AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_ecoli_reg_100.orf -o00530_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 Input sequences: #1 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #2 yadI 104 putative PTS enzyme II B component #3 hlpA 121 histone-like protein, located in outer membrane or nucleoid #4 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #5 dniR 71 transcriptional regulator for nitrite reductase (cytochrome c552) #6 prpB 238 putative phosphonomutase 2 #7 ushA 217 UDP-sugar hydrolase (5'-nucleotidase) #8 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #9 ybeX 89 putative transport protein #10 ybeZ 113 putative ATP-binding protein in pho regulon #11 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #12 nagB_nagE 332 nagB: glucosamine-6-phosphate deaminase, nagE: PTS system, N-acetylglucosamine-specific enzyme IIABC #13 seqA 184 negative modulator of initiation of replication #14 pgm 25 phosphoglucomutase #15 hrsA 108 protein modification enzyme, induction of ompC #16 ycaI 129 orf, hypothetical protein #17 msbA 36 ATP-binding transport protein; multicopy suppressor of htrB #18 htrB 224 heat shock protein #19 rne 80 RNase E, membrane attachment, mRNA turnover, maturation 5S RNA #20 ptsG 294 PTS system, glucose-specific IIBC component #21 cls 300 cardiolipin synthase, a major membrane phospholipid; novobiocin sensitivity #22 ydcH 72 orf, hypothetical protein #23 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #24 malX 174 PTS system, maltose and glucose-specific II ABC #25 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #26 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #27 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #28 manX 300 PTS enzyme IIAB, mannose-specific #29 msbB 119 suppressor of htrB, heat shock protein #30 wcaA 34 putative regulator #31 BIME92 24 BIME #32 wza 300 putative polysaccharide export protein #33 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #34 gatZ 28 putative tagatose 6-phosphate kinase 1 #35 gatY 197 tagatose-bisphosphate aldolase 1 #36 fruB 300 PTS system, fructose-specific IIA/fpr component #37 ptsH 300 PTS system protein HPr #38 ptsI 44 PEP-protein phosphotransferase system enzyme I #39 crr 40 PTS system, glucose-specific IIA component #40 mltB_srlA 255 mltB: membrane-bound lytic murein transglycosylase B, srlA: PTS system, glucitol/sorbitol-specific IIC component, one of two #41 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #42 mltA 208 membrane-bound lytic murein transglycosylase A #43 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #44 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #45 mutY 160 adenine glycosylase; G.C --> T.A transversions #46 yggX 27 orf, hypothetical protein #47 mltC 61 membrane-bound lytic murein transglycosylase C #48 agaZ 248 putative tagatose 6-phosphate kinase 2 #49 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #50 murA 54 first step in murein biosynthesis;UDP-N-glucosamine 1-carboxyvinyltransferase #51 yrbA 144 orf, hypothetical protein #52 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #53 nanA 121 N-acetylneuraminate lyase (aldolase); catabolism of sialic acid; not K-12? #54 glgB 272 1,4-alpha-glucan branching enzyme #55 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #56 kdtA 300 3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase) #57 glvB 24 PTS system, arbutin-like IIB component #58 glvC 34 PTS system, arbutin-like IIC component #59 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #60 glmS 161 L-glutamine:D-fructose-6-phosphate aminotransferase #61 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #62 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #63 frvA 300 PTS system, fructose-specific IIA component #64 frwC 300 PTS system, fructose-like enzyme II component #65 pflD 50 formate acetyltransferase 2 #66 murB 300 UDP-N-acetylenolpyruvoylglucosamine reductase #67 aceB 268 malate synthase A #68 aceA 29 isocitrate lyase #69 BIME206 22 BIME #70 aceK 27 isocitrate dehydrogenase kinase/phosphatase #71 sgaT 291 orf, hypothetical protein #72 treB 118 PTS system enzyme II, trehalose specific #73 sgcA 130 putative PTS system enzyme II A component #74 slt 183 soluble lytic murein transglycosylase Motif number 1 CAGTTTAGCACAAAGAGCCTCGAAACCCAAATTC 1 21 0 CAAAGCCCGA 0.95431 -80 GTTAGTTAATCAAAACGCCGTCGTTAATCACCAA 9 46 0 CAAAGCCTCT 0.809794 -44 TAGAGAAATGAAAAAAGCACCCGACAGGTGCTTT 16 38 0 AAAAGCACCA 0.807723 -92 AAGACTGGGCGAAATTGCCGCGCTTGTAAATAAC 18 122 0 GAAAGCCCGT 0.730064 -103 TGAGAACGTAAAAAAAGCACCCATACTCAGGAGC 20 261 1 AAAAGCACCT 0.807723 -34 TGCAGTTGTTAAAAAAGCCGCCTGGCTGGCGGCT 23 20 0 AAAAGCCCCG 0.955146 -43 AAAACTGCCCTCATCGACGATTAT 27 285 0 AAAAGCCTCT 0.762546 -14 TGTAGCGGCGCAACTTGCCCCGCACCAAATAAAA 29 53 0 CAACGCCCGA 0.855849 -67 GAAAGGCAAAAAAACGGCCTCCCGATAGGGAAGC 35 71 0 AAAAGCCCCG 0.955146 -127 AAATCAAAAGCGCCACGAATAGTCAAAAT 36 6 1 AAAAGCCCGA 0.940315 -295 GTTTTATTACCAAACGGCAACCTAATCTAATCAG 40 34 1 CAAAGCACCA 0.847775 -222 ACGAAGATAACAAACCGCCGCGTTTAATGAAATG 42 152 0 CAAAGCCCGT 0.95431 -57 AAAACAAACACAACACGCACCCGGA 47 47 1 CAACGCACCG 0.617324 -15 CATAAATAAGCAAAAAGCCTCGCTGATAAATCAG 51 77 0 CAAAGCCCGT 0.95431 -68 ATTTTTAGCGAAAATCGCCGCCTTGTTGCTTTTT 55 61 1 AAAAGCCCCT 0.954333 -240 TGATATCACACAAAAGGCCGTCGACTGGACAGTT 55 158 1 CAAAGCCTCA 0.809794 -143 GTCTTATGCCAAAAACGCCACGTGTTTACGTGGC 62 15 1 AAAAGCCCGG 0.941362 -225 GATATAAAAGCAAAACGCCACGTAAACACGTGGC 62 31 0 CAAAGCCCGA 0.95431 -209 GTAGAAACGCAAAAAGGCCATCCGTCAGGATGGC 66 194 0 AAAAGCCTCG 0.765928 -107 CAGATACGGTAAACTAGCCTCGTTTTTGCATCAG 66 267 1 AAACGCCCGT 0.817464 -34 TTCGGAAATAAAAAAGGCACCCGAAGGTGCCTGA 67 53 0 AAAAGCACCA 0.807723 -216 **** *** ** * Masking position 3 Map Score: 22.1614 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 431 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 CTCATTCTTACGATTGCGGCAGGCCGTGTTA 4 47 1 CGATGCGGCA 0.861285 -58 TTAAAGATGCCTAATCCGCCAACGGCTTACA 12 291 1 CTAACCGCCA 0.722622 -42 TGACGCTATCCGCTGCCGGGATTTATTCATA 13 118 1 CGCTCCGGGA 0.798982 -67 ACGCTGCATGCGCCAGCGCCCCACTTCCGTT 21 124 1 CGCCGCGCCC 0.78498 -177 ACTTTCCTAAGCCGCCAGCCAGGCGGC 23 7 1 CTAACCGCCA 0.722622 -56 TCGATGCCGGTACGGGTAATCG 25 2 1 CGATCCGGTA 0.663979 -49 AACATCCATTCGCAGCCGGTACGCAGTCAGT 29 13 1 CGCACCGGTA 0.841215 -107 CATCCAGACACGCTACCGCCCCTGGCTTTTT 32 110 0 CGCTCCGCCC 0.957499 -191 CGCACCTGCCATTTAACAAGG 34 1 1 CGCACTGCCA 0.688523 -28 ATGTTTACACCGCATCCGGCATAAAAACACG 35 26 1 CGCACCGGCA 0.984677 -172 TTATCATGCTTGCATCCGGCAACTAACTTTG 45 56 0 TGCACCGGCA 0.833475 -105 TGCCGGAGCACGCCTCCGGCAACTTGCATAA 47 17 1 CGCCCCGGCA 0.97121 -45 AATTCATATCCGCTACCGGCGAATCGCCCAT 50 14 0 CGCTCCGGCG 0.933948 -41 ATCTGGGGCGCGATGCCGCCCCTGTTAGTGC 54 25 1 CGATCCGCCC 0.903966 -248 GTCCGGCTACCTCTGCCGCCACATTAACAAA 55 228 1 CTCTCCGCCA 0.847687 -73 TCCCCGCTGACGAAAGCGCCATTTTCGACCA 61 171 0 CGAAGCGCCA 0.851034 -130 GTGCCAGAGATGCCTCCGGCACAATATTTTA 63 20 1 TGCCCCGGCA 0.731592 -281 TGTGGGAAAGCGAACCCGCCCTTGCGAGCGG 65 20 0 CGAACCGCCC 0.913388 -31 CGTTCAAATCCGCTCCCGGCGGATTTGTCCT 66 89 0 CGCTCCGGCG 0.934599 -212 ATACTTTTGACGAAGGCGGCAGGGATCGCAG 73 59 0 CGAAGCGGCA 0.874215 -72 **** ****** Masking position 8 Map Score: 18.7555 Number of sites scoring better than the average of aligned sites = 2121 Number in coding regions = 1748 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 ACGCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGT 12 156 1 TTTGGATCAC 0.978243 -177 TATGTGATCAATTTCACTTGATTGAAA 15 92 0 TATGGATCAC 0.948801 -17 CCTCGCAGAGTTTTGAACAGTTTTCACCCTTTCGTTA 16 90 1 TTTTAATCAC 0.577297 -40 TATTGTCGTTTTTGTGATCGTTATCTCGATATTTAAA 35 124 1 TTTGGATCTC 0.743598 -74 TCCCGGGTTCTTTTAAAAATCAGTCACAAGTAAGGTA 38 13 1 TTTTAATCAC 0.577297 -32 TATCTTTCATTTTGCGATCAAAATAACACTTTTAAAT 40 76 0 TTTGGATAAC 0.641328 -180 ATTTTTTATATTTGTGAAACCGGTCACCTGAATATTT 41 84 0 TTTGGATCAC 0.978243 -173 CATATAAATATTTGTGATCTACAACACGCCTTATCTA 44 71 0 TTTGGAACAC 0.743598 -230 AAATATCAATTATGTAATATGCATCACGATATGCGGT 44 112 1 TATGAATCAC 0.751469 -189 TAATGCCCGTTTTCAGAACACTTTCACAAGCGACTAA 45 17 0 TTTCGATCAC 0.909974 -144 AGATAATGGTTTTCTGATCTGATTCACAAAAGAAACA 48 134 0 TTTCGATCAC 0.909974 -115 GAAAGCTTATAATGCGATCTGCTTCACTAAAGTGGCA 53 11 0 AATGGATCAC 0.689138 -111 GTATATCGTTTATCAGACAAGCATCACTTCAGAGGTA 53 92 1 TATCGATCAC 0.806426 -30 TCAAAACAAAAATGTGACACTACTCACATTTAAATGC 55 23 1 AATGGATCAC 0.689138 -278 ACACAAGCGTTTTGTGATGAACGTCACGTCAATTACC 55 96 1 TTTGGATCAC 0.978243 -205 CCCCTATATTTATGTGATTGATATCACACAAAAGGCC 55 140 1 TATGGATCAC 0.948801 -161 GAAAGCGCCATTTTCGACCATCGTCACGCCTTTTGTC 61 154 0 TTTTGATCAC 0.89328 -147 TTGTCCAGCTTTTGGCAGATTTGTCACATGGCAGGCC 64 55 0 TTTGCATCAC 0.767705 -246 TAACCGTCAATTTGCGACGCGTCTCACAAGACGCTGT 64 100 1 TTTGGATCAC 0.978243 -201 TGTGGAATTATTTGCGGGTCGCGTCACATTTAATCAT 71 226 1 TTTGGGTCAC 0.811261 -66 TCACTCTAATTTTCAAAAGTAATCACAACAAGATTA 71 266 0 TTTTAATCAC 0.577297 -26 **** ** **** Masking position 3 Map Score: 22.1588 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 56 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 GCGTTTCAGTTAACGTTTCAGGCAATGTTTC 6 83 0 TACGTTTCAG 0.930281 -156 ATCCGCAAATATGCGTTTCAGTTAACGTTTC 6 95 0 ATCGTTTCAG 0.903027 -144 TCCACAATCGAATCGATTCAGATAAGGGCTA 28 220 0 AACGATTCAG 0.965742 -81 TGCTTTCTTGAAACGTTTCAGCGCGATCTTG 36 203 1 AACGTTTCAG 0.971014 -98 TGCTGAATTGAAACGATTCAGCCTCTATGAG 36 267 0 AACGATTCAG 0.965742 -34 GCGCGAAATTAATCGTTACAGGAAAAGCCAA 37 60 1 AACGTTACAG 0.809759 -241 CAAATCATAAAATCGATTCAGCTTTGGCTTT 37 83 0 AACGATTCAG 0.965742 -218 GGTTTCTTAATTCCGTTTCAGCATCGGCATT 41 176 1 TTCGTTTCAG 0.787648 -81 CGCAAGCTACTCTCGTTTCAGTGACTTTCAT 48 101 1 TCCGTTTCAG 0.757139 -148 CTGGACAGTTAACCGATTCAGTGCCAGATTT 55 182 1 AACGATTCAG 0.965742 -119 GTCGATCGTTAAGCGATTCAGCACCTTACCT 67 23 1 AACGATTCAG 0.965742 -246 ** ******** Masking position 10 Map Score: 12.9896 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 23 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 GCAATGAAACGCGGTGAAACATTGCCTGAA 6 68 1 GCGGTGAAAC 0.874095 -171 AGGAGCCAGGGCAGGGATAACAA 11 4 0 GCAGGGATAA 0.488929 -56 AATTTTGGTTGCGGGCGAAAAAATGCGACA 18 164 1 GCGGGCGAAA 0.877594 -61 CGACTAAGCTGCGGGCAAAGTAACGCCTTT 19 33 0 GCGGGCAAAG 0.95812 -48 AAATAAAAACGCGGGAAAAGCACTGGTCAG 21 221 0 GCGGGAAAAG 0.960728 -80 TCAGTAAATTGCGCGAGAAGATAAAACGTT 24 124 0 GCGCGAGAAG 0.621015 -51 TTTATTTGGTGCGGGGCAAGTTGCGCCGCT 29 54 1 GCGGGGCAAG 0.8501 -66 AGACAAGATCGCGCTGAAACGTTTCAAGAA 36 207 0 GCGCTGAAAC 0.577687 -94 TGCACAATCGGCGGGAAAAATATTCAGGTG 41 67 1 GCGGGAAAAA 0.957539 -190 AAGCAATTGAGCAGGGAAACCGGTGTTTTG 44 212 0 GCAGGGAAAC 0.840359 -89 GTACCGTCCGGCGGTAAAAATAAAATACTC 44 256 0 GCGGTAAAAA 0.837981 -45 ATCCAGTTTTGCGGTAAAAC 57 1 0 GCGGTAAAAC 0.791574 -24 ACCCGGGCTTGCAGGCAAAAAAGAGATCTA 58 14 0 GCAGGCAAAA 0.785756 -21 ACCGCACTAAGCGGGCAAAACCTGAAAAAA 59 38 1 GCGGGCAAAA 0.95473 -96 GCTTTCGTCAGCGGGGATAATCCGTTATTG 61 185 1 GCGGGGATAA 0.846181 -116 GCCCTTGCGAGCGGGAGAAGAAC 65 4 0 GCGGGAGAAG 0.892663 -47 AGAATATATTGCGCGGAAAAATTTAAAAAC 72 63 0 GCGCGGAAAA 0.890379 -56 CTGGGATTAGGCGGGGAAAAAGGCTACACT 74 60 0 GCGGGGAAAA 0.976316 -124 GATCACCCTCGCAGTAAAAGTAAAAAAGTG 74 96 1 GCAGTAAAAG 0.493857 -88 ********** Masking position 9 Map Score: 13.7214 Number of sites scoring better than the average of aligned sites = 956 Number in coding regions = 834 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 6 CTCAGGCCTGCCGTTCCGGTGGGCCTTGTTTTTT 10 13 1 CCTCGGTGGC 0.744047 -101 TGAATAATTTCCTTATAGGCCGGTGA 10 98 1 CCTTGGCCGT 0.832265 -16 GAAAAAAGCACCCGACAGGTGCTTTTCTCTCGTT 16 29 0 CCGCGGTGCT 0.882812 -101 AAAAAAGCCGCCTGGCTGGCGGCTTAGGAAAGT 23 10 0 CCGCGGCGGT 0.994824 -53 TAACCCTAAGCCAGGTTGGCGCTTTTTTTCTCAT 36 238 1 CCGTGGCGCT 0.77403 -63 CAATACAGTCCATTGCTGGCGGGTGTTGACCGCT 37 163 0 CATCGGCGGT 0.963083 -138 GAACTAAAGTCTAGCCTGGCGGTTCGACTTTAGC 37 244 0 CTGCGGCGGT 0.943794 -57 GGCAGGTTTGCCGGACAGGCGGTTAACGCCATAT 51 26 0 CCGCGGCGGT 0.994824 -119 TTGCTTGATTCACGTCAGGCCGTTTTTTTCAGGT 59 69 1 CAGCGGCCGT 0.965679 -65 AATTTTTGCACAGGACTGGTGGGTTTGGAACGGA 62 148 1 CAGCGGTGGT 0.928784 -92 AGATTTGTCACATGGCAGGCCGTTGCCGTGCGCT 64 42 0 CAGCGGCCGT 0.965679 -259 CGTTCAAATCCGCTCCCGGCGGATTTGTCCTACT 66 86 0 CGTCGGCGGT 0.921582 -215 CTGCCCGCCACCCTCCGGGCCGTTGCTTCGCAAC 66 119 0 CCTCGGCCGT 0.978825 -182 AAGCAGAAGGCCATCCTGACGGATGGCCTTTTTG 66 185 1 CCTCGACGGT 0.837009 -116 CCCGCCTAATCCCAGCCGGTCGATCACCCTCGCA 74 75 1 CCACGGTCGT 0.693708 -109 ** * * ***** * Masking position 8 Map Score: 14.0043 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 752 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 CCGTATTTTTATTTTGCTGCAAATTGTACTGCC 12 51 1 ATTTGCTGCA 0.538698 -282 GAATTTAACCATTATGCCCGATAAATTCATCCT 15 31 1 ATTTGCCCGA 0.768123 -78 TAATTGCTATATCATGCCGCGGATTTTTACTTT 18 35 0 ATCTGCCGCA 0.972664 -190 GGTACGGGTAATCGTGCCGGTAAGAAAAGAGAG 25 19 1 ATCTGCCGGA 0.913093 -32 GTAGCGGCGCAACTTGCCCCGCACCAAATAAAA 29 53 0 AACTGCCCCA 0.607228 -67 ATGGCAAAAAATTGTGCAGCACATCAAACTTTT 36 124 1 ATTTGCAGCA 0.673119 -177 GTCATTAAACATTATGCCGCTAAAGGAAGAATT 37 118 0 ATTTGCCGCA 0.956697 -183 ATGGTAAAGCATCACGCCCCGCACAAGGAAGCG 40 197 0 ATCCGCCCCA 0.79832 -59 CTGTGCTGCAATCTTGCCCCCAACAACAGTGAA 45 128 1 ATCTGCCCCA 0.947557 -33 CTTGCAGGCAGGTTTGCCGGACAGGCGGTTAAC 51 33 0 GGTTGCCGGA 0.492034 -112 CAAATGGCCCGTTGTGCCGCACAACAGACCGCC 52 36 0 GTTTGCCGCA 0.93358 -82 CAGGGGCGGCATCGCGCCCCAGATTTAATGAAT 54 16 0 ATCCGCCCCA 0.79832 -257 TTTTTTTGGAGTTTTGCCGCAAAGCGGTAGAGG 59 104 1 GTTTGCCGCA 0.93358 -30 ATAAACCGGAAGCATGCCGCAAAACAGCGTCTT 64 127 0 AGCTGCCGCA 0.892523 -174 TATGGCGGGCGTCCTGCCCGCCACCCTCCGGGC 66 133 0 GTCTGCCCGA 0.77243 -168 CCGTTTTTAAATTTTTCCGCGCAATATATTCTG 72 61 1 ATTTTCCGCA 0.507853 -58 CGCGCAATATATTCTGCAGCCAACCAAAAATGT 72 78 1 ATTTGCAGCA 0.673119 -41 CAATGCAGCGTCATGCCGCGTAATAGATTTAT 74 162 0 GTCTGCCGCA 0.957694 -22 *** ****** * Masking position 13 Map Score: 14.8298 Number of sites scoring better than the average of aligned sites = 729 Number in coding regions = 674 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 TTGTGCTAAACTGGCCCGCCGAATGTATAGT 1 42 1 CTGGCCGCCG 0.91911 -59 TTCTCAGGCCTGCCGTTCCGGTGGG 10 5 1 CAGGCTGCCG 0.980121 -109 AGCGTCAAGCCTGGCTTGCAGAAAAACTCGG 13 94 0 CTGGCTGCAG 0.933074 -91 CATGCAGCGTCAGGCTAGCCGACGTAAATCG 21 103 0 CAGGCAGCCG 0.931641 -198 ACTGGTCTTTCAGGCATCCAGACACGCTACC 32 124 0 CAGGCTCCAG 0.936885 -177 GACTTGCAGGCAGGTTTGCCGGACAGGCGGT 51 37 0 CAGGTTGCCG 0.87253 -108 CAAAAAACCTCGGGCTTCCAGCCTGCGCGAC 55 255 1 CGGGCTCCAG 0.962409 -46 TACCCGGGCTTGCAGGCAAAAAAGA 58 20 0 CGGGCTGCAG 0.983715 -15 CCCATGTGACCGGGTTAGCCGGCCAGAA 60 8 0 CGGGTAGCCG 0.787103 -154 CCCGTTTTTTCGGGCGCCCCGAGCCTTGTAG 60 98 0 CGGGCCCCCG 0.925248 -64 CCCGAAAAAACGGGCATACAGGTTGACCGAC 60 115 1 CGGGCTACAG 0.871907 -47 CAGTTTATGGCGGGCGTCCTGCCCGCCACCC 66 140 0 CGGGCTCCTG 0.880404 -161 ***** ***** Masking position 9 Map Score: 12.0201 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 400 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 ATTCTTACGATTGCGGCAGGCCGTGTTATT 4 50 1 TTGCGGCAGG 0.715827 -55 ATAGACAAGTCTGCGTCCGGTGAAGATAAA 7 144 0 CTGCGTCCGG 0.925491 -74 CGGCAGCGGATAGCGTCAAGCCTGGCTTGC 13 106 0 TAGCGTCAAG 0.662784 -79 TGCGTATCCACAGCATCAGGAAGTGCATTC 21 42 0 CAGCATCAGG 0.906139 -259 CTGGCGCATGCAGCGTCAGGCTAGCCGACG 21 110 0 CAGCGTCAGG 0.983053 -191 AAGCACTGGTCAGCGTCGGGGGTGGGGGTA 21 204 0 CAGCGTCGGG 0.908745 -97 TTCATTTCAGCAGCGTCAGCAGCCAATCAG 36 55 0 CAGCGTCAGC 0.829489 -246 TGTGCAAAATTTGCGTCAGGGAGAGGCTGC 42 121 1 TTGCGTCAGG 0.94889 -88 CTTATCATGCTTGCATCCGGCAACTAACTT 45 58 0 TTGCATCCGG 0.493965 -103 TCAGTTGATACTGCGTCATGGTGAGATAAA 48 182 0 CTGCGTCATG 0.876967 -67 ACCTTAATTTAAGCGTCAGGTGGATGTTTT 61 105 0 AAGCGTCAGG 0.850453 -196 TGCCGCAAAACAGCGTCTTGTGAGACGCGT 64 116 0 CAGCGTCTTG 0.549169 -185 AGCCTCGTTTTTGCATCAGGAAAGCAGCT 66 282 1 TTGCATCAGG 0.755488 -19 CCTGAAAAAATAGTGTCAGGATTAATCAAA 71 53 0 TAGTGTCAGG 0.607832 -239 CAATGCAGCGTCATGCCGCGTAATA 74 169 0 CAGCGTCATG 0.91317 -15 ********** Masking position 7 Map Score: 10.5553 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 1030 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 10 GATACTCTTCCTGTCAAAATATAA 4 91 0 ATCTTCCTGT 0.913981 -14 ATGCTTGCGCCTTTTTCCTGTGGCGTGAATA 10 73 1 CTTTTCCTGT 0.780233 -41 TGCCCGATAAATTCATCCTGTAAATAATACA 15 45 1 ATCATCCTGT 0.929491 -64 TTTATTTTAAATTTTCCCGTCAAAGAGTTA 26 10 1 ATTTTCCCGT 0.69176 -75 TTGGCAGAGTAATTATCCTGTGCACTATTAA 32 265 0 ATTATCCTGT 0.927057 -36 AATTGAAACGATTCAGCCTCTATGAGAAAAA 36 262 0 ATCAGCCTCT 0.48484 -39 TTGATTCAGCCTGTCGGAACTGGT 37 4 1 ATCAGCCTGT 0.817568 -297 TTCAGCTTTGGCTTTTCCTGTAACGATTAAT 37 67 0 GTTTTCCTGT 0.658603 -234 GGCGGTTCGACTTTAGCCTGTATTGTTAGCG 37 230 0 CTTAGCCTGT 0.599586 -71 CGGATTTTATCCTGTTATCAGTAGG 41 242 0 TTTATCCTGT 0.867476 -15 AATATTATCCTGTAGAGGAGAGA 43 15 0 TTTATCCTGT 0.867476 -13 AAATCATCCTCTTTATCGACTC 46 16 0 ATCATCCTCT 0.734637 -12 GCTTGTCTTCCTGTTTTATTGTGT 54 259 0 TTCTTCCTGT 0.845498 -14 CTTTACCATTACTTTTCCCGTTTTTGACTTA 56 228 0 ATTTTCCCGT 0.69176 -73 AAAACCCCCCTGTTTTCCTGTTTATTCATTG 61 59 1 TTTTTCCTGT 0.840663 -242 TTATTGAACAATTTATCCTCTGTCCATTTCA 61 209 1 ATTATCCTCT 0.727451 -92 TGCCGTGCGCTCTTATCCTGTAAACAGAAAA 64 22 0 TTTATCCTGT 0.867476 -279 GTTTCTACAAACTCTTCCTGTCGTCATATCT 66 220 1 ATCTTCCTGT 0.913981 -81 * ********* Masking position 3 Map Score: 10.486 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 170 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 11 AGGAAAGTCACTTTTTCAGGGTTGCGATGT 7 11 1 CTTTTTCAGG 0.861653 -207 ATTGCGCCGGTTTTTTTTGGCCTGAGTTCT 27 51 1 TTTTTTTTGG 0.726987 -248 ATGAAATCAATTTTTTTAGGACTGATGCCA 32 182 1 TTTTTTTAGG 0.893916 -119 ATTTTTTCAGGCCGGATATGG 51 2 1 TTTTTTCAGG 0.9676 -143 ATCAAGCAATTTTTTTCAGGTTTTGCCCGC 59 48 0 TTTTTTCAGG 0.9676 -86 GTCAGGCCGTTTTTTTCAGGTTTTTTTTTG 59 82 1 TTTTTTCAGG 0.9676 -52 TTTTTCAGGTTTTTTTTTGGAGTTTTGCCG 59 93 1 TTTTTTTTGG 0.726987 -41 TGTATGCCCGTTTTTTCGGGCGCCCCGAGC 60 105 0 TTTTTTCGGG 0.888046 -57 AAAAATGTAGTTTTTTCAAGGTGAAGCGGT 61 247 1 TTTTTTCAAG 0.722929 -54 CCTGACACTATTTTTTCAGGAAGGCAATGA 71 63 1 TTTTTTCAGG 0.9676 -229 ********** Masking position 5 Map Score: 8.40632 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 60 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TTGATAAAGGGTGATAGCCGTCAAAACTCCTCTC 2 39 0 GTGACGTCAA 0.776162 -66 CGTGTCTTTTGTGAGTTTTGTCACCAAATATCGT 12 159 1 GTGATGTCAC 0.903214 -174 TTTCAATCAAGTGAAATTGATCACATA 15 92 1 GTGAGATCAC 0.809024 -17 AAGTTGAAACGTGATAGCCGTCAAACAAATTGGC 20 145 1 GTGACGTCAA 0.776162 -150 TGCCCGAAATGTGAAGAGGGTCATAACCACAGGT 27 102 1 GTGAGGTCAT 0.787678 -197 TTTAAATATCGAGATAACGATCACAAAAACGACA 35 127 0 GAGAGATCAC 0.580903 -71 TTTTATATTTGTGAAACCGGTCACCTGAATATTT 41 84 0 GTGAGGTCAC 0.832822 -173 TAGATAAGGCGTGTTGTAGATCACAAATATTTAT 44 71 1 GTGTGATCAC 0.556489 -230 CCCAACAACAGTGAATTCGGTGACC 45 146 1 GTGAGGTGAC 0.805735 -15 TGTTTCTTTTGTGAATCAGATCAGAAAACCATTA 48 134 1 GTGAGATCAG 0.681313 -115 TGCCACTTTAGTGAAGCAGATCGCATTATAAGCT 53 11 1 GTGAGATCGC 0.879282 -111 GCATTTAAATGTGAGTAGTGTCACATTTTTGTTT 55 26 0 GTGATGTCAC 0.903214 -275 CAAGCGTTTTGTGATGAACGTCACGTCAATTACC 55 99 1 GTGACGTCAC 0.513714 -202 CTATATTTATGTGATTGATATCACACAAAAGGCC 55 143 1 GTGATATCAC 0.639903 -158 GACAAAAGGCGTGACGATGGTCGAAAATGGCGCT 61 154 1 GTGAGGTCGA 0.785349 -147 ACAGCGTCTTGTGAGACGCGTCGCAAATTGACGG 64 103 0 GTGACGTCGC 0.900354 -198 **** ****** Masking position 11 Map Score: 11.8325 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 199 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 13 GTCAAAATATAAGAAACGACAATAATAACACG 4 71 0 AAAACGACAA 0.745676 -34 ATTCAGAAGAATTTAACGAAAGGGTGAAAACT 16 108 0 ATAACGAAAG 0.8511 -22 TGAAATCGAAAACAAACGACAGGAT 35 183 1 AAAACGACAG 0.967646 -15 TTAATGACGTACGAAACGTCAGCGGTCAACAC 37 143 1 AAAACGTCAG 0.825013 -158 GCAAAACGAAATGAAACGAAAGTTTTACGAAA 48 20 0 AAAACGAAAG 0.973161 -229 TGAGATAAAAATAAAACGAAAGATAATGGTTT 48 159 0 AAAACGAAAG 0.973161 -90 ATCAACTGAAACAAAACGAAAGATTAATATCG 48 203 1 AAAACGAAAG 0.973161 -46 CAAATAAAACGAAAGGCTCAGTCGA 66 4 1 AAAACGAAAG 0.973161 -297 CAAACAACAGATAAAACGAAAGGCCCAGTCTT 66 36 0 AAAACGAAAG 0.973161 -265 * ********* Masking position 6 Map Score: 7.28403 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 25 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 TTCTTGTCATCGGCTCCGTTCGCCGTTATGATCGG 5 18 1 CGGCCCGTCG 0.953534 -54 ATCCCTGCCCTGGCTCCTTGCTCAGGGCAATATTT 11 16 1 TGGCCCTTCG 0.713043 -44 TGCAGCCCTGTGGCACAATGGTCAACATAATACCC 13 43 0 TGGCCAATCA 0.722931 -142 CGCGGCAATTTCGCCCAGTCTTCAGCCACAAATTT 18 134 1 TCGCCAGTCG 0.801322 -91 TGGTTATTCACCGCCCAATTTTCGGCGGTGAACTT 20 53 0 CCGCCAATCG 0.917667 -242 ACGCATATTTCGGCGCGATTGCCCCTCAAGCCAAC 21 67 1 CGGCCGATCC 0.81028 -234 TTTTATCTTCTCGCGCAATTTACTGAATCCAGATT 24 128 1 TCGCCAATCG 0.804558 -47 CTTTTCTTACCGGCACGATTACCCGTACCGGCATC 25 13 0 CGGCCGATCG 0.964755 -38 CAAAAAAAACCGGCGCAATGGCCGGTTTCCGTTGT 27 35 0 CGGCCAATCG 0.942201 -264 GATAGTGTAGCGGCGCAACTTGCCCCGCACCAAAT 29 57 0 CGGCCAACCC 0.612695 -63 CCACGAGATGCGGCCCAATTTACTGCTTAGGAGAA 39 12 1 CGGCCAATCG 0.980067 -29 AATCGGCAAACGGTGCAGTACACTGCGTTGATTGC 41 27 0 CGGTCAGTCG 0.859465 -230 CCGATTGTCCTTGCACAATCGGCGGGAAAAATATT 41 56 1 TTGCCAATCG 0.643071 -201 ACCGTACAAATGGCCCGTTGTGCCGCACAACAGAC 52 40 0 TGGCCGTTCG 0.509196 -78 TTGACCTGAACGGCGCAGCACTCTGTGCATCCTCT 54 180 0 CGGCCAGCCG 0.909717 -93 AATCGGTTAACTGTCCAGTCGACGGCCTTTTGTGT 55 165 0 CTGTCAGTCG 0.37884 -136 CATTGAAACTCGGCCCCATTTTCAAATCTACATAG 56 130 0 CGGCCCATCA 0.750761 -171 GAGGCATCTCTGGCACATTGGGCAA 63 1 0 TGGCCATTCA 0.391631 -300 TCCCGGTACGGTTTTCTGTTTACAGGAT 64 4 1 CGGTCGGTCG 0.772568 -297 **** **** * * Masking position 6 Map Score: 11.832 Number of sites scoring better than the average of aligned sites = 1056 Number in coding regions = 989 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 15 AATTCTGTATTCGGCGTTGAGACTTCCTTC 7 97 0 TCGGCGTTGA 0.878473 -121 TTAATCACCAACGGCGGGGACGTCTGCCAG 9 27 0 ACGGCGGGGA 0.962269 -63 CGCCCAATTTTCGGCGGTGAACTTTACTCG 20 47 0 TCGGCGGTGA 0.981113 -248 CGCCGAAAATTGGGCGGTGAATAACCACGT 20 61 1 TGGGCGGTGA 0.85903 -234 CCTTGCACAATCGGCGGGAAAAATATTCAG 41 64 1 TCGGCGGGAA 0.957407 -193 AGGGTACCGTCCGGCGGTAAAAATAAAATA 44 259 0 CCGGCGGTAA 0.757129 -42 GGCGCTTTCGTCAGCGGGGATAATCCGTTA 61 182 1 TCAGCGGGGA 0.920428 -119 TTTGACGAAGGCGGCAGGGATCGCAGAAGG 73 55 0 GCGGCAGGGA 0.853444 -76 GTCAAAAGTATCGACGGGGATCGCTACCAG 73 79 1 TCGACGGGGA 0.920548 -52 TTAACCCGAATCGGCATGGAGTCAACGACG 73 110 1 TCGGCATGGA 0.775932 -21 CGGCTGGGATTAGGCGGGGAAAAAGGCTAC 74 63 0 TAGGCGGGGA 0.927258 -121 GGGTGATCGACCGGCTGGGATTAGGCGGGG 74 74 0 CCGGCTGGGA 0.858708 -110 ********** Masking position 10 Map Score: 6.58617 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 525 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096