AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_ecoli_reg_300.orf -o00790_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/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 Input sequences: #1 fixA 300 probable flavoprotein subunit, carnitine metabolism #2 fixC 50 flavoprotein; electron transport #3 yaaU 56 putative transport protein #4 yabF 107 putative NAD(P)H oxidoreductase #5 folA 191 dihydrofolate reductase type I; trimethoprim resistance #6 yabB 300 orf, hypothetical protein #7 murC 53 L-alanine adding enzyme, UDP-N-acetyl-muramate:alanine ligase #8 ftsZ 60 cell division; forms circumferential ring; tubulin-like GTP-binding protein and GTPase #9 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #10 yacA 155 orf, hypothetical protein #11 secA 61 preprotein translocase; secretion protein #12 mutT 59 7,8-dihydro-8-oxoguanine-triphosphatase, prefers dGTP, causes AT-GC transversions #13 pcnB 92 poly(A) polymerase I #14 yadB 36 putative tRNA synthetase #15 dksA 177 dnaK suppressor protein #16 yaiB 300 orf, hypothetical protein #17 phoA 31 alkaline phosphatase #18 nfnB 93 oxygen-insensitive NAD(P)H nitroreductase #19 ybdF 64 orf, hypothetical protein #20 ybdJ 65 orf, hypothetical protein #21 ybdK 300 orf, hypothetical protein #22 lipB 166 protein of lipoate biosynthesis #23 ybeD 109 orf, hypothetical protein #24 dacA 138 D-alanyl-D-alanine carboxypeptidase, fraction A; penicillin-binding protein 5 #25 mrdA 30 cell elongation, e phase; peptidoglycan synthetase; penicillin-binding protein 2 #26 ybeB 300 orf, hypothetical protein #27 helD 122 DNA helicase IV #28 nemA 36 N-ethylmaleimide reductase #29 gloA 80 lactoylglutathione lyase #30 rnt 102 RNase T, degrades tRNA #31 lhr 92 member of ATP-dependent helicase superfamily II #32 ntpA 117 dATP pyrophosphohydrolase #33 aspS 276 aspartate tRNA synthetase #34 folE 257 GTP cyclohydrolase I #35 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #36 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #37 dedA 82 orf, hypothetical protein #38 usg 65 putative PTS system enzyme II A component #39 pdxB 98 erythronate-4-phosphate dehyrogenase #40 hmpA 300 dihydropteridine reductase, ferrisiderophore reductase activity #41 ygcM 300 putative 6-pyruvoyl tetrahydrobiopterin synthase #42 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #43 ygdP 300 putative invasion protein #44 ygiG 101 putative kinase #45 folP 44 7,8-dihydropteroate synthase #46 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #47 ftsJ 125 cell division protein #48 yhhN 140 putative enzyme #49 zntA 73 zinc-transporting ATPase #50 gmk 251 guanylate kinase #51 rpoZ 54 RNA polymerase, omega subunit #52 rep 174 rep helicase, a single-stranded DNA dependent ATPase #53 dapF 300 diaminopimelate epimerase #54 uvrD 83 DNA-dependent ATPase I and helicase II #55 pldA 146 outer membrane phospholipase A #56 recQ 126 ATP-dependent DNA helicase #57 dnaB 82 replicative DNA helicase; part of primosome #58 mgtA 300 Mg2+ transport ATPase, P-type 1 #59 lplA 27 lipoate-protein ligase A #60 smp 105 orf, hypothetical protein Motif number 1 AAGCGTAAACCGTCGTCGACTGGTGCGAGGATGATGTTGA 5 122 0 CTGCGTGCGG 0.984323 -70 AAGATATGTCCTAAAATGCCGCTCGCGTCGCAAACTGACA 6 15 1 CAGCCCGCGG 0.617196 -286 GCCGTTCCATCACGTTTACCACAGGCGGGAA 14 16 1 CTACCGGCGA 0.944937 -21 GGTTAATTTACATTCTGGTCGCGTGCGCAAATACGCTTTT 15 25 1 CTGCCTGCGA 0.963145 -153 GAAGTCGGAGCGGCTGGGCGAGATGCGGAAGTTCTGGAAT 21 235 0 CGGGGTGCGA 0.891863 -66 ACAATTTCTACAAAGTCGTGTCTGGCGGAAAAAGTCTGGC 26 13 0 CTGGCGGCGA 0.965029 -288 ACAAAAATGGCGATGCAATCTGCGGCGCGGGGTGGGATGA 26 56 1 CCACGGGCGG 0.830625 -245 CTGGATTTGCCCTGAACGTCTAAGGCGATGATGTCCTGAC 26 258 0 CAGCAGGCGG 0.85216 -43 TCCAACATTGCGAGCGGCGTAAAGCCGCCGCT 29 3 1 CTGGGGGCGA 0.976231 -78 GCTAACGCTGCGACTTGGTCACCTGCGCAGCAGGGGGCAT 33 218 1 CTGCCTGCGG 0.976845 -59 TACAGCCTGATTATTGTGCGTGAGGCGGCGCACATAATCC 34 164 0 TGGGGGGCGG 0.784298 -94 ACTTTGCCCCCACGCAGGGCGGAGGCGTCACACCTGCAGG 34 217 1 CAGCGGGCGA 0.942783 -41 TATAGGCGGTCCTGTTGGACAACGGCGAACAGTATAACCG 40 25 1 CTGCAGGCGC 0.84753 -276 TCGGTACAAATACAGTCATCTGATGCGGGAAC 45 3 0 TTACGTGCGA 0.615537 -42 GGGGATAACTCATCGTAACCAATTGCGTAAATTTTTACGC 47 83 0 CTACATGCGA 0.726138 -43 TTACTCTCTTCAGCCTGACGGGCTGCGGTCTGAAAGGTCC 53 108 1 CTAGGTGCGC 0.661665 -193 GCGTCTCTACCGGTTTGGTCGGCGGCGGTGCGTTTTTATC 53 167 0 CTGCGGGCGG 0.992428 -134 CGGATAAAAACGATCGCGCCACTGGCGATGGTCCATCCCA 53 225 1 CGGCCGGCGG 0.973621 -76 ATATACCCAGCTTTTTGGCGGAGGGCGTTGCGCTTCTCCG 54 26 1 CTGGAGGCGG 0.934929 -58 AAACAGGCGCTATTTTCAGCGCCTGCGCGAGAAACTGCAA 56 79 0 TTACCTGCGA 0.518228 -48 GTTTTAATCTCCGTCGAGGGAGAGGCGTGGGATCAGGTTC 58 120 0 CGGGGGGCGG 0.965266 -181 CGTCTTTTCACGGCGTTACCGGATGCGTAAGGCCGTGACG 58 174 1 CTACGTGCGA 0.92445 -127 AGTACAGAAATGTCTTCAGGCGTGGCGAAGCCTTACCTGA 58 244 0 TTAGGGGCGG 0.731786 -57 GCAATGGATACAAGGTAGCCTCATGCGTTATTTTCCCTGC 60 36 0 CTGCCTGCGA 0.963145 -70 * * * * * **** * Masking position 15 Map Score: 24.3149 Number of sites scoring better than the average of aligned sites = 2568 Number in coding regions = 2316 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 2 TCACCAATATTGAAAACACGGCGTAGCAAAAAG 1 164 0 TGAAAAGGCG 0.596269 -137 GAAATTGTGGGGCAAAGTGGGAATAAGGGGTGA 6 271 1 GGCAAAGGAA 0.982789 -30 AAATTCGACTGGCAAATCTGGCACTCTCTCCGG 10 32 1 GGCAAAGGCA 0.983103 -124 AGACGTTCAGGGCAAATCCAGCATCACCGACTG 26 277 1 GGCAAAAGCA 0.806767 -24 AACATCGTTATGCAAATACGGAAGTGAAAGTTA 34 75 0 TGCAAAGGAA 0.878418 -183 GTCTGTTGGGGGCAAAAATGGCATTATGCGTCC 36 85 1 GGCAAAGGCA 0.983103 -71 CAATTAAGATGCAAAAAAAGGAAGACCAT 40 282 1 GCAAAAGGAA 0.688973 -19 AATTACTACGGGAAAACCCGGAGCATTCTGAAT 43 80 0 GGAAAAGGAG 0.919712 -221 ATCCCTCATCGGAAAATGCGGAAATAAGCATAC 48 15 1 GGAAAAGGAA 0.957791 -126 AAAGCCGAGTGGCAAAAACGGAGTCTGCGAGGA 50 54 1 GGCAAAGGAG 0.966473 -198 GTGAATGACAGGCAAATGCGGAAGCAGCTACGC 50 114 1 GGCAAAGGAA 0.982789 -138 TTGAGTGGTTGGCAAATCTGGAATCCAGCATCC 56 18 1 GGCAAAGGAA 0.982789 -109 TTCGAAGCAGGGAAAATAACGCATGAGGCTACC 60 30 1 GGAAAACGCA 0.710896 -76 ****** **** Masking position 6 Map Score: 14.8932 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 272 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 TCCACTCTGGCAGGGCTGCATTTT 2 4 1 ACTCTGGCAG 0.575893 -47 ATTTTATATTCTGCTGGCGAGTCCACGCTCT 5 86 0 CTGCTGGCGG 0.945552 -106 ATGATTACGGCCTCAGGCGACAGGCACAAAT 8 28 1 CCTCAGGCGC 0.948209 -33 ATCACGTTTACCACAGGCGGGAA 14 24 1 CCACAGGCGG 0.720626 -13 ACCTTGTAATCTGCTGGCACGCAAAATTACT 18 57 1 CTGCTGGCAG 0.943639 -37 AGCCAAATTGCTTCAGGCACCATCAGTTCAC 21 184 1 CTTCAGGCAC 0.96689 -117 AAACTCCCGCCTTCTGGCGGGAGTTGCTATT 23 65 1 CTTCTGGCGG 0.93055 -45 CGTAAAGCAGGCATCTGATGTGTCA 24 5 1 AAGCAGGCAC 0.658275 -134 AATGCACTACCGGCAGGCATCTGACTTTCCG 24 66 0 CGGCAGGCAC 0.866622 -73 CATTGCATGTCATCAGGCATCGACTCGA 31 8 0 CATCAGGCAC 0.895249 -85 ACATGCAATGATTCAGGCATCTATAGTGAGG 31 29 1 ATTCAGGCAC 0.835484 -64 CAGGGGGCATCCGCCGGCAGCTAAGTTAAGG 33 248 1 CCGCCGGCAC 0.769439 -29 ATGATTTCTCCTGCAGGTGTGACGCCTCCGC 34 235 0 CTGCAGGTGG 0.781907 -23 AAACGATTACCTTCAGGCTACGCAAGGCTTT 40 106 1 CTTCAGGCTC 0.771816 -195 GTTAGCCAAAAAGCAGGCAGGAC 44 89 1 AAGCAGGCAG 0.681116 -13 GCGTTTTTATCTGCAGGCGGGAAATAGAGCG 53 147 0 CTGCAGGCGG 0.977543 -154 GCTTTATTACCTTCAGGTAAGGCTTCGCCAC 58 232 1 CTTCAGGTAG 0.72729 -69 ACAGAAATGTCTTCAGGCGTGGCGAAGCCTT 58 250 0 CTTCAGGCGG 0.971086 -51 GTATCCATTGCTTCTGGCAACATTAAGTCTC 60 65 1 CTTCTGGCAC 0.92095 -41 ********* * Masking position 6 Map Score: 16.4204 Number of sites scoring better than the average of aligned sites = 1872 Number in coding regions = 1687 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 4 AAATTTCTTTTTGCTACGCCGTGTTTTCAATAT 1 158 1 TTGCCGCCTG 0.965693 -143 GGCTGCATTTTGGCCCTGCCGCTGACAGGGAGC 2 24 1 TGGCTGCCCT 0.933935 -27 TTGTAGCGATGCCTTTTGCATCGTAT 7 4 1 TAGCTGCCTT 0.721753 -50 CTGGCTTAAATGGCCATGCGGTGAGTTTTTTTC 16 36 1 TGGCTGCGTG 0.86147 -265 GCGCCGCAGATTGCATCGCCATTTTTGTAAAAC 26 51 0 TTGCCGCCTT 0.93208 -250 TCGGTGATGCTGGATTTGCCCTGAACGTCTAAG 26 274 0 TGGATGCCTG 0.79673 -27 TTATTGTAATTGCCGCTGCCTTTCATCAGCAGA 34 114 0 TGCCTGCCTT 0.904402 -144 GCAGGTGTGACGCCTCCGCCCTGCGTGGGGGCA 34 221 0 CGCCCGCCTG 0.808932 -37 GCAGAGCCAGTGGCCCTGCCCTTATCAGTTA 35 9 0 TGGCTGCCTT 0.973083 -61 GCAGGGCCACTGGCTCTGCCCTTTTGCTATTCT 35 23 1 TGGCTGCCTT 0.973083 -47 ATTTGCCTATGCCTTGTACTCGTCAT 37 67 0 TGCCTGCCTG 0.950993 -16 AGCAAAGCTGTTTCTGCGCCCTGTCAGCGCCCA 41 15 1 TTTCCGCCTG 0.649621 -286 CTACGTCACATGGCCGCGCCGTGTATAATAAGC 50 185 1 TGGCCGCCTG 0.991683 -67 TGGCACCGCCGCGTAAAAATAGG 54 71 0 TGGCCGCCCG 0.979004 -13 TCCTTATTATTTGCGGCGCTTTTTTCACTTACC 58 75 1 TTGCCGCTTT 0.437092 -226 CCTTCAGGTAAGGCTTCGCCACGCCTGAAGACA 58 241 1 AGGCCGCCCG 0.810193 -60 **** **** ** Masking position 8 Map Score: 15.2938 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 693 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 GGAGTTTACGGAGCTGAGGAAAAGCTTGTCAAGCC 6 227 0 GGAGGAAAGC 0.963143 -74 ATGAAGATAAGTTGTGCGGAAAAGTGCTTAAGAAA 10 129 0 GTCGGAAAGT 0.965449 -27 ACTTGACAACTGTGTGAGGAAAAGCGTATTTGCGC 15 49 0 TTAGGAAAGC 0.811494 -129 TTAGATAATTGCTATCCGGAAAAGCATCTGCTATT 15 91 1 GTCGGAAAGC 0.989791 -87 TCGATAGTGCGTGTTAAGGAGAAGCAAC 15 160 1 GGAGGAAAGC 0.963143 -18 ACCAGGAGCCGGGTAACGGAGAAGCGAG 22 4 0 GGCGGAAAGC 0.990581 -163 TTTTACTCATTCTCCACGGAGATGCCGTTTTGTAT 22 82 1 TTCGGAATGC 0.709754 -85 TGAGACGAGAGTTAACCGGACAAGTGTGCCATAAT 39 58 0 GTCGGAAAGT 0.965449 -41 AACCGCCGTAGAGTACCGGAAAGGCTGTTTTTTCG 41 255 0 GGCGGAAGGC 0.956523 -46 GTAAAAATAGGTTGGGCGGAGAAGCGCAACGCCCT 54 47 0 GTCGGAAAGC 0.991189 -37 GAAAAGACGGGCTTACCGGAAAAGTTTTAATCTCC 58 148 0 GTCGGAAAGT 0.964404 -153 * * **** **** Masking position 10 Map Score: 12.1577 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 77 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 AACGCCCTCTATTCACCCGAAACAAAAATG 1 29 0 ATTCACCCGA 0.737695 -272 GTAGTCATATATTCACGCGGCTTATAGTCA 4 48 0 ATTCACGCGG 0.977048 -60 ACAAAGGCGTAATCACGCGGGCTACCT 4 91 1 AATCACGCGG 0.977048 -17 CTTACGAGCCAATCTCCCAGGCT 22 154 1 AATCTCCCAG 0.686546 -13 ACGTTAACAAAGTCACGCGGAAAGTCAGAT 24 49 1 AGTCACGCGG 0.939634 -90 TATCTATTTGATTCACCCAGGGGGAAAACT 26 174 1 ATTCACCCAG 0.846126 -127 CCTGCATGATATTCACGGGGAATAGCGTTA 31 73 1 ATTCACGGGG 0.846445 -20 AGTGTGCCATAATCTCGCGGCCAGGCATAC 39 41 0 AATCTCGCGG 0.944309 -58 TTTCGTCTGAAATCTCCCGG 46 1 0 AATCTCCCGG 0.934284 -99 ACTTTTAGTAATTCACCTGGGATGGACCAT 53 252 0 ATTCACCTGG 0.757186 -49 TTACTCCAATCACGCGGGTACAGAAAC 53 284 0 AATCACGCGG 0.977048 -17 ********** Masking position 1 Map Score: 10.4945 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 153 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 AACATCTGACTTTCAATATTGGTGATCCATA 1 115 1 TTTCATATTG 0.971365 -186 AAAAAGAAATTTTCAATATTGTTTTATGGAT 1 139 0 TTTCATATTG 0.971365 -162 TACGCCGTGTTTTCAATATTGGTGAGGAACT 1 172 1 TTTCATATTG 0.971365 -129 TAAATCCAACTTTCAATATTGTTAAGTTCCT 1 196 0 TTTCATATTG 0.971365 -105 CGTGTGACATTTTCAATATTGGTGATTAAAG 1 231 1 TTTCATATTG 0.971365 -70 TTACTGTGGTTTTCAGTAATGGGCGGCAATT 27 22 1 TTTCATAATG 0.875661 -101 TAAACACGTTTTTCATTATGGATTGCCTGTA 53 59 0 TTTCATATGG 0.912571 -242 ***** ***** Masking position 5 Map Score: 7.41512 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 20 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ATATTGATTCAGAAAAGAGAGAAATCTGAAC 4 14 0 AGAAAAAGAG 0.623876 -94 AATAGCTGTAAGAAAAAATCCCTCATCGTCA 6 100 0 AGAAAAATCC 0.552375 -201 TATAAAATTCAAAAAAAAACGACTGGTTCAC 10 69 0 AAAAAAAACG 0.755197 -87 AAAGTGCTTAAGAAAACAGCGTTCGCACCGT 10 113 0 AGAAAAAGCG 0.970969 -43 ATTCAGGACAAAAAAATAGCGGCTAATCATA 13 13 0 AAAAAAAGCG 0.948814 -80 CTTGCGGCAAAAATTAGCGACTCGGGTAA 13 74 0 AAAAATAGCG 0.598205 -19 ATGGTAAGCGAGAAAAATGCGCTATAGATTT 18 16 0 AGAAAATGCG 0.834614 -78 TGAGTCATGCAGAAAAAAACGGGTTCAGCTT 21 95 0 AGAAAAAACG 0.847707 -206 TGATGGAATTAAAAAAGTGCCCTACTATAGC 24 98 0 AAAAAATGCC 0.470466 -41 TGCATCTTATAAAAAATAGCCCTGCAATGTA 40 239 0 AAAAAAAGCC 0.854828 -62 AGATAATGCGAAAAAACAGCCTTTCCGGTAC 41 247 1 AAAAAAAGCC 0.854828 -54 TTTCGCTGAAAGAGAACAGCGATTGAAATGC 42 108 0 AGAGAAAGCG 0.799259 -43 ACAACTGTGTTAAAAACAGCGTCAGGATACT 46 53 0 TAAAAAAGCG 0.810879 -47 TCCGCTTACGAAAAAATAACGAATTCAAGGA 48 114 1 AAAAAAAACG 0.755197 -27 CATTAGACTTAGAAAATATCGGGTCGTAACG 52 13 0 AGAAAAATCG 0.795276 -162 GCGCAGGCGCTGAAAATAGCGCCTGTTTTTA 56 91 1 TGAAAAAGCG 0.885536 -36 CTCCGGTAAGTGAAAAAAGCGCCGCAAATAA 58 81 0 TGAAAAAGCG 0.885536 -220 ****** **** Masking position 5 Map Score: 12.9834 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 532 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 9 AGGCGCAGAATCCTGCGCCTTTTACTTCAACAGTTAGC 12 13 0 TCCCCTACTC 0.961422 -47 CCGCATCTCGCCCAGCCGCTCCGACTTCTATACTGAAT 21 247 1 CCCCCGACTC 0.985682 -54 AAAATTCTTGTCCGCCAGCTCGGTCTTCAGCCTTACGA 22 123 1 TCCCCGTCTC 0.975721 -44 AAGTGTAATTTCCGTCCCCATATACTAAGCATCAGTAA 23 26 1 TCCCCTACTA 0.846187 -84 TATCATCCCACCCCGCGCCGCAGATTGCATCGCCATTT 26 60 0 CCCCCGATTC 0.956904 -241 TCAGGGCAAATCCAGCATCACCGACTGC 26 283 1 TCCCCGACTC 0.994456 -18 GCTGCCTCTTCGTTGACTGCCTTCGCTCAT 32 98 0 TGCCCGACTC 0.974703 -20 ATTTTCAGGAAGCGTCCTCGCAGACTCCGTTTTTGCCA 50 63 0 AGCCCGACTC 0.844329 -189 ATCGTTTTTATCCGGCACCGTGGATTGCGTTTGCGTCT 53 201 0 TCCCCGATTC 0.982993 -100 AAATCTGGAATCCAGCATCCAGGATTACCCTCTCAGAG 56 31 1 TCCCCGATTC 0.983009 -96 CCCACGCCTCTCCCTCGACGGAGATTAAAACTTTTCCG 58 129 1 TCCCCGATTA 0.927378 -172 AAGGAGTCCCTCCGCACTGTCTGAAACAGTACAG 58 277 0 TCCCCGTCTA 0.898694 -24 *** * * **** * Masking position 16 Map Score: 13.0168 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 148 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TGGTTTGATACGTAACGCCGCACTGACTCT 3 14 1 CGTAACGCCG 0.966451 -43 GGGAATAAGGGGTGAGGCTGGC 6 289 1 GGTGAGGCTG 0.951082 -12 GTGCCTGTCGCCTGAGGCCGTAATCATCGT 8 25 0 CCTGAGGCCG 0.923793 -36 GAGATTGGCTCGTAAGGCTGAAGACCGAGC 22 140 0 CGTAAGGCTG 0.965902 -27 TATTTAATTACGTTACGCCGGAGCTGAC 23 92 1 CGTTACGCCG 0.819534 -18 GCAGTCGGTGATGCTGGATTTGCCCT 26 285 0 GGTGATGCTG 0.655887 -16 TTGCGAGCGGCGTAAAGCCGCCGCTATACT 29 18 1 CGTAAAGCCG 0.816734 -63 GTGACATACAGCTAACGCTGCGACTTGGTC 33 208 1 GCTAACGCTG 0.75985 -69 GATTATTGTGCGTGAGGCGGCGCACATAAT 34 166 0 CGTGAGGCGG 0.884616 -92 GTAGAGTACCGGAAAGGCTGTTTTTTCGCA 41 253 0 GGAAAGGCTG 0.63592 -48 TATAGAGTATCCTGACGCTGTTTTTAACAC 46 48 1 CCTGACGCTG 0.827192 -52 GACCGCAGCCCGTCAGGCTGAAGAGAGTAA 53 108 0 CGTCAGGCTG 0.868739 -193 AAACTTTTCCGGTAAGCCCGTCTTTTCACG 58 156 1 GGTAAGCCCG 0.719714 -145 TTACGCATCCGGTAACGCCGTGAAAAGACG 58 174 0 GGTAACGCCG 0.950988 -127 TTACCGGATGCGTAAGGCCGTGACGTTTTA 58 189 1 CGTAAGGCCG 0.978476 -112 ********** Masking position 5 Map Score: 12.6221 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 547 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 GGCAGGGCCAAAATGCAGCCCTGCCAGAGT 2 14 0 AAATGCAGCC 0.827219 -37 CGATAAAAAAAATTGTCGCCACTATACGTA 5 162 0 AATTGTCGCC 0.938083 -30 ATATGTCCTAAAATGCCGCTCGCGTCGCAA 6 18 1 AAATGCCGCT 0.847587 -283 ATTTCGGGACAATTGTCGCCGAATCGGCTT 26 110 0 AATTGTCGCC 0.938083 -191 AAAACGTTACAATTGCCGCCCATTACTGAA 27 33 0 AATTGCCGCC 0.98717 -90 AATACGGATAAATTGCAGCGCGCATTATGA 30 72 0 AATTGCAGCG 0.744418 -31 GAGTTCACTCAGTTGCCGCCTCGATGCAAC 32 39 0 AGTTGCCGCC 0.947303 -79 TTTCCAGTATAATAGCCGCCTTTTTTCATT 33 173 1 AATAGCCGCC 0.923833 -104 TAATTATTGTAATTGCCGCTGCCTTTCATC 34 120 0 AATTGCCGCT 0.946231 -138 ********** Masking position 1 Map Score: 7.39347 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 562 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 12 AAACGTGATGGAACGGCTGTAA 14 1 0 GAGGCTGTAA 0.812178 -36 CCACTTTATATCGGGCCTGAAATCAGACTCTA 33 95 0 TCGCCTGAAA 0.742061 -182 CTACGTTGGCTACAGCCTGAAATGTTCCGAGC 37 21 0 TAGCCTGAAA 0.932409 -62 CCAACGTAGTTACAGCCTGAAAGATGACGAGT 37 44 1 TAGCCTGAAA 0.932409 -39 TGTCCAACAGGACCGCCTATAAAGGCCAAAAA 40 14 0 GAGCCTATAA 0.766017 -287 CGCACCTTTGGAGCGCCTGAAACCTGCGGCGC 42 76 1 GAGCCTGAAA 0.979956 -75 ATTTGAATGTGACCGCGTGTAAGCCGCTAACC 52 104 0 GAGCGTGTAA 0.812178 -71 TTTCATTATGGATTGCCTGTAAAGTTCATCGC 53 48 0 GAGCCTGTAA 0.970926 -253 GTAATACAGTGAGTGCCTTAAACACGTTTTTC 53 76 0 GAGCCTTAAA 0.827377 -225 CCCGATTGCCTGAAATAAAAACAGG 56 112 0 GAGCCTGAAA 0.979956 -15 ** ******** Masking position 8 Map Score: 6.09305 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 191 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 GATTACGCCTTTGTTTTCCCACAAAGTGTAGTCATATA 4 67 0 TTTTTCCCAG 0.963774 -41 AGCCGCTATTTTTTTGTCCTGAATGATGTTTGACACTA 13 20 1 TTTTTCCAAG 0.963111 -73 AGCGGCCTCATTTTTCCCCCGAACATGGGGATCGATAG 15 129 1 TTTTCCCAAG 0.817585 -49 GTCTGTATTTCCTTATCCAAAGTATGGAGAAGTTAAC 16 274 0 TCTTTCCAGG 0.80755 -27 CATACTTTGCTTATTCTCCTTCGCCTAAAGGAACGTTT 19 37 1 TTTTTCCCGA 0.641014 -28 ATCGTCAAAATTCTTCGCCACCAGTCAGCACTGCCATA 21 126 1 TTTTGCCCAG 0.820376 -175 CAGGATAAAATTCTTGTCCGCCAGCTCGGTCTTCAGCC 22 117 1 TTTTTCCCAG 0.963774 -50 CTCCAGGATTTTGTTATCGACAAAATTGATGACCTCAA 26 218 1 TTTTTCGAAG 0.735205 -83 CTTTTTATCCTCAAAATGGCTAACAGATT 29 62 0 TTTTTCCAAG 0.963111 -19 TTCGACCACTTTTTTATCCAAAGTTTCGGGCTGTTATG 36 26 1 TTTTTCCAGG 0.963774 -130 TGCAAGCTCTTTATTCTCCAAAGCCTTGCGTAGCCTGA 40 118 0 TTTTTCCAGG 0.963774 -183 CGGCGGTGCGTTTTTATCTGCAGGCGGGAAATAGAGCG 53 147 0 TTTTTCTAGG 0.65623 -154 GGCGCGATCGTTTTTATCCGGCACCGTGGATTGCGTTT 53 207 0 TTTTTCCCAG 0.963774 -94 ** ** *** ** * Masking position 5 Map Score: 6.45509 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 71 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 CAAAATGCAGCCCTGCCAGAGTGGA 2 6 0 CCCTGCCAGA 0.85891 -45 TTGGCCCTGCCGCTGACAGGGAGCTCTT 2 33 1 CGCTGACAGG 0.938661 -18 TGGCACTCTCTCCGGCCAGGTGAACCAGTC 10 50 1 TCCGGCCAGG 0.716255 -106 AGAAGAATATCCCTGACAATGGTGTTTTAA 20 28 1 CCCTGACAAT 0.683794 -38 AGGGGAGTTACCCGACCAGGAGCCGGGTAA 22 23 0 CCCGACCAGG 0.717063 -144 AACAAAGTCACGCGGAAAGTCAGATGCCTG 24 54 1 CGCGGAAAGT 0.648986 -85 GAGTGCTTTACCCTGCAAGTTTTCCCCCTG 26 191 0 CCCTGCAAGT 0.889199 -110 GAACCTGGTTCGATGCCAGTTTTATCTTTG 36 119 0 CGATGCCAGT 0.628165 -37 TAGCAAAGCTCCCTGCCAATGTTACAGCAG 38 28 0 CCCTGCCAAT 0.871313 -38 GCCATAATCTCGCGGCCAGGCATACTTGCG 39 36 0 CGCGGCCAGG 0.974998 -63 TAAAAAATAGCCCTGCAATGTAAATGGTTC 40 231 0 CCCTGCAATG 0.641543 -70 GTTTTATGGGCGCTGACAGGGCGCAGAAAC 41 24 0 CGCTGACAGG 0.938661 -277 AATAAGCATACCCTGCCAGTTATGGTGTTG 48 37 1 CCCTGCCAGT 0.971399 -104 TTATACACGGCGCGGCCATGTGACGTAGCC 50 183 0 CGCGGCCATG 0.845382 -69 CTCGCGCAGGCGCTGAAAATAGCGCCTGTT 56 88 1 CGCTGAAAAT 0.309472 -39 ********** Masking position 8 Map Score: 8.22167 Number of sites scoring better than the average of aligned sites = 1752 Number in coding regions = 1658 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 15 TTGTTTCATTGTAATGCGGCGAGTCCAGGGA 5 54 1 GTAATGGGCG 0.885024 -138 TACGCTTTACGTATAGTGGCGACAATTTTTT 5 155 1 GTATAGGGCG 0.973738 -37 TATTAACTCCGCAACGCGGGGCGTTTGAGAT 11 35 1 GCAACGGGGG 0.81098 -27 TGTTGTTTTAGTATAGCGGCGGCTTTACGCC 29 26 0 GTATAGGGCG 0.973738 -55 TGTCGATGCAGTAAAGATGCGGGCGCGATGA 30 30 0 GTAAAGTGCG 0.865039 -73 CATTCGCGTTGCATCGAGGCGGCAACTGAGT 32 32 1 GCATCGGGCG 0.970703 -86 CACCTTTATAGCAAACTGGCGTAGAGTCTGA 33 74 1 GCAAACGGCG 0.914831 -203 ATATAAAGTGGTAACGAGGCGTTCCAGCGCG 33 116 1 GTAACGGGCG 0.968337 -161 TCGCGGCCAGGCATACTTGCGAAGATTTCAG 39 26 0 GCATACTGCG 0.649966 -73 CTTGCTTCCAGTTTAGTGGCGAGGGTGGACG 48 72 0 GTTTAGGGCG 0.839153 -69 ****** **** Masking position 9 Map Score: 4.50854 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 473 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357