AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_ecoli_reg_300.orf -o00230_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: BIME6 21 BIME Input sequences: #1 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 rpsB 300 30S ribosomal subunit protein S2 #9 tsf 257 protein chain elongation factor EF-Ts #10 pyrH 146 uridylate kinase #11 frr 291 ribosome releasing factor #12 yaeM 91 putative ATP-binding component of a transport system #13 yaeS 185 orf, hypothetical protein #14 cdsA 120 CDP-diglyceride synthetase #15 yaeT 29 orf, hypothetical protein #16 hlpA 121 histone-like protein, located in outer membrane or nucleoid #17 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #18 dnaE 36 DNA polymerase III, alpha subunit #19 dnaQ 64 DNA polymerase III, epsilon subunit #20 gpt 260 guanine-hypoxanthine phosphoribosyltransferase #21 ybaN 69 putative gene 58 #22 apt 152 adenine phosphoribosyltransferase #23 dnaX 128 DNA polymerase III, tau and gamma subunits; DNA elongation factor III #24 ybaB 52 orf, hypothetical protein #25 htpG 109 chaperone Hsp90, heat shock protein C 62.5 #26 adk 180 adenylate kinase activity; pleiotropic effects on glycerol-3-phosphate acyltransferase activity #27 gsk 151 inosine-guanosine kinase #28 ushA 217 UDP-sugar hydrolase (5'-nucleotidase) #29 ybbT 229 orf, hypothetical protein #30 ybbU 77 putative regulator #31 gcl 89 glyoxylate carboligase #32 ybbQ 99 putative oxidoreductase #33 ybbV 31 orf, hypothetical protein #34 ybbX 59 putative hydrolase #35 purE 117 phosphoribosylaminoimidazole carboxylase = AIR carboxylase, catalytic subunit #36 ppiB 173 peptidyl-prolyl cis-trans isomerase B (rotamase B) #37 leuS 234 leucine tRNA synthetase #38 yceD 159 orf, hypothetical protein #39 rpmF 51 50S ribosomal subunit protein L32 #40 plsX 110 glycerolphosphate auxotrophy in plsB background #41 fabH 67 3-oxoacyl-[acyl-carrier-protein] synthase III; acetylCoA ACP transacylase #42 acpP 210 acyl carrier protein #43 fabF 87 3-oxoacyl-[acyl-carrier-protein] synthase II #44 pabC 119 4-amino-4-deoxychorismate lyase #45 ycfC 35 orf, hypothetical protein #46 ymfC 201 orf, hypothetical protein #47 prsA 150 phosphoribosylpyrophosphate synthetase #48 hemM 213 an enzyme in main pathway of synthesis of 5-aminolevulinate, possibly glutamyl-tRNA dehydrogenase #49 malX 174 PTS system, maltose and glucose-specific II ABC #50 add 103 adenosine deaminase #51 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #52 holE 138 DNA polymerase III, theta subunit #53 yebK 300 orf, hypothetical protein #54 pykA 127 pyruvate kinase II, glucose stimulated #55 shiA 300 putative transport protein, shikimate #56 amn 101 AMP nucleosidase #57 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #58 nrdB 21 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #59 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #60 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #61 cvpA 165 membrane protein required for colicin V production #62 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #63 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #64 dedA 82 orf, hypothetical protein #65 usg 65 putative PTS system enzyme II A component #66 pdxB 98 erythronate-4-phosphate dehyrogenase #67 purC 66 phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase #68 BIME121 112 BIME #69 dapA 79 dihydrodipicolinate synthase #70 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #71 ppk 171 polyphosphate kinase #72 guaA 68 GMP synthetase (glutamine-hydrolyzing) #73 guaB 161 IMP dehydrogenase #74 ndk 148 nucleoside diphosphate kinase #75 b2520 47 orf, hypothetical protein #76 purL 300 phosphoribosylformyl-glycineamide synthetase = FGAM synthetase #77 ygaM 139 orf, hypothetical protein #78 nrdH 247 glutaredoxin-like protein; hydrogen donor #79 cysD 251 ATP:sulfurylase (ATP:sulfate adenylyltransferase), subunit 2 #80 relA 47 (p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor #81 ygcA 56 putative enzyme #82 pnp 177 polynucleotide phosphorylase; cytidylate kinase activity #83 rpsO 148 30S ribosomal subunit protein S15 #84 rbfA 74 ribosome-binding factor A #85 infB 24 protein chain initiation factor IF-2 #86 nusA 27 transcription pausing; L factor #87 yhbC 200 orf, hypothetical protein #88 metY 300 tRNA #89 rpoA 25 RNA polymerase, alpha subunit #90 rpsD 33 30S ribosomal subunit protein S4 #91 rpsM 146 30S ribosomal subunit protein S13 #92 rpmJ 31 50S ribosomal subunit protein L36 #93 rpsH 33 30S ribosomal subunit protein S8, and regulator #94 rplN 164 50S ribosomal subunit protein L14 #95 rplC 32 50S ribosomal subunit protein L3 #96 rpsJ 237 30S ribosomal subunit protein S10 #97 yheD 179 putative export protein A for general secretion pathway (GSP) #98 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #99 ftsY 149 cell division membrane protein #100 gmk 251 guanylate kinase #101 rpoZ 54 RNA polymerase, omega subunit #102 yicP 96 probable adenine deaminase (synthesis xanthine) #103 dnaA 300 DNA biosynthesis; initiation of chromosome replication; can be transcription regulator #104 gppA 135 guanosine pentaphosphatase; exopolyphosphatase #105 rhlB 76 putative ATP-dependent RNA helicase #106 cyaA 300 adenylate cyclase #107 polA 300 DNA polymerase I, 3' --> 5' polymerase, 5' --> 3' and 3' --> 5' exonuclease #108 rpoB 300 RNA polymerase, beta subunit #109 rpoC 76 RNA polymerase, beta prime subunit #110 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #111 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #112 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #113 hflK 85 protease specific for phage lambda cII repressor #114 yjeT 81 orf, hypothetical protein #115 purA 103 adenylosuccinate synthetase #116 cpdB 189 2':3'-cyclic-nucleotide 2'-phosphodiesterase #117 nrdD 300 anaerobic ribonucleoside-triphosphate reductase #118 holC 52 DNA polymerase III, chi subunit #119 BIME233 22 BIME #120 pepA 266 aminopeptidase A/I #121 holD 102 DNA polymerase III, psi subunit #122 deoC 257 2-deoxyribose-5-phosphate aldolase #123 deoA 83 thymidine phosphorylase #124 deoB 51 phosphopentomutase #125 deoD 56 purine-nucleoside phosphorylase Motif number 1 AATCCATCAAAAAACCAGGCTTGAGTATAGC 3 48 0 AAAACAGGCT 0.66729 -27 ATAAAAGTGAAAAAGGGGGCCATATGCAGGC 9 189 0 AAAAGGGGCC 0.849458 -69 TTATCAAAAAGGAGCCGCCTGAGGGCG 10 7 1 AAAAGAGCCG 0.798879 -140 TTGAACGACAAAAACGCCGCTCAGTAGATCC 12 15 1 AAAAGCCGCT 0.918454 -77 AATAAAAAGCAAAACGCCGCCAGCCGATCCG 12 49 0 AAAAGCCGCC 0.888255 -43 GGATAATCCGGCTACAGAGAGTC 13 3 1 ATAACCGGCT 0.630454 -183 GGCAGTGCGTAAAAAGACGCGGACTCATGTG 20 139 1 AAAAGACGCG 0.890287 -122 TAAGCCGTAGATAAACAGGCTGGGACACTTC 20 238 1 ATAACAGGCT 0.415103 -23 TGATACGTTTAAAACGCGCCGTGAGTACCAC 22 110 1 AAAAGCGCCG 0.905199 -43 ATTTTGTCAAAAAAACCCGCTCCGCAGAGCG 31 25 0 AAAACCCGCT 0.820019 -65 AAAGCTAAGAAAAAAGGCCCGCAAGCGGACC 44 36 0 AAAAGGCCCG 0.858222 -84 CAATTCTCTGATAAGGAGCCGGT 44 107 1 ATAAGAGCCG 0.584297 -13 CAATTACTCCAAAAGGGGGCGCTCTCTTTTA 48 80 0 AAAAGGGGCG 0.932646 -134 TCCGAATGAAATAACGCCGCGATGGCGATAA 54 60 0 ATAAGCCGCG 0.873458 -68 AGATAGTGTGAAAATGACCCTCTTGCAAGTG 57 166 0 AAAAGACCCT 0.684284 -135 CGCATCAATAAAAATGGCGCTGAAAAAATAT 61 57 0 AAAAGGCGCT 0.883117 -109 TCATATCAGAAAAAAGGGCCGGATGATTCCA 68 22 0 AAAAGGGCCG 0.864963 -91 TACGCTCTGTATAATGCCGCGGCAATATTTA 73 114 1 ATAAGCCGCG 0.873458 -48 AGGTTTACGCAAAATGCCGCTCATTTATGAG 76 118 0 AAAAGCCGCT 0.918454 -183 CAGATTCTTTATAATGACGCCCGTTTCCCCC 76 243 1 ATAAGACGCC 0.539198 -58 AGAAAAGTCCATAAAGCCGCGATGAACCTCA 77 75 1 ATAAGCCGCG 0.873458 -65 GTGAATCACAAAAATCCCCCTACCCCGTCAC 78 77 1 AAAACCCCCT 0.67821 -171 CGAGTTTCAGAAAAGGGGGCCTGAGTGGCCC 82 17 1 AAAAGGGGCC 0.849458 -161 GTCAGCTTGAAAAAAGGGGCCACTCAGGCCC 82 33 0 AAAAGGGGCC 0.849458 -145 AATTAATTTTAAAAAGGGGCTAACAGCCCCT 84 33 1 AAAAGGGGCT 0.888829 -42 TCTCCTGACAAAAAAGGGGCTGTTAGCCCCT 84 47 0 AAAAGGGGCT 0.888829 -28 GGATGAGGTGAAAAGCCCGCG 86 17 1 AAAACCCGCG 0.887525 -11 GTTCAGTTATATAAAGCCCCGATTTATCGGG 87 120 1 ATAAGCCCCG 0.761508 -81 CAAGACATAAAAAAAGGGCCTAAAGCCCAGT 87 177 0 AAAAGGGCCT 0.787164 -24 ACAAACCTGGAAAACGAGGCG 90 1 0 AAAAGAGGCG 0.895689 -33 AAGCGGTGTTATAATGCCGCGCCCTCGATAT 94 82 1 ATAAGCCGCG 0.873458 -83 TGAAACTAAAAAAACCAGGCGCGAAAAGTGG 106 179 1 AAAACAGGCG 0.776464 -122 ATTCCCCAGCAAAAGCCCGCTTTATACCTTT 110 50 1 AAAACCCGCT 0.820019 -251 CCCCGTGTAAAAAAACAGCCCGAAACC 112 7 0 AAAACAGCCC 0.395693 -69 CGCATCCGGCAAAAGCCGCCTCATACTCTTT 123 47 1 AAAACCGCCT 0.690424 -37 **** ****** Masking position 4 Map Score: 34.1208 Number of sites scoring better than the average of aligned sites = 1070 Number in coding regions = 870 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 2 AGCTTGCCGCCTTTCTGCAACTCGAACTAT 9 34 0 CTTTCTGCAA 0.740734 -224 CGCCGCCAGCCGATCCGCAAGGATCTACTG 12 36 0 CGATCCGCAA 0.811956 -56 ATCATCTGCACTTTCCGCAAATTATCTCGC 26 55 1 CTTTCCGCAA 0.975501 -126 AATCTAACGGCTTTCGGCAATTACTCCAAA 48 98 0 CTTTCGGCAA 0.808959 -116 CCGCTATTATCGTTGCGTAATGTGATTTAT 49 74 1 CGTTGCGTAA 0.815488 -101 CGATTTTTTACGTTGCGCAATTGGGG 50 7 0 CGTTGCGCAA 0.972169 -97 CGTAAAAAATCGTTGCGCAATCGTGGATTT 50 25 1 CGTTGCGCAA 0.972169 -79 TTTTGGAATTCTTTCCGCAATAGTTTCATG 57 266 0 CTTTCCGCAA 0.975501 -35 TTGTTTAACACTTTGCGTAACGTACACTGG 83 74 1 CTTTGCGTAA 0.812639 -75 AACGCAACAACTTTGCGCAAAAAGTGTGAG 100 149 1 CTTTGCGCAA 0.971656 -103 AAATGGAACACTTTCCGCAATGCCTGTTGC 108 201 0 CTTTCCGCAA 0.975501 -100 AATTCGCGAGCGTTGCGCAAACGTTTTCGT 110 174 1 CGTTGCGCAA 0.972169 -127 TTTTCCGGTGCTTTCCGCAATCGCCATCCG 117 209 0 CTTTCCGCAA 0.975501 -92 ********** Masking position 9 Map Score: 18.021 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 44 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 AATCACTTCGCACGGGCAGGTTTTGGCACC 6 160 0 CACGGGCAGG 0.773788 -34 GCAGTTTGGTCACGGCCAGCGCGCAGCAAC 11 94 1 CACGGCCAGC 0.948536 -198 GGATGGCGAGCACTGCCCGGGGCCAAAATG 11 146 1 CACTGCCCGG 0.905965 -146 AAAAGCAAAACGCCGCCAGCCGATCCGCAA 12 46 0 CGCCGCCAGC 0.96614 -46 TGGCGAACCCCACCGGCGGCAACAGAAACA 14 81 0 CACCGGCGGC 0.842317 -40 ACAATAATAACACGGCCTGCCGCAATCGTA 17 55 0 CACGGCCTGC 0.954447 -50 TTTAACCTTTGACCGCCTGCGCCTGTGCTC 22 67 0 GACCGCCTGC 0.895056 -86 AAAACAGGACCACTGGCTGCC 37 224 1 CACTGGCTGC 0.806127 -11 AAGGTATCGTCGCCGCCCGGTTTGGTCTTT 40 63 0 CGCCGCCCGG 0.933098 -48 CAGGACGCTGCCAGCGAACTCGCAG 41 6 1 CGCTGCCAGC 0.932934 -62 GCGGTCGAACGACCGCCTGGAGATGTTCAC 43 11 0 GACCGCCTGG 0.895056 -77 GCGGTCGTTCGACCGCCTGAGTTTTATCTT 43 25 1 GACCGCCTGA 0.678731 -63 CTCTTTAATACACCGCCTGGAAAGGATCAT 47 67 1 CACCGCCTGG 0.978705 -84 TTTCTGGGCGCACTGCCGGAAAGCGAATCC 51 238 0 CACTGCCGGA 0.776596 -63 GCCATAATCTCGCGGCCAGGCATACTTGCG 66 36 0 CGCGGCCAGG 0.928595 -63 ATTCACGGGACACTGCCTGGATATTATGGC 71 132 0 CACTGCCTGG 0.957276 -40 TAATTCACATCACCGCCTGCAAGTATGTGT 99 36 0 CACCGCCTGC 0.978705 -114 TGTCAGGATCCACTGCCAGACCTCATTTTA 106 19 0 CACTGCCAGA 0.829998 -282 TAGCACAATCCGCTGCCGGGTTTTAACCCG 109 37 0 CGCTGCCGGG 0.908271 -40 TGGCTATAATCGCCGCCAGTATCAATTGAG 121 20 0 CGCCGCCAGT 0.736652 -83 ********** Masking position 5 Map Score: 18.9484 Number of sites scoring better than the average of aligned sites = 2091 Number in coding regions = 1994 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 CATCATCGGTAACGTTGCGCGTGACAAACGGTCA 2 213 0 AAGTGCGCGA 0.943869 -42 AAATAAGGGTAAGATTCCGCGTAAGTATCGCGGG 11 25 1 AAATCCGCGA 0.744186 -267 GAGGGGAAAATAGGTTGCGCGAGATTATAGAGAT 20 194 0 TAGTGCGCGA 0.938213 -67 CATTTCAACGTCGAGTGCGCGAAAGGCTGTTTTG 37 121 1 TCATGCGCGA 0.698292 -114 ATAATTCGCACACATTGCGGGTTACTGCTTTATT 38 66 0 CAATGCGGGA 0.502043 -94 CATAACCACGCAGACTGCGCGCAACATGAGCATT 42 26 0 CAATGCGCGA 0.898317 -185 TGCCGTCATGAAAGATGCGCGTTATTAGGCTATA 46 148 1 AAGTGCGCGA 0.943869 -54 CTGGATTCAGTAAATTGCGCGAGAAGATAAAACG 49 126 0 TAATGCGCGA 0.958366 -49 TTCTGGATATAAAAGTGCGCACCATTATAAAAAC 50 67 0 AAATGCGCAA 0.761575 -37 AATTTCAGCGTATAATGCGCGCCAATTGACTCTT 51 59 1 TAATGCGCGA 0.958366 -242 TTGTCTGACCTAAGGTGCGCGAAAGCCACTTTTT 57 105 1 TAGTGCGCGA 0.938213 -196 CGCCATTTTTATTGATGCGCGGGAAGGAAATCCC 61 69 1 ATGTGCGCGA 0.532879 -97 CGAGAATAATGCTCGGAACATTTCAGGC 64 5 1 AAATGCTCGA 0.65286 -78 GACATCTGCCAATATTGCTCGCCATAATATCCAG 71 112 1 AAATGCTCGA 0.65286 -60 TGTTGCTCATTATAATCCGCGCCATCTCGTACGC 74 87 1 TAATCCGCGA 0.724284 -62 TTTTTTGTAAAATAATGCGCTTAAGGGAGAGCAG 88 88 1 AAATGCGCTA 0.690323 -213 GTTAAGTATGTATAATGCGCGGGCTTGTCGTAGT 96 55 1 TAATGCGCGC 0.68755 -183 GATCATAGCCTAAACTGCGCAAGAGATCTTCTGT 103 121 0 TAATGCGCAA 0.742558 -180 GACCGTAAAGAAAGATGCGCTACATACAAGTGTA 106 97 0 AAGTGCGCTA 0.595225 -204 ACGTTTTCGTTACAATGCGGGCGAAAAATAAGGA 110 194 1 TAATGCGGGA 0.724284 -107 CGATTCTGAAAAAATTGCGCACGATACGTCTCAA 111 21 0 AAATGCGCAA 0.761575 -65 ** * ****** * Masking position 6 Map Score: 15.8103 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 288 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 GTCTTTTACTGGCTCTTCTCGCTAACCCAACCGGT 4 43 1 GTCTTCCGCA 0.815894 -258 GATGACACGAAGGTCATCCGGCATTACA 26 4 0 ATCATCGGCT 0.84229 -177 GATGACCTTCGTGTCATCCGGCATTTTTCTTTTCA 26 21 1 GTCATCGGCT 0.975603 -160 CACTTTCCGCAAATTATCTCGCCATTAACCGTTTC 26 63 1 ATTATCCGCT 0.498555 -118 TGTCTGTCGCATCCCGCTCTGCGGAGCGGG 31 6 1 GGCATCCGCT 0.96218 -84 CCGCACGATCGGATCATCACGCAATGTATGCTGAT 36 76 0 GTCATCCGCT 0.975603 -98 TCCTCACTAAGCTTCATCACGCAGATGCGTGA 40 8 0 GTCATCCGCA 0.953484 -103 TGTTCCAGACGTTGCATCGCGCTCTTTAATACACC 47 46 1 GGCATCCGCT 0.96218 -105 TTATGCCTTTGCGGCATCGGGCAATGCGT 61 5 0 GGCATCGGCT 0.96218 -161 TACAGGGCTGGAATCATCCGGCCCTTTTTTCTGAT 68 14 1 GTCATCGGCT 0.975603 -99 TCTTAACTGAGGTTCATCGCGGCTTTATGGACTTT 77 78 0 GTCATCCGGT 0.734628 -62 GGATTTTTGTGATTCACCAGGCAAAAAGAAACCCC 78 59 0 GTCACCGGCA 0.696893 -189 AACCCGACGCGTATCATCGCGCCGTATCTTCATTT 78 205 1 GTCATCCGCT 0.975603 -43 CTCTCAATCGATATCTTCTGGCGCTTCAGTGGTAG 98 213 0 ATCTTCGGCT 0.535891 -32 CTGCAAGTATGTGTTATCTGGCGGATTGAGCAATT 99 15 0 GTTATCGGCA 0.792355 -135 GATCCTGACAGGCGTTTCACGCCGTTGTAATAAGG 106 39 1 GGTTTCCGCT 0.505916 -262 ATGCGTCTACGCCTTATCCGGCCTACGGGTAGATA 123 17 0 GTTATCGGCA 0.792355 -67 ATAAGGCGTAGACGCATCCGGCAAAAGCCGCCTCA 123 35 1 GGCATCGGCA 0.92878 -49 * ***** *** * Masking position 8 Map Score: 13.8273 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 423 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TTGACCGCAGCCGGAAAACGGTAAAAGCAC 2 63 0 CCGGAAAACG 0.89427 -192 CTATTCATTCGCGGAATCTGTTAATAAAGC 6 94 0 GCGGAATCTG 0.812159 -100 AAAGGGCACCCCGGAATATGTGCCGATACG 8 220 0 CCGGAATATG 0.841366 -81 CATCTGCGGCGCGAAATATGAAGGGGGAGA 9 122 1 GCGAAATATG 0.550115 -136 ATTAAGTAAACCGGAATCTGAAG 18 24 1 CCGGAATCTG 0.876811 -13 GAGATAATTTGCGGAAAGTGCAGATGATGA 26 53 0 GCGGAAAGTG 0.902049 -128 CGGTATATAACCGAAAAGTGACTGAGCGTA 41 47 1 CCGAAAAGTG 0.851934 -21 AAAGAATCTGCCGAAAACTGTGCGGGCCAG 47 99 0 CCGAAAACTG 0.851934 -52 GGGCGCACTGCCGGAAAGCGAATCCGGTAT 51 233 0 CCGGAAAGCG 0.919032 -68 TTACGAGCTTGCGAAAACTGTAAACGCTTA 53 53 1 GCGAAAACTG 0.777538 -248 TCCTAAACGCCCGAAATCCGGTGCCTTAAG 79 90 1 CCGAAATCCG 0.669151 -162 AAAACCAGGCGCGAAAAGTGGTAACGGTTA 106 189 1 GCGAAAAGTG 0.777538 -112 AACAGGCATTGCGGAAAGTGTTCCATTTTC 108 203 1 GCGGAAAGTG 0.902049 -98 ATTTTGTTGACCGGAAAATGGAACACTTTC 108 216 0 CCGGAAAATG 0.918678 -85 GCGGAAAGCACCGGAAAACGAAACGAAAAA 117 221 1 CCGGAAAACG 0.89427 -80 AACGAAAAAACCGGAAAACGCCTTTCCCAA 117 242 1 CCGGAAAACG 0.89427 -59 ********** Masking position 5 Map Score: 13.7573 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 334 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 ATATTTCGCGCCGCAGATGCGTTATCTTCG 9 111 0 CCGCAGATGC 0.953322 -147 TGGGGGTCGCTTTTGCTGAAGTATCG 14 7 1 TCGCTTTTGC 0.623329 -114 CTCCTTACCATCCCATTTGCACCGGAGGGT 16 96 0 TCCCATTTGC 0.699251 -26 AGCACAACAATCGCAGTTGCAATTATTGCG 22 11 1 TCGCAGTTGC 0.934338 -142 ACCGTTTCAGCCCCAGGTGCCTTTCTTGAG 26 90 1 CCCCAGGTGC 0.79093 -91 AAGCTTCATCACGCAGATGCGTGA 40 5 0 ACGCAGATGC 0.779279 -106 TTTGGTCTTTCCCCAGTTGCCTGGGGAAAA 40 43 0 CCCCAGTTGC 0.947754 -68 CAGGACGCAAACGCATATGCAACGTGGTGG 46 48 0 ACGCATATGC 0.58385 -154 CCCCAATTGCGCAACGTAAA 50 1 1 CCCCAATTGC 0.640076 -103 ACATAAAAGTCCGCATATGCACAAAATGGC 55 56 0 CCGCATATGC 0.890301 -245 GTGCTCCAGACCGCAGTTGCGGTTATAGGG 87 91 1 CCGCAGTTGC 0.977835 -110 ACTACACTCCTCGCTGTTGCTTCATGGCAC 99 125 0 TCGCTGTTGC 0.806367 -25 GTAGCTGCTTCCGCATTTGCCTGTCATTCA 100 115 0 CCGCATTTGC 0.946036 -137 TAACTCATGTCCGCTGTTGCGATGACTTCG 120 185 0 CCGCTGTTGC 0.928116 -82 ********** Masking position 8 Map Score: 10.734 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 434 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 GATTAACACTAGCGTAGAGATGACGAGTACGTTAG 2 174 1 AGCGTGAACG 0.55338 -81 ATGACAAAAACGCGTAACAAAAGTGTCTATAATCA 4 124 1 CGCGTAAGTG 0.834553 -177 GTCCTCTCCCGCGTGAGAAATACGCTTCCCCGTA 7 60 0 CGCGTAAACG 0.929771 -24 GGTAAGATTCCGCGTAAGTATCGCGGGGGCGTAAG 11 32 1 CGCGTAAGCG 0.939023 -260 GACCAAACTGCCTGCAACAATAACGCCTTATAACC 11 70 0 CCTGCAAACG 0.586859 -222 TGTGTTAATACCCGTCGTCATCGCGGCGTTGTTTC 14 52 1 CCCGTGAGCG 0.964396 -69 GCAGACCACCAGCGTTACAATGGCGAACCCCACCG 14 96 0 AGCGTAAGCG 0.834556 -25 ACGTTTAAAACGCGCCGTGAGTACCACCGTAACAA 22 114 1 CGCGCGAACC 0.506788 -39 CTAACACAGCCCCGTCAGAACGGCGAGGCTGAATG 23 58 0 CCCGTAAGCG 0.980065 -71 CAGTTAACCACCCGTAAAAACAACC 27 137 1 CCCGTAAACC 0.819606 -15 TACCCGCAATAAAAATGGCCGATATCA 33 3 1 CCCGCAAATG 0.715608 -29 TATGCTGATTCGCGCGGGAAATATGGGTATTATAC 36 50 0 CGCGCGAATG 0.456434 -124 CCCAAACGTCCGCGTCAAAACAGCCTTTCGCGCAC 37 135 0 CGCGTAAGCC 0.860582 -100 AAAGCAGTAACCCGCAATGTGTGCGAATTATTGGC 38 69 1 CCCGCATGCG 0.661746 -91 CGTGCGAATTACCGCTAAAATCGCGTTTTCCTGCA 68 71 0 ACCGCAAGCG 0.849635 -42 GTTTGCTTTCCCTGTTAGAATTGCGCCGAATTTTA 70 237 1 CCTGTAAGCG 0.824771 -61 TTATTTTTCTACCGCAAGTAACGCGTGGGGACCCA 70 269 1 ACCGCAAGCG 0.849498 -29 TACCCCCGTAATTAAAGCGCCAGCTCTGC 71 5 1 CCCGTAAGCG 0.979932 -167 CAGGCAGTGTCCCGTGAATAAAACGGAGTAAAAGT 71 143 1 CCCGTAAACG 0.9563 -29 GCCACAATGGCCCGTTAGCAACGTCGAATAATTAT 75 12 0 CCCGTAAGTC 0.633722 -36 CTTTTCTGAAAGCGTTGTGAATGCGCAATCAGGTA 77 47 0 AGCGTGAGCG 0.735589 -93 TGATTTGCTACCCGTCATGACTGTGATTCCGCCAA 106 265 0 CCCGTAAGTG 0.892908 -36 TTCCGCAATGCCTGTTGCTATCACGCTTAAACCAT 108 184 0 CCTGTGAACG 0.536085 -117 CGCTGTAGCGCCCGTCATCCGTACGCTCTGCTTTT 117 23 1 CCCGTACACG 0.6558 -278 ***** * * *** Masking position 4 Map Score: 16.5351 Number of sites scoring better than the average of aligned sites = 1135 Number in coding regions = 1060 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 9 TTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGT 1 22 0 TTTACCGCGG 0.663499 -31 GCGTGAGAAATACGCTTCCCCGTAAGCGCATGGTAAACT 7 45 0 TCTCCCGCGC 0.744825 -39 TCTTGTAAATTCAGCTAACCCTTGTGGGGCTGCGCTGAA 10 55 1 TCTACCGGGG 0.652883 -92 GCCTTATAACCAGACTTACGCCCCCGCGATACTTACGCG 11 42 0 CCTACGGCGA 0.63223 -250 TTTTTACGCACTGCCTCTCCCTGACGCGGGATAAAGTGG 20 115 0 CCTTCCGCGG 0.983874 -146 ATGCACATCTTGTGCTGTCCGTAGCGTGGGCAGCACAAG 23 22 0 TCTTCCGTGG 0.592593 -107 AATGTTAACACAATCTGACGGGAGCGCGCGAGACGCAGC 27 91 0 CCTACGGCGC 0.897227 -61 TTATTGAAACCAAGCTGACCGGTCGGCGGTGGTTGAACG 29 177 1 CCTACCGCGG 0.966613 -53 TCACCTCTCCTTCGAGCGCTACTGGTTTG 46 1 1 TCTTCCGCGC 0.952403 -201 TTTTTCGATGTCACCTATCCTTAGAGCGAGGCACCACCA 51 186 1 TCTTCCGCGA 0.797577 -115 CGAATGAGATTAATTTATCGCCATCGCGGCGTTATTTCA 54 46 1 TTTTCGGCGG 0.66123 -82 ATTTCTGTGACATACTATCGGATGTGCGGTAATTGTATG 56 58 1 CCTTCGGCGG 0.966284 -44 ACGGATTATACCTCCTTTCTTCAAGGCGGCAATATTCTT 70 22 1 CCTTCTGCGG 0.78802 -276 GCAAAAAATGCTTGCTATCCCCGAAGGGCGGGTTACTAT 73 52 0 CCTTCCGGGC 0.83331 -110 AACCGCGGGCCTACCTTACCTGATTGCGCATTCACAACG 77 31 1 CCTACCGCGC 0.948987 -109 TTTGCCTTCTCCTGCTCTCCCTTAAGCGCATTATTTTAC 88 94 0 CCTTCCGCGC 0.975149 -207 CGTTAAAAATCCCCATATCGAGGGCGCGGCATTATAACA 94 88 0 CATTCGGCGG 0.727614 -77 CATTAAATTTTCCAATATGCGGCGTAAATCGT 103 4 1 TTTTCCGCGG 0.806169 -297 ACAAGTCGACCCATCTGTCCATTGAGCGGACAGTTTGTG 108 253 0 CCTTCCGCGG 0.983889 -48 AAATTTACATATCGCTGTAGCGCCCGTCATCCG 117 5 1 TATTCGGCGC 0.466737 -296 * ** *** **** Masking position 6 Map Score: 13.9942 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 346 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 CATAGCATTTTTATCCATAAGATTAGCGGA 4 210 1 TTATCCATAA 0.516593 -91 GTGTTCTCCACAAAGGAATGTAG 16 4 1 TTCTCCACAA 0.502524 -118 CGCAACTCAATTACCCACACATGTCTAAAC 36 21 0 TTACCCACAC 0.632365 -153 CCTTCCTGAGTTATCCACAAAGTTATGCAC 57 139 1 TTATCCACAA 0.90941 -162 GACCACTTTTTTATCCAAAGTTTCGGGCTG 63 29 1 TTATCCAAAG 0.630343 -127 TGGCGCAGGTTTACGCAAAATGCCGCTCAT 76 125 0 TTACGCAAAA 0.539919 -176 ATGAGAGGCTTTACCCACATAGAGCTGGGT 82 135 1 TTACCCACAT 0.671752 -43 CCAGTGTACGTTACGCAAAGTGTTAAACAA 83 74 0 TTACGCAAAG 0.446737 -75 CACTGAATTTTTATGCAAAATAAATGAGTT 88 14 1 TTATGCAAAA 0.515706 -287 TTTGCATTTTTTACCCAAAACGAGTAGAAT 88 266 1 TTACCCAAAA 0.729062 -35 TGTGAATAAATTACGCACAAAATGTGACAT 98 95 0 TTACGCACAA 0.826213 -150 GACCGTGATTTTATCCACAAGTTCAATGCA 98 129 0 TTATCCACAA 0.90941 -116 TTTTCCCGATTTATCCACAGGACTTTCCAG 103 81 0 TTATCCACAG 0.873592 -220 TGTAAATAATTTATGCACAAAGTTATCCAC 107 157 1 TTATGCACAA 0.808168 -144 ATGCACAAAGTTATCCACATGACGATTTGC 107 169 1 TTATCCACAT 0.653411 -132 GTGGCATCCTTTACCCATAATCTGATAAAC 107 268 1 TTACCCATAA 0.539264 -33 TTATACCTTTTTACGCACAGAGTTATCCAC 110 71 1 TTACGCACAG 0.765944 -230 ACGCACAGAGTTATCCACAATCATCAATGT 110 83 1 TTATCCACAA 0.90941 -218 CGCCATCCGCTTATCCACAACGCCGCACCT 117 188 0 TTATCCACAA 0.90941 -113 TAAGAACAGGTTATCCACAGAAATTGGGAA 117 265 0 TTATCCACAG 0.873592 -36 ********** Masking position 2 Map Score: 11.8463 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 80 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 AGACCAGGTAGTACACGTTTGGTTAGGGGGCCTG 9 160 1 GAACGTTGGT 0.90001 -98 AGAGAGCAAGGAAAACGGTTGCGTGGCTGTGAAA 35 31 0 GAACGTTGCT 0.987192 -87 AACAGAAAAAGAAAACGTTTGCGTAGGGATTTCC 61 94 0 GAACGTTGCT 0.987192 -72 TCCTGCAGACGCACACGTTTGCGTATCATATCAG 68 44 0 GAACGTTGCT 0.987192 -69 AAGCAGTCTCGCAAACGTTTGCTTTCCCTGTTAG 70 221 1 GAACGTTGCT 0.987192 -77 TATACAGAGCGTAACCGATTGCATCTACCCCTTT 73 93 0 GACCGTTGCT 0.967301 -69 ATGCGCTGACGAAACCGTTTGCGTGGAAATAAAA 76 209 0 GACCGTTGCT 0.967301 -92 TTCATTTGTTGAATACTTTTGCCTTCTCCTGCTC 88 116 0 GAACTTTGCT 0.858619 -185 ACTTTACTAGCAATACGCTTGCGTTCGGTGGTTA 96 25 1 CAACGTTGCT 0.90001 -213 TTATTTCACCGGATACGCTTTCGTAAAGCAATAG 105 31 1 GAACGTTTCT 0.922326 -46 CGAGCGTTGCGCAAACGTTTTCGTTACAATGCGG 110 180 1 GAACGTTTCT 0.922326 -121 * * *** **** * Masking position 3 Map Score: 12.3997 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 11 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 TTTCACAGCCACGCAACCGTTTTCCTTGCT 35 31 1 ACGCAACCGT 0.850561 -87 GAAAAAAGGCCCGCAAGCGGACCTTTTATA 44 29 0 CCGCAAGCGG 0.81742 -91 GTATCGCAGGACGCAAACGCATATGCAACG 46 54 0 ACGCAAACGC 0.850767 -148 GGAAATCCCTACGCAAACGTTTTCTTTTTC 61 94 1 ACGCAAACGT 0.955249 -72 CTGATATGATACGCAAACGTGTGCGTCTGC 68 44 1 ACGCAAACGT 0.955249 -69 CTAACAGGGAAAGCAAACGTTTGCGAGACT 70 225 0 AAGCAAACGT 0.748888 -73 GAATTGAAAAACGCCAGCGGCAGAGCTGGC 71 29 0 ACGCCAGCGG 0.817715 -143 TTTTATTTCCACGCAAACGGTTTCGTCAGC 76 209 1 ACGCAAACGG 0.9613 -92 TAACCACCGAACGCAAGCGTATTGCTAGTA 96 29 0 ACGCAAGCGT 0.947722 -209 TGCTTGATTCATGCAAGCGGCATTAATACT 97 67 0 ATGCAAGCGG 0.69412 -113 CTATTGCTTTACGAAAGCGTATCCGGTGAA 105 35 0 ACGAAAGCGT 0.758398 -42 CCGCATTGTAACGAAAACGTTTGCGCAACG 110 184 0 ACGAAAACGT 0.730873 -117 ATCCATTTTTAAGCAAACGGTGATTTTGAA 115 82 1 AAGCAAACGG 0.775518 -22 ********** Masking position 6 Map Score: 8.19162 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 109 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 AGGGCGGCTTCTTTTTGTGCCCATCTTGTA 10 32 1 CTTTTTGTGC 0.936704 -115 GAGTCCGCGTCTTTTTACGCACTGCCTCTC 20 135 0 CTTTTTACGC 0.729504 -126 CTTTTTGTCCTTGTAACATA 29 220 0 CTTTTTGTCC 0.808385 -10 GCAACATGAGCATTTTGTGCAAATCGCGG 42 10 0 CATTTTGTGC 0.84595 -201 TAACGCAAATCATTTTGCACTAATTATTAC 42 61 0 CATTTTGCAC 0.699046 -150 TGAGTTTTATCTTTTTGTCCCACTAGAATC 43 42 1 CTTTTTGTCC 0.808385 -46 TTATCTATTCCTTTTTGTAATAACTTTTTT 52 12 1 CTTTTTGTAA 0.428084 -127 ATCAGGGTGCCATTTTGTGCATATGCGGAC 55 48 1 CATTTTGTGC 0.84595 -253 ACGCCATCGACTTTTTATGCCTTTGCGGCA 61 24 0 CTTTTTATGC 0.649663 -142 TTTACACAACCTTTTTGCACGTCTTTTCCC 70 193 0 CTTTTTGCAC 0.862252 -105 GCATCTACCCCTTTTTGCAAAAAATGCTTG 73 77 0 CTTTTTGCAA 0.521207 -85 ATCCACGCCACATTTTGTCAACGTTTATTG 88 180 0 CATTTTGTCA 0.213986 -121 CTCTATGTCACATTTTGTGCGTAATTTATT 98 91 1 CATTTTGTGC 0.84595 -154 CTTGCTCACACTTTTTGCGCAAAGTTGTTG 100 153 0 CTTTTTGCGC 0.9556 -99 ACCGTTACCACTTTTCGCGCCTGGTTTTTT 106 187 0 CTTTTCGCGC 0.69533 -114 AGTCACCAGCCTTTTTGCGCTGTAAGGCGC 108 46 1 CTTTTTGCGC 0.9556 -255 CGCTTTATACCTTTTTACGCACAGAGTTAT 110 67 1 CTTTTTACGC 0.729504 -234 AGTTACAGCACTTTTTGCACTCAAAAATGA 115 33 0 CTTTTTGCAC 0.862252 -71 TGTTTTATCCTTTTTGTGACATAACAAAG 125 38 0 CTTTTTGTGA 0.72017 -19 ********** Masking position 5 Map Score: 14.3553 Number of sites scoring better than the average of aligned sites = 591 Number in coding regions = 539 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 14 TTATCATACCTGTCATTCAATGCCGTGCCTAAC 2 119 1 TTCTTCATGC 0.972032 -136 TTTTCCTTGCTCTCTTTCCGTGCTATTCTCTGT 35 50 1 TTCTTCCTGC 0.961159 -68 ACTGCTTTATTTTCGTTCAGTGCTGATAACAAA 38 44 0 TTCTTCATGC 0.972032 -116 TGCATTTCGATTTCTTTCAGTGCGGAAATCGTC 53 254 1 TTCTTCATGC 0.972032 -47 AGCGTGTTATACTCTTTCCCTGCAATGGGTTCC 98 15 1 ATCTTCCTGC 0.776885 -230 GACAACGGGGTCTCTTTCCCTGCTACGGAACCC 98 41 0 TTCTTCCTGC 0.961159 -204 GCAACGAGGTTATCATTCACTGTTTTATCAGAC 98 156 0 TTCTTCATGT 0.773102 -89 CGCATTTGCCTGTCATTCACTGCAATAAAGACG 100 101 0 TTCTTCATGC 0.972032 -151 ACTACTGCTGTGCCTTTCAATGCTTGTTTCTAT 108 98 1 TCCTTCATGC 0.878762 -203 CGCGAATTTTTCTCTTTCAATGGTGATCACAAT 110 149 0 TTCTTCATGG 0.83471 -152 * ** **** *** Masking position 7 Map Score: 6.66899 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 13 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 CTATTTTATTTGCCATTTTGGCCCCGGGCAGTGCTC 11 153 0 TGCCAGCCCG 0.954881 -139 GAAGGGGTAATGCTAACACAGCCCCGTCAGAACGGC 23 69 0 TGCTAGCCCG 0.889285 -60 CACGATCCCCTGCCAACTTAGCGGCCTAAAAAAGCA 32 32 0 TGCCAGCGCC 0.954878 -68 CGTGCGGTTATGCTATAACACCACCCTATATATGAC 36 104 1 TGCTACCCCC 0.749771 -70 GGTTGCCTTTTGCCAATAATTCGCACACATTGCGGG 38 79 0 TGCCATCCAC 0.689188 -81 GAAAGGATCATGCCTGGCCCGCACAGTTTTCGGCAG 47 86 1 TGCCTGCCAG 0.446441 -65 GGGAGAAACTTGCTTTCTGGGCGCACTGCCGGAAAG 51 245 0 TGCTTGCCAC 0.558618 -56 AATTCCGGCTTGCCATCCTGGCTCACTCTTAGTAAC 52 83 1 TGCCAGCCAC 0.953827 -56 CAAGTCAGGGTGCCAGACCGGCACCCTCAGCGAAGG 59 13 0 TGCCAGCCCC 0.988701 -82 ATAAGGGCAGGGCCACTGGCTCTGCCCTTTTGCTAT 62 17 1 GGCCATCGCC 0.470409 -53 GGACGCATAATGCCATTTTTGCCCCCAACAGACCAT 63 82 0 TGCCAGCCCC 0.988701 -74 GTTGGACATCTGCCAATATTGCTCGCCATAATATCC 71 108 1 TGCCAGCCGC 0.902968 -64 TGAAAAAAGGGGCCACTCAGGCCCCCTTTTCTGAAA 82 21 0 GGCCAGCCCC 0.971606 -157 CGACTATAATTGCTACTACAGCTCCCCACGAAAAAG 117 154 1 TGCTAGCCCC 0.97077 -147 GCCAACATATGGCTATAATCGCCGCCAGTATCAATT 121 23 0 GGCTAGCGCC 0.758507 -80 TCGACGAATTTGCTATATTTGCGCCCCTGACAACAG 121 65 1 TGCTAGCCCC 0.97077 -38 ***** ** *** Masking position 12 Map Score: 15.0823 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 251 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185