AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_aful_reg_300.orf -o00640_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) AF1641 31 enoyl-CoA hydratase (fad-4) 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 AF0366 218 acetyl-CoA synthetase (acs-2) #6 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #7 AF0439 82 transcriptional regulatory protein, AsnC family #8 AF0442 300 succinoglycan biosynthesis regulator (exsB) #9 AF0481 64 proteasome, subunit beta (psmB) #10 AF0483 101 conserved hypothetical protein #11 AF0484 33 GTP cyclohydrolase II (ribA-1) #12 AF0487 57 penicillin G acylase #13 AF0495 265 A. fulgidus predicted coding region AF0495 #14 AF0496 57 conserved hypothetical transmembrane protein #15 AF0497 132 DNA polymerase B1 (polB) #16 AF0498 197 acyl-coA dehydrogenase (acd-3) #17 AF0673 155 mercuric resistance operon regulatory protein (merR) #18 AF0677 165 acetyl-CoA synthetase (acs-3) #19 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #20 AF0685 140 enoyl-CoA hydratase (fad-2) #21 AF0845 73 acyl-CoA dehydrogenase (acd-5) #22 AF0846 112 Na+/H+ antiporter (nhe2) #23 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #24 AF0970_AF0971 101 AF0970: A. fulgidus predicted coding region AF0970, AF0971: conserved hypothetical protein #25 AF0973 108 bile acid-inducible operon protein F (baiF-1) #26 AF1026 150 acyl-CoA dehydrogenase (acd-7) #27 AF1141 35 acyl-CoA dehydrogenase (acd-8) #28 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #29 AF1287_AF1289 600 AF1287: acetyl-CoA synthetase (acs-6), AF1289: conserved hypothetical protein #30 AF1540 143 succinyl-CoA synthetase, beta subunit (sucC-1) #31 AF1542 135 conserved hypothetical protein #32 AF1642 50 histidyl-tRNA synthetase (hisS) #33 AF1695 50 thiamine biosynthesis protein (apbA) #34 AF1696 28 small multidrug export protein (qacE) #35 AF1697 49 conserved hypothetical protein #36 AF1699 102 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #37 AF2057 35 acyl-CoA dehydrogenase (acd-10) #38 AF2186 65 succinyl-CoA synthetase, beta subunit (sucC-2) #39 AF2187 174 A. fulgidus predicted coding region AF2187 #40 AF2216 131 methylmalonyl-CoA decarboxylase, biotin carboxyl carrier subunit (mmdC) #41 AF2219 137 methylmalonyl-CoA mutase, subunit alpha, C-terminus (mcmA2) #42 AF2244 300 acyl-CoA dehydrogenase (acd-11) #43 AF2275 63 acyl-CoA dehydrogenase (acd-12) #44 AF2277 49 DNA polymerase, bacteriophage-type #45 AF2389-C 300 acetyl-CoA synthetase, putative #46 AF2426 85 conserved hypothetical protein #47 AF2429 30 enoyl-CoA hydratase (fad-5) Motif number 1 GAAAACTTTAACTTTTTGTCAAAATA 1 285 0 AATTTAATTT 0.787566 -16 GTTCACCTCCAATTTATAACATTTAATGAGCAAA 4 62 0 ATTATAATTT 0.944287 -25 TTTGCGCAAAAGTGTTTTAATTTTCGCAAAAATT 5 98 1 ATTTTTATTT 0.829736 -121 GTAGTCGTGTAATATTTAATGTTTTCGTGAAATA 6 48 0 ATTTTAATTT 0.955435 -32 GTAAACTAAAAATATAAAAATTTTATGTTTGCCA 7 50 0 ATTAAAATTT 0.883517 -33 GAAATTTGAAATTATTTAATTTTTATGTTTTGAC 12 25 0 ATTTTAATTT 0.956293 -33 TATGCTTAAAAGGATTTAAAGTTTGGTGTGATTG 15 100 0 AGTTTAATTT 0.698229 -33 GCTATATCTGATTCTTAAAATTTTAAAGATAAAA 16 121 1 ATTTAAATTT 0.907301 -77 TATACTAAGGACTATATAAATTTTTTTGCATTTA 17 44 1 ATTATAATTT 0.944287 -112 CGGCTTTAGGACTTTATAATATTTCCCATCTAAT 17 120 0 ATTATAATTT 0.944299 -36 TCTCATTTTCAAAATATAAGATTTGCCACTTTGT 21 40 0 AATATAATTT 0.798895 -34 ATTTTTATTTTTATATTTTTGTTTTTAACA 23 7 1 ATTTATATTT 0.68646 -199 TATTTCTACAATTTTTTAAAGTTTGAAATCGAAA 25 11 1 ATTTTAATTT 0.955435 -98 GTAATTTTCAAATGTATAAGTTTTTCGATTTCAA 25 33 0 ATTATAATTT 0.944287 -76 CCTACCGAAAAGTTTTAAATCTTTCGCAATTTTA 26 118 0 ATTTAAATTT 0.907483 -33 ATTGTTCTGAAAACTTAAAACTTTTCATTTAATT 29 506 1 AATTAAATTT 0.486516 -95 GTTACTATTTAAATTTTTTGGAAAAGA 30 4 1 ATTTTAATTT 0.955435 -140 TCAATTTTTCAATATAAAAAATTTTCGGAATTTC 30 36 0 ATTAAAATTT 0.883517 -108 AATTCGCTCAACTCTAAAACCTTTTAAACACCCT 32 12 1 ATTAAAATTT 0.883696 -39 CATTTAAAATATTTTTTTAGCTTTCAAAACCTTT 36 38 1 ATTTTTATTT 0.83007 -65 TAACACGCAGAAAATATAAGGTTTTGGT 37 18 1 AATATAATTT 0.798895 -18 TCTTTTTGTGATTATTTAAATTTTGCCAAGTTAA 42 271 0 ATTTTAATTT 0.955435 -30 AATACAAAAGATTTTATTAATTTTACGCTATTTT 43 40 0 ATTATTATTT 0.790962 -24 * * ***** *** Masking position 5 Map Score: 28.5435 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 41 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 GATGGAGCTTCTGCTCCATCAGCCCAAAGAACCT 1 65 0 CGCCACAGCC 0.847529 -236 TTCACTCCTCAAACAACCACCTCCCGTACTCAAA 1 224 0 AACCCCCTCC 0.648791 -77 CTTGGACATGCTTCTTGAACCTCCCAAACTCAAC 8 96 1 CTCGACCTCC 0.871116 -205 TTTGTCCGCTCGGCAACCCCCGCTCAGATGAAAA 8 203 1 CGCCCCCGCT 0.965411 -98 TATGTTTTGACTAATCCAGCCTCCG 12 2 0 CAACACCTCC 0.615182 -56 TCTTGCAGTCCCTCTCGCTCATCTGCTCCCATCT 15 28 0 CTCGCCATCT 0.746995 -105 TTGAGATTCTCTTCGACGGCATCCCGCTTGATAA 29 33 0 CTCCGCATCC 0.853454 -568 GCAACTCCTACTTTGCCCACCTCTCCGTCTGCAA 29 87 1 CTTCCCCTCT 0.908817 -514 GTGCTCAAGCCCGTCTCACCCTCTTCGAGCAGCA 29 168 1 CGTCACCTCT 0.703356 -433 AGAACTGCCTCATAGTCCACAGCCTTCCGCGGTA 29 244 1 CTACCCAGCC 0.769618 -357 TTCCGCCATTCTGCCTGCACATCCAACCACCTTT 30 89 0 CGCGCCATCC 0.900157 -55 TGGCGTCCACCTTCAACCGCCGCTAAGGCTGATG 31 37 0 CTCCCCCGCT 0.96417 -99 TAGGCAGAACCTTCTGCCCCCTCTACAACTTAAT 39 84 1 CTCCCCCTCT 0.977506 -91 CGATTTATCGCAGCTACCGCAGCCAGAAACTCTT 40 30 0 CGCCCCAGCC 0.960374 -102 TCCCTGAGCTCAACCACTCCCTCCTTCTCTCTCA 40 69 0 CACCTCCTCC 0.733943 -63 TCTCTCAACCTCGCCGCCATCTTCCAGTTTCT 40 110 0 CTCCGCATCT 0.664227 -22 CCGGAAAAGACCTTCTCCACCGCCTCAGCCTGAG 42 56 1 CTTCCCCGCC 0.947834 -245 TATAGAAGAGCTGTTTCCGCCTCAGGCTGAGGCG 42 76 0 CGTCCCCTCA 0.765635 -225 AACAGCTCTTCTATACCCTCCTCCTTTAAAATGC 42 95 1 CATCCCCTCC 0.91791 -206 GAGATGCTTTCAGCAAGCTCCTCCACCTTCACCA 42 143 1 CGCGCCCTCC 0.968321 -158 CCAGAGGAGGCTTACGCCTCCTCCTACATAACTT 45 66 1 CTACCCCTCC 0.948161 -235 ATATAGTTGCCTTCGTCATCCTCAGGAAGGGATA 45 237 1 CTCCACCTCA 0.759013 -64 * ** ** ***** Masking position 10 Map Score: 18.8549 Number of sites scoring better than the average of aligned sites = 2408 Number in coding regions = 2300 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 TTAATTTTCGCAAAAATTTTCATTTTTAAT 5 114 1 CAAAAATTTT 0.784872 -105 TAATGGCAAACATAAAATTTTTATATTTTT 7 47 1 CATAAAATTT 0.724533 -36 TCAATAGAGAAAAAAGATTTTTAA 9 5 0 AAAAAGATTT 0.794404 -60 ATTTTGGACTAAAAAAATTTTCATAAACAA 13 31 0 AAAAAAATTT 0.78837 -235 AAATTTTAAAGATAAAATTTGTTTTGACAA 16 138 1 GATAAAATTT 0.639197 -60 ACCTAAATGCAAAAAAATTTATATAGTCCT 17 51 0 AAAAAAATTT 0.78837 -105 GAGTATTAGACAAAACATTTTTAACTAACA 18 27 0 CAAAACATTT 0.689911 -139 ACGCACGAGAAAAAAGATTTTATATAACAA 19 27 0 AAAAAGATTT 0.794404 -119 TTTTTAAAGGAAAGATTTATCTTGCAAG 20 9 1 GGAAAGATTT 0.842717 -132 CGGCACATTACGTAAAATTTAAGTATTAAC 23 183 1 CGTAAAATTT 0.608827 -23 GTTCATAAATGAAAAAATTTAAAT 24 88 1 GAAAAAATTT 0.89722 -14 AAATTTATTTGAAAAAATTTCGTAAAAATA 26 55 0 GAAAAAATTT 0.89722 -96 GATAAAATTGCGAAAGATTTAAAACTTTTC 26 116 1 CGAAAGATTT 0.888327 -35 AACTCCTACCGAAAAGTTTTAAATCTTTCG 26 126 0 GAAAAGTTTT 0.718223 -25 TGAATTAAATGAAAAGTTTTAAGTTTTCAG 29 512 0 GAAAAGTTTT 0.718223 -89 ATTTCTTTTCCAAAAAATTTAAATAGTAAC 30 11 0 CAAAAAATTT 0.928368 -133 AAAGAAATTCCGAAAATTTTTTATATTGAA 30 33 1 CGAAAATTTT 0.683444 -111 GGAATTAATCCGAAAAATTTTTACCTATAT 41 98 1 CGAAAAATTT 0.884649 -40 AATACAAAAGATTTTATTAATTTT 43 50 0 CAAAAGATTT 0.930761 -14 ********** Masking position 8 Map Score: 13.0428 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 60 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 GAAAACTTTAACTTTTTGTCAAAATAAGTTTTTCT 1 276 0 TTATTTAAAT 0.938583 -25 TCTTAAAAAATTGAATTATGCTCAAAGTGTGAGCA 4 8 0 TTATTTAAAT 0.938583 -79 GCAAAAGTGTTTTAATTTTCGCAAAAATTTTCATTTTT 5 103 1 TTATTCAAAT 0.659637 -116 ATACTTACACTTTAATTGCAATTAAAATTGCCATTTAA 7 12 1 TTATTTAAAT 0.938583 -71 GGAGTTTGATTTCAGGTGTAATAAAAGTATCCAAACCT 10 70 0 TTAGTTAAAT 0.865976 -32 ATGATATAGGTTACCTTCTTGTCAAATTCTTCTTTGCG 13 211 1 TTCTTTAAAT 0.690331 -55 AAATTGCAAGTTGATGGAAGTTCAAAGTTATGCGAATA 16 47 0 TTAGGTAAAT 0.782054 -151 AATAGATATATTTATTTATTGTTAAAATCTATTTTAAA 18 126 0 TTATTTAAAT 0.938583 -40 TAAAAGCTTTTTTGATGTTCATGAAATTTCAAAATTGC 22 44 1 TTGTGTAAAT 0.694969 -69 ACAACTAATGTTGATTGATATTTAAAATGAGTGTATCT 24 50 0 TTATGTAAAT 0.894591 -52 AGATTTTGATTTGACATACTTTGAAATTTATTTGAAAA 26 70 0 TTAATTAAAT 0.619234 -81 AATCAAAATCTTAAATTGAGATAAAATTGCGAAAGATT 26 97 1 TTATTTAAAT 0.938583 -54 TTTCATTTAATTCAATTCGAATCAAAATTCTTAAATAC 29 528 1 TTATTTAAAT 0.938583 -73 CAACCACCTTTTAAGTTCGATTTAACATTCTCAATTTT 30 62 0 TTATTTAACT 0.659637 -82 CGGAAGTCCTTTTGGTTTCGTTGAAAATGGGGTGGT 30 118 1 TTGTTTAAAT 0.804021 -26 CGCTCTAATGTTTAAGGCAAATTAAAATAGTTTGCTGA 44 22 0 TTAGGTAAAT 0.782054 -28 ** * ** * *** * Masking position 14 Map Score: 9.97878 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 11 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TGTTATAAATTGGAGGTGAACT 4 75 1 TGGAGGTGAA 0.584245 -12 AAAATGGGATTGAAAGTGGACGTGTAAATC 8 38 1 TGAAAGTGGA 0.830755 -263 GTAGAAGGTGGATTTCAAAGTT 8 289 0 AGAAGGTGGA 0.925198 -12 TTGAGTAGTGTGGAGGAGTAT 25 98 1 TGGAGGAGTA 0.649205 -11 GTAAGAATTATAAAGGAGGATTCCAAATAT 26 25 0 TAAAGGAGGA 0.866031 -126 GGACACCAACAGAAGATGGAAGATGCTGCT 29 195 0 AGAAGATGGA 0.691586 -406 TAGCGGCGGTTGAAGGTGGACGCCATCACC 31 46 1 TGAAGGTGGA 0.976885 -90 TATCTGAGAGAGAAGGAGGGAGTGGTTGAG 40 65 1 AGAAGGAGGG 0.703803 -67 GTTGGCATTTTAAAGGAGGAGGGTATAGAA 42 103 0 TAAAGGAGGA 0.866031 -198 CTTGAAGTGGTGAAGGTGGAGGAGCTTGCT 42 154 0 TGAAGGTGGA 0.976885 -147 GTTAAACAATTGAAAAAGGATTTAAATAGA 42 246 0 TGAAAAAGGA 0.53959 -55 GCAAAAGTTATGTAGGAGGAGGCGTAAGCC 45 74 0 TGTAGGAGGA 0.876115 -227 TTATTTCGGCTGGAGAAGGATTACTGGATG 45 118 1 TGGAGAAGGA 0.835904 -183 TCGGACGAGCTGAAGGAGGAGCTGAGAGAG 45 278 1 TGAAGGAGGA 0.98235 -23 ********** Masking position 4 Map Score: 12.0551 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 695 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CTAAACTCCCCCCTTAAAGTCCG 5 206 0 AACTCCCCCC 0.97491 -13 GGGTTCGAATCCCTCCCCCCGCATTTAGTT 8 136 0 CCCTCCCCCC 0.969741 -165 CCTGAAATCAAACTCCCACC 10 92 1 AACTCCCACC 0.976497 -10 CATAACTTTGAACTTCCATCAACTTGCAAT 16 53 1 AACTTCCATC 0.782926 -145 GCATGAACTCCTACCGAAAAGTTTT 26 136 0 AACTCCTACC 0.852349 -15 CATCGCTGTCCACGCCCATCAGAGTTGGAA 29 127 1 CACGCCCATC 0.83772 -474 TTCGAGCAGCATCTTCCATCTTCTGTTGGT 29 191 1 ATCTTCCATC 0.532654 -410 TGTTCGGATAAACTCCCCTCGTGAAGGGAA 29 280 1 AACTCCCCTC 0.960438 -321 TGAGCTCAACCACTCCCTCCTTCTCTCTCA 40 69 0 CACTCCCTCC 0.896105 -63 AACAATCCAACCCTCCCATCAAAAGAGACA 45 146 0 CCCTCCCATC 0.955378 -155 CTTAATCCTAATCTCCCCTCTAACTCCCTT 45 191 0 ATCTCCCCTC 0.88468 -110 ATAGCTCTAACCCTCCTACCATTCTTCCAA 46 30 0 CCCTCCTACC 0.826427 -56 ********** Masking position 6 Map Score: 9.28404 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 421 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CATTCTTGCGAGAGTGAACCATCCACAAACGAATGG 1 19 1 AGATGACCCC 0.708705 -282 ACACCCTTTCAGCAGGTAGCTTCCTCAGAAAAGCTT 1 189 0 AGCGGTCCCC 0.905675 -112 GACGAAAAGAAGATTTACACGTCCACTTTCAATCCC 8 43 0 AGATTACCCC 0.851946 -258 TAGGGGTTCGAGGGTTCGAATCCCTCCCCCCGCATT 8 141 0 AGGTTCACCC 0.706931 -160 ACCCGGGTCGAGGAGTCCGCAGCCCCTCAGGATATC 20 75 0 AGGGTCCCCC 0.976476 -66 TGTTTATCGGAGGTTTTCCCGACCTCTGGCAAAGAT 28 114 0 AGGTTTCCCC 0.975248 -108 GCTGTGCTCAAGCCCGTCTCACCCTCTTCGAGCAGC 29 165 1 AGCCGTCCCC 0.802042 -436 CTCTCTGCCCAGCTTTTTGCAACCACGGTTTGAGAC 29 415 1 AGCTTTCCCC 0.961491 -186 CTCTGAGAACAGGCGTCATCAGCCTTAGCGGCGGTT 31 21 1 AGGGTCCCCT 0.686937 -115 GAATCGGTATGGGTGATGGCGTCCACCTTCAACCGC 31 51 0 GGGGATCCCC 0.505877 -85 CAATAGGCAGAACCTTCTGCCCCCTCTACAACTTAA 39 81 1 AACTTCCCCC 0.604552 -94 AGGGTTTTACCCGCCGCTGTGGGCATT 42 2 1 GGGTTTCCCC 0.913623 -299 TTGCCGGAAAAGACCTTCTCCACCGCCTCAGCCTGA 42 53 1 AGACTTCCCC 0.789284 -248 ATGTAGGAGGAGGCGTAAGCCTCCTCTGGGTGAAAC 45 59 0 AGGGTACCCC 0.954811 -242 CTTATATAGTTGCCTTCGTCATCCTCAGGAAGGGAT 45 234 1 TGCTTCCCCC 0.740032 -67 AGGTTTATACCTCCCCATTCTACCCT 47 1 1 AGGTTACCCC 0.958729 -30 *** *** * ** * Masking position 13 Map Score: 6.88265 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 461 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 CCCGTACTCAAACACCCTTTCAGCAGGTAGCTTCC 1 201 0 ACCCCTTCCA 0.901115 -100 ATATGAAGTCATCGCCCTTTAAACCACAATATTCA 8 254 0 ACCCCTTACC 0.922275 -47 GTTGAAATAGAGTTCCCTTACAAACGTTTTTGTAC 10 24 0 ATCCCTTCAC 0.855456 -78 GATTTATCTCAGCACGCTTTCGCAAGTTTTTTAAA 18 97 1 ACCGCTTCAA 0.946722 -69 CTTCGACGGCATCCCGCTTGATAAGGTCTCGACGT 29 22 0 ACCGCTTAAG 0.79294 -579 AGTTGCCGTTGACACGCTTAAGGACTTTGAGATTC 29 58 0 GCCGCTTAAC 0.898789 -543 GGACAGCGATGACCCGCTTGCAGACGGAGAGGTGG 29 103 0 GCCGCTTCAC 0.960271 -498 AACAACCTCCCTTACCTACATTTTTAATC 29 582 0 ACCCCTTCAC 0.986861 -19 AAACCTTTTAAACACCCTTGCCGAAGCTTGAGC 32 28 1 ACCCCTTCAA 0.954942 -23 AACAATGCAGATCCCGCTTGCAGTCGACCCAAACG 45 27 0 ACCGCTTCTC 0.908491 -274 TCTCCCCTCTAACTCCCTTAATCACCAAACTACAA 45 175 0 ACCCCTTAAC 0.96503 -126 * * ***** * ** Masking position 8 Map Score: 3.9206 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 194 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 AATGAATTTAAATTTGCTCATTAAATGTTA 4 50 1 AATTTGCTCA 0.917138 -37 CTTTTGCGCAAATTTGCTCACAATTGCACT 5 80 0 AATTTGCTCA 0.917138 -139 TTGCCCCGTTAATCTGCTCCAAACTATAAT 13 153 1 AATCTGCTCC 0.965434 -113 CGTTCTCGCAATTTCGCTCCTTGCAGCCCT 14 26 1 ATTTCGCTCC 0.729586 -32 CCCTCTCGCTCATCTGCTCCCATCTCAATT 15 23 0 CATCTGCTCC 0.853474 -110 GCCTGTACCGAATTTGTTCCAATTAATACT 23 134 0 AATTTGTTCC 0.774123 -72 AAATTCGCTCAACTCTAAAAC 32 2 1 AATTCGCTCA 0.843999 -49 TTCCGGCAAAAATCTGCTCCTCGCAATGCC 42 32 0 AATCTGCTCC 0.965434 -269 GGTGCATTAAAAATTGCTCCTCGTTAAACT 42 192 1 AAATTGCTCC 0.915997 -109 CAGATTGCTGAAATAGCTCC 46 76 1 AAATAGCTCC 0.661492 -10 ********** Masking position 8 Map Score: 4.71746 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 110 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 GCCTTAGGGCTATTTTAAAAAGCAAAAACAA 9 40 1 TATTTTAAAA 0.766745 -25 TGATTCTTAAAATTTTAAAGATAAAATTTGT 16 129 1 AATTTTAAAA 0.922731 -69 TGTTAAAATCTATTTTAAAAAACTTGCGAAA 18 114 0 TATTTTAAAA 0.766745 -52 ATACGAAGTGAATTTTAAAGAGAGGCAACAG 19 74 1 AATTTTAAAA 0.922731 -72 CAGATTTGTTAATTATAAAAA 24 1 0 AATTATAAAA 0.602966 -101 CAGATACACTCATTTTAAATATCAATCAACA 24 49 1 CATTTTAAAA 0.734502 -53 TTCGATTTCAAACTTTAAAAAATTGTAGAAA 25 13 0 AACTTTAAAA 0.736328 -96 CCTTATGGGTAATTTTAAATAACTCTCCTTT 28 190 1 AATTTTAAAA 0.920503 -32 CTTTTCCAAAAAATTTAAATAGTAAC 30 6 0 AAATTTAAAA 0.7686 -138 CATTCCAAATAATTTTAAATAAGTTGGCTCG 41 22 0 AATTTTAAAA 0.920503 -116 TAACTTGGCAAAATTTAAATAATCACAAAAA 42 272 1 AAATTTAAAA 0.7686 -29 ********* * Masking position 7 Map Score: 7.22056 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 13 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 AACGGTAACTTCCTGTTTTCCC 3 1 0 TCGTTTTCCC 0.987857 -131 AACAGGAAGTTACCGTTTTCCCCCGAACAACA 3 16 1 TCGTTTTCCC 0.987857 -116 TTCTTTGCGTTCATGTTTTCCCACGCGTAGAA 13 240 1 TAGTTTTCCC 0.97305 -26 CTTGTTTATCGGAGGTTTTCCCGACCTCTGGC 28 120 0 GAGTTTTCCC 0.942078 -102 TTTAAGGTTCTGCAGTTTTCCCAATAAACTTT 35 26 0 TCGTTTTCCC 0.987857 -24 * * ******** Masking position 6 Map Score: 1.79742 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 11 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 12 ACAACAACTGACGAAATGAGCACGATTTGTTT 3 42 1 ACGAAATGAA 0.820616 -90 GAATACTCATACGAAATTATTATTCAATAAAA 3 97 1 ACGAAATTAA 0.871767 -35 TTCATATTTCACGAAAACATTAAATATTACAC 6 44 1 ACGAAAACAA 0.82506 -36 ATCTCTGATGACGAAAAGAAGATTTACACGTC 8 56 0 ACGAAAAGAA 0.665563 -245 AGCCAATCACACCAAACTTTAAATCCTTTTAA 15 97 1 ACCAAACTTA 0.636808 -36 AAGGTTATATACCAAATCTAGAACCTGTGCT 16 177 1 ACCAAATCTA 0.636807 -21 TCACCTGAAGACCAAACCATGAGGTGGTACA 22 10 0 ACCAAACCAA 0.925814 -103 GAAAGGCTGTACGAAATTATTAAAGTTATTTG 22 85 0 ACGAAATTAA 0.871767 -28 TTTGAAAATTACCAAATTATTAATACTGCATG 25 55 1 ACCAAATTAA 0.830716 -54 CCCATTTTCAACGAAACCAAAAGGACTTCCGC 30 117 0 ACGAAACCAA 0.945321 -27 TTTATTACGAAACCAAAAGTTTATTGGG 35 7 1 ACGAAACCAA 0.945321 -43 TCCCTTAATCACCAAACTACAAACAATCCAAC 45 165 0 ACCAAACTAA 0.886693 -136 ********* * Masking position 6 Map Score: 4.87464 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 38 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 CATCCACAAACGAATGGGAAGATAGAGAGG 1 38 1 CGAATGGGAA 0.955007 -263 CTCTATGCGTAGAGTTGGAA 6 1 0 AGAGTTGGAA 0.930467 -79 CTGCATTTTTCGAGTTGAAATAGAGTTCCC 10 42 0 CGAGTTGAAA 0.703285 -60 ATTATTCTACGCGTGGGAAAACATGAACG 13 247 0 CGCGTGGGAA 0.899418 -19 TTCCAGAATTCGAATTGGAAAATTCGTTCG 16 17 0 CGAATTGGAA 0.930467 -181 CACGCCCATCAGAGTTGGAAAGTCGAAGGC 29 137 1 AGAGTTGGAA 0.930467 -464 AGAAAAGGAAAGAATGGGAAGAGAAATGTC 29 448 0 AGAATGGGAA 0.930467 -153 GAGCAGGGTAGAATGGGGAGGTATAAACC 47 12 0 AGAATGGGGA 0.780426 -19 ********** Masking position 10 Map Score: 2.39692 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 38 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 GCTTCCTCAGAAAAGCTTGGTAAGGAGTCTCC 1 175 0 AAAAGCTTGA 0.906237 -126 AACCTCAAGAAAAGCTTTGAAA 2 2 0 AAAAGCTTTA 0.958088 -21 CAATAGAGAAAAAAGATTTTTAA 9 2 0 AAAAGATTTA 0.778845 -63 TTCAAGTACAAAAACGTTTGTAAGGGAACTCT 10 19 1 AAAACGTTTA 0.817559 -83 ACCAAACTTTAAATCCTTTTAAGCATAATTGG 15 107 1 AAATCCTTTA 0.541669 -26 AGTATTAGACAAAACATTTTTAACTAACAACT 18 24 0 AAAACATTTA 0.665416 -142 ATCTATTTTAAAAAACTTGCGAAAGCGTGCTG 18 106 0 AAAAACTTGA 0.457824 -60 TGAACATCAAAAAAGCTTTTAATTCACCTGAA 22 33 0 AAAAGCTTTA 0.958088 -80 GTGTATCTGCAAAAGCTTTATATTGCCAGATT 24 26 0 AAAAGCTTTA 0.958088 -76 ACTCCTACCGAAAAGTTTTAAATCTTTCGCAA 26 123 0 AAAAGTTTTA 0.666354 -28 CGTGGTTGCAAAAAGCTGGGCAGAGAGAAGAA 29 410 0 AAAAGCTGGA 0.567357 -191 GCTCAACTCTAAAACCTTTTAAACACCCTTGC 32 17 1 AAAACCTTTA 0.928109 -34 AAATTAACGGAAAAGGTTTTGAAAGCTAAAAA 36 51 0 AAAAGGTTTA 0.88808 -52 GCTGCTTAGAAAAACCGTTACAAGACTCAAAG 39 43 1 AAAACCGTTA 0.653165 -132 AAACAATTGAAAAAGGATTTAAATAGAACACA 42 241 0 AAAAGGATTA 0.438511 -60 ********* * Masking position 3 Map Score: 3.60307 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 129 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 15 TGGAGCTTCTGCTCCATCAGCCCAAAGAAC 1 67 0 GCTCCATCAG 0.902261 -234 TGGAGCAGAAGCTCCATCTGTTTGATTCTT 1 81 1 GCTCCATCTG 0.882254 -220 CCAAGTAAAAGATATCTCTGATGACGAAAA 8 71 0 GATATCTCTG 0.641034 -230 GAACTATGTGGCTATATCTGATTCTTAAAA 16 111 1 GCTATATCTG 0.948939 -87 ACGAGAAAAGGCTATATCAGCCAGATATAG 39 126 1 GCTATATCAG 0.958152 -49 GGCTATTGCTGCTATATCTGGCTGATATAG 39 137 0 GCTATATCTG 0.948939 -38 GCGATAAATCGCTATCTGAGAGAGAAGGAG 40 53 1 GCTATCTGAG 0.765304 -79 ATGCTCTCTCAGCTCCTCCTTC 45 289 0 GCTCTCTCAG 0.948748 -12 GGAGCTATTTCAGCAATCTGCTA 46 73 0 GCTATTTCAG 0.849592 -13 ********** Masking position 7 Map Score: 3.71623 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 92 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555