AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_mthe_reg_300.orf -o00450_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 Input sequences: #1 MTH278 300 ferredoxin #2 MTH384 249 unknown #3 MTH387 24 conserved protein #4 MTH388 35 unknown #5 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #6 MTH394 55 unknown #7 MTH397 40 formate hydrogenlyase, subunit 7 #8 MTH399 23 polyferredoxin #9 MTH400 33 polyferredoxin #10 MTH403 187 formylmethanofuran:tetrahydromethanopterin formyltransferase II #11 MTH405 130 polyferredoxin #12 MTH587 263 methionyl-tRNA synthetase #13 MTH927 139 ferredoxin #14 MTH928 300 cobalamin biosynthesis protein N #15 MTH1026 222 phosphatidylserine decarboxylase #16 MTH1027 39 CDP-diacylglycerol-serine O-phosphatidyltransferase #17 MTH1029 41 unknown #18 MTH1030 30 unknown #19 MTH1031 59 conserved protein #20 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #21 MTH1133 21 polyferredoxin (MvhB) #22 MTH1136 171 methyl viologen-reducing hydrogenase, delta subunit #23 MTH1137 116 conserved protein (FlpA) #24 MTH1138 51 methyl viologen-reducing hydrogenase, delta subunit homolog FlpD #25 MTH1141 300 conserved protein (FlpE) #26 MTH1246 30 NADH dehydrogenase I, subunit N #27 MTH1251 147 conserved protein #28 MTH1252 143 conserved protein #29 MTH1253 135 unknown #30 MTH1468 35 ferredoxin #31 MTH1469 57 molybdenum transport ATP-binding protein homolog #32 MTH1470 44 molybdenum transport protein ModA related protein #33 MTH1471 56 O-antigen transporter homolog #34 MTH1472 30 O-antigen transporter homolog #35 MTH1475 56 unknown #36 MTH1476 127 tryptophan synthase, beta subunit homolog #37 MTH1636 101 S-adenosylhomocysteine hydrolase #38 MTH1819 134 ferredoxin Motif number 1 TCGCGAGGTTGACCTGAGTGCTCCCATCTCCTAT 1 35 1 GACGGTGTCC 0.942467 -266 ATGAATCTTTTATCATGGGGTTGCTTATACTTTG 1 255 0 TACTGGGTGC 0.806385 -46 TTTTTACTGATATCTGAAGGGTCCCTCTACAGAA 2 124 0 TACGAGGTCC 0.979566 -126 TTTTTACTAATATCTGGAGGTTTCTCTACAGAAA 2 162 0 TACGAGGTTC 0.955945 -88 TCACCATTAACACCGGAATGATTCTATTATCATA 5 14 0 CACGATGTTC 0.936056 -28 TCCAGGGATTCAGCCGAGGGATCCGACGTCCTCT 10 132 0 CACGGGGTCC 0.992755 -56 CCCATAAAGGTATCGAAGTGTTCCATCACATCGA 12 33 1 TACAGTGTCC 0.816329 -231 TCCAGTACCTCAGCGGCGTGTTGCCGTGATTATG 12 118 1 CACGGTGTGC 0.980259 -146 ATATCCATTATAACTGCGGGGGTCCTCAGCTGCC 13 46 1 TACGGGGGTC 0.885809 -94 GTGTTCCCTTCACCAGAGGTTTTCAGCAAAATGC 20 109 0 CACGGGTTTC 0.766262 -121 TATAATAAATTATCAGGGTGTTCCCTTCACCAGA 20 126 0 TACGGTGTCC 0.987429 -104 ACTCCCCTTCCACCAGAAGGCTCCTATGAAAC 22 9 0 CACGAGGTCC 0.981133 -163 CTTAACTCTGTAATGGCGTGTTGCGGGTTGTTCT 25 45 1 TATGGTGTGC 0.707564 -256 AACATGAGCGTATCAGAATGATTCCATTTATAAG 29 11 0 TACGATGTTC 0.931007 -125 ATGATGATTTCATCAGTAGGGACCAGTTCCAGCC 36 94 1 CACGAGGACC 0.826408 -34 TCCAAGATGTTAACCGGGTGATGCA 37 87 1 TACGGTGTGC 0.978621 -15 ** * * *** *** Masking position 2 Map Score: 17.3612 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 307 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 GCCTCATCCTATGTTTATATGTTATGGCTCT 1 99 0 ATTTTATATG 0.946512 -202 GCCTCATCCTATGTTTATATGTTATGGCTCT 1 143 0 ATTTTATATG 0.946512 -158 GAGTATTTATATGTTTATATGTTATGGCTCT 1 187 0 ATTTTATATG 0.946512 -114 AAAAAAGGCCATAATTTTATTAAGAGGTCTT 2 191 1 ATATTTTATT 0.452221 -59 ACCAGTAATCATCTATATATTC 3 2 0 ATTATATATT 0.694046 -23 TTTCAATTTTTTTATTTTTCAGGAAA 13 6 1 ATTTTTTATT 0.845474 -134 ATTAAGAAAGATTTATATATGGACCTGTGGA 13 110 1 ATTATATATG 0.803657 -30 AAATTAAGTAATAATTATATGAAAATTTAAT 14 189 0 ATATTATATG 0.727517 -112 CTTTTTATTAATTTTTTTATTACATATTCTT 14 230 0 ATTTTTTATT 0.845474 -71 TCCACCAACCATTTTTTTATTTTCAGGGAC 18 11 1 ATTTTTTATT 0.845474 -20 TGTGTGGTTAAAATTTTTATTATTTTTAATA 22 45 0 AATTTTTATT 0.558615 -127 AATTTCCGAAAATTTTATATGTGTGGTTAAA 22 64 0 AATTTATATG 0.803644 -108 TTTTAGGAACATTTATATATGTAATAC 25 284 1 ATTATATATG 0.803657 -17 TTATATAGAAAACTTTATATTATCATAAATA 27 86 1 AATTTATATT 0.694035 -62 TGATACGCTCATGTTTTTATTACAGCACTAT 29 30 1 ATTTTTTATT 0.845478 -106 AGCACTATAGATATTAATATGGGATAAGTTA 29 53 1 ATTTAATATG 0.727517 -83 CTGAAGTCCAATATTAATATGGGGCTATTGC 38 98 0 ATTTAATATG 0.727517 -37 ** ******** Masking position 8 Map Score: 15.5753 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 31 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TTATAATTTTCGCGAGGTTGACCTGAGTGCTC 1 26 1 CCGAGGTTAC 0.741677 -275 TTGCTTATACTTTGGGGTTAACCCTTTATAGT 1 237 0 TTGGGGTTAC 0.763209 -64 AATCTTTTATCATGGGGTTGCTTATACTTTGG 1 254 0 CTGGGGTTCT 0.95922 -47 CCATCATGTCCTGGAGGTTCCTATGGAGTCAC 2 20 1 CGGAGGTTCT 0.944159 -230 TTACTAATATCTGGAGGTTTCTCTACAGAAAC 2 161 0 CGGAGGTTCT 0.944159 -89 TAAATGCGTGATGTTGATGTCCT 8 7 1 CTGATGTTAT 0.899136 -17 TGCTTGCGTCCAGGAGGTCCTCTGCCTCCTCA 10 75 0 CGGAGGTCTC 0.476512 -113 CGTCCTCTCCCCGGATGTTCTTTCTGACCTCC 10 108 0 CGGATGTTTT 0.695513 -80 TGTGCTGAGGCCTGATGTTGATCCCGTGAACC 11 48 1 CTGATGTTAT 0.899136 -83 GTACTGTTTTCATGAGGTCCATTAAGAAAGAT 13 90 1 CTGAGGTCAT 0.834255 -50 CATATCACATTCTGAGGTTCATCATATGGTGT 15 84 1 TTGAGGTTAT 0.775016 -139 AGGTTCATCATATGGTGTTCATATCGCTGTGA 15 98 1 TTGGTGTTAT 0.612159 -125 GAACATTTCACATGGAGTTCACAGCGATATGA 15 116 0 CTGGAGTTAC 0.813963 -107 TTTCTTCTCACATGGAGTTCACGGTGACATGA 15 146 0 CTGGAGTTAC 0.813963 -77 AATAAATTATCAGGGTGTTCCCTTCACCAGAG 20 125 0 CGGGTGTTCC 0.845385 -105 AGGACTCATGGGGTTATTACGGCAGCCT 27 7 1 CTGGGGTTTT 0.901908 -141 TGTATTCTGACTTGAGGTTAATTGATGCCTGC 28 110 1 CTGAGGTTAT 0.962676 -34 ATTGATGCCTGCGGAGGTTTATAA 28 130 1 GGGAGGTTAT 0.779917 -14 AATGGGCCCGGGGGGTGTTAATCTCAG 37 6 0 GGGGTGTTAT 0.618863 -96 CGGTTAACATCTTGGAGTTCCTTGTCTGTAGA 37 71 0 CTGGAGTTCT 0.810047 -31 * ******* ** Masking position 8 Map Score: 14.5206 Number of sites scoring better than the average of aligned sites = 774 Number in coding regions = 716 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 AAGGCAGTAGCTGATGCCGGTCCCGAATCAGAGC 1 70 1 CTGACGGTCC 0.975909 -231 TAAACATAGGATGAGGCAGTTCCCGCAAACAGAG 1 113 1 ATGACGTTCC 0.985331 -188 TTTATATGTTATGGCTCTGTTTGCGGGAACTGCC 1 127 0 ATGGCGTTGC 0.930533 -174 TAAACATAGGATGAGGCAGTTCCCGCAAACAGAG 1 157 1 ATGACGTTCC 0.985331 -144 TTTATATGTTATGGCTCTGTTTGCGGGAACTGCC 1 171 0 ATGGCGTTGC 0.930533 -130 TAACACCGGAATGATTCTATTATCATAAAC 5 7 0 ATGACATTTC 0.694733 -35 TGTGGTTTCCCTGAATCCAGTACCTCAGCGGCGT 12 103 1 CTGACAGTCC 0.950321 -161 AATAACTCACCTGTTCCCATTACCGGTAATATGA 15 187 0 CTGTCATTCC 0.819748 -36 AAGGTTACTTATGAAACAATTTCCGAAAATTTTA 22 78 0 ATGACATTCC 0.969436 -94 GTATTAAAATCTGAACCCATTCCCTGCATTTTTA 23 15 1 CTGACATTCC 0.966498 -102 AACAAGGAGGATGACCCTGTCCCCGGCGGATACA 31 13 0 ATGACGTCCC 0.907391 -45 TGTAGAACCTATGGCGCCGGTTCTTTATATCTTT 32 21 0 ATGGCGGTCT 0.84054 -24 CACCTCATGGCTGGAACTGGTCCCTACTGATGAA 36 102 0 CTGGCGGTCC 0.976348 -26 CAATATTAATATGGGGCTATTGCTAAAAATAGTT 38 87 0 ATGGCATTCT 0.789645 -48 **** * *** ** Masking position 2 Map Score: 14.7465 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 198 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 ATATAGATGATTACTGGTGA 3 15 1 TTACTGGTGA 0.972757 -10 CATTCCGGTGTTAATGGTGATGAG 5 28 1 TTAATGGTGA 0.965229 -14 TTTACCACCTTTCTGGTGAAA 21 3 0 TTTCTGGTGA 0.978963 -19 TACAGTGACTTTGAAGGTGAAACAAT 23 101 1 TTGAAGGTGA 0.84302 -16 AGTTTGATGGTGATTTTCGAGCC 24 4 1 TTGATGGTGA 0.967707 -48 AAAATTGGATTTTATTGTGATTTTCATGTA 25 227 1 TTTATTGTGA 0.77991 -74 GGCGCCGGCCTTACTGGTGAGCAACATCGC 28 36 0 TTACTGGTGA 0.972757 -108 CAACTCTTTATTTCTGGTGATTCA 34 17 1 TTTCTGGTGA 0.978963 -14 GACTTCAGTTTTTAGGGTGACATC 38 121 1 TTTAGGGTGA 0.905666 -14 ********** Masking position 8 Map Score: 10.6049 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 6 TTAAACGTATTTACTTAAATTTTTTTCCGGTTC 11 75 0 TTATTATTTT 0.914033 -56 AACACAACCCTTTATTACCTTTTAAACGTATTT 11 96 0 TTTTTATTTT 0.901747 -35 GCGTGATGAATGTATTAAATTTTCATATAATTA 14 176 1 TGTTTATTTT 0.743559 -125 CATATAATTATTACTTAATTTTTATTAGAGCAA 14 199 1 TTATTATTTT 0.914033 -102 TTTAAGACTTTTTATTAATTTTTTTATTACATA 14 235 0 TTTTTATTTT 0.901747 -66 GCCACCTGTTTTACTTATAATCTGGTGTAGTCA 16 15 0 TTATTAATCT 0.822481 -25 AAATAAGAAATTAATTAATTTTTTGTTTTGG 17 9 0 TTATTATTTT 0.914033 -33 AATTAATTTCTTATTTAATATTTTAT 17 26 1 TTATTAATTT 0.901747 -16 ACCCTGATAATTTATTATAATCTGAGTTCTGAA 20 141 1 TTTTTAATCT 0.799975 -89 TCTTGATTAATTATTTAAATTCTGAAGGCAAAG 20 183 1 TTATTATTCT 0.84295 -47 TAGATGATTATTTTTTAATATTTAACGTGGTTT 25 94 0 TTTTTAATTT 0.887921 -207 TCATCTATTATGAATTATAATTTCCTGCCAGAA 25 120 1 TGATTAATTT 0.743559 -181 GATCCCCTATTTTATTACGATTTATATAGAAAA 27 65 1 TTTTTAATTT 0.887921 -83 *** *** **** Masking position 7 Map Score: 10.0198 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 17 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 TGCCGGTCCCGAATCAGAGCCATAACATATAA 1 84 1 GAATCAACCA 0.922617 -217 AACATAGGATGAGGCAGTTCCCGCAAACAGAG 1 115 1 GAGGCATCCC 0.786261 -186 AACATAGGATGAGGCAGTTCCCGCAAACAGAG 1 159 1 GAGGCATCCC 0.786261 -142 GGTTCCTATGGAGTCACATCCACTTACCGGTT 2 35 1 GAGTCAACCA 0.869543 -215 AATTCCAGCTGCAGCAAAACCC 9 22 1 GCAGCAACCC 0.972845 -12 ATGCTGAATGTAAGCACATCCAGGGATTCAGC 10 152 0 TAAGCAACCA 0.871397 -36 TGAGCATCACAACCATGCTGAATGT 10 173 0 GCATCAACCA 0.971154 -15 ACATCAGGCCTCAGCACACCCAGATTCCCGGA 11 34 0 TCAGCAACCA 0.950332 -97 CAAGGCCAGATCAGCATGCCCAAAACTGCGGT 12 67 0 TCAGCAGCCA 0.891608 -197 GCTTAAATTAGCATCCCTTCCATACTGAGTTA 23 71 1 GCATCCTCCA 0.718085 -46 ATCTATTAGGGCCGCATGGCCATAATTTTAGA 25 165 1 GCCGCAGCCA 0.899154 -136 TCAGAATACAGCATCAAAACCCTGGAATCCCA 28 88 0 GCATCAACCC 0.957125 -56 ACTGATGAAATCATCATTTCCATGCAGTAAGA 36 79 0 TCATCATCCA 0.860797 -49 CGGCTCATTCTCCTCACAACCATCAGCTGCTC 38 44 1 TCCTCAACCA 0.820657 -91 ****** * *** Masking position 5 Map Score: 9.4666 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 316 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 GTTATGGCTCTGTTTGCGGGAACTGCCTCATC 1 122 0 TGTGCGGGAA 0.940905 -179 GTTATGGCTCTGTTTGCGGGAACTGCCTCATC 1 166 0 TGTGCGGGAA 0.940905 -135 TAAGTGGATGTGACTCCATAGGAACCTCCAGG 2 29 0 TGTCCATAGG 0.462335 -221 GAGTGGTGGATGAGTTCAGGAGAGTGTTCAGA 10 17 1 TGTTCAGGAG 0.910379 -171 CCTCCATGCTTGCGTCCAGGAGGTCCTCTGCC 10 81 0 TGTCCAGGAG 0.976196 -107 TTTAATGTGCTGGATCCGGGAATCTGGGTGTG 11 20 1 TGTCCGGGAA 0.96887 -111 GGCCTGATGTTGATCCCGTGAACCGGAAAAAA 11 56 1 TGCCCGTGAA 0.68652 -75 GCTGAGGTACTGGATTCAGGGAAACCACAACC 12 100 0 TGTTCAGGGA 0.778733 -164 ATCTGGTTCATGATTCAAGGAGGAGTTTGAG 12 243 1 TGTCAAGGAG 0.69883 -21 ATATCCATTATAACTGCGGGGGTCCTCAGCTG 13 46 1 TATGCGGGGG 0.753699 -94 AAAACAGTACTGTTTTCATGAGGTCCATTAAG 13 84 1 TGTTCATGAG 0.62833 -56 GGTTAATTGATGCCTGCGGAGGTTTATAA 28 125 1 TGTGCGGAGG 0.862641 -19 AGGATGACCCTGTCCCCGGCGGATACATC 31 8 0 TGCCCGGCGG 0.813544 -50 CGTTTCTGGATGGCTCCGGGAGAAAAAAATCA 35 35 0 TGTCCGGGAG 0.989842 -22 AAATAATTAATGGGCCCGGGGGGTGTTAATCT 37 14 0 TGCCCGGGGG 0.978116 -88 ** ******** Masking position 1 Map Score: 10.0813 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 668 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 TTTAGGTCTAACTCACCTTTTTTAAAAAGATT 2 223 1 ATCACCTTTT 0.727637 -27 AGGACATCAACATCACGCATTTA 8 2 0 CTCACGCTTT 0.956729 -22 TAATGGATATCCTCACGTATTTCCTGAAAAAT 13 24 0 CTCACGTTTT 0.964127 -116 TTAATACATTCATCACGCGTTATTGCATAATT 14 162 0 CTCACGCTTA 0.832042 -139 CCGCCACCTGTTTTACTTATAAT 16 27 0 CCCACCTTTT 0.954159 -13 TCCACCAACCATTTTTTTATTTTC 18 3 1 CCCAACCTTT 0.862851 -28 AATTCCTCACCTGTTAGATTCCTCAT 26 15 0 CTCACCTTTA 0.89296 -16 GCCTCTTCCCCTTCAAGTGTTTAATCATCGGA 27 35 1 CTCAAGTTTT 0.908041 -113 ATCCGTCAACTCTTTATTTCTGGTG 34 4 1 CTCAACTTTT 0.931878 -27 TGCATCACCCGGTTAACATCTTGG 37 88 0 CTCACCCGTT 0.84021 -14 GATCCATCATCAGGTATTTTTAGCAACAA 38 8 1 CTCAGGTTTT 0.816454 -127 CTCCATCCATCACCAACTATTTTTAGCAATAG 38 73 1 CCCAACTTTT 0.88436 -62 * ****** *** Masking position 5 Map Score: 7.88917 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 77 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 CTGCCTTGATAGGAGATGGGAGCACTCAGG 1 47 0 AGGAGATGGG 0.927888 -254 CCAGGACATGATGGGGTGGGAAT 2 4 0 ATGGGGTGGG 0.847684 -246 CTGCGGTTCGATGTGATGGAACACTTCGAT 12 44 0 ATGTGATGGA 0.64472 -220 TCTGGCCTTGAGGTTGTGGTTTCCCTGAAT 12 89 1 AGGTTGTGGT 0.780377 -175 ATCATATTACCGGTAATGGGAACAGGTGAG 15 186 1 CGGTAATGGG 0.854947 -37 ATAAAAATGCAGGGAATGGGTTCAGATTTT 23 20 0 AGGGAATGGG 0.914175 -97 GCTTTGATAAAAGTGGTGGGTTAATAAAAA 23 43 0 AAGTGGTGGG 0.834411 -74 TGGAATTCTAAGGTGATGGT 24 42 1 AGGTGATGGT 0.92888 -10 CGGATTTTTCCGGAAGTGGGCCAGCAATTC 29 114 1 CGGAAGTGGG 0.693593 -22 AGTAGGGGTGAGGTGGTGGAGGGGT 35 6 0 AGGTGGTGGA 0.947492 -51 TGTACATCAAAGGGAATGGTTAATAAACA 36 10 0 AGGGAATGGT 0.75034 -118 TGTAGATAATAGGTTGTGGGTCATCACTTA 37 47 0 AGGTTGTGGG 0.926434 -55 TAAAAATAGTTGGTGATGGATGGAGCAGCT 38 68 0 TGGTGATGGA 0.623993 -67 ********** Masking position 7 Map Score: 7.174 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 501 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 CGAAAACGACTATGAAAATCCTTAAAATTTATTAC 2 83 1 TATGAATTTA 0.807717 -167 ATATAAATCTTTTTAAAAAAGGTGAG 2 234 0 TATAAATTTA 0.930034 -16 TTTACTTCTATATAAATTTATTTGAGTCCATGTCT 12 158 0 TATAAATTTA 0.930051 -106 CAGGTCCATATATAAATCTTTCTTAATGGACCTCA 13 102 0 TATAAATCTA 0.961064 -38 CCGTTATATTTATAAAAATTTTTAATTTCTTGAGT 14 85 1 TATAAATTTA 0.929281 -216 TAAATTTTCATATAATTATTACTTAATTTTTATTA 14 191 1 TATAATTCTA 0.724557 -110 GTGGATATGGTATGAAGATTATTTAAGACTTTTTA 14 254 0 TATGAATTTA 0.807688 -47 AGTACATGAGTATATATATCTTTCACCGGCATATC 15 55 1 TATATATTTA 0.585914 -168 TAACCACACATATAAAATTTTCGGAAATTGTTTCA 22 66 1 TATAAATCGA 0.79582 -106 GAGTGGTAAGTATAAAGGTTACTTATGAAACAATT 22 91 0 TATAAATCTA 0.961113 -81 GTATTACATATATAAATGTTCCTAAAATTTAAAAG 25 276 0 TATAAATCTA 0.961119 -25 TTTATGATAATATAAAGTTTTCTATATAAATCGTA 27 80 0 TATAAATCTT 0.724561 -68 TAAATAGTTCTTTAAAGATATCTTACTGCATGGAA 36 59 1 TTTAAATCTA 0.724557 -69 ****** * ** * Masking position 9 Map Score: 8.35306 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 16 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 GATGAGGCAGTTCCCGCAAACAGAGCCATA 1 122 1 TTCCCGCAAA 0.933134 -179 GATGAGGCAGTTCCCGCAAACAGAGCCATA 1 166 1 TTCCCGCAAA 0.933134 -135 CCTCACGTATTTCCTGAAAAATAAAAAAAT 13 16 0 TTCCTGAAAA 0.966845 -124 GTCCCTGAAAATAAAAAAATG 18 20 0 TCCCTGAAAA 0.872099 -11 ACAGGGCATTTTGCTGAAAACCTCTGGTGA 20 104 1 TTGCTGAAAA 0.947171 -126 TATGAAACAATTTCCGAAAATTTTATATGT 22 73 0 TTTCCGAAAA 0.81254 -99 GCTGGCCCACTTCCGGAAAAATCCGTATAC 29 109 0 TTCCGGAAAA 0.914314 -27 CCGCGGTTTGTTGCTAAAAATACCTGATGA 38 17 0 TTGCTAAAAA 0.779334 -118 TATGGGGCTATTGCTAAAAATAGTTGGTGA 38 82 0 TTGCTAAAAA 0.779334 -53 ********** Masking position 8 Map Score: 3.88009 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 28 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ACCCCATCATGTCCTGGAGGTTCCTATGGA 2 17 1 GTCCTGGAGG 0.953426 -233 CCATGCTTGCGTCCAGGAGGTCCTCTGCCT 10 80 0 GTCCAGGAGG 0.975015 -108 CCTGGACGCAAGCATGGAGGTCAGAAAGAA 10 93 1 AGCATGGAGG 0.943837 -95 ATGCTGATCTGGCCTTGAGGTTGTGGTTTC 12 82 1 GGCCTTGAGG 0.944946 -182 TGGTTCATGATTCAAGGAGGAGTTTGAG 12 246 1 TTCAAGGAGG 0.791935 -18 ACGATCCAAAAGCAAGGAGGAAACTCT 22 155 1 AGCAAGGAGG 0.96973 -17 CTAAAATTATGGCCATGCGGCCCTAATAGA 25 166 0 GGCCATGCGG 0.884325 -135 CGTCGGGTTCAACAAGGAGGATGACCCTGT 31 27 0 AACAAGGAGG 0.832105 -31 GACCAGTTCCAGCCATGAGGTGAT 36 114 1 AGCCATGAGG 0.953765 -14 ********** Masking position 3 Map Score: 6.5096 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 575 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 GCATCAGCTACTGCCTTGATAGGAGATGGG 1 57 0 CTGCCTTGAT 0.449678 -244 ATAAATACTCCTCCAGTGAAAGATTAGGAA 1 208 1 CTCCAGTGAA 0.9331 -93 CCGACGTCCTCTCCCCGGATGTTCTTTCTG 10 114 0 CTCCCCGGAT 0.83256 -74 ATGTAAGCACATCCAGGGATTCAGCCGAGG 10 147 0 ATCCAGGGAT 0.591757 -41 CCTGATGTTGATCCCGTGAACCGGAAAAAA 11 58 1 ATCCCGTGAA 0.841866 -73 GAGGTACTGGATTCAGGGAAACCACAACCT 12 99 0 ATTCAGGGAA 0.648799 -165 AAAAGCTTTTCTCCAGGGTACTGTCAATCA 19 30 0 CTCCAGGGTA 0.766387 -30 GTTAATAAAAATGCAGGGAATGGGTTCAGA 23 24 0 ATGCAGGGAA 0.922045 -93 GCTTCAATCCAGTGATCCTAACTGGA 25 7 1 ATCCAGTGAT 0.812142 -294 CTCTGAGTCGCTGCAGCGATGTTGCTCACC 28 21 1 CTGCAGCGAT 0.70186 -123 CCCTGAAATGCTCCACGGAATGCCCCAACA 33 27 0 CTCCACGGAA 0.922986 -30 GCGGTATATGCCCTGAAATGCTCCACG 33 40 0 ATGCCCTGAA 0.607863 -17 AGATATCTTACTGCATGGAAATGATGATTT 36 74 1 CTGCATGGAA 0.79368 -54 ********** Masking position 2 Map Score: 4.13549 Number of sites scoring better than the average of aligned sites = 758 Number in coding regions = 702 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 15 GCACACCCAGATTCCCGGATCCAGCACATTAA 11 21 0 ACCCGGATCC 0.877572 -110 GGTTTTCAGGTTTTCCGGGGCCTATGTAAATC 20 43 0 TTCCGGGGCC 0.972711 -187 ATACACATCTTTACCCCGGGACTGACAGGGCA 20 80 1 TCCCCGGGAC 0.938918 -150 GCTCACCAGTAAGGCCGGCGCCAATGACTTTG 28 44 1 AGCCGGCGCC 0.981082 -100 GATGTATCCGCCGGGGACAGGGTCATCC 31 7 1 TGCCGGGGAC 0.95311 -51 AAAGATATAAAGAACCGGCGCCATAGGTTCTA 32 21 1 AACCGGCGCC 0.949411 -24 CTGATTTTTTTCTCCCGGAGCCATCCAGAAAC 35 34 1 TCCCGGAGCC 0.984657 -23 TGAGATTAACACCCCCCGGGCCCATTAATTAT 37 12 1 ACCCCGGGCC 0.98516 -90 * ********* Masking position 6 Map Score: 2.25335 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 149 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925