AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00061_aful_reg_300.orf -o00061_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) 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 AF0220 180 biotin carboxylase (acc) #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 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #21 AF0685 140 enoyl-CoA hydratase (fad-2) #22 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #23 AF0970 101 A. fulgidus predicted coding region AF0970 #24 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #25 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #26 AF1119 111 A. fulgidus predicted coding region AF1119 #27 AF1121 34 transcriptional regulatory protein, AsnC family #28 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #29 AF1173 180 A. fulgidus predicted coding region AF1173 #30 AF1174 61 A. fulgidus predicted coding region AF1174 #31 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #32 AF1191 32 dihydroxynaphthoic acid synthase (menB) #33 AF1192 50 conserved hypothetical protein #34 AF1195 27 activator 1, replication factor C, 53 KD subunit #35 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #36 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #37 AF1208 165 conserved hypothetical protein #38 AF1210 108 conserved hypothetical protein #39 AF1289 300 conserved hypothetical protein #40 AF1641 31 enoyl-CoA hydratase (fad-4) #41 AF1642 50 histidyl-tRNA synthetase (hisS) #42 AF2009 101 heme biosynthesis protein (nirJ-2) #43 AF2010 46 A. fulgidus predicted coding region AF2010 #44 AF2011 175 conserved hypothetical protein #45 AF2013 275 coenzyme F390 synthetase (ftsA-3) #46 AF2014 63 sugar transporter, putative #47 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #48 AF2244 300 acyl-CoA dehydrogenase (acd-11) #49 AF2271 177 A. fulgidus predicted coding region AF2271 #50 AF2272 87 A. fulgidus predicted coding region AF2272 #51 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #52 AF2409 42 iron-sulfur cluster binding protein #53 AF2410 43 A. fulgidus predicted coding region AF2410 #54 AF2411 41 conserved hypothetical protein #55 AF2412 39 thiamine biosynthesis protein (thiC) #56 AF2414 67 conserved hypothetical protein #57 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) #58 AF2426 85 conserved hypothetical protein #59 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 AAGGATTGTCAAAAATTTTTTAC 3 26 1 AAAAATTTTA 0.691782 -13 GTTAATTAAAAAAAATTTTATAAAATGATTTG 6 17 0 AAAAATTATA 0.872681 -79 AATTAACAACAAAAAGTTAATTAAAAAAAATT 6 32 0 AAAAATTATT 0.841505 -64 TAAATTCCTTAAAAATTTAATATTTGCTCATT 9 26 1 AAAAATTATA 0.872682 -34 GATATCACAGAAAAACTTATTTTGACAAAAAG 11 268 1 AAAAATTTTT 0.634868 -33 TTATTTTGACAAAAAGTTAAAGTTTTC 11 284 1 AAAAATTAAG 0.829389 -17 TTATCATCTTAAAAAATTGAATTATGCTCAAA 14 20 0 AAAAATTAAT 0.832287 -67 TCTATTTGAAAAAAGGTTTTTAAATCGGTGGC 15 142 1 AAAAGTTTTA 0.720706 -39 CTATATATCCAAAAAATTTAAGTTTGCTCTGC 16 91 0 AAAAATTAAG 0.829388 -78 CTAAAAATATAAAAATTTTATGTTTGCCATTA 18 47 0 AAAAATTATG 0.838734 -36 CGCACGAGAAAAAAGATTTTATATAACAAACC 20 24 0 AAAAGTTTAT 0.651234 -122 GTGTATCTGCAAAAGCTTTATATTGCCAGATT 23 26 0 AAAAGTTATA 0.887331 -76 TTCATAAATGAAAAAATTTAAAT 23 89 1 AAAAATTAAA 0.864985 -13 ACTCCTACCGAAAAGTTTTAAATCTTTCGCAA 24 17 1 AAAAGTTAAA 0.880399 -134 GCAAAATCTGAAAAATTTGAATGGCTTCAGAA 25 99 1 AAAAATTAAT 0.832289 -95 GTAAAAAGCGAAAAGTTTTAAAAGGCTGAAAA 25 158 1 AAAAGTTAAA 0.880399 -36 TTATCTGAGCAAAAAATTTAAATTATTGAAGT 26 77 1 AAAAATTAAA 0.864985 -35 AAAAGTTTATTTTTCTGAGACA 27 1 1 AAAAGTTTTT 0.666538 -34 ATAATTATGGAAAAGCTTAAATGGTTTGAATT 29 33 0 AAAAGTTAAT 0.850791 -148 TTGTAATCTCAAAAGATTAAAATACTCTTCAA 30 26 1 AAAAGTTAAA 0.880399 -36 TTTAGCTTCAAAAAAGTTAATTTAAGTATGTT 37 142 0 AAAAATTATT 0.841505 -24 AAGGGTGTTTAAAAGGTTTTAGAGTTGAGCGA 41 15 0 AAAAGTTTAG 0.646661 -36 ATTTAGTTCCAAAAGGTTAAATATCTGGATGC 42 25 0 AAAAGTTAAT 0.850791 -77 TTAAAAAGCTAAAAATTTTATGCAAATAAATA 46 28 0 AAAAATTATG 0.838734 -36 GGTGGCATATAAAAAATTTTTTTATTTGTTTT 49 25 1 AAAAATTTTT 0.433385 -153 ACAAAAAAGAAAAAGGTTAAAACTTAGTCAAC 49 143 1 AAAAGTTAAA 0.880399 -35 AATAAAATGGAAAAACTTAATACAT 51 43 1 AAAAATTATA 0.872682 -15 GGCAGTTGAAAAGGTTTATGTTGATGCTGC 52 9 1 AAAAGTTATG 0.856649 -34 TTTTTAAAAAAGTTCATATAGTATGAAA 54 7 1 AAAAATTATA 0.872682 -35 ***** ** *** Masking position 7 Map Score: 35.6997 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 195 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 2 TGCCTTTCAATCCCATTTTGGTCTGATTTCAACCCGTCAGG 1 56 0 TCCTTTATTA 0.982909 -245 TTACTTTCAATCCCATTTTGGTCTGATTTCAACTGTTCCTT 1 124 0 TCCTTTATTA 0.982909 -177 TGCCTTTCAATCCCATTTTGGTCTGATTTCAACTTGGGAGC 1 197 0 TCCTTTATTA 0.982909 -104 ATTTACGTAATCCCACTTTAGTCTGATTTCAAAAAACGCCG 2 67 0 TCCTTTATTA 0.982909 -200 TTTTTTTAATTAACTTTTTGTTGTTAATTAATTATTTATCA 6 35 1 TACTTTATTA 0.926982 -61 TGGTAAGGAGTCTCCAGTTCATCAAAATTCAGGCTCATGTG 11 149 0 TCCTTTATTA 0.982909 -152 TGCTCACACTTTGAGCATAATTCAATTTTTTAAG 14 4 1 TCCTTGATTA 0.8864 -83 AGTTCACCTCCAATTTATAACATTTAATGAGCAAATT 14 60 0 CCCTTTATTA 0.879419 -27 GATACTTACACTTTAATTGCAATTAAAATTGCCATT 18 6 1 TTCTTTATTA 0.942957 -77 CCACTTTCAATCCCATTTTGGTCTGATTTCAACTTACTGTG 19 16 0 TCCTTTATTA 0.982909 -285 AATCCGCCTGTACCGAATTTGTTCCAATTAATACTTGATAT 22 128 0 TACTTTATTA 0.926982 -78 TTTAAATCTTTCGCAATTTTATCTCAATTTAAGATTTTGAT 24 33 1 TCCTTTATTA 0.982909 -118 TTTTAAAACTTTTCGCTTTTTACGAAATTAAATAAGTATTT 25 140 0 TTCTTAATTA 0.602114 -54 AATACCACCTTGTTAGTACTTGAATTCAAACCA 29 3 1 TACTTTATTA 0.926982 -178 AACAGGGAGATTTCTCATTACTTATACTTTAACTATCTGTT 35 31 0 TTCTTTATTA 0.942957 -35 AATACCTTTTTTACCGGTTTATGTCAATTTATGTGATTTAG 38 38 1 TTCTTTATTA 0.942957 -71 ** * ** * * ** * Masking position 9 Map Score: 26.4478 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 TAATGTCTCGCTTTCAATCCCATTT 1 1 0 CTTTAATCTT 0.961539 -300 CGTCGTCTGCCTTTCAATCCCATTTTGGTCTGATT 1 69 0 CTTTAATCTT 0.961539 -232 GATGTTCTTACTTTCAATCCCATTTTGGTCTGATT 1 137 0 CTTTAATCTT 0.961539 -164 TCGCCATTGCCTTTCAATCCCATTTTGGTCTGATT 1 210 0 CTTTAATCTT 0.961539 -91 AAAGCCACCGATTTAAAAACCTTTTTTCAAATAGA 15 142 0 ATTTAAACTT 0.86394 -39 TGGTACTCCGATTTTAAAAACTGTTGCATAGTTTG 16 22 1 ATTTAAACTT 0.86394 -147 TTAAATGGCAATTTTAATTGCAATTAAAGTGTAAG 18 15 0 ATTTAATCTT 0.851496 -68 TACACGTCCACTTTCAATCCCATTTTGGTCTGATT 19 29 0 CTTTAATCTT 0.961539 -272 CTTCATATAACTTTGAAATCCACCTTCTAC 19 281 1 CTTTAAACCT 0.745918 -20 TGTTGCCTCTCTTTAAAATTCACTTCGTATGCTTT 20 69 0 CTTTAAACTT 0.965139 -77 ATTTGACATACTTTGAAATTTATTTGAAAAAATTT 24 72 1 CTTTAAATTT 0.828019 -79 TGTCTTTAACTATTTTTTCAGCCTTTTA 25 176 0 CTTTACTTTT 0.581132 -18 ATTACTTATACTTTAACTATCTGTTGGAAAAAATA 35 21 0 CTTTACTCTT 0.888615 -45 TTTACCTTTTCTTTAACAGATTTTTCGAATTGTTC 37 28 1 CTTTACATTT 0.605742 -138 AGATTTTTCTCTCTTAAATACCTTTTTTACCGGTT 38 22 1 CTCTAAACTT 0.745918 -87 ACTCTAAAACCTTTTAAACACCCTTGCCGAAGCTT 41 22 1 CTTTAAACTT 0.965139 -29 AAGGCAGTGGCTTTTAAAGCCTTTTGCTGCAAACG 45 183 1 CTTTAAACTT 0.965139 -93 ATTTTTTATTATTTGAAAAACGTTTGCAGGGTGAT 47 11 1 ATTTAAACTT 0.86394 -28 ATTGTGTTCTATTTAAATCCTTTTTCAATTGTTTA 48 239 1 ATTTAATTTT 0.499285 -62 **** *** * ** Masking position 4 Map Score: 23.6213 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 102 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 TTAGAAAATCTTTTTCCTCTTGCCACGCTTG 1 260 0 TTTTTCTCTT 0.64612 -41 CAGCAATTGTTTTTTACTTTTCCTCTTTTTT 2 20 0 TTTTTCTTTT 0.871814 -247 TTTTTTCTTATTTATGAACCAG 5 2 1 TTTTTTTATT 0.797289 -72 TTTATAAAATTTTTTTTAATTAACTTTTTGT 6 25 1 TTTTTTAATT 0.710616 -71 TTTTTAACTTTTCTTTGTCAAT 7 2 1 TTTTACTTTT 0.628725 -53 TTGCCGAGAATTTTATTTATTTCGATAAATT 15 50 0 TTTTATTATT 0.494772 -131 AAACATAAAATTTTTATATTTTTAGTTTACT 18 54 1 TTTTTTATTT 0.838181 -29 ATTTTTATTTTTATATTTTTGT 22 2 1 TTTTTTTTTT 0.892431 -204 TATTTTTATATTTTTGTTTTTAACACGCTGT 22 16 1 TTTTTTTTTT 0.892431 -190 TTTTTATAATTAACAAATCTG 23 1 1 TTTTTTAATT 0.710616 -101 ATTTAAATTTTTTCATTTATGAACACAA 23 84 0 TTTTTCATTT 0.809388 -18 TTTTAATTTTTATTTTTTCCAACAGAT 35 7 1 TTTTTTTTTT 0.892431 -59 CTCCTTCACTTTTTTCTTATTAAAATACCAT 36 273 0 TTTTTTTATT 0.797289 -28 AAAATAAAAATTTTACTATTTAGGCC 43 6 0 TTTTATATTT 0.563262 -41 AATAGTAAAATTTTTATTTTTGTTAGCATGT 43 17 1 TTTTTTTTTT 0.892431 -30 GGGCACTCAATTTTTACACTTGAAGTAAAGA 44 80 1 TTTTTCACTT 0.532697 -96 TGCATAAAATTTTTAGCTTTTTAATTCTTTA 46 36 1 TTTTACTTTT 0.628725 -28 ATTTTTTATTATTTGAAAAACGT 47 3 1 TTTTTTTATT 0.797289 -36 ATATAAAAAATTTTTTTATTTGTTTTGATTA 49 31 1 TTTTTTATTT 0.838181 -147 AGTTTTAACCTTTTTCTTTTTTGTTTAACCA 49 136 0 TTTTTTTTTT 0.892431 -42 ATGTATTAAGTTTTTCCATTTTATTCGTTAT 51 37 0 TTTTTCATTT 0.809388 -21 ***** ***** Masking position 4 Map Score: 21.6746 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 72 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 CCATTTTGGTCTGATTTCAACCCGTCAGGAC 1 54 0 CGATTTCAAC 0.984884 -247 CCATTTTGGTCTGATTTCAACTGTTCCTTGA 1 122 0 CGATTTCAAC 0.984884 -179 TTGGGAGCTACCGAGTCCAACACAAGTTTAT 1 174 0 CGAGTCCAAC 0.838393 -127 CCATTTTGGTCTGATTTCAACTTGGGAGCTA 1 195 0 CGATTTCAAC 0.984884 -106 CCACTTTAGTCTGATTTCAAAAAACGCCGGC 2 65 0 CGATTTCAAA 0.972258 -202 GCTAAAGCCACCGATTTAAAAACCTTTTTTC 15 149 0 CGATTTAAAA 0.829624 -32 TAGTGGTACTCCGATTTTAAAAACTGTTGCA 16 19 1 CGATTTTAAA 0.734143 -150 CCATTTTGGTCTGATTTCAACTTACTGTGTT 19 14 0 CGATTTCAAC 0.984884 -287 GTAGAAGGTGGATTTCAAAGTTATATGAA 19 282 0 TGATTTCAAA 0.697735 -19 ACTCCTCGACCCGGGTTCAACTCCCGGCGGG 21 95 1 CGGGTTCAAC 0.838393 -46 ACGTAATGTGCCGATTTAAAAATAGATAATC 22 165 0 CGATTTAAAA 0.829624 -41 CATTGCCTTGCAGATTTCAACAAAAGTGGAA 28 43 0 CGATTTCAAC 0.984884 -69 AGCCGGTGACCCGAGTTCAAATCTCGGCGGC 45 100 0 CGAGTTCAAA 0.946502 -176 * ********* Masking position 9 Map Score: 17.8852 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 65 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 GTCTCGCTTTCAATCCCATTT 1 1 0 CAACCCATTT 0.990221 -300 GTCTGCCTTTCAATCCCATTTTGGTCTGATT 1 69 0 CAACCCATTT 0.990221 -232 TTCTTACTTTCAATCCCATTTTGGTCTGATT 1 137 0 CAACCCATTT 0.990221 -164 CATTGCCTTTCAATCCCATTTTGGTCTGATT 1 210 0 CAACCCATTT 0.990221 -91 CGTCCACTTTCAATCCCATTTTGGTCTGATT 19 29 0 CAACCCATTT 0.990221 -272 ATATGTTAATCAAAGCAATTTC 33 39 1 CAAGCAATTT 0.793265 -12 TTATTCCCGGCACCCCCATTTCGGAAATTGT 39 238 1 CACCCCATTT 0.964186 -63 AAAACTTAGTCAACCCAATTTGACAGC 49 161 1 CAACCAATTT 0.95865 -17 *** ******* Masking position 8 Map Score: 13.847 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 25 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 ATCCCATTTTGGTCTGATTTCAACCCGTCAG 1 57 0 GGTCTGATTC 0.993189 -244 ATCCCATTTTGGTCTGATTTCAACTGTTCCT 1 125 0 GGTCTGATTC 0.993189 -176 ATCCCATTTTGGTCTGATTTCAACTTGGGAG 1 198 0 GGTCTGATTC 0.993189 -103 ATCCCACTTTAGTCTGATTTCAAAAAACGCC 2 68 0 AGTCTGATTC 0.934629 -199 AACTCTCGTCGGTCTGAGTTTTGTTTCCTTG 2 127 0 GGTCTGATTT 0.96635 -140 ATCCCATTTTGGTCTGATTTCAACTTACTGT 19 17 0 GGTCTGATTC 0.993189 -284 AAAACTTTTCGGTAGGAGTTCATGC 24 5 0 GGTAGGATTC 0.886283 -146 AAGCTTAAATGGTTTGAATTCAAGTACTAAC 29 22 0 GGTTTGATTC 0.949791 -159 TAGGTATGAATTTCGATGTGAAG 44 163 0 GGTATGATTT 0.867873 -13 ******* *** Masking position 7 Map Score: 13.8245 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 29 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GACGACGTACACTACTGGGGCGTTGTCAAGGAACA 1 97 1 ACTGGGGCGG 0.84663 -204 TCTGATTTCAACTTGGGAGCTACCGAGTCCAACAC 1 182 0 ACGGAGCTAG 0.74756 -119 GTTCTTTGGGCTGATGGAGCAGAAGCTCCATCTGT 11 67 1 CTGGAGCAGG 0.825878 -234 TATCCGCTACCCCACGGGGGCGACGTGGAAAAATT 21 44 0 CCGGGGGCGG 0.994575 -97 TAGCGGATATCCTGAGGGGCTGCGGACTCCTCGAC 21 70 1 CCGGGGCTGG 0.98939 -71 GGTTCAACTCCCGGCGGGGGCATGGAATTTTTAAT 21 108 1 CCGGGGGCAG 0.979394 -33 CGTTATCACCCTGTAGGGGCCAGTGCCTTCCGGAA 36 54 0 CTGGGGCCAG 0.967534 -247 TCACCGCACACCGCAGGAGGTGGCGATGGCTGCAG 39 17 1 CCGGAGGTGG 0.961369 -284 CTGCCAGATACTGTCTGAGCTGCAGTTCCAGAAAA 45 28 0 CTTGAGCTGG 0.64444 -248 CGCCAGTTCAATGATGGGGCCGCCGAGATTTGAAC 45 82 1 ATGGGGCCGG 0.967537 -194 ATCCTCTCGGCTTTGGGAGCCGGTGACCCGAGTTC 45 113 0 CTGGAGCCGG 0.981906 -163 TTTAATCATTACAGAGGGGCCGTAGGGTAGCCTGG 45 150 0 ACGGGGCCGG 0.988257 -126 GTTTTACCCGCCGCTGTGGGCATTGCGAGGAGCAG 48 14 1 CCGTGGGCAG 0.743139 -287 TGAAAATTATCCGAGGGAGCCGAAGGTTTGGGAGA 57 27 1 CCGGAGCCGG 0.99351 -89 ** ******* * Masking position 9 Map Score: 15.4915 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 263 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TAAAAAAATTAGAAAATCTTTTTCCTCTTG 1 269 0 AGAAAATCTT 0.913262 -32 GATTTGCTGGAGAAGAGCTTTAGGCGGTTT 2 160 0 AGAAGAGCTT 0.926312 -107 ATCAGAAAATCTTATAAGGATTG 3 4 1 AGAAAATCTT 0.913262 -35 CCTTCTAAAGATAAAAGCTGTTATGAATCA 4 58 0 ATAAAAGCTG 0.809249 -47 TGAGTGCTAAATAAAGGCTGTTATGAACTG 5 30 0 ATAAAGGCTG 0.642055 -44 TAGCTTCCTCAGAAAAGCTTGGTAAGGAGT 11 179 0 AGAAAAGCTT 0.96746 -122 GGGATATCACAGAAAAACTTATTTTGACAA 11 266 1 AGAAAAACTT 0.722033 -35 AACCTCAAGAAAAGCTTTGAAA 12 6 0 AGAAAAGCTT 0.96746 -17 CTCAAAATAAAGAAAGGCTTTTATGTTGAG 16 134 1 AGAAAGGCTT 0.926312 -35 GGTTTGTTATATAAAATCTTTTTTCTCGTG 20 24 1 ATAAAATCTT 0.713103 -122 ACGAAACAAAATAAAATCTTTGTCTTCAAA 25 23 1 ATAAAATCTT 0.713103 -171 TGATAATTATGGAAAAGCTTAAATGGTTTG 29 37 0 GGAAAAGCTT 0.80135 -144 CTGCAGTTCCAGAAAAGCTGACAGGTTGAT 45 14 0 AGAAAAGCTG 0.947288 -262 GAGGCGGTGGAGAAGGTCTTTTCCGGCAAA 48 52 0 AGAAGGTCTT 0.653045 -249 AGGAGGGTATAGAAGAGCTGTTTCCGCCTC 48 87 0 AGAAGAGCTG 0.883698 -214 ********** Masking position 4 Map Score: 15.2211 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 253 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 TTAAACGGTTAAAGCTTAATGAATAAATTTGGTGGTG 2 190 0 AATTAATAAA 0.937437 -77 CCAAACGCCCAAACCTTAAATACCAAACCGCCCATCG 2 233 1 AATTAAAAAA 0.79837 -34 ATTAACAACAAAAAGTTAATTAAAAAAAATTTTATAA 6 26 0 AATTAATAAA 0.937437 -70 GTTGTTAATTAATTATTTATCAGGATATTTTTTCTGA 6 54 1 AATTTATAAA 0.798364 -42 GTAACAATTATTAATGAGCAAATATTAAATTT 9 38 0 AATTAATAAA 0.937435 -22 AATTTTACGAAACATTTATTGAACATAACAATTAATC 10 71 1 AATTATTAAA 0.654023 -33 AGTATTCATAAATACTTTATCATCATAAATAAACAAA 13 67 0 AATTTATAAA 0.798364 -65 ACTCATACGAAATTATTATTCAATAAAAAAGGGGTGG 13 101 1 AATTATTAAA 0.654014 -31 AGCATAATTCAATTTTTTAAGATGATAATGAATTTAA 14 24 1 AATTTAAAAA 0.511322 -63 TCCAATTTATAACATTTAATGAGCAAATTTAAATTCA 14 52 0 AATTAATAAA 0.937437 -35 TGCCTTAGATAACAATTTATCGAAATAAATAAAATTC 15 37 1 AATTTATGAA 0.449747 -144 TATTTCACGAAAACATTAAATATTACACGACTACTTT 17 48 1 AATTAAAAAA 0.79837 -32 GGGGGCATGGAATTTTTAATGTCAATAA 21 123 1 AATTAATTAA 0.531389 -18 CTTTAATGTCAATAATTAATTACGAGAGCAAATGAAA 22 67 1 AATTAATAAA 0.937435 -139 TGAATATATCAAGTATTAATTGGAACAAATTCGGTAC 22 123 1 AATTAATGAA 0.755681 -83 ATATTGCCAGATTTGTTAATTATAAAAA 23 2 0 ATTTAATAAA 0.504092 -100 TGGATAAGGTTATGATTAATTAAAAAAC 40 2 0 TATTAATAAA 0.503799 -30 TAACTTGGCAAAATTTAAATAATCACAAAAAGAGCCT 48 272 1 AATAAATAAA 0.504096 -29 CTGAGATATTAAATTTTAATCAAAACAAATAAAAAAA 49 41 0 AATTAATAAA 0.937437 -137 TTTTGACTTTAATGGTTAAACAAAAAAGAAAAAGGTT 49 124 1 AATTAAAAAA 0.79837 -54 ** ***** * * * Masking position 6 Map Score: 15.6975 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 0 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 TAGTGTACGTCGTCTGCCTTTCAATCCCAT 1 81 0 CGTCTGCCTT 0.796555 -220 TCTGATTTCAACTGTTCCTTGACAACGCCC 1 114 0 ACTGTTCCTT 0.484124 -187 GCAAAAGTCGCCATTGCCTTTCAATCCCAT 1 222 0 CCATTGCCTT 0.717978 -79 GACCCTCAATCCTGCGCCTTTGTCCGCTCG 19 185 1 CCTGCGCCTT 0.954081 -116 TACACCACCTTGTTTAACTCT 20 135 0 ACACCACCTT 0.580082 -11 ACCATTGCCGCCTCTGCCTCTTTTGAGCAT 31 19 0 CCTCTGCCTC 0.921102 -85 CCTGTAGGGGCCAGTGCCTTCCGGAAGTCC 36 50 0 CCAGTGCCTT 0.942714 -251 TCGGTGTACTCGACTTCCTCCGGGATGATA 36 196 0 CGACTTCCTC 0.520064 -105 AATACACCTCCTTCACTTTTTTC 36 288 0 ACACCTCCTT 0.790509 -13 GCAGCCATCGCCACCTCCTGCGGTGTGCGG 39 20 0 CCACCTCCTG 0.885727 -281 ATTGAGTGCCCCAGTGCCTGAGCTACATAA 44 61 0 CCAGTGCCTG 0.838684 -115 GACAAGACTGCCTGCTCCTTTATCCTTCTT 44 107 0 CCTGCTCCTT 0.907504 -69 GCTTTAAAAGCCACTGCCTTTAATCATTAC 45 173 0 CCACTGCCTT 0.969979 -103 AAGACCTTCTCCACCGCCTCAGCCTGAGGC 48 62 1 CCACCGCCTC 0.959854 -239 TCTTCTATACCCTCCTCCTTTAAAATGCCA 48 101 1 CCTCCTCCTT 0.95065 -200 TCAGCAAGCTCCTCCACCTTCACCACTTCA 48 152 1 CCTCCACCTT 0.875809 -149 ********** Masking position 9 Map Score: 11.5508 Number of sites scoring better than the average of aligned sites = 1094 Number in coding regions = 1034 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 12 AATCTACATTCATAAAAAAATTAGAAA 1 284 0 ATTCATAAAA 0.840574 -17 GGTGTTCAGAAAAAAGAGGAAAA 2 4 1 GTTCAGAAAA 0.838008 -263 TTATGAATCAGTTCATAACAAAATTATCTG 4 38 0 GTTCATAACA 0.943456 -67 TTATGAACTGATTCATAACAGCTTTTATCT 4 50 1 ATTCATAACA 0.843298 -55 TTATGAACTGGTTCATAAATAAGAAAAAA 5 10 0 GTTCATAAAT 0.883399 -64 TTATGAACCAGTTCATAACAGCCTTTATTT 5 22 1 GTTCATAACA 0.943456 -52 ACCACCATTTGTTCAGAAAAAATATCCTGA 6 73 0 GTTCAGAAAA 0.838008 -23 GGAGTCTCCAGTTCATCAAAATTCAGGCTC 11 154 0 GTTCATCAAA 0.720862 -147 TCGTATGAGTATTCATAAATACTTTATCAT 13 81 0 ATTCATAAAT 0.709096 -51 AAACCACAATATTCATAAATCCTATGCAGA 19 239 0 ATTCATAAAT 0.709096 -62 CATTAGTTGTGTTCATAAATGAAAAAATTT 23 78 1 GTTCATAAAT 0.883399 -24 TGGGCATAGTGCTCATAACAAACATCAACA 29 107 1 GCTCATAACA 0.724647 -74 CAATCTCCTGTTTCATAACATTCACTAAGC 53 19 0 TTTCATAACA 0.620594 -25 ********** Masking position 5 Map Score: 7.39008 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 ACGATTATCGCAGCAATTGTTTTTTACTTTT 2 30 0 CAGCAATGTT 0.860841 -237 ATAAAATTCTCGGCAACTGCTACAAATCAAA 15 65 1 CGGCAACGCT 0.980377 -116 GCAGCAAACTATGCAACAGTTTTTAAAATCG 16 30 0 ATGCAACGTT 0.718891 -139 TTTTAAAGAGAGGCAACAGTTAGTATAATGT 20 86 1 AGGCAACGTT 0.85699 -60 ATGAGTGTATCTGCAAAAGCTTTATATTGCC 23 31 0 CTGCAAAGCT 0.853295 -71 GAGGCAGAGGCGGCAATGGTTAGGTTCTGAT 31 29 1 CGGCAATGTT 0.964344 -75 ACCCCCATTTCGGAAATTGTTGAGTTTATCA 39 249 1 CGGAAATGTT 0.856536 -52 TCTATCACCCTGCAAACGTTTTTCAAATAA 47 19 0 CTGCAAAGTT 0.833916 -20 CAGCCTGAGGCGGAAACAGCTCTTCTATACC 48 81 1 CGGAAACGCT 0.916869 -220 CTTTCACTTCCAGCAACTGCTTTCTACATAT 50 64 0 CAGCAACGCT 0.919533 -24 AATACAAATTCGGCAATTGTTGAA 56 4 0 CGGCAATGTT 0.964344 -64 TAGCAGATTGCTGAAATAGCTCC 58 73 1 CTGAAATGCT 0.746931 -13 ******* *** Masking position 6 Map Score: 8.68619 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 164 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 GAAGTTACCGTTTTCCCCCGAACAACAACTGAC 13 21 1 TTTTCCCGAC 0.880741 -111 ACCTCAAAATTTTTTCCCACCTGACTATATAAC 29 75 0 TTTTCCCCCG 0.94406 -106 GTTATGAGCACTATGCCCACCTCAAAATTTTTT 29 93 0 CTATCCCCCC 0.961597 -88 TTCCAGTACATTTTTCCCTGCCCGGAG 32 16 1 TTTTCCCGCC 0.977127 -17 CTGTGAAGACTTATGCCCACAACATCCACGTCT 39 59 0 TTATCCCCAC 0.898534 -242 GATGAAGTGTTTATTCCCGGCACCCCCATTTCG 39 228 1 TTATCCCGCC 0.971969 -73 TTAAAAAACGGTTTTCCCGCCAGTTCAATGATG 45 65 1 GTTTCCCCCG 0.817598 -211 AGGGTTTTACCCGCCGCTGTGGGCATT 48 5 1 TTTTCCCCCC 0.984402 -296 AACAGCTCTTCTATACCCTCCTCCTTTAAAATG 48 95 1 CTATCCCCCC 0.961597 -206 TACCTCCCCATTCTACCCTGCTC 59 18 1 TTCTCCCGCC 0.939834 -13 **** *** ** * Masking position 4 Map Score: 6.99769 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 142 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 15 GAATAAATTTGGTGGTGGATTTGCTGGAGA 2 177 0 GGTGGTGGAT 0.965572 -90 TTTCTAATTTGGAGGTGTTTAG 4 93 1 GGAGGTGTTT 0.584986 -12 CTTCCCATTCGTTTGTGGATGGTTCACTCT 11 29 0 GTTTGTGGAT 0.687898 -272 TTTGAGTACGGGAGGTGGTTGTTTGAGGAG 11 224 1 GGAGGTGGTT 0.929237 -77 GGAGGTGGTTGTTTGAGGAGTGAAATTATT 11 234 1 GTTTGAGGAG 0.408234 -67 GTAGAAGGTGGATTTCAAAGTTA 19 288 0 GAAGGTGGAT 0.783595 -13 TTCCTCTCTTGTTGGTGGTTCGGTGTACTC 36 215 0 GTTGGTGGTT 0.824825 -86 AAAAAGTGAAGGAGGTGTATT 36 290 1 GGAGGTGTAT 0.798576 -11 GCACACCGCAGGAGGTGGCGATGGCTGCAG 39 22 1 GGAGGTGGCG 0.86351 -279 GCTGATCCTCGTTGGTGGAGTTATTCCGAC 39 164 1 GTTGGTGGAG 0.915807 -137 CTCAGGCTGAGGCGGTGGAGAAGGTCTTTT 48 60 0 GGCGGTGGAG 0.876358 -241 GCATTTTAAAGGAGGAGGGTATAGAAGAGC 48 99 0 GGAGGAGGGT 0.843801 -202 AAGTGGTGAAGGTGGAGGAGCTTGCTGAAA 48 150 0 GGTGGAGGAG 0.897732 -151 AGAGGAAGGCGTATGTGGATTATGCAATAT 57 68 1 GTATGTGGAT 0.743766 -48 TGGAAGAATGGTAGGAGGGTTAGAGCTATG 58 31 1 GTAGGAGGGT 0.718384 -55 ********** Masking position 5 Map Score: 6.49315 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 1072 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899