AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_bsub_reg_300.orf -o00010_bsub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/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 ybfT 218 similar to glucosamine-6-phosphate isomerase #2 ycgA 300 similar to hypothetical proteins #3 ycgB 115 ycgB #4 amyE 148 alpha-amylase #5 lctE 176 L-lactate dehydrogenase #6 ycnL 164 ycnL #7 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #8 yflL 66 similar to hypothetical proteins #9 treP 192 phosphotransferase system (PTS) trehalose-specific enzyme IIBC component #10 glvA 300 6-phospho-alpha-glucosidase #11 yfiA 64 similar to hypothetical proteins #12 yhfR 70 similar to phosphoglycerate mutase (glycolysis) #13 yhfU 134 similar to biotin biosynthesis #14 yhfV 138 similar to methyl-accepting chemotaxis protein #15 yhfW 111 similar to hypothetical proteins #16 ykvY 300 similar to Xaa-Pro dipeptidase #17 ykvZ 281 similar to transcriptional regulator (LacI family) #18 glcT 62 transcriptional antiterminator (BglG family) #19 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #20 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #21 moeB 50 molybdopterin biosynthesis protein #22 yknU 223 similar to ABC transporter (ATP-binding protein) #23 yknW 109 yknW #24 fruR 279 transcriptional regulator (DeoR family) #25 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #26 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #27 ypqE 137 similar to phosphotransferase system enzyme II #28 yqiS 124 similar to phosphate butyryltransferase #29 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #30 yqgQ 109 yqgQ #31 yqgP 89 similar to hypothetical proteins #32 yqgO 66 yqgO #33 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #34 yraG 248 similar to spore coat protein #35 adhA 300 NADP-dependent alcohol dehydrogenase #36 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #37 levR 300 transcriptional regulator (NifA/NtrC family) #38 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #39 ytcD 183 ytcD #40 pykA 42 pyruvate kinase #41 pfk 183 6-phosphofructokinase #42 yttI 300 similar to acetyl-CoA carboxylase #43 gbsA 198 glycine betaine aldehyde dehydrogenase #44 pgi 111 glucose-6-phosphate isomerase #45 yugK 103 similar to NADH-dependent butanol dehydrogenase #46 yugJ 229 similar to NADH-dependent butanol dehydrogenase #47 eno 29 enolase #48 tpi 30 triose phosphate isomerase #49 pgk 300 phosphoglycerate kinase #50 gap 46 glyceraldehyde-3-phosphate dehydrogenase #51 yvbQ 297 yvbQ #52 araE 137 permease #53 fbaA 180 fructose-1,6-bisphosphate aldolase #54 spo0F 165 two-component response regulator #55 sacP 300 phosphotransferase system (PTS) sucrose-specific enzyme IIBC component #56 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #57 licR 162 transcriptional regulator (antiterminator) #58 yxzF 28 yxzF #59 yxlJ 128 similar to DNA-3-methyladenine glycosidase #60 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component #61 iolI 85 alternate gene name: yxdH; myo-inositol catabolism #62 iolD 203 alternate gene name: yxdD; myo-inositol catabolism #63 iolC 23 alternate gene name: yxdC; myo-inositol catabolism #64 iolB 74 alternate gene name: yxdB; myo-inositol catabolism #65 iolA 300 methylmalonate-semialdehyde dehydrogenase #66 yyzE 300 similar to phosphotransferase systeme enzyme II #67 fbp 300 fructose-1,6-bisphosphatase Motif number 1 AGAATTTTGTTAACGCTTACATTTAAAATTA 4 25 0 TACGCTTACA 0.892691 -124 CTCTATGTTAAAACGCTTACAGTCCCTATAC 7 79 0 AACGCTTACA 0.964436 -94 CACTTTTTTATAGCGCTTTCATCCTAGTCTG 9 91 0 TACGCTTTCA 0.922439 -102 ACCTCCTTGATAACGTTTACAATTCCATTTA 10 274 0 TACGTTTACA 0.782553 -27 CTTCCAGTTTAACCGTTTACATTTGCCCTTT 19 144 0 AACGTTTACA 0.921456 -95 ACGCCTGTGAATTCGTTGTCATGATTTTTAG 19 179 1 ATCGTTGTCA 0.727612 -60 TATGTAGAATAAACGCTTACAGAAAATCATT 22 83 0 AACGCTTACA 0.964436 -141 AAACCGAAAATAGCGTTTACAATGAAATTGT 24 223 1 TACGTTTACA 0.782553 -57 TTCAAAATGAATACGTTTTCATTAGGAGGTG 24 255 1 ATCGTTTTCA 0.837267 -25 AAGAACCGTCAATCGTTTTCATCGCTGATTT 25 44 0 AACGTTTTCA 0.943733 -257 GTCAAGAAGAAAACGCTGACAAAAAAGCCAG 30 32 0 AACGCTGACA 0.933685 -78 CAGTTGTGTTAAGCGTTTTCATTGTTATTTC 36 111 0 AACGTTTTCA 0.943733 -79 TTATTTTTGAATGCGCTGTCAACCTTGTCGT 42 15 1 ATCGCTGTCA 0.860621 -286 TTTTTTTGTCAAACGCTGTCATCCTCAATTC 42 108 0 AACGCTGTCA 0.952671 -193 ATGTTGAGTAAAGCGTTTTCATTTAAACCTT 52 101 0 AACGTTTTCA 0.943733 -37 TAGTTGACGAAAACGCTATCATGATTTATGA 55 130 1 AACGCTATCA 0.756925 -171 CAGATTAAGAATACGCTTTCATCATAAATCA 55 151 0 ATCGCTTTCA 0.922439 -150 CATATTATGAAATCGCTTTCATAAACACTCA 56 52 0 AACGCTTTCA 0.974855 -76 CCAAAAATGAAAGCGTTGACATCTCACGAAT 60 52 1 AACGTTGACA 0.858975 -249 GCCAAGAATTAAACGCTTTCAAAAACACCAA 65 196 0 AACGCTTTCA 0.974855 -105 TAGCATAAACCGCTTACAATGATAGTTA 66 8 1 AACGCTTACA 0.964436 -293 TTCGTTTTGGTTACGCTTTCATTATAATTGT 66 81 0 TTCGCTTTCA 0.784868 -220 ** ******** Masking position 7 Map Score: 35.4181 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 166 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 TCTTCCGCTTCCTCCTTTCAAACCGATGTGA 4 63 0 CCCCTTTCAA 0.673646 -86 ATATAAACCCTCCCTGTTTTGTTTGTCGCT 7 153 0 CTCCTGTTTT 0.809796 -20 GTAAAAACCACCTTTTCTTTTTATGATA 8 49 0 CCCCTTTTCT 0.876013 -18 AGAGGCTCACCCTGCTTTTTAATGTCATATT 9 11 1 CCGCTTTTTA 0.841392 -182 TTCTCGACATCGTCCTTTTTTATCTGCATTA 17 32 1 CGCCTTTTTT 0.894965 -250 AAGAATTGACCTCCTCTTTTTACTAGTCTG 19 219 0 CCCCTCTTTT 0.851614 -20 TAAGTCACCTCTTCCTTTCTTTTAAACAGTC 25 278 0 CTCCTTTCTT 0.901157 -23 TATCGCCACCGCCTTTTTTAACCAGATTA 27 9 1 CCCCTTTTTT 0.984373 -129 TGTTTCGACTCCGCCTTTTATTATGCAAGTT 28 88 0 CCCCTTTTAT 0.963769 -37 CTGTTACCACCTTTCTTGTTTCGACTC 28 108 0 CCCCTTTCTT 0.970541 -17 GGAAAGGAAGCTGGCTTTTTTGTCAGCGTTT 30 22 1 CTGCTTTTTT 0.908213 -88 TTTCGGAGCGCCAGCTGTTATAATGAAAAAA 31 50 1 CCGCTGTTAT 0.786686 -40 TTTCAAAGCTCTGGCTTTTTTCTTACACCTC 33 241 0 CTGCTTTTTT 0.908213 -60 GAAAAAGGTTCTGGCTTTTTTTCTATTCCGA 33 268 1 CTGCTTTTTT 0.908213 -33 ATTGATGTAACCTCCTTTTATCAACGTTACA 34 228 0 CCCCTTTTAT 0.963769 -21 ATTGACAAAGCTGGCTTTTATGCGTATATGT 37 186 0 CTGCTTTTAT 0.806897 -115 CCAGTCATTCCGCCCTTTCTTCTTGACTTGA 44 27 1 CGCCTTTCTT 0.816731 -85 TCAAACGTTCCTTCCTTTTTTGCTGGACATT 51 274 0 CTCCTTTTTT 0.945746 -24 GTCTTTTCCTGCTTTCTTTCATGATTGA 55 8 1 CCGCTTTCTT 0.949241 -293 CTATTTCTCCCCCTTTTATTTAAACAAAA 55 282 0 CCCCTTTTAT 0.963769 -19 TCCCGGCTGTTTTTTTATAGGTC 57 3 1 CCGCTGTTTT 0.897256 -160 TGGTTGGCCCTCCTTTTTTGAACGGTAAC 59 9 1 CCCCTTTTTT 0.984373 -120 CCGCCTTTCACCAGCTTTTTTTGTATCAAAT 60 236 0 CCGCTTTTTT 0.972793 -65 TGAAAGGCGGCCACCTTTCATCCAGCAGTCC 60 257 1 CCCCTTTCAT 0.932943 -44 GTGTATACCTCCTTTTTATGGGGGGACT 60 283 0 CCCCTTTTTA 0.90334 -18 ** ******** Masking position 6 Map Score: 32.018 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 343 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 260 Fraction of orfs with sites within 600 bp upstream = 0.0417604 Motif number 3 AAAAACGTATGACATTTAAAATGCCTGACGCCT 2 102 1 GACATAAAAG 0.839091 -199 ACAATTTTTTAAAAATAAAAAGGCTCCTGGTT 7 10 0 AAAATAAAAG 0.93837 -163 CTTGGCCGATAAAAAAGAAAAAGGCTTAAAAAG 14 73 1 AAAAAAAAAG 0.926109 -66 AAAAGGCTTAAAAAGCCAAAAAGTAAAAATTAT 14 91 1 AAAACAAAAG 0.723285 -48 TAGAAATAAAAAAGGACTTTGTTCT 17 3 1 GAAAAAAAAG 0.866794 -279 CTTTCAGCTAAAAACACAAAAAGATATCTGGTA 17 197 1 AAAAAAAAAG 0.926109 -85 AAATTGAAGCAAAATTGAAAGTGTGGTTAAATA 27 64 1 AAAATAAAGG 0.812315 -74 AAAGGAAATGAAAAGATAAAGGGGTTTTCTGAA 29 12 0 AAAAAAAAGG 0.780832 -141 AGCGATTCTTAAAACAAAAAATGATACCGAGTG 34 161 1 AAAAAAAAAG 0.926109 -88 TTGTTGTTGAAACACTTAAAACGAAAAAAATAA 36 65 0 AACATAAAAG 0.909453 -125 TGGCTGAAATAACAATGAAAACGCTTAACACAA 36 106 1 AACATAAAAG 0.909453 -84 TTGCCCTAAAAACAATGAAAAGGGATCTCCATC 41 115 0 AACATAAAAG 0.909453 -69 ATATATTCACGAAAAAGAAAAAGTATGCTTCCG 42 237 1 GAAAAAAAAG 0.866794 -64 AAACATGAGGAAAAGTCAAAAAGAAAAATCAAA 43 78 1 AAAATAAAAG 0.93837 -121 AGTCAAAAAGAAAAATCAAAATGGGACTTTGAC 43 91 1 AAAATAAAAG 0.93837 -108 ATAAGTTGACAAAAAAGAAAAAGGGAAGCAGCC 45 32 0 AAAAAAAAAG 0.926109 -72 TTTGAAAATCAAAAGGAGAGACAAAA 47 4 1 GAAATAAAAG 0.887704 -26 AGTATACAACAAAAGAGAAAATGCTCAGAAAAT 54 42 1 AAAAAAAAAG 0.926109 -124 AGTCAACACCAAAAATGAAAGCGTTGACATCTC 60 44 1 AAAATAAAGG 0.812315 -257 TATACCTACAAACAAATAAAACGACCCGTCAGG 60 95 1 AACAAAAAAG 0.8921 -206 TGCTTTTAGAGACAATTAAAACGAGAGAAAGAG 67 249 0 GACATAAAAG 0.839091 -52 **** * **** * Masking position 8 Map Score: 24.4058 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 285 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 4 TTCACATCGGTTTGAAAGGAGGAAGCGGAAGAA 4 62 1 TTAAGGAGGA 0.956185 -87 ATTGTAAACGTTATCAAGGAGGTCGTCAT 10 282 1 TTAAGGAGGT 0.917681 -19 AATTATATTTTTCCCAAGGGGGATCATTGTA 14 118 1 TTAAGGGGGA 0.892277 -21 CTATCTTTTCATACATAGGAAGCAGGCATTGTT 15 45 0 ATTAGGAAGC 0.379605 -67 GTAACGTTCAATCGCAGGGGGGTTGTTCCGTTT 16 144 0 ATAGGGGGGT 0.535794 -157 TGCATTGCAAATGGCAGGGAGGAACAAGAA 16 281 1 ATAGGGAGGA 0.856176 -20 TTGTTAGATATTCTCAAGGAGGTTTTGAA 23 91 1 TTAAGGAGGT 0.917681 -19 TGAATACGTTTTCATTAGGAGGTGAAGC 24 262 1 TTTAGGAGGT 0.60284 -18 TGACTGTTTAAAAGAAAGGAAGAGGTGACTTAG 25 277 1 AAAAGGAAGA 0.602465 -24 GTTGAAGTGAATGAGAAGGGAGAAAATACA 27 118 1 ATAAGGGAGA 0.707327 -20 AGGTGGAATATGGAAAGGAAGCTGGCTTTTTT 30 10 1 ATAAGGAAGC 0.817979 -100 CATAAGCGTATTCATAAGGAAGCGGTCAGTCAA 30 58 0 TTAAGGAAGC 0.828518 -52 AAAAGTATGGTTTTATAGGAGGCACTCGAT 34 8 0 TTTAGGAGGC 0.677116 -241 ACAACACATCTTACAAAGGAGGAACATC 39 6 0 TTAAGGAGGA 0.956185 -178 GGCTGAAGATTTCAGAAGGAAGTGAACCAA 40 23 1 TTAAGGAAGT 0.777632 -20 TAGGTAAGGTTTCATAGGGAGGATGGAGATCCC 41 94 1 TTAGGGAGGA 0.864869 -90 TGCATTCTCCATATGAGGGAAGCTGGCCTGCCC 46 78 1 ATAGGGAAGC 0.568586 -152 CATAATAAAAAATCTAAGGAGGAGATGTC 46 211 1 AAAAGGAGGA 0.828507 -19 ATGCAAACCATTTTGAAGGAGGATCTCCTAGGC 49 278 1 TTAAGGAGGA 0.956185 -23 TCTCTCACTTATTTAAAGGAGGAAACAATC 50 27 1 ATAAGGAGGA 0.953047 -20 ACAATCAGGCTACATAAGGAGGACATTCGAC 53 160 1 TAAAGGAGGA 0.838556 -21 ATATTGTACGTTATAAAGGAGGATTCACTT 54 8 0 TTAAGGAGGA 0.956185 -158 TTTTTGTTTAAATAAAAGGGGGAGAAATAG 55 281 1 AAAAGGGGGA 0.647102 -20 CAGTCCCCCCATAAAAAGGAGGTATACAC 60 282 1 ATAAGGAGGT 0.91204 -19 TGCGTTTTAGATATGAAGGGAGTTCGGCAGGAA 61 47 0 ATAAGGGAGT 0.552487 -39 ATCCATGTAGATGGAAAGGAAGAGCCTTTTGTC 62 106 1 ATAAGGAAGA 0.864267 -98 ATGTGTTTACTAATGAAGGAGGCAATAAGA 65 281 1 TAAAGGAGGC 0.785675 -20 ** ******** Masking position 8 Map Score: 27.1039 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 166 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 5 GTCTGATTTATGAACAAAAAAGAAACCATC 5 51 0 TGAACAAAAA 0.449958 -126 AGTAAGTGGATGATAAAAAATGTGAAAATG 6 69 1 TGATAAAAAA 0.692226 -96 GACTTTAAGATTACAAAAAAGGTAAAAAAA 10 126 1 TTACAAAAAA 0.676442 -175 CATGATAAGATGACATAAAAGATAAGGAGA 21 22 1 TGACATAAAA 0.673447 -29 GAATAAACGCTTACAGAAAATCATTGTATG 22 78 0 TTACAGAAAA 0.4498 -146 TTTCTTCTCTTGACAAAATATTTTTTCCGC 29 53 0 TGACAAAATA 0.627278 -100 AAGAAAACGCTGACAAAAAAGCCAGCTTCC 30 27 0 TGACAAAAAA 0.954449 -83 GCTGTTATAATGAAAAAAAACTATTGGAGC 31 63 1 TGAAAAAAAA 0.692226 -27 ATTGCCCACGTGATAAAAAATCTACGTTAC 33 180 1 TGATAAAAAA 0.692226 -121 AAATAATCAATGACAAAAAATGAATCTTAT 37 33 0 TGACAAAAAA 0.954449 -268 TTAAGGAATGTCACAAAAAATAAACGTGAG 41 30 0 TCACAAAAAA 0.637313 -154 TGACAGCGTTTGACAAAAAAAGTACAATAG 42 118 1 TGACAAAAAA 0.954449 -183 TAACATAAGTTGACAAAAAAGAAAAAGGGA 45 39 0 TGACAAAAAA 0.954449 -65 TGTCCCGCTATGACAAAAAACGTCCCGTCA 51 241 0 TGACAAAAAA 0.954449 -57 TGACAGAAAATGCAAACAAG 52 1 1 TGACAGAAAA 0.891229 -137 TACGTTTCCATGACCGAAAATCGTGAAGAT 62 145 0 TGACCGAAAA 0.748753 -59 AACCAAGAAATGACCAAAAAGTAACCTGTT 65 116 1 TGACCAAAAA 0.884005 -185 ********** Masking position 7 Map Score: 15.334 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 127 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 6 TGCGCAAATGAAAGCAATCATAAATAAGAGGAC 2 137 0 AAAGAACATA 0.910957 -164 GGACTTACCGAAAGAAACCATCAATGATGGTTT 5 26 1 AAAGAACATA 0.910957 -151 TATGAACAAAAAAGAAACCATCATTGATGGTTT 5 40 0 AAAGAACATA 0.910957 -137 CATAGAGTCAAAGGGAAGCATCATTCTCTGAAC 7 103 1 AAGGAACATA 0.870946 -70 ATGTAAACTTAAATTAAAAATCAGTTGACATAA 13 57 1 AAATAAAATA 0.730044 -78 TTTATCGGCCAAGGGAAACATGAATGAAGCTGC 14 53 0 AAGGAACATA 0.870946 -86 AAAAAGCCAAAAAGTAAAAATTATATTTTTCCC 14 100 1 AAAGAAAATA 0.827255 -39 GAATATGGAAAAATTAAGAATAAATCTGATTGG 15 77 1 AAATAAAATA 0.730044 -35 TAGAAATAAAAAAGGACTTTGTTCTC 17 4 1 AAATAAAAGA 0.767116 -278 AGTTTACACCAAATAAAGAAGAACCGTCAATCG 25 60 0 AAATAAAAGA 0.767116 -241 GTCCCCTTCAAAAGTAATAATCAGTAAACAGTT 37 92 0 AAAGAAAATA 0.827255 -209 ACATGAGGAAAAGTCAAAAAGAAAAATCAAAAT 43 80 1 AAGTAAAAGA 0.684833 -119 CTGTGAAATCAAGTCAAGAAGAAAGGGCGGAAT 44 33 0 AAGTAAAAGA 0.684833 -79 TAAAATAATTAAAGAAAGCAGAAATGATTTTTT 51 201 1 AAAGAACAGA 0.925713 -97 GGAAATAGGAAAATCAAACAGAATACATACAAT 54 102 1 AAATAACAGA 0.875574 -64 ATTTTCGTCAAAAGTAAGCAGTATTGTATGTAT 54 124 0 AAAGAACAGA 0.925713 -42 CTCAATCATGAAAGAAAGCAGGAAAAGAC 55 7 0 AAAGAACAGA 0.925713 -294 AAATTTGCGTAAATGAAAAAGGATCGCTGTGTC 55 221 1 AAATAAAAGA 0.767116 -80 TTCTAGAACAAAAGTAATCATAAAGATT 60 6 0 AAAGAACATA 0.910957 -295 TAATACCCATAAGTCAATCATAAACACTACATT 65 69 0 AAGTAACATA 0.792144 -232 TCGTAATGAAAAGTAAAACATCAATATTGACTA 67 103 1 AAGTAACATA 0.792144 -198 **** ** *** * Masking position 7 Map Score: 20.3837 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 307 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 GCTTACATTTAAAATTATCACAATCACTCTA 4 10 0 AAAATACACA 0.518671 -139 ATACTTCACAAACAAAAAGACATCAAAGAGAA 5 133 1 AACAAAGACA 0.67545 -44 GTGGATGATAAAAAATGTGAAAATGTGTTGAA 6 74 1 AAAAAGGAAA 0.69007 -91 GTTGAACAGCAACAAAACGAAACAGAAGGGAC 6 100 1 AACAAAGAAA 0.799165 -65 CAAAAAAGGTAAAAAAACCAAATCTCTCAGAC 10 139 1 AAAAAACAAA 0.753664 -162 CTCTATGGGAAAAAACACTAAAGTTGATCAAA 10 195 1 AAAAAATAAA 0.608952 -106 ATTAAATAAAAAAATCATCAAATGTTCGAAAG 17 59 1 AAAATACAAA 0.673237 -223 CCTCTCAACCAAAAACATGAAATTAAACCCTT 17 88 0 AAAAAAGAAA 0.905159 -194 TAACCCAATTAAAATGAAGAAACCCATGTGAT 17 159 1 AAAATAGAAA 0.865358 -123 CTTACAGCTAAAAATCATGACAACGAATTCAC 19 185 0 AAAATAGACA 0.77072 -54 AATTTATTAGAAAAACATGAAACTTTTTGATA 23 44 1 AAAAAAGAAA 0.905159 -66 AAATTCGACAAAAATAAGGACAATTGTACGAC 24 99 0 AAAATAGACA 0.77072 -181 CTATATTTCTAAAAAGACCAAACGCAACAATC 33 124 1 AAAAAACAAA 0.753664 -177 TATGGATGTACAAAACAGGAAAGGAGCAATAG 36 166 1 CAAAAAGAAA 0.432545 -24 AGCGTTTGACAAAAAAAGTACAATAGTTTCGG 42 122 1 AAAAAATACA 0.448871 -179 TAAGATAAAGAACATAAAGAAATAACTTAACG 43 43 0 AACATAGAAA 0.728236 -156 ATCTTAACGAAACATGAGGAAAAGTCAAAAAG 43 69 1 AACATAGAAA 0.728236 -130 TAAGGTTGTTAAAAACATTAAATTTTTATTTA 43 147 1 AAAAAATAAA 0.608952 -52 AAAAAGGGGAAATAGCCGTTTG 45 1 1 AAAAAGGAAA 0.69007 -103 ATACAGCACGAAAAACGTGAAACCGTCTGTTC 49 248 0 AAAAAGGAAA 0.69007 -53 CCACCCTGTTAAAATAATTAAAGAAAGCAGAA 51 192 1 AAAATATAAA 0.511877 -106 CAAAAAGAAGAAACAAATGAATC 53 2 1 AAAAAAGAAA 0.905159 -179 ACAAATCGGCAACATAATGACATGATTCATTT 53 25 0 AACATAGACA 0.583595 -156 TAATATAATAAAAATAATGAAAAAATGTAGTG 65 46 1 AAAATAGAAA 0.865358 -255 AAACGCTTTCAAAAACACCAAAAAAATAAATG 65 185 0 AAAAAACAAA 0.753664 -116 ***** * **** Masking position 4 Map Score: 14.1508 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 492 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 8 AAGCAATCATAAATAAGAGGACATAGGCGT 2 129 0 AAATAAGAGG 0.416635 -172 CGGAAGAATGAAGTAAGAGGGATTTTTGAC 4 87 1 AAGTAAGAGG 0.835769 -62 AATAGATCTTAATGAAGAGGGTGTATGA 6 9 0 AATGAAGAGG 0.670582 -156 AGACGGAGACAAGTAAGTGGATGATAAAAA 6 58 1 AAGTAAGTGG 0.604782 -107 ATTATCATAAAAAGAAAAGGTGGTTTTTAC 8 47 1 AAAGAAAAGG 0.427884 -20 ATAAGGTTGAAAAGGAGTGATTTCA 15 6 0 AAAGGAGTGA 0.355736 -106 TGTCAGTATACAGGAAGAGGAGCAGGAAAT 16 177 1 CAGGAAGAGG 0.678115 -124 ACTCCCTATAAAGTAAGAGACTCACTCCAT 22 118 1 AAGTAAGAGA 0.791877 -106 GTTTAAAAGAAAGGAAGAGGTGACTTAGT 25 282 1 AAGGAAGAGG 0.947007 -19 ATAACGGTTGAAGTGAATGAGAAGGGAGAA 27 112 1 AAGTGAATGA 0.250437 -26 CTGGACAATAAAGGAAATGAAAAGATAAAG 29 24 0 AAGGAAATGA 0.545063 -129 GCGTATTCATAAGGAAGCGGTCAGTCAAGA 30 56 0 AAGGAAGCGG 0.588015 -54 ATTCTCGAATAAGGGACAGGAAAG 32 5 0 AAGGGACAGG 0.495657 -62 AAGTCTGAATAAGTAAATGATTTTAGTTTG 33 36 1 AAGTAAATGA 0.25439 -265 AAGATTTCAGAAGGAAGTGAACCAA 40 28 1 AAGGAAGTGA 0.800705 -15 CCCTAAAAACAATGAAAAGGGATCTCCATC 41 115 0 AATGAAAAGG 0.377742 -69 TAATTTTCTAAAGGAAAAGAGGGTCAGT 43 9 0 AAGGAAAAGA 0.799374 -190 AGTTCATATAAAGTGAAAGATGAAACATTA 44 69 1 AAGTGAAAGA 0.526316 -43 TAAAAAATCTAAGGAGGAGATGTC 46 216 1 AAGGAGGAGA 0.611666 -14 TTGAAAATCAAAAGGAGAGACAAAACTC 47 12 1 AAAGGAGAGA 0.647421 -18 AAACTGCTATAAGGAAGTGGAACAG 48 16 1 AAGGAAGTGG 0.843104 -15 TTCATGGAAAAAGGGAAAGGGAGTCCGTCC 49 67 0 AAGGGAAAGG 0.839193 -234 TCCTTTAAATAAGTGAGAGATATTTATATT 50 17 0 AAGTGAGAGA 0.788403 -30 TGAAAGAAAGCAGGAAAAGAC 55 2 0 CAGGAAAAGA 0.319593 -299 GTTTAAATAAAAGGGGGAGAAATAG 55 286 1 AAGGGGGAGA 0.606679 -15 TAAATTCTATAATGGAGAGAATGGCAAGTC 57 65 0 AATGGAGAGA 0.598464 -98 CATGTTTAAGGAAGAGGCAATCAGGGG 58 8 1 AAGGAAGAGG 0.947007 -21 ATATTCCCTGAATGGAAAGATTTTAAAACA 59 41 1 AATGGAAAGA 0.3077 -88 AAAATCGGTAAAAGGAGAGGTCGATTC 59 112 1 AAAGGAGAGG 0.710646 -17 TGTAGATGGAAAGGAAGAGCCTTTTGTCGA 62 111 1 AAGGAAGAGC 0.599784 -93 TCTTTTAATCAAGTAAGAGAAGTAAGAGAA 65 15 0 AAGTAAGAGA 0.791877 -286 ATGTCGGGGAAAGTGAGAGATTATACGAGA 66 124 1 AAGTGAGAGA 0.788403 -177 ********** Masking position 2 Map Score: 19.1294 Number of sites scoring better than the average of aligned sites = 1152 Number in coding regions = 875 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 9 CCATAATACCATTTGCCCTCCCAATATGAAA 1 56 1 ATTTCCCTCC 0.93234 -163 GGTTTTGGGAATTTCCGCTCCTTTTATCGGG 16 71 0 ATTTCGCTCC 0.766559 -230 GCTTCACCTCCTAATGAAAAC 24 269 0 GCTTACCTCC 0.734838 -11 GAAGATGAACGTTTTCCCTCTATTATATATC 26 32 1 GTTTCCCTCT 0.866525 -83 CATTATAACAGCTGGCGCTCCGAAACGCCTA 31 44 0 GCTGCGCTCC 0.918352 -46 AACGCGCATTATTTTCCCTCCAAACTAAAAT 33 55 0 ATTTCCCTCC 0.93234 -246 TTTGAAGGGGACTGGCCCTCCAGAACTGAGC 37 113 1 ACTGCCCTCC 0.961264 -188 ACTGACCCTCTTTTCCTTTAG 43 1 1 ACTGCCCTCT 0.860083 -198 GCTGCTGTCCCTCCATAACGGTAT 44 98 0 GCTGCCCTCC 0.979253 -14 TTATAGGTCAGTTTTCCCTCTAGTCCTCCGG 57 25 1 GTTTCCCTCT 0.866525 -138 TGGTTGGCCCTCCTTTTTTGAAC 59 3 1 GTTGCCCTCC 0.972354 -126 **** ****** Masking position 3 Map Score: 7.96624 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 49 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 GCCGTACAAGCCGGCGGGCAGCAATCG 3 7 0 CCGGCGGCAG 0.960644 -109 AAAAAACCGGCCGTATGGCAGACCGGTTTTT 13 16 0 CCGTAGGCAG 0.962805 -119 AAACCGGACGGCATTTCAGCCGTC 22 4 1 CCGGAGGCAT 0.941518 -220 TACAGAAAAACCGGACGGCTGAAATGCCGTC 22 17 0 CCGGAGGCTG 0.984028 -207 ACTTTCATCCCGGGATCGCAGCATGATTACA 35 96 1 CGGGACGCAG 0.844102 -205 GCACGATGTTCCGGAAGGCATT 42 289 1 CCGGAGGCAT 0.941518 -12 GGGGAAATAGCCGTTTGGCTGCTTCCCTTTT 45 16 1 CCGTTGGCTG 0.809252 -88 ACTCAACATTCGGGAGGGCAGGGAA 52 123 1 CGGGAGGCAG 0.978887 -15 GGGAGTTCGGCAGGAAGGCTGTCGCCATATC 61 32 0 CAGGAGGCTG 0.873092 -54 CACATGGACGCCGTTCGGCTGTTCGTCGT 64 9 0 CCGTTGGCTG 0.809252 -66 GTAATGACGCCGGGATGGTAGCATCGATTTC 66 273 0 CGGGAGGTAG 0.785092 -28 ***** ***** Masking position 1 Map Score: 8.12888 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 187 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 TGGAATATATGAAACAGACAAGGTTACCCTA 9 62 0 GAAACAGCAA 0.800142 -131 TCATACATAGGAAGCAGGCATTGTTCATAAC 15 39 0 GAAGCAGCAT 0.909085 -73 TATTCATAAGGAAGCGGTCAGTCAAGAAGAA 30 52 0 GAAGCGGCAG 0.93726 -58 AAATGAAGTTGAAGCATACAGAAAATACACT 34 190 0 GAAGCATCAG 0.660915 -59 TATAAGCTGAGAAACAGTCAGTAATTAATGC 35 133 0 GAAACAGCAG 0.789213 -168 CCCTTGCCTTAAAGCAGACTTTAAGGTTTAT 35 198 1 AAAGCAGCTT 0.447988 -103 TAAGAACCAAAAAGCAGCCAGCGCTCCGCAC 38 27 0 AAAGCAGCAG 0.921625 -179 AAGAAAAAGGGAAGCAGCCAAACGGCTATTT 45 20 0 GAAGCAGCAA 0.969365 -84 CGCTATAATGAAAGCGGACAAGGGAAGGGGA 49 39 1 AAAGCGGCAA 0.863902 -262 TGTGACTGGTAAAGCAGGCAAGACCTAAAAT 55 194 1 AAAGCAGCAA 0.92633 -107 TGTTACTGCGAAAGCAGGCAAAACCTAAATG 60 130 1 AAAGCAGCAA 0.92633 -171 GTTTACTAATGAAGGAGGCAATAAGA 65 285 1 GAAGGAGCAA 0.75544 -16 GATTGGTGCTGAAGCGGTCTACCCCTAAAGC 66 230 1 GAAGCGGCTA 0.7654 -71 ******* *** Masking position 3 Map Score: 6.40289 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 434 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 12 TGCAAATACTGAACAGCTATTCCTCTTTAATA 20 47 1 GAACAGCTTC 0.783429 -90 GAACGAGCAAAAACAGCGATTCTTAAAACAAA 34 147 1 AAACAGCTTC 0.967294 -102 AAACAGTTTTTTCATATGAACC 36 1 1 AAACAGTTTT 0.56375 -189 GGAAGCAGCCAAACGGCTATTTCCCCTTTTT 45 10 0 AAACGGCTTT 0.620173 -94 TGCTGGTAAAAAACAGATTTTCCATTGTAACA 45 64 0 AAACAGATTC 0.75298 -40 CGCTTTAATGAAACAGCCCTTTCTACGGGAAG 51 14 1 AAACAGCTTT 0.886667 -284 ATCCCAATATAAACAGCCCTTCCCGTAGAAAG 51 32 0 AAACAGCTTC 0.958716 -266 AAAGATTTTAAAACAGCCGTTTTTTTTGATCT 59 56 1 AAACAGCTTT 0.548176 -73 CGTAAACAGCCACTCCTCACTTG 63 9 0 AAACAGCCTC 0.866561 -15 CAAGAGCTTAAAACAGCTTTTCAGTACAGGTT 67 200 0 AAACAGCTTC 0.923547 -101 ******* *** Masking position 3 Map Score: 5.30263 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 123 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 TTATTTGATTTTTTGAAGACTTACTTCGGAGTCA 4 113 0 TTGAAGATTC 0.759604 -36 TTGCAAAAGTTTGTGAAGTGTTGCACAATATAAA 5 93 1 TTGAAGTTTC 0.946329 -84 GTCTTTTTGTTTGTGAAGTATTTCACATTTATAT 5 120 0 TTGAAGTTTC 0.946329 -57 ATGTTTTTGGTTGAGAGGTTTTACAGCAAGACAG 17 102 1 TTGAGGTTTC 0.965478 -180 ACCAGCATCATTTGGAGGTTTTACT 45 89 1 TTGAGGTTTC 0.965478 -15 TGGCACGATATTGTGAAGTATTTCACAATTAATT 55 47 1 TTGAAGTTTC 0.946329 -254 CATCTACTAGTTAGGAGGTTTTTCTC 57 147 1 TTGAGGTTTC 0.965478 -16 TTATTCTCTTTTAGGAGGTGATGCAGCATTTGAT 60 209 1 TTGAGGTATC 0.833664 -92 ** ***** ** * Masking position 6 Map Score: 4.08689 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 17 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 ACAATATATGAAGCGATTGCGCAAATGAAA 2 157 0 AAGCGATTGC 0.799509 -144 TTCATTGCAGAAGCGCAGGCTGTTATTGTA 3 52 1 AAGCGCAGGC 0.937358 -64 CAGCACCCTTAAGAGCTGGCATGGAACTTG 28 64 1 AAGAGCTGGC 0.826964 -61 AGGCGTTTCGGAGCGCCAGCTGTTATAATG 31 45 1 GAGCGCCAGC 0.813267 -45 ACCTTTTTCAAAGCTCTGGCTTTTTTCTTA 33 247 0 AAGCTCTGGC 0.903329 -54 AGTCAGTGCGGAGCGCTGGCTGCTTTTTGG 38 22 1 GAGCGCTGGC 0.963073 -184 AAGCTGATATAAGCGAGGGCAGGCCAGCTT 46 97 0 AAGCGAGGGC 0.773588 -133 CCTTAGGCGAAAGCGCCGGCAAAGCTGCTT 49 144 0 AAGCGCCGGC 0.987356 -157 AGAATTTAATCAGCGCCTGCGCAGTTGTTA 62 62 0 CAGCGCCTGC 0.886184 -142 CATCCTGCTCAAGCGCCTGCCCGATCCCTA 62 176 0 AAGCGCCTGC 0.970867 -28 AAGCTGTTTTAAGCTCTTGCTTACCCCATT 67 213 1 AAGCTCTTGC 0.799509 -88 ********** Masking position 2 Map Score: 5.28922 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 277 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 15 TTCATTCTCCCCATTCTGTATG 1 1 1 TTCATTCCCC 0.942135 -218 TGCATTTTATTTCCTGCTCCTCTTCCTGTATA 16 183 0 TTCCTGCCCC 0.953344 -118 CCGTTATCCCTTCATTCACCACTATTTAACCA 27 87 0 TTCATTCCCC 0.942135 -51 ACAATCCATTCTCCTCACAGGCACCA 39 168 0 TCCATTCCCC 0.977932 -16 TCTCCATTCACCTCAGCAACATAT 41 170 0 TCCATTCCCC 0.977932 -14 TGTGAAGGGTTCTCTTCACCGCATGTCATCAA 42 179 0 TCTCTTCCCC 0.901594 -122 TCCGTCCCCTTCCCTTGTCCGCTTTCATTATA 49 42 0 TCCCTTGCCC 0.874135 -259 TTCCCTGCCCTCCCGAATGTTGA 52 125 0 TCCCTGCCTC 0.845018 -13 CCCGCCGAACTCCATGCTCAGC 61 1 0 TCCATGCCAC 0.877517 -85 AAGCAACCATTTCATGCACAACAGGTTACTTT 65 133 0 TTCATGCCAC 0.724684 -168 CCAATCACATTCTCTTCCCCGCCTACGGCCTC 66 172 0 TCTCTTCCCC 0.901594 -129 ******* ** * Masking position 5 Map Score: 4.79438 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 118 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035