AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_aful_reg_300.orf -o00380_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 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 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #9 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #10 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #11 AF0439 82 transcriptional regulatory protein, AsnC family #12 AF0442 300 succinoglycan biosynthesis regulator (exsB) #13 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #14 AF0685 140 enoyl-CoA hydratase (fad-2) #15 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #16 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #17 AF0970 101 A. fulgidus predicted coding region AF0970 #18 AF0991 260 glutaryl-CoA dehydrogenase (gcdH) #19 AF1025 150 3-hydroxyacyl-CoA dehydrogenase (hbd-4) #20 AF1119 111 A. fulgidus predicted coding region AF1119 #21 AF1121 34 transcriptional regulatory protein, AsnC family #22 AF1122 111 3-hydroxyacyl-CoA dehydrogenase (hbd-5) #23 AF1173 180 A. fulgidus predicted coding region AF1173 #24 AF1174 61 A. fulgidus predicted coding region AF1174 #25 AF1177 103 3-hydroxyacyl-CoA dehydrogenase (hbd-6) #26 AF1191 32 dihydroxynaphthoic acid synthase (menB) #27 AF1192 50 conserved hypothetical protein #28 AF1195 27 activator 1, replication factor C, 53 KD subunit #29 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #30 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #31 AF1208 165 conserved hypothetical protein #32 AF1210 108 conserved hypothetical protein #33 AF1215 101 cell division protein, putative #34 AF1641 31 enoyl-CoA hydratase (fad-4) #35 AF1642 50 histidyl-tRNA synthetase (hisS) #36 AF1694 50 tryptophanyl-tRNA synthetase (trpS) #37 AF1778 105 stage V sporulation protein (spoVG) #38 AF1779 57 2-hydroxyacid dehydrogenase, putative #39 AF1855 180 2,3-dihydrosybenzoate-AMP ligase (entE) #40 AF1975 99 glutamyl-tRNA reductase (hemA) #41 AF1976 93 26S protease regulatory subunit 4 #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 AF2233 87 peroxidase / catalase (perA) #48 AF2271 177 A. fulgidus predicted coding region AF2271 #49 AF2272 87 A. fulgidus predicted coding region AF2272 #50 AF2273 57 3-hydroxyacyl-CoA dehydrogenase (hbd-10) #51 AF2426 85 conserved hypothetical protein #52 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 GAAAAAGATTTTCTAATTTTTTTATGAATGTA 1 275 1 TTCTAATTTT 0.519542 -26 CAGCAATTGTTTTTTACTTTTCCTCTTTTTTC 2 19 0 TTTTTATTTC 0.378003 -248 TTGACAATCCTTATAAGATTTTCTGAT 3 6 0 TTATAATTTT 0.862995 -33 GTAAAAAATTTTTGACAATCCTT 3 26 0 TAAAAATTTT 0.449421 -13 ACAAATCATTTTATAAAATTTTTTTTAATTAA 6 16 1 TTATAATTTT 0.862995 -80 AATTTTTTTTAATTAACTTTTTGTTGTTAATT 6 32 1 AATTAATTTT 0.830616 -64 TTTTTAACTTTTCTTTGTCAAT 7 1 1 TTTTTATTTT 0.872708 -54 TTTTAAATTTTCGCTCCTTTGC 8 1 1 TTTTAATTTC 0.599416 -123 CAGAACGACCATTAAAGATTTTGCAGCAAACT 9 51 0 ATTAAATTTT 0.861904 -118 GTCGTGTAATATTTAATGTTTTCGTGAAATAT 10 47 0 ATTTAATTTT 0.938904 -33 AAACATAAAATTTTTATATTTTTAGTTTACTT 11 54 1 TTTTTATTTT 0.872708 -29 GGTTTGTTATATAAAATCTTTTTTCTCGTGCG 13 24 1 ATAAAATTTT 0.699564 -122 GATTGACTTTATTTAAATTTTTTGGATTTTCA 15 41 1 ATTTAATTTT 0.938904 -57 ATTTTTATTTTTATATTTTTGTTTTTAAC 16 8 1 TTTTTATTTT 0.872708 -198 AATCTGGCAATATAAAGCTTTTGCAGATACAC 17 26 1 TATAAATTTT 0.686295 -76 ATTTAAATTTTTTCATTTATGA 17 90 0 ATTTAATTTT 0.938904 -12 TTGCGAAAGATTTAAAACTTTTCGGTAGGAGT 19 17 0 TTTAAATTTT 0.872708 -134 TTTTATCTCAATTTAAGATTTTGATTTGACAT 19 49 1 ATTTAATTTT 0.938904 -102 CACTTCAATAATTTAAATTTTTTGCTCAGATA 20 78 0 ATTTAATTTT 0.938904 -34 TGTCTCAGAAAAATAAACTTTT 21 1 0 AAATAATTTT 0.646618 -34 AATTCAAACCATTTAAGCTTTTCCATAATTAT 23 33 1 ATTTAATTTT 0.938904 -148 TTGAAGAGTATTTTAATCTTTTGAGATTACAA 24 26 0 TTTTAATTTT 0.944074 -36 TTTTAATTTTTATTTTTTCCAACAGATA 29 7 1 TTTTTATTTT 0.872708 -59 CTATTTGTAGTATTTACCTTTTCTTTAACAGA 31 16 1 TATTTATTTT 0.686295 -150 AACATACTTAAATTAACTTTTTTGAAGCTAAA 31 142 1 AATTAATTTT 0.830616 -24 ACGCTTTTTATTTAAACCTTTTTCCCAACTTT 33 61 0 TTTAAATTTT 0.872708 -41 GCAAGGGTGTTTAAAAGGTTTTAGAGTTGAGC 35 17 0 TTAAAATTTT 0.718964 -34 CTTCAAAACCTTTTTATCTTTTCTGGGTTCAA 38 29 1 TTTTTATTTT 0.872708 -29 TATGCTGACAATTTAACCTTTTCTAAAAAGAT 39 34 1 ATTTAATTTT 0.938904 -147 TAACCTTTTCTAAAAAGATTTTGCGGTAGTTT 39 47 1 TAAAAATTTT 0.449432 -134 CCATTTTATCATTTTAATTTTTGCTTTTCAGC 40 29 1 ATTTTATTTT 0.861904 -71 CACAAGTGCTTTTTAAGTTTTTTATTCAGCAA 40 62 0 TTTTAATTTT 0.944074 -38 TTATCCCTCAATTTTATTTTTTGCTTCCCTCT 41 69 0 ATTTTATTTT 0.861904 -25 GCATCCAGATATTTAACCTTTTGGAACTAAAT 42 25 1 ATTTAATTTT 0.938904 -77 TGCTAACAAAAATAAAAATTTTACTATTTAGG 43 13 0 AATAAATTTT 0.665719 -34 CGTAAGCTTAATAATAAGTTTTATAACCTTCA 44 136 1 ATAATATTTT 0.486088 -40 TTGCATAAAATTTTTAGCTTTTTAATTCTTTA 46 35 1 TTTTTATTTT 0.872708 -29 ACATCTTAGTAAAAAACATTTTTCTTCTAGAA 47 23 1 AAAAAATTTT 0.42539 -65 ATGGTGGCATATAAAAAATTTTTTTATTTGTT 48 23 1 ATAAAATTTT 0.699591 -155 ATTACCTGAGATATTAAATTTTAATCAAAACA 48 51 0 ATATTATTTT 0.699602 -127 GTTGACTAAGTTTTAACCTTTTTCTTTTTTGT 48 143 0 TTTTAATTTT 0.944074 -35 ATGTATTAAGTTTTTCCATTTTATT 50 43 0 TATTAATTTT 0.843423 -15 ****** **** Masking position 6 Map Score: 52.0373 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 156 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 2 TAATGTCTCGCTTTCAATCCCATTT 1 2 0 CTTTAACCAT 0.983561 -299 CGTCGTCTGCCTTTCAATCCCATTTTGGTCTGAT 1 70 0 CTTTAACCAT 0.983561 -231 GATGTTCTTACTTTCAATCCCATTTTGGTCTGAT 1 138 0 CTTTAACCAT 0.983561 -163 TCGCCATTGCCTTTCAATCCCATTTTGGTCTGAT 1 211 0 CTTTAACCAT 0.983561 -90 TACACGTCCACTTTCAATCCCATTTTGGTCTGAT 12 30 0 CTTTAACCAT 0.983561 -271 AGTCATCGCCCTTTAAACCACAATATTCATAAAT 12 249 0 CTTTAAACAT 0.825003 -52 CTTCATATAACTTTGAAATCCACCTTCTAC 12 281 1 CTTTAACCAC 0.870317 -20 TGTTGCCTCTCTTTAAAATTCACTTCGTATGCTT 13 70 0 CTTTAATCAT 0.963379 -76 GGGCATGGAATTTTTAATGTCAATAA 14 125 1 TTTTAATCAT 0.893005 -16 GATACACTCATTTTAAATATCAATCAACATTAGT 17 51 1 TTTTAATCAT 0.893005 -51 GGATTTGAGGCTTTAAAAGCAAATTTAAAGCTTT 18 61 1 CTTTAACAAT 0.847949 -200 TCAATTTTTGTTTTAAAGACCTTTAAGGTAAATT 18 133 1 TTTTAACCTT 0.741209 -128 ATTTGACATACTTTGAAATTTATTTGAAAAAATT 19 72 1 CTTTAATTAT 0.581681 -79 TTTAAGTATGTTTTCAATATCATTACATATCATT 31 120 0 TTTTAATCAT 0.893005 -46 AAATTAACTTTTTTGAAGCTAAATC 31 151 1 TTTTAATAAT 0.437545 -15 CTCTAAAACCTTTTAAACACCCTTGCCGAAGCTT 35 23 1 TTTTAACCCT 0.706514 -28 TGACAATGAACTTTCAATATCTTTAATTTTAAAA 39 87 0 CTTTAATCTT 0.798762 -94 CAGCAAAAGGCTTTAAAAGCCACTGCCTTTAATC 45 178 0 CTTTAACCAT 0.983561 -98 **** ** *** * Masking position 4 Map Score: 23.0605 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 75 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TCCTGACGGGTTGAAATCAGACCAAAATGG 1 55 1 TTGAAATCAG 0.971764 -246 CAAGGAACAGTTGAAATCAGACCAAAATGG 1 123 1 TTGAAATCAG 0.971764 -178 TAAACTTGTGTTGGACTCGGTAGCTCCCAA 1 175 1 TTGGACTCGG 0.946637 -126 AGCTCCCAAGTTGAAATCAGACCAAAATGG 1 196 1 TTGAAATCAG 0.971764 -105 CCGGCGTTTTTTGAAATCAGACTAAAGTGG 2 66 1 TTGAAATCAG 0.971764 -201 GCAACAGTTTTTAAAATCGGAGTACCACTA 9 19 0 TTAAAATCGG 0.798135 -150 ACACAGTAAGTTGAAATCAGACCAAAATGG 12 15 1 TTGAAATCAG 0.971764 -286 CCGCCGGGAGTTGAACCCGGGTCGAGGAGT 14 95 0 TTGAACCCGG 0.965924 -46 ATTATCTATTTTTAAATCGGCACATTACGT 16 166 1 TTTAAATCGG 0.798135 -40 TCCACTTTTGTTGAAATCTGCAAGGCAATG 22 44 1 TTGAAATCTG 0.877263 -68 ACTTAAAGAATTGGACCCGGATGGTATTTT 30 253 1 TTGGACCCGG 0.899553 -48 GACAGAATTGAACCCAGAAAAGATAAA 38 41 0 TTGAACCCAG 0.946551 -17 CCGCCGAGATTTGAACTCGGGTCACCGGCT 45 101 1 TTGAACTCGG 0.982502 -175 ********** Masking position 5 Map Score: 19.4862 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 85 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 CTTTCAATCCCATTTTGGTCTGATTTCAACCCG 1 61 0 CATTTTCTGA 0.98161 -240 CTTTCAATCCCATTTTGGTCTGATTTCAACTGT 1 129 0 CATTTTCTGA 0.98161 -172 CTTTCAATCCCATTTTGGTCTGATTTCAACTTG 1 202 0 CATTTTCTGA 0.98161 -99 AAGATTTTCTAATTTTTTTATGAATGTAGATT 1 279 1 AATTTTATGA 0.788955 -22 TTTACTTTTCCTCTTTTTTCTGAACACC 2 6 0 CTTTTTCTGA 0.953141 -261 TACGTAATCCCACTTTAGTCTGATTTCAAAAAA 2 72 0 CATTTTCTGA 0.98161 -195 AAAGTCAGATAATTTTGTTATGAACTGATTCAT 4 33 1 AATTTTATGA 0.788955 -72 ATTTATCAGGATATTTTTTCTGAACAAATGGTG 6 68 1 ATTTTTCTGA 0.895398 -28 CAAAAAATTTAAGTTTGCTCTGCCAATAGTCCA 9 81 0 AATTTTCTGC 0.752947 -88 CTTTCAATCCCATTTTGGTCTGATTTCAACTTA 12 21 0 CATTTTCTGA 0.98161 -280 CCTATGCAGAATTTTTCATCTGAGCGGGGGTTG 12 216 0 ATTTTTCTGA 0.895398 -85 AAATCTTTCGCAATTTTATCTCAATTTAAGATT 19 36 1 CATTTTCTCA 0.828051 -115 TTAGAGTGAGCATTTTTATCTGAGCAAAAAATT 20 62 1 CATTTTCTGA 0.98161 -50 TTTTGTGTTGATGTTTGTTATGAGCACTATGCC 23 109 0 ATTTTTATGA 0.58756 -72 ACACCTCCTTCACTTTTTTCTTATTAAAATACC 30 275 0 CATTTTCTTA 0.76466 -26 ** *** ***** Masking position 6 Map Score: 21.1636 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 45 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TCTCGCTTTCAATCCCATTT 1 1 0 AATCCCATTT 0.970489 -300 TCTGCCTTTCAATCCCATTTTGGTCTGATT 1 69 0 AATCCCATTT 0.970489 -232 TCTTACTTTCAATCCCATTTTGGTCTGATT 1 137 0 AATCCCATTT 0.970489 -164 ATTGCCTTTCAATCCCATTTTGGTCTGATT 1 210 0 AATCCCATTT 0.970489 -91 AAATTTACGTAATCCCACTTTAGTCTGATT 2 80 0 AATCCCACTT 0.968509 -187 CGCGAATCCCCTCTTAAGCAGAGA 5 60 0 AATCCCCTCT 0.887706 -14 GTCCACTTTCAATCCCATTTTGGTCTGATT 12 29 0 AATCCCATTT 0.970489 -272 ATAACTTTGAAATCCACCTTCTAC 12 287 1 AATCCACCTT 0.653788 -14 TCATATTTGGAATCCTCCTTTATAATTCTT 19 119 0 AATCCTCCTT 0.769049 -32 TTTAGTAAAAAATTCCACTTTTGTTGAAAT 22 31 1 AATTCCACTT 0.707883 -81 TAATAAGTTAAATCCTATCTGTGAC 32 94 1 AATCCTATCT 0.685722 -15 ********** Masking position 2 Map Score: 13.1222 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 59 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GCTACCGAGTCCAACACAAGTTTATGAGATGTT 1 166 0 CCAACACATT 0.616822 -135 TCCAGCAAATCCACCACCAAATTTATTCATTAA 2 179 1 CCACCACATT 0.971803 -88 CTAAACACCTCCAAATTAGAAAATAGG 4 88 0 ACACCTCATT 0.913857 -17 ACAACCACCATTTGTTCAGAAAAAATA 6 79 0 CCACCATTTC 0.651386 -17 ATTAAATATTACACGACTACTTTTTTCA 10 62 1 ACACGACATT 0.782465 -18 AAGAAGATTTACACGTCCACTTTCAATCCCATT 12 40 0 ACACGTCATT 0.589323 -261 ATCGCCCTTTAAACCACAATATTCATAAATCCT 12 246 0 AAACCACATT 0.600734 -55 TACACCACCTTGTTTAACTCTATT 13 132 0 ACACCACTTT 0.945015 -14 AACACCTCCAGATTTCTTGAGCTT 15 2 1 ACACCTCATT 0.913857 -96 GCTACCACCTTTTTTCTGTATTTA 18 247 0 CTACCACTTT 0.761033 -14 TTTTTCTGAGACACCATTTTCTTCG 21 20 1 ACACCATTTT 0.809185 -15 AATACCACCTTGTTAGTACTTGAA 23 2 1 ATACCACTTT 0.710744 -179 AGCACTATGCCCACCTCAAAATTTTTTCCCACC 23 87 0 CCACCTCATT 0.932201 -94 AAATTCTTATATACCACTTTGTTTGAGAGTAAC 37 60 1 ATACCACTTT 0.710744 -46 ATCACCACCTCTACCTTAAAAATTATG 39 5 1 CCACCTCATT 0.932201 -176 CCGGGAGTCTCCACCATTTTATCATTTTAATTT 40 16 1 CCACCATTTC 0.651386 -84 TTTTTATATGCCACCATCAACTTCTCAAC 48 7 0 CCACCATATT 0.894779 -171 AACTTTTTTACACCATAAGTTCAAGGATAACG 50 10 1 ACACCATATC 0.690452 -48 ******* * ** Masking position 12 Map Score: 12.8719 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 376 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 TGCAAAAGTCGCCATTGCCTTTCAATCCCA 1 223 0 GCCATTGCCT 0.985642 -78 TATTAGTGTAGGCATTGCCTTGCAGATTTC 22 56 0 GGCATTGCCT 0.940264 -56 AACCATTGCCGCCTCTGCCTCTTTTGAGCA 25 20 0 GCCTCTGCCT 0.963231 -84 CCCTGTAGGGGCCAGTGCCTTCCGGAAGTC 30 51 0 GCCAGTGCCT 0.990671 -250 AATTGAGTGCCCCAGTGCCTGAGCTACATA 44 62 0 CCCAGTGCCT 0.960549 -114 GGCTTTAAAAGCCACTGCCTTTAATCATTA 45 174 0 GCCACTGCCT 0.990671 -102 ********** Masking position 6 Map Score: 5.79333 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 TTAGAAAATCTTTTTCCTCTTGCCACGCTTG 1 260 0 TTTTTCTCTT 0.686933 -41 CAGCAATTGTTTTTTACTTTTCCTCTTTTTT 2 20 0 TTTTTCTTTT 0.784022 -247 TTTTTTCTTATTTATGAACCAG 5 2 1 TTTTTTTATT 0.674001 -72 TTTATAAAATTTTTTTTAATTAACTTTTTGT 6 25 1 TTTTTTAATT 0.768061 -71 AAACATAAAATTTTTATATTTTTAGTTTACT 11 54 1 TTTTTTATTT 0.855813 -29 TTATTTAAATTTTTTGGATTTTCAGTAAGAT 15 49 1 TTTTTGATTT 0.672889 -49 ATTTTTATTTTTATATTTTTGTTTTTAA 16 8 1 TTTTTTATTT 0.855813 -198 TTTTTATAATTAACAAATCTG 17 1 1 TTTTTTAATT 0.768061 -101 ATTTAAATTTTTTCATTTATGAACACAA 17 84 0 TTTTTCATTT 0.853249 -18 TTTTAATTTTTATTTTTTCCAACAGAT 29 7 1 TTTTTTTTTT 0.787495 -59 CTCCTTCACTTTTTTCTTATTAAAATACCAT 30 273 0 TTTTTTTATT 0.674001 -28 CTTTAACAGATTTTTCGAATTGTTCAAGCGA 31 38 1 TTTTTGAATT 0.534378 -128 GGCGTTGCTGTTTTTAAACTTGCCTTTATCG 33 23 1 TTTTTAACTT 0.535276 -79 TTTAGGAAATTTTTTAAAATTAAAGATATTG 39 76 1 TTTTTAAATT 0.515302 -105 ATCATTTTAATTTTTGCTTTTCAGCATTGCT 40 36 1 TTTTTCTTTT 0.784022 -64 AATAGTAAAATTTTTATTTTTGTTAGCATGT 43 17 1 TTTTTTTTTT 0.787495 -30 GGGCACTCAATTTTTACACTTGAAGTAAAGA 44 80 1 TTTTTCACTT 0.778488 -96 ATATAAAAAATTTTTTTATTTGTTTTGATTA 48 31 1 TTTTTTATTT 0.855813 -147 TCTCAGGTAATTTTTTAACTTCTGCAGTTAA 48 72 1 TTTTTAACTT 0.535276 -106 AGTTTTAACCTTTTTCTTTTTTGTTTAACCA 48 136 0 TTTTTTTTTT 0.787495 -42 ATGTATTAAGTTTTTCCATTTTATTCGTTAT 50 37 0 TTTTTCATTT 0.853249 -21 ***** ***** Masking position 5 Map Score: 20.2108 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 107 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 9 ATCAAGTTATTTTAATCAAAAGTCAGATAAT 4 15 1 TTAATCAAAA 0.750265 -90 CAATGGGCGATTTAAGCAAAGGAGCGAAAAT 8 17 0 TTAAGCAAAG 0.929777 -107 ATTAAAGATTTTGCAGCAAACTATGCAACAG 9 42 0 TTCAGCAAAC 0.76777 -127 TTTTTAAAGGAAAGATTTATCTTG 14 4 1 TTAAGGAAAG 0.762029 -137 ATTATTGACATTAAAGCTAAATACAGTACGC 16 52 0 TTAAGCTAAA 0.766091 -154 TTAAAGGTCTTTAAAACAAAAATTGAAGTTT 18 128 0 TTAAACAAAA 0.616889 -133 TTTAAAGACCTTTAAGGTAAATTTTATGTTG 18 144 1 TTAAGGTAAA 0.441978 -117 GCCTTGCAGATTTCAACAAAAGTGGAATTTT 22 39 0 TTCAACAAAA 0.531925 -73 GTTCAATCAAAACATTGAAGAG 24 50 0 TTAATCAAAA 0.75027 -12 ATTAAAAATTACAGCAAAATAGTAATATA 27 9 1 TTCAGCAAAA 0.919289 -42 GAAAAATCTGTTAAAGAAAAGGTAAATACTA 31 23 0 TTAAGAAAAG 0.670669 -143 TTTCGAATTGTTCAAGCGAAGCTCGTTTAAA 31 50 1 TTAAGCGAAG 0.611826 -116 ATTAACTTTTTTGAAGCTAAATC 31 153 1 TTAAGCTAAA 0.766091 -13 GGAAAAAGGTTTAAATAAAAAGCGTATTAAA 33 68 1 TTAATAAAAA 0.316045 -34 AGAATTTTGATTGCAGGAAACGTTAGATTAA 37 36 0 TTCAGGAAAC 0.444313 -70 TAAAAAGGTTTTGAAGCAAAAGCCAAACTCT 38 14 0 TTAAGCAAAA 0.941651 -44 ATTTTTACACTTGAAGTAAAGAAGGATAAAG 44 89 1 TTAAGTAAAG 0.446281 -87 TGAGCTGCAGTTCCAGAAAAGCTGACAGGTT 45 17 0 TTCAGAAAAG 0.589703 -259 ACGAATGCGTTTGCAGCAAAAGGCTTTAAAA 45 194 0 TTCAGCAAAA 0.919289 -82 GATATTAAATTTTAATCAAAACAAATAAAAA 48 43 0 TTAATCAAAA 0.750265 -135 ** ******** Masking position 2 Map Score: 9.72892 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 181 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 TGAATAAATTTGGTGGTGGATTTGCTGGAG 2 178 0 TGGTGGTGGA 0.841452 -89 TTTTCTAATTTGGAGGTGTTTAG 4 92 1 TGGAGGTGTT 0.952339 -13 GGATTGAAAGTGGACGTGTAAATCTTCTTT 12 44 1 TGGACGTGTA 0.842346 -257 GAGTTAAACAAGGTGGTGTA 13 136 1 AGGTGGTGTA 0.952339 -10 TCAAGAAATCTGGAGGTGTT 15 1 0 TGGAGGTGTT 0.952339 -97 CAAATATGAGTGGTGGTAAAA 19 140 1 TGGTGGTAAA 0.521886 -11 AGTACTAACAAGGTGGTATT 23 1 0 AGGTGGTATT 0.775494 -180 CGTAACGTTGAGGACGTGTTGAATAACAGC 30 155 1 AGGACGTGTT 0.842346 -146 AAAAAAGTGAAGGAGGTGTATT 30 289 1 AGGAGGTGTA 0.952339 -12 TTTAAGGTAGAGGTGGTGAT 39 1 0 AGGTGGTGAT 0.863281 -180 ********** Masking position 7 Map Score: 4.38575 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 495 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 11 CCGGGTTCAACTCCCGGCGGGGGCATGGAAT 14 105 1 CTCCGGCGGG 0.966385 -36 CTCCGGGCAGGGAAAAATGTA 26 22 0 CTCCGGCAGG 0.980684 -11 AAGTTCTGGACTTCCGGAAGGCACTGGCCCC 30 43 1 CTTCGGAAGG 0.981426 -258 GCTCTTAGCGCTTCATGAAGGACGTAACGTT 30 133 1 CTTCTGAAGG 0.923588 -168 GTGTACTCGACTTCCTCCGGGATGATAATTT 30 192 0 CTTCTCCGGG 0.703575 -109 GCTCAAGCTTCGGCAAGGGTGTTTAAAA 35 33 0 CTTCGCAAGG 0.949228 -18 ATGGTGGAGACTCCCGGAACGG 40 2 0 CTCCGGAACG 0.948254 -98 TATTTGGAGGCTTCCGGAACGTAGAGGGAAG 41 47 1 CTTCGGAACG 0.949227 -47 **** ****** Masking position 2 Map Score: 3.59979 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 159 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 TCTGATTTCAAAAAACGCCGGCAAAAACGATTATCGC 2 50 0 AAAAGGAAAA 0.930793 -217 ATTAACAACAAAAAGTTAATTAAAAAAAATTTTATAA 6 26 0 AAAATTAAAA 0.737726 -70 TTGTTCAGAAAAAATATCCTGATAAATAATTAATTAA 6 58 0 AAAATGAAAT 0.894507 -38 GTTAAAAACAAAAATATAAAAATAAAAAT 16 3 0 AAAATAAAAA 0.737726 -203 CAGTACGCTAAAAACAGCGTGTTAAAAACAAAAATAT 16 23 0 AAAAGGAAAA 0.930793 -183 TGAGCGTTTAAAAAGATTTCGGAAAAAGTTTGCCAAT 18 198 0 AAAATGAAAA 0.960346 -63 TAAACGCTCAAAAAAAGAATGTTAAATACAGAAAAAA 18 225 1 AAAAGGAAAT 0.824836 -36 AATTTATTTGAAAAAATTTCGTAAAAATAGTAAGAAT 19 88 1 AAAATGAAAA 0.960346 -63 ACATCAACACAAAAGTTAACGGTAAAATAATAACAAT 23 128 1 AAAATGAAAA 0.960346 -53 CGGGCAGGGAAAAATGTACTGGAAAATAC 26 3 0 AAAATGAAAT 0.894507 -30 ATTAAAAATTACAGCAAAATAGTAATATAT 27 4 1 AAAATGAAAT 0.894507 -47 AAAGTTGGGAAAAAGGTTTAAATAAAAAGCGTATTAA 33 61 1 AAAATAAAAA 0.737726 -41 AAACTACCGCAAAATCTTTTTAGAAAAGGTTAAATTG 39 42 0 AAAATTAAAA 0.737726 -139 AATCCCTTAAAAAATTTCCCGATTAAAGTTGGTAATG 39 139 0 AAAATGTAAA 0.674503 -42 AGCAAAAAATAAAATTGAGGGATAAAAT 41 76 1 AAAAGGAAAA 0.930793 -18 TAAAAAGCTAAAAATTTTATGCAAATAAATATGCATA 46 22 0 AAAATGAATA 0.674503 -42 **** * * **** Masking position 4 Map Score: 15.2884 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 55 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 CAGACGACGTACACTACTGGGGCGTTGTCAA 1 95 1 ACACTACGGG 0.952591 -206 AATCGGAGTACCACTACTGGGTGG 9 4 0 CCACTACGGG 0.983441 -165 AACCCTCGAACCCCTACGGGACAGGACCCTC 12 161 1 CCCCTACGGA 0.963581 -140 GATATCCGCTACCCCACGGGGGCGACGTGGA 14 50 0 ACCCCACGGG 0.979307 -91 AAATTCCATGCCCCCGCCGGGAGTTGAACCC 14 107 0 CCCCCGCGGG 0.980917 -34 AAGGCACTGGCCCCTACAGGGTGATAACGCA 30 60 1 CCCCTACGGG 0.993658 -241 ******* *** Masking position 7 Map Score: 4.00265 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 44 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 TTTCAACTTGGGAGCTACCGAGTCCAACACA 1 181 0 GGAGCACCGA 0.891744 -120 CATCTGAGCGGGGGTTGCCGAGCGGACAAAG 12 202 0 GGGGTGCCGA 0.989114 -99 TCGCCCCCGTGGGGTAGCGGATATCCTGAGG 14 56 1 GGGGTGCGGA 0.984249 -85 GATATCCTGAGGGGCTGCGGACTCCTCGACC 14 75 1 GGGGCGCGGA 0.992305 -66 GTTTAAACGAGGTGTGGCTGATATGTAGAGT 31 74 1 GGTGTGCTGA 0.885602 -92 GTTCAATGATGGGGCCGCCGAGATTTGAACT 45 87 1 GGGGCGCCGA 0.994563 -189 CTCGGCTTTGGGAGCCGGTGACCCGAGTTCA 45 112 0 GGAGCGGTGA 0.844241 -164 ***** ***** Masking position 11 Map Score: 3.14922 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 48 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 GGAGAAGAGCTTTAGGCGGTTTTAAACTCTC 2 151 0 TTTAGCGGTT 0.957113 -116 TTTGGGGATTTTTAAACGGTTAAAGCTTAAT 2 207 0 TTTAACGGTT 0.794151 -60 GTATTTAAGGTTTGGGCGTTTGGGGATTTTT 2 225 0 TTTGGCGTTT 0.924593 -42 CTTTCTTTATTTTGAGTGGTTTGAAGCCTAT 9 119 0 TTTGGTGGTT 0.886851 -50 GTTCGTTGAGTTTGGGAGGTTCAAGAAGCAT 12 103 0 TTTGGAGGTT 0.91824 -198 ATATTCAATTTTTACGCGTTTAGATTTTTCA 16 99 0 TTTAGCGTTT 0.904978 -107 TTCGTTATATTTTTTGAGGTTCAAGGTTTGA 18 24 0 TTTTGAGGTT 0.682752 -237 ACATTCTTTTTTTGAGCGTTTAAAAAGATTT 18 216 0 TTTGGCGTTT 0.924593 -45 AATGATATTATTTAAGTGTTTCTTATTAGTG 22 78 0 TTTAGTGTTT 0.722073 -34 GGCAAGGGTGTTTAAAAGGTTTTAGAGTTGA 35 19 0 TTTAAAGGTT 0.601279 -32 **** ****** Masking position 3 Map Score: 3.43781 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 74 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911