AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00120_aful_reg_300.orf -o00120_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 Purged sequences: AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) 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 AF0018 22 3-ketoacyl-CoA thiolase (acaB-1) #9 AF0025 300 cyanate transport protein (cynX) #10 AF0033 36 acyl carrier protein synthase (acaA-1) #11 AF0135 59 conserved hypothetical protein #12 AF0136 103 A. fulgidus predicted coding region AF0136 #13 AF0194 300 A. fulgidus predicted coding region AF0194 #14 AF0195 22 A. fulgidus predicted coding region AF0195 #15 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #16 AF0197 86 acetyl-CoA synthetase (acs-1) #17 AF0283 168 3-ketoacyl-CoA thiolase (acaB-7) #18 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #19 AF0439 82 transcriptional regulatory protein, AsnC family #20 AF0442 300 succinoglycan biosynthesis regulator (exsB) #21 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #22 AF0970 101 A. fulgidus predicted coding region AF0970 #23 AF1029 193 long-chain-fatty-acid--CoA ligase (fadD-5) #24 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #25 AF1289 300 conserved hypothetical protein #26 AF2009 101 heme biosynthesis protein (nirJ-2) #27 AF2010 46 A. fulgidus predicted coding region AF2010 #28 AF2011 175 conserved hypothetical protein #29 AF2013 275 coenzyme F390 synthetase (ftsA-3) #30 AF2014 63 sugar transporter, putative #31 AF2100 106 acetolactate synthase, large subunit (ilvB-4) #32 AF2244 300 acyl-CoA dehydrogenase (acd-11) #33 AF2409 42 iron-sulfur cluster binding protein #34 AF2410 43 A. fulgidus predicted coding region AF2410 #35 AF2411 41 conserved hypothetical protein #36 AF2412 39 thiamine biosynthesis protein (thiC) #37 AF2414 67 conserved hypothetical protein #38 AF2416 115 3-ketoacyl-CoA thiolase (acaB-12) Motif number 1 AATGTCTCGCTTTCAATCCCATTT 1 2 0 TTCAATCCAT 0.951162 -299 TCCTGACGGGTTGAAATCAGACCAAAATGGGAT 1 55 1 TTAAATCGAC 0.964331 -246 GTCGTCTGCCTTTCAATCCCATTTTGGTCTGAT 1 70 0 TTCAATCCAT 0.951162 -231 CAAGGAACAGTTGAAATCAGACCAAAATGGGAT 1 123 1 TTAAATCGAC 0.964331 -178 ATGTTCTTACTTTCAATCCCATTTTGGTCTGAT 1 138 0 TTCAATCCAT 0.951162 -163 AGCTCCCAAGTTGAAATCAGACCAAAATGGGAT 1 196 1 TTAAATCGAC 0.964331 -105 CGCCATTGCCTTTCAATCCCATTTTGGTCTGAT 1 211 0 TTCAATCCAT 0.951162 -90 CCGGCGTTTTTTGAAATCAGACTAAAGTGGGAT 2 66 1 TTAAATCGAT 0.938039 -201 GCAACAGTTTTTAAAATCGGAGTACCACTACTG 17 16 0 TTAAATCGAT 0.938039 -153 ACACAGTAAGTTGAAATCAGACCAAAATGGGAT 20 15 1 TTAAATCGAC 0.964331 -286 ACACGTCCACTTTCAATCCCATTTTGGTCTGAT 20 30 0 TTCAATCCAT 0.951162 -271 GTCATCGCCCTTTAAACCACAATATTCATAAAT 20 249 0 TTAAACCCAT 0.742198 -52 ATTATCTATTTTTAAATCGGCACATTACGTAAA 21 166 1 TTAAATCGCC 0.752011 -40 ATACACTCATTTTAAATATCAATCAACATTAGT 22 52 1 TTAAATACAT 0.691792 -50 TTTTTTCTTATTAAAATACCATCCGGGTCCAAT 24 262 0 TTAAATACAC 0.800333 -39 GTGACCCGAGTTCAAATCTCGGCGGCCCCATCA 29 93 0 TTAAATCCGC 0.837166 -183 GCTGCAAGAGTTTAAAACCCATCGAATACGATT 31 32 0 TTAAAACCAC 0.776227 -75 CCCTCCTCCTTTAAAATGCCAACAGCATAACTT 32 110 1 TTAAATGCAC 0.771117 -191 CTCGGATAATTTTCAATCGCATCGGTGACCC 38 9 0 TTCAATCCAC 0.972051 -107 ** ***** ** * Masking position 2 Map Score: 24.6069 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 104 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 TCTGCCTTTCAATCCCATTTTGGTCTGATTTCAACCC 1 62 0 AACCCTTTCG 0.995526 -239 TCTTACTTTCAATCCCATTTTGGTCTGATTTCAACTG 1 130 0 AACCCTTTCG 0.995526 -171 ATTGCCTTTCAATCCCATTTTGGTCTGATTTCAACTT 1 203 0 AACCCTTTCG 0.995526 -98 AAATTTACGTAATCCCACTTTAGTCTGATTTCAAAAA 2 73 0 AACCCTTTCG 0.995528 -194 AGGCGGTTTTAAACTCTCGTCGGTCTGAGTTTTGTTT 2 132 0 AACTCTCTCG 0.870802 -135 CGCGAATCCCCTCTTAAGCAGAGATGAGTGC 5 53 0 AACCCTTGCG 0.992028 -21 ACAACCACCATTTGTTCAGAAAAAATATC 6 77 0 AACACTTTCG 0.971666 -19 GTGTTCCTTCAACCCCTACTCAATCTCCTTCTATTAG 12 15 0 AACCCTCTCC 0.900093 -89 TCCCGTACTCAAACACCCTTTCAGCAGGTAGCTTCCT 13 200 0 AACACTTGCG 0.950426 -101 GTCCACTTTCAATCCCATTTTGGTCTGATTTCAACTT 20 22 0 AACCCTTTCG 0.995526 -279 TTTGTCTTCAAAGCCCCAATTGAGCTTTTAGTGAATT 23 41 1 AACCCTTGCT 0.885279 -153 CACTTCATCAACCCCCATCTTTTTCAGCTCGACAATA 25 200 0 ACCCCTTTCG 0.974499 -101 ** *** ** ** * Masking position 1 Map Score: 21.0809 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 44 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 AATCATTTTATAAAATTTTTTTTAATTAAC 6 19 1 TAAAATTTTT 0.909107 -77 TTTTTTTTAATTAACTTTTTGTTGTTAATT 6 34 1 TTAACTTTTT 0.920145 -62 TGAGCAAATATTAAATTTTTAAGGAATTTA 11 26 0 TTAAATTTTT 0.938921 -34 GAAAACTTTAACTTTTTGTCAAAATAA 13 284 0 TTAACTTTTT 0.920145 -17 TTGAGCATAATTCAATTTTTTAAGATGATA 16 21 1 TTCAATTTTT 0.857513 -66 CAGAGCAAACTTAAATTTTTTGGATATATA 17 92 1 TTAAATTTTT 0.938921 -77 ATGGCAAACATAAAATTTTTATATTTTTAG 19 49 1 TAAAATTTTT 0.909107 -34 ACTTGATATATTCAATTTTTACGCGTTTAG 21 107 0 TTCAATTTTT 0.857513 -99 ATTTAAATTTTTTCATTTATGA 22 90 0 TTAAATTTTT 0.938921 -12 CTGAAGCCATTCAAATTTTTCAGATTTTGC 23 99 0 TCAAATTTTT 0.762395 -95 TTCAGCCTTTTAAAACTTTTCGCTTTTTAC 23 158 0 TAAAACTTTT 0.803027 -36 ATACACCTCCTTCACTTTTTTCTTATTAAA 24 280 0 TTCACTTTTT 0.818377 -21 ATCCAGATATTTAACCTTTTGGAACTAAAT 26 27 1 TTAACCTTTT 0.818377 -75 GCCTAAATAGTAAAATTTTTATTTTTGTTA 27 12 1 TAAAATTTTT 0.909107 -35 TTTATTTGCATAAAATTTTTAGCTTTTTAA 30 30 1 TAAAATTTTT 0.909107 -34 AGCATCAACATAAACCTTTTCAACTGCC 33 9 0 TAAACCTTTT 0.753326 -34 ********** Masking position 4 Map Score: 20.586 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 39 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 TGACGGGTTGAAATCAGACCAAAATGGGATTGAAAGGC 1 58 1 AATCAGCAGG 0.997421 -243 GGAACAGTTGAAATCAGACCAAAATGGGATTGAAAGTA 1 126 1 AATCAGCAGG 0.997421 -175 TCCCAAGTTGAAATCAGACCAAAATGGGATTGAAAGGC 1 199 1 AATCAGCAGG 0.997421 -102 GCGTTTTTTGAAATCAGACTAAAGTGGGATTACGTAAA 2 69 1 AATCAGCAGG 0.997421 -198 AAGGAAACAAAACTCAGACCGACGAGAGTTTAAAACCG 2 128 1 AATCAGCAGG 0.997421 -139 AGTTCATCAAAATTCAGGCTCATGTGAGGCTTAACGTA 13 137 0 AATCAGCAGG 0.997421 -164 CAGTAAGTTGAAATCAGACCAAAATGGGATTGAAAGTG 20 18 1 AATCAGCAGG 0.997421 -283 ** **** * * * * Masking position 12 Map Score: 17.9394 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 Motif number 5 CAAGAGGAAAAAGATTTTCTAATTTTTTTA 1 269 1 AAGATTTTCT 0.933036 -32 AAACCGCCTAAAGCTCTTCTCCAGCAAATC 2 160 1 AAGCTCTTCT 0.956155 -107 CAATCCTTATAAGATTTTCTGAT 3 4 0 AAGATTTTCT 0.933036 -35 TGATTCATAACAGCTTTTATCTTTAGAAGG 4 58 1 CAGCTTTTAT 0.863298 -47 CAGTTCATAACAGCCTTTATTTAGCACTCA 5 30 1 CAGCCTTTAT 0.761226 -44 ACTCCTTACCAAGCTTTTCTGAGGAAGCTA 13 179 1 AAGCTTTTCT 0.977375 -122 TTGTCAAAATAAGTTTTTCTGTGATATCCC 13 266 0 AAGTTTTTCT 0.808976 -35 TTTCAAAGCTTTTCTTGAGGTT 14 6 1 AAGCTTTTCT 0.977375 -17 CTCAACATAAAAGCCTTTCTTTATTTTGAG 17 134 0 AAGCCTTTCT 0.956155 -35 TTTGAAGACAAAGATTTTATTTTGTTTCGT 23 23 0 AAGATTTTAT 0.735026 -171 ATCAACCTGTCAGCTTTTCTGGAACTGCAG 29 14 1 CAGCTTTTCT 0.969438 -262 TTTGCCGGAAAAGACCTTCTCCACCGCCTC 32 52 1 AAGACCTTCT 0.780261 -249 GAGGCGGAAACAGCTCTTCTATACCCTCCT 32 87 1 CAGCTCTTCT 0.941222 -214 ********** Masking position 2 Map Score: 16.2506 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 192 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 GCCTAAAGCTCTTCTCCAGCAAATCCACCACCAAAT 2 165 1 CTCTCACACC 0.970268 -102 CCTTCAACCCCTACTCAATCTCCTTCTATTAGCTCT 12 11 0 CTCTCACCTC 0.973417 -93 GCCCAAAGAACCTCTCTATCTTCCCATTCGTTTGTG 13 42 0 CCCTCACCCA 0.97714 -259 GATGGAGCTTCTGCTCCATCAGCCCAAAGAACCTCT 13 63 0 CTCTCACCCA 0.991101 -238 AATAATTTCACTCCTCAAACAACCACCTCCCGTACT 13 228 0 CTCTCACCAC 0.954057 -73 CTTGGACATGCTTCTTGAACCTCCCAAACTCAACGA 20 96 1 CTCTTACCCA 0.950624 -205 GTTACTACTTGAACGAAACAAAATAAAATC 23 5 1 CTCTTACACA 0.747862 -189 CGGAAAAGACCTTCTCCACCGCCTCAGCCTGAGGCG 32 57 1 CTCTCACCCA 0.991101 -244 GGAAACAGCTCTTCTATACCCTCCTCCTTTAAAATG 32 92 1 CTCTAACCTC 0.782129 -209 TTTCAGCAAGCTCCTCCACCTTCACCACTTCAAGTT 32 150 1 CTCTCACCCC 0.995301 -151 CATACGCCTTCCTCTCAATCTTCTCCCAAACCTTCG 38 47 0 CCCTCACCCC 0.987849 -69 ** *** * * * ** Masking position 8 Map Score: 14.9854 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 706 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 AATCTACATTCATAAAAAAATTAGAA 1 285 0 TCTAATAAAA 0.624977 -16 AACTGGTTCATAAATAAGAAAAAA 5 1 0 TAAAAAAAAA 0.938019 -73 GATAAATAATTAATTAACAACAAAAAGTTAATTA 6 41 0 TAATAAAAAA 0.79997 -55 ATCGTTTGATTAAATATTGATAAAAGTTATTGAC 9 272 0 TAAAATAAAA 0.892608 -29 CAATGCTATCAAAAAAGGCAAATCTTAAATAA 10 9 1 TCAAAAGAAA 0.775425 -28 AAATACTTTATCATCATAAATAAACAAATCGTGC 15 61 0 TCATATAAAA 0.624994 -71 ACGAAATTATTATTCAATAAAAAAGGGGTGGTGG 15 107 1 TATTAAAAAA 0.513809 -25 GTTTGAAGCCTATATATCCAAAAAATTTAAGTTT 17 98 0 TATAATAAAA 0.687151 -71 TTCAAACCACTCAAAATAAAGAAAGGCTTTTATG 17 125 1 TCAAATAAAA 0.863143 -44 TTATGTTGAGTAAATAAAGGCAAAA 17 154 1 TAAAAAGAAA 0.819835 -15 GAAAGTAAACTAAAAATATAAAAATTTTATGTTT 19 54 0 TAAAATAAAA 0.892609 -29 AAAACAAAAATATAAAAATAAAAAT 21 2 0 TATAAAAAAA 0.799957 -204 TTAGTTGTGTTCATAAATGAAAAAATTTAAAT 22 80 1 TCATAAAAAA 0.752143 -22 GGATGGTATTTTAATAAGAAAAAAGTGAAGGAGG 24 271 1 TTAAAAAAAA 0.598317 -30 ACACTTGAAGTAAAGAAGGATAAAGGAGCAGGCA 28 95 1 TAAAAAAAAA 0.938019 -81 TTTATGCAAATAAATATGCATAAAATGCACACT 30 10 0 TAAAATAAAA 0.892609 -54 GGAAATTTAAAGAATTAAAAAGCTAAAAATT 30 43 0 TAAAAAAAAA 0.938019 -21 ATACGATTAATCAAAAAGAATAAATAATC 31 6 0 TCAAAAAAAA 0.919894 -101 TTTGCCAAGTTAAACAATTGAAAAAGGATTTAAA 32 250 0 TAAAAAGAAA 0.819829 -51 TGGCAAAATTTAAATAATCACAAAAAGAGCCTGC 32 277 1 TAAAAAAAAA 0.938019 -24 **** ** * *** Masking position 1 Map Score: 17.3393 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 31 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 ATCCCATTTTGGTCTGATTTCAACCCGTCAG 1 57 0 GGTCTGATTC 0.993474 -244 ATCCCATTTTGGTCTGATTTCAACTGTTCCT 1 125 0 GGTCTGATTC 0.993474 -176 ATCCCATTTTGGTCTGATTTCAACTTGGGAG 1 198 0 GGTCTGATTC 0.993474 -103 ATCCCACTTTAGTCTGATTTCAAAAAACGCC 2 68 0 AGTCTGATTC 0.951807 -199 AACTCTCGTCGGTCTGAGTTTTGTTTCCTTG 2 127 0 GGTCTGATTT 0.97649 -140 ATCCCATTTTGGTCTGATTTCAACTTACTGT 20 17 0 GGTCTGATTC 0.993474 -284 TAGGTATGAATTTCGATGTGAAG 28 163 0 GGTATGATTT 0.843449 -13 ******* *** Masking position 7 Map Score: 12.4834 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 24 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ATTTTCTAATTTTTTTATGAATGTAGATT 1 282 1 TTTTTTATGA 0.644229 -19 ACTTTTCCTCTTTTTTCTGAACACC 2 6 0 TTTTTTCTGA 0.871506 -261 ATCCTTATAAGATTTTCTGAT 3 2 0 GATTTTCTGA 0.586346 -37 TTTTTTCTTATTTATGAACC 5 1 1 TTTTTTCTTA 0.700967 -73 TATCAGGATATTTTTTCTGAACAAATGGTG 6 71 1 TTTTTTCTGA 0.871506 -25 GCAGTATATCTTTTTTATTGTCGGACTGCG 9 77 1 TTTTTTATTG 0.533587 -224 TCAAAAAGCGGTTTTTATGGTAGTGGTCAT 9 218 0 GTTTTTATGG 0.856582 -83 TCCTTACCAAGCTTTTCTGAGGAAGCTACC 13 181 1 GCTTTTCTGA 0.901601 -120 GTCAAAATAAGTTTTTCTGTGATATCCCGA 13 264 0 GTTTTTCTGT 0.794546 -37 TTTCAAAGCTTTTCTTGAGGTT 14 8 1 GCTTTTCTTG 0.852698 -15 CCACCACCCCTTTTTTATTGAATAATAATT 15 111 0 TTTTTTATTG 0.533587 -21 ATAAAGAAAGGCTTTTATGTTGAGTAAATA 17 140 1 GCTTTTATGT 0.435995 -29 CCTCCTTCACTTTTTTCTTATTAAAATACC 24 275 0 TTTTTTCTTA 0.700967 -26 TCTTTCTTCCTCTTTTCTGGCAGCTTGGTT 25 281 0 TCTTTTCTGG 0.902749 -20 CAACCTGTCAGCTTTTCTGGAACTGCAGCT 29 16 1 GCTTTTCTGG 0.94366 -260 AAACGCATTCGTTTTTCAGGATGGTGAAGT 29 213 1 GTTTTTCAGG 0.642449 -63 GACGTTTTTCTTGCAGCATCAAC 33 30 0 GTTTTTCTTG 0.885475 -13 ********** Masking position 5 Map Score: 11.653 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 434 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 GAGGAAAAAGATTTTCTAATTTTTTTATGAA 1 272 1 ATTTCTAATT 0.877301 -29 CCACCACCAAATTTATTCATTAAGCTTTAAC 2 189 1 ATTTTTCATT 0.952684 -78 TAGAAGGCCTATTTTCTAATTTGGAGGTGTT 4 81 1 ATTTCTAATT 0.877301 -24 AAAATTTAATATTTGCTCATTAATAATTGTT 11 37 1 ATTTCTCATT 0.956174 -23 AATGAGCACGATTTGTTTATTTATGATGATA 15 56 1 ATTTTTTATT 0.723153 -76 ATGAATTTAAATTTGCTCATTAAATGTTATA 16 51 1 ATTTCTCATT 0.956174 -36 ATATTGCCAGATTTGTTAATTATAAAAA 22 8 0 ATTTTTAATT 0.868414 -94 ATTTAAATTTTTTCATTTATGAACACA 22 85 0 ATTTTTCATT 0.952692 -17 GACATGCGATATTTATTCATTACGCCTGAAT 26 75 0 ATTTTTCATT 0.952684 -27 GATTATTTATTCTTTTTGATTAATC 31 5 1 ATTTTTCTTT 0.739149 -102 **** ****** Masking position 7 Map Score: 9.14012 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 15 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TGGGATTGAAAGGCAATGGCGACTTTTGCA 1 223 1 AGGCAATGGC 0.919424 -78 AGCTAATAGAAGGAGATTGAGTAGGGGTTG 12 13 1 AGGAGATTGA 0.579256 -91 GAGCGGACAAAGGCGCAGGATTGAGGGTCC 20 184 0 AGGCGCAGGA 0.900785 -117 GACTTCCGGAAGGCACTGGCCCCTACAGGG 24 51 1 AGGCACTGGC 0.966878 -250 CGCACACCGCAGGAGGTGGCGATGGCTGCA 25 21 1 AGGAGGTGGC 0.978564 -280 TATGTAGCTCAGGCACTGGGGCACTCAATT 28 62 1 AGGCACTGGG 0.898903 -114 AGAAGGATAAAGGAGCAGGCAGTCTTGTCG 28 108 1 AGGAGCAGGC 0.952616 -68 TAATGATTAAAGGCAGTGGCTTTTAAAGCC 29 174 1 AGGCAGTGGC 0.959295 -102 CCTCAGGCTGAGGCGGTGGAGAAGGTCTTT 32 61 0 AGGCGGTGGA 0.953739 -240 GGCATTTTAAAGGAGGAGGGTATAGAAGAG 32 100 0 AGGAGGAGGG 0.831752 -201 GTGAAGGTGGAGGAGCTTGCTGAAAGCATC 32 145 0 AGGAGCTTGC 0.925831 -156 GTTATGAAACAGGAGATTGCGAAA 34 30 1 AGGAGATTGC 0.829913 -14 ********** Masking position 1 Map Score: 11.4148 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 452 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 12 AATGCGGGGGGAGGGATTCGAACCCTCGAACC 20 141 1 GAGGTTCGAA 0.828265 -160 TCCTGTCCCGTAGGGGTTCGAGGGTTCGAATC 20 155 0 TAGGTTCGAG 0.709088 -146 CATCTGAGCGGGGGTTGCCGAGCGGACAAAGG 20 201 0 GGGGGCCGAG 0.99418 -100 TGCTACCGTCGAGGTATCCGGGAGTTGT 24 7 0 GAGGTCCGGG 0.969398 -294 TATCATCCCGGAGGAAGTCGAGTACACCGAAC 24 196 1 GAGGGTCGAG 0.989988 -105 TTTCCGAAATGGGGGTGCCGGGAATAAACACT 25 233 0 GGGGGCCGGG 0.991846 -68 GTTCAATGATGGGGCCGCCGAGATTTGAACTC 29 87 1 GGGGGCCGAG 0.99418 -189 TCATTACAGAGGGGCCGTAGGGTAGCCTGGTG 29 148 0 GGGGGTAGGG 0.88204 -128 GCCTCAGGCTGAGGCGGTGGAGAAGGTCTTTT 32 60 0 GAGGGTGGAG 0.934925 -241 AAAATTATCCGAGGGAGCCGAAGGTTTGGGAG 38 29 1 GAGGGCCGAA 0.964612 -87 **** ****** Masking position 4 Map Score: 10.3218 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 227 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 ACTCAAACACCCTTTCAGCAGGTAGCTTCC 13 201 0 CCTTTCAGCA 0.923116 -100 CCATTAAAGATTTTGCAGCAAACTATGCAA 17 45 0 TTTTGCAGCA 0.910483 -124 ATGAATTTTGCCTTGCAGCTCTATGCGTAG 18 19 0 CCTTGCAGCT 0.948811 -61 CTTTAACTATTTTTTCAGCCTTTTAAAACT 23 171 0 TTTTTCAGCC 0.782548 -23 AACCCCCATCTTTTTCAGCTCGACAATATC 25 198 0 TTTTTCAGCT 0.812763 -103 CTTCCTCTTTTCTGGCAGCTTGGTTTTGAT 25 276 0 TCTGGCAGCT 0.8961 -25 AGAATCAACCTGTCAGCTTTTCTGGAAC 29 9 1 CCTGTCAGCT 0.789042 -267 AAACGAATGCGTTTGCAGCAAAAGGCTTTA 29 197 0 GTTTGCAGCA 0.852066 -79 GGTTTTAAACTCTTGCAGCCTGACAAAATC 31 46 1 TCTTGCAGCC 0.949054 -61 AACTTGAGATGCTTTCAGCAAGCTCCTCCA 32 138 1 GCTTTCAGCA 0.891807 -163 GACGTTTTTCTTGCAGCATCAACATAAA 33 25 0 TCTTGCAGCA 0.965134 -18 ********** Masking position 7 Map Score: 8.82304 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 328 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 AAAAAAGAGGAAAAGTAAAAAACAATTGCTG 2 20 1 AAAATAAAAA 0.892423 -247 TAGGCCTTCTAAAGATAAAAGCTGTTATGAA 4 61 0 AAAGTAAAAG 0.75426 -44 TTGACAAAGAAAAGTTAAAAA 7 1 0 AAAGTAAAAA 0.942192 -54 AGTAAACTAAAAATATAAAAATTTTATGTTT 19 54 0 AAATTAAAAA 0.816384 -29 ACAAAAATATAAAAATAAAAAT 21 2 0 AAAATAAAAA 0.892423 -204 ACAGCGTGTTAAAAACAAAAATATAAAAATA 21 16 0 AAAACAAAAA 0.760986 -190 TATTGACATTAAAGCTAAATACAGTACGCTA 21 50 0 AAAGTAAATA 0.801745 -156 ACATGCTAACAAAAATAAAAATTTTACTATT 27 17 0 AAAATAAAAA 0.892423 -30 AAAGAATTAAAAAGCTAAAAATTTTATGCAA 30 35 0 AAAGTAAAAA 0.942192 -29 TAACTTGGCAAAATTTAAATAATCACAAAAA 32 272 1 AAATTAAATA 0.52453 -29 AAAAAGGCGCAAAGGCAAAAAAACTTTGCCC 36 12 0 AAAGCAAAAA 0.862171 -28 **** ****** Masking position 7 Map Score: 6.16587 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 32 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 15 TCTCCAGCAAATCCACCACCAAATTTATTC 2 177 1 ATCCACCACC 0.972974 -90 CTAAACACCTCCAAATTAGAAA 4 93 0 AAACACCTCC 0.77165 -12 AGAGTGAACCATCCACAAACGAATGGGAAG 13 29 1 ATCCACAAAC 0.680987 -272 CTCCTCAAACAACCACCTCCCGTACTCAAA 13 224 0 AACCACCTCC 0.960508 -77 TAACTTTGAAATCCACCTTCTAC 20 288 1 ATCCACCTTC 0.933182 -13 GAGTACACCGAACCACCAACAAGAGAGGAA 24 215 1 AACCACCAAC 0.859544 -86 AATACACCTCCTTCACTTTTT 24 290 0 ATACACCTCC 0.894557 -11 CTGCAGCCATCGCCACCTCCTGCGGTGTGC 25 22 0 CGCCACCTCC 0.921485 -279 GTCGGAATAACTCCACCAACGAGGATCAGC 25 164 0 CTCCACCAAC 0.926682 -137 AAAAGACCTTCTCCACCGCCTCAGCCTGAG 32 60 1 CTCCACCGCC 0.930275 -241 CAGCAAGCTCCTCCACCTTCACCACTTCAA 32 153 1 CTCCACCTTC 0.919932 -148 ATATTGCATAATCCACATACGCCTTCCTCT 38 68 0 ATCCACATAC 0.783574 -48 ********** Masking position 5 Map Score: 10.9049 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 447 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604