AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_aful_reg_100.orf -o00310_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 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 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #6 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #7 AF0439 82 transcriptional regulatory protein, AsnC family #8 AF0442 300 succinoglycan biosynthesis regulator (exsB) #9 AF0685 140 enoyl-CoA hydratase (fad-2) #10 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #11 AF0991 260 glutaryl-CoA dehydrogenase (gcdH) #12 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #13 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #14 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #15 AF1191 32 dihydroxynaphthoic acid synthase (menB) #16 AF1192 50 conserved hypothetical protein #17 AF1195 27 activator 1, replication factor C, 53 KD subunit #18 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #19 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #20 AF1208 165 conserved hypothetical protein #21 AF1305 72 D-arabino 3-hexulose 6-phosphate formaldehyde lyase (hps-2) #22 AF1306 77 conserved hypothetical protein #23 AF1641 31 enoyl-CoA hydratase (fad-4) #24 AF1642 50 histidyl-tRNA synthetase (hisS) #25 AF1855 180 2,3-dihydrosybenzoate-AMP ligase (entE) #26 AF2013 275 coenzyme F390 synthetase (ftsA-3) #27 AF2014 63 sugar transporter, putative #28 AF2271 177 A. fulgidus predicted coding region AF2271 #29 AF2272 87 A. fulgidus predicted coding region AF2272 #30 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #31 AF2426 85 conserved hypothetical protein #32 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 AGTTAATTAAAAAAAATTTTATAAAATGATTTGTC 3 15 0 AAAAATTTAA 0.954233 -81 ATTTGTTCAGAAAAAATATCCTGATAAATAATTAA 3 62 0 AAAAATATAT 0.849366 -34 CTATATATCCAAAAAATTTAAGTTTGCTCTGCCAA 5 88 0 AAAAATTTTT 0.849349 -81 CTAAAAATATAAAAATTTTATGTTTGCCATTAAAT 7 44 0 AAAAATTTTT 0.848391 -39 CTTGAACCTCAAAAAATATAACGAAACTTTCGGAT 11 30 1 AAAAATATAA 0.758796 -231 AAGATTTCGGAAAAAGTTTGCCAATAAAGATGTAG 11 188 0 AAAAATTTAT 0.973939 -73 AATTTATTTGAAAAAATTTCGTAAAAATAGTAAGA 12 88 1 AAAAATTTAA 0.954233 -63 CACTAATAAGAAACACTTAAATAATATCATTATCA 13 78 1 AAACATTAAT 0.738514 -34 TTTAGCTTCAAAAAAGTTAATTTAAGTATGTTTTC 20 139 0 AAAAATTAAA 0.870916 -27 GCGAACTCCAAAAAATTTATTACATATCCGGAGAC 21 40 1 AAAAATTAAT 0.923671 -33 GCTTAACGAAAAAAAATTTTAAAATGGCGGTTGTA 22 45 1 AAAAATTTAT 0.973939 -33 CTTTAATTTTAAAAAATTTCCTAAACTACCGCAAA 25 66 0 AAAAATTTAA 0.954233 -115 GTCAACATTTAAACAATTTTAACATTACCAACTTT 25 117 1 AAACATTTAT 0.89714 -64 CAAATCCCTTAAAAAATTTCCCGATTAAAGTTGGT 25 143 0 AAAAATTTAT 0.973939 -38 TTAAAAAGCTAAAAATTTTATGCAAATAAATATGC 27 25 0 AAAAATTTAA 0.954233 -39 GGTGGCATATAAAAAATTTTTTTATTTGTTTTGAT 28 25 1 AAAAATTTAT 0.973853 -153 AATAAAATGGAAAAACTTAATACAT 30 43 1 AAAAATTAAT 0.923671 -15 ***** *** ** Masking position 7 Map Score: 22.4529 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 58 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 CCAAATCAAGTTATTTTAATCAAAAGTCAGATAA 1 11 1 TTTTATCAAA 0.810713 -94 TTTTTTCTTATTTATGAACCAGTTC 2 2 1 TTTTATTTAT 0.541373 -72 TTTTATAAAATTTTTTTTAATTAACTTTTTGTTG 3 24 1 TTTTAATTAA 0.742788 -72 AATTAACTTTTTGTTGTTAATTAATTATTTATCA 3 42 1 TTTTAATTAA 0.750611 -54 ATCAGGATATTTTTTCTGAACAAATGGTGGTTGT 3 72 1 TTTTAACAAA 0.55402 -24 TCTTTGTCAATTATCGTTATTAAAAAGAGAACTT 4 22 1 TTTCATTAAA 0.931085 -33 ATGGCAATTTTAATTGCAATTAAAGTGTAAGTAT 7 12 0 TATTATTAAA 0.587375 -71 AAAAATTTTATGTTTGCCATTAAATGGCAATTTT 7 35 0 TGTTATTAAA 0.678437 -48 TTATTGACATTAAAAATTCCATGC 9 127 0 TTTTATTAAA 0.958602 -14 TCGTAATTAATTATTGACATTAAAGCTAAATACA 10 58 0 TTTTATTAAA 0.958602 -148 TGTACCGAATTTGTTCCAATTAATACTTGATATA 10 127 0 TTTTATTAAT 0.724802 -79 ATTTAAAGCTTTATTAGGATTTACTTTGGTTTAT 11 83 1 TTTTATTTAC 0.498032 -178 CTACCACCTTTTTTCTGTATTTAACATTCTTTTT 11 236 0 TTTCATTTAA 0.858253 -25 TTTCGCAATTTTATCTCAATTTAAGATTTTGATT 12 41 1 TTTCATTTAA 0.858259 -110 TTTTACGAAATTTTTTCAAATAAATTTCAAAGTA 12 80 0 TTTTAATAAA 0.8613 -71 TCTATTACCATTTTTAGTAAAAAATTCCACTTTT 13 19 1 TTTTAAAAAA 0.440878 -93 CTCCTTCACTTTTTTCTTATTAAAATACCATCCG 19 270 0 TTTTATTAAA 0.958601 -31 TTTAGGAAATTTTTTAAAATTAAAGATATTGAAA 25 76 1 TTTTATTAAA 0.958601 -105 TGAAAGTTCATTGTCAACATTTAAACAATTTTAA 25 105 1 TTTCATTTAA 0.858263 -76 CCCTTAAAAAATTTCCCGATTAAAGTTGGTAATG 25 139 0 ATTCATTAAA 0.594245 -42 TTATGCATATTTATTTGCATAAAATTTTTAGCTT 27 21 1 TTTTATAAAA 0.730091 -43 ATTTTTTTATTTGTTTTGATTAAAATTTAATATC 28 40 1 TTTTATTAAA 0.9586 -138 ATACTACGACATCTCTGCATTAAAACGATTATGT 29 32 0 ATTCATTAAA 0.594245 -56 ** ** ****** Masking position 4 Map Score: 18.7925 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 40 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 TTAATTAAAAAAAATTTTATAAAATGATTTGT 3 16 0 AAAATTATAA 0.592515 -80 AATTAACAACAAAAAGTTAATTAAAAAAAATT 3 32 0 AAAATTAATT 0.772601 -64 ATTGACAAAGAAAAGTTAAAAA 4 1 0 AAAATAAAAA 0.923482 -54 ATATTTCACGAAAACATTAAATATTACACGAC 6 47 1 AAAATTAAAT 0.923482 -33 AAGTAAACTAAAAATATAAAAATTTTATGTTT 7 54 0 AAAATAAAAA 0.923482 -29 GTTAAAAACAAAAATATAAAAATAAAAAT 10 8 0 AAAATAAAAA 0.923482 -198 AAATCCTAATAAAGCTTTAAATTTGCTTTTAA 11 73 0 AAAGTTAAAT 0.71357 -188 GCTCAAAAAAAGAATGTTAAATACAGAAAAAA 11 230 1 AGAATTAAAT 0.71357 -31 TAAAATTGCGAAAGATTTAAAACTTTTCGGTA 12 22 0 AAAGTTAAAA 0.807517 -129 ATGTCAAATCAAAATCTTAAATTGAGATAAAA 12 49 0 AAAATTAAAT 0.923482 -102 TATCTGTTGGAAAAAATAAAAATTAAAA 18 7 0 AAAATAAAAA 0.923482 -59 TCTGTTAAAGAAAAGGTAAATACTACAAATAG 20 16 0 AAAATAAATA 0.772601 -150 TTTAGCTTCAAAAAAGTTAATTTAAGTATGTT 20 142 0 AAAATTAATT 0.772601 -24 TTAACGAAAAAAAATTTTAAAATGGCGGTTGT 22 47 1 AAAATTAAAA 0.953104 -31 ATCTTTTTAGAAAAGGTTAAATTGTCAGCATA 25 34 0 AAAATTAAAT 0.923482 -147 TAAAGAATTAAAAAGCTAAAAATTTTATGCAA 27 35 0 AAAATAAAAA 0.923482 -29 AATTAACTGCAGAAGTTAAAAAATTACCTGAG 28 73 0 AGAATAAAAA 0.71357 -105 ACAAAAAAGAAAAAGGTTAAAACTTAGTCAAC 28 143 1 AAAATTAAAA 0.953104 -35 AATAAAATGGAAAAACTTAATACAT 30 43 1 AAAATTAATA 0.851223 -15 **** ****** Masking position 7 Map Score: 23.9376 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 55 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 4 CTGCAAGGCAAAATTCATATTTCACGAAAACATTAA 6 31 1 AATTCTTTAG 0.957007 -49 ATTGCAATTAAAATTGCCATTTAATGGCAAACATAA 7 26 1 AATTGTTTAG 0.947287 -57 GGATTTATGAATATTGTGGTTTAAAGGGCGATGACT 8 247 1 AATTGTTTAG 0.947287 -54 TTTAAAGGAAAGATTTATCTTGCAAGAGTCCAATTT 9 13 1 AATTTTTGAG 0.734766 -128 TTAGCGTACTGTATTTAGCTTTAATGTCAATAATTA 10 49 1 GATTTTTTAG 0.836017 -157 AATACTTGATATATTCAATTTTTACGCGTTTAGATT 10 104 0 AATTCTTTAG 0.957007 -102 TTCGTTAATACTTAAATTTTACGTAATGTGCCG 10 183 0 AACTTTTTAG 0.836017 -23 ATATAACGAAACTTTCGGATTTGAGGCTTTAAAAGC 11 45 1 ATTTCTTTAG 0.837366 -216 ATAAAGCTTTAAATTTGCTTTTAAAGCCTCAAATCC 11 61 0 AATTTTTTAG 0.956226 -200 GAGAAACTTCAATTTTTGTTTTAAAGACCTTTAAGG 11 125 1 ATTTTTTTAG 0.834786 -136 CTGCAACATAAAATTTACCTTAAAGGTCTTTAAAAC 11 142 0 AATTTTTAAG 0.651461 -119 TCTGTATTTAACATTCTTTTTTTGAGCGTTTAAAAA 11 221 0 AATTCTTTGG 0.738418 -40 TCTCAATTTAAGATTTTGATTTGACATACTTTGAAA 12 54 1 AATTTTTTAA 0.519997 -97 GTGATAACGCAGATTGGTGTTTACGGTTTTGATGAG 19 80 1 AATTGTTTCG 0.695027 -221 TGCTGCAAACGCATTCGTTTTTCAGGATGGTGAAGT 26 207 1 GATTCTTTAG 0.838581 -69 TTAAAGTCAAAAATTTACCTTTCAAGTTAACAATTA 28 100 0 AATTTTTTAG 0.956226 -78 CTATTTCAGCAATCTGCTATTTGACGTTTCCCATAG 31 56 0 ATCTGTTTAG 0.492417 -30 * **** *** * * Masking position 10 Map Score: 13.0827 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 28 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 AACTGATTCATAACAGCTTTTATCTTTAGAA 1 55 1 TAACAGTTTT 0.943904 -50 AACCAGTTCATAACAGCCTTTATTTAGCACT 2 27 1 TAACAGCTTT 0.920476 -47 AATCATTTTATAAAATTTTTTTTAATTAACT 3 19 1 TAAAATTTTT 0.678297 -77 GCAAACTATGCAACAGTTTTTAAAATCGGAG 5 27 0 CAACAGTTTT 0.710511 -142 AGAACGACCATTAAAGATTTTGCAGCAAACT 5 51 0 TTAAAGTTTT 0.827249 -118 TTACTCAACATAAAAGCCTTTCTTTATTTTG 5 136 0 TAAAAGCTTT 0.910495 -33 AAAATTTACCTTAAAGGTCTTTAAAACAAAA 11 138 0 TTAAAGTCTT 0.669387 -123 TTTCTGTATTTAACATTCTTTTTTTGAGCGT 11 228 0 TAACATCTTT 0.623326 -33 ACGTGTTGAATAACAGCTCTTTTGAAATTAT 19 168 1 TAACAGTCTT 0.876762 -133 ACCTTTTCTTTAACAGATTTTTCGAATTGTT 20 31 1 TAACAGTTTT 0.943904 -135 AGCGTAAATCAAAAAGTCCTTC 22 2 0 AAAAAGCCTT 0.516803 -76 TCGTTAAGCAAAACAGATATTAGCGTAAATC 22 23 0 AAACAGTATT 0.439849 -55 ACCGCCATTTTAAAATTTTTTTTCGTTAAGC 22 45 0 TAAAATTTTT 0.678297 -33 CAAGGGTGTTTAAAAGGTTTTAGAGTTGAGC 24 17 0 TAAAAGTTTT 0.936647 -34 AACCTTTTCTAAAAAGATTTTGCGGTAGTTT 25 48 1 AAAAAGTTTT 0.785524 -133 TTTTTTAAAATTAAAGATATTGAAAGTTCAT 25 85 1 TTAAAGTATT 0.473298 -96 GCAGTGGCTTTTAAAGCCTTTTGCTGCAAAC 26 186 1 TTAAAGCTTT 0.767121 -90 ****** **** Masking position 5 Map Score: 11.2413 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 137 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 GGATTCGAACCCTCGAACCCCTACGGGACA 8 154 1 CCTCGAACCC 0.953344 -147 TTTGTCCGCTCGGCAACCCCCGCTCAGATG 8 203 1 CGGCAACCCC 0.977658 -98 AATTTTTCCACGTCGCCCCCGTGGGGTAGC 9 44 1 CGTCGCCCCC 0.962518 -97 CTCAGGATATCCGCTACCCCACGGGGGCGA 9 56 0 CCGCTACCCC 0.978323 -85 GTCGAGGAGTCCGCAGCCCCTCAGGATATC 9 75 0 CCGCAGCCCC 0.988134 -66 GCTGCGGACTCCTCGACCCGGGTTCAACTC 9 88 1 CCTCGACCCG 0.930732 -53 ACCATTGCCGCCTCTGCCTCTTTTGAGCAT 14 19 0 CCTCTGCCTC 0.863018 -85 CTTTCTCGGGCCTCAGGCCCATGTTGTACT 14 74 0 CCTCAGGCCC 0.896299 -30 CAAATCAATTCGGCGAACTCCAAAAAATTT 21 28 1 CGGCGAACTC 0.792227 -45 GTTCAAATCTCGGCGGCCCCATCATTGAAC 26 87 0 CGGCGGCCCC 0.993102 -189 ********** Masking position 4 Map Score: 8.86167 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 292 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 7 AATCGGAGTACCACTACTGGGTGG 5 4 0 CCACTACGGG 0.941452 -165 AACCCTCGAACCCCTACGGGACAGGACCCTC 8 161 1 CCCCTACGGA 0.938365 -140 CGCTCGGCAACCCCCGCTCAGATGAAAAATT 8 209 1 CCCCCGCCAG 0.944227 -92 TTCCACGTCGCCCCCGTGGGGTAGCGGATAT 9 49 1 CCCCCGTGGG 0.951897 -92 AAATTCCATGCCCCCGCCGGGAGTTGAACCC 9 107 0 CCCCCGCGGG 0.996103 -34 AGTACATTTTTCCCTGCCCGGAG 15 20 1 TCCCTGCCGG 0.933418 -13 AAGGCACTGGCCCCTACAGGGTGATAACGCA 19 60 1 CCCCTACGGG 0.99133 -241 ******* *** Masking position 4 Map Score: 4.79691 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 102 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TTTTTTCTTATTTATGAACCAG 2 3 1 TTTTCTTATT 0.600791 -71 TTTTTAACTTTTCTTTGTCAATTATCGT 4 9 1 TTTTCTTTGT 0.907005 -46 TACCAGTAAGTTCTCTTTTTAATAACGATA 4 33 0 TTCTCTTTTT 0.85594 -22 CGTGTAAATCTTCTTTTCGTCATCAGAGAT 8 58 1 TTCTTTTCGT 0.740128 -243 CCGCATTTAGTTCTGTTCGTTGAGTTTGGG 8 118 0 TTCTGTTCGT 0.75457 -183 ATTTTTATTTTTATATTTTTGT 10 3 1 TTTTATTTTT 0.76128 -203 ATTTTTATATTTTTGTTTTTAACACGCTGT 10 17 1 TTTTGTTTTT 0.682128 -189 GTATTTAACATTCTTTTTTTGAGCGTTTAA 11 224 0 TTCTTTTTTT 0.660705 -37 TTTTAATTTTTATTTTTTCCAACAGAT 18 8 1 TTTTATTTTT 0.76128 -58 AAGAGCTTCATTCTCTTCGTTTGCTCATCA 19 109 0 TTCTCTTCGT 0.8968 -192 TCCTTCACTTTTTTCTTATTAAAATACCAT 19 273 0 TTTTCTTATT 0.600791 -28 AATTTCTATTTGTAGTATTTACC 20 4 1 TTCTATTTGT 0.833978 -162 ATTTTAAAATTTTTTTTCGTTAAGCAAAAC 22 40 0 TTTTTTTCGT 0.744076 -38 TAAAAAATTTTTTTATTTGTTTTGATTAAA 28 34 1 TTTTATTTGT 0.836814 -144 GTTTTAACCTTTTTCTTTTTTGTTTAACCA 28 136 0 TTTTCTTTTT 0.858466 -42 AGTTTTTCCATTTTATTCGTTATCCTTGAA 30 30 0 TTTTATTCGT 0.823451 -28 ********** Masking position 6 Map Score: 12.8307 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 138 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ATTGTGGTTTAAAGGGCGATGACTTCATATAAC 8 259 1 AAAGGGATGC 0.93603 -42 GTAGAAGGTGGATTTCAAAGTTATAT 8 285 0 GAAGGGATTC 0.926635 -16 CAAATTCGGTACAGGCGGATTATCTATTTTTAA 10 148 1 ACAGGGATTT 0.967195 -58 TAAGAATTATAAAGGAGGATTCCAAATATGAGT 12 118 1 AAAGGGATTC 0.979404 -33 AGCCAACAGGGAGATTTCTCATTACTTA 18 48 0 ACAGGGATTC 0.986916 -18 ACTGGCCCCTACAGGGTGATAACGCAGATTGGT 19 65 1 ACAGGGATAC 0.939974 -236 AGAAAAGCTGACAGGTTGATTCT 26 1 0 ACAGGGATTT 0.967196 -275 TGTTAACTTGAAAGGTAAATTTTTGACTTTAAT 28 104 1 AAAGGAATTT 0.674874 -74 ***** **** * Masking position 9 Map Score: 3.96959 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 64 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ATCAAGTTATTTTAATCAAAAGTCAGATAA 1 15 1 TTTAATCAAA 0.877216 -90 ATTAAAGATTTTGCAGCAAACTATGCAACA 5 43 0 TTGCAGCAAA 0.8572 -126 TTAAAGGTCTTTAAAACAAAAATTGAAGTT 11 129 0 TTAAAACAAA 0.722917 -132 GCCTTGCAGATTTCAACAAAAGTGGAATTT 13 40 0 TTTCAACAAA 0.869423 -72 ATTAAAAATTACAGCAAAATAGTAATAT 16 9 1 TTACAGCAAA 0.847578 -42 TAATATATATGTTAATCAAAGCAATTTC 16 33 1 GTTAATCAAA 0.829458 -18 AGATATTAGCGTAAATCAAAAAGTCCTTC 22 10 0 GTAAATCAAA 0.633702 -68 ATTTTTTTTCGTTAAGCAAAACAGATATTA 22 32 0 GTTAAGCAAA 0.919369 -46 ATTGTCAACATTTAAACAATTTTAACATTA 25 114 1 TTTAAACAAT 0.579313 -67 ACGAATGCGTTTGCAGCAAAAGGCTTTAAA 26 195 0 TTGCAGCAAA 0.8572 -81 AGCTAAAAATTTTATGCAAATAAATATGCA 27 24 0 TTTATGCAAA 0.628548 -40 GATATTAAATTTTAATCAAAACAAATAAAA 28 44 0 TTTAATCAAA 0.877216 -134 GACTTTAATGGTTAAACAAAAAAGAAAAAG 28 128 1 GTTAAACAAA 0.82952 -50 GGAGCTATTTCAGCAATCTGCTATTTG 31 69 0 TTTCAGCAAT 0.74587 -17 ********** Masking position 8 Map Score: 7.03622 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 123 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 GATATTTTTTCTGAACAAATGGTGGTTGT 3 77 1 CTGAACATGG 0.771854 -19 AATGGTCGTTCTGGACTATTGGCAGAGCAAAC 5 70 1 CTGGACTTGG 0.967851 -99 CGTGGAAAAATTGGACTCTTGCAAGATAAATC 9 24 0 TTGGACTTGC 0.845565 -117 TCGACCCGGGTTCAACTCCCGGCGGGGGCATG 9 100 1 TTCAACTCGG 0.884811 -41 TATACTCCTTTGGACGACTGGATTTGA 17 10 1 TTGGACGTGG 0.953849 -18 AGAGAAAGTTCTGGACTTCCGGAAGGCACTGG 19 38 1 CTGGACTCGG 0.968759 -263 GGCCCCATCATTGAACTGGCGGGAAAACCGTT 26 71 0 TTGAACTCGG 0.96636 -205 GTGACCCGAGTTCAAATCTCGGCGGCCCCATC 26 94 0 TTCAAATCGG 0.570426 -182 TTCGTTATCCTTGAACTTATGGTGTAAAAAAG 30 13 0 TTGAACTTGG 0.963656 -45 TATGTGTGTTTTGGAAGAATGGTAGGAGGGTT 31 20 1 TTGGAAGTGG 0.781322 -66 ******* *** Masking position 5 Map Score: 2.93608 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 73 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 TTTATAAAATTTTTTTTAATTAACTTTTTG 3 25 1 TTTTTTTAAT 0.594424 -71 TCCTATGCAGAATTTTTCATCTGAGCGGGG 8 220 0 AATTTTTCAT 0.718663 -81 GGGGGCATGGAATTTTTAATGTCAATAA 9 123 1 AATTTTTAAT 0.855925 -18 TACGCGTTTAGATTTTTCATTTGCTCTCGT 10 88 0 GATTTTTCAT 0.833853 -118 ATTTTGCTGTAATTTTTAAT 16 1 0 AATTTTTAAT 0.855925 -50 GACCCGGATGGTATTTTAATAAGAAAAAAG 19 266 1 GTATTTTAAT 0.724786 -35 GTTTTTTAATTAATCATAAC 23 1 1 GTTTTTTAAT 0.904525 -31 CGGGAAAACCGTTTTTTAATACTGCCAGAT 26 54 0 GTTTTTTAAT 0.904525 -222 AAAATTTTTAGCTTTTTAATTCTTTAAATT 27 41 1 GCTTTTTAAT 0.810168 -23 CTGAGATATTAAATTTTAATCAAAACAAAT 28 48 0 AAATTTTAAT 0.622844 -130 ********** Masking position 5 Map Score: 2.75009 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 44 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 13 AACTAAATGCGGGGGGAGGGATTCGAACCC 8 136 1 GGGGGGAGGG 0.958109 -165 AACTCCCGGCGGGGGCATGGAATTTTTAAT 9 113 1 GGGGGCATGG 0.935148 -28 CCAATAAAGATGTAGGATGGTTCAACTGCA 11 173 0 TGTAGGATGG 0.685856 -88 CTACCGTCGAGGTATCCGGGAGTTGT 19 7 0 GGTATCCGGG 0.851991 -294 ATACCTCGACGGTAGCAGAGAAAGTTCTGG 19 22 1 GGTAGCAGAG 0.841602 -279 TCTCGGCTTTGGGAGCCGGTGACCCGAGTT 26 114 0 GGGAGCCGGT 0.861812 -162 GGGGCCGTAGGGTAGCCTGGTGATCCTCTC 26 140 0 GGTAGCCTGG 0.971044 -136 TCTGTCATGAGGGAGGCAGGATTTAAATAC 26 241 0 GGGAGGCAGG 0.899146 -35 TTGGAAGAATGGTAGGAGGGTTAGAGCTAT 31 30 1 GGTAGGAGGG 0.980039 -56 GAGCAGGGTAGAATGGGGAGGTATAA 32 15 0 GGTAGAATGG 0.827246 -16 ********** Masking position 2 Map Score: 4.50724 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 423 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 GTTCATAACAGCCTTTATTTAGCACTCATCT 2 32 1 GCCTTTATTA 0.973865 -42 CAACATAAAAGCCTTTCTTTATTTTGAGTGG 5 131 0 GCCTTTCTTA 0.943777 -38 TTTTGCCTTTATTTACTCAACATAA 5 154 0 GCCTTTATTA 0.973865 -15 ATTACGCCTCTATTACCATTTTTAGT 13 6 1 GCCTCTATTC 0.918671 -106 TGCCGCCTCTGCCTCTTTTGAGCATATTCCC 14 13 0 GCCTCTTTTA 0.90375 -91 AAAAGCCACTGCCTTTAATCATTACAGAGGG 26 167 0 GCCTTTAATA 0.901893 -109 ********* * Masking position 6 Map Score: 0.769332 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 11 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 15 ACAACCACCATTTGTTCAGAAA 3 84 0 AACCACCATT 0.962576 -12 AAAATCGGAGTACCACTACTGGGTGG 5 7 0 TACCACTACT 0.785682 -162 AATAGTCCAGAACGACCATTAAAGATTTTG 5 60 0 AACGACCATT 0.80975 -109 GCTACCACCTTTTTTCTGTATT 11 249 0 TACCACCTTT 0.954291 -12 TTTTACCACCACTCATATTTGGA 12 138 0 TACCACCACT 0.970439 -13 CAGCCCTTACAACCGCCATTTTAAAATTTT 22 57 0 AACCGCCATT 0.872281 -21 ATCACCACCTCTACCTTAAAAA 25 3 1 CACCACCTCT 0.902139 -178 ATTTTAACATTACCAACTTTAATCGGGAAA 25 132 1 TACCAACTTT 0.699826 -49 ********** Masking position 2 Map Score: 0.781081 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 142 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727