AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_ecoli_reg_300.orf -o00520_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 dniR 71 transcriptional regulator for nitrite reductase (cytochrome c552) #2 yagE 273 putative lyase/synthase #3 yagG 226 putative permease #4 galE 260 UDP-galactose-4-epimerase #5 modF 67 ATP-binding component of molybdate transport system #6 modE 128 molybdate uptake regulatory protein #7 ychK 73 orf, hypothetical protein #8 hnr 91 Hnr protein #9 galU 201 glucose-1-phosphate uridylyltransferase #10 rspA 205 starvation sensing protein #11 b1582 134 orf, hypothetical protein #12 ugd 248 UDP-glucose 6-dehydrogenase #13 gnd 300 gluconate-6-phosphate dehydrogenase, decarboxylating #14 rfbA 57 glucose-1-phosphate thymidylyltransferase #15 rfbB 300 dTDP-glucose 4,6 dehydratase #16 galF 174 homolog of Salmonella UTP--glucose-1-P uridyltransferase, probably a UDP-gal transferase #17 wcaK 61 putative galactokinase (EC 2.7.1.6). #18 BIME91 82 BIME #19 wcaJ 54 putative colanic acid biosynthsis UDP-glucose lipid carrier transferase #20 cpsG 104 phosphomannomutase #21 gmd 25 GDP-D-mannose dehydratase #22 wcaA 34 putative regulator #23 BIME92 24 BIME #24 wza 300 putative polysaccharide export protein #25 gatD 47 galactitol-1-phosphate dehydrogenase #26 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #27 gatY 197 tagatose-bisphosphate aldolase 1 #28 BIME96 27 BIME #29 b2097 184 orf, hypothetical protein #30 pdxB 98 erythronate-4-phosphate dehyrogenase #31 mltB 255 membrane-bound lytic murein transglycosylase B #32 mltA 208 membrane-bound lytic murein transglycosylase A #33 mutY 160 adenine glycosylase; G.C --> T.A transversions #34 yggX 27 orf, hypothetical protein #35 mltC 61 membrane-bound lytic murein transglycosylase C #36 glgB 272 1,4-alpha-glucan branching enzyme #37 asd 192 aspartate-semialdehyde dehydrogenase #38 trxA 76 thioredoxin 1 #39 rhoL 140 rho operon leader peptide #40 rho 84 transcription termination factor Rho; polarity suppressor #41 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #42 slt 183 soluble lytic murein transglycosylase Motif number 1 CGGACCGTACACCCCAAAGGGGAGAGGGGACT 2 77 1 ACCCAAGGGG 0.611759 -197 CCCGGCCCTCTCCCCAAAGGGGCGAGGGGGAA 2 124 0 TCCCAAGGGG 0.77854 -150 GTGCTGACCTTGCCGGAGGCGGCCTTAGCACC 4 18 1 TGCCGAGCGG 0.994914 -243 TCATACCATAAGCCTAATGGAGCGAATT 4 243 1 AGCCAAGGAG 0.612534 -18 AAGTTAATTCTGACAGGCGCAGGTGGCAATAG 8 32 1 TGACGGGCAG 0.850735 -60 GTATATCAGCACCCCGAAGGGGCTAAGTTCTG 9 121 0 ACCCGAGGGG 0.919652 -81 ACGCAAAACGTACCAGGAGGGTGTTTATATTG 11 63 1 TACCGGGGGT 0.596032 -72 GGCAAAAAAAAGCCCGGTGCAATATACGCCGG 12 40 0 AGCCGGGCAA 0.836344 -209 GTAGCTGTAAAGCCAGGGGCGGTAGCGTGCAT 15 207 1 AGCCGGGCGG 0.989232 -94 ATAAATTTGATGCCAGGTGAGGCTGCGTTTGT 17 31 0 TGCCGGGAGG 0.915499 -31 CGACAACGGTTGCCGGATGCGGCGTAAAACGC 18 28 1 TGCCGAGCGG 0.994914 -55 TCGCATTCATTGCCTGATGCGACGT 20 4 0 TGCCGAGCGA 0.9752 -101 TAGTTGGCCCTGACCGAAGCGGCCAATTTTAT 20 61 0 TGACGAGCGG 0.951587 -44 GTAGCTAAAAAGCCAGGGGCGGTAGCGTGTCT 24 104 1 AGCCGGGCGG 0.989232 -197 TTTTTACCTGAGGGGGAGGTTATCCC 25 5 1 TACCGAGGGG 0.941528 -43 CGTGTTTTTATGCCGGATGCGGTGTAAACATA 27 25 0 TGCCGAGCGG 0.994914 -173 CGGTAGTCACTGCCCGATACGGACTTTACATA 31 167 0 TGCCGAACGG 0.876207 -89 TAACAGATTCAACCAGGGGCAAGTATGGTAAA 31 222 0 AACCGGGCAA 0.470541 -34 GAGCAGCCTCTCCCTGACGCAAATTTTGCACA 32 121 0 TCCCGAGCAA 0.750104 -88 CAAAGTTAGTTGCCGGATGCAAGCATGATAAG 33 56 1 TGCCGAGCAA 0.915839 -105 TTATGCAAGTTGCCGGAGGCGTGCTCCGGCAC 35 16 0 TGCCGAGCGT 0.944771 -46 TATTACGCACTAACAGGGGCGGCATCGCGCCC 36 30 0 TAACGGGCGG 0.781738 -243 GTGAAAGATGTGCCAAGAGGAGACCGGCACAT 37 135 1 TGCCAGGGAG 0.787047 -58 **** ** **** Masking position 4 Map Score: 32.4035 Number of sites scoring better than the average of aligned sites = 3014 Number in coding regions = 2393 Number in noncoding regions = 621 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 2 ACTGCACCGAGCCATCTTTTCCCCCTCGCC 2 106 1 GCCATCTTTT 0.705544 -168 TTATAGAACAGCGTTCGTTTATTTAACGAT 2 243 0 GCGTTCGTTT 0.814292 -31 GCATGAAACCGCGTCTTTTTTCAGATAAAA 4 79 1 GCGTCTTTTT 0.915265 -182 CAAGAATTTAGCCGTTTTTTATGCGCGATT 4 148 0 GCCGTTTTTT 0.944755 -113 GCTTTGCGTGGCGTTCGTTTTCCGTCACAA 6 85 1 GCGTTCGTTT 0.814292 -44 ATGCTAACTCGCCTCCTTTTCAGAACTTAG 9 101 1 GCCTCCTTTT 0.876408 -101 GCAAATATACGCCTTTTTTTGTGATCACTC 10 99 1 GCCTTTTTTT 0.958055 -107 ATTGCACCGGGCTTTTTTTTGCCAAATATC 12 49 1 GCTTTTTTTT 0.778704 -200 GAATCTTCCTGCCGTTGTTTTATATAAACC 15 17 1 GCCGTTGTTT 0.890945 -284 TTTGTTCGTTGCCGCTTTTT 17 1 0 GCCGCTTTTT 0.911791 -61 AGGTGAGGCTGCGTTTGTTTTGTTCGTTGC 17 19 0 GCGTTTGTTT 0.895146 -43 AGCAAAGTGCGCGTGTTTTTATGCCGGATG 27 38 0 GCGTGTTTTT 0.849526 -160 CTATCGGGAGGCCGTTTTTTTGCCTTTCAC 27 77 1 GCCGTTTTTT 0.944755 -121 GTCGTTACGGGCGAGTTTTTCCATCTTTTG 29 158 0 GCGAGTTTTT 0.535551 -27 AATCACTAAAGCCTATTTTTTGTGCAAAAT 32 101 1 GCCTATTTTT 0.725695 -108 TCTTCGTTGCGCCTTATTTTTTAACCTGAA 32 179 1 GCCTTATTTT 0.692122 -30 TGCGACTTTGGCTGCTTTTTGTATGGTGAA 37 110 1 GCTGCTTTTT 0.614268 -83 AAGCGTTTTTTTCCTGCAAAGA 37 181 0 GCGTTTTTTT 0.947006 -12 ********** Masking position 8 Map Score: 16.0485 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 360 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 GGTCAGCTTTGCGTGGCGTTCGTTTTCCGT 6 80 1 GCGTGGCGTT 0.980402 -49 TAAAATTGAGGCCCGGCGTATATTGCACCG 12 28 1 GCCCGGCGTA 0.907847 -221 CCATCGAACAACGTAGCGTTAAAACTTTTA 12 168 1 ACGTAGCGTT 0.77001 -81 ATCCACAACGAAGCGGCGTAACATCACAAG 16 65 1 AAGCGGCGTA 0.798832 -110 CGGTTGCCGGATGCGGCGTAAAACGCCTTA 18 34 1 ATGCGGCGTA 0.798832 -49 GTGTAAACATACGTGGCAGTGCTAT 27 6 0 ACGTGGCAGT 0.743218 -192 GCTTCCTTGTGCGGGGCGTGATGCTTTACC 31 198 1 GCGGGGCGTG 0.916386 -58 ATTTCATTAAACGCGGCGGTTTGTTATCTT 32 153 1 ACGCGGCGGT 0.967406 -56 AAAACTGGACGCCCGGCGTGAGTCATGCTA 39 42 1 GCCCGGCGTG 0.92246 -99 CCACGTAAACACGTGGCGTTTTTGGCATAA 41 18 0 ACGTGGCGTT 0.982143 -222 CCACGTGTTTACGTGGCGTTTTGCTTTTAT 41 32 1 ACGTGGCGTT 0.982143 -208 AACATCGCCAGCGCGGCATTAAGATTACAG 41 64 0 GCGCGGCATT 0.944013 -176 AGTGTCCGTAACGTGGCGTAAACGGCAATG 42 122 1 ACGTGGCGTA 0.970085 -62 TAAATCTATTACGCGGCATGACGCTGCATT 42 163 1 ACGCGGCATG 0.929573 -21 ********** Masking position 7 Map Score: 15.2643 Number of sites scoring better than the average of aligned sites = 1314 Number in coding regions = 1259 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 ACCCCAAAGGGGAGAGGGGACTGCACCGAG 2 87 1 GGAGAGGGGA 0.910123 -187 TCCCCAAAGGGGCGAGGGGGAAAAGATGGC 2 116 0 GGCGAGGGGG 0.983876 -158 GCCCCTTTGGGGAGAGGGCCGGGGTGAGGG 2 133 1 GGAGAGGGCC 0.919526 -141 AGAGGGCCGGGGTGAGGGGCAATATGTGAT 2 145 1 GGTGAGGGGC 0.970287 -129 ACCGTTGGCCGGAGAGGGTGCTAAGGCCGC 4 36 0 GGAGAGGGTG 0.988194 -225 TTTGATGCCAGGTGAGGCTGCGTTTGTTTT 17 28 0 GGTGAGGCTG 0.963585 -34 CCCCACTGCGGGTAAGGGGCTAATAACAGG 19 28 1 GGTAAGGGGC 0.834188 -27 GACTGCATGCTGAGAGGGTGTGAAAAATTA 24 56 1 TGAGAGGGTG 0.92803 -245 TTTGCGTCAGGGAGAGGCTGCTCATTTCAT 32 130 1 GGAGAGGCTG 0.970239 -79 CCTCACTTCAGGTAAGGCTGTGAATACTCA 36 141 0 GGTAAGGCTG 0.803019 -132 TTACTTTTACTGCGAGGGTGATCGACCGGC 42 89 0 TGCGAGGGTG 0.896662 -95 ********** Masking position 5 Map Score: 10.9012 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 162 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 GAAAAGATGGCTCGGTGCAGTCCCCTCTCCCCTT 2 93 0 CCGTGCAGCC 0.974893 -181 GTTGAGATATATCGTTGGCGTCACAAAAGCAAAA 3 94 1 ACGTGGCGCC 0.895453 -133 TGATGTGACGAGCGTTACCCACTCGCGCTAAACC 15 151 0 ACGTACCCCC 0.869328 -150 GGTATTAATGCACGCTACCGCCCCTGGCTTTACA 15 212 0 CCGTACCGCC 0.995718 -89 GGCATCCAGACACGCTACCGCCCCTGGCTTTTTA 24 109 0 CCGTACCGCC 0.995718 -192 GTAGTCACTGCCCGATACGGACTTTACATAACTC 31 163 0 CCGTACGGCT 0.889684 -93 TTCCGGTTTACACCCTGCCGTCGCTGTGCTGCAA 33 105 1 CCCTGCCGCC 0.977526 -56 AAATCTGGGGCGCGATGCCGCCCCTGTTAGTGCG 36 23 1 CCGTGCCGCC 0.996671 -250 CCGTTTACGCCACGTTACGGACACTTTTTTACTT 42 113 0 CCGTACGGCC 0.98799 -71 * ** ***** * * Masking position 6 Map Score: 9.25884 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 195 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 GCGGTTTCATGCCTGCATGCGTCGAACCGT 4 61 0 GCCTGCATGC 0.732466 -200 AGTTAATTCTGAGAGCATGAA 12 238 1 GAGAGCATGA 0.843601 -11 ATTCCAGGCCGCGAGCATTCAGCGCGGTGA 13 259 1 GCGAGCATTC 0.910936 -42 CACATCATAGGCATGCATGCAGTGCTCTGG 15 178 1 GCATGCATGC 0.49902 -123 AGGGGCGGTAGCGTGCATTAATACCTCTAT 15 221 1 GCGTGCATTA 0.732291 -80 CATATTACTTCAGAGCATGCTGTGAAATAA 15 270 0 CAGAGCATGC 0.788948 -31 CGACGCCTGCATTCGCACCGCCCC 23 5 1 GCCTGCATTC 0.725324 -20 TCTCATCAACGACTGCATGCTGAGAGGGTG 24 46 1 GACTGCATGC 0.837373 -255 TGAAATCTTCGCAAGTATGCCTGGCCGCGA 30 27 1 GCAAGTATGC 0.625909 -72 TCCGTGGATGCGCACTATACT 32 2 1 CCGTGGATGC 0.767624 -207 GTTGCCGGATGCAAGCATGATAAGGCCGTG 33 64 1 GCAAGCATGA 0.842327 -97 GGACGACGCAGAGAGGATGCACAGAGTGCT 36 169 1 GAGAGGATGC 0.866909 -104 CCGTAAACAGGCATGGATGATCCTGCCATA 40 11 1 GCATGGATGA 0.633811 -74 AATTTTCTCTGAGAGCATGCATT 41 227 1 GAGAGCATGC 0.952405 -13 ********** Masking position 7 Map Score: 9.56699 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 576 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 GACCGATCATAACGGCGAACGGAGCCGATGACAAGAAA 1 17 0 AAGAACGGGA 0.964111 -55 ATCGGAAGGGAAGAGGGAGTGCGGGAAATTTAAGCTGG 2 175 0 AAGAGTGGAA 0.853182 -99 GCAAACGATAACGCGGGCTAAATTTGCATT 9 3 1 AAGAACGGTA 0.945554 -199 AAAAAGCGGCAACGAACAAAACAAACGCAGC 17 4 1 AAGAACGCAA 0.865193 -58 TCATCAGAAAAAATGTTAGCGCGGTCAAGTTTTCACCG 29 88 0 AAGAGCGGAA 0.986622 -97 GAATCGAGCCAACAGAAAACGCTGAAAAAACATCCAAA 29 124 1 AAGAACGGAA 0.982129 -61 AGTTTGAATAAAAGGATAGCGAGGGGAATGAGTTGAGT 31 129 1 AAGAGCGGAA 0.986622 -127 GGTTGCATGAAAACGCGAGCGGAGTATAGTGCGCATCC 32 16 0 AAGAGCGGTA 0.958858 -193 GTTAAAAAATAAGGCGCAACGAAGATAACAAACCGCCG 32 166 0 AACAACGGAA 0.865193 -43 GCCTTACCTGAAGTGAGGACGACGCAGAGAGGATGCAC 36 153 1 AAGGACGGGA 0.834954 -120 TTAAGATAAAACGGGAAGCGTTGGAAATTACAAGATT 39 114 0 AAGAGCGGAA 0.986622 -27 ** * **** * ** Masking position 2 Map Score: 8.65573 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 114 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 CGCCTTTTTTTGTGATCACTCCGGCTTTTTTCGA 10 108 1 TGTGAATCCG 0.948085 -98 CCGCTTTTCATGCGATACATTATGCTCATCATGA 13 26 1 TGCGACTTAG 0.763081 -275 TATACTTATTTGCGAACATTCCAGGCCGCGAGCA 13 242 1 TGCGAATCCG 0.991635 -59 TGTTGCGAATCTTCCTGCCGTTGTTTT 15 4 1 TGCGACTCCG 0.988289 -297 ATTTGCGACCATTCCTGGAAAAATGGA 16 4 1 TGCGAATCCG 0.991635 -171 TAAGGCGTTTTACGCCGCATCCGGCAACCGTTGT 18 30 0 TACGCCTCCG 0.740897 -53 CAGGCATACTTGCGAAGATTTCAGGTATAAGGAT 30 16 0 TGCGAATTCG 0.967065 -83 AGGCCGTGGCTGCGGAAAGTTCCGGTTTACACCC 33 86 1 TGCGGATTCG 0.872781 -75 ATGAAACATCTGCGCTTACTCCTGTATTACGCAC 36 52 0 TGCGCATCCG 0.980758 -221 CAGGTAAGGCTGTGAATACTCATGTATTCAGCCA 36 129 0 TGTGAATCAG 0.737695 -144 CCATCAGTAATGCGACTTATCCTGCTTTGTTAGC 37 50 0 TGCGATTCCG 0.955041 -143 ***** * *** * Masking position 10 Map Score: 10.0058 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 260 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 TAAAACTTTCTTGTCATCGGCTCCGTTCGCCGTT 1 9 1 TTTGCACGTC 0.965986 -63 TATATCCCACTTTGTGCAGCGATTACTGACAGGGAT 5 40 0 TTGTCACGTC 0.932315 -28 GGACTGTTCGTGTTTTGAACGTGTTCATATTTCTGT 9 164 0 TTTTGACGTC 0.895316 -38 TAGTTTTTGCATCTTGTTCGTGATGGTGG 14 4 1 TTTTCACTTC 0.8523 -54 CTGCCACGTATGTTTACACCGCATCCGGCATAAAAA 27 17 1 TTTTCACGTC 0.985085 -181 AAACACGCGCACTTTGCTACGGCTTCCCTATCGGGA 27 50 1 ATTTCTCGTC 0.720938 -148 TATTAAGTGGTATTGTCATCGCGTACCTTACATTAC 29 32 0 TTTGCACGTC 0.965986 -153 CTTTTGGATGTTTTTTCAGCGTTTTCTGTTGGCTCG 29 128 0 TTTTCACGTC 0.985085 -57 AAGGTTGACTTTATTTCACCGGATACGCTTTCGTAA 38 41 0 TATTCACGTC 0.902853 -36 TGAATCTTGTAATTTCCAACGCTTCCCGTTTTATCT 39 112 1 ATTTCACGTC 0.948347 -29 * *** ** ** * * Masking position 14 Map Score: 6.87531 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 69 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 GTAATGCAAATTTAGCCCGCGTTATCGTTT 9 13 0 TTTAGCCCGC 0.912691 -189 TACTTGTGATGTTACGCCGCTTCGTTGTGG 16 67 0 GTTACGCCGC 0.919835 -108 GATAAGGCGTTTTACGCCGCATCCGGCAAC 18 36 0 TTTACGCCGC 0.982149 -47 CGGATCTTCCCTTACCCCACTGCGGGTAAG 19 14 1 CTTACCCCAC 0.822196 -41 TTTGTCGTTATTTACACCGCGGTTTCGCAT 20 30 0 TTTACACCGC 0.972215 -75 GCCACGTATGTTTACACCGCATCCGGCATA 27 19 1 TTTACACCGC 0.972215 -179 CGCGGTCAAGTTTTCACCGCAAAGGTATTT 29 77 0 TTTTCACCGC 0.896713 -108 CAACCTTTTTTTTACCCCGATCACGGATTT 32 49 1 TTTACCCCGA 0.932389 -160 AAGTTCGAGATTTACCCCAAGTTTAAGAAC 40 55 1 TTTACCCCAA 0.773551 -30 AGTGTAGCCTTTTTCCCCGCCTAATCCCAG 42 60 1 TTTTCCCCGC 0.956916 -124 GTCATTGCCGTTTACGCCACGTTACGGACA 42 124 0 TTTACGCCAC 0.931641 -60 ********** Masking position 3 Map Score: 13.0388 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 282 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 11 CTACCATGTCCCCGAACAAGTGTTCACTATGTC 2 42 1 CCGACAAGTT 0.699138 -232 CGGGAAATATTCCGCAGACGGTTTTATCTCTTA 3 17 0 TCGCGACGGT 0.880344 -210 CGGAATATTTCCCGCAGACGGCTTTGTTGTTTT 3 36 1 CCGCGACGGT 0.983094 -191 AGCACCCTCTCCGGCCAACGGTTCGACGCATGC 4 44 1 CCGCAACGGT 0.978339 -217 TTTTTAAGTGCCATCTGAAGGCTTTTGAAAAAA 13 71 0 CCTCGAAGGT 0.7625 -230 AGATATTTAGCCAGAAAACGTATTTTATCAAAT 13 112 1 CCGAAACGTT 0.819566 -189 TGTTTTCGGTTCCGACAACGGTTGCCGGATGCG 18 16 1 TCGAAACGGT 0.805306 -67 GAGCACAGAACCGTAGGACGGATAAGGCGTTTT 18 53 0 CCTAGACGGT 0.853968 -30 CCAACTATTGCCTGAAAAAGGGTAACGAT 20 86 1 CCGAAAAGGT 0.928525 -19 AGCATCACGCCCCGCACAAGGAAGCGGTAGTCA 31 190 0 CCGCCAAGGA 0.7109 -66 TTTTTTTTACCCCGATCACGGATTTGGCATGAT 32 54 1 CCGACACGGT 0.976792 -155 AAACAGTGCCGGAGCACGCCTCCGGCAACTT 35 9 1 CCGACACGCT 0.830942 -53 TAACCAACTAAAGGTTGACTTTATTT 38 61 0 CCACAAAGGT 0.585782 -16 ** ** ***** * Masking position 8 Map Score: 6.07897 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 800 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 AGACGGCTTTGTTGTTTTTGAAATTTATTA 3 51 1 GTTGTTTTTG 0.771038 -176 ATTACGTTATTTTGCTTTTGTGACGCCAAC 3 107 0 TTTGCTTTTG 0.922412 -120 AGCGGCCAATTTTATTTTTGTCGTTATTTA 20 46 0 TTTATTTTTG 0.739457 -59 AATGAAATTATTTGTTTTTAAATATCGAGA 27 147 0 TTTGTTTTTA 0.880039 -51 ATCCTGTCGTTTGTTTTCGATTTCAAAAT 27 179 0 TTTGTTTTCG 0.771038 -19 GCTTTAGTGATTTGTTTTTGTTCAAAATCA 32 83 0 TTTGTTTTTG 0.93512 -126 GCGTGTTGTGTTTGTTTTTATGCAAGTTGC 35 35 0 TTTGTTTTTA 0.880039 -27 TACGTGGCGTTTTGCTTTTATATCTGTAAT 41 41 1 TTTGCTTTTA 0.858177 -199 CGGACACTTTTTTACTTTTACTGCGAGGGT 42 100 0 TTTACTTTTA 0.543698 -84 ********** Masking position 6 Map Score: 2.58959 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 91 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 CCGTACACCCCAAAGGGGAGAGGGGACTGC 2 81 1 CAAAGGGGAG 0.933259 -193 GCCCTCTCCCCAAAGGGGCGAGGGGGAAAA 2 122 0 CAAAGGGGCG 0.980221 -152 TTTATCTGAAAAAAGACGCGGTTTCATGCC 4 78 0 AAAAGACGCG 0.735557 -183 CATAGCATAACAAAGATGCGAAAAGTGTGA 4 207 0 CAAAGATGCG 0.928092 -54 CTGACCGCACAAAAGGGGAGTGCTTTTCTG 6 56 0 AAAAGGGGAG 0.837067 -73 TAAGTTCTGAAAAGGAGGCGAGTTAGCATA 9 100 0 AAAGGAGGCG 0.7599 -102 GAAATTCGATCAAAGTTGCGATTTGATAAA 13 135 0 CAAAGTTGCG 0.728226 -166 ATTACGCACTAACAGGGGCGGCATCGCGCC 36 31 0 AACAGGGGCG 0.791546 -242 GAAAGATGTGCCAAGAGGAGACCGGCACAT 37 137 1 CCAAGAGGAG 0.708506 -56 TTTTTTCCTGCAAAGATGTGTGCTGTATAA 37 167 0 CAAAGATGTG 0.590378 -26 TCACGATAAACATAGAGGCGAAGTCCAAC 42 10 0 CATAGAGGCG 0.865528 -174 ********** Masking position 5 Map Score: 2.06672 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 390 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 14 GGCTAAATTTGCATTACCTGCTAATGTCGGC 9 26 1 GATTACCTGC 0.611056 -176 CTTTTGTCAACCATTCACAGCGCAAATATAC 10 78 1 CATTCACAGC 0.961819 -128 GTTCGATTCCTTGCATCGCTTGTC 10 192 0 CATTCCTTGC 0.781671 -14 TGATTCTACACCATCCACTGCGGACGCAAAA 11 40 1 CATCCACTGC 0.925679 -95 AATGCTACTGCAATCCACAACGAAGCGGCGT 16 53 1 CATCCACAAC 0.501742 -122 CCGCGGTTTCGCATTCATTGCCTGATGCGAC 20 13 0 GATTCATTGC 0.877539 -92 AATTTTTATTCAATTAACTGCAAGGTAAATG 24 216 1 CATTAACTGC 0.886992 -85 ATCCTGTGCACTATTAATAGCAATGTCGCCA 24 251 0 CATTAATAGC 0.590442 -50 CAAGGAAGCGGTAGTCACTGCCCGATACGGA 31 176 0 GAGTCACTGC 0.871655 -80 GGTCACCGAATTCACTGTTGTTGGGGGC 33 143 0 GATTCACTGT 0.622006 -18 GAATACATGAGTATTCACAGCCTTACCTGAA 36 134 1 GATTCACAGC 0.941044 -139 TCCTGCCATACCATTCACAACATTAAGTTCG 40 31 1 CATTCACAAC 0.761187 -54 TTTATGCTAACCAGTCATTGCCGTTTACGCC 42 136 0 CAGTCATTGC 0.781515 -48 * ********* Masking position 3 Map Score: 1.08354 Number of sites scoring better than the average of aligned sites = 780 Number in coding regions = 708 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 15 ATTCCGCAGACGGTTTTATCTCTTAAAATA 3 12 0 CGGTTTTATC 0.710362 -215 TTGCCGGAGGCGGCCTTAGCACCCTCTCCG 4 27 1 CGGCCTTAGC 0.854867 -234 CAAATTTAGCCCGCGTTATCGTTTGC 9 7 0 CCGCGTTATC 0.957713 -195 TATATGCTTACGGCTTTATATTACGGGTGA 13 174 0 CGGCTTTATA 0.797711 -127 GCGGCGTAAAACGCCTTATCCGTCCTACGG 18 46 1 ACGCCTTATC 0.89211 -37 TACGCCTTATACGAACAACAC 28 2 1 ACGCCTTATA 0.671938 -26 TCCGCAGCCACGGCCTTATCATGCTTGCAT 33 72 0 CGGCCTTATC 0.969019 -89 AAATCATCCTCTTTATCGACTCACGCG 34 11 0 CCTCTTTATC 0.68279 -17 CCAACGCTTCCCGTTTTATCTTAA 39 127 1 CCGTTTTATC 0.808011 -14 GCCTTTTTCCCCGCCTAATCCCAGCCGGTC 42 66 1 CCGCCTAATC 0.930154 -118 CAGCGTCATGCCGCGTAATAGATTTATGCT 42 159 0 CCGCGTAATA 0.581932 -25 ********** Masking position 8 Map Score: 1.78683 Number of sites scoring better than the average of aligned sites = 874 Number in coding regions = 607 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226