AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_bsub_reg_300.orf -o00130_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 metS 300 methionyl-tRNA synthetase #2 yabD 78 similar to hypothetical proteins #3 yabE 155 similar to hypothetical proteins #4 yabF 144 similar to hypothetical proteins #5 spoIIE 300 serine phosphatase #6 yabS 84 similar to hypothetical proteins #7 yabT 88 yabT #8 yacA 103 similar to cell-cycle protein #9 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #10 yacB 194 similar to hypothetical proteins #11 yacC 85 similar to hypothetical proteins #12 yacD 46 similar to protein secretion PrsA homolog #13 cysK 75 cysteine synthetase A #14 pabB 166 para-aminobenzoate synthase (subunit A) #15 ndhF 300 NADH dehydrogenase (subunit 5) #16 yclB 89 similar to phenylacrylic acid decarboxylase #17 yerQ 300 similar to hypothetical proteins #18 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #19 yhfI 151 similar to hypothetical proteins #20 yisP 300 alternate gene name: yucD; similar to phytoene synthase #21 trpE 215 anthranilate synthase #22 aroB 61 3-dehydroquinate synthase #23 aroF 69 chorismate synthase #24 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #25 ndk 115 nucleoside diphosphate kinase #26 gerCA 162 heptaprenyl diphosphate synthase component I #27 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #28 mtrA 187 GTP cyclohydrolase I #29 hbs 300 non-specific DNA-binding protein HBsu #30 dnaG 33 DNA primase #31 yqxD 157 alternate gene name: yqfM; similar to hypothetical proteins #32 yqfL 25 similar to hypothetical proteins #33 yqzB 132 similar to hypothetical proteins #34 glyQ 296 glycyl-tRNA synthetase (alpha subunit) #35 yqxN 300 alternate gene name: yqfI; similar to hypothetical proteins #36 yqeT 24 similar to ribosomal protein L11 methyltransferase #37 dnaJ 199 heat-shock protein #38 dnaK 23 class I heat-shock protein (chaperonin) #39 grpE 71 heat-shock protein #40 hrcA 119 transcriptional regulator #41 hemN 52 coproporphyrinogen III oxidase #42 lepA 133 GTP-binding protein #43 spoIIP 62 spoIIP #44 gpr 203 spore protease #45 aadK 300 aminoglycoside 6-adenylyltransferase #46 yrhE 300 similar to formate dehydrogenase #47 yteU 21 similar to hypothetical proteins from B. subtilis #48 yteQ 94 similar to sugar transport protein #49 yteP 215 similar to hypothetical proteins from B. subtilis #50 menE 90 O-succinylbenzoic acid-CoA ligase #51 menB 34 dihydroxynapthoic acid synthetase #52 menF 288 menaquinone-specific isochorismate synthase #53 yufT 300 similar to NADH dehydrogenase #54 dhbB 27 isochorismatase #55 dhbE 28 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E) #56 dhbC 25 isochorismate synthase #57 dhbA 193 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase #58 yuiI 138 yuiI #59 yuiH 100 similar to sulfite oxidase #60 ywaB_dltA 600 ywaB: alternate gene name: ipa-6d; similar to quinone biosynthesis, dltA: D-alanyl-D-alanine carrier protein ligase (Dcl) Motif number 1 CCTTTGGGCGGGAGCTTTTTGACATTCTGAT 1 266 1 GGGCTTTTTG 0.791616 -35 TTTTGCGCCCTCTGTTTTTTTCGTTATAATA 4 34 1 TCGTTTTTTT 0.610205 -111 TCTTGCAGAAGCCGATTTTTTTCATTTTTAG 5 130 1 GCGATTTTTT 0.802618 -171 GCGTCAGCCGGCAGTTTTTTTAGAAAGAAAG 10 15 0 GCGTTTTTTT 0.959066 -180 GCTGACGCTGGCAGTTTTTTTATGTAAATGA 10 38 1 GCGTTTTTTT 0.959066 -157 CACTTCCTACGCGGTTTCTTTCATAAATCAA 11 49 0 GCGTTTCTTT 0.857229 -37 CGGTTCGCCGGGAGTTTTTTTATATTTCGTG 14 27 1 GGGTTTTTTT 0.955571 -140 TTTGAAGTTGTCGGCTTTTTTGTTGGAAAAA 15 181 1 TCGCTTTTTT 0.611144 -120 ATGATAAGGAGGCGCTTTCTT 16 1 0 GGGCTTTCTT 0.884319 -89 CAGCTGAAAAGCTGATTTTTTTATTGAAACA 24 152 1 GCGATTTTTT 0.802618 -85 TCCCAGTCTCGCTGTCTTTTTGTCCTAGTAT 24 208 0 GCGTCTTTTT 0.915509 -29 CCCTTAGAAAGGGGCTTTTCTGTGAAGAAAT 28 54 0 GGGCTTTTCT 0.783576 -134 TCCTCAGAGTGCAGTTTTTCTTAAAAAGCCG 29 159 1 GCGTTTTTCT 0.797102 -142 CATAGAGACGGGAGTTTTTTGGTTGCTGCCG 34 240 1 GGGTTTTTTG 0.790964 -57 TGAAGTTTTTGGCGCTTTTTTTGGGTGAGTT 40 15 1 GGGCTTTTTT 0.955738 -105 GTCTTGTACTGCGGCTTCTTTCTGTAAAGAA 41 22 1 GCGCTTCTTT 0.857711 -31 ACAGGGGCCTCCTTCACATTAAGT 44 190 0 GGGCCTCCTT 0.475338 -14 TTCTAATATCGGTGTCTTTTTTTCAGGTGGA 49 77 1 GGGTCTTTTT 0.908649 -139 TGCGGTCCAAGCTGTTTTCTTTTCAATACAG 50 46 1 GCGTTTTCTT 0.892413 -45 TCAAGGCGCAGCAGTCTTTTTCGCTGGATGT 57 136 1 GCGTCTTTTT 0.915509 -58 ATTTGATCAAGGTGCCTTTTTTATTCGGGAA 58 85 1 GGGCCTTTTT 0.908976 -54 ACCGCAAGAAGGCGTTTTCTTTCTTATTATA 60 469 0 GGGTTTTCTT 0.883915 -132 GGAAGCAAAAGGAGTTTTTTATTAAGCTGCC 60 538 1 GGGTTTTTTA 0.581108 -63 ** ******** Masking position 7 Map Score: 20.8708 Number of sites scoring better than the average of aligned sites = 943 Number in coding regions = 662 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 2 TCGTATATAATCAAATGAAATAAAAAACTTTGGTTCG 1 56 0 TAAAAAAAAA 0.952159 -245 ATTAAAAATCTTTAATGAAAATAAAAAAAGTCTGTTC 1 106 0 TTAAAAAAAA 0.801551 -195 CGGAATGTTGTCTAAAAATGAAAAAAATCGGCTTCTG 5 135 0 TTAAAAAAAA 0.801551 -166 TAGGATTTTGTCAAAAGAAGGTAACAATACCAAAGAA 5 218 0 TAAAAAACAA 0.856821 -83 GCTTTACAATTAAAAACAAGTAAAAAAGAAAATAGAG 14 129 1 TAAAAAAAAA 0.952159 -38 TTAAAGGAAATGAAAACATAGCATAAAGTAAAGACCA 15 50 1 TAAAAATAAA 0.791916 -251 TACTATGAGTTAAAAAAATCGCAACAAAATGTACATA 17 215 0 TAAAAAACAA 0.856821 -86 TCAATCACGCTGAAAAGATGACAAAATCCTAAAACGA 18 64 0 TAAAAAAAAT 0.574504 -192 GTAAACCTTTACAAAACAGAACAAAAACCGGCGGCGT 24 48 0 AAAAAAAAAA 0.791916 -189 GGATGAAAAAAGGAAAAAAAGGAATATTCG 29 4 1 TAAAAAAAAA 0.952159 -297 GTAAATATCTTGTAATCAAACAAAAAACTTATAAATG 33 56 0 TTAAAAAAAA 0.801551 -77 ATATTTAATAATAAATGATCATATAAAAAGATGGACC 34 16 0 AAAAAATAAA 0.421206 -281 TATCTTCTTTTTAAAGAACTGGAAAAAGAGAACATGG 35 182 1 TAAAAAAAAA 0.952159 -119 TTGCCCGGGATAAAAGGAATTGAAAAATCATAATTCA 37 125 1 TAAAAAAAAA 0.952159 -75 AACAAAAGTATCAAACCACAAGAAAAATGTCAATTAT 40 46 0 TAAAAAAAAA 0.952159 -74 CATTTGCTGAATAAATCATGCTAAAAAGAGAACCTTC 44 139 0 AAAAAAAAAA 0.791916 -65 CCATCTTTCTTTCAAGAAGTCAAAAAAAGCCATGTAT 46 260 0 TCAAAAAAAA 0.703198 -41 TATTTTGAGGTCAAAAGAACTCATAAAAATCCATTAC 53 73 1 TAAAAATAAA 0.791916 -228 AAGGGAATGATAAAAGCAAATAAAAAAGGCGATAAAA 53 252 0 TAAAAAAAAA 0.952159 -49 CAACATGATTTTAAATTAGGTTAACAAAAAGGAGGCC 59 71 1 TAAAAAACAA 0.856821 -30 * *** * ***** Masking position 8 Map Score: 16.9933 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 162 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 CTTGAAACCTCCTAATCAGAATGTCAAA 1 283 0 GACCTCCTCA 0.748919 -18 TATTTCCTCCAAGACAAAATAAAAAC 4 129 0 ATCCTCCACA 0.914769 -16 GATCCCCTCCGCCGCTACCATATTTG 5 2 1 ATCCTCCGCT 0.844504 -299 TAACACTTTCAACCCCTCCAAGCAAAGAAGAAGCA 8 33 0 AACCTCCAAA 0.811383 -71 AATGTCCTCCTCACAATGAGCAGGTA 8 88 0 ATCCTCCTAA 0.919751 -16 TACTAAACCTCCTATACACTTCCTACGC 11 68 0 TACCTCCTCA 0.874007 -18 AAGAAAGCGCCTCCTTATCATACCTTTTAG 16 6 1 AGCCTCCTCA 0.94287 -84 TCAAAAAAATTGGTCCTCCTTCAATATACCCATTT 19 110 0 TGCCTCCTAT 0.874911 -42 AATGTCCTCCTATCTTTTCAAAAAAA 19 136 0 ATCCTCCTTT 0.849364 -16 GTTCTATGTCCTCCACCAATGAATACATTT 28 168 0 ATCCTCCAAT 0.886783 -20 GCCTTTCACCTCCTCCCAAAAGGATACAT 29 282 0 TTCCTCCTAA 0.869378 -19 TTCAAGCACCTCCACTTTTCTTTCATAAG 34 278 0 AGCCTCCATT 0.745151 -19 TCTTGACCAGATGTCCTCCATTTCATGTTAAACAA 35 37 0 ATCCTCCACA 0.914769 -264 TTGAATAACCTCCTGCTATGTAA 38 5 0 ATCCTCCTAT 0.930977 -19 TGAATCCCTCCAGCGCTTGTCTAGTAA 43 46 0 AACCTCCACT 0.890873 -17 GTGTTTCACCTCCTAAGATACAACCTGTA 44 5 1 TTCCTCCTAT 0.886783 -199 ACAGGGGCCTCCTTCACATTAAGTACCT 44 186 0 GGCCTCCTCA 0.804726 -18 TACATGTTCCTCCGTTTCAGCCTTAATAT 45 282 0 TGCCTCCGCA 0.705286 -19 ATTCATATTCCCCTCCATCTTTCTTTCAAGAA 46 279 0 TTCCTCCATT 0.655346 -22 ATGATGACCTCCTTTTATTCTCTATGTG 51 17 0 ATCCTCCTAT 0.930977 -18 CCATAAAAGGAAAACCTCCTATATTCCTCCACCCG 52 82 0 AACCTCCTTT 0.784684 -207 CTGCAAAGATAAGACCTCCTTTTCTCGTTCTCAAT 53 201 0 AACCTCCTCT 0.93359 -100 GTTGTATCCCTCCAGCAATTCATTCTGT 55 10 0 TACCTCCAAT 0.746182 -19 TCTCATGAACCTCCTTTAAATTCAG 56 6 0 TGCCTCCTAA 0.855976 -20 ** ****** ** Masking position 7 Map Score: 17.7288 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 223 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 4 GTCCCTTACAGCGTTTTTCTATAAAAGTTCTACA 3 42 1 GCTTTTTCTA 0.73406 -114 TTCGCTTTCTTTCTAAAAAAACTGCCGG 10 5 1 CTTCTTTCTA 0.750858 -190 CTGCTTTCAGCCCCTTTTCTCAAATTAAAAACCC 12 21 0 CCCTTTTCTA 0.933944 -26 TTATTTATCTCTATTTTTTTCCAACAAAAAAGCC 15 193 0 CTTTTTTTTA 0.327657 -108 TCTAAATTCTCCCTTTTTTAAAACTCATTATT 15 279 0 CTCCTTTTTA 0.716687 -22 TTCAATATACCCATTTTTCTTGAAAAAAGCATGT 19 92 0 CCTTTTTCTA 0.871358 -60 CGAAATCGTAACATCTTTCTGATAATTAATCAAT 25 45 0 ACTCTTTCTA 0.610896 -71 TCACAGAAAAGCCCCTTTCTAAGGGGCTTTTCAT 28 60 1 GCCCTTTCTG 0.785947 -128 AAACGCAAGTACTTCTTTCTCTCACTGCAACATA 34 50 0 ACTCTTTCTA 0.610896 -247 AAAATCCCAGCCTCTTTTTTAAAATTGCTCAAGA 34 144 0 CCCTTTTTTA 0.850423 -153 TCAAGCACCTCCACTTTTCTTTCATAAGTTGACT 34 272 0 CCCTTTTCTA 0.933944 -25 CACAAGAAACCCACCTTTCTGTAGTTAAACTAGC 35 100 0 CCCCTTTCTG 0.900103 -201 GAAGTTTTTGGCGCTTTTTTTGGGTGAGTTATAA 40 16 1 GCCTTTTTTG 0.372542 -104 TTGTACTGCGGCTTCTTTCTGTAAAGAAGGTGAA 41 25 1 GCTCTTTCTA 0.872841 -28 ATATCGTTTTCCTTCTTTTTGTCAATCTCTCATA 45 13 1 CCTCTTTTTA 0.871358 -288 ATATTCCCCTCCATCTTTCTTTCAAGAAGTCAAA 46 273 0 CCTCTTTCTA 0.94396 -28 GGCGCCCCCTCCTTTTTTGCA 47 1 0 CCCCTTTTTA 0.933944 -21 TCTAATATCGGTGTCTTTTTTTCAGGTGGACCGG 49 78 1 GTTCTTTTTA 0.330592 -138 TTTTTCCTAGCCTCCTTTCACGGATTCTTGCATT 49 192 0 CCCCTTTCAA 0.673686 -24 ATACAAATAACCTCTTTTTTGTTAGACTTATTTT 53 45 1 CCCTTTTTTA 0.850423 -256 AAATTATATCGCACTTTTCTGCAAGCTGCCACGC 53 121 0 GCCTTTTCTA 0.852106 -180 ATGGGCCTCCTTTTTGTTAACCTAATTTA 59 82 0 CCCCTTTTTA 0.933944 -19 CTTCCTCTTCCTTTCTATTAAAAGGCTTAC 60 581 0 CTCCTTTCTA 0.86284 -20 ** ******* * Masking position 7 Map Score: 17.1913 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 509 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 5 CGTTGCCTGTCATTATAGCGAAAGCACAGATAGG 5 251 0 CTTTAGGAAG 0.660619 -50 GAATGTTATTCTTGGAAGAGAAATTCACTTTTTT 14 82 1 CTGAAGGAAT 0.629924 -85 CCCTTGTAGTCTAGGAAGGGGGAGCATTGGAGCG 17 92 0 CAGAAGGGAG 0.909138 -209 CCTTTGAAGTCTAGGAAGGGCGAGCATCGGAGCA 18 104 1 CAGAAGGGAG 0.909138 -152 AATGAAATCACTACAAAGGGGAAAGAGGGA 19 7 0 CACAAGGAAA 0.686143 -145 AGCGTTAATGCGATGAAGGGAGAAGAAGTC 23 50 1 CATAAGGGAA 0.567559 -20 AAAATGAGAGCAAGTAAGAGAAAGACAATTAAAC 29 189 0 CAGAAGGAAG 0.96714 -112 TACGAATAAACTATTATGGGTAAG 31 144 1 CATATGGAAG 0.612715 -14 CTTTACATAGCTATGAAGTGAAAAGGTG 33 115 1 CATAAGGAAA 0.794266 -18 CTTGGCCGCTCCTGCTTGAGGAAGGTGCGGAA 35 279 1 CTGTTGGAAG 0.420758 -22 TGTTCACCTCCCTCAAAGTGTAAGGAGAAGGACA 39 46 0 CTCAAGGAAG 0.836023 -26 GTACGTGAAAGAGAAAAGCAACCCAGA 42 4 1 CTGAAGGAAA 0.891291 -130 CAATGTAAAACAAGAAAGAGAAAAGTTCCCTATC 42 41 0 CAGAAGGAAA 0.910492 -93 ACTCTATGAACAAGCTAGAGGAAGTAGAACTGT 43 10 0 CAGTAGGAAG 0.864189 -53 GAATACATCACATTCAAGAGTAAAAAAATCTATA 45 231 1 CTTAAGGAAA 0.756794 -70 AATCTTTATACCTGCAAGGGCAAGAATGGAATGT 60 289 1 CTGAAGGAAG 0.95955 -312 TGTACCTGTTCGTTCAAGTGAAAGCAGAAACCTA 60 414 1 CTTAAGGAAG 0.900008 -187 CTTTTAATAGAAAGGAAGAGGAAG 60 587 1 AAGAAGGAAG 0.578895 -14 * ** *** * *** Masking position 13 Map Score: 12.0451 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 213 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TCGAGCGTCTAATAAGCAGAAAATGCACTTT 4 68 0 AAAAGCAGAA 0.77344 -77 GTTGTTAGTGAAAAAAGTGAATTTCTCTTCC 14 95 0 AAAAAGTGAA 0.879249 -72 AGGGTTTTTCAACAAGCTGAAAGCCTCAG 17 9 0 AAAAGCTGAA 0.936544 -292 AGGGTTTTCAATCAAGCTGAAAGAATGTTAA 17 122 1 ATAAGCTGAA 0.826966 -179 AAAGGTTTACATTAAAGTGAATAAAGGGTTG 24 75 1 ATAAAGTGAA 0.702193 -162 AACGATCTAAAATCAGCTGAAAAGCTGATTT 24 139 1 AACAGCTGAA 0.842965 -98 TCTGTGAAGAAATAAAGTGTATGTAAGCTAG 28 36 0 AAAAAGTGTA 0.702193 -152 ATGTTTGTCCAACAAAGTGAAGAATTTCTGT 29 128 0 AAAAAGTGAA 0.879249 -173 TCTTTCTGTAAAGAAGGTGAATCCG 41 38 1 AAAAGGTGAA 0.943056 -15 AATGTAAAACAAGAAAGAGAAAAGTTCCCTA 42 43 0 AAAAAGAGAA 0.627459 -91 GCGGCTCTACAAAAAACTGAATATTCATGTA 45 109 1 AAAAACTGAA 0.866474 -192 GGAAAATTTTAACCAAGTGAAATGTCCTGAG 46 45 0 AACAAGTGAA 0.725906 -256 CCTTAATTCTAAGAAGGTGTAAACACACATG 46 217 0 AAAAGGTGTA 0.842835 -84 GATTAATTGTATTAAGGTGAAGTGGATGTTA 49 15 0 ATAAGGTGAA 0.842835 -201 ATCAATCCTGATCAAGCTGAAGGAAAG 53 7 0 ATAAGCTGAA 0.826966 -294 TAAAAAACAAAACAAGCAGTATCATCAAATA 60 68 1 AAAAGCAGTA 0.525044 -533 GCAATTAATGAAACAGCTGTATGAAAAACCC 60 129 0 AACAGCTGTA 0.634804 -472 ** ******** Masking position 5 Map Score: 10.2438 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 529 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 7 GATCTTAAAGGCTAAGATGGTATCATAGATAA 1 181 1 GCAAGAGGTA 0.611253 -120 TTTGTGTTTCGACAAGAAAGGAGTTTTTCACT 2 56 1 GAAAGAAGGA 0.94873 -23 ATCCTATGAGGAGAAGAAAGCATGTAGAACTT 3 66 0 GAAAGAAGCA 0.879244 -90 TATAGCGAAAGCACAGATAGGATTTTGTCAAA 5 240 0 GCCAGAAGGA 0.698642 -61 TAACAGGTGGGAGATGAGAGGA 5 289 1 GAATGAAGGA 0.711766 -12 ATTTCTTCTGGCGAAGATGGGAATATATGAAT 6 29 1 GCAAGAGGGA 0.962729 -56 AAGTAAAAAAGAAAATAGAGGAATGATACAA 14 146 1 GAAATAAGGA 0.511486 -21 CAATCACGCTGAAAAGATGACAAAATCCTAAA 18 68 0 GAAAGAGACA 0.599363 -188 CAATTTTTTTGAAAAGATAGGAGGACATT 19 133 1 GAAAGAAGGA 0.94873 -19 CAAGGAGAATGAGAAGATGGCATGAGAGGATA 21 176 0 GAAAGAGGCA 0.895861 -40 AAGCGTTAATGCGATGAAGGGAGAAGAAGTC 23 49 1 GCATGAGGGA 0.775133 -21 AATAAATCATGCTAAAAAGAGAACCTTCAATG 44 135 0 GCAAAAGAGA 0.45541 -69 ATTATAAAGGGATAAAACAGGATGTGATCATA 49 123 1 GAAAAAAGGA 0.775018 -93 TGTCTGTATTGAAAAGAAAACAGCTTGGACCG 50 48 0 GAAAGAAACA 0.558737 -43 TGTAAGAGCTGCAAAGATAAGACCTCCTTTTC 53 212 0 GCAAGAAAGA 0.791755 -89 TAAAAAAGGCGATAAAATAGCAAGATGTAAGA 53 237 0 GAAAAAAGCA 0.575454 -64 TGCGTATTTTGCCAAGAAGGGAATGATAAAAG 53 273 0 GCAAGAGGGA 0.962729 -28 GGCATTTAGAGCGAAGAAAGGAATTGATGAT 57 173 1 GCAAGAAGGA 0.956261 -21 TGTGATTGTCGAAAAAACGGGAAGGGAATTTT 60 169 0 GAAAAAGGGA 0.802761 -432 ** **** **** Masking position 7 Map Score: 16.7154 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 217 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 AAAAAACGCTAGCGGGTTTTGTAAGAGCTT 3 12 1 AGCGGGTTTT 0.967504 -144 TTATGTATTCAGAGGGTTTTGCGCCCTCTG 4 18 1 AGAGGGTTTT 0.927039 -127 TTGGCTCAGCTGCGGCTTTTACAATCATCC 10 69 1 TGCGGCTTTT 0.772104 -126 GCTCTTTAGCGGGTTTTTAATTTGAGA 12 8 1 AGCGGGTTTT 0.967504 -39 ACAACGAATGCGAGGGTTTTTCAACAAGCT 17 22 0 CGAGGGTTTT 0.888368 -279 TCCTAGACTACAAGGGTTTTCAATCAAGCT 17 110 1 CAAGGGTTTT 0.637254 -191 CATATAACGCCGCCGGTTTTTGTTCTGTTT 24 42 1 CGCCGGTTTT 0.664778 -195 CCCCTTAGAAAGGGGCTTTTCTGTGAAGAA 28 56 0 AGGGGCTTTT 0.88377 -132 CCCCTTTCTAAGGGGCTTTTCATATTTCAA 28 71 1 AGGGGCTTTT 0.88377 -117 AAGACAATTAAACGGCTTTTTAAGAAAAAC 29 172 0 AACGGCTTTT 0.825897 -129 ATTGCCTTATAAAGGCTTTTCCCGGTTCCC 46 15 1 AAAGGCTTTT 0.668806 -286 TCCACTTGACAGCGGGTTTTTCATACAGCT 60 116 1 AGCGGGTTTT 0.967504 -485 ********** Masking position 7 Map Score: 9.22123 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 169 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 GGCCCGTTGGTCAAGCGGTTAAGACACCGC 5 40 1 TCAAGCGGTT 0.899204 -261 CCTCTCATCTCCCACCTGTTATATTCGTTG 5 280 0 CCCACCTGTT 0.739286 -21 GGCCCCTTTACCAAGCTGTTTACGCAATGT 7 60 0 CCAAGCTGTT 0.962913 -29 TATACACTTCCTACGCGGTTTCTTTCATAA 11 54 0 CTACGCGGTT 0.777699 -32 TTGTGTATTTCTAAGCTGTTCTTATCGTA 21 10 0 CTAAGCTGTT 0.8 -206 GCTGGCTGTCCCCGCTGTTAAAAGCAAAT 26 10 1 CCCCGCTGTT 0.957811 -153 GGCTGTATCCTCCCGCTGTTTGCGAGCATT 26 37 0 TCCCGCTGTT 0.892959 -126 ACGAGAGTTCTCCCGCGGTTCCACCCTAGT 34 188 0 TCCCGCGGTT 0.886386 -109 GCAGGAGCGGCCAAGAGGTTTATAAAATTG 35 264 0 CCAAGAGGTT 0.656737 -37 CCGCAAAGTCTCAAGCTGTTGGTTTACTAG 50 21 0 TCAAGCTGTT 0.905116 -70 ACTTTGCGGTCCAAGCTGTTTTCTTTTCAA 50 42 1 CCAAGCTGTT 0.962913 -49 ********** Masking position 9 Map Score: 6.24664 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 413 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 AATGTCAAAAAGCTCCCGCCCAAAGGACGA 1 262 0 AGCTCCCGCC 0.876529 -39 TTTCTAAAAAAACTGCCGGCTGACGCTGGC 10 20 1 AACTGCCGGC 0.983671 -175 TACATAAAAAAACTGCCAGCGTCAGCCGGC 10 34 0 AACTGCCAGC 0.840337 -161 AAAAAGCCAAAACTCCCGGTTCGCCGGGAG 14 11 1 AACTCCCGGT 0.840337 -156 AATATAAAAAAACTCCCGGCGAACCGGGAG 14 23 0 AACTCCCGGC 0.983671 -144 GAATCCTGAAAATTGTCGGCTTCACTTCAA 15 126 0 AATTGTCGGC 0.746091 -175 GAAATTTTGAAGTTGTCGGCTTTTTTGTTG 15 176 1 AGTTGTCGGC 0.676602 -125 ACCGCGGGAGAACTCTCGTCCCTATGTTTG 34 199 1 AACTCTCGTC 0.769962 -98 GCAACCAAAAAACTCCCGTCTCTATGCTTG 34 236 0 AACTCCCGTC 0.922254 -61 TTTTTTATTAAGCTGCCGGCTGAAAAAAAG 60 552 1 AGCTGCCGGC 0.977217 -49 ********** Masking position 4 Map Score: 5.29876 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 269 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 ATTATATACGACAAAATTCGACACGAACAGA 1 82 1 ACAAAATTCA 0.856083 -219 CCTTCTTTTGACAAAATCCTATCTGTGCTTT 5 234 1 ACAAAATCCA 0.967957 -67 CAGAATGTTGACAAAATCCTAAAACAGTTTT 18 34 1 ACAAAATCCA 0.967957 -222 TGAAAAGATGACAAAATCCTAAAACGAAAAC 18 60 0 ACAAAATCCA 0.967957 -196 ATAACAGATTACAAAAATCAATAACTGTTTT 19 46 1 ACAAAAATCA 0.757302 -106 ACAAAACAGAACAAAAACCGGCGGCGTTATA 24 44 0 ACAAAAACCG 0.787342 -193 TTTGGCACAGCCAAAAACCCAGGATAGAGCG 31 18 0 CCAAAAACCA 0.787342 -140 GTTGCTGAGAACAAAATCCCAGCCTCTTTTT 34 159 0 ACAAAATCCA 0.967957 -138 TAGACTCATAACAAGATCCTATTACAAATCC 46 127 0 ACAAGATCCA 0.8759 -174 ********* * Masking position 6 Map Score: 4.33688 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 25 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 TGCTTTCAGCCCCTTTTCTCAAATTAAAAA 12 24 0 CCCTTTTCTC 0.743898 -23 AAGAGAAATTCACTTTTTTCACTAACAACA 14 97 1 CACTTTTTTC 0.775716 -70 TCTAAATTCTCCCTTTTTTAAAACTCATTA 15 281 0 CCCTTTTTTA 0.547423 -20 CTTCAATATACCCATTTTTCTTGAAAAAAG 19 97 0 CCCATTTTTC 0.662142 -55 TAACAATTAGCCCTTTTTTCCGTGATTCCT 20 109 1 CCCTTTTTTC 0.962821 -192 TGCCATTCAACCCTTTATTCACTTTAATGT 24 83 0 CCCTTTATTC 0.848457 -154 CCCAAATTCACATTTATTTCTTAATCTATG 26 127 0 CATTTATTTC 0.420549 -36 GCTTACATACACTTTATTTCTTCACAGAAA 28 39 1 ACTTTATTTC 0.437228 -149 AACGAATATTCCTTTTTTTCCTTTTTTCAT 29 13 0 CCTTTTTTTC 0.947486 -288 TACTTGCTCTCATTTTTTTCTGAGACAGGT 29 207 1 CATTTTTTTC 0.706719 -94 CTTGGCTTTGACTTTTTTTCTTGCCCGGGA 37 105 1 ACTTTTTTTC 0.720632 -95 GATACACCTGCCCTTAATTCTAAGAAGGTG 46 229 0 CCCTTAATTC 0.62774 -72 GGCGCCCCCTCCTTTTTTGCA 47 2 0 CCTTTTTTGC 0.669286 -20 AATATCGGTGTCTTTTTTTCAGGTGGACCG 49 81 1 TCTTTTTTTC 0.50517 -135 ATGATGACCTCCTTTTATTCTCTATGTGAA 51 15 0 CCTTTTATTC 0.795951 -20 AATTCCCTTCCCGTTTTTTCGACAATCACA 60 171 1 CCGTTTTTTC 0.790037 -430 AATGACTTCTCCCTTATTTCACAAGATACC 60 497 0 CCCTTATTTC 0.88636 -104 TAAAAGGCTTACTTTTTTTCAGCCGGCAGC 60 563 0 ACTTTTTTTC 0.720632 -38 ********** Masking position 5 Map Score: 9.51486 Number of sites scoring better than the average of aligned sites = 862 Number in coding regions = 686 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 13 TAATCAAATGAAATAAAAAACTTTGGTTCGAAAGTCTT 1 48 0 ATAAAATTGT 0.715673 -253 TCTTTAATGAAAATAAAAAAAGTCTGTTCGTGTCGAAT 1 97 0 ATAAAATCTT 0.913338 -204 AGAATAATTAAAATTAAAAATCTTTAATGAAAATAAAA 1 117 0 ATAAAATTTT 0.896605 -184 GAATTGTTACACGTGAAACACCTTTTGTTTATCA 2 7 0 ATAACATTTT 0.558493 -72 AGTTTCATGAATATACAAAAGTTTTTATTTTGTCTTGG 4 109 1 ATAAAATTTT 0.896605 -36 TGTTGTCTAAAAATGAAAAAAATCGGCTTCTGCAAGAG 5 129 0 ATAAAATCGT 0.75364 -172 GGATATGAATATCTTTAAAATACCTGCTCATTGTGAGG 8 68 1 ATAAAACCTT 0.605891 -36 ATAATCTATCAATTTCAAAATTTTTTGTCAA 13 4 0 ATAAAATTTT 0.896605 -72 TGATATATCCATATGAAAAATATCTATTAAATCTATAA 16 48 0 ATAAAATCTT 0.913337 -42 CCTGCCAGTTATATTCAAAAAATTTCATCACTAAACTC 20 49 1 ATAAAATTTT 0.896605 -252 CTTAATATCTAACTGTAAAACGTCTTATAGATTTTTTT 45 252 0 ATAAAATCTT 0.913338 -49 TGACGATCAGATGCTCAAAAAGTTTCATTTTTTCCCTA 60 209 1 ACAAAATTTT 0.558493 -392 CACTTTTTAAAAGTTAAAAAGATCTTTTGACTCCAGGT 60 353 0 ATAAAATCTT 0.913338 -248 AGTGTAATGTACTTAAAAAAATTTTTCTGTACCTGTTC 60 387 1 ATAAAATTTT 0.896605 -214 * * **** *** * Masking position 10 Map Score: 5.93711 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 56 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 ACTATATTAAAGGAAATGAAAACATAGCATAA 15 44 1 AGGAAATGAA 0.832221 -257 ATTGGAGCGGAGCGAATGTAGAATTCGTGAGC 17 69 0 AGCGAATGGA 0.943221 -232 AATCAAGCTGAAAGAATGTTAAGGATGACAAA 17 131 1 AAAGAATGAA 0.552914 -170 ATCGGAGCACAGCGAATGTTGAATTCGTGAGC 18 129 1 AGCGAATGGA 0.943221 -127 CAGGCCTGACAACGAATGCGAAGGTTTGCCTA 18 170 1 AACGAATGAA 0.770962 -86 TCTAGTTTTAAGCGAAAGAAAAACTTGGCCTA 18 223 0 AGCGAAAGAA 0.778285 -33 TTGTATATGAAGAAAATGCCGATTCTTACTTT 20 247 0 AGAAAATGGA 0.719767 -54 ACCGCATTAGAGAAAATGTGGAGAATATGAGA 22 20 1 AGAAAATGGA 0.719767 -42 TACCTGCGTAAGCGAATGAAAAGATAAAACTC 26 92 1 AGCGAATGAA 0.952888 -71 AGAGCAAGTAAGAGAAAGACAATTAAACGGCT 29 185 0 AGAGAAAGAA 0.563259 -116 CTGAACTGTGAAGAAATGATAATAAACGAACT 29 248 1 AAGAAATGAA 0.452205 -53 TTTCTCAAACAGGAAATGTTGATACGTATCTT 35 156 1 AGGAAATGGA 0.802915 -145 ACTCTCAATAAGCGAGTGCTAATTCTATAACA 40 79 0 AGCGAGTGAA 0.732924 -41 TGATTTATTCAGCAAATGGCAACAATATAGGT 44 158 1 AGCAAATGAA 0.894866 -46 TTTGCCAAGAAGGGAATGATAAAAGCAAATAA 53 266 0 AGGGAATGAA 0.921794 -35 ******** ** Masking position 5 Map Score: 6.26676 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 219 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 15 CGCCGTGAAAGGGCGGTGTCTTAACCGCTTG 5 51 0 GGGGGTGTCT 0.547379 -250 TGCTTACTGTGGGAGGAGGTAAGGA 9 83 1 GGGGGAGGTA 0.678126 -15 AAGATGGCATGAGAGGATAAAATACTATATA 21 164 0 GAGGGATAAA 0.421994 -52 AATCAATCCGGGGCGGAGAAATTTCTTAATA 25 21 0 GGGGGAGAAA 0.974723 -95 CATAATGATGGGGTGGAGAAT 25 105 1 GGGGGAGAAT 0.932019 -11 CGCAAACAGCGGGAGGATACAGCCAATTCTT 26 43 1 GGGGGATACA 0.793455 -120 TCCTTTTGGGAGGAGGTGAAAGGC 29 287 1 AGGGGTGAAA 0.757143 -14 GCAAACTAACGGGGGGATAAT 32 15 1 GGGGGATAAT 0.797607 -11 AGCGACCTTAGGGCGGTGTAAGCTAAGGATG 34 94 1 GGGGGTGTAA 0.907534 -203 TACACTTTGAGGGAGGTGAACACA 39 58 1 GGGGGTGAAC 0.837101 -14 GTTGTATCTTAGGAGGTGAAACAC 44 4 0 AGGGGTGAAA 0.757143 -200 CGATAAAGCAGGGGGGATTAAAGTGTGTCAA 45 60 1 GGGGGATTAA 0.815332 -241 CATAAATGGCGGGTGGAGGAATATAGGAGGT 52 73 1 GGGGGAGGAA 0.943121 -216 *** ******* Masking position 6 Map Score: 3.73744 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 121 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459