AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -irpoH_tpal_opreg_300.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0027 225 hemolysin, putative #2 TP0029 107 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) #3 TP0030 118 heat shock protein (groEL) #4 TP0071 203 ATP-dependent Clp protease subunit B (clpB) #5 TP0099 194 uridylate kinase (smbA) #6 TP0185 147 signal peptidase I (sip) #7 TP0186 54 oxygen-independent coproporphyrinogen III oxidase, putative #8 TP0187 63 translation elongation factor TU (tuf) #9 TP0188 71 ribosomal protein S10 (rpsJ) #10 TP0189 46 ribosomal protein L3 (rplC) #11 TP0192 55 ribosomal protein L2 (rplB) #12 TP0207 187 ribosomal protein L15 (rplO) #13 TP0214 23 T. pallidum predicted coding region TP0214 #14 TP0215 205 grpE protein (grpE) #15 TP0216 115 heat shock protein 70 (dnaK) #16 TP0489 300 conserved hypothetical protein #17 TP0492 23 DNA primase (dnaG) #18 TP0506 300 trigger factor (tig) #19 TP0524 135 ATP-dependent protease LA (lon-2) #20 TP0682 92 cell division protein (ftsJ) #21 TP0758 118 ribosomal protein S21 (rpsU) #22 TP0765 300 cell division protein (ftsH) #23 TP0844 92 glyceraldehyde 3-phosphate dehydrogenase (gap) #24 TP0984 143 heat shock protein 90 (htpG) #25 TP1013 204 chaperonin (groES) Motif number 1 AGAAAGAGGACTCCGCGCGGTCTCCGGA 1 8 1 GGACCCGCGC 0.888144 -218 TGTGTCAAGAGCACACCCTCCACTACAATGA 1 47 0 GCACCCCTCC 0.959324 -179 ACCTTAAAAGGTGCCCCCCCCCAGCGGGGAG 1 89 1 GTGCCCCCCC 0.81359 -137 CATCCTTGGACCCCTCCCCGCTGGGGGGGGG 1 102 0 CCCCCCCCGC 0.926298 -124 CTACGCCTTACCGCGGCCTGCCAAAGCGCAC 4 66 1 CCGCGCCTGC 0.796068 -138 GGTGTACATGGTATGCGGTGCGCTTTGGCAG 4 83 0 GTATCGGTGC 0.6084 -121 GAACACTCCATCGCCCCGTGCACGCTGGGAC 5 103 1 TCGCCCGTGC 0.895985 -92 TGTGTATCTGGCATTGCGTCCCAGCGTGCAC 5 120 0 GCATGCGTCC 0.802498 -75 CTATCCGGTAGCATCCGGCGCCATGAGGGGC 6 62 0 GCATCGGCGC 0.876263 -86 AAAACGGCGTCCCTCCCAGACACGGCA 6 131 0 GCGTCCTCCC 0.747588 -17 GGTGCGTGCTGCGCATCGTGCTGTTCCTTTT 7 31 1 GCGCTCGTGC 0.847862 -24 AACTCCAAACACACTCCGCGCCGCAAACGC 9 10 0 ACACCCGCGC 0.975626 -62 CTAAAACCGCACCCACCTTGCAAAATAACTC 9 36 0 ACCCCCTTGC 0.709842 -36 TGCGGTAGCTGCGTAAGGTGCCAGAGCGGTG 11 19 1 GCGTAGGTGC 0.603723 -37 ACCGTCCGACGCACCGGCTCCCTCTGACCGA 12 53 0 GCACGGCTCC 0.606557 -135 TCCTCCACCCGCACCAGGTGCGAAACAGCTC 12 158 0 GCACAGGTGC 0.4905 -30 AAGTAACGAGAGACGCCGCCCTCGGTCAAGA 14 140 0 AGACCCGCCC 0.508673 -66 TGACCTCTCAGCATACCCTGCCTG 15 4 0 GCATCCCTGC 0.96111 -112 CGGCTATACTGCGCGCCCTGCAGGCAGGGCG 15 67 1 GCGCCCCTGC 0.583957 -49 TGTATAGGATACCCGCCCTGCCTGCAGGGCG 15 80 0 ACCCCCCTGC 0.905671 -36 AAATCCTTCCGCACCGCGCGCACGCGCACGA 16 261 0 GCACGCGCGC 0.501132 -40 CTTGCCGSATSTCTTCCGTGCGAGAGTGGTG 18 49 1 STCTCCGTGC 0.393814 -252 GTCCCTCCTCTCGCAGGGCGCCTGTGCGGGA 18 134 1 TCGCGGGCGC 0.72235 -167 GGTTCGATCCCCGTTTCCCGCTTTTTCAGCG 18 209 1 CCGTTCCCGC 0.36803 -92 CCGCAACGCCTCGCACGGTCCAAGCAGGATG 18 248 0 TCGCCGGTCC 0.652367 -53 TAAACGTCTTGCACGACCTGCGGGGGCGCAG 19 34 1 GCACACCTGC 0.68408 -102 CGGGGGCGCAGTATACCGCGCAGGTATATTT 19 54 1 GTATCCGCGC 0.885666 -82 CATTGACTTTTCGTCCCTTGCCTGGATACTA 19 107 1 TCGTCCTTGC 0.475646 -29 GACAGCTCCCACACATCGTGCTCGCACAAAA 20 36 0 ACACTCGTGC 0.709816 -57 ACCTTCCTACACGCCCCCCATGCTATGTG 20 74 0 ACACCCCCCC 0.870324 -19 TCCCCTGCACGCACACCCTACGTGTC 21 6 0 GCACCCCTAC 0.631827 -113 AAGCACTCCTGCCTCCCCTGCACGCACACCC 21 19 0 GCCTCCCTGC 0.938481 -100 TGTGTGAGAGCCGTACGGCGCA 22 2 0 CCGTCGGCGC 0.788976 -299 GTGTATCATGGGCCGGCGTGCCCGCGCGCAC 22 59 1 GGCCGCGTGC 0.532894 -242 GCTCCCTTTTGCAGTGCGCGCGGGCACGCCG 22 72 0 GCAGGCGCGC 0.551531 -229 TTTTAAGTTCTCCCCCCGCCCTCAAAAAGGC 22 163 1 TCCCCCGCCC 0.839433 -138 TCACGCGAAAGACCTCCGCGCAGAAATTCGC 22 203 1 GACCCCGCGC 0.733891 -98 GCAGAAATTCGCGTAAGGTGCTCTCGCTCGT 22 222 1 GCGTAGGTGC 0.603723 -79 GCTCTCGCTCGTGCTCCTTGCTCTTTGTGCG 22 241 1 GTGCCCTTGC 0.721147 -60 TGCTCTTTGTGCGCTGCTTGCTCTTGCAAAC 22 259 1 GCGCGCTTGC 0.861256 -42 AAAAGAGCACACATCCCGCGCAACGCTATCT 23 55 0 ACATCCGCGC 0.927782 -38 TTGCCCAACCTCCTCTAAAAAGA 23 80 0 GCCCACCTCC 0.606798 -13 GGAACAGGTGGTACACGCTGCCCGATGAACA 24 31 0 GTACCGCTGC 0.732451 -113 AGTCTGTGCTACACTTCGCGCGCGGTCTGTG 24 83 1 ACACTCGCGC 0.778574 -61 AAAGATTCCATTACGCCGCGCACAGACCGCG 24 103 0 TTACCCGCGC 0.764756 -41 GACCCTCTGTGCATACCTCCCTTTCCCACGG 25 71 1 GCATCCTCCC 0.731647 -134 CCTCCCTTTCCCACGGCGCGCTACAGTTCTC 25 86 1 CCACGCGCGC 0.669683 -119 TGTATAGAATGCGCCCCGCGCGGTGCGTGTA 25 136 1 GCGCCCGCGC 0.51104 -69 GTGCGTGTAGGCATACGGCGCAAACGTGAAG 25 158 1 GCATCGGCGC 0.949362 -47 **** ****** Masking position 11 Map Score: 63.0222 Number of sites scoring better than the average of aligned sites = 5224 Number in coding regions = 4782 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 2 CTTAAAAGGTGCCCCCCCCCAGCGGGGAGG 1 91 1 GCCCCCCCCC 0.97059 -135 CATCCTTGGACCCCTCCCCGCTGGGGGGGG 1 103 0 CCCCTCCCCG 0.955795 -123 TGGTGTTTTAGCCCTTCGGGGGAATTACGT 1 155 1 GCCCTTCGGG 0.562047 -71 AAAAGTACGGCCCCATCCTGTGTACTTACT 2 17 0 CCCCATCCTG 0.956945 -91 CACCCCTGTTCTCCACCGCGACTACTCCCG 4 110 1 CTCCACCGCG 0.940679 -94 GTGTAGAACACTCCATCGCCCCGTGCACGC 5 98 1 CTCCATCGCC 0.90673 -97 GGTGCGTGCTGCGCATCGTGCTGTTCCTTT 7 31 1 GCGCATCGTG 0.894198 -24 CAGCCTAAAACCGCACCCACCTTGCAAAAT 9 41 0 CCGCACCCAC 0.768358 -31 CCAGCGTTATACGCACCCTCTTTGTCATGC 12 11 0 ACGCACCCTC 0.810488 -177 GAACCGTCCGACGCACCGGCTCCCTCTGAC 12 56 0 ACGCACCGGC 0.51671 -132 AAACAGCTCGCACCATCCCCAAGACGGCAG 12 137 0 CACCATCCCC 0.855337 -51 AACCTAACTCCTCCACCCGCACCAGGTGCG 12 167 0 CTCCACCCGC 0.854415 -21 TCGCGCATCCTCGTGATATGAG 14 3 1 GCGCATCCTC 0.932958 -203 TTTGCCATAACACCCTCGCGGTAATGCCGT 14 173 0 CACCCTCGCG 0.689802 -33 TGCTCCAGAACTCCATCCTGACCTCTCAGC 15 23 0 CTCCATCCTG 0.885383 -93 CGGCTATACTGCGCGCCCTGCAGGCAGGGC 15 67 1 GCGCGCCCTG 0.921779 -49 TGTATAGGATACCCGCCCTGCCTGCAGGGC 15 81 0 ACCCGCCCTG 0.715517 -35 TGAAATCCTTCCGCACCGCGCGCACGCGCA 16 264 0 CCGCACCGCG 0.972683 -37 GTCCCCTCCTCCGCCACTGAAATCC 16 286 0 CTCCTCCGCC 0.853854 -15 GGTTGGGTGTCTGCATCCTGTTGGGCGAGT 18 14 1 CTGCATCCTG 0.857671 -287 GAGGGTTCAAGTCCCTCCTCTCGCAGGGCG 18 124 1 GTCCCTCCTC 0.793336 -177 CAGCGCTTTGCTGCATCCTGCTTGGACCGT 18 235 1 CTGCATCCTG 0.857671 -66 ATACCTACGTCCGCAACGCCTCGCACGGTC 18 259 0 CCGCAACGCC 0.778959 -42 GCGCGGTATACTGCGCCCCCGCAGGTCGTG 19 45 0 CTGCGCCCCC 0.913602 -91 GAAAGCACTCCTGCCTCCCCTGCACGCACA 21 22 0 CTGCCTCCCC 0.872323 -97 CGACCCTCCCCTGAAAAAAAC 21 108 0 GACCCTCCCC 0.721939 -11 TAAGTTCTCCCCCCGCCCTCAAAAAGGCCC 22 166 1 CCCCGCCCTC 0.960173 -135 CCTCAAAAAGGCCCTTCGTCGTCACGCGAA 22 182 1 GCCCTTCGTC 0.799732 -119 TCACGCGAAAGACCTCCGCGCAGAAATTCG 22 203 1 GACCTCCGCG 0.604816 -98 TTGCCCAACCTCCTCTAAAAAG 23 81 0 GCCCAACCTC 0.742312 -12 GAGAACTGTAGCGCGCCGTGGGAAAGGGAG 25 87 0 GCGCGCCGTG 0.890111 -118 TGTATAGAATGCGCCCCGCGCGGTGCGTGT 25 136 1 GCGCCCCGCG 0.939891 -69 ********** Masking position 4 Map Score: 33.6942 Number of sites scoring better than the average of aligned sites = 2185 Number in coding regions = 1855 Number in noncoding regions = 330 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 GGACCCCTCCCCGCTGGGGGGGGGCACCTTT 1 95 0 CCCTGGGGGG 0.748145 -131 CCCAACCTCCCAACTCGCAGGAGCCTACTTC 4 14 1 CACTCGCAGG 0.9525 -190 GTTTTTTCTACCGCTTGCAGGGGACTTACGG 4 137 0 CCCTTGCAGG 0.984366 -67 CACTCCATCGCCCCGTGCACGCTGGGACGCA 5 106 1 CCCGTGCACG 0.948481 -89 GAAACCCTCTCGCCGGCATCGTAACG 5 179 0 CCCTCGCCGG 0.971366 -16 TAGGCTGCCGTGTCTGGGAGGGACGCCGTTT 6 126 1 TGCTGGGAGG 0.424559 -22 AGGTGCGAAACAGCTCGCACCATCCCCAAGA 12 143 0 CACTCGCACC 0.513237 -45 CTATACTGCGCGCCCTGCAGGCAGGGCGGGT 15 70 1 CGCCTGCAGG 0.896723 -46 CTAGCAAAAACGCCTGGAACGAAACGCCAGG 16 187 0 CGCTGGAACG 0.750801 -114 TCCTTCCGCACCGCGCGCACGCGCACGAAAA 16 258 0 CCCGCGCACG 0.978794 -43 CGATTCCACCACTCTCGCACGGAAGAATC 18 55 0 ACCTCGCACG 0.863333 -246 GGATCTAGTGCCTCTGGCATGAGGGTTCAAG 18 104 1 CCCTGGCATG 0.9041 -197 TCAAGTCCCTCCTCTCGCAGGGCGCCTGTGC 18 130 1 CCCTCGCAGG 0.993076 -171 ACGTCCGCAACGCCTCGCACGGTCCAAGCAG 18 252 0 CGCTCGCACG 0.985973 -49 TCCTAGTAAACGTCTTGCACGACCTGCGGGG 19 28 1 CGCTTGCACG 0.96551 -108 GGTATACTGCGCCCCCGCAGGTCGTGCAAGA 19 40 0 GCCCCGCAGG 0.743782 -96 CGCTAGCCTACCCCTGGTAGGCTGTGTTTTT 21 83 1 CCCTGGTAGG 0.871339 -36 TATCATGGGCCGGCGTGCCCGCGCGCACTGC 22 62 1 CGCGTGCCCG 0.690513 -239 TCTTTTTTAACCTCTGGGAGGATAC 24 129 1 CCCTGGGAGG 0.892185 -15 ** ******** Masking position 7 Map Score: 24.2889 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 344 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AATGAACTGCGTGTCCGGAGACCGCGCGGAGTCC 1 18 0 GTGTCAACCG 0.837482 -208 CTACAGGAATGTGTGCGCAAAGGGGTGAGAGC 2 86 1 GTGTCAAGGG 0.977105 -22 CCCAGACACGGCAGCCTAACACGGCGATAATCGA 6 110 0 GCAGCAACGG 0.868368 -38 TTTTGTCTGTGCGTTGCGATACGGAAGAGGTAGG 10 21 1 GCGTGAACGG 0.983366 -26 GCATTCAATGGTGGAGAAAGACGGGAGTCCTGCC 12 108 1 GTGGGAACGG 0.986552 -80 ATCGTGGTCGGTGTAGTCAGACGGTAAATAGGTG 14 103 1 GTGTGAACGG 0.9863 -103 GGAGTTTCCCGAGTGGTCAAAGGGAGCAGACTGT 16 62 1 GAGTGAAGGG 0.921208 -239 AAGGATTTCAGTGGCGGAGGAGGGGAC 16 284 1 GTGGGGAGGG 0.959038 -17 ATGCAGCAAAGCGCTGAAAAAGCGGGAAACGGGG 18 217 0 GCGCGAAGCG 0.879595 -84 AGTACCGTTATACGGCGTGTTTGCC 20 2 1 GTACGAACGG 0.91412 -91 GACACGTAGGGTGTGCGTGCAGGGGAGGCAGGAG 21 11 1 GTGTCGAGGG 0.914209 -108 GTGCCCGCGCGCACTGCAAAAGGGAGCCTTAACT 22 76 1 GCACGAAGGG 0.917859 -225 AGAGGGTCCAGTGGCGTGATAGGGACACCGAACA 25 45 0 GTGGGAAGGG 0.989447 -160 GGAAAGGGAGGTATGCACAGAGGGTCCAGTGGCG 25 63 0 GTATCAAGGG 0.909705 -142 ACTGTAGCGCGCCGTGGGAAAGGGAGGTATGCAC 25 79 0 GCCGGAAGGG 0.891183 -126 CGCGCGGTGCGTGTAGGCATACGGCGCAAACGTG 25 152 1 GTGTGAACGG 0.9863 -53 **** * * **** Masking position 11 Map Score: 22.4557 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 142 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 TGTGTCAAGAGCACACCCTCCACTACAATGA 1 47 0 GCACACCCCC 0.969471 -179 CCCCCGAAGGGCTAAAACACCAGAACCGAAG 1 146 0 GCTAAAACCC 0.569436 -80 AACGGAAAGAACACTCACACGTAATTCCCCC 1 172 0 ACACTCACCG 0.705117 -54 CAGCAGCACTACCAACACACCGAACGCAGCG 1 205 0 ACCAACACCC 0.846632 -21 CAACTTAATTGCACGAATACCGCAAAAGTAC 2 39 0 GCACGAATCC 0.806415 -69 ACCCCTTTGCGCACACATTCCTGTAGAACAC 2 81 0 GCACACATCC 0.954252 -27 GCTCTCACCCCTTTGCGCACA 2 97 0 GCTCTCACCC 0.84872 -11 AAGCGGTAGAAAAAACATACCGATGACGAGA 4 152 1 AAAAACATCC 0.215068 -52 TACACGGGCGACACAGACTCCTAGTTCTTGT 5 72 0 ACACAGACCC 0.906558 -123 ACGATGCGCAGCACGCACCACAAATGCGGCG 7 19 0 GCACGCACAC 0.783411 -36 AAATAACTCCAAACACACTCCGCGCCGCAAA 9 14 0 AAACACACCC 0.856225 -58 CCCACCTTGCAAAATAACTCCAAACACACTC 9 25 0 AAAATAACCC 0.144477 -47 CACAGACAAAACACACACGCC 10 1 0 ACACACACCC 0.981231 -46 CTCCTTTTTTGCCATAACACCCTCGCGGTAA 14 179 0 GCCATAACCC 0.57582 -27 ACAGCAGCTAGCAAAAACGCCTGGAACGAAA 16 194 0 GCAAAAACCC 0.920811 -107 CTTCCGCACCGCGCGCACGCGCACGAAAAGA 16 256 0 GCGCGCACCG 0.578735 -45 ATCGGCAAGCAAAAACTCGCCCAACAGGA 18 29 0 GCAAAAACCG 0.605276 -272 AGGGACTTGAACCCTCATGCCAGAGGCACTA 18 109 0 ACCCTCATCC 0.472339 -192 AGCTATTCCCGCACAGGCGCCCTGCGAGAGG 18 140 0 GCACAGGCCC 0.687336 -161 CGCACAAAAGGCAAACACGCCGTATAACGGT 20 14 0 GCAAACACCC 0.978077 -79 ACCTTCCTACACGCCCCCCATGCTATGTG 20 74 0 ACACGCCCCC 0.899442 -19 TGCCTCCCCTGCACGCACACCCTACGTGTC 21 10 0 GCACGCACCC 0.990907 -109 CGTTTCTTCCGAAAGCACTCCTGCCTCCCCT 21 31 0 GAAAGCACCC 0.79567 -88 TCTAAAAAGAGCACACATCCCGCGCAACGCT 23 59 0 GCACACATCC 0.954252 -34 TTGCCCAACCTCCTCTAAAAAGA 23 80 0 GCCCAACCCC 0.735862 -13 ATTACGCCGCGCACAGACCGCGCGCGAAGTG 24 94 0 GCACAGACGC 0.704961 -50 CCGTATGCCTACACGCACCGCGCGGGGCGCA 25 145 0 ACACGCACGC 0.783862 -60 ******** ** Masking position 11 Map Score: 25.523 Number of sites scoring better than the average of aligned sites = 1705 Number in coding regions = 1544 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 6 GAGACCGCGCGGAGTCCTCTTTCT 1 3 0 GGGTCTCTTT 0.9727 -223 TGTAGTGGAGGGTGTGCTCTTGACACAAGGGC 1 51 1 GGGTCTCTTG 0.970072 -175 AAGGATGTATGGCGTTGTCTCTTCGGTTCTGG 1 126 1 GGGTGTCTCT 0.981667 -100 GAATTACGTGTGAGTGTTCTTTCCGTTTCCGC 1 176 1 TGGTTTCTTT 0.766816 -50 GCCGCGGTAAGGCGTAGCCTTTTATATTTTCT 4 51 0 GGGTGCCTTT 0.929842 -153 GGGACTTACGGGAGTAGTCGCGGTGGAGAACA 4 116 0 GGGTGTCGCG 0.928849 -88 CGTAGTCTAGTGAGTGTTCTCTGTGC 5 5 0 TGGTTTCTCT 0.781014 -190 ACGGTAAATAGGTGTTTTCTTGACCGAGGGCG 14 123 1 GGGTTTCTTG 0.926848 -83 CTTGACCGAGGGCGGCGTCTCTCGTTACTTTT 14 141 1 GGGGGTCTCT 0.885336 -65 TAAATCTGTTGGCGTTGTCTTCCAAGGTTCGA 16 95 1 GGGTGTCTTC 0.911471 -206 GGGTAGTGTCTGACTTGTCTTTCCCTGGCGTT 16 164 1 TGCTGTCTTT 0.494282 -137 AGGGGAGGCAGGAGTGCTTTCGGAAGAAACGA 21 31 1 GGGTCTTTCG 0.6655 -88 ACGATTGACAGGGGACGTCTTTTGCGCTAGCC 21 59 1 GGGAGTCTTT 0.829321 -60 ATCATGGGCCGGCGTGCCCGCGCGCACTGCAA 22 63 1 GGGTCCCGCG 0.716954 -238 TTGCGCGGGATGTGTGCTCTTTTTAGAGGAGG 23 63 1 TGGTCTCTTT 0.893762 -30 ** ** ****** Masking position 2 Map Score: 10.3644 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 213 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 CTAGTGAGTGTTCTCTGTGC 5 1 0 TTCTCTGTGC 0.96142 -194 CTAGTTCTTGTATTCTGTGCAAAAACCGAC 5 53 0 TATTCTGTGC 0.932917 -142 GATCCAAAGGGTCTCTTTGCGTTACGATGC 5 160 1 GTCTCTTTGC 0.647431 -35 AATGAGATGGGTTCCTGTGCCCCTCATGGC 6 44 1 GTTCCTGTGC 0.967 -104 CGTGTGTGTTTTGTCTGTGCGTTGCGATAC 10 13 1 TTGTCTGTGC 0.97319 -34 GTGGTTGTCCGTTTCTGTGCTTGGCAGTTA 14 54 1 GTTTCTGTGC 0.976279 -152 TTGCCGSATSTCTTCCGTGCGAGAGTGGTG 18 50 1 TCTTCCGTGC 0.891962 -251 CTCTCGCAGGGCGCCTGTGCGGGAATAGCT 18 141 1 GCGCCTGTGC 0.921955 -160 CACTTTTTGTTTTCCCGTGCT 22 290 1 TTTCCCGTGC 0.92323 -11 TTCCGGTTGGTTTACTGTGCTGCATAGTCT 24 58 1 TTTACTGTGC 0.88747 -86 CTGTGCTGCATAGTCTGTGCTACACTTCGC 24 72 1 TAGTCTGTGC 0.919813 -72 ********** Masking position 8 Map Score: 10.256 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 164 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 ACAATGAACTGCGTGTCCGGAGACCGCGCGGA 1 22 0 GCGTGTCGAG 0.98769 -204 GCTGCGTTCGGTGTGTTGGTAGTGCTGCTG 1 206 1 GTGTGTGGAG 0.957009 -20 GTAGGCTCCTGCGAGTTGGGAGGTTGGGAAT 4 10 0 GCGAGTGGAG 0.904858 -194 GGTATGCGGTGCGCTTTGGCAGGCCGCGGTAA 4 73 0 GCGCTTGGAG 0.694052 -131 TTGCGTCCCAGCGTGCACGGGGCGATGGAGTG 5 106 0 GCGTGCCGGG 0.936348 -89 GCGTTTGCGGCGCGGAGTGTGT 9 1 1 GCGTTTCGCG 0.864529 -71 GCGGCGCGGAGTGTGTTTGGAGTTATTTTGCA 9 17 1 GTGTGTTGAG 0.922921 -55 GGCGTGTGTGTTTTGTCTGTGCG 10 2 1 GCGTGTTGTT 0.785418 -45 GAGGGAGCCGGTGCGTCGGACGGTTCGGTCTT 12 60 1 GTGCGTGGCG 0.825339 -128 TACCCGCCCTGCCTGCAGGGCGCGCAGTATAG 15 70 0 GCCTGCGGCG 0.780216 -46 CCCTAAGTTGGCTTGTTCGTTTGGGGAGTTTC 16 38 1 GCTTGTCGTT 0.19588 -263 CTTTTCGTGCGCGTGCGCGCGGTGCGGAAGGA 16 257 1 GCGTGCCGGG 0.936344 -44 GGCGGTTGGGTGTCTGCATCCTGTTGGGC 18 8 1 GGGTGTTGAT 0.570982 -293 CCTAAGTCTAGCGTGTCTGCCGATTCCACCAC 18 74 0 GCGTGTTGCG 0.981942 -227 CCGTTATACGGCGTGTTTGCCTTTTGTGCGAG 20 15 1 GCGTGTTGCT 0.93064 -78 AGCATGGGGGGCGTGTAGGAAGGT 20 79 1 GCGTGTGGAG 0.991083 -14 GACACGTAGGGTGTGCGTGCAGGGGAGGCAGG 21 11 1 GTGTGCTGAG 0.851194 -108 CCCGCGCGGTGCGTGTAGGCATACGGCGCAAA 25 150 1 GCGTGTGGAT 0.96482 -55 ****** ** ** Masking position 9 Map Score: 18.6414 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 645 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 CAAGAGCACACCCTCCACTACAATGAACTG 1 43 0 CCCTCCACTA 0.869401 -183 TTAAGGTGCTCACGCCCTTGTGTCAAGAGC 1 66 0 CACGCCCTTG 0.791765 -160 GCATACCATGTACACCCCTGTTCTCCACCG 4 98 1 TACACCCCTG 0.898164 -106 CCCGTCTTTCTCCACCATTGAATGCAACTT 12 103 0 TCCACCATTG 0.883906 -85 ACCACCCCTCCATTGCCCAACTG 13 9 0 CCCTCCATTG 0.943885 -15 GTCCCCTCCTCCGCCACTGAAATCCTTCC 16 282 0 TCCGCCACTG 0.974016 -19 GTCTGCCGATTCCACCACTCTCGCACGGAA 18 62 0 TCCACCACTC 0.891529 -239 GGGTTCAAGTCCCTCCTCTCGCAGGGCGCC 18 126 1 CCCTCCTCTC 0.764927 -175 AAGGTGGCGCTCTACCACTGAGCTATTCCC 18 161 0 TCTACCACTG 0.828727 -140 AAGCACTCCTGCCTCCCCTGCACGCACACC 21 20 0 GCCTCCCCTG 0.941855 -99 TTTGCGCTAGCCTACCCCTGGTAGGCTGTG 21 79 1 CCTACCCCTG 0.925278 -40 CGACCCTCCCCTGAAAAAAACAC 21 106 0 CCCTCCCCTG 0.989886 -13 GTGTCCCTATCACGCCACTGGACCCTCTGT 25 51 1 CACGCCACTG 0.942814 -154 ********** Masking position 9 Map Score: 12.2281 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 290 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 CACACGTAATTCCCCCGAAGGGCTAAAACAC 1 157 0 TCCCCCAAGG 0.939853 -69 GCTCTTCCAAAGGAAATATACCC 8 51 0 TCTTCCAAGG 0.987653 -13 ATATGAGGTTCCGTCCCAAGGACGTTAGGTG 14 26 1 CCGTCCAAGG 0.951094 -180 TAGAGCGCCACCTTGCCAAGGTGGAAGTCGC 18 177 1 CCTTGCAAGG 0.73471 -124 CGTAGGTATTTCTTCCTAAGGATCTGGGCTT 18 280 1 TCTTCCAAGG 0.987653 -21 GTCAATCGTTTCTTCCGAAAGCACTCCTGCC 21 37 0 TCTTCCAAAG 0.908805 -82 GTATCCTCCCAGAGGTTAAAAAAGA 24 129 0 CCTCCCGAGG 0.921765 -15 TTCTCTTGATTCTTCAAAAGGAAATGTATAG 25 112 1 TCTTCAAAGG 0.908647 -93 ****** **** Masking position 9 Map Score: 5.43728 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 35 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 CTTTTAAGGTGCTCACGCCCTTGTGTCAAG 1 69 0 GCTCACGCCC 0.95534 -157 CTTAAAAGGTGCCCCCCCCCAGCGGGGAGG 1 91 1 GCCCCCCCCC 0.898694 -135 GCTCTCACCCCTTTGCGCAC 2 98 0 GCTCTCACCC 0.983451 -10 GTACACCCCTGTTCTCCACCGCGACTACTC 4 107 1 GTTCTCCACC 0.66033 -97 TTCGGTCACCGCTCTGGCACCTTACGCAGC 11 26 0 GCTCTGGCAC 0.929259 -30 CGATTCCACCACTCTCGCACGGAAGAAT 18 56 0 ACTCTCGCAC 0.890454 -245 GCAAGGTGGCGCTCTACCACTGAGCTATTC 18 163 0 GCTCTACCAC 0.878126 -138 CCCACACATCGTGCTCGCACAAAAGGCAAA 20 30 0 GTGCTCGCAC 0.814935 -63 TACACTGACAGCTCCCACACATCGTGCTCG 20 43 0 GCTCCCACAC 0.94443 -50 GCGCCGTACGGCTCTCACACAGTCTGTCGA 22 12 1 GCTCTCACAC 0.977916 -289 GGTTTTTTAAGTTCTCCCCCCGCCCTCAAA 22 159 1 GTTCTCCCCC 0.964404 -142 CGCGTAAGGTGCTCTCGCTCGTGCTCCTTG 22 231 1 GCTCTCGCTC 0.959212 -70 ********** Masking position 4 Map Score: 11.609 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 223 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 GTCTTTTGAACGCTTTTTTCTCGTCATCGG 4 171 0 CGCTTTTTTC 0.73758 -33 GTTTTTACGTCGGTTTTTGCACAGAATACA 5 45 1 CGGTTTTTGC 0.933485 -150 GATCCAAAGGGTCTCTTTGCGTTACGATGC 5 160 1 GTCTCTTTGC 0.546269 -35 AGAACCGCAAGGCTTTTTTCAATTACCAT 6 10 0 GGCTTTTTTC 0.544766 -138 AAAGCCTTGCGGTTCTTTGCAATGAGATGG 6 24 1 GGTTCTTTGC 0.850042 -124 GTTATACGCACCCTCTTTGTCATGC 12 6 0 CCCTCTTTGT 0.631107 -182 TCGGACGGTTCGGTCTTTGGGTTTGAGGAA 12 75 1 CGGTCTTTGG 0.664858 -113 TTTCTTCTCCTTTTTTGCCATAACACCC 14 188 0 CCTTTTTTGC 0.904134 -18 TTCGTTCCAGGCGTTTTTGCTAGCTGCTGT 16 195 1 GCGTTTTTGC 0.884223 -106 CTCTCGCAGGGCGCCTGTGCGGGAATAGCT 18 141 1 GCGCCTGTGC 0.720227 -160 TCCCCGTTTCCCGCTTTTTCAGCGCTTTGC 18 216 1 CCGCTTTTTC 0.56647 -85 GGCGTGTTTGCCTTTTGTGCGAGCACGATG 20 24 1 CCTTTTGTGC 0.828888 -69 TGACAGGGGACGTCTTTTGCGCTAGCCTAC 21 64 1 CGTCTTTTGC 0.728538 -55 CGACGTTTCACCTTCTTTTCGTGTATCATG 22 39 1 CCTTCTTTTC 0.773147 -262 GCACGTCAATCCCTCTTTGCTGTAGGGCTC 23 13 0 CCCTCTTTGC 0.97003 -80 ACTTCGCGCGCGGTCTGTGCGCGGCGTAAT 24 95 1 CGGTCTGTGC 0.928604 -49 CGCCACTGGACCCTCTGTGCATACCTCCCT 25 63 1 CCCTCTGTGC 0.94326 -142 ********** Masking position 6 Map Score: 11.9652 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 540 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 13 GTGCTCACGCCCTTGTGTCAAGAGCACACCCT 1 59 0 CCTTTTCAAG 0.801502 -167 GTTCAAAAGACCTATAATCACGCC 4 190 1 CCTAATCACG 0.938346 -14 ACACGGCGTACCCATTCTCACGACCAC 8 6 0 CCCATTCACG 0.910487 -58 TGGGACGGAACCTCATATCACGAGGATGCGCG 14 12 0 CCTCTTCACG 0.985584 -194 AGCTGCTGTGCCTCTTGTCACTTTCTTGAGTG 16 216 1 CCTCTTCACT 0.844209 -85 AAAAGAACATCCTGCACTCAAGAAAGTGACAA 16 230 0 CCTGATCAAG 0.756326 -71 TGCCTACATTCCCGTATTTTTCT 17 10 0 CCTAATCCCG 0.926231 -14 GGTTCAAGTCCCTCCTCTCGCAGGGCGCCTGT 18 127 1 CCTCTTCGCA 0.817174 -174 CGGGTTCGATCCCCGTTTCCCGCTTTTTCAGC 18 207 1 CCCCTTCCCG 0.951597 -94 AAAGTCAATGCCTCCATTCGAGGCCTTTTAAA 19 85 0 CCTCATCGAG 0.930155 -51 AGGGCGCCTAGTATCCAGGCAAGGGACG 19 118 0 CCTATTCCAG 0.916373 -18 GCGTTCCTCCTCATAACGAGTCATATCTTC 25 185 0 CCTCTACGAG 0.748348 -20 **** * ***** Masking position 9 Map Score: 4.55201 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 96 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 14 AGAAAGAGGACTCCGCGCGGTCTCCGGA 1 9 1 GACTCCGCGC 0.659717 -217 GTGTCAAGAGCACACCCTCCACTACAATGA 1 47 0 CACACCCTCC 0.842561 -179 GCACTACCAACACACCGAACGCAGCGGAAA 1 201 0 CACACCGAAC 0.833936 -25 AGCCTAAAACCGCACCCACCTTGCAAAATA 9 40 0 CGCACCCACC 0.847284 -32 TCACCAGCGTTATACGCACCCTCTTTGTCA 12 14 0 TATACGCACC 0.3649 -174 CACAGAAACGGACAACCACCTAACGTCCTT 14 43 0 GACAACCACC 0.839183 -163 ACCGTCTGACTACACCGACCACGATGCGAC 14 98 0 TACACCGACC 0.951838 -108 AGTAACGAGAGACGCCGCCCTCGGTCAAGA 14 140 0 GACGCCGCCC 0.882056 -66 TCGAATCCTTGACTCCCCACTTTCGTCTTC 16 123 1 GACTCCCCAC 0.894178 -178 ACAGGATGCAGACACCCAACCGCC 18 5 0 GACACCCAAC 0.956939 -296 TCGAACCCGCGACTTCCACCTTGGCAAGGT 18 186 0 GACTTCCACC 0.685677 -115 ACCTTCCTACACGCCCCCCATGCTATG 20 76 0 TACACGCCCC 0.902304 -17 GTTTTTTAAGTTCTCCCCCCGCCCTCAAAA 22 160 1 TTCTCCCCCC 0.592189 -141 GCGTGATAGGGACACCGAACAGATCTCCTC 25 36 0 GACACCGAAC 0.918822 -169 GCCGTATGCCTACACGCACCGCGCGGGGCG 25 147 0 TACACGCACC 0.910349 -58 ********** Masking position 10 Map Score: 6.03012 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 418 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 15 CGCCATACATCCTTGGACCCCTCCCCGCTGGGGGGG 1 104 0 CGGACCCCCC 0.942332 -122 CAAAGAGACCCTTTGGATCCAGGCCCTGTGTGTATC 5 143 0 CGGATCACCC 0.99562 -52 GCTCTTCCAAAGGAAATATACCCGAATTCAAAT 8 41 0 CGGAAAACCC 0.822256 -23 ATCTCGAGGTCTAGGGTTCGAATCCCTAAGTTGGCT 16 15 1 CGGTTCACCC 0.994609 -286 GCGTTGTCTTCCAAGGTTCGAATCCTTGACTCCCCA 16 106 1 CGGTTCACCT 0.947607 -195 ACACGCTAGACTTAGGATCTAGTGCCTCTGGCATGA 18 90 1 CGGATCAGCC 0.970611 -211 GCCTCTGGCATGAGGGTTCAAGTCCCTCCTCTCGCA 18 113 1 TGGTTCACCC 0.947607 -188 TGGCGCTCTACCACTGAGCTATTCCCGCACAGGCGC 18 151 0 CTGAGCACCC 0.872715 -150 AGGTGGAAGTCGCGGGTTCGATCCCCGTTTCCCGCT 18 195 1 CGGTTCACCC 0.994609 -106 * ***** * *** Masking position 15 Map Score: 5.95167 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 26 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925