AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_aful_reg_300.orf -o00650_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 Purged sequences: AF1449 33 pyruvate formate-lyase 2 (pflD) AF1641 31 enoyl-CoA hydratase (fad-4) 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 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #17 AF1119 111 A. fulgidus predicted coding region AF1119 #18 AF1121 34 transcriptional regulatory protein, AsnC family #19 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #20 AF1173 180 A. fulgidus predicted coding region AF1173 #21 AF1174 61 A. fulgidus predicted coding region AF1174 #22 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #23 AF1191 32 dihydroxynaphthoic acid synthase (menB) #24 AF1192 50 conserved hypothetical protein #25 AF1195 27 activator 1, replication factor C, 53 KD subunit #26 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #27 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #28 AF1208 165 conserved hypothetical protein #29 AF1210 108 conserved hypothetical protein #30 AF1446 63 A. fulgidus predicted coding region AF1446 #31 AF1448 114 transcriptional regulatory protein, AsnC family #32 AF1461 87 iron-sulfur cluster binding protein, putative #33 AF1462 136 A. fulgidus predicted coding region AF1462 #34 AF1642 50 histidyl-tRNA synthetase (hisS) #35 AF1665 147 ornithine cyclodeaminase (arcB) #36 AF1667 158 sulfate adenylyltransferase (sat) #37 AF1669 48 adenylylsulfate reductase, subunit B (aprB) #38 AF1671 64 coenzyme F390 synthetase (ftsA-2) #39 AF1695 50 thiamine biosynthesis protein (apbA) #40 AF1696 28 small multidrug export protein (qacE) #41 AF1697 49 conserved hypothetical protein #42 AF1699 102 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #43 AF1720 182 acetolactate synthase, large subunit (ilvB-1) #44 AF1778 105 stage V sporulation protein (spoVG) #45 AF1779 57 2-hydroxyacid dehydrogenase, putative #46 AF2009 101 heme biosynthesis protein (nirJ-2) #47 AF2010 46 A. fulgidus predicted coding region AF2010 #48 AF2011 175 conserved hypothetical protein #49 AF2013 275 coenzyme F390 synthetase (ftsA-3) #50 AF2014 63 sugar transporter, putative #51 AF2100 106 acetolactate synthase, large subunit (ilvB-4) #52 AF2271 177 A. fulgidus predicted coding region AF2271 #53 AF2272 87 A. fulgidus predicted coding region AF2272 #54 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #55 AF2426 85 conserved hypothetical protein #56 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 TAAAAAAATTAGAAAATCTTTTTCCTCTTGCC 1 267 0 AAAAACTTTT 0.891863 -34 GTAAAAAATTTTTGACAATCCTT 3 26 0 TAAAATTTTT 0.875893 -13 CAAATCATTTTATAAAATTTTTTTTAATTAAC 6 17 1 TTAAATTTTT 0.900733 -79 AATTTTTTTTAATTAACTTTTTGTTGTTAATT 6 32 1 ATTAATTTTT 0.795012 -64 GCAGAGCAAACTTAAATTTTTTGGATATATAG 8 91 1 CTAAATTTTT 0.888858 -78 TAATGGCAAACATAAAATTTTTATATTTTTAG 10 47 1 CTAAATTTTT 0.888858 -36 GGTTTGTTATATAAAATCTTTTTTCTCGTGCG 12 24 1 AAAAACTTTT 0.891863 -122 AATCTGGCAATATAAAGCTTTTGCAGATACAC 15 26 1 TTAAACTTTT 0.919834 -76 ATTTAAATTTTTTCATTTATGAA 15 89 0 TTAAATTTTT 0.900733 -13 TTGCGAAAGATTTAAAACTTTTCGGTAGGAGT 16 17 0 TTAAACTTTT 0.919834 -134 ACTTCAATAATTTAAATTTTTTGCTCAGATAA 17 77 0 TTAAATTTTT 0.900733 -35 TGTCTCAGAAAAATAAACTTTT 18 1 0 AATAACTTTT 0.793074 -34 AATTCAAACCATTTAAGCTTTTCCATAATTAT 20 33 1 ATTAACTTTT 0.830626 -148 TATGCCCACCTCAAAATTTTTTCCCACCTGAC 20 83 0 TAAAATTTTT 0.875893 -98 TTGAAGAGTATTTTAATCTTTTGAGATTACAA 21 26 0 TTTAACTTTT 0.841332 -36 AACATACTTAAATTAACTTTTTTGAAGCTAAA 28 142 1 ATTAATTTTT 0.795012 -24 TCGCTCAACTCTAAAACCTTTTAAACACCCTT 34 15 1 CAAAACTTTT 0.887687 -36 AAAATTGAATAGAAAAATTTTTCTTACAGCAT 35 75 1 AAAAATTTTT 0.867187 -73 GTAGAAAATTTTTTGAACTCCTTT 36 3 1 AAAAATTTTT 0.819618 -156 AGCTCTAAAATTTTTCTTTTTTCTA 38 4 1 TTAAATTTTT 0.900739 -61 AGGCAATGCAATAAAAACTTTTAGATTTAGAA 38 31 0 AAAAACTTTT 0.892396 -34 GCAGTTTTCCCAATAAACTTTTGGTTTCGTAA 41 15 0 CATAACTTTT 0.785062 -35 TTTTTAGCTTTCAAAACCTTTTCCGTTAATTT 42 51 1 TAAAACTTTT 0.899674 -52 AAACCTTTTCCGTTAATTTTTTATTCTTTTAA 42 64 1 CTTAATTTTT 0.787054 -39 CCTGGGCGAACCAAAACTTTTTAAAGCGCATG 43 68 1 CAAAATTTTT 0.862077 -115 GGCTTTTGCTTCAAAACCTTTTTATCTTTTCT 45 21 1 TAAAACTTTT 0.899674 -37 GCATCCAGATATTTAACCTTTTGGAACTAAAT 46 25 1 ATTAACTTTT 0.830626 -77 GGCCTAAATAGTAAAATTTTTATTTTTGTTA 47 10 1 ATAAATTTTT 0.893528 -37 TATTTATTTGCATAAAATTTTTAGCTTTTTAA 50 28 1 CTAAATTTTT 0.888858 -36 GGTGGCATATAAAAAATTTTTTTATTTGTTTT 52 25 1 AAAAATTTTT 0.49125 -153 GTTGACTAAGTTTTAACCTTTTTCTTTTTTGT 52 143 0 TTTAACTTTT 0.841332 -35 ATGTATTAAGTTTTTCCATTTTATT 54 43 0 TTTAATTTTT 0.807452 -15 * **** ***** Masking position 6 Map Score: 44.7533 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 157 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 2 CAAGCGTGGCAAGAGGAAAAAGATTTTCTAA 1 260 1 AAGAGAAAAA 0.909221 -41 AAAAAAGAGGAAAAGTAAAAAACAATTGCTG 2 20 1 AAAAGAAAAA 0.944954 -247 ACTGGTTCATAAATAAGAAAAAA 5 3 0 AAATAGAAAA 0.676789 -71 ATTGACAAAGAAAAGTTAAAAA 7 2 0 AAAAGTAAAA 0.856196 -53 AGTAAACTAAAAATATAAAAATTTTATGTTT 10 54 0 AAATAAAAAA 0.860325 -29 ACAAAAATATAAAAATAAAAAT 14 2 0 AAAAAAAAAA 0.932171 -204 ACAGCGTGTTAAAAACAAAAATATAAAAATA 14 16 0 AAAAAAAAAA 0.932171 -190 TTGTGTTCATAAATGAAAAAATTTAAAT 15 84 1 AAATGAAAAA 0.884977 -18 ATCTGTTGGAAAAAATAAAAATTAAAA 26 7 0 AAAAAAAAAA 0.932171 -59 AAAGGTATTTAAGAGAGAAAAATCTGCCGTT 29 16 0 AAGAGGAAAA 0.772982 -93 GAAAGTTTTTAAGAGGGAAAAATCCAATTAC 30 26 1 AAGAGGAAAA 0.772982 -38 TACCGCAAAAAAAAAAAAAAACGAACAGGAG 33 56 0 AAAAAAAAAA 0.932171 -81 TAGATTTAGAAAAAAGAAAAATTTTAGAGCT 38 11 0 AAAAAAAAAA 0.932171 -54 GGATGCTTAAAAGAATAAAAAATTAACGGAA 42 71 0 AAGAAAAAAA 0.889114 -32 TCCTTTAGAAAAGAAGTAAAAGCTGTACTAC 43 145 0 AAGAATAAAA 0.73552 -38 TTGAACCCAGAAAAGATAAAAAGGTTTTGAA 45 30 0 AAAAGTAAAA 0.856196 -28 GGCCTAAATAGTAAAATTTTTATTTT 47 6 1 AAATATAAAA 0.681153 -41 ACATGCTAACAAAAATAAAAATTTTACTATT 47 17 0 AAAAAAAAAA 0.932171 -30 TCTTTACTTCAAGTGTAAAAATTGAGTGCCC 48 80 0 AAGTGAAAAA 0.817817 -96 TAAAGAATTAAAAAGCTAAAAATTTTATGCA 50 36 0 AAAAGTAAAA 0.856196 -28 TAATCAAAACAAATAAAAAAATTTTTTATAT 52 31 0 AAATAAAAAA 0.860325 -147 TGGTTAAACAAAAAAGAAAAAGGTTAAAACT 52 136 1 AAAAAAAAAA 0.932171 -42 ATAACGAATAAAATGGAAAAACTTAATACAT 54 37 1 AAATGAAAAA 0.884977 -21 ***** ***** Masking position 8 Map Score: 30.9404 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 66 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 TAATGTCTCGCTTTCAATCCCATTT 1 2 0 CTTTAATCCT 0.98101 -299 CGTCGTCTGCCTTTCAATCCCATTTTGGTCTGAT 1 70 0 CTTTAATCCT 0.98101 -231 GATGTTCTTACTTTCAATCCCATTTTGGTCTGAT 1 138 0 CTTTAATCCT 0.98101 -163 TCGCCATTGCCTTTCAATCCCATTTTGGTCTGAT 1 211 0 CTTTAATCCT 0.98101 -90 GTAAGTTCTCTTTTTAATAACGATAATTGACAAA 7 24 0 TTTTAATACT 0.77063 -31 TACACGTCCACTTTCAATCCCATTTTGGTCTGAT 11 30 0 CTTTAATCCT 0.98101 -271 AGTCATCGCCCTTTAAACCACAATATTCATAAAT 11 249 0 CTTTAACACT 0.701153 -52 TGTTGCCTCTCTTTAAAATTCACTTCGTATGCTT 12 70 0 CTTTAAATCT 0.774259 -76 TTGTTTAACTCTATTAATCCCTCTATATAAACAT 12 113 0 CTATAATCCT 0.78705 -33 GGGCATGGAATTTTTAATGTCAATAA 13 125 1 TTTTAATTCT 0.885362 -16 GATACACTCATTTTAAATATCAATCAACATTAGT 15 51 1 TTTTAATTCT 0.885362 -51 TTTAAGTATGTTTTCAATATCATTACATATCATT 28 120 0 TTTTAATTCT 0.885362 -46 GATTTTTCTCTCTTAAATACCTTTTTTACCGGTT 29 23 1 TCTTAATCCT 0.754145 -86 CTCTAAAACCTTTTAAACACCCTTGCCGAAGCTT 34 23 1 TTTTAACCCT 0.918777 -28 GTAGAAAATTTTTTGAACTCCTTTGCCTTTTATT 36 11 1 TTTTAACCCT 0.918777 -148 AATTGCGCGGTTTTGAATGTCTTTGAAAATTCGA 36 60 1 TTTTAATTCT 0.885362 -99 TAAAAAAATATTTTAAATGCCGATTCTGGTTGAA 42 23 0 TTTTAATCCT 0.966586 -80 ATTTTTTTAGCTTTCAAAACCTTTTCCGTTAATT 42 48 1 CTTTAAACCT 0.927781 -55 CAGCAAAAGGCTTTAAAAGCCACTGCCTTTAATC 49 178 0 CTTTAAACCT 0.927781 -98 **** *** ** * Masking position 4 Map Score: 27.4503 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 54 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 TGCCTTTCAATCCCATTTTGGTCTGATTTCAACCCGTCAGGA 1 55 0 TCTTTATTAA 0.982743 -246 TTACTTTCAATCCCATTTTGGTCTGATTTCAACTGTTCCTTG 1 123 0 TCTTTATTAA 0.982743 -178 TGCCTTTCAATCCCATTTTGGTCTGATTTCAACTTGGGAGCT 1 196 0 TCTTTATTAA 0.982743 -105 ATTTACGTAATCCCACTTTAGTCTGATTTCAAAAAACGCCGG 2 66 0 TCTTTATTAA 0.982743 -201 TTTTTTTAATTAACTTTTTGTTGTTAATTAATTATTTATCAG 6 35 1 TCTTTATTAT 0.948141 -61 GATACTTACACTTTAATTGCAATTAAAATTGCCATTT 10 6 1 TCTTTATTAA 0.982733 -77 CCACTTTCAATCCCATTTTGGTCTGATTTCAACTTACTGTGT 11 15 0 TCTTTATTAA 0.982743 -286 AATCCGCCTGTACCGAATTTGTTCCAATTAATACTTGATATA 14 127 0 TCTTTATTAT 0.948141 -79 TTTAAATCTTTCGCAATTTTATCTCAATTTAAGATTTTGATT 16 33 1 TCTTTATTAA 0.982743 -118 AATACCACCTTGTTAGTACTTGAATTCAAACCAT 20 3 1 TCTTTATTAA 0.982743 -178 AACAGGGAGATTTCTCATTACTTATACTTTAACTATCTGTTG 26 30 0 TCTTTATTAA 0.982743 -36 AATACCTTTTTTACCGGTTTATGTCAATTTATGTGATTTAGA 29 38 1 TCTTTATTAT 0.948141 -71 GGTTGGATTGTAACACTTTCATTGTAAATAAAGTTTACCTTA 31 83 0 TCTTTAATAA 0.858363 -32 * * ** * * ** ** Masking position 16 Map Score: 24.4587 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 5 CTTTCAATCCCATTTTGGTCTGATTTCAACCC 1 62 0 CATTTGTCTG 0.984343 -239 CTTTCAATCCCATTTTGGTCTGATTTCAACTG 1 130 0 CATTTGTCTG 0.984343 -171 CTTTCAATCCCATTTTGGTCTGATTTCAACTT 1 203 0 CATTTGTCTG 0.984343 -98 TTTACTTTTCCTCTTTTTTCTGAACACC 2 7 0 CTTTTTTCTG 0.817472 -260 TACGTAATCCCACTTTAGTCTGATTTCAAAAA 2 73 0 CATTTATCTG 0.890764 -194 CAAAAAATTTAAGTTTGCTCTGCCAATAGTCC 8 82 0 AATTTGTCTG 0.792829 -87 CTTTCAATCCCATTTTGGTCTGATTTCAACTT 11 22 0 CATTTGTCTG 0.984343 -279 CCTCCCCCCGCATTTAGTTCTGTTCGTTGAGT 11 123 0 CATTAGTCTG 0.860872 -178 AAATCTTTCGCAATTTTATCTCAATTTAAGAT 16 36 1 CATTTTTCTC 0.828742 -115 TTAGAGTGAGCATTTTTATCTGAGCAAAAAAT 17 62 1 CATTTTTCTG 0.97849 -50 TTTTCCAGTACATTTTTCCCTGCCCGGAG 23 14 1 CATTTTCCTG 0.954422 -19 ACACCTCCTTCACTTTTTTCTTATTAAAATAC 27 276 0 CATTTTTCTT 0.852014 -25 AAAGATAAAACAATTTTGCCTGCCCTTCGAGA 35 28 1 CATTTTCCTG 0.954422 -120 TTTTTCTATTCAATTTTTCCTTCAATAGATGC 35 60 0 CATTTTCCTT 0.725988 -88 ** **** **** Masking position 5 Map Score: 19.0603 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 44 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 AAATGGGATTGAAAGCGAGAC 1 2 1 AATGGGATTG 0.985296 -299 ATCAGACCAAAATGGGATTGAAAGGCAGAC 1 70 1 AATGGGATTG 0.985296 -231 ATCAGACCAAAATGGGATTGAAAGTAAGAA 1 138 1 AATGGGATTG 0.985296 -163 ATCAGACCAAAATGGGATTGAAAGGCAATG 1 211 1 AATGGGATTG 0.985296 -90 ATCAGACCAAAATGGGATTGAAAGTGGACG 11 30 1 AATGGGATTG 0.985296 -271 CCTTCGAAGTAATTGGATTTTTCCCTCTTA 30 35 0 AATTGGATTT 0.703355 -29 GCTGTCAAATTGGGTTGACTAAGTTTT 52 161 0 AATTGGGTTG 0.849048 -17 ********** Masking position 2 Map Score: 11.0882 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 22 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ATGGGATTGAAAGGCAGACGACGTACACTAC 1 81 1 AAGGCAACGA 0.817229 -220 ATGGGATTGAAAGGCAATGGCGACTTTTGCA 1 222 1 AAGGCATGGC 0.987792 -79 CGAGCGGACAAAGGCGCAGGATTGAGGGTCC 11 184 0 AAGGCGAGGA 0.936899 -117 TGAAATCTGCAAGGCAATGCCTACACTAATA 19 55 1 AAGGCATGCC 0.955824 -57 ATGCTCAAAAGAGGCAGAGGCGGCAATGGTT 22 19 1 GAGGCAAGGC 0.944055 -85 GGACTTCCGGAAGGCACTGGCCCCTACAGGG 27 50 1 AAGGCATGGC 0.987792 -251 TCGAAAATAAAAGGCAAAGGAGTTCAAAAAA 36 19 0 AAGGCAAGGA 0.971855 -140 ATGCAGAGTTAAGGCAATGCAATAAAAACTT 38 43 0 AAGGCATGCA 0.902282 -22 AAGAAGGATAAAGGAGCAGGCAGTCTTGTCG 48 107 1 AAGGAGAGGC 0.752455 -69 GTAATGATTAAAGGCAGTGGCTTTTAAAGCC 49 173 1 AAGGCATGGC 0.987792 -103 ****** **** Masking position 2 Map Score: 10.2444 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 161 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 8 ATTAAAGATTTTGCAGCAAACTATGCAACA 8 43 0 TTGCAGCAAA 0.938917 -126 TTTTTAAAGGAAAGATTTATCTT 13 4 1 TTAAAGGAAA 0.869626 -137 ATTATTGACATTAAAGCTAAATACAGTACG 14 53 0 TTAAAGCTAA 0.713091 -153 ATTAAAAATTACAGCAAAATAGTAATAT 24 9 1 TTACAGCAAA 0.89371 -42 GAAAAATCTGTTAAAGAAAAGGTAAATACT 28 24 0 TTAAAGAAAA 0.507966 -142 ATTAACTTTTTTGAAGCTAAATC 28 153 1 TTGAAGCTAA 0.819627 -13 GAGTAAATTGTTACCGCAAAAAAAAAAAAA 33 68 0 TTACCGCAAA 0.692539 -69 AGAGCATCTATTGAAGGAAAAATTGAATAG 35 57 1 TTGAAGGAAA 0.924232 -91 TTGAAAAGTATTAAAGTTAATGTCAAGTTT 35 114 0 TTAAAGTTAA 0.3281 -34 GAATAAAAAATTAACGGAAAAGGTTTTGAA 42 60 0 TTAACGGAAA 0.638563 -43 CTACTTACCTTTGTAGGAAA 43 1 0 TTGTAGGAAA 0.63188 -182 AGAATTTTGATTGCAGGAAACGTTAGATTA 44 37 0 TTGCAGGAAA 0.917306 -69 TAAAAAGGTTTTGAAGCAAAAGCCAAACTC 45 15 0 TTGAAGCAAA 0.944134 -43 ATTTTTACACTTGAAGTAAAGAAGGATAAA 48 89 1 TTGAAGTAAA 0.768933 -87 ACGAATGCGTTTGCAGCAAAAGGCTTTAAA 49 195 0 TTGCAGCAAA 0.938917 -81 ********** Masking position 9 Map Score: 9.75344 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 125 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 TTCTAATTTTTTTATGAATGTAGATT 1 285 1 TTTAGTTATT 0.962711 -16 ACATAAAATTTTTATATTTTTAGTTTACTTTCATAC 10 56 1 TTTAATTTTT 0.60584 -27 CGCTTGAAGTTTAGGTTTGTTATATAAAATCTTTT 12 10 1 TTTAGTTTAT 0.666304 -136 ATTTTTATTTTTATATTTTTGTTTTTAAC 14 4 1 TTTATTTTTT 0.741456 -202 ATATTCAATTTTTACGCGTTTAGATTTTTCATTTGC 14 94 0 TTTAGTTATT 0.962711 -112 ATTTAAATTTTTTCATTTATGAACACA 15 85 0 TTTAATTATT 0.749911 -17 TTTATCTCAATTTAAGATTTTGATTTGACATACTTT 16 50 1 TTTAGTTTTT 0.929745 -101 AATGATATTATTTAAGTGTTTCTTATTAGTGTAGGC 19 73 0 TTTAGTTTAT 0.666304 -39 ATTCAAACCATTTAAGCTTTTCCATAATTATCATTA 20 34 1 TTTAGTTATA 0.661457 -147 GGTCCAATTCTTTAAGTGTGTCGATTTCCTCTCTTG 27 234 0 TTTAGTTATT 0.962711 -67 GCTTTAAGGTTCTGCAGTTTTCCCAATA 41 32 0 TTTAGTTAGT 0.766033 -18 CAAAGTGGTATATAAGAATTTTGATTGCAGGAAACG 44 45 0 TATAGTTATT 0.661457 -61 AGTGTGCATTTTATGCATATTTATTTGCATAAAAT 50 10 1 TTTAGTTATT 0.962708 -54 TTTTTAGCTTTTTAATTCTTTAAATTTCC 50 45 1 TTTATTTATT 0.848364 -19 GATTATTTATTCTTTTTGATTAATCGTATTC 51 6 1 TTTATTTATT 0.848364 -101 ACTCGATTTATGATTATAATTTTAAAAAGTTT 51 85 0 TTTAGTTTTT 0.929745 -22 AAAAAATTTTTTTATTTGTTTTGATTAAAATTTAAT 52 35 1 TTTATTTATT 0.848364 -143 ATGTATTAAGTTTTTCCATTTTATTCGTTA 54 38 0 ATTAGTTATT 0.661457 -20 **** * * * *** Masking position 9 Map Score: 12.9414 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 20 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 TCCAGCAAATCCACCACCAAATTTATTCAT 2 179 1 CCACCACCAA 0.983749 -88 CTAAACACCTCCAAATTAGAAAAT 4 91 0 ACACCTCCAA 0.899697 -14 ATTTACACGTCCACTTTCAATCCCATTTTG 11 37 0 CCACTTTCAA 0.775395 -264 ACTTTGAAATCCACCTTCTAC 11 290 1 CCACCTTCTA 0.860433 -11 AGCACTATGCCCACCTCAAAATTTTTTCCC 20 90 0 CCACCTCAAA 0.899697 -91 GTACACCGAACCACCAACAAGAGAGGAAAT 27 217 1 CCACCAACAA 0.887028 -84 TCTGCTCCACCTTCGAAGTAATTGGA 30 48 0 CCACCTTCGA 0.901355 -16 TCAACTCACCTCCAACCTTTTCATA 37 34 0 TCACCTCCAA 0.899697 -15 TTCATCACTCCCACCACCAGCATGCGCTTT 43 90 0 CCACCACCAG 0.919353 -93 TTAAAACCACCTCTAACTCCTTTAGA 43 167 0 CCACCTCTAA 0.899697 -16 TTTTTATATGCCACCATCAACTTCTCAAC 52 10 0 CCACCATCAA 0.962732 -168 ********** Masking position 3 Map Score: 7.36118 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 219 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 ATGTCCTGACGGGTTGAAATCAGACCAAAAT 1 52 1 GGGTTGAATC 0.95289 -249 TCATAAACTTGTGTTGGACTCGGTAGCTCCC 1 172 1 GTGTTGGATC 0.822034 -129 GGTAGCTCCCAAGTTGAAATCAGACCAAAAT 1 193 1 AAGTTGAATC 0.657935 -108 TTGCCGGCGTTTTTTGAAATCAGACTAAAGT 2 63 1 TTTTTGAATC 0.44021 -204 GGAACACAGTAAGTTGAAATCAGACCAAAAT 11 12 1 AAGTTGAATC 0.657935 -289 AGGGGTTCGAGGGTTCGAATCCCTCCCCCCG 11 145 0 GGGTTCGATC 0.905652 -156 TCCTCGACCCGGGTTCAACTCCCGGCGGGGG 13 97 1 GGGTTCAATC 0.850132 -44 AATTCCACTTTTGTTGAAATCTGCAAGGCAA 19 41 1 TTGTTGAATC 0.836282 -71 AAGCTTAAATGGTTTGAATTCAAGTACTAAC 20 22 0 GGTTTGAATC 0.831404 -159 AATACCATCCGGGTCCAATTCTTTAAGTGTG 27 250 0 GGGTCCAATC 0.762029 -51 TTATACAATGTGGTTCGACTCTACATATCAG 28 91 0 TGGTTCGATC 0.797301 -75 GTAGAAAATTTTTTGAACTCCTTTGCCTTT 36 10 1 TTTTTGAATC 0.439691 -149 ATGCCGATTCTGGTTGAATTCTGATTCAAC 42 10 0 TGGTTGAATC 0.92789 -93 TATCTTTTCTGGGTTCAATTCTGTC 45 43 1 GGGTTCAATC 0.959933 -15 CGTCTCCTCGATGTTCAAATCTATCGGGCCC 48 22 0 ATGTTCAATC 0.713635 -154 CCGGTGACCCGAGTTCAAATCTCGGCGGCCC 49 98 0 GAGTTCAATC 0.572118 -178 ******** ** Masking position 4 Map Score: 13.385 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 116 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 ACTTTTCCTCTTTTTTCTGAACACC 2 6 0 TTTTTTCTGA 0.84865 -261 TTAGAAGGCCTATTTTCTAATTTGGAGGTG 4 80 1 TATTTTCTAA 0.812734 -25 TTTTTTCTTATTTATGAACC 5 1 1 TTTTTTCTTA 0.780988 -73 TATCAGGATATTTTTTCTGAACAAATGGTG 6 71 1 TTTTTTCTGA 0.84865 -25 TTTTACGAAATTTTTTCAAATAAATTTCAA 16 84 0 TTTTTTCAAA 0.854542 -67 ATTCTTACTATTTTTACGAAATTTTTTCAA 16 95 0 TTTTTACGAA 0.540362 -56 AAAAGTTTATTTTTCTGAGACACCATTT 18 9 1 ATTTTTCTGA 0.754874 -26 AAAGTGGAATTTTTTACTAAAAATGGTAAT 19 22 0 TTTTTACTAA 0.660436 -90 TTAATTTTTATTTTTTCCAACAGATAGTTA 26 13 1 TTTTTTCCAA 0.725768 -53 CCTCCTTCACTTTTTTCTTATTAAAATACC 27 275 0 TTTTTTCTTA 0.780988 -26 TCTTTAACAGATTTTTCGAATTGTTCAAGC 28 37 1 ATTTTTCGAA 0.836544 -129 GGAAACCGTATTTTTTCAAAAGCTCTTTCA 33 15 0 TTTTTTCAAA 0.854542 -122 GAATAGAAAAATTTTTCTTACAGCATCTCA 35 81 1 ATTTTTCTTA 0.661987 -67 CTTTGCCTTTTATTTTCGAAGAGTTTGAAA 36 31 1 TATTTTCGAA 0.724009 -128 AAAACCGCGCAATTTTCAAACTCTTCGAAA 36 44 0 AATTTTCAAA 0.475982 -115 AAGGTTTTCGAATTTTCAAAGACATTCAAA 36 71 0 AATTTTCAAA 0.475982 -88 TCATTAAAATATTTTTCGAAACCTTTATAT 36 104 1 ATTTTTCGAA 0.836544 -55 CTTTTCATACATTTTTCTAAAAAAAAATTA 37 13 0 ATTTTTCTAA 0.894369 -36 AAAATTTTTCTTTTTTCTAAATCTAAAAGT 38 17 1 TTTTTTCTAA 0.939086 -48 AGCTTTTACTTCTTTTCTAAAGGAGTTAGA 43 152 1 TCTTTTCTAA 0.661601 -31 ********** Masking position 5 Map Score: 11.6253 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 88 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 AGAACTAAATGCGGGGGGAGGGATTCGAACCCT 11 134 1 GGGGGAGGGA 0.922574 -167 TTCATCTGAGCGGGGGTTGCCGAGCGGACAAAG 11 202 0 CGGGGGCCGA 0.973745 -99 CTACCCCACGGGGGCGACGTGGAAAAATTGGAC 13 40 0 GGGCGGTGGA 0.87861 -101 CGTCGCCCCCGTGGGGTAGCGGATATCCTGAGG 13 54 1 GGGGGGCGGA 0.993162 -87 CGGATATCCTGAGGGGCTGCGGACTCCTCGACC 13 73 1 GGGGGGCGGA 0.993162 -68 TCAACTCCCGGCGGGGGCATGGAATTTTTAATG 13 111 1 GGGGGATGGA 0.963563 -30 ATTATCATCCCGGAGGAAGTCGAGTACACCGAA 27 194 1 CGAGGGTCGA 0.853276 -107 CCACCAACAAGAGAGGAAATCGACACACTTAAA 27 227 1 GGAGGATCGA 0.890687 -74 GATTAAGGGAGGGGCCCGATAGATTTGAA 48 7 1 GGAGGCCCGA 0.895837 -169 GATTTGAACATCGAGGAGACGGATGAAGGTTAT 48 32 1 TGAGGACGGA 0.717743 -144 CAGTTCAATGATGGGGCCGCCGAGATTTGAACT 49 85 1 AGGGGGCCGA 0.931368 -191 * **** ***** Masking position 13 Map Score: 5.66401 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 14 ATTGGGCATGTCCTGACGGGTTGAAATCAG 1 45 1 TCCTGACGGG 0.922095 -256 GGTTTTAAACTCTCGTCGGTCTGAGTTTTG 2 135 0 TCTCGTCGGT 0.773068 -132 TGGTTCTCGATGGGCGGTTTGGTA 2 253 0 TCTCGATGGG 0.789735 -14 GAGGGTCCTGTCCCGTAGGGGTTCGAGGGT 11 162 0 TCCCGTAGGG 0.956582 -139 TCCACGTCGCCCCCGTGGGGTAGCGGATAT 13 50 1 CCCCGTGGGG 0.901024 -91 GTAGCGGATATCCTGAGGGGCTGCGGACTC 13 69 1 TCCTGAGGGG 0.832098 -72 CGGGTTCAACTCCCGGCGGGGGCATGGAAT 13 106 1 TCCCGGCGGG 0.981311 -35 CTCCCGGATACCTCGACGGTAGCAGAGAAA 27 15 1 CCTCGACGGT 0.701165 -286 TGCGTTATCACCCTGTAGGGGCCAGTGCCT 27 61 0 CCCTGTAGGG 0.730008 -240 GAAATTATCATCCCGGAGGAAGTCGAGTAC 27 191 1 TCCCGGAGGA 0.723686 -110 CAATAGATGCTCTCGAAGGGCAGGCAAAAT 35 40 0 TCTCGAAGGG 0.925131 -108 CGAGTTCAAATCTCGGCGGCCCCATCATTG 49 90 0 TCTCGGCGGC 0.775669 -186 ********** Masking position 2 Map Score: 4.67965 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 265 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 AATCAAGTTATTTTAATCAAAAGTCAGATAA 4 14 1 TTTAATCAAA 0.927009 -91 GTTCAATCAAAACATTGAAGA 21 51 0 GTCAATCAAA 0.919935 -11 GTAATATATATGTTAATCAAAGCAATTTC 24 32 1 TTTAATCAAA 0.927494 -19 TGATTTAGAAGATTAATCAAATATAATAAGT 29 71 1 GTTAATCAAA 0.953041 -38 ATTTCGTTACTCTCAAACAAAGTGGTATATA 44 67 0 TTCAAACAAA 0.726218 -39 CATCGAATACGATTAATCAAAAAGAATAAAT 51 15 0 GTTAATCAAA 0.953041 -92 AGATATTAAATTTTAATCAAAACAAATAAAA 52 44 0 TTTAATCAAA 0.927009 -134 TGACTTTAATGGTTAAACAAAAAAGAAAAAG 52 127 1 GTTAAACAAA 0.881375 -51 * ********* Masking position 6 Map Score: 4.01787 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 10 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863