AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00071_aful_reg_300.orf -o00071_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) AF0195 22 A. fulgidus predicted coding region AF0195 AF0672 27 medium-chain acyl-CoA ligase (alkK-3) AF2243 38 3-ketoacyl-CoA thiolase (fadA-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 AF0025 300 cyanate transport protein (cynX) #10 AF0089 300 long-chain-fatty-acid--CoA ligase (fadD-1) #11 AF0135 59 conserved hypothetical protein #12 AF0136 103 A. fulgidus predicted coding region AF0136 #13 AF0194 300 A. fulgidus predicted coding region AF0194 #14 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #15 AF0197 86 acetyl-CoA synthetase (acs-1) #16 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #17 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #18 AF0439 82 transcriptional regulatory protein, AsnC family #19 AF0442 300 succinoglycan biosynthesis regulator (exsB) #20 AF0481 64 proteasome, subunit beta (psmB) #21 AF0483 101 conserved hypothetical protein #22 AF0484 33 GTP cyclohydrolase II (ribA-1) #23 AF0487 57 penicillin G acylase #24 AF0495 265 A. fulgidus predicted coding region AF0495 #25 AF0496 57 conserved hypothetical transmembrane protein #26 AF0497 132 DNA polymerase B1 (polB) #27 AF0498 197 acyl-coA dehydrogenase (acd-3) #28 AF0673 155 mercuric resistance operon regulatory protein (merR) #29 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #30 AF0685 140 enoyl-CoA hydratase (fad-2) #31 AF0687 228 long-chain-fatty-acid--CoA ligase (fadD-3) #32 AF0837 63 cell division protein pelota (pelA) #33 AF0838 27 TRK potassium uptake system protein (trkA-2) #34 AF0840 125 long-chain-fatty-acid--CoA ligase (fadD-4) #35 AF0845 73 acyl-CoA dehydrogenase (acd-5) #36 AF0846 112 Na+/H+ antiporter (nhe2) #37 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #38 AF0970 101 A. fulgidus predicted coding region AF0970 #39 AF0991 260 glutaryl-CoA dehydrogenase (gcdH) #40 AF1025_AF1026 150 AF1025: 3-hydroxyacyl-CoA dehydrogenase (hbd-4), AF1026: acyl-CoA dehydrogenase (acd-7) #41 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #42 AF1119 111 A. fulgidus predicted coding region AF1119 #43 AF1121 34 transcriptional regulatory protein, AsnC family #44 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #45 AF1141 35 acyl-CoA dehydrogenase (acd-8) #46 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #47 AF1173 180 A. fulgidus predicted coding region AF1173 #48 AF1174 61 A. fulgidus predicted coding region AF1174 #49 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #50 AF1191 32 dihydroxynaphthoic acid synthase (menB) #51 AF1192 50 conserved hypothetical protein #52 AF1195 27 activator 1, replication factor C, 53 KD subunit #53 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #54 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #55 AF1208 165 conserved hypothetical protein #56 AF1210 108 conserved hypothetical protein #57 AF1289 300 conserved hypothetical protein #58 AF1510 24 long-chain-fatty-acid--CoA ligase (fadD-6) #59 AF1512 71 conserved hypothetical protein #60 AF1513 257 A. fulgidus predicted coding region AF1513 #61 AF1514 199 A. fulgidus predicted coding region AF1514 #62 AF1641 31 enoyl-CoA hydratase (fad-4) #63 AF1642 50 histidyl-tRNA synthetase (hisS) #64 AF1768 300 dipeptide ABC transporter, permease protein (dppB) #65 AF1772 82 long-chain-fatty-acid--CoA ligase (fadD-7) #66 AF1928 142 tungsten formylmethanofuran dehydrogenase, subunit D (fwdD-2) #67 AF1932 84 long-chain-fatty-acid--CoA ligase (fadD-8) #68 AF2009 101 heme biosynthesis protein (nirJ-2) #69 AF2010 46 A. fulgidus predicted coding region AF2010 #70 AF2011 175 conserved hypothetical protein #71 AF2013 275 coenzyme F390 synthetase (ftsA-3) #72 AF2014 63 sugar transporter, putative #73 AF2057 35 acyl-CoA dehydrogenase (acd-10) #74 AF2100 106 acetolactate synthase, large subunit (ilvB-4) #75 AF2244 300 acyl-CoA dehydrogenase (acd-11) #76 AF2271 177 A. fulgidus predicted coding region AF2271 #77 AF2272 87 A. fulgidus predicted coding region AF2272 #78 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #79 AF2275 63 acyl-CoA dehydrogenase (acd-12) #80 AF2277 49 DNA polymerase, bacteriophage-type #81 AF2368 40 long-chain-fatty-acid--CoA ligase (fadD-9) #82 AF2369 33 A. fulgidus predicted coding region AF2369 #83 AF2370 170 conserved hypothetical protein #84 AF2409 42 iron-sulfur cluster binding protein #85 AF2410 43 A. fulgidus predicted coding region AF2410 #86 AF2411 41 conserved hypothetical protein #87 AF2412 39 thiamine biosynthesis protein (thiC) #88 AF2414 67 conserved hypothetical protein #89 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) #90 AF2426 85 conserved hypothetical protein #91 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 TTGACAATCCTTATAAGATTTTCTGAT 3 6 0 TTATAATTTT 0.599629 -33 AAATCATTTTATAAAATTTTTTTTAATTAACT 6 18 1 ATAAAATTTT 0.756382 -78 GAAAACTTTAACTTTTTGTCAAAATAA 13 284 0 CTTTAATTTT 0.525068 -17 CAGAACGACCATTAAAGATTTTGCAGCAAACT 16 51 0 ATTAAATTTT 0.837043 -118 GCAGAGCAAACTTAAATTTTTTGGATATATAG 16 91 1 CTTAAATTTT 0.622334 -78 TTTACTCAACATAAAAGCCTTTCTTTATTTTG 16 136 0 ATAAAACTTT 0.659337 -33 GTCGTGTAATATTTAATGTTTTCGTGAAATAT 17 47 0 ATTTAATTTT 0.775091 -33 TTAAAAATCTTTTTTCTCTATT 20 1 1 TTAAAACTTT 0.581679 -64 CACACCAAACTTTAAATCCTTTTAAGCATAAT 26 104 1 TTTAAACTTT 0.696854 -29 CAAATTTTATCTTTAAAATTTTAAGAATCAGA 27 127 0 CTTTAATTTT 0.525068 -71 ACTAAGGACTATATAAATTTTTTTGCATTTAG 28 47 1 ATATAATTTT 0.675812 -109 GGTTTGTTATATAAAATCTTTTTTCTCGTGCG 29 24 1 ATAAAATTTT 0.75652 -122 TAAGTATTTTTTAAAAACTTTTCTCTTCTAGT 34 92 0 TTAAAATTTT 0.690622 -34 CTTCAGGTGAATTAAAAGCTTTTTTGATGTTC 36 32 1 ATTAAACTTT 0.761883 -81 AAATCTGGCAATATAAAGCTTTTGCAGATACA 38 25 1 ATATAACTTT 0.564939 -77 ATTTAAATTTTTTCATTTATGAA 38 89 0 TTTAAATTTT 0.786796 -13 TTAAAAGCAAATTTAAAGCTTTATTAGGATTT 39 73 1 ATTTAACTTT 0.682205 -188 TTGCGAAAGATTTAAAACTTTTCGGTAGGAGT 40 17 0 TTTAAATTTT 0.786796 -134 TTTTATCTCAATTTAAGATTTTGATTTGACAT 40 49 1 ATTTAATTTT 0.775091 -102 TTTTCAGCCTTTTAAAACTTTTCGCTTTTTAC 41 158 0 TTTAAATTTT 0.786796 -36 ACTTCAATAATTTAAATTTTTTGCTCAGATAA 42 77 0 TTTAAATTTT 0.786796 -35 ATAACTCTCCTTTTAACATTTTTC 46 208 1 TTTTAATTTT 0.712307 -14 AATTCAAACCATTTAAGCTTTTCCATAATTAT 47 33 1 ATTTAATTTT 0.775091 -148 TTGAAGAGTATTTTAATCTTTTGAGATTACAA 48 26 0 TTTTAATTTT 0.712307 -36 AATAATTACTATTTAAAGTTTTCCTTTCTTTT 60 223 0 ATTTAATTTT 0.775091 -35 ATAATCCCAAATAAAAAGCTTTATAAAAACAA 61 30 0 ATAAAACTTT 0.659337 -170 CTTATAATATATAAAAGCCTTTTTCCGCTTTT 61 173 0 ATAAAACTTT 0.659337 -27 GCAAGGGTGTTTAAAAGGTTTTAGAGTTGAGC 63 17 0 TTAAAATTTT 0.690622 -34 AGTGAGAACTATTAAAATTTTTTTAAATGTGG 65 49 0 ATTAAATTTT 0.837043 -34 CGTAGTGTTTATTAAAAGTTTTTTTTATATAT 66 36 0 ATTAAATTTT 0.837043 -107 GCATCCAGATATTTAACCTTTTGGAACTAAAT 68 25 1 ATTTAATTTT 0.775091 -77 GGCAGTGGCTTTTAAAGCCTTTTGCTGCAAAC 71 185 1 TTTAAACTTT 0.696854 -91 ATTTTTAGCTTTTTAATTCTTTAAATTTCC 72 44 1 TTTTAACTTT 0.60665 -20 CACGCAGAAAATATAAGGTTTTGGT 73 21 1 ATATAATTTT 0.675812 -15 TTGTGTTCTATTTAAATCCTTTTTCAATTGTT 75 240 1 TTTAAACTTT 0.696854 -61 ATGGTGGCATATAAAAAATTTTTTTATTTGTT 76 23 1 ATAAAATTTT 0.756521 -155 GTTGACTAAGTTTTAACCTTTTTCTTTTTTGT 76 143 0 TTTTAATTTT 0.712307 -35 CGTAAAATTAATAAAATCTTTTGTATT 79 47 1 ATAAAATTTT 0.75652 -17 TTGTGATTAACTTAAAAATTTTACGAAA 81 7 0 CTTAAATTTT 0.622334 -34 CACAGCGCGGATAAAATATTTT 82 1 0 ATAAAATTTT 0.75652 -33 ****** **** Masking position 6 Map Score: 46.8653 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 58 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 GCTTACGCGTTGCACCCGGCGGGGAGGAGGCCGTTTCAT 10 38 1 TCGGCGGGGG 0.923994 -263 CGGAAGGCCCCTGAGAAGGGGCGGAGGAGGAACAGAAAC 10 132 0 CAGGGGGGGG 0.992167 -169 AGGGGCCTTCCGCCACAGCGGGTGGGGGGACTTTCCTCC 10 159 1 CCGCGGGGGG 0.650999 -142 GTCGGAGAAACATTACAGTGGGAGCGGCGGTGGGCGGCT 10 206 0 CCGTGGGGGG 0.966829 -95 AATTTTTCATCTGAGCGGGGGTTGCCGAGCGGACAAAGG 19 201 0 CCGGGGGCGG 0.996185 -100 GATATCCGCTACCCCACGGGGGCGACGTGGAAAAATTGG 30 42 0 AAGGGGGCGG 0.876708 -99 CCGCCGGGAGTTGAACCCGGGTCGAGGAGTCCGCAGCCC 30 86 0 TCCGGGGGGG 0.924012 -55 GGGGAATATGCTCAAAAGAGGCAGAGGCGGCAATGGTTA 49 12 1 CAGAGGGGGG 0.97811 -92 TTGAAATTATCATCCCGGAGGAAGTCGAGTACACCGAAC 54 189 1 CCGAGGGCGG 0.989055 -112 GCCTTCACCGCACACCGCAGGAGGTGGCGATGGCTGCAG 57 13 1 CCCAGGGGGG 0.947937 -288 TCAACAATTTCCGAAATGGGGGTGCCGGGAATAAACACT 57 233 0 CAGGGGGCGG 0.99001 -68 ATTCAGCCCCGGCTATGAGGCGTTAGGCCGGG 60 4 1 CCGGCTGGGG 0.731197 -254 CTATGAGGCGTTAGGCCGGGGTTGCCGAGCGGTAAGGCG 60 23 1 TCGGGGGCGG 0.984037 -235 CCCGCCAGTTCAATGATGGGGCCGCCGAGATTTGAACTC 71 80 1 CAGGGGGCGG 0.99001 -196 GTGTATCTTTCTGTCATGAGGGAGGCAGGATTTAAATAC 71 241 0 CAGAGGGCAG 0.649751 -35 TGTTTCCGCCTCAGGCTGAGGCGGTGGAGAAGGTCTTTT 75 60 0 TCGAGGGGGG 0.965362 -241 * * **** * ** * Masking position 14 Map Score: 22.4356 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 198 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TCTGCCTTTCAATCCCATTTTGGTCTGATTTCAACCCGTCAGG 1 56 0 ATCTTTATTA 0.975161 -245 TCTTACTTTCAATCCCATTTTGGTCTGATTTCAACTGTTCCTT 1 124 0 ATCTTTATTA 0.975161 -177 ATTGCCTTTCAATCCCATTTTGGTCTGATTTCAACTTGGGAGC 1 197 0 ATCTTTATTA 0.975161 -104 AAATTTACGTAATCCCACTTTAGTCTGATTTCAAAAAACGCCG 2 67 0 ATCTTTATTA 0.975161 -200 ATTTTTTTTAATTAACTTTTTGTTGTTAATTAATTATTTATCA 6 33 1 ATCTTTATTA 0.975161 -63 CTTGGTAAGGAGTCTCCAGTTCATCAAAATTCAGGCTCATGTG 13 149 0 ATCTTTATTA 0.975161 -152 GATACTTACACTTTAATTGCAATTAAAATTGCCATT 18 4 1 ATCTTTATTA 0.975161 -79 GTCCACTTTCAATCCCATTTTGGTCTGATTTCAACTTACTGTG 19 16 0 ATCTTTATTA 0.975161 -285 TGGAGAATGAAATTGCAAGTTGATGGAAGTTCAAAGTTATGCG 27 51 0 ATCTTTATTA 0.975161 -147 ACTATGTGGCTATATCTGATTCTTAAAATTTTAAAGATAAAAT 27 113 1 TTCTTTATTA 0.942567 -85 ATAATCCGCCTGTACCGAATTTGTTCCAATTAATACTTGATAT 37 128 0 TTCTTTATTA 0.942567 -78 GTTTTAAATCTTTCGCAATTTTATCTCAATTTAAGATTTTGAT 40 31 1 TTCTTTATTA 0.942567 -120 AATACCACCTTGTTAGTACTTGAATTCAAACCA 47 1 1 ATCTTTATTA 0.975161 -180 CCAACAGGGAGATTTCTCATTACTTATACTTTAACTATCTGTT 53 31 0 GTCTTTATTA 0.880856 -35 TAAATACCTTTTTTACCGGTTTATGTCAATTTATGTGATTTAG 56 36 1 TTCTTTATTA 0.942567 -73 * * * ** * * ** * Masking position 18 Map Score: 24.814 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 32 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 ACATTCATAAAAAAATTAGAAAATCTTTTTCCT 1 273 0 AAAAAGAAAA 0.719263 -28 GGTGTTCAGAAAAAAGAGGAAAAGTAAAAAACA 2 11 1 AAAAAGAAAA 0.719263 -256 GAACTGGTTCATAAATAAGAAAAAA 5 3 0 ATAAAGAAAA 0.811124 -71 CAACAAAAAGTTAATTAAAAAAAATTTTATAAA 6 25 0 TTAATAAAAA 0.720012 -71 TAAATTCATTATCATCTTAAAAAATTGAATTAT 15 27 0 ATCATAAAAA 0.585685 -60 AAAGTAAACTAAAAATATAAAAATTTTATGTTT 18 54 0 AAAAAAAAAA 0.773316 -29 AGGGCTATTTTAAAAAGCAAAAACAAAGTG 20 45 1 TAAAAAAAAA 0.720012 -20 GGAACTCTATTTCAACTCGAAAAATGCAGGTTT 21 43 1 TTCAAGAAAA 0.572913 -59 CAACAACAAAATAATAAAGAAAA 24 1 0 ATAATGAAAA 0.719263 -265 GATAAATACCTAAATGCAAAAAAATTTATATAG 28 55 0 TAAATAAAAA 0.605397 -101 GTAAATTTTTTTAAAATTAAAAATTGACACCAA 31 203 1 TTAAAAAAAA 0.811692 -26 AAACAAAAATATAAAAATAAAAAT 37 2 0 ATAAAAAAAA 0.85115 -204 AAACAGCGTGTTAAAAACAAAAATATAAAAATA 37 16 0 TTAAAAAAAA 0.811692 -190 GCCAGATTTGTTAATTATAAAAA 38 1 0 TTAATAAAAA 0.720012 -101 AGTTGTGTTCATAAATGAAAAAATTTAAAT 38 82 1 ATAAAAAAAA 0.85115 -20 AAAAGAATGTTAAATACAGAAAAAAGGTGGTAG 39 237 1 TAAATGAAAA 0.535362 -24 TTGCGAAAATATAATCCAAAAAAGTAATTCACT 41 70 0 ATAATAAAAA 0.773316 -124 ATATTTTCGCAAAATCTGAAAAATTTGAATGGC 41 91 1 AAAATAAAAA 0.670536 -103 TTTAATTTCGTAAAAAGCGAAAAGTTTTAAAAG 41 149 1 TAAAAGAAAA 0.658857 -45 GCTTCAAGTAAAAAATGGGTCTATA 45 21 0 TTCAAAAAAA 0.641083 -15 GGATGGTATTTTAATAAGAAAAAAGTGAAGGAG 54 271 1 TTAATAAAAA 0.720012 -30 GCTTCGCTTGAACAATTCGAAAAATCTGTTAAA 55 39 0 AACAAGAAAA 0.514954 -127 TATTAAACGTGAAAAAGTAAGTAT 58 10 0 TTAAAGAAAA 0.763998 -15 CGTTTAGAAAATAATTCGAAAAAAG 59 3 0 ATAATAAAAA 0.773316 -69 TCGTATAATAATCAATCAAAAAAGAAAGGAAAA 60 204 1 ATCAAAAAAA 0.703219 -54 TTCAAACTTATAAAAGCGGAAAAAGGCTTTTAT 61 162 1 TAAAAGAAAA 0.658857 -38 GAGACAATTTATAAAACAAAAAAGAAAAAA 67 8 0 ATAAAAAAAA 0.85115 -77 AAATTGTCTCTTAATTGTAAAAAGCTCATGATA 67 31 1 TTAATAAAAA 0.720012 -54 TTAAAGAATTAAAAAGCTAAAAATTTTATGCAA 72 35 0 AAAAAAAAAA 0.773316 -29 ATTTATGATTATAATTTTAAAAAGTTTGCTAAG 74 79 0 ATAATAAAAA 0.773316 -28 TGCCAAGTTAAACAATTGAAAAAGGATTTAAAT 75 249 0 AACAAAAAAA 0.585685 -52 CAAAATTTAAATAATCACAAAAAGAGCCTGC 75 280 1 ATAATAAAAA 0.773316 -21 TTTTAATCAAAACAAATAAAAAAATTTTTTATA 76 32 0 AACAAAAAAA 0.585685 -146 TGTTTAACCATTAAAGTCAAAAATTTACCTTTC 76 113 0 TTAAAAAAAA 0.811692 -65 AGGATAACGAATAAAATGGAAAAACTTAATACA 78 34 1 ATAAAGAAAA 0.811124 -24 ***** ***** Masking position 4 Map Score: 27.0442 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 117 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 TCTGCCTTTCAATCCCATTTTGGTCTGATTTCAAC 1 64 0 AATCCTTGTC 0.987201 -237 TCTTACTTTCAATCCCATTTTGGTCTGATTTCAAC 1 132 0 AATCCTTGTC 0.987201 -169 ATTGCCTTTCAATCCCATTTTGGTCTGATTTCAAC 1 205 0 AATCCTTGTC 0.987201 -96 AAATTTACGTAATCCCACTTTAGTCTGATTTCAAA 2 75 0 AATCCTTGTC 0.987201 -192 ACAACCACCATTTGTTCAGAAAAAATA 6 79 0 AACCCTTTTC 0.904935 -17 CAGCCCAAAGAACCTCTCTATCTTCCCATTCGTTT 13 45 0 AACCCTTTTC 0.904935 -256 GTCCACTTTCAATCCCATTTTGGTCTGATTTCAAC 19 24 0 AATCCTTGTC 0.987201 -277 TGGACGTGTAAATCTTCTTTTCGTCATCAGAGATA 19 54 1 AATCTTTGTC 0.914654 -247 TCTAATATCCAATCGCTATTTTGTCAGATAAATCA 28 86 1 AATCCTTGTC 0.987201 -70 TTATCATTATAACCGTTATATAGTCAGGTGGGAAA 47 61 1 AACCTTTGTC 0.856966 -120 AGTAATGAGAAATCTCCCTGTTGGCT 53 50 1 AATCCTTGGC 0.929783 -16 TTTTTAAGTTAATCACAATTTTTTCGTATC 81 21 1 AATCCTTTTC 0.944529 -20 **** * * * *** Masking position 2 Map Score: 16.9877 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 36 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GATTCATAACAGCTTTTATCTTTAGAAGGCCTA 4 59 1 AGTTTATTTT 0.732009 -46 ATATCACAGAAAAACTTATTTTGACAAAAAGTT 13 269 1 AACTTATTTG 0.847527 -32 AAAAATATAAAAATTTTATGTTTGCCATTAAAT 18 44 0 AATTTATTTT 0.895345 -39 GAAATTATTTAATTTTTATGTTTTGACTAATCC 23 19 0 AATTTATTTT 0.895392 -39 TTGTCAAAACAAATTTTATCTTTAAAATTTTAA 27 135 0 AATTTATTTT 0.895345 -63 TTTTAAAGGAAAGATTTATCTTGCAAGAGTCCA 30 12 1 AATTTATTTG 0.925642 -129 AATGGGCAGGAAAATTGATGTTTTGCAAGACAG 31 128 1 AATTGATTTT 0.73197 -101 ACAAAGTGGCAAATCTTATATTTTGAAAATGAG 35 40 1 AACTTATTTT 0.792578 -34 GTATCTGCAAAAGCTTTATATTGCCAGATTTGT 38 23 0 AATTTATTTG 0.925642 -79 CCTTTAAGGTAAATTTTATGTTGCAGTTGAACC 39 152 1 AATTTATTTG 0.925641 -109 TTGAAGACAAAGATTTTATTTTGTTTCGTTCAA 41 19 0 AGTTTATTTG 0.798893 -175 AACTCAACTTAAAGCTTATATTGGTTAAAGAAC 42 21 0 AACTTATTTG 0.847527 -91 AAAAGTTTATTTTTCTGAGACACC 43 2 1 AATTTATTTT 0.895345 -33 TTTTAATTTTTATTTTTTCCAACAGAT 53 5 1 AATTTATTTT 0.895392 -61 AGAATAATAAAGCTTTGATTTTGGTGCAGTCGT 59 33 0 AGTTGATTTG 0.559018 -39 TAAATAGTAAAATTTTTATTTTTGTTAGCATGT 69 15 1 AATTTATTTT 0.895392 -32 ACCAAAACCTTATATTTTCTGCGTGTT 73 19 0 AACTTATTTT 0.792578 -17 AAAGTTTGCTAAGGTTGATTTTGTCAGGCTGCA 74 59 0 AATTGATTTG 0.798893 -48 GGCAGTTGAAAAGGTTTATGTTGATGCTGCAAG 84 11 1 AATTTATTTG 0.925642 -32 ** ***** *** Masking position 6 Map Score: 20.2473 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 21 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 7 GGGTTGAAATCAGACCAAAATGGGATTGAAAGGC 1 62 1 CAGAAATGGG 0.987073 -239 CAGTTGAAATCAGACCAAAATGGGATTGAAAGTA 1 130 1 CAGAAATGGG 0.987073 -171 AAGTTGAAATCAGACCAAAATGGGATTGAAAGGC 1 203 1 CAGAAATGGG 0.987073 -98 TTTTTGAAATCAGACTAAAGTGGGATTACGTAAA 2 73 1 CAGAAGTGGG 0.956829 -194 GCACTCATCTCTGCTTAAGAGGGGATTCGCG 5 53 1 CTGAAAGGGG 0.936779 -21 AATTATTATTCAATAAAAAAGGGGTGGTGGT 14 111 1 CAAAAAGGGG 0.755022 -21 AAGTTGAAATCAGACCAAAATGGGATTGAAAGTG 19 22 1 CAGAAATGGG 0.987073 -279 TGCTGGAAGGCTGGAAGAAATGGGCAGGAAAATT 31 110 1 CTGGAATGGG 0.765248 -119 TGTTGTAGGGCAGTTAAATAGTGGCAGACAAC 35 9 0 CAGAAAGTGG 0.854662 -65 ATGTTAAATACAGAAAAAAGGTGGTAGC 39 243 1 CAGAAGGTGG 0.630574 -18 GCTTCAAGTAAAAAATGGGTCTATATTTC 45 17 0 AAGAAATGGG 0.822947 -19 GACATACATGCAGTACAACATGGGCCTGAGGCCC 49 63 1 CAGAAATGGG 0.987073 -41 TATTGTCGAGCTGAAAAAGATGGGGGTTGATGAA 57 200 1 CTGAAATGGG 0.957168 -101 GAGCAGGGTAGAATGGGGAGGTATAAA 91 14 0 CAGAGATGGG 0.917618 -17 *** ** ***** Masking position 13 Map Score: 17.6917 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 60 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GGGTTGAAATCAGACCAAAATGGGATTGAAAG 1 62 1 CAGAAAAATG 0.960327 -239 CAGTTGAAATCAGACCAAAATGGGATTGAAAG 1 130 1 CAGAAAAATG 0.960327 -171 AAGTTGAAATCAGACCAAAATGGGATTGAAAG 1 203 1 CAGAAAAATG 0.960327 -98 GGTGTTCAGAAAAAAGAGGAAAAGTAAA 2 7 1 CAGAAAAGAG 0.697565 -260 TTTTTGAAATCAGACTAAAGTGGGATTACGTA 2 73 1 CAGAAAAGTG 0.95218 -194 CCCTCTTAAGCAGAGATGAGTGCTAAATAAAG 5 44 0 CAGATGAGTG 0.607271 -30 AAGTTGAAATCAGACCAAAATGGGATTGAAAG 19 22 1 CAGAAAAATG 0.960327 -279 ACTCAACGAACAGAACTAAATGCGGGGGGAGG 19 123 1 CAGATAAATG 0.84432 -178 ATTTTTTGCTCAGATAAAAATGCTCACTCTAA 42 62 0 CAGAAAAATG 0.960325 -50 CTCCGGGCAGGGAAAAATGTACTGGAAAA 50 14 0 CAGGAAAATG 0.893494 -19 GTATTTTAATAAGAAAAAAGTGAAGGAGGTGT 54 276 1 AAGAAAAGTG 0.588277 -25 GAGCAGGGTAGAATGGGGAGGTATA 91 16 0 CAGGAGAATG 0.744077 -15 **** ****** Masking position 9 Map Score: 9.31804 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 = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 AATATCCTGATAAATAATTAATTAACAACAA 6 52 0 TAAATAATTA 0.62659 -44 TGTAAATTCCTTAAAAATTTAATATTTGCTC 11 24 1 TTAAAAATTA 0.683552 -36 GTGATATCCCGAAATAATTTCACTCCTCAAA 13 245 0 GAAATAATTC 0.717566 -56 ATTATCATCTTAAAAAATTGAATTATGCTCA 15 22 0 TAAAAAATTA 0.762122 -65 ACATAAAAATTAAATAATTTCAAATTTCATC 23 31 1 TAAATAATTC 0.793422 -27 TTATTGACATTAAAAATTCCATGCCCCCGC 30 121 0 TTAAAAATTC 0.838092 -20 TTTTTTAAAATTAAAAATTGACACCAATAC 31 209 1 TTAAAAATTA 0.683825 -20 CACATCAGAATAAAAAATTCCTTCTTTTATT 34 59 0 TAAAAAATTC 0.884631 -67 ACAAATAACTTTAATAATTTCGTACAGCCTT 36 84 1 TTAATAATTC 0.726364 -29 ATCTAAACGCGTAAAAATTGAATATATCAAG 37 105 1 GTAAAAATTA 0.604178 -101 GTTCATAAATGAAAAAATTTAAAT 38 88 1 GAAAAAATTA 0.69269 -14 AAATTTATTTGAAAAAATTTCGTAAAAATAG 40 87 1 GAAAAAATTC 0.843459 -64 CCATTTTTAGTAAAAAATTCCACTTTTGTTG 44 26 1 TAAAAAATTC 0.884631 -86 ATTAAAAATTACAGCAAAATAG 51 2 1 TTAAAAATTC 0.837935 -49 AATTTCCCGATAAATAATTACTATTTAAAGT 60 236 0 TAAATAATTC 0.798065 -22 GATTTCGGGAGAAATAATTAACGGAAGAGTG 64 174 0 GAAATAATTA 0.532521 -127 TGATAAACCTTAAATAATTCCAGAAACACCG 67 59 1 TAAATAATTC 0.807732 -26 TACTTCAAGTGTAAAAATTGAGTGCCCCAGT 70 76 0 GTAAAAATTA 0.604178 -100 CAACGGTGCATTAAAAATTGCTCCTCGTTAA 75 188 1 TTAAAAATTC 0.838092 -113 CTGCAGAAGTTAAAAAATTACCTGAGATATT 76 68 0 TAAAAAATTC 0.884465 -110 ********* * Masking position 8 Map Score: 15.2449 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 42 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 GTTCATAACAGCCTTTATTTAGCACTCATCT 5 32 1 GCCTTTTTTA 0.968995 -42 CAACATAAAAGCCTTTCTTTATTTTGAGTGG 16 131 0 GCCTTTTTTA 0.968995 -38 TTTTGCCTTTATTTACTCAACATAA 16 154 0 GCCTTTTTTA 0.968995 -15 ACTAACTGTTGCCTCTCTTTAAAATTCACTT 29 79 0 GCCTCTTTTA 0.968388 -67 GTTGTCTGCCACTATTTAACTGCCCTAC 35 8 1 GCCACTTTTA 0.845911 -66 TGCCGCCTCTGCCTCTTTTGAGCATATTCCC 49 13 0 GCCTCTTTGA 0.890548 -91 CGCTAAAAACGCCTTTTTTTAAAAGTATAAA 61 82 1 GCCTTTTTTA 0.968995 -118 TTGCCTTTGCGCCTTTTTTTAAACT 87 25 1 GCCTTTTTTA 0.968995 -15 ****** **** Masking position 11 Map Score: 8.25528 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 11 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TCAAGTTATTTTAATCAAAAGTCAGATAAT 4 16 1 TTAATCAAAA 0.941179 -89 TAAATCTATCTTTATCAAAAAGCGGTTTTT 9 232 0 TTTATCAAAA 0.787282 -69 TTATCAATATTTAATCAAACGATTCTCC 9 283 1 TTAATCAAAC 0.669878 -18 AACATAACAATTAATCAAAAAT 12 92 1 TTAATCAAAA 0.941179 -12 GAGTCTCCAGTTCATCAAAATTCAGGCTCA 13 153 0 TTCATCAAAA 0.684641 -148 ACTTTAACTTTTTGTCAAAATAAGTTTTTC 13 277 0 TTTGTCAAAA 0.447766 -24 GGAGGCTGGATTAGTCAAAACATAAAAATT 23 12 1 TTAGTCAAAA 0.778045 -46 GTTCAATCAAAACATTGAAGAG 48 50 0 TCAATCAAAA 0.778045 -12 AATATATATGTTAATCAAAGCAATTTC 51 34 1 TTAATCAAAG 0.669878 -17 ATTTAGAAGATTAATCAAATATAATAAGTT 56 73 1 TTAATCAAAT 0.5779 -36 AATTGTTGAGTTTATCAAAACCAAGCTGCC 57 263 1 TTTATCAAAA 0.787282 -38 CGTATAATAATCAATCAAAAAAGAAAGGAA 60 205 1 TCAATCAAAA 0.778045 -53 AGAAAACTACTTAAGCAAAAAACTACTGTG 61 116 0 TTAAGCAAAA 0.655731 -84 GTTTTTTAATTAATCATAACCTTATCCAT 62 10 1 TTAATCATAA 0.562395 -22 TCGAATACGATTAATCAAAAAGAATAAATA 74 14 0 TTAATCAAAA 0.941179 -93 ATATTAAATTTTAATCAAAACAAATAAAAA 76 43 0 TTAATCAAAA 0.941179 -135 ACTTTAATGGTTAAACAAAAAAGAAAAAGG 76 129 1 TTAAACAAAA 0.562395 -49 AATTTTTAAGTTAATCACAATTTTTTCGTA 81 19 1 TTAATCACAA 0.655739 -22 ********** Masking position 1 Map Score: 10.2035 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 9 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 TAGTCTGATTTCAAAAAACGCCGGCAAAAA 2 60 0 TCAAAAAACG 0.763582 -207 CGTTTAAAAATCCCCAAACGCCCAAACCTT 2 220 1 TCCCCAAACG 0.907613 -47 GAGTGAACCATCCACAAACGAATGGGAAGA 13 30 1 TCCACAAACG 0.942039 -271 TAACTTTTTGTCAAAATAAGTTTTTCTGTG 13 273 0 TCAAAATAAG 0.358441 -28 TTTTAAACGCTCAAAAAAAGAATGTTAAAT 39 222 1 TCAAAAAAAG 0.748575 -39 GAAAATATAATCCAAAAAAGTAATTCACTA 41 69 0 TCCAAAAAAG 0.87616 -125 CTTGCAGATTTCAACAAAAGTGGAATTTTT 44 38 0 TCAACAAAAG 0.863109 -74 TCGGAATAACTCCACCAACGAGGATCAGCA 57 163 0 TCCACCAACG 0.688007 -138 TTTTGGAAATTCCACAGAAGTAATTTTCCG 60 147 0 TCCACAGAAG 0.702655 -111 CTGTGGAATTTCCAAAAAAGCAAGCATAAA 60 160 1 TCCAAAAAAG 0.87616 -98 CGAGAAATAATCCCCAAACGACATAATCCC 61 54 0 TCCCCAAACG 0.907613 -146 CCTATCACCAAAAGTTTTTGAGGA 66 129 0 TCACCAAAAG 0.792147 -14 GAGCTGCAGTTCCAGAAAAGCTGACAGGTT 71 17 0 TCCAGAAAAG 0.685232 -259 ATTTAAATAATCACAAAAAGAGCCTGC 75 284 1 TCACAAAAAG 0.642812 -17 TATTGCATAATCCACATACGCCTTCCTCTC 89 67 0 TCCACATACG 0.753081 -49 ********** Masking position 8 Map Score: 7.07747 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 97 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 AGTTCAGGCATTCTTCGGAAATGACCACTAC 9 198 1 TTCTTCGAAA 0.749198 -103 ATCATCGCATTTCCCCGCACCGGTCTCGTTT 10 105 1 TTCCCCGACC 0.709185 -196 AGTTACCGTTTTCCCCCGAACAACAACTGAC 14 23 1 TTCCCCCAAC 0.924131 -109 TAAGTTTATATTCCCCCGACCAACTTTTTTC 22 13 1 TTCCCCCACC 0.793738 -21 TGGCTGTATCTTCTTCGCAACTAAAATTAAG 26 71 0 TTCTTCGAAC 0.752726 -62 TCATAGCCTTTTCTCCGCAAATTATATAACT 31 20 1 TTCTCCGAAA 0.937505 -209 ATCTTCTTTCTCCCCAAACTTCTCTAT 33 10 0 TTCTCCCAAA 0.959479 -18 CTGGCAAAGATTCTCTCGAAAACAGGTGTTT 46 94 0 TTCTCTCAAA 0.629489 -128 TGGGGATTATTTCTCGCTAAAAACGCCTTTT 61 68 1 TTCTCGCAAA 0.715753 -132 CGTTAATTATTTCTCCCGAAATCGACATGGT 64 182 1 TTCTCCCAAA 0.959474 -119 AAGAAAGAGCTTCTCCGAAAATCCATTCATT 83 61 0 TTCTCCGAAA 0.937018 -110 CCTCTCAATCTTCTCCCAAACCTTCGGCTCC 89 42 0 TTCTCCCAAC 0.960204 -74 CCTCCTACCATTCTTCCAAAACACACATATA 90 18 0 TTCTTCCAAA 0.824995 -68 ******* *** Masking position 9 Map Score: 6.73387 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 125 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 GGAAGCTACCTGCTGAAAGGGTGTTTGAGT 13 201 1 TGCTGAAAGG 0.913471 -100 TTGCATAGTTTGCTGCAAAATCTTTAATGG 16 45 1 TGCTGCAAAA 0.804544 -124 CTACGCATAGAGCTGCAAGGCAAAATTCAT 17 19 1 AGCTGCAAGG 0.924987 -61 ACTGGTAGAGGGCTGCAAGGAGCGAAATTG 25 34 0 GGCTGCAAGG 0.923586 -24 ATGGAGGAGCTGCTGGAAGGCTGGAAGAAA 31 100 1 TGCTGGAAGG 0.737115 -129 AGTTTTAAAAGGCTGAAAAAATAGTTAAAG 41 171 1 GGCTGAAAAA 0.585122 -23 ATATTTCTCCAGCTGCAATGACCGCTGCTG 46 19 1 AGCTGCAATG 0.631443 -203 TGGGAGTATCTGCTGACAGAACTTGTTTAT 46 143 0 TGCTGACAGA 0.772556 -79 GATATTGTCGAGCTGAAAAAGATGGGGGTT 57 198 1 AGCTGAAAAA 0.589974 -103 ATCAAAACCAAGCTGCCAGAAAAGAGGAAG 57 276 1 AGCTGCCAGA 0.798694 -25 GTTCCAGAAAAGCTGACAGGTTGATTCT 71 9 0 AGCTGACAGG 0.72511 -267 TAAAGCCTTTTGCTGCAAACGCATTCGTTT 71 197 1 TGCTGCAAAC 0.638979 -79 GATTTTGTCAGGCTGCAAGAGTTTAAAACC 74 46 0 GGCTGCAAGA 0.908634 -61 TGGAGGAGCTTGCTGAAAGCATCTCAAGTT 75 138 0 TGCTGAAAGC 0.788805 -163 TTTATGTTGATGCTGCAAGAAAAACGTC 84 25 1 TGCTGCAAGA 0.940752 -18 AATAGCAGATTGCTGAAATAGCTCC 90 71 1 TGCTGAAATA 0.546871 -15 ********** Masking position 4 Map Score: 7.14917 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 416 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 15 AAAAAAGTTGGTCGGGGGAATATAAACTTAA 22 12 0 GCGGGGGAAT 0.772837 -22 TGTTAATTGAGATGGGAGCAGATGAGCGAGA 26 19 1 GTGGGAGCAG 0.903313 -114 TTCAACTCCCGGCGGGGGCATGGAATTTTTA 30 110 1 GCGGGGGCAT 0.979345 -31 CAATCGTCGGATTGGGGGCAGCAGCGGTCAT 46 36 0 ATGGGGGCAG 0.752273 -186 AAAAAATTTTGAGGTGGGCATAGTGCTCATA 47 93 1 GGGTGGGCAT 0.850858 -88 GTTAGGTTCTGATGGGGACATACATGCAGTA 49 47 1 GTGGGGACAT 0.844525 -57 CGGATACCTCGACGGTAGCAGAGAAAGTTCT 54 19 1 GCGGTAGCAG 0.56365 -282 AGACGTGGATGTTGTGGGCATAAGTCTTCAC 57 59 1 GTGTGGGCAT 0.960657 -242 TATCGCTCCGGCTGGGAGCATAAGATTCATT 64 75 1 GTGGGAGCAT 0.94354 -226 TTTACCCGCCGCTGTGGGCATTGCGAGGAGC 75 16 1 GTGTGGGCAT 0.960657 -285 CTCAAGTTATGCTGTTGGCATTTTAAAGGAG 75 115 0 GTGTTGGCAT 0.843512 -186 TTGAGAAGTTGATGGTGGCATATAAAAAATT 76 12 1 GTGGTGGCAT 0.94354 -166 * ********* Masking position 10 Map Score: 6.80438 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 134 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987