AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_tpal_reg_300.orf -o00230_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0002 242 DNA polymerase III, subunit beta (dnaN) #2 TP0045 300 adenosine deaminase, putative #3 TP0053 170 ribonucleoside-diphosphate reductase, subunit beta (nrdB) #4 TP0103 64 ATP-dependent DNA helicase, putative #5 TP0104 246 5'-nucleotidase (ushA) #6 TP0105 166 DNA polymerase I (polA) #7 TP0185 147 signal peptidase I (sip) #8 TP0186 54 oxygen-independent coproporphyrinogen III oxidase, putative #9 TP0187 63 translation elongation factor TU (tuf) #10 TP0188 71 ribosomal protein S10 (rpsJ) #11 TP0189 46 ribosomal protein L3 (rplC) #12 TP0192 55 ribosomal protein L2 (rplB) #13 TP0207 187 ribosomal protein L15 (rplO) #14 TP0231 100 conserved hypothetical protein #15 TP0232 99 T. pallidum predicted coding region TP0232 #16 TP0233 30 anti-sigma F factor antagonist, putative #17 TP0234 234 ribosomal protein L33 (rpmG) #18 TP0235 149 preprotein translocase subunit (secE) #19 TP0237 106 ribosomal protein L11 (rplK) #20 TP0240 108 ribosomal protein L7/L12 (rplL) #21 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #22 TP0278 127 T. pallidum predicted coding region TP0278 #23 TP0279 45 ribosomal protein S1 (rpsA) #24 TP0283 177 lipopolysaccharide core biosynthesis protein (kdtB) #25 TP0284 104 T. pallidum predicted coding region TP0284 #26 TP0289 22 T. pallidum predicted coding region TP0289 #27 TP0290 54 conserved hypothetical protein #28 TP0291 36 T. pallidum predicted coding region TP0291 #29 TP0524 135 ATP-dependent protease LA (lon-2) #30 TP0595 23 adenylate kinase (adk) #31 TP0596 107 polynucleotide adenylyltransferase (pcnB) #32 TP0598 36 T. pallidum predicted coding region TP0598 #33 TP0604 103 ribosome recycling factor #34 TP0605 90 translation elongation factor TS (tsf) #35 TP0607 249 T. pallidum predicted coding region TP0607 #36 TP0608 300 T. pallidum predicted coding region TP0608 #37 TP0642 140 phosphomannomutase (manB) #38 TP0669 153 DNA polymerase III, subunit alpha (dnaE) #39 TP0671 30 sn-1,2-diacylglycerol cholinephosphotransferase, putative #40 TP0672 134 glycyl-tRNA synthetase (glyS) #41 TP0673 177 glutamyl-tRNA synthetase (gltX) #42 TP0734 81 purine nucleoside phosphorylase (deoD) #43 TP0736 233 hydrogenase, gamma chain (hydG) #44 TP0886 147 polyribonucleotide nucleotidyltransferase (pnp) #45 TP0891 175 translation initiation factor 2 (infB) #46 TP0892 49 N utilization substance protein A (nusA) #47 TP0893 174 conserved hypothetical protein #48 TP0895 21 T. pallidum predicted coding region TP0895 #49 TP0900 38 T. pallidum predicted coding region TP0900 #50 TP0901 40 conserved hypothetical integral membrane protein #51 TP1005 58 DNA polymerase III, subunits gamma and tau (dnaH) #52 TP1006 108 DNA gyrase, subunit B (gyrB) #53 TP1007 42 thymidylate synthase-complementing protein (thy1) #54 TP1008 126 ribonucleoside-diphosphate reductase, subunit alpha (nrdA) #55 TP1009 96 glycerol-3-phosphate dehydrogenase (gpsA) #56 TP1010 125 nucleoside-diphosphate kinase (ndk) #57 TP1011 34 peptidyl-tRNA hydrolase (pth) #58 TP1012 204 RNA polymerase sigma-43 factor (sigA) #59 TP1039 226 adenine phosphoribosyltransferase (apt) Motif number 1 CAACCGATGTGAGCGTGGTGGGGTTTGTTAGC 2 37 1 GGGTGGTGGG 0.779773 -264 GTATTGGGCAGGGAAACCTGCGAGTGTGTTCT 2 119 0 GGAACCTGCG 0.713044 -182 ACACAAGACACAGAGCCCTGCAGACAGACATT 3 71 1 CGGCCCTGCA 0.733812 -100 GGTCTAGGTTCCGTACCGTGCGGGCACGGAAC 5 190 1 CGACCGTGCG 0.948425 -57 TCCGCTCGATGTGTTCCGTGCCCGCACGGTAC 5 202 0 GGTCCGTGCC 0.862864 -45 CTATCCGGTAGCATCCGGCGCCATGAGGGGCA 7 61 0 GACCGGCGCC 0.802313 -87 TGTGTAGGCGCCGCATTTGTGGTGC 8 4 1 GAGCGCCGCA 0.770389 -51 CGCATTTGTGGTGCGTGCTGCGCATCGTGCTG 8 22 1 GGGTGCTGCG 0.960901 -33 TCGTGAGAATGGGTACGCCGTGTACTATTTGA 9 15 1 GGACGCCGTG 0.780211 -49 GCGTTTGCGGCGCGGAGTGTGTTT 10 3 1 GTGCGGCGCG 0.954712 -69 TGTGTTTTGTCTGTGCGTTGCGATACGGAAGA 11 17 1 CGGCGTTGCG 0.744145 -30 CGGTAAGCTGCGGTAGCTGCGT 12 1 1 CGAAGCTGCG 0.515264 -55 TGCGGTAGCTGCGTAAGGTGCCAGAGCGGTGA 12 19 1 GGAAGGTGCC 0.774402 -37 TCGGTCAGAGGGAGCCGGTGCGTCGGACGGTT 13 53 1 GACCGGTGCG 0.903128 -135 AACCCAAAGACCGAACCGTCCGACGCACCGGC 13 66 0 CGACCGTCCG 0.724834 -122 GGAGAAAGACGGGAGTCCTGCCGTCTTGGGGA 13 120 1 GGGTCCTGCC 0.858679 -68 CTGCCGTCTTGGGGATGGTGCGAGCTGTTTCG 13 137 1 GGATGGTGCG 0.953037 -51 GAGCTGTTTCGCACCTGGTGCGGGTGGAGGAG 13 158 1 GACTGGTGCG 0.637951 -30 TTGACCGGTAGTATGCGGTGCCTGGTATAGGT 14 56 1 GAGCGGTGCC 0.955373 -45 GGGCATTCTGGTAGGCGGTGTGTGGTTTTGAG 15 23 1 GAGCGGTGTG 0.783191 -77 GTAACAGAAAGAGTGTCGTGTGAATTTCAATA 15 63 1 GGGTCGTGTG 0.694925 -37 GAGCCGCCCGGAGGCCGGCCCGCATTGTATAA 17 93 0 GGCCGGCCCG 0.843722 -142 ACAGGACTCCCCGAGCCGCCCGGAGGCCGGCC 17 105 0 CGGCCGCCCG 0.886326 -130 TTTTTTGCATGCGTCCGGCGCGTCGTTGTGTG 21 20 1 GGCCGGCGCG 0.982174 -243 TTTCGTGTGGGAGGGCGTCGCGCTTTTGAGTA 21 64 1 GGGCGTCGCG 0.920958 -199 CTTGAGTGGAGGGGACGGCGTCTCCCCTGTGT 21 169 1 GGACGGCGTC 0.753123 -94 GTGGTATAGGGAGCACCGTGTCGGTTCGGTGC 21 223 1 GGACCGTGTC 0.638796 -40 AGCGTTCGCGCCGTGCGGTGCGCACGTTGTGT 24 18 1 CGGCGGTGCG 0.987399 -160 TAAACGTCTTGCACGACCTGCGGGGGCGCAGT 29 34 1 GAGACCTGCG 0.556525 -102 CGGGGGCGCAGTATACCGCGCAGGTATATTTT 29 54 1 GAACCGCGCA 0.635995 -82 GTGTGCCCTCCGCGGTCTCTTT 34 1 1 GGGCCCTCCG 0.922031 -90 AGGAGAGCGGGCGGACGGCCCCTGAGTTGCCA 35 19 1 GGACGGCCCC 0.863698 -231 CCACGTAAACGGGCGCCCCGCGCCTACGCTCC 35 63 0 GGGCCCCGCG 0.989132 -187 ACGCCACGGCGCACGCCCTGCGCGGCATCTGC 36 46 1 GAGCCCTGCG 0.939383 -255 CATCTGCATGGAACGCCGCGCAGGACTGGGGA 36 71 1 GAGCCGCGCA 0.824572 -230 ACTGGGGAGAGCGAACCGTGCGAAAAAGCGTC 36 95 1 GGACCGTGCG 0.985543 -206 CCCGGTCACAGAAGACCGCGCCTCGGCCGCTC 36 161 0 GAACCGCGCC 0.846949 -140 CTATGTCGTACGGCGTGGTCCCGGTCACAGAA 36 180 0 CGGTGGTCCC 0.452666 -121 GCGGGTGAACGATTACCGCGCCTATAAGACTC 36 261 1 GTACCGCGCC 0.659573 -40 CGATCTCTGTGAGGTCGCCGCGGGTGCTGACA 40 75 1 GGTCGCCGCG 0.926599 -60 AGGGGGGAAGGTGAGCGGCGCGTCACC 40 118 1 GGGCGGCGCG 0.996853 -17 CCGCGTGAAGCGGCATCCTGCGTGGTAGGAAG 41 42 1 CGATCCTGCG 0.608444 -136 ACAGGGAGGCGGTCACGGTGCATGAGGAGTGT 41 80 1 GTACGGTGCA 0.468003 -98 TCACAGGGATGCTTGCGCCCCGGAGGGGGATG 41 125 1 GTGCGCCCCG 0.576135 -53 GAGAAAAGCAGCGGTCGGCGCGTTAGTTGCCT 43 115 1 GGTCGGCGCG 0.965585 -119 AAGTTTCGCAGTGCGTGCCGCCGAGGGGTTGT 44 26 1 GGGTGCCGCC 0.91399 -122 GGCTGTGCCAGGGCTTGGTGCGGCCTGCGATA 44 105 1 GGTTGGTGCG 0.826911 -43 TAACGTGCACCGGCGTGGTGCGGAGGTGCCGC 47 26 1 CGGTGGTGCG 0.936418 -149 ACATGCTAGAGTGAGCCCCGCGAGGGGTGCGT 47 151 1 GGGCCCCGCG 0.989133 -24 ACCCAAAAGGGAGTGCGGTGCACGG 50 26 1 GGGCGGTGCA 0.972977 -15 GTATTTCCATGTGAGTGGTGCCGTCTGACAGG 51 26 1 GGGTGGTGCC 0.955372 -33 GCTTCCCCCACAGAGACGCGCGGAAGAAAACA 54 19 0 CGGACGCGCG 0.815424 -108 AAAGTTTAGGGTCTGCGGTGCGTGTTCTTTTT 55 11 1 GCGCGGTGCG 0.895956 -86 AAAGAATGGTGGGTACGCTGGCGCGCCACGTG 56 80 1 GGACGCTGGC 0.552959 -46 GTGCGTGTAGGCATACGGCGCAAACGTGAAGA 58 36 0 GAACGGCGCA 0.734806 -169 AGAATGCGCCCCGCGCGGTGCGTGTAGGCATA 58 53 0 CGGCGGTGCG 0.987399 -152 GAGAACTGTAGCGCGCCGTGGGAAAGGGAGGT 58 109 1 GGGCCGTGGG 0.92244 -96 * * ******** Masking position 10 Map Score: 72.3249 Number of sites scoring better than the average of aligned sites = 4066 Number in coding regions = 3700 Number in noncoding regions = 366 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 CATTACTTAGCCCACCTCCTCTAGGAAATTTTCG 2 151 1 CCCACCTCCG 0.782143 -150 TATGTGCAGCACCCTTCTTTCCGCTCCTAACGTG 6 101 0 ACCCTTCTCC 0.401885 -66 AAAACGGCGTCCCTCCCAGACACGGCAGCCTAAC 7 124 0 CCCTCCCACG 0.931233 -24 ACACGGCGTACCCATTCTCACGACCAC 9 4 0 CCCATTCTCC 0.670852 -60 AACCCCTCCATCAGCCTAAAACCGC 10 57 0 ACCCCTCCCC 0.724791 -15 GTTATACGCACCCTCTTTGTCATGC 13 2 0 CCCTCTTTCG 0.641425 -186 CCGACGCACCGGCTCCCTCTGACCGATCGTACTC 13 45 0 GGCTCCCTGC 0.473796 -143 ATCCTCTCTCCTTTCCGTCCCGCACCTATACC 14 79 0 TCCTTTCCCG 0.767615 -22 AGGCCATCCCCACTAGCGGTTTCGCA 16 15 0 GCCATCCCCG 0.804777 -16 GTGACGCGCCTTTCTTTCTGGGGCAGGCTGG 17 8 1 GCCTTTCTCG 0.672558 -227 AGCACGAAACACCTCCCTAAACAGGCAGCCAACC 17 40 0 ACCTCCCTAG 0.57312 -195 ACCACCCCTCCTCACATCCACAGACGGA 17 217 0 CCCCTCCTCC 0.937367 -18 AAGGTTCGAGTCCTTCCTGGCCTGAGTGCTTTCG 18 114 1 TCCTTCCTCG 0.866803 -36 AAAAGCGCGACGCCCTCCCACACGAAAGGGTGTC 21 57 0 CGCCCTCCCG 0.898282 -206 GAGACGCCGTCCCCTCCACTCAAGTGAGGAGAAC 21 159 0 CCCCTCCACG 0.790793 -104 GCACTCCCCCCTCAAGCTGCACCGAACCG 21 244 0 CCCCCCTCGG 0.639307 -19 CCAGCGCACTCCCTTCCCCACATGGACTGCCGCT 22 44 0 CCCTTCCCCG 0.986591 -84 GAGCTCTCTACGCTTCCTAGCTACACAACGTGCG 24 38 0 CGCTTCCTCC 0.900852 -140 TATATTCGCACCCACTCCGTCAACTCCTCGCGGA 24 88 0 CCCACTCCCC 0.888747 -90 CCCGAGAAGGAGCTCCCTGTCAAGACCAACTAGG 31 66 0 AGCTCCCTCG 0.829979 -42 CTACCCCGCCCATCCTCCCCCGAGAAGGAGCT 31 86 0 CCCATCCTCG 0.920589 -22 CACGCCTGCTTGCTCCCCATCCTGCAGGGTGGCA 33 32 0 TGCTCCCCCG 0.900933 -72 GAGAAGCACGAGCTCCCCCACGCCTGCTTGCTCC 33 50 0 AGCTCCCCCC 0.8544 -54 GTACCCCTCCTGACAGCATTTTCCGAT 34 74 0 CCCCTCCTCC 0.937367 -17 GCCGTCCGCCCGCTCTCCTTCAGCAGG 35 4 0 CGCTCTCCCC 0.906569 -246 GCGCCTACGCTCCTTCCAGTCAAGCTGGCAACTC 35 42 0 TCCTTCCACG 0.5147 -208 TCTTCTGTGGACCTTCCCAGGCCCGCAGCAGGTT 35 187 0 ACCTTCCCGC 0.658746 -63 TCGCACGGTTCGCTCTCCCCAGTCCTGCGCGGCG 36 84 0 CGCTCTCCAC 0.487563 -217 GCGCCTCGGCCGCTCCTCATCTAGAGAGTAAGTT 36 142 0 CGCTCCTCCG 0.813458 -159 CCATTACAATGCCCCTCTATCCTGTGGTGCCGTA 37 82 1 GCCCCTCTCG 0.717345 -59 TATATTTTTATCCACCCTTGCAGGGTTTTTGCTC 38 58 0 TCCACCCTCG 0.800758 -96 GTTGTTGTCCGCTCTCTGCGCGCGGGGAAA 39 10 1 CGCTCTCTGC 0.562412 -21 CCGCTCACCTTCCCCCCTGTCTAGCATACTGTCA 40 102 0 TCCCCCCTCG 0.889391 -33 CCCTGTCTTCCCCTTCCTACCACGCAGGATGCCG 41 52 0 CCCTTCCTCG 0.975305 -126 CACCGTGACCGCCTCCCTGTCTTCCCCTTCCTAC 41 66 0 GCCTCCCTCC 0.910986 -112 TATCGCACATCCCCCTCCGGGGCGCAAGCATCCC 41 130 0 CCCCCTCCGG 0.859134 -48 CGCTCGCCCTCCCCGGGGGCCGATTATCGC 41 158 0 CCCTCCCCGC 0.960948 -20 CGTCACTCCCTCCCTTCGTGGGGCCTAGACC 42 61 0 CCCTCCCTGG 0.953497 -21 GTAAACCTCCCCGACACGTATATCTGTT 43 5 1 ACCTCCCCCG 0.962274 -229 GTTCATCGGACCCTTCTCGGCGCCGATGGCGTTT 43 36 1 CCCTTCTCCC 0.789518 -198 TGTACTATCATCCATCCCTCCGAGAGTTTGGTCG 43 196 1 TCCATCCCCG 0.780637 -38 GCACGCACCCCTCGCGGGGCTCACTCT 47 158 0 CGCACCCCGG 0.799905 -17 TCGTTCTTTACGCTTCCCCCACAGAGACGCGCGG 54 28 0 CGCTTCCCAG 0.720062 -99 GATTCCTAACCCCTCCCCTGATCCTCACCTTTCT 55 73 0 CCCTCCCCAC 0.907359 -24 TCTCTTTTTACCCTTCCTTCACCGTATGGTGAGT 56 21 0 CCCTTCCTAG 0.794772 -105 GTGCATACCTCCCTTTCCCACGGCGCGCTACAGT 58 113 0 CCCTTTCCCC 0.928239 -92 ******** * * Masking position 3 Map Score: 51.8418 Number of sites scoring better than the average of aligned sites = 1552 Number in coding regions = 1276 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 3 CCAAACAAAAACCGCACACAAGCTTGTGAAG 1 120 0 ACCGCACCAA 0.812709 -123 TGTACACGCGAACACACTGCACATGTGA 2 8 0 AACACACGCA 0.879364 -293 CGTCGTATAGAACACACTCGCAGGTTTCCCT 2 111 1 AACACACCGC 0.809951 -190 CTACCCTGTGCCCGCACTCAGGAGGAGGTTT 3 146 1 CCCGCACCAG 0.806153 -25 AGTAATGCTAACCACTCGGCCATAAAAATGC 5 96 0 ACCACTCGCC 0.776187 -151 CGGAACCTAGACCACACCGTATCGGAGACAC 5 172 0 ACCACACGTA 0.4978 -75 GTGTTCCGTGCCCGCACGGTACGGAACCTAG 5 193 0 CCCGCACGTA 0.50546 -54 AATAACTCCAAACACACTCCGCGCCGCAAAC 10 13 0 AACACACCCG 0.939607 -59 TCAGCCTAAAACCGCACCCACCTTGCAAAAT 10 41 0 ACCGCACCAC 0.912518 -31 GCACAGACAAAACACACACGCC 11 2 0 AACACACCGC 0.809951 -45 TCCGTATCGCAACGCACAGACAAAACACACA 11 15 0 AACGCACGAC 0.871273 -32 TCCTTCGGTCACCGCTCTGGCACCTTACGCA 12 28 0 ACCGCTCGGC 0.681939 -28 AGAACTCAAAACCACACACCGCCTACCAGAA 15 28 0 ACCACACCCG 0.961871 -72 CACCTTTTCGAAAGCACTCAGGCCAGGAAGG 18 125 0 AAAGCACCAG 0.495295 -25 TGCGCATTGCAACACTCTCCACCCTGGAAGA 19 17 0 AACACTCCCA 0.458197 -90 AAAAAACAACAAAACACCCGAAACCAACGCG 19 65 0 AAAACACCGA 0.224512 -42 GGACAGGAAGACAGCACCCCAGAAGCCTGAC 20 50 0 ACAGCACCCA 0.815909 -59 CGTAATACTCCCCACACAGGGGAGACGCCGT 21 183 0 CCCACACGGG 0.743496 -80 TGCTCCCTATACCACACGCTCTACCGTAATA 21 207 0 ACCACACCTC 0.693699 -56 TCTGATCACCAGCGCACTCCCTTCCCCACAT 22 55 0 AGCGCACCCC 0.801818 -73 CAACGTGCGCACCGCACGGCGCGAACGCTTC 24 16 0 ACCGCACGCG 0.984645 -162 TTTATATTCGCACCCACTCCGTCAACTCCTC 24 93 0 CACCCACCCG 0.760316 -85 CTGAACTTTAAAAGCACAGCCCCGAAGATCA 25 58 0 AAAGCACGCC 0.873628 -47 CACCCAAAAAACAACACGGCAACT 27 4 0 ACAACACGCA 0.65871 -51 TTTCCCTAAAAAAGCACTGCCCTCT 28 5 0 AAAGCACGCC 0.873628 -32 CSCCGCACAGCGAGCAGCATCT 32 2 1 SCCGCACGCG 0.984645 -35 ACACCACGCACACCAGATGCTGCTC 32 22 0 CACGCACCCA 0.87721 -15 TTCCCCTCACAACACAGTGCGGCAAGAGAGA 33 80 0 AACACAGGCG 0.490812 -24 GCGGGATTTGAACCCACCGCCTTTGGCTCCG 35 112 1 AACCCACGCC 0.893289 -138 AGTCGGAGCTACAGCACAGCATTCTAGGATT 38 104 0 ACAGCACGCA 0.823417 -50 CCCTCGGCGGCACGCACTGCGAAACTTCCCC 44 22 0 CACGCACGCG 0.944065 -126 CCTATGCACAACCCCTCGGCGGCACGCACTG 44 34 0 ACCCCTCGCG 0.607489 -114 GTCACCGGTGAACGCACAGCCTGCTCACTAG 45 61 0 AACGCACGCC 0.976924 -115 TGAGGGTGCTAACGCACTCGGGCGGCACCTC 47 48 0 AACGCACCGG 0.905827 -127 CCGTGCACCGCACTCCCTTTTGGGTAG 50 24 0 ACCGCACCCC 0.984904 -17 CGCGCGGAAGAAAACACCCCCGTG 54 4 0 AAAACACCCC 0.731159 -123 CTTTACGCTTCCCCCACAGAGACGCGCGGAA 54 26 0 CCCCCACGAG 0.463856 -101 AAGAACACGCACCGCAGACCCTAAACTTT 55 9 0 ACCGCAGCCC 0.793474 -88 CGTATGCCTACACGCACCGCGCGGGGCGCAT 58 51 1 CACGCACGCG 0.944062 -154 ******* *** Masking position 5 Map Score: 41.685 Number of sites scoring better than the average of aligned sites = 1399 Number in coding regions = 1255 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 4 GTTAGGTTTCCCCAAACCTACCCACAAAACAGGGACCACC 3 31 1 CCACCCCAAC 0.949457 -140 GCGCGTAACTCGCGGAATATACAAGGCAACTGTATGTTCT 5 58 0 CCAACAGCAC 0.966109 -189 CGGCGTCCCTCCCAGACACGGCAGCCTAACACGGCGATAA 7 114 0 CCACCACTAC 0.764678 -34 GTCAACCAAACACGCAAACAGCAGGATAACACGGAGTACA 14 21 0 CCAACAGTAC 0.948531 -80 CGAAACACCTCCCTAAACAGGCAGCCAACCAGCCTGCCCC 17 30 0 CCAACACAAC 0.983514 -205 CGCCTCACCTCACACATCAAGCACGAAACACCTCCCTAAA 17 53 0 CCATCAGAAA 0.739212 -182 CCCACAAATCCCCGGAAAACACCAGAAAACCCCGTGCGTA 18 28 0 CCAACCGAAC 0.990701 -122 CCGAAACCAACGCGTAAGCGGCAGGCAATCATGCGCATTG 19 39 0 CCAACAGAAC 0.98992 -68 CTCTCCTTATGACGTAAAAAACAACAAAACACCCGAAACC 19 71 0 GCAACACAAC 0.823747 -36 GCACTCCCCCCTCAAGCTGCACCGAACCGACACGGTGC 21 235 0 CCAACACAAC 0.983514 -28 GTGGGAAGCACGGATAGATCCTGCCACCCTGCAGGATG 33 9 1 CCATCCGCAC 0.853005 -95 TGGGAAGGTCCACAGAAGAGGCGGGCAACCGTATTCCATA 35 202 1 CCAACGGAAC 0.953448 -48 GAGGACTGCACGCAAAACCTGCCAGGAAACAATGATGAGA 43 79 1 CCAACCGAAC 0.990701 -155 TTAAAACTCTCACACAAGGGCCCACAAAAATGAGGATACG 47 111 0 CCAACCCAAA 0.908708 -64 AAAAAGATTTCGCTGAAACTTCACGAAATCTCGGTGAAAA 59 138 0 CCAACAGAAC 0.98992 -89 TCCACCAAGCCTCCCAACAAACCGGTAAGATCATTGAC 59 199 1 CCAACCGAAA 0.942483 -28 * * ** ** * ** * Masking position 6 Map Score: 17.1128 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 37 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 CACACAAGCTTGTGAAGAAAGTATATTTTTT 1 106 0 TGTGAAGAAG 0.812264 -137 GGGTTTGTTAGCAAGGGGACGTTGATCTGTT 2 57 1 GCAAGGGACG 0.392982 -244 ACAAAGACAATCAGCAGCACGAACAGATCAA 2 78 0 TCAGCAGACG 0.759883 -223 TGGCACAGCCTGTAAAGAACGTAGTTCTTTA 6 38 0 TGTAAAGACG 0.584046 -129 TGCCACGTTAGGAGCGGAAAGAAGGGTGCTG 6 98 1 GGAGCGGAAG 0.917289 -69 CTGCCGTGTCTGGGAGGGACGCCGTTTT 7 130 1 TGGGAGGACG 0.790851 -18 AACAGCACGATGCGCAGCACGCACCACAAAT 8 25 0 TGCGCAGACG 0.690426 -30 GATAAAAGGAACAGCACGATGCGCAGCA 8 37 0 GGAACAGACG 0.822539 -18 ATAACGCTGGTGAGGAGTACGATCGGTCAGA 13 31 1 TGAGGAGACG 0.919126 -157 TGCATTCAATGGTGGAGAAAGACGGGAGTCC 13 107 1 GGTGGAGAAG 0.913395 -81 GCCTGGTATAGGTGCGGGACGGAAAGGAGAG 14 75 1 GGTGCGGACG 0.949932 -26 TCCACTCAAGTGAGGAGAACGCGACCCAACC 21 148 0 TGAGGAGACG 0.919126 -115 TGGTGCAGTACGCTGAAGTAAT 26 11 0 GGTGCAGACG 0.960677 -12 GCTTTTTTAGGGAAAAGGAAGATCGC 28 21 1 GGAAAAGAAG 0.60686 -16 GTGGGAAGCACGGATAGATCCT 33 2 1 TGGGAAGACG 0.829632 -102 CCCTGCAGGATGGGGAGCAAGCAGGCGTGGG 33 37 1 TGGGGAGAAG 0.772187 -67 GTGCGGCAAGAGAGAAGCACGAGCTCCCCCA 33 64 0 AGAGAAGACG 0.621994 -40 CTCACAACACAGTGCGGCAAGAGAGAAGCAC 33 75 0 AGTGCGGAAG 0.504127 -29 CTGCGTGGTAGGAAGGGGAAGACAGGGAGGC 41 59 1 GGAAGGGAAG 0.608384 -119 GTGCGACAGAGCTGAAGAAAGGCTTTTCTTT 43 148 1 GCTGAAGAAG 0.645536 -86 GCACAACCCCTCGGCGGCACGCACTGCGAAA 44 29 0 TCGGCGGACG 0.577109 -119 ACGTCCTTCGGGTAAGGCACGGAGCATGGA 49 19 1 GGTAAGGACG 0.672193 -20 CTCGTCTGTGTGAGCAGCAAGAGTATTGCCT 52 25 1 TGAGCAGAAG 0.883639 -84 CGCGCGTCTCTGTGGGGGAAGCGTAAAGAAC 54 29 1 TGTGGGGAAG 0.813236 -98 GTTTCCTCTTGCTGAAGAAAGGTGAGGATCA 55 58 1 GCTGAAGAAG 0.645536 -39 CTCACCATACGGTGAAGGAAGGGTAAAAAGA 56 22 1 GGTGAAGAAG 0.890559 -104 GTATGAAATAGGAGCAGGACGCG 57 22 1 GGAGCAGACG 0.963761 -13 TTTAAAGTTTGGAGGAGAAAGAACG 59 5 0 GGAGGAGAAG 0.919867 -222 ******* *** Masking position 9 Map Score: 27.9861 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 661 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 AACACATCGAGCGGACGCGTCTGTTCGTGGAGG 5 219 1 GCGGCGCTTG 0.976469 -28 AAGTGCCTATCCGGTAGCATCCGGCGCCATGAG 7 66 0 CCGGAGCTCG 0.940952 -82 GCCGTGTTAGGCTGCCGTGTCTGGGAGGGACGC 7 119 1 GCTGCGTTTG 0.610602 -29 GTTTGGTTGACCGGTAGTATGCGGTGCCTGGTA 14 50 1 CCGGAGTTCG 0.907945 -51 TCAATCCCGCTCGGAAGCTTCCGTCTGTGGATG 17 198 1 TCGGAGCTCG 0.733672 -37 CGCATGATTGCCTGCCGCTTACGCGTTGGTTTC 19 44 1 CCTGCGCTCG 0.766552 -63 CAACGACGCGCCGGACGCATGCAAAAAAAACCA 21 15 0 CCGGCGCTCA 0.715269 -248 GCGCTCGTCTTCCTCGGAAGACT 22 1 1 GCGCCGTTCC 0.94965 -127 TGGCAAATAAGCGGCAGTCCATGTGGGGAAGGG 22 35 1 GCGGAGTCTG 0.538428 -93 ACCGCACGGCGCGAACGCTTCTCCTC 24 4 0 GCGACGCTTC 0.476329 -174 TGTGCCCTCCGCGGTCTCTTTTGGGATGTGTGT 34 12 1 GCGGCTCTTG 0.791398 -79 CAGGGGCCGTCCGCCCGCTCTCCTTCAGCAGG 35 10 0 CCGCCGCCCC 0.715795 -240 TAGGCGCGGGGCGCCCGTTTACGTGGGTAAGAG 35 69 1 GCGCCGTTCG 0.981266 -181 CGGCCGAGGCGCGGTCTTCTGTGACCGGGACCA 36 164 1 GCGGCTTTTG 0.701326 -137 CGTCCTTTCTGCGGGAGTGTTTCTGATACTCTA 36 227 0 GCGGAGTTTC 0.732639 -74 CACAGAGATCGCGCCCGCCTTTGAACACATCCC 40 53 0 GCGCCGCTTG 0.972379 -82 ACCGCGTGAAGCGGCATCCTGCGTGGTAGGAAG 41 41 1 GCGGATCTCG 0.729883 -137 CCCCTCCGGGGCGCAAGCATCCCTGTGAGGCCC 41 120 0 GCGCAGCTCC 0.900289 -58 TTCGGTAACCTCGCGCGTGTACGCTCAGCGCAT 42 21 0 TCGCCGTTCG 0.82999 -61 ACGTCAACATCCGCCCGTGTACGAGAGGTAGTT 45 101 0 CCGCCGTTCG 0.965801 -75 TGCGGAGGTGCCGCCCGAGTGCGTTAGCACCCT 47 44 1 CCGCCGATCG 0.750333 -131 GTAGTGTGTAGCGGGCGTATCCTCATTTTTGTG 47 96 1 GCGGCGTTCT 0.742516 -79 AGTCTATAGTGCGCTCGTCTGTGTGAGCAGCAA 52 12 1 GCGCCGTTTG 0.95612 -97 GTGTTTTCTTCCGCGCGTCTCTGTGGGGGAAGC 54 18 1 CCGCCGTTTG 0.921558 -109 TACACGTGGCGCGCCAGCGTACCCACCATTCTT 56 81 0 GCGCAGCTCC 0.900289 -45 **** *** * ** Masking position 2 Map Score: 29.2997 Number of sites scoring better than the average of aligned sites = 1138 Number in coding regions = 1033 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 TGCAGTGTGTTCGCGTGTACAACCGATGTGA 2 18 1 TCGCGTGACA 0.810296 -283 CGCACCTGGTGCGGGTGGAGGAGTTAGGTTA 13 167 1 GCGGGTGAGG 0.936236 -21 CGTAGAGAGCTCGCGTGAACACCGATTTTCC 24 60 1 TCGCGTGACA 0.810296 -118 CTGAAGGAGAGCGGGCGGACGGCCCCTGAGT 35 15 1 GCGGGCGACG 0.959551 -235 GGCGCGGGGCGCCCGTTTACGTGGGTAAGAG 35 71 1 GCCCGTTACG 0.854814 -179 ACAGCTGCTTGCCGGTCCACGCCCTTCCACA 36 14 0 GCCGGTCACG 0.932297 -287 GAAAGGACGCGCGGGTGAACGATTACCGCGC 36 251 1 GCGGGTGACG 0.993395 -50 CGACTGCTTATCGGGTGCACCGTTTTTTGTT 38 130 1 TCGGGTGACC 0.84997 -24 CGGTAACCTCGCGCGTGTACGCTCAGCGCAT 42 21 0 GCGCGTGACG 0.989617 -61 ACCAGACGTCACCGGTGAACGCACAGCCTGC 45 68 0 ACCGGTGACG 0.926977 -108 GTCAACATCCGCCCGTGTACGAGAGGTAGTT 45 101 0 GCCCGTGACG 0.98796 -75 TCCGCACCACGCCGGTGCACGTTACAGACTG 47 19 0 GCCGGTGACG 0.992336 -156 CAAAAGGGAGTGCGGTGCACGG 50 29 1 TGCGGTGACG 0.80304 -12 ******* *** Masking position 9 Map Score: 15.9048 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 198 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 TATTCTTTTATCCACCACTTATCCCCATCGAATTC 1 23 0 TCACCACCCC 0.795141 -220 GCAGCACGAACAGATCAACGTCCCCTTGCTAACAA 2 61 0 CAATCAACCC 0.401592 -240 AACCTACCCACAAAACAGGGACCACCACACAAGAC 3 45 1 CAAACAGCAC 0.638784 -126 GACCACCACACAAGACACAGAGCCCTGCAGACAGA 3 64 1 CAGACACCCC 0.960667 -107 GGCGTCCCTCCCAGACACGGCAGCCTAACACGGCG 7 118 0 CCGACACGCC 0.754383 -30 CAAAATAACTCCAAACACACTCCGCGCCGCAAACG 10 12 0 CCAACACCGC 0.674877 -60 CCTCCATCAGCCTAAAACCGCACCCACCTTGCAAA 10 43 0 CCAAAACCCC 0.6862 -29 AACGCACAGACAAAACACACACGCC 11 1 0 CAAACACGCC 0.69223 -46 CCACACACCGCCTACCAGAATGCCCTGCTACAGGC 15 13 0 CCACCAGCCC 0.972308 -87 AAACAGGCAGCCAACCAGCCTGCCCCAGAAAGAAA 17 21 0 CCACCAGCCC 0.972308 -214 ACACATCAAGCACGAAACACCTCCCTAAACAGGCA 17 47 0 CAGAAACCCC 0.569025 -188 CAGAAGCAACACAGACAGGACTCCCCGAGCCGCCC 17 116 0 ACGACAGCCC 0.716207 -119 ATCCCCGGAAAACACCAGAAAACCCCGTGCGTAAC 18 26 0 AAACCAGCCC 0.735404 -124 TGACGTAAAAAACAACAAAACACCCGAAACCAACG 19 67 0 AAAACAACCC 0.466013 -40 AGCCTGACCGCCTAACACATACCCCGTAACTAAGT 20 23 0 CCAACACCCC 0.975875 -86 ACCCAACCCGCATGCCAAAATGCCGAGAACAAGTA 21 121 0 CAGCCAACCG 0.579312 -142 GAACTACACAAAAAACAGGCAGCACTATTTATATT 24 116 0 AAAACAGCAC 0.17391 -62 AGGAAGCATTCATACCACCGTGCCGAATTACAAAA 31 34 0 CAACCACCCG 0.847664 -74 CTACCCCGCCCATCCTCCCCCGAGAAGGA 31 89 0 CCGCCCACCC 0.526289 -19 ACGGATAGATCCTGCCACCCTGCAGGATGGGGAGC 33 20 1 CCGCCACCAG 0.463967 -84 ACATGCCTACCCAGACACACATCCCAAAAGAGACC 34 24 0 CCGACACCCC 0.973496 -67 ACATCCCCTGCATACCTCTTTTCCCTATAGCCCGC 40 25 0 CAACCTCCCC 0.668226 -110 GGCGAAGGTGCAGACCAAAAGCCCTT 46 2 0 CAACCAACCT 0.402303 -48 AGCGTGCTTGCATAACACTGTCCACTGTGTAGGCT 53 12 1 CAAACACCAC 0.753935 -31 ATACACGTGGCGCGCCAGCGTACCCACCATTCTTT 56 80 0 CGGCCAGCCC 0.742025 -46 GTGTCCCTATCACGCCACTGGACCCTCTGTGCATA 58 140 0 CAGCCACCCC 0.973496 -65 GATAGGGACACCGAACAGATCTCCTCTGGTTTATC 58 164 1 CCAACAGCCT 0.587695 -41 TAATTCTCAATCCACCAAGCCTCCCAACAAACCGG 59 189 1 TCACCAACCC 0.514058 -38 ** ***** *** Masking position 6 Map Score: 15.9731 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 473 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 9 AGGTTCCGTACCGTGCGGGCACGGAACACA 5 195 1 CCGTGCGGGC 0.826695 -52 GCATCCGGCGCCATGAGGGGCACAGGAACC 7 53 0 CCATGAGGGG 0.668623 -95 CACGCACCACAAATGCGGCGCCTACACA 8 9 0 AAATGCGGCG 0.174732 -46 CATATCTGTTACGCACGGGGTTTTCTGGTG 18 19 1 ACGCACGGGG 0.777335 -131 GCACACAACGACGCGCCGGACGCATGCAAA 21 23 0 ACGCGCCGGA 0.539883 -240 CGGCATTTTGGCATGCGGGTTGGGTCGCGT 21 131 1 GCATGCGGGT 0.439877 -132 GGCGTCTCCCCTGTGTGGGGAGTATTACGG 21 185 1 CTGTGTGGGG 0.431101 -78 ATAGGGAGCACCGTGTCGGTTCGGTGCAGC 21 228 1 CCGTGTCGGT 0.542322 -35 AAGCGGCAGTCCATGTGGGGAAGGGAGTGC 22 43 1 CCATGTGGGG 0.834998 -85 AGCGTTCGCGCCGTGCGGTGCGCACGTTGT 24 18 1 CCGTGCGGTG 0.738145 -160 TTGTTCAGGAACATGCGGCGAACTACACAA 24 140 0 ACATGCGGCG 0.78333 -38 TTCCTGAACAACGTGAGGGGTTGCCGTGC 24 159 1 ACGTGAGGGG 0.890388 -19 GTCTTGCACGACCTGCGGGGGCGCAGTATA 29 39 1 ACCTGCGGGG 0.755905 -97 GCGCAGTATACCGCGCAGGTATATTTTTTA 29 59 1 CCGCGCAGGT 0.635274 -77 GGGAGCAAGCAGGCGTGGGGGAGCTCGTGC 33 49 1 AGGCGTGGGG 0.761675 -55 GAAGGAGCGTAGGCGCGGGGCGCCCGTTTA 35 60 1 AGGCGCGGGG 0.914827 -190 CATGCAGATGCCGCGCAGGGCGTGCGCCGT 36 51 0 CCGCGCAGGG 0.852443 -250 CGCAGAAAGGACGCGCGGGTGAACGATTAC 36 247 1 ACGCGCGGGT 0.946541 -54 TCCGCTCTCTGCGCGCGGGGAAA 39 18 1 GCGCGCGGGG 0.95928 -13 TACTGTCAGCACCCGCGGCGACCTCACAGA 40 80 0 ACCCGCGGCG 0.618653 -55 GGTGACGCGCCGCTCACCTTCCCC 40 121 0 ACGCGCCGCT 0.594368 -14 CTGAGCGTACACGCGCGAGGTTACCGAAAC 42 26 1 ACGCGCGAGG 0.780733 -56 GGTTACCGAAACGTGTGGGTCTAGGCCCCA 42 44 1 ACGTGTGGGT 0.819004 -38 GAACAGATATACGTGTCGGGGAGGTTTAC 43 10 0 ACGTGTCGGG 0.826697 -224 CACCTCCGCACCACGCCGGTGCACGTTACA 47 24 0 CCACGCCGGT 0.618545 -151 AGAGTGAGCCCCGCGAGGGGTGCGTGC 47 158 1 CCGCGAGGGG 0.939644 -17 TAAAAAGAGAAAGTGTGGGGAGGACTTGCA 56 45 1 AAGTGTGGGG 0.544151 -81 CCTAGCTAATACACGTGGCGCGCCAGCGTA 56 93 0 ACACGTGGCG 0.636891 -33 CCTACACGCACCGCGCGGGGCGCATTCTAT 58 57 1 CCGCGCGGGG 0.90805 -148 ********** Masking position 5 Map Score: 28.5934 Number of sites scoring better than the average of aligned sites = 1155 Number in coding regions = 1040 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 10 ATATCCGTATGTGGAAGGGCATAGACT 4 48 1 GTGGAAGGGC 0.975923 -17 GAAAAGCAGATTGGCACAGCCTGTAAAGAA 6 50 0 TTGGCACAGC 0.779116 -117 TATATTTCCTTTGGAAGAGC 9 54 1 TTGGAAGAGC 0.894983 -10 GCTGCGTAAGGTGCCAGAGCGGTGACCGAA 12 26 1 GTGCCAGAGC 0.976578 -30 TTGCCTGTAGCAGGGCATTCTGGTAG 15 7 1 GTAGCAGGGC 0.956769 -93 TGTAGCTCAGTTGGCAGAGCGCAACCATGG 17 149 1 TTGGCAGAGC 0.967953 -86 AGTAGCTCTAATGGCAGAGCGTCGGTCTCC 18 70 1 ATGGCAGAGC 0.922803 -80 ACCCTTTCGTGTGGGAGGGCGTCGCGCTTT 21 60 1 GTGGGAGGGC 0.959638 -203 CTTTGTGGAAGGGCGTGGACCGGC 36 5 1 GTGGAAGGGC 0.975923 -296 TTGAAAAAGTGTACCAGAGCCACTACACTG 37 11 0 GTACCAGAGC 0.865292 -130 GCAGGTGGCTGTGCCAGGGCTTGGTGCGGC 44 99 1 GTGCCAGGGC 0.982442 -49 ********** Masking position 6 Map Score: 13.5513 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 92 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CAGCCAACCAGCCTGCCCCAGAAAGAAAGGC 17 18 0 GCCTGCCCCG 0.976272 -217 TACAATGCGGGCCGGCCTCCGGGCGGCTCGG 17 96 1 GCCGGCCTCG 0.992652 -139 GCGCATGATTGCCTGCCGCTTACGCGTTGGT 19 43 1 GCCTGCCGCT 0.79789 -64 GCGCGTCGTTGTGTGCCTCTGACACCCTTTC 21 37 1 GTGTGCCTCG 0.909879 -226 AGAGCGGGCGGACGGCCCCTGAGTTGCCAGC 35 22 1 GACGGCCCCG 0.857703 -228 CGGATAGAGCGTTGGCCTCCGGAGCCAAAGG 35 131 0 GTTGGCCTCG 0.70885 -119 GTAACCTGCTGCGGGCCTGGGAAGGTCCACA 35 185 1 GCGGGCCTGG 0.929512 -65 CACAGAAGAGGCGGGCAACCGTATTCCATAC 35 212 1 GCGGGCAACG 0.765117 -38 TTTGCTCGCAGCGTACCACGGGATCATAGCT 38 34 0 GCGTACCACG 0.84117 -120 CAACTAACGCGCCGACCGCTGCTTTTCTCAT 43 113 0 GCCGACCGCG 0.956868 -121 GTTTCGCAGTGCGTGCCGCCGAGGGGTTGTG 44 28 1 GCGTGCCGCG 0.98359 -120 TACACACTACGCGGGCCTCGGTTACTGTGAG 47 75 0 GCGGGCCTCG 0.992646 -100 CCCGCCTACCTCCGCTGCGTG 48 8 0 GCCTACCTCG 0.935345 -14 ********* * Masking position 6 Map Score: 12.3661 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 122 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TGTACAACCGATGTGAGCGTGGTGGGGTTT 2 33 1 ATGTGAGCGT 0.678279 -268 CGTATAACGCTGGTGAGGAGTACGATCGGT 13 28 1 TGGTGAGGAG 0.906347 -160 TTGATGTGTGAGGTGAGGCGTTATACAATG 17 73 1 AGGTGAGGCG 0.870147 -162 GGTAAGGTTGAGGTCAGCGGTTCAATCCCG 17 177 1 AGGTCAGCGG 0.731258 -58 CCGTCTGTGGATGTGAGGAGGGGTGGT 17 218 1 ATGTGAGGAG 0.924214 -17 CCCTCCACTCAAGTGAGGAGAACGCGACCC 21 152 0 AAGTGAGGAG 0.816999 -111 TTCCTGAACAACGTGAGGGGTTGCCGTGC 24 159 1 ACGTGAGGGG 0.858024 -19 CCGCACTGTGTTGTGAGGGGAAAAG 33 89 1 TTGTGAGGGG 0.855398 -15 CCTGCTGAAGGAGAGCGGGCGGACGGCC 35 9 1 AGGAGAGCGG 0.85488 -241 CTTACTCTCTAGATGAGGAGCGGCCGAGGC 36 144 1 AGATGAGGAG 0.586486 -157 CATGCACTTTTTGTGAGCATTGCACAGAGC 37 43 1 TTGTGAGCAT 0.282779 -98 GTACTTTTAAAGGTGAGGAAGCGCTC 37 125 1 AGGTGAGGAA 0.629411 -16 ACAGGGGGGAAGGTGAGCGGCGCGTCACC 40 116 1 AGGTGAGCGG 0.976522 -19 CCCGTGTTGCTAGTGAGCAGGCTGTGCGTT 45 52 1 TAGTGAGCAG 0.519398 -124 TTGTATTTCCATGTGAGTGGTGCCGTCTGA 51 24 1 ATGTGAGTGG 0.607467 -35 GCGCTCGTCTGTGTGAGCAGCAAGAGTATT 52 22 1 GTGTGAGCAG 0.570792 -87 GCTGATGAAAAGGAGAGCGGTCAGTT 52 93 1 AGGAGAGCGG 0.85488 -16 TGCTGAAGAAAGGTGAGGATCAGGGGAGGG 55 67 1 AGGTGAGGAT 0.811014 -30 GGTGAGGATCAGGGGAGGGGTTAGGAATC 55 78 1 AGGGGAGGGG 0.860344 -19 ********** Masking position 6 Map Score: 12.8357 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 186 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 CTATGCCCTTCCACATACGGATATTCTTTTT 4 41 0 CCACAACGGA 0.954481 -24 AATATCCTCCACGAACAGACGCGTCCGCT 5 228 0 CCACGACAGA 0.829278 -19 CTCCTCACATCCACAGACGGAAGCTTCCGAG 17 207 0 CCACAACGGA 0.954481 -28 GTAATACTCCCCACACAGGGGAGACGCCGTC 21 182 0 CCACAAGGGG 0.884436 -81 GCACTCCCTTCCCCACATGGACTGCCGCTTA 22 42 0 CCCCAATGGA 0.862298 -86 TTTTAAAAGGCCTCGAATGGAGGCATTGACT 29 84 1 CCTCGATGGA 0.875996 -52 CCCGCGGCGACCTCACAGAGATCGCGCCCGC 40 68 0 CCTCAAGAGA 0.89095 -67 ATTTTCAGGGCCTCACAGGGATGCTTGCGCC 41 113 1 CCTCAAGGGA 0.970497 -65 GGTCTAGGCCCCACGAAGGGAGGGAGTGACG 42 61 1 CCACGAGGGA 0.974382 -21 TCGACCAAACTCTCGGAGGGATGGATGATAG 43 200 0 TCTCGAGGGA 0.70832 -34 TTTACGCTTCCCCCACAGAGACGCGCGGAAG 54 25 0 CCCCAAGAGA 0.871004 -102 ***** ***** Masking position 7 Map Score: 7.91413 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 48 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 14 AGCTTGTGTGCGGTTTTTGTTTGGTAATTCTCG 1 127 1 CGTTTTTTTG 0.967097 -116 GTTCGTGCTGCTGATTGTCTTTGTCCCGTCGTA 2 85 1 CGTTGTTTTG 0.943324 -216 ATTACTTCTACAGGTTTTTTATGCAATTTTATA 5 121 1 CGTTTTTATG 0.948245 -126 GTTTGCGGCGCGGAGTGTGTTTGGAGTTATTTT 10 13 1 CGGTGTTTTG 0.815525 -59 TGTCTGGTTTTTTTTGCATGCGTCCG 21 4 1 CGTTTTTTTG 0.967097 -259 CTACTTGCATCTGGTTTTCTATGTCGTACGGCG 36 197 0 CGTTTTTATG 0.948245 -104 ATTGCACAGACAGGTTTTTTATGAAAGA 41 6 0 CGTTTTTATG 0.948245 -172 AGCTGAAGAAAGGCTTTTCTTTGACAAATCTGC 43 157 1 AGTTTTTTTG 0.766478 -77 * * **** **** Masking position 6 Map Score: 3.43695 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 12 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 GGCGTAGACACTGAATTCGATGGGGATAAGTGGTG 1 11 1 CTGATTCGGG 0.859031 -232 TCTGCATCCTCTTGCGTAAAACAATA 2 285 0 CTGATCCTGG 0.979756 -16 CCTGCTTGCTCCCCATCCTGCAGGGTGGCAGGATC 33 27 0 CCCATCCTGG 0.940839 -77 GAGGCCAACGCTCTATCCGAATGAGCTAATCTTCC 35 143 1 CTCATCCGGG 0.934718 -107 CTTCCCTGCTCTGTAACCTGCTGCGGGCCTGGGAA 35 173 1 CTGAACCTGG 0.938649 -77 TACAATGCCCCTCTATCCTGTGGTGCCGTAAATAG 37 86 1 CTCATCCTGG 0.983534 -55 AAGGCAGTCGCTCTATCCGGGTGAGCTATGATCCC 38 11 1 CTCATCCGGG 0.984734 -143 CCACACGTTTCGGTAACCTCGCGCGTGTACGCTCA 42 27 0 CGGAACCTGG 0.802521 -55 ATATCTCTCCGTCCGAACGCGGATTATGGGC 54 106 0 CTCGTCCGGG 0.932965 -21 *** ***** * * Masking position 8 Map Score: 4.17044 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 16 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432