AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00410_aful_reg_300.orf -o00410_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: AF0672 27 medium-chain acyl-CoA ligase (alkK-3) Input sequences: #1 AF0194 300 A. fulgidus predicted coding region AF0194 #2 AF0195 22 A. fulgidus predicted coding region AF0195 #3 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #4 AF0197 86 acetyl-CoA synthetase (acs-1) #5 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #6 AF0439 82 transcriptional regulatory protein, AsnC family #7 AF0442 300 succinoglycan biosynthesis regulator (exsB) #8 AF0481 64 proteasome, subunit beta (psmB) #9 AF0483 101 conserved hypothetical protein #10 AF0484 33 GTP cyclohydrolase II (ribA-1) #11 AF0487 57 penicillin G acylase #12 AF0495 265 A. fulgidus predicted coding region AF0495 #13 AF0496 57 conserved hypothetical transmembrane protein #14 AF0497 132 DNA polymerase B1 (polB) #15 AF0498 197 acyl-coA dehydrogenase (acd-3) #16 AF0673 155 mercuric resistance operon regulatory protein (merR) #17 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #18 AF0685 140 enoyl-CoA hydratase (fad-2) #19 AF0845 73 acyl-CoA dehydrogenase (acd-5) #20 AF0846 112 Na+/H+ antiporter (nhe2) #21 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #22 AF0970 101 A. fulgidus predicted coding region AF0970 #23 AF1026 150 acyl-CoA dehydrogenase (acd-7) #24 AF1141 35 acyl-CoA dehydrogenase (acd-8) #25 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #26 AF1289 300 conserved hypothetical protein #27 AF1641 31 enoyl-CoA hydratase (fad-4) #28 AF1642 50 histidyl-tRNA synthetase (hisS) #29 AF2057 35 acyl-CoA dehydrogenase (acd-10) #30 AF2244 300 acyl-CoA dehydrogenase (acd-11) #31 AF2275 63 acyl-CoA dehydrogenase (acd-12) #32 AF2277 49 DNA polymerase, bacteriophage-type #33 AF2334 33 spermidine synthase (speE) #34 AF2426 85 conserved hypothetical protein #35 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 GATATCACAGAAAAACTTATTTTGACAAAAAG 1 268 1 AAAACTTATT 0.957991 -33 GAAAACTTTAACTTTTTGTCAAA 1 288 0 AAAATTTAAT 0.861917 -13 TTTCAAAGCTTTTCTTGAGGTT 2 4 1 CAAACTTTTT 0.814094 -19 TAAAAATATAAAAATTTTATGTTTGCCATTAA 6 46 0 AAAATTTATT 0.934019 -37 TTAAAAATCTTTTTTCTCTATTGAA 8 4 1 AAAACTTTTT 0.887827 -61 GTCCCAGCAAAAAACCATATTTCATGATATAG 12 188 1 AAAACATATT 0.60762 -78 CCAATCACACCAAACTTTAAATCCTTTTAAGC 14 99 1 CAAATTTAAT 0.775404 -34 GTTGTCAAAACAAATTTTATCTTTAAAATTTT 15 137 0 CAAATTTATT 0.886744 -61 CTAAATGCAAAAAAATTTATATAGTCCTTAGT 16 47 0 AAAATTTATT 0.934016 -109 TTTGTTATATAAAATCTTTTTTCTCGTGCGTA 17 26 1 AAAACTTTTT 0.887827 -120 TTTTTAAAGGAAAGATTTATCTTGCAAGAGTC 18 11 1 AAAGTTTATT 0.809754 -130 AACAAAGTGGCAAATCTTATATTTTGAAAATG 19 39 1 CAAACTTATT 0.92661 -35 CAGGTGAATTAAAAGCTTTTTTGATGTTCATG 20 35 1 AAAACTTTTT 0.887827 -78 TGTATCTGCAAAAGCTTTATATTGCCAGATTT 22 25 0 AAAGTTTATT 0.809754 -77 TCATAAATGAAAAAATTTAAAT 22 90 1 AAAATTTAAT 0.861917 -12 ATGTCAAATCAAAATCTTAAATTGAGATAAAA 23 91 1 AAAACTTAAT 0.909632 -60 CTCCTACCGAAAAGTTTTAAATCTTTCGCAAT 23 122 0 AAAGTTTAAT 0.652397 -29 ACCAAAACCTTATATTTTCTGCGTG 29 21 0 AAAACTTATT 0.958032 -15 TTTAACTTGGCAAAATTTAAATAATCACAAAA 30 270 1 CAAATTTAAT 0.775404 -31 TAAAATTAATAAAATCTTTTGTATT 31 49 1 AAAACTTTTT 0.887859 -15 **** ***** * Masking position 8 Map Score: 23.3451 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 44 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 2 TTGGGCTGATGGAGCAGAAGCTCCATCTGT 1 72 1 GGAGCAGAAG 0.818506 -229 TTTGAGTACGGGAGGTGGTTGTTTGAGGAG 1 224 1 GGAGGTGGTT 0.79759 -77 CATCTGAGCGGGGGTTGCCGAGCGGACAAA 7 203 0 GGGGTTGCCG 0.870106 -98 ATTATAGTTTGGAGCAGATTAACGGGGCAA 12 153 0 GGAGCAGATT 0.844149 -113 AATTGAGATGGGAGCAGATGAGCGAGAGGG 14 23 1 GGAGCAGATG 0.934518 -110 GCTACCCCACGGGGGCGACGTGGAAAAATT 18 44 0 GGGGGCGACG 0.820274 -97 TCGCCCCCGTGGGGTAGCGGATATCCTGAG 18 56 1 GGGGTAGCGG 0.852888 -85 GATATCCTGAGGGGCTGCGGACTCCTCGAC 18 75 1 GGGGCTGCGG 0.939616 -66 CGTCGGATTGGGGGCAGCAGCGGTCATTGC 25 33 0 GGGGCAGCAG 0.887019 -189 TTACCCATAAGGAGGTGATTTAAATCAAAT 25 172 0 GGAGGTGATT 0.846962 -50 GCACACCGCAGGAGGTGGCGATGGCTGCAG 26 22 1 GGAGGTGGCG 0.906626 -279 GAAAAAGATGGGGGTTGATGAAGTGTTTAT 26 212 1 GGGGTTGATG 0.838302 -89 TTTCCGAAATGGGGGTGCCGGGAATAAACA 26 235 0 GGGGGTGCCG 0.959581 -66 GGCATTGCGAGGAGCAGATTTTTGCCGGAA 30 32 1 GGAGCAGATT 0.844149 -269 GCATTTTAAAGGAGGAGGGTATAGAAGAGC 30 99 0 GGAGGAGGGT 0.761304 -202 TGGTGAAGGTGGAGGAGCTTGCTGAAAGCA 30 147 0 GGAGGAGCTT 0.896824 -154 ********** Masking position 4 Map Score: 12.8096 Number of sites scoring better than the average of aligned sites = 1546 Number in coding regions = 1432 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 AGTCGTGTAATATTTAATGTTTTCGTGAAATATGAATT 5 42 0 TTTATTCTGA 0.803562 -38 TTGTTTTTGCTTTTTAAAATAGCCCTAAGGCAACCTTC 8 33 0 TTTATACTAA 0.829547 -32 ATATAACCTTTACTTAATGTTGTCAAAACAAATTTTAT 15 149 0 TTTATTCAAA 0.968451 -49 ATTAAAAGCTTTTTTGATGTTCATGAAATTTCAAAATT 20 42 1 TTTATTTAAA 0.66908 -71 TTCGTTAATACTTAAATTTTACGTAATGTGCCGATT 21 180 0 TTTATTCTAA 0.951492 -26 GCAATAACGGTGATTAAATTCGGCGAAACACCTGTTTT 25 69 1 TTTATCCAAA 0.921762 -153 AAAGGAGAGTTATTTAAAATTACCCATAAGGAGGTGAT 25 183 0 TTTATTCATA 0.916061 -39 AACCCCCATCTTTTTCAGCTCGACAATATCGTCTGTCG 26 190 0 TTTATCCATA 0.807271 -111 ATTTCGGAAATTGTTGAGTTTATCAAAACCAAGCTGCC 26 255 1 TTTATTCAAA 0.968451 -46 GTTTTTTAATTAATCATAACCTTATCCAT 27 2 1 TTTATACTAA 0.829547 -30 CCTTTTTCAATTGTTTAACTTGGCAAAATTTAAATAAT 30 257 1 TTTATTCAAA 0.968451 -44 ATCAGCAAACTATTTTAATTTGCCTTAAACATTAGAGC 32 21 1 TTTATTCTAA 0.951492 -29 AGCAATCTGCTATTTGACGTTTCCCATAGCTCTAACCC 34 47 0 TTTATTCATA 0.916063 -39 * ** * ** * *** Masking position 7 Map Score: 7.40944 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 51 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 GAAGGTGGATTTCAAAGTTATATGAAGTCATCGCCC 7 272 0 TTAAATTGAA 0.966793 -29 ATTAAATAATTTCAAATTTCATCGAAGCT 11 39 1 TTAAATTGAA 0.971221 -19 TTGATGGAAGTTCAAAGTTATGCGAATATTCCAGAA 15 39 0 TTAAATTGAA 0.971164 -159 GAGAATGAAATTGCAAGTTGATGGAAGTTCAAAGTT 15 56 0 TTCAATTGAA 0.943296 -142 AAATTTTATCTTTAAAATTTTAAGAATCAGATATAG 15 122 0 TTAAATTGAA 0.971456 -76 TGTCTGCAATTTTGAAATTTCATGAACATCAAAAAA 20 51 0 TTGAATTGAA 0.900403 -62 TTTATAATTCTTACTATTTTTACGAAATTTTTTCAA 23 41 1 TTCTATTGAA 0.723956 -110 TTGACATACTTTGAAATTTATTTGAAAAAATTTCGT 23 62 0 TTAAATTGAA 0.970903 -89 TGCGAAAGATTTAAAACTTTTCGGTAGGAGTTCATG 23 124 1 TTAAATTGTA 0.827271 -27 TTTAAAAGGTTTTAGAGTTGAGCGAATTT 28 4 0 TTAGATTGAA 0.888303 -47 ** *** ** *** Masking position 8 Map Score: 8.21677 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 15 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 CCCGAACAACAACTGACGAAATGAGCACGATT 3 37 1 ATGACGAAAT 0.788718 -95 GTTTGCCATTAAATGGCAATTTTAATTGCAAT 6 26 0 ATGGCAATTT 0.654045 -57 ACCCCCGCTCAGATGAAAAATTCTGCATAGGA 7 218 1 ATGAAAAATT 0.767785 -83 ACTCTATTTCAACTCGAAAAATGCAGGTTTGG 9 46 1 ATCGAAAAAT 0.68599 -56 CCAGAATTCGAATTGGAAAATTCGTTCGTGAG 15 13 0 ATGGAAAATT 0.879483 -185 CTAATGATTTATCTGACAAAATAGCGATTGGA 16 93 0 ATGACAAAAT 0.915046 -63 CACGGGGGCGACGTGGAAAAATTGGACTCTTG 18 35 0 ATGGAAAAAT 0.953586 -106 TAATTAACAAATCTGGCAATATAAAGCTTTTG 22 17 1 ATGGCAATAT 0.841775 -85 TTGTGTTCATAAATGAAAAAATTTAAAT 22 84 1 ATGAAAAAAT 0.902909 -18 TTTGAAATTTATTTGAAAAAATTTCGTAAAAA 23 57 0 ATGAAAAAAT 0.902899 -94 CGGTCATTGCAGCTGGAGAAATATACTGGGGC 25 11 0 ATGGAGAAAT 0.876852 -211 CAATTGTTTAACTTGGCAAAATTTAAATAATC 30 264 1 ATGGCAAAAT 0.959289 -37 * ********* Masking position 9 Map Score: 6.78487 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 90 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 GAGGTTCTTTGGGCTGATGGAGCAGAAGCT 1 64 1 GGGCTGATGG 0.946007 -237 CAATAAAAAAGGGGTGGTGGT 3 121 1 GGGGTGGTGG 0.930747 -11 AACTAAATGCGGGGGGAGGGATTCGAACCC 7 136 1 GGGGGGAGGG 0.955522 -165 AACTCCCGGCGGGGGCATGGAATTTTTAAT 18 113 1 GGGGGCATGG 0.873883 -28 CCTGCGGTGTGCGGTGAAGGCCA 26 4 0 GCGGTGAAGG 0.94232 -297 ACCGCAGGAGGTGGCGATGGCTGCAGTGGA 26 26 1 GTGGCGATGG 0.96781 -275 TCTTGCTTTAGTGCCGAAGGTCATAAACTA 26 101 1 GTGCCGAAGG 0.901553 -200 GGCTGAGGCGGTGGAGAAGGTCTTTTCCGG 30 56 0 GTGGAGAAGG 0.916825 -245 AAAACTTGAAGTGGTGAAGGTGGAGGAGCT 30 158 0 GTGGTGAAGG 0.973166 -143 ********** Masking position 3 Map Score: 5.60102 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 467 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 AAACATAAAATTTTTATATTTTTAGTTTACT 6 54 1 TTTTTATTTT 0.89787 -29 CACTTTGTTTTTGCTTTTTAAAATAGCC 8 47 0 TTTTTGCTTT 0.89776 -18 CTTACAAACGTTTTTGTACTTGAAATAAAAC 9 12 0 TTTTTGTCTT 0.766116 -90 AATTATTTAATTTTTATGTTTTGACTAATCC 11 19 0 TTTTTATTTT 0.89787 -39 GTCAAAACAAATTTTATCTTTAAAATTTTAA 15 135 0 ATTTTATTTT 0.527644 -63 TATATAAATTTTTTTGCATTTAGGTATTTAT 16 56 1 TTTTTGCTTT 0.89776 -100 ATTTTTATTTTTATATTTTTGT 21 2 1 TTTTTATTTT 0.89787 -204 TATTTTTATATTTTTGTTTTTAACACGCTGT 21 16 1 TTTTTGTTTT 0.933421 -190 TTTTTATAATTAACAAATCTG 22 1 1 TTTTTATATT 0.709625 -101 ATTTAAATTTTTTCATTTATGAACACAA 22 84 0 TTTTTTCTTT 0.575987 -18 GCAGGCTCTTTTTGTGATTATTTAAATTT 30 282 0 TTTTTGTATT 0.795801 -19 ******* *** Masking position 5 Map Score: 5.48563 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 39 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TACACTTTAATTGCAATTAAAATTGCCATTT 6 17 1 TTGCATTAAA 0.926683 -66 AATTTTATGTTTGCCATTAAATGGCAATTTT 6 35 0 TTGCATTAAA 0.926726 -48 CACTTTGTTTTTGCTTTTTAAAATAGCCCTA 8 44 0 TTGCTTTTAA 0.574886 -21 GTTTTTGTACTTGAAATAAAACC 9 3 0 TTGAATAAAA 0.770362 -99 TTCCATCAACTTGCAATTTCATTCTCCAACA 15 66 1 TTGCATTTCA 0.803336 -132 TTATTGACATTAAAAATTCCATGC 18 127 0 TTGAATTAAA 0.931112 -14 GTCTGCAATTTTGAAATTTCATGAACATCAA 20 55 0 TTGAATTTCA 0.813675 -58 TAATTAATTATTGACATTAAAGCTAAATACA 21 58 0 TTGAATTAAA 0.931112 -148 CTAATGTTGATTGATATTTAAAATGAGTGTA 22 53 0 TTGAATTTAA 0.919193 -49 TTGACATACTTTGAAATTTATTTGAAAAAAT 23 67 0 TTGAATTTAT 0.591153 -84 AAATCTTAAATTGAGATAAAATTGCGAAAGA 23 102 1 TTGAATAAAA 0.770408 -49 **** ****** Masking position 7 Map Score: 5.53864 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 20 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 GAAGCTACCTGCTGAAAGGGTGTTTGAGTA 1 202 1 GCTGAAAGGG 0.969115 -99 TACGCATAGAGCTGCAAGGCAAAATTCATA 5 20 1 GCTGCAAGGC 0.93426 -60 CTGGTAGAGGGCTGCAAGGAGCGAAATTGC 13 33 0 GCTGCAAGGA 0.974916 -25 TATTTCTCCAGCTGCAATGACCGCTGCTGC 25 20 1 GCTGCAATGA 0.92721 -202 GGGAGTATCTGCTGACAGAACTTGTTTATC 25 142 0 GCTGACAGAA 0.842121 -80 GGTGGCGATGGCTGCAGTGGATGAAGACGT 26 35 1 GCTGCAGTGG 0.773761 -266 ATATTGTCGAGCTGAAAAAGATGGGGGTTG 26 199 1 GCTGAAAAAG 0.674433 -102 TCAAAACCAAGCTGCCAGAAAAGAGGAAGA 26 277 1 GCTGCCAGAA 0.894804 -24 GGAGGAGCTTGCTGAAAGCATCTCAAGTTA 30 137 0 GCTGAAAGCA 0.848215 -164 ATAGCAGATTGCTGAAATAGCTCC 34 72 1 GCTGAAATAG 0.839596 -14 ********** Masking position 3 Map Score: 4.2656 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 529 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 TGATTCTTTGGATGAGTTCATTTATTGGTAC 1 103 1 GTGAGTTCAT 0.811887 -198 TAATCTTCGTGGTGTTTGCATCCATACATGG 12 86 0 GTGTTTGCAT 0.94593 -180 ATCAACATTAGTTGTGTTCATAAATGAAAAA 22 73 1 GTGTGTTCAT 0.94593 -29 AGACGTGGATGTTGTGGGCATAAGTCTTCAC 26 59 1 GTGTGGGCAT 0.987866 -242 TTTACCCGCCGCTGTGGGCATTGCGAGGAGC 30 16 1 GTGTGGGCAT 0.987866 -285 CTCAAGTTATGCTGTTGGCATTTTAAAGGAG 30 115 0 GTGTTGGCAT 0.964923 -186 * ********* Masking position 3 Map Score: 2.93112 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 57 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 TTCATATAACTTTGAAATCCACCTTCTAC 7 282 1 TTTAATCCCT 0.975816 -19 GTTTTTGCTTTTTAAAATAGCCCTAAGGCAACCT 8 35 0 TTTAATGCCT 0.839351 -30 GGTTTGGATACTTTTATTACACCTGAAATCAAAC 9 71 1 CTTATTCCCT 0.82826 -31 ATTAAGTTTATATTCCCCCGACCAACTTTT 10 7 1 TTTATTCCCG 0.888715 -27 GTTGCCTCTCTTTAAAATTCACTTCGTATGCTTT 17 69 0 TTTAATCCTT 0.919256 -77 ATCAAAAAAGCTTTTAATTCACCTGAAGACCAAA 20 26 0 CTTAATCCCT 0.945502 -87 TATATTTTTGTTTTTAACACGCTGTTTTTAGCGT 21 22 1 TTTAACCCTG 0.777056 -184 ACCACTCATATTTGGAATCCTCCTTTATAATTCT 23 18 1 TTTAATCCCT 0.975816 -133 CTCTAAAACCTTTTAAACACCCTTGCCGAAGCTT 28 23 1 TTTAACCCTT 0.830372 -28 CGAGGAGCAATTTTTAATGCACCGTTGAAAACTT 30 181 0 TTTAATCCCG 0.966362 -120 *** *** * *** Masking position 6 Map Score: 3.91237 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 52 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 GAAATAGAGTTCCCTTACAAACGTTTTTGT 9 26 0 TCCCTTACAA 0.893579 -76 CAATTGCGTTTCCTTTACAACAATTTTGGA 12 53 0 TCCTTTACAA 0.95827 -213 GATAAATCTTTCCTTTAAAAA 18 2 0 TCCTTTAAAA 0.936892 -139 TTTGGAATCCTCCTTTATAATTCTTACTAT 23 28 1 TCCTTTATAA 0.936892 -123 TATACCCTCCTCCTTTAAAATGCCAACAGC 30 106 1 TCCTTTAAAA 0.936892 -195 ATCCCGTCAATCCTTTATTAGCTT 33 20 1 TCCTTTATTA 0.785524 -14 ********** Masking position 5 Map Score: 2.51004 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 36 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 13 GGGAGGTGGTTGTTTGAGGAGTGAAATTAT 1 233 1 TGTTTGAGGA 0.700902 -68 CGTCAGTTGTTGTTCGGGGGAAAACGGTAA 3 25 0 TGTTCGGGGG 0.975122 -107 GTCCCGTAGGGGTTCGAGGGTTCGAATCCC 7 153 0 GGTTCGAGGG 0.975122 -148 CAAAGGCGCAGGATTGAGGGTCCTGTCCCG 7 177 0 GGATTGAGGG 0.93873 -124 ATTTTTCATCTGAGCGGGGGTTGCCGAGCG 7 209 0 TGAGCGGGGG 0.901555 -92 GAAAAAAGTTGGTCGGGGGAATATAAACT 10 15 0 TGGTCGGGGG 0.984034 -19 CTGTACTGGTAGAGGGCTGCAAGGAG 13 42 0 TGGTAGAGGG 0.881037 -16 AGTTGAACCCGGGTCGAGGAGTCCGCAGCC 18 87 0 GGGTCGAGGA 0.923875 -54 CACAATCGTCGGATTGGGGGCAGCAGCGGT 25 39 0 GGATTGGGGG 0.95175 -183 ********** Masking position 6 Map Score: 6.47063 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 159 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 GGGAAAACAGGAAGTTACCG 3 1 1 GGGAAAACAG 0.980551 -131 TGTTGTTCGGGGGAAAACGGTAACTTCCTG 3 18 0 GGGAAAACGG 0.987339 -114 TTCTACGCGTGGGAAAACATGAACGCAAAG 12 242 0 GGGAAAACAT 0.957221 -24 GCCAGAGGTCGGGAAAACCTCCGATAAACA 25 120 1 GGGAAAACCT 0.949509 -102 AACTACATAAGGGAATACGGGGGCAATCCA 26 126 1 GGGAATACGG 0.959516 -175 ********** Masking position 5 Map Score: 2.36352 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 15 GAGTCTCCAGTTCATCAAAATTCAGGCTCAT 1 152 0 TTCATCAAAT 0.691312 -149 ACTTTAACTTTTTGTCAAAATAAGTTTTTCT 1 276 0 TTTGTCAAAT 0.691439 -25 GATTTGTTTATTTATGATGATAAAGTATTTA 3 65 1 TTTATGATAT 0.855771 -67 TGATAAAGTATTTATGAATACTCATACGAAA 3 82 1 TTTATGAAAC 0.903744 -50 AATTCAATTTTTTAAGATGATAATGAATTTA 4 29 1 TTTAAGATAT 0.431388 -58 CTGCATAGGATTTATGAATATTGTGGTTTAA 7 240 1 TTTATGAAAT 0.937462 -61 TTTGTTGTTGTTTATGAAAATTTTTTTAGTC 12 24 1 TTTATGAAAT 0.937391 -242 ATTTTGAAATTTCATGAACATCAAAAAAGCT 20 48 0 TTCATGAAAT 0.851927 -65 AATTTTTTCATTTATGAACACAACTAATGTT 22 76 0 TTTATGAAAC 0.903744 -26 AATTGTTGAGTTTATCAAAACCAAGCTGCCA 26 263 1 TTTATCAAAC 0.785114 -38 GCAGGCTCTTTTTGTGATTATTTAAATTTTG 30 280 0 TTTGTGATAT 0.696202 -21 ******** ** Masking position 7 Map Score: 3.60427 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 27 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172