AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_mthe_reg_300.orf -o00910_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MTH1710 21 carbon monoxide dehydrogenase, alpha subunit Input sequences: #1 MTH106 137 tungsten formylmethanofuran dehydrogenase, subunit C homolog #2 MTH185 125 conserved protein #3 MTH186 26 unknown #4 MTH187 142 conserved protein #5 MTH189 99 unknown #6 MTH278 300 ferredoxin #7 MTH384 249 unknown #8 MTH387 24 conserved protein #9 MTH388 35 unknown #10 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #11 MTH394 55 unknown #12 MTH397 40 formate hydrogenlyase, subunit 7 #13 MTH399 23 polyferredoxin #14 MTH400 33 polyferredoxin #15 MTH403 187 formylmethanofuran:tetrahydromethanopterin formyltransferase II #16 MTH405 130 polyferredoxin #17 MTH413 300 conserved protein #18 MTH644 145 conserved protein #19 MTH645 24 collagenase #20 MTH648 65 ribosomal protein L37 #21 MTH649 300 conserved protein #22 MTH700 110 conserved protein #23 MTH702 27 acetyl-CoA synthetase related protein #24 MTH927 139 ferredoxin #25 MTH928 300 cobalamin biosynthesis protein N #26 MTH1026 222 phosphatidylserine decarboxylase #27 MTH1027 39 CDP-diacylglycerol-serine O-phosphatidyltransferase #28 MTH1029 41 unknown #29 MTH1030 30 unknown #30 MTH1031 59 conserved protein #31 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #32 MTH1120 132 nifH / minD related protein #33 MTH1133 21 polyferredoxin (MvhB) #34 MTH1136 171 methyl viologen-reducing hydrogenase, delta subunit #35 MTH1137 116 conserved protein (FlpA) #36 MTH1138 51 methyl viologen-reducing hydrogenase, delta subunit homolog FlpD #37 MTH1141 300 conserved protein (FlpE) #38 MTH1246 30 NADH dehydrogenase I, subunit N #39 MTH1251 147 conserved protein #40 MTH1252 143 conserved protein #41 MTH1253 135 unknown #42 MTH1468 35 ferredoxin #43 MTH1469 57 molybdenum transport ATP-binding protein homolog #44 MTH1470 44 molybdenum transport protein ModA related protein #45 MTH1471 56 O-antigen transporter homolog #46 MTH1472 30 O-antigen transporter homolog #47 MTH1475 56 unknown #48 MTH1476_MTH1477 127 MTH1476: tryptophan synthase, beta subunit homolog , MTH1477: unknown #49 MTH1478 135 conserved protein #50 MTH1480 144 conserved protein #51 MTH1481 142 isopropylmalate synthase #52 MTH1510 109 NH(3)-dependent NAD+ synthetase #53 MTH1552 139 formate dehydrogenase, alpha subunit homolog #54 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #55 MTH1560 107 nitrogenase NifH subunit #56 MTH1563 37 nitrogenase NifD subunit #57 MTH1567 235 catalytic subunit of nitrate reductase (flp) #58 MTH1570 74 glutamine synthetase #59 MTH1571 300 molybdopterin biosynthesis protein MoeB homolog #60 MTH1582 44 carbonic anhydrase #61 MTH1667 219 unknown #62 MTH1668 84 conserved protein #63 MTH1669 148 conserved protein #64 MTH1672 41 conserved protein #65 MTH1674 151 conserved protein #66 MTH1708 300 carbon monoxide dehydrogenase, alpha subunit #67 MTH1819 134 ferredoxin Motif number 1 GCCATGGTAAACCCTTCACCCCATCACACT 5 19 0 ACCCTTCACC 0.873676 -81 ACATATAAATACTCCTCCAGTGAAAGATTA 6 204 1 ACTCCTCCAG 0.626713 -97 TCTGATTAAATCCCTTCCATTTTCATTCCA 11 22 0 TCCCTTCCAT 0.89135 -34 ACTCTCCTGAACTCATCCACCACTCTGAAG 15 12 0 ACTCATCCAC 0.628146 -176 AGGTCCTCTGCCTCCTCAATAACCGTTATG 15 63 0 CCTCCTCAAT 0.636191 -125 TAAATTTATTACCCCTCCCCGGTAATAGAT 17 266 1 ACCCCTCCCC 0.970999 -35 AAATAACAGTCCCCCTCCACATACTGACCT 18 87 0 CCCCCTCCAC 0.98361 -59 AAGTTGATCCACCCTTCCCCTTACAATTAA 20 13 0 ACCCTTCCCC 0.969952 -53 CCTGGGATCCCCCCATCCATGAGAGATGCA 21 134 0 CCCCATCCAT 0.825525 -167 ATGATAAATGTCTCTTCCCTTAATAAAGTT 22 47 0 TCTCTTCCCT 0.78698 -64 ATCAGGGTGTTCCCTTCACCAGAGGTTTTC 31 119 0 TCCCTTCACC 0.853374 -111 TAATACCACTCCCCTTCCACCAGAAGGCTC 34 20 0 CCCCTTCCAC 0.98301 -152 TAAATTAGCATCCCTTCCATACTGAGTTAC 35 74 1 TCCCTTCCAT 0.89135 -43 ATTACGGCAGCCTCTTCCCCTTCAAGTGTT 39 26 1 CCTCTTCCCC 0.963038 -122 ACCCCTCCACCACCTCACCC 47 1 1 ACCCCTCCAC 0.961912 -56 GACAGACATACCTCCTCAACATGGGGGAGT 50 122 1 CCTCCTCAAC 0.813694 -23 CCTCTTCACCTCACTCTCTA 53 1 1 CCTCTTCACC 0.84808 -139 AGCCTCAAGTTCCCTTCCATCTATTCTAAA 53 111 0 TCCCTTCCAT 0.89135 -29 GATAATAAAACCCCTTCCCTGAACCGAACT 59 82 1 CCCCTTCCCT 0.968466 -219 GTTTATATAACCCCCTCCCGCTGGTACTGT 61 154 0 CCCCCTCCCG 0.939654 -66 ********** Masking position 6 Map Score: 24.5156 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 646 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 GGAATATGAAGACATCATAAAAACCCCCAGCTTCCAA 2 92 0 GCCTAACCCC 0.986417 -34 TCAGATATCAGGACATCCCATATGAG 3 7 0 GTCGAACCCA 0.699923 -20 CAATGAGCTGTTCAACAGCGGGTTCCCCTATTTCAGA 4 18 0 TCCGGGTCCC 0.73395 -125 TGTTACCCAGGGCTGCTGCGGCCCCCCTCCTAACAGA 4 78 0 GCCGGCCCCC 0.913212 -65 TTTCGCGAGGTTGACCTGAGTGCTCCCATCTCCTATC 6 33 1 TGCGGGTCCC 0.467046 -268 AAGTGGATGTGACTCCATAGGAACCTCCAGGACATGA 7 23 0 GCCTGACCTC 0.785718 -227 TTTTTTTACTGATATCTGAAGGGTCCCTCTACAGAAG 7 123 0 GTCGAGTCCC 0.802493 -127 CTCCATGCTTGCGTCCAGGAGGTCCTCTGCCTCCTCA 15 75 0 GGCGAGCCTC 0.691603 -113 CATCCGGGGAGAGGACGTCGGATCCCTCGGCTGAATC 15 123 1 GGCTGACCCT 0.55066 -65 GTGGGTTCTGGAGGTCTTTATATCCCCTGAGAACCCT 17 78 0 GGCTAACCCC 0.946913 -223 GAACCCGGTTTCTGAAAAACCCACCTTCAATGT 18 7 1 GTCGAACCCA 0.699923 -139 CATTCCAGGGTCCGCCCTGGGATCCCCCCATCCATGA 21 142 0 TCCTGACCCC 0.93536 -159 TGTTTTACATGGCAGCTGAGGACCCCCGCAGTTATAA 24 53 0 GCCGGACCCC 0.98727 -87 AGGGGAAGAGGCTGCCGTAATAACCCCATGAGTCCT 39 10 0 GTCTAACCCC 0.955176 -138 CAAGTCAGAATACAGCATCAAAACCCTGGAATCCCAG 40 87 0 TCCTAACCCT 0.597473 -57 CACGGGTCCTGTCATCATAACATCCCCCGCCGGTGCT 49 30 0 GCCTAACCCC 0.986423 -106 TCCAGGTTCAGCCTCAAGTTCCCTTCCATCTAT 53 117 0 TCCTAGTCCC 0.721089 -23 ACTGTTTTTCGATTTCAGAATGGCTCCAGAGGACCGC 59 109 1 GTCGAGCTCC 0.516484 -192 AAGGCTGTGGTCCTACAGGATGACCCCCTCATGATTT 59 226 1 TCCGAGCCCC 0.965353 -75 CTTCGTAATAGCCATCAGAATGTCCCCTGGAAACTGG 61 30 1 GCCGAGCCCC 0.990161 -190 ATTTCCAGGAGATTCCTTGATATCCCCAGTTTCCAGG 61 55 0 GTCTAACCCC 0.955188 -165 CAGCAGATTCGGCTCCATAAAAACCACAACAATAAAC 62 13 1 GCCTAACCAC 0.74299 -72 ATTACCATTATACACCCTGAGACCCCCGGCAATGGTC 66 117 0 TCCTAACCCC 0.952647 -184 * * * * * * **** Masking position 6 Map Score: 20.174 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 783 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 CAGTGACTGGATTTATAATTTTCGCGAGGTTG 6 14 1 ATTTATATTT 0.710535 -287 CTGGAGGAGTATTTATATGTTTATATGTTATG 6 192 0 ATTTATATTT 0.710535 -109 ATATAAATCTTTTTAAAAAAGG 7 238 0 ATATAAATTT 0.908835 -12 AAACGTATTTACTTAAATTTTTTTCCGGTTCA 16 74 0 ACTTAAATTT 0.582488 -57 TATTCTACTAATATATAAGTTTTCTTGCACTG 21 196 0 ATATATATTT 0.764463 -105 ATTATGTGGAACTTAAACATTTAAGATGAGAA 22 16 1 ACTTAAATTT 0.582488 -95 TTCCTGAAAAATAAAAAAATTGAAA 24 4 0 ATAAAAATTG 0.479868 -136 ACAGGTCCATATATAAATCTTTCTTAATGGAC 24 106 0 ATATAAATTT 0.908835 -34 CGTTATATTTATAAAAATTTTTAATTTCTTGA 25 86 1 ATAAAAATTT 0.76446 -215 GTACATGAGTATATATATCTTTCACCGGCATA 26 56 1 ATATATATTT 0.764452 -167 TCATTCCATTAAAAGCTTTTCTCCAGGGT 30 41 0 ATTAAAATTT 0.710535 -19 TTAACCACACATATAAAATTTTCGGAAATTGT 34 65 1 ATATAAATTT 0.908835 -107 ATTTATGATAATATAAAGTTTTCTATATAAAT 39 84 0 ATATAAATTT 0.908835 -64 TTAAAGAACTATTTAAAACTTTACTGTACATA 48 42 0 ATTTAAATTT 0.882898 -86 GTGGGCTACAATTAAAAGCTTTTACACACAGT 51 79 0 ATTAAAATTT 0.710535 -64 CCACACACCTATATATATATTTTTCTATTTGA 54 11 1 ATATATATTT 0.763885 -61 CTATTTAAATTTTTTGGTAAATGG 55 94 0 ATTTAAATTT 0.882898 -14 GCCTAATCTTATTTAAAATTTTATAAAGGGGC 63 47 0 ATTTAAATTT 0.882898 -102 TACTACCTTTATAAAAATTTTTCCTATACCTG 65 69 0 ATAAAAATTT 0.76446 -83 CATTCATATAATATAAAGGTTGAAGTGATTAT 66 29 1 ATATAAATTG 0.739161 -272 TGGAATCTATATATAAACTTTGTGCATTGTCG 66 219 0 ATATAAATTG 0.739161 -82 ******* *** Masking position 10 Map Score: 18.9199 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 9 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 TCCGGTTCAGTGTGATGGGGTGAAGGGT 5 6 1 TTATGTGTGG 0.770176 -94 CATCCTATGTTTATATGTTATGGCTCTGATTCG 6 93 0 TTTTGTTTGG 0.930656 -208 CATCCTATGTTTATATGTTATGGCTCTGTTTGC 6 137 0 TTTTGTTTGG 0.930656 -164 ATTTATATGTTTATATGTTATGGCTCTGTTTGC 6 181 0 TTTTGTTTGG 0.930656 -120 GGGTTGATCTTTAATGTGCTGGATCCGGGAAT 16 10 1 TTATGTGTGG 0.770176 -121 CAATCCATGATTCTGTGATGAGGCCCCTGTGGG 17 110 0 TTTTGATAGG 0.605069 -191 ATTTAATTATGTGGAACTTAAACA 22 2 1 TTATTATTGG 0.541333 -109 TTTCAATTTTTTTATTTTTCAGGAAATACGTGA 24 11 1 TTATTTTAGG 0.87041 -129 GGTGAGTTATTTGTTTGTAAAGG 26 210 1 TTTTGTAAGG 0.635862 -13 AATTAATTAATTTTTTGTTTTGG 28 1 0 TTTTGTTTGG 0.930656 -41 CCAACCATTTTTTTATTTTCAGGGAC 29 15 1 TTTTTTTAGG 0.87041 -16 ATATGTATCCTTATATTTTCAGGTTATCTATTA 32 99 0 TTTTTTTAGG 0.87041 -34 GGATCGATGATTAATTTTACAGGAGGAGTATA 52 10 0 TTATTTAAGG 0.520208 -100 CTATTTAAATTTTTTGGTAAATGGTTA 55 91 0 TTATTTTTGG 0.892855 -17 AATTCATCTTTTCTGTTTTAAGGATAAAAAAGT 59 11 0 TTTTTTTAGG 0.87041 -290 ATACGGGAAGTTTATTGTTGTGGTTTTTATGGA 62 26 0 TTATGTTTGG 0.930656 -59 TAATGATGTTTTTAATTTTATGGAATCTATATA 66 238 0 TTATTTTTGG 0.892855 -63 AATATTGGACTTCAGTTTTTAGGGTGACATC 67 114 1 TTATTTTAGG 0.87041 -21 ** * **** *** Masking position 6 Map Score: 18.1238 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 68 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TCCCATTTCTGGAAAGACCAGGTAGATAAT 1 56 0 GGAAAGACCA 0.460923 -82 CTCATATGGGATGTCCTGATATCTGA 3 8 1 GGGATGTCCT 0.852485 -19 CAACTGCTCTGGGATCTCCAATGTTACCCA 4 106 0 GGGATCTCCA 0.908927 -37 CTCTGTTTGCGGGAACTGCCTCATCCTATG 6 117 0 GGGAACTGCC 0.813348 -184 CTCTGTTTGCGGGAACTGCCTCATCCTATG 6 161 0 GGGAACTGCC 0.813348 -140 GGTTCATGCAGGGATCACCCCCCTTGATTC 17 231 1 GGGATCACCC 0.973515 -70 GGTCCGCCCTGGGATCCCCCCATCCATGAG 21 141 0 GGGATCCCCC 0.947663 -160 CTCTGGTGAAGGGAACACCCTGATAATTTA 31 125 1 GGGAACACCC 0.923226 -105 TTCAACAAGGAGGATGACCCTGTCCCCGGC 43 20 0 AGGATGACCC 0.917885 -38 AATGCTCCACGGAATGCCCCAACAATGACA 45 21 0 GGAATGCCCC 0.845371 -36 TCTTTCCCACAGGATCTCCAGTGATAGGCT 59 178 1 AGGATCTCCA 0.727861 -123 GTGGTCCTACAGGATGACCCCCTCATGATT 59 232 1 AGGATGACCC 0.917885 -69 AATAGCCATCAGAATGTCCCCTGGAAACTG 61 36 1 AGAATGTCCC 0.772423 -184 GGGATATCAAGGAATCTCCTGGAAATATAA 61 66 1 GGAATCTCCT 0.589055 -154 CCTGAGCGGAGGGATGACCATTGCCGGGGG 66 102 1 GGGATGACCA 0.908167 -199 ATAAATGGTGGGGATGTGCCAGATAGGCGG 66 160 0 GGGATGTGCC 0.937665 -141 GGTTGTGAGGAGAATGAGCCGCGGTTTGTT 67 35 0 AGAATGAGCC 0.486816 -100 ********** Masking position 4 Map Score: 14.1075 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 651 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 GCCGGTCCCGAATCAGAGCCATAACATATAAA 6 85 1 AACAGACCAT 0.921081 -216 CAGTTCCCGCAAACAGAGCCATAACATATAAA 6 129 1 AACAGACCAT 0.921081 -172 CAGTTCCCGCAAACAGAGCCATAACATATAAA 6 173 1 AACAGACCAT 0.921081 -128 TGCTGAATGTAAGCACATCCAGGGATTCAGCC 15 151 0 AACACACCAG 0.817654 -37 TGAGCATCACAACCATGCTGAATGTA 15 172 0 CACACACCAT 0.980629 -16 CATCAGGCCTCAGCACACCCAGATTCCCGGAT 16 33 0 CACACACCAG 0.921965 -98 CTTCAAGAGTTAACACAACCCTTTATTACCTT 16 108 0 TACACACCCT 0.732893 -23 TCCATCAAGGAACCACAGCCCTCTGAACACAA 17 41 1 AACACACCCT 0.929659 -260 ACTTTACGTGCACCACATGCATCTCTCATGGA 21 117 1 CACACAGCAT 0.900939 -184 GGCCTATGTAAATCAGATACCTGAGATTCTCC 31 25 0 AACAGAACCT 0.571941 -205 CAGAATACAGCATCAAAACCCTGGAATCCCAG 40 87 0 CACAAACCCT 0.732893 -57 ACCCCTCCACCACCTCACCCCTACTGATTTTT 47 11 1 CACTCACCCT 0.736631 -46 TCCAGCAAAACAACACAAACATCAACTCACCC 49 92 0 CACACAACAT 0.893898 -44 ATGGCACGGTCATCAGATGCATTGCAGCCCTC 50 90 1 CACAGAGCAT 0.846736 -55 TGATTTATATCAACACACACATAGTATTATGC 59 257 1 CACACAACAT 0.893898 -44 AGGCCTTATCCTTCAGATCCATATC 64 4 0 CTCAGACCAT 0.724613 -38 GGCTCATTCTCCTCACAACCATCAGCTGCTCC 67 45 1 CCCACACCAT 0.865228 -90 ** **** **** Masking position 7 Map Score: 12.3274 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 330 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 GCGGGAACTGCCTCATCCTATGTTTATATGTTAT 6 105 0 CCCACCTTTT 0.983788 -196 GCGGGAACTGCCTCATCCTATGTTTATATGTTAT 6 149 0 CCCACCTTTT 0.983788 -152 ATTCCCACCCCATCATGTCCTGGAGGTTCCT 7 8 1 CCCACATTCT 0.969066 -242 CATTTTCATTCCACATCATGTCTT 11 1 0 CCCACATTTT 0.951392 -55 TTCTTTACCTCAGCATTTGCTCTTTATTGAT 12 20 0 CCCACATTCT 0.969066 -21 CCGCCACCTGTTTTACTTATAATC 27 26 0 CCCCCCTTTT 0.971367 -14 ATCATAACATCCCCCGCCGGTGCTGCATGGTGGA 49 20 0 CCCCCCGTCT 0.903114 -116 ACAAACATCAACTCACCCTATACTCAATACTCCT 49 76 0 ACCACCTTCT 0.874514 -60 CCCATCACCCTGTACTCAATACTCCA 49 120 0 CACACCTTCT 0.874514 -16 CCTCTTCACCTCACTCTCTACTCATAACCTTT 53 9 1 CCCATCTTCT 0.874514 -131 TGGTAATAATCCTCCGCCTATCTGGCACATCCCC 66 147 1 CCCCCCTTTG 0.853455 -154 TCTGGCACATCCCCACCATTTATTAAAAAGGTCC 66 167 1 CCCACATTTT 0.951392 -134 ** ** *** * ** Masking position 11 Map Score: 9.92235 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 132 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 TCACCAGTAATCATCTATAT 8 15 0 TCACCAGTAA 0.936673 -10 CTCATCACCATTAACACCGGAATG 10 28 0 TCACCATTAA 0.931757 -14 TTTCACCAGAAAGGTGGTAAA 33 3 1 TCACCAGAAA 0.959564 -19 ATTGTTTCACCTTCAAAGTCACTGTA 35 101 0 TCACCTTCAA 0.699112 -16 GGCTCGAAAATCACCATCAAACT 36 4 0 TCACCATCAA 0.936464 -48 TACATGAAAATCACAATAAAATCCAATTTT 37 227 0 TCACAATAAA 0.656788 -74 GCGATGTTGCTCACCAGTAAGGCCGGCGCC 40 36 1 TCACCAGTAA 0.936673 -108 TGAATCACCAGAAATAAAGAGTTG 46 17 0 TCACCAGAAA 0.959564 -14 TGATAAAGTTTCACCATAAAAAGGACACTG 53 55 1 TCACCATAAA 0.956339 -85 GATGTCACCCTAAAAACTGAAGTC 67 121 0 TCACCCTAAA 0.836538 -14 ********** Masking position 3 Map Score: 8.91314 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 72 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AAAATATTCTCCTTAAAATATATAATTATC 1 32 1 CCTTAAAATA 0.805663 -106 AAATGGGAAACCTTAAATTACAGCATGGAA 1 78 1 CCTTAAATTA 0.784799 -60 ATCATTACAGCCTTAAAATATTATCCCATG 2 53 0 CCTTAAAATA 0.805663 -73 CTATGAAAATCCTTAAAATTTATTACTAAA 7 92 1 CCTTAAAATT 0.859486 -158 CCCTGAGAACCCTTAAATTTGTGTTCAGAG 17 61 0 CCTTAAATTT 0.843276 -240 CTTGATTCCGGGTTAAATTTATTACCCCTC 17 253 1 GGTTAAATTT 0.873054 -48 CTATCCTAGATTAAAATTTAGCCGGATT 21 283 0 GATTAAAATT 0.641346 -18 TTATATGTGTGGTTAAAATTTTTATTATTT 34 51 0 GGTTAAAATT 0.886598 -121 TTTTATCAAAGCTTAAATTAGCATCCCTTC 35 61 1 GCTTAAATTA 0.844097 -56 ACGGTTAAATGATTAAAATTGGATTTTATT 37 213 1 GATTAAAATT 0.641346 -88 GGTTAAATTTCTCTGAGTCG 40 1 1 GGTTAAATTT 0.873054 -143 ATGACTTTGAGGTTAAATTTCTGGGATTCC 40 67 1 GGTTAAATTT 0.873054 -77 CATTTTATCTGCTTAAATTTCTGTGGGCTA 51 103 0 GCTTAAATTT 0.888745 -40 TTTGGTAAATGGTTAAAATAAAGAACAAAA 55 76 0 GGTTAAAATA 0.841242 -32 TTTGAAATACGTTAAAATACCTGTAGATG 57 10 1 CGTTAAAATA 0.781139 -226 ********** Masking position 5 Map Score: 9.86256 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 22 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 TATTGAGGAGGCAGAGGACCTCCTGGACGCA 15 72 1 GCGAGGACCT 0.683462 -116 GGGATTCAGCCGAGGGATCCGACGTCCTCTC 15 131 0 CGGGGATCCG 0.648768 -57 TGTGCTGGATCCGGGAATCTGGGTGTGCTGA 16 25 1 CCGGAATCTG 0.670128 -106 TGATGTTGATCCCGTGAACCGGAAAAAAATT 16 60 1 CCGTGAACCG 0.915558 -71 CTTTATATCCCCTGAGAACCCTTAAATTTGT 17 69 0 CCGAGAACCC 0.887072 -232 AAAAACCTGGGCCGGGATCCTGTCGAAAACT 17 149 0 GCGGGATCCT 0.900463 -152 CAGGGTCCGCCCTGGGATCCCCCCATCCATG 21 143 0 CCGGGATCCC 0.964261 -158 CATTATAACTGCGGGGGTCCTCAGCTGCCAT 24 51 1 GCGGGGTCCT 0.881181 -89 TGTTCATATCGCTGTGAACTCCATGTGAAAT 26 113 1 GCGTGAACTC 0.491992 -110 CCCCGGAAAACCTGAAAACCGGAATATACAC 31 55 1 CCGAAAACCG 0.699071 -175 AGGGCATTTTGCTGAAAACCTCTGGTGAAGG 31 106 1 GCGAAAACCT 0.401407 -124 AAATAATCCTCCTGTGATCCTGTGAGAATAA 32 11 1 CCGTGATCCT 0.893905 -122 GCTTCAATCCAGTGATCCTAACTGGAAGG 37 9 1 CCGTGATCCT 0.893905 -292 GCATCAAAACCCTGGAATCCCAGAAATTTAA 40 79 0 CCGGAATCCC 0.872923 -65 TTACCTGGCACCCGGGAACCCGGGTTATAAC 51 25 1 CCGGGAACCC 0.96093 -118 CTTGATTCCCCGTGGTCTGGCATTTTATC 51 124 0 CCGTGGTCTG 0.712852 -19 CAGAATGGCTCCAGAGGACCGCCCCAGACAT 59 124 1 CCGAGGACCG 0.882073 -177 CAGATATAAGGCTGTGGTCCTACAGGATGAC 59 219 1 GCGTGGTCCT 0.737854 -82 GCCCTGGAGACTTAAAGGGCTTC 61 3 1 CCGGAGACTT 0.518165 -217 CAGAATGTCCCCTGGAAACTGGGGATATCAA 61 45 1 CCGGAAACTG 0.649352 -175 ATGACCATTGCCGGGGGTCTCAGGGTGTATA 66 115 1 CCGGGGTCTC 0.8492 -186 ** ******** Masking position 4 Map Score: 16.0914 Number of sites scoring better than the average of aligned sites = 1145 Number in coding regions = 1082 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 TAAGGCTGTAATGATAAAAATAGTTTGGAAG 2 68 1 ATATAAAAAT 0.7463 -58 AAAAGACCTCTTAATAAAATTATGGCCTTTT 7 193 0 TTATAAAATT 0.825148 -57 GGAGATGATAAAATTCCAGCTGCAG 14 5 1 ATATAAAATT 0.626559 -29 TGCCGTTATATTTATAAAAATTTTTAATTTC 25 83 1 TTATAAAAAT 0.892171 -218 TATTCTTGCTCTAATAAAAATTAAGTAATAA 25 206 0 CTATAAAAAT 0.82224 -95 GGTATTAAAAATAATAAAAATTTTAACCACA 34 43 1 ATATAAAAAT 0.7463 -129 AAGTGGTGGGTTAATAAAAATGCAGGGAATG 35 32 0 TTATAAAAAT 0.892172 -85 AATTTAAGCTTTGATAAAAGTGGTGGGTTAA 35 49 0 TTATAAAAGT 0.633099 -68 TATATAAATGTTCCTAAAATTTAAAAGGCAT 37 272 0 TTCTAAAATT 0.66614 -29 TGGGGATACTCTTATAAAAATTGAATTTAAT 57 38 1 CTATAAAAAT 0.82224 -198 TGTGGTGCAACTCATAAAATTAGATGAATCT 57 125 1 CTATAAAATT 0.72514 -111 AACTGGCCCCTTTATAAAATTTTAAATAAGA 63 42 1 TTATAAAATT 0.825148 -107 GTTTACTACCTTTATAAAAATTTTTCCTATA 65 73 0 TTATAAAAAT 0.892171 -79 CCGCGGTTTGTTGCTAAAAATACCTGATGAT 67 16 0 TTCTAAAAAT 0.777694 -119 TATGGGGCTATTGCTAAAAATAGTTGGTGAT 67 81 0 TTCTAAAAAT 0.777694 -54 ** ******** Masking position 6 Map Score: 9.93221 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 8 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 12 CTAACATCCCCTGTTTTAACATGTTT 1 122 0 ATCCCCTTTT 0.927595 -16 CATCATAAAAACCCCCAGCTTCCAAACTATT 2 86 0 ACCCCCACTT 0.885536 -40 CAACAGCGGGTTCCCCTATTTCAGATAGGAG 4 12 0 TTCCCCTTTT 0.643195 -131 GCTGCTGCGGCCCCCCTCCTAACAGATTTGT 4 73 0 CCCCCCTCTA 0.875569 -70 TTAGGTCTAACTCACCTTTTTTAAAAAGATT 7 224 1 CTCACCTTTT 0.830614 -26 TAAATCCCCTCTTTTCTGATTAAA 11 42 0 ATCCCCTTTT 0.927595 -14 TTTTTATTAACCCACCACTTTTATCAAAGCT 35 43 1 CCCACCATTT 0.731883 -74 AATTCCTCACCTGTTAGATTCCTCAT 38 15 0 CTCACCTTTA 0.768708 -16 TAATCATCGGATCCCCTATTTTATTACGATT 39 56 1 ATCCCCTTTT 0.927595 -92 TTATAAGAGTATCCCCATCTACAGGTATTTT 57 24 0 ATCCCCACTA 0.864573 -212 ATTCCTTGATATCCCCAGTTTCCAGGGGACA 61 50 0 ATCCCCATTT 0.896726 -170 TGGAAATATAATCCCCTTCTAACTCTGTAAA 61 85 1 ATCCCCTCTA 0.904024 -135 GAAAACACCACCTACTTATATATACCT 65 7 1 ACCACCTCTT 0.827691 -145 CTGGCACATCCCCACCATTTATTAAAAAGGT 66 168 1 CCCACCATTA 0.649136 -133 TGCTCCATCCATCACCAACTATTTTTAGCAA 67 71 1 ATCACCACTA 0.728748 -64 ******* *** Masking position 10 Map Score: 7.9408 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 133 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 13 ATAAACATATAAATACTCCTCCAGTGAAAG 6 200 1 AAATACTCCT 0.766267 -101 CCCCGTAAATAATCCTGAATGAGAAC 9 20 0 AAATAATCCT 0.945678 -16 CATTTATCATTAATAATCATTATTAATTTT 22 67 1 TAATAATCAT 0.744017 -44 AATGCAGATAAAATATTCATTAATTATGCA 25 141 1 AAATATTCAT 0.622396 -160 AAAAAGTCTTAAATAATCTTCATACCATAT 25 255 1 AAATAATCTT 0.729228 -46 AAATAATCCTCCTGTGATCC 32 1 1 AAATAATCCT 0.945678 -132 AAATATTAAAAAATAATCATCTATTATGAA 37 104 1 AAATAATCAT 0.92843 -197 ATATTATCATAAATAATCATGTTAATTATT 39 102 1 AAATAATCAT 0.92843 -46 CCTACTGATGAAATCATCATTTCCATGCAG 48 84 0 AAATCATCAT 0.818045 -44 CCTCCTGTAAAATTAATCATCGATCCAAGA 52 17 1 AATTAATCAT 0.600406 -93 TTTAAATCATCCTTCAAGTAAGT 56 25 0 AAATCATCCT 0.85782 -13 TGTATAATGGTAATAATCCTCCGCCTATCT 66 140 1 TAATAATCCT 0.795938 -161 ********** Masking position 2 Map Score: 6.02788 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 8 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 AGTTTGGAAGCTGGGGGTTTTTATGATGTCTT 2 89 1 CGGGGGTTTT 0.866568 -37 ATTCAACCTCCCTGAGGTCATTTCCTTCCATC 5 65 1 CTGAGGTCTT 0.818999 -35 AATCTTTTATCATGGGGTTGCTTATACTTTGG 6 254 0 CTGGGGTTCT 0.816012 -47 CCATCATGTCCTGGAGGTTCCTATGGAGTCAC 7 20 1 CGGAGGTTCT 0.945952 -230 TTACTAATATCTGGAGGTTTCTCTACAGAAAC 7 161 0 CGGAGGTTCT 0.945952 -89 TAAATGCGTGATGTTGATGTCCT 13 7 1 CTGATGTTAT 0.770371 -17 CGTCCTCTCCCCGGATGTTCTTTCTGACCTCC 15 108 0 CGGATGTTTT 0.733075 -80 TGTGCTGAGGCCTGATGTTGATCCCGTGAACC 16 48 1 CTGATGTTAT 0.770371 -83 CCTGTGGGTTCTGGAGGTCTTTATATCCCCTG 17 86 0 CGGAGGTCTT 0.866568 -215 CTGTCTTTCTCCTCAGGTTCATGCAGGGATCA 17 216 1 CTCAGGTTAT 0.615863 -85 GTACTGTTTTCATGAGGTCCATTAAGAAAGAT 24 90 1 CTGAGGTCAT 0.88806 -50 CATATCACATTCTGAGGTTCATCATATGGTGT 26 84 1 TTGAGGTTAT 0.535517 -139 CACAGGATCACAGGAGGATTATTT 32 3 0 CGGAGGATAT 0.715467 -130 AGGACTCATGGGGTTATTACGGCAGCCT 39 7 1 CTGGGGTTTT 0.818999 -141 TGTATTCTGACTTGAGGTTAATTGATGCCTGC 40 110 1 CTGAGGTTAT 0.956164 -34 ATTGATGCCTGCGGAGGTTTATAA 40 130 1 GGGAGGTTAT 0.710364 -14 GGAGTATATACGGGAAGTTTATTGTTGTGGTT 62 34 0 CGGAAGTTAT 0.655851 -51 * ******* ** Masking position 12 Map Score: 10.3925 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 277 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 AGCAGTTGAACCCCTCATAAAGGCT 4 128 1 CCCCTCATAA 0.759487 -15 GTAAACCCTTCACCCCATCACACTGAACCG 5 13 0 CACCCCATCA 0.971027 -87 AAGTATAAGCAACCCCATGATAAAAGATTC 6 257 1 AACCCCATGA 0.895388 -44 ATTCCCACCCCATCATGTCCTGGAG 7 6 1 CACCCCATCA 0.971027 -244 GCAGGGATCACCCCCCTTGATTCCGGGTTA 17 238 1 CCCCCCTTGA 0.854722 -63 GCCCTGGGATCCCCCCATCCATGAGAGATG 21 136 0 CCCCCCATCC 0.867312 -165 GATTACACCTCATCAGCGTCAGGAA 22 96 0 CACCTCATCA 0.946297 -15 TTTCTTAATGGACCTCATGAAAACAGTACT 24 89 0 GACCTCATGA 0.7909 -51 CTGCCGTAATAACCCCATGAGTCCT 39 6 0 AACCCCATGA 0.895388 -142 ATCACCTCATGGCTGGAACTGG 48 116 0 CACCTCATGG 0.844452 -12 ACAGGATGACCCCCTCATGATTTATATCAA 59 240 1 CCCCTCATGA 0.960544 -61 ********** Masking position 8 Map Score: 6.53515 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 173 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604