AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_mthe_reg_100.orf -o00790_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 MTH122 127 mutator MutT related protein #3 MTH151 75 methyl coenzyme M reductase system, component A2 homolog #4 MTH187 142 conserved protein #5 MTH189 99 unknown #6 MTH238 106 tungsten formylmethanofuran dehydrogenase, subunit C homolog #7 MTH281 259 conserved protein #8 MTH310 178 conserved protein #9 MTH312 50 ATP-dependent helicase #10 MTH342 226 succinoglycan biosynthesis transport protein #11 MTH403 187 formylmethanofuran:tetrahydromethanopterin formyltransferase II #12 MTH409 258 unknown #13 MTH410 62 unknown #14 MTH472 140 DNA helicase II #15 MTH504 214 H(2)-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase homolog (III) #16 MTH511 240 DNA helicase II #17 MTH551 118 DNA helicase II related protein #18 MTH619 23 sensory transduction histidine kinase #19 MTH738 24 conserved protein #20 MTH739 286 conserved protein #21 MTH753 292 conserved protein #22 MTH777 48 conserved protein #23 MTH778 68 unknown #24 MTH779 300 conserved protein #25 MTH927 139 ferredoxin #26 MTH1015 63 methyl coenzyme M reductase system, component A2 #27 MTH1016 65 conserved protein #28 MTH1018 31 conserved protein #29 MTH1020 109 conserved protein #30 MTH1062 134 N5-methyl-tetrahydromethanopterin:coenzyme M methyltransferase, subunit A homolog #31 MTH1073 67 cation antiporter #32 MTH1132 300 methyl coenzyme M reductase II, beta subunit #33 MTH1163 83 N5-methyl-tetrahydromethanopterin:coenzyme M methyltransferase, subunit E #34 MTH1167 31 methyl coenzyme M reductase I, D protein #35 MTH1169 203 unknown #36 MTH1259 300 formylmethanofuran:tetrahydromethanopterin formyltransferase #37 MTH1300 221 coenzyme F420-reducing hydrogenase, alpha subunit #38 MTH1315 28 mutator MutT protein #39 MTH1318 231 conserved protein #40 MTH1336 73 mutator MutT protein homolog #41 MTH1355 124 arsenate reductase #42 MTH1383 52 DNA repair protein RadA #43 MTH1385 300 replication factor A related protein #44 MTH1464 168 coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin dehydrogenase #45 MTH1493 78 cation transporting P-type ATPase related protein #46 MTH1494 266 conserved protein #47 MTH1511 109 arsenical pump-driving ATPase #48 MTH1512 300 H(2)-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase homolog (II) #49 MTH1516 152 cation-transporting P-ATPase PacL #50 MTH1534 40 aryldialkylphosphatase related protein #51 MTH1535 43 heavy-metal transporting CPx-type ATPase #52 MTH1552 139 formate dehydrogenase, alpha subunit homolog #53 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #54 MTH1752 300 coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase #55 MTH1804 176 conserved protein #56 MTH1894 34 aspartate aminotransferase homolog #57 MTH1895 170 conserved protein Motif number 1 ATACCACACAGAAATATTTATGGGAGATGTATTT 6 45 1 GAAATTAGGG 0.829383 -62 ACTTAAAGTATTCACATTCATAGGGTTATAAAAA 8 39 1 TTAATTAAGG 0.846996 -140 GGAATACCTGAAAATATTGAGGGGTTATCAATCC 12 45 1 AAAATTAGGG 0.90592 -214 GAAAAATGACGTCACTTTAAGGGGAGCTGTTGAA 12 96 1 GTATTTAGGG 0.804749 -163 GTGCGAATAGATTTGATTGATGGGAATATTAATG 14 93 0 ATTATTAGGG 0.796137 -48 TCGCACTGATATATCATTCAGGGGTTCATC 14 121 1 ATTATTAGGG 0.796137 -20 CAATCAGGAAAAAACTTTAATAGGGTGAGGCTCC 15 159 1 AAATTTAAGG 0.755467 -56 GCTGTGCATCTATAATTTCAGAGGTGATGTT 16 8 0 TAATTTAAGG 0.772162 -233 AGTTATTATGAAGAATTTAATAGGCTGATGAATT 16 106 0 AAATTTAAGG 0.755467 -135 AAACCATAGAATAACATTTATGGG 16 227 1 ATAATTAGGG 0.91891 -14 ATCTATACACATGAATTTGATGGGACAGTTAATT 21 27 1 ATATTTAGGG 0.890883 -266 GCATGCCAGTTTTTCATTAAGGGGTCCATGCTAA 21 93 0 TTTATTAGGG 0.81075 -200 GATGGCGCTTTATTAATTGAGGGGTTGACTGTAC 21 242 0 TATATTAGGG 0.784497 -51 CCAATGATTTTTAAGTTTAAAGGGAGTCACCGGG 24 17 0 TTATTTAGGG 0.899561 -284 AGGTTAACTTTAAATATTAAAAGGCTTAATGTAT 24 251 0 TAAATTAAGG 0.824683 -50 AATGAATATTTAAAGATTTAAGGGAGATTAAA 42 31 1 TAAATTAGGG 0.913519 -22 TCCTTTAGCAGAATAATTGAAGGGTTCATAAAGG 43 17 1 GATATTAGGG 0.6262 -284 TTATGGTATTAAGATTTTGAGAGGATACAGTGGC 45 37 0 AAATTTAAGG 0.755467 -42 CTTCGATCTCTTCTCTTTTAAGGGACCTTGTCCG 46 178 0 TTTTTTAGGG 0.755294 -89 TGGATCGATGATTAATTTTACAGGAGGAGTATA 47 87 1 ATATTTAAGG 0.784285 -23 AAATTCCATATTAAGATTTAAAGGTCTTAAATAT 48 135 0 TTAATTAAGG 0.846996 -166 TATATACCTATATAGATTTAGGGGCTGATCTAC 50 10 0 TAAATTAGGG 0.913519 -31 TAAACTGATCTTTAAATTAAAAGGTTCATTCTAT 54 188 1 TTAATTAAGG 0.846996 -113 TAAATAACAAATTATTTTTATAGGCCGGATAAAG 54 258 1 ATATTTAAGG 0.784285 -43 ** * *** * *** Masking position 7 Map Score: 23.5338 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 102 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 TCGCCACCGGCTCCATGAATATATACT 3 59 0 CCCCGCCATG 0.954797 -17 AGGAGGGGGGCCGCAGCAGCCCTGGGTAACATTG 4 84 1 CCCAGCCCTG 0.993992 -59 TTCTTTAGGGTCTCAAAGTCCCTGCGGTAATAAG 7 113 1 TCCAACCCTG 0.951029 -147 CATCCCTGGGCCTCAATGACCCTCTCAGCGGCAG 10 32 0 CCCAACCCTC 0.876559 -195 ATGAAGGATCCCCAAAAGGCCATGAACAGTTATA 10 63 1 CCAAACCATG 0.663686 -164 ACGGTGCGGATCACAGTCGCCATTCAGTATCTGA 10 138 0 TCCAGCCATT 0.839646 -89 TCCTCTGCCTCCTCAATAACCGTTATGATCGGGT 11 56 0 CCCAACCGTT 0.808247 -132 AGGTATCTTTCAACAGCTCCCCTTAAAGTGACGT 12 104 0 CACAGCCCTT 0.836751 -155 TTTAAATGCATCGCAGACACCATGGCTGTCCCCG 20 130 0 TCCAGCCATG 0.960259 -157 CTGCGGGGGTCCTCAGCTGCCATGTAAAACAGTA 25 59 1 CCCAGCCATG 0.989071 -81 ACCCTTATGCTATCAGCAACCCTGATTTTTTATG 27 32 0 TACAGCCCTG 0.863291 -34 TTATGAGATTCCACAGGGACCATGGGTAAGTTCC 29 40 0 CCCAGCCATG 0.989071 -70 ACCATCCGCATCCCAGCAACCGTGAAAAATATAC 44 64 1 TCCAGCCGTG 0.921942 -105 TTACATTCCACCAGATCCATGATTCAACCTG 51 23 0 CCCCACCATG 0.902791 -21 CCAGGTTCAGCCTCAAGTTCCCTTCCATCTATTC 52 115 0 CCCAACCCTT 0.940345 -25 CTCCGGAATCCCTCAGTACTCCTGCTTACTGTTT 55 49 1 CCCAGTCCTG 0.891357 -128 GTTGCCGGTTCACCAAGGCCCCTGTATGAAAGCC 55 125 0 CACAACCCTG 0.912276 -52 ** *** ***** Masking position 13 Map Score: 19.2431 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 826 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 GTTACCCAGGGCTGCTGCGGCCCCCCTCCTAACAG 4 79 0 GCCGGGCCCC 0.997887 -64 GAGAATGCTCCCGGTGCGTGCCTGGCACGGC 9 30 0 GCCGTGGTGC 0.891574 -21 ATACTGAATGGCGACTGTGATCCGCACCGTTCCCA 10 142 1 GCCGGACCGC 0.961545 -85 GGTTATTGAGGAGGCAGAGGACCTCCTGGACGCAA 11 69 1 GACGGGCCTC 0.975481 -119 GGACATCCCGGTGACTCCCTTTAAACTT 24 4 1 CACGTGCTCC 0.813956 -297 ATCATTCCAGGCCACAGGGAAGTGCCCAATGATTT 24 41 0 GCCGGAGTGC 0.7494 -260 GCCGGGATTTGAACCCGGGGCCTCCGCCATGCCAA 24 175 1 GACGGGCTCC 0.988024 -126 GTTTTACATGGCAGCTGAGGACCCCCGCAGTTATA 25 54 0 GCCGGGCCCC 0.997886 -86 GTAAAACCATGAATCTGAGGGCCCCTAGGAATAAT 36 211 0 GACGGGCCCC 0.996144 -90 GCCTCTTTAACCTTCTGATGTCCCCATATGTTCAC 43 91 1 CCCGTGCCCC 0.961599 -210 ATGATTATCGGCGGCAGGGTGCCTCCAG 46 4 0 GCCGGTCCTC 0.825847 -263 TGTATTTTAGGATGCTGGGGGCTCCTAATTTTTTC 48 213 1 GACGGGCTCC 0.988024 -88 TCTGAGCTGTGCAGCAGTGGACCGCAATATTT 54 8 0 GCCGGGCCGC 0.995364 -293 GCACAGCTCAGATCCTGATGAGCCCGGCCCACCAT 54 31 1 GACGTGGCCC 0.968645 -270 GGTAGCTCCTGATCCTGATGAGCCCGGCTCACTAC 54 82 1 GACGTGGCCC 0.968645 -219 ** * * ** **** Masking position 7 Map Score: 21.4341 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 259 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 CCTGCGTGACAAGGTTTATATACTGTGTGGT 7 227 1 AAGTTTATAT 0.837832 -33 TTGATAGATAAATTTTTTTATAACCCTATGA 8 56 0 AATTTTTTAT 0.792542 -123 AATCCTCAGAAATCTTTAAATGTGTTTAATA 8 85 1 AATTTTAAAT 0.89438 -94 ATTGAATATAAATTTTTTTATTGAATTCATC 16 83 1 AATTTTTTAT 0.792542 -158 GGAAACAGTAAATTTATTAATCGTGTGGATT 17 55 1 AATTATTAAT 0.558251 -64 AATTAACACGACTATTTAAATGCATCGCAGA 20 147 0 ACTTTTAAAT 0.730931 -140 AAGCTAAAAAAAGGTTTAAATATGACTTTAG 20 218 1 AAGTTTAAAT 0.867319 -69 TGTTTTTTAAACTGTTTTTATTGTCCTGCAT 24 129 0 ACTTTTTTAT 0.550673 -172 TTTCAATTTTTTTATTTTTCAGGAA 25 5 1 AATTTTTTAT 0.792542 -135 TCCATTAAGAAAGATTTATATATGGACCTGT 25 107 1 AAGTTTATAT 0.837832 -33 TTTGCACCGGAAGATTTATATGTCATTAACT 30 65 1 AAGTTTATAT 0.837832 -70 GTCGAAAGCTTTATATGTAAAAACAC 35 188 0 AAGTTTATAT 0.837832 -16 AAAAGTGAAAACTATTTATATCATTTTATAG 37 127 0 ACTTTTATAT 0.682239 -95 AATAGTTTTCACTTTTTTTATAATTGAAAAA 37 142 1 ACTTTTTTAT 0.550673 -80 GATGTATCCAAATTTATAAATATATCTGAAT 41 67 0 AATTATAAAT 0.688852 -58 ATCTCCCTTAAATCTTTAAATATTCATTAAG 42 28 0 AATTTTAAAT 0.89438 -25 CTTTGATAATAAGATTTAAATATATAGTAAT 43 204 1 AAGTTTAAAT 0.867319 -97 AATTATAAATAATATTTTAATCATTTAATTT 44 24 0 AATTTTTAAT 0.828579 -145 GCTTAATCATAATCTTTAAATCATAAAATAC 44 111 1 AATTTTAAAT 0.89438 -58 TGAGATGGAAAATTTTTTAATAAAAGATGGT 48 80 0 AATTTTTAAT 0.828579 -221 ATTACTTAACAATATATTAATGTTAG 48 285 1 AATTATTAAT 0.558252 -16 CAAATAGAAAAATATATATATAGGTGTGTGG 53 11 0 AATTATATAT 0.636334 -61 AGATAATCGAAAGTTTTAAATAACAATGTCA 54 226 0 AAGTTTAAAT 0.867319 -75 AGGCCGGATAAAGTTTTAAATGGTGATAAAT 54 279 1 AAGTTTAAAT 0.867319 -22 AGATCAGCTGAATTTATAAATCATGCTAGAC 57 19 1 AATTATAAAT 0.688852 -152 *** ******* Masking position 5 Map Score: 21.9295 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 26 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 AGCAGTTGAACCCCTCATAAAGGCT 4 128 1 CCCTCTAAGG 0.97967 -15 ATTATCCCAGCGCCTCTTCCTGGAATACCACAC 6 21 1 CCCTCTCTGG 0.981956 -86 AGATGTAACGCCCTCCTTCCTGGCCATCTGATT 7 82 1 CCTCCTCTGG 0.900427 -178 TCCCCCCATCCAGTATCTGGCCGT 9 2 1 CCCCCTCAGT 0.949872 -49 CTTTCAACAGCTCCCCTTAAAGTGACGTCATTT 12 99 0 CCCCCTAAGT 0.933863 -160 TATTTATAACCACCCCATGATGGTCTGAAATAT 15 66 1 CCCCCTATGG 0.987201 -149 GATTATCTCCCCATTATGGGTTCTTGATC 22 30 0 CCCCCTATGG 0.987201 -19 TGGAAATGGTCACCTCATGAAGGAGCTATCCAT 32 193 0 CCCTCTAAGG 0.97967 -108 CTCACCTTCCTGGTGTTAACAAC 37 1 1 CCACCTCTGG 0.900427 -221 ACCAGACTCCTCCTGCAGGCATCTATTT 38 10 0 CCCTCTCAGG 0.984772 -19 CCATTCACCTCTTCAAGGTAAAAACAAT 39 214 0 CCCTCTAAGG 0.97967 -18 * **** * **** Masking position 8 Map Score: 15.7784 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 141 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 CAGAGCAGTTGAACCCCTCATAAAGGCT 4 125 1 GAACCCCTCA 0.982863 -18 CGGCCATGGTAAACCCTTCACCCCATCACA 5 21 0 AAACCCTTCA 0.659556 -79 GGCCTTTTGGGGATCCTTCATCCCTGGGCC 10 54 0 GGATCCTTCA 0.852087 -173 AGAGGACGTCGGATCCCTCGGCTGAATCCC 11 132 1 GGATCCCTCG 0.916666 -56 TCCCTCGGCTGAATCCCTGGATGTGCTTAC 11 145 1 GAATCCCTGG 0.849546 -43 ATGGGATTGATAACCCCTCAATATTTTCAG 12 52 0 TAACCCCTCA 0.790687 -207 GATGAACCCCTGAATGATATATC 14 128 0 GAACCCCTGA 0.942362 -13 TGAAATCCCTCAAAGTCATACT 20 3 1 AAATCCCTCA 0.805541 -284 CATAAAATTCGAATCCTTTAATTAACTGTC 21 50 0 GAATCCTTTA 0.567562 -243 CTATTAGCATGGACCCCTTAATGAAAAACT 21 90 1 GGACCCCTTA 0.801186 -203 AAGGTACAGTCAACCCCTCAATTAATAAAG 21 239 1 CAACCCCTCA 0.848457 -54 GGTTGACCTGGGATCCTTGGAGGGAGATGA 36 109 1 GGATCCTTGG 0.476993 -192 GAACCTTTATGAACCCTTCAATTATTCTGC 43 24 0 GAACCCTTCA 0.94344 -277 GTATATGAATGAACTCCTCACAAGGATGGA 46 117 1 GAACTCCTCA 0.751952 -150 GGTCACATATGAATCCCTCGAGGACCTTTC 54 137 0 GAATCCCTCG 0.95194 -164 TAACCCTCCGGAATCCCTCAGTACTCCTGC 55 44 1 GAATCCCTCA 0.972727 -133 ********** Masking position 3 Map Score: 12.4853 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 596 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 AGTGGTTCAATTCTGGGAGGTGGTCTATTTC 2 67 0 TTCTGGAGGT 0.957483 -61 TCCGGTTCAGTGTGATGGGGTGAAGG 5 6 1 TTCAGGTGAT 0.63346 -94 AGGAAATGACCTCAGGGAGGTTGAATGCACA 5 60 0 CTCAGGAGGT 0.904137 -40 CCATAAATATTTCTGTGTGGTATTCCAGGAA 6 37 0 TTCTGGTGGT 0.963084 -70 AAGGTTTATATACTGTGTGGTACAAGGTACT 7 237 1 TACTGGTGGT 0.91601 -23 ACTTCAGAGTGGTGGATGAGTTC 11 3 1 TTCAGGTGGT 0.937027 -185 TGTGCTTACATTCAGCATGGTTGTGATGCTC 11 166 1 TTCAGATGGT 0.72956 -22 ACCAGAAACCTACAGAGAGGTAATAGAGATA 12 205 1 TACAGGAGGT 0.843001 -54 CTTCTGCTTCCTCTGTGCGGTACTTCATCTG 21 193 0 CTCTGGCGGT 0.835748 -100 TTCATAGAGATACTGAATGGTGAATCCAC 30 9 0 TACTGATGGT 0.66412 -126 TTGCCCCCAGTTCTGAGAGATTAT 34 4 0 TTCTGGAGAT 0.723417 -28 AACCATAGATCACTGTAAGGTAAGCATTGTT 39 189 1 CACTGAAGGT 0.556202 -43 ACATCAATAGATCTGTGTGGTAGTTATAAGG 41 93 1 ATCTGGTGGT 0.785909 -32 TCCTCATTATCTCTGAGAGGTGGTGGTCTAT 46 214 0 CTCTGGAGGT 0.942975 -53 ***** ***** Masking position 11 Map Score: 10.743 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 218 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 GATGGAAGGAAATGACCTCAGGGAGGTTGAATG 5 64 0 ATGACCAGGG 0.911675 -36 ATAACTGTTCATGGCCTTTTGGGGATCCTTCAT 10 63 0 AGGCCTTGGG 0.779253 -164 TATTAACTTCAGGGCCCTTTGAATGCTTCTAGT 15 107 0 AGGCCCTGAA 0.849312 -108 ATTGCATAACAATGCCCTCAGGATAACAAAGCA 20 62 0 ATGCCCAGGA 0.978192 -225 ATCTTTCTTAATGGACCTCATGAAAACAGTACT 25 89 0 AGGACCATGA 0.63538 -51 AGATTTATATATGGACCTGTGGAATATACGAT 25 118 1 AGGACCTGGA 0.963344 -22 ATTCACAGTCACTGCCCCATGGGTCCAGAGCCG 35 51 0 ATGCCCTGGG 0.970917 -153 AGTGACTGTGAATGACCAGAGGATGATTATTAT 35 71 1 ATGACCAGGA 0.942792 -133 CATGAATCTGAGGGCCCCTAGGAATAATAAGAG 36 206 0 AGGCCCAGGA 0.983659 -95 ATTTTCACAGACTGCCCCATGGACCACTTGCTG 43 54 0 ATGCCCTGGA 0.981585 -247 CTCACATGGTATTGCCCCATGGAGCAGTTTAAG 57 74 1 ATGCCCTGGA 0.981585 -97 * ***** **** Masking position 1 Map Score: 8.46534 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 228 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 9 TCATCCATGATTGGGGTTCAGGACATATAAAT 2 103 0 TGGGTTCAGG 0.934205 -25 CCTTTGAGATCCCTGTTTCTGGTGAAGGCACT 7 194 1 CTGTTTCTGG 0.699341 -66 TACAATTTAATGTTTTTTCATGTACTTAAAGT 8 16 1 TTTTTTCATG 0.388993 -163 TCTGCTTTAATCATGTTTCAGGTGCTAAAAT 10 206 1 TTGTTTCAGG 0.872483 -21 TGTAGGTTTCTGGTTTTTCTGGCCCTTTCCTG 12 187 0 TTTTTTCTGG 0.773749 -72 TTAATAATTCCTTGTGTTCAGGCCCTTTAATC 14 34 1 CGTGTTCAGG 0.70697 -107 CAGATAGTAATTCTGGTTCATGATTCCAGAGG 15 24 0 TTGGTTCATG 0.569179 -191 TTAACCAGACTTTTGGTTCAGGGAAACAGTAA 17 34 1 TTGGTTCAGG 0.876495 -85 ATCTCCCCATTATGGGTTCTTGATCATTCACC 22 23 0 TGGGTTCTTG 0.725517 -26 ACCCCATATCTCTGGTTTCAGGGTCCGGATTT 23 35 1 TGGTTTCAGG 0.931922 -34 TTCAATTTTTTTATTTTTCAGGAAATACGTGA 25 12 1 TTTTTTCAGG 0.773749 -128 GCTGATAGCATAAGGGTCCTGGCCCCC 27 49 1 TGGGTCCTGG 0.614282 -17 CACCTTTTTTTGGGTTTTCTGGATTTTTTATA 35 159 0 TGTTTTCTGG 0.872483 -45 GTAAATAATTTTTGTTCTCTGGGTGCGTTTTA 36 77 1 TGTTCTCTGG 0.599833 -224 AGTAAATATTTTTGTTCTCTGGTGCTGTAATA 36 145 1 TGTTCTCTGG 0.599833 -156 TAATAACTTATTAGTTTTCAGGAGCTCACCAA 43 231 1 TGTTTTCAGG 0.872483 -70 TACTCCTGCTTACTGTTTCTGGAAGCCTCCTT 55 65 1 TTGTTTCTGG 0.872483 -112 ATCAACCTTCTCGGGTTCTTGATGATGACAT 57 150 0 CGGGTTCTTG 0.47329 -21 * ********* Masking position 9 Map Score: 10.4683 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 411 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 CTGTTTTATTTGAAAACCCCCTTCCCGGTATT 8 112 0 TGAACCCCCT 0.930647 -67 CAGGATTCTATGGAAACCTCCAGGTATCTTTC 12 127 0 TGAACCTCCA 0.924898 -132 ATGAAAACCCCCACCACAGTATA 17 106 0 TGAACCCCCA 0.930647 -13 ACATTGGTGATGGATAGCTCCTTCATGAGGTG 32 184 1 TGATGCTCCT 0.677145 -117 AAAAAGTTTGTGCAATGCACCTTCGTTAAT 33 9 0 TGAAGCACCT 0.903486 -75 ACTTTTTAAGTGTAATGCACCTAATTTTTTTT 33 34 1 TGAAGCACCT 0.903486 -50 AATTATTTACTATAACCCTCCAGTAAAGAAAC 36 55 0 TAAACCTCCA 0.728559 -246 GCTGATAGCATGTACCCCACCAGGACGTATAT 46 91 1 TGACCCACCA 0.891454 -176 TATACTCCTCCTGTAAAATTAA 47 98 0 TAACCCTCCT 0.640253 -12 GACTTACACTTGAAATGCACCACTCATGTTAT 49 36 0 TGAAGCACCA 0.903486 -117 GCATTTCAAGTGTAAGTCCCCTTGATGAAGCT 49 50 1 TGAATCCCCT 0.568132 -103 ATTTACACTTGAAACACACCACCCTCATTAT 49 132 0 TGAAACACCA 0.548378 -21 TTACATTCCACCAGATCCATGAT 51 31 0 TAATCCACCA 0.375536 -13 TTACTGTTTCTGGAAGCCTCCTTGGATGGTTC 55 74 1 TGAACCTCCT 0.925217 -103 GGTTCTACAGTGCACCGCCCCTCAGGCTTTCA 55 101 1 TGACGCCCCT 0.870549 -76 TCATGGCACTTAAACTGCTCCATGGGGCAATA 57 83 0 TAACGCTCCA 0.573583 -88 ** ** ****** Masking position 4 Map Score: 9.06322 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 287 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 AAGGAGAATATTTTATCATTAAATGAGAATTGT 1 13 0 TTTTTATTAA 0.869543 -125 TAATGTTTTGTTTGGTTATTAAATCTGTACCGG 14 65 0 TTTGTATTAA 0.795336 -76 TGAATATAAATTTTTTTATTGAATTCATCAGCC 16 85 1 TTTTTATTAA 0.925125 -156 ACTTTTATAGTTTTTCCATTGAATTCTCATGGC 16 188 0 TTTTCATTAA 0.611094 -53 CTGGAATGATTTTTTTATTTTAATAAGGAAACC 24 66 1 TTTTTTTTAA 0.812667 -235 TGCATTTATTTTTACTGATTAAATGAAGTTTTT 24 101 0 TTTATATTAA 0.731604 -200 CATTAAGCCTTTTAATATTTAAAGTTAACCTTA 24 254 1 TTTATTTTAA 0.525303 -47 ATCCTTTTTTCTTATTCAATAGAGTCATA 32 7 1 TTTTTATTAA 0.925294 -294 AAATTTACTATTTTATTAATAAAACTGATGGGG 32 251 0 TTTTTAATAA 0.627487 -50 AAATAGTAAATTTTATTAATAAATAAATAAAAC 32 271 1 TTTTTAATAA 0.627487 -30 TGCACCTAATTTTTTTTATTCAAAAAAATAAAA 33 49 1 TTTTTATTAA 0.925125 -35 TTTTCACTTTTTTTATAATTGAAAAACTTATAA 37 147 1 TTTTTATTAA 0.924111 -75 TAAATAATATTTTAATCATTTAATTTAATATTG 44 17 0 TTTATATTAA 0.737141 -152 TTATTAAGTATTTTATGATTTAAAGATTATGAT 44 116 0 TTTTTATTAA 0.924111 -53 ATTTTGGCATTTTTTTCTTTGAAAAAATTAGGA 48 235 0 TTTTTTTTAA 0.812667 -66 ATAAAAATAATTTGTTATTTAAAGATAATCGAA 54 246 0 TTTGTTTTAA 0.578028 -55 **** * *** ** Masking position 10 Map Score: 12.4838 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 12 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 TCCTCATCCATGATTGGGGTTCAGGACATAT 2 107 0 TCTATGGGGT 0.917054 -21 ATGTGTTTAATACCGGGAAGGGGGTTTTCAAATAA 8 104 1 TCGGAGGGGT 0.981863 -75 TTTCAAATCTTCCAGGGTATGGGATTGATAACCCC 12 65 0 TCGGATGGGT 0.841453 -194 GGTTCATGATTCCAGAGGTGGGGGTTTTGCC 15 7 0 TCGGTGGGGT 0.994197 -208 TTAAAGTTTTTTCCTGATTGGGGATTTTATGGGCC 15 144 0 TCTATGGGGT 0.917054 -71 TAAATGAATATACTGTGGTGGGGGTTTTCAT 17 98 1 TCGGTGGGGT 0.994197 -21 GCTTAATGTATACTTTGTTGGGGCTGGTAGCTCAG 24 227 0 TCTGTGGGGT 0.982501 -74 TTTTCACGGTTGCTGGGATGCGGATGGTTAAAATT 44 57 0 TCGGTGCGGT 0.961378 -112 GAAATATGAATCCGGTGATGGCGGTTGCCGGTTCA 55 147 0 TCGGTGGCGT 0.961378 -30 * * * * ***** * Masking position 1 Map Score: 7.37806 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 56 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 CTGTTGAACAGCTCATTGAGGCCCTTGATGA 4 37 1 GCTCATGAGG 0.768759 -106 GTGCATTCAACCTCCCTGAGGTCATTTCCTT 5 61 1 CCTCCTGAGG 0.555326 -39 AGAATCCTGGCTTCCCGGTGGGAACCAGTCT 8 147 0 CTTCCGGTGG 0.695632 -32 CCGCTGAGAGGGTCATTGAGGCCCAGGGATG 10 35 1 GGTCATGAGG 0.867368 -192 CGATCATAACGGTTATTGAGGAGGCAGAGGA 11 59 1 GGTTATGAGG 0.432877 -129 TCCATGCTTGCGTCCAGGAGGTCCTCTGCCT 11 80 0 CGTCCGGAGG 0.815275 -108 ACACCATGGCTGTCCCCGAGGATAAAAGATA 20 117 0 TGTCCCGAGG 0.628562 -170 TCATTGGGCACTTCCCTGTGGCCTGGAATGA 24 44 1 CTTCCTGTGG 0.759044 -257 ACTTACCCATGGTCCCTGTGGAATCTCATAA 29 43 1 GGTCCTGTGG 0.948127 -67 ATGGATAGCTCCTTCATGAGGTGACCATTTC 32 193 1 CCTTCTGAGG 0.717894 -108 AAATAGATGCCTGCAGGAGGAGTCTGGT 38 10 1 CCTGCGGAGG 0.549124 -19 TCCAGCAAGTGGTCCATGGGGCAGTCTGTGA 43 52 1 GGTCCTGGGG 0.938094 -249 CATTCATATACGTCCTGGTGGGGTACATGCT 46 97 0 CGTCCGGTGG 0.92638 -170 TCAAAGGAAAGGTCCTCGAGGGATTCATATG 54 131 1 GGTCCCGAGG 0.938061 -170 CACTTAAACTGCTCCATGGGGCAATACCATG 57 78 0 GCTCCTGGGG 0.904998 -93 ***** ***** Masking position 3 Map Score: 9.63513 Number of sites scoring better than the average of aligned sites = 1144 Number in coding regions = 1111 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 ATATAATGGACCAGCACTTCAGGTGAACGG 2 16 0 CCAGCACTTC 0.813829 -112 TCGCCACCGGCTCCATGAATATA 3 63 0 CCACCGGCTC 0.948071 -13 GAAAATTATCCCAGCGCCTCTTCCTGGAAT 6 17 1 CCAGCGCCTC 0.782758 -90 GGCAAAACCCCCACCTCTGGAATCATG 15 8 1 CCCCCACCTC 0.965357 -207 ATGAAAACCCCCACCACAGTATATTCA 17 102 0 CCCCCACCAC 0.900233 -17 ATGGCGGAGGCCCCGGGTTCAAATCCCGGC 24 175 0 CCCCGGGTTC 0.695474 -126 AAAACCACCACTTCAAACTTTTTT 29 96 0 CCACCACTTC 0.951089 -14 AAGACCACCATTACACTTAAAGAT 31 5 1 CCACCATTAC 0.553551 -63 TGGTTTTTTGCCCCCAGTTCTGAGAGATTA 34 12 0 CCCCCAGTTC 0.951874 -20 AGCATGTACCCCACCAGGACGTATATGAAT 46 97 1 CCACCAGGAC 0.655771 -170 AAGAGATAGACCACCACCTCTCAGAGATAA 46 209 1 CCACCACCTC 0.968949 -58 GATTCCACGGCTTCAGTTGTATCT 46 253 0 CCACGGCTTC 0.691857 -14 AAATTAGGAGCCCCCAGCATCCTAAAATAC 48 214 0 CCCCCAGCAT 0.489276 -87 GGTTGCACAGCCACCAGCTTCATCAAGGGG 49 67 0 CCACCAGCTT 0.768147 -86 TTACATTCCACCAGATCCATGATTCAA 51 27 0 CCACCAGATC 0.874991 -17 TGAGCCCGGCCCACCATATCATGAAGTCAT 54 49 1 CCACCATATC 0.547509 -252 ACATTGTATTCCCGGAGTTCCATGAGATTA 57 124 0 CCCGGAGTTC 0.499896 -47 ********** Masking position 2 Map Score: 11.0184 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 679 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 15 CGTTCCCAGTTTATCTTCAGGATAGCCAGA 10 169 1 TTATCTTCAG 0.938127 -58 CTGGATGTGCTTACATTCAGCATGGTTGTG 11 161 1 TTACATTCAG 0.725257 -27 GGCCCTGTTATTAACTTCAGGGCCCTTTGA 15 118 0 TTAACTTCAG 0.808234 -97 ATAAAAAAATTTATATTCAATAATTTTAAT 16 74 0 TTATATTCAA 0.635035 -167 CTGTACCTTATTATCTTCAGTCACCTTCTG 21 218 0 TTATCTTCAG 0.938127 -75 GCATAAGCGGTTATATTCAGATTAATACTG 32 57 1 TTATATTCAG 0.918685 -244 CGGTAATAAATTATATTTAGAGCTCTCCAC 35 23 0 TTATATTTAG 0.805757 -181 CCCCTTCATGTTATCTTCAGTGTCCTTTTT 52 72 0 TTATCTTCAG 0.938127 -68 AAGGGGACTGTTAAATTTAGAATAGATGGA 52 96 1 TTAAATTTAG 0.533151 -44 AAACTTTCGATTATCTTTAAATAACAAATT 54 241 1 TTATCTTTAA 0.461785 -60 TTCCATGAGATTATATTTAGGTTCATGGCA 57 107 0 TTATATTTAG 0.805757 -64 ********** Masking position 3 Map Score: 5.60079 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555