AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_ecoli_reg_300.orf -o00650_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 Input sequences: #1 leuO 300 probable transcriptional activator for leuABCD operon #2 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #3 pdhR 300 transcriptional regulator for pyruvate dehydrogenase complex #4 aceE 160 pyruvate dehydrogenase (decarboxylase component) #5 rpsB 300 30S ribosomal subunit protein S2 #6 tsf 257 protein chain elongation factor EF-Ts #7 pyrH 146 uridylate kinase #8 frr 291 ribosome releasing factor #9 yaeM 91 putative ATP-binding component of a transport system #10 yaeS 185 orf, hypothetical protein #11 cdsA 120 CDP-diglyceride synthetase #12 yaeT 29 orf, hypothetical protein #13 hlpA 121 histone-like protein, located in outer membrane or nucleoid #14 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #15 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #16 ybaC 151 putative lipase (EC 3.1.1.-) #17 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #18 ybeX 89 putative transport protein #19 ybeZ 113 putative ATP-binding protein in pho regulon #20 yleA 145 orf, hypothetical protein #21 sdhC 300 succinate dehydrogenase, cytochrome b556 #22 ybiY 31 putative pyruvate formate-lyase 2 activating enzyme #23 pflB 54 formate acetyltransferase 1 #24 focA 300 probable formate transporter (formate channel 1) #25 htrB 224 heat shock protein #26 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #27 ycjL 121 probable amidotransferase subunit #28 ycjC 26 orf, hypothetical protein #29 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #30 goaG 37 4-aminobutyrate aminotransferase #31 ydbO 284 orf, hypothetical protein #32 ydcH 72 orf, hypothetical protein #33 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #34 gadB 300 glutamate decarboxylase isozyme #35 rspA 205 starvation sensing protein #36 b1582 134 orf, hypothetical protein #37 msbB 119 suppressor of htrB, heat shock protein #38 yebA 78 orf, hypothetical protein #39 yebL 24 putative adhesin #40 wcaA 34 putative regulator #41 BIME92 24 BIME #42 wza 300 putative polysaccharide export protein #43 gatD 47 galactitol-1-phosphate dehydrogenase #44 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #45 gatZ 28 putative tagatose 6-phosphate kinase 1 #46 gatY 197 tagatose-bisphosphate aldolase 1 #47 BIME96 27 BIME #48 b2097 184 orf, hypothetical protein #49 atoS 214 sensor protein AtoS for response regulator AtoC #50 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #51 atoB 30 acetyl-CoA acetyltransferase #52 pdxB 98 erythronate-4-phosphate dehyrogenase #53 b2654 300 orf, hypothetical protein #54 b2657 171 putative enzyme #55 b2658 138 orf, hypothetical protein #56 b2659 230 orf, hypothetical protein #57 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #58 yqeF 251 putative acyltransferase #59 tdcE 33 probable formate acetyltransferase 3 #60 tdcC 21 anaerobically inducible L-threonine, L-serine permease #61 tdcB 98 threonine dehydratase, catabolic #62 tdcA 188 transcriptional activator of tdc operon #63 gadA 210 glutamate decarboxylase isozyme #64 yhjA 300 putative cytochrome C peroxidase (EC 1.11.1) #65 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #66 ivbL 300 ilvB operon leader peptide #67 ilvL 300 ilvGEDA operon leader peptide #68 ilvG_1 139 acetolactate synthase II, large subunit, cryptic, interrupted #69 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #70 trxA 76 thioredoxin 1 #71 rhoL 140 rho operon leader peptide #72 rho 84 transcription termination factor Rho; polarity suppressor #73 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #74 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #75 frwC 300 PTS system, fructose-like enzyme II component #76 pflD 50 formate acetyltransferase 2 #77 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit Motif number 1 CCGCCTGAGGGCGGCTTCTTTTTGTGCCCA 7 25 1 GCGGCTTCTT 0.788559 -122 GATCTACTGAGCGGCGTTTTTGTCGTTCAA 9 15 0 GCGGCGTTTT 0.985731 -77 GGATCGGCTGGCGGCGTTTTGCTTTTTATT 9 50 1 GCGGCGTTTT 0.985731 -42 GTCAGATATGCCGTGGTTTTACACGGCTTT 10 106 1 CCGTGGTTTT 0.451319 -80 GTGGTTTTACACGGCTTTTTTTTGTATAGG 10 118 1 ACGGCTTTTT 0.784305 -68 CGTCGTCATCGCGGCGTTGTTTCTGTTGCC 11 64 1 GCGGCGTTGT 0.868495 -57 GTGATTAACGACGGCGTTTTGATTAACTAA 18 49 1 ACGGCGTTTT 0.865575 -41 TGCAATGCTTGCGCCTTTTTCCTGTGGCGT 19 69 1 GCGCCTTTTT 0.729778 -45 GCGTTGTAACGTGTCGTTTTCGCATCTGGA 21 125 1 GTGTCGTTTT 0.621059 -176 ACCTTCTTAAGTGGATTTTTTATTTACTGC 23 26 0 GTGGATTTTT 0.438976 -29 ATATCATGCCGCGGATTTTTACTTTCCCAT 25 30 0 GCGGATTTTT 0.795602 -195 CGCCAGCCAGGCGGCTTTTTTAACAACTGC 33 23 1 GCGGCTTTTT 0.975008 -40 TGTGATCACTCCGGCTTTTTTCGATCTTTA 35 118 1 CCGGCTTTTT 0.914974 -88 GCAGTCAGTACCGGCTTTTTTTATTTGGTG 37 35 1 CCGGCTTTTT 0.914974 -85 GCTACCGCCCCTGGCTTTTTAGCTACCAAT 42 100 0 CTGGCTTTTT 0.683864 -201 AGCAAAGTGCGCGTGTTTTTATGCCGGATG 46 38 0 GCGTGTTTTT 0.627414 -160 GTTTGCGCCGGCGGGGTTTTGGAATCGTGT 65 24 0 GCGGGGTTTT 0.96193 -82 CGCAAACCGGGCGGGGTTTTTCGTTTAAGC 65 47 1 GCGGGGTTTT 0.96193 -59 CCTCGCTCCGGCGGGGTTTTTTGTTATCTG 66 160 1 GCGGGGTTTT 0.96193 -141 ACGTAAACACGTGGCGTTTTTGGCATAAGA 73 16 0 GTGGCGTTTT 0.932829 -224 ACGTGTTTACGTGGCGTTTTGCTTTTATAT 73 34 1 GTGGCGTTTT 0.932829 -206 ********** Masking position 7 Map Score: 26.8829 Number of sites scoring better than the average of aligned sites = 1049 Number in coding regions = 892 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 2 GAGATGTGATCTGCCCGGCATTAAACCGCA 6 225 0 CTGCCCGGCA 0.543566 -33 AAAGAAGCCGCCCTCAGGCGGCTCCTTTTT 7 16 0 CCCTCAGGCG 0.511755 -131 ACCAGACTTACGCCCCCGCGATACTTACGC 8 43 0 CGCCCCCGCG 0.951094 -249 CCGGTTGCTGCGCGCTGGCCGTGACCAAAC 8 97 0 CGCGCTGGCC 0.636257 -195 ATGGCGAGCACTGCCCGGGGCCAAAATGGC 8 148 1 CTGCCCGGGG 0.542831 -144 AAGCAAAACGCCGCCAGCCGATCCGCAAGG 9 44 0 CCGCCAGCCG 0.792662 -48 AATGGCGAACCCCACCGGCGGCAACAGAAA 11 83 0 CCCACCGGCG 0.637274 -38 GTTCTTTGCGTGGCCCGGCGATCTTATATT 13 63 0 TGGCCCGGCG 0.810303 -59 AATAATAACACGGCCTGCCGCAATCGTAAG 14 53 0 CGGCCTGCCG 0.950099 -52 CTGCGTCTCGCGCGCTCCCGTCAGATTGTG 16 51 0 CGCGCTCCCG 0.71184 -101 TTCTCAGGCCTGCCGTTCCGGTGGG 19 6 1 AGGCCTGCCG 0.673297 -108 TGGCTGCGTTCGCTCCCCCGAATCACTTAC 29 121 0 CGCTCCCCCG 0.493346 -154 AACGGGCATACGGCCCGGGGATCTCTGCGC 29 204 1 CGGCCCGGGG 0.916716 -71 GGGATCTCTGCGCCCTGACGTTCACAAACT 29 221 1 CGCCCTGACG 0.861787 -54 AAAAAGCCGCCTGGCTGGCGGCTTAGGAAA 33 13 0 CTGGCTGGCG 0.812357 -50 CCCGCTCTGTCGCCCTGGCGTTTAATAATT 38 39 1 CGCCCTGGCG 0.93666 -40 GGCAAAAAAACGGCCTCCCGATAGGGAAGC 46 71 0 CGGCCTCCCG 0.864843 -127 CATAATCTCGCGGCCAGGCATACTTGCGAA 52 34 0 CGGCCAGGCA 0.726605 -65 ATTCCAAAACCCCGCCGGCGCAAACCGGGC 65 29 1 CCCGCCGGCG 0.940044 -77 GACGAAACCTCGCTCCGGCGGGGTTTTTTG 66 153 1 CGCTCCGGCG 0.932162 -148 GCGGCACCAGCGGCCAGACGTTCTCAAGTT 69 244 0 CGGCCAGACG 0.700498 -57 GCCGCTGGTGCCGCCTGGCGCCAGTAATTC 69 260 1 CCGCCTGGCG 0.967543 -41 TAAAAACTGGACGCCCGGCGTGAGTCATGC 71 40 1 ACGCCCGGCG 0.708895 -101 ATCTTAATGCCGCGCTGGCGATGTTAGGAA 73 69 1 CGCGCTGGCG 0.962146 -171 CGCACGGCAACGGCCTGCCATGTGACAAAT 75 44 1 CGGCCTGCCA 0.754114 -257 AAGCTGCTCCCGGGCTTGCGAAAGCCCATG 75 281 0 CGGGCTTGCG 0.723104 -20 AAAGCGAACCCGCCCTTGCGAGCGGGAGAA 76 15 0 CGCCCTTGCG 0.842071 -36 CTACTCGCAACGCGACGGCGAGACAAATTT 77 16 1 CGCGACGGCG 0.53941 -279 ********** Masking position 5 Map Score: 23.1031 Number of sites scoring better than the average of aligned sites = 3709 Number in coding regions = 3547 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 3 TATTCACCAAATCAATATCAAAAAAAATCGCAA 1 120 0 ATAATATCAA 0.653075 -181 TTTAATTGAATTAAAAATCACAAAATTGGTAAG 3 29 1 TTAAAATCAA 0.718715 -272 TTGAGACAGAATAAAAAGCAAAACGCCGCCAGC 9 56 0 ATAAAAGCAA 0.642233 -36 CGCAGCCAGTTTCAATATCAGCAGGCGGGATCG 16 76 1 TTAATATCAA 0.602748 -76 CCCGAATAGGTTGAAAAACAGGATTGAT 25 207 1 TTAAAAACAA 0.820781 -18 TGCTTAACCTATGAAAATCAAAAGCTTACTCGC 26 199 0 ATAAAATCAA 0.760196 -102 TCGTGAATTAATTAAAAACACGAATCACATTGT 31 237 0 ATAAAAACAA 0.850344 -48 TATTTTTTCATTGAAAAACAATACAATATGAAA 34 148 0 TTAAAAACAA 0.820781 -153 ATATCTCACGATAAATAACATTAGGATTTTGTT 34 192 1 ATAATAACAA 0.771383 -109 GGACTCGTGTTTAAATAACAAAATCCTAATGTT 34 208 0 TTAATAACAA 0.731153 -93 TATCTGGTCGATAAAAAACAGTAAATGGCTTCA 56 81 0 ATAAAAACAA 0.850344 -150 TCTTATTGTGATCAAAAGCAACAAATTAGTAAC 56 201 0 ATAAAAGCAA 0.642233 -30 AAGTTAAAGTATAAAAATCAGCATAAACCCTGA 62 26 0 ATAAAATCAA 0.760196 -163 TTAAATACCTTTAAATATCAACAAGTTAAAGTA 62 48 0 TTAATATCAA 0.602748 -141 CAGGCTTAATTTAAATAACAAAATCCTAAGCAG 63 118 0 TTAATAACAA 0.731153 -93 TGTTCTGAAAATGAAAAACAACACCAAATCGGT 64 62 0 ATAAAAACAA 0.850344 -239 TATTTTATTTTTAAAAAACAACAATTTATATTG 67 169 1 TTAAAAACAA 0.820781 -132 TTTTTTTGACCTTAAAAACATAACCGAGGAGCA 68 60 1 CTAAAAACAA 0.516917 -80 GGAGCAGACAATGAATAACAGCACAAAATTCTG 68 87 1 ATAATAACAA 0.771383 -53 ** ******* * Masking position 2 Map Score: 13.5703 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 124 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 TTTATATCTGTGCGGTTTAATGCCGGGCAGA 6 215 1 TGCGGTTAAT 0.654197 -43 CTTGTGGGGCTGCGCTGAAAAGCGACGTACA 7 75 1 TGCGCTAAAA 0.868026 -72 GTTGTCGAAGTACGCAGTAAATAAAAAATCC 23 13 1 TACGCATAAA 0.608094 -42 TAGCGGAGGATGCGGAAAAAATTCAACTCAT 24 106 1 TGCGGAAAAA 0.938491 -195 TTTATGCAAATACGGAGTAAATATTTGATTA 24 169 0 TACGGATAAA 0.67245 -132 ACGCTACATTTGCGCATTAAAAATTATTTGT 25 93 1 TGCGCATAAA 0.930359 -132 TCGCCATTACTGCGCTTTAAATGACCTTTAT 27 85 0 TGCGCTTAAA 0.883986 -37 GTATAGCAACTGCGGAAAACATTAATGCACT 31 109 1 TGCGGAAACA 0.689992 -176 AGACACAGAATGCGCATAAAAATAACAGCAT 34 92 1 TGCGCAAAAA 0.920204 -209 GTCAATAGCCTGCGGATGAAATCAATTTTTT 42 167 1 TGCGGAGAAA 0.824402 -134 TTATGCCGGATGCGGTGTAAACATACGTGGC 46 19 0 TGCGGTTAAA 0.90976 -179 TAAATACCTTTGCGGTGAAAACTTGACCGCG 48 76 1 TGCGGTAAAA 0.896933 -109 TTGCTTCCATTGCGGATAAATCCTACTTTTT 63 158 1 TGCGGAAAAT 0.741145 -53 TTAGCCCTCTTGCGCACTAAAAAAATCGATC 77 134 1 TGCGCATAAA 0.930359 -161 ****** **** Masking position 9 Map Score: 7.57376 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 191 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TGCAACGCGTGCATTTTGTCCCCTTTTTCCTCG 1 51 0 GCATTTCCCC 0.947989 -250 CGGGAATTCTCGAGCTTGCCGCCTTTCTGCAAC 6 43 0 CGAGTTCGCC 0.910123 -215 TAGGGGGCCTGCATATGGCCCCCTTTTTCACTT 6 183 1 GCATTGCCCC 0.774392 -75 ATTTTATTTGCCATTTTGGCCCCGGGCAGTGCT 8 154 0 CCATTTCCCC 0.863515 -138 TAAGTTTACAGGATTTTTACCCCTAAGGGCTGA 20 39 1 GGATTTCCCC 0.972697 -107 ATGTATTGTCGCATTTTTTCGCCCGCAACCAAA 25 167 0 GCATTTCGCC 0.903146 -58 TACGGCCCGGGGATCTCTGCGCCCTGACGTTCA 29 212 1 GGATTCCGCC 0.77439 -63 TACCTGAGGGGGAGGTTATCCCCCTTAACAATC 43 15 1 GGAGTTCCCC 0.981783 -33 CACCTGAGGCGGAGCTTCGCCCCTTTGAAATAC 49 50 0 GGAGTTCCCC 0.982741 -165 TTTAATGCATGGAGGTTTTCCCATTCATCCTTA 54 130 0 GGAGTTCCCA 0.803594 -42 GTTAAGTATGGGAGATTAACGCCCTATCTACCC 58 69 1 GGAGTTCGCC 0.965891 -183 ACATTAAGTTCGAGATTTACCCCAAGTTTAAGA 72 50 1 CGAGTTCCCC 0.951908 -35 **** ** **** Masking position 3 Map Score: 10.118 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 115 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ACGTTTAGTTGCCGCGCTTTTATATGCGCTT 4 52 0 GCGCGCTTTT 0.958331 -109 TCGGAAGTCCGGCGCGCTTTATACCACAAAT 5 129 0 GGGCGCTTTA 0.856844 -172 GCGACATTGTACGTCGCTTTTCAGCGCAGCC 7 82 0 ACTCGCTTTT 0.59784 -65 GATCTACTGAGCGGCGTTTTTGTCGTTCAAG 9 14 0 GCGCGTTTTT 0.602357 -78 TGGGGGTCGCTTTTGCTGAAGTAT 11 4 1 GGTCGCTTTT 0.963257 -117 TCAGCAGGCGGGATCGCATTTTCATGGCAGT 16 93 1 GGTCGCATTT 0.923876 -59 GGGCGAAATTGCCGCGCTTGTAAATAACAAA 25 119 0 GCGCGCTTGT 0.879022 -106 ACACCTTTCAGCATCGCTTTTCGCCATTATA 26 28 0 GCTCGCTTTT 0.957573 -273 TAAAATGATTGGATCGCATTAAAAAAGTAGG 34 269 0 GGTCGCATTA 0.731127 -32 TCGATTCCTTGCATCGCTTGTCGTGATGCAT 35 183 0 GCTCGCTTGT 0.877006 -23 GCAGGAATATGGAGCGCATTTGAGGGTGTAT 55 77 1 GGGCGCATTT 0.925189 -62 GTTATGAGGCGGATCGCATTTTTGTACTGAT 75 165 1 GGTCGCATTT 0.923876 -136 CGCAAGGGCGGGTTCGCTTTCCCACAGGAGT 76 25 1 GGTCGCTTTC 0.831564 -26 ** ******** Masking position 9 Map Score: 8.12632 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 224 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 CTGGACGGAAGCGACAATCTCACTTTGTGTAAC 5 179 1 GCACAATCAC 0.88002 -122 GGATGAGCGAGCGAAGATAACGCATCTGCGGCG 6 100 1 GCAAGATCGC 0.853038 -158 TTACGCCCCCGCGATACTTACGCGGAATCTTAC 8 33 0 GCATACTCGC 0.819744 -259 CAAACTGCCTGCAACAATAACGCCTTATAACCA 8 69 0 GCACAATCGC 0.961962 -223 GGTCGCTTTTGCTGAAGTATCGCCTGATATCTG 11 15 1 GCGAAGTCGC 0.596418 -106 TAAAGTCATCGCTACACTACCACTACATTCCTT 13 23 0 GCACACTCAC 0.883795 -99 CATCTTTATTGCAATGCTTGCGCCTTTTTCCTG 19 60 1 GCATGCTCGC 0.757451 -54 TGCATTCCTGGCTACTATTTCGCAAGAGCAAGT 20 121 1 GCACTATCGC 0.731563 -25 CACATTTTACGCTACATTTGCGCATTAAAAATT 25 85 1 GCACATTCGC 0.873622 -140 ATTTACAAGCGCGGCAATTTCGCCCAGTCTTCA 25 125 1 GCGCAATCGC 0.533499 -100 TCAAATTTTTGCAAAGCTGACACCTTTCAGCAT 26 45 0 GCAAGCTCAC 0.633913 -256 AAGTTGCGCCGCTACACTATCACCAGATTGATT 37 71 1 GCACACTCAC 0.883704 -49 GGACAAGTGTGCCATAATCTCGCGGCCAGGCAT 52 43 0 GCATAATCGC 0.876835 -56 CAAAATTCGTGCCGAAATTGCGCGTTCTGCGCG 66 55 1 GCGAAATCGC 0.883715 -246 ATCACGCTCGGCAGAAATCACGCTCTGGATGAA 74 62 0 GCGAAATCGC 0.884668 -128 GCGCAAGAGGGCTAAATTATCACTGAAGATGAT 77 116 0 GCAAATTCAC 0.527159 -179 ** ***** *** Masking position 8 Map Score: 10.5441 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 699 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 8 ACAAAATGCACGCGTTGCAAAACCTATCCT 1 65 1 CGCGTTGCAA 0.632382 -236 CGCATATAAAAGCGCGGCAACTAAACGTAG 4 55 1 AGCGCGGCAA 0.969926 -106 CTTCATATTTCGCGCCGCAGATGCGTTATC 6 115 0 CGCGCCGCAG 0.952818 -143 TCACGGCCAGCGCGCAGCAACCGGAGCGTA 8 103 1 CGCGCAGCAA 0.917803 -189 GTTATTTACAAGCGCGGCAATTTCGCCCAG 25 122 1 AGCGCGGCAA 0.969926 -103 AAGCGCAATGCGCCCGGCAATCTATACACA 29 34 1 CGCCCGGCAA 0.921117 -241 TTTTATTTGGTGCGGGGCAAGTTGCGCCGC 37 53 1 TGCGGGGCAA 0.700237 -67 GTGATAGTGTAGCGGCGCAACTTGCCCCGC 37 64 0 AGCGGCGCAA 0.817477 -56 CAATCCTGCTCTCGCCGCAATCATGATATG 64 97 1 CTCGCCGCAA 0.793303 -204 TAACATCGCCAGCGCGGCATTAAGATTACA 73 65 0 AGCGCGGCAT 0.803839 -175 GATCTGATCACGCTCGGCAGAAATCACGCT 74 71 0 CGCTCGGCAG 0.731939 -119 AGGATAAGAGCGCACGGCAACGGCCTGCCA 75 34 1 CGCACGGCAA 0.88737 -267 TCTTGTGAGACGCGTCGCAAATTGACGGTT 75 101 0 CGCGTCGCAA 0.89977 -200 ********** Masking position 9 Map Score: 7.01995 Number of sites scoring better than the average of aligned sites = 865 Number in coding regions = 813 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ATAATTTTTACCAGAAAAATCA 4 1 0 CCGAAAAACA 0.963046 -160 TGAACTCTCGCCGGAAAGCTCAATAAGACAGG 4 87 0 CCGAAAGCCA 0.965126 -74 GGGACAGGTTCCAGAAAACTCAACGTTATTAG 4 121 1 CCGAAAACCA 0.955547 -40 CAGTTAACCACCCGTAAAAACAACC 16 4 0 CCGTAAAACA 0.804237 -148 TGTCTGGATGCCTGAAAGACCAGTCTGAATTA 42 131 1 CCGAAAGACA 0.971058 -170 AACAGAAAACGCTGAAAAAACATCCAAAAGAT 48 134 1 GCGAAAAACA 0.791082 -51 CGGCTGGTAACCGCAAAGCACACTGTATTATG 66 112 0 CCCAAAGCCA 0.80084 -189 CTGTATCGTTCCTGAAAAAACAGTTGCTGCCA 69 57 0 CCGAAAAACA 0.963046 -244 AACACATCACCCGGAAAGACCAGGTTGAAGCG 69 154 1 CCGAAAGACA 0.971058 -147 ** ****** ** Masking position 6 Map Score: 4.65908 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 98 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 CATATGCAGGCCCCCTAACCAAACGTGTAC 6 170 0 CCCCCTAACC 0.93537 -88 CTGGCTTATAGGCCCGTAACTCGCATGGTT 24 200 0 GGCCCGTAAC 0.726717 -101 CGCATTTTTTCGCCCGCAACCAAAATTTGT 25 161 0 CGCCCGCAAC 0.946082 -64 TGCGTTCGCTCCCCCGAATCACTTACCTGA 29 117 0 CCCCCGAATC 0.88343 -158 GGCGCAACTTGCCCCGCACCAAATAAAAAA 37 51 0 GCCCCGCACC 0.943862 -69 GGGAGGTTATCCCCCTTAACAATCAGGAGT 43 24 1 CCCCCTTAAC 0.825883 -24 TGGAAAAACTCGCCCGTAACGACCAGGATT 48 165 1 CGCCCGTAAC 0.917756 -20 AATGTTAACTCCCCCTAACCTGTTGCTTTA 56 125 1 CCCCCTAACC 0.93537 -106 TTAATTTGATCGCCCGAACAGCAATGTTTG 63 11 1 CGCCCGAACA 0.728466 -200 CGAACTAAGACCCCCGCACCGAAAGGTCCG 68 25 1 CCCCCGCACC 0.986025 -115 TCAAAAAAAACCCCCGGACCTTTCGGTGCG 68 39 0 CCCCCGGACC 0.963396 -101 ********** Masking position 8 Map Score: 6.28733 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 189 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 CCAAATCAATATCAAAAAAAATCGCAAAAC 1 117 0 ATCAAAAAAA 0.838514 -184 TTACAAGATGGGCACAAAAAGAAGCCGCCC 7 33 0 GGCACAAAAA 0.803979 -114 TAAATCGCGAATCATAAAAAGCAAAGGATC 31 51 1 ATCATAAAAA 0.808232 -234 AGCCGGAGTGATCACAAAAAAAGGCGTATA 35 104 0 ATCACAAAAA 0.835785 -102 CACCGCATCCGGCATAAAAACACGCGCACT 46 33 1 GGCATAAAAA 0.772542 -165 AGGAGTGAAAGGCAAAAAAACGGCCTCCCG 46 81 0 GGCAAAAAAA 0.807115 -117 CGAGATAACGATCACAAAAACGACAATATG 46 122 0 ATCACAAAAA 0.835785 -76 GGCTCGATTCATCAGAAAAAATGTTAGCGC 48 104 0 ATCAGAAAAA 0.777485 -81 CCTGATTTTTGTCAAAAAAA 62 1 0 GTCAAAAAAA 0.863213 -188 CAAAATCCTAAGCAGAAAAACGACTTTTTA 63 103 0 AGCAGAAAAA 0.698509 -108 AGACAAAGCCATCATAAAAAACAGGGAGAT 64 211 0 ATCATAAAAA 0.808232 -90 TATTAAACGCATCATAAAAATCGGCCAAAA 67 206 1 ATCATAAAAA 0.808232 -95 TGTTTTTAAGGTCAAAAAAAACCCCCGGAC 68 50 0 GTCAAAAAAA 0.863213 -90 GAGACTTAAGGTCAAAAAAACAGAAGGGTA 74 15 0 GTCAAAAAAA 0.863213 -175 ********** Masking position 6 Map Score: 8.0373 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 76 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 TGATTAACTAACATGAGAACCCATACGACGC 18 68 1 ACATGAAACC 0.546386 -22 TAGGTTAAGCAAATCATCACCGCACTGACTA 26 221 1 AAATCACACC 0.902952 -80 GAGTTTGCAAAAATGAAAACCCACTGCTAGA 27 37 1 AAATGAAACC 0.683001 -85 CCTTATACGAACAACACCACCCC 47 15 1 ACAACACACC 0.87746 -13 CACCGCCGAGAAATCATCACCTTAACCTCTG 49 155 1 AAATCACACC 0.902952 -60 CTGAAAATGAAAAACAACACCAAATCGGTAT 64 60 0 AAAACACACC 0.927581 -241 GGGTCACAATAACTCACCACCGTGAGGGAAG 64 276 1 AACTCACACC 0.915095 -25 AATATTGTTAAACACAAAACCAACAAGGTCC 66 277 1 AACACAAACC 0.8704 -24 TTTGACCTTAAAAACATAACCGAGGAGCAGA 68 64 1 AAAACAAACC 0.852892 -76 ATCCATGGCCAACACATCACCCGGAAAGACC 69 144 1 AACACACACC 0.936858 -157 ATCTGGTACGACCAGATCACCTTGCGGATTC 74 158 1 ACCAGACACC 0.809292 -32 TTATCCTGTAAACAGAAAACCGTACCGGGA 75 10 0 AACAGAAACC 0.774568 -291 ****** **** Masking position 6 Map Score: 4.26777 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 279 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AAAATGCAGAATAAACCAGACATTCATGTC 2 30 0 ATAAACCAGA 0.75209 -198 GGAAAGCTCAATAAGACAGGTTCTACGTTT 4 77 0 ATAAGACAGG 0.858117 -84 GAGAGCCCTTATAGACCAGGTAGTACACGT 6 148 1 ATAGACCAGG 0.709385 -110 TTACGGGCCTATAAGCCAGGCGAGATATGA 24 211 1 ATAAGCCAGG 0.938347 -90 TTTTTGTTCTGTAAGCCGGGTAAGCGCAAT 29 13 1 GTAAGCCGGG 0.668805 -262 AAACCAGCTCATAAGCCGGGAGAACAACCT 40 15 1 ATAAGCCGGG 0.932629 -20 TTGGTAGCTAAAAAGCCAGGGGCGGTAGCG 42 101 1 AAAAGCCAGG 0.740667 -200 TCGATAATTAATAAAACAGATTTAAGCATT 53 159 1 ATAAAACAGA 0.546595 -142 TTATATATAGATAAAGCAGGAATATGGAGC 55 62 1 ATAAAGCAGG 0.708571 -77 ATCTGCCCCGATAAAACGGGGCAGATAATA 56 22 1 ATAAAACGGG 0.858117 -209 GCAATTTACCATAAACCAGGTTAAGTATGG 58 50 1 ATAAACCAGG 0.94361 -202 AAGCCATCATAAAAAACAGGGAGATACGCT 64 206 0 AAAAAACAGG 0.555119 -95 TTAAGATAAAACGGGAAGCGTTGGA 71 126 0 ATAAAACGGG 0.858117 -15 ATAACTTGCGATAAACCGGAAGCATGCCGC 75 140 0 ATAAACCGGA 0.733994 -161 ********** Masking position 3 Map Score: 5.89316 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 216 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 14 AATCGTTAAAAAACTCCTTTCCTACGTAAA 3 96 1 AAACTCCTTT 0.919674 -205 AATAAACTCCTTACCATCCCATT 13 109 0 AAACTCCTTA 0.94837 -13 ACAAAAACTCCTTTCAAATTACGT 16 138 0 AAACTCCTTT 0.919674 -14 TAACAGCATAAAACACCTTACCACCACCCA 34 114 1 AAACACCTTA 0.766997 -187 TTTAAACTCCTTAAAATGATTGG 34 288 0 AAACTCCTTA 0.94837 -13 AAAAACTCCTGATTGTTAAGGG 43 36 0 AAACTCCTGA 0.912293 -12 TTCGAACTCCTTAAATTTATTTG 63 198 0 GAACTCCTTA 0.912293 -13 GAGGAACTCCTGTGGGAAAGCGA 76 38 0 GAACTCCTGT 0.785942 -13 ********** Masking position 3 Map Score: 3.24956 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 16 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 15 AAAGTCTACATTTGTGCATAGTTACAACTTT 3 123 1 TTTTGCATAG 0.970837 -178 ACACGGCTTTTTTTTGTATAGGCTTCAGTAT 10 126 1 TTTTGTATAG 0.867643 -60 CCAAATCAAATTTTTGCAAAGCTGACACCTT 26 52 0 TTTTGCAAAG 0.856443 -249 CTTGAATGATTTTGTGTATAGATTGCCGGGC 29 45 0 TTTTGTATAG 0.867643 -230 ACTGTGCAAATTTCTGCATAGCAAGTTTTGG 50 13 0 TTTTGCATAG 0.970837 -183 AGTGCGCAATTTTCTGCATAGCCGCTCATTC 50 41 1 TTTTGCATAG 0.970837 -155 AAAAGTCGTTTTTCTGCTTAGGATTTTGTTA 63 105 1 TTTTGCTTAG 0.839948 -106 TTTGACGTATTTAGTGCATAGTTGAGTATCG 66 28 0 TTATGCATAG 0.839948 -273 AAATGGTTAATTTTTGCACAGGACTGGTGGG 73 140 1 TTTTGCACAG 0.898396 -100 *** ******* Masking position 5 Map Score: 4.79812 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 11 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