AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00071_aful_reg_100.orf -o00071_aful_100.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: AF0033 36 acyl carrier protein synthase (acaA-1) AF0672 27 medium-chain acyl-CoA ligase (alkK-3) AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) Input sequences: #1 AF0006 104 corrinoid methyltransferase protein (mtaC-1) #2 AF0008 73 oxalate/formate antiporter (oxlT-1) #3 AF0014 95 A. fulgidus predicted coding region AF0014 #4 AF0016 54 A. fulgidus predicted coding region AF0016 #5 AF0018 22 3-ketoacyl-CoA thiolase (acaB-1) #6 AF0025 300 cyanate transport protein (cynX) #7 AF0089 300 long-chain-fatty-acid--CoA ligase (fadD-1) #8 AF0135 59 conserved hypothetical protein #9 AF0136 103 A. fulgidus predicted coding region AF0136 #10 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #11 AF0197 86 acetyl-CoA synthetase (acs-1) #12 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #13 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #14 AF0439 82 transcriptional regulatory protein, AsnC family #15 AF0442 300 succinoglycan biosynthesis regulator (exsB) #16 AF0498 197 acyl-coA dehydrogenase (acd-3) #17 AF0673 155 mercuric resistance operon regulatory protein (merR) #18 AF0685 140 enoyl-CoA hydratase (fad-2) #19 AF0687 228 long-chain-fatty-acid--CoA ligase (fadD-3) #20 AF0840 125 long-chain-fatty-acid--CoA ligase (fadD-4) #21 AF0845 73 acyl-CoA dehydrogenase (acd-5) #22 AF0846 112 Na+/H+ antiporter (nhe2) #23 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #24 AF0991 260 glutaryl-CoA dehydrogenase (gcdH) #25 AF1025_AF1026 150 AF1025: 3-hydroxyacyl-CoA dehydrogenase (hbd-4), AF1026: acyl-CoA dehydrogenase (acd-7) #26 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #27 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #28 AF1141 35 acyl-CoA dehydrogenase (acd-8) #29 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #30 AF1173 180 A. fulgidus predicted coding region AF1173 #31 AF1174 61 A. fulgidus predicted coding region AF1174 #32 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #33 AF1191 32 dihydroxynaphthoic acid synthase (menB) #34 AF1192 50 conserved hypothetical protein #35 AF1195 27 activator 1, replication factor C, 53 KD subunit #36 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #37 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #38 AF1208 165 conserved hypothetical protein #39 AF1289 300 conserved hypothetical protein #40 AF1510 24 long-chain-fatty-acid--CoA ligase (fadD-6) #41 AF1512 71 conserved hypothetical protein #42 AF1513 257 A. fulgidus predicted coding region AF1513 #43 AF1641 31 enoyl-CoA hydratase (fad-4) #44 AF1642 50 histidyl-tRNA synthetase (hisS) #45 AF1768 300 dipeptide ABC transporter, permease protein (dppB) #46 AF1772 82 long-chain-fatty-acid--CoA ligase (fadD-7) #47 AF1928 142 tungsten formylmethanofuran dehydrogenase, subunit D (fwdD-2) #48 AF1932 84 long-chain-fatty-acid--CoA ligase (fadD-8) #49 AF2013 275 coenzyme F390 synthetase (ftsA-3) #50 AF2014 63 sugar transporter, putative #51 AF2057 35 acyl-CoA dehydrogenase (acd-10) #52 AF2100 106 acetolactate synthase, large subunit (ilvB-4) #53 AF2244 300 acyl-CoA dehydrogenase (acd-11) #54 AF2271 177 A. fulgidus predicted coding region AF2271 #55 AF2272 87 A. fulgidus predicted coding region AF2272 #56 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #57 AF2275 63 acyl-CoA dehydrogenase (acd-12) #58 AF2277 49 DNA polymerase, bacteriophage-type #59 AF2368 40 long-chain-fatty-acid--CoA ligase (fadD-9) #60 AF2369 33 A. fulgidus predicted coding region AF2369 #61 AF2370 170 conserved hypothetical protein #62 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) #63 AF2426 85 conserved hypothetical protein #64 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 AAACGGCCTCCTCCCCGCCGGGTGCAACGCGTAAGCGGC 7 35 0 CCCCCGGGCG 0.842994 -266 GTTTCTGTTCCTCCTCCGCCCCTTCTCAGGGGCCTTCCG 7 132 1 CCCCCCCTCG 0.996068 -169 GGAGGAAAGTCCCCCCACCCGCTGTGGCGGAAGGCCCCT 7 159 0 CCCCCCCGTG 0.562693 -142 AGCCGCCCACCGCCGCTCCCACTGTAATGTTTCTCCGAC 7 206 1 CCCCCCCGTG 0.994386 -95 CCTTTGTCCGCTCGGCAACCCCCGCTCAGATGAAAAATT 15 201 1 CCGCCCCGCG 0.997477 -100 CCAATTTTTCCACGTCGCCCCCGTGGGGTAGCGGATATC 18 42 1 CCGCCCCTGT 0.913009 -99 GGGCTGCGGACTCCTCGACCCGGGTTCAACTCCCGGCGG 18 86 1 CCCCCCGGTA 0.89093 -55 TAACCATTGCCGCCTCTGCCTCTTTTGAGCATATTCCCC 32 12 0 CCCCCCCTTG 0.988963 -92 GTTCGGTGTACTCGACTTCCTCCGGGATGATAATTTCAA 37 189 0 CCGCCCCGGG 0.994424 -112 CTGCAGCCATCGCCACCTCCTGCGGTGTGCGGTGAAGGC 39 13 0 CCCCCCGGGG 0.979565 -288 GACTTATGCCCACAACATCCACGTCTTCATCCACTGCAG 39 46 0 CCACCCCTCA 0.894264 -255 AGTGTTTATTCCCGGCACCCCCATTTCGGAAATTGTTGA 39 233 1 CCGCCCCTTG 0.985952 -68 CGCCTTACCGCTCGGCAACCCCGGCCTAACGCCTCATAG 42 23 0 CCGCCCCGCA 0.988496 -235 GAGTTCAAATCTCGGCGGCCCCATCATTGAACTGGCGGG 49 80 0 CCGCCCCTCG 0.994979 -196 GTATTTAAATCCTGCCTCCCTCATGACAGAAAGATACAC 49 241 1 CTGCCCCTGG 0.808456 -35 ATCTGCTCCTCGCAATGCCCACAGCGGCGGGTAAAACCC 53 12 0 CCATCCCGCG 0.871816 -289 AAAAGACCTTCTCCACCGCCTCAGCCTGAGGCGGAAACA 53 60 1 CCCCCCCGCA 0.990966 -241 CAAGCTCCTCCACCTTCACCACTTCAAGTTTTCAACGGT 53 156 1 CCCTCCCTCT 0.720126 -145 * ** * ** * ** * Masking position 9 Map Score: 28.0133 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 534 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 AGTTAATTAAAAAAAATTTTATAAAATGATTT 3 18 0 AAAATTTTAT 0.872561 -78 GTAAATTCCTTAAAAATTTAATATTTGCTCAT 8 25 1 TAAATTTAAT 0.787679 -35 ATTTGCTCATTAAATGTTATAAATTGGAGGTG 11 61 1 TAAATTATAA 0.605138 -26 AGTTTGCTGCAAAATCTTTAATGGTCGTTCTG 12 51 1 AAAATTTAAT 0.884634 -118 ATATTTCACGAAAACATTAAATATTACACGAC 13 47 1 AAAATTAAAT 0.846369 -33 ACTAAAAATATAAAAATTTTATGTTTGCCATT 14 48 0 TAAATTTTAT 0.768574 -35 ATCTGATTCTTAAAATTTTAAAGATAAAATTT 16 126 1 TAAATTTAAA 0.704106 -72 CAACATTAAGTAAAGGTTATATACCAAATCTA 16 165 1 TAAATTATAT 0.704953 -33 CTAAATGCAAAAAAATTTATATAGTCCTTAGT 17 47 0 AAAATTATAT 0.831607 -109 ACTAGAAGAGAAAAGTTTTTAAAAAATACTTA 20 92 1 AAAATTTTAA 0.815124 -34 AACAAAGTGGCAAATCTTATATTTTGAAAATG 21 39 1 CAAATTATAT 0.662435 -35 TGAACATCAAAAAAGCTTTTAATTCACCTGAA 22 33 0 AAAATTTTAA 0.815124 -80 TAAATCCTAATAAAGCTTTAAATTTGCTTTTA 24 74 0 TAAATTTAAA 0.704106 -187 ACTCCTACCGAAAAGTTTTAAATCTTTCGCAA 25 17 1 AAAATTTAAA 0.831037 -134 ATGTCAAATCAAAATCTTAAATTGAGATAAAA 25 49 0 AAAATTAAAT 0.846369 -102 GCTTTGAAGACAAAGATTTTATTTTGTTTCGT 26 23 0 CAAATTTTAT 0.732008 -171 GTAAAAAGCGAAAAGTTTTAAAAGGCTGAAAA 26 158 1 AAAATTTAAA 0.831037 -36 GAAAAATGTTAAAAGGAGAGTTAT 29 208 0 AAAATTAAAA 0.779425 -14 ATAATTATGGAAAAGCTTAAATGGTTTGAATT 30 33 0 AAAATTAAAT 0.846369 -148 TTGTAATCTCAAAAGATTAAAATACTCTTCAA 31 26 1 AAAATTAAAA 0.779425 -36 TTGGAAAAAATAAAAATTAAAA 36 1 0 TAAATTAAAA 0.630942 -65 AAAAGAAAGGAAAACTTTAAATAGTAATTATT 42 223 1 AAAATTAAAT 0.846369 -35 GCTCAACTCTAAAACCTTTTAAACACCCTTGC 44 17 1 AAAATTTTAA 0.815124 -34 GTGTATCTGGCAAAAATTTAATGGGCTAATCT 45 40 1 CAAATTTAAT 0.752906 -261 CCACATTTAAAAAAATTTTAATAGTTCTCACT 46 49 1 AAAATTTAAT 0.884634 -34 ATATATAAAAAAAACTTTTAATAAACACTACG 47 36 1 AAAATTTAAT 0.884634 -107 AAGCTCATGATAAACCTTAAATAATTCCAGAA 48 52 1 TAAATTAAAT 0.727175 -33 ATTAAAAAGCTAAAAATTTTATGCAAATAAAT 50 29 0 TAAATTTTAT 0.768574 -35 ACCAAAACCTTATATTTTCTGCGTG 51 21 0 AAAATTATAT 0.831607 -15 TCAACCTTAGCAAACTTTTTAAAATTATAATC 52 74 1 CAAATTTTAA 0.636628 -33 TTTAACTTGGCAAAATTTAAATAATCACAAAA 53 270 1 CAAATTAAAT 0.686435 -31 AACAAATAAAAAAATTTTTTATATGCCACCAT 54 23 0 AAAATTTTAT 0.872998 -155 ACAAAAAAGAAAAAGGTTAAAACTTAGTCAAC 54 143 1 AAAATTAAAA 0.779425 -35 AATACAAAAGATTTTATTAATTTTACG 57 47 0 AAAATTTTAT 0.872994 -17 TTTCGTAAAATTTTTAAGTTAATCACA 59 6 1 TAAATTTTAA 0.68083 -35 AAAATATTTTATCCGCGCTGTG 60 1 1 AAAATTTTAT 0.872994 -33 **** ****** Masking position 7 Map Score: 40.5079 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 80 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 3 TTTTTTCTTATTTATGAACCAGTTCATAACAGCC 2 4 1 TTTTTTTTTT 0.898257 -70 TTGTTGTTAATTAATTATTTATCAGGATATTTTTTCTGAAC 3 52 1 TTATTTTTTT 0.879043 -44 TACCTTTCGCTTTTTACTTTGAGCTAATTTTTAATAGTCGT 7 243 0 TTTTATTTTT 0.898257 -58 ACATAAAATTTTTATATTTTTAGTTTACTTTCATACT 14 56 1 TTTTATTTTT 0.898257 -27 TTGGTGTCAATTTTTAATTTTAAAAAAATTTACTATATTGA 19 195 0 TTTTATTTTT 0.898256 -34 ACAAATAACTTTAATAATTTCGTACAGCCTTTCCACATT 22 84 1 TTATATTTTT 0.879043 -29 ATTTTTATTTTTATATTTTTGTTTTTAACACGCT 23 4 1 TTTTTTTATT 0.656208 -202 TTTATAATTCTTACTATTTTTACGAAATTTTTTCAAATAAA 25 90 0 TTATATTTTT 0.879043 -61 TTTTAGTGAATTACTTTTTTGGATTATATTTTCGCAAAATC 26 66 1 TTATTTTTTT 0.879043 -128 TATTTAAGTGTTTCTTATTAGTGTAGGCATTGCCTTGCAGA 27 60 0 TTTTTTTATT 0.656208 -52 CATATAATTGTTATTATTTTACCGTTAACTTTTGTGTTGAT 30 130 0 TTATATTTTT 0.879043 -51 AACATATATATTACTATTTTGCTGTAATTTTTAAT 34 5 0 TTATATTTTT 0.879043 -46 AAATCAAAGCTTTATTATTCTCAACCAGATTGTTTCT 41 45 1 TTTTTTTCTT 0.673255 -27 AAAGTTTTCCTTTCTTTTTTGATTGATTATTATACGAATAA 42 200 0 TTTTTTTTTT 0.898257 -58 GTTTTTTAATTAATCATAACCTTATCCATTC 43 3 1 TTTTATTATT 0.656208 -29 TCTCTTCCTTTTTCTTGTTTCATGATTAGTTTCGTAACCTC 45 109 0 TTTTTTTTTT 0.898257 -192 TAAAAAAATTTTAATAGTTCTCACTCTAATTAACAAT 46 56 1 TTATATTCTT 0.629097 -27 AAAAATTTTTTTATTTGTTTTGATTAAAATTTAATATCTCA 54 36 1 TTATTTTTTT 0.879043 -142 TTTTAACCTTTTTCTTTTTTGTTTAACCATTAAAGTCAAAA 54 124 0 TTTTTTTTTT 0.898257 -54 ACAAAAGATTTTATTAATTTTACGCTATTTTTTGTGAAAGA 57 30 0 TTATATTTTT 0.879043 -34 *** ** *** ** Masking position 9 Map Score: 17.313 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 53 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 TTTTTTTTAATTAACTTTTTGTTGTTAATT 3 34 1 TTAACTTTTT 0.862552 -62 TACCAGTAAGTTCTCTTTTTAATAACGATA 4 33 0 TTCTCTTTTT 0.822664 -22 TAAAATACCTTTCGCTTTTTACTTTGAGCT 7 259 0 TTCGCTTTTT 0.856579 -42 TGAGCAAATATTAAATTTTTAAGGAATTTA 8 26 0 TTAAATTTTT 0.828822 -34 TTGAGCATAATTCAATTTTTTAAGATGATA 11 21 1 TTCAATTTTT 0.862552 -66 CAGAGCAAACTTAAATTTTTTGGATATATA 12 92 1 TTAAATTTTT 0.828822 -77 CATAAAATTTTTATATTTTTAGTTTACTTT 14 57 1 TTATATTTTT 0.734155 -26 ATTTTTATTTTTATATTTTTGTTTTTAACA 23 11 1 TTATATTTTT 0.734155 -195 TTTTACGCGTTTAGATTTTTCATTTGCTCT 23 91 0 TTAGATTTTT 0.780479 -115 ACTTGATATATTCAATTTTTACGCGTTTAG 23 107 0 TTCAATTTTT 0.862552 -99 GAAAGTTTCGTTATATTTTTTGAGGTTCAA 24 31 0 TTATATTTTT 0.734155 -230 TTTGAGAAACTTCAATTTTTGTTTTAAAGA 24 122 1 TTCAATTTTT 0.862552 -139 TTTAAAACTTTTCGCTTTTTACGAAATTAA 26 150 0 TTCGCTTTTT 0.856579 -44 ATACACCTCCTTCACTTTTTTCTTATTAAA 37 280 0 TTCACTTTTT 0.890514 -21 CATACTTAAATTAACTTTTTTGAAGCTAAA 38 144 1 TTAACTTTTT 0.862552 -22 GATTAGCCCATTAAATTTTTGCCAGATACA 45 41 0 TTAAATTTTT 0.828822 -260 TATTTAACCGTTCTCTTTTTGGGCGAGGAG 47 84 0 TTCTCTTTTT 0.822664 -59 CATAAAATTTTTAGCTTTTTAATTCTTTAA 50 38 1 TTAGCTTTTT 0.821686 -26 ********** Masking position 6 Map Score: 22.7863 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 54 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 GTGCAATCTAATTTGTTTTTAAATCCTGTAAT 6 125 0 ATTTGTTTAA 0.789682 -176 TGCGAATGCAATTTAACTTAAAGGGGCATTGG 6 161 1 ATTTACTTAA 0.870386 -140 GAAATATGAATTTTGCCTTGCAGCTCTATGCG 13 22 0 TTTTGCTTCA 0.674365 -58 TCAAAACAAATTTTATCTTTAAAATTTTAAGA 16 133 0 TTTTACTTAA 0.747548 -65 CCATCTAATGATTTATCTGACAAAATAGCGAT 17 97 0 ATTTACTGCA 0.429838 -59 TAAAGGAAAGATTTATCTTGCAAGAGTCCAAT 18 15 1 ATTTACTTCA 0.726188 -126 TGGTGTCAATTTTTAATTTTAAAAAAATTTAC 19 203 0 TTTTATTTAA 0.483183 -26 TATTAAAGTTATTTGTCTGCAATTTTGAAATT 22 68 0 ATTTGCTGAA 0.771707 -45 ATTTTTATATTTTTGTTTTTAACACGCTGTTT 23 17 1 TTTTGTTTAA 0.623443 -189 AGCGTACTGTATTTAGCTTTAATGTCAATAAT 23 51 1 ATTTACTTAA 0.870388 -155 AAAGCTTTAAATTTGCTTTTAAAGCCTCAAAT 24 63 0 ATTTGTTTAA 0.789682 -198 AAACTTCAATTTTTGTTTTAAAGACCTTTAAG 24 128 1 TTTTGTTTAA 0.623443 -133 GCAACATAAAATTTACCTTAAAGGTCTTTAAA 24 144 0 ATTTACTTAA 0.870389 -117 ATACTTTGAAATTTATTTGAAAAAATTTCGTA 25 79 1 ATTTATTGAA 0.376056 -72 AAAATAAAATCTTTGTCTTCAAAGCCCCAATT 26 30 1 CTTTGCTTAA 0.617369 -164 AGATACTCCCATTTGATTTAAATCACCTCCTT 29 162 1 ATTTGTTTAA 0.789682 -60 AATAACAATTATATGGCTTTAAACGTACTATT 30 156 1 ATATGCTTAA 0.434078 -25 GATTTAGCTTCAAAAAAGTTAAT 38 153 0 ATTTACTTAA 0.870389 -13 AAAGTCAAAAATTTACCTTTCAAGTTAACAAT 54 102 0 ATTTACTTCA 0.726188 -76 AAAGGTAAATTTTTGACTTTAATGGTTAAACA 54 114 1 TTTTGCTTAA 0.839839 -64 AACTATTTTAATTTGCCTTAAACATTAGAGCG 58 28 1 ATTTGCTTAA 0.922432 -22 ***** *** ** Masking position 8 Map Score: 14.7925 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 74 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 GTTGCACCCGGCGGGGAGGAGGCCGTTTCATC 7 46 1 GCGGGGAGGG 0.96124 -255 CGAGACCGGTGCGGGGAAATGCGATGATTCCG 7 101 0 GCGGGGAAGC 0.966955 -200 CCCACCCGCTGTGGCGGAAGGCCCCTGAGAAG 7 153 0 GTGGCGGAGC 0.628302 -148 TTCCGCCACAGCGGGTGGGGGGACTTTCCTCC 7 166 1 GCGGGTGGGG 0.873316 -135 TACAGTGGGAGCGGCGGTGGGCGGCTGACCGA 7 200 0 GCGGCGGGGC 0.927685 -101 GTTGTTGTTCGGGGGAAAACGGTAACTTCCTG 10 18 0 GGGGGAAAGG 0.813257 -114 AGAACTAAATGCGGGGGGAGGGATTCGAACCC 15 134 1 GCGGGGGAGG 0.983645 -167 GGGTTGCCGAGCGGACAAAGGCGCAGGATTGA 15 190 0 GCGGACAAGC 0.675318 -111 CTACCCCACGGGGGCGACGTGGAAAAATTGGA 18 41 0 GGGGCGAGGG 0.872912 -100 TCAACTCCCGGCGGGGGCATGGAATTTTTAAT 18 111 1 GCGGGGGAGG 0.983644 -30 TATATAATTTGCGGAGAAAAGGCTATGAGGTG 19 16 0 GCGGAGAAGG 0.83862 -213 TCGTCGGATTGGGGGCAGCAGCGGTCATTGCA 29 32 0 GGGGGCACGC 0.777387 -190 GGGGGAATATGCTCAAAAGAGG 32 1 1 GGGGGAAAGC 0.773098 -103 TTTCCGAAATGGGGGTGCCGGGAATAAACACT 39 233 0 GGGGGTGCGG 0.708192 -68 TCGAACCCACGCGGGCGAACGCCCACACGCTC 42 72 0 GCGGGCGAGC 0.958369 -186 TCATTACAGAGGGGCCGTAGGGTAGCCTGGTG 49 148 0 GGGGCCGAGG 0.894976 -128 ******* * ** Masking position 4 Map Score: 14.2327 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 281 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 TTCTAAAGATAAAAGCTGTTATGAATCAGTTCATA 1 51 0 AAAAGCTTTA 0.94267 -54 ACCAGTTCATAACAGCCTTTATTTAGCACTCATCT 2 28 1 AACAGCTTTA 0.953957 -46 ACAACCACCATTTGTTCAGAAAAAATAT 3 78 0 ACCACCTTTA 0.863734 -18 CACTACCATAAAAACCGCTTTTTGATAAAGATAGA 6 223 1 AAAACCTTTA 0.927873 -78 ACCACCACCCCTTTTTTATTGAATAATA 10 114 0 ACCACCTTTA 0.863735 -18 TACTCAACATAAAAGCCTTTCTTTATTTTGAGTGG 12 131 0 AAAAGCTTTA 0.942669 -38 CAGGTGAATTAAAAGCTTTTTTGATGTTCATGAAA 22 35 1 AAAAGCTTTT 0.600837 -78 TTGAGGCTTTAAAAGCAAATTTAAAGCTTTATTAG 24 65 1 AAAAGCATTA 0.584532 -196 GCTACCACCTTTTTTCTGTATTTAACAT 24 243 0 ACCACCTTTG 0.462373 -18 AATTCGGCGAAACACCTGTTTTCGAGAGAATCTTT 29 85 1 AACACCTTTA 0.941893 -137 CGTGTTGAATAACAGCTCTTTTGAAATTATCATCC 37 169 1 AACAGCTTTA 0.953957 -132 GCTCAACTCTAAAACCTTTTAAACACCCTTGCCGA 44 17 1 AAAACCTTAA 0.523977 -34 AACTGGCGGGAAAACCGTTTTTTAATACTGCCAGA 49 55 0 AAAACCTTTA 0.927873 -221 TTTTTGCCGGAAAAGACCTTCTCCACCGCCTCAGC 53 50 1 AAAAGATTTA 0.621295 -251 CTGAGGCGGAAACAGCTCTTCTATACCCTCCTCCT 53 85 1 AACAGCTTTA 0.953957 -216 AATACAAAAGATTTTATTAATTTTACGCTA 57 44 0 AAAAGATTTA 0.621295 -20 ****** ** * * Masking position 10 Map Score: 7.34349 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 45 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GTTGTTAATTAATTATTTATCAGGATATTT 3 54 1 AATTATTTAT 0.353074 -42 AACTTTTATCAATATTTAATCAAACGATTC 6 278 1 AATATTTAAT 0.71218 -23 ACTTTGAGCTAATTTTTAATAGTCGTCGGA 7 239 0 AATTTTTAAT 0.912252 -62 GCAAATATTAAATTTTTAAGGAATTTACAT 8 23 0 AATTTTTAAG 0.585392 -37 GTAACAATTATTAATGAGCAAATAT 8 45 0 AATTATTAAT 0.648262 -15 TTTAATGAGCAAATTTAAATTCATTATCAT 11 45 0 AAATTTAAAT 0.295352 -42 TTTGCTGCAAAATCTTTAATGGTCGTTCTG 12 53 1 AATCTTTAAT 0.475 -116 GTAGTCGTGTAATATTTAATGTTTTCGTGA 13 52 0 AATATTTAAT 0.71218 -28 GGCAAACATAAAATTTTTATATTTTTAGTT 14 51 1 AAATTTTTAT 0.476858 -32 TCCTATGCAGAATTTTTCATCTGAGCGGGG 15 220 0 AATTTTTCAT 0.486447 -81 GGGGGCATGGAATTTTTAATGTCAATAA 18 123 1 AATTTTTAAT 0.912252 -18 TATTGGTGTCAATTTTTAATTTTAAAAAAA 19 208 0 AATTTTTAAT 0.912252 -21 TAAAAGAAGGAATTTTTTATTCTGATGTGC 20 61 1 AATTTTTTAT 0.754805 -65 CTTTAATGTCAATAATTAATTACGAGAGCA 23 67 1 AATAATTAAT 0.304857 -139 CCTTATGGGTAATTTTAAATAACTCTCCTT 29 190 1 AATTTTAAAT 0.586013 -32 ATTTTGCTGTAATTTTTAAT 34 1 0 AATTTTTAAT 0.912252 -50 TTTTAATTTTTATTTTTTCCAACA 36 5 1 AATTTTTATT 0.332739 -61 TTTAAATAGTAATTATTTATCGGGAAATTC 42 238 1 AATTATTTAT 0.353074 -20 GTATCTGGCAAAAATTTAATGGGCTAATCT 45 42 1 AAAATTTAAT 0.422862 -259 ACATTTAAAAAAATTTTAATAGTTCTCACT 46 51 1 AAATTTTAAT 0.754805 -32 ATATAAAAAAAACTTTTAATAAACACTACG 47 38 1 AACTTTTAAT 0.486447 -105 AACGAGGAGCAATTTTTAATGCACCGTTGA 53 187 0 AATTTTTAAT 0.912252 -114 TAACTTGGCAAAATTTAAATAATCACAAAA 53 272 1 AAATTTAAAT 0.295352 -29 CAAATAAAAAAATTTTTTATATGCCACCAT 54 23 0 AATTTTTTAT 0.754805 -155 CTGAGATATTAAATTTTAATCAAAACAAAT 54 48 0 AAATTTTAAT 0.754805 -130 TTTCGTAAAATTTTTAAGTTAATCACAA 59 9 1 AATTTTTAAG 0.585392 -32 AAAATATTTTATCCGCGCTGTG 60 3 1 AATATTTTAT 0.422862 -31 TCCCTCGGATAATTTTCAATCGCATCGGTG 62 15 0 AATTTTCAAT 0.453649 -101 ********** Masking position 6 Map Score: 16.2506 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 44 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 9 TCTCTCCCAATTTTACGAAACATTTATTGA 9 63 1 TTTTACGAAA 0.871246 -41 AAAATTCATATTTCACGAAAACATTAAATA 13 40 1 TTTCACGAAA 0.722853 -40 TTGGCAAACTTTTTCCGAAATCTTTTTAAA 24 199 1 TTTTCCGAAA 0.950147 -62 TTCTTACTATTTTTACGAAATTTTTTCAAA 25 94 0 TTTTACGAAA 0.871246 -57 ATTTTTCAGATTTTGCGAAAATATAATCCA 26 85 0 TTTTGCGAAA 0.587003 -109 ACTTTTCGCTTTTTACGAAATTAAATAAGT 26 144 0 TTTTACGAAA 0.871246 -50 GTATTTTCCAGTACATTTTTCCC 33 4 1 TTTTCCAGTA 0.336572 -29 AAACTCAACAATTTCCGAAATGGGGGTGCC 39 246 0 ATTTCCGAAA 0.738159 -55 ACAGAAGTAATTTTCCGGTAAGATTCAACA 42 134 0 TTTTCCGGTA 0.672785 -124 CTTCTGTGGAATTTCCAAAAAAGCAAGCAT 42 157 1 ATTTCCAAAA 0.41023 -101 GAATTTCCCGATAAATAATTACT 42 245 0 TTTCCCGATA 0.627193 -13 TTAAACTTTGCCAAAAGCGCGCTGGA 47 7 1 TTTGCCAAAA 0.568533 -136 GGAGCAGATTTTTGCCGGAAAAGACCTTCT 53 42 1 TTTGCCGGAA 0.718547 -259 CATAACAATCTTTCACAAAAAATAGCGTAA 57 22 1 TTTCACAAAA 0.390795 -42 AACTTAAAAATTTTACGAAA 59 1 0 TTTTACGAAA 0.871246 -40 GAACTCTTTTCCAAAATAAAGGTAAG 61 7 1 TTTTCCAAAA 0.826372 -164 ATCCATTCATTTTTCCGGAATCGTTTACGT 61 42 0 TTTTCCGGAA 0.904639 -129 AAGAAAGAGCTTCTCCGAAAATCCATTCAT 61 62 0 TTCTCCGAAA 0.689979 -109 ********** Masking position 2 Map Score: 10.782 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 205 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 AGGCCGTTTCATCCGGAGCGGGTGACCTCA 7 65 1 ATCCGGAGCG 0.804317 -236 TCCATGCCCCCGCCGGGAGTTGAACCCGGG 18 104 0 CGCCGGGAGT 0.839199 -37 AAAGCCTCAAATCCGAAAGTTTCGTTATAT 24 45 0 ATCCGAAAGT 0.576369 -216 CCGTCGAGGTATCCGGGAGTTGT 37 4 0 ATCCGGGAGT 0.777226 -297 AGTTCTGGACTTCCGGAAGGCACTGGCCCC 37 44 1 TTCCGGAAGG 0.581532 -257 CTTGCTTTAGTGCCGAAGGTCATAAACTAC 39 102 1 TGCCGAAGGT 0.778026 -199 AACGCCTCATAGCCGGGGCTGAAT 42 5 0 AGCCGGGGCT 0.930216 -253 GATACAACAGCGCCGGGGGTGGGATTCGAA 42 99 0 CGCCGGGGGT 0.906474 -159 TAAACACCCTTGCCGAAGCTTGAGC 44 36 1 TGCCGAAGCT 0.689549 -15 TTATGCTCCCAGCCGGAGCGATAAAAAGAT 45 68 0 AGCCGGAGCG 0.934611 -233 CGGCTCCCAAAGCCGAGAGGATCACCAGGC 49 126 1 AGCCGAGAGG 0.830933 -150 AATAAAGGTAAGCCGGAACGTAAACGATTC 61 25 1 AGCCGGAACG 0.884945 -146 TATCCGAGGGAGCCGAAGGTTTGGGAGAAG 62 34 1 AGCCGAAGGT 0.897954 -82 ********** Masking position 4 Map Score: 5.00256 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 241 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 CTAAACACCTCCAAATTAGAAAA 1 92 0 AACACCTCCA 0.820995 -13 GGTCTCGTTTCTGTTCCTCCTCCGCCCCTTC 7 126 1 CTTTCCTCCT 0.666515 -175 GGGTGGGGGGACTTTCCTCCTTTCGGTCAGC 7 178 1 ACTTCCTCCT 0.850933 -123 ACCCCTACTCAATCTCCTTCTATTAGCTCT 9 10 0 AACTCCTTCT 0.871737 -94 TAACTTTGAAATCCACCTTCTAC 15 288 1 ATCACCTTCT 0.59573 -13 AGCCTTCCAGCAGCTCCTCCATCAGACTGTA 19 91 0 CACTCCTCCA 0.761027 -138 TCAGAATAAAAAATTCCTTCTTTTATTTCCG 20 55 0 AATTCCTTCT 0.706476 -71 ATTTGATTTAAATCACCTCCTTATGGGTAAT 29 172 1 AACACCTCCT 0.940017 -50 AATACACCTCCTTCACTTTTTT 37 289 0 ATCACCTCCT 0.890448 -12 TTCCGGCAAAAATCTGCTCCTCGCAATGCCC 53 31 0 AACTGCTCCT 0.870716 -270 GCTCTTCTATACCCTCCTCCTTTAAAATGCC 53 99 1 ACCTCCTCCT 0.941586 -202 TGCTTTCAGCAAGCTCCTCCACCTTCACCAC 53 147 1 AACTCCTCCA 0.916467 -154 GGTGCATTAAAAATTGCTCCTCGTTAAACTC 53 192 1 AATTGCTCCT 0.704586 -109 GCCTTTATCTTCCTCCTGTGCTTCAGA 62 99 0 ATTTCCTCCT 0.873186 -17 ** ******** Masking position 8 Map Score: 6.20756 Number of sites scoring better than the average of aligned sites = 994 Number in coding regions = 930 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 TTTATTTTGAGTGGTTTGAAGCCTATATATCCA 12 112 0 GGTTGAAGCC 0.976271 -57 TGCGGGGGGAGGGATTCGAACCCTCGAACCCCT 15 143 1 GGTTGAACCC 0.957202 -158 TGCCCCCGCCGGGAGTTGAACCCGGGTCGAGGA 18 97 0 GGGTGAACCC 0.983748 -44 AGCTCAATTGGGGCTTTGAAGACAAAGATTTTA 26 34 0 GGTTGAAGAC 0.842089 -160 CGCCGGGGGTGGGATTCGAACCCACGCGGGCGA 42 86 0 GGTTGAACCC 0.957202 -172 TGGGGCCGCCGAGATTTGAACTCGGGTCACCGG 49 96 1 GGTTGAACTC 0.933621 -180 CAGGCTGCAAGAGTTTAAAACCCATCGAATACG 52 35 0 GGTTAAACCC 0.549497 -72 GCCCACAGCGGCGGGTAAAACCCT 53 2 0 GGGTAAACCC 0.936948 -299 * * ** ****** Masking position 9 Map Score: 6.02861 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 8 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 TTGCTCATTAATAATTGTTAC 8 49 1 ATAATTGTTA 0.673084 -11 ATTTTTGATTAATTGTTATGTTCAATAA 9 86 0 TTAATTGTTA 0.909752 -18 AATTTGCTCATTAAATGTTATAAATTGGAG 11 60 1 TTAAATGTTA 0.673077 -27 AATGGCAATTTTAATTGCAATTAAAGTGTA 14 17 0 TTAATTGCAA 0.782657 -66 AAATTGCCATTTAATGGCAAACATAAAATT 14 36 1 TTAATGGCAA 0.532201 -47 AATGGTAAACTTAATTGCAAGTTTATTGCT 20 22 0 TTAATTGCAA 0.782657 -104 ATATCAAGTATTAATTGGAACAAATTCGGT 23 128 1 TTAATTGGAA 0.573257 -78 TTAAAGCCATATAATTGTTATTATTTTACC 30 148 0 ATAATTGTTA 0.673084 -33 ATTACAATGTTTAAATGTTAGC 31 3 0 TTAAATGTTA 0.673077 -59 ATCCTAATAGTTAATTGTTAAAAGTTATCC 46 20 1 TTAATTGTTA 0.909752 -63 AAATTGTCTCTTAATTGTAAAAAGCTCATG 48 31 1 TTAATTGTAA 0.865606 -54 ACTTCTGCAGTTAATTGTTAACTTGAAAGG 54 89 1 TTAATTGTTA 0.909752 -89 ATTTTTGACTTTAATGGTTAAACAAAAAAG 54 122 1 TTAATGGTTA 0.761036 -56 ********** Masking position 4 Map Score: 6.01917 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 4 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 CAATTTTAATTGCAATTAAAGTGTAAGTATC 14 11 0 TGCAATAAAG 0.544514 -72 GGAAAAAGTTTGCCAATAAAGATGTAGGATG 24 184 0 TGCCATAAAG 0.809046 -77 TTAAAAAGATTTCGGAAAAAGTTTGCCAATA 24 197 0 TTCGGAAAAG 0.735428 -64 CGAAAATATAATCCAAAAAAGTAATTCACTA 26 69 0 ATCCAAAAAG 0.654072 -125 CCTTGCAGATTTCAACAAAAGTGGAATTTTT 27 38 0 TTCAAAAAAG 0.821619 -74 AAAACCAAGCTGCCAGAAAAGAGGAAGAAAG 39 279 1 TGCCAAAAAG 0.949774 -22 TAGAAAATAATTCGAAAAAAG 41 1 0 TTCGAAAAAG 0.832557 -71 TTTTTGGAAATTCCACAGAAGTAATTTTCCG 42 147 0 TTCCAAGAAG 0.737006 -111 TCTGTGGAATTTCCAAAAAAGCAAGCATAAA 42 159 1 TTCCAAAAAG 0.942277 -99 TGAGCTGCAGTTCCAGAAAAGCTGACAGGTT 49 17 0 TTCCAAAAAG 0.942277 -259 CGAATGCGTTTGCAGCAAAAGGCTTTAAAAG 49 193 0 TGCAGAAAAG 0.748923 -83 AGCAGATTTTTGCCGGAAAAGACCTTCTCCA 53 44 1 TGCCGAAAAG 0.913581 -257 ***** ***** Masking position 9 Map Score: 5.1547 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 52 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 GATAATTGACAAAGAAAAGTTAAAAA 4 3 0 AAAAAAGAAA 0.929551 -52 TATGTTGAGTAAATAAAGGCAAAA 12 155 1 AAAAAAGAAA 0.929551 -14 AAAAACAAAAATATAAAAATAAAAAT 23 3 0 ATAAAAAAAA 0.513338 -203 AACGCTCAAAAAAAGAATGTTAAATACAGAAAAA 24 227 1 AAAGAAGAAA 0.827558 -34 TTAAATTGAGATAAAATTGCGAAAGATTTAAAAC 25 31 0 ATAAATGAAA 0.683937 -120 TAAAAGGCTGAAAAAATAGTTAAAGACA 26 176 1 AAAAATGAAA 0.90343 -18 CTGTTGGAAAAAATAAAAATTAAAA 36 2 0 AAAAAAAAAA 0.820151 -64 AAAATCTGTTAAAGAAAAGGTAAATACTACAAAT 38 18 0 AAAAAAGAAA 0.929551 -148 AATCAATCAAAAAAGAAAGGAAAACTTTAAATAG 42 213 1 AAAGAAGAAA 0.827558 -45 GAAGGCTCGAAAACGATAGTGAAAAAGAACCATG 45 207 0 AAAGATGAAA 0.772863 -94 ACAATTTATAAAACAAAAAAGAAAAAA 48 4 0 AAAAAAAAAA 0.820151 -81 TTGCCAAGTTAAACAATTGAAAAAGGATTTAAAT 53 249 0 AAAAATGAAA 0.90343 -52 GGCAAAATTTAAATAATCACAAAAAGAGCCTGC 53 278 1 AAAAATAAAA 0.763777 -23 ATTTTAATCAAAACAAATAAAAAAATTTTTTATA 54 32 0 AAAAAAAAAA 0.820151 -146 TTTAATGGTTAAACAAAAAAGAAAAAGGTTAAAA 54 131 1 AAAAAAAAAA 0.820151 -47 AGGATAACGAATAAAATGGAAAAACTTAATACAT 56 34 1 ATAAATGAAA 0.683937 -24 AATCTTTCACAAAAAATAGCGTAAAATTAATAAA 57 28 1 AAAAATGTAA 0.429029 -36 *** *** * *** Masking position 6 Map Score: 11.3238 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 49 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604