AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_bsub_reg_300.orf -o00710_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: iolG 22 myo-inositol 2-dehydrogenase Input sequences: #1 yjlC 300 yjlC #2 yjlD 39 similar to NADH dehydrogenase #3 yjmA 197 similar to glucuronate isomerase #4 yjmB 67 similar to Na+:galactoside symporter #5 yjmC 104 similar to malate dehydrogenase #6 ykrV 94 similar to aspartate aminotransferase #7 ykrW 196 similar to ribulose-bisphosphate carboxylase #8 yloB 115 similar to calcium-transporting ATPase #9 yloC 82 similar to hypothetical proteins #10 yloD 233 similar to guanylate kinase #11 yloI 80 similar to pantothenate metabolism flavoprotein #12 def 26 polypeptide deformylase #13 yneA 149 yneA #14 ynzC 63 ynzC #15 tkt 168 transketolase #16 aspB 22 aspartate aminotransferase #17 ypmA 142 ypmA #18 dinG 125 ATP-dependent helicase #19 panB 245 ketopantoate hydroxymethyltransferase #20 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #21 ypjD 300 alternate gene name: jojD #22 citH 43 malate dehydrogenase #23 citC 163 isocitrate dehydrogenase #24 citZ 300 citrate synthase II #25 pykA 42 pyruvate kinase #26 pfk 183 6-phosphofructokinase #27 yttI 300 similar to acetyl-CoA carboxylase #28 malS 81 malate dehydrogenase (decarboxylating) #29 ytnP 145 ytnP #30 ytmQ 206 similar to hypothetical proteins #31 pckA 300 phosphoenolpyruvate carboxykinase #32 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #33 tpi 30 triose phosphate isomerase #34 pgk 300 phosphoglycerate kinase #35 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #36 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #37 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #38 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #39 ywlB 66 alternate gene name: ipc-28d #40 spoIIR 140 alternate gene name: ipc-27d, csfX #41 fbaA 180 fructose-1,6-bisphosphate aldolase #42 spo0F 165 two-component response regulator #43 ywfB 151 alternate gene name: ipa-80d #44 ywfA 209 alternate gene name: ipa-79d; similar to chloramphenicol resistance #45 rocB 73 alternate gene name: ipa-77d #46 rocA 226 pyrroline-5 carboxylate dehydrogenase #47 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #48 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #49 iolI 85 alternate gene name: yxdH; myo-inositol catabolism #50 iolD 203 alternate gene name: yxdD; myo-inositol catabolism #51 iolC 23 alternate gene name: yxdC; myo-inositol catabolism #52 iolB 74 alternate gene name: yxdB; myo-inositol catabolism #53 iolA 300 methylmalonate-semialdehyde dehydrogenase #54 fbp 300 fructose-1,6-bisphosphatase Motif number 1 TGCTTTCTGGCAATGTCTTTTTTTATGTTTATG 3 55 1 CTTCTTTTTT 0.961927 -143 CCTTTGGGATCAATCTCTTTTTTGAAAATGAAA 3 100 0 CTTCTTTTTT 0.961927 -98 CCAAATTTTTCTTTACTTTTTTCATTTAACCAT 6 23 1 CTCTTTTTTC 0.669654 -72 TCCCTCTGTCCCAGTCCTTTTTTGGATCAAGGC 19 110 0 CGCCTTTTTT 0.851103 -136 ATTTAGAAAACATTTTATTTTTCTTATATAGAA 23 113 0 CTTATTTTTC 0.814238 -51 AAAATGTAAGCATTTTCTTTTTGGGGGAGAGAA 24 194 1 CTTCTTTTTG 0.888668 -107 CGGAAGCATACTTTTTCTTTTTCGTGAATATAT 27 237 0 CTTCTTTTTC 0.973781 -64 AAAAGACCCGCAAGCTCGTTTTTCCAGTGTATC 30 134 0 CGTCGTTTTT 0.674523 -73 TGAAACCTTCCTTTATCGTTTTTTGTGTTTTGC 31 277 0 CTTCGTTTTT 0.80903 -24 TCTGTGTCACTCCCTTTTTTTGATGGTTGT 32 8 1 CTCCTTTTTT 0.921165 -140 GACGGACTCCCTTTCCCTTTTTCCATGAAGACC 34 68 1 CTCCTTTTTC 0.944984 -233 TAGGGCAGATCGCAGTCTTTTTCGGCACAGGGC 34 200 0 CATCTTTTTC 0.737585 -101 AACGAAGTCGCCGTTTCTTTTTTCTTCATATAT 36 26 1 CTTCTTTTTT 0.961927 -50 TAACAGCTTGCTAGATTTTTTTCACCCTGCACG 40 50 1 CGTTTTTTTC 0.681958 -91 ATTTTCTGAGCATTTTCTCTTTTGTTGTATACT 42 42 0 CTTCTCTTTT 0.687383 -124 AGGTGATCACCTTTCTCTTTTTCCGATCTTGAA 46 85 0 CTTCTTTTTC 0.973781 -142 GAGATGTTTTCAGTCTCTTTTTTTGTGGATTCA 47 35 1 CTTCTTTTTT 0.961927 -142 TTTTTCACCTCATTGTTTTTTTGGCCGGCTGTA 47 153 0 CTTTTTTTTG 0.485074 -24 TGGACGATTTCCCTCTCTTTTTCTAGTAACATC 48 79 0 CTTCTTTTTC 0.973781 -222 TCGCGAATTACCAGTTCTTTTTCTTAAAAATTA 48 207 0 CGTCTTTTTC 0.947832 -94 CCCACCTTTACTCGATCTTTTTCAA 50 3 0 CGTCTTTTTC 0.947832 -201 CAATCATAAACACTACATTTTTTCATTATTTTT 53 55 0 CTCATTTTTT 0.579654 -246 TATGCATCCGCCATTTATTTTTTTGGTGTTTTT 53 174 1 CTTATTTTTT 0.748855 -127 * * ******** Masking position 10 Map Score: 25.8513 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 679 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 TGAATAAGTCAAAATCCTTTACTCTCTCTGAA 1 87 0 AAAACCTTTC 0.947777 -214 ATCAAAAAACCTCTTCAAACTGCAAT 7 181 0 AAAACCTCTC 0.924795 -16 ACTAGATCAAAAAAAGTTTTACAACTGAT 14 8 0 AAAAGTTTTC 0.754765 -56 GTTAAACTCCTTTATTGCATTTTGT 14 49 0 AAACCCTTTT 0.866459 -15 CACACCGCAAAAGCCGCTTTATGCGGCTT 17 8 0 AAGCGCTTTT 0.61311 -135 TTTGAGAGTAAAACGGTTTTGCCGCTCCATTT 18 49 1 AAACGTTTTC 0.808501 -77 GCATCACACAAAACCCCTTTTCCTTCCATTAG 21 168 1 AAACCCTTTC 0.961381 -133 TAAGAAAAATAAAATGTTTTCTAAATATGAAT 23 120 1 AAAAGTTTTT 0.445119 -44 TTCCCCGAAAAAACGCCTTTATTTGCGGGTTT 24 14 0 AAACCCTTTT 0.866459 -287 TGCTGGAACTAAAACCCTTTGCTTTTGAAAGA 24 156 0 AAAACCTTTC 0.947776 -145 CTGATTTCATACAAGCCTTTCCGAGCACGTCA 27 59 1 ACAACCTTTC 0.744027 -242 CCCATGTATAAAAACGCTCTGTTTTGAACAAT 30 46 0 AAAAGCTCTT 0.762053 -161 GTCTGCTGGAACACTCCTTTCCCATGTATAAA 30 66 0 ACACCCTTTC 0.799482 -141 TTGACATTGCAAACCCTTTTACGATAAGATAT 31 130 0 AAACCTTTTC 0.808501 -171 CGGCTTTCAGAAAACGCTCTGTGATAGAGAAA 34 100 1 AAAAGCTCTT 0.762053 -201 ACCGCGTTTTAAGCAGCTTTGCCGGCGCTTTC 34 134 1 AAGCGCTTTC 0.858759 -167 CTTCTAGCGAAAAAAGCTTTCCACCCTAGCAT 41 128 0 AAAAGCTTTC 0.946984 -53 CCTATAATTAAAAACCCTTTTTAAAGGGTTTT 43 27 1 AAAACCTTTT 0.824992 -125 AAAAAGCTCTCCGGGAGGCCGG 44 1 1 AAAAGCTCTC 0.92479 -209 TAACACGTAAAAAAAGCTCTCCGGCCTCCCGG 44 21 0 AAAAGCTCTC 0.92479 -189 TCTTTCTCAAACACCTCTTCCATAATCTTC 44 190 0 AAACCCTCTC 0.944043 -20 TCTGCAGAAAAAGCGCTTTTTCATAATTCGCG 48 235 0 AAGCCTTTTC 0.507672 -66 TCCCTTCGACAAAAGGCTCTTCCTTTCCATCT 50 114 0 AAAAGCTCTC 0.924792 -90 CAAGAGCTTAAAACAGCTTTTCAGTACAGGTT 54 200 0 AAACGCTTTC 0.960345 -101 **** ***** * Masking position 8 Map Score: 27.3935 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 449 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 3 CTTAAAAGCGTGAGACAGGGAGAGGCACTACCCTTTC 1 232 1 TAGAGGGACA 0.862916 -69 GTTAACATTTTGAAATAGAATGAAAGACGGTGAGGAC 3 171 1 TAAAGAGAGA 0.759932 -27 CCCAAAAAACTGAAAAGGAAGGAGGCACTTGC 5 83 1 TAAAGAGACA 0.961311 -22 AATTATAGCATGAAATGGGACGAGTCAGAATAAGCAT 8 40 1 TAAAGAGACA 0.961311 -76 GTTCTCATAATAAAAGGGCAATAGACACGCTATTACC 9 33 0 TAAAGATACA 0.484925 -50 GTCTGCGCCAATCAAACGGATGATTCAGGATGCAAGA 10 164 1 ACAAGAGACA 0.513414 -70 CAATATTTGTTCAAACTGGAGGATGAAAAA 17 123 1 TAAAGAGAAA 0.745699 -20 AGCGTTTATATTATAGTGGATGAAAAAGAAAACAGCA 21 202 1 TATAGAGAAA 0.504223 -99 TGAGGCTTACTTAAAAAGCACGATGCAAGTATTTCTC 24 222 0 TAAAGAGACA 0.961311 -79 ACTATTATGCTCAGAAAGGAAGAGGCAGG 28 63 1 TAGAGAGACA 0.852918 -19 ATTTATTATGTTCAACTGAGTGAGACAACCAAGGTGC 31 17 0 TCAAGGGACA 0.909668 -284 CAACCATCAAAAAAAGGGAGTGACACAGA 32 3 0 AAAAGGGACA 0.754159 -145 TTCTTGACATTGCAAAGGTGTGAATCAA 32 130 1 TCAAGGGACA 0.909668 -18 GAAAAGCACATCATATGGTGTGAATCAAAGAGCGGAC 35 72 1 TATAGGGACA 0.903425 -85 TCCTTGTCCATAATAGGGCTAGAAACAAAGCACGGAG 40 97 1 TATAGTGACA 0.617902 -44 ATATTGTACGTTATAAAGGAGGATTCACTT 42 4 0 TATAGAGACA 0.896025 -162 TTGAGAGAAATAAAATCGTGCGATTCTTTAGCGGATC 45 12 1 TAAAGGGACT 0.634993 -62 ATCAAAAAGTTGAAATCGTGCGATCCGCTAAAGAATC 45 33 0 TAAAGGGACG 0.720546 -41 CGCATATGAATAAAAATGCAAGAATCATGCCATTTTC 46 167 0 TAAAGAGACA 0.961311 -60 TTGAAAAAGATCGAGTAAAGGTGGGATC 50 2 1 TAAAGTGAAA 0.354948 -202 TGTATGTGTTTACTAATGAAGGAGGCAATAAGA 53 278 1 TCTAGAGACA 0.762896 -23 TTAGAGACAATTAAAACGAGAGAAAGAGGTGCCAAAT 54 240 0 TAAAGGGAGA 0.77458 -61 * *** * * ** ** Masking position 5 Map Score: 18.2628 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 155 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 AATTCTTAAGACACAGAGGTGGAAC 4 53 1 AACGAGGGGA 0.875686 -15 AGTGCCCAAAAAACTGAAAAGGAAGGAGGCACT 5 79 1 AACGAAAGGA 0.646034 -26 GAATGCAGGAAGAATGAGAGGGTGTA 8 4 0 AAAGAGAGGT 0.579948 -112 CGATAATTATAGCATGAAATGGGACGAGTCAGA 8 36 1 ACAGAAAGGG 0.698769 -80 GGTACAACACATAAGGAAGGGGATTTTT 15 151 1 AAAGAAGGGA 0.957236 -18 ACCTTCCGTTACAACGAGAAGGATTCTTCACTT 19 164 0 AAAGAGAGGA 0.937818 -82 ATCTCCTCTAAACATGAGGAGGAGAAAAC 19 227 1 ACAGAGGGGA 0.938003 -19 TGAAGATTTCAGAAGGAAGTGAACCAA 25 26 1 AAAGAAGGAA 0.785051 -17 TGCCCTAAAAACAATGAAAAGGGATCTCCATCC 26 114 0 AAAGAAAGGG 0.846962 -70 ATGCTAAGAAAAAACGAGGAGAAACTTCCGCTA 32 65 0 AAAGAGGGAA 0.854854 -83 CAAAACTGCTATAAGGAAGTGGAACAG 33 14 1 AAAGAAGGGA 0.957236 -17 ATGAAAGCGGACAAGGGAAGGGGACGGACTCCC 34 46 1 AAAGGAAGGG 0.698769 -255 TCTTCATGGAAAAAGGGAAAGGGAGTCCGTCCC 34 66 0 AAAGGAAGGG 0.698769 -235 GACAACGCTAATAAAGAAGTGGATAAGTATGTG 38 23 0 AAAGAAGGGA 0.957236 -134 AAAGAACGCAAAAACGGGGTGAACGG 39 51 1 AAAGGGGGAA 0.711701 -16 CTAGAAACAAAGCACGGAGAGGAACGGTGGGGA 40 115 1 ACAGGAGGGA 0.797266 -26 TATATTTCATAACACGAGGGGGACTACAT 46 208 1 ACAGAGGGGA 0.938003 -19 GGCCAAAAAAACAATGAGGTGAAAAAG 47 160 1 AAAGAGGGAA 0.854854 -17 ATGTTACTAGAAAAAGAGAGGGAAATCGTCCAT 48 80 1 AAAGAGAGGA 0.937818 -221 TTCTGCCAATAGAAAGAGGAGGGCTTCTCT 52 55 1 AAAGAGGGGG 0.955277 -20 * ** **** *** Masking position 1 Map Score: 22.149 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 418 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 5 GCGTGAGACAGGGAGAGGCACTACCCTTTC 1 239 1 GGGAGAGGCA 0.878201 -62 AACTGAAAAGGAAGGAGGCACTTGC 5 90 1 GAAGGAGGCA 0.941196 -15 ATCAAGAGCAGGCAGAGGGACGAGCCCGAT 7 54 1 GGCAGAGGGA 0.957059 -143 AAAGGACTGGGACAGAGGGATGAAACTCGC 19 123 1 GACAGAGGGA 0.909815 -123 GGTTTCATAGGGAGGATGGAGATCCCTTTT 26 101 1 GGAGGATGGA 0.715382 -83 TGCTCAGAAAGGAAGAGGCAGG 28 70 1 GGAAGAGGCA 0.941196 -12 GACCTGGCTTGACGGAGGCGTGACGCATAT 29 113 1 GACGGAGGCG 0.937881 -33 GACGCATATGGACGGAGGCGCC 29 134 1 GACGGAGGCG 0.937881 -12 ATCCCGAGCTGGCGGAGGGACAGGCCCTAT 31 80 0 GGCGGAGGGA 0.980095 -221 GAGCAGAGGCATCTTCGACTT 48 2 1 AGCAGAGGCA 0.757625 -299 AAAAATAAATGGCGGATGCATATTTACATA 53 166 0 GGCGGATGCA 0.930421 -135 GTTTACTAATGAAGGAGGCAATAAGA 53 285 1 GAAGGAGGCA 0.941196 -16 ********** Masking position 6 Map Score: 12.4867 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 275 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 TAAGTCGGTTGCCGGGCTTCATCGGGCTCGT 7 73 0 GCCGGCTTCA 0.979506 -124 ATTGACGCAAGCCAGCCTCCAATGGTTCT 23 9 0 GCCAGCTCCA 0.969324 -155 GAAACCGGTTGCTGGGCTTCATAGGGCCTGT 31 60 1 GCTGGCTTCA 0.806789 -241 AAGGGAAGGGGACGGACTCCCTTTCCCTTTT 34 58 1 GACGGCTCCC 0.968627 -243 TTTTCTGAAAGCCGGTCTTCATGGAAAAAGG 34 83 0 GCCGGCTTCA 0.979506 -218 AAAAAAGCTCTCCGGCCTCCCGGAGAGCTTT 44 13 0 TCCGGCTCCC 0.939773 -197 GCCATATCCCGCCGAACTCCATGCTCAGC 49 9 0 GCCGACTCCA 0.950886 -77 GGGATATGGCGACAGCCTTCCTGCCGAACTC 49 30 1 GACAGCTTCC 0.788021 -56 CAGCCTTCCTGCCGAACTCCCTTCATATCTA 49 42 1 GCCGACTCCC 0.968627 -44 GCCAGACTCCCCCATCTGCGT 49 75 0 GCCAGCTCCC 0.980529 -11 ***** ***** Masking position 8 Map Score: 11.1875 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 143 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ATAGCAAACACAAAAAACTCCAATTCGATT 1 56 0 CAAAAAACTC 0.74924 -245 CTACCCTTTCCAAAAAAATCAGCAAACTGC 1 259 1 CAAAAAAATC 0.720021 -42 ATCAAAAAACCTCTTCAAACTG 7 185 0 CAAAAAACCT 0.628111 -12 AGTACTAGATCAAAAAAAGTTTTACAACTG 14 13 0 CAAAAAAAGT 0.886797 -51 TGAAACAGTTGAGAAAAAGTCGTCAGACAT 15 109 1 GAGAAAAAGT 0.429333 -60 TTCTGCAAGCCAAAAAACCTTCCGTTACAA 19 183 0 CAAAAAACCT 0.628111 -63 TGATTTCCCCGAAAAAACGCCTTTATTTGC 24 20 0 GAAAAAACGC 0.847272 -281 CAGCGTTTGACAAAAAAAGTACAATAGTTT 27 121 1 CAAAAAAAGT 0.886797 -180 TAGCAAAACACAAAAAACGATAAAGGAAGG 31 275 1 CAAAAAACGA 0.693086 -26 ATACAACCATCAAAAAAAGGGAGTGACACA 32 13 0 CAAAAAAAGG 0.620305 -135 TAGCATTCGTCAAAAAACGTGATATAATGT 32 92 1 CAAAAAACGT 0.901004 -56 GACCGGCTTTCAGAAAACGCTCTGTGATAG 34 97 1 CAGAAAACGC 0.867455 -204 GCATACAGCACGAAAAACGTGAAACCGTCT 34 252 0 CGAAAAACGT 0.604129 -49 CACGCATAGGCTAAAAAAGCGGGGCGTGTC 37 41 1 CTAAAAAAGC 0.507088 -38 CGTGCAGGGTGAAAAAAATCTAGCAAGCTG 40 53 0 GAAAAAAATC 0.423219 -88 CCTAGTTATGGAGAAAAAGCGATCTGAGTA 41 71 1 GAGAAAAAGC 0.616449 -110 TGTCTTCTAGCGAAAAAAGCTTTCCACCCT 41 133 0 CGAAAAAAGC 0.737261 -48 CCCATACAAACAAAAAAACCCTTTAAAAAG 43 43 0 CAAAAAAACC 0.756429 -109 ATGTAACACGTAAAAAAAGCTCTCCGGCCT 44 26 0 TAAAAAAAGC 0.424852 -184 GCGTAAAGAGCAAAAAACGCAAAATAAATT 46 51 1 CAAAAAACGC 0.951084 -176 GTCTTTTGCTGAAAAAACTTGTTGAATCGA 46 135 0 GAAAAAACTT 0.285233 -92 TTTGAATCCACAAAAAAAGAGACTGAAAAC 47 40 0 CAAAAAAAGA 0.66029 -137 TAAAAAAGGGCAAAAAAAGTCGAAGATGCC 48 18 0 CAAAAAAAGT 0.886797 -283 GCGTCCTCTGCAGAAAAAGCGCTTTTTCAT 48 243 0 CAGAAAAAGC 0.849238 -58 ********** Masking position 5 Map Score: 16.153 Number of sites scoring better than the average of aligned sites = 1474 Number in coding regions = 1192 Number in noncoding regions = 282 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 8 GCAAGTGCCTCCTTCCTTTTCAGTTTTT 5 87 0 CCTCCTTCCT 0.747438 -18 TCCGCTCGTCCACTCCCCTGCTCTCTTAT 8 97 0 TCCACTCCCT 0.893344 -19 AAAAATCCCCTTCCTTATGTGTTGTA 15 153 0 TCCCCTTCCT 0.987357 -16 GTTTTGCCGCTCCATTTCCGTACAAAACGTG 18 64 1 TCCATTTCCT 0.915044 -62 CAAAACCCCTTTTCCTTCCATTAGATAGCGT 21 176 1 TTTCCTTCCT 0.847569 -125 TTGGTTCACTTCCTTCTGAAATCTT 25 28 0 TTCACTTCCT 0.940253 -15 CTGTTCCACTTCCTTATAGCAGTTT 33 16 0 TCCACTTCCT 0.979916 -15 AGGGAGTCCGTCCCCTTCCCTTGTCCGCTTT 34 49 0 TCCCCTTCCT 0.987357 -252 GGGGACGGACTCCCTTTCCCTTTTTCCATGA 34 65 1 TCCCTTTCCT 0.945173 -236 CACATACTTATCCACTTCTTTATTAGCGTTG 38 23 1 TCCACTTCTT 0.77782 -134 TTAAAAAACATTTACTTCCATGGAAAATGAT 48 169 1 TTTACTTCCT 0.776487 -132 CAAAAGGCTCTTCCTTTCCATCTACATGGAT 50 106 0 TTCCTTTCCT 0.847569 -98 ********* * Masking position 6 Map Score: 10.4404 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 217 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 9 TTTATCTAAAAATAAACAATTGAATAAGTC 1 109 0 AATAAACAAT 0.683371 -192 AAAGGTAAAATAAAAACAAATCAAAATGTT 3 138 1 TAAAAACAAA 0.540973 -60 CATAGGTTCGAAAAAACAATTGACAGAAAC 13 73 1 AAAAAACAAT 0.920009 -77 TAAAAATGCGAACAAACATTCCTGTTGGAG 13 127 1 AACAAACATT 0.408737 -23 AAATTAGATTAAAAAACATATTTTTTATTT 21 132 0 AAAAAACATA 0.540973 -169 CTATTCTCATTATAAACAATAATCAGACAT 24 89 0 TATAAACAAT 0.451295 -212 AAATTTTATTTAAAAACAATTTATTTAATT 26 58 1 TAAAAACAAT 0.814228 -126 ATCATTGCCCTAAAAACAATGAAAAGGGAT 26 122 0 TAAAAACAAT 0.814228 -62 ATGCACACACAAAAAACAATAAATAGTATA 31 209 1 AAAAAACAAT 0.920009 -92 AGCAAAACACAAAAAACGATAAAGGAAGGT 31 276 1 AAAAAACGAT 0.609454 -25 CAATATTTTCAAAAAACATTGACAGTTCAA 43 82 1 AAAAAACATT 0.814228 -70 GTAAATAGAGAAAAAACAATGCTAAACTAT 44 142 1 AAAAAACAAT 0.920009 -68 CTCTTTACGCAAAAAACAAATGCAAAATTA 46 31 0 AAAAAACAAA 0.755656 -196 CAGCCGGCCAAAAAAACAATGAGGTGAAAA 47 155 1 AAAAAACAAT 0.920009 -22 AATATTCCTTAAAAAACATTTACTTCCATG 48 161 1 AAAAAACATT 0.814228 -140 ********** Masking position 5 Map Score: 12.6101 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 194 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 10 TACTCTCTCTGAAAATAGCAAACACAAAAA 1 70 0 GAAAATAGCA 0.80581 -231 AAATAATACTGAATATGGCAAGATGAAAAA 1 138 1 GAATATGGCA 0.914739 -163 TCCTTTTAATGAATCTGGCATTGCCAAAAG 3 11 1 GAATCTGGCA 0.66892 -187 GTTCTCATAATAAAAGGGCAATAGACACGC 9 40 0 TAAAAGGGCA 0.697574 -43 TATAAGAGGAATACGGCAATATCGTATT 15 9 1 GAATACGGCA 0.913164 -160 GCTTGCAGAAGAAAACGGCAGATCATCTCC 19 203 1 GAAAACGGCA 0.963505 -43 GGCTGATGTGGAAAAGGGCATAAAGCAAAA 21 15 1 GAAAAGGGCA 0.963505 -286 GGATGAAAAAGAAAACAGCAAACGTGCTTA 21 219 1 GAAAACAGCA 0.802658 -82 AGGGGGGGGTGAAAATGGAAACAATGAAAA 29 67 1 GAAAATGGAA 0.679724 -79 CAAAAGACAAGAAAATGGCATGATTCTTGC 46 157 1 GAAAATGGCA 0.964203 -70 TCCTATTTTAAAAAAGGGCAAAAAAAGTCG 48 26 0 AAAAAGGGCA 0.697574 -275 ********** Masking position 3 Map Score: 6.50402 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 278 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 AAACTGGGTAGTAAACATTTATTTTTGTAA 1 165 1 GTAAACATTT 0.953231 -136 TTATGACAGCGTTAACATTTCATTTTCAAA 3 83 1 GTTAACATTT 0.914468 -115 AAATGTTAACGTTAACATTTTGATTTGTTT 3 151 0 GTTAACATTT 0.914468 -47 AAATGTTAACGTTAACATTTTGAAATAGAA 3 161 1 GTTAACATTT 0.914468 -37 GCAAACGTGCTTAAACATTTGTCAAACGTA 21 236 1 TTAAACATTT 0.666458 -65 TTCATATTTAGAAAACATTTTATTTTTCTT 23 121 0 GAAAACATTT 0.762641 -43 AAAATTATAGGTAAACATTTAACAAATGTC 24 64 1 GTAAACATTT 0.953231 -237 CCAGTAAAATGTAAGCATTTTCTTTTTGGG 24 189 1 GTAAGCATTT 0.84408 -112 CAAAAGGGAGGTAATCATTTGTTAAAGGAT 27 209 1 GTAATCATTT 0.785065 -92 ********** Masking position 4 Map Score: 6.31995 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 12 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 GTAGGGGTTTCGCTTGGAGAGTGCCCAAAAA 5 60 1 CGCTTGAGAG 0.900149 -45 TGAGGTTAGCCTCTTGTTCAGACATCAAAAT 23 39 1 CTCTTGTCAG 0.858876 -125 CATCGTGCTTCGCTTGATCAGACGGTACGGA 27 266 0 CGCTTGTCAG 0.979131 -35 GCGATAACTCCGCTAGGGCAGATCGCAGTCT 34 215 0 CGCTAGGCAG 0.956424 -86 GCGGAGTTATCGCTTGAACAGACGGTTTCAC 34 233 1 CGCTTGACAG 0.979099 -68 ATTTAATCAGCGCCTGCGCAGTTGTTAAGCG 50 58 0 CGCCTGGCAG 0.970176 -146 ATCGGGCAGGCGCTTGAGCAGGATGCAGGCC 50 181 1 CGCTTGGCAG 0.990619 -23 ****** **** Masking position 10 Map Score: 4.03732 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 66 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 CACTCTCCAAGCGAAACCCCTACAAACACAT 5 52 0 GCGAACCCCT 0.728601 -53 CGGACGAGAAACGAAACCTCTTTAGACGCGA 7 151 1 ACGAACCTCT 0.68696 -46 ATCAAAAAACCTCTTCAAACTGCA 7 183 0 AAAAACCTCT 0.415951 -14 AAGAAAAGCCCCCTTTATCGGGG 18 3 1 GAAAACCCCC 0.765441 -123 TTAGAAAGTGAAGAATCCTTCTCGTTGTAAC 19 159 1 AAGAACCTTC 0.847034 -87 TCTGCAAGCCAAAAAACCTTCCGTTACAACG 19 181 0 AAAAACCTTC 0.596511 -65 TGTAATACCTGTAAAACCGCCCTCAGCCAGA 21 46 1 GTAAACCGCC 0.58874 -255 TGAACGAAACCTCCTATCATCCTC 21 287 0 ACGAACCTCC 0.891535 -14 ATAAACGTGAAGCCTTTGGCTCACGTT 26 7 1 GTGAACCTTT 0.732142 -177 ATGCGGTGAAGAGAACCCTTCACAAAAGGGA 27 187 1 GAGAACCTTC 0.941252 -114 TATTGACATTGCAAACCCTTTTACGATAAGA 31 133 0 GCAAACCTTT 0.484405 -168 ATGAAACCTTCCTTTATCGTT 31 290 0 ATGAACCTTC 0.779655 -11 AAAAAACGAGGAGAAACTTCCGCTAGAATTG 32 59 0 GAGAACTTCC 0.5891 -89 CACGAAAAACGTGAAACCGTCTGTTCAAGCG 34 243 0 GTGAACCGTC 0.748217 -58 AAGTGAATCCTCCTTTATAACGT 42 3 1 GTGAACCTCC 0.948646 -163 TTTGAGAAGCCTCCGCAAAATAAT 46 4 1 GAGAACCTCC 0.966565 -223 AGAGAAGCCCTCCTCTTTCTAT 52 63 0 GAGAACCCTC 0.871367 -12 ***** ***** Masking position 5 Map Score: 6.55339 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 369 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 14 GAGAGTGCCCAAAAAACTGAAAAGGAAGGAGG 5 76 1 AAAAATGAAA 0.637021 -29 ACCTTCTAAAAAAATCTTGAAATGATAGTCCA 6 65 0 AAAATTGAAA 0.831542 -30 CGTATATACTGAAATTATAAAAATGCGAACAA 13 110 1 GAAATTAAAA 0.503104 -40 TTTTACTCTCAAAATCTTAAAAGAAAACCCCC 18 30 0 AAAATTAAAA 0.812673 -96 TGCATACGACAAAAGTGTAACACGTTTTGTAC 18 83 0 AAAAGTAACA 0.403833 -43 GGCATAAAGCAAAAGTGTAATACCTGTAAAAC 21 31 1 AAAAGTAATA 0.649438 -270 GCAAGGAAAAAGCCTAAAACTAGCCATAA 22 8 1 AAAAGTAAAA 0.79781 -36 ATACAGCACGAAAAACGTGAAACCGTCTGTTC 34 248 0 AAAAATGAAA 0.637021 -53 TAATCCTTTTGAAAGTATAAAAGATGTCCTGT 38 85 0 GAAAGTAAAA 0.479414 -72 ACTTTTGACGAAAATCATAATATTGGGGTGTA 42 142 1 AAAATTAATA 0.670705 -24 ATGTTTTTTGAAAATATTGATAATTATTCCCA 43 69 0 AAAATTGATA 0.698571 -83 AAATTTACTTAAAATTTTAAAAGATTGGTTGG 43 125 1 AAAATTAAAA 0.812673 -27 GATTTAAATGAAAATAATAAAACTTATAAATA 44 97 1 AAAATTAAAA 0.812673 -113 CCTCCTGATCAAAAAGTTGAAATCGTGCGATC 45 45 0 AAAAATGAAA 0.637021 -29 ACTTCCATGGAAAATGATGATAGATTAATTTT 48 182 1 AAAATTGATA 0.698571 -119 TTACTTGATTAAAAGATTAATATAATAAAAAT 53 29 1 AAAAGTAATA 0.649438 -272 TAATATAATAAAAATAATGAAAAAATGTAGTG 53 46 1 AAAATTGAAA 0.831542 -255 ***** ***** Masking position 8 Map Score: 6.07037 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 275 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 15 CTTGAACTCCCCCTAATTCGTC 16 6 0 ATCCCCCTAT 0.970221 -17 GTTTTCTCCTCCTCATGTTTAGAGGA 19 230 0 TTCCTCCTAT 0.953576 -16 GTCGAATGTCCTCCTTATGTAGCCTGAT 41 163 0 TTCCTCCTAT 0.953576 -18 AAATTGTCCTCCTGATCAAAAAGTTG 45 58 0 TTCCTCCTAT 0.953576 -16 ATGTAGTCCCCCTCGTGTTATGAAAT 46 211 0 ATCCCCCTGT 0.909297 -16 TCTTCATTGGATTCACCCTTATCATCATGCAA 47 84 0 ATCACCCTAT 0.80865 -93 GACATTTCCCCCTAATTGATTGTTGA 48 285 0 TTCCCCCTAT 0.976971 -16 * ******* ** Masking position 9 Map Score: 1.96485 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 18 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