AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_aful_reg_100.orf -o00240_aful_100.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 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #4 AF0197 86 acetyl-CoA synthetase (acs-1) #5 AF0204 72 conserved hypothetical protein #6 AF0252 251 CTP synthase (pyrG) #7 AF0384 97 conserved hypothetical protein #8 AF0385 28 conserved hypothetical protein #9 AF0497 132 DNA polymerase B1 (polB) #10 AF0764 138 LSU ribosomal protein L7AE (rpl7AE) #11 AF0876 300 5'-nucleotidase (nt5) #12 AF0971 101 conserved hypothetical protein #13 AF1117 62 DNA-directed RNA polymerase, subunit E' (rpoE1) #14 AF1118 111 A. fulgidus predicted coding region AF1118 #15 AF1127 213 LSU ribosomal protein L18E (rpl18E) #16 AF1131 75 DNA-directed RNA polymerase, subunit K (rpoK) #17 AF1232 63 conserved hypothetical protein #18 AF1309 85 conserved hypothetical protein #19 AF1342 126 thymidine phosphorylase (deoA-2) #20 AF1553 28 conserved hypothetical protein #21 AF1554 21 thioredoxin reductase (trxB) #22 AF1664 147 ribonucleotide reductase (nrd) #23 AF1731 21 A. fulgidus predicted coding region AF1731 #24 AF1740 89 conserved hypothetical protein #25 AF1765 74 conserved hypothetical protein #26 AF1886 32 DNA-directed RNA polymerase, subunit B'' (rpoB2) #27 AF1926 57 conserved hypothetical protein #28 AF1927 142 conserved hypothetical protein #29 AF2252 78 argininosuccinate synthetase (argG) #30 AF2277 49 DNA polymerase, bacteriophage-type #31 AF2285 104 SSU ribosomal protein S13P (rps13P) Motif number 1 CTTTTACGGTTTTAAACTTTCTCCCGTATGCT 2 85 0 TTTAAATTCT 0.965793 -32 TGATAATGAATTTAAATTTGCTCATTAAATGT 4 46 1 TTTAAATGCT 0.720075 -41 CACACCAAACTTTAAATCCTTTTAAGCATAAT 9 104 1 TTTAAACTTT 0.946848 -29 TGTTAATCCATTTAAATCTTGTGATTACCATC 10 27 1 TTTAAATTGT 0.922562 -112 CCCGTGCAGTTTTAAAAGTTTTGGTAACACTG 10 68 0 TTTAAATTTT 0.979471 -71 GCTTCAGGGTTAAAAATGTTTTCGACTTGTGT 11 83 0 TAAAAATTTT 0.560896 -218 ATTTAAATTTTTTCATTTATGAA 12 2 1 TTTAAATTTT 0.979471 -100 AATCTGGCAATATAAAGCTTTTGCAGATACAC 12 65 0 TATAAATTTT 0.844397 -37 ACTTCAATAATTTAAATTTTTTGCTCAGATAA 14 24 1 TTTAAATTTT 0.979471 -88 CATTACGTAATTTAAATCTTTGCCGCATGTTA 15 59 0 TTTAAATTTG 0.812983 -155 ATATTAAGTATTTAAAAACTTTCTGAAAACTG 18 52 0 TTTAAACTTT 0.946848 -34 TGTCGTCAGCTTTAAAACCTTTTCAGGTGAGA 19 21 1 TTTAAACTTT 0.946848 -106 GTTGTTTATGTTTAAAAATTCTCACCTGAAAA 19 40 0 TTTAAATTCT 0.965793 -87 TTTTAAAAAACTTTGACCCAATCT 20 3 1 TTAAAACTTT 0.807442 -26 TGACATTAACTTTAATACTTTTCAAGAAGACA 22 18 0 TTTAATTTTT 0.763973 -130 GGTGTCGGATTTTAAAATTTTTACATGGCGGT 24 58 0 TTTAAATTTT 0.979471 -32 GTGAGGATTATTAAAAATTTCTCACCAAACGC 25 38 0 TTAAAATTCT 0.869211 -37 ACAAATACTATTTAACCGTTCTCTTTTTGGGC 28 42 1 TTTAACTTCT 0.839341 -101 GTAGTGTTTATTAAAAGTTTTTTTTATATATC 28 97 1 TTAAAATTTT 0.918236 -46 CAGGAAGTTTTTTAACTTTTGTTTAATCTCAA 29 25 1 TTTAACTTGT 0.687939 -54 TGCGGAGAGGTTTAAATCTTTTGAGATTAAAC 29 45 0 TTTAAATTTT 0.979471 -34 TGTAAGGATATTTAAAGGTTATGTGCCCCCCT 31 55 0 TTTAAATTAT 0.813703 -50 ****** **** Masking position 1 Map Score: 31.3576 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 53 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 TTTTACGGTTTTAAACTTTCTCCCGTATGCT 2 85 0 TTAAACTTCT 0.70421 -32 AATTTGCTCATTAAATGTTATAAATTGGAGG 4 60 1 TTAAATTTAT 0.717918 -27 ACACCAAACTTTAAATCCTTTTAAGCATAAT 9 105 1 TTAAATCTTT 0.868406 -28 CCGTGCAGTTTTAAAAGTTTTGGTAACACTG 10 68 0 TTAAAATTTT 0.944089 -71 TGATTCCCTATAAAAGTTTCTTCGGATGGAG 11 217 0 TAAAAGTTCT 0.59616 -84 ATTTAAATTTTTTCATTTATGAA 12 3 1 TTAAATTTTT 0.896611 -99 CTTCAATAATTTAAATTTTTTGCTCAGATAA 14 25 1 TTAAATTTTT 0.896611 -87 TCAACTCAACTTAAAGCTTATATTGGTTAAA 14 77 1 TTAAAGTTAT 0.713858 -35 TATTAAGTATTTAAAAACTTTCTGAAAACTG 18 52 0 TTAAAACTTT 0.927604 -34 GTCGTCAGCTTTAAAACCTTTTCAGGTGAGA 19 22 1 TTAAAACTTT 0.927604 -105 TTGTTTATGTTTAAAAATTCTCACCTGAAAA 19 40 0 TTAAAATTCT 0.926701 -87 TGAACTTCAAAAACTCTGAAAGAATAT 19 110 0 TCAAAACTCT 0.705483 -17 TTTTAAAAAACTTTGACCCAATCT 20 4 1 TAAAAACTTT 0.747713 -25 GTGTCGGATTTTAAAATTTTTACATGGCGGT 24 58 0 TTAAAATTTT 0.943948 -32 TGAGGATTATTAAAAATTTCTCACCAAACGC 25 38 0 TAAAAATTCT 0.745146 -37 TAAGACTTCCTCAAAAACTTTTGGTGATAGG 28 11 0 TCAAAACTTT 0.761869 -132 GTAGTGTTTATTAAAAGTTTTTTTTATATAT 28 97 1 TTAAAATTTT 0.944089 -46 GCGGAGAGGTTTAAATCTTTTGAGATTAAAC 29 45 0 TTAAATTTTT 0.89687 -34 GTAAGGATATTTAAAGGTTATGTGCCCCCCT 31 55 0 TTAAAGTTAT 0.713858 -50 ****** **** Masking position 9 Map Score: 18.3689 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 113 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 GCTTAAATAATTATGAAGAAATTATACTCCATGCCGAGTTC 2 18 0 TGGAAAAACA 0.694475 -99 TTTTCATGAATGCTGTTGGAGGTATGAGTAAATAACGATTT 6 49 0 TGGGAGAGAA 0.804412 -203 ACGTAGGAGGTCACGCCGAAAGTAGAGCCAAGACTTATAAA 7 48 1 TGGAAAAAAA 0.95035 -50 TTAATTTTAGTTGCGAAGAAGATACAGCCAATCACACCAAA 9 72 1 TGGAAGAAAA 0.986242 -61 TAACACTGATATGTGATGATGGTAATCACAAGATTTAAATG 10 35 0 AGGATGATAA 0.483806 -104 GTTCGTTGCAGGAGGAGTTATTTAAAAATATCGCTGA 11 7 1 TGGGAGATAA 0.901281 -294 TTAAAGGCACACAAGTCGAAAACATTTTTAACCCTGAAGCT 11 75 1 AGGAAAATAA 0.607864 -226 TAAAAGTTTCTTCGGATGGAGGCAATTAAAAACCAATGTGC 11 197 0 TGGGAGATAA 0.901281 -104 GTTTTTAGCCTTCCGCGGAAGGAACATTAAAAATTAACATG 15 25 1 TGGAAGAAAA 0.986244 -189 GGAAGCTGGCAGAGGAGGAAGTCAAATCCAAACCTCGTTAC 15 137 1 AGGAAGAAAA 0.943127 -77 CAGTGAACCTACAGCGAAAGGTATATATAATCTTTCGTAT 17 34 0 TGAAAGAAAA 0.802238 -30 TTTCTCGCTATCGTGAAGAAGTTATAGATAATGTTGTTTAT 19 63 0 TGGAAGAAAA 0.986243 -64 CAGTTATGGTAGATAAGAAAGATAAAACAATTTTG 22 123 0 TGGATAAAAA 0.755491 -25 CACCAAAAGTTTTTGAGGAAGTCTTAACAAATACTATTTAA 28 16 1 TGGAAGTAAA 0.852033 -127 CCGTTCTCTTTTTGGGCGAGGAGAAAAATAATAGTCTTTCG 28 57 1 TGGAGGAAAA 0.90678 -86 TTTAAATCTTTTGAGATTAAACAAAAGTTAAAAAACTTCCT 29 26 0 TGTAAAAAAA 0.656331 -53 CGCTCTAATGTTTAAGGCAAATTAAAATAGTTTGCT 30 24 0 TGTAAGAAAA 0.877349 -26 * * **** * * ** Masking position 21 Map Score: 13.4728 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 329 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 ATTGAATTATGCTCAAAGTGTGAGCA 4 7 0 GCTCAAAGTG 0.883125 -80 ATCGTTTCATGCAAAAAATGAAAGT 5 6 0 GCAAAAAATG 0.938036 -67 TATGTACAGAGCAAAGATTGTTGCTGAAAA 11 263 1 GCAAAGATTG 0.746302 -38 TCCGCGGAAGGCTAAAAACGATTTCGATAT 15 14 0 GCTAAAAACG 0.85529 -200 GAGCGAGTCAGCAAAAAATGAGGCGCCA 15 196 1 GCAAAAAATG 0.938036 -18 ATCTATTGAAGGAAAAATTGAATAGAAAAA 22 77 0 GGAAAAATTG 0.853774 -71 TCGAAGGGCAGGCAAAATTGTTTTATCTTT 22 111 1 GGCAAAATTG 0.903017 -37 GGCAAAAGTGAGGTAAAAAT 23 12 0 GGCAAAAGTG 0.923002 -10 TGAAATCTGCAAAAAGAGAAAGGTGAGA 26 9 1 GCAAAAAGAG 0.869704 -24 AAAAGTATTAGCCCAAATCGCTATGCTGGT 27 14 0 GCCCAAATCG 0.903885 -44 TTTTCTCCTCGCCCAAAAAGAGAACGGTTA 28 54 0 GCCCAAAAAG 0.772095 -89 TTAAACTTTGCCAAAAGCGCGCTGGATAT 28 124 0 GCCAAAAGCG 0.959973 -19 CGAATTAAATGCTAAAATTGGAATAATCCT 31 18 1 GCTAAAATTG 0.920799 -87 ********** Masking position 5 Map Score: 9.63792 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 233 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 GCTCATTTCGTCAGTTGTTGTTCGGGGGAA 3 33 0 TCAGTTGTTG 0.526628 -99 AACTTTGCTTTGCGCTGATATCGTTTCATG 5 25 0 TGCGCTGATA 0.739749 -48 AAGCTCGTTTGCAGCAGTTGTCGTGCTGAA 6 182 1 GCAGCAGTTG 0.652244 -70 ATTTGCGCCCTCCGGAGTTGAGACA 6 237 1 TCCGGAGTTG 0.845003 -15 GTGAATATTTTCAGGTGAGG 7 1 0 TCAGGTGAGG 0.895197 -97 GTCTTGGTGCTCCGCTGTTGTGAATATTTT 7 20 0 TCCGCTGTTG 0.867686 -78 AATTGAGATGGGAGCAGATGAGCGAGAGGG 9 23 1 GGAGCAGATG 0.840907 -110 ATTTGATGAAGGAGGTGATGAC 10 127 1 GGAGGTGATG 0.952233 -12 GTTCGTTGCAGGAGGAGTTATTTAAAAATA 11 11 1 GGAGGAGTTA 0.403289 -290 AAAATAATCAGGCGGTGATGGG 11 289 1 GGCGGTGATG 0.969748 -12 CAGCAAAGGCTGCGGTGATGATTTT 13 48 1 TGCGGTGATG 0.970347 -15 AGCTTTAAGTTGAGTTGATGATTATTAGAG 14 65 0 TGAGTTGATG 0.758172 -47 CGGTCAAAACTACGCTGAGGTGTAGTTGAT 15 94 1 TACGCTGAGG 0.639535 -120 TAAAACCTTTTCAGGTGAGAATTTTTAAAC 19 33 1 TCAGGTGAGA 0.567805 -94 AATCCCGTCATGCGGAGAGGTTTAAATCTT 29 57 0 TGCGGAGAGG 0.895092 -22 CTTCCTCTTAGACGGTGATGTT 31 93 1 GACGGTGATG 0.847129 -12 ********** Masking position 4 Map Score: 10.666 Number of sites scoring better than the average of aligned sites = 1971 Number in coding regions = 1862 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 GAATTATTTGTTGAGGATTTAAACTTTGCT 5 46 0 TTGAGGATTT 0.959506 -27 GAGAGGACACGCGAGGATTTCCAGAAGCTT 6 92 0 GCGAGGATTT 0.874182 -160 GAATTTCCCATTGAGGATGGGATTCCAGAT 6 209 1 TTGAGGATGG 0.945029 -43 ACACTGATATGTGATGATGGTAATCACAAG 10 44 0 GTGATGATGG 0.901835 -95 GAATGATGATTTGATGAAGGAGGTGATGAC 10 119 1 TTGATGAAGG 0.502309 -20 AAAGGCTGCGGTGATGATTTT 13 52 1 GTGATGATTT 0.926806 -11 GATTATTAGAGTGAGCATTTTTATCTGAGC 14 46 0 GTGAGCATTT 0.824088 -66 TTAAGTTGAGTTGATGATTATTAGAGTGAG 14 61 0 TTGATGATTA 0.755143 -51 ACCTTTTCAGGTGAGAATTTTTAAACATAA 19 37 1 GTGAGAATTT 0.75966 -90 TGAAGTTTTGTGGGGATGTTAATTTTGTT 24 10 1 GTGGGGATGT 0.876237 -80 TCGGATGTTCGTGAGGATTATTAAAAATTT 25 50 0 GTGAGGATTA 0.95226 -25 CCAAAAGTTTTTGAGGAAGTCTTAACAAAT 28 18 1 TTGAGGAAGT 0.831408 -125 CCCCCTTCAATTGAGGATTATTCCAATTTT 31 31 0 TTGAGGATTA 0.914742 -74 ********** Masking position 7 Map Score: 7.36548 Number of sites scoring better than the average of aligned sites = 738 Number in coding regions = 683 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 ATATAACCAAGCAAAAGCTTAAATAATTAT 2 45 0 GCAAAAGCTT 0.970636 -72 TATATCAAGTGCAATAGCATACGGGAGAAA 2 70 1 GCAATAGCAT 0.868752 -47 ACTCATACCTCCAACAGCATTCATGAAAAG 6 61 1 CCAACAGCAT 0.970216 -191 GCGAGGATTTCCAGAAGCTTCCTTTTCATG 6 82 0 CCAGAAGCTT 0.915791 -170 GAGTGTATCTGCAAAAGCTTTATATTGCCA 12 63 1 GCAAAAGCTT 0.970636 -39 AAATCCGACACCAACAGCATGC 24 78 1 CCAACAGCAT 0.970216 -12 AAATTTCTCACCAAACGCTTTTATAAGTTC 25 26 0 CCAAACGCTT 0.905361 -49 GGCACCAGCATAGCGATTTGG 27 2 1 GCACCAGCAT 0.874766 -56 CCTATCACCAAAAGTTTTTGAGGAAGT 28 8 1 CCAAAAGTTT 0.800558 -135 ********** Masking position 3 Map Score: 6.92766 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 68 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 ACCTCCTCTCCTTTTACGGTT 2 106 0 ACCCCTCTCC 0.963591 -11 ACCACCACCCCTTTTTTATTG 3 121 0 ACCCCACCCC 0.953202 -11 AGTTCACCTCCAATTTATAACATTTA 4 71 0 ACCCCAATTT 0.882148 -16 AACCACTTCAACTTCCAATTCCGACTTGCAG 6 121 0 ACTCCAATTC 0.869739 -131 TTCGTTCTCCTCAACCACTTCAACTTCCAAT 6 133 0 TCACCACTTC 0.774556 -119 TCCAGATATAATCTCCTCTTCGTTCTCCTCA 6 151 0 ATCCCTCTTC 0.913868 -101 AAATGGATTAACATCCTATTTTTTATGAT 10 9 0 ACACCTATTT 0.605393 -130 GTCATCACCTCCTTCATCAAATCA 10 125 0 ATCCCTCCTT 0.566988 -14 CTCTGTACATACCACCAATTCTAGCATGATT 11 243 0 ACCCCAATTC 0.971353 -58 TTTGGATTTGACTTCCTCCTCTGCCAGCTTC 15 138 0 ACTCCTCCTC 0.893691 -76 TCACTACTAAACACCCACTTCAT 18 3 0 ACACCACTTC 0.967387 -83 GCAACCCCTACTTCCCCATGG 21 8 0 ACCCTACTTC 0.882946 -14 *** ******* Masking position 5 Map Score: 4.95945 Number of sites scoring better than the average of aligned sites = 1570 Number in coding regions = 1487 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 ACCAAGCAAAAGCTTAAATAATTATGAAGA 2 40 0 AGCTTAAATA 0.696604 -77 ATACTTTATCATCATAAATAAACAAATCGT 3 63 0 ATCATAAATA 0.911189 -69 CGTATGAGTATTCATAAATACTTTATCATC 3 80 0 TTCATAAATA 0.803384 -52 ATTCATTATCATCTTAAAAAATTGAATTAT 4 27 0 ATCTTAAAAA 0.828349 -60 TTCCGCCTTAATTTTAAATACCGCAAAAAA 6 21 0 ATTTTAAATA 0.899778 -231 TTGGATGCATTATAAATAACTCTTACCC 8 11 0 ATTATAAATA 0.884303 -18 ATCATAAAAAATAGGATGTT 10 1 1 ATCATAAAAA 0.803386 -138 TTCAGCGATATTTTTAAATAACTCCTCCTG 11 19 0 TTTTTAAATA 0.752586 -282 AGATACACTCATTTTAAATATCAATCAACA 12 43 0 ATTTTAAATA 0.899778 -59 AGATTTGTTAATTATAAAAA 12 92 1 ATTATAAAAA 0.751986 -10 TTTCAGAAAGTTTTTAAATACTTAATATAA 18 56 1 TTTTTAAATA 0.752586 -30 ********** Masking position 6 Map Score: 7.16677 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 15 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 GCTCTACTTTCGGCGTGACCTCCTACGTCTTGGT 7 42 0 CGCGACTCCT 0.92755 -56 TCTTGCAGTCCCTCTCGCTCATCTGCTCCCATCT 9 28 0 CTCGCCATCT 0.945633 -105 GCGAGAGGGACTGCAAGATCACATTATCTTAATT 9 44 1 CGCGACACAT 0.945707 -89 CGTTGTCCTACCGCTAGACTACCCGCGCTTGTCA 11 123 0 CGCGATACCC 0.914762 -178 GTTCGAATCCCGGCCCGCGCACATTGGTTTTTAA 11 179 1 CGCGCCACAT 0.942162 -122 CCCATCACCGCCTGATTATTTTCAGCAACAA 11 280 0 CGCGATATTT 0.645805 -21 CCTCCTCTGCCAGCTTCCTTATCTTGCTCATATC 15 121 0 CGCCCTATCT 0.805633 -93 GTCCCGAACGCCGCAGGATCACCAGG 16 3 0 CGCGACACCA 0.940772 -73 GTTCAAATCTCGGCGGCCCCATCTGCTTTAAGGG 16 49 1 CGCCCCATCT 0.943608 -27 TTTGCCTGCCCTTCGAGAGCATCTATTGAAGGAA 22 93 0 CTCGACATCT 0.948976 -55 TTTTAATAATCCTCACGAACATCCGAGGAGC 25 54 1 CTCGACATCC 0.888853 -21 * ** ** ***** Masking position 4 Map Score: 3.18646 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 453 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 TGTCTCAACTCCGGAGGGCGCAAATCTG 6 234 0 CTCCGGAGGG 0.956431 -18 CGGGCTAACGCCTCGGAAGGGCGTTGTCCT 11 148 0 CCTCGGAAGG 0.989847 -153 ATAAAAGTTTCTTCGGATGGAGGCAATTAA 11 209 0 CTTCGGATGG 0.978036 -92 AATGTTCCTTCCGCGGAAGGCTAAAAACGA 15 23 0 CCGCGGAAGG 0.983255 -191 GCTCCTCGGATGTTCGTGAGGAT 25 62 0 CCTCGGATGT 0.950558 -13 ********** Masking position 7 Map Score: 1.57848 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 39 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 12 GCTTTTGCTTGGTTATATCAAGTGCAATAGCAT 2 57 1 GTATATAAGT 0.972581 -60 TCCTTATCTTGCTCATATCAACTACACCTCAGC 15 107 0 GTATATAACT 0.872119 -107 CTGCAACCGATTATATTAAGTATTTAAAAAC 18 65 0 GTATATAAGT 0.972574 -21 AAGTATTAAAGTTAATGTCAAGTTTTCTTGAGA 22 30 1 GTATGTAAGT 0.928424 -118 AATTGTGTGGGGTGATAAAAAGTATTAGCCCAA 27 28 0 GTATAAAAGT 0.964591 -30 CTTTCGTAGTGTTTATTAAAAGTTTTTTTTATA 28 92 1 GTATTAAAGT 0.870451 -51 AAAATAGTTTGCTGATAAGAAGTTTT 30 4 0 GTATAAAAGT 0.964581 -46 * * **** **** Masking position 5 Map Score: 3.30075 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 TGGTAATTGTTTAAAGAATATGGACG 1 6 0 TTAAAGAAAT 0.946874 -92 GAGCTGAGCATTAAAGAGTATTGTAAATGAT 1 66 0 TTAAAGAGAT 0.866968 -32 TCAACTCAACTTAAAGCTTATATTGGTTAAA 14 77 1 TTAAAGCTAT 0.841514 -35 CTTATATTGGTTAAAGAACATCATATAGC 14 93 1 TTAAAGAAAT 0.946874 -19 CACCCCTTAAAGCAGATGGGGCCGCCG 16 59 0 TTAAAGCAAT 0.955601 -17 TCAAAAACTCTGAAAGAATATTAACTTTTTC 19 100 0 TGAAAGAAAT 0.845778 -27 GCTCTAATGTTTAAGGCAAATTAAAATAGTT 30 28 0 TTAAGGCAAT 0.868812 -22 ******** ** Masking position 4 Map Score: 1.65919 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 6 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 14 ********** No masking Map Score: 2.74513e-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 Motif number 15 ********** No masking Map Score: 2.74513e-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