AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_synecho_ctra_300.orf -o224_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCY09374 77 Synechocystis #2 RCY24913 188 Synechocystis #3 RCY27579 201 Synechocystis #4 RCY35636 89 Synechocystis #5 RCY46112 116 Synechocystis #6 RCY22383 35 Synechocystis #7 RCY11108 217 Synechocystis #8 RCY05884 180 Synechocystis #9 RCY44898 206 Synechocystis #10 RCY15128 40 Synechocystis #11 RCY23001 94 Synechocystis #12 RCY43048 300 Synechocystis #13 RCT00037 281 Chlamydia_trachomatis #14 RCT00184 126 Chlamydia_trachomatis #15 RCT00185 300 Chlamydia_trachomatis #16 RCT00476 19 Chlamydia_trachomatis #17 RCT00477 107 Chlamydia_trachomatis #18 RCT00478 286 Chlamydia_trachomatis #19 RCT00480 43 Chlamydia_trachomatis #20 RCT00481 65 Chlamydia_trachomatis #21 RCT00482 20 Chlamydia_trachomatis #22 RCT00483 21 Chlamydia_trachomatis #23 RCT00484 55 Chlamydia_trachomatis #24 RCT00485 22 Chlamydia_trachomatis #25 RCT00488 21 Chlamydia_trachomatis #26 RCT00489 27 Chlamydia_trachomatis #27 RCT00493 16 Chlamydia_trachomatis #28 RCT00495 32 Chlamydia_trachomatis #29 RCT00497 18 Chlamydia_trachomatis #30 RCT00499 23 Chlamydia_trachomatis #31 RCT00502 300 Chlamydia_trachomatis Motif number 1 CTATGCCAACGACGATCGCCAGGAAAAGGG 2 111 0 GACGATCGCC 0.678868 -78 ACAACCCGGCGGCGATCGCCAATGTAGGAT 3 128 1 GGCGATCGCC 0.499374 -74 TAAGTAATCCGCCCATTGGGGAAATTTGGC 5 21 0 GCCCATTGGG 0.891279 -96 CCCCCCGATCGGCGATCGCCAAATGCCCCT 5 85 1 GGCGATCGCC 0.499374 -32 AGCCCATTTAGCCCAAGCCCACC 6 23 1 GCCCAAGCCC 0.930338 -13 AAAAAACCTTGCCAATCCGGTTCACAC 7 8 0 GCCAATCCGG 0.748063 -210 GTAGTGCAACGGCGATCGCCTCTCCGCTAA 7 172 1 GGCGATCGCC 0.499374 -46 GGGAGATCTGGCCCAATGGGAGTCATGCTT 8 82 1 GCCCAATGGG 0.937458 -99 CAAGATGCTTGACCAATGGGAACTAAGCCC 8 124 1 GACCAATGGG 0.790865 -57 AATCAATCCAGGCGATCGGGCTTAGTTCCC 8 141 0 GGCGATCGGG 0.728099 -40 AAATTCCTCGGCCAAGGCGGTTTAATCCT 11 10 1 GGCCAAGGCG 0.941367 -85 TACTGCCAATGACCAATGGGACTTAGGCAT 12 182 1 GACCAATGGG 0.790865 -119 AGGCATTGGAGCCAAATGCCTAAGTCCCAT 12 197 0 GCCAAATGCC 0.816683 -104 ATCTTACCCAGCCCAACGCCTGGAGTGGTT 12 234 1 GCCCAACGCC 0.842333 -67 ACTTGCACGGGCCAAAGCCCAAGGGATTTT 18 164 0 GCCAAAGCCC 0.754727 -123 ATATACCATTGCCCATTCGCCGCCTTTGTT 31 143 1 GCCCATTCGC 0.86017 -158 TTTAGCAAACGGCCATGCCCTCCATCCTGC 31 216 0 GGCCATGCCC 0.748783 -85 ********** Masking position 5 Map Score: 18.2139 Number of sites scoring better than the average of aligned sites = 8960 Number in coding regions = 8180 Number in noncoding regions = 780 Number of orfs with sites within 600 bp upstream = 492 Fraction of orfs with sites within 600 bp upstream = 0.0790235 Motif number 2 AAAATTTAATCCCTTTTCCTGGCGATCGTCGTTGG 2 101 1 CCTTCCGGCA 0.965634 -88 ATAAACTGAACCCCCCGATCGGCGATCGCCAAATG 5 75 1 CCCCATGGCA 0.950783 -42 TCGCCAAATGCCCCTGGCTAGGTTAAG 5 100 1 CCCTCTGGTA 0.990591 -17 GATCGCCTCTCCGCTAACTGGGTTACAAACATTAC 7 185 1 CCCTCTGGTA 0.990587 -33 AGGAAATTAACCGTTAAATGGGTTACGATCAAAGC 9 34 0 CCTTATGGTA 0.923581 -173 GAGAGCAGTTCCTCCACCTGGGCCAGAGGAAATTA 9 60 0 CCCCCTGGCA 0.992089 -147 AGAATTTTAGCTTTTTGCTTGGTGACCCTTTCCTC 9 124 1 CTTTCTGGTA 0.860749 -83 TGCTTGGTGACCCTTTCCTCGGTGACCTAAACTGC 9 139 1 CCTTCTGGTA 0.987413 -68 TCTTGTTCTGCCTTTGTCTGGGCTACCATTTGGTG 12 116 1 CCTTCTGGCA 0.993343 -185 AAATCCACTCCTTTATCTAAGCGAATTCTAAAAA 14 103 0 CCTTCTAGCA 0.958311 -24 GTCTACCATTCCACCATCTGAGCAAAAACGACGAG 18 118 0 CCCCCTAGCA 0.950787 -169 ** ** ** *** * Masking position 15 Map Score: 14.9785 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 467 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 ACTGTGCCAAAACAGTCTGAAGCAAAAGAGATTA 2 31 0 AAAGCTGAAA 0.820307 -158 GAGTCGGGCCCTAAGGCAGAATAAAGATTGAACT 2 62 0 CTAGCAGAAA 0.94273 -127 GGGAAAAATGCCAGAAGCATCGATGGTTG 2 170 0 AATGCAGAAA 0.928669 -19 TTTTAAAAGACAGAGACAGTAAAAAATAAAGTCC 4 45 0 CAAGCAGTAA 0.973853 -45 TTTCTAGGAAAACTGGCAGTAATAAACTGAACCC 5 54 1 AATGCAGTAA 0.904372 -63 TGGCTTGGGGCTTTGACAGTAGCAACGACTTTGC 7 114 1 CTTGCAGTAA 0.884268 -104 AGATCTCCCCCAAAGTCAGCATAACCCTTCCCCG 8 57 0 CAAGCAGCAA 0.931593 -124 GTAGCCCAGACAAAGGCAGAACAAGACAATCAGG 12 108 0 CAAGCAGAAA 0.98087 -193 TCCCATTGGTCATTGGCAGTAATATCGCTCAAAA 12 169 0 CATGCAGTAA 0.959676 -132 AACCTCTGCACAAAGGCATTAAAAAGTTGCGTCT 13 114 0 CAAGCATTAA 0.71041 -168 ACATAGTGAAAAAAGCCCGAAGAAAACCTTTGTC 14 25 0 AAAGCCGAAA 0.793259 -102 CCTTGTTTTCATTTGTCAGAAGAAACGAAGCTTA 15 55 1 ATTGCAGAAA 0.806942 -246 ATCGCAAAAACAAAGCCTGAAAAATCGTTCTAGG 31 52 0 CAAGCTGAAA 0.919923 -249 ** ** ***** * Masking position 11 Map Score: 10.6102 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 268 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 AATCTTTATTCTGCCTTAGGGCCCGACTCCC 2 67 1 CTGCCTTGGG 0.981931 -122 GAATGCTTTAACGCCTTGGGTAAATGGGGGA 3 32 1 ACGCCTTGGT 0.849778 -170 CCAAATGCCCCTGGCTAGGTTAAG 5 103 1 CTGGCTAGTT 0.838717 -14 ACTGTTGTCGATGGCTTGGGGCTTTGACAGT 7 103 1 ATGGCTTGGG 0.924218 -115 AAGGGTTATGCTGACTTTGGGGGAGATCTGG 8 62 1 CTGACTTGGG 0.841963 -119 TCCAGGCGATCGGGCTTAGTTCCCATTGGTC 8 134 0 CGGGCTTGTT 0.78749 -47 TAGTTTTTCAATGGCTTTGGGGCC 9 193 1 ATGGCTTGGG 0.924218 -14 AAGGATTAAACCGCCTTGGCCGAGGAATTT 11 10 0 CCGCCTTGCC 0.782131 -85 TTGTCTTGTTCTGCCTTTGTCTGGGCTACCA 12 113 1 CTGCCTTGTC 0.964893 -188 TTGGAGCCAAATGCCTAAGTCCCATTGGTCA 12 191 0 ATGCCTAGTC 0.740159 -110 CAACTTTTTAATGCCTTTGTGCAGAGGTTTT 13 119 1 ATGCCTTGTG 0.949715 -163 TTTAGGGTCGCTGCCTAAGTGTATCTGTTTG 15 102 1 CTGCCTAGTG 0.939788 -199 AACGATTTTTCAGGCTTTGTTTTTGCGATTT 31 57 1 CAGGCTTGTT 0.714306 -244 TGCCCATTCGCCGCCTTTGTTTGCTTTAAGG 31 152 1 CCGCCTTGTT 0.940033 -149 ******* *** Masking position 6 Map Score: 10.5717 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 614 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 ACGATCAAAGCTGTTTTCCCTTTAGGTTTCG 9 14 0 CTGTTTTCCT 0.870953 -193 ATCACTTCAACATTTTTTCCTAAACCAGGAA 11 39 0 CATTTTTTCT 0.923467 -56 TCACGGGGAAATTTTTTCACTTTTGAACAAT 12 16 0 ATTTTTTCCT 0.845258 -285 GATGCCACTGCATTTATTCCT 12 290 1 CATTTATTCT 0.629332 -11 AGTTTTATCTCTTTTTTTTCTAACTAAAGTC 13 51 0 CTTTTTTTCT 0.971378 -231 ATCTCTAATCCTTCTTTTTCTCTATATAAAA 13 165 0 CTTCTTTTCT 0.921644 -117 TTTCTTCGGGCTTTTTTCACTATGTCTTTTC 14 34 1 CTTTTTTCCT 0.975195 -93 TTCACTATGTCTTTTCTCCCTCTCTCTTTAG 14 49 1 CTTTTCTCCT 0.937845 -78 CTGAGCACATCTTTTTTCTCTGGTTCTTGAG 18 206 1 CTTTTTTCCT 0.975195 -81 ACCAACCCTAAATTTTTTTCTAGCGTGTTGC 20 21 0 AATTTTTTCT 0.626377 -45 GTTATTCTTCTCTTCCTTCTTTA 30 7 0 CTTCTCTTCT 0.818653 -17 CATTCGCCGCCTTTGTTTGCTTTAAGGAGCC 31 156 1 CTTTGTTTCT 0.853506 -145 ******** ** Masking position 7 Map Score: 8.65335 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 259 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 TCAGGGGTTGATTTTTTAAGGTT 3 1 0 ATTTAAGGTT 0.865087 -201 TTTTTGGATAATTGTTAAGGGTTAAAGCCTGTA 4 12 1 ATTTAGGGTT 0.984946 -78 GCCTGGATTGATTTTTGAGGGTTGCCTGATTTT 8 158 1 ATTTAGGGTT 0.984945 -23 CACATGCTGTAGTGTTGAGAGTTTTATCTCTTT 13 68 0 ATTTAGAGTT 0.927972 -214 ACAGTGCAAAATAATTTAGGGTCGCTGCCTAAG 15 88 1 AATTAGGGTC 0.94461 -213 CTAATAGACGACTTTTAAGAGTCTTTATATAAA 15 264 1 ATTTAGAGTC 0.913992 -37 TGTGGCGAGGACTCTTTAGGGTCCTCGTCGTTT 18 95 1 ATTTAGGGTC 0.981807 -192 ACGCTAGAAAAAAATTTAGGGTTGGTCGTACTT 20 26 1 AATTAGGGTT 0.953859 -40 ACCTAGAACGATTTTTCAGGCTTTGTTTTTGCG 31 51 1 ATTTAGGCTT 0.90482 -250 * * ** ****** Masking position 6 Map Score: 8.69615 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 60 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 CAACAAATGATCCACCAACCATCGATGCTT 2 155 1 TCCACCAACC 0.877865 -34 TAGGTACTTCTCCCCCATTTACCCAAGGCG 3 43 0 TCCCCCATTT 0.730089 -159 CAGCAAAAAAGCCTCCAGCCCTCGATAATC 3 87 0 GCCTCCAGCC 0.963602 -115 TAGTCAGTATCCCCCCATCCTACATTGGCG 3 144 0 CCCCCCATCC 0.980452 -58 TTTTCGCATTTCGACCATCC 4 80 1 TCGACCATCC 0.810078 -10 TACTGTCAAAGCCCCAAGCCATCGACAACA 7 105 0 GCCCCAAGCC 0.803867 -113 GACTTTGCTGGCCCCCATCCCATTAAAAGC 7 140 1 GCCCCCATCC 0.986497 -78 GGAGAGCAGTTCCTCCACCTGGGCCAGAGG 9 66 0 TCCTCCACCT 0.835968 -141 CAAGAGGGATTCCCCTATCTCTAATCCTTC 13 182 0 TCCCCTATCT 0.748134 -100 TATTTTGACATCCTCCAGCGGCTGAAGTCA 13 210 0 TCCTCCAGCG 0.860225 -72 TGTCTACCATTCCACCATCTGAGCAAAAAC 18 124 0 TCCACCATCT 0.936451 -163 AACGGCCATGCCCTCCATCCTGCAAGAGCG 31 209 0 CCCTCCATCC 0.962304 -92 ********** Masking position 7 Map Score: 7.50861 Number of sites scoring better than the average of aligned sites = 1271 Number in coding regions = 1152 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 8 CAGTCTGAAGCAAAAGAGATTATCAGATTTT 2 22 0 CAAAAGGATT 0.911938 -167 CGATCGCCAGGAAAAGGGATTAAATTTTTCC 2 98 0 GAAAAGGATT 0.711632 -91 GCCAGTTTTCCTAGAAAGATTAAGTAATCCG 5 40 0 CTAGAAGATT 0.90848 -77 GCCCGATCGCCTGGATTGATTTTTGAGGGTT 8 150 1 CTGGATGATT 0.809753 -31 TTTCCTAAACCAGGAAGGATTAAACCGCCTT 11 24 0 CAGGAAGATT 0.92743 -71 TGAATCCACTGTGGAGTGATTACGAAAAAGT 12 44 1 GTGGAGGATT 0.900823 -257 AGCCCAACGCCTGGAGTGGTTGAATTAGAAT 12 243 1 CTGGAGGGTT 0.877719 -58 CGGCTGAAGTCAAGAGGGATTCCCCTATCTC 13 191 0 CAAGAGGATT 0.976639 -91 CTAGTAAAACCTAGAACGATTTTTCAGGCTT 31 43 1 CTAGAAGATT 0.90848 -258 GCGACATCCACACAAGAGATTTTTCTTGACG 31 107 0 CACAAGGATT 0.761133 -194 CTCCATCCTGCAAGAGCGATTTCCACGACAA 31 196 0 CAAGAGGATT 0.976639 -105 ****** **** Masking position 5 Map Score: 6.34854 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 151 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 GTTCTAGTCAGTATCCCCCCATCCTACATT 3 148 0 GTATCCCCCC 0.88954 -54 CAATTCAGCCAAATTTCCCCAATGGGCGGA 5 14 1 AAATTTCCCC 0.92792 -103 CCATTGGGCCAGATCTCCCCCAAAGTCAGC 8 71 0 AGATCTCCCC 0.974276 -110 TATCCCATAGGAATCTCCCCTTAAACCTGA 10 17 0 GAATCTCCCC 0.988923 -24 AAAAGTGAAAAAATTTCCCCGTGAATCCAC 12 23 1 AAATTTCCCC 0.92792 -278 GGTTGAATTAGAATCGCCCCTTTAATTTTC 12 260 1 GAATCGCCCC 0.983626 -41 ACGAAATCAGGAATCTCCCAAAAGGCTTTA 17 14 0 GAATCTCCCA 0.908836 -94 AACGCTTCACAGACCGCCCCCGGTGCCTAA 31 253 0 AGACCGCCCC 0.871285 -48 ********** Masking position 3 Map Score: 5.62633 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 246 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 10 GGTGTTTGACTAAAATCTGATAATCTCT 2 9 1 ACTAAAATCT 0.633917 -180 ACATCCCAGCAAAAAAGCCTCCAGCCCTCG 3 93 0 AAAAAAGCCT 0.958278 -109 CAGGCTATCAAAAAAAACCTTGCCAATCCG 7 19 0 AAAAAAACCT 0.934854 -199 GAAAAACTACACAAAATCCTGTCTTTTAGC 9 172 0 ACAAAATCCT 0.679609 -35 TTTTTTTCTAACTAAAGTCTTTTCCTAGAA 13 40 0 ACTAAAGTCT 0.734857 -242 CTATTTAAAGAAAAAAACCTCTGCACAAAG 13 133 0 AAAAAAACCT 0.934854 -149 AAAAAGCCCGAAGAAAACCTTTGTCTTCGG 14 20 0 AAGAAAACCT 0.792164 -107 AGACATAGTGAAAAAAGCCCGAAGAAAACC 14 31 0 AAAAAAGCCC 0.783673 -96 TCGTTTTCGTAAAAAAGTCTCTTAATAGAT 15 189 1 AAAAAAGTCT 0.868457 -112 TAGTAAAGCCTTTTGGGAGAT 17 2 1 AGTAAAGCCT 0.906033 -106 AAGCTCCACTAGTAAAACCTAGAACGATTT 31 35 1 AGTAAAACCT 0.857635 -266 AAATCGCAAAAACAAAGCCTGAAAAATCGT 31 58 0 AACAAAGCCT 0.859165 -243 CTTAGCGTCAAGAAAAATCTCTTGTGTGGA 31 102 1 AGAAAAATCT 0.745989 -199 ********** Masking position 5 Map Score: 7.67924 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 258 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 ATTAGGTACTTCTCCCCCATTTACCCAAGG 3 45 0 TCTCCCCCAT 0.77393 -157 GGCGATCGCCTCTCCGCTAACTGGGTTACA 7 182 1 TCTCCGCTAA 0.865867 -36 TTGGGCCAGATCTCCCCCAAAGTCAGCATA 8 68 0 TCTCCCCCAA 0.955979 -113 TGGAGGAACTGCTCTCCTAAAGTTGCTAAA 9 79 1 GCTCTCCTAA 0.944034 -128 CCCATAGGAATCTCCCCTTAAACCTGATTG 10 14 0 TCTCCCCTTA 0.96515 -27 CTTTTCTCCCTCTCTCTTTAGAATGATTCA 14 59 1 TCTCTCTTTA 0.678334 -68 GAGTTAAATAGCTCTCCTCATCTATAAATC 18 253 0 GCTCTCCTCA 0.860485 -34 AACACTCTCTCCTAAAAATTA 22 7 0 TCTCTCCTAA 0.971838 -15 AACCTGTCTCCTTATGAC 29 5 0 TGTCTCCTTA 0.757606 -14 ********** Masking position 3 Map Score: 2.9775 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 291 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 12 CTTTTGCTTCAGACTGTTTTGGCACAGTTCAATCTTT 2 37 1 AGATTTTAAG 0.851872 -152 CGAAATGCGAAAAATTTTAAAAGACAGAGACAGTAAA 4 56 0 AAATTAAAAG 0.735269 -34 ATTTCTAGGAAAAGACTTTAGTTAGAAAAAAAAGAGA 13 38 1 AAATTTAAAA 0.633328 -244 TCTATATAAAAGACTATTTAAAGAAAAAAACCTCTGC 13 139 0 AGATTTAAAA 0.91811 -143 ATAGAGAAAAAGAAGGATTAGAGATAGGGGAATCCCT 13 171 1 AGAATTAAAG 0.851872 -111 CACTATAAAAAGATACTTTACAAACAGATACACTTAG 15 116 0 AGATTTAAAG 0.978384 -185 AAGTCTTCCGAGACTCTTAAACAAGAGTCCTTCACTA 15 148 0 AGATTAAAAG 0.947446 -153 CTAATACCTCAGACTATCTATTAAGAGACTTTTTTAC 15 197 0 AGATCTAAAG 0.894998 -104 ACGACTTTTAAGAGTCTTTATATAAAGAACGGAGAAG 15 271 1 AGATTTAAAG 0.978384 -30 GCTTTTTTTTAGAACTTTAACATACAATCCATTGTAG 18 21 1 AGATTAAAAA 0.817041 -266 CTAGAACTTTTAGGTAAAGTTT 24 3 1 AGATTTAAAG 0.978384 -20 *** **** * ** Masking position 14 Map Score: 6.11634 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 35 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ATCGCCAGGAAAAGGGATTAAATTTTTCCGGG 2 95 0 AAAGATTAAA 0.563644 -94 AAGGCAAAGTTAACAACTAAAAATGTCCACTT 8 12 0 TAAACTAAAA 0.497994 -169 TGCTCTCCTAAAGTTGCTAAAACTTGCTGAAA 9 88 1 AAGGCTAAAA 0.838991 -119 GTCACCAAGCAAAAAGCTAAAATTCTCCCGTT 9 118 0 AAAGCTAAAA 0.96512 -89 TCGGTGACCTAAACTGCTAAAAGACAGGATTT 9 157 1 AAAGCTAAAA 0.96512 -50 GGATTGTTCAAAAGTGAAAAAATTTCCCCGTG 12 14 1 AAAGAAAAAA 0.801952 -287 GTTAGAAAAAAAAGAGATAAAACTCTCAACAC 13 58 1 AAAGATAAAA 0.910443 -224 GAATTCTAAAAAAATAATAAAATTCATGAATC 14 83 0 AAAAATAAAA 0.741496 -44 TTTTTTACGAAAACGACAAAAAGTCTTCCGAG 15 173 0 AAAACAAAAA 0.756678 -128 ATTGTATGTTAAAGTTCTAAAAAAAAGCAATG 18 17 0 AAATCTAAAA 0.755496 -270 CCCACACCAAAAATCGCAAAAACAAAGCCTGA 31 66 0 AAAGCAAAAA 0.916815 -235 *** ******* Masking position 10 Map Score: 3.87466 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 244 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 14 GACGATCGCCAGGAAAAGGGATTAAATTTT 2 101 0 AGGAAAAGGG 0.726411 -88 CGATCGTCGTTGGCATAGCTCGATCCTATG 2 123 1 TGGCATAGCT 0.677531 -66 CGCAGGGAAAAGGAAAGGCTCAGCTTGAGT 3 180 0 AGGAAAGGCT 0.938325 -22 CAAATGCCCCTGGCTAGGTTAAG 5 104 1 TGGCTAGGTT 0.590103 -13 TGAACCGGATTGGCAAGGTTTTTTTTGATA 7 14 1 TGGCAAGGTT 0.925535 -204 TCCCAGGTAAAGGCAAAGTTAACAACTAAA 8 23 0 AGGCAAAGTT 0.937393 -158 TAGGTCACCGAGGAAAGGGTCACCAAGCAA 9 138 0 AGGAAAGGGT 0.961172 -69 GTGAGTCCGAAGACAAAGGTTTTCTTCGGG 14 14 1 AGACAAAGGT 0.67853 -113 GGAGGATCCGAGGCATGGGTGTCTGACGGC 15 20 1 AGGCATGGGT 0.913389 -281 TACACAATAAAGGAAAGGGTTACTAACGAA 17 39 0 AGGAAAGGGT 0.961172 -69 CACGCACGACTGGAAAAGCTACAATGGATT 18 46 0 TGGAAAAGCT 0.83138 -241 TAGAACTTTTAGGTAAAGTTT 24 12 1 AGGTAAAGTT 0.660106 -11 ********** Masking position 8 Map Score: 5.71533 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 611 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 15 TGTCTTTTAAAATTTTTCGCATTTCGACCAT 4 67 1 AATTTTTCGA 0.947701 -23 GCGCAAAAGTACTTTTTCGTAATCACTCCAC 12 54 0 ACTTTTTCGA 0.966094 -247 ACGAAAAAGTACTTTTGCGCATTGTACTCAC 12 65 1 ACTTTTGCGA 0.959386 -236 ATAAATAACTACTATTGCGAATACTTAT 13 264 1 ACTATTGCGA 0.853538 -18 TGATGCTAATTTTTCGAAAACACTGACT 19 8 1 AATTTTTCGA 0.947701 -36 TAATTTTTAGGAGAGAGTGTT 22 2 1 AATTTTTAGA 0.737071 -20 ********* * Masking position 6 Map Score: 0.387684 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 53 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701