AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_aful_reg_300.orf -o00280_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: AF0033 36 acyl carrier protein synthase (acaA-1) AF0672 27 medium-chain acyl-CoA ligase (alkK-3) 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 AF0018 22 3-ketoacyl-CoA thiolase (acaB-1) #9 AF0135 59 conserved hypothetical protein #10 AF0136 103 A. fulgidus predicted coding region AF0136 #11 AF0194 300 A. fulgidus predicted coding region AF0194 #12 AF0195 22 A. fulgidus predicted coding region AF0195 #13 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #14 AF0197 86 acetyl-CoA synthetase (acs-1) #15 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #16 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #17 AF0439 82 transcriptional regulatory protein, AsnC family #18 AF0442 300 succinoglycan biosynthesis regulator (exsB) #19 AF0481 64 proteasome, subunit beta (psmB) #20 AF0483 101 conserved hypothetical protein #21 AF0484 33 GTP cyclohydrolase II (ribA-1) #22 AF0487 57 penicillin G acylase #23 AF0495 265 A. fulgidus predicted coding region AF0495 #24 AF0496 57 conserved hypothetical transmembrane protein #25 AF0497 132 DNA polymerase B1 (polB) #26 AF0498 197 acyl-coA dehydrogenase (acd-3) #27 AF0673 155 mercuric resistance operon regulatory protein (merR) #28 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #29 AF0685 140 enoyl-CoA hydratase (fad-2) #30 AF0845 73 acyl-CoA dehydrogenase (acd-5) #31 AF0846 112 Na+/H+ antiporter (nhe2) #32 AF0932 41 conserved hypothetical protein #33 AF0933 22 branched-chain amino acid aminotransferase (ilvE) #34 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #35 AF0970 101 A. fulgidus predicted coding region AF0970 #36 AF1025_AF1026 150 AF1025: 3-hydroxyacyl-CoA dehydrogenase (hbd-4), AF1026: acyl-CoA dehydrogenase (acd-7) #37 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #38 AF1119 111 A. fulgidus predicted coding region AF1119 #39 AF1121 34 transcriptional regulatory protein, AsnC family #40 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #41 AF1141 35 acyl-CoA dehydrogenase (acd-8) #42 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #43 AF1173 180 A. fulgidus predicted coding region AF1173 #44 AF1174 61 A. fulgidus predicted coding region AF1174 #45 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #46 AF1191 32 dihydroxynaphthoic acid synthase (menB) #47 AF1192 50 conserved hypothetical protein #48 AF1195 27 activator 1, replication factor C, 53 KD subunit #49 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #50 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #51 AF1208 165 conserved hypothetical protein #52 AF1210 108 conserved hypothetical protein #53 AF1289 300 conserved hypothetical protein #54 AF1641 31 enoyl-CoA hydratase (fad-4) #55 AF1642 50 histidyl-tRNA synthetase (hisS) #56 AF2009 101 heme biosynthesis protein (nirJ-2) #57 AF2010 46 A. fulgidus predicted coding region AF2010 #58 AF2011 175 conserved hypothetical protein #59 AF2013 275 coenzyme F390 synthetase (ftsA-3) #60 AF2014 63 sugar transporter, putative #61 AF2057 35 acyl-CoA dehydrogenase (acd-10) #62 AF2216 131 methylmalonyl-CoA decarboxylase, biotin carboxyl carrier subunit (mmdC) #63 AF2219 137 methylmalonyl-CoA mutase, subunit alpha, C-terminus (mcmA2) #64 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #65 AF2244 300 acyl-CoA dehydrogenase (acd-11) #66 AF2271 177 A. fulgidus predicted coding region AF2271 #67 AF2272 87 A. fulgidus predicted coding region AF2272 #68 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #69 AF2275 63 acyl-CoA dehydrogenase (acd-12) #70 AF2277 49 DNA polymerase, bacteriophage-type #71 AF2409 42 iron-sulfur cluster binding protein #72 AF2410 43 A. fulgidus predicted coding region AF2410 #73 AF2411 41 conserved hypothetical protein #74 AF2412 39 thiamine biosynthesis protein (thiC) #75 AF2414 67 conserved hypothetical protein #76 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) #77 AF2426 85 conserved hypothetical protein #78 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 ATCAGAAAATCTTATAAGGATTGTCAA 3 6 1 AAAATTATAA 0.786259 -33 AAGGATTGTCAAAAATTTTTTAC 3 26 1 AAAATTTTTA 0.786145 -13 GTTAATTAAAAAAAATTTTATAAAATGATTTG 6 17 0 AAAATTTATA 0.871188 -79 AATTAACAACAAAAAGTTAATTAAAAAAAATT 6 32 0 AAAATTAATT 0.752742 -64 TAAATTCCTTAAAAATTTAATATTTGCTCATT 9 26 1 AAAATTAATA 0.819417 -34 GATATCACAGAAAAACTTATTTTGACAAAAAG 11 268 1 AAAATTATTT 0.623363 -33 AGTTTGCTGCAAAATCTTTAATGGTCGTTCTG 15 51 1 AAAATTTAAT 0.871189 -118 CAAAATAAAGAAAGGCTTTTATGTTGAGTAAA 15 136 1 AAAGTTTTAT 0.519882 -33 ATATTTCACGAAAACATTAAATATTACACGAC 16 47 1 AAAATTAAAT 0.819417 -33 TGGCAAACATAAAATTTTTATATTTTTAGTTT 17 50 1 AAAATTTATA 0.871189 -33 CAATAGAGAAAAAAGATTTTTAA 19 2 0 AAAATTTTTA 0.786145 -63 GTTGTTTATGAAAATTTTTTTAGTCCAAAATT 23 30 1 AAAATTTTTA 0.786258 -236 ATTATGCTTAAAAGGATTTAAAGTTTGGTGTG 25 104 0 AAAGTTTAAA 0.747943 -29 CCTAAATGCAAAAAAATTTATATAGTCCTTAG 27 48 0 AAAATTTATA 0.871062 -108 CGCACGAGAAAAAAGATTTTATATAACAAACC 28 24 0 AAAATTTTAT 0.786145 -122 TGAACATCAAAAAAGCTTTTAATTCACCTGAA 31 33 0 AAAATTTTAA 0.845748 -80 AACGGAAAAACGTTTTAAATCAGCTGAT 32 7 1 AAAATTTTAA 0.845748 -35 GTGTATCTGCAAAAGCTTTATATTGCCAGATT 35 26 0 AAAATTTATA 0.871189 -76 TTCATAAATGAAAAAATTTAAAT 35 89 1 AAAATTTAAA 0.909752 -13 ACTCCTACCGAAAAGTTTTAAATCTTTCGCAA 36 17 1 AAAATTTAAA 0.909753 -134 ATGTCAAATCAAAATCTTAAATTGAGATAAAA 36 49 0 AAAATTAAAT 0.819417 -102 CTTTGAAGACAAAGATTTTATTTTGTTTCGTT 37 22 0 AAAGTTTATT 0.57186 -172 GTAAAAAGCGAAAAGTTTTAAAAGGCTGAAAA 37 158 1 AAAATTTAAA 0.909753 -36 TTATCTGAGCAAAAAATTTAAATTATTGAAGT 38 77 1 AAAATTTAAA 0.909752 -35 AAAAGTTTATTTTTCTGAGACA 39 1 1 AAAATTATTT 0.623469 -34 GAAAAATGTTAAAAGGAGAGTTAT 42 208 0 AAAATTAAAA 0.871189 -14 ATAATTATGGAAAAGCTTAAATGGTTTGAATT 43 33 0 AAAATTAAAT 0.819417 -148 TTGTAATCTCAAAAGATTAAAATACTCTTCAA 44 26 1 AAAATTAAAA 0.871189 -36 TTTAGCTTCAAAAAAGTTAATTTAAGTATGTT 51 142 0 AAAATTAATT 0.752742 -24 GCTCAACTCTAAAACCTTTTAAACACCCTTGC 55 17 1 AAAATTTTAA 0.845748 -34 ATTTAGTTCCAAAAGGTTAAATATCTGGATGC 56 25 0 AAAATTAAAT 0.819417 -77 CCTAAATAGTAAAATTTTTATTTTTGTTAGCA 57 13 1 AAAATTTATT 0.819416 -34 GTTTGCAGCAAAAGGCTTTAAAAGCCACTGCC 59 185 0 AAAGTTTAAA 0.747943 -91 GGAAATTTAAAGAATTAAAAAGCTAAAAAT 60 44 0 AAAGTTAAAA 0.665646 -20 ACCAAAACCTTATATTTTCTGCGTG 61 21 0 AAAATTATAT 0.71165 -15 AACAATTGAAAAAGGATTTAAATAGAACACAA 65 240 0 AAAGTTTAAA 0.747943 -61 GGTGGCATATAAAAAATTTTTTTATTTGTTTT 66 25 1 AAAATTTTTT 0.458427 -153 ACAAAAAAGAAAAAGGTTAAAACTTAGTCAAC 66 143 1 AAAATTAAAA 0.871189 -35 AATAAAATGGAAAAACTTAATACAT 68 43 1 AAAATTAATA 0.819417 -15 AATACAAAAGATTTTATTAATTTTACG 69 47 0 AAAATTTTAT 0.786145 -17 **** ****** Masking position 7 Map Score: 44.101 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 107 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 2 CCTGACGGGTTGAAATCAGACCAAAATGGGATTGAAAGGCA 1 56 1 TAATAAAGGA 0.976919 -245 AAGGAACAGTTGAAATCAGACCAAAATGGGATTGAAAGTAA 1 124 1 TAATAAAGGA 0.976919 -177 GCTCCCAAGTTGAAATCAGACCAAAATGGGATTGAAAGGCA 1 197 1 TAATAAAGGA 0.976919 -104 CGGCGTTTTTTGAAATCAGACTAAAGTGGGATTACGTAAAT 2 67 1 TAATAAAGGA 0.976919 -200 TGATAAATAATTAATTAACAACAAAAAGTTAATTAAAAAAA 6 35 0 TAATAAAGTA 0.92405 -61 CACATGAGCCTGAATTTTGATGAACTGGAGACTCCTTACCA 11 149 1 TAATAAAGGA 0.976919 -152 CTTAAAAAATTGAATTATGCTCAAAGTGTGAGCA 14 4 0 TAATCAAGGA 0.8344 -83 AATTTGCTCATTAAATGTTATAAATTGGAGGTGAACT 14 60 1 TAATAAAGGG 0.8344 -27 AATGGCAATTTTAATTGCAATTAAAGTGTAAGTATC 17 6 0 TAATAAAGAA 0.92405 -77 CACAGTAAGTTGAAATCAGACCAAAATGGGATTGAAAGTGG 18 16 1 TAATAAAGGA 0.976919 -285 CGCATAACTTTGAACTTCCATCAACTTGCAATTTCATTCTC 26 51 1 TAATAAAGAA 0.92405 -147 ATTTTATCTTTAAAATTTTAAGAATCAGATATAGCCACATA 26 115 0 TAATAAAGTA 0.92405 -83 ATATCAAGTATTAATTGGAACAAATTCGGTACAGGCGGATT 34 128 1 TAATAAAGTA 0.92405 -78 ATCAAAATCTTAAATTGAGATAAAATTGCGAAAGATTTAAA 36 33 0 TAATAAAGGA 0.976919 -118 TGGTTTGAATTCAAGTACTAACAAGGTGGTATT 43 3 0 TAATAAAGTA 0.92405 -178 AACAGATAGTTAAAGTATAAGTAATGAGAAATCTCCCTGTT 49 31 1 TAATAAAGAA 0.92405 -35 CTAAATCACATAAATTGACATAAACCGGTAAAAAAGGTATT 52 38 0 TAATAAAGAA 0.92405 -71 * ** * * ** * ** Masking position 13 Map Score: 30.3311 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 28 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 AAATGGGATTGAAAGCGAGACATT 1 4 1 TGGATTGAAA 0.934125 -297 CCCATTTTGGTCTGATTTCAACCCGTCAGGA 1 55 0 TCGATTTCAA 0.92848 -246 CAGACCAAAATGGGATTGAAAGGCAGACGAC 1 72 1 TGGATTGAAA 0.934125 -229 CCCATTTTGGTCTGATTTCAACTGTTCCTTG 1 123 0 TCGATTTCAA 0.92848 -178 CAGACCAAAATGGGATTGAAAGTAAGAACAT 1 140 1 TGGATTGAAA 0.934125 -161 CCCATTTTGGTCTGATTTCAACTTGGGAGCT 1 196 0 TCGATTTCAA 0.92848 -105 CAGACCAAAATGGGATTGAAAGGCAATGGCG 1 213 1 TGGATTGAAA 0.934125 -88 CCCACTTTAGTCTGATTTCAAAAAACGCCGG 2 66 0 TCGATTTCAA 0.92848 -201 CCCATTTTGGTCTGATTTCAACTTACTGTGT 18 15 0 TCGATTTCAA 0.92848 -286 CAGACCAAAATGGGATTGAAAGTGGACGTGT 18 32 1 TGGATTGAAA 0.934125 -269 GAGTTAATCAGCTGATTTAAAACGTTTTTCC 32 14 0 GCGATTTAAA 0.864361 -28 TACGTAATGTGCCGATTTAAAAATAGATAAT 34 166 0 GCGATTTAAA 0.864361 -40 GCATTGCCTTGCAGATTTCAACAAAAGTGGA 40 44 0 GCGATTTCAA 0.892001 -68 CCCATAAGGAGGTGATTTAAATCAAATGGGA 42 168 0 GGGATTTAAA 0.888001 -54 TTTAATCTTTTGAGATTACAATGTTTAAATG 44 16 0 TGGATTACAA 0.672383 -46 TGTCAATTTATGTGATTTAGAAGATTAATCA 52 59 1 TGGATTTAGA 0.731921 -50 TTATGAAACAGGAGATTGCGAAA 72 31 1 GGGATTGCGA 0.719227 -13 GGGTCACCGATGCGATTGAAAATTATCCGAG 76 11 1 TGGATTGAAA 0.934125 -105 ** ******** Masking position 6 Map Score: 21.2779 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 139 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AAAAAAGAGGAAAAGTAAAAAACAATTGCTGC 2 20 1 AAAATAAAAA 0.759789 -247 ACTGGTTCATAAATAAGAAAAAA 5 2 0 AAATAAAAAA 0.855905 -72 AACAAAAAGTTAATTAAAAAAAATTTTATAAA 6 25 0 TAATAAAAAA 0.806005 -71 ATTGACAAAGAAAAGTTAAAAA 7 1 0 AAAATAAAAA 0.759789 -54 AAGTAAACTAAAAATATAAAAATTTTATGTTT 17 54 0 AAAAAAAAAA 0.907131 -29 GGGCTATTTTAAAAAGCAAAAACAAAGTG 19 46 1 AAAAGAAAAA 0.833805 -19 TGGATTAGTCAAAACATAAAAATTAAATAATT 22 18 1 AAAAAAAAAA 0.907131 -40 GATAAATACCTAAATGCAAAAAAATTTATATA 27 56 0 TAAAGAAAAA 0.778235 -100 GTTAAAAACAAAAATATAAAAATAAAAAT 34 8 0 AAAAAAAAAA 0.907131 -198 CCAGATTTGTTAATTATAAAAA 35 1 0 TAATAAAAAA 0.806005 -101 GTTGTGTTCATAAATGAAAAAATTTAAAT 35 83 1 TAAAGAAAAA 0.778235 -19 TGCGAAAATATAATCCAAAAAAGTAATTCACT 37 70 0 TAATCAAAAA 0.619002 -124 TATTTTCGCAAAATCTGAAAAATTTGAATGGC 37 92 1 AAATTAAAAA 0.657935 -102 TATCTGTTGGAAAAAATAAAAATTAAAA 49 7 0 AAAAAAAAAA 0.907131 -59 GATGGTATTTTAATAAGAAAAAAGTGAAGGAG 50 272 1 TAATAAAAAA 0.806005 -29 TACATGCTAACAAAAATAAAAATTTTACTATT 57 17 0 CAAAAAAAAA 0.723929 -30 TAAAGAATTAAAAAGCTAAAAATTTTATGCAA 60 35 0 AAAACAAAAA 0.792516 -29 TTAGCGGAATTAATCCGAAAAATTTTTACCTA 63 93 1 TAATCAAAAA 0.619001 -45 AACGTTTTTCAAATAATAAAAAAT 64 3 0 AAATAAAAAA 0.855905 -36 AAAATTTAAATAATCACAAAAAGAGCCTGC 65 281 1 TAATAAAAAA 0.806005 -20 TTAATCAAAACAAATAAAAAAATTTTTTATAT 66 31 0 CAAAAAAAAA 0.723929 -147 GTTTAACCATTAAAGTCAAAAATTTACCTTTC 66 113 0 TAAATAAAAA 0.688711 -65 ATGGTTAAACAAAAAAGAAAAAGGTTAAAACT 66 135 1 AAAAAAAAAA 0.907131 -43 GATAACGAATAAAATGGAAAAACTTAATACAT 68 36 1 AAAAGAAAAA 0.833805 -22 **** * ***** Masking position 8 Map Score: 19.285 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 73 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 TTCAATAAAAAAGGGGTGGTGGT 13 119 1 AGGGGGTGGT 0.792474 -13 AGAACTAAATGCGGGGGGAGGGATTCGAACCCT 18 134 1 GGGGGAGGGA 0.781748 -167 TTCATCTGAGCGGGGGTTGCCGAGCGGACAAAG 18 202 0 CGGGGGCCGA 0.973082 -99 CTACCCCACGGGGGCGACGTGGAAAAATTGGAC 29 40 0 GGGCGGTGGA 0.775252 -101 CGTCGCCCCCGTGGGGTAGCGGATATCCTGAGG 29 54 1 GGGGGGCGGA 0.986045 -87 CGGATATCCTGAGGGGCTGCGGACTCCTCGACC 29 73 1 GGGGGGCGGA 0.986045 -68 TCAACTCCCGGCGGGGGCATGGAATTTTTAATG 29 111 1 GGGGGATGGA 0.87992 -30 ATTATCATCCCGGAGGAAGTCGAGTACACCGAA 50 194 1 CGAGGGTCGA 0.916541 -107 CCACCAACAAGAGAGGAAATCGACACACTTAAA 50 227 1 GGAGGATCGA 0.781299 -74 AATTTCCGAAATGGGGGTGCCGGGAATAAACAC 53 234 0 AGGGGGCCGG 0.782349 -67 GATTAAGGGAGGGGCCCGATAGATTTGAA 58 7 1 GGAGGCCCGA 0.770794 -169 CAGTTCAATGATGGGGCCGCCGAGATTTGAACT 59 85 1 AGGGGGCCGA 0.957929 -191 CTGAGAGAGAAGGAGGGAGTGGTTGAGCTCAGG 62 68 1 AGAGGGTGGT 0.650556 -64 CCGCCTCAGGCTGAGGCGGTGGAGAAGGTCTTT 65 61 0 CGAGGGTGGA 0.916541 -240 TGAAAATTATCCGAGGGAGCCGAAGGTTTGGGA 76 27 1 CGAGGGCCGA 0.946292 -89 GGAGAAGATTGAGAGGAAGGCGTATGTGGATTA 76 57 1 GGAGGGGCGT 0.738312 -59 * **** ***** Masking position 6 Map Score: 11.1461 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 461 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 6 TTAAACGGTTAAAGCTTAATGAATAAATTTGGTGGTG 2 190 0 AATTAATAAA 0.884265 -77 CCAAACGCCCAAACCTTAAATACCAAACCGCCCATCG 2 233 1 AATTAAAAAA 0.860302 -34 ATTAACAACAAAAAGTTAATTAAAAAAAATTTTATAA 6 26 0 AATTAATAAA 0.884265 -70 GTTGTTAATTAATTATTTATCAGGATATTTTTTCTGA 6 54 1 AATTTATAAA 0.752964 -42 GTAACAATTATTAATGAGCAAATATTAAATTT 9 38 0 AATTAATAAA 0.884265 -22 AATTTTACGAAACATTTATTGAACATAACAATTAATC 10 71 1 AATTATTAAA 0.752972 -33 AGTATTCATAAATACTTTATCATCATAAATAAACAAA 13 67 0 AATTTATAAA 0.752964 -65 ACTCATACGAAATTATTATTCAATAAAAAAGGGGTGG 13 101 1 AATTATTAAA 0.752972 -31 AGCATAATTCAATTTTTTAAGATGATAATGAATTTAA 14 24 1 AATTTAAAAA 0.710715 -63 TCCAATTTATAACATTTAATGAGCAAATTTAAATTCA 14 52 0 AATTAATAAA 0.884265 -35 TATTTCACGAAAACATTAAATATTACACGACTACTTT 16 48 1 AATTAAAAAA 0.860302 -32 CTGATTCTTAAAATTTTAAAGATAAAATTTGTTTTGA 26 128 1 AATTAAAAAA 0.860302 -70 AACATTAAGTAAAGGTTATATACCAAATCTAGAACCT 26 166 1 AATTATAAAA 0.710718 -32 GCACGAGAAAAAAGATTTTATATAACAAACCTAAACT 28 18 0 AATTTTAAAA 0.494988 -128 CTTTAATGTCAATAATTAATTACGAGAGCAAATGAAA 34 67 1 AATTAATAAA 0.884265 -139 CTGAGATATTAAATTTTAATCAAAACAAATAAAAAAA 66 41 0 AATTAATAAA 0.884265 -137 TTTTGACTTTAATGGTTAAACAAAAAAGAAAAAGGTT 66 124 1 AATTAAAAAA 0.860302 -54 AACTTTTTTACACCATAAGTTCAAGGA 68 1 1 AATTTTAAAA 0.494988 -57 ** ***** * * * Masking position 7 Map Score: 16.8908 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 11 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 GTCAGATAATTTTGTTATGAACTGATTCAT 4 36 1 TTTGTTATGA 0.81033 -69 GATTTGTTTATTTATGATGATAAAGTATTT 13 65 1 TTTATGATGA 0.735959 -67 AATTCAATTTTTTAAGATGATAATGAATTT 14 29 1 TTTAAGATGA 0.449258 -58 AAAGCCTTTCTTTATTTTGAGTGGTTTGAA 15 125 0 TTTATTTTGA 0.828354 -44 AAGAAAGGCTTTTATGTTGAGTAAATAAAG 15 143 1 TTTATGTTGA 0.86958 -26 AAAGATAAAATTTGTTTTGACAACATTAAG 26 145 1 TTTGTTTTGA 0.910872 -53 CTTCGTATGCTTTGTATTGATTAGTACGCA 28 52 0 TTTGTATTGA 0.646826 -94 AATTTAAGATTTTGATTTGACATACTTTGA 36 58 1 TTTGATTTGA 0.749434 -93 CAATATAAGCTTTAAGTTGAGTTGATGATT 38 31 1 TTTAAGTTGA 0.661169 -81 TGTGTTGATGTTTGTTATGAGCACTATGCC 43 109 0 TTTGTTATGA 0.81033 -72 ACCGTTAACTTTTGTGTTGATGTTTGTTAT 43 121 0 TTTGTGTTGA 0.933861 -60 TTCTGGCAGCTTGGTTTTGATAAACTCAAC 53 267 0 TTGGTTTTGA 0.598524 -34 AATTTTTTTATTTGTTTTGATTAAAATTTA 66 39 1 TTTGTTTTGA 0.910872 -139 GTTGAAAAGGTTTATGTTGATGCTGCAAGA 71 15 1 TTTATGTTGA 0.86958 -28 ********** Masking position 10 Map Score: 8.6909 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 35 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GTCAGTTGTTGTTCGGGGGAAAACGGTAACTTC 13 21 0 GTCGGGAAAA 0.870479 -111 ATCTTTGCCAGAGGTCGGGAAAACCTCCGATAA 42 114 1 GGGCGGAAAA 0.897353 -108 GTTATATAGTCAGGTGGGAAAAAATTTTGAGGT 43 75 1 CGGGGGAAAA 0.946919 -106 AAAAAATTTTGAGGTGGGCATAGTGCTCATAAC 43 93 1 GGGGGGATAG 0.956495 -88 CTCCGGGCAGGGAAAAATGTACTGGAA 46 16 0 GGCGGGAAAA 0.977591 -17 AGACGTGGATGTTGTGGGCATAAGTCTTCACAG 53 59 1 GTGGGGATAA 0.887354 -242 CGAAATGGGGGTGCCGGGAATAAACACTTCATC 53 228 0 GGCGGGATAA 0.96753 -73 CATCATTGAACTGGCGGGAAAACCGTTTTTTAA 59 65 0 CGGGGGAAAC 0.806502 -211 AATGCCCACAGCGGCGGGTAAAACCCT 65 5 0 GGGGGGAAAA 0.986818 -296 CATTTTAAAGGAGGAGGGTATAGAAGAGCTGTT 65 95 0 GGGGGGATAG 0.956495 -206 GAGCAGGGTAGAATGGGGAGGTA 78 18 0 GGCGGGAGAA 0.930667 -13 * ** *** **** Masking position 10 Map Score: 6.08603 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 148 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 GTTTTTGCCGGCGTTTTTTGAAATCAGACTA 2 59 1 GCGTTTTTGA 0.77297 -208 GTTCATAACAGCCTTTATTTAGCACTCATCT 5 32 1 GCCTTTTTTA 0.961449 -42 TTTCAAAGCTTTTCTTGAGGTT 12 8 1 GCTTTTTTGA 0.696711 -15 CAACATAAAAGCCTTTCTTTATTTTGAGTGG 15 131 0 GCCTTTTTTA 0.961449 -38 TTTTGCCTTTATTTACTCAACATAA 15 154 0 GCCTTTTTTA 0.961449 -15 ACTAACTGTTGCCTCTCTTTAAAATTCACTT 28 79 0 GCCTCTTTTA 0.953642 -67 GTTGTCTGCCACTATTTAACTGCCCTAC 30 8 1 GCCACTTTTA 0.764311 -66 TGCCGCCTCTGCCTCTTTTGAGCATATTCCC 45 13 0 GCCTCTTTGA 0.944345 -91 TTGCCTTTGCGCCTTTTTTTAAACT 74 25 1 GCCTTTTTTA 0.961449 -15 ****** **** Masking position 6 Map Score: 5.91659 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TTCTTTGGGCTGATGGAGCAGAAGCTCCATC 11 68 1 TATGGAGCAG 0.621054 -233 GTAGAAGGTGGATTTCAAAGTTA 18 288 0 AAAGGTGGAT 0.46581 -13 ATAGAGTTAAACAAGGTGGTGTA 28 133 1 AAAGGTGGTG 0.764986 -13 GTAAGAATTATAAAGGAGGATTCCAAATATG 36 117 1 TAAGGAGGAT 0.825446 -34 AAAATTACCCATAAGGAGGTGATTTAAATCA 42 175 0 AAAGGAGGTG 0.901531 -47 AAGAAAAAAGTGAAGGAGGTGTATT 50 286 1 TAAGGAGGTG 0.946388 -15 GAAGCTCGTTTAAACGAGGTGTGGCTGATAT 51 67 1 TAACGAGGTG 0.859698 -99 ATAGATTTGAACATCGAGGAGACGGATGAAG 58 29 1 AATCGAGGAG 0.578572 -147 TAAAGAAGGATAAAGGAGCAGGCAGTCTTGT 58 105 1 TAAGGAGCAG 0.879732 -71 GTTGGCATTTTAAAGGAGGAGGGTATAGAAG 65 102 0 TAAGGAGGAG 0.971457 -199 CTTGAAGTGGTGAAGGTGGAGGAGCTTGCTG 65 153 0 TAAGGTGGAG 0.923668 -148 TATCATGAGTTTAACGAGGAGCAATTTTTAA 65 198 0 TAACGAGGAG 0.921962 -103 * ********* Masking position 3 Map Score: 5.39094 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 716 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 TGCAAAAGTCGCCATTGCCTTTCAATCCCA 1 223 0 GCCATTGCCT 0.87666 -78 GGACCCTCAATCCTGCGCCTTTGTCCGCTC 18 184 1 TCCTGCGCCT 0.837687 -117 AACCATTGCCGCCTCTGCCTCTTTTGAGCA 45 20 0 GCCTCTGCCT 0.931098 -84 CCCTGTAGGGGCCAGTGCCTTCCGGAAGTC 50 51 0 GCCAGTGCCT 0.963038 -250 TGCAGCCATCGCCACCTCCTGCGGTGTGCG 53 21 0 GCCACCTCCT 0.963038 -280 AATTGAGTGCCCCAGTGCCTGAGCTACATA 58 62 0 CCCAGTGCCT 0.874483 -114 CGACAAGACTGCCTGCTCCTTTATCCTTCT 58 108 0 GCCTGCTCCT 0.931098 -68 GGCTTTAAAAGCCACTGCCTTTAATCATTA 59 174 0 GCCACTGCCT 0.963038 -102 AAAGACCTTCTCCACCGCCTCAGCCTGAGG 65 61 1 TCCACCGCCT 0.908681 -240 CTCTTCTATACCCTCCTCCTTTAAAATGCC 65 100 1 CCCTCCTCCT 0.783244 -201 GATGCTTTCAGCAAGCTCCTCCACCTTCAC 65 145 1 GCAAGCTCCT 0.783554 -156 TTTCGCAATCTCCTGTTTCATAAC 72 30 0 GCAATCTCCT 0.496866 -14 ********** Masking position 10 Map Score: 8.54248 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 318 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 TACAAACGTTTTTGTACTTGAAATAAAACC 20 9 0 TTTACTTGAA 0.939022 -93 GGGAACTCTATTTCAACTCGAAAAATGCAGGT 20 42 1 TTTACTCGAA 0.725544 -60 TTTGTTCCAATTAATACTTGATATATTCAATT 34 120 0 TTAACTTGAT 0.640761 -86 TTCGTTAATACTTAAATTTTACGTAA 34 190 0 TTAACTTAAA 0.54817 -16 GTTACTACTTGAACGAAACAAAA 37 2 1 TTAACTTGAA 0.939022 -192 ATAGACCCATTTTTTACTTGAAGC 41 22 1 TTTACTTGAA 0.939022 -14 TACCACCTTGTTAGTACTTGAATTCAAACCAT 43 13 1 TTAACTTGAA 0.939022 -168 GCACTCAATTTTTACACTTGAAGTAAAGAAGG 58 82 1 TTTACTTGAA 0.93902 -94 ATTTTTTATTATTTGAAAAACGTTTGC 64 6 1 TTAATTTGAA 0.524925 -33 AATGCACCGTTGAAAACTTGAAGTGGTGAAGG 65 168 0 TGAACTTGAA 0.842194 -133 TGCAGTTAATTGTTAACTTGAAAGGTAAATTT 66 94 1 TGTACTTGAA 0.842197 -84 AAAGGTAAATTTTTGACTTTAATGGTTAAACA 66 114 1 TTTACTTTAA 0.548199 -64 *** ******* Masking position 6 Map Score: 4.60517 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 10 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 GCAAAAACGATTATCGCAGCAATTGTTTTT 2 37 0 TTATCGCAGC 0.904328 -230 TATGAATTTTGCCTTGCAGCTCTATGCGTA 16 20 0 GCCTTGCAGC 0.870205 -60 GCAATTTCGCTCCTTGCAGCCCTCTACCAG 24 33 1 TCCTTGCAGC 0.966324 -25 GCAGCAGCGGTCATTGCAGCTGGAGAAATA 42 20 0 TCATTGCAGC 0.903888 -202 GATAAACAAGTTCTGTCAGCAGATACTCCC 42 142 1 TTCTGTCAGC 0.804631 -80 TCTTCCTCTTTTCTGGCAGCTTGGTTTTGA 53 277 0 TTCTGGCAGC 0.97675 -24 CCTGAAGAGTTTCTGGCTGCGGTAGCTGCG 62 26 1 TTCTGGCTGC 0.868812 -106 AGATAGCGATTTATCGCAGCTACCGCAGCC 62 40 0 TTATCGCAGC 0.904328 -92 GACGTTTTTCTTGCAGCATCAACATAA 71 26 0 TTCTTGCAGC 0.972058 -17 ********** Masking position 4 Map Score: 4.55833 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 130 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 GGGATTACGTAAATTTATTTGTGGAAAGTGT 2 94 1 AAATTTATTG 0.754005 -173 AGTTCATAACAAAATTATCTGACTTTTGATT 4 28 0 AAAATTATTG 0.912841 -77 AAAATTTTATAAAATGATTTGTCGTGA 6 7 0 AAAATGATTG 0.540157 -89 TAAAAATATAAAAATTTTATGTTTGCCATTA 17 47 0 AAAATTTTTG 0.842978 -36 GGTGGATTTCAAAGTTATATGAAGTCATCGC 18 274 0 AAAGTTATTG 0.863585 -27 ATGGAAGTTCAAAGTTATGCGAATATTCCAG 26 41 0 AAAGTTATCG 0.72801 -157 TTTTATCTTTAAAATTTTAAGAATCAGATAT 26 124 0 AAAATTTTAG 0.590756 -74 AGGACTATATAAATTTTTTTGCATTTAGGTA 27 51 1 AAATTTTTTG 0.611071 -105 CGAAATTATTAAAGTTATTTGTCTGCAATTT 31 75 0 AAAGTTATTG 0.863582 -38 ACATACTTTGAAATTTATTTGAAAAAATTTC 36 77 1 AAATTTATTG 0.754005 -74 CAGGTGGGAAAAAATTTTGAGGTGGGCATAG 43 85 1 AAAATTTTAG 0.590756 -96 TAAAATAATAACAATTATATGGCTTTAAACG 43 150 1 ACAATTATTG 0.540175 -31 GAGGCCCGAGAAAGTTATGAGGGA 45 90 1 AAAGTTATAG 0.629933 -14 TAAAAAGCTAAAAATTTTATGCAAATAAATA 60 28 0 AAAATTTTTG 0.842978 -36 CAACTTATTTAAAATTATTTGGAATGAACTT 63 27 1 AAAATTATTG 0.912811 -111 CATATAGGTAAAAATTTTTCGGATTAATTCC 63 98 0 AAAATTTTCG 0.694175 -40 CAGAAGTTAAAAAATTACCTGAGATATTAAA 66 65 0 AAAATTACTG 0.540175 -113 GATGCGATTGAAAATTATCCGAGGGAGCCGA 76 19 1 AAAATTATCG 0.815776 -97 ******** ** Masking position 5 Map Score: 9.59466 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 46 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 15 CTTTTCCTCTTTTTTCTGAACACC 2 4 0 TTTTTCTGAC 0.668724 -263 ATCAGGATATTTTTTCTGAACAAATGGTGGT 6 72 1 TTTTTCTGAC 0.668724 -24 TCAAAATAAGTTTTTCTGTGATATCCCGAAA 11 262 0 TTTTTCTGGA 0.775802 -39 CTGTTGCATAGTTTGCTGCAAAATCTTTAAT 15 42 1 GTTTGCTGAA 0.922166 -127 TAGTTCTTAGTATTTCTGTAATCTTCGTGGT 23 104 0 TATTTCTGAA 0.58524 -162 AAATATGGTTTTTTGCTGGGACTGCTTATTA 23 179 0 TTTTGCTGGA 0.891572 -87 AAAAGTTTATTTTTCTGAGACACCATTTTC 39 10 1 TTTTTCTGGA 0.775802 -25 AAAATTCCACTTTTGTTGAAATCTGCAAGGC 40 39 1 TTTTGTTGAA 0.502739 -73 TATATTACTATTTTGCTGTAATTTTTAAT 47 9 0 TTTTGCTGAA 0.947 -42 AACCTGTCAGCTTTTCTGGAACTGCAGCTCA 59 17 1 CTTTTCTGAA 0.586101 -259 TTTTAAAGCCTTTTGCTGCAAACGCATTCGT 59 194 1 TTTTGCTGAA 0.947 -82 AGGAGCAGATTTTTGCCGGAAAAGACCTTCT 65 41 1 TTTTGCCGAA 0.707972 -260 AGGTGGAGGAGCTTGCTGAAAGCATCTCAAG 65 140 0 GCTTGCTGAA 0.651409 -161 AATTAAAATAGTTTGCTGATAAGAAGTTTT 70 10 0 GTTTGCTGTA 0.578468 -40 TCAAATAGCAGATTGCTGAAATAGCTCC 77 68 1 GATTGCTGAA 0.689757 -18 ******** ** Masking position 4 Map Score: 3.55641 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 230 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548