AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ifadR_aful_opreg_100.orf -g0.49 -x5 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 = 0 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 AF0840 125 long-chain-fatty-acid--CoA ligase (fadD-4) #10 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #11 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #12 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #13 AF1191 32 dihydroxynaphthoic acid synthase (menB) #14 AF1192 50 conserved hypothetical protein #15 AF1195 27 activator 1, replication factor C, 53 KD subunit #16 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #17 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #18 AF1510 24 long-chain-fatty-acid--CoA ligase (fadD-6) #19 AF1512 71 conserved hypothetical protein #20 AF1513 257 A. fulgidus predicted coding region AF1513 #21 AF1768 300 dipeptide ABC transporter, permease protein (dppB) #22 AF1772 82 long-chain-fatty-acid--CoA ligase (fadD-7) #23 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #24 AF2244 300 acyl-CoA dehydrogenase (acd-11) #25 AF2271 177 A. fulgidus predicted coding region AF2271 #26 AF2272 87 A. fulgidus predicted coding region AF2272 #27 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #28 AF2368 40 long-chain-fatty-acid--CoA ligase (fadD-9) #29 AF2369 33 A. fulgidus predicted coding region AF2369 #30 AF2370 170 conserved hypothetical protein Motif number 1 TCATTTTATAAAATTTTTTTTAATTAACTTTTTGTT 3 21 1 AAATTTTATA 0.682763 -75 AGAGCAAACTTAAATTTTTTGGATATATAGGCTTCA 5 93 1 TAATTTTATT 0.854569 -76 AGTAGTCGTGTAATATTTAATGTTTTCGTGAAATAT 6 47 0 TAATTTATTT 0.746483 -33 TGGCAAACATAAAATTTTTATATTTTTAGTTTACTT 7 50 1 AAATTTTTTT 0.966874 -33 GTATTTTTTAAAAACTTTTCTCTTCTAGTAGCACAT 9 85 0 AAATTTTTTT 0.967539 -41 ACTCCTACCGAAAAGTTTTAAATCTTTCGCAATTTT 10 17 1 AAATTTTTCT 0.730342 -134 TATCTCAATTTAAGATTTTGATTTGACATACTTTGA 10 52 1 TAATTTTTTA 0.884496 -99 TATTTTTACGAAATTTTTTCAAATAAATTTCAAAGT 10 81 0 AAATTTTATA 0.682759 -70 CTTTGAAGACAAAGATTTTATTTTGTTTCGTTCAAG 11 18 0 AAATTTTTTT 0.967539 -176 TTTAGTGAATTACTTTTTTGGATTATATTTTCGCAA 11 67 1 TACTTTTTTT 0.694605 -127 GAAGCCATTCAAATTTTTCAGATTTTGCGAAAATAT 11 91 0 AAATTTCTTT 0.749686 -103 TCAGCCTTTTAAAACTTTTCGCTTTTTACGAAATTA 11 151 0 AAATTTTTTT 0.967529 -43 TTTTAATTTTTATTTTTTCCAACAGATA 16 3 1 TTATTTTTTT 0.60533 -63 CACCAAAATCAAAGCTTTATTATTCTCAACCAGATT 19 40 1 AAATTTATTT 0.780971 -32 AATTACTATTTAAAGTTTTCCTTTCTTTTTTGATTG 20 216 0 TAATTTTTTT 0.961484 -42 AGAACTATTAAAATTTTTTTAAATGTGGGATAACTT 22 41 0 AAATTTTATT 0.875248 -42 GGCATATAAAAAATTTTTTTATTTGTTTTGATTAAA 25 28 1 AAATTTTTTT 0.967536 -150 ATATCTCAGGTAATTTTTTAACTTCTGCAGTTAATT 25 69 1 TAATTTTTTT 0.961434 -109 ACTTGAAAGGTAAATTTTTGACTTTAATGGTTAAAC 25 109 1 TAATTTTTTA 0.88434 -69 GACTAAGTTTTAACCTTTTTCTTTTTTGTTTAACCA 25 136 0 TAATTTTTTT 0.961484 -42 ATGTATTAAGTTTTTCCATTTTATTCGTTATC 27 36 0 TAATTTTTTT 0.961484 -22 TTTCGTAAAATTTTTAAGTTAATCACAATTTT 28 7 1 AAATTTTTTA 0.899125 -34 *** **** ** * Masking position 8 Map Score: 28.4927 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 57 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 ACACCTCCAAATTAGAAAATAGGCCTTCTAA 1 80 0 ATAGAAAATA 0.835404 -25 TGGTTCATAAATAAGAAAAAA 2 1 0 ATAGAAAAAA 0.935469 -73 CCACCATTTGTTCAGAAAAAATATCCTGATA 3 71 0 TTAGAAAAAA 0.935468 -25 GGCTTTTATGTTGAGTAAATAAAGGCAAAA 5 149 1 TTAGTAAATA 0.659186 -20 CTAGTAGCACATCAGAATAAAAAATTCCTTC 9 66 0 ATAGAATAAA 0.700606 -60 TTTGAAATTTATTTGAAAAAATTTCGTAAAA 10 83 1 ATTGAAAAAA 0.695604 -68 TTTGAAAAAATTTCGTAAAAATAGTAAGAAT 10 94 1 TTCGTAAAAA 0.886334 -57 TTTTCAGATTTTGCGAAAATATAATCCAAAA 11 82 0 TTCGAAAATA 0.877525 -112 ACTTATTTAATTTCGTAAAAAGCGAAAAGTT 11 144 1 TTCGTAAAAA 0.886334 -50 TATTACCATTTTTAGTAAAAAATTCCACTTT 12 21 1 TTAGTAAAAA 0.846656 -91 TGGTATTTTAATAAGAAAAAAGTGAAGGAGG 17 274 1 ATAGAAAAAA 0.935469 -27 TTAGAAAATAATTCGAAAAAAG 19 2 0 ATCGAAAAAA 0.953411 -70 GGTGCAGTCGTTTAGAAAATAATTCGAAAAA 19 13 0 TTAGAAAATA 0.835403 -59 ATTGATTATTATACGAATAAAACATGAGTTT 20 189 0 ATCGAATAAA 0.767627 -69 GATACGAAAAAATTGTGATTAA 28 29 0 ATCGAAAAAA 0.953411 -12 ACGTAAACGATTCCGGAAAAATGAATGGATT 30 42 1 TTCGGAAAAA 0.778421 -129 ** ******** Masking position 7 Map Score: 16.4382 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 65 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 CGCGAATCCCCTCTTAAGCAGAG 2 61 0 GCGAATCCCC 0.991151 -13 GTTCGAGGGTTCGAATCCCTCCCCCCGCATTT 8 140 0 TCGAATCCCC 0.973482 -161 ATTCGAACCCTCGAACCCCTACGGGACAGGAC 8 156 1 TCGAACCCCC 0.975474 -145 TTGTCCGCTCGGCAACCCCCGCTCAGATGAAA 8 204 1 GGCAACCCCC 0.987965 -97 AAATCTGCAAGGCAATGCCTACACTAATAAGA 12 57 1 GGCAATGCCC 0.980888 -55 CCCTGTAGGGGCCAGTGCCTTCCGGAAGTCCA 17 49 0 GCCAGTGCCC 0.940519 -252 CTTACCGCTCGGCAACCCCGGCCTAACGCCTC 20 27 0 GGCAACCCCC 0.987965 -231 ACCCACGCGGGCGAACGCCCACACGCTCTCCA 20 68 0 GCGAACGCCC 0.987967 -190 CCGCGTGGGTTCGAATCCCACCCCCGGCGCTG 20 90 1 TCGAATCCCC 0.973482 -168 ATCTGCTCCTCGCAATGCCCACAGCGGCGGGT 24 19 0 CGCAATGCCC 0.907975 -282 ********* * Masking position 4 Map Score: 12.5776 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 64 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TTCTAAAGATAAAAGCTGTTATGAATCAGTTCATAAC 1 49 0 AAAGTTATAC 0.973908 -56 CAAATTAGAAAATAGGCCTTCTAAAGATAAAAGCTGT 1 67 0 AAAGTTCTAA 0.933218 -38 ACCAGTTCATAACAGCCTTTATTTAGCACTCATCTCT 2 28 1 AAAGTTATAC 0.973908 -46 TACTCAACATAAAAGCCTTTCTTTATTTTGAGTGGTT 5 129 0 AAAGTTCTAT 0.882208 -40 AAAAATTCTGCATAGGATTTATGAATATTGTGGTTTA 8 233 1 CAAGTTATAA 0.683838 -68 ACTAGAAGAGAAAAGTTTTTAAAAAATACTTATCACC 9 92 1 AAAGTTAAAT 0.702352 -34 TATAATCCAAAAAAGTAATTCACTAAAAGCTCAATTG 11 57 0 AAAGTTCAAA 0.817729 -137 ATAATTTCAAAAGAGCTGTTATTCAACACGTCCTCAA 17 162 0 AAAGTTATAC 0.973908 -139 GAAAACTTTAAATAGTAATTATTTATCGGGAAATTC 20 232 1 AAAGTTATAC 0.973907 -26 TTTTTGCCGGAAAAGACCTTCTCCACCGCCTCAGCCT 24 50 1 AAAGTTCTAC 0.974382 -251 CTGAGGCGGAAACAGCTCTTCTATACCCTCCTCCTTT 24 85 1 AAAGTTCTAC 0.974382 -216 AATAGAACACAATTGTAGTTATATATCATGAGTTTAA 24 215 0 AATGTTATAC 0.798878 -86 AAACAATTGAAAAAGGATTTAAATAGAACACAATTGT 24 236 0 AAAGTTAAAA 0.814906 -65 ** ** **** * * Masking position 15 Map Score: 12.0308 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 16 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 GTAGAAGGTGGATTTCAAAGTTA 8 288 0 GAAGGTGGAT 0.792302 -13 TAAGAATTATAAAGGAGGATTCCAAATATG 10 118 1 AAAGGAGGAT 0.944846 -33 CCAGTCGTCCAAAGGAGTATA 15 2 0 AAAGGAGTAT 0.704158 -26 TTTGATGAGCAAACGAAGAGAATGAAGCTC 17 107 1 AAACGAAGAG 0.843245 -194 AGAAAAAAGTGAAGGAGGTGTATT 17 287 1 GAAGGAGGTG 0.849163 -14 GAAACAAGAAAAAGGAAGAGAGGCTTTAGC 21 129 1 AAAGGAAGAG 0.961583 -172 AGAAATAATTAACGGAAGAGTGGCACTACA 21 166 0 AACGGAAGAG 0.81121 -135 TTGGCATTTTAAAGGAGGAGGGTATAGAAG 24 102 0 AAAGGAGGAG 0.987278 -199 TTGAAGTGGTGAAGGTGGAGGAGCTTGCTG 24 153 0 GAAGGTGGAG 0.945297 -148 ATCATGAGTTTAACGAGGAGCAATTTTTAA 24 198 0 TAACGAGGAG 0.724454 -103 GAAAGGTGTAGCACAGCGCGG 29 23 0 AAAGGTGTAG 0.793107 -11 TGAGTGAGCTAAAGAAAGAGCTTCTCCGAA 30 73 0 AAAGAAAGAG 0.64234 -98 ********** Masking position 2 Map Score: 7.96831 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 1204 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 TTAATTAAAAAAAATTTTATAAAATGATTT 3 18 0 AAAATTTTAT 0.817922 -78 ATTAACAACAAAAAGTTAATTAAAAAAAAT 3 33 0 AAAAGTTAAT 0.797478 -63 ATTGACAAAGAAAAGTTAAAAA 4 3 0 AAAAGTTAAA 0.63455 -52 GTAGTCGTGTAATATTTAATGTTTTCGTGA 6 52 0 AATATTTAAT 0.869356 -28 TAAAAATATAAAAATTTTATGTTTGCCATT 7 48 0 AAAATTTTAT 0.817922 -35 TAAAAGAAGGAATTTTTTATTCTGATGTGC 9 61 1 AATTTTTTAT 0.752013 -65 AGGCTGAAAAAATAGTTAAAGACA 11 180 1 AATAGTTAAA 0.63455 -14 ATTTTGCTGTAATTTTTAAT 14 1 0 AATTTTTAAT 0.817922 -50 GTATCTGGCAAAAATTTAATGGGCTAATCT 21 42 1 AAAATTTAAT 0.869357 -259 GGAAAATCCTAATAGTTAATTGTTAAAAGT 22 15 1 AATAGTTAAT 0.797478 -68 ACATTTAAAAAAATTTTAATAGTTCTCACT 22 51 1 AAATTTTAAT 0.817922 -32 AACGAGGAGCAATTTTTAATGCACCGTTGA 24 187 0 AATTTTTAAT 0.817922 -114 ATCCTTTTTCAATTGTTTAACTTGGCAAAA 24 255 1 AATTGTTTAA 0.441736 -46 TTAACTTGGCAAAATTTAAATAATCACAAA 24 271 1 AAAATTTAAA 0.745824 -30 CAAATAAAAAAATTTTTTATATGCCACCAT 25 23 0 AATTTTTTAT 0.752013 -155 TGTTTTGATTAAAATTTAATATCTCAGGTA 25 51 1 AAAATTTAAT 0.869357 -127 TATCTCAGGTAATTTTTTAACTTCTGCAGT 25 70 1 AATTTTTTAA 0.572132 -108 ATAAAATGGAAAAACTTAATACAT 27 44 1 AAAACTTAAT 0.474479 -14 TTTCGTAAAATTTTTAAGTTAATCACA 28 8 1 AAATTTTTAA 0.572132 -33 AAAATATTTTATCCGCGCTGTG 29 3 1 AATATTTTAT 0.817922 -31 ********** Masking position 6 Map Score: 17.6997 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 34 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 7 ACTGATTCATAACAGCTTTTATCTTTAGAA 1 56 1 AACAGCTTTT 0.724128 -49 ACCAGTTCATAACAGCCTTTATTTAGCACT 2 28 1 AACAGCCTTT 0.929827 -46 CAAACTATGCAACAGTTTTTAAAATCGGAG 5 27 0 AACAGTTTTT 0.834874 -142 TACTCAACATAAAAGCCTTTCTTTATTTTG 5 136 0 AAAAGCCTTT 0.716471 -33 ACTAGAAGAGAAAAGTTTTTAAAAAATACT 9 92 1 AAAAGTTTTT 0.606293 -34 CGTGTTGAATAACAGCTCTTTTGAAATTAT 17 169 1 AACAGCTCTT 0.930377 -132 CATTGCGAGGAGCAGATTTTTGCCGGAAAA 24 34 1 AGCAGATTTT 0.696659 -267 TTTTTGCCGGAAAAGACCTTCTCCACCGCC 24 50 1 AAAAGACCTT 0.637409 -251 CTGAGGCGGAAACAGCTCTTCTATACCCTC 24 85 1 AACAGCTCTT 0.930377 -216 GGATTTTCGGAGAAGCTCTTTCTTTAGCTC 30 68 1 AGAAGCTCTT 0.805962 -103 ********** Masking position 4 Map Score: 6.44106 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 184 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 CGAATCCCTCCCCCCGCATTTAGTTCTGTTCGT 8 128 0 CCCCGCTTAG 0.903652 -173 CGCTCGGCAACCCCCGCTCAGATGAAAAATTCT 8 209 1 CCCCGCAGAT 0.865501 -92 CTCCGGGCAGGGAAAAATGTACT 13 20 0 CCCGGGGGGA 0.829979 -13 TCTGCGTTATCACCCTGTAGGGGCCAGTGCCTT 17 60 0 CCCCTGGGGG 0.922064 -241 ATTCAGCCCCGGCTATGAGGCGTTAGGCC 20 7 1 CCCGGCTGAG 0.978438 -251 AGCGGTAAGGCGCACGCCTGGAGAGCGTGTGGG 20 50 1 CCACGCGGAG 0.87954 -208 TGTGGGCGTTCGCCCGCGTGGGTTCGAATCCCA 20 77 1 CCCCGCGGGT 0.985173 -181 GATACAACAGCGCCGGGGGTGGGATTCGAACCC 20 96 0 CCCGGGTGGG 0.960028 -162 CTTTTTATCGCTCCGGCTGGGAGCATAAGATTC 21 70 1 CCCGGCGGAG 0.598999 -231 AGGGTTTTACCCGCCGCTGTGGGCATTGCGAGG 24 11 1 CGCCGCTGGG 0.951835 -290 * ***** **** Masking position 1 Map Score: 5.48195 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 191 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 AATGAATCTTATGCTCCCAGCCGGAGCGATA 21 75 0 ATGCTCCAGC 0.983694 -226 GCTCCTCGCAATGCCCACAGCGGCGGGTAAA 24 16 0 ATGCCCCAGC 0.992697 -285 CTCCTTTAAAATGCCAACAGCATAACTTGAG 24 115 1 ATGCCACAGC 0.988748 -186 ATAACTTGAGATGCTTTCAGCAAGCTCCTCC 24 136 1 ATGCTTCAGC 0.956741 -165 AATTTTTTATATGCCACCATCAACTTCTCAA 25 12 0 ATGCCACATC 0.943941 -166 ****** **** Masking position 9 Map Score: 2.22461 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 44 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ACCACTCAAAATAAAGAAAGGCTTTTATGTT 5 130 1 ATAAGAAAGG 0.720902 -39 GAGGATTCCAAATATGAGTGGTGGTAAAA 10 132 1 AAATGAGTGG 0.931515 -19 AAATCTGAAAAATTTGAATGGCTTCAGAACC 11 102 1 AATTGAATGG 0.740159 -92 TGCAGATTTCAACAAAAGTGGAATTTTTTAC 12 35 0 AAAAAAGTGG 0.645101 -77 CCGAACCACCAACAAGAGAGGAAATCGACAC 17 222 1 AAAAGAGAGG 0.964806 -79 TAATCAATCAAAAAAGAAAGGAAAACTTTAA 20 212 1 AAAAGAAAGG 0.935121 -46 AACAAGAAAAAGGAAGAGAGGCTTTAGCATC 21 131 1 AGAAGAGAGG 0.951264 -170 AAATAATTAACGGAAGAGTGGCACTACACGT 21 163 0 CGAAGAGTGG 0.755694 -138 GTTAATTGTTAACTTGAAAGGTAAATTTTTG 25 98 1 AATTGAAAGG 0.771947 -80 CGATTCCGGAAAAATGAATGGATTTTCGGAG 30 49 1 AAATGAATGG 0.877321 -122 CTAACAAGTCAGTTAGAGAGGATTTCCGTTG 30 101 0 AGTAGAGAGG 0.886034 -70 ** ******** Masking position 7 Map Score: 3.55944 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 344 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 TCAAGTTATTTTAATCAAAAGTCAGATAAT 1 16 1 TTAATCAAAA 0.964843 -89 CAACAAAAAGTTAATTAAAAAAAATTTTAT 3 28 0 TTAATTAAAA 0.753974 -68 AATATATATGTTAATCAAAGCAATTTC 14 34 1 TTAATCAAAG 0.879361 -17 CGTATAATAATCAATCAAAAAAGAAAGGAA 20 205 1 TCAATCAAAA 0.879361 -53 CAAAATTTAAATAATCACAAAAAGAGCCTG 24 280 1 ATAATCACAA 0.735797 -21 ATATTAAATTTTAATCAAAACAAATAAAAA 25 43 0 TTAATCAAAA 0.964843 -135 ACTTTAATGGTTAAACAAAAAAGAAAAAGG 25 129 1 TTAAACAAAA 0.831026 -49 AATTTTTAAGTTAATCACAATTTTTTCGTA 28 19 1 TTAATCACAA 0.939542 -22 ********** Masking position 4 Map Score: 3.46331 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 13 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 AGATAATTTTGTTATGAACTGATTCATAAC 1 39 1 GTTATGAACT 0.95577 -66 AATAAAGGCTGTTATGAACTGGTTCATAAA 2 21 0 GTTATGAACT 0.95577 -53 TTTAATGGTCGTTCTGGACTATTGGCAGAG 5 67 1 GTTCTGGACT 0.981024 -102 AGCAGAGAAAGTTCTGGACTTCCGGAAGGC 17 35 1 GTTCTGGACT 0.981024 -266 ********** Masking position 5 Map Score: 1.13856 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 6 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 TGAAAAAAGTAGTCGTGTAATAT 6 67 0 AAAAAGTAGT 0.660569 -13 GTTTGCCATTAAATGGCAATTTTAATTGCA 7 28 0 AAATGGCAAT 0.61998 -55 AATTTCGTAAAAATAGTAAGAATTATAAAG 10 102 1 AAATAGTAAG 0.921075 -49 ATATAATCCAAAAAAGTAATTCACTAAAAG 11 65 0 AAAAAGTAAT 0.91177 -129 TTTTTACTAAAAATGGTAATAGAGGCGTAA 12 12 0 AAATGGTAAT 0.769459 -100 AATTACAGCAAAATAGTAATATATATGTTA 14 17 1 AAATAGTAAT 0.896868 -34 ATTAAACGTGAAAAAGTAAGTAT 18 4 0 AAAAAGTAAG 0.932742 -21 GGAATTTCCAAAAAAGCAAGCATAAAAACT 20 164 1 AAAAAGCAAG 0.871445 -94 TAATCAATCAAAAAAGAAAGGAAAACTTTA 20 212 1 AAAAAGAAAG 0.713076 -46 GGAAAACTTTAAATAGTAATTATTTATCGG 20 231 1 AAATAGTAAT 0.896868 -27 ATGAAACAAGAAAAAGGAAGAGAGGCTTTA 21 127 1 AAAAAGGAAG 0.786482 -174 ********** Masking position 3 Map Score: 6.7744 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 32 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 TCCAACTCTACGCATAGAGCTGCAAGGCAAAATT 6 12 1 CGCGAGCTCA 0.996479 -68 CTTCATGAAGCGCTAAGAGCTTCATTCTCTTCGT 17 119 0 CGCGAGCTCA 0.996524 -182 TTCTCAGAAGTGCCATGAGCTTCAAACGTGCATC 21 238 1 TGCGAGCTCA 0.986329 -63 ATATTTTATCCGCGCTGTGCTACACCTTTC 29 14 1 CGCGTGCTCA 0.991264 -20 *** ***** ** Masking position 11 Map Score: 0.103293 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 ********** No masking Map Score: -3.87713e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0