AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_ecoli_reg_300.orf -o00052_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: gatZ 28 putative tagatose 6-phosphate kinase 1 Input sequences: #1 yadG 108 putative ATP-binding component of a transport system #2 yadI 104 putative PTS enzyme II B component #3 lacZ 122 beta-D-galactosidase #4 lacI 76 transcriptional repressor of the lac operon #5 mhpR 76 transcriptional regulator for mhp operon #6 brnQ 300 branched chain amino acid transport system II carrier protein #7 proY 75 proline permease transport protein #8 malZ 155 maltodextrin glucosidase #9 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #10 seqA 184 negative modulator of initiation of replication #11 pgm 25 phosphoglucomutase #12 hrsA 108 protein modification enzyme, induction of ompC #13 galE 260 UDP-galactose-4-epimerase #14 modF 67 ATP-binding component of molybdate transport system #15 modE 128 molybdate uptake regulatory protein #16 yceD 159 orf, hypothetical protein #17 rpmF 51 50S ribosomal subunit protein L32 #18 plsX 110 glycerolphosphate auxotrophy in plsB background #19 fabH 67 3-oxoacyl-[acyl-carrier-protein] synthase III; acetylCoA ACP transacylase #20 acpP 210 acyl carrier protein #21 fabF 87 3-oxoacyl-[acyl-carrier-protein] synthase II #22 pabC 119 4-amino-4-deoxychorismate lyase #23 ptsG 294 PTS system, glucose-specific IIBC component #24 ychK 73 orf, hypothetical protein #25 hnr 91 Hnr protein #26 galU 201 glucose-1-phosphate uridylyltransferase #27 rspA 205 starvation sensing protein #28 b1582 134 orf, hypothetical protein #29 malX 174 PTS system, maltose and glucose-specific II ABC #30 pfkB 286 6-phosphofructokinase II; suppressor of pfkA #31 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #32 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #33 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #34 osmE 201 activator of ntrL gene #35 manX 300 PTS enzyme IIAB, mannose-specific #36 galF 174 homolog of Salmonella UTP--glucose-1-P uridyltransferase, probably a UDP-gal transferase #37 wcaK 61 putative galactokinase (EC 2.7.1.6). #38 BIME91 82 BIME #39 wcaJ 54 putative colanic acid biosynthsis UDP-glucose lipid carrier transferase #40 cpsG 104 phosphomannomutase #41 gmd 25 GDP-D-mannose dehydratase #42 wcaA 34 putative regulator #43 BIME92 24 BIME #44 wza 300 putative polysaccharide export protein #45 gatD 47 galactitol-1-phosphate dehydrogenase #46 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #47 gatY 197 tagatose-bisphosphate aldolase 1 #48 BIME96 27 BIME #49 b2097 184 orf, hypothetical protein #50 fruB 300 PTS system, fructose-specific IIA/fpr component #51 pdxB 98 erythronate-4-phosphate dehyrogenase #52 glk 203 glucokinase #53 ptsH 300 PTS system protein HPr #54 ptsI 44 PEP-protein phosphotransferase system enzyme I #55 crr 40 PTS system, glucose-specific IIA component #56 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #57 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #58 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #59 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #60 ebgR 218 regulator of ebg operon #61 ebgA 147 evolved beta-D-galactosidase, alpha subunit; cryptic gene #62 agaZ 248 putative tagatose 6-phosphate kinase 2 #63 BIME157 76 BIME #64 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #65 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #66 yrbG 209 orf, hypothetical protein #67 rpoN 47 RNA polymerase, sigma(54 or 60) factor; nitrogen and fermentation regulation #68 yhbH 22 probable sigma-54 modulation protein #69 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #70 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #71 glvB 24 PTS system, arbutin-like IIB component #72 glvC 34 PTS system, arbutin-like IIC component #73 yidW 300 regulator protein for dgo operon #74 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #75 bglG 285 positive regulation of bgl operon #76 BIME185 97 BIME #77 pstC 86 high-affinity phosphate-specific transport system, cytoplasmic membrane component #78 pstS 300 high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein #79 trxA 76 thioredoxin 1 #80 rhoL 140 rho operon leader peptide #81 rho 84 transcription termination factor Rho; polarity suppressor #82 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #83 frvA 300 PTS system, fructose-specific IIA component #84 b3913 146 orf, hypothetical protein #85 yiiP 148 putative transport system permease protein #86 pfkA 180 6-phosphofructokinase I #87 frwC 300 PTS system, fructose-like enzyme II component #88 pflD 50 formate acetyltransferase 2 #89 melA 282 alpha-galactosidase #90 sgaT 291 orf, hypothetical protein #91 treB 118 PTS system enzyme II, trehalose specific #92 treR 300 repressor of treA,B,C #93 sgcA 130 putative PTS system enzyme II A component #94 sgcC 286 putative PTS system enzyme IIC component #95 sgcX 300 putative lyase/synthase Motif number 1 TCAACACAATAAAAAACCACGGGGCATCGCA 7 41 0 AAAAAACACG 0.59803 -35 GGAGTATATGAATAAATCCCGGCAGCGGATA 10 124 0 AATAAACCCG 0.690771 -61 TTTTATCTGAAAAAAGACGCGGTTTCATGCC 13 78 0 AAAAAGCGCG 0.722827 -183 AAAAGCTAAGAAAAAAGGCCCGCAAGCGGAC 22 37 0 AAAAAAGCCC 0.815681 -83 CTGTGTAATAAATAAAGGGCGCTTAGATGCC 23 195 1 AATAAAGGCG 0.74743 -100 TGAGAACGTAAAAAAAGCACCCATACTCAGG 23 261 1 AAAAAACACC 0.533051 -34 GAGTGATCACAAAAAAAGGCGTATATTTGCG 27 98 0 AAAAAAGGCG 0.919361 -108 TATAAAGATCGAAAAAAGCCGGAGTGATCAC 27 119 0 GAAAAAGCCG 0.599774 -87 AACGAATTATAAAAAGGCGCGAATAACTTAG 30 98 1 AAAAAGCGCG 0.722827 -189 CAAAATTTTAAATAAAGCTCCAATAAATCAT 30 201 1 AATAAACTCC 0.356023 -86 TCAGGCCAAAAAAAACCGGCGCAATGGCCGG 33 45 0 AAAAACGGCG 0.805511 -254 TCACGGGCTTGAAAAAGCGCCCAATGTATTC 34 142 1 GAAAAACGCC 0.772308 -60 CGATATCTAAAATAAATCGCGAAACGCAGGG 35 178 1 AATAAACGCG 0.815358 -123 CATCCGGCATAAAAACACGCGCACTTTGCTA 47 38 1 AAAAACCGCG 0.860729 -160 GTGAAAGGCAAAAAAACGGCCTCCCGATAGG 47 76 0 AAAAAAGGCC 0.897416 -122 CAAAAGATGGAAAAACTCGCCCGTAACGACC 49 158 1 AAAAACCGCC 0.825849 -27 CTCTATGAGAAAAAAAGCGCCAACCTGGCTT 50 245 0 AAAAAACGCC 0.928846 -56 CGCGTCTGTTAAAAACTGGCGCTAACAATAC 53 211 1 AAAAACGGCG 0.805511 -90 CGACGTGACGGAAAAATGCCGATGCTGAAAC 57 190 0 GAAAAAGCCG 0.599774 -67 TCAAGGTAATAAAAAAGGTCGCCGAAGCACC 59 17 0 AAAAAAGTCG 0.650377 -284 GTTTTCAGTAAATAAAGCGCGTTTCTTTGAC 60 133 0 AATAAACGCG 0.815358 -86 CCACATTAACAAAAAACCTCGGGCTTCCAGC 70 246 1 AAAAAACTCG 0.735159 -55 AAAAACACCCCTTCTTATGTT 70 290 0 AAAAACCCCC 0.705787 -11 AAAAACCTGAAAAAAACGGCCTGACGTGAAT 74 76 0 AAAAAAGGCC 0.897416 -58 TTTTATAAACAAAAAAACCCGACTTCACCAG 75 253 0 AAAAAACCCG 0.8959 -33 TTTTGTTTATAAAAAAGGTCCTTGCT 75 270 1 AAAAAAGTCC 0.588031 -16 ATAACAGGAAGAAAAATGCCCCGCTTACGCA 78 11 0 GAAAAAGCCC 0.534857 -290 ATTGAGGATAAAAAAAACCCCCACAGCATGT 85 56 0 AAAAAACCCC 0.868483 -93 CCGGTAAGTGAAAAAAGCGCCGCAAATAATA 92 134 1 AAAAAACGCC 0.928846 -167 AATGAGGATGAATAAAACGCGGTAACTGTTA 95 115 0 AATAAACGCG 0.815358 -186 ****** **** Masking position 5 Map Score: 27.7711 Number of sites scoring better than the average of aligned sites = 711 Number in coding regions = 486 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 2 AGGATTTCCTCCTGAACCGGCTTACAGAACGCA 8 15 0 CCTGCCGGCT 0.974443 -141 AGGAGGAAATCCTGATCCGGCTATTCCGAAAGT 8 35 1 CCTGCCGGCA 0.933986 -121 CGAAAGTTATCCGCCCCCGTCCTCCTCCCCCAA 8 61 1 CCGCCCGTCT 0.935296 -95 TTGACGCTATCCGCTGCCGGGATTTATTCATAT 10 117 1 CCGCCCGGGT 0.919882 -68 GGTGCTAAGGCCGCCTCCGGCAAGGTCAGCACT 13 17 0 CCGCCCGGCA 0.984877 -244 GGCCTTAGCACCCTCTCCGGCCAACGGTTCGAC 13 38 1 CCCTCCGGCA 0.945743 -223 GTTCTCTCCCCTGACTGGCTTTACTCAATAG 25 71 0 CCCTCTGGCT 0.890939 -21 GGCACGATTACCCGTACCGGCATCGA 31 4 0 CCCGCCGGCT 0.988931 -47 ACAAACGCAGCCTCACCTGGCATCAAATTTATG 37 31 1 CCTCCTGGCT 0.897678 -31 GCGTTTTACGCCGCATCCGGCAACCGTTGTCGG 38 27 0 CCGCCCGGCA 0.984877 -56 GCGTAAAACGCCTTATCCGTCCTACGGTTCTGT 38 49 1 CCTTCCGTCT 0.622798 -34 AGACACGCTACCGCCCCTGGCTTTTTAGCTACC 44 103 0 CCGCCTGGCT 0.968275 -198 TATGTTTACACCGCATCCGGCATAAAAACACGC 47 25 1 CCGCCCGGCT 0.994334 -173 CAGGGAGCCTGCCTTTCCGGCGTTGTTGTTATG 52 122 1 GCCTCCGGCT 0.902493 -82 GCGTAAAACACCGTACCCGGCCTGGAGTTTTA 77 10 0 CCGTCCGGCT 0.985864 -77 GTGTTTTACGCCGCATCCGGCATTACAAAATGA 77 32 1 CCGCCCGGCT 0.994334 -55 TAATCTTAATGCCGCGCTGGCGATGTTAGGAAA 82 67 1 GCCGCTGGCA 0.531836 -173 ACCAGATTAACCCGAATCGGCATGGAGTCAACG 93 104 1 CCCGTCGGCT 0.797721 -27 CTTGTGGCATGCGGTACCGGCATGTCGACTTCA 94 19 1 GCGGCCGGCT 0.963149 -268 **** ***** * Masking position 9 Map Score: 27.6523 Number of sites scoring better than the average of aligned sites = 881 Number in coding regions = 517 Number in noncoding regions = 364 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 ATTCACCACCCTGAATTGACTCTCTTCC 4 59 0 CCCTGAATTG 0.514268 -18 CCAATGATCTGAAGTTGAAACGTGATAGCCGT 23 134 1 GGTTGAAACG 0.63414 -161 GACTTTTTTTGTGGCTGAAAGGAGTATACGGT 33 186 0 GGCTGAAAGG 0.878593 -113 CTAACCCGTTGCTACTGAAACGACAAGCGACA 34 50 1 GACTGAAACG 0.845238 -152 CAAGCGACAGCGGGCTGAATGGTGGTTAAAAC 34 73 1 CGCTGAATGG 0.815912 -129 CTGTAAAATGGTTGCTGAATTATAGCTTGTTC 36 141 0 GGCTGAATTA 0.565081 -34 GGCTGCTGACGCTGCTGAAATGAAATTGCTGA 50 61 1 GGCTGAAATG 0.927429 -240 GCTTTCCTTGCGTGCTGAAACAGAAGTATTAT 50 172 1 CGCTGAAACA 0.765586 -129 AAGACAAGATCGCGCTGAAACGTTTCAAGAAA 50 206 0 CGCTGAAACG 0.966979 -95 TTTTCTCATAGAGGCTGAATCGTTTCAATTCA 50 263 1 GGCTGAATCG 0.975449 -38 GTTCTCCTCTCTTGCTGAATTGAAACGATTCA 50 278 0 CGCTGAATTG 0.886711 -23 CGCTGCAATTGGTGCTGAAACGATAAAGTAAT 52 67 1 GGCTGAAACG 0.977571 -137 CCAGTTCCGACAGGCTGAATCAA 53 2 0 CGCTGAATCA 0.748566 -299 AGGAAAAGCCAAAGCTGAATCGATTTTATGAT 53 79 1 AGCTGAATCG 0.723525 -222 GAAAAATGCCGATGCTGAAACGGAATTAAGAA 57 179 0 GGCTGAAACG 0.977571 -78 GCGTTTCTTTGACGCTGTAACGGTAACACAGC 60 114 0 GGCTGTAACG 0.737621 -105 CATAATGAAAGTCACTGAAACGAGAGTAGCTT 62 104 0 GACTGAAACG 0.845238 -145 TGCGAAATCTGGCACTGAATCGGTTAACTGTC 70 185 0 GACTGAATCG 0.832738 -116 CGCATGTTTGCAGCCTGAATCGTAAACTCTCT 84 90 1 CCCTGAATCG 0.783123 -57 ACAATCACTTCCTGCTGAATTGATTCAGGTCA 86 67 0 CGCTGAATTG 0.886711 -114 TTGGGCGGTAGTGGCTGAAATGCCCTGTTCAG 94 86 0 GGCTGAAATG 0.927429 -201 * ********* Masking position 6 Map Score: 21.3259 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 494 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 4 GGGAGAGGAGTTTTGACGGCTATCACCCTTTATCAACAAT 2 37 1 TTTGATCACT 0.950002 -68 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCC 3 15 1 ATTGATCACT 0.906845 -108 CGCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGTTATT 9 125 0 TTTGATCACA 0.933096 -176 TATGTGATCAATTTCACTTGATTGAAATTAT 12 88 0 ATTGATCACA 0.877394 -21 TGCGCTTTTTATCTGAAAAAAGACGCGGTTTCATGCCTGC 13 75 0 ATTGAACGCT 0.485671 -186 GTGCCAATTTGTTTGACGGCTATCACGTTTCAACTTCAGA 23 141 0 GTTGATCACT 0.749805 -154 TGACCTGTGGTTATGACCCTCTTCACATTTCGGGCAAATA 33 98 0 TTTGATCACT 0.950002 -201 ATTGTCGTTTTTGTGATCGTTATCTCGATATTTAAAAACA 47 125 1 TTTGATCTCA 0.561025 -73 TTTTTTATATTTGTGAAACCGGTCACCTGAATATTTTTCC 57 80 0 TTTGATCACA 0.933159 -177 ATATAAATATTTGTGATCTACAACACGCCTTATCTATTGC 59 67 0 TTTGAACACT 0.794073 -234 GATAATGGTTTTCTGATCTGATTCACAAAAGAAACATAAT 62 130 0 TTTGATCACA 0.933155 -119 TGGCATTTAAATGTGAGTAGTGTCACATTTTTGTTTTGAT 70 22 0 ATTGATCACT 0.906845 -279 CACAAGCGTTTTGTGATGAACGTCACGTCAATTACCTCTC 70 97 1 TTTGATCACA 0.933159 -204 CCCTATATTTATGTGATTGATATCACACAAAAGGCCGTCG 70 141 1 ATTGATCACA 0.877345 -160 ATTGATAAAAATATGACCATGCTCGCAGTTATTAACTTTG 75 84 0 ATTGATCGCT 0.823101 -202 CCGAGCGCCTTTTTGACTCTGTACACGGTTAACACTT 76 71 1 TTTGAACACT 0.794073 -27 AAACAGCGTCTTGTGAGACGCGTCGCAAATTGACGGTTAC 87 99 0 TTTGATCGCT 0.891499 -202 TTATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGAT 87 156 1 TTTGATCGCT 0.900764 -145 GGTCGAATAATTGTGAGAACGTTCACGTGAAAACGCGCAA 95 244 0 TTTGATCACA 0.933154 -57 ** *** **** * Masking position 4 Map Score: 18.7827 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 32 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 ACTGATTTTCGGCTAAGGAGGAAGGCG 2 88 1 GGTGGGAAGC 0.960014 -17 CGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCC 3 47 0 GCTAGGAAAC 0.713659 -76 TCTGTAAGCCGGTTCAGGAGGAAATCCTGATCCGGC 8 20 1 GGTGGGAAAC 0.98049 -136 GCTCCCCGTTGGATCGGGGATAAACCGTAATTGAGG 17 16 1 GGTGGAAAAC 0.893207 -36 TTTTCCCCAGGCAACTGGGGAAAGACCAAACCGGGC 18 43 1 GCAGGGAAGC 0.838468 -68 CGCAACATGAGCATTTTGTGCAAATCGCGG 20 5 0 GCTTGGAAAC 0.713659 -206 TCTCACGCGTGGCAAGGGGGGAGAGCCTCGCCGTGT 23 230 0 GGAGGGAGAC 0.704174 -65 TTTTGAATAAGCATGTGGCGAAAACAGATTTTTATT 30 149 1 GCTGGGAAAA 0.81464 -138 AACGGTTGCCGGATGCGGCGTAAAACGCCTTATCCG 38 32 1 GGTGGGAAAC 0.98049 -51 TCTGTCAATAGCCTGCGGATGAAATCAATTTTTTTA 44 164 1 GCTGGTAAAC 0.893207 -137 TTTTTATGCCGGATGCGGTGTAAACATACGTGGCAG 47 17 0 GGTGGGAAAA 0.81464 -181 CGCCAACCTGGCTTAGGGTTAAAGACAAGATCGCGC 50 223 0 GCTGGTAAGC 0.799827 -78 ATCTGACCCCGCATAAGGAATAGAAC 52 1 0 GCTGGAAGAC 0.646935 -203 AAAATGACATGCGTCGGGCAGAAATCTGAAAAGGGA 73 106 0 GCTGGAAAAC 0.893206 -195 GAGAGGGTTAGGGTGAGGGGAAAACCGTGTCAGCAA 76 13 0 GGTGGGAAAC 0.98049 -85 TTGTAATGCCGGATGCGGCGTAAAACACCGTACCCG 77 24 0 GGTGGGAAAC 0.98049 -63 AACCCCCACAGCATGTGGGGGAAGACAGGGATGGTG 85 36 0 GCTGGGAAGC 0.960014 -113 CGCCCCTCTGGGAAGAGGGTGAAAACCGTGCTCCCA 89 72 0 GGAGGTAAAC 0.643908 -211 ** * ** * *** * Masking position 12 Map Score: 17.2388 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 369 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 TATTGTGACGGAAAACGAACGCCACGCAAAGCTGA 15 82 0 GAAAAAGCAC 0.649939 -47 GTCATAGAGTCAAAGAAAAAGGCAGCCTGTGGTTG 16 110 0 CAAAAAGCAG 0.68367 -50 GACATCTAACGCCAGGGTTAGACGT 18 96 0 GACAAAGCAG 0.846816 -15 TTTTGAAATCGAAAACAAACGACAGGAT 47 180 1 GAAAAAGCAG 0.956783 -18 ATTCCTTCATGACAGGTAATGTAAGGTACGCGATG 49 17 1 GACAAAGAAG 0.849473 -168 ACTGGATCACGAAAATAAACGGCAGCACTGTCCGG 61 44 0 GAAAAAGCAG 0.956783 -104 TAGGCAAAACGAAATGAAACGAAAGTTTTACGAAA 62 20 0 GAAAAAGAAG 0.957629 -229 ATTCACAAAAGAAACATAATGAAAGTCACTGAAAC 62 115 0 GAAAAAGAAG 0.957629 -134 TGGTGAGATAAAAATAAAACGAAAGATAATGGTTT 62 159 0 AAAAAAGAAG 0.724135 -90 AGTATCAACTGAAACAAAACGAAAGATTAATATCG 62 200 1 GAAAAAGAAG 0.957629 -49 AGATCAAAACGAAAGAAAAAGAAAGGCCTTACGGG 63 42 0 GAAAAAGAAG 0.957629 -35 TCGTTGAAAGAAAAGATAAAGGAAGCAAAAGGGAT 64 11 0 AAAAAAGAAG 0.724135 -181 GGAGAAAAAAGAAATAAAACGAAATTTGTGATCGT 64 42 0 GAAAAAGAAT 0.561174 -150 CAAGTGAAATGAAACGAAAGGCAAGTGAAAGCGAC 64 128 1 GAAAAAGAAG 0.957629 -64 GCCATGCTTAGAAAATCAACGCAAGACGAAGGGTG 66 15 0 GAAAAAGAAG 0.957629 -195 GGCTAAAAAGTAAAACAAATGCCAGCTTTCGCTAA 66 101 0 TAAAAAGCAG 0.593202 -109 **** ** * *** Masking position 8 Map Score: 16.1557 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 29 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TCCTCCTGAACCGGCTTACAGAACGCAAGGA 8 8 0 CGGCTTCAGC 0.922306 -148 AGCGTCAAGCCTGGCTTGCAGAAAAACTCGGAAT 10 91 0 CGGCTTCAGA 0.985745 -94 TGCGGAGTGTCTGGCTGACAGATAATCGTCGATG 33 264 1 CGGCTGCAGA 0.928685 -35 ACTGGTCTTTCAGGCATCCAGACACGCTACCGCC 44 121 0 CGGCATCAGA 0.933878 -180 TACGGCTTTCCTTGCGTGCTGAAACAGAAGTATT 50 168 1 CTGCGTCTGA 0.566975 -133 GCCGGAAAGGCAGGCTCCCTGTAAATATCGATCT 52 109 0 CGGCTCCTGA 0.895879 -95 CAAAAAACCTCGGGCTTCCAGCCTGCGCGACAGC 70 255 1 CGGCTTCAGT 0.952914 -46 TACCCGGGCTTGCAGGCAAAAAAGAGAT 72 17 0 CGGCTTCAGA 0.985745 -18 AAAATATGACCATGCTCGCAGTTATTAACTTTGT 75 83 0 CTGCTCCAGA 0.936079 -203 TGACTCACGCCGGGCGTCCAGTTTTTAGCGACGG 80 33 0 CGGCGTCAGT 0.864749 -108 AATGCATGCTCTCAGAGAAAATTATTAG 82 222 0 CTGCTCCAGA 0.936079 -18 CAGAAAACCTCCGGCTTCCAGGTTGAGCATTCCC 89 210 0 CGGCTTCAGT 0.952914 -73 CGTGAAAAGACGGGCTTACCGGAAAAGTTTTAAT 92 58 1 CGGCTTCCGA 0.916013 -243 TAACGTTACCCGTGCATTCAGCAATGGGTAAAGT 92 239 0 CTGCATCAGA 0.818539 -62 ATGGCGCCGCCCTGCTCACAGGGATCAACGACGA 94 212 1 CTGCTCCAGA 0.936079 -75 * ***** *** * Masking position 9 Map Score: 13.486 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 319 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 AACTCCTCTCCCCCAAATCCAGAGGAGAGGAAATAGC 2 12 0 CCCATCGGGG 0.956347 -93 ACGGTTTATCCCCGATCCAACGGGGAGCACCAA 17 7 0 CCCCCAGGGG 0.98396 -45 TTATTCACCGCCCAATTTTCGGCGGTGAACTTTACTC 23 48 0 CCCTTCGGGG 0.886317 -247 CGCTTAGATGCCCTGTACACGGCGAGGCTCTCCCCCC 23 214 1 CCCACCGGAG 0.956387 -81 GGTGATTCTACACCATCCACTGCGGACGCAAAACGTA 28 38 1 CACCCCGGGC 0.687296 -97 GCTACTGCAATCCACAACGAAGCGGCGTAACATCACA 36 56 1 TCCACAGGGG 0.862752 -119 GTTATTAGCCCCTTACCCGCAGTGGGGTAAGGGAAGA 39 18 0 CCTCCCGGGG 0.928501 -37 CAATAGTTGGCCCTGACCGAAGCGGCCAATTTTATTT 40 59 0 CCCCCAGGGC 0.951187 -46 GAGGTTATCCCCCTTAACAATCAGGAGTTTTT 45 26 1 CCCACACGGG 0.832133 -22 AAGCATCACGCCCCGCACAAGGAAGCGGTAGTCACTG 56 53 1 CCCACAGAGG 0.766505 -203 GATAAGCACTTCCTCTACAATGGGGGCGCACATCAGG 60 173 1 TCCACAGGGC 0.666319 -46 CTCACCCTAACCCTCTCCCCAGAGGGGCGAGGGGACC 76 32 1 CCCCCCGGGG 0.992876 -66 CCCTGTCTTCCCCCACATGCTGTGGGGGTTTTTTTTA 85 42 1 CCCATCGGGG 0.65306 -107 ACGGTTTTCACCCTCTTCCCAGAGGGGCGAGGGGACT 89 79 1 CCCTCCGGGG 0.981986 -204 CGGGAACGTTCCCGAAACGCAGCGAAGATCACAATTT 91 27 0 CCCACCGGAG 0.956389 -92 AATGGCGCCGCCCTGCTCACAGGGATCAACGACGACG 94 211 1 CCCTCCGGAC 0.712376 -76 GAGGGAGCGTCCTGCAACAAAGTGGTGCTATAACAGT 95 85 1 CCTACAGGGG 0.862752 -216 *** ** * * ** * Masking position 14 Map Score: 15.2042 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 270 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 CTCTGGATTTGGGGGAGAGGAGTTTTGACG 2 25 1 GGGGGAGAGG 0.959656 -80 AAGGATATTTGGGGGAGGAGGACGGGGGCG 8 72 0 GGGGGAGGAG 0.867027 -84 CATTAGGCTATGGCAAGGTGATCAGATTTT 8 121 1 TGGCAAGGTG 0.684084 -35 TTCTCACGCGTGGCAAGGGGGGAGAGCCTC 23 237 0 TGGCAAGGGG 0.939705 -58 ACCCCACTGCGGGTAAGGGGCTAATAACAG 39 27 1 GGGTAAGGGG 0.899704 -28 AATAAAAGGATAGCGAGGGGAATGAGTTGA 56 112 0 TAGCGAGGGG 0.832278 -144 TTGCGTCAATGGGCAAGGTGGGCTTGCATT 62 76 0 GGGCAAGGTG 0.844942 -173 GAGAGGGTTAGGGTGAGGGGAAAACCGTGT 76 19 0 GGGTGAGGGG 0.957581 -79 CTCGCCCCTCTGGGGAGAGGGTTAGGGTGA 76 33 0 TGGGGAGAGG 0.904327 -65 CTCCCCAGAGGGGCGAGGGGACCGACCGAG 76 46 1 GGGCGAGGGG 0.98997 -52 CTCGCCCCTCTGGGAAGAGGGTGAAAACCG 89 80 0 TGGGAAGAGG 0.789744 -203 CTTCCCAGAGGGGCGAGGGGACTCTCCGAG 89 93 1 GGGCGAGGGG 0.98997 -190 AATCTCCGTCGAGGGAGAGGCGTGGGATCA 92 89 1 GAGGGAGAGG 0.750597 -212 ********** Masking position 6 Map Score: 12.4535 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 138 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 GTTGGGAGTATTTCCCGCTAAAATTGTTTAAA 6 203 1 TTCCGCTAAA 0.823961 -98 GGCAGTACAATTTGCAGCAAAATAAAAATACG 9 238 1 TTGCGCAAAA 0.943257 -63 CCGTAGTGAACATGCTGCCACACTAACAATTC 22 81 1 CTGCGCCACA 0.70549 -39 AAAAGTTTGATGTGCTGCACAATTTTTTGCCA 50 125 0 TTGCGCACAA 0.866674 -176 CATTAAACATTATGCCGCTAAAGGAAGAATTG 53 117 0 TTGCGCTAAA 0.8742 -184 ACGGCAGCACTGTCCGGCAAAAACGATTGCCG 61 29 0 TTCCGCAAAA 0.918011 -119 ATTTTGACTTTATGCGGCTAAAAAGTAAAACA 66 119 0 TTGCGCTAAA 0.874202 -91 AGAATCGTACTCTCCTGCTAAAACGTCGCAAA 67 22 0 TTCCGCTAAA 0.823966 -26 AATGGCCCGTTGTGCCGCACAACAGACCGCCA 69 35 0 TTGCGCACAA 0.866674 -83 TCCGGCTACCTCTGCCGCCACATTAACAAAAA 70 229 1 TTGCGCCACA 0.761859 -72 GTTTTACCGCAAAACTGGATCCCG 71 3 1 TTACGCAAAA 0.592214 -22 CCTCTACCGCTTTGCGGCAAAACTCCAAAAAA 74 105 0 TTGCGCAAAA 0.943257 -29 GCCAGAGATGCCTCCGGCACAATATTTTAAAT 83 22 1 CTCCGCACAA 0.766254 -279 TGCAAGAAGACTTCCGGCAACAGATTTCATTT 86 134 1 CTCCGCAACA 0.823183 -47 AAACCGGAAGCATGCCGCAAAACAGCGTCTTG 87 126 0 CTGCGCAAAA 0.925629 -175 GAAGAGGGAGCGTCCTGCAACAAAGTGGTGCT 95 82 1 CTCCGCAACA 0.823183 -219 * *** ****** Masking position 3 Map Score: 11.1639 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 216 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 TTGGCAAAAGGCAACCACAGGCTGCCTTTTTC 16 99 1 GCAAACAGGC 0.802567 -61 GGCGCAGGTGGCAATAGCATGCCACTATTGAG 25 47 1 GCAAGCATGC 0.788535 -45 GAAACGACAAGCGACAGCGGGCTGAATGGTGG 34 66 1 GCGAGCGGGC 0.944835 -136 CCTTTTTCAGGCAATAGTTGGCCCTGACCGAA 40 75 0 GCAAGTTGGC 0.525481 -30 GGGGCGGTGCGAATGCAGGCGTCG 43 5 0 GCGAGCAGGC 0.989119 -20 CAACAACGCCGGAAAGGCAGGCTCCCTGTAAA 52 118 0 GGAAGCAGGC 0.946645 -86 GCTAAAAATGGAGAATGCAGGCGTGATCACAT 60 73 1 GAGAGCAGGC 0.877549 -146 TTTCTATTAAGCAAATGCAAGCCCACCTTGCC 62 63 1 GCAAGCAAGC 0.7887 -186 GCCGTGGTTAGCGAAAGCTGGCATTTGTTTTA 66 94 1 GCGAGCTGGC 0.966798 -116 TGTAGATACTGCGAAATCTGGCACTGAATCGG 70 194 0 GCGATCTGGC 0.786915 -107 TACCCGGGCTTGCAGGCAAAAAAGAGA 72 18 0 GGGCGCAGGC 0.81788 -17 AATCTGAAAAGGGATATCAGGCGCTAAACAGG 73 88 0 GGGATCAGGC 0.782729 -213 GATTGTTACTGCATTCGCAGGCAAAACCTGAC 75 207 1 GCATGCAGGC 0.857571 -79 GAAACAATAGGCAATCGCAGGCGGAGCAAACA 87 231 0 GCAAGCAGGC 0.982585 -70 **** ****** Masking position 12 Map Score: 9.36349 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 517 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 12 CCCTTTTACTGGCTAAACCAGAAAACTTATTTTATC 9 83 0 GGAAAAAAAC 0.940787 -218 CCAGGCAACTGGGGAAAGACCAAACCGGGCGGCGAC 18 49 1 GGAAAAAACC 0.714769 -62 ATTCTAGTGGGACAAAAAGATAAAACTCAGGCGGTC 21 35 0 GAAAAAAAAC 0.709615 -53 GTGAATGGTTGACAAAAGATGAAATAGAATACCTTT 27 60 0 GAAAAAAATA 0.342741 -146 ACTCTTTGACGGGAAAATTTAAAATAAA 32 3 0 GGAAAAAATA 0.772232 -82 TTCAGATAAGGGCTACAACCAAAAACCCCTGCGTTT 35 199 0 GGACAAAAAC 0.668313 -102 TCAGCAATTAGGAAAAATGGCAAAAAATTGTGCAGC 50 108 1 GGAAAAAAAA 0.92652 -193 ACCGTCCGGCGGTAAAAATAAAATACTCGTGCGGTT 59 248 0 GGAAAAATAC 0.576175 -53 AAAGTTCAATGGAGAAAAAAGAAATAAAACGAAATT 64 51 0 GGAAAAAATA 0.772232 -141 AAGTACATTGGGATAAATCATAAAAAACTAATGA 65 9 0 GGAAAAAAAA 0.92652 -158 GACTTTATGCGGCTAAAAAGTAAAACAAATGCCAGC 66 110 0 GGAAAAAAAC 0.940787 -100 GCACTAAGCGGGCAAAACCTGAAAAAAATTGCTTGA 74 41 1 GGAAAAAAAA 0.92652 -93 ACCGCTTTGCGGCAAAACTCCAAAAAAAAACCTGAA 74 96 0 GGAAAAAAAA 0.92652 -38 GATACATTGTGAGTAAATCACAAAAATAATGAATAA 83 106 1 GAAAAAAAAA 0.659791 -195 CAACTTCCCTGGCAAAAAGTCAAAAAATGGTCATTG 90 87 0 GGAAAAAAAA 0.92652 -205 TATATTGCGCGGAAAAATTTAAAAACGGGAACGTTC 91 53 0 GGAAAAAAAC 0.940787 -66 ** *** ***** Masking position 7 Map Score: 9.7567 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 58 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 GGCAGCGGATAGCGTCAAGCCTGGCTTGCAGAAAA 10 100 0 AGTCAGCGGC 0.974051 -85 GTAGATTTCATGCATCACGACAAGCGATGCAAGGA 27 174 1 TGTCAGCAGC 0.930069 -32 AGTATGGTAAAGCATCACGCCCCGCACAAGGAAGC 56 44 1 AGTCAGCCGC 0.87829 -212 AAAAATTGCTTGATTCACGTCAGGCCGTTTTTTTC 74 64 1 TGTCAGCGGC 0.990341 -70 TAAGTTAGCATGACTCACGCCGGGCGTCCAGTTTT 80 42 0 TGTCAGCGGC 0.990341 -99 CCTGCTGAATTGATTCAGGTCAGGCCAAATGGCGG 86 54 0 TGTCAGCGGC 0.990341 -127 TTGGCAGATTTGTCACATGGCAGGCCGTTGCCGTG 87 46 0 TGACAGCGGC 0.948387 -255 CTTGAATAACTTCATCATGGCAGGCGAATCTGCAG 89 241 0 TTTCAGCGGC 0.919679 -42 ** *** * * *** Masking position 7 Map Score: 6.09435 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 19 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 GGTATCGTCGCCGCCCGGTTTGGTCTTTCCCCAG 18 57 0 CCGCCGGTGT 0.550472 -54 GTTTGTCCTCCAGGGAGGGAAAAAATGATT 21 68 0 CCTCCGGAGA 0.672618 -20 GCCGTTATTGTTTCCAGGGAGATTATTT 24 5 0 TTTCCGGAAT 0.505846 -69 TTAAATTCTCCTGGACTGTTCGTGTTTTGA 26 182 0 TCTCCGGCGT 0.948135 -20 ATATAAACACCCTCCTGGTACGTTTTGCGTCCGC 28 59 0 CCTCCGGAGT 0.960018 -76 ATTCGTTACCTTTCCAGGGACGCTAATCTTTGAT 30 71 0 TTTCCGGAGT 0.9509 -216 TGACTCCATTTTTCCAGGAATGGTCGCAAAT 36 8 0 TTTCCGGAGT 0.9509 -167 AGCTTTGGCTTTTCCTGTAACGATTAATTTCGCG 53 61 0 TTTCCGTAGT 0.748662 -240 TTTCCTCTCCAGTTCAGATTACTGCGATA 62 230 0 TCTCCGTCGT 0.73765 -19 TAAAACTCCAGGCCGGGTACGGTGTTTT 77 5 1 ACTCCGGCGT 0.67922 -82 GGGCATTTTTCTTCCTGTTATGTTTTTAATCAAA 78 21 1 CTTCCGTAGT 0.642917 -280 AATGTCTCCTGGGAGGATTCATAAAGCA 78 283 0 TCTCCGGAGT 0.975445 -18 ATTCCTGGAATTTGCTGGCATGTTATGCAATTTG 82 100 1 TTTGCGGAGT 0.602732 -140 ACATATTACATCTCCCGGTAAGTTATATTTCCCT 83 72 1 TCTCCGGAGT 0.975445 -229 GCAGATCTCCTGGCTTGCTTGAATAACTT 89 264 0 TCTCCGGTGT 0.890272 -19 TTTTGACTTTTTGCCAGGGAAGTTGTTGTTGATT 90 98 1 TTGCCGGAGT 0.828642 -194 ***** ** * * * Masking position 7 Map Score: 9.48083 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 175 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 15 GCGCTTAGATGCCCTGTACACGGCGAGGCT 23 213 1 GCCCTGTACA 0.909333 -82 TAGCAATGTCGCCATGCACATTTACCTTGC 44 235 0 GCCATGCACA 0.942429 -66 AAAGCATCACGCCCCGCACAAGGAAGCGGT 56 52 1 GCCCCGCACA 0.961459 -204 AACACCGGTTTCCCTGCTCAATTGCTTTCA 59 215 1 TCCCTGCTCA 0.936238 -86 TAAATTGAGCGCCATGCTTAGAAAATCAAC 66 30 0 GCCATGCTTA 0.805562 -180 ACAACAGACCGCCATGCACATGCTAATTGC 69 19 0 GCCATGCACA 0.942429 -99 GAAGAAAAATGCCCCGCTTACGCA 78 5 0 GCCCCGCTTA 0.863269 -296 CGTTTTAACGTCCCTGCTCAG 92 2 0 TCCCTGCTCA 0.936238 -299 TGGCTGAAATGCCCTGTTCAGTCAGGAACT 94 77 0 GCCCTGTTCA 0.936238 -210 TAATGGCGCCGCCCTGCTCACAGGGATCAA 94 210 1 GCCCTGCTCA 0.988364 -77 ********** Masking position 10 Map Score: 7.31691 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 208 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987