AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_mthe_reg_100.orf -o00910_mthe_100.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 Input sequences: #1 MTH106 137 tungsten formylmethanofuran dehydrogenase, subunit C homolog #2 MTH187 142 conserved protein #3 MTH189 99 unknown #4 MTH278 300 ferredoxin #5 MTH384 249 unknown #6 MTH387 24 conserved protein #7 MTH388 35 unknown #8 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #9 MTH394 55 unknown #10 MTH397 40 formate hydrogenlyase, subunit 7 #11 MTH399 23 polyferredoxin #12 MTH400 33 polyferredoxin #13 MTH405 130 polyferredoxin #14 MTH413 300 conserved protein #15 MTH644 145 conserved protein #16 MTH700 110 conserved protein #17 MTH702 27 acetyl-CoA synthetase related protein #18 MTH927 139 ferredoxin #19 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #20 MTH1120 132 nifH / minD related protein #21 MTH1133 21 polyferredoxin (MvhB) #22 MTH1136 171 methyl viologen-reducing hydrogenase, delta subunit #23 MTH1246 30 NADH dehydrogenase I, subunit N #24 MTH1251 147 conserved protein #25 MTH1468 35 ferredoxin #26 MTH1469 57 molybdenum transport ATP-binding protein homolog #27 MTH1470 44 molybdenum transport protein ModA related protein #28 MTH1471 56 O-antigen transporter homolog #29 MTH1472 30 O-antigen transporter homolog #30 MTH1475 56 unknown #31 MTH1476 127 tryptophan synthase, beta subunit homolog #32 MTH1481 142 isopropylmalate synthase #33 MTH1510 109 NH(3)-dependent NAD+ synthetase #34 MTH1560 107 nitrogenase NifH subunit #35 MTH1563 37 nitrogenase NifD subunit #36 MTH1567 235 catalytic subunit of nitrate reductase (flp) #37 MTH1570 74 glutamine synthetase #38 MTH1571 300 molybdopterin biosynthesis protein MoeB homolog #39 MTH1582 44 carbonic anhydrase #40 MTH1667 219 unknown #41 MTH1708 300 carbon monoxide dehydrogenase, alpha subunit #42 MTH1710 21 carbon monoxide dehydrogenase, alpha subunit #43 MTH1819 134 ferredoxin Motif number 1 AGCTGTTCAACAGCGGGTTCCCCTATTTCAGA 2 18 0 CAGCGGGCCC 0.975834 -125 CCCAGGGCTGCTGCGGCCCCCCTCCTAACAGA 2 78 0 CTGCGGCCCC 0.94751 -65 CGAGGTTGACCTGAGTGCTCCCATCTCCTATC 4 38 1 CTGAGTGCCC 0.935282 -263 TTTGCGGGAACTGCCTCATCCTATGTTTATAT 4 110 0 CTGCCTCCCT 0.769312 -191 TTTGCGGGAACTGCCTCATCCTATGTTTATAT 4 154 0 CTGCCTCCCT 0.769312 -147 CCATCATGTCCTGGAGGTTCCTATGGAGTCAC 5 20 1 CTGGAGGCCT 0.937629 -230 TTACTGATATCTGAAGGGTCCCTCTACAGAAG 5 123 0 CTGAAGGCCC 0.939285 -127 TTACTAATATCTGGAGGTTTCTCTACAGAAAC 5 161 0 CTGGAGGTCT 0.792852 -89 GGGGTGATCCCTGCATGAACCTGAGGAGAAAG 14 220 0 CTGCATGCCT 0.925048 -81 CCAGGCGGTGTCCCCTGTGTGGT 17 15 0 CAGGCGGTCC 0.856966 -13 TCCATTATAACTGCGGGGGTCCTCAGCTGCCA 18 49 1 CTGCGGGTCC 0.918555 -91 AATAAATTATCAGGGTGTTCCCTTCACCAGAG 19 125 0 CAGGGTGCCC 0.970719 -105 CCCCTTCCACCAGAAGGCTCCTATGAAAC 22 8 0 CAGAAGGCCT 0.844856 -164 GTTATTACGGCAGCCTCTTCCCCTTCAAGTGT 24 23 1 CAGCCTCCCC 0.887295 -125 CCGCCGGGGACAGGGTCATCCTCCTTGTTGAA 26 18 1 CAGGGTCCCT 0.839141 -40 CGTTTCTGGATGGCTCCGGGAGAAAAA 30 40 0 CTGGATGTCC 0.890562 -17 TTTTCGATTTCAGAATGGCTCCAGAGGACCGC 38 114 1 CAGAATGTCC 0.746694 -187 AAGCAGATGTCTGGGGCGGTCCTCTGGAGCCA 38 129 0 CTGGGGCTCC 0.821299 -172 TATCTGCTTGCAGCATGAGCCTATCACTGGAG 38 193 0 CAGCATGCCT 0.918372 -108 TGTGGTCCTACAGGATGACCCCCTCATGATTT 38 231 1 CAGGATGCCC 0.966817 -70 TAATAGCCATCAGAATGTCCCCTGGAAACTGG 40 35 1 CAGAATGCCC 0.920496 -185 ******* *** Masking position 3 Map Score: 29.2041 Number of sites scoring better than the average of aligned sites = 1297 Number in coding regions = 1228 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 CTGCTGCGGCCCCCCTCCTAACAGATTTGT 2 73 0 CCCCCTCCTA 0.86714 -70 TAAACCCTTCACCCCATCACACTGAACCGG 3 12 0 ACCCCATCAC 0.953906 -88 GACCTGAGTGCTCCCATCTCCTATCAAGGC 4 45 1 CTCCCATCTC 0.766604 -256 ATTCCCACCCCATCATGTCCTGGAGG 5 7 1 ACCCCATCAT 0.879935 -243 TTCTGATTAAATCCCTTCCATTTTCATTCC 9 23 0 ATCCCTTCCA 0.836179 -33 TAAATCCCCTCTTTTCTGATTAA 9 43 0 ATCCCCTCTT 0.538779 -13 TAAATTTATTACCCCTCCCCGGTAATAGAT 14 266 1 ACCCCTCCCC 0.956283 -35 AAATAACAGTCCCCCTCCACATACTGACCT 15 87 0 CCCCCTCCAC 0.956283 -59 TATCAGGGTGTTCCCTTCACCAGAGGTTTT 19 120 0 TTCCCTTCAC 0.886386 -110 TTAATACCACTCCCCTTCCACCAGAAGGCT 22 21 0 TCCCCTTCCA 0.908207 -151 GGCAGCCTCTTCCCCTTCAAGTGTTTAATC 24 31 1 TCCCCTTCAA 0.92335 -117 TTTATAGCTCCCTTCTCTTTAGTACCA 24 131 0 CTCCCTTCTC 0.865006 -17 ACCCCTCCACCACCTCACCC 30 1 1 ACCCCTCCAC 0.963811 -56 TATAAGAGTATCCCCATCTACAGGTATTTT 36 24 0 TCCCCATCTA 0.790759 -212 TTTCAGTCTTATCCCATCAAATTTCCTTAT 36 84 0 ATCCCATCAA 0.761082 -152 AGATAATAAAACCCCTTCCCTGAACCGAAC 38 81 1 ACCCCTTCCC 0.970726 -220 CTACAGGATGACCCCCTCATGATTTATATC 38 238 1 ACCCCCTCAT 0.858057 -63 GTTCTCCCTCCATAAATTAATTA 39 4 1 CTCCCTCCAT 0.709796 -41 GGAAATATAATCCCCTTCTAACTCTGTAAA 40 86 1 TCCCCTTCTA 0.880564 -134 TGTTTATATAACCCCCTCCCGCTGGTACTG 40 155 0 ACCCCCTCCC 0.933422 -65 ATCTGGCACATCCCCACCATTTATTAAAAA 41 166 1 TCCCCACCAT 0.747404 -135 ********** Masking position 5 Map Score: 22.9263 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 896 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 GGTAGATAATTATATATTTTAAGGAGAATATTTT 1 32 0 TATTTTTAGG 0.637811 -106 TAATTTAAGGTTTCCCATTTCTGGAAAGACCAGG 1 64 0 TTTATTTTGG 0.884704 -74 TCATCCTATGTTTATATGTTATGGCTCTGATTCG 4 93 0 TTTTGTTTGG 0.896888 -208 TCATCCTATGTTTATATGTTATGGCTCTGTTTGC 4 137 0 TTTTGTTTGG 0.896888 -164 TATTTATATGTTTATATGTTATGGCTCTGTTTGC 4 181 0 TTTTGTTTGG 0.896888 -120 GTTCCAGTTGTTCCTTTTTTCTGGCCTCCTAAAC 15 42 1 TTCTTTTTGG 0.941621 -104 TTTCAATTTTTTTATTTTTCAGGAAATACGTGA 18 10 1 TTTTTTTAGG 0.960958 -130 GATGTGTATATTCCGGTTTTCAGGTTTTCCGGGG 19 55 0 TTCTTTTAGG 0.935753 -175 TATATGTATCCTTATATTTTCAGGTTATCTATTA 20 99 0 CTTTTTTAGG 0.887063 -34 ATCCGTCAACTCTTTATTTCTGGTGATTCA 29 10 1 CTCATTTTGG 0.591669 -21 ACTGTTCAGTTTTTGCTTTTTTGTTCTTTATTTT 34 58 1 TTTTTTTTGT 0.717559 -50 CTATTTAAATTTTTTGGTAAATGGTTA 34 91 0 TTTTTTTTGG 0.964611 -17 CCCATCAAATTTCCTTATTTAAGGAATATCCTTA 36 68 0 TTCATTTAGG 0.803932 -168 GAATTCATCTTTTCTGTTTTAAGGATAAAAAAGT 38 11 0 TTTTTTTAGG 0.960958 -290 AAACGTGATTTTTGTTTTTTCAGAAGAATTCATC 38 36 0 TTTTTTTAGA 0.696431 -265 ACCGAACTGTTTTTCGATTTCAGAATGGCTCCAG 38 104 1 TTTATTTAGA 0.392406 -197 GACACAGACATTCCGTTTTTCTGTTTATATAACC 40 172 0 TTCTTTTTGT 0.600538 -48 ATAATGATGTTTTTAATTTTATGGAATCTATATA 41 238 0 TTTTTTTTGG 0.964611 -63 TAATATTGGACTTCAGTTTTTAGGGTGACATC 43 113 1 CTTTTTTAGG 0.887063 -22 *** **** *** Masking position 9 Map Score: 18.4155 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 77 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 GTTAGGAGGGGGGCCGCAGCAGCCCTGGGTAAC 2 81 1 GGGCCCGCGC 0.861815 -62 GTTATGGCTCTGTTTGCGGGAACTGCCTCATCC 4 121 0 TGTTTCGGAC 0.825429 -180 GTTATGGCTCTGTTTGCGGGAACTGCCTCATCC 4 165 0 TGTTTCGGAC 0.825429 -136 GGGTTTTGCTGCAGCTGGAATTTTA 12 19 0 GTTTTCGCGC 0.841377 -15 ATTTTTTTCCGGTTCACGGGATCAACATCAGGC 13 57 0 GGTTCCGGTC 0.885933 -74 CAAATTTAAGGGTTCTCAGGGGATATAAAGACC 14 70 1 GGTTCCGGGA 0.959114 -231 CCGGCCCAGGTTTTTACAGGCGCATATCTGTAT 14 165 1 TTTTTCGGGC 0.81275 -136 TAACTGCGGGGGTCCTCAGCTGCCATGTAAAAC 18 56 1 GGTCCCGCGC 0.980072 -84 CCGGTTTTCAGGTTTTCCGGGGCCTATGTAAAT 19 44 0 GGTTTCGGGC 0.981404 -186 CTTCACCAGAGGTTTTCAGCAAAATGCCCTGTC 19 103 0 GGTTTCGCAA 0.555985 -127 GTTTCATAGGAGCCTTCTGGTGG 22 1 1 GTTTCTGGGC 0.553513 -171 AGGATGACCCTGTCCCCGGCGGATACATC 26 7 0 TGTCCCGCGA 0.801784 -51 TACTGATTTTTTTCTCCCGGAGCCATCCAGAAA 30 32 1 TTTCTCGGGC 0.80958 -25 TTATAACCCGGGTTCCCGGGTGCCAGGTAATTT 32 22 0 GGTTCCGGGC 0.990847 -121 TGTCTGGGGCGGTCCTCTGGAGCCATTCTGAAA 38 121 0 GGTCCCGGGC 0.99031 -180 GCCATCAGAATGTCCCCTGGAAACTGGGGATAT 40 40 1 TGTCCCGGAA 0.672808 -180 ***** * ** ** Masking position 9 Map Score: 15.6754 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 619 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 GAGCCATAACATATAAACATAGGATGAGGCAG 4 100 1 ATATAAATAG 0.830549 -201 GAGCCATAACATATAAACATAGGATGAGGCAG 4 144 1 ATATAAATAG 0.830549 -157 GAGCCATAACATATAAACATATAAATACTCCT 4 188 1 ATATAAATAT 0.752592 -113 ATATAAATCTTTTTAAAAAAGG 5 238 0 ATATAAATTT 0.933672 -12 GATGGTCCACATATTAAAGATGGGTGAAGAG 15 125 1 ATATTAAATG 0.326359 -21 TTCCTGAAAAATAAAAAAATTGAAA 18 4 0 ATAAAAATTG 0.631774 -136 ACAGGTCCATATATAAATCTTTCTTAATGGAC 18 106 0 ATATAAATTT 0.933672 -34 TTAACCACACATATAAAATTTTCGGAAATTGT 22 65 1 ATATAAATTT 0.933672 -107 ATTTATGATAATATAAAGTTTTCTATATAAAT 24 84 0 ATATAAATTT 0.933672 -64 TTAAAGAACTATTTAAAACTTTACTGTACATA 31 42 0 ATTTAAATTT 0.665964 -86 AGCATCACTGATATAAGTTTTTCTACCTCTTT 33 49 1 ATATAAGTTT 0.612238 -61 CTATTTAAATTTTTTGGTAAATGG 34 94 0 ATTTAAATTT 0.665964 -14 GGGGATACTCTTATAAAAATTGAATTTAATAA 36 39 1 TTATAAATTG 0.631774 -197 GTGTGTGTTGATATAAATCATGAGGGGGTCAT 38 245 0 ATATAAAATG 0.762523 -56 CCTTTATATTATATGAATGTTTGATATAGTGA 41 16 0 ATATGAATTT 0.640955 -285 CATTCATATAATATAAAGGTTGAAGTGATTAT 41 29 1 ATATAAATTG 0.957754 -272 TGGAATCTATATATAAACTTTGTGCATTGTCG 41 219 0 ATATAAATTG 0.957754 -82 CAATAGCCCCATATTAATATTGGACTTCAGTT 43 99 1 ATATTAATTG 0.773789 -36 ******* *** Masking position 2 Map Score: 12.8469 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 14 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 ACAAATCTGTTAGGAGGGGGGCCGCAGCAG 2 73 1 TAGGAGGGGG 0.775607 -70 TCCGGTTCAGTGTGATGGGGTGAAGGGTTT 3 11 1 TGTGATGGGG 0.758329 -89 CATATAAACATAGGATGAGGCAGTTCCCGC 4 109 1 TAGGATGAGG 0.931423 -192 CATATAAACATAGGATGAGGCAGTTCCCGC 4 153 1 TAGGATGAGG 0.931423 -148 ATAAAGAGCAAATGCTGAGGTAAAGAA 10 24 1 AATGCTGAGG 0.879484 -17 GGAATCTGGGTGTGCTGAGGCCTGATGTTG 13 38 1 TGTGCTGAGG 0.952386 -93 TTGTGTTCAGAGGGCTGTGGTTCCTTGATG 14 43 0 AGGGCTGTGG 0.875064 -258 TCCATGATTCTGTGATGAGGCCCCTGTGGG 14 110 0 TGTGATGAGG 0.900537 -191 CGCATATCTGTATGCAGAGGGTTTGAATTC 14 185 1 TATGCAGAGG 0.778549 -116 TCCAGGTCAGTATGTGGAGGGGGACTGTTA 15 84 1 TATGTGGAGG 0.537435 -62 TTCTGGTGGAAGGGGAGTGGTATTAAAAAT 22 25 1 AGGGGAGTGG 0.34612 -147 AAAAATCAGTAGGGGTGAGGTGGTGGAGGG 30 13 0 AGGGGTGAGG 0.869196 -44 AAGCAGATATAAGGCTGTGGTCCTACAGGA 38 216 1 AAGGCTGTGG 0.832257 -85 TATCGCACCCTGAGCGGAGGGATGACCATT 41 94 1 TGAGCGGAGG 0.753042 -207 ATGTGCCAGATAGGCGGAGGATTATTACCA 41 147 0 TAGGCGGAGG 0.956585 -154 ********** Masking position 4 Map Score: 9.51111 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 509 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TTTTAAGGAGAATATTTTATCATTAAATGAGAATT 1 15 0 AATTTTATTA 0.631166 -123 CCTGTTTTAACATGTTTTTTAATGAACAATTTTCC 1 104 0 CATTTTATGA 0.892074 -34 TCAGATCATGAATCTTTTATCATGGGGTTGCTTAT 4 261 0 AATTTTATGG 0.965068 -40 AAAAATTAATAATGATTATTAATGATAAATGTCTC 16 63 0 AATTTTATGA 0.959758 -48 TCCATATATAAATCTTTCTTAATGGACCTCATGAA 18 98 0 AATTTTATGG 0.965068 -42 TCAGAATTTAAATAATTAATCAAGAATAATATTAT 19 173 0 AATTTTAAGA 0.734213 -57 TGTCCAAGACAATATTTATTAATGGTTACCGAGAT 20 55 0 AATTTTATGG 0.965068 -78 TGGTAAGTATAAAGGTTACTTATGAAACAATTTCC 22 88 0 AAATTTATGA 0.734213 -84 CAATAATTAACATGATTATTTATGATAATATAAAG 24 98 0 CATTTTATGA 0.892074 -50 GACAATTATTAATGATTTATAATGATGTTTTTAAT 41 255 0 AATTTTATGA 0.959758 -46 TGTTGCTAAAAATACCTGATGATGGATC 43 4 0 AATCTTATGG 0.825867 -131 TATTGCTAAAAATAGTTGGTGATGGATGGAGCAGC 43 69 0 AATTTTATGG 0.965068 -66 *** ** * **** Masking position 12 Map Score: 9.84177 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 10 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 AAACATGTTAAAACAGGGGATGTTAG 1 122 1 AAACAGGGGA 0.979717 -16 CTCCTATCTGAAATAGGGGAACCCGCTGTT 2 12 1 AAATAGGGGA 0.975609 -131 GCCCTGGGTAACATTGGAGATCCCAGAGCA 2 102 1 ACATTGGAGA 0.763556 -41 TTTAATCAGAAAAGAGGGGATTTA 9 42 1 AAAGAGGGGA 0.94742 -14 TACTACCACACAGGGGACACCGCCTGG 17 8 1 ACACAGGGGA 0.964729 -20 AATCGTAATAAAATAGGGGATCCGATGATT 24 57 0 AAATAGGGGA 0.975609 -91 ACGTTTCTTTAAATTGGAGATAATAAAACC 38 64 1 AAATTGGAGA 0.850809 -237 TGTCCCCTGGAAACTGGGGATATCAAGGAA 40 50 1 AAACTGGGGA 0.967855 -170 ********** Masking position 3 Map Score: 8.28394 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 48 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ACTCAGGTCAACCTCGCGAAAATTATAAATCC 4 22 0 ACCTCGAAAA 0.920042 -279 ATATAAATACTCCTCCAGTGAAAGATTAGGAA 4 206 1 TCCTCGTGAA 0.941089 -95 AAAAAAAAGTTTCTGTAGAGAAACCTCCAGAT 5 153 1 TTCTGGAGAA 0.702274 -97 AATTTAAGGGTTCTCAGGGGATATAAAGACCT 14 72 1 TTCTCGGGAT 0.502917 -229 TGGGCCGGGATCCTGTCGAAAACTGGCCTTCA 14 141 0 TCCTGGAAAA 0.891989 -160 CCCTGCATGAACCTGAGGAGAAAGACAGCGAA 14 212 0 ACCTGGAGAA 0.878983 -89 TTCTTAATGGACCTCATGAAAACAGTACTGTT 18 86 0 ACCTCGAAAA 0.920042 -54 TTTGCTGAAAACCTCTGGTGAAGGGAACACCC 19 113 1 ACCTCGTGAA 0.91542 -117 AAATAATCCTCCTGTGATCCTGTGAGAA 20 7 1 TCCTCGTGAT 0.775469 -126 TATACTCCTCCTGTAAAATTAATCATC 33 6 1 TCCTCGTAAA 0.925187 -104 TCCCATTTTCTTCTCATGAAAACTGTTCAGTT 34 37 1 TTCTCGAAAA 0.768066 -71 TCACTGGAGATCCTGTGGGAAAGATTCTTCAG 38 170 0 TCCTGGGAAA 0.872024 -131 ATATCAAGGAATCTCCTGGAAATATAATCCCC 40 69 1 ATCTCGGAAA 0.73262 -151 ***** ***** Masking position 11 Map Score: 7.13061 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 227 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 ATCTGAAATAGGGGAACCCGCTGTTGAACA 2 17 1 GGGGAACCCG 0.872565 -126 GCTCTGTTTGCGGGAACTGCCTCATCCTAT 4 118 0 CGGGAACTGC 0.880347 -183 GCTCTGTTTGCGGGAACTGCCTCATCCTAT 4 162 0 CGGGAACTGC 0.880347 -139 ATTATATTCACAGAAACCGGTAAGTGGATG 5 51 0 CAGAAACCGG 0.897105 -199 CTTTAATGTGCTGGATCCGGGAATCTGGGT 13 19 1 CTGGATCCGG 0.909541 -112 ATGTTGATCCCGTGAACCGGAAAAAAATTT 13 62 1 CGTGAACCGG 0.951301 -69 CAGTTTTCGACAGGATCCCGGCCCAGGTTT 14 148 1 CAGGATCCCG 0.588382 -153 GTGGGTTTTTCAGAAACCGGGTTC 15 5 0 CAGAAACCGG 0.897105 -141 TAATAAAATAGGGGATCCGATGATTAAACA 24 52 0 GGGGATCCGA 0.775508 -96 CATCCTCCTTGTTGAACCCGACGATGTTGT 26 34 1 GTTGAACCCG 0.535236 -24 CACCTCATGGCTGGAACTGGTCCCTACTGA 31 106 0 CTGGAACTGG 0.897104 -22 ACCTGGCACCCGGGAACCCGGGTTATAACT 32 27 1 CGGGAACCCG 0.733478 -116 CACAATATAAGGGAAACCGAAGATTAGTAA 41 60 0 GGGAAACCGA 0.684603 -241 ********** Masking position 5 Map Score: 8.59316 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 418 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 11 ATAAACATATAAATACTCCTCCAGTGAAAG 4 200 1 AAATACTCCT 0.845199 -101 CCCCGTAAATAATCCTGAATGAGAAC 7 20 0 AAATAATCCT 0.958963 -16 CATTTATCATTAATAATCATTATTAATTTT 16 67 1 TAATAATCAT 0.789855 -44 AAATAATCCTCCTGTGATCC 20 1 1 AAATAATCCT 0.958963 -132 ATATTATCATAAATAATCATGTTAATTATT 24 102 1 AAATAATCAT 0.922445 -46 CCTACTGATGAAATCATCATTTCCATGCAG 31 84 0 AAATCATCAT 0.853241 -44 CCTCCTGTAAAATTAATCATCGATCCAAGA 33 17 1 AATTAATCAT 0.652175 -93 TTTAAATCATCCTTCAAGTAAGT 35 25 0 AAATCATCCT 0.919502 -13 TGTATAATGGTAATAATCCTCCGCCTATCT 41 140 1 TAATAATCCT 0.880733 -161 ********** Masking position 4 Map Score: 6.07036 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 14 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 12 GAGGTTGAATGCACACTGAAGGTCCGGCCAT 3 44 0 GACACTGAAG 0.927023 -56 TCCTGAATGAGAACATGGAAGCC 7 3 0 GACATGGAAG 0.972664 -33 GATGTGGAATGAAAATGGAAGGGATTTAATC 9 18 1 GAAATGGAAG 0.845721 -38 CCCGGATCCAGCACATTAAAGATCAACCC 13 9 0 GACATTAAAG 0.921842 -122 GGAACAACTGGAACATTGAAGGTGGGTTTTT 15 25 0 GACATTGAAG 0.957325 -121 ATATTGTCTTGGACAGCAAAGAGTTAATAGA 20 75 1 GACAGCAAAG 0.921558 -58 GTACATATATGTACATCAAAGGGAATGGTTA 31 18 0 GACATCAAAG 0.934397 -110 GTACATATATGTACAGTAAAGTTTTAAATAG 31 35 1 GACAGTAAAG 0.906791 -93 AAACAGTTCGGTTCAGGGAAGGGGTTTTATT 38 85 0 GTCAGGGAAG 0.788537 -216 TATTATGCAAGAACATGAAAGAGGGTTTGA 38 281 1 GACATGAAAG 0.949259 -20 ACAATATAAGGGAAACCGAAGATTAGTAATA 41 58 0 GAAACCGAAG 0.702674 -243 * ********* Masking position 5 Map Score: 8.51771 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 83 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 ATTGTTCATTAAAAAACATGTTAAAACAGG 1 109 1 AAAAAACATG 0.663852 -29 AGATGGAAGGAAATGACCTCAGGGAGGTTG 3 68 0 AAATGACCTC 0.806309 -32 TTAGACCTAAAAAAGACCTCTTAATAAAAT 5 204 0 AAAAGACCTC 0.921315 -46 TCAGGGGATATAAAGACCTCCAGAACCCAC 14 85 1 TAAAGACCTC 0.894796 -216 TATGCGCCTGTAAAAACCTGGGCCGGGATC 14 161 0 TAAAAACCTG 0.86664 -140 GTTTTCAGCAAAATGCCCTGTCAGTCCCGG 19 95 0 AAATGCCCTG 0.582788 -135 GGTTTTCTGTAAATTACCTGGCACCCGGGA 32 12 1 AAATTACCTG 0.805506 -131 GAAATACGTTAAAATACCTGTAGATGGGGA 36 14 1 AAAATACCTG 0.920942 -222 TTAATTTAACTAAATACCTGGATGTAAATC 36 215 1 TAAATACCTG 0.894312 -21 GCTGAACACATAAAGACATGGACCTTTTTA 41 190 0 TAAAGACATG 0.785867 -111 TCCATAAAATTAAAAACATCATTATAAATC 41 247 1 TAAAAACATC 0.423271 -54 TTTGTTGCTAAAAATACCTGATGATGGATC 43 11 0 AAAATACCTG 0.920942 -124 ********** Masking position 3 Map Score: 5.39244 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 70 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 CGGTCCCGAATCAGAGCCATAACATATAAA 4 87 1 TCAGAGCCAT 0.945365 -214 GTTCCCGCAAACAGAGCCATAACATATAAA 4 131 1 ACAGAGCCAT 0.967048 -170 GTTCCCGCAAACAGAGCCATAACATATAAA 4 175 1 ACAGAGCCAT 0.967048 -126 CCCCATGATAAAAGATTCATGATCTGAAGA 4 269 1 AAAGATTCAT 0.678731 -32 GGGCCTCATCACAGAATCATGGATTGAAGG 14 117 1 ACAGAATCAT 0.771852 -184 GTCTTTCTCCTCAGGTTCATGCAGGGATCA 14 218 1 TCAGGTTCAT 0.897539 -83 CGTATATTCCACAGGTCCATATATAAATCT 18 118 0 ACAGGTCCAT 0.95224 -22 TCCGCCGGGGACAGGGTCATCCTCCTTGTT 26 17 1 ACAGGGTCAT 0.959502 -41 CACCATTCAGTGTCATTGTTGGGGCA 28 7 1 TCAGTGTCAT 0.728028 -50 ACATATACAGTCAGATTCATCTAATTTTAT 36 138 0 TCAGATTCAT 0.889933 -98 CATTTATTAAAAAGGTCCATGTCTTTATGT 41 183 1 AAAGGTCCAT 0.754398 -118 ********** Masking position 3 Map Score: 8.54112 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 232 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 GATGGGGTGAAGGGTTTACCATGGCCGGACC 3 24 1 AGGGTTACCA 0.91061 -76 GGAACTATAAAGGGTTAACCCCAAAGTATAA 4 234 1 AGGGTTACCC 0.977975 -67 AGGTTCATGCAGGGATCACCCCCCTTGATTC 14 230 1 AGGGATACCC 0.99184 -71 CCTCTGGTGAAGGGAACACCCTGATAATTTA 19 124 1 AGGGAAACCC 0.956107 -106 GTTCAACAAGGAGGATGACCCTGTCCCCGGC 26 20 0 GAGGATACCC 0.895449 -38 CATGCCATGGAGGCATAACCC 37 64 1 AGGCATACCC 0.952632 -11 TGTGGTCCTACAGGATGACCCCCTCATGATT 38 231 1 CAGGATACCC 0.895456 -70 CCCTGAGCGGAGGGATGACCATTGCCGGGGG 41 101 1 AGGGATACCA 0.965321 -200 ****** **** Masking position 8 Map Score: 6.36624 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 107 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617