AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_aful_reg_300.orf -o00310_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0003 300 A. fulgidus predicted coding region AF0003 #2 AF0004 266 RNase L inhibitor #3 AF0005 38 A. fulgidus predicted coding region AF0005 #4 AF0006 104 corrinoid methyltransferase protein (mtaC-1) #5 AF0008 73 oxalate/formate antiporter (oxlT-1) #6 AF0014 95 A. fulgidus predicted coding region AF0014 #7 AF0016 54 A. fulgidus predicted coding region AF0016 #8 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #9 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #10 AF0439 82 transcriptional regulatory protein, AsnC family #11 AF0442 300 succinoglycan biosynthesis regulator (exsB) #12 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #13 AF0685 140 enoyl-CoA hydratase (fad-2) #14 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #15 AF0970 101 A. fulgidus predicted coding region AF0970 #16 AF0991 260 glutaryl-CoA dehydrogenase (gcdH) #17 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #18 AF1119 111 A. fulgidus predicted coding region AF1119 #19 AF1121 34 transcriptional regulatory protein, AsnC family #20 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #21 AF1173 180 A. fulgidus predicted coding region AF1173 #22 AF1174 61 A. fulgidus predicted coding region AF1174 #23 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #24 AF1191 32 dihydroxynaphthoic acid synthase (menB) #25 AF1192 50 conserved hypothetical protein #26 AF1195 27 activator 1, replication factor C, 53 KD subunit #27 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #28 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #29 AF1208 165 conserved hypothetical protein #30 AF1210 108 conserved hypothetical protein #31 AF1305 72 D-arabino 3-hexulose 6-phosphate formaldehyde lyase (hps-2) #32 AF1306 77 conserved hypothetical protein #33 AF1641 31 enoyl-CoA hydratase (fad-4) #34 AF1642 50 histidyl-tRNA synthetase (hisS) #35 AF1855 180 2,3-dihydrosybenzoate-AMP ligase (entE) #36 AF2009 101 heme biosynthesis protein (nirJ-2) #37 AF2010 46 A. fulgidus predicted coding region AF2010 #38 AF2011 175 conserved hypothetical protein #39 AF2013 275 coenzyme F390 synthetase (ftsA-3) #40 AF2014 63 sugar transporter, putative #41 AF2271 177 A. fulgidus predicted coding region AF2271 #42 AF2272 87 A. fulgidus predicted coding region AF2272 #43 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #44 AF2426 85 conserved hypothetical protein #45 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 AAAAAATTAGAAAATCTTTTTCCTCTTGCC 1 267 0 AAAATCTTTT 0.945701 -34 ATCAGAAAATCTTATAAGGATTGTC 3 6 1 AAAATCTTAT 0.865478 -33 AGGATTGTCAAAAATTTTTTAC 3 27 1 AAAATTTTTT 0.962406 -12 ATCATTTTATAAAATTTTTTTTAATTAACT 6 20 1 AAAATTTTTT 0.962406 -76 AGTTTGCTGCAAAATCTTTAATGGTCGTTC 8 51 1 AAAATCTTTA 0.797285 -118 AGAGCAAACTTAAATTTTTTGGATATATAG 8 93 1 TAAATTTTTT 0.92567 -76 TAAAAATATAAAAATTTTATGTTTGCCATT 10 48 0 AAAATTTTAT 0.909412 -35 TTTGTTATATAAAATCTTTTTTCTCGTGCG 12 26 1 AAAATCTTTT 0.945701 -120 ATTTAAATTTTTTCATTTATGAA 15 89 0 TAAATTTTTT 0.92567 -13 ACCTTTAAGGTAAATTTTATGTTGCAGTTG 16 151 1 TAAATTTTAT 0.805477 -110 AACTTTTTCCGAAATCTTTTTAAACGCTCA 16 205 1 GAAATCTTTT 0.89784 -56 ATGTCAAATCAAAATCTTAAATTGAGATAA 17 51 0 AAAATCTTAA 0.565575 -100 CTATTTTTACGAAATTTTTTCAAATAAATT 17 88 0 GAAATTTTTT 0.932024 -63 TTCAATAATTTAAATTTTTTGCTCAGATAA 18 77 0 TAAATTTTTT 0.92567 -35 TGCCCACCTCAAAATTTTTTCCCACCTGAC 21 83 0 AAAATTTTTT 0.962406 -98 GGATATGTAATAAATTTTTTGGAGTTCGCC 31 39 0 TAAATTTTTT 0.92567 -34 CCGCCATTTTAAAATTTTTTTTCGTTAAGC 32 45 0 AAAATTTTTT 0.962406 -33 AAACTACCGCAAAATCTTTTTAGAAAAGGT 35 49 0 AAAATCTTTT 0.945701 -132 GGTAGTTTAGGAAATTTTTTAAAATTAAAG 35 71 1 GAAATTTTTT 0.932024 -110 TGGTAATGTTAAAATTGTTTAAATGTTGAC 35 117 0 AAAATTGTTT 0.710573 -64 CTTTAATCGGGAAATTTTTTAAGGGATTTG 35 148 1 GAAATTTTTT 0.932024 -33 CCTAAATAGTAAAATTTTTATTTTTGTTAG 37 13 1 AAAATTTTTA 0.859223 -34 TAAAAAGCTAAAAATTTTATGCAAATAAAT 40 29 0 AAAATTTTAT 0.909412 -35 AACAAATAAAAAAATTTTTTATATGCCACC 41 25 0 AAAATTTTTT 0.962406 -153 CCTGAGATATTAAATTTTAATCAAAACAAA 41 49 0 TAAATTTTAA 0.455795 -129 ********** Masking position 5 Map Score: 39.6948 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 60 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 TAATGTCTCGCTTTCAATCCCATTT 1 2 0 CTTTAACCAT 0.986253 -299 CGTCGTCTGCCTTTCAATCCCATTTTGGTCTGAT 1 70 0 CTTTAACCAT 0.986253 -231 GATGTTCTTACTTTCAATCCCATTTTGGTCTGAT 1 138 0 CTTTAACCAT 0.986253 -163 TCGCCATTGCCTTTCAATCCCATTTTGGTCTGAT 1 211 0 CTTTAACCAT 0.986253 -90 TACACGTCCACTTTCAATCCCATTTTGGTCTGAT 11 30 0 CTTTAACCAT 0.986253 -271 AGTCATCGCCCTTTAAACCACAATATTCATAAAT 11 249 0 CTTTAAACAT 0.849691 -52 CTTCATATAACTTTGAAATCCACCTTCTAC 11 281 1 CTTTAACCAC 0.889469 -20 TGTTGCCTCTCTTTAAAATTCACTTCGTATGCTT 12 70 0 CTTTAATCAT 0.969273 -76 GGGCATGGAATTTTTAATGTCAATAA 13 125 1 TTTTAATCAT 0.909155 -16 GATACACTCATTTTAAATATCAATCAACATTAGT 15 51 1 TTTTAATCAT 0.909155 -51 GGATTTGAGGCTTTAAAAGCAAATTTAAAGCTTT 16 61 1 CTTTAACAAT 0.86991 -200 TCAATTTTTGTTTTAAAGACCTTTAAGGTAAATT 16 133 1 TTTTAACCTT 0.774486 -128 ATTTGACATACTTTGAAATTTATTTGAAAAAATT 17 72 1 CTTTAATTAT 0.625096 -79 TTTAAGTATGTTTTCAATATCATTACATATCATT 29 120 0 TTTTAATCAT 0.909155 -46 AAATTAACTTTTTTGAAGCTAAATC 29 151 1 TTTTAATAAT 0.482614 -15 CTCTAAAACCTTTTAAACACCCTTGCCGAAGCTT 34 23 1 TTTTAACCCT 0.742705 -28 TGACAATGAACTTTCAATATCTTTAATTTTAAAA 35 87 0 CTTTAATCTT 0.826373 -94 CAGCAAAAGGCTTTAAAAGCCACTGCCTTTAATC 39 178 0 CTTTAACCAT 0.986253 -98 **** ** *** * Masking position 4 Map Score: 25.0798 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 75 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TGCCTTTCAATCCCATTTTGGTCTGATTTCAACCCGTCAGGA 1 55 0 TCTTTATTAA 0.985047 -246 TTACTTTCAATCCCATTTTGGTCTGATTTCAACTGTTCCTTG 1 123 0 TCTTTATTAA 0.985047 -178 TGCCTTTCAATCCCATTTTGGTCTGATTTCAACTTGGGAGCT 1 196 0 TCTTTATTAA 0.985047 -105 ATTTACGTAATCCCACTTTAGTCTGATTTCAAAAAACGCCGG 2 66 0 TCTTTATTAA 0.985047 -201 TTTTTTTAATTAACTTTTTGTTGTTAATTAATTATTTATCAG 6 35 1 TCTTTATTAT 0.954852 -61 GATACTTACACTTTAATTGCAATTAAAATTGCCATTT 10 6 1 TCTTTATTAA 0.985034 -77 CCACTTTCAATCCCATTTTGGTCTGATTTCAACTTACTGTGT 11 15 0 TCTTTATTAA 0.985047 -286 AATCCGCCTGTACCGAATTTGTTCCAATTAATACTTGATATA 14 127 0 TCTTTATTAT 0.954852 -79 TTTAAATCTTTCGCAATTTTATCTCAATTTAAGATTTTGATT 17 33 1 TCTTTATTAA 0.985047 -118 AATACCACCTTGTTAGTACTTGAATTCAAACCAT 21 3 1 TCTTTATTAA 0.985047 -178 AACAGGGAGATTTCTCATTACTTATACTTTAACTATCTGTTG 27 30 0 TCTTTATTAA 0.985047 -36 AATACCTTTTTTACCGGTTTATGTCAATTTATGTGATTTAGA 30 38 1 TCTTTATTAT 0.954852 -71 TGCGGTAGTTTAGGAAATTTTTTAAAATTAAAGATATTGAAA 35 68 1 TGTTTATTAA 0.865427 -113 * * ** * * ** ** Masking position 16 Map Score: 25.7354 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 24 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 AGCAATTGTTTTTTACTTTTCCTCTTTTTT 2 20 0 TTTTACTTTT 0.806872 -247 AAATTTATTCATTAAGCTTTAACCGTTTAA 2 197 1 ATTAAGCTTT 0.800732 -70 CGGTTTGGTATTTAAGGTTTGGGCGTTTGG 2 233 0 TTTAAGGTTT 0.668404 -34 TCATAACAGCTTTTATCTTTAGAAGGCCTA 4 62 1 TTTTATCTTT 0.80486 -43 ATTTTTTTTAATTAACTTTTTGTTGTTAAT 6 33 1 ATTAACTTTT 0.781531 -63 TTTGTTGTTAATTAATTATTTATCAGGATA 6 51 1 ATTAATTATT 0.363582 -45 TTTTTAACTTTTCTTTGTCAAT 7 3 1 TTTAACTTTT 0.881232 -52 TCGTGTAATATTTAATGTTTTCGTGAAATA 9 48 0 TTTAATGTTT 0.63919 -32 AATATAAAAATTTTATGTTTGCCATTAAAT 10 44 0 TTTTATGTTT 0.499379 -39 ATTTTTATTTTTATATTTTTGT 14 3 1 TTTTATTTTT 0.702318 -203 AGCGTACTGTATTTAGCTTTAATGTCAATA 14 51 1 ATTTAGCTTT 0.693502 -155 TGCTCTCGTAATTAATTATTGACATTAAAG 14 67 0 ATTAATTATT 0.363582 -139 TTACGTAAAATTTAAGTATTAACGAA 14 190 1 TTTAAGTATT 0.574178 -16 ATTCAAACCATTTAAGCTTTTCCATAATTA 21 34 1 TTTAAGCTTT 0.892871 -147 TGAAGAGTATTTTAATCTTTTGAGATTACA 22 27 0 TTTAATCTTT 0.879879 -35 TTTTAATTTTTATTTTTTCCA 27 2 1 TTTAATTTTT 0.80732 -64 TATTTGTAGTATTTACCTTTTCTTTAACAG 29 17 1 ATTTACCTTT 0.778832 -149 ACATACTTAAATTAACTTTTTTGAAGCTAA 29 143 1 ATTAACTTTT 0.781531 -23 ATGCTGACAATTTAACCTTTTCTAAAAAGA 35 35 1 TTTAACCTTT 0.928425 -146 CATCCAGATATTTAACCTTTTGGAACTAAA 36 26 1 TTTAACCTTT 0.928425 -76 AAAATAAAAATTTTACTATTTAGGCC 37 7 0 TTTTACTATT 0.541632 -40 ATAGTAAAATTTTTATTTTTGTTAGCATGT 37 18 1 TTTTATTTTT 0.702318 -29 AGCCACTGCCTTTAATCATTACAGAGGGGC 39 165 0 TTTAATCATT 0.674451 -111 TGCATAAAATTTTTAGCTTTTTAATTCTTT 40 36 1 TTTTAGCTTT 0.824347 -28 AAAGTCAAAAATTTACCTTTCAAGTTAACA 41 104 0 ATTTACCTTT 0.778832 -74 TTCTTTTTTGTTTAACCATTAAAGTCAAAA 41 124 0 TTTAACCATT 0.785808 -54 TTGACTAAGTTTTAACCTTTTTCTTTTTTG 41 144 0 TTTAACCTTT 0.928425 -34 ATGTATTAAGTTTTTCCATTTTAT 43 44 0 ATTAAGTTTT 0.696837 -14 ********** Masking position 5 Map Score: 24.8147 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 182 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 5 CTTTCAATCCCATTTTGGTCTGATTTCAACCC 1 62 0 CATTTTTCTG 0.979707 -239 CTTTCAATCCCATTTTGGTCTGATTTCAACTG 1 130 0 CATTTTTCTG 0.979707 -171 CTTTCAATCCCATTTTGGTCTGATTTCAACTT 1 203 0 CATTTTTCTG 0.979707 -98 ATTAGAAAATCTTTTTCCTCTTGCCACGCTTG 1 260 0 CTTTTTTCTT 0.80672 -41 TTTACTTTTCCTCTTTTTTCTGAACACC 2 7 0 CTCTTTTCTG 0.889254 -260 TACGTAATCCCACTTTAGTCTGATTTCAAAAA 2 73 0 CACTTTTCTG 0.961234 -194 CTTTATTTAGCACTCATCTCTGCTTAAGAGGG 5 44 1 CACTCATCTG 0.576414 -30 CTTTCAATCCCATTTTGGTCTGATTTCAACTT 11 22 0 CATTTTTCTG 0.979707 -279 CCTCCCCCCGCATTTAGTTCTGTTCGTTGAGT 11 123 0 CATTTATCTG 0.87929 -178 TATATAAAATCTTTTTTCTCGTGCGTACTAAT 12 31 1 CTTTTTTCGT 0.681911 -115 TTAGAGTGAGCATTTTTATCTGAGCAAAAAAT 18 62 1 CATTTTTCTG 0.979706 -50 TTTTCCAGTACATTTTTCCCTGCCCGGAG 24 14 1 CATTTTCCTG 0.946119 -19 CTAAGAGCTTCATTCTCTTCGTTTGCTCATCA 28 109 0 CATTCTTCGT 0.706565 -192 ACACCTCCTTCACTTTTTTCTTATTAAAATAC 28 276 0 CACTTTTCTT 0.868772 -25 TCTTAAATACCTTTTTTACCGGTTTATGTCAA 30 33 1 CTTTTTCCGG 0.74493 -76 TAAGTTTTTCCATTTTATTCGTTATCCTTGAA 43 30 0 CATTTTTCGT 0.868772 -28 TATACCTCCCCATTCTACCCTGCTC 45 16 1 CATTCTCCTG 0.86462 -15 ****** **** Masking position 4 Map Score: 20.6638 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 125 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ATTCATAAAAAAATTAGAAAATCTTTTTCCT 1 273 0 AAATTAAAAA 0.919322 -28 AAAAAGAGGAAAAGTAAAAAACAATTGCTGC 2 21 1 AAAGTAAAAA 0.682125 -246 AAACACCTCCAAATTAGAAAATAGGCCTTCT 4 82 0 AAATTAAAAA 0.919322 -23 ACTGGTTCATAAATAAGAAAAAA 5 3 0 AAATAAAAAA 0.866651 -71 AACAAAAAGTTAATTAAAAAAAATTTTATAA 6 26 0 TAATTAAAAA 0.812817 -70 AAGTAAACTAAAAATATAAAAATTTTATGTT 10 55 0 AAAATAAAAA 0.826496 -28 GTTAAAAACAAAAATATAAAAATAAAAAT 14 9 0 AAAATAAAAA 0.826496 -197 CCAGATTTGTTAATTATAAAAA 15 2 0 TAATTAAAAA 0.812817 -100 TTGTGTTCATAAATGAAAAAATTTAAAT 15 84 1 AAATGAAAAA 0.703825 -18 TATCTGTTGGAAAAAATAAAAATTAAAA 27 8 0 AAAAAAAAAA 0.730959 -58 GATGGTATTTTAATAAGAAAAAAGTGAAGGA 28 272 1 TAATAAAAAA 0.71237 -29 AGGTTATGATTAATTAAAAAAC 33 2 0 TAATTAAAAA 0.812817 -30 TAATCAAAACAAATAAAAAAATTTTTTATAT 41 31 0 AAATAAAAAA 0.866651 -147 TTAACTGCAGAAGTTAAAAAATTACCTGAGA 41 72 0 AAGTTAAAAA 0.607237 -106 ATGGTTAAACAAAAAAGAAAAAGGTTAAAAC 41 135 1 AAAAAAAAAA 0.730959 -43 ****** **** Masking position 6 Map Score: 11.2702 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 27 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 CTTTTCCTCTTTTTTCTGAACACC 2 4 0 TTTTTTGAAC 0.921118 -263 TCAGATAATTTTGTTATGAACTGATTCATAA 4 37 1 TTGTTTGAAC 0.913949 -68 TAAATAAAGGCTGTTATGAACTGGTTCATAA 5 22 0 CTGTTTGAAC 0.805947 -52 ATCAGGATATTTTTTCTGAACAAATGGTGGT 6 72 1 TTTTTTGAAC 0.921118 -24 TGCAGAATTTTTCATCTGAGCGGGGGTTGCC 11 214 0 TTCATTGAGC 0.597416 -87 TTTTATATTTTTGTTTTTAACACGCTGTTTT 14 19 1 TTGTTTTAAC 0.755443 -187 TTTTAACACGCTGTTTTTAGCGTACTGTATT 14 33 1 CTGTTTTAGC 0.712454 -173 TTTAACATTCTTTTTTTGAGCGTTTAAAAAG 16 220 0 TTTTTTGAGC 0.959923 -41 AGTGAGCATTTTTATCTGAGCAAAAAATTTA 18 66 1 TTTATTGAGC 0.794514 -46 AAAAGTTTATTTTTCTGAGACACCATTTTC 19 10 1 TTTTTTGAGA 0.558704 -25 GTGTTGATGTTTGTTATGAGCACTATGCCCA 21 107 0 TTGTTTGAGC 0.956113 -74 CCGCCTCTGCCTCTTTTGAGCATATTCCCCC 23 11 0 CTCTTTGAGC 0.78236 -93 GTGTTTACGGTTTTGATGAGCAAACGAAGAG 28 96 1 TTTTGTGAGC 0.903533 -205 CTAATATCTGTTTTGCTTAACGAAAAAAAAT 32 31 1 TTTTGTTAAC 0.570457 -47 AAAATTTTTATTTTTGTTAGCATGTAGCTAA 37 23 1 TTTTTTTAGC 0.874471 -24 CCTTTTTCTTTTTTGTTTAACCATTAAAGTC 41 128 0 TTTTGTTAAC 0.570457 -50 ***** ***** Masking position 7 Map Score: 9.95932 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 218 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 TGGGATTGAAAGGCAATGGCGACTTTTGCA 1 223 1 AGGCAATGGC 0.988022 -78 GAAATCTGCAAGGCAATGCCTACACTAATA 20 56 1 AGGCAATGCC 0.94978 -56 TGCTCAAAAGAGGCAGAGGCGGCAATGGTT 23 20 1 AGGCAGAGGC 0.969209 -84 GACTTCCGGAAGGCACTGGCCCCTACAGGG 28 51 1 AGGCACTGGC 0.992223 -250 TATGTAGCTCAGGCACTGGGGCACTCAATT 38 62 1 AGGCACTGGG 0.966947 -114 TAATGATTAAAGGCAGTGGCTTTTAAAGCC 39 174 1 AGGCAGTGGC 0.992223 -102 ********** Masking position 5 Map Score: 6.47339 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 AGAACTAAATGCGGGGGGAGGGATTCGAACCCT 11 134 1 GGGGGAGGGA 0.928176 -167 TTCATCTGAGCGGGGGTTGCCGAGCGGACAAAG 11 202 0 CGGGGGCCGA 0.975742 -99 CTACCCCACGGGGGCGACGTGGAAAAATTGGAC 13 40 0 GGGCGGTGGA 0.887004 -101 CGTCGCCCCCGTGGGGTAGCGGATATCCTGAGG 13 54 1 GGGGGGCGGA 0.993692 -87 CGGATATCCTGAGGGGCTGCGGACTCCTCGACC 13 73 1 GGGGGGCGGA 0.993692 -68 TCAACTCCCGGCGGGGGCATGGAATTTTTAATG 13 111 1 GGGGGATGGA 0.966307 -30 ATTATCATCCCGGAGGAAGTCGAGTACACCGAA 28 194 1 CGAGGGTCGA 0.863149 -107 CCACCAACAAGAGAGGAAATCGACACACTTAAA 28 227 1 GGAGGATCGA 0.898343 -74 GATTAAGGGAGGGGCCCGATAGATTTGAA 38 7 1 GGAGGCCCGA 0.90317 -169 GATTTGAACATCGAGGAGACGGATGAAGGTTAT 38 32 1 TGAGGACGGA 0.733891 -144 CAGTTCAATGATGGGGCCGCCGAGATTTGAACT 39 85 1 AGGGGGCCGA 0.936357 -191 * **** ***** Masking position 13 Map Score: 7.22973 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 220 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 TTAATGAATAAATTTGGTGGTGGATTTGCTG 2 181 0 AATTGGTGGT 0.965656 -86 CCTATTTTCTAATTTGGAGGTGTTTAG 4 88 1 AATTGGAGGT 0.89884 -17 TTTTTCTGAACAAATGGTGGTTGT 6 82 1 CAATGGTGGT 0.895669 -14 AGGATTTATGAATATTGTGGTTTAAAGGGCG 11 246 1 AAATTGTGGT 0.87679 -55 AATAGAGTTAAACAAGGTGGTGTA 12 132 1 AAAAGGTGGT 0.949082 -14 TAAATACAGAAAAAAGGTGGTAGC 16 247 1 AAAAGGTGGT 0.949083 -14 TTCAAGTACTAACAAGGTGGTATT 21 4 0 AAAAGGTGGT 0.949082 -177 GGTGGGAAAAAATTTTGAGGTGGGCATAGTG 21 87 1 AATTTGAGGT 0.605679 -94 AAAAAATTTTAAAATGGCGGTTGTAAGGGCT 32 55 1 AAATGGCGGT 0.916204 -23 GTTGAGAAGTTGATGGTGGCATATAAA 41 7 1 AATTGATGGT 0.710694 -171 ** ******** Masking position 2 Map Score: 6.15198 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 74 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 TTGACAACGCCCCAGTAGTGTACGTCGTCTG 1 95 0 CCCGTAGTGT 0.962329 -206 CCACCCAGTAGTGGTACTCCGATT 8 4 1 CCCGTAGTGG 0.986919 -165 GAGGGTCCTGTCCCGTAGGGGTTCGAGGGTT 11 161 0 TCCGTAGGGG 0.970653 -140 TCCACGTCGCCCCCGTGGGGTAGCGGATATC 13 50 1 CCCGTGGGGT 0.983259 -91 GGGTTCAACTCCCGGCGGGGGCATGGAATTT 13 107 1 CCCGCGGGGG 0.984599 -34 TGCGTTATCACCCTGTAGGGGCCAGTGCCTT 28 60 0 CCCGTAGGGG 0.994671 -241 *** ******* Masking position 5 Map Score: 4.68098 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 44 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 GGATTCGAACCCTCGAACCCCTACGGGACA 11 154 1 CCTCGAACCC 0.803665 -147 TTTGTCCGCTCGGCAACCCCCGCTCAGATG 11 203 1 CGGCAACCCC 0.950135 -98 AATTTTTCCACGTCGCCCCCGTGGGGTAGC 13 44 1 CGTCGCCCCC 0.962194 -97 CTCAGGATATCCGCTACCCCACGGGGGCGA 13 56 0 CCGCTACCCC 0.930482 -85 GTCGAGGAGTCCGCAGCCCCTCAGGATATC 13 75 0 CCGCAGCCCC 0.958565 -66 GCTGCGGACTCCTCGACCCGGGTTCAACTC 13 88 1 CCTCGACCCG 0.92608 -53 ATTAAAAATTCCATGCCCCCGCCGGGAGTT 13 113 0 CCATGCCCCC 0.791822 -28 GTTCAAATCTCGGCGGCCCCATCATTGAAC 39 87 0 CGGCGGCCCC 0.989563 -189 CTTTGGGAGCCGGTGACCCGAGTTCAAATC 39 108 0 CGGTGACCCG 0.814094 -168 CCAGGCTACCCTACGGCCCCTCTGTAATGA 39 150 1 CTACGGCCCC 0.832161 -126 ********** Masking position 8 Map Score: 4.66875 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 174 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 13 CATGCCCAATAAATTGTGTTAATGTCTCGCT 1 24 0 AAATTGGTTA 0.696181 -277 ACATCTCATAAACTTGTGTTGGACTCGGTAG 1 167 1 AACTTGGTTG 0.824532 -134 GGGATTACGTAAATTTATTTGTGGAAAGTGT 2 94 1 AAATTTTTTG 0.852745 -173 TGATTAAAATAACTTGATTTGG 4 2 0 AACTTGTTTG 0.837829 -103 AAAATTTTATAAAATGATTTGTCGTGA 6 7 0 AAAATGTTTG 0.616677 -89 TCATTTTATAAAATTTTTTTTAATTAACTTT 6 21 1 AAATTTTTTT 0.561094 -75 ACATACTTTGAAATTTATTTGAAAAAATTTC 17 77 1 AAATTTTTTG 0.852745 -74 TATAAGCTTTAAGTTGAGTTGATGATTATTA 18 34 1 AAGTTGGTTG 0.718576 -78 GAAATTGCTTTGATTAACATAT 25 39 0 AAATTGTTTG 0.942373 -12 AGGAAAATTGAGTTTGGCAAATCAA 31 5 1 AAATTGGTTT 0.766496 -68 GGAGTTCGCCGAATTGATTTGCCAAACTCAA 31 18 0 GAATTGTTTG 0.704618 -55 CGCCATTTTAAAATTTTTTTTCGTTAAGCAA 32 43 0 AAATTTTTTT 0.561094 -35 GGCATATAAAAAATTTTTTTATTTGTTTTGA 41 28 1 AAATTTTTTA 0.471509 -150 GCTGTCAAATTGGGTTGACTAAGTTTT 41 161 0 AAATTGGTTG 0.937003 -17 ****** **** Masking position 2 Map Score: 5.16025 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 53 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 14 TGGTGGTGGATTTGCTGGAGAAGAGCTTTA 2 168 0 TTTGCTGGAG 0.938332 -99 TGTTGCATAGTTTGCTGCAAAATCTTTAAT 8 43 1 TTTGCTGCAA 0.96618 -126 ATATTACTATTTTGCTGTAATTTTTAAT 25 9 0 TTTGCTGTAA 0.912845 -42 ACCTGTCAGCTTTTCTGGAACTGCAGCTCA 39 18 1 TTTTCTGGAA 0.86555 -258 TTTAAAGCCTTTTGCTGCAAACGCATTCGT 39 195 1 TTTGCTGCAA 0.96618 -81 GTAGAAAGCAGTTGCTGGAAGTGAAAGGGT 42 68 1 GTTGCTGGAA 0.938332 -20 ********** Masking position 6 Map Score: 1.31261 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 55 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 TTTGCTGCAAAATCTTTAATGGTCGTTCTG 8 53 1 AATCTTTAAT 0.415322 -116 TTGGCAGAGCAAACTTAAATTTTTTGGATA 8 88 1 AAACTTAAAT 0.858033 -81 GATACTTACACTTTAATTGCAATTAAA 10 8 1 ACACTTTAAT 0.807997 -75 TAACAAACCTAAACTTCAAGCG 12 3 0 AAACTTCAAG 0.767744 -143 TTCGTTAATACTTAAATTTTACGTAAT 14 189 0 ATACTTAAAT 0.724461 -17 CTTCTTTGAGAAACTTCAATTTTTGTTTTA 16 118 1 AAACTTCAAT 0.867514 -143 GTCAAATCAAAATCTTAAATTGAGATAAAA 17 49 0 AATCTTAAAT 0.659907 -102 CTCTGTCATAACACTTCAATAATTTAAATT 18 91 0 ACACTTCAAT 0.925673 -21 CTAATAAGAAACACTTAAATAATATCATTA 20 80 1 ACACTTAAAT 0.91997 -32 AGATTAAAATACTCTTCAATGTTTTGATTG 22 39 1 ACTCTTCAAT 0.799934 -23 GGAAATCGACACACTTAAAGAATTGGACCC 28 241 1 ACACTTAAAG 0.853008 -60 TATTGAAAACATACTTAAATTAACTTTTTT 29 135 1 ATACTTAAAT 0.724461 -31 CTCAATTTTTACACTTGAAGTAAAGAAGGA 38 85 1 ACACTTGAAG 0.641012 -91 ********** Masking position 8 Map Score: 6.99873 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 29 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548