothetical proteins #26 yfjM 195 yfjM #27 yfjL 29 alternate gene name: yztA #28 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #29 citA 108 citrate synthase I #30 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #31 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #32 mmgD 33 citrate synthase III #33 mmgC 27 acyl-CoA dehydrogenase #34 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #35 mmgA 137 acetyl-CoA acetyltransferase #36 yqiK 78 similar to glycerophosphodiester phosphodiesterase #37 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #38 sodA 178 superoxide dismutase #39 yqgC 109 yqgC #40 yrhG 262 similar to formate dehydrogenase #41 yrhF 300 yrhF #42 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #43 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #44 ysfA 118 ysfA #45 ysfB 68 similar to hypothetical proteins #46 ysfC 102 similar to glycolate oxidase subunit #47 citC 163 isocitrate dehydrogenase #48 citZ 300 citrate synthase II #49 gbsA 198 glycine betaine aldehyde dehydrogenase #50 yvfH 300 similar to L-lactate permease #51 rocA 226 pyrroline-5 carboxylate dehydrogenase #52 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #53 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #54 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #55 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) Motif number 1 AGGTCTCCGGAACACCCTGCAATCCCGAGC 2 95 0 AACACCCTGC 0.874126 -506 CTGATAAAGAAAAAACCCGGTAAGCATTTA 7 24 1 AAAAACCCGG 0.595541 -248 GAATTAATAAAAAACCCGGCGCTAAATGCT 7 46 0 AAAACCCGGC 0.931261 -226 GACGAAAACGAAAAGCCCGCTTAATAACTG 9 171 1 AAAAGCCCGC 0.962835 -80 ACCAAACAGCCGGCTGACCAGGCT 13 5 1 AACAGCCGGC 0.982935 -222 GCAGCAAAAAAACAGCCTGGTCAGCCGGCT 13 18 0 AACAGCCTGG 0.834316 -209 AGCCCGCCGTACAAGCCGGCGGGCAGCAAT 16 13 0 ACAAGCCGGC 0.818918 -103 TGAATAACTCAAAAGCCCGCCGTACAAGCC 16 26 0 AAAAGCCCGC 0.962835 -90 ATGTTACAATAACAGCCTGCGCTTCTGCAA 16 56 0 AACAGCCTGC 0.956257 -60 TAAATGTGAAAAGCCGCCGCATATCATC 22 9 1 AAAAGCCGCC 0.952801 -75 GTTTGCAGAAAAAAACCGCCTGATGATATG 22 30 0 AAAAACCGCC 0.832802 -54 TTCCAACCTCAACACCCCGCAATCTAAGAA 23 171 0 AACACCCCGC 0.917458 -20 AAGACCGGATATCACCCGGCCTTTGACAAT 28 42 0 ATCACCCGGC 0.76786 -190 GAATTGCTCAAACAGCCGCCGACGCGGCTT 34 84 1 AACAGCCGCC 0.96462 -66 ATCCGCACATAAAAGCCGCGTCGGCGGCTG 34 96 0 AAAAGCCGCG 0.823008 -54 GGCTGCGTCAAACAGCCTCCTTCTAACAAC 35 21 0 AACAGCCTCC 0.911876 -117 TATATAAGAAAAAAACCGGGCGCTGTCACC 45 23 0 AAAAACCGGG 0.707939 -46 AATAAAAACCTCCCAGTATGTAA 47 151 0 AAAAACCTCC 0.65403 -13 CAAAAACCCGCAAATAAAGGC 48 2 1 AAAAACCCGC 0.864724 -299 ATAAGCCTCCTTGACGTAAA 49 189 0 ATAAGCCTCC 0.580716 -10 GCTTTAAAAAATCAGCCCGCCAATTCCTTT 52 115 0 ATCAGCCCGC 0.863486 -62 GCGCTTACATTACAGCCGGCCAAAAAAACA 52 143 1 TACAGCCGGC 0.779778 -34 ********** Masking position 4 Map Score: 23.7355 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 450 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 GTACCCAGGTTTTCCCCTCTTTCACAGAGC 2 484 1 TTTCCCCTCT 0.920892 -117 TTACCAGACATCTCCCCCCACAAGAATTGG 10 72 1 TCTCCCCCCA 0.933131 -229 ACTGAAATTTTATCCCCTCAATGAAGAATT 12 270 1 TATCCCCTCA 0.703859 -31 TATTTCGATCCATCCCCTCTGTTTGAAAAT 15 39 0 CATCCCCTCT 0.732891 -262 ATCTTCCCCCTCGGCAAATAC 20 2 1 TCTTCCCCCT 0.958406 -191 TTCGACAGAATCCCCCCCCGACTTTCTAAC 23 40 1 TCCCCCCCCG 0.835339 -151 TTTCCTCTCCCCCTTTATATGATA 26 182 0 CTCTCCCCCT 0.909241 -14 TTCTATTCTCCCTCTGATTAATATT 29 6 1 TTCTCCCTCT 0.920892 -103 TTGTATTCCCCCTATCCTTTTCT 29 96 0 TATTCCCCCT 0.850915 -13 AAAACGTTCATCTTCCCTCTCGATTATGCA 31 17 0 TCTTCCCTCT 0.94063 -98 AAGATGAACGTTTTCCCTCTATTATATATC 31 33 1 TTTTCCCTCT 0.907858 -82 GATAGCCCCTCTCCCTCTAGTAATCTAG 42 16 0 CTCTCCCTCT 0.873233 -18 ATCTGTCTCCCCTCTCTCCTGCGTA 43 6 1 TCTCCCCTCT 0.949287 -287 ATTCTGTAATCCTCCCCCCTGTTTGAGCTA 43 41 0 CCTCCCCCCT 0.941553 -252 TTCATTTTACTCCTCCCTCAAAAGGGCGTC 43 180 0 TCCTCCCTCA 0.905617 -113 GTGCTAAATCTCTTCCCCCACTTCTTTCAA 43 242 0 TCTTCCCCCA 0.921942 -51 GGCGTTCCCCCTCATCATGTTTTT 45 55 0 TTCCCCCTCA 0.875776 -14 GCAAGTATTTCTCTCCCCCAAAAAGAAAAT 48 205 0 CTCTCCCCCA 0.837007 -96 TATTTCTCCCCCTTTTATTTAAA 54 4 1 TTCTCCCCCT 0.944227 -297 ********** Masking position 5 Map Score: 19.5293 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 64 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 GTTTGCAACCTTTCTTTACGCCGTTTTTGTGTGCATT 3 169 1 TTTCTTTTTT 0.737777 -132 TGATGCTCCCTTTTAATTAACTGTTTTAGCGGAGGAT 4 80 1 TTTTATTTTT 0.499376 -221 TAGAGCAATTTTTTGTTAATGATTTGTAATTGGCTTG 5 94 0 TTTTTTTTGT 0.834098 -108 GACTCCTGACTTTTATTTCTGCCTTTTATTCCTTTTA 8 51 1 TTTTTTTTTT 0.897649 -146 GTCAGACCATTTTTTTTCCAGCTCTGTGACCTTGTCT 9 117 0 TTTTTTCTGT 0.831178 -134 GGGCTTTTCGTTTTCGTCTATCTCTTTAGCTACCGGT 9 152 0 TTTTGTCTTT 0.875475 -99 TTTCAAAATGTTTTTGTCGTATTTTGTATGATTCTGT 12 57 0 TTTTGTTTGT 0.804521 -244 TGTTTTTTGTCGCTTCCTTTTCTCCTTTAT 23 4 1 TTTTGTCTTT 0.875475 -187 AATCCCTTTATTTTGTTAGCCTTTTTTGAATCAAGCA 26 17 0 TTTTTTTTTT 0.897649 -179 TCCAGGTTTATTTTAGTCAAGAATTGTGTAAAAATCC 26 49 0 TTTTGTTTGT 0.804521 -147 ATCCGGGTCTTTTTTGTACGCAGCTTTTACTCAGCCT 26 96 1 TTTTGTCTTT 0.875475 -100 GACGTATTTATTTCCTTGGAAATCTTT 28 1 0 TTTCTTCTTT 0.733704 -231 ATATCCGGTCTTTTTTTTGCATGCTGTAAAACGAGAC 28 60 1 TTTTTTCTGT 0.831178 -172 GATTAATATTTTTAATTAATTCCCTTTAAAATATTGA 29 26 1 TTTATTCTTT 0.634642 -83 CCGTCAATCGTTTTCATCGCTGATTTTCAATAAATGT 30 33 0 TTTTATTTTT 0.499376 -268 GACCTCCTAGTTTGATTAAGCAATTTTAAAGTTTACA 31 81 0 TTTGTTTTTT 0.681737 -34 ACACAGGTTATTTGAGTGCTGCCTTTTTTATTGCCTT 40 190 1 TTTGGTTTTT 0.636824 -73 TATGTACGCGTTTTCTTGACGCCCTTTTGAGGGAGGA 43 163 1 TTTTTTCTTT 0.895708 -130 AGAGAGTTTCAGTTTCATTTTTTGTATGTTTCT 46 7 1 TTTCGTTTTT 0.69726 -96 CATGGAAGGCTTTGCTTTTTTTCTTTTACAATAGATT 46 45 1 TTTGTTTTTT 0.681737 -58 AAAAAACGCCTTTATTTGCGGGTTTTTG 48 2 0 TTTATTTTTT 0.639486 -299 ACCTATAATTTTTTTTTTCCATTCTGTGATTTCCCCG 48 39 0 TTTTTTCTGT 0.831178 -262 CCATTTTGATTTTTCTTTTTGACTTTTCCTCATGTTT 49 78 0 TTTTTTTTTT 0.897649 -121 ACATTAAATTTTTATTTAACAAACTTTATTTACGTCA 49 161 1 TTTATTCTTT 0.634642 -38 TTCATATATTTTTTTGTTTTAATCTGTTTATATTTCA 50 46 1 TTTTGTCTGT 0.801205 -255 TGAACGCAAATTTATTTTGCGTTTTTTGCTCTTTACG 51 52 0 TTTATTTTTT 0.639486 -175 ACTGAGATGTTTTCAGTCTCTTTTTTTGTGGATTCAA 52 32 1 TTTCGTTTTT 0.69726 -145 CACCTCATTGTTTTTTTGGCCGGCTGTAATGTAAGCG 52 144 0 TTTTTTCTGT 0.831178 -33 CATCTTCGACTTTTTTTGCCCTTTTTTAAAATAGGAT 53 20 1 TTTTTTTTTT 0.897649 -281 CATGATAGCGTTTTCGTCAACTATTTTTTTAGTTAAA 54 168 1 TTTTGTTTTT 0.877741 -133 TTTTTGTCTATTTTGTTGCTTATTTATGTCGGC 55 7 0 TTTTTTTTAT 0.330155 -294 TTGAGCAATATTTTTTTCGTCTATTTTGTGAATTACT 55 202 1 TTTTTTTTTT 0.897649 -99 **** ** **** Masking position 7 Map Score: 21.5296 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 106 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 TTTTCGCATCTGGAAGCAGTGTTTTGCATGAC 2 41 0 TGAAGCATGT 0.853404 -560 GGCCTCTATCTGTAAGCGCTTTTATTAATTTT 13 176 0 TGAAGCGTTT 0.982649 -51 ATATGGATTATGTTAGCAATTTCTGTTATGAT 20 117 1 TGTAGCATTT 0.79007 -76 AACTAGAAATTGTAAGCGCTGTCTATCTTCTG 35 102 1 TGAAGCGTGT 0.942655 -36 GAAGAAGTAATGGAGGCGTTTTATT 40 248 1 TGAGGCGTTT 0.906735 -15 TTATAATTTATGTACGCGTTTTCTTGACGCCC 43 155 1 TGACGCGTTT 0.947067 -138 TTCTTTCAATTGTAAGCACTTTATTAAGATTT 43 219 0 TGAAGCATTT 0.952507 -74 TACAATAGATTGAAAGCGTTTTTTGACAGGGG 46 71 1 TGAAGCGTTT 0.982649 -32 GCCAGTAAAATGTAAGCATTTTCTTTTTGGGG 48 188 1 TGAAGCATTT 0.952507 -113 TGGCGCCATATGTAAGCGGTTTCTATAGATGA 50 253 0 TGAAGCGTTT 0.982649 -48 TTTCCGATCTTGAACGCAAATTTATTTTGCGT 51 67 0 TGACGCAATT 0.54317 -160 CCGGCTGTAATGTAAGCGCTTTAAAAAATCAG 52 130 0 TGAAGCGTTT 0.982649 -47 TGATTTATGATGAAAGCGTATTCTTAATCTGA 54 138 0 TGAAGCGATT 0.913995 -163 TCATAAATCATGATAGCGTTTTCGTCAACTAT 54 160 1 TGTAGCGTTT 0.913995 -141 ** ***** *** Masking position 1 Map Score: 18.2145 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 41 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 CTTTCTTTACGCCGTTTTTGTGTGCATTCA 3 178 1 GCCGTTTTTG 0.800679 -123 TACGTGATGTGCGTGTTTTGCGAGTTAAGA 9 49 0 GCGTGTTTTG 0.800679 -202 TGCCCCTTTCGTGTTTTTTCTGG 14 4 0 GTGTTTTTTC 0.645924 -26 ATACATCTCGGCGTTTTTAGAAAACGGTGT 20 44 1 GCGTTTTTAG 0.730482 -149 TATTTTGTTAGCCTTTTTTGAATCAAGCAC 26 16 0 GCCTTTTTTG 0.969396 -180 GTAAATCCGGGTCTTTTTTGTACGCAGCTT 26 92 1 GTCTTTTTTG 0.829698 -104 CTCCGTTTTTGCGTTTTTTGTCTA 32 5 0 GCGTTTTTTG 0.969396 -29 TTCACAGCGAGCCTTTCTTCATTCAATGTA 38 121 0 GCCTTTCTTC 0.747575 -58 TTTGAGTGCTGCCTTTTTTATTGCCTTTCT 40 200 1 GCCTTTTTTA 0.69445 -63 CTTTTTTATTGCCTTTCTTGCATAACTGTG 40 212 1 GCCTTTCTTG 0.887758 -51 TCTATACATGGCTTTTTTTGACTTCTTGAA 41 20 0 GCTTTTTTTG 0.861828 -281 GGAAGGCTTTGCTTTTTTTCTTTTACAATA 46 48 1 GCTTTTTTTC 0.700197 -55 TAGATTGAAAGCGTTTTTTGACAGGGGGAT 46 76 1 GCGTTTTTTG 0.969396 -27 GCAAATAAAGGCGTTTTTTCGGGGAAATCA 48 20 1 GCGTTTTTTC 0.922244 -281 AATTTATTTTGCGTTTTTTGCTCTTTACGC 51 51 0 GCGTTTTTTG 0.969396 -176 CGAATTTTAGGTCTTTTTTGTTTAAATAAA 54 24 0 GTCTTTTTTG 0.829698 -277 ********** Masking position 6 Map Score: 14.0217 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 213 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 CGGTGGTGGTTAGGGTATTACTTCACATACCCTATGGA 1 129 1 TGAATTCACT 0.935218 -172 ATCTGACCTCTGGTTCACAATTTCCCAATTAAAACTCA 10 121 1 TGAATTCCCA 0.925007 -180 CACATTTATATTGTGCAACACTTCACAAACTTTTGCAA 18 93 0 TGAATTCACA 0.933925 -84 GTCTTTTTGTTTGTGAAGTATTTCACATTTATATTGTG 18 116 0 TGAATTCACT 0.579768 -61 TAAACACACATGGCGGAATAGTTCACTAGCAAGTCTTA 41 78 1 TGAATTCACA 0.929112 -223 AAAAAAATTATAGGTAAACATTTAACAAATGTCTGATT 48 61 1 TGAATTAACA 0.819605 -240 TAAAAATTAATTGTGAAATACTTCACAATATCGTGCCA 54 236 1 TGAATTCACA 0.499879 -65 GAAAAAAATATTGCTCAATATTTCACAAATGTGTCAAA 55 182 0 TGAATTCACA 0.979061 -119 AACCGAGACTTTGATCAGTAATTCACAAAATAGACGAA 55 217 0 TGAATTCACA 0.979061 -84 AACTGTTAATTTGCTCACTACTTCACAAATAGAACCGA 55 249 0 TGAATTCACA 0.979061 -52 * * * * ***** * Masking position 10 Map Score: 10.4178 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 10 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 GTCTGTTGCTCATCTCCTTGTCACACGTTGTG 10 242 0 CTCTCCTGTC 0.944885 -59 CATTCTTCCGCTTCCTCCTTTCAAACCGATGT 17 65 0 CTCCTCTTTC 0.905485 -84 TTTGAACCAGCTCCTTCTTTTCGTAAATGATG 20 85 1 CCCTTCTTTC 0.931534 -108 TGTTTTTTGTCGCTTCCTTTTCTCCTTTATTC 23 11 1 CCTTCCTTTC 0.684456 -180 GTTCCCACTCTTTTCCTCATATGTA 27 15 0 CCACTCTTTC 0.490984 -15 CAATGATCGACGTATTTATTTCCTTGGAAATC 28 14 0 CTATTTTTTC 0.405881 -218 TTGTATTCCCCCTATCCTTTTCTGTTATTATA 29 87 0 CTATCCTTTC 0.848411 -22 ACTAAGTCACCTCTTCCTTTCTTTTAAACAG 30 280 0 CTCTTCTTTC 0.960784 -21 TTTACTCTGTCTTCTTCATGTCTTCCTTGTAT 39 71 0 CTCTTCTGTC 0.931534 -39 GCCTCCATTACTTCTTCTTTTCTCACAGTTAT 40 233 0 CTCTTCTTTC 0.960784 -30 CATCTTTCTTTCAAGAAGTCAA 41 1 1 CTCTTTTTTC 0.790278 -300 TTCACCCATCCCCCTGTCAAAAAACGCT 46 85 0 CTCCCCTGTC 0.870197 -18 ATATAACATCTCCTTTTCAATAAATTTC 48 283 0 CTCTCCTTTC 0.968623 -18 AGAATCATGCCATTTTCTTGTCTTTTGCTGAA 51 152 0 CTTTTCTGTC 0.632551 -75 GGACGATTTCCCTCTCTTTTTCTAGTAACATC 53 79 0 CTCTCTTTTC 0.826031 -222 GCTTTCTCCTCCATTTCCGGTTAAAAC 55 284 0 CCCTCCTTTC 0.944885 -17 * ***** **** Masking position 9 Map Score: 11.723 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 103 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 ATGCAAAACACTGCTTCCAGATGCGAAAAC 2 44 1 CTGCTTCCAG 0.697455 -557 ACAGCCTATACTGCCGCCAGGTCTCCGGAA 2 113 0 CTGCCGCCAG 0.728832 -488 TTGCGTAAGACTGCCGGAACTTAAATTTGC 2 559 0 CTGCCGGAAC 0.931282 -42 GTTTGCTCGTCTGCCACCACGTTGCATATG 5 158 0 CTGCCACCAC 0.783466 -44 AATCCAGCCGCTGCTGCAAGGCCGTAAAGG 6 233 0 CTGCTGCAAG 0.929463 -25 ATACAATTCTCTGCTGCAAGATGAATAATG 7 113 1 CTGCTGCAAG 0.929463 -159 GCGCAAAAATCAGCTGCCACACAACACAAC 9 215 1 CAGCTGCCAC 0.772877 -36 TGTGTTTCGGCTGCTGGCATACTCATATTT 15 64 0 CTGCTGGCAT 0.820036 -237 TCAAATTCACCTGCCGGCACAATATATGAA 15 175 0 CTGCCGGCAC 0.72355 -126 TTTCTGCAAACTGCCGGAATGAGAACAGAC 22 49 1 CTGCCGGAAT 0.800842 -35 CCCATTAAACCTGCCGCCAGCATTTC 38 7 0 CTGCCGCCAG 0.728832 -172 ATTTTACTGGCTGCTGGAACTAAAACCCTT 48 169 0 CTGCTGGAAC 0.905072 -132 ********** Masking position 9 Map Score: 10.7441 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 889 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CCGTCGGTATTTTACAAAATTGTTAACAAT 1 88 0 TTTACAAAAT 0.64899 -213 GTATAGGCTGTTCACAAAATCATTACAATT 2 132 1 TTCACAAAAT 0.829689 -469 GTAATTTGTATTTAATAAATACGATCGATA 4 33 1 TTTAATAAAT 0.463698 -268 CTATGCGTTGTTCAATAAATTCGAACATAG 6 107 0 TTCAATAAAT 0.694948 -151 GAAGTAAGTCTTCAAAAAATCAAATAAGGA 17 120 1 TTCAAAAAAT 0.866785 -29 AAAACCAGCGTTCACAATATCCTCAAAATA 23 112 0 TTCACAATAT 0.69579 -79 CCTAGAAATATTCAAAATATTCTAATCATT 24 22 1 TTCAAAATAT 0.753382 -228 ATTAATTCCCTTTAAAATATTGATTATTTT 29 40 1 TTTAAAATAT 0.536911 -69 AAATATAATATTTAAAAAATAATCAATATT 29 55 0 TTTAAAAAAT 0.711773 -54 ATCGCTGATTTTCAATAAATGTATTCGCTT 30 25 0 TTCAATAAAT 0.694948 -276 TTTTATTCATTTTAAAAAATTTGAGAATAG 37 67 0 TTTAAAAAAT 0.711773 -234 ACATCTCCTTTTCAATAAATTTCCCCTTTA 48 276 0 TTCAATAAAT 0.694948 -25 TTTGATTTTTTTCAAAATATAATGCTAGGT 50 188 1 TTCAAAATAT 0.753382 -113 ATGTAAGCGCTTTAAAAAATCAGCCCGCCA 52 123 0 TTTAAAAAAT 0.711773 -54 TGTGAAATACTTCACAATATCGTGCCATAC 54 247 1 TTCACAATAT 0.69579 -54 TGATCAGTAATTCACAAAATAGACGAAAAA 55 214 0 TTCACAAAAT 0.829689 -87 ********** Masking position 4 Map Score: 10.1088 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 62 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 CTCGCCGCTCTGTGAAAGAGGGGAAAACCTGGG 2 487 0 TTAAGAGGGG 0.855032 -114 AAAACAAACATATAAATCACAGGAGTCGCCC 8 176 1 TTAACACAGG 0.612673 -21 GGAGATGTCTGGTAAAGAAAAGGGCAATCCTCA 10 54 0 GTAAAAAAGG 0.590459 -247 ATTGGGAAATTGTGAACCAGAGGTCAGATAAGC 10 117 0 TTAACAGAGG 0.941872 -184 TCTGATATTTTATAAAAAAGCGGTAAATCACTG 13 65 0 TTAAAAGCGG 0.805203 -162 TAATTAATATTTTCAAACAGAGGGGATGGATCG 15 31 1 TTAACAGAGG 0.941872 -270 TGAAAGCAATCATAAATAAGAGGACATAGGCGT 15 129 0 CTAAAAGAGG 0.628975 -172 AACTAAATCTTATAAAACAAAGGGGAATAATCG 21 46 1 TTAACAAAGG 0.837153 -26 TTAACCAGAATATAAAAAATAGGGTAGATAATC 25 136 1 TTAAAATAGG 0.483996 -165 TAATTAAAAATATTAATCAGAGGGAGAATAGAA 29 11 0 TTAACAGAGG 0.941872 -98 CTAATGACTGTTTAAAAGAAAGGAAGAGGTGAC 30 273 1 TTAAGAAAGG 0.695196 -28 AACATGATGAAAAAGGGGATTTGAATGG 34 6 1 GTAAAAGGGG 0.788509 -144 GTATATTATAGCTCAAACAGGGGGGAGGATTAC 43 33 1 GTAACAGGGG 0.809241 -260 ATTTCGCACTTATCAAACAGGGGGTAAAGTA 43 272 1 TTAACAGGGG 0.93004 -21 AATAACATCATGTTAAAAAAAGGAGCGCCACAT 44 16 0 TTAAAAAAGG 0.818775 -103 AATTTTGATGTCTGAACAAGAGGCTAACCTCAT 47 38 0 TTAAAAGAGG 0.934386 -126 CCAGTTTATGTTTCAAGGAGGGGTTTGGG 50 282 1 TTAAGAGGGG 0.855032 -19 TTTTATCCTATTTTAAAAAAGGGCAAAAAAAGT 53 28 0 TTAAAAAGGG 0.787537 -273 GTCTTTTTTGTTTAAATAAAAGGGGGAGAAATA 54 11 0 TTAAAAAAGG 0.818775 -290 GTATTCTTAATCTGAATAAGCGGGATTGTGACT 54 120 0 TTAAAAGCGG 0.805203 -181 * * ** ****** Masking position 3 Map Score: 16.1266 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 70 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 CCGCCCGACAATACTGGAGATGAAT 11 270 1 ATACTGGAGA 0.925994 -15 TAATTACTGTATAATGGAGACTACAGAATC 12 35 1 ATAATGGAGA 0.957231 -266 ACCGATGTGAAGACTGGAGAATTTTGTTAA 17 43 0 AGACTGGAGA 0.93546 -106 GAATGAGAACAGACTGGAGACGAATAGAT 22 65 1 AGACTGGAGA 0.93546 -19 ATTCTGTCGAATAAAGGAGAAAAGGAAGCG 23 21 0 ATAAAGGAGA 0.88836 -170 ATTTGCGGTTATAAAGGAGATGCTGACC 24 232 1 ATAAAGGAGA 0.88836 -18 TCTTGCATTTATAATGGTGAACCCTAAATA 28 196 1 ATAATGGTGA 0.83374 -36 TCAAACTGCATAATCGAGAGGGAAGATGA 31 10 1 ATAATCGAGA 0.704157 -105 CAAAATAAGTATAATGGAGAAAACTTTAGG 36 44 1 ATAATGGAGA 0.957231 -35 ATCTTTGACCAGAATGGAGAATTTGTAAAG 37 251 0 AGAATGGAGA 0.962862 -50 GGGAAATCACAGAATGGAAAAAAAAAATTA 48 41 1 AGAATGGAAA 0.650386 -260 TCGGAAAAAGAGAAAGGTGATCACCTGTTA 51 92 1 AGAAAGGTGA 0.673766 -135 ********** Masking position 3 Map Score: 9.28204 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 38 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 ACCCGGCGCTAAATGCTTACCGGGTTTTTT 7 33 0 AAATGCTTAC 0.924019 -239 ATAATGAACCAACTGCTTACGCGGCATTAA 11 233 1 AACTGCTTAC 0.856 -52 AAATTAATAAAAGCGCTTACAGATAGAGGC 13 177 1 AAGCGCTTAC 0.954841 -50 AGAATTTTGTTAACGCTTACATTTAAAATT 17 26 0 TAACGCTTAC 0.741785 -123 GATTGATAAGAAATGCTTTCGCATGCGATA 25 200 1 AAATGCTTTC 0.712961 -101 TATCTGTTTTCAATGCTTACGATGTAAACT 31 59 1 CAATGCTTAC 0.808236 -56 AGAAGATAGACAGCGCTTACAATTTCTAGT 35 103 0 CAGCGCTTAC 0.879923 -35 GGCGTCAAGAAAACGCGTACATAAATTATA 43 156 0 AAACGCGTAC 0.780984 -137 AATCTTAATAAAGTGCTTACAATTGAAAGA 43 220 1 AAGTGCTTAC 0.91918 -73 CCCTGTCAAAAAACGCTTTCAATCTATTGT 46 72 0 AAACGCTTTC 0.821987 -31 CCCAAAAAGAAAATGCTTACATTTTACTGG 48 189 0 AAATGCTTAC 0.924019 -112 CATCTATAGAAACCGCTTACATATGGCGCC 50 254 1 AACCGCTTAC 0.917023 -47 TGATTTTTTAAAGCGCTTACATTACAGCCG 52 131 1 AAGCGCTTAC 0.954841 -46 ********** Masking position 2 Map Score: 11.9813 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 CAACCTGGCTTTACCCGTTTTTTATTTGGC 2 519 0 TTACCCGTTT 0.577481 -82 TGAATGGGCGATGCCCCGTTGCTTGTTGAC 6 31 1 ATGCCCCGTT 0.851519 -227 AAATTGCCCGTTTGTGAACCACT 8 4 1 TTGCCCGTTT 0.933073 -193 GTCAGGAGTCATGCCCGTTTGCAAACAAGT 8 31 0 ATGCCCGTTT 0.91369 -166 CTGATGAGGATTGCCCTTTTCTTTACCAGA 10 50 1 TTGCCCTTTT 0.876482 -251 GCCCATTGCCCCTTTCGTGTTTTTT 14 15 0 TTGCCCCTTT 0.950773 -15 CGGTCGTGACATCCCCCTTTGTCACGCGGT 15 204 0 ATCCCCCTTT 0.882394 -97 TTCCGATTATTCCCCTTTGTTTTATAAG 21 54 0 ATTCCCCTTT 0.784146 -18 CGCAAAATAATTGCCCTGTTA 25 2 0 TTGCCCTGTT 0.735087 -299 TTTCCTCTCCCCCTTTATATGATATC 26 180 0 CTCCCCCTTT 0.809476 -16 TTCCATTCAAATCCCCTTTTTCATCATGTT 34 11 0 ATCCCCTTTT 0.733801 -139 TCATTCATTCATGCCCGTTTCAAAGCATAC 35 59 1 ATGCCCGTTT 0.91369 -79 TATAAAGGCTTTTCCCGGTTCCCCTCAGGA 41 255 0 TTTCCCGGTT 0.574544 -46 TTTCAATAAATTTCCCCTTTAAGAGTGTTG 48 267 0 TTTCCCCTTT 0.827115 -34 TCGACTTTTTTTGCCCTTTTTTAAAATAGG 53 25 1 TTGCCCTTTT 0.876482 -276 TATTTCTCCCCCTTTTATTTAAACA 54 6 1 CTCCCCCTTT 0.809476 -295 ********** Masking position 2 Map Score: 14.4465 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 97 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 14 CTGTTTTAGCGGAGGATGCGGAAAAAATTCAA 4 100 1 GGAGGGCGGA 0.986897 -201 TGAGATAATAGTGAGAAGCGGAGCACTCTGAA 7 216 0 GTGAGGCGGA 0.845846 -56 AGGATATATGGGAAGGAGCGGATGTGAAAGAA 13 145 1 GGAAGGCGGA 0.971503 -82 CGGTTTGAAAGGAGGAAGCGGAAGAATGAAGT 17 69 1 GGAGGGCGGA 0.986897 -80 GCGGTTATAAAGGAGATGCTGACC 24 236 1 AGGAGGCTGA 0.660342 -14 TATCATATAAAGGGGGAGAGGAAA 26 182 1 AGGGGGAGGA 0.893593 -14 ACGCAAAAACGGAGGTTGAGGAT 32 21 1 GGAGGGAGGA 0.920656 -13 TATTCCATCCGGGGGTGGCCGAG 33 15 1 GGGGGGCCGA 0.910625 -13 CGCAGGTCAGATGGGGAGCGGAATTGCTCAAA 34 64 1 ATGGGGCGGA 0.883365 -86 ATGTGAATCCAGAGGCCGCGGAGGCAGGA 34 131 1 AGAGGGCGGA 0.979191 -19 TACAATTGAAAGAAGTGGGGGAAGAGATTTAG 43 237 1 AGAAGGGGGA 0.733909 -56 AAATATATGAAGAAGTAGCGGATGCCCTATTA 50 25 0 AGAAGGCGGA 0.955157 -276 ***** ***** Masking position 12 Map Score: 10.4189 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 230 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 TTAGAAAGGGTCACACGCATGCCCCAATAGAA 3 237 0 TCACAGCAGC 0.941623 -64 GACACTTTATTCACAATCCTGCCACAGAGATA 6 58 1 TCACATCCGC 0.963143 -200 AAATTTCAGTTCACCGGCCAGCGGCACCGTAA 12 248 0 TCACCGCCGC 0.978399 -53 AAGCGGTAAATCACTGTCCGGCCGGGATTCTG 13 49 0 TCACTTCCGC 0.786188 -178 GCGGTCAAATTCACCTGCCGGCACAATATATG 15 177 0 TCACCGCCGC 0.978399 -124 AATGAATAACTCAAAAGCCCGCCGTACAAGCC 16 26 0 TCAAAGCCGC 0.969875 -90 TCCAGTCTGTTCTCATTCCGGCAGTTTGCAGA 22 51 0 TCTCATCCGC 0.735513 -33 TTCCAACCTCAACACCCCGCAATCTAAGAA 23 171 0 TCAACCCCGC 0.723388 -20 TCCAAAAAGTTCAAAAGCAAGGCCACTAAGAA 25 85 1 TCAAAGCAGG 0.667393 -216 TCGATCATTGTCAAAGGCCGGGTGATATCCGG 28 36 1 TCAAAGCCGG 0.909737 -196 TTCCTTGTATTCACACGCATGCAACGATACAA 39 49 0 TCACAGCAGC 0.941623 -61 TAGGCAGCATTCAAACGCCTGGTTTGACACAG 40 164 1 TCAAAGCCGG 0.909737 -99 GCTTTACCAGTCACAATCCCGCTTATTCAGAT 54 112 1 TCACATCCGC 0.963143 -189 ***** *** ** Masking position 1 Map Score: 11.5536 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 270 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