AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_mthe_reg_300.orf -o00330_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: MTH5 22 ribosomal protein L8 (E.coli L2) MTH44 27 ribosomal protein Sa (E.coli S2) MTH892 21 ATP-dependent protease LA related protein Input sequences: #1 MTH1 170 conserved protein #2 MTH9 46 ribosomal protein L35 (E.coli L29) #3 MTH21 109 ribosomal protein L19 #4 MTH31 30 ribosomal protein L14 #5 MTH34 236 ribosomal protein S18 (E.coli S13) #6 MTH40 58 DNA-dependent RNA polymerase, subunit N #7 MTH42 171 DNA-dependent RNA polymerase, subunit K #8 MTH43 51 enolase #9 MTH47 21 conserved protein #10 MTH48 73 conserved protein #11 MTH52 189 aspartate aminotransferase related protein #12 MTH147 23 phenylacrylic acid decarboxylase #13 MTH148 47 conserved protein #14 MTH150 75 conserved protein #15 MTH243 231 conserved protein #16 MTH248 195 conserved protein #17 MTH249 64 conserved protein #18 MTH250 23 tRNA intron endonuclease #19 MTH251 54 tryptophanyl-tRNA synthetase #20 MTH252 22 conserved protein #21 MTH253 75 threonine synthase #22 MTH254 206 histone HMtB #23 MTH255 269 ribosomal protein L7a #24 MTH256 49 ribosomal protein S28 #25 MTH261 24 translation initiation factor eIF-2, gamma subunit #26 MTH262 24 conserved protein #27 MTH611 84 prolyl-tRNA synthetase #28 MTH868 45 agmatine ureohydrolase #29 MTH869 103 translation initiation factor, eIF-5A #30 MTH890 145 conserved protein #31 MTH891 59 conserved protein #32 MTH893 60 integrase-recombinase protein #33 MTH894 179 conserved protein #34 MTH895 51 conserved protein #35 MTH1107 107 oxaloacetate decarboxylase, alpha subunit #36 MTH1192 76 conserved protein #37 MTH1193 146 transcriptional regulator #38 MTH1194 35 acetylpolyamine aminohydolase #39 MTH1254 135 argininosuccinate synthase #40 MTH1445 64 glycinamide ribonucleotide synthetase #41 MTH1449 135 dihydroxy-acid dehydratase #42 MTH1495_MTH1496 194 MTH1495: ornithine cyclodeaminase, MTH1496: amidase #43 MTH1601 246 aspartate aminotransferase #44 MTH1692 113 conserved protein #45 MTH1694 207 aspartate aminotransferase related protein #46 MTH1894 34 aspartate aminotransferase homolog #47 MTH1895 170 conserved protein Motif number 1 ATATTTAAACTTTCCGCTGGTGAGG 1 5 0 TTCCGCTGGT 0.893223 -166 TTAAAAAGTTTTTTCGCTGGACTGGAAAATA 3 29 0 TTTCGCTGGA 0.89241 -81 AGAAGCCGGATCACTGCTGGAAAACAAAAAA 11 69 0 TACTGCTGGA 0.64642 -121 ATTATCATGTAGTCCACTGGAGTTAATAAAA 11 128 0 ATCCACTGGA 0.763474 -62 TCAGGACAGAAACCTCCTGGAACAGATTAAC 13 17 1 ACCTCCTGGA 0.773626 -31 TCTGATTTTTTTTCTCATGGTACTTACAATA 15 146 1 TTCTCATGGT 0.692122 -86 GTCACACTCTCCCCTGGATTATAGGTAA 15 214 0 TTCCCCTGGA 0.990433 -18 CCAGCGGAATATTCCCCAGGAACACGGAAGG 16 87 0 ATCCCCAGGA 0.6698 -109 CCTGGGGAATATTCCGCTGGAGGGGTGCTGG 16 98 1 ATCCGCTGGA 0.942503 -98 CCCCAGATAGAGTTCCCTGGAAAACCAGCAC 16 122 0 ATTCCCTGGA 0.882451 -74 CCCTGAAGGATTTCCCCTGGAGGGTCAGGGT 16 161 1 TTCCCCTGGA 0.990433 -35 GTTAAAGGGGTCTTCCATGGATGACTGCAGC 17 13 0 TTTCCATGGA 0.900495 -52 ACCCCGTTTAATTTCCCTGGTTAATTCAGGT 21 11 1 ATTCCCTGGT 0.591883 -65 AACTTCAAGTTGTCCGATGAAAAATAGAAAA 22 50 0 TTCCGATGAA 0.791022 -157 GGGTTGAAGGTGCCCCATGAACCAACCGATG 22 118 1 TCCCCATGAA 0.762124 -89 CAGAATACGATTTCTCATGAAAATCTGTATC 23 134 1 TTCTCATGAA 0.690307 -136 ATTGGTGTAATTACCGATGGATGGTAGAAAA 23 244 1 TACCGATGGA 0.772067 -26 AAATATATTTTTCCCTGGAGATAAACACT 27 66 0 TTTCCCTGGA 0.951994 -19 TTTTATATAATGTCCACTGAATTAATAGATA 29 38 1 TTCCACTGAA 0.620249 -66 CTTTCCTCCATGAATCTGTTAAAA 30 4 1 TCTCCATGAA 0.380299 -142 ATTATTTATCCCCTGAATCAGAAAATG 38 7 1 TTCCCCTGAA 0.951994 -29 TTCTTTGGGTTTTCTCCTGGTGGGAGCTGGA 43 40 1 TTCTCCTGGT 0.831256 -207 AAGAGGTGATTAACTGATGGATCGCGGCTTC 43 96 0 TACTGATGGA 0.454835 -151 CCTTCTTCTCTTTCGCATGGATACTCCTGTG 45 174 1 TTCGCATGGA 0.755546 -34 CACATGGTATTGCCCCATGGAGCAGTTTAAG 47 76 1 TCCCCATGGA 0.943585 -95 ACCTAAATATAATCTCATGGAACTCCGGGAA 47 115 1 ATCTCATGGA 0.814992 -56 * ********* Masking position 9 Map Score: 25.9045 Number of sites scoring better than the average of aligned sites = 1169 Number in coding regions = 1094 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 AGCTTTGCTCCTCCTGGGTTCAAATCCCAGTC 5 119 1 CTCCTGGGCA 0.978303 -118 GAACTCGGGTCTCCAGCGTTCCGGTGCTGACC 7 85 0 CTCCAGCGCC 0.881375 -87 TTTTTATTAACTCCAGTGGACTACATGATAAT 11 127 1 CTCCAGTGCT 0.831069 -63 CATGGGCCATCCCCTGGGCACAGCCTCTCGCC 15 15 0 CCCCTGGGCA 0.935017 -217 AATATTATACCTTGAGGGGCCCCGGGTCCCGT 16 42 1 CTTGAGGGCC 0.900945 -154 GGTGCTGGTTTTCCAGGGAACTCTATCTGGGG 16 121 1 TTCCAGGGCT 0.781053 -75 AGGGGAAATCCTTCAGGGCGCTGACACCCCAG 16 147 0 CTTCAGGGCT 0.970023 -49 AACCCTGACCCTCCAGGGGAAATCCTTCAGGG 16 161 0 CTCCAGGGAA 0.83483 -35 ACCTCCCGTGAGTGCTGGTTGAG 18 8 0 CCCGTGAGCT 0.511438 -16 TAGTGTTTATCTCCAGGGAAAAATATATTT 27 65 1 CTCCAGGGAA 0.83483 -20 TTCAGGCAATCTTCTGGCTCCTGACCTGAATT 33 39 0 CTTCTGGCCT 0.608672 -141 CGATCCCTCCTGAGGGCCTGCGGCCTGA 41 7 1 CTCCTGAGCC 0.923772 -129 GCCACATCCACCTGAGGGAACTTGCAGAGGCT 41 102 1 CCTGAGGGCT 0.740147 -34 GGGTTTTCTCCTGGTGGGAGCTGGAGCTCAGG 43 46 1 CTGGTGGGCT 0.635288 -201 CTGAATCAGGCTCCTGAGCTCCAGCTCCCACC 43 58 0 CTCCTGAGCC 0.923772 -189 TGGATCGCGGCTTCAGGGACCTGAATCAGGCT 43 78 0 CTTCAGGGCT 0.970023 -169 TTAATCACCTCTTCAGGGCCCCATGACTGGCT 43 114 1 CTTCAGGGCC 0.970565 -133 GAGAATCTTCTGAGATCAAAAATAAATA 46 7 1 CTTCTGAGCA 0.783343 -28 ACTTAAACTGCTCCATGGGGCAATACCATGTG 47 76 0 CTCCATGGCA 0.730367 -95 ******** ** Masking position 6 Map Score: 16.8136 Number of sites scoring better than the average of aligned sites = 1070 Number in coding regions = 1021 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 TGCATTGTGGAAATATTTATAAATAAATCCG 1 135 1 AAAATTTATA 0.675448 -36 GTCCAGCGAAAAAACTTTTTAAGGGGATACC 3 38 1 AAACTTTTTA 0.687144 -72 GATGTATCATATAACTGTATATTATGACATC 5 37 0 ATACTGTATA 0.752014 -200 ATCAATCGATAACTTTATATATTTTTATT 6 9 1 ATACTTTATA 0.928537 -50 TACTGACATAATAACTTTATGCG 14 63 1 ATACTTTATG 0.777191 -13 AAAATTAGCGATATATTTATATAGGATTATA 22 164 1 ATAATTTATA 0.650059 -43 AATTGGCAGCAAAACTTTATATGTGATGAAG 23 44 1 AAACTTTATA 0.93572 -226 TTTCTCATGAAAATCTGTATCCAGCAAGTTT 23 144 1 AAACTGTATC 0.477002 -126 AAGTGGGTGAGTACCTTTATATGTTCTCGGT 23 180 0 GTACTTTATA 0.622326 -90 ACATTATATAAAAGCTTTATAGGAATTCAGT 29 20 0 AAACTTTATA 0.93572 -84 TGGCCCTTTAATAACTTGATAATATCTATAT 30 122 0 ATACTTGATA 0.607344 -24 CAATCCCAATTTACCTTTATATCCATAAATT 33 147 1 TTACTTTATA 0.526465 -33 ATCTTCAGATAAACATTTATAAGGGAACATC 37 37 1 AAAATTTATA 0.675448 -110 ATTCACTTAAAAAACTTTATAATATAACTTT 37 107 1 AAACTTTATA 0.93572 -40 GGGATAACTTTATCCACATTTATA 43 4 1 ATACTTTATC 0.777191 -243 GGACTCATGTAAATCTTTTTAAATGGACAGA 43 179 1 AAACTTTTTA 0.687145 -68 TGATCATTGCAAACCTTTATGTCAACCACCA 44 47 0 AAACTTTATG 0.796247 -67 *** ******* Masking position 6 Map Score: 11.795 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 21 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 AGTTATATGATACATCCTGTGCCGGGATAGCCTAGC 5 52 1 TCTTGCCGGG 0.988429 -185 GTCCGGAAACTTCTTCAATGGCTGGGAGGATGGACC 7 29 0 TCTAGCTGGG 0.979595 -143 GGTTTATAATTCCTTTTTTAACAGGGTATCCCTGAG 11 27 1 TCTTACAGGG 0.796909 -163 GTGATCCGGCTTCTTCACAGGCTGGGGATTCAGCAC 11 86 1 TCTCGCTGGG 0.918149 -104 AGAGATTCTTTGCCTGTAATGCCGGGGTGATAAACT 15 77 0 TCTAGCCGGG 0.99119 -155 TGCCATAGGTTACCTATAATCCAGGGGAGAGTGTGA 15 205 1 TCTACCAGGG 0.964245 -27 GGGCCCCGGGTCCCGTGATGCCCGGGAGGCCTTCCG 16 58 1 TCGACCCGGG 0.955891 -138 GCTGGAGGGGTGCTGGTTTTCCAGGGAACTCTATCT 16 113 1 TCGTCCAGGG 0.896428 -83 CAAGCACTCGTGGATATACTGCTGGGTTGAAGGTGC 22 95 1 TGTAGCTGGG 0.801046 -112 TTTCTATTAATCCTTGTTTTCCTGGGCGTCTTACTG 23 81 1 TCTTCCTGGG 0.943212 -189 CTGGGCGTCTTACTGGATGATCCGGGATAATTCAGA 23 102 1 TCGTTCCGGG 0.759353 -168 TAACCAGTCATTCCTCAAAAGGAGGGTTTAC 31 39 1 TCTAGGAGGG 0.907587 -21 GTTCGATGAGTGCATGATCCGCAAGGTTTAAGTGGA 32 30 1 TCTTGCAAGG 0.717623 -31 GCCTGAATTCTTCCTTCAAGGGCGGGCTTAATTTTT 33 64 1 TCTAGGCGGG 0.949185 -116 GAGTTTCCGGTCCATGGACCGCCGGGACAGCCATGA 42 83 1 TCTAGCCGGG 0.991188 -112 * * * * ****** Masking position 1 Map Score: 17.2663 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 185 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TATGATACATCCTGTGCCGGGATAGCCTAG 5 57 1 CCTGTGCCGG 0.960088 -180 GGTTCAAATCCCAGTCCCGGCGTCGGTTAA 5 135 1 CCAGTCCCGG 0.950952 -102 CTCCAGCGTTCCGGTGCTGACCATCCCCGT 7 77 0 CCGGTGCTGA 0.861016 -95 AATAAAAATTGCTGTGCTGAATCCCCAGCC 11 105 0 GCTGTGCTGA 0.900967 -85 CCAGGAGGTTTCTGTCCTGATTTTTT 13 7 0 TCTGTCCTGA 0.797076 -41 TCTTCTGGCTCCTGACCTGAATTTTATTGA 33 32 0 CCTGACCTGA 0.817098 -148 CACCCTCGAGGCAGTCATGGCAGCTATTAA 42 53 0 GCAGTCATGG 0.833983 -142 TACTGTCATGGCTGTCCCGGCGGTCCATGG 42 94 0 GCTGTCCCGG 0.948957 -101 TGAAAATCAGCCAGTCATGGGGCCCTGAAG 43 124 0 CCAGTCATGG 0.91829 -123 TAAAAACAGTCCAGTCATGGT 45 2 0 CCAGTCATGG 0.91829 -206 CATGGATACTCCTGTGCTGATGTGATAAA 45 189 1 CCTGTGCTGA 0.953358 -19 ********** Masking position 2 Map Score: 7.71422 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 304 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TCTGTCCGGATTTATTTATAAATATTTCCAC 1 141 0 TTTATTTTAA 0.508896 -30 CGCATAAAGTTATTATGTCAGTAAAACTAT 14 56 0 TTATTATTCA 0.349201 -20 AGAATCTGATTTTTTTTCTCATGGTACTTAC 15 142 1 TTTTTTTTCA 0.733189 -90 ACTTACAATATTTATTTACCATCAGCGATAA 15 167 1 TTTATTTCCA 0.683427 -65 CTGACCTTCTTATTTCTCATTT 20 4 0 CTTATTTTCA 0.869396 -19 TTTAAGCTTTTCTATTTTTCATCGGACAACT 22 43 1 TCTATTTTCA 0.683427 -164 CAACTTGAAGTTAATTTCTCACCCTCCAAGC 22 69 1 TTAATTTTCA 0.808919 -138 GCAGCAAAACTTTATATGTGATGAAGCTTTA 23 49 1 TTTATATTGA 0.689368 -221 CTCTGATTATTTTATATATCAGTATCGTCAT 30 86 1 TTTATATTCA 0.930392 -60 TTAATTTATTTTTCATTTATTTCAA 33 5 1 TTTATTTTCA 0.944516 -175 AAGGGCGGGCTTAATTTTTCAGAAGGTCAGT 33 81 1 TTAATTTTCA 0.808914 -99 CCTTATATTTCAAGTTGAAGTG 42 2 1 CTTATATTCA 0.839401 -193 GTTGATCAGACTTATATCTCACTTCAACTTG 42 21 0 CTTATATTCA 0.839401 -174 TTTATCCACATTTATATATCATTCTTTGGGT 43 19 1 TTTATATTCA 0.930392 -228 CGCCTTTATTTATTTTTGATCTCAGAAGA 46 16 0 TTTATTTTGA 0.738659 -19 ATCAGCTGAATTTATAAATCATGCTAGACAG 47 21 1 TTTATAATCA 0.533511 -150 ******* *** Masking position 5 Map Score: 8.20708 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 14 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 GTGGTCTGTGGTTTTACTTGCCCAGTCTGCAT 1 108 1 GTTTTCTTCC 0.930813 -63 CTATTTTAATGTTTTTCTTGGAGGCAT 7 155 1 GTTTTCTTGA 0.923441 -17 AGTTCTAATAGTTTTACTGACATAATAACTTT 14 49 1 GTTTTCTGCA 0.97119 -27 AGGGGTGCTGGTTTTCCAGGGAACTCTATCTG 16 118 1 GTTTTCAGGA 0.782194 -78 TAATTTTAAGGTTTTTCTGAGCCATCGGTTGG 22 139 0 GTTTTCTGGC 0.963547 -68 CACATATAAAGTTTTGCTGCCAATTAAAAAGG 23 37 0 GTTTTCTGCA 0.97119 -233 ATTAATCCTTGTTTTCCTGGGCGTCTTACTGG 23 86 1 GTTTTCTGGC 0.963547 -184 CTGGTTTTTCTACCATCCATCGGTA 23 255 0 GTTTTCTACA 0.813866 -15 AATCAGAGGTGTGTTTCTGGGCTATATTTAAA 30 62 0 GTGTTCTGGC 0.832713 -84 ATACGCTCATGTTTTTATTACAGCACTATAGA 39 93 0 GTTTTATTCA 0.689081 -43 CTCATCCGTGGTTTTAATTTCATTTCCAACAC 42 124 1 GTTTTATTCA 0.689081 -71 ***** *** ** Masking position 5 Map Score: 6.80988 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 50 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AGGGTAGCTTGGTCCATCCTCCCAGCCATTG 7 19 1 GGCCATCCTC 0.989256 -153 GTTCCGGTGCTGACCATCCCCGTTCCAGTTG 7 69 0 TGCCATCCCC 0.957261 -103 CCATCCCCTGGGCACAGCCTCTCGCCCATA 15 10 0 GGACAGCCTC 0.97132 -222 CCGGAATCATGGGCCATCCCCTGGGCACAGC 15 23 0 GGCCATCCCC 0.992812 -209 CATTTATAAGGGAACATCCCCTATCTTATAA 37 50 1 GGACATCCCC 0.984666 -97 GTTTAATTGAGGTTCAGCCTCGGGTAGGTAA 45 137 1 GGTCAGCCTC 0.950517 -71 ** ******** Masking position 6 Map Score: 4.54048 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 74 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AAAAGTTACTGAGGTGATTTA 4 20 1 GGGTGATTTA 0.864708 -11 AGTTTATTATGAGGTGTTTTA 8 41 1 GGGTGTTTTA 0.7432 -11 AAACCTCCTGGAACAGATTAACGGGGCAAGA 13 26 1 GACAGATTAA 0.72798 -22 CTGTAATGCCGGGGTGATAAACTGATAACTG 15 69 0 GGGTGATAAA 0.709877 -163 CCATACACAAGTACTGATTAAAG 17 52 1 GACTGATTAA 0.807254 -13 CCTCCCGTGAGTGCTGGTTGAG 18 2 0 GGCTGGTTGA 0.866623 -22 GGGCCCTGAAGAGGTGATTAACTGATGGATC 43 104 0 GGGTGATTAA 0.95832 -143 CTTTTTAAATGGACAGATTAAAAATAGATAC 43 193 1 GACAGATTAA 0.72798 -54 TTTTCGTGGTGTGGTGGTTGACATAAAGGTT 44 36 1 GGGTGGTTGA 0.911138 -78 TTTCGTGGTTGTAGTGGTTGATGTAAAGGTG 44 88 1 GAGTGGTTGA 0.746661 -26 AAACCCTAAAGTGGAGTTTAATTGAGGTTCA 45 122 1 GGGAGTTTAA 0.869326 -86 ATGCTAGACAGCGGAGATTAATGAACCTTCA 47 41 1 GGGAGATTAA 0.936273 -130 TTGCCCCATGGAGCAGTTTAAGTGCCATGAA 47 85 1 GGCAGTTTAA 0.808273 -86 * ********* Masking position 11 Map Score: 6.13312 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 251 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 CAAATCCCAGTCCCGGCGTCGGTTAAAGCA 5 139 1 TCCCGGCGTC 0.949304 -98 TGGTCCATCCTCCCAGCCATTGAAGAAGTT 7 28 1 TCCCAGCCAT 0.882245 -144 CGAGTTCAAATCTCGGCGGTCCCATCAAAT 7 110 1 TCTCGGCGGT 0.87958 -62 ACGGAAGGCCTCCCGGGCATCACGGGACCC 16 65 0 TCCCGGGCAT 0.964335 -131 ATCCTTGTTTTCCTGGGCGTCTTACTGGAT 23 90 1 TCCTGGGCGT 0.76196 -180 CTGACATAGTTCCCGGCCACATCCACCTGA 41 87 1 TCCCGGCCAC 0.977415 -49 GTCATGGCTGTCCCGGCGGTCCATGGACCG 42 90 0 TCCCGGCGGT 0.986756 -105 TTTACATGAGTCCCGGCCAGCCATCAGTAA 43 162 0 TCCCGGCCAG 0.95921 -85 GACATTGTATTCCCGGAGTTCCATGAGATT 47 125 0 TCCCGGAGTT 0.810938 -46 ********** Masking position 1 Map Score: 4.51396 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 187 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TTTGCTGATAAACCCGAAAAATTTCAGGTA 3 65 0 AACCCGAAAA 0.975824 -45 AGGAATTATAAACCCCAGAAAACAGAAAAA 11 11 0 AACCCCAGAA 0.8838 -179 AAGTTAATTCAACACGAGAAGAATGATATT 11 156 0 AACACGAGAA 0.939264 -34 GCAGCATCTAAACCCGAAGAGATTCTTTGC 15 100 0 AACCCGAAGA 0.958083 -132 ACCAGGAGAAAACCCAAAGAATGATATATA 43 31 0 AACCCAAAGA 0.747775 -216 CAACCACCACACCACGAAAACCGGCACACC 44 26 0 ACCACGAAAA 0.899339 -88 AACCACTACAACCACGAAAACCGGCAGGGT 44 77 0 ACCACGAAAA 0.899339 -37 CATCATCAAGAACCCGAGAAGGTTGAT 47 154 1 AACCCGAGAA 0.975347 -17 ********** Masking position 7 Map Score: 3.72398 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 47 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 CGAAAAAACTTTTTAAGGGGATACCTGAAATT 3 44 1 TTTAAGGGGT 0.959451 -66 TATTCACAGGGTGCATATGTA 9 1 1 TTTCACAGGT 0.952013 -21 GATGGAAAATTTTTAAGGGCGTTAAAAT 10 56 1 TTTAAGGGCT 0.734272 -18 TTTTTCTGTTTTCTGGGGTTTATAATTCCT 11 9 1 TTTCTGGGGT 0.760466 -181 ATAATTCCTTTTTTAACAGGGTATCCCTGAGA 11 32 1 TTTAACAGGT 0.944832 -158 TGATCCGGCTTCTTCACAGGCTGGGGATTCAG 11 87 1 TTTCACAGGT 0.952013 -103 TGGCTGCATCTGTTAAAGGGGTCTTCCATGGA 17 23 0 TTTAAAGGGT 0.754249 -42 TACTATATCATTTTAACAGATTCATGGAGGAA 30 13 0 TTTAACAGAT 0.574367 -133 CGGGCTTAATTTTTCAGAAGGTCAGTGACTTC 33 86 1 TTTCAGAAGT 0.629324 -94 CAACATGTCATGTTAACAGGTTCAACCTGGAA 34 19 1 TTTAACAGGT 0.944832 -33 ATCATTTTCTGATTCAGGGGATAAATAAT 38 8 0 GTTCAGGGGT 0.824727 -28 AAACAAAGTTTATTAAGAGGTTTGTTTAATAT 45 82 1 TTTAAGAGGT 0.953328 -126 * ******** * Masking position 4 Map Score: 4.40386 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 109 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 ATCCTGTGCCGGGATAGCCTAGCCAGGTAAGG 5 65 1 GGGAGCCTAG 0.951651 -172 ACCGGAACGCTGGAGACCCGAGTTCAAATCTC 7 92 1 TGGACCCGAG 0.958876 -80 TCGATTTGATGGGACCGCCGAGATTTGAACTC 7 111 0 GGGAGCCGAG 0.990095 -61 TTCTTTCTCAGGGATACCCTGTTAAAAAAGGA 11 37 0 GGGACCCTGT 0.854813 -153 CTGTGCCCAGGGGATGGCCCATGATTCCGGTT 15 24 1 GGGAGCCCAT 0.803842 -208 ATTCTTTGCCTGTAATGCCGGGGTGATAAACT 15 77 0 TGTAGCCGGG 0.918506 -155 CCCGGGTCCCGTGATGCCCGGGAGGCCTTCCG 16 62 1 GTGACCCGGG 0.904861 -134 AAGGTAAATTGGGATTGCCAGTATATATAACT 33 132 0 GGGAGCCAGT 0.882706 -48 TTCCGGTCCATGGACCGCCGGGACAGCCATGA 42 87 1 TGGAGCCGGG 0.993058 -108 GATTTACTGATGGCTGGCCGGGACTCATGTAA 43 159 1 TGGCGCCGGG 0.964206 -88 TATAATCTCATGGAACTCCGGGAATACAATGT 47 122 1 TGGATCCGGG 0.941085 -49 **** ****** Masking position 8 Map Score: 6.71004 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 321 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 AATGCTGAATACAAGGAGGTTTCTTGA 3 93 1 AAAGGAGGTT 0.925187 -17 AATTCACTCTTACTGGAGGTTAATGA 5 221 1 TCTGGAGGTT 0.946782 -16 AAAAACATTAAAATAGAGGTTCTTGGATTCG 7 140 0 AATAGAGGTT 0.398388 -32 TTGAATTAACTTCTGGAGGATAAATC 11 174 1 TCTGGAGGAT 0.831804 -16 GTTAATCTGTTCCAGGAGGTTTCTGTCCTGA 13 17 0 TCAGGAGGTT 0.952885 -31 GAAGGATTTCCCCTGGAGGGTCAGGGTTTGA 16 165 1 CCTGGAGGGT 0.898595 -31 CACTCATTCTAACAGGAGGTAAGATTA 29 87 1 ACAGGAGGTA 0.824382 -17 TTTAACAGATTCATGGAGGAAAG 30 3 0 TATGGAGGAA 0.48506 -143 GTCATTCCTCAAAAGGAGGGTTTAC 31 45 1 AAAGGAGGGT 0.92648 -15 TGCTGTGTATTTAAGGAAGTTCCTACTATGT 35 50 1 TAAGGAAGTT 0.447706 -58 GGGAAAATAAAAAAGGAGGGTAATTA 37 6 0 AAAGGAGGGT 0.92648 -141 GCCGCAGGCCCTCAGGAGGGATCG 41 4 0 CCAGGAGGGA 0.730362 -132 GCAGAGGCTGTTAAGGAGGGT 41 125 1 TAAGGAGGGT 0.935892 -11 ATCCACTTTAATCTGGAGGTTTT 43 234 1 ACTGGAGGTT 0.938864 -13 AAGTGGAGTTTAATTGAGGTTCAGCCTCGGG 45 130 1 TATTGAGGTT 0.434115 -78 * ********* Masking position 7 Map Score: 9.61743 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 710 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 15 TATTAATATCTGTCCGGATTTATTTATAAAT 1 149 0 TGTCCGGATT 0.97465 -22 ATTGAAGAAGTTTCCGGACTTTTCAACTGGA 7 46 1 TTTCCGGATT 0.960381 -126 AGGAGGTTTCTGTCCTGATTTTTT 13 4 0 TGTCCTGATT 0.960381 -44 TTCTGGCTCCTGACCTGAATTTTATTGAAAT 33 29 0 TGACCTGATT 0.880492 -151 AGCCAGAAGATTGCCTGAATTCTTCCTTCAA 33 52 1 TTGCCTGATT 0.926845 -128 TATACGGATTTTTCCGGAAGTGGGCCAGCAA 39 16 0 TTTCCGGAGT 0.865561 -120 TAGGATAATGTGGCCTGATTTTATTACAGAG 45 40 1 TGGCCTGATT 0.952598 -168 TGACATTGTATTCCCGGAGTTCCATGAGATT 47 125 0 TTCCCGGATT 0.916106 -46 ******** ** Masking position 8 Map Score: 3.89707 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432