AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_bsub_reg_300.orf -o00520_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 Input sequences: #1 yfnI 300 alternate gene name: yetP; similar to hypothetical proteins #2 yfnH 235 similar to glucose-1-phosphate cytidylyltransferase #3 yjbJ 203 similar to lytic transglycosylase #4 yjbK 124 yjbK #5 yjlC 300 yjlC #6 yjlD 39 similar to NADH dehydrogenase #7 yjmA 197 similar to glucuronate isomerase #8 yjmB 67 similar to Na+:galactoside symporter #9 yjmC 104 similar to malate dehydrogenase #10 yngA 300 yngA #11 xsa 216 beta-xylosidase #12 etfA 35 electron transfer flavoprotein (alpha subunit) #13 ysiA 104 similar to transcriptional regulator (TetR/AcrR family) #14 lcfA 188 long chain acyl-CoA synthetase #15 yshC 73 similar to DNA polymerase beta #16 yshA 133 yshA #17 araP 35 integral membrane protein #18 araN 30 sugar-binding protein #19 araA 207 L-arabinose isomerase #20 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #21 ysdC 183 similar to endo-1,4-beta-glucanase #22 ytdA_ytcA 171 ytdA: alternate gene name: yzwA; similar to UTP-glucose-1-phosphate uridylyltransferase, ytcA: similar to NDP-sugar dehydrogenase #23 yugK 103 similar to NADH-dependent butanol dehydrogenase #24 yugJ 229 similar to NADH-dependent butanol dehydrogenase #25 gtaB 245 UTP-glucose-1-phosphate uridylyltransferase #26 lytD 128 N-acetylglucosaminidase (major autolysin) (CWBP90) #27 pmi 264 mannose-6-phosphate isomerase #28 galK 80 galactokinase #29 ywcC 300 alternate gene name: ipa-33d #30 galE 114 UDP-glucose 4-epimerase #31 yxkA 129 similar to hypothetical proteins Motif number 1 TCTCGGAAATAAAAAAAGGATTTCTTTTGTCA 1 94 0 AAAAAAGGAT 0.82635 -207 TGTATAACCAAAAAAAGAGCCTTGAGCGAAGG 2 41 0 AAAAAAAGCT 0.892351 -195 AACCAACTTGAAAAAATAGATTCCATTTGGTC 2 72 1 AAAAAAAGAT 0.90539 -164 TTTGTTTAAAAAAGGAGAGCATT 4 2 0 AAAGGAAGCT 0.860467 -123 AAATTGATATAAAGGACGGAGGATATACG 6 21 1 AAAGGAGGAG 0.83109 -19 TTTCATTTTCAAAAAAGAGATTGATCCCAAAG 7 100 1 AAAAAAAGAT 0.90539 -98 AAAAAACTGAAAAGGAAGGAGGCACTTGC 9 86 1 AAAGGAGGAG 0.83109 -19 TTTCAGACACAAAAAACAGCCGTTCAATGCGG 10 162 1 AAAAAAAGCG 0.920135 -139 ATACTCTTGAAAAAAACAGCCGCATTGAACGG 10 181 0 AAAAAAAGCG 0.920135 -120 TATTATGAGAAAAAGAAAGATTTACCTTTCTT 14 99 1 AAAAGAAGAT 0.90702 -90 AAAAGTGTAAAAAAAGGAGATTATTAC 16 6 0 AAAAAGAGAT 0.853237 -128 TTATTAAATGAATGGAAAGACGAGCCTCCCGC 16 65 0 AATGGAAGAG 0.754549 -69 CGTCCTATTGAATAAAAAGCCGGGCTCTGCCC 19 29 1 AATAAAAGCG 0.781633 -179 GCTTTTTTTAAAAGAAAAGATTGACAGTATAA 19 64 1 AAAGAAAGAT 0.874749 -144 AATCCACCTCAATAGGCGGATTCTTCCGTATC 20 12 0 AATAGGGGAT 0.477961 -185 TGTACAGACAAAAAAATAGAATCCACCTCAAT 20 31 0 AAAAAAAGAT 0.90539 -166 CACTTTTTCTAAAAGAAAGCTGTAAAAACATA 21 75 1 AAAAGAAGCG 0.921533 -109 ATATCCTATTAAAAAAGGGCTGGTTCGTGATT 22 49 1 AAAAAAGGCG 0.851392 -123 CAAAAAAGAAAAAGGGAAGCAGCCAAACGGCT 23 24 0 AAAGGGAGCG 0.838891 -80 TGATGCTGGTAAAAAACAGATTTTCCATTGTA 23 67 0 AAAAAAAGAT 0.90539 -37 ATAGAATAAGAAAGAGGAGAAGGA 26 115 1 AAAGAGAGAG 0.855009 -14 ATTTGTATCAAAAAAGGAGAATTATTCTTATC 27 50 1 AAAAAGAGAT 0.853237 -215 TTGAAGGGGTAATGAAAAGATGATGCTTTGTA 27 143 1 AATGAAAGAG 0.75098 -122 TGTCATAGGAAAAAGGCAGCTTATACGGGCGT 27 182 1 AAAAGGAGCT 0.836959 -83 TCTATGAAGAAATAAGGGGAATAAAAAATAAA 28 39 1 AATAAGGGAT 0.473179 -42 AGAACGAGAAAATAGAGAGAGGGATTCAT 31 111 1 AATAGAAGAG 0.808146 -19 ****** *** * Masking position 2 Map Score: 26.7655 Number of sites scoring better than the average of aligned sites = 1490 Number in coding regions = 1192 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 2 CTATTTTTCGTTTTTGCTAGTTTATGTTATTCTTA 1 24 1 TTTTTTTTTT 0.945081 -277 CCTTCATTTCGTTTCACATTTTTTTCTCGGAAATA 1 115 0 GTTTCATTTT 0.381532 -186 ATGGAATCTATTTTTTCAAGTTGGTTGTATAACCA 2 63 0 TTTTTATTGT 0.803326 -173 GTAAATCTTATTTTTACTATTATCTCTTTAGATGT 4 79 0 TTTTTTTATT 0.452192 -46 CGAATTGGAGTTTTTTGTGTTTGCTATTTTCAGAG 5 59 1 TTTTTTTTGT 0.862096 -242 GATTTTGACTTATTCAATTGTTTATTTTTAGATAA 5 103 1 TATTCTTTTT 0.510296 -198 TGGCAATGTCTTTTTTTATGTTTATGACAGCGTTA 7 62 1 TTTTTATTTT 0.918326 -136 AACGTTAACATTTTGATTTGTTTTTATTTTACCTT 7 139 0 TTTTGTTTTT 0.578842 -59 GAACTGGATACATTTATTCATTGATAAGATGGGGC 10 102 1 CATTTTTTGT 0.424354 -199 GTATACCCGCTTTTTCATGTTTTGTTCATATTTTA 10 227 1 TTTTTTTTTT 0.945081 -74 TGTTCATATTTTATTAATTGTTTATTCAACACTGT 10 249 1 TTATTTTTTT 0.452192 -52 AAAGTCCGGGTTTTTTCATATTTATAAATACATAC 11 29 1 TTTTTATTTT 0.918326 -188 GTCAACGACATTTTCTATTGTTTTTATATTTGTAC 11 64 0 TTTTCTTTTT 0.786522 -153 TGATAAGAAGGATTTTCAGGTTTGTCAAGTTTATT 13 29 0 GATTTATTTT 0.44902 -76 AGCGGGAATCTTTTTGTTAATTGGTCTTATATATC 14 58 1 TTTTTTTTGT 0.862096 -131 ATTTACCTTTCTTTTTCTTTTTTTTGCCGTCCATC 14 118 1 CTTTTTTTTT 0.877673 -71 AATAATCTCCTTTTTTTACACTTTTCGCTGTATAT 16 13 1 TTTTTACTTT 0.604275 -121 ACAAAATATTTATTTATAGGTTTATTTTCCTATCA 19 125 1 TATTTATTTT 0.760771 -83 AAGTGAAACCTTTTTCTATGCTTTTCGTATTACAT 21 45 0 TTTTTACTTT 0.604275 -139 CGGGTATATGTTTTTACAGCTTTCTTTTAGAAAAA 21 78 0 TTTTTATTTT 0.918326 -106 GGCTGCTTCCCTTTTTCTTTTTTGTCAACTTATGT 23 32 1 CTTTTTTTTT 0.877673 -72 CATTTTAAATCATTTCATTCTTGATTCAAATAAAA 25 76 1 CATTTTTTGT 0.424354 -170 TTTCAATATGTTTTTACACATTTTTATGATATCGG 25 160 0 TTTTTATTTT 0.918326 -86 ATATTGACGGTTTTTATTAATTTGTATCAAAAAAG 27 31 1 TTTTTTTTTT 0.945081 -234 ATATGTGCAGCTTTTCAAGCTTTGTTTCAGCCTTT 27 87 0 CTTTTATTTT 0.824187 -178 CACCTTTCTGGTTTTTATTTTTTATTCCCCTTATT 28 49 0 GTTTTTTTTT 0.815155 -32 ATCCAGTCAGTATTTAATTGTTTATTATTATAAAT 29 134 0 TATTTTTTTT 0.82956 -167 TATTAATAGTTTTTTCATATTTTTTAGC 30 4 0 TTTTTTTTTT 0.945081 -111 ***** * *** * Masking position 4 Map Score: 21.3667 Number of sites scoring better than the average of aligned sites = 1429 Number in coding regions = 1052 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 349 Fraction of orfs with sites within 600 bp upstream = 0.0560553 Motif number 3 GATTTTGTTTGGAAAGAAGGAATTGGAAGG 1 258 1 GGAAAGAAGG 0.878012 -43 AGAAGGAATTGGAAGGCAGGATATAAAGAG 1 272 1 GGAAGGCAGG 0.856711 -29 GGGCTTGGCGATGAAGAAGGTGCTGATTGC 3 177 0 ATGAAGAAGG 0.757376 -27 TTTACAGGGCGGAAAGGAAGAGCATC 4 109 1 GGAAAGGAAG 0.813966 -16 ACTGCTTATAGTAAAGGAGAATTGGAT 5 284 1 GTAAAGGAGA 0.741292 -17 ATTGATATAAAGGACGGAGGATATACG 6 23 1 AGGACGGAGG 0.909511 -17 AAAACTGAAAAGGAAGGAGGCACTTGC 9 88 1 AGGAAGGAGG 0.971932 -17 TCATTTCTATAGGAAGGAACGATGAACA 13 87 1 AGGAAGGAAC 0.502429 -18 GGGGACGGAGAATAGATGGAA 14 2 1 GGGACGGAGA 0.68424 -187 GGATTCTCGCGGAATGGAGGAGAAACG 16 117 1 GGAATGGAGG 0.91755 -17 CGATTTGACAGGAAGGGAGGATAAATAATC 20 135 1 GGAAGGGAGG 0.966067 -62 GCTTTCTAAAATAAAGGAGGTTGAACAAAA 20 177 1 ATAAAGGAGG 0.930023 -20 GATCATCACCATAAGGGAGGTGCCTTCACA 21 13 0 ATAAGGGAGG 0.901404 -171 TTGTATAATAAGAATGCAGGACTGATGAAG 21 151 1 AGAATGCAGG 0.591464 -33 TGCAGGACTGATGAAGGAGGGTTTGGAAC 21 165 1 ATGAAGGAGG 0.94723 -19 CAGTAATCTTGTAAAGGAGCTCAGGTG 22 8 0 GTAAAGGAGC 0.855449 -164 AAAAGAAAAAGGGAAGCAGCCAAACGGCTA 23 23 0 GGGAAGCAGC 0.764042 -81 CATTCTCCATATGAGGGAAGCTGGCCTGCC 24 80 1 ATGAGGGAAG 0.566227 -150 CAAGGTGCTGGGAAAGAAGCTGATATAAGC 24 113 0 GGAAAGAAGC 0.665031 -117 TTTTTCGATCATAAGGAAGGTGCCTTTTAA 25 226 1 ATAAGGAAGG 0.613885 -20 AGCCAGCGCGATGATGGAGGCGAGTACAAC 29 11 1 ATGATGGAGG 0.828371 -290 ATAACTTGCAGTGAAGGAGATATTTC 31 7 0 GTGAAGGAGA 0.794658 -123 ********** Masking position 4 Map Score: 18.4866 Number of sites scoring better than the average of aligned sites = 1030 Number in coding regions = 674 Number in noncoding regions = 356 Number of orfs with sites within 600 bp upstream = 383 Fraction of orfs with sites within 600 bp upstream = 0.0615162 Motif number 4 TGTGTGCCTTTGAAAAAAGAAATAGATACCGAGTATA 1 57 0 TAAAAGAAAT 0.941016 -244 AAGGCACACATGACAAAAGAAATCCTTTTTTTATTTC 1 84 1 TAAAAGAAAT 0.941016 -217 GAGCTCGATATGATAAAATGAATCTGTACTTTGTTTA 4 26 0 TAAAATGAAT 0.841789 -99 ATTATTTTTATCTAAAAATAAACAATTGAATAAGTCA 5 108 0 TAAAATAAAT 0.955174 -193 CACAATCATTTACAAAAATAAATGTTTACTACCCAGT 5 167 0 TAAAATAAAT 0.955174 -134 CAATCTCTTTTTTGAAAATGAAATGTTAACGCTGTCA 7 86 0 TAAAATGAAT 0.841789 -112 TTCATATTATGAGAAAAAGAAAGATTTACCTTTCTTT 14 95 1 GAAAAGAAAT 0.684006 -94 CCCCGGCTTTTTTTAAAAGAAAAGATTGACAGTATAA 19 59 1 TAAAAGAAAT 0.941016 -149 AATAGTCAATTACTATAATAAAATTGTTCGTACAAAA 19 94 1 TATAATAAAT 0.774762 -114 GTACTAATGATAGGAAAATAAACCTATAAATAAATAT 19 130 0 TAAAATAAAT 0.955174 -78 TGCCCCTTTCTCATAAAATAAAACGCTTTCAAATACA 19 175 0 TAAAATAAAT 0.955174 -33 TGTAAGCGCTTTCTAAAATAAAGGAGGTTGAACAAAA 20 170 1 TAAAATAAAG 0.729898 -27 GTTTCACTTTTTCTAAAAGAAAGCTGTAAAAACATAT 21 71 1 TAAAAGAAAT 0.941016 -113 TCCCAGCACCTTGCAAAATAAAACCATCTGGTATGCT 24 130 1 TAAAATAAAT 0.955174 -100 GGACCTTATTTATAATAATAAACAATTAAATACTGAC 29 127 1 TATAATAAAT 0.774762 -174 ATAGTATGTAAATGAAAATAAATCATTTAGCCTATTA 29 167 1 AAAAATAAAT 0.661095 -134 * ******** * Masking position 8 Map Score: 17.6744 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 131 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 GTTTGCTGATTTTTTTGGAAAGGGTAGTGCCTCTCC 5 250 0 TTTTGAGGTA 0.932375 -51 GTAAATAAAATGTGTTTGTAGGGGTTTCGCTTGGAG 9 43 1 TTTTGAGGTT 0.970572 -62 ACACTCCGTTTATATTTGTATGTTTTCAGACACAAA 10 139 1 TTTTGAGTTT 0.902967 -162 ATTTGTTGATATGGATTACTATAGCGG 10 284 0 TTTTAAGGTT 0.921134 -17 TGTTTTTATATTTGTACGTATGTATTTATAAATATG 11 45 0 TTTAGAGTTT 0.635868 -172 GTTTGTCAAGTTTATTCATAGGCGTTCTCTTTTT 13 9 0 TTTTAAGCTT 0.8719 -96 CGGCGAGCAGTATTTTCGCAAGCTTTTCCATCTATT 14 21 0 TTTTGAGCTT 0.950543 -168 GTACAAAATATTTATTTATAGGTTTATTTTCCTATC 19 123 1 TTTTAAGTTA 0.579419 -85 ACGTATCTTTTGTATTTGAAAGCGTTTTATTTTATG 19 165 1 TTTTGAGCTT 0.950543 -43 CAACCTCCTTTATTTTAGAAAGCGCTTACAAATTAG 20 164 0 TTTTGAGCCT 0.737095 -33 GGATAAAGCTTGTTTAAAAATGGTTTATCCGATATC 25 132 1 TTTAAAGGTT 0.68669 -114 TAGGAAGCGTTTTCTTTGAAGGGGTAATGAAAAGAT 27 128 1 TTTTGAGGTA 0.932375 -137 GCGGTATTTATTTCTTTAAACGGTTATGCTATTCGG 29 222 0 TTTTAAGGTA 0.830007 -79 AAACAGGTCATTTTTTAGGAGGGTTTACATC 30 94 1 TTTTGAGGTT 0.970572 -21 * * ** * * ** ** Masking position 10 Map Score: 10.7902 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 139 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 AAACATAAATATTCCGGCTTGCCGCGGTGTATTT 1 206 1 ACCGGCTCCG 0.970326 -95 TTGGTCACCAAGGCTGGCTTTCTCTCATATCATT 2 98 1 ACTGGCTCTC 0.719072 -138 TGAAACTTGAAAGCGGGCTTTCCGTATTCTGAGT 3 103 0 ACGGGCTCCG 0.994964 -101 GCTGAGCGGGCTTGGCGATGAAGAAGG 3 187 0 GCGGGCTGCG 0.966989 -17 CCTTTTAATGAATCTGGCATTGCCAAAAGCATTC 7 12 1 ACTGGCTGCC 0.926757 -186 AAACATGAAAAAGCGGGTATACCGCTCAATAGTC 10 215 0 ACGGGTTCCG 0.939639 -86 ATGAATGGAAAGACGAGCCTCCCGCTGTTATGAT 16 56 0 ACGAGCTCCG 0.939634 -78 ATTGGAGCTCGGGCTGGCCGTCCTATTGAA 19 7 1 GCGGGCGCCG 0.946562 -201 TTGAATAAAAAGCCGGGCTCTGCCCCCGGCTTTT 19 36 1 ACGGGCCGCC 0.950228 -172 CATATGAGGGAAGCTGGCCTGCCCTCGCTTATAT 24 87 1 ACTGGCTCCC 0.969986 -143 GGCGTTTGTAAGAGGGGCGCACCGGGAAAATGAT 27 209 1 AGGGGCCCCG 0.90843 -56 * ***** * *** Masking position 7 Map Score: 6.68344 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 228 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ACAGTAGATTTTGAAACCGGATTGAAATCG 2 132 1 TTGAAACCGG 0.872465 -104 TGAAACCGGATTGAAATCGGACAAATTATC 2 143 1 TTGAAATCGG 0.821926 -93 GAACTGAAACTTGAAAGCGGGCTTTCCGTA 3 111 0 TTGAAAGCGG 0.976378 -93 ATCTCTAAAATCGAAAGGGGAGGTTTT 14 172 1 TCGAAAGGGG 0.832038 -17 CATTCAAAAAGTGAAAGCGGGGAGGTTCTC 17 16 1 GTGAAAGCGG 0.934747 -20 TCTTTTGTATTTGAAAGCGTTTTATTTTAT 19 170 1 TTGAAAGCGT 0.74784 -38 TTTATTTTATGAGAAAGGGGCAGTTTAC 19 190 1 GAGAAAGGGG 0.848014 -18 TCCTTTATTTTAGAAAGCGCTTACAAATTA 20 165 0 TAGAAAGCGC 0.814663 -32 ACGAAAAGCATAGAAAAAGGTTTCACTTTT 21 52 1 TAGAAAAAGG 0.59819 -132 AGCAACTGGGCAGAAAGCGGAATCACGAAC 22 71 0 CAGAAAGCGG 0.886155 -101 TAAAAACATATTGAAAAGGGTAAATAGAGA 25 179 1 TTGAAAAGGG 0.855384 -67 GTTTTTTTATTAGAAAATGGAAGTGATTCA 26 34 1 TAGAAAATGG 0.59819 -95 TATTTCTTCATAGAAAACGGCAGATCATAT 28 23 0 TAGAAAACGG 0.938218 -58 ********** Masking position 5 Map Score: 7.53322 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 481 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 GATGAAAAAGAGCCTTGAGCGGGCGC 2 6 1 AAAAAGCCTT 0.886278 -230 TATAACCAAAAAAAGAGCCTTGAGCGAAGGC 2 40 0 AAAAAGCCTT 0.886278 -196 TCAGACACAAAAAACAGCCGTTCAATGCGGC 10 164 1 AAAAAGCCGT 0.9783 -137 ACTCTTGAAAAAAACAGCCGCATTGAACGGC 10 180 0 AAAAAGCCGC 0.942806 -121 AACAAAACATGAAAAAGCGGGTATACCGCTC 10 222 0 GAAAAGCGGG 0.861096 -79 TATAAATATGAAAAAACCCGGACTTTTAAAG 11 24 0 AAAAACCCGG 0.882569 -193 TCCTATTGAATAAAAAGCCGGGCTCTGCCCC 19 31 1 TAAAAGCCGG 0.92337 -177 TTTTCTTTTAAAAAAAGCCGGGGGCAGAGCC 19 51 0 AAAAAGCCGG 0.983063 -157 ATTTTCAAGTGAAATAGTCGTATGGTTAGCG 21 113 1 GAAAAGTCGT 0.76464 -71 AAAAAGGGGAAATAGCCGTTTGGCTGCTT 23 9 1 GAAAAGCCGT 0.973812 -95 **** ****** Masking position 6 Map Score: 6.96329 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 386 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 GATACCGAGTATAAGAATAACATAAACTAG 1 40 0 ATAAGAATAA 0.845213 -261 TTATTTTTAGATAAAAATAATACTGAATAT 5 124 1 ATAAAAATAA 0.613622 -177 CTTTTAAGGCATAAGAATAAGGATTGTGAA 5 210 0 ATAAGAATAA 0.845213 -91 TAAAGGTAAAATAAAAACAAATCAAAATGT 7 137 1 ATAAAAACAA 0.832566 -61 AATTAATAAAATATGAACAAAACATGAAAA 10 238 0 ATATGAACAA 0.938502 -63 ATAGTAATCCATATCAACAAAT 10 289 1 ATATCAACAA 0.61874 -12 GTATTTATAAATATGAAAAAACCCGGACTT 11 30 0 ATATGAAAAA 0.67952 -187 ACGTACAAATATAAAAACAATAGAAAATGT 11 62 1 ATAAAAACAA 0.832566 -155 GAACAGATATATAAGACCAATTAACAAAAA 14 68 0 ATAAGACCAA 0.897765 -121 TTTTCTCATAATATGAACAGATATATAAGA 14 82 0 ATATGAACAG 0.847339 -107 ACGTGTTATGATAAGAACTAGGATTCTCGC 16 97 1 ATAAGAACTA 0.57863 -37 GGATATTGATATATGACCAGTAATCTTGTA 22 25 0 ATATGACCAG 0.740317 -147 CTATGAGTATATAAAACTAGTTTATTTATC 26 89 0 ATAAAACTAG 0.228801 -40 CTTTTCCTCGATAAGAATAATTCTCCTTTT 27 61 0 ATAAGAATAA 0.845213 -204 CTATGACAACATATGTACAAAGCATCATCT 27 160 0 ATATGTACAA 0.550705 -105 AAAATGACTAATATAACCAATGGACCTTAT 29 106 1 ATATAACCAA 0.695091 -195 GCTAAAAAATATGAAAAAACTATTAATA 30 9 1 ATATGAAAAA 0.67952 -106 ********** Masking position 3 Map Score: 5.52785 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 410 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 10 ACGAAAGAAACCTTCATTTCGTTTCACATT 1 130 0 CCTTCATTTC 0.923451 -171 CCTTCCAATTCCTTCTTTCCAAACAAAATC 1 258 0 CCTTCTTTCC 0.817219 -43 GATGCTCTTCCTTTCCGCCCTGTAA 4 110 0 TCTTCCTTTC 0.868004 -15 TTGCCAAAAGCATTCCTTTCCGAGTGCTTT 7 31 1 CATTCCTTTC 0.940764 -167 GCAAGTGCCTCCTTCCTTTTCAGTTTTTTG 9 85 0 CCTTCCTTTT 0.776107 -20 AGTGTTAGCCCCATCTTATCAATGAATAAA 10 114 0 CCATCTTATC 0.702068 -187 GCCTCTGATCATTCCTTTCATACGGATAT 11 198 0 CATTCCTTTC 0.940764 -19 ACCTGAAAATCCTTCTTATCATGAAATTAT 13 43 1 CCTTCTTATC 0.860796 -62 AATGAATAGTCATTCATTTCTATAGGAAGG 13 74 1 CATTCATTTC 0.757711 -31 GCAAGCTTTTCCATCTATTCTCCGTCCCC 14 10 0 CCATCTATTC 0.771511 -179 GGAGGCTCGTCTTTCCATTCATTTAATAAA 16 68 1 CTTTCCATTC 0.56483 -66 CTGCGTTACCCCTTCCATTCGAGGTGCGGG 18 11 0 CCTTCCATTC 0.942769 -20 ATTATACTGTCAATCTTTTCTTTTAAAAAA 19 67 0 CAATCTTTTC 0.765004 -141 ATTTATCCTCCCTTCCTGTCAAATCGACTG 20 131 0 CCTTCCTGTC 0.906215 -66 GTACAAAGCATCATCTTTTCATTACCCCTT 27 146 0 TCATCTTTTC 0.574093 -119 ********** Masking position 4 Map Score: 9.16442 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 441 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 11 TTTTTGAACAAAATTTGAACGTGAAT 5 6 0 AAATTTAACG 0.82424 -295 TTTGAAAATGAAATGTTAACGCTGTCATAAA 7 82 0 AAATGTAACG 0.973085 -116 AAACAAATCAAAATGTTAACGTTAACATTTT 7 151 1 AAATGTAACG 0.973085 -47 GAAAACATACAAATATAAACGGAGTGTTAGC 10 135 0 AAATATAACG 0.82424 -166 ATATGTTCGTACATGTCAACGACATTTTCTA 11 82 0 ACATGTAACG 0.960519 -135 GAGTCAGCATGAATGTAAGCGCTTTTAAAGT 11 124 0 GAATGTAGCG 0.844667 -93 TGATGGAAACATATGTGAACGTCTGGGGGTT 15 48 1 ATATGTAACG 0.899188 -26 AAACAAATACGCATGTAAACGTAACAATTTG 31 43 0 GCATGTAACG 0.932325 -87 ****** **** Masking position 8 Map Score: 3.69604 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 44 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 AACAAAATCAAGGCATCACACAACAATAAAT 1 236 0 AGGCATCCAC 0.825434 -65 CAATCTATCAAGGCATTTCCCCGATAATTTG 2 164 0 AGGCATTCCC 0.976174 -72 AGACAGGGAGAGGCACTACCCTTTCCAAAAA 5 244 1 AGGCACTCCC 0.989814 -57 TCAGTTTTTTGGGCACTCTCCAAGCGAAACC 9 65 0 GGGCACTTCC 0.959547 -40 ATAAAAAGCCGGGCTCTGCCCCCGGCTTTTT 19 40 1 GGGCTCTCCC 0.822151 -168 TGTGTGAAGGCACCTCCCTTATGGTGAT 21 8 1 AGGCACCCCC 0.990802 -176 GAATCTATACATGCATTCTCCATATGAGGGA 24 67 1 ATGCATTTCC 0.653469 -163 TTAAAAGGCACCTTCCTTATGATCGA 25 230 0 AGGCACCTCC 0.976928 -16 ******* *** Masking position 4 Map Score: 4.65566 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 68 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 CAAATGGTTGTAATAAAAATGATATGGTGCG 1 175 1 TATAAAAATG 0.885779 -126 AAAGAGATAATAGTAAAAATAAGATTTACAG 4 85 1 TATAAAAATA 0.657645 -40 AAAAACTGGGTAGTAAACATTTATTTTTGTA 5 163 1 TATAAACATT 0.626807 -138 GTTAACGCTGTCATAAACATAAAAAAAGACA 7 68 0 TCTAAACATA 0.830968 -130 TCCATTCATTTAATAAACGTGTTATGATAAG 16 81 1 TATAAACGTG 0.746266 -53 ACCGAAAATTTCCTGAACATGACGATATACG 20 95 1 TCTGAACATG 0.773088 -102 ATTCTTATTATACAAAACATGGCGCTAACCA 21 135 0 TAAAAACATG 0.664925 -49 GAATATCATGTAATAAACATGAGCTGAGGGG 22 143 1 TATAAACATG 0.944851 -29 TTATCCGATATCATAAAAATGTGTAAAAACA 25 156 1 TCTAAAAATG 0.899833 -90 TTTCTCTCCTTCTTAAACATATTGACGGTTT 27 13 1 TCTAAACATA 0.830968 -252 TCATTTAGCCTATTAAAAATGACCCCTGGGA 29 189 1 TATAAAAATG 0.885778 -112 CGATTAAACTTCTTAAAAATGGATGTGGACC 30 41 1 TCTAAAAATG 0.899833 -74 ** ******** Masking position 6 Map Score: 4.90357 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 119 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 14 TGAAAAAGAGCCTTGAGCGGGCGCATTGCC 2 13 1 CCTTGAGCGG 0.976141 -223 AAAAAAAGAGCCTTGAGCGAAGGCAATGCG 2 34 0 CCTTGAGCGA 0.80044 -202 CGCTCAGCGATACTGAGCGGACACTTTG 8 9 0 TACTGAGCGG 0.955961 -59 CGCTCAGTATCGCTGAGCGGATCACTATCC 8 20 1 CGCTGAGCGG 0.958624 -48 AAAACAGCCGCATTGAACGGCTGTTTTTTG 10 171 0 CATTGAACGG 0.814632 -130 AGTATAAGACTATTGAGCGGTATACCCGCT 10 208 1 TATTGAGCGG 0.963392 -93 CCATCTGGTATGCTGATCGGTGAGAGCTGA 24 153 1 TGCTGATCGG 0.804539 -77 AAAACTAGTTTATTTATCGGCACGCGCATG 26 77 0 TATTTATCGG 0.54239 -52 ACCGGATCAATCTTTAGCGGTATTTATTTC 29 244 0 TCTTTAGCGG 0.862215 -57 ********** Masking position 6 Map Score: 2.66453 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 294 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 ACCTGCTCTTTATATCCTGCCTTCCAATTC 1 277 0 TATATCCTGC 0.79358 -24 CGTATATCCTCCGTCCTTTATA 6 28 0 TATATCCTCC 0.963582 -12 AATCGAACACTAACTCCTCCAAAAGTTTCT 10 64 0 TAACTCCTCC 0.951409 -237 CGTTTCTCCTCCATTCCGCGAG 16 122 0 TTTCTCCTCC 0.888499 -12 AATTAGATTATTTATCCTCCCTTCCTGTCA 20 140 0 TTTATCCTCC 0.880312 -57 GTTCCAAACCCTCCTTCATCAGTC 21 170 0 CAAACCCTCC 0.7916 -14 AGTAAAACCTCCAAATGATGCT 23 92 0 TAAAACCTCC 0.764081 -12 GACATCTCCTCCTTAGATTTTT 24 218 0 CATCTCCTCC 0.924958 -12 GATGTAAACCCTCCTAAAAAATGA 30 101 0 TAAACCCTCC 0.898312 -14 GAAATATCTCCTTCACTGCAAGTT 31 5 1 TATCTCCTTC 0.737551 -125 ********** Masking position 8 Map Score: 5.54692 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 135 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011