AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ifadR_aful_opreg_300.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 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 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #9 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #10 AF0439 82 transcriptional regulatory protein, AsnC family #11 AF0442 300 succinoglycan biosynthesis regulator (exsB) #12 AF0837 63 cell division protein pelota (pelA) #13 AF0838 27 TRK potassium uptake system protein (trkA-2) #14 AF0840 125 long-chain-fatty-acid--CoA ligase (fadD-4) #15 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #16 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #17 AF1119 111 A. fulgidus predicted coding region AF1119 #18 AF1121 34 transcriptional regulatory protein, AsnC family #19 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #20 AF1191 32 dihydroxynaphthoic acid synthase (menB) #21 AF1192 50 conserved hypothetical protein #22 AF1195 27 activator 1, replication factor C, 53 KD subunit #23 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #24 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #25 AF1510 24 long-chain-fatty-acid--CoA ligase (fadD-6) #26 AF1512 71 conserved hypothetical protein #27 AF1513 257 A. fulgidus predicted coding region AF1513 #28 AF1514 199 A. fulgidus predicted coding region AF1514 #29 AF1768 300 dipeptide ABC transporter, permease protein (dppB) #30 AF1772 82 long-chain-fatty-acid--CoA ligase (fadD-7) #31 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #32 AF2244 300 acyl-CoA dehydrogenase (acd-11) #33 AF2271 177 A. fulgidus predicted coding region AF2271 #34 AF2272 87 A. fulgidus predicted coding region AF2272 #35 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #36 AF2368 40 long-chain-fatty-acid--CoA ligase (fadD-9) #37 AF2369 33 A. fulgidus predicted coding region AF2369 #38 AF2370 170 conserved hypothetical protein Motif number 1 CCCAAACGCCCAAACCTTAAATACCAAACCGC 2 232 1 CAAATTAAAT 0.825142 -35 ATCAGAAAATCTTATAAGGATTGTCAA 3 6 1 AAAATTATAA 0.65937 -33 TAAGGATTGTCAAAAATTTTTTAC 3 25 1 CAAATTTTTT 0.424171 -14 AGTTAATTAAAAAAAATTTTATAAAATGATTT 6 18 0 AAAATTTTAT 0.837783 -78 AATTAACAACAAAAAGTTAATTAAAAAAAATT 6 32 0 AAAATTAATT 0.810069 -64 AGTTTGCTGCAAAATCTTTAATGGTCGTTCTG 8 51 1 AAAATTTAAT 0.937627 -118 CTATATATCCAAAAAATTTAAGTTTGCTCTGC 8 91 0 AAAATTTAAG 0.745677 -78 ATATTTCACGAAAACATTAAATATTACACGAC 9 47 1 AAAATTAAAT 0.912467 -33 TGGCAAACATAAAATTTTTATATTTTTAGTTT 10 50 1 AAAATTTATA 0.736253 -33 ACTAGAAGAGAAAAGTTTTTAAAAAATACTTA 14 92 1 AAAATTTTAA 0.736253 -34 ACTCCTACCGAAAAGTTTTAAATCTTTCGCAA 15 17 1 AAAATTTAAA 0.872165 -134 ATGTCAAATCAAAATCTTAAATTGAGATAAAA 15 49 0 AAAATTAAAT 0.912467 -102 GCTTTGAAGACAAAGATTTTATTTTGTTTCGT 16 23 0 CAAATTTTAT 0.735711 -171 GCAAAATCTGAAAAATTTGAATGGCTTCAGAA 16 99 1 AAAATTGAAT 0.641515 -95 GTAAAAAGCGAAAAGTTTTAAAAGGCTGAAAA 16 158 1 AAAATTTAAA 0.872165 -36 TATCTGAGCAAAAAATTTAAATTATTGAAGTG 17 78 1 AAAATTAAAT 0.912467 -34 AAAAGTTTATTTTTCTGAGACA 18 1 1 AAAATTATTT 0.635715 -34 GCACCAAAATCAAAGCTTTATTATTCTCAACC 26 39 1 CAAATTTATT 0.735754 -33 AAAAGAAAGGAAAACTTTAAATAGTAATTATT 27 223 1 AAAATTAAAT 0.912467 -35 ATCCCAAATAAAAAGCTTTATAAAAACAAACA 28 27 0 AAAATTTATA 0.736253 -173 GTGTATCTGGCAAAAATTTAATGGGCTAATCT 29 40 1 CAAATTTAAT 0.871827 -261 CCACATTTAAAAAAATTTTAATAGTTCTCACT 30 49 1 AAAATTTAAT 0.937624 -34 TTTAACTTGGCAAAATTTAAATAATCACAAAA 32 270 1 CAAATTAAAT 0.825142 -31 GGTGGCATATAAAAAATTTTTTTATTTGTTTT 33 25 1 AAAATTTTTT 0.459568 -153 ACAAAAAAGAAAAAGGTTAAAACTTAGTCAAC 33 143 1 AAAATTAAAA 0.825511 -35 AATAAAATGGAAAAACTTAATACAT 35 43 1 AAAATTAATA 0.65937 -15 TTTCGTAAAATTTTTAAGTTAATCACAA 36 7 1 AAAATTTAAG 0.745779 -34 AAAATATTTTATCCGCGCTGTG 37 1 1 AAAATTTTAT 0.859895 -33 **** ****** Masking position 7 Map Score: 28.5 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 107 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 2 TTCAATCCCATTTTGGTCTGATTTCAACCCGTCA 1 58 0 TTTTTGATTT 0.87072 -243 TTCAATCCCATTTTGGTCTGATTTCAACTGTTCC 1 126 0 TTTTTGATTT 0.87072 -175 TTCAATCCCATTTTGGTCTGATTTCAACTTGGGA 1 199 0 TTTTTGATTT 0.87072 -102 AGGAAAAAGATTTTCTAATTTTTTTATGAATGTA 1 273 1 TTTTTTTTTT 0.902399 -28 TGTTTTTTACTTTTCCTCTTTTTTCTGAACACC 2 10 0 TTTTTTTTTT 0.902399 -257 TTAATTAACTTTTTGTTGTTAATTAATTATTTAT 6 40 1 TTTTTTAATT 0.813413 -56 TTTTTAACTTTTCTTTGTCAATTAT 7 2 1 TTTTTTTCTT 0.818937 -53 TTTTGCCTTTATTTACTCAACATA 8 155 0 TTTTTTATTT 0.934259 -14 AATTTTTATATTTTTAGTTTACTTTCATACT 10 62 1 TTTTTTACTT 0.874246 -21 TTCAATCCCATTTTGGTCTGATTTCAACTTACTG 11 18 0 TTTTTGATTT 0.87072 -283 CAATTTAAGATTTTGATTTGACATACTTTGAAAT 15 57 1 TTTTTGACAT 0.586417 -94 TTTGACATACTTTGAAATTTATTTGAAAAAATTT 15 73 1 TTTGTTATTT 0.752635 -78 GTGAATTACTTTTTTGGATTATATTTTCGCAAAA 16 71 1 TTTTTTATAT 0.859467 -123 AATCCAGTTTGATAATGATATTATTTAAGTG 19 91 0 TTTGTGATAT 0.382927 -21 TTTTAATTTTTATTTTTTCCAACA 23 1 1 TTTTTTTATT 0.739327 -65 ATACTTACTTTTTCACGTTTAATA 25 10 1 TTTTTTTAAT 0.549662 -15 CTTTTTTCGAATTATTTTCTAAACGAC 26 4 1 TTTTTTATTT 0.934259 -68 AAACATGAGTTTTTATGCTTGCTTTTTTGGAAAT 27 167 0 TTTTTTGCTT 0.768582 -91 TTTTCCTTTCTTTTTTGATTGATTATTATACGAA 27 203 0 TTTTTTGATT 0.675602 -55 GATTATGTCGTTTGGGGATTATTTCTCGCTAAAA 28 56 1 TTTGTTATTT 0.752635 -144 ATAAAAGCCTTTTTCCGCTTTTATAAGTTTGAAA 28 161 0 TTTTTTTTAT 0.799152 -39 CTCTCTTCCTTTTTCTTGTTTCATGATTAGTTTC 29 117 0 TTTTTTTCAT 0.660606 -184 ATTTAAATCCTTTTTCAATTGTTTAACTTGGCAA 32 249 1 TTTTTTGTTT 0.871616 -52 GCAGGCTCTTTTTGTGATTATTTAAATTTTGCC 32 278 0 TTTTTTATTT 0.934259 -23 TATAAAAAATTTTTTTATTTGTTTTGATTAAAAT 33 32 1 TTTTTTGTTT 0.871616 -146 GAAAGGTAAATTTTTGACTTTAATGGTTAAACAA 33 113 1 TTTTTTTAAT 0.549663 -65 ATGTATTAAGTTTTTCCATTTTATTCGTTATCCT 35 34 0 TTTTTTTTAT 0.799152 -24 **** ****** Masking position 9 Map Score: 26.5235 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 167 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 GTTGAAATCAGACCAAAATGGGATTGAAAGGCAGA 1 64 1 GAAAAGGGTT 0.985371 -237 GTTGAAATCAGACCAAAATGGGATTGAAAGTAAGA 1 132 1 GAAAAGGGTT 0.985371 -169 GTTGAAATCAGACCAAAATGGGATTGAAAGGCAAT 1 205 1 GAAAAGGGTT 0.985371 -96 TGCCACCTATGCAAAAGTCGCCATTGCCTTTCAAT 1 227 0 GCAAGGCCTT 0.803655 -74 TTTGAAATCAGACTAAAGTGGGATTACGTAAATTT 2 75 1 GAAAAGGGTT 0.985371 -192 ACCTCCAAATTAGAAAATAGGCCTTCTAAAGATAA 4 74 0 TAAAAGGCTT 0.651496 -31 ACTCATCTCTGCTTAAGAGGGGATTCGCG 5 55 1 GCAAGGGGTT 0.962774 -19 TATTTTTTCTGAACAAATGGTGGTTGT 6 79 1 GAAAAGTGTT 0.912104 -17 GTTGAAATCAGACCAAAATGGGATTGAAAGTGGAC 11 24 1 GAAAAGGGTT 0.985371 -277 TTCACTAAAAGCTCAATTGGGGCTTTGAAGACAAA 16 41 0 GCAATGGGTT 0.904597 -153 ATTATTTCTCGCTAAAAACGCCTTTTTTTAAAAGT 28 73 1 GCAAAGCCTT 0.928344 -127 ACTTATAAAAGCGGAAAAAGGCTTTTATATATTAT 28 167 1 GCAAAGGCTT 0.973906 -33 TCAGCCTGAGGCGGAAACAGCTCTTCTATACCCTC 32 80 1 GCAAAGCTTT 0.712859 -221 GATACGAAAAAATTGTGATTAACTTAAAAA 36 21 0 GAAAAGTGTT 0.912104 -20 ** *** *** ** Masking position 6 Map Score: 17.5295 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 130 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TAATGTCTCGCTTTCAATCCCATTT 1 4 0 CTTTAACCCA 0.983429 -297 CGTCGTCTGCCTTTCAATCCCATTTTGGTCTG 1 72 0 CTTTAACCCA 0.983429 -229 GATGTTCTTACTTTCAATCCCATTTTGGTCTG 1 140 0 CTTTAACCCA 0.983429 -161 TCGCCATTGCCTTTCAATCCCATTTTGGTCTG 1 213 0 CTTTAACCCA 0.983429 -88 GATATATAGGCTTCAAACCACTCAAAATAAAG 8 114 1 CTTCAACACT 0.843275 -55 TACACGTCCACTTTCAATCCCATTTTGGTCTG 11 32 0 CTTTAACCCA 0.983429 -269 GGGTTCGAGGGTTCGAATCCCTCCCCCCGCAT 11 142 0 GTTCAACCCT 0.892737 -159 GGATTCGAACCCTCGAACCCCTACGGGACAGG 11 154 1 CCTCAACCCT 0.870255 -147 AGTCATCGCCCTTTAAACCACAATATTCATAA 11 251 0 CTTTAACACA 0.882475 -50 CTTCATATAACTTTGAAATCCACCTTCTAC 11 281 1 CTTTAATCCA 0.79629 -20 AAATCTTTGTCTTCAAAGCCCCAATTGAGCTT 16 36 1 CTTCAACCCC 0.95039 -158 GCCCGCGTGGGTTCGAATCCCACCCCCGGCGC 27 88 1 GTTCAACCCA 0.941339 -170 GGAAACAGCTCTTCTATACCCTCCTCCTTTAA 32 92 1 CTTCATCCCT 0.819022 -209 **** ** **** Masking position 6 Map Score: 18.889 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 113 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 AATCTACATTCATAAAAAAATTAGAAAA 1 283 0 TTCATAAAAA 0.881615 -18 GGTGTTCAGAAAAAAGAGGAAAAG 2 5 1 TTCAGAAAAA 0.859685 -262 TTAGTCTGATTTCAAAAAACGCCGGCAAAA 2 61 0 TTCAAAAAAC 0.767194 -206 TCAAGTTATTTTAATCAAAAGTCAGATAAT 4 16 1 TTAATCAAAA 0.679001 -89 AAAAAGTTAATTAAAAAAAATTTTATAAAA 6 24 0 TTAAAAAAAA 0.820295 -72 CCACCATTTGTTCAGAAAAAATATCCTGAT 6 72 0 TTCAGAAAAA 0.859685 -24 CGCTAACACTTTTATAAAACCGCAATCCAG 12 37 1 TTTATAAAAC 0.581404 -27 TTGAAATTTATTTGAAAAAATTTCGTAAAA 15 84 1 TTTGAAAAAA 0.722149 -67 TTGAAAAAATTTCGTAAAAATAGTAAGAAT 15 95 1 TTCGTAAAAA 0.830873 -56 CTTATTTAATTTCGTAAAAAGCGAAAAGTT 16 145 1 TTCGTAAAAA 0.830873 -49 ATTACCATTTTTAGTAAAAAATTCCACTTT 19 22 1 TTAGTAAAAA 0.72882 -90 CCTTGCAGATTTCAACAAAAGTGGAATTTT 19 39 0 TTCAACAAAA 0.812459 -73 TAGAAAATAATTCGAAAAAAG 26 2 0 TTCGAAAAAA 0.846257 -70 AATAAAAAGCTTTATAAAAACAAACAGTCG 28 23 0 TTTATAAAAA 0.77781 -177 AGTTTATACTTTTAAAAAAAGGCGTTTTTA 28 85 0 TTTAAAAAAA 0.797565 -115 AGAAAACTACTTAAGCAAAAAACTACTGTG 28 116 0 TTAAGCAAAA 0.635062 -84 CGGAAATCGCTTAAGAAAACTACTTAAGCA 28 129 0 TTAAGAAAAC 0.569662 -71 TTATCCCACATTTAAAAAAATTTTAATAGT 30 44 1 TTTAAAAAAA 0.797565 -39 TTTTTTATTATTTGAAAAACGTTTGCAGGG 31 12 1 TTTGAAAAAC 0.506546 -27 ATATTAAATTTTAATCAAAACAAATAAAAA 33 43 0 TTAATCAAAA 0.679001 -135 ACTTTAATGGTTAAACAAAAAAGAAAAAGG 33 129 1 TTAAACAAAA 0.703256 -49 ********** Masking position 2 Map Score: 14.2738 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 146 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 AATCGTTTTTGCCGGCGTTTTTTGAAATCA 2 55 1 GCCGGCGTTT 0.906344 -212 AGAACTAAATGCGGGGGGAGGGATTCGAAC 11 134 1 GCGGGGGGAG 0.958624 -167 TTTCATCTGAGCGGGGGTTGCCGAGCGGAC 11 206 0 GCGGGGGTTG 0.992626 -95 TCAAGTAAAAGCGGTCGTTGAACA 12 5 0 GCGGTCGTTG 0.880493 -59 ACGCCTCATAGCCGGGGCTGAAT 27 4 0 GCCGGGGCTG 0.987601 -254 GAGGCGTTAGGCCGGGGTTGCCGAGCGGTA 27 27 1 GCCGGGGTTG 0.994376 -231 ATACAACAGCGCCGGGGGTGGGATTCGAAC 27 98 0 GCCGGGGGTG 0.993224 -160 ********** Masking position 4 Map Score: 8.4791 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 58 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 AATTTTATAAAATGATTTGTCGTGA 6 1 0 ATATTTTCGA 0.980043 -95 GTTGTTAATTAATTATTTATCAGGATATTTTTTCT 6 54 1 ATATTTTCGA 0.980043 -42 GCAAGGCAAAATTCATATTTCACGAAAACATTAAA 9 33 1 ATATATTCGA 0.955283 -47 TTTAAATAGTAATTATTTATCGGGAAATTC 27 238 1 ATATTTTCGA 0.980043 -20 CTCTTCCGTTAATTATTTCTCCCGAAATCGACATG 29 176 1 ATATTTTCGA 0.980043 -125 ACACAATTGTAGTTATATATCATGAGTTTAACGAG 32 211 0 ATATATTCGA 0.955283 -90 CCGAAAATCCATTCATTTTTCCGGAATCGTTTACG 38 43 0 ATATTTTCGA 0.980043 -128 * * **** ** ** Masking position 5 Map Score: 8.33015 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 3 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 AGGCCTTCTAAAGATAAAAGCTGTTATGAA 4 61 0 AAGATAAAAG 0.737003 -44 AGATGAGTGCTAAATAAAGGCTGTTATGAA 5 33 0 TAAATAAAGG 0.778026 -41 CCACTCAAAATAAAGAAAGGCTTTTATGTT 8 131 1 TAAAGAAAGG 0.84755 -38 TTATGTTGAGTAAATAAAGGCAAAA 8 154 1 TAAATAAAGG 0.778026 -15 GTGCTACTAGAAGAGAAAAGTTTTTAAAAA 14 87 1 AAGAGAAAAG 0.816342 -39 CGAAGAAAATGGTGTCTCAGAA 18 23 0 AAGAAAATGG 0.648562 -12 GTATTTTAATAAGAAAAAAGTGAAGGAGGT 24 276 1 AAGAAAAAAG 0.775408 -25 AATCAATCAAAAAAGAAAGGAAAACTTTAA 27 213 1 AAAAGAAAGG 0.923131 -45 TTTATACTTTTAAAAAAAGGCGTTTTTAGC 28 83 0 TAAAAAAAGG 0.811969 -117 ATCATGAAACAAGAAAAAGGAAGAGAGGCT 29 124 1 AAGAAAAAGG 0.945479 -177 TTAAACAAAAAAGAAAAAGGTTAAAACTTA 33 139 1 AAGAAAAAGG 0.945479 -39 CAGTTGCTGGAAGTGAAAGGGT 34 76 1 AAGTGAAAGG 0.703784 -12 ACTCTTTTCCAAAATAAAGGTAAGCCGGAA 38 13 1 AAAATAAAGG 0.88333 -158 ********** Masking position 6 Map Score: 10.1608 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 144 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 GTGGTGGATTTGCTGGAGAAGAGCTTTAGG 2 166 0 TGCTGGAGAA 0.775668 -101 TTGCATAGTTTGCTGCAAAATCTTTAATGG 8 45 1 TGCTGCAAAA 0.633541 -124 TTTGAAAAAATTTCGTAAAAATAGTAAGAA 15 94 1 TTTCGTAAAA 0.759647 -57 TGGATTATATTTTCGCAAAATCTGAAAAAT 16 85 1 TTTCGCAAAA 0.752302 -109 ACTTATTTAATTTCGTAAAAAGCGAAAAGT 16 144 1 TTTCGTAAAA 0.759647 -50 GGGAAAAATGTACTGGAAAATAC 20 4 0 TACTGGAAAA 0.717556 -29 TTTAACTATCTGTTGGAAAAAATAAAAATT 23 15 0 TGTTGGAAAA 0.823869 -51 TGTTGAATCTTACCGGAAAATTACTTCTGT 27 134 1 TACCGGAAAA 0.864813 -124 CCATGTCGATTTCGGGAGAAATAATTAACG 29 182 0 TTCGGGAGAA 0.60594 -119 AGCAGATTTTTGCCGGAAAAGACCTTCTCC 32 44 1 TGCCGGAAAA 0.949827 -257 TTTCGTAAAATTTTTAAGTT 36 1 1 TTTCGTAAAA 0.759647 -40 CTTACCTTTATTTTGGAAAAGAGTTC 38 7 0 TTTTGGAAAA 0.835836 -164 ACGTAAACGATTCCGGAAAAATGAATGGAT 38 42 1 TTCCGGAAAA 0.958184 -129 ATGAATGGATTTTCGGAGAAGCTCTTTCTT 38 62 1 TTTCGGAGAA 0.867863 -109 ********** Masking position 7 Map Score: 9.50524 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 234 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 TGGGCGTTTGGGGATTTTTAAACGGTTAAAG 2 213 0 GGATTTTTAA 0.821796 -54 AGGATTGTCAAAAATTTTTTAC 3 27 1 AAATTTTTTA 0.791371 -12 AAGTAGTCGTGTAATATTTAATGTTTTCGTG 9 53 0 GAATATTTAA 0.609836 -27 AATAAAAGAAGGAATTTTTTATTCTGATGTG 14 59 1 GAATTTTTTA 0.954385 -67 AAGGTGATAAGTATTTTTTAAAAACTTTTCT 14 100 0 GATTTTTTAA 0.609934 -26 CTATTTTTACGAAATTTTTTCAAATAAATTT 15 87 0 GAATTTTTTC 0.752298 -64 CAACAAAAGTGGAATTTTTTACTAAAAATGG 19 26 0 GAATTTTTTA 0.954385 -86 CTATTTTGCTGTAATTTTTAAT 21 2 0 GAATTTTTAA 0.940769 -49 ACTTTAAATAGTAATTATTTATCGGGAAATT 27 236 1 GAATTATTTA 0.796427 -22 TTAACGAGGAGCAATTTTTAATGCACCGTTG 32 188 0 GAATTTTTAA 0.940783 -113 GGCTCTTTTTGTGATTATTTAAATTTTGCCA 32 277 0 GGATTATTTA 0.532625 -24 AACAAATAAAAAAATTTTTTATATGCCACCA 33 24 0 AAATTTTTTA 0.791371 -154 AATATCTCAGGTAATTTTTTAACTTCTGCAG 33 68 1 GAATTTTTTA 0.954371 -110 TTTCGTAAAATTTTTAAGTTAATCACA 36 7 1 AAATTTTTAA 0.742287 -34 * ********* Masking position 5 Map Score: 11.097 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 63 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 TAGTGTACGTCGTCTGCCTTTCAATCCCAT 1 81 0 CGTCTGCCTT 0.889996 -220 TCTGATTTCAACTGTTCCTTGACAACGCCC 1 114 0 ACTGTTCCTT 0.6423 -187 GCAAAAGTCGCCATTGCCTTTCAATCCCAT 1 222 0 CCATTGCCTT 0.648397 -79 GACCCTCAATCCTGCGCCTTTGTCCGCTCG 11 185 1 CCTGCGCCTT 0.971975 -116 CCTGTAGGGGCCAGTGCCTTCCGGAAGTCC 24 50 0 CCAGTGCCTT 0.922603 -251 TCGGTGTACTCGACTTCCTCCGGGATGATA 24 196 0 CGACTTCCTC 0.619856 -105 AATACACCTCCTTCACTTTTTTC 24 288 0 ACACCTCCTT 0.747166 -13 GCTCTCCAGGCGTGCGCCTTACCGCTCGGC 27 46 0 CGTGCGCCTT 0.915664 -212 TGCTAAAGCCTCTCTTCCTTTTTCTTGTTT 29 130 0 TCTCTTCCTT 0.71327 -171 CCGGCAAAAATCTGCTCCTCGCAATGCCCA 32 30 0 TCTGCTCCTC 0.627596 -271 AAGACCTTCTCCACCGCCTCAGCCTGAGGC 32 62 1 CCACCGCCTC 0.93939 -239 TCTTCTATACCCTCCTCCTTTAAAATGCCA 32 101 1 CCTCCTCCTT 0.967762 -200 TCAGCAAGCTCCTCCACCTTCACCACTTCA 32 152 1 CCTCCACCTT 0.86173 -149 ********** Masking position 9 Map Score: 4.72541 Number of sites scoring better than the average of aligned sites = 1562 Number in coding regions = 1484 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 TGTCCTGACGGGTTGAAATCAGACCAAAAT 1 53 1 GGTTGAAATC 0.957371 -248 GTCAAGGAACAGTTGAAATCAGACCAAAAT 1 121 1 AGTTGAAATC 0.949111 -180 GTAGCTCCCAAGTTGAAATCAGACCAAAAT 1 194 1 AGTTGAAATC 0.949111 -107 TGCCGGCGTTTTTTGAAATCAGACTAAAGT 2 64 1 TTTTGAAATC 0.818977 -203 GACCGACGAGAGTTTAAAACCGCCTAAAGC 2 144 1 AGTTTAAAAC 0.680178 -123 GAACACAGTAAGTTGAAATCAGACCAAAAT 11 13 1 AGTTGAAATC 0.949111 -288 CTTCATATAACTTTGAAATCCACCTTCTAC 11 281 1 CTTTGAAATC 0.91065 -20 CTACCGAAAAGTTTTAAATCTTTCGCAATT 15 21 1 GTTTTAAATC 0.651917 -130 TTTTTTCAGCCTTTTAAAACTTTTCGCTTT 16 162 0 CTTTTAAAAC 0.529274 -32 ATTCCACTTTTGTTGAAATCTGCAAGGCAA 19 42 1 TGTTGAAATC 0.909059 -70 GCTTTTATAAGTTTGAAAACCGGAAATCGC 28 149 0 GTTTGAAAAC 0.817733 -51 TTTAATGCACCGTTGAAAACTTGAAGTGGT 32 173 0 CGTTGAAAAC 0.921116 -128 ********** Masking position 6 Map Score: 11.0772 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 146 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TCTAAAGATAAAAGCTGTTATGAATCAGTTC 4 54 0 AAGCTGTTAT 0.96899 -51 GTGCTAAATAAAGGCTGTTATGAACTGGTTC 5 26 0 AAGCTGTTAT 0.968994 -48 AAAATAAAGAAAGGCTTTTATGTTGAGTAAA 8 137 1 AAGCTTTTAT 0.974286 -32 TTGAGACGCTAACACTTTTATAAAACCGCAA 12 31 1 AAACTTTTAT 0.787882 -33 CTTTGAAGACAAAGATTTTATTTTGTTTCGT 16 23 0 AAGATTTTAT 0.787884 -171 AACTCAACTTAAAGCTTATATTGGTTAAAGA 17 23 0 AAGCTTATAT 0.856586 -89 TAATTTCAAAAGAGCTGTTATTCAACACGTC 24 167 0 AGGCTGTTAT 0.879541 -134 TGAGAATAATAAAGCTTTGATTTTGGTGCAG 26 37 0 AAGCTTTGAT 0.898502 -35 AAAGCGGAAAAAGGCTTTTATATATTATAAG 28 174 1 AAGCTTTTAT 0.974286 -26 ** ******** Masking position 6 Map Score: 6.27061 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 11 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 AGACGACGTACACTACTGGGGCGTTGTCAAGGA 1 96 1 CACTCTGGGG 0.993647 -205 ATCGGAGTACCACTACTGGGTGG 8 1 0 CACTCTGGGG 0.995717 -168 ACCACTTCTGGATTGCGGTTTTATA 12 49 0 CACTCTGGAG 0.965861 -15 CGGTAAGGCGCACGCCTGGAGAGCGTGTGGGCG 27 52 1 CACGCTGGAG 0.94312 -206 TTAAGCAAAAAACTACTGTGGAGTTTATACTTT 28 103 0 AACTCTGTGG 0.874938 -97 AAGCTCATGGCACTTCTGAGAAGGCTCGAAAAC 29 227 0 CACTCTGAGG 0.978312 -74 **** ***** * Masking position 7 Map Score: 2.72533 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 17 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 AGCGAGACATTAACACAATTTATTGGGCATG 1 24 1 TAACCAATTT 0.803891 -277 CTACCGAGTCCAACACAAGTTTATGAGATGT 1 167 0 CAACCAAGTT 0.943391 -134 ACACTTTCCACAAATAAATTTACGTAATCCC 2 94 0 CAAAAAATTT 0.625942 -173 CCAAATCAAGTTATTTTAATCA 4 2 1 CAAACAAGTT 0.882951 -103 TCACGACAAATCATTTTATAAAATTTT 6 7 1 CAAACATTTT 0.582433 -89 TTCGCAATTTTATCTCAATTTAAGATTTTGA 15 42 1 TATCCAATTT 0.593066 -109 GAAATTTTTTCAAATAAATTTCAAAGTATGT 15 77 0 CAAAAAATTT 0.625942 -74 TAATAATCATCAACTCAACTTAAAGCTTATA 17 34 0 CAACCAACTT 0.861434 -78 ATATGTTAATCAAAGCAATTTC 21 39 1 CAAACAATTT 0.923336 -12 TTGCTGAAAGCATCTCAAGTTATGCTGTTGG 32 128 0 CATCCAAGTT 0.855596 -173 AAAACTTAGTCAACCCAATTTGACAGC 33 161 1 CAACCAATTT 0.963779 -17 TTTTTAAGTTAATCACAATTTTTTCGTATC 36 21 1 AATCCAATTT 0.452502 -20 **** ****** Masking position 7 Map Score: 3.61037 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 64 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665