AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ifruR_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ycnL 164 ycnL #2 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #3 mtlD 52 mannitol-1-phosphate dehydrogenase #4 yjdC 300 similar to transcriptional antiterminator (BglG family) #5 yjdD 147 similar to fructose phosphotransferase system enzyme II #6 ykvY 300 similar to Xaa-Pro dipeptidase #7 ykvZ 281 similar to transcriptional regulator (LacI family) #8 glcT 62 transcriptional antiterminator (BglG family) #9 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #10 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #11 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #12 moeB 50 molybdopterin biosynthesis protein #13 yknU 223 similar to ABC transporter (ATP-binding protein) #14 yknW 109 yknW #15 fruR 279 transcriptional regulator (DeoR family) #16 pps 300 phosphoenolpyruvate synthase #17 kdgK 37 2-keto-3-deoxygluconate kinase #18 kdgR 221 transcriptional regulator (LacI family) #19 ypqE 137 similar to phosphotransferase system enzyme II #20 gapB 205 glyceraldehyde-3-phosphate dehydrogenase #21 ytcD 183 ytcD #22 citC 163 isocitrate dehydrogenase #23 citZ 300 citrate synthase II #24 pykA 42 pyruvate kinase #25 pfk 183 6-phosphofructokinase #26 yttI 300 similar to acetyl-CoA carboxylase #27 pckA 300 phosphoenolpyruvate carboxykinase #28 pgk 300 phosphoglycerate kinase #29 gap 46 glyceraldehyde-3-phosphate dehydrogenase #30 yvbQ 297 yvbQ #31 araE 137 permease #32 crh 23 catabolite repression HPr-like protein #33 yvcL 22 similar to hypothetical proteins #34 yvcJ 24 similar to hypothetical proteins #35 yvcI 300 similar to mutator MutT protein #36 yvkC 300 similar to pyruvate,water dikinase Motif number 1 GACAATTTTTTAAAAATAAAAAGGCTCCTGGTT 2 10 0 TATAAAAAGG 0.816292 -163 TTCCGGAAGCTTCGGTAAAAAACGAAACTTTTGT 4 178 1 TGAAAAAACG 0.752373 -123 CATTTTTCCCTATAACAAAAAAAGCAAGGAATAA 5 20 0 TAAAAAAAAG 0.947296 -128 TACCATAGGTTCCGGTAATAAAGGCATTTTTCCC 5 44 0 TGAATAAAGG 0.691858 -104 TACCGGAACCTATGGTAAAAAAAGCGATTTTAAT 5 61 1 TGAAAAAAAG 0.939648 -87 ATGATAGAGCTGTAATAATAAAAGCCCACCATCT 6 33 1 TAAATAAAAG 0.824539 -268 TAGAAATAAAAAAGGACTTTGTTC 7 1 1 TATAAAAAAG 0.889573 -281 TTTTATTTAATGCAGATAAAAAAGGACGATGTCG 7 36 0 TATAAAAAAG 0.889573 -246 TGAATGCATTGAAAAAAGGTTTGACGTG 8 5 1 TAGAAAAAAG 0.851538 -58 GTAATAAAGCTTTAAGTTAAAAGGAGAATGATAA 10 72 1 TATTAAAAGG 0.461907 -26 TGATTTCTACTATGAATATAAAAGACTTTTTTCA 15 47 1 TGTATAAAAG 0.645942 -233 TTCTTCTTATTTTAATGAAAAAAGTCTTTTATAT 15 62 0 TAGAAAAAAG 0.851538 -218 TCTGTTTTTGTGCAATATAAAAAGAACCTGGGAA 16 153 0 TAATAAAAAG 0.776404 -148 AGACGCATAATCTGGTTAAAAAAGGCGGTGGCGA 19 13 0 TGTAAAAAAG 0.874656 -125 GAGTAAGCTATATAAATAAAAAAGAGCAGATTCA 21 56 1 TATAAAAAAG 0.889573 -128 AAACATATCGTTAAGAAATAAAAGTACGTACTTT 21 114 1 TAAATAAAAG 0.824539 -70 GATGACAGCGTTTGACAAAAAAAGTACAATAGTT 26 116 1 TGAAAAAAAG 0.939648 -185 AAAGCCGGTCTTCATGGAAAAAGGGAAAGGGAGT 28 73 0 TAGAAAAAGG 0.759831 -228 TATGTCCCGCTATGACAAAAAACGTCCCGTCATA 30 239 0 TGAAAAAACG 0.752373 -59 ACATATAATGTCCAGCAAAAAAGGAAGGAACGTT 30 268 1 TAAAAAAAGG 0.908376 -30 AAAAAGTGTATTCATTATAAAAAGGGGGTCAATT 35 86 0 TAATAAAAAG 0.776404 -215 CTTTTATTTATGGACAAAAAAAGGACACGGATAA 35 137 0 TAAAAAAAGG 0.908376 -164 GACTTGATGATGTAATAAAAAAAGTGCCGCTGAT 36 38 0 TAAAAAAAAG 0.947296 -263 GCCGCCAGATTCCGAGAATAAAAGAAAATAGGCA 36 73 1 TGAATAAAAG 0.802784 -228 AAACACAGGCTCCGCAATAAAAAGACTAGAGAGA 36 241 1 TGATAAAAAG 0.750487 -60 AAAAACAAAATGAATGAAGAAAAGAGGGGTTTCA 36 274 1 TAAAGAAAAG 0.632118 -27 * * ******** Masking position 1 Map Score: 27.3534 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 499 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 2 CACATTTTCACATTTTTTATCATCCACTTAC 1 70 0 CATTTTTATC 0.657203 -95 AACCAGGAGCCTTTTTATTTTTAAAAAATTG 2 11 1 CTTTTTTTTT 0.928288 -162 TTATTCCTTGCTTTTTTTGTTATAGGGAAAA 5 20 1 CTTTTTTGTT 0.92855 -128 TTTTCTAATGCATTTTATTTCCTGCTCCTCT 6 192 0 CATTTTTTTC 0.885179 -109 AACAAAGTCCTTTTTTATTTCTA 7 3 0 TTTTTTTTTC 0.767671 -279 TACCAGATATCTTTTTGTGTTTTTAGCTGAA 7 199 0 CTTTTTTGTT 0.92855 -83 TTGCTCATGCCTTTTTGTTGTGTAAAAGGGC 9 120 1 CTTTTTTTGT 0.759707 -119 TGCATGAGGTTTTTTTATGTTTAGTGATTTC 15 23 1 TTTTTTTGTT 0.772062 -257 TTCCCAGGTTCTTTTTATATTGCACAAAAAC 16 153 1 CTTTTTTATT 0.762984 -148 CTCTTGTCAATATTTTTTTTTGAAGGGGAGA 16 274 1 TATTTTTTTT 0.672305 -27 TAGGAAAAATCATTTTATTTTCTATATAAGA 22 94 1 CATTTTTTTT 0.887281 -70 ATTTAGAAAACATTTTATTTTTCTTATATAG 22 115 0 CATTTTTTTT 0.887281 -49 TTACCTATAATTTTTTTTTTCCATTCTGTGA 23 47 0 TTTTTTTTTC 0.767671 -254 AAAATGTAAGCATTTTCTTTTTGGGGGAGAG 23 194 1 CATTTTTTTT 0.887281 -107 AACTATTGTACTTTTTTTGTCAAACGCTGTC 26 119 0 CTTTTTTGTC 0.927155 -182 CGGAAGCATACTTTTTCTTTTTCGTGAATAT 26 239 0 CTTTTTTTTT 0.928288 -62 TCCTTTATCGTTTTTTGTGTTTTGCTAATTG 27 271 0 TTTTTTTGTT 0.772062 -30 GCAGAAATGATTTTTTTTGGCTATGACGGGA 30 218 1 TTTTTTTGGC 0.447579 -80 ATCTTGTTTGCATTTTCTGTCA 31 2 0 CATTTTTGTC 0.88558 -136 TATCCGTGTCCTTTTTTTGTCCATAAATAAA 35 138 1 CTTTTTTGTC 0.927155 -163 ATCAGCGGCACTTTTTTTATTACATCATCAA 36 38 1 CTTTTTTATT 0.762984 -263 ACTGTATGCCTATTTTCTTTTATTCTCGGAA 36 82 0 TATTTTTTTT 0.672305 -219 TCTCTCTAGTCTTTTTATTGCGGAGCCTGTG 36 244 0 CTTTTTTTGC 0.755881 -57 TTTCTTCATTCATTTTGTTTTTCTCTCTAGT 36 265 0 CATTTTTTTT 0.887281 -36 ****** **** Masking position 6 Map Score: 27.3047 Number of sites scoring better than the average of aligned sites = 854 Number in coding regions = 602 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 3 TACCAGAGTCCCTTCTGTTTCGTTTTGTTGC 1 108 0 CCTTCTTTTC 0.504051 -57 ATATAAACCCTCCCTGTTTTGTTTGTCGC 2 154 0 CCTCCCGTTT 0.961563 -19 AGGGATTATTCCTTGCTTTTTTTGTTATAGG 5 15 1 CCTTGCTTTT 0.668212 -133 TTCCTGCTCCTCTTCCTGTATACTGACAGTA 6 174 0 TCTTCCGTAT 0.781062 -127 CATTGTTCTGTCTTCCATTGTAACAGGTTTT 6 252 0 TCTTCCTTGT 0.68061 -49 GTTCTCGACATCGTCCTTTTTTATCTGCATT 7 31 1 TCGTCCTTTT 0.773194 -251 ACGAGAATGAACTTCCCGTTTTTTTCCCTCA 9 71 0 ACTTCCGTTT 0.681066 -168 CAGGCGTAAGTCTTCCAGTTTAACCGTTTAC 9 155 0 TCTTCCGTTT 0.911395 -84 AAGAATTGACCTCCTCTTTTTACTAGTCTG 9 219 0 CCTCCTTTTT 0.763309 -20 GGCTGAAATGCCGTCCGGTTT 13 1 0 CCGTCCGTTT 0.937826 -223 GGCATTTCAGCCGTCCGGTTTTTCTGTATTT 13 20 1 CCGTCCGTTT 0.937826 -204 TTTTTGATATCCTTCCCGTACTATTTGTTAG 14 67 1 CCTTCCGTAC 0.732221 -43 TATCGCCACCGCCTTTTTTAACCAGATTA 19 9 1 CCGCCTTTTT 0.546294 -129 AATAAAAACCTCCCAGTATGTAATTCATA 22 145 0 CCTCCCGTAT 0.896657 -19 CAAATGATTACCTCCCTTTTGTGAAGGGTTC 26 199 0 CCTCCCTTTG 0.812508 -102 ATGAAACCTTCCTTTATCGTTTTTTGT 27 284 0 CCTTCCTTAT 0.925585 -17 GAGTCCGTCCCCTTCCCTTGTCCGCTTTCAT 28 46 0 CCTTCCTTGT 0.893274 -255 GACGGACTCCCTTTCCCTTTTTCCATGAAGA 28 68 1 CTTTCCTTTT 0.576063 -233 TATAAACAGCCCTTCCCGTAGAAAGGGCTGT 30 26 0 CCTTCCGTAG 0.732221 -272 CTCAAACGTTCCTTCCTTTTTTGCTGGACAT 30 275 0 CCTTCCTTTT 0.972872 -23 AAGATCTCCCCTTTTCTTTACGG 32 9 0 TCTCCCTTTT 0.849711 -15 GACAATCTTTTCTTCTATTTTACAGCATATT 35 211 0 TCTTCTTTTT 0.570074 -90 ****** **** Masking position 9 Map Score: 15.8074 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 674 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 4 CGAAGATACCAAATCACTTTTCTTCATCATGTT 4 21 1 AAACCTTTCT 0.924864 -280 AAGAGTATAAAAATCGCTTTTTTCCGGAAGCTT 4 157 1 AAACCTTTTT 0.966792 -144 TTATAGGGAAAAATGCCTTTATTACCGGAACCT 5 39 1 AAAGCTTTTT 0.936821 -109 CAGCTCATTAAAATCGCTTTTTTTACCATAGGT 5 68 0 AAACCTTTTT 0.966792 -80 TAGAAATAAAAAAGGACTTTGTTCTCGACATCG 7 11 1 AAAGCTTTTT 0.93682 -271 CTATGAATATAAAAGACTTTTTTCATTAAAATA 15 56 1 AAAGCTTTTT 0.935652 -224 ATGTTAGGAAAAATCATTTTATTTTCTATATAA 22 90 1 AAACTTTTTT 0.840715 -74 TCATATTTAGAAAACATTTTATTTTTCTTATAT 22 117 0 AAACTTTTTT 0.840652 -47 TTCCCCGAAAAAACGCCTTTATTTGCGGGTTTT 23 13 0 AAAGCTTTTT 0.936821 -288 TGCTGGAACTAAAACCCTTTGCTTTTGAAAGAA 23 155 0 AAACCTTTCT 0.924864 -146 ATTTTATTTAAAAACAATTTATTTAATTGTATA 25 60 1 AAACATTTTT 0.676131 -124 AAGAAAGCAGAAATGATTTTTTTTGGCTATGAC 30 212 1 AAAGTTTTTT 0.728792 -86 GGTTTAAATGAAAACGCTTTACTCAACATTCGG 31 103 1 AAACCTTTCT 0.924864 -35 TTTTATAATGAATACACTTTTTTGGCACGGATT 35 98 1 AATCCTTTTT 0.727015 -203 ATTTGAAACCCCTCTTTTCTTCATTCAT 36 283 0 AAACCTCTTT 0.797981 -18 *** * **** ** Masking position 2 Map Score: 18.7118 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 128 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 AGGTGAAGAATTGGAGTATTTTTATGAATTTC 4 96 1 TTGAGTTTTT 0.731358 -205 GGGATGAAGATGGTGGGCTTTTATTATTACAG 6 42 0 TGGGGGTTTT 0.806068 -259 CTTTCGAACATTTGATGATTTTTTTATTTAAT 7 59 0 TTTATGTTTT 0.874607 -223 AAGGGTTTAATTTCATGTTTTTGGTTGAGAGG 7 88 1 TTTATGTTTT 0.874607 -194 CCAGATATCTTTTTGTGTTTTTAGCTGAAAGG 7 196 0 TTTGTGTTTT 0.804969 -86 GTGAATTCGTTGTCATGATTTTTAGCTGTAAG 9 185 1 TGTATGTTTT 0.804969 -54 ACCTTCAATATTGAAGGCTTTTCATA 14 5 0 TTGAGGTTTT 0.9223 -105 GCCTTCAATATTGAAGGTTTTTGGAAATTTAT 14 19 1 TTGAGGTTTT 0.9223 -91 TATCAAAAAGTTTCATGTTTTTCTAATAAATT 14 44 0 TTTATGTTTT 0.874607 -66 TTTTTTTATGTTTAGTGATTTCTACTATGAAT 15 32 1 TTTGTGTTTC 0.460038 -248 TTGAATGAATTTGAATGATTTTAGTTGCCTAA 15 193 1 TTGATGTTTT 0.925683 -87 AATCCTAAAGTTGGGTTCTTTTTGAACTTACT 16 41 0 TTGGTTTTTT 0.62832 -260 TTTAAAATTATGGTATTCTTTTGTTGTAACGG 18 157 1 TGGATTTTTT 0.62832 -65 AATTACATACTGGGAGGTTTTTATT 22 149 1 TGGAGGTTTT 0.875374 -15 ACGCCTTTATTTGCGGGTTTTTG 23 2 0 TTGGGGTTTT 0.875374 -299 GGAGATCCCTTTTCATTGTTTTTAGGGCAATG 25 118 1 TTTATTTTTT 0.615343 -66 TTCTGCTTTCTTTAATTATTTTAACAGGGTGG 30 192 0 TTTATTTTTT 0.615343 -106 GTAACACATGTGTAATGCTTTTCGGTTATGAT 35 45 1 TGTATGTTTT 0.804969 -256 TATCATTTAATTGTAGGTTTTCAGGAAAATGC 36 190 0 TTGAGGTTTC 0.710164 -111 *** *** **** Masking position 9 Map Score: 15.0822 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 328 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 AAACGGAACAACCCCCCTGCGATTGAACGTTAC 6 144 1 ACCCCCCTAT 0.869269 -157 TTCTTGTTCCTCCCTGCCATTTGCAATGCA 6 281 0 TCCTCCCTAT 0.942184 -20 GAACAGCTATTCCTCTTTAATAAACAGACAAGC 11 57 1 TCCTCTTTAA 0.575715 -80 CTACATATGTTACTCCCTATAAAGTAAGAGACT 13 107 1 TACTCCCTAA 0.591598 -117 TTCAAAACCTCCTTGAGAATATCTAACAA 14 91 0 ACCTCCTTAA 0.89262 -19 GTTCGTAGAGTCCCCATTCATAAA 16 2 0 TCCCCATTAA 0.630965 -299 TCTACATCTCCCCTTCAAAAAAAAATATT 16 282 0 TCTCCCCTAA 0.840306 -19 TATATTTCCCCCTTGGTTAGGATTTCAGC 18 7 1 TCCCCCTTTA 0.829948 -215 TGTATTTTCTCCCTTCTCATTCACTTCAAC 19 118 0 TCTCCCTTAT 0.720678 -20 GATGTTCCTCCTTTGTAAGATGTGTTGT 21 6 1 TCCTCCTTAA 0.962506 -178 TTGGTTCACTTCCTTCTGAAATCTTCAGCC 24 23 0 ACTTCCTTAA 0.543056 -20 GGGATCTCCATCCTCCCTATGAAACCTTACCTA 25 94 0 TCCTCCCTAA 0.966898 -90 GCCTAGGAGATCCTCCTTCAAAATGGTTTGCAT 28 278 0 TCCTCCTTAA 0.962506 -23 GATTGTTTCCTCCTTTAAATAAGTGAGAGA 29 27 0 TCCTCCTTAT 0.934735 -20 AATAAACAATTCCACCCTGTTAAAATAATTAAA 30 181 1 TCCACCCTAA 0.804306 -117 CTTTCTCCCCCCTGACTTGTCTTT 34 7 0 TCCCCCCTTT 0.755992 -18 AAAGTAATTGACCCCCTTTTTATAATGAATACA 35 81 1 ACCCCCTTAT 0.853883 -220 ******** ** Masking position 8 Map Score: 11.7704 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 178 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 7 TATAGGGACTGTAAGCGTTTTAACATAGAG 2 80 1 GTAAGCGTTT 0.936978 -93 TACTATATAAGAAACCGTTTACATTATAAA 4 226 0 GAAACCGTTT 0.961519 -75 AGTTATGCTCTTAACGGTTTTGGGAATTTC 6 87 0 TTAACGGTTT 0.599517 -214 TCAAATGTTCGAAAGGGTTTAATTTCATGT 7 76 1 GAAAGGGTTT 0.891465 -206 CCTTGATCTGGAATGCGTTTCATACAATAT 7 240 0 GAATGCGTTT 0.667566 -42 GTCTTCCAGTTTAACCGTTTACATTTGCCC 9 147 0 TTAACCGTTT 0.799917 -92 ATGATTTTCTGTAAGCGTTTATTCTACATA 13 84 1 GTAAGCGTTT 0.936978 -140 AAATATTTTGGTAACGGTTTCAAAGAAAAT 18 53 1 GTAACGGTTT 0.863784 -169 TTCTTTTGTTGTAACGGTTTTGAAATCGGT 18 172 1 GTAACGGTTT 0.863784 -50 TCATATATTTGAAACCGATTTCAAAACCGT 18 185 0 GAAACCGATT 0.710923 -37 AATTGAGGATGACAGCGTTTGACAAAAAAA 26 109 1 GACAGCGTTT 0.748509 -192 AAATAACAGAGAAACCGGTTGCTGGGCTTC 27 50 1 GAAACCGGTT 0.784712 -251 CGAAAAACGTGAAACCGTCTGTTCAAGCGA 28 242 0 GAAACCGTCT 0.772222 -59 GCTGTTTCATTAAAGCGTTT 30 1 0 TAAAGCGTTT 0.838145 -297 GAATGTTGAGTAAAGCGTTTTCATTTAAAC 31 104 0 TAAAGCGTTT 0.838145 -34 ********** Masking position 10 Map Score: 13.4665 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 208 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 CAGTCCCTATACAATTGAAAGTAAAGAGGACT 2 59 0 ACAATTAAGT 0.860162 -114 AAAAATAAGGACAATTGTACGACATTTTCTTC 15 90 0 ACAATTTAGA 0.772027 -190 AGGATATAATAAAATTATAAGATGGATATCTA 16 233 0 AAAATTTAGA 0.83626 -68 GGTTTCAAAGAAAATTTTAGGATAAATAGTGA 18 68 1 AAAATTTAGA 0.83626 -154 AAATTGAAGCAAAATTGAAAGTGTGGTTAAAT 19 64 1 AAAATTAAGT 0.902693 -74 ACATATTGATAAAAATCAACGATTATAACGCT 20 102 0 AAAAATAAGA 0.696285 -104 TCTTATATAGAAAATAAAATGATTTTTCCTAA 22 93 0 AAAATAAAGA 0.696285 -71 CTATATAAGAAAAATAAAATGTTTTCTAAATA 22 115 1 AAAATAAAGT 0.635119 -49 ATGGAAAAAAAAAATTATAGGTAAACATTTAA 23 54 1 AAAATTTAGT 0.795 -247 GAATGTCACAAAAAATAAACGTGAGCCAAAGG 25 23 0 AAAAATAAGT 0.635143 -161 GTTTTTAAATAAAATTTAAGGAATGTCACAAA 25 43 0 AAAATTAAGA 0.92434 -141 TACTTATATTAAAATTTAACGAAAATTACATT 31 59 0 AAAATTAAGA 0.92434 -79 ATAAGTACGTACAATTGAAGGTTTAAATGAAA 31 84 1 ACAATTAAGT 0.860162 -54 CTGAAAACCTACAATTAAATGATAGTGTTTAC 36 198 1 ACAATTAAGA 0.890065 -103 ****** ** ** Masking position 4 Map Score: 8.48822 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 110 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 TTATACTCTTTGAGTTTGCTATGTAATGTATATT 4 133 0 TGATTGCTTT 0.919147 -168 TTTGTCTCTATGATTTTGTTTTATAATGTAAACG 4 207 1 TGATTGTTTT 0.859448 -94 TTCTTCATTTTAATTGGGTTATGTCTCACTGTTC 7 146 0 TAATGGTTTT 0.610487 -136 CTTACGCCTGTGAATTCGTTGTCATGATTTTTAG 9 176 1 TGATCGTTTA 0.900967 -63 GTATTCAAAATGAATACGTTTTCATTAGGAGGTG 15 252 1 TGATCGTTTA 0.896774 -28 CCGGCTGATTTGAATCTGCTCTTTTTTATTTATA 21 66 0 TGATTGCTTT 0.919147 -118 ACATTATTTTTGAATGCGCTGTCAACCTTGTCGT 26 12 1 TGATCGCTTA 0.935782 -289 GACCTGACTTGGTTCTTTCGAATAGAAG 28 5 1 TGATGGTTTT 0.887291 -296 ATATTGTCGATGAATTGGCTCTTAACAGTTGAAT 30 150 1 TGATGGCTTA 0.944305 -148 TACTGGGTTTTAATTCCGCTGTAACACATGTGTA 35 25 1 TAATCGCTTA 0.771456 -276 TTAATTCAGATGATTTTGCTGTAACTGGAATTCT 35 171 0 TGATTGCTTA 0.929427 -130 AATTAAGGAATGAATATGCTGTAAAATAGAAGAA 35 199 1 TGATTGCTTA 0.929426 -102 AATGAATAGTTAAGTTGGTTATATTATCCTGAAA 36 130 0 TAATGGTTTT 0.610487 -171 *** * **** * * Masking position 3 Map Score: 7.49001 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 150 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 AATAGATCTTAATGAAGAGGGTGTATGA 1 9 0 AATGAAGAGG 0.839779 -156 ATTTTTTAAAAATAAAAAGGCTCCTGGTT 2 10 0 AATAAAAAGG 0.685841 -163 AGGTTCCGGTAATAAAGGCATTTTTCCCTA 5 42 0 AATAAAGGCA 0.624438 -106 TGCATTAGAAAATGAAGGCGTCGTGAAAGG 6 211 1 AATGAAGGCG 0.834278 -90 TAGAAATAAAAAAGGACTTTGTTC 7 5 1 AATAAAAAAG 0.575462 -277 ATCTGCATTAAATAAAAAAATCATCAAATG 7 53 1 AATAAAAAAA 0.474054 -229 ACCCAATTAAAATGAAGAAACCCATGTGAT 7 161 1 AATGAAGAAA 0.683944 -121 GGGGATTTAGAAAGAAGGGAATCT 7 268 1 AAAGAAGGGA 0.382313 -14 TTCTTATTTTAATGAAAAAAGTCTTTTATA 15 63 0 AATGAAAAAA 0.644717 -217 TTCACCTCCTAATGAAAACGTATTCATTTT 15 258 0 AATGAAAACG 0.814651 -22 TAATCTGGTTAAAAAAGGCGGTGGCGATA 19 10 0 AAAAAAGGCG 0.316162 -128 AATAGTGGTGAATGAAGGGATAACGGTTGA 19 93 1 AATGAAGGGA 0.769981 -45 AAGCTATATAAATAAAAAAGAGCAGATTCA 21 60 1 AATAAAAAAG 0.575462 -124 AAAACCCGCAAATAAAGGCGTTTTTTCGGG 23 13 1 AATAAAGGCG 0.714324 -288 CCCTAAAAACAATGAAAAGGGATCTCCATC 25 115 0 AATGAAAAGG 0.814651 -69 GAAGCGCTATAATGAAAGCGGACAAGGGAA 28 35 1 AATGAAAGCG 0.808484 -266 TAAAATAATTAAAGAAAGCAGAAATGATTT 30 201 1 AAAGAAAGCA 0.341683 -97 TGAAGGTTTAAATGAAAACGCTTTACTCAA 31 99 1 AATGAAAACG 0.814651 -39 CCGTAAAGAAAAGGGGAGATCTT 32 5 1 AAAGAAAAGG 0.448329 -19 CCCTTTTTATAATGAATACACTTTTTTGGC 35 94 1 AATGAATACA 0.200046 -207 TTTGTCCATAAATAAAAGAGAATTCCAGTT 35 153 1 AATAAAAGAG 0.56558 -148 TGCCTCCCACAATGAAGAGACATTGACAAT 35 236 0 AATGAAGAGA 0.777046 -65 GAAGCGGTATAATAAAGAGACGATGACAGG 35 270 1 AATAAAGAGA 0.633848 -31 TTGATGATGTAATAAAAAAAGTGCCGCTGA 36 39 0 AATAAAAAAA 0.474054 -262 AGATTCCGAGAATAAAAGAAAATAGGCATA 36 79 1 AATAAAAGAA 0.46401 -222 CAGGCTCCGCAATAAAAAGACTAGAGAGAA 36 246 1 AATAAAAAGA 0.59211 -55 AAACAAAATGAATGAAGAAAAGAGGGGTTT 36 276 1 AATGAAGAAA 0.683944 -25 ********** Masking position 5 Map Score: 17.46 Number of sites scoring better than the average of aligned sites = 1445 Number in coding regions = 1142 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 343 Fraction of orfs with sites within 600 bp upstream = 0.0550916 Motif number 11 AGAGTCAAAGGGAAGCATCATTCTCTGAACAT 2 106 1 GGAAGCTATT 0.787996 -67 AGGAAACCTCCTTTAAAGTGTGA 5 135 0 GGAAACTCTT 0.787996 -13 TGTTCTCGGTGGCAGCTGTCTTGCTGTAAAAC 7 119 0 GGCAGCGCTT 0.981042 -163 AGAACCATTGGAGGCTGGCTTGCGTCAATGA 22 10 1 GGAGGCGCTT 0.981042 -154 TGTAAAAACATGAGGCTTACTTAAAAAGCACG 23 237 0 TGAGGCTCTT 0.784632 -64 CAGACGGTACGGAAGCATACTTTTTCTTTTTC 26 247 0 GGAAGCTCTT 0.970833 -54 TAAAAGCCAGGGCAGCGGCCTTAGGCGAAAGC 28 160 0 GGCAGCGCTT 0.981042 -141 CTCGGAATCTGGCGGCGGACTTGATGATGTAA 36 57 0 GGCGGCGCTT 0.980666 -244 ****** * *** Masking position 11 Map Score: 3.30835 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 174 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 ATTGAAAGTAAAGAGGACTTTGGCACATGACTGTG 2 43 0 AAGAGACTGA 0.93647 -130 AGTATACAGGAAGAGGAGCAGGAAATAAAATGCAT 6 181 1 AAGAGAGGGA 0.947031 -120 TAGAAATAAAAAAGGACTTTGTTCTCGACATCGT 7 10 1 AAAAGACTGC 0.718796 -272 ATGCAGATAAAAAAGGACGATGTCGAGAACAAAGT 7 26 0 AAAAGACTGG 0.718796 -256 TCAGACTAGTAAAAAGAGGAGGTCAATTCTT 9 218 1 AAAAAAGGGA 0.695404 -21 GCTTTAAGTTAAAAGGAGAATGATAAAA 10 80 1 AAAAGAGTGA 0.924521 -18 GGAAATTAAGAAAAGAACCTGGTGAAATTTCCCAG 16 125 1 AAAAGACGGA 0.962974 -176 GTGCAATATAAAAAGAACCTGGGAAATTTCACCAG 16 143 0 AAAAGACGGA 0.962974 -158 GCCCTCAACTAAGAGGAGGTTGGGAAGAG 17 19 1 AAGAGAGTGA 0.917634 -19 ATCTGGTTAAAAAAGGCGGTGGCGATA 19 3 0 AAAAGCGGGA 0.741429 -135 GGCTTACTTAAAAAGCACGATGCAAGTATTTCTCT 23 221 0 AAAAGACTGA 0.941882 -80 GCTATAATGAAAGCGGACAAGGGAAGGGGACGGAC 28 40 1 AAGCGACGGA 0.775317 -261 TATGGACAAAAAAAGGACACGGATAACTGGAGAAT 35 128 0 AAAAGACGGA 0.962974 -173 TGTAAAATAGAAGAAAAGATTGTCAATGTCTCTTC 35 218 1 AAGAAAGTGA 0.564072 -83 ***** ** ** * Masking position 2 Map Score: 7.86002 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 183 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 13 GTGGATGATAAAAAATGTGAAAATGTGTTG 1 74 1 AAAAATGTGA 0.745681 -91 AACATGATGAAGAAAAGTGATTTGGTATCT 4 24 0 AGAAAAGTGA 0.826061 -277 AAGCTTCCGGAAAAAAGCGATTTTTATACT 4 160 0 AAAAAAGCGA 0.814552 -141 ACCTATGGTAAAAAAAGCGATTTTAATGAG 5 68 1 AAAAAAGCGA 0.814552 -80 CCTCTCAACCAAAAACATGAAATTAAACCC 7 90 0 AAAAACATGA 0.821433 -192 ATTGAGGGAAAAAAACGGGAAGTTCATTCT 9 69 1 AAAAACGGGA 0.813533 -170 AATTTATTAGAAAAACATGAAACTTTTTGA 14 44 1 AAAAACATGA 0.821433 -66 GTTAATATGGAGAAACGTGAAAGATTTTGA 15 157 1 AGAAACGTGA 0.896709 -123 TCACAGGCACCAAAAAGTGACTATAGCACT 21 150 0 CAAAAAGTGA 0.674788 -34 AGAGTGTTGTAAAAACATGAGGCTTACTTA 23 246 0 AAAAACATGA 0.821433 -55 ATAAACGTGAAGCCTTTGGC 25 1 1 ATAAACGTGA 0.848769 -183 GTCACAAAAAATAAACGTGAGCCAAAGGCT 25 21 0 ATAAACGTGA 0.848769 -163 ATACAGCACGAAAAACGTGAAACCGTCTGT 28 250 0 AAAAACGTGA 0.967647 -51 TTCCTCCTTTAAATAAGTGAGAGATATTTA 29 21 0 AAATAAGTGA 0.583327 -26 AATCCGTGCCAAAAAAGTGTATTCATTATA 35 101 0 AAAAAAGTGT 0.599647 -200 TGATGTAATAAAAAAAGTGCCGCTGATTAG 36 35 0 AAAAAAGTGC 0.689433 -266 ********** Masking position 5 Map Score: 9.96721 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 361 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 14 CTGTTTTGTTTGTCGCTGTAAGATACAAAA 2 140 0 TGTCGCTGTA 0.723189 -33 TTTTATGAATTTCTGCTGAATATACATTAC 4 115 1 TTCTGCTGAA 0.754812 -186 GTGGCAGCTGTCTTGCTGTAAAACCTCTCA 7 113 0 TCTTGCTGTA 0.821843 -169 TTTTTGTGTTTTTAGCTGAAAGGAGAAGAT 7 189 0 TTTAGCTGAA 0.7391 -93 TGTCATGATTTTTAGCTGTAAGGTCAGACT 9 195 1 TTTAGCTGTA 0.919617 -44 AGCCGTCCGGTTTTTCTGTATTTCATTGGC 13 28 1 TTTTTCTGTA 0.635455 -196 TATGGTATTCTTTTGTTGTAACGGTTTTGA 18 165 1 TTTTGTTGTA 0.635455 -57 ATCTTCAGCCTTCAGCTGTACA 24 3 0 TTCAGCTGTA 0.827354 -40 TTCCTTCCTTTTTTGCTGGACATTATATGT 30 268 0 TTTTGCTGGA 0.837733 -30 TGGGTTTTAATTCCGCTGTAACACATGTGT 35 28 1 TTCCGCTGTA 0.88533 -273 ATTCAGATGATTTTGCTGTAACTGGAATTC 35 172 0 TTTTGCTGTA 0.956723 -129 ********** Masking position 10 Map Score: 2.96845 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 282 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 15 CTGTTTTTCTATCCTTCCTGTCAGTATCTA 4 281 0 ATCCTTCCTG 0.739715 -20 ACGGCTGAAATGCCGTCCGGTTT 13 4 0 TGCCGTCCGG 0.972131 -220 ACGGCATTTCAGCCGTCCGGTTTTTCTGTA 13 18 1 AGCCGTCCGG 0.972131 -206 ACTTTTTGATATCCTTCCCGTACTATTTGT 14 65 1 ATCCTTCCCG 0.936832 -45 ATTTCATACAAGCCTTTCCGAGCACGTCAT 26 62 1 AGCCTTTCCG 0.83112 -239 AAAAGTATGCTTCCGTACCGTCTGATCAAG 26 255 1 TTCCGTACCG 0.699072 -46 AATGCCTTCCGGAACATCGTGC 26 289 0 TGCCTTCCGG 0.96654 -12 TTCCCTGCCCTCCCGAATGTTGAGT 31 123 0 TGCCCTCCCG 0.944727 -15 ********** Masking position 6 Map Score: 1.71764 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 207 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049