AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -irpoH_tpal_opreg_100.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 TP0030 118 heat shock protein (groEL) #2 TP0071 203 ATP-dependent Clp protease subunit B (clpB) #3 TP0099 194 uridylate kinase (smbA) #4 TP0215 205 grpE protein (grpE) #5 TP0216 115 heat shock protein 70 (dnaK) #6 TP0489 300 conserved hypothetical protein #7 TP0492 23 DNA primase (dnaG) #8 TP0506 300 trigger factor (tig) #9 TP0524 135 ATP-dependent protease LA (lon-2) #10 TP0682 92 cell division protein (ftsJ) #11 TP0758 118 ribosomal protein S21 (rpsU) #12 TP0765 300 cell division protein (ftsH) #13 TP0844 92 glyceraldehyde 3-phosphate dehydrogenase (gap) #14 TP0984 143 heat shock protein 90 (htpG) #15 TP1013 204 chaperonin (groES) Motif number 1 TCCCAACCTCCCAACTCGCAGGAGCCTACTTCA 2 13 1 CCCTCGCAGA 0.916167 -191 CCGCGGCCTGCCAAAGCGCACCGCATACCATGT 2 76 1 CCAGCGCACG 0.903397 -128 TGTTTTTTCTACCGCTTGCAGGGGACTTACGGG 2 136 0 ACCTTGCAGG 0.84994 -68 GCATTGCGTCCCAGCGTGCACGGGGCGATGGAG 3 108 0 CCCGTGCACG 0.976792 -87 GAAACCCTCTCGCCGGCATCGTAACGC 3 178 0 CCCTCGCCGC 0.935534 -17 GTAACGAGAGACGCCGCCCTCGGTCAAGAAAAC 4 136 0 ACCGCCCTCG 0.875437 -70 TAACGGCTATACTGCGCGCCCTGCAGGCAGGGC 5 64 1 ACCGCGCCCG 0.995098 -52 ACCTTGGAAGACAACGCCAACAGATTTACAGTC 6 90 0 ACCGCCAACG 0.746389 -211 CACGAAAAGAACATCCTGCACTCAAGAAAGTGA 6 233 0 ACCCTGCACC 0.808404 -68 ATCCTTCCGCACCGCGCGCACGCGCACGAAAAG 6 257 0 ACCGCGCACC 0.993186 -44 CGGCAAGCAAAAACTCGCCCAACAGGATGCAG 8 24 0 AACTCGCCCA 0.775212 -277 CCGATTCCACCACTCTCGCACGGAAGAATCG 8 54 0 CACTCGCACG 0.965633 -247 TTCAAGTCCCTCCTCTCGCAGGGCGCCTGTGCG 8 129 1 TCCTCGCAGG 0.856527 -172 ACCACTGAGCTATTCCCGCACAGGCGCCCTGCG 8 145 0 TACCCGCACG 0.560658 -156 TACGTCCGCAACGCCTCGCACGGTCCAAGCAGG 8 251 0 ACCTCGCACG 0.99503 -50 CTCCTAGTAAACGTCTTGCACGACCTGCGGGGG 9 27 1 ACCTTGCACA 0.835935 -109 TGCGCGGTATACTGCGCCCCCGCAGGTCGTGCA 9 43 0 ACCGCCCCCC 0.96995 -93 TCCCACACATCGTGCTCGCACAAAAGGCAAACA 10 28 0 CGCTCGCACA 0.800795 -65 TGTTACACTGACAGCTCCCACACATCGTGCTCG 10 43 0 ACCTCCCACC 0.969546 -50 ACCTTCCTACACGCCCCCCATGCTATGT 10 75 0 CCCACGCCCC 0.938535 -18 TCCTGCCTCCCCTGCACGCACACCCTACGTGTC 11 11 0 CCCACGCACC 0.960554 -108 GCTAGCGCAAAAGACGTCCCCTGTCAATCGTTT 11 57 0 AACGTCCCCG 0.525763 -62 TGCGCCGTACGGCTCTCACACAGTCTGTCGA 12 9 1 ACCTCTCACC 0.757346 -292 GGCCGGCGTGCCCGCGCGCACTGCAAAAGGGAG 12 69 1 CCCGCGCACG 0.997164 -232 GGGTTTTTTAAGTTCTCCCCCCGCCCTCAAAAA 12 158 1 AGCTCCCCCG 0.794017 -143 ACGCGAAAGACCTCCGCGCAGAAATTCGCGTAA 12 205 1 CCCGCGCAGA 0.946438 -96 AAAAGAGCACACATCCCGCGCAACGCTATCTGA 13 53 0 ACCCCGCGCA 0.736222 -40 TCTGTGCTACACTTCGCGCGCGGTCTGTGCGCG 14 85 1 ACCGCGCGCG 0.98191 -59 AGATTCCATTACGCCGCGCACAGACCGCGCGCG 14 99 0 ACCGCGCACG 0.99692 -45 GTGCATACCTCCCTTTCCCACGGCGCGCTACAG 15 79 1 CCTTCCCACG 0.671341 -126 AAATGTATAGAATGCGCCCCGCGCGGTGCGTGT 15 133 1 AACGCCCCGG 0.686435 -72 GCGCCGTATGCCTACACGCACCGCGCGGGGCGC 15 146 0 CCCACGCACG 0.981846 -59 ** ******* * Masking position 9 Map Score: 50.9315 Number of sites scoring better than the average of aligned sites = 1929 Number in coding regions = 1744 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 2 ATGGTATGCGGTGCGCTTTGGCAGGCCGCGGTAAGGCG 2 69 0 GGCTTTGAGG 0.89164 -135 ACCGCTTGCAGGGGACTTACGGGAGTAGTCGCGGTGGA 2 121 0 GGCTTAGGGG 0.959515 -83 CGGGGCGATGGAGTGTTCTACACGGGCGACACAGACTC 3 83 0 GGTTCTCCGG 0.915537 -112 GTCGCATCGTGGTCGGTGTAGTCAGACGGTAAATAGGT 4 98 1 GTGTGTGCGG 0.696871 -108 CGGTAAATAGGTGTTTTCTTGACCGAGGGCGGCGTCTC 4 124 1 GGTTCTGCGG 0.900608 -82 CAGGCAGGGTATGCTGAGAGGTCAGGATGGA 5 4 1 GAGTATCGGG 0.887226 -112 GGCAGGGCGGGTATCCTATACAGAGGAGTTGAGGGTT 5 89 1 GACTATCGGG 0.924495 -27 TTGTTCGTTTGGGGAGTTTCCCGAGTGGTCAAAGGGAG 6 50 1 GGGTTTCGGG 0.991133 -251 CGCGCGGTGCGGAAGGATTTCAGTGGCGGAGGAGGGGA 6 272 1 GAGATTCGGG 0.568856 -29 ATCCTGTTGGGCGAGTTTTTGCTTGCCGSATSTCTTCC 8 28 1 GGTTTTGTGG 0.705292 -273 GGAGGGACTTGAACCCTCATGCCAGAGGCACTAGATCC 8 104 0 GACTCAGCGG 0.505112 -197 ACCTGCGGGGGCGCAGTATACCGCGCAGGTATATTTTT 9 49 1 GGGTATCGGG 0.975065 -87 CTGGTAGGCTGTGTTTTTTTCAGGGGAGGGTCG 11 96 1 GGTTTTCGGG 0.980619 -23 ACTGCAAAAGGGAGCCTTAACTGAGATGAATACGCGCT 12 88 1 GACTTACGGG 0.850732 -213 TGACGACGAAGGGCCTTTTTGAGGGCGGGGGGAGAACT 12 168 0 GGTTTTGGGG 0.976898 -133 TTTCTGCGCGGAGGTCTTTCGCGTGACGACGAAGGGCC 12 191 0 GGCTTTGGGG 0.993171 -110 CGCGGGATGTGTGCTCTTTTTAGAGGAGGTTGGGCAA 13 66 1 GGCTTTTGGG 0.919733 -27 TCACGGGTTCTTTTGTCTGGTGTTCATCGGGC 14 5 1 GGCTTTGCGG 0.986611 -139 CACCTGTTCCGGTTGGTTTACTGTGCTGCATAGTCTGT 14 52 1 GTGTTTCGGG 0.907194 -92 CACTTCGCGCGCGGTCTGTGCGCGGCGTAATGGAATCT 14 94 1 GGCTGTCCGT 0.649721 -50 TAAACCAGAGGAGATCTGTTCGGTGTCCCTATCACGCC 15 29 1 GGCTGTCGGC 0.844356 -176 CCGTGGGAAAGGGAGGTATGCACAGAGGGTCCAGTGGC 15 64 0 GGGTATCCGG 0.951993 -141 GAAGAATCAAGAGAACTGTAGCGCGCCGTGGGAAAGGG 15 89 0 GGCTGTGGGG 0.987765 -116 * * **** * * * * Masking position 15 Map Score: 30.2929 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 488 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 ATGAAAAGATGTGAAGTGTTGCCAAGAATCTT 1 31 1 GTGAGTGTGC 0.639777 -88 CTTTGGCAGGCCGCGGTAAGGCGTAGCCTTTT 2 60 0 CCGCGTAGGC 0.957186 -144 ACGGGAGTAGTCGCGGTGGAGAACAGGGGTGT 2 109 0 TCGCGTGAGA 0.876947 -95 CATAACACCCTCGCGGTAATGCCGTAAAAGTA 4 166 0 TCGCGTATGC 0.941201 -40 CCTGCAGGGCGCGCAGTATAGCCGTTACCTAG 5 59 0 GCGCGTAAGC 0.989131 -57 GTGCGCGTGCGCGCGGTGCGGAAGGATTTCAG 6 263 1 GCGCGTGGGA 0.988061 -38 GTCCCTCCTCTCGCAGGGCGCCTGTGCGGGAA 8 134 1 TCGCGGGGCC 0.912054 -167 CGCTTTTTCAGCGCTTTGCTGCATCCTGCTTG 8 227 1 GCGCTTGTGC 0.86859 -74 CTTGGACCGTGCGAGGCGTTGCGGACGTAGGT 8 255 1 GCGAGCGTGC 0.720953 -46 ACCTGCGGGGGCGCAGTATACCGCGCAGGTAT 9 49 1 GCGCGTAACC 0.976857 -87 TGCGCCGTACGGCTCTCACACAG 12 2 1 GCGCGTAGGC 0.99565 -299 CAATCCCTCTTTGCTGTAGGGCTCCC 13 5 0 TTGCGTAGGC 0.822243 -88 AGACTATGCAGCACAGTAAACCAACCGGAACA 14 56 0 GCACGTAACC 0.676716 -88 CAGACCGCGCGCGAAGTGTAGCACAGACTATG 14 80 0 GCGAGTGAGC 0.959144 -64 GAACTGTAGCGCGCCGTGGGAAAGGGAGGTAT 15 83 0 GCGCGTGGAA 0.855865 -122 TACACGCACCGCGCGGGGCGCATTCTATACAT 15 135 0 GCGCGGGGCA 0.905521 -70 CTTCACGTTTGCGCCGTATGCCTACACGCACC 15 157 0 GCGCGTAGCC 0.990673 -48 **** *** *** Masking position 6 Map Score: 21.0299 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 919 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 TAGGCTCCTGCGAGTTGGGAGGTTGGGAAT 2 9 0 CGGTTGGGGG 0.610351 -195 TTTTCTACCGCTTGCAGGGGACTTACGGGAGT 2 133 0 CTGCAGGGAC 0.88004 -71 TGCGTCCCAGCGTGCACGGGGCGATGGAGTGT 3 105 0 CGGCACGGGC 0.991463 -90 CTGACTACACCGACCACGATGCGACCTGCATC 4 91 0 CGCCACGAGC 0.619144 -115 CAGGCAGGGTATGCTGAGAGGT 5 1 1 CAGCAGGGAT 0.874845 -115 GCCTGCAGGGCGCGCAGTATAGCCGTTACCTA 5 60 0 CGGCAGTAAG 0.348795 -56 GCGCGCCCTGCAGGCAGGGCGGGTATCCTATA 5 77 1 CAGCAGGGGG 0.979652 -39 CACTTTCTTGAGTGCAGGATGTTCTTTTCGTG 6 234 1 AGGCAGGAGT 0.69768 -67 TTCCACCACTCTCGCACGGAAGAATCGGCA 8 51 0 CTGCACGGAG 0.720007 -250 AGTCCCTCCTCTCGCAGGGCGCCTGTGCGGGA 8 133 1 CTGCAGGGGC 0.969157 -168 GCTGAAAAAGCGGGAAACGGGGATCGAACCCG 8 207 0 CGGAAACGGG 0.241095 -94 TCGCACGGTCCAAGCAGGATGCAGCAAAGCGC 8 237 0 CAGCAGGAGC 0.946661 -64 CTGCTTGGACCGTGCGAGGCGTTGCGGACGTA 8 252 1 CGGCGAGGGT 0.894308 -49 CCCCGCAGGTCGTGCAAGACGTTTACTAGGAG 9 27 0 CGGCAAGAGT 0.914867 -109 GCCTAGTATCCAGGCAAGGGACGAAAAGTCAA 9 109 0 CAGCAAGGAC 0.792168 -27 GCCTTTTGTGCGAGCACGATGTGTGGGAGCTG 10 33 1 CGGCACGAGT 0.945055 -60 GCATGGGGGGCGTGTAGGAAGGT 10 80 1 CGGTAGGAGG 0.887692 -13 GACACGTAGGGTGTGCGTGCAGGG 11 3 1 CAGTAGGGGT 0.788691 -116 GTAGGGTGTGCGTGCAGGGGAGGCAGGAGTGC 11 16 1 CGGCAGGGAG 0.980377 -103 GCAGTGCGCGCGGGCACGCCGGCCCATGATAC 12 61 0 CGGCACGCGG 0.865986 -240 CGCAGAAATTCGCGTAAGGTGCTCTCGCTCGT 12 221 1 CGGTAAGGGC 0.900459 -80 CAGCGCACAAAGAGCAAGGAGCACGAGCGAGA 12 243 0 AGGCAAGGGC 0.809419 -58 TTTGCAAGAGCAAGCAGCGCACAAAGAGCAAG 12 257 0 CAGCAGCGAC 0.667827 -44 TGGTGTTCATCGGGCAGCGTGTACCACCTGTT 14 28 1 CGGCAGCGGT 0.950325 -116 GCGCACAGACCGCGCGCGAAGTGTAGCACAGA 14 85 0 CGGCGCGAGT 0.800504 -59 CTACACGCACCGCGCGGGGCGCATTCTATACA 15 136 0 CGGCGGGGGC 0.984156 -69 ** ****** ** Masking position 4 Map Score: 37.2594 Number of sites scoring better than the average of aligned sites = 1531 Number in coding regions = 1394 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 TCCTGCGAGTTGGGAGGTTGGGAAT 2 5 0 TGGGAGGTGG 0.927819 -199 CTCATATCACGAGGATGCGCGA 4 2 0 GAGGATGGCG 0.94783 -204 CAGTTACCATTGGGATGCAGGTCGCATCGTG 4 78 1 TGGGATGAGG 0.946628 -128 GATTTCAGTGGCGGAGGAGGGGAC 6 287 1 GCGGAGGGGG 0.984889 -14 AGAAAAATACGGGAATGTAGGCA 7 11 1 GGGAATGAGG 0.893677 -13 CTAGTGCCTCTGGCATGAGGGTTCAAGTCCC 8 108 1 TGGCATGGGG 0.901724 -193 GCGAGGCGTTGCGGACGTAGGTATTTCTTCC 8 265 1 GCGGACGAGG 0.975341 -36 TTAAAAGGCCTCGAATGGAGGCATTGACTTT 9 86 1 TCGAATGAGG 0.498905 -50 GTGTAACACATAGCATGGGGGGCGTGTAGGA 10 68 1 TAGCATGGGG 0.851136 -25 TGTGCGTGCAGGGGAGGCAGGAGTGCTTTCG 11 22 1 GGGGAGGAGG 0.990683 -97 GTTTTTTTCAGGGGAGGGTCG 11 108 1 GGGGAGGTCG 0.938629 -11 CAGTGCGCGCGGGCACGCCGGCCCATGATAC 12 61 0 GGGCACGCGG 0.898646 -240 GGGCCTTTTTGAGGGCGGGGGGAGAACTTAA 12 165 0 GAGGGCGGGG 0.901349 -136 TCTTTCGCGTGACGACGAAGGGCCTTTTTGA 12 184 0 GACGACGAGG 0.803276 -117 AAAGAGCAAGGAGCACGAGCGAGAGCACCTT 12 236 0 GAGCACGGCG 0.901277 -65 GCTCTTTTTAGAGGAGGTTGGGCAA 13 78 1 GAGGAGGTGG 0.967743 -15 GACTCGTTATGAGGAGGAACGC 15 193 1 GAGGAGGACG 0.954643 -12 ******* *** Masking position 7 Map Score: 19.4279 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 510 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 AAGGACGTTAGGTGGTTGTCCGTTTCTGTGC 4 43 1 GGTGGTTTCC 0.381965 -163 CTGCAGGCAGGGCGGGTATCCTATACAGAGG 5 84 1 GGCGGGTTCC 0.971846 -32 TTGTTCGTTTGGGGAGTTTCCCGAGTGGTCA 6 50 1 GGGGAGTTCC 0.750836 -251 TTTCGTTCCAGGCGTTTTTGCTAGCTGCTGT 6 194 1 GGCGTTTTGC 0.954289 -107 GGCGGTTGGGTGTCTGCATCCTGTTGG 8 7 1 TGGGTGTTGC 0.904928 -294 TCCTAAGTCTAGCGTGTCTGCCGATTCCACC 8 76 0 AGCGTGTTGC 0.922114 -225 CCTCTCGCAGGGCGCCTGTGCGGGAATAGCT 8 140 1 GGCGCCTTGC 0.785381 -161 ACCGTTATACGGCGTGTTTGCCTTTTGTGCG 10 14 1 GGCGTGTTGC 0.994467 -79 TAGCATGGGGGGCGTGTAGGAAGGT 10 78 1 GGCGTGTGGA 0.746973 -15 GACACGTAGGGTGTGCGTGCAGGGGAGGCA 11 10 1 GGTGTGCTGC 0.889356 -109 GTGCAGGGGAGGCAGGAGTGCTTTCGGAAGA 11 27 1 GGCAGGATGC 0.70038 -92 ATCATGGGCCGGCGTGCCCGCGCGCACTGCA 12 63 1 GGCGTGCCGC 0.891119 -238 AGCGTTGCGCGGGATGTGTGCTCTTTTTAGA 13 59 1 GGGATGTTGC 0.931689 -34 CCGTGGGAAAGGGAGGTATGCACAGAGGGTC 15 71 0 GGGAGGTTGC 0.909215 -134 CCCCGCGCGGTGCGTGTAGGCATACGGCGCA 15 149 1 TGCGTGTGGC 0.858353 -56 ******* *** Masking position 2 Map Score: 12.3157 Number of sites scoring better than the average of aligned sites = 560 Number in coding regions = 511 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 AGATACACACAGGGCCTGGATCCAAAGGGTCTC 3 142 1 AGGGTGATCC 0.992815 -53 CCCTGCAGGCAGGGCGGGTATCCTATACAGAGG 5 82 1 AGGGGTATCC 0.897312 -34 AAGCCAACTTAGGGATTCGAACCCTAGACCTCG 6 19 0 AGGGTGAACC 0.995509 -282 GTGGGGAGTCAAGGATTCGAACCTTGGAAGACA 6 110 0 AAGGTGAACC 0.961173 -191 CTCATGCCAGAGGCACTAGATCCTAAGTCTAGC 8 94 0 AGGCTGATCC 0.958108 -207 CTGCGAGAGGAGGGACTTGAACCCTCATGCCAG 8 117 0 AGGGTGAACC 0.995509 -184 AAGCGGGAAACGGGGATCGAACCCGCGACTTCC 8 199 0 CGGGTGAACC 0.992097 -102 TTTTTGAGGGCGGGGGGAGAACTTAAAAAACCC 12 158 0 CGGGGGAACT 0.888119 -143 **** * ***** Masking position 10 Map Score: 8.82486 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 17 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 GTCATCGGTATGTTTTTTCTACCGCTTGCA 2 149 0 TGTTTTTTCT 0.570627 -55 TTTTTACGTCGGTTTTTGCACAGAATACAA 3 46 1 GGTTTTTGCA 0.874304 -149 ACGGTAAATAGGTGTTTTCTTGACCGAGGG 4 123 1 GGTGTTTTCT 0.870646 -83 TTTCTTCTCCTTTTTTGCCATAACACCCT 4 187 0 CTTTTTTGCC 0.859165 -19 ATCTGTTGGCGTTGTCTTCCAAGGTTCGAA 6 98 1 GTTGTCTTCC 0.768998 -203 TCGTTCCAGGCGTTTTTGCTAGCTGCTGTG 6 196 1 CGTTTTTGCT 0.900568 -105 GGCGGTTGGGTGTCTGCATCCTGTTGGG 8 9 1 GGTGTCTGCA 0.875878 -292 CTGTTGGGCGAGTTTTTGCTTGCCGSATST 8 31 1 AGTTTTTGCT 0.583533 -270 CTAAGTCTAGCGTGTCTGCCGATTCCACCA 8 75 0 CGTGTCTGCC 0.955617 -226 CGTTATACGGCGTGTTTGCCTTTTGTGCGA 10 16 1 CGTGTTTGCC 0.967021 -77 CCCTGTCAATCGTTTCTTCCGAAAGCACTC 11 42 0 CGTTTCTTCC 0.893419 -77 GGTAGGCTGTGTTTTTTTCAGGGGAGGGTC 11 98 1 GTTTTTTTCA 0.518174 -21 CAAACCACTTTTTGTTTTCCCGTGCT 12 285 1 TTTGTTTTCC 0.552919 -16 ********** Masking position 5 Map Score: 6.13933 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 371 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 GCGTGATTATAGGTCTTTTGAACGCTTTTT 2 183 0 AGGTCTTTTG 0.952642 -21 TGGATCCAAAGGGTCTCTTTGCGTTACGAT 3 158 1 GGGTCTCTTT 0.765734 -37 ACCGAGGGCGGCGTCTCTCGTTACTTTTAC 4 145 1 GCGTCTCTCG 0.928951 -61 GGGAGGCAGGAGTGCTTTCGGAAGAAACGA 11 33 1 AGTGCTTTCG 0.865648 -86 TTGACAGGGGACGTCTTTTGCGCTAGCCTA 11 63 1 ACGTCTTTTG 0.859689 -56 TTCTGCGCGGAGGTCTTTCGCGTGACGACG 12 198 0 AGGTCTTTCG 0.962822 -103 ATTCGCGTAAGGTGCTCTCGCTCGTGCTCC 12 228 1 GGTGCTCTCG 0.91438 -73 TCACGGGTTCTTTTGTCTGGTGTTC 14 6 1 GGTTCTTTTG 0.929485 -138 GGCGCGCTACAGTTCTCTTGATTCTTCAAA 15 100 1 AGTTCTCTTG 0.929485 -105 ********** Masking position 6 Map Score: 5.62245 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 90 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 TGTGTGTATCTGGCATTGCGTCCCAGCGTGCACG 3 119 0 TGGTTCGTCC 0.995089 -76 CCTCGTGATATGAGGTTCCGTCCCAAGGACGTTA 4 19 1 TGATTCGTCC 0.987528 -187 GGACGTTAGGTGGTTGTCCGTTTCTGTGCTTGGC 4 45 1 TGGGTCGTTC 0.87445 -161 GGGTAGTGTCTGACTTGTCTTTCCCTGGCGTTTC 6 164 1 TGATGCTTCC 0.896617 -137 TGTCTTTCCCTGGCGTTTCGTTCCAGGCGTTTTT 6 179 1 TGGTTCGTCC 0.995091 -122 ATGGAGGCATTGACTTTTCGTCCCTTGCCTGGAT 9 100 1 TGATTCGTCC 0.987536 -36 TCGTGTATCATGGGCCGGCGTGCCCGCGCGCACT 12 57 1 TGGCGCGTCC 0.983906 -244 ACAGCAAAGAGGGATTGACGTGCCGATCTTTTTT 13 20 1 GGGTGCGTCC 0.981039 -73 *** ** *** ** Masking position 11 Map Score: 8.24297 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 34 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TATGCGGTGCGCTTTGGCAGGCCGCGGTAA 2 73 0 GCTTTGGCAG 0.944815 -131 GTTTTTTCTACCGCTTGCAGGGGACTTACG 2 138 0 CCGCTTGCAG 0.881521 -66 GGATCTAGTGCCTCTGGCATGAGGGTTCAA 8 104 1 CCTCTGGCAT 0.744339 -197 TCAAGTCCCTCCTCTCGCAGGGCGCCTGTG 8 130 1 CCTCTCGCAG 0.920146 -171 CCCGTTTCCCGCTTTTTCAGCGCTTTGCTG 8 218 1 GCTTTTTCAG 0.855174 -83 AAGCCCAGATCCTTAGGAAGAAATACCTAC 8 281 0 CCTTAGGAAG 0.617127 -20 GTTAAGGCTCCCTTTTGCAGTGCGCGCGGG 12 79 0 CCTTTTGCAG 0.981391 -222 ATCCATTCGGGTTTTTTAAGTTCTCCCCCC 12 150 1 GTTTTTTAAG 0.187974 -151 CGACGAAGGGCCTTTTTGAGGGCGGGGGGA 12 173 0 CCTTTTTGAG 0.838224 -128 ACGTGCCGATCTTTTTTCAGATAGCGTTGC 13 37 1 CTTTTTTCAG 0.702692 -56 TCTTTTTTAACCTCTGGGAGGATAC 14 129 1 CCTCTGGGAG 0.925144 -15 CTATACATTTCCTTTTGAAGAATCAAGAGA 15 113 0 CCTTTTGAAG 0.937028 -92 ********** Masking position 9 Map Score: 5.05978 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 331 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 CTCATATCACGAGGATGCGCGA 4 3 0 GAGGATGCGC 0.900024 -203 GCTGAGAGGTCAGGATGGAGTTCTGGAGCA 5 23 1 CAGGATGGAG 0.942107 -93 AAGAAAGTGACAAGAGGCACAGCAGCTAGC 6 213 0 CAAGAGGCAC 0.873309 -88 TTCTTGAGTGCAGGATGTTCTTTTCGTGCG 6 238 1 CAGGATGTTC 0.833107 -63 ACTCGCCCAACAGGATGCAGACACCCAACC 8 14 0 CAGGATGCAG 0.974635 -287 CGCCCTGCGAGAGGAGGGACTTGAACCCTC 8 124 0 GAGGAGGGAC 0.968703 -177 ACGGTCCAAGCAGGATGCAGCAAAGCGCTG 8 235 0 CAGGATGCAG 0.974635 -66 TGTGCGTGCAGGGGAGGCAGGAGTGCTTTC 11 22 1 GGGGAGGCAG 0.920521 -97 GCTCTTTTTAGAGGAGGTTGGGCAA 13 78 1 GAGGAGGTTG 0.86983 -15 CCAACCGGAACAGGTGGTACACGCTGCCCG 14 38 0 CAGGTGGTAC 0.812913 -106 GACTCGTTATGAGGAGGAACGC 15 193 1 GAGGAGGAAC 0.919013 -12 ********** Masking position 4 Map Score: 8.29355 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 275 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 CATCAAATTACCGCATAATACGA 1 2 0 CGCATAATAG 0.811351 -117 CCAAAGCGCACCGCATACCATGTACACCCCTG 2 86 1 CGCATACCAG 0.991549 -118 ACGATGCGACCTGCATCCCAATGGTAACTGCC 4 76 0 CGCATCCCAT 0.8492 -130 CCTGACCTCTCAGCATACCCTGCCTG 5 5 0 CGCATACCCG 0.990744 -111 TGCGGGGGCGCAGTATACCGCGCAGGTATATT 9 52 1 CGTATACCGG 0.827526 -84 CGTCCCTTGCCTGGATACTAGGCGCCCT 9 118 1 CGGATACTAG 0.864336 -18 GAAAGCACTCCTGCCTCCCCTGCACGCACACC 11 20 0 CGCCTCCCCG 0.964807 -99 GAAAAAAACACAGCCTACCAGGGGTAGGCTAG 11 85 0 CGCCTACCAG 0.982806 -34 GTTTACTGTGCTGCATAGTCTGTGCTACACTT 14 67 1 CGCATAGTCG 0.860995 -77 * ******** * Masking position 6 Map Score: 3.86501 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 127 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 ********** No masking Map Score: 1.94221e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 1.94221e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0