AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_ecoli_reg_100.orf -o00230_ecoli_100.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 surA 52 survival protein #2 imp 254 organic solvent tolerance #3 polB 74 DNA polymerase II #4 araB 300 L-ribulokinase #5 guaC 224 GMP reductase #6 hpt 193 hypoxanthine phosphoribosyltransferase #7 dgt 83 deoxyguanosine triphosphate triphosphohydrolase #8 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #9 dnaE 36 DNA polymerase III, alpha subunit #10 dnaQ 64 DNA polymerase III, epsilon subunit #11 gpt 260 guanine-hypoxanthine phosphoribosyltransferase #12 apt 152 adenine phosphoribosyltransferase #13 dnaX 128 DNA polymerase III, tau and gamma subunits; DNA elongation factor III #14 adk 180 adenylate kinase activity; pleiotropic effects on glycerol-3-phosphate acyltransferase activity #15 gsk 151 inosine-guanosine kinase #16 ushA 217 UDP-sugar hydrolase (5'-nucleotidase) #17 ybbT 229 orf, hypothetical protein #18 ybbU 77 putative regulator #19 gcl 89 glyoxylate carboligase #20 ybbQ 99 putative oxidoreductase #21 ybbV 31 orf, hypothetical protein #22 ybbX 59 putative hydrolase #23 purE 117 phosphoribosylaminoimidazole carboxylase = AIR carboxylase, catalytic subunit #24 leuS 234 leucine tRNA synthetase #25 pabC 119 4-amino-4-deoxychorismate lyase #26 ycfC 35 orf, hypothetical protein #27 ymfC 201 orf, hypothetical protein #28 prsA 150 phosphoribosylpyrophosphate synthetase #29 add 103 adenosine deaminase #30 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #31 holE 138 DNA polymerase III, theta subunit #32 pykA 127 pyruvate kinase II, glucose stimulated #33 amn 101 AMP nucleosidase #34 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #35 nrdB 21 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #36 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #37 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #38 cvpA 165 membrane protein required for colicin V production #39 purC 66 phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase #40 BIME121 112 BIME #41 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #42 ppk 171 polyphosphate kinase #43 guaA 68 GMP synthetase (glutamine-hydrolyzing) #44 guaB 161 IMP dehydrogenase #45 ndk 148 nucleoside diphosphate kinase #46 purL 300 phosphoribosylformyl-glycineamide synthetase = FGAM synthetase #47 nrdH 247 glutaredoxin-like protein; hydrogen donor #48 cysD 251 ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 #49 relA 47 (p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor #50 ygcA 56 putative enzyme #51 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #52 rpoA 25 RNA polymerase, alpha subunit #53 rpsD 33 30S ribosomal subunit protein S4 #54 rpsM 146 30S ribosomal subunit protein S13 #55 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #56 gmk 251 guanylate kinase #57 rpoZ 54 RNA polymerase, omega subunit #58 yicP 96 probable adenine deaminase (synthesis xanthine) #59 dnaA 300 DNA biosynthesis; initiation of chromosome replication; can be transcription regulator #60 gppA 135 guanosine pentaphosphatase; exopolyphosphatase #61 cyaA 300 adenylate cyclase #62 polA 300 DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3' --> 5' exonuclease #63 rpoB 300 RNA polymerase, beta subunit #64 rpoC 76 RNA polymerase, beta prime subunit #65 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #66 purA 103 adenylosuccinate synthetase #67 cpdB 189 2':3'-cyclic-nucleotide 2'-phosphodiesterase #68 nrdD 300 anaerobic ribonucleoside-triphosphate reductase #69 holC 52 DNA polymerase III, chi subunit #70 BIME233 22 BIME #71 pepA 266 aminopeptidase A/I #72 holD 102 DNA polymerase III, psi subunit #73 deoC 257 2-deoxyribose-5-phosphate aldolase #74 deoA 83 thymidine phosphorylase #75 deoB 51 phosphopentomutase #76 deoD 56 purine-nucleoside phosphorylase Motif number 1 ATTGACCGCAGCCGGAAAACGGTAAAAGCAC 2 63 0 GCGGAAAACG 0.973426 -192 TTTTTTGGATGGAGTGAAACG 4 290 1 GGGTGAAACG 0.90771 -11 AAAAATGAGTGCACGAAAGCGAAATTGATGA 5 52 1 GCCGAAAGCG 0.925845 -173 CCATGCGCTTACGGGGAAGCGTATTTCTCAC 7 51 1 ACGGGAAGCG 0.841941 -33 ATTGAATCGAACTGTAAAACGACAAGTCTGA 10 30 1 ACGTAAAACG 0.750966 -35 CTGCGCCTGTGCTCGAAAACGCCAGAATGTA 12 50 0 GCCGAAAACG 0.962296 -103 TGGCAGGCTCTGAAACGCTGGAAGGTG 13 112 0 GCCTGAAACG 0.922318 -17 AAGGCACCTGGGGCTGAAACGGTTAATGGCG 14 82 0 GGCTGAAACG 0.872655 -99 AAGAAAAAAGGCCCGCAAGCGGACCTTTTAT 25 30 0 GCCGCAAGCG 0.892226 -90 CCGTATCGCAGGACGCAAACGCATATGCAAC 27 55 0 GGCGCAAACG 0.907128 -147 TGGGCGCACTGCCGGAAAGCGAATCCGGTAT 30 233 0 GCGGAAAGCG 0.947144 -68 GTGTGCGTCTGCAGGAAAACGCGATTTTAGC 40 62 1 GCGGAAAACG 0.973426 -51 GATTTTATTTCCACGCAAACGGTTTCGTCAG 46 207 1 CCCGCAAACG 0.791858 -94 TGTACCCAAGGGGGGGAAACGGGCGTCATTA 46 254 0 GGGGGAAACG 0.964791 -47 CTCCAACAAACCTGGAAAACGAGGCG 53 6 0 CCGGAAAACG 0.891714 -28 GTTGTTGCTACCACTGAAGCGCCAGAAGATA 55 206 1 CCCTGAAGCG 0.566295 -39 TTATTACAACGGCGTGAAACGCCTGTCAGGA 61 41 0 GGGTGAAACG 0.907709 -260 ACGAAAAAATGGTCTAAAACGTGATCAATTT 61 146 0 GGCTAAAACG 0.840948 -155 GTAGTCAAACAGTGTGAAACGCTACTGGCGC 63 72 0 AGGTGAAACG 0.692852 -229 TGCGGAAAGCACCGGAAAACGAAACGAAAAA 68 220 1 ACGGAAAACG 0.893633 -81 AAACGAAAAAACCGGAAAACGCCTTTCCCAA 68 241 1 ACGGAAAACG 0.893633 -60 ATGCGTCAGTGGTGGCAAACGCATCAGGATC 73 73 0 GGGGCAAACG 0.933417 -185 ** ******** Masking position 7 Map Score: 25.9514 Number of sites scoring better than the average of aligned sites = 976 Number in coding regions = 918 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 ATCATCTGCACTTTCCGCAAATTATCTCGC 14 55 1 CTTTCCGCAA 0.98254 -126 CGATTTTTTACGTTGCGCAATTGGGG 29 7 0 CGTTGCGCAA 0.982193 -97 CGTAAAAAATCGTTGCGCAATCGTGGATTT 29 25 1 CGTTGCGCAA 0.982193 -79 TTTTGGAATTCTTTCCGCAATAGTTTCATG 34 266 0 CTTTCCGCAA 0.98254 -35 AACGCAACAACTTTGCGCAAAAAGTGTGAG 56 149 1 CTTTGCGCAA 0.98254 -103 AAATGGAACACTTTCCGCAATGCCTGTTGC 63 201 0 CTTTCCGCAA 0.98254 -100 AATTCGCGAGCGTTGCGCAAACGTTTTCGT 65 174 1 CGTTGCGCAA 0.982193 -127 TTTTCCGGTGCTTTCCGCAATCGCCATCCG 68 209 0 CTTTCCGCAA 0.98254 -92 ********** Masking position 9 Map Score: 16.2503 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 TCCGCTAATCTTATGGATAAAAATGCTATG 4 210 0 TTATGGATAA 0.750338 -91 GTGCATAACTTTGTGGATAACTCAGGAAGG 34 139 0 TTGTGGATAA 0.964368 -162 ACCCAGCTCTATGTGGGTAAAGCCTCTCAT 51 135 0 ATGTGGGTAA 0.817817 -43 ATGTCACATTTTGTGCGTAATTTATTCACA 55 95 1 TTGTGCGTAA 0.849538 -150 CAATGCAAGCTTGTGAATAAATTACGCACA 55 106 0 TTGTGAATAA 0.682329 -139 TGCATTGAACTTGTGGATAAAATCACGGTC 55 129 1 TTGTGGATAA 0.964368 -116 CTGGAAAGTCCTGTGGATAAATCGGGAAAA 59 81 1 CTGTGGATAA 0.938469 -220 GTGGATAACTTTGTGCATAAATTATTTACA 62 157 0 TTGTGCATAA 0.876794 -144 GCAAATCGTCATGTGGATAACTTTGTGCAT 62 169 0 ATGTGGATAA 0.871293 -132 GTTTATCAGATTATGGGTAAAGGATGCCAC 62 268 0 TTATGGGTAA 0.677358 -33 GTGGATAACTCTGTGCGTAAAAAGGTATAA 65 71 0 CTGTGCGTAA 0.759971 -230 ACATTGATGATTGTGGATAACTCTGTGCGT 65 83 0 TTGTGGATAA 0.964368 -218 AGGTGCGGCGTTGTGGATAAGCGGATGGCG 68 188 1 TTGTGGATAA 0.964368 -113 TTCCCAATTTCTGTGGATAACCTGTTCTTA 68 265 1 CTGTGGATAA 0.938469 -36 ********** Masking position 9 Map Score: 15.541 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 28 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AGCCGGAAAACGGTAAAAGCACCTTTATAT 2 55 0 CGGTAAAAGC 0.456104 -200 CGAGAAGAGCCAGTAAAAGACGCAGTGACG 4 34 0 CAGTAAAAGA 0.691896 -267 CTAATCAATGCGGCGCAAGACTGCGAAATT 5 139 0 CGGCGCAAGA 0.817032 -86 GTAGCGTGGGCAGCACAAGACTGGCGATAA 13 11 0 CAGCACAAGA 0.891403 -118 ACGCTACGGACAGCACAAGATGTGCATTCA 13 34 1 CAGCACAAGA 0.891403 -95 GAAATCAGGTCAGGGAGAGAAGT 16 205 1 CAGGGAGAGA 0.695338 -13 TGTCTGAATTCAGGAAAAGCGAAATTTAAA 20 69 1 CAGGAAAAGC 0.90332 -31 CAGAGAATAGCACGGAAAGAGAGCAAGGAA 23 52 0 CACGGAAAGA 0.748237 -66 CTTTTATATCCAGAAAAAGAGTGCGACC 29 86 1 CAGAAAAAGA 0.691896 -18 CGCATTCTAACAGAAAAAGAAAACGTTTGC 38 106 0 CAGAAAAAGA 0.691896 -60 GCACACCAGACAGCAAAAGATTTTAAAACG 39 21 1 CAGCAAAAGA 0.946663 -46 CCCAGGCGCGCGGCGAAAGAAGACTTGTGC 41 165 0 CGGCGAAAGA 0.906152 -133 GCAATTCTAACAGGGAAAGCAAACGTTTGC 41 231 0 CAGGGAAAGC 0.907323 -67 CCCTTGGGTACACCGAAAGCTTAGAAGACG 46 273 1 CACCGAAAGC 0.744939 -28 GAACCCATTGCAGGGAAAGAGTATAACACG 55 17 0 CAGGGAAAGA 0.931561 -228 GGTTCCGTAGCAGGGAAAGAGACCCCGTTG 55 42 1 CAGGGAAAGA 0.931561 -203 GATGAAATACCGGGAAGAGACAACGGGGTC 55 62 0 CGGGAAGAGA 0.530709 -183 ATAGCCTAAACTGCGCAAGAGATCTTCTGT 59 121 0 CTGCGCAAGA 0.549173 -180 AAAAGATTTTCACGAAAAGCGGTGAAAAAC 62 219 1 CACGAAAAGC 0.671061 -82 CTGCATTCCCCAGCAAAAGCCCGCTTTATA 65 46 1 CAGCAAAAGC 0.927357 -255 TATTTAAATCCACCACAAGAAGCCCCATTT 69 33 1 CACCACAAGA 0.641865 -20 AGCTAAAATCCTGCAAAAGACGAGTTTTTA 71 25 0 CTGCAAAAGA 0.715407 -242 TAGACGCATCCGGCAAAAGCCGCCTCATAC 74 43 1 CGGCAAAAGC 0.868902 -41 ********** Masking position 8 Map Score: 17.9182 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 607 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 CCAATCAAACGAAACCAGGCTATACTCAAG 3 30 1 GAAACCAGGC 0.885063 -45 AATCCATCAAAAAACCAGGCTTGAGTATAG 3 49 0 AAAACCAGGC 0.859377 -26 ACTATGCCTTCAAATCGGGCTTATCGCGAG 7 18 0 CAAATCGGGC 0.71689 -66 GTTGTCAACACAAGACAGGCTTGCGAGATA 11 73 1 CAAGACAGGC 0.903423 -188 TAAGCCGTAGATAAACAGGCTGGGACACTT 11 238 1 ATAAACAGGC 0.734316 -23 GCGATTGCCTCAAGAAAGGCACCTGGGGCT 14 98 0 CAAGAAAGGC 0.524711 -83 GCTTGGTTTCAATAACAGGCAATCTAAAAC 17 162 0 AATAACAGGC 0.734316 -68 TAAAAGCTAAGAAAAAAGGCCCGCAAGCGG 25 39 0 GAAAAAAGGC 0.68248 -81 TCAACGACTCAAAAACAGGCACTCACGTTG 30 123 1 AAAAACAGGC 0.935292 -178 ATCATATCAGAAAAAAGGGCCGGATGATTC 40 24 0 AAAAAAGGGC 0.485459 -89 CGCCCGACATGAAGTCGGGCGAAGAGAA 43 9 0 GAAGTCGGGC 0.79295 -60 AAGAAACCCCGAAGACAGGCTTCGGGGTCA 47 39 0 GAAGACAGGC 0.941356 -209 TGAGTATCCTGAAAACGGGCTTTTCAGCAT 54 95 1 GAAAACGGGC 0.909693 -52 TCCGCTGTAGATAGTCAGGCAGATATACAA 56 12 1 ATAGTCAGGC 0.512382 -240 TATTGCAGTGAATGACAGGCAAATGCGGAA 56 107 1 AATGACAGGC 0.708964 -145 TGAAACTAAAAAAACCAGGCGCGAAAAGTG 61 179 1 AAAACCAGGC 0.859377 -122 TGACGGGTAGCAAATCAGGCGATACGTC 61 283 1 CAAATCAGGC 0.820731 -18 CCATAATCTGATAAACAGGCACGGACATT 62 282 1 ATAAACAGGC 0.734316 -19 GCCTGAGAAATCAGGCTGATGGCTGG 63 7 1 GAAATCAGGC 0.887085 -294 AGAGCGTACGGATGACGGGCGCTACAGCGA 68 22 0 GATGACGGGC 0.629316 -279 ********** Masking position 8 Map Score: 13.8014 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 596 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 CGTTTGTCACGCGCAACGTTACCGATGATGGAACAATAA 2 217 1 GCGCACCAGT 0.958307 -38 CTGTAACAAAGCGGGACCAAAGCCATGACAAAAACGCGT 4 100 1 GCGGGCGAGC 0.887286 -201 CATAAGATTAGCGGATCCTACCTGACGCTTTTTATCGCA 4 225 1 GCGGACCAGT 0.881151 -76 TCGCAGTCTTGCGCCGCATTGATTAGTGCGTATGATAGC 5 143 1 GCGCCCAATC 0.536652 -82 AAGGGTAAGAGCGCAACTCCAGTGACGCTATCATACGCA 5 169 0 GCGCACGAGT 0.969551 -56 GGTTTTGGCACCGCAACAAAGCGCAAGACACGCAGTATA 6 133 0 CCGCACCAGC 0.716062 -61 TTCCCCGTAAGCGCATGGTAAACTATGCCTTCAAATCGG 7 30 0 GCGCAGAAGC 0.865831 -54 TCGAGCACAGGCGCAGGCGGTCAAAGGTTAAACAACTGT 12 65 1 GCGCAGCAGT 0.792566 -88 AGGCCCGCAAGCGGACCTTTTATAAGGGTGGAAAATGAC 25 14 0 GCGGACAAGT 0.915096 -106 GCCTAATAACGCGCATCTTTCATGACGGCAAACAATAGG 27 139 0 GCGCACAAGC 0.974888 -63 CGAAAACTGTGCGGGCCAGGCATGATCCTTTCCAGGCGG 28 79 0 GCGGGCAACT 0.423568 -72 CCCCAATTGCGCAACGTAAAAAATCGTTGCGCAATCG 29 9 1 GCGCACAACT 0.775448 -95 TACAATTACCGCACATCCGATAGTATGTCACAGAAATGT 33 56 0 GCACACAAGC 0.563037 -46 TTTCCTTCCCGCGCATCAATAAAAATGGCGCTGAAAAAA 38 60 0 GCGCACAAGC 0.974888 -106 CTGTTAGAATGCGCCCCGAACAGGATGACAGGGCGTAAA 38 123 1 GCGCCCAAGC 0.945458 -43 TTCTTTCGCCGCGCGCCTGGGGAAAAGACGTGCAAAAAG 41 174 1 GCGCGCGAGC 0.960637 -124 TCATTATAATCCGCGCCATCTCGTACGCTGGTACAGACA 45 93 1 CCGCGCCAGT 0.588796 -56 GCAGAGGTTCGCGCGGCTAATGAGAGGCTTTACCCACAT 51 116 1 GCGCGCGAGT 0.954556 -62 TCACATGGCCGCGCCGTGTATAATAAGCTCGTATGTAGG 56 190 1 GCGCCTAAGT 0.611997 -62 AAGATCTCTTGCGCAGTTTAGGCTATGATCCGCGGTCCC 59 125 1 GCGCATGAGT 0.770971 -176 CTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAA 61 101 1 GCGCACTAGT 0.780499 -200 GTTGATGTTGGCGGAATCACAGTCATGACGGGTAGCAAA 61 258 1 GCGGATGAGC 0.557826 -43 GAAAACGTTTGCGCAACGCTCGCGAATTTTTCTCTTTCA 65 163 0 GCGCACGATT 0.680258 -138 TCGTTACAATGCGGGCGAAAAATAAGGATGCCCCGTTAG 65 200 1 GCGGGGAAGT 0.541682 -101 TGCTATATTTGCGCCCCTGACAACAGGAGCGATTCGCT 72 75 1 GCGCCCAAGG 0.66935 -28 ***** * * * * * Masking position 15 Map Score: 18.1797 Number of sites scoring better than the average of aligned sites = 1189 Number in coding regions = 1052 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 TGAGAATACCACTTTATCCCGCGTCAGGGAGA 11 107 1 ATTATCCCGC 0.668012 -154 GATGACACGAAGGTCATCCGGCATTACA 14 7 0 ATCATCCGGC 0.957288 -174 GATGACCTTCGTGTCATCCGGCATTTTTCTTT 14 21 1 GTCATCCGGC 0.989061 -160 TGTCTGTCGCATCCCGCTCTGCGGAGC 19 6 1 GGCATCCCGC 0.982222 -84 TGTTCCAGACGTTGCATCGCGCTCTTTAATAC 28 46 1 GGCATCGCGC 0.956989 -105 TTATGCCTTTGCGGCATCGGGCAATGCGT 38 8 0 GGCATCGGGC 0.973593 -158 AAAACATCCGGCACACCAGACA 39 1 1 AACATCCGGC 0.823102 -66 TACAGGGCTGGAATCATCCGGCCCTTTTTTCT 40 14 1 GTCATCCGGC 0.989068 -99 AACCCGACGCGTATCATCGCGCCGTATCTTCA 47 205 1 GTCATCGCGC 0.953569 -43 ATGCGTCTACGCCTTATCCGGCCTACGGGTAG 74 20 0 GTTATCCGGC 0.932319 -64 ATAAGGCGTAGACGCATCCGGCAAAAGCCGCC 74 35 1 GGCATCCGGC 0.989324 -49 * ********* Masking position 6 Map Score: 12.6749 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 108 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 ACCACGTAATCCGCAGTGCGGTTAATTGAAATGGA 1 22 1 CCGCGCGGAA 0.922072 -31 CTTGTGCTGCCCACGCTACGGACAGCACAAGATGT 13 22 1 CCACCCGGAG 0.926507 -107 GCTGCGTCTCGCGCGCTCCCGTCAGATTGTGTTAA 15 91 1 GCGCCCCGAG 0.974892 -61 CGTTCAACCACCGCCGACCGGTCAGCTTGGTTTCA 17 181 0 CCGCGCGGAG 0.988362 -49 CTGTCGCATCCCGCTCTGCGGAGCGGGTTTTTTTG 19 14 1 CCGCCCGGCG 0.983638 -76 CAAACCAGTAGCGCTCGAAGGAGAGGTGA 27 5 0 GCGCCAGGAG 0.949493 -197 TGGTGGTGCCTCGCTCTAAGGATAGGTGACATCGA 30 190 0 TCGCCAGGAG 0.782722 -111 TGCTTTCTGGGCGCACTGCCGGAAAGCGAATCCGG 30 236 0 GCGCCCCGAA 0.843621 -65 CATACAATTACCGCACATCCGATAGTATGTCACAG 33 62 0 CCGCCCCGAG 0.988394 -40 TTTTATTGATGCGCGGGAAGGAAATCCCTACGCAA 38 75 1 GCGCGAGGAT 0.517845 -91 CGATAGTAACCCGCCCTTCGGGGATAGCAAGCATT 44 50 1 CCGCCCGGAT 0.966412 -112 AGGCTATGATCCGCGGTCCCGATCGTTTTGCAGGA 59 144 1 CCGCGCCGCG 0.910428 -157 CACAAACTGTCCGCTCAATGGACAGATGGGTCGAC 63 253 1 CCGCCTGGAG 0.942258 -48 TACGCCTTATCCGGCCTACGGGTAGATACGTCTC 74 10 0 CCGGCCGGAG 0.948399 -74 **** * *** ** Masking position 2 Map Score: 11.1945 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 409 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TGTACTGGCTGTACGCAATAATTGCAACTGCGATTGT 12 17 0 GTGCTTGCAA 0.835472 -136 TGCTTTTTTAGGCCGCTAAGTTGGCAGGGGATCGTGT 20 32 1 GGGCTGGCAG 0.96945 -68 GTTACTAAGAGTGAGCCAGGATGGCAAGCCGGAATTG 31 82 0 GTGCTGGCAA 0.908898 -57 CCTTCGCTGAGGGTGCCGGTCTGGCACCCTGACTTGC 36 13 1 GGGCTGGCAC 0.956112 -82 TGTCAGACTTGCAGGCAGACTTTGCAGGATTTCGGCG 36 56 0 GCGCTTGCAG 0.90396 -39 GGATATTATGGCGAGCAATATTGGCAGATGTCCAACT 42 107 0 GCGCTGGCAG 0.948698 -65 TTCGGGGATAGCAAGCATTTTTTGCAAAAAGGGGTAG 44 66 1 GCGCTTGCAA 0.937609 -96 TACAGCCATTGGCGGCACGCGTTGCTAATTCACGATG 46 168 1 GGGCTTGCTA 0.783951 -133 TTTCAGAAAAGGGGGCCTGAGTGGCCCCTTTTTTCAA 51 21 1 GGGCTGGCCC 0.924122 -157 GTTGGGTTGAGCTGGCTAGATTAGCCAGCCAATCTTT 54 36 1 GCGCTAGCCA 0.893632 -111 CTTTTTCGTGGGGAGCTGTAGTAGCAATTATAGTCGA 68 153 0 GGGCTAGCAA 0.96267 -148 AATTGATACTGGCGGCGATTATAGCCATATGTTGGCG 72 23 1 GGGCTAGCCA 0.935135 -80 CTGTTGTCAGGGGCGCAAATATAGCAAATTCGTCGAT 72 64 0 GGGCTAGCAA 0.96267 -39 ** ** ****** Masking position 12 Map Score: 7.80881 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 295 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 TCTCATTCTTACGATTGCGGCAGGCCGTGTTATTATTGT 8 46 1 AGTGCGCGCG 0.989138 -59 TAACCTTTGACCGCCTGCGCCTGTGCTCGAAAACGCCAG 12 56 0 CGTGCGCGCG 0.972682 -97 GCCTTTCTTGAGGCAATCGCCTGTTGGTGGTATCGTTTA 14 108 1 AGATCGCGGG 0.892582 -73 ACTAACATACCTGTATGCGTCGTCTGAAGGAAGTCTCAA 16 72 1 CGTGCGCTGG 0.822028 -146 CATCATAGACAAGTCTGCGTCCGGTGAAGATAAATCTGC 16 139 0 AGTGCGCGGG 0.993373 -79 GAAGAACCTCAGGCATGCGTCCATTGGTGGAAAGAATCT 28 120 0 AGTGCGCAGG 0.979541 -31 CAGACTTTGCAGGATTTCGGCGGGAGTTGCAAGTCAGGG 36 39 0 AGTTCGCGGG 0.97954 -56 TGATACGCAAACGTGTGCGTCTGCAGGAAAACGCGATTT 40 50 1 AGTGCGCGGA 0.94149 -63 TCTTTTCCCCAGGCGCGCGGCGAAAGAAGACTTGTGCCA 41 163 0 AGCGCGCAGG 0.874701 -135 GAATTGAAAAACGCCAGCGGCAGAGCTGGCGCTTTAATT 42 20 0 AGAGCGCGCG 0.940491 -152 TTCCACGCAAACGGTTTCGTCAGCGCATCAGATTCTTTA 46 215 1 AGTTCGCGCC 0.724059 -86 TTGCGATTTGCCGATTTCGGCAGGTCTGGTCCCTAAAGG 49 11 1 CGTTCGCGCG 0.919178 -37 CCTATCGTTAATGAATGCGCCAACTGTGATAGTGTCATC 67 61 1 AGTGCGCAGA 0.837113 -129 TATCTTAGCGACGATTTCGACGACTCAAGAGAATAAATG 71 74 0 AGTTCGCACG 0.902808 -193 TCACTTTCAAATGAATGCGTCAGTGGTGGCAAACGCATC 73 79 0 AGTGCGCGGG 0.993373 -179 TAAGGCGTAGACGCATCCGGCAAAAGCCGCCTCATACTC 74 36 1 AGTCCGCAGG 0.845618 -48 * * **** * * * * Masking position 9 Map Score: 18.0227 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 328 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ACGTCATTGTAAGGAACCACTGCCATGAAAATGC 15 31 1 AAGACCCGCC 0.794119 -121 GACGGGAGCGCGCGAGACGCAGCCAGTTTCAATA 15 80 0 CGCAACCGCC 0.877615 -72 ATTCAGACAACACGATCCCCTGCCAACTTAGCGG 20 44 0 CACACCCGCC 0.985512 -56 GACACAAGCACACATTCCTCTGCACGCTTTTTCG 30 159 1 CACTCCCGCA 0.70013 -142 GGTGCCAGACCGGCACCCTCAGCGAAGGCA 36 7 0 CGGACCCGCG 0.931595 -88 ACCTGTAAATCGCAAGCTCCAGCAGTTTTTTTCC 42 59 1 CGCACTCGCA 0.698152 -113 TCATTAGCCGCGCGAACCTCTGCAACGGAAGATC 51 105 0 CGCACCCGCA 0.972311 -73 TTCCCTGCTACGGAACCCATTGCAGGGAAAGAGT 55 25 0 CGGACCTGCA 0.665691 -220 GAGGGTGACGCACGAACCGCTGTCTGCGGTTATA 59 193 0 CACACCCGTC 0.895903 -108 AAACGCCTGTCAGGATCCACTGCCAGACCTCATT 61 22 0 CAGACCCGCC 0.983211 -279 TCGGAGTTAGCACAATCCGCTGCCGGGTTTTAAC 64 40 0 CACACCCGCC 0.985512 -37 ATTTTGCCCACGGTAACCACAGTCAAAATTGTGA 65 122 1 CGGACCCGTC 0.922234 -179 GCAATTCTATCTGTAGCCACCGCCGTTGTCTTTA 71 224 1 CTGACCCGCC 0.923999 -43 *** * ** * *** Masking position 12 Map Score: 9.19098 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 527 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 ATCGGTAACGTTGCGCGTGACAAACGGTCA 2 213 0 TTGCGCGTGA 0.6814 -42 TACCGGTTGGGTTAGCGAGAAGAGCCAGTA 4 49 0 GTTAGCGAGA 0.773048 -252 TCCATCTTTTGTTCGCCAAACTTTACGGCC 8 14 1 GTTCGCCAAA 0.623929 -91 CTGGTTTTTAGTGCGCCAGATCTCTATAAT 11 175 1 GTGCGCCAGA 0.967541 -86 GGAAAATAGGTTGCGCGAGATTATAGAGAT 11 194 0 TTGCGCGAGA 0.955343 -67 TCTGACGGGAGCGCGCGAGACGCAGCCAGT 15 87 0 GCGCGCGAGA 0.907419 -65 TCAACGTCGAGTGCGCGAAAGGCTGTTTTG 24 125 1 GTGCGCGAAA 0.944255 -110 CTGACCTAAGGTGCGCGAAAGCCACTTTTT 34 109 1 GTGCGCGAAA 0.944255 -192 GAAAGCAAACGTTTGCGAGACTGCTTTACA 41 217 0 GTTTGCGAGA 0.703755 -81 GTGAGCGAGATCAAATTCTA 44 1 1 GTGAGCGAGA 0.935203 -161 TTGCGTAAACCTGCGCCAGATGGCAACTTA 46 137 1 CTGCGCCAGA 0.920702 -164 GTAGCAACAACTGTGCCAGAGCTTAAGAGC 55 187 0 CTGTGCCAGA 0.617329 -58 ATAGCCTAAACTGCGCAAGAGATCTTCTGT 59 121 0 CTGCGCAAGA 0.689906 -180 AGTGACCTGTTTGAGCGAGAA 64 2 0 TTGAGCGAGA 0.823116 -75 TAGCTGAGTTTTTCGCGAAAAATTCAGCTA 65 245 1 TTTCGCGAAA 0.405737 -56 ********** Masking position 10 Map Score: 8.66064 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 405 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 CGGATCCTACCTGACGCTTTTTATCGCAACTCT 4 236 1 CTGACGTTTA 0.687432 -65 TTATAGAGATCTGGCGCACTAAAAACCAGTATT 11 171 0 CTGGCGCTAA 0.819692 -90 CCAGTACATTCTGGCGTTTTCGAGCACAGGCGC 12 46 1 CTGGCGTTCA 0.89867 -107 AATCACGCAACTTGCGGATTTAAAAGGGGATAC 17 17 0 CTTGCGTTTA 0.922027 -213 AGCGGCAGAGCTGGCGCTTTAATTACGGGGGTA 42 11 0 CTGGCGTTAT 0.843962 -161 AGCTCTGCCGCTGGCGTTTTTCAATTCACCTGT 42 32 1 CTGGCGTTTA 0.970922 -140 ACTGCTGGAGCTTGCGATTTACAGGTGAATTGA 42 52 0 CTTGCGTTAA 0.910772 -120 GACTTCATGTCGGGCGATTTATATTATCTGTTT 43 23 1 CGGGCGTTAA 0.893234 -46 TTCTTGCGAGTTTCAGAAAAGGGGG 51 3 1 CTTGCGTTTA 0.922027 -175 CAGAAGATCTCTTGCGCAGTTTAGGCTATGATC 59 122 1 CTTGCGGTTA 0.650968 -179 TGAAACGCTACTGGCGCCTTACAGCGCAAAAAG 63 56 0 CTGGCGTTAA 0.966469 -245 CAGGTCACTGCTGTCGGGTTAAAACCCGGCAGC 64 23 1 CTGTCGTTAA 0.654987 -54 CGAGTTTTTACGGGCGTATTTAAA 71 2 0 CGGGCGTTTA 0.906474 -265 TAAAATTCACCTTGCGAGTTTGTTAGTATTCTA 73 211 0 CTTGCGTTTT 0.689342 -47 ****** *** * Masking position 10 Map Score: 9.14571 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 304 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 GTAACGTTGCGCGTGACAAACGGTCAGAGACT 2 207 0 GCGTAAAACG 0.613908 -48 CTGTAACAAAGCGGGACCAAAGCCATGACAAA 4 100 1 GCGGACAAAG 0.956026 -201 TGACAAAAACGCGTAACAAAAGTGTCTATAAT 4 125 1 GCGTAAAAAG 0.832852 -176 GTCTATAATCACGGCAGAAAAGTCCACATTGA 4 148 1 ACGGAAAAAG 0.754631 -153 TGGGATTGTAGCGTAAAAAAAGACAATTTCGC 5 115 1 GCGTAAAAAG 0.832852 -110 GCGCTTTGTTGCGGTGCCAAAACCTGCCCGTG 6 148 1 GCGGGCAAAA 0.827295 -46 TGCCAACTTAGCGGCCTAAAAAAGCATTGTCT 20 26 0 GCGGCAAAAA 0.690738 -74 CCAAACGTCCGCGTCAAAACAGCCTTTCGCGC 24 137 0 GCGTAAACAG 0.507035 -98 ACGGAACAAGTCGGAATAAAAGCTAAGAAAAA 25 53 0 TCGGAAAAAG 0.851594 -67 AAGCTGAGTTTCGGTGACAACGTCACCTTGTT 28 18 1 TCGGGCAACG 0.553719 -133 CGCGTTACTTGCGGTAGAAAAATAAAATTCGG 41 262 0 GCGGAAAAAA 0.876079 -36 CGTGAATAAAACGGAGTAAAAGTGGTA 42 155 1 ACGGGAAAAG 0.733071 -17 AAGACAGGCTTCGGGGTCAAAGACGCGTATTT 47 26 0 TCGGGCAAAG 0.795421 -222 TCATACTATGGCGGTAAAAAAATTTGCATGGT 48 26 0 GCGGAAAAAA 0.876079 -226 GTTGATGTTGGCGGAATCACAGTCATGACGGG 61 258 1 GCGGACACAG 0.817777 -43 TTCACGAAAAGCGGTGAAAAACTCATGTTTTC 62 227 1 GCGGGAAAAC 0.697731 -74 TCGTTACAATGCGGGCGAAAAATAAGGATGCC 65 200 1 GCGGCAAAAA 0.690738 -101 CGCATCACCTTCGGCATAAAAGGAAAAGAAG 73 10 0 TCGGAAAAAG 0.851594 -248 CATAACAAAGGCGGAGTCAACGCTCCGCCCAA 76 16 0 GCGGGCAACG 0.861019 -41 **** * ***** Masking position 9 Map Score: 8.18515 Number of sites scoring better than the average of aligned sites = 1100 Number in coding regions = 936 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 15 ACCTGTCATTCAATGCCGTGCCTAACACCA 2 126 1 CAATGCCGTG 0.862467 -129 ACGCACTAATCAATGCGGCGCAAGACTGCG 5 144 0 CAATGCGGCG 0.859604 -81 AGCCCCGTCAGAACGGCGAGGCTGAATGCA 13 56 0 GAACGGCGAG 0.602598 -73 CTGAAACGGTTAATGGCGAGATAATTTGCG 14 70 0 TAATGGCGAG 0.687824 -111 AAGGAAGTCTCAACGCCGAATACAGAATTT 16 98 1 CAACGCCGAA 0.822705 -120 CTGTGCCCTCTAAAGCCGAGAGTTGTGCAC 23 79 1 TAAAGCCGAG 0.569066 -39 TATTAGGCTATAATGCGGCAATTCATAATC 27 170 1 TAATGCGGCA 0.5232 -32 CCGAATGAAATAACGCCGCGATGGCGATAA 32 60 0 TAACGCCGCG 0.935604 -68 ACGCTCTGTATAATGCCGCGGCAATATTTA 44 115 1 TAATGCCGCG 0.922808 -47 GTGATGAAAGCAAAGCCGAGTGGCAAAAAC 56 43 1 CAAAGCCGAG 0.736599 -209 TTCCTTATTACAACGGCGTGAAACGCCTGT 61 46 0 CAACGGCGTG 0.779486 -255 GAAATATCCCGAATGCCGCGTGTTACCGTT 61 231 1 GAATGCCGCG 0.871293 -70 CTAACGCCCCTAACGGGGCATCCTTATTTT 65 218 0 TAACGGGGCA 0.382158 -83 CGCTTATCCACAACGCCGCACCTTTTTCGT 68 181 0 CAACGCCGCA 0.921119 -120 TCTGACGTGCCAATGCCGTAATAACGTTAA 71 147 1 CAATGCCGTA 0.704145 -120 AAACTTCTTACAATGGCGCATCACCTTCGG 73 28 0 CAATGGCGCA 0.816729 -230 ********** Masking position 3 Map Score: 5.81305 Number of sites scoring better than the average of aligned sites = 1848 Number in coding regions = 1763 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798