AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_bsub_reg_100.orf -o00010_bsub_100.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 Input sequences: #1 ybfT 218 similar to glucosamine-6-phosphate isomerase #2 lctE 176 L-lactate dehydrogenase #3 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #4 yflL 66 similar to hypothetical proteins #5 treP 192 phosphotransferase system (PTS) trehalose-specific enzyme IIBC component #6 glvA 300 6-phospho-alpha-glucosidase #7 yfiA 64 similar to hypothetical proteins #8 yhfR 70 similar to phosphoglycerate mutase (glycolysis) #9 yhfU 134 similar to biotin biosynthesis #10 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #11 fruR 279 transcriptional regulator (DeoR family) #12 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #13 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #14 ypqE 137 similar to phosphotransferase system enzyme II #15 yqiS 124 similar to phosphate butyryltransferase #16 yqgQ 109 yqgQ #17 yraG 248 similar to spore coat protein #18 adhA 300 NADP-dependent alcohol dehydrogenase #19 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #20 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #21 pykA 42 pyruvate kinase #22 pfk 183 6-phosphofructokinase #23 gbsA 198 glycine betaine aldehyde dehydrogenase #24 pgi 111 glucose-6-phosphate isomerase #25 eno 29 enolase #26 tpi 30 triose phosphate isomerase #27 pgk 300 phosphoglycerate kinase #28 gap 46 glyceraldehyde-3-phosphate dehydrogenase #29 yvbQ 297 yvbQ #30 fbaA 180 fructose-1,6-bisphosphate aldolase #31 sacP 300 phosphotransferase system (PTS) sucrose-specific enzyme IIBC component #32 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #33 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component #34 iolI 85 alternate gene name: yxdH; myo-inositol catabolism #35 iolG 22 myo-inositol 2-dehydrogenase #36 iolD 203 alternate gene name: yxdD; myo-inositol catabolism #37 yyzE 300 similar to phosphotransferase systeme enzyme II #38 fbp 300 fructose-1,6-bisphosphatase Motif number 1 ATGCAATCCGTTCTTTTTCATTGAGACCATA 1 30 1 TCTTTTTCAT 0.726141 -189 AACCAGGAGCCTTTTTATTTTTAAAAAA 3 8 1 ACCTTTTTAT 0.482837 -165 ACTTTTTTATAGCGCTTTCATCCTAGTCTGG 5 90 0 ACGCTTTCAT 0.959425 -103 CCCCTCCGTATCCGTTTTTATAACTTGTATA 5 167 0 TCGTTTTTAT 0.74322 -26 CGTACAAAAGAACCTTTTCATAAGAATTGGA 6 60 1 ACCTTTTCAT 0.920588 -241 TTCCAGTTTAACCGTTTACATTTGCCCTTTT 10 143 0 ACGTTTACAT 0.678484 -96 CGCCTGTGAATTCGTTGTCATGATTTTTAGC 10 180 1 TCGTTGTCAT 0.71871 -59 TCAAAATGAATACGTTTTCATTAGGAGGTGA 11 256 1 TCGTTTTCAT 0.972928 -24 GTATTCGCTTTACATTTTCATCAA 12 4 0 TCATTTTCAT 0.600587 -297 AGAACCGTCAATCGTTTTCATCGCTGATTTT 12 43 0 ACGTTTTCAT 0.972928 -258 AAAAGCCAGCTTCCTTTCCATATTCCACCT 16 10 0 TCCTTTCCAT 0.814816 -100 CTTTTTTGTCAGCGTTTTCTTCTTGACTGAC 16 36 1 ACGTTTTCTT 0.76636 -74 TTCTTGACTGACCGCTTCCTTATGAATACGC 16 55 1 ACGCTTCCTT 0.450281 -55 AACTATCATAAGCGTATTCATAAGGAAGCGG 16 66 0 ACGTATTCAT 0.632881 -44 AGTTGTGTTAAGCGTTTTCATTGTTATTTCA 19 110 0 ACGTTTTCAT 0.972928 -80 AGGATGGAGATCCCTTTTCATTGTTTTTAGG 22 113 1 TCCTTTTCAT 0.920588 -71 CTTTCATTATAGCGCTTCTATTCGAAAGAAC 27 22 0 ACGCTTCTAT 0.419548 -279 CCTTCCCTTGTCCGCTTTCATTATAGCGCTT 27 36 0 TCGCTTTCAT 0.959425 -265 CAATATTCGCAGAGTTTTCATGCCGCGTCGT 29 125 0 AAGTTTTCAT 0.66019 -173 AAATCATGATAGCGTTTTCGTCAACTATTTT 31 126 0 ACGTTTTCGT 0.733826 -175 AGATTAAGAATACGCTTTCATCATAAATCAT 31 150 0 TCGCTTTCAT 0.959425 -151 GACACAGCGATCCTTTTTCATTTACGCAAAT 31 223 0 TCTTTTTCAT 0.726141 -78 ATATTATGAAATCGCTTTCATAAACACTCAG 32 51 0 ACGCTTTCAT 0.959425 -77 GTGAGATGTCAACGCTTTCATTTTTGGTGTT 33 48 0 ACGCTTTCAT 0.959425 -253 CAAAAGGCTCTTCCTTTCCATCTACATGGAT 36 106 0 TCCTTTCCAT 0.814816 -98 CGATCCCTAATACGTTTCCATGACCGAAAAT 36 154 0 TCGTTTCCAT 0.931698 -50 TCGTTTTGGTTACGCTTTCATTATAATTGTA 37 80 0 TCGCTTTCAT 0.959425 -221 TATTGATGTTTTACTTTTCATTACGAAGCTT 38 98 0 TACTTTTCAT 0.385253 -203 * ********* Masking position 11 Map Score: 32.6265 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 612 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 2 GTAAAAACCACCTTTTCTTTTTATGATA 4 49 0 CCCCTTTTCT 0.976494 -18 AGAGGCTCACCCTGCTTTTTAATGTCATATT 5 11 1 CCGCTTTTTA 0.77292 -182 ATCAGATCCCCCCATTTTCTTTCTATTATA 7 45 0 CCCATTTTCT 0.753993 -20 TGCCATACGGCCGGTTTTTTTGCGTTCATTA 9 27 1 CCGTTTTTTT 0.629031 -108 GAATGAACTTCCCGTTTTTTTCCCTCAATCA 10 67 0 CCGTTTTTTT 0.629031 -172 AAGAATTGACCTCCTCTTTTTACTAGTCTG 10 219 0 CCCCTCTTTT 0.796993 -20 TAAGTCACCTCTTCCTTTCTTTTAAACAGTC 12 278 0 CTCCTTTCTT 0.874637 -23 TATCGCCACCGCCTTTTTTAACCAGATTA 14 9 1 CCCCTTTTTT 0.979225 -129 TGTTTCGACTCCGCCTTTTATTATGCAAGTT 15 88 0 CCCCTTTTAT 0.938509 -37 CTGTTACCACCTTTCTTGTTTCGACTC 15 108 0 CCCCTTTCTT 0.976269 -17 AAAAAGCCAGCTTCCTTTCCATATTCCACCT 16 11 0 CTCCTTTCCA 0.566147 -99 GGAAAGGAAGCTGGCTTTTTTGTCAGCGTTT 16 22 1 CTGCTTTTTT 0.731197 -88 ATTGATGTAACCTCCTTTTATCAACGTTACA 17 228 0 CCCCTTTTAT 0.938509 -21 ACTGACCCTCTTTTCCTTTAGAAAATT 23 7 1 CCCTTTTCCT 0.793094 -192 TCCAGTCATTCCGCCCTTTCTTCTTGACTTG 24 26 1 CCCCCTTTCT 0.775796 -86 TCAAACGTTCCTTCCTTTTTTGCTGGACATT 29 274 0 CTCCTTTTTT 0.88881 -24 GTCTTTTCCTGCTTTCTTTCATGATTGA 31 8 1 CCGCTTTCTT 0.93333 -293 CTATTTCTCCCCCTTTTATTTAAACAAAA 31 282 0 CCCCTTTTAT 0.938509 -19 CCGCCTTTCACCAGCTTTTTTTGTATCAAAT 33 236 0 CCGCTTTTTT 0.941313 -65 TGAAAGGCGGCCACCTTTCATCCAGCAGTCC 33 257 1 CCCCTTTCAT 0.930174 -44 GTGTATACCTCCTTTTTATGGGGGGACT 33 283 0 CCCCTTTTTA 0.90911 -18 ACAAACGATCCCACCTTTACTCGATCTTTTT 36 14 0 CCCCTTTACT 0.78044 -190 ACAAAAGGCTCTTCCTTTCCATCTACATGGA 36 107 0 CTCCTTTCCA 0.566147 -97 AGATTGTTTGCCTCATTTCTTCCACTTAAAA 38 158 0 CCCATTTCTT 0.752176 -143 ** ******** Masking position 8 Map Score: 28.8974 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 574 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 365 Fraction of orfs with sites within 600 bp upstream = 0.0586251 Motif number 3 GACTCTATGTTAAAACGCTTACAGTCCCTATAC 3 79 0 TAAACGCTCA 0.953264 -94 AGACTAGGATGAAAGCGCTATAAAAAAGTGTTG 5 92 1 GAAACGCTAA 0.745339 -101 AAATGGAATTGTAAACGTTATCAAGGAGGTCGT 6 275 1 GTAACGTTCA 0.910917 -26 GTCTTCCAGTTTAACCGTTTACATTTGCCCTTT 10 144 0 TTAACGTTCA 0.779447 -95 TTACGCCTGTGAATTCGTTGTCATGATTTTTAG 10 177 1 GAATCGTTCA 0.930142 -62 TATTCAAAATGAATACGTTTTCATTAGGAGGTG 11 253 1 GAATCGTTCA 0.930142 -27 AGAAGAACCGTCAATCGTTTTCATCGCTGATTT 12 44 0 TCAACGTTCA 0.674586 -257 CAGTCAAGAAGAAAACGCTGACAAAAAAGCCAG 16 32 0 GAAACGCTCA 0.983338 -78 CACAGTTGTGTTAAGCGTTTTCATTGTTATTTC 19 111 0 TTAACGTTCA 0.779447 -79 GGCCTTAGGCGAAAGCGCCGGCAAAGCTGCTTA 27 143 0 GAAACGCCCA 0.882136 -158 AATAGTTGACGAAAACGCTATCATGATTTATGA 31 128 1 GAAACGCTCA 0.983338 -173 TTCAGATTAAGAATACGCTTTCATCATAAATCA 31 151 0 GAATCGCTCA 0.950275 -150 ATCATATTATGAAATCGCTTTCATAAACACTCA 32 52 0 GAAACGCTCA 0.983338 -76 CACCAAAAATGAAAGCGTTGACATCTCACGAAT 33 50 1 GAAACGTTCA 0.976257 -251 GCCCGATCCCTAATACGTTTCCATGACCGAAAA 36 155 0 TAATCGTTCA 0.821484 -49 TAGCATAAACCGCTTACAATGATAGTTA 37 6 1 TAAACGCTCA 0.953264 -295 CAATTATAATGAAAGCGTAACCAAAACGAAGGG 37 82 1 GAAACGTACA 0.778676 -219 **** **** ** Masking position 3 Map Score: 26.1912 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 147 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 CCATCATTGATGGTTTCTTTCGGTAAGTCC 2 26 0 TGGTTTCTTT 0.844665 -151 CCATCAATGATGGTTTCTTTTTTGTTCATA 2 43 1 TGGTTTCTTT 0.844665 -134 TCTTATGAAAAGGTTCTTTTGTACGATTCG 6 55 0 AGGTTCTTTT 0.835255 -246 CTGAGAGATTTGGTTTTTTTACCTTTTTTG 6 139 0 TGGTTTTTTT 0.915049 -162 GCCATACGGCCGGTTTTTTTGCGTTCATTA 9 28 1 CGGTTTTTTT 0.797512 -107 AACATGCATGAGGTTTTTTTATGTTTAGTG 11 19 1 AGGTTTTTTT 0.949712 -261 GAAAGGAAGCTGGCTTTTTTGTCAGCGTTT 16 23 1 TGGCTTTTTT 0.611088 -87 TAGTGCTGTCAGGTTTCTTTGGTATCATTA 17 56 0 AGGTTTCTTT 0.905069 -193 CTTATAAATCAGGTTCATTTTAAATGGTTT 18 158 1 AGGTTCATTT 0.531824 -143 TCATTTTAAATGGTTTTTTTAAAAAACCCT 18 172 1 TGGTTTTTTT 0.915049 -129 CTTTAAGGCAAGGGTTTTTTAAAAAAACCA 18 182 0 AGGGTTTTTT 0.733682 -119 ATTTTAATACAGGTTTATTTTTTTCGTTTT 19 51 1 AGGTTTATTT 0.808847 -139 GGCGAATTTTAGGTCTTTTTTGTTTAAATA 31 265 1 AGGTCTTTTT 0.71929 -36 TGTGTCATTTAGGTTTTTTTATTCTCTTTT 33 191 1 AGGTTTTTTT 0.949712 -110 GCCTTTCACCAGCTTTTTTTGTATCAAATG 33 235 0 AGCTTTTTTT 0.612971 -66 ********** Masking position 8 Map Score: 14.0735 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 128 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 GTGACACCCCCTCAAAGAGATAG 1 206 0 ACACCCCCTC 0.897037 -13 CATGTGCCAAAGTCCTCTTTACTTTCAATT 3 49 1 AGTCCTCTTT 0.501101 -124 ATGACGACCTCCTTGATAACGTTT 6 287 0 CGACCTCCTT 0.838044 -14 AAGAATTGACCTCCTCTTTTTACTAG 10 223 0 TGACCTCCTC 0.890701 -16 GCTTCACCTCCTAATGAAAACGT 11 267 0 TCACCTCCTA 0.814242 -13 AACTAATACAACACCGCTTAACATGGATTA 12 92 0 ACACCGCTTA 0.704983 -209 ACTAAGTCACCTCTTCCTTTCTTTTA 12 285 0 TCACCTCTTC 0.806033 -16 AGTTCTCGACCTCCTAGTTTGATTAA 13 99 0 CGACCTCCTA 0.817072 -16 TATCGCCACCGCCTTTTTTAACCAG 14 6 1 CCACCGCCTT 0.862803 -132 TCTTGTTTCGACTCCGCCTTTTATTATGCA 15 92 0 ACTCCGCCTT 0.70535 -33 TCTTCTTGACTGACCGCTTCCTTATGAATA 16 53 1 TGACCGCTTC 0.834721 -57 GTTGGACACCCCTTATCAATTATGC 20 191 0 ACACCCCTTA 0.704983 -15 CCCCTTCCCTTGTCCGCTTTCATTATAGCG 27 39 0 TGTCCGCTTT 0.581186 -262 AAAGGGAGTCCGTCCCCTTCCCTTGTCCGC 27 52 0 CGTCCCCTTC 0.694122 -249 GTCGAATGTCCTCCTTATGTAGCCTG 30 165 0 TGTCCTCCTT 0.691278 -16 CTATTTCTCCCCCTTTTATTTAAAC 31 286 0 TCTCCCCCTT 0.731279 -15 GTAAAAGACCCCCTAGAGTTTGATC 32 113 0 AGACCCCCTA 0.824136 -15 AAATGCTGCATCACCTCCTAAAAGAGAATA 33 210 0 TCACCTCCTA 0.814242 -91 GACATTTCACCCACCCCTTCGTTTTGGTTA 37 99 0 CCACCCCTTC 0.837301 -202 CTTTAGGGGTAGACCGCTTCAGCACCAATC 37 230 0 AGACCGCTTC 0.816265 -71 ********** Masking position 9 Map Score: 13.0403 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 348 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 6 TTGCATACAGAATGGGGAGAATGAA 1 6 0 AATGGGGAGA 0.871709 -213 CAGATTCGAAAATGGGGGAATTTCAT 7 7 0 AATGGGGGAA 0.871709 -58 ATAGAAAGAAAATGGGGGGATCTGAT 7 49 1 AATGGGGGGA 0.966424 -16 CATACGTTAATATGGAGAAACGTGAAAGAT 11 152 1 TATGGAGAAA 0.544476 -128 ACAGATATATAATAGAGGGAAAACGTTCAT 13 36 0 AATAGAGGGA 0.786117 -79 AATAGTGGTGAATGAAGGGATAACGGTTGA 14 93 1 AATGAAGGGA 0.772562 -45 ATTATACCGTTATGGAGGGACAGCAGC 24 95 1 TATGGAGGGA 0.955453 -17 TTGAAAATCAAAAGGAGAGACAAAACTC 25 12 1 AAAGGAGAGA 0.740047 -18 GAGATATTTATATTGAGGGA 28 1 0 TATTGAGGGA 0.585526 -46 TCACTTATTTAAAGGAGGAAACAATC 28 31 1 AAAGGAGGAA 0.740047 -16 GTATCCTAGTTATGGAGAAAAAGCGATCTG 30 67 1 TATGGAGAAA 0.544476 -114 TTGTTTAAATAAAAGGGGGAGAAATAG 31 284 1 AAAAGGGGGA 0.560236 -17 ACCTCCTTTTTATGGGGGGACTGCTGGATG 33 275 0 TATGGGGGGA 0.951239 -26 GCGTTTTAGATATGAAGGGAGTTCGGCAGG 34 49 0 TATGAAGGGA 0.697174 -37 AAGATCGAGTAAAGGTGGGATCGTTTGTGG 36 17 1 AAAGGTGGGA 0.629199 -187 ********** Masking position 2 Map Score: 9.60541 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 243 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 7 CATTTATATTGTGCAACACTTCACAAACTTTTGCAA 2 93 0 GTGAAACAAA 0.976258 -84 CAATATAAATGTGAAATACTTCACAAACAAAAAGAC 2 118 1 GTGAAACAAA 0.976258 -59 GTGAAATCCTCCAAAAAGTAATCAAA 9 119 0 GTGAACCAAA 0.962622 -16 CCTTTTTGTTGTGTAAAAGGGCAAATGTAAACGGTT 10 129 1 GTGAAACAAT 0.839348 -110 CCGAAATGAAGTTGAAGCATACAGAAAATACACTCG 17 188 0 GTTAACCAAA 0.864487 -61 TTATCGTTATGTTGAAGACACCATAAAACATAAATA 18 225 1 GTTAAACAAA 0.910598 -76 AGAATATCAGGCGTAAGAACCAAAAAGCAGCCAGCG 20 35 0 GCGAAAAAAA 0.669883 -171 CTGATATTCTGTGCAAGAAAACATAAGATGCATCAT 20 61 1 GTGAAACAAA 0.976258 -145 ACAGCTGAAGGCTGAAGATTTCAGAAGGAAGTGAAC 21 14 1 GCTAAACAAA 0.864487 -29 AAAATTAATTGTGAAATACTTCACAATATCGTGCCA 31 47 0 GTGAAACAAA 0.976258 -254 GATTGTTACTGCGAAAGCAGGCAAAACCTAAATGGT 33 127 1 GCGAACCAAA 0.941624 -174 *** ** * ** ** Masking position 6 Map Score: 8.07161 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 56 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 CAAAAAAACCGGCCGTATGGCAGACCGGTTTTT 9 16 0 GGCGTAGCAG 0.892641 -119 GGTGGAATATGGAAAGGAAGCTGGCTTTTTTGT 16 12 1 GGAAGGGCTG 0.827138 -98 AGGGCAGTCAGTGCGGAGCGCTGGCTGCTTTTT 20 17 1 GTGGGAGCTG 0.913161 -189 ACCCAAAGGGCGGAATCCAGTCATTCCGCC 24 8 1 GGGGGACCAG 0.91884 -104 ATACCGTTATGGAGGGACAGCAGC 24 98 1 GGAGGAGCAG 0.978463 -14 AACTCCGCTAGGGCAGATCGCAGTCTTTTTCGG 27 208 0 GGGAGAGCAG 0.959185 -93 GGTCATGCTAGGGTGGAAAGCTTTTTTCGCTAG 30 124 1 GGGGGAGCTT 0.953189 -57 TTCTCTTTTAGGAGGTGATGCAGCATTTGATAC 33 212 1 GGAGTGGCAG 0.776577 -89 TCCTTTTTATGGGGGGACTGCTGGATGAAAGGT 33 269 0 GGGGGAGCTG 0.993223 -32 AAGGGAGTTCGGCAGGAAGGCTGTCGCCATATC 34 32 0 GGCGGAGCTG 0.981079 -54 CCATCTACATGGATGTACTGCTGGTTTAAGAAT 36 87 0 GGAGTAGCTG 0.932462 -117 TTCGCTTTAGGGGTAGACCGCTTCAGCACCAAT 37 231 0 GGGAGAGCTT 0.818019 -70 *** *** **** Masking position 11 Map Score: 9.03897 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 277 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 GTATAGGGACTGTAAGCGTTTTAACATAGA 3 79 1 TGTAAGCGTT 0.936269 -94 CAGACTAGGATGAAAGCGCTATAAAAAAGT 5 91 1 TGAAAGCGCT 0.93639 -102 TAAATGGAATTGTAAACGTTATCAAGGAGG 6 274 1 TGTAAACGTT 0.865939 -27 AAAGGGCAAATGTAAACGGTTAAACTGGAA 10 144 1 TGTAAACGGT 0.783129 -95 ACAATTTCATTGTAAACGCTATTTTCGGTT 11 224 0 TGTAAACGCT 0.783129 -56 CACCTCCTAATGAAAACGTATTCATTTTGA 11 256 0 TGAAAACGTA 0.78943 -24 AAATCAGCGATGAAAACGATTGACGGTTCT 12 44 1 TGAAAACGAT 0.741777 -257 TATAATAGAGGGAAAACGTTCATCTTCCCT 13 29 0 GGAAAACGTT 0.579517 -86 CTGGCTTTTTTGTCAGCGTTTTCTTCTTGA 16 32 1 TGTCAGCGTT 0.650724 -78 GAAATAACAATGAAAACGCTTAACACAACT 19 111 1 TGAAAACGCT 0.866174 -79 AGCGCTATAATGAAAGCGGACAAGGGAAGG 27 37 1 TGAAAGCGGA 0.826595 -264 TCATAAATCATGATAGCGTTTTCGTCAACT 31 131 0 TGATAGCGTT 0.6926 -170 TGATTTATGATGAAAGCGTATTCTTAATCT 31 151 1 TGAAAGCGTA 0.895032 -150 TGAGTGTTTATGAAAGCGATTTCATAATAT 32 52 1 TGAAAGCGAT 0.867259 -76 ACACCAAAAATGAAAGCGTTGACATCTCAC 33 49 1 TGAAAGCGTT 0.963413 -252 TAACTATCATTGTAAGCGGTTTATGCTA 37 9 0 TGTAAGCGGT 0.891457 -292 ACAATTATAATGAAAGCGTAACCAAAACGA 37 81 1 TGAAAGCGTA 0.895032 -220 ********** Masking position 5 Map Score: 20.4462 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 141 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 10 ATGACGACCTCCTTGATAACGT 6 289 0 GACGACCTCC 0.934789 -12 TTATATTTTAGCCGATCCCCAGTTTGCCAA 12 182 0 GCCGATCCCC 0.91166 -119 AAGGGAAGGGGACGGACTCCCTTTCCCTTT 27 58 1 GACGGACTCC 0.977048 -243 TTTTCTGAAAGCCGGTCTTCATGGAAAAAG 27 84 0 GCCGGTCTTC 0.842453 -217 CTGGCTTTTAGACGAACTGCCCTGTGCCGA 27 182 1 GACGAACTGC 0.850802 -119 CATTTTGAAGGAGGATCTCCTAGGC 27 286 1 GAGGATCTCC 0.894268 -15 CACAGATTGCGAGAGTCTCCTCCTGCACCT 33 165 0 GAGAGTCTCC 0.614992 -136 GCCATATCCCGCCGAACTCCATGCTCAGC 34 10 0 GCCGAACTCC 0.984283 -76 CAGCCTTCCTGCCGAACTCCCTTCATATCT 34 42 1 GCCGAACTCC 0.984283 -44 GCCAGACTCCCCCATCTGCG 34 76 0 GCCAGACTCC 0.921487 -10 ********** Masking position 7 Map Score: 5.22058 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 153 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 AATTTCTGAAAATTTGTTATAAAAGAAGGATA 1 93 0 AATTTGTTAA 0.820078 -126 AAAAACACTAAAGTTGATCAAATGACCTAAGT 6 205 1 AAGTTGTAAA 0.840762 -96 ATAGACGCATAATCTGGTTAAAAAAGGCGGTG 14 17 0 AATCTGTAAA 0.844619 -121 TAAACCTTAAAGTCTGCTTTAAGGCAAGGGTT 18 196 0 AGTCTGTTAA 0.822192 -105 TGTACTGGCGAATTTGTTTTAATGTGTTATAC 20 131 1 AATTTGTTAA 0.820078 -75 TGTTAGATTAAGGTTGTTAAAAACATTAAATT 23 139 1 AGGTTGTAAA 0.794958 -60 TCTCAAAACTGCTATAAGGAAGTGGAA 26 6 1 AAACTGTTAA 0.697459 -25 AGCGCCGGCAAAGCTGCTTAAAACGCGGTCGT 27 131 0 AAGCTGTAAA 0.879441 -170 TTAGTTAAATAGTTTGATATAACATGTAGACA 31 93 0 AGTTTGTTAA 0.769951 -208 GGACATTACAAAATTGATCAAACTCTAGGGGG 32 98 1 AAATTGTAAA 0.590221 -30 GATACAAAAAAAGCTGGTGAAAGGCGGCCACC 33 240 1 AAGCTGTAAA 0.879441 -61 GAAAGGCCATAGTTTGATTTAAAGCTTCGTAA 38 77 1 AGTTTGTTAA 0.769951 -224 CTGTACTGAAAAGCTGTTTTAAGCTCTTGCTT 38 203 1 AAGCTGTTAA 0.894189 -98 ****** * *** Masking position 11 Map Score: 5.18002 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 233 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 12 TGTCATTACGAATTTAGCACCGCCCTTATC 1 139 0 AATTTAGCAC 0.622454 -80 AGTAAAGAGGACTTTGGCACATGACTGTGA 3 42 0 ACTTTGGCAC 0.955396 -131 ATGATGCTTCCCTTTGACTCTATGTTAAAA 3 97 0 CCTTTGACTC 0.688587 -76 TCCCGTAACACGTTTGGCGCACTTAGGTCA 6 227 0 CGTTTGGCGC 0.920963 -74 AGTTCAGCAAACTTTGGCGCAAATTCTCCT 18 21 0 ACTTTGGCGC 0.962778 -280 AAACGTGAAGCCTTTGGCTCACGTTTATTT 22 13 1 CCTTTGGCTC 0.957546 -171 TGGGATGCACCATTTGGCGCTTTCTGTATA 29 58 1 CATTTGGCGC 0.952072 -240 TTGTAGGTATACTTTAGCACTAGATTCGTG 33 76 0 ACTTTAGCAC 0.808348 -225 TTGCTTACCCCATTTGGCACCTCTTTCTCT 38 229 1 CATTTGGCAC 0.942693 -72 ********** Masking position 5 Map Score: 4.01068 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 157 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 AATGATGGTTTCTTTTTTGTTCATAAATCA 2 48 1 TCTTTTTTGT 0.768592 -129 ATAAACCCTCCCTGTTTTGTTTGTCGCTGT 3 151 0 CCTGTTTTGT 0.945311 -22 GGTTTTTTTACCTTTTTTGTAATCTTAAAG 6 128 0 CCTTTTTTGT 0.966213 -173 TTTGCCAAAACCTTTTATGTAGGATAGTTA 12 160 0 CCTTTTATGT 0.832302 -141 CTGTTACCACCTTTCTTGTTTCGACTCCG 15 106 0 CCTTTCTTGT 0.795083 -19 AAGGAAGCTGGCTTTTTTGTCAGCGTTTTC 16 25 1 GCTTTTTTGT 0.736263 -85 CACTCGGTATCATTTTTTGTTTTAAGAATC 17 164 0 CATTTTTTGT 0.863254 -85 TTGCTCCTTTCCTGTTTTGTACATCCATAT 19 165 0 CCTGTTTTGT 0.945311 -25 GGGCAATGATCATGTTATGTTTAATCATAT 22 142 1 CATGTTATGT 0.398402 -42 GACTTTTCCTCATGTTTCGTTAAGATAAAG 23 65 0 CATGTTTCGT 0.506019 -134 GACGGTTTCACGTTTTTCGTGCTGTATGCA 27 253 1 CGTTTTTCGT 0.646575 -48 TATGACGGGACGTTTTTTGTCATAGCGGGA 29 239 1 CGTTTTTTGT 0.872036 -59 AACGTTCCTTCCTTTTTTGCTGGACATTAT 29 272 0 CCTTTTTTGC 0.795083 -26 GAATTTTAGGTCTTTTTTGTTTAAATAAAA 31 268 1 TCTTTTTTGT 0.768592 -33 CTTTCACCAGCTTTTTTTGTATCAAATGCT 33 233 0 CTTTTTTTGT 0.714157 -68 ********** Masking position 5 Map Score: 10.0692 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 363 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 14 AGCACCGCCCTTATCAAACTGTCAATATTAATTT 1 120 0 TTAAACTGTA 0.939458 -99 CTTTTTATTTTTAAAAAATTGTCACAGTCATGTG 3 21 1 TTAAATTGTA 0.72829 -152 AATCAATCATTTTACAACCTGTAAAGGGGATGTG 4 16 0 TTTAACTGTA 0.957837 -51 ATTCCCCCATTTTCGAATCTGTAATTGTATATAA 7 16 1 TTTAACTGTA 0.957476 -49 GTCTATAGGGTTTGTAAACTGTAAATTCGACAAA 11 119 0 TTTAACTGTA 0.957838 -161 AACTGTATTATTTCGAAGTTGTAAAAAACTAATA 12 114 0 TTTAATTGTA 0.796776 -187 ATGAACCTGATTTATAAGCTGAGAAACAGTCAGT 18 142 0 TTTAACTGAA 0.761713 -159 TAACATATGGTTTTTAAACTGTCAAAGTCCCATT 23 110 0 TTTAACTGTA 0.957838 -89 GTGGAATTGTTTATTCAACTGTTAAGAGCCAATT 29 162 0 TTACACTGTA 0.763934 -136 TTACTTTTCATTACGAAGCTTTAAATCAAACTAT 38 85 0 TTAAACTTTA 0.575452 -216 *** ** **** * Masking position 7 Map Score: 3.12441 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 22 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 ATTTTAATGAAAAAAGTCTTTTATATTCATA 11 57 0 AAAAAGTCTT 0.710058 -223 CCTTTCTTTTAAACAGTCATTAGACGTGCAT 12 265 0 AAACAGTCTT 0.93446 -36 GAACGAGCAAAAACAGCGATTCTTAAAACAA 17 147 1 AAACAGCGTT 0.813859 -102 ATAAGCTGAGAAACAGTCAGTAATTAATGCA 18 132 0 AAACAGTCGT 0.91037 -169 AAACAGTTTTTTCATATGAAC 19 1 1 AAACAGTTTT 0.816658 -189 GAAAAACGTGAAACCGTCTGTTCAAGCGATA 27 240 0 AAACCGTCGT 0.679305 -61 CGCTTTAATGAAACAGCCCTTTCTACGGGAA 29 14 1 AAACAGCCTT 0.957892 -284 ATCCCAATATAAACAGCCCTTCCCGTAGAAA 29 33 0 AAACAGCCTT 0.957892 -265 TTTGATACAAAAAAAGCTGGTGAAAGGCGGC 33 237 1 AAAAAGCTGT 0.478541 -64 CAAGAGCTTAAAACAGCTTTTCAGTACAGGT 38 201 0 AAACAGCTTT 0.88148 -100 ******** ** Masking position 3 Map Score: 2.98843 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 217 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714