AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_aful_reg_300.orf -o00240_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: AF2251 30 competence-damage protein, putative Input sequences: #1 AF0060 97 A. fulgidus predicted coding region AF0060 #2 AF0106 116 aspartate carbamoyltransferase, catalytic subunit (pyrB) #3 AF0194 300 A. fulgidus predicted coding region AF0194 #4 AF0195 22 A. fulgidus predicted coding region AF0195 #5 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #6 AF0197 86 acetyl-CoA synthetase (acs-1) #7 AF0204 72 conserved hypothetical protein #8 AF0252 251 CTP synthase (pyrG) #9 AF0384 97 conserved hypothetical protein #10 AF0385 28 conserved hypothetical protein #11 AF0481 64 proteasome, subunit beta (psmB) #12 AF0483 101 conserved hypothetical protein #13 AF0484 33 GTP cyclohydrolase II (ribA-1) #14 AF0487 57 penicillin G acylase #15 AF0495 265 A. fulgidus predicted coding region AF0495 #16 AF0496 57 conserved hypothetical transmembrane protein #17 AF0497 132 DNA polymerase B1 (polB) #18 AF0764 138 LSU ribosomal protein L7AE (rpl7AE) #19 AF0876 300 5'-nucleotidase (nt5) #20 AF0971 101 conserved hypothetical protein #21 AF1117 62 DNA-directed RNA polymerase, subunit E' (rpoE1) #22 AF1118 111 A. fulgidus predicted coding region AF1118 #23 AF1127 213 LSU ribosomal protein L18E (rpl18E) #24 AF1131 75 DNA-directed RNA polymerase, subunit K (rpoK) #25 AF1232 63 conserved hypothetical protein #26 AF1309 85 conserved hypothetical protein #27 AF1342 126 thymidine phosphorylase (deoA-2) #28 AF1553 28 conserved hypothetical protein #29 AF1554 21 thioredoxin reductase (trxB) #30 AF1664 147 ribonucleotide reductase (nrd) #31 AF1731 21 A. fulgidus predicted coding region AF1731 #32 AF1740 89 conserved hypothetical protein #33 AF1765 74 conserved hypothetical protein #34 AF1886 32 DNA-directed RNA polymerase, subunit B'' (rpoB2) #35 AF1926 57 conserved hypothetical protein #36 AF1927 142 conserved hypothetical protein #37 AF2252 78 argininosuccinate synthetase (argG) #38 AF2277 49 DNA polymerase, bacteriophage-type #39 AF2285 104 SSU ribosomal protein S13P (rps13P) #40 AF2287 80 carotenoid biosynthetic gene ERWCRTS, putative #41 AF2289 216 mevalonate kinase (mvk) Motif number 1 CTTTTACGGTTTTAAACTTTCTCCCGTATGCT 2 85 0 TTTAAATTCT 0.91198 -32 TTTCAAAGCTTTTCTTGAGGTT 4 2 1 TTCAAATTTT 0.909854 -21 TTAAAAATCTTTTTTCTCTATT 11 1 1 TTAAAACTTT 0.861427 -64 AGAGTTCCCTTACAAACGTTTTTGTACTTGAA 12 19 0 TACAAATTTT 0.681719 -83 AATTTTGGACTAAAAAAATTTTCATAAACAAC 15 30 0 TAAAAATTTT 0.750514 -236 CACACCAAACTTTAAATCCTTTTAAGCATAAT 17 104 1 TTTAAACTTT 0.924065 -29 TGTTAATCCATTTAAATCTTGTGATTACCATC 18 27 1 TTTAAATTGT 0.746362 -112 CCCGTGCAGTTTTAAAAGTTTTGGTAACACTG 18 68 0 TTTAAATTTT 0.965218 -71 GCTTCAGGGTTAAAAATGTTTTCGACTTGTGT 19 83 0 TAAAAATTTT 0.750509 -218 ATTTAAATTTTTTCATTTATGAA 20 2 1 TTTAAATTTT 0.965217 -100 AATCTGGCAATATAAAGCTTTTGCAGATACAC 20 65 0 TATAAATTTT 0.854839 -37 ACTTCAATAATTTAAATTTTTTGCTCAGATAA 22 24 1 TTTAAATTTT 0.965217 -88 CATTACGTAATTTAAATCTTTGCCGCATGTTA 23 59 0 TTTAAATTTG 0.698016 -155 ATATTAAGTATTTAAAAACTTTCTGAAAACTG 26 52 0 TTTAAACTTT 0.924065 -34 GTCGTCAGCTTTAAAACCTTTTCAGGTGAGAA 27 22 1 TTAAAATTTT 0.934105 -105 GTTGTTTATGTTTAAAAATTCTCACCTGAAAA 27 40 0 TTTAAATTCT 0.91198 -87 TGAACTTCAAAAACTCTGAAAGAATAT 27 110 0 TTCAAACTCT 0.623004 -17 TTTTAAAAAACTTTGACCCAATCT 28 3 1 TTAAAACTTT 0.861427 -26 TGACATTAACTTTAATACTTTTCAAGAAGACA 30 18 0 TTTAATTTTT 0.609305 -130 GGTGTCGGATTTTAAAATTTTTACATGGCGGT 32 58 0 TTTAAATTTT 0.965218 -32 GTGAGGATTATTAAAAATTTCTCACCAAACGC 33 38 0 TTAAAATTCT 0.841086 -37 GTAGTGTTTATTAAAAGTTTTTTTTATATATC 36 97 1 TTAAAATTTT 0.934105 -46 TGCGGAGAGGTTTAAATCTTTTGAGATTAAAC 37 45 0 TTTAAATTTT 0.965218 -34 TGTAAGGATATTTAAAGGTTATGTGCCCCCCT 39 55 0 TTTAAATTAT 0.665038 -50 ****** **** Masking position 10 Map Score: 30.9911 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 83 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 ACCTCCTCTCCTTTTACGGTTTT 2 104 0 CCTCCTCTCT 0.972101 -13 TGAACTGGAGACTCCTTACCAAGCTTTTCTGA 3 169 1 ACTCCTTACA 0.716311 -132 CAGCAGGTAGCTTCCTCAGAAAAGCTTGGTAA 3 184 0 CTTCCTCAAA 0.899658 -117 AAATAATTTCACTCCTCAAACAACCACCTCCC 3 233 0 ACTCCTCAAA 0.716311 -68 TTTCCAGAAGCTTCCTTTTCATGAATGCTGTT 8 73 0 CTTCCTTTCT 0.818171 -179 TCCTCTTCGTTCTCCTCAACCACTTCAACTTC 8 137 0 TCTCCTCACA 0.952282 -115 CCAGATATAATCTCCTCTTCGTTCTCCTCAAC 8 149 0 TCTCCTCTCT 0.909218 -103 TACAATTGCGTTTCCTTTACAACAATTTTGGA 15 53 0 TTTCCTTTCA 0.77242 -213 CCTCTGCCAGCTTCCTTATCTTGCTCATATCA 23 120 0 CTTCCTTACT 0.773588 -94 GATTTGACTTCCTCCTCTGCCAGCTTCCTTAT 23 133 0 CCTCCTCTCA 0.989181 -81 TTTGTTAAGACTTCCTCAAAAACTTTTGGTGA 36 15 0 CTTCCTCAAA 0.899658 -128 CTATTATTTTTCTCCTCGCCCAAAAAGAGAAC 36 59 0 TCTCCTCGCA 0.859956 -84 TACAGGCTTGCTTCCTCTTAGACGGTGATGTT 39 83 1 CTTCCTCTAA 0.921922 -22 GGTGGTCAATCTTCCTCTTCGAAGTGC 40 6 0 CTTCCTCTCA 0.980399 -75 CCTGACTCAACCTCCTCTTCGAGGCAGATTTT 40 40 0 CCTCCTCTCA 0.989181 -41 ******** * * Masking position 6 Map Score: 14.912 Number of sites scoring better than the average of aligned sites = 1587 Number in coding regions = 1512 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 CCTTTTACGGTTTTAAACTTTCTCCCGTAT 2 88 0 TTTTAAACTT 0.746959 -29 TTTGACAAAAAGTTAAAGTTTTC 3 288 1 AGTTAAAGTT 0.631804 -13 ATGATAATGAATTTAAATTTGCTCATTAAA 6 45 1 ATTTAAATTT 0.890304 -42 TTTGTTGAGGATTTAAACTTTGCTTTGCGC 7 40 0 ATTTAAACTT 0.870037 -33 TTTTTGCGGTATTTAAAATTAAGGCGGAAA 8 22 1 ATTTAAAATT 0.903867 -230 GCTTAAAAGGATTTAAAGTTTGGTGTGATT 17 101 0 ATTTAAAGTT 0.897887 -32 ATGTTAATCCATTTAAATCTTGTGATTACC 18 26 1 ATTTAAATCT 0.851368 -113 TTACCAAAACTTTTAAAACTGCACGGGGAA 18 73 1 TTTTAAAACT 0.745292 -66 ATTTAAATTTTTTCATTTAT 20 1 1 ATTTAAATTT 0.890304 -101 TTACATTCTTAGTTAAATTTATATTGCTTC 21 12 1 AGTTAAATTT 0.612979 -51 CACTTCAATAATTTAAATTTTTTGCTCAGA 22 23 1 ATTTAAATTT 0.890304 -89 CGGAAGGAACATTAAAAATTAACATGCGGC 23 40 1 ATTAAAAATT 0.765315 -174 ACATTACGTAATTTAAATCTTTGCCGCATG 23 62 0 ATTTAAATCT 0.851368 -152 ATATTAAGTATTTAAAAACTTTCTGAAAAC 26 54 0 TTTAAAAACT 0.503686 -32 CCTGAAAAGGTTTTAAAGCTGACGACAATT 27 18 0 TTTTAAAGCT 0.732367 -109 GTTGTTTATGTTTAAAAATTCTCACCTGAA 27 42 0 TTTAAAAATT 0.58982 -85 TGGTGTCGGATTTTAAAATTTTTACATGGC 32 61 0 TTTTAAAATT 0.805673 -29 CGTGAGGATTATTAAAAATTTCTCACCAAA 33 41 0 ATTAAAAATT 0.765315 -34 CGTAGTGTTTATTAAAAGTTTTTTTTATAT 36 96 1 ATTAAAAGTT 0.753069 -47 ATCTCAAAAGATTTAAACCTCTCCGCATGA 37 50 1 ATTTAAACCT 0.825319 -29 ********** Masking position 3 Map Score: 16.287 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 52 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 4 ATGCTGAGTATGAGCTGAGCATTAAAGAGT 1 78 0 TGAGCTGAGC 0.714064 -20 AGAGGTTCTTTGGGCTGATGGAGCAGAAGC 3 63 1 TGGGCTGATG 0.889054 -238 AACTTTGCTTTGCGCTGATATCGTTTCATG 7 25 0 TGCGCTGATA 0.842443 -48 TGCGCCCTCCGGAGTTGAGACA 8 240 1 GGAGTTGAGA 0.553983 -12 GTGAATATTTTCAGGTGAGG 9 1 0 TCAGGTGAGG 0.848069 -97 AATTGAGATGGGAGCAGATGAGCGAGAGGG 17 23 1 GGAGCAGATG 0.746642 -110 ATTTGATGAAGGAGGTGATGAC 18 127 1 GGAGGTGATG 0.960246 -12 AAAATAATCAGGCGGTGATGGG 19 289 1 GGCGGTGATG 0.967058 -12 CAGCAAAGGCTGCGGTGATGATTTT 21 48 1 TGCGGTGATG 0.967708 -15 AGCTTTAAGTTGAGTTGATGATTATTAGAG 22 65 0 TGAGTTGATG 0.809981 -47 CGGTCAAAACTACGCTGAGGTGTAGTTGAT 23 94 1 TACGCTGAGG 0.768237 -120 TAAAACCTTTTCAGGTGAGAATTTTTAAAC 27 33 1 TCAGGTGAGA 0.568543 -94 CTTAATTGTGTGGGGTGATAAAAAGTATTA 35 34 0 TGGGGTGATA 0.714525 -24 AATCCCGTCATGCGGAGAGGTTTAAATCTT 37 57 0 TGCGGAGAGG 0.859067 -22 CTTCCTCTTAGACGGTGATGTT 39 93 1 GACGGTGATG 0.773219 -12 CTATTATGGAGGAGCTGAGGGATTACGAGG 41 72 0 GGAGCTGAGG 0.958339 -145 ********** Masking position 8 Map Score: 11.5607 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 1330 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 TCATAATTATTTAAGCTTTTGCTTGGTTATAT 2 43 1 TTAATTTTGC 0.936758 -74 AAACGGTAACTTCCTGTTTTCCC 5 2 0 TTCCTTTTCC 0.898384 -130 AAACAGGAAGTTACCGTTTTCCCCCGAACAAC 5 15 1 TTACTTTTCC 0.846108 -117 ACTTTCATTTTTTGCATGAAACGAT 7 4 1 TTCATTTTGC 0.959708 -69 GAGGATGGGATTCCAGATTTGCGCCCTCCGGA 8 221 1 TTCCATTTGC 0.479684 -31 CTTCTTTGCGTTCATGTTTTCCCACGCGTAGA 15 239 1 TTCATTTTCC 0.954359 -27 ATTTAAATTTTTTCATTTATGAAC 20 3 1 TTAATTTTTC 0.59219 -99 TCTGGCAATATAAAGCTTTTGCAGATACACTC 20 63 0 TAAATTTTGC 0.70511 -39 TTCAATAATTTAAATTTTTTGCTCAGATAAAA 22 26 1 TAAATTTTGC 0.70511 -86 ATTACGTAATTTAAATCTTTGCCGCATGTTAA 23 58 0 TTAACTTTGC 0.667745 -156 TGGCGCCTCATTTTTTGCTGACTCGCTC 23 196 0 CTCATTTTGC 0.856061 -18 AATTTTTCTATTCAATTTTTCCTTCAATAGAT 30 75 1 TTCATTTTCC 0.954359 -73 AATTTTTACCTCACTTTTGCC 31 10 1 CTCATTTGCC 0.56592 -12 CATCTCACCTTTCTCTTTTTGCAGATTTCA 34 9 0 TTCTTTTTGC 0.717092 -24 TTAAACTTTGCCAAAAGCGCGC 36 131 0 TTAATTTGCC 0.76454 -12 ACAAAATTCTTTAAGTTTTTCCCGTAGTCTAA 41 192 1 TTAATTTTCC 0.928591 -25 **** ****** Masking position 8 Map Score: 10.68 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 109 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 ATCAAACAGATGGAGCTTCTGCTCCATCAGCC 3 75 0 TGGGCTTCGC 0.95303 -226 ACTCGAAAAATGCAGGTTTGGATACTTTTATT 12 57 1 TGCGGTTTGA 0.857571 -45 TATGGTTTTTTGCTGGGACTGCTTATTATAGT 15 175 0 TGCGGGACGC 0.940168 -91 TCTGGCAAAATTCGGGTTCAGCGATATTTTTA 19 33 0 TTCGGTTCGC 0.900055 -268 TTGTCATTGCTGGAGCTTCAGGGTTAAAAATG 19 97 0 TGGGCTTCGG 0.95303 -204 CCGCAGCCTTTGCTGGGTCGGGAAGCAATATA 21 31 0 TGCGGGTCGG 0.991125 -32 CTGGTGATCCTGCGGCGTTCGGGACGCCGTGA 24 12 1 TGCGCGTTGG 0.895454 -64 AATTTTTACATGGCGGTTCAGCTAACGAAACA 32 43 0 TGGGGTTCGC 0.978602 -47 CCTCTATCTTTGCCGGTTCCGGCTCAACGACC 41 42 1 TGCGGTTCGG 0.990392 -175 CAGCCTCCGCTGCGGGGTCGGAGGTGTAGACG 41 114 1 TGCGGGTCGA 0.974183 -103 *** ***** ** Masking position 1 Map Score: 8.83269 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 126 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 TGGAGCTTCTGCTCCATCAGCCCAAAGAACC 3 66 0 GCTCCATCAC 0.843643 -235 TAATTTCACTCCTCAAACAACCACCTCCCGT 3 231 0 CCTCAAACAC 0.829488 -70 TTTACTCATACCTCCAACAGCATTCATGAAA 8 58 1 CCTCCAACAC 0.969303 -194 TTCGGCGTGACCTCCTACGTCTTGGTGCTCC 9 37 0 CCTCCTACGC 0.920293 -61 TCGGCTCTTCCCTAATTCCCCGTGCAGTTTT 18 87 0 CCTAATTCCC 0.636331 -52 GTCATCACCTCCTTCATCAAATCATCAT 18 121 0 CCTCCTTCAC 0.978827 -18 TTAAATAACTCCTCCTGCAACGAAC 19 5 0 CCTCCTGCAC 0.934317 -296 TTTTTAATTGCCTCCATCCGAAGAAACTTTT 19 206 1 CCTCCATCCA 0.853132 -95 GCAACCCCTACTTCCCCATGG 29 5 0 CCTACTTCCC 0.919078 -17 TCCATAATAGCCTCCATCCTCCCAGCCTCCG 41 92 1 CCTCCATCCC 0.986617 -125 ACCGTCTACACCTCCGACCCCGCAGCGGAGG 41 117 0 CCTCCGACCC 0.948486 -100 ********* * Masking position 3 Map Score: 8.92429 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 589 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 CGTCCATATTCTTTAAACAATTACCA 1 6 1 ATATCTTTAA 0.873793 -92 ATCATTTACAATACTCTTTAATGCTCAGCTC 1 66 1 ATATCTTTAA 0.873793 -32 TTGAGGAGTGAAATTATTTCGGGATATCACA 3 246 1 AAATATTTCG 0.625824 -55 ATGAAATTTGAAATTATTTAATTTTTATGTT 14 30 0 AAATATTTAA 0.771447 -28 ATTATGCTTAAAAGGATTTAAAGTTTGGTGT 17 105 0 AAAGATTTAA 0.63419 -28 ATTTAAATTTTTTCATTTATGAACA 20 5 1 AAATTTTTCA 0.525243 -97 TTTAACCAATATAAGCTTTAAGTTGAGTTGA 22 77 0 ATAGCTTTAA 0.780513 -35 GCTATATGATGTTCTTTAACCAATATAAG 22 93 0 ATGTCTTTAA 0.43712 -19 GGAAGGCTAAAAACGATTTCGATATGAG 23 8 0 AAAGATTTCG 0.462092 -206 AAAGGTATATATAATCTTTCGTATCTGGGAC 25 27 0 ATATCTTTCG 0.774302 -37 TAGTATCCCTAAATTATTTCACTACTAAACA 26 21 0 AAATATTTCA 0.777828 -65 CAGTTTTCAGAAAGTTTTTAAATACTTAATA 26 52 1 AAATTTTTAA 0.516121 -34 GAAAAAGTTAATATTCTTTCAGAGTTTTTGA 27 100 1 ATATCTTTCA 0.877769 -27 GTCTTAACAAATACTATTTAACCGTTCTCTT 36 36 1 ATATATTTAA 0.771447 -107 GAGAAAAATAATAGTCTTTCGTAGTGTTTAT 36 77 1 ATATCTTTCG 0.774302 -66 GTTTAATCTCAAAAGATTTAAACCTCTCCGC 37 45 1 AAAGATTTAA 0.63419 -34 AGGGGGGCACATAACCTTTAAATATCCTTAC 39 55 1 ATACCTTTAA 0.502477 -50 TGTTTGCACAAAATTCTTTAAGTTTTTCCCG 41 185 1 AAATCTTTAA 0.873793 -32 *** ******* Masking position 7 Map Score: 7.96633 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 116 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 9 ACCAGTAGAACTCGGCATGGAGTATAATTTCT 2 11 1 CTCGCAGGAG 0.990578 -106 CAAACACCCTTTCAGCAGGTAGCTTCCTCAGA 3 196 0 TTCGCAGTAG 0.821942 -105 CGCGTGTCCTCTCTGCAAGTCGGAATTGGAAG 8 109 1 CTCGCAGTCG 0.981556 -143 TGTCTCAACTCCGGAGGGCGCAAATCTGGA 8 232 0 CTCGGAGGCG 0.981615 -20 TAGGAGGTCACGCCGAAAGTAGAGCCAAGACT 9 51 1 CGCGAAGTAG 0.846372 -47 ACTGGTAGAGGGCTGCAAGGAGCGAAATTGCG 16 32 0 GGCGCAGGAG 0.895347 -26 GGGCTAACGCCTCGGAAGGGCGTTGTCCTACC 19 145 0 CTCGAAGGCG 0.973755 -156 ATAAAAGTTTCTTCGGATGGAGGCAATTAAAA 19 207 0 CTTGGAGGAG 0.813608 -94 ATTTAAACCTCTCCGCATGACGGGATTGT 37 60 1 CTCGCAGACG 0.954553 -19 *** *** **** Masking position 7 Map Score: 3.70616 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 184 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 TCCGCCTTAATTTTAAATACCGCAAAAAAGC 8 19 0 TTTTAAATAC 0.958841 -233 TTGGATGCATTATAAATAACTCTTACCC 10 9 0 TTATAAATAC 0.872088 -20 CTTAGGGCTATTTTAAAAAGCAAAAACAAAG 11 42 1 TTTTAAAAAC 0.930007 -23 TCAGCGATATTTTTAAATAACTCCTCCTGCA 19 17 0 TTTTAAATAC 0.958841 -284 GATACACTCATTTTAAATATCAATCAACATT 20 41 0 TTTTAAATAC 0.958841 -61 TTTTTATAATTAACAAATCTGGCA 20 88 0 TTATAATTAC 0.666147 -14 ATACGAAAGATTATATATACCTTTCGCTGTA 25 34 1 TTATATATAC 0.561287 -30 TTCAGAAAGTTTTTAAATACTTAATATAATC 26 57 1 TTTTAAATAT 0.586451 -29 TTTTAAAAAACTTTGACCCAA 28 1 1 TTTTAAAAAC 0.930002 -28 CATGTAAAAATTTTAAAATCCGACACCAACA 32 63 1 TTTTAAAATC 0.566677 -27 GGTGAGAAATTTTTAATAATCCTCACGAACA 33 44 1 TTTTAATAAC 0.795439 -31 TAAAAAAAACTTTTAATAAACACTACGAAAG 36 92 0 TTTTAATAAC 0.795249 -51 TAAAAGTTTTTTTTATATATCCAGCGCGCTT 36 108 1 TTTTATATAC 0.813835 -35 GGCACATAACCTTTAAATATCCTTACAGGCT 39 60 1 CTTTAAATAC 0.77264 -45 ********* * Masking position 5 Map Score: 11.8587 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 16 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 11 TTGAGTACGGGAGGTGGTTGTTTGAGGAGT 3 225 1 GAGGTGGTTG 0.983949 -76 CAATAAAAAAGGGGTGGTGGT 5 121 1 GGGGTGGTGG 0.941037 -11 ATTGGAAGTTGAAGTGGTTGAGGAGAACGA 8 133 1 GAAGTGGTTG 0.974779 -119 AATCATGCTAGAATTGGTGGTATGTACAGA 19 243 1 GAATTGGTGG 0.808808 -58 ATGAAGTGGGTGTTTAGTAGTG 26 3 1 GAAGTGGGTG 0.956305 -83 CCATGGGGAAGTAGGGGTTGC 29 8 1 GAAGTAGGGG 0.735626 -14 CTGCCTCGAAGAGGAGGTTGAGTCAGGATA 40 45 1 GAGGAGGTTG 0.916569 -36 GAGGGATTACGAGGTCGTTGAGCCGGAACC 41 56 0 GAGGTCGTTG 0.921785 -161 ********** Masking position 7 Map Score: 4.73179 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 479 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 GCAGGTAGCTTCCTCAGAAAAGCTTGGTAAGGAGT 3 179 0 TCCAAAACTT 0.701557 -122 ATTTCGGGATATCACAGAAAAACTTATTTTGACAA 3 261 1 ACCAAAACTT 0.926074 -40 AACCTCAAGAAAAGCTTTGAAA 4 7 0 ACCAAAAGCT 0.723182 -16 AATTTTAAATACCGCAAAAAAGCCTACCAGC 8 7 0 ACCAAAACCT 0.919315 -245 GATACAGCCAATCACACCAAACTTTAAATCCTTTT 17 92 1 ACCAAAATTT 0.924775 -41 AATTGCCTCCATCCGAAGAAACTTTTATAGGGAAT 19 211 1 ACGAAAATTT 0.706397 -90 AAATGAGTGTATCTGCAAAAGCTTTATATTGCCAG 20 59 1 ACGCAAGTTT 0.659733 -43 TGAACTTCAAAAACTCTGAAAGAATAT 27 110 0 ACTCAAATCT 0.493685 -17 TTCTTACAGCATCTCAAGAAAACTTGACATTAACT 30 39 0 ACCAAAACTT 0.926074 -109 CAAAATTAACATCCCCACAAAACTTCA 32 3 0 ACCCAAACTT 0.938365 -87 CCTATCACCAAAAGTTTTTGAGGAAGTC 36 4 1 ACCCAAGTTT 0.908314 -139 AACCTCTGAAAACCCAGGAAGTTTTTTAACTTTTG 37 11 1 ACCAAAGTTT 0.890728 -68 AGGAAGATTGACCACCTGAAAATCTGCCTCGAAGA 40 22 1 ACCCAAATCT 0.931457 -59 AAGATCGTTTTTCACCCGAAGTTCTACACCGTCTA 41 140 0 TCCCAAGTCT 0.628375 -77 * * ** *** *** Masking position 9 Map Score: 5.3422 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 230 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 13 GTGCAATAGCATACGGGAGAAAGTTTAAAA 2 78 1 ATACGGGAGA 0.741203 -39 GGGTGTTTGAGTACGGGAGGTGGTTGTTTG 3 219 1 GTACGGGAGG 0.978542 -82 GTCAGTTGTTGTTCGGGGGAAAACGGTAAC 5 24 0 GTTCGGGGGA 0.971554 -108 GAAAAAAGTTGGTCGGGGGAATATAAACTT 13 14 0 GGTCGGGGGA 0.958303 -20 GCCTTTGCTGGGTCGGGAAGCAATATAAAT 21 28 0 GGTCGGGAAG 0.916032 -35 ATCCTGCGGCGTTCGGGACGCCGTGACCCG 24 18 1 GTTCGGGACG 0.960046 -58 CTCCTCGGATGTTCGTGAGGATTATTAAAA 33 54 0 GTTCGTGAGG 0.931494 -21 ********** Masking position 5 Map Score: 1.0042 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 90 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 14 CTGCTCCATCAGCCCAAAGAACCTCTCTAT 3 59 0 AGCCCAAAGA 0.929096 -242 AAACGATATCAGCGCAAAGCAAAGTTTAAA 7 29 1 AGCGCAAAGC 0.934195 -44 GTGGTTGAGGAGAACGAAGAGGAGATTATA 8 146 1 AGAACGAAGA 0.772747 -106 ACAACAGCGGAGCACCAAGACGTAGGAGGT 9 29 1 AGCACCAAGA 0.928185 -69 CGCCGAAAGTAGAGCCAAGACTTATAAATG 9 61 1 AGAGCCAAGA 0.94877 -37 GGAAAACATGAACGCAAAGAAGAATTTGAC 15 231 0 AACGCAAAGA 0.856826 -35 TGGTATGTACAGAGCAAAGATTGTTGCTGA 19 260 1 AGAGCAAAGA 0.957153 -41 ********** Masking position 7 Map Score: 0.261204 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 50 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 ********** No masking Map Score: 1.09306e-11 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