AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00061_aful_reg_100.orf -o00061_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) 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 AF0135 59 conserved hypothetical protein #7 AF0136 103 A. fulgidus predicted coding region AF0136 #8 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #9 AF0197 86 acetyl-CoA synthetase (acs-1) #10 AF0220 180 biotin carboxylase (acc) #11 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #12 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #13 AF0439 82 transcriptional regulatory protein, AsnC family #14 AF0442 300 succinoglycan biosynthesis regulator (exsB) #15 AF0685 140 enoyl-CoA hydratase (fad-2) #16 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #17 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #18 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #19 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #20 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #21 AF1191 32 dihydroxynaphthoic acid synthase (menB) #22 AF1192 50 conserved hypothetical protein #23 AF1195 27 activator 1, replication factor C, 53 KD subunit #24 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #25 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #26 AF1208 165 conserved hypothetical protein #27 AF1289 300 conserved hypothetical protein #28 AF1641 31 enoyl-CoA hydratase (fad-4) #29 AF1642 50 histidyl-tRNA synthetase (hisS) #30 AF2013 275 coenzyme F390 synthetase (ftsA-3) #31 AF2014 63 sugar transporter, putative #32 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #33 AF2244 300 acyl-CoA dehydrogenase (acd-11) #34 AF2271 177 A. fulgidus predicted coding region AF2271 #35 AF2272 87 A. fulgidus predicted coding region AF2272 #36 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #37 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) #38 AF2426 85 conserved hypothetical protein #39 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 AATTAACAACAAAAAGTTAATTAAAAAAAATT 3 32 0 AAAATTAATT 0.850354 -64 ATTGACAAAGAAAAGTTAAAAA 4 1 0 AAAATAAAAA 0.801477 -54 TAAATTCCTTAAAAATTTAATATTTGCTCATT 6 26 1 AAAATTAATA 0.899894 -34 GGGAAAACAGGAAGTTACCGTTTTC 8 4 1 AAAAGGAAGT 0.693534 -128 TATCATCTTAAAAAATTGAATTATGCTCAAAG 9 19 0 AAAATGAATT 0.84412 -68 TATATATCCAAAAAATTTAAGTTTGCTCTGCC 11 90 0 AAAATTAAGT 0.796288 -79 ATATTTCACGAAAACATTAAATATTACACGAC 12 47 1 AAAATTAAAT 0.811236 -33 AAGTAAACTAAAAATATAAAAATTTTATGTTT 13 54 0 AAAATAAAAA 0.801477 -29 GTTAAAAACAAAAATATAAAAATAAAAAT 16 8 0 AAAATAAAAA 0.801477 -198 CTAAACGCGTAAAAATTGAATATATCAAGTAT 16 107 1 AAAATGAATA 0.89547 -99 ATGTCAAATCAAAATCTTAAATTGAGATAAAA 17 49 0 AAAATTAAAT 0.811236 -102 AAATTTCGTAAAAATAGTAAGAATTATAAAGG 17 101 1 AAAAGTAAGA 0.789769 -50 AATATAATCCAAAAAAGTAATTCACTAAAAGC 18 64 0 AAAAGTAATT 0.775389 -130 ATATTTTCGCAAAATCTGAAAAATTTGAATGG 18 91 1 AAAATGAAAA 0.86629 -103 TTTTTTACTAAAAATGGTAATAGAGGCGTAAT 19 11 0 AAAAGTAATA 0.845229 -101 AGATTTCAACAAAAGTGGAATTTTTTACTAAA 19 31 0 AAAAGGAATT 0.766889 -81 AAATTACAGCAAAATAGTAATATATATGTTAA 22 16 1 AAAAGTAATA 0.845229 -35 TATCTGTTGGAAAAAATAAAAATTAAAA 24 7 0 AAAATAAAAA 0.801477 -59 TCTGTTAAAGAAAAGGTAAATACTACAAATAG 26 16 0 AAAATAAATA 0.842225 -150 TTTAGCTTCAAAAAAGTTAATTTAAGTATGTT 26 142 0 AAAATTAATT 0.850354 -24 AAGCTGCCAGAAAAGAGGAAGAAAGA 27 285 1 AAAAGGAAGA 0.781659 -16 TAAAGAATTAAAAAGCTAAAAATTTTATGCAA 31 35 0 AAAATAAAAA 0.801477 -29 TGCACCGTTGAAAACTTGAAGTGGTGAAGGTG 33 166 0 AAAATGAAGT 0.788362 -135 TTAACTTGGCAAAATTTAAATAATCACAAAAA 33 271 1 AAAATAAATA 0.842225 -30 ACAAAAAAGAAAAAGGTTAAAACTTAGTCAAC 34 143 1 AAAATTAAAA 0.871773 -35 AATAAAATGGAAAAACTTAATACAT 36 43 1 AAAATTAATA 0.899894 -15 **** ****** Masking position 4 Map Score: 28.4537 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 121 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 ATAGGGTGTTCCTTCAACCCCTACTCAATCTCCTTCT 7 20 0 CCCCCCCCTA 0.992476 -84 ACCACCACCCCTTTTTTATTGAATAATA 8 114 0 CCCCCCTTTA 0.982475 -18 GGGTTCGAATCCCTCCCCCCGCATTTAGTTCTGTTCG 14 129 0 CCCCCCGTTA 0.978832 -172 CTTTGTCCGCTCGGCAACCCCCGCTCAGATGAAAAAT 14 202 1 TCCCCCCCTA 0.942949 -99 GGTCGAGGAGTCCGCAGCCCCTCAGGATATCCGCTAC 15 69 0 TCCCCCCAGA 0.741504 -72 GGCTGCGGACTCCTCGACCCGGGTTCAACTCCCGGCG 15 87 1 TCCCCCGTTA 0.852819 -54 AATACACCTCCTTCACTTTTTTCTTATTAAAAT 25 278 0 CCCCACTTTC 0.894703 -23 TCCACTGCAGCCATCGCCACCTCCTGCGGTGTGCGGT 27 19 0 CCCCACCCTC 0.952362 -282 TAGTTTATGACCTTCGGCACTAAAGCAAGATGAGCAC 27 94 0 CCCCACTAGA 0.733792 -207 TGGATTGCCCCCGTATTCCCTTATGTAGTTTATGACC 27 119 0 CCACCCTTGA 0.665202 -182 GTGTTTATTCCCGGCACCCCCATTTCGGAAATTGTTG 27 234 1 CCCCCCCTTG 0.952475 -67 GCTTTGGGAGCCGGTGACCCGAGTTCAAATCTCGGCG 30 102 0 CCTCCCGTTA 0.683528 -174 ACCAGGCTACCCTACGGCCCCTCTGTAATGATTAAAG 30 149 1 CCCCCCCTGA 0.991157 -127 GTATTTAAATCCTGCCTCCCTCATGACAGAAAGATAC 30 241 1 CCCCCCTTGC 0.9531 -35 CCGGAAAAGACCTTCTCCACCGCCTCAGCCTGAGGCG 33 56 1 CCCCACCCTA 0.976661 -245 GCAAGCTCCTCCACCTTCACCACTTCAAGTTTTCAAC 33 155 1 CCCCACCTTA 0.979107 -146 TTTTTATATGCCACCATCAACTTCTCAAC 34 3 0 CCCCAACCTA 0.775112 -175 TTCTCCCAAACCTTCGGCTCCCTCGGATAATTTTCAA 37 26 0 CCCCTCCCGA 0.868286 -90 TAGCTCTAACCCTCCTACCATTCTTCCAAAACACACA 38 22 0 CCCCCATTTC 0.688069 -64 ** * **** ** * Masking position 8 Map Score: 19.4053 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 677 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 AAAAGTTAATTAAAAAAAATTTTATAAAATGA 3 21 0 TAAAAAATTT 0.74277 -75 TCACCTCCAATTTATAACATTTAATGAGCAAA 9 62 0 TTATAACTTT 0.684955 -25 TAGGCTAAGCTGTAAATCGTTTTCGGTGCCTT 10 11 1 TTAAATCTTT 0.816738 -170 AGCCACCGATTTAAAAACCTTTTTTCAAATAG 10 143 0 TAAAAACTTT 0.924425 -38 TACTCCGATTTTAAAAACTGTTGCATAGTTTG 11 25 1 TAAAAACGTT 0.83797 -144 AAACTAAAAATATAAAAATTTTATGTTTGCCA 13 50 0 TTAAAAATTT 0.848635 -33 TTGCGAAAGATTTAAAACTTTTCGGTAGGAGT 17 17 0 TTAAAACTTT 0.959595 -134 TTTTCAGCCTTTTAAAACTTTTCGCTTTTTAC 18 158 0 TTAAAACTTT 0.959595 -36 TTCGCTCAACTCTAAAACCTTTTAAACACCCT 29 14 1 TTAAAACTTT 0.959595 -37 CTGGCAGTATTAAAAAACGGTTTTCCCGCCAG 30 56 1 TAAAAACGTT 0.83797 -220 GGCAGTGGCTTTTAAAGCCTTTTGCTGCAAAC 30 185 1 TTAAAGCTTT 0.789291 -91 TTTTATTATTTGAAAAACGTTTGCAGGGTGAT 32 14 1 TAAAAACTTT 0.924425 -25 TTGTGTTCTATTTAAATCCTTTTTCAATTGTT 33 240 1 TTAAATCTTT 0.816738 -61 GATGGTGGCATATAAAAAATTTTTTTATTTGT 34 22 1 TTAAAAATTT 0.848635 -156 GAACTTATGGTGTAAAAAAGTT 36 1 0 TTAAAAAGTT 0.703307 -57 * ****** *** Masking position 6 Map Score: 15.6866 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 21 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 GTCAGATAATTTTGTTATGAACTGATTCATAACAG 1 36 1 TTTTTGACGA 0.485562 -69 TTTTTTCTTATTTATGAACCAGTTC 2 1 1 TTTTTTATAT 0.916312 -73 ATTTTATAAAATTTTTTTTAATTAACTTTTTGTTG 3 23 1 ATTTTTATAA 0.589632 -73 TAATTAACTTTTTGTTGTTAATTAATTATTTATCA 3 41 1 TTTTTTATAA 0.923027 -55 TATCAGGATATTTTTTCTGAACAAATGGTGGTTGT 3 71 1 TTTTTGACAA 0.681828 -25 TTCTTTGTCAATTATCGTTATTAAAAAGAGAACTT 4 21 1 ATTTTTATAA 0.589633 -34 AATTTAATATTTGCTCATTAATAATTGTTAC 6 39 1 TTGTTTATAT 0.51139 -21 ATTTTTGATTAATTGTTATGTTCAAT 7 88 0 TTTTTTATGT 0.821088 -16 TGATAAAGTATTTATGAATACTCATACGAAATTAT 8 82 1 TTTTATATAT 0.567049 -50 CACCACCCCTTTTTTATTGAATAATAATTTCGTAT 8 105 0 TTTTTGATAT 0.878386 -27 AAAGCCTTTCTTTATTTTGAGTGGTTTGAAGCCTA 11 120 0 TTTTTGATGT 0.751702 -49 AAGAAAGGCTTTTATGTTGAGTAAATAAAGGCAAA 11 143 1 TTTTTGATAA 0.887929 -26 TATTTAAGTGTTTCTTATTAGTGTAGGCATTGCCT 19 66 0 TTTTTTATTA 0.491023 -46 AACAGGGAGATTTCTCATTACTTATACTTTAACTA 24 37 0 TTTTTTATAT 0.916312 -29 CCTCCTTCACTTTTTTCTTATTAAAATACCATCCG 25 270 0 TTTTTTATAA 0.922928 -31 GTTTTTTAATTAATCATAACCTTATCC 28 3 1 TTTTTTATAT 0.916309 -29 AGTGTGCATTTTATGCATATTTATTTGCATAAAA 31 10 1 TTTTATATAT 0.567064 -54 ATTTTTTATTATTTGAAAAACGTTTG 32 2 1 TTTTTTATGA 0.834285 -37 GCAGGCTCTTTTTGTGATTATTTAAATTTTGCCAA 33 276 0 TTTTTTATAA 0.923142 -25 AATTTTTTTATTTGTTTTGATTAAAATTTAATATC 34 39 1 TTTTTGATAA 0.887828 -139 ACCTTTTTCTTTTTTGTTTAACCATTAAAGTCAAA 34 125 0 TTTTTTACAT 0.756832 -53 *** * *** * ** Masking position 5 Map Score: 15.3847 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 18 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTTGTTGTTAATTAATTATTTATCAGGATA 3 51 1 ATTAATTATT 0.714418 -45 ATGAGCAAATATTAAATTTTTAAGGAATTT 6 27 0 ATTAAATTTT 0.540404 -33 ATATTTGCTCATTAATAATTGTTAC 6 45 1 ATTAATAATT 0.860482 -15 TTTTTTATTGAATAATAATTTCGTATGAGT 8 101 0 AATAATAATT 0.512469 -31 CAGAACGACCATTAAAGATTTTGCAGCAAA 11 53 0 ATTAAAGATT 0.753213 -116 TCACGAAAACATTAAATATTACACGACTAC 12 52 1 ATTAAATATT 0.871227 -28 CCCCGCTCAGATGAAAAATTCTGCATAGGA 14 220 1 ATGAAAAATT 0.702752 -81 TTATTGACATTAAAAATTCCATGCCCCC 15 123 0 ATTAAAAATT 0.941881 -18 TGCTCTCGTAATTAATTATTGACATTAAAG 16 67 0 ATTAATTATT 0.714418 -139 ATTAAAAATTACAGCAAAAT 22 1 1 ATTAAAAATT 0.941881 -50 TGTTGGAAAAAATAAAAATTAAAA 24 5 0 AATAAAAATT 0.737582 -61 TCAACGGTGCATTAAAAATTGCTCCTCGTT 33 187 1 ATTAAAAATT 0.941881 -114 ATGGTGGCATATAAAAAATTTTTTTATTTG 34 23 1 ATAAAAAATT 0.614665 -155 ATTTGTTTTGATTAAAATTTAATATCTCAG 34 48 1 ATTAAAATTT 0.737726 -130 CACCGATGCGATTGAAAATTATCCGAGGGA 37 15 1 ATTGAAAATT 0.687401 -101 ********** Masking position 5 Map Score: 8.93833 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 13 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 CTAAATGCGGGGGGAGGGATTCGAACCCTCGA 14 138 1 GGGAGGGATC 0.803563 -163 GCGGACAAAGGCGCAGGATTGAGGGTCCTGTC 14 180 0 GGCAGGATTA 0.7649 -121 CTCCGGGCAGGGAAAAATGTACTGGA 21 17 0 GGCAGGGAAA 0.971663 -16 CGAAATGGGGGTGCCGGGAATAAACACTTCAT 27 229 0 GGCCGGGAAA 0.965763 -72 TGCCAGAAAAGAGGAAGAAAGA 27 289 1 GGGAAGAAAA 0.773825 -12 CATCATTGAACTGGCGGGAAAACCGTTTTTTA 30 66 0 CGGCGGGAAA 0.854304 -210 AATGCCCACAGCGGCGGGTAAAACCCT 33 6 0 GGGCGGGTAA 0.975641 -295 GCCTCAGCCTGAGGCGGAAACAGCTCTTCTAT 33 77 1 GGGCGGAAAA 0.952958 -224 CATTTTAAAGGAGGAGGGTATAGAAGAGCTGT 33 96 0 GGGAGGGTAA 0.979874 -205 TGAAGCACAGGAGGAAGATAAAGGC 37 101 1 GGGAAGATAA 0.713078 -15 AGGGTAGAATGGGGAGGTATAAACCT 39 5 0 GGGAGGTATA 0.726848 -26 GAGCAGGGTAGAATGGGGAGGT 39 19 0 GGCAGGGTAA 0.961401 -12 * ******** * Masking position 7 Map Score: 6.82153 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 445 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TCTCTCCCAATTTTACGAAACATTTATTGA 7 63 1 TTTTACGAAA 0.968464 -41 ATTACTTGGATTTTACGTATTCTTGCAGTT 10 113 1 TTTTACGTAT 0.759666 -68 AAAATTCATATTTCACGAAAACATTAAATA 12 40 1 TTTCACGAAA 0.84797 -40 AATACTTAAATTTTACGTAATGTGCCGATT 16 180 0 TTTTACGTAA 0.909084 -26 TTCTTACTATTTTTACGAAATTTTTTCAAA 17 94 0 TTTTACGAAA 0.968464 -57 ATTTTTCAGATTTTGCGAAAATATAATCCA 18 85 0 TTTTGCGAAA 0.85656 -109 ACTTTTCGCTTTTTACGAAATTAAATAAGT 18 144 0 TTTTACGAAA 0.968464 -50 AAGTGGAATTTTTTACTAAAAATGGTAATA 19 21 0 TTTTACTAAA 0.75617 -91 CTTTAACAGATTTTTCGAATTGTTCAAGCG 26 38 1 TTTTTCGAAT 0.641883 -128 ********** Masking position 3 Map Score: 7.46021 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 13 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 GTTTATTTATGATGATAAAGTATTTATGAATACTCA 8 70 1 GTGAAGTTTA 0.984732 -62 AATTTTTTAAGATGATAATGAATTTAAATTTGCTCA 9 34 1 GTGAAGATTA 0.965587 -53 TTGGGGCTTTGAAGACAAAGATTTTATTTTGTTTCG 18 24 0 GAGAAGATTA 0.853483 -170 AGGACGTAACGTTGAGGACGTGTTGAATAACAGCTC 25 151 1 GTGAAGTTTA 0.984732 -150 AAAGATGGGGGTTGATGAAGTGTTTATTCCCGGCAC 27 215 1 GTGAAGTTTA 0.984732 -86 CGTTTTTCAGGATGGTGAAGTATTTAAATCCTGCCT 30 222 1 GTGGAGTTTA 0.952029 -54 GTCAAATTGGGTTGACTAAGTTTTAACCTTTTTCTT 34 149 0 GTGAAGTTTA 0.984732 -29 * *** * ** ** * Masking position 8 Map Score: 4.22189 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 12 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ATTTTGAGGAATGTTGCAATA 5 12 1 ATGTTGCAAT 0.622271 -11 ATACGTATTCTTGTTGCAATTACTTGGATT 10 95 1 TTGTTGCAAT 0.912666 -86 GTTGCATAGTTTGCTGCAAAATCTTTAATG 11 44 1 TTGCTGCAAA 0.932756 -125 AATTCCACTTTTGTTGAAATCTGCAAGGCA 19 41 1 TTGTTGAAAT 0.834978 -71 TATTACTATTTTGCTGTAATTTTTAAT 22 8 0 TTGCTGTAAT 0.859355 -43 TTAAAGCCTTTTGCTGCAAACGCATTCGTT 30 196 1 TTGCTGCAAA 0.932756 -80 GTGGAGGAGCTTGCTGAAAGCATCTCAAGT 33 139 0 TTGCTGAAAG 0.912194 -162 TAGAAAGCAGTTGCTGGAAGTGAAAGGGT 35 69 1 TTGCTGGAAG 0.859032 -19 AAATAGCAGATTGCTGAAATAGCTCC 38 70 1 TTGCTGAAAT 0.939167 -16 ********** Masking position 5 Map Score: 4.65558 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 155 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 10 TTTAGAAGGCCTATTTTCTAATTTGGAGGTGT 1 79 1 CTTTTTTAAT 0.906028 -26 ATTTTATAAAATTTTTTTTAATTAACTTTTTG 3 23 1 ATTTTTTAAT 0.773467 -73 GCATAATTCAATTTTTTAAGATGATAATGAAT 9 25 1 ATTTTTAGAT 0.484298 -62 ATTTAAAAACCTTTTTTCAAATAGAACTGCAA 10 135 0 CTTTTTAAAT 0.944146 -46 ACTATGCAACAGTTTTTAAAATCGGAGTACCA 11 22 0 AGTTTTAAAT 0.654094 -147 GGCGGATTATCTATTTTTAAATCGGCACATTA 16 161 1 CTTTTTAAAT 0.944148 -45 TTGATTTGACATACTTTGAAATTTATTTGAAA 17 69 1 ATCTTTAAAT 0.733681 -82 TTTTTACGAAATTTTTTCAAATAAATTTCAAA 17 83 0 ATTTTTAAAT 0.856814 -68 ATTTGGAATCCTCCTTTATAATTCTTACTATT 17 113 0 CTCTTTTAAT 0.816072 -38 TGAATAACAGCTCTTTTGAAATTATCATCCCG 25 174 1 CTTTTTAAAT 0.944147 -127 ACCTCCTTCACTTTTTTCTTATTAAAATACCA 25 274 0 CTTTTTTTAT 0.506422 -27 GGCGGGAAAACCGTTTTTTAATACTGCCAGAT 30 54 0 CCTTTTTAAT 0.623373 -222 ACCCTGCAAACGTTTTTCAAATAATAAAAAAT 32 11 0 CGTTTTAAAT 0.842286 -28 CTATACCCTCCTCCTTTAAAATGCCAACAGCA 33 105 1 CTCTTTAAAT 0.886094 -196 ** **** **** Masking position 11 Map Score: 6.70768 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 40 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 ACCAGTTCATAACAGCCTTTATTTAGCACTC 2 28 1 AACGCCTTTA 0.902142 -46 GGGTTGAAGGAACACCCTATACATCATCTCT 7 37 1 AACCCCTATA 0.75696 -67 GGAAAACGGTAACTTCCTGTTTTCCC 8 6 0 AACTCCTGTT 0.696582 -126 ATATGAAGTCATCGCCCTTTAAACCACAATA 14 258 0 ATCCCCTTTA 0.953816 -43 AAAATAGATAATCCGCCTGTACCGAATTTGT 16 147 0 ATCGCCTGTA 0.944552 -59 CATATTTGGAATCCTCCTTTATAATTCTTAC 17 117 0 ATCTCCTTTA 0.913133 -34 GTAATGAGAAATCTCCCTGTTGGCT 24 51 1 ATCCCCTGTT 0.861299 -15 AATCTGCGTTATCACCCTGTAGGGGCCAGTG 25 64 0 ATCCCCTGTA 0.965175 -237 AATACACCTCCTTCACTTTTTTCTT 25 286 0 CACTCCTTCA 0.596684 -15 CTTTAAAAGCCACTGCCTTTAATCATTACAG 30 171 0 CACGCCTTTA 0.83753 -105 TCTATCACCCTGCAAACGTTTTTC 32 25 0 ATCCCCTGCA 0.905709 -14 CTTCTATACCCTCCTCCTTTAAAATGCCAAC 33 102 1 CTCTCCTTTA 0.85458 -199 *** ******* Masking position 8 Map Score: 5.3981 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 181 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 GAGGGTCCTGTCCCGTAGGGGTTCGAGGGTT 14 161 0 TCCGTAGGGG 0.804345 -140 GAATTTTTCATCTGAGCGGGGGTTGCCGAGC 14 210 0 TCGAGCGGGG 0.937533 -91 ATCCGCTACCCCACGGGGGCGACGTGGAAAA 15 47 0 CCCGGGGGCG 0.921852 -94 CGGGTTCAACTCCCGGCGGGGGCATGGAATT 15 106 1 TCCGGCGGGG 0.946407 -35 CTCCGGGCAGGGAAAAATGTAC 21 21 0 TCGGGCAGGG 0.754444 -12 GCATAAGTCTTCACAGCGGTGCTCATCTTGC 27 76 1 TCCAGCGGTG 0.964508 -225 AGATGCTGATCCTCGTTGGTGGAGTTATTCC 27 160 1 CCCGTTGGTG 0.588033 -141 CGAGTTCAAATCTCGGCGGCCCCATCATTGA 30 89 0 TCCGGCGGCC 0.928399 -187 CTCGCAATGCCCACAGCGGCGGGTAAAACCC 33 12 0 CCCAGCGGCG 0.968087 -289 TAATTTTCAATCGCATCGGTGACCC 37 5 0 TCCATCGGTG 0.884633 -111 ** ******** Masking position 2 Map Score: 2.8546 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 251 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 TTTTAATCAAAAGTCAGATAATTTTGTTATGAA 1 24 1 AAGTAGAAAT 0.414068 -81 ACAAAAAGTTAATTAAAAAAAATTTTATAAAAT 3 23 0 AATTAAAAAT 0.592794 -73 AATTCCTTAAAAATTTAATATTTGCTCATTAAT 6 28 1 AAATTAAATT 0.597739 -32 CAATTTATCGAAATAAATAAAATTCTCGGCAAC 10 49 1 AAATAATAAT 0.333496 -132 CAACTGCTACAAATCAAATACGTATTCTTGTTG 10 78 1 AAATAAAACT 0.593641 -103 AGTAAACTAAAAATATAAAAATTTTATGTTTGC 13 52 0 AAATTAAAAT 0.608834 -31 AAGCATGTCCAAGTAAAAGATATCTCTGATGAC 14 76 0 AAGTAAAATT 0.880849 -225 TTTTTAAAGGAAAGATTTATCTTGCAAG 15 6 1 AAAGAAAATT 0.465276 -135 CAGCGTGTTAAAAACAAAAATATAAAAATAAAA 16 13 0 AAAAAAAATT 0.508666 -193 TTACGAGAGCAAATGAAAAATCTAAACGCGTAA 16 86 1 AAATAAAATT 0.885797 -120 AAACGCGTAAAAATTGAATATATCAAGTATTAA 16 109 1 AAATGAAATT 0.629567 -97 TGGGGCTTTGAAGACAAAGATTTTATTTTGTTT 18 26 0 AAGAAAAATT 0.496621 -168 GCTTTTTACGAAATTAAATAAGTATTTATTCTC 18 134 0 AAATAAAAAT 0.885813 -60 AAGAATTAAAAAGCTAAAAATTTTATGCAAATA 31 32 0 AAGCAAAATT 0.453321 -32 GGAAATTTAAAGAATTAAAAAGCTAA 31 48 0 AATTAAAAAT 0.592624 -16 AAATTTTGCCAAGTTAAACAATTGAAAAAGGAT 33 255 0 AAGTAAAAAT 0.880805 -46 TAATCAAAACAAATAAAAAAATTTTTTATATGC 34 29 0 AAATAAAAAT 0.885559 -149 GTTTTGATTAAAATTTAATATCTCAGGTAATTT 34 52 1 AAATTAAATT 0.611346 -126 TTAACTGCAGAAGTTAAAAAATTACCTGAGATA 34 70 0 AAGTAAAAAT 0.880805 -108 TTAACCATTAAAGTCAAAAATTTACCTTTCAAG 34 110 0 AAGTAAAATT 0.880596 -68 ATAACGAATAAAATGGAAAAACTTAATACAT 36 37 1 AAATGAAAAT 0.62957 -21 **** *** ** * Masking position 13 Map Score: 8.08009 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 42 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 14 ACAACCACCATTTGTTCAGAAAAAATATCCTGA 3 73 0 TTTGTTCAAA 0.877426 -23 GCATTTATGCTCATGTAAATTCCTTAAA 6 6 1 TATGCTCAAA 0.956959 -54 AAATTTAATATTTGCTCATTAATAATTGTTAC 6 38 1 TTTGCTCAAT 0.869808 -22 GATTAATTGTTATGTTCAATAAATGTTTCGTAA 7 75 0 TATGTTCAAA 0.813956 -29 TGAATTTAAATTTGCTCATTAAATGTTATAAAT 9 52 1 TTTGCTCAAA 0.976484 -35 AAAATTTAAGTTTGCTCTGCCAATAGTCCAGAA 11 78 0 TTTGCTCTAA 0.929625 -91 AGATTTTTCATTTGCTCTCGTAATTAATTATTG 16 76 0 TTTGCTCTAA 0.930527 -130 GGGGGAATATGCTCAAAAGAGGCAGAGGCG 20 8 1 TATGCTCAGA 0.838571 -96 ATTCTCTTCGTTTGCTCATCAAAACCGTAAACA 25 97 0 TTTGCTCAAA 0.95534 -204 ******** ** Masking position 6 Map Score: 6.19305 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 22 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 TATCCAAAAAATTTAAGTTTGCTCTGCCAA 11 88 0 ATTTAAGTTT 0.773522 -81 TTTAATTGCAATTAAAGTGTAAGTATC 13 8 0 ATTAAAGTGT 0.708608 -75 ATTACGTAAAATTTAAGTATTAACGAA 16 189 1 ATTTAAGTAT 0.918281 -17 TGTCTTTAACTATTTTTTCAGCC 18 181 0 CTTTAACTAT 0.795786 -13 TAATGATATTATTTAAGTGTTTCTTATTAG 19 80 0 ATTTAAGTGT 0.931365 -32 ATTACTTATACTTTAACTATCTGTTGGAAA 24 26 0 CTTTAACTAT 0.795786 -40 GGGTCCAATTCTTTAAGTGTGTCGATTTCC 25 241 0 CTTTAAGTGT 0.930074 -60 AAAAAAGTTAATTTAAGTATGTTTTCAATA 26 135 0 ATTTAAGTAT 0.918281 -31 ********** Masking position 5 Map Score: 1.52432 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 11 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925