AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_synecho_reg_100.orf -o199_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RCY41239 17 Synechocystis Input sequences: #1 RCY25702 300 Synechocystis #2 RCY23794 104 Synechocystis #3 RCY53156 108 Synechocystis #4 RCY31741 108 Synechocystis #5 RCY09512 82 Synechocystis #6 RCY38222 137 Synechocystis #7 RCY33689 119 Synechocystis #8 RCY05922 107 Synechocystis #9 RCY14231 101 Synechocystis #10 RCY17023 68 Synechocystis #11 RCY34894 39 Synechocystis #12 RCY03648 59 Synechocystis #13 RCY03870 91 Synechocystis #14 RCY00359 106 Synechocystis #15 RCY25341 23 Synechocystis #16 RCY37057 40 Synechocystis #17 RCY34487 29 Synechocystis #18 RCY46798 32 Synechocystis #19 RCY53151 73 Synechocystis #20 RCY50421 39 Synechocystis #21 RCY31267 300 Synechocystis #22 RCY46651 107 Synechocystis #23 RCY25755 109 Synechocystis #24 RCY40141 87 Synechocystis #25 RCY11977 246 Synechocystis #26 RCY00456 110 Synechocystis #27 RCY08095 101 Synechocystis #28 RCY42619 279 Synechocystis #29 RCY36500 280 Synechocystis #30 RCY02337 187 Synechocystis #31 RCY08595 300 Synechocystis #32 RCY07893 147 Synechocystis #33 RCY44389 59 Synechocystis #34 RCY35764 206 Synechocystis #35 RCY36190 150 Synechocystis #36 RCY49047 96 Synechocystis #37 RCY44729 201 Synechocystis #38 RCY16852 164 Synechocystis #39 RCY50281 225 Synechocystis #40 RCY44485 300 Synechocystis #41 RCY17020 157 Synechocystis #42 RCY50817 112 Synechocystis #43 RCY14811 300 Synechocystis #44 RCY17622 25 Synechocystis #45 RCY16281 94 Synechocystis #46 RCY23988 96 Synechocystis #47 RCY23271 201 Synechocystis #48 RCY11277 49 Synechocystis #49 RCY29451 106 Synechocystis Motif number 1 TCTTCCCCCCATCCCTGTCCTGTT 4 2 1 CTCCCCCCTC 0.646003 -107 GGCAAAAAAGAATGTCCCTAGCGGG 4 94 1 ATGTCCCTGG 0.49082 -15 TTAAATTAACTCTCCCCACTGAGGGGAAGCATT 6 44 0 TTCCCCACGG 0.707549 -94 CAAATATAGGTTGCTCCATTGGCCAACCTATGC 7 30 0 TGCTCCATGC 0.821608 -90 AACCAAAATCCTTCCCCATAGCCTGGGAGAGAG 9 18 1 CTCCCCATGC 0.922146 -84 GCTGAAGGCCCCAAGCCTTTACTAAGT 10 5 1 AGGCCCCAGC 0.783614 -64 CTTGATTGAAACGCTCCATCGACGTAACTGAAT 21 128 1 AGCTCCATGC 0.768424 -173 ACAAGCAGAAAGGCTCCCCGGACATAAAGCGAC 21 212 0 AGCTCCCCGC 0.947229 -89 TCTAATCCTCCTGCCCCCTTAATTGCCTTGCCC 22 62 1 CGCCCCCTAT 0.678477 -46 CTTAATTGCCTTGCCCCCTAATCTCAATCTTGG 22 79 1 TGCCCCCTAC 0.869525 -29 TCTGGGGGTATCGCCCCCCTGGTAACCTCTCCC 23 11 1 TGCCCCCCGT 0.917488 -99 CCCCTGGTAACCTCTCCCCGGCCTTCCCTAACC 23 26 1 CTCTCCCCGC 0.967975 -84 ACACAATAAAAATGCCCCTTGGCGATCGCCGGG 25 182 0 ATGCCCCTGC 0.904976 -65 CAGTAATTTACCGACCCCTTGGCTCCACTGAGT 28 14 0 CGACCCCTGC 0.63874 -266 GATTGCCGGCAATCCCCCCAGTCAATATTCCTC 28 245 1 ATCCCCCCGC 0.96845 -35 TTACCAAAAGCCTGTCCATGGACTGCAATACCC 29 56 0 CTGTCCATGC 0.712824 -225 GATTAACCCCTAGCTCCCCGGCCACCCTAACGA 29 103 1 TGCTCCCCGC 0.96141 -178 TGCGGAGGGCCGTCCCCCATGGTAACAGAGTAA 30 22 1 CTCCCCCAGT 0.742954 -166 ACTTTGCCTTTCTGTCCATTGCCCCAGGTAAAA 30 54 1 TTGTCCATGC 0.622715 -134 CAGGTAAAAATTGCTCCCTGGCGATCGCCAATT 30 78 1 TGCTCCCTGG 0.788734 -110 TTTTGGCGGGATTCCCCCTAAAGGTTAAGATGG 30 109 1 ATCCCCCTAG 0.453868 -79 GGTTTGTGAATTGCTCCACAAGCTAAACAAACT 30 143 1 TGCTCCACAC 0.54367 -45 AGGGTCTCCACTTCCCCCCAGACATTACAACAG 31 99 1 CTCCCCCCGC 0.984632 -202 ACGATATTTATCGGCCCCTGGATGGGAAACCGG 31 249 0 TGGCCCCTGT 0.775279 -52 CTGACTGGGCCAGCCCCACTGACTATTCAACTT 32 68 1 CGCCCCACGC 0.954589 -80 TGGGGTTGAGTTGCCCCCACGCCTCCCTGGGTT 34 41 1 TGCCCCCAGC 0.918798 -166 TTTCAGGAAAATTCCCCCTAGATTTAGTTGCAG 34 77 1 ATCCCCCTGT 0.818643 -130 TTATTTATCTCCGCCCCCCCACTTTCC 37 185 1 CGCCCCCCAT 0.751324 -17 CATAAACCTTTGTGTCCCCAAGCAGTGTGATAT 39 155 1 TTGTCCCCAC 0.617316 -71 AAGTTTCGAGCTTCCCCATTGGTCTTGGTTTTA 40 13 1 CTCCCCATGT 0.713784 -288 CCATATCCCCCTTCCCCCCAGAGGGTATTGTAC 40 103 1 CTCCCCCCGG 0.932188 -198 TACTGAGTTCACTGTCCCATGGCGGGGATGTGA 41 63 0 ATGTCCCAGC 0.579517 -95 ATCATTCATTTCTCTCCATTATCTGGATGCAAG 43 114 1 TTCTCCATAC 0.401663 -187 TGGGACAAAATCTGCCCCTGGTCATTGGCCG 45 9 0 TTGCCCCTGC 0.92967 -86 AGGGGCAGATTTTGTCCCAAGACTAATTTGTGC 45 23 1 TTGTCCCAGC 0.656703 -72 AATATCTGCTCCACTGGTCGAGAACTAG 48 6 1 CGCTCCACGT 0.676165 -44 CGAGAACTAGACTGTCCCCAATCATTCCAAC 48 29 1 ATGTCCCCAC 0.537511 -21 * ******* * * Masking position 7 Map Score: 37.7862 Number of sites scoring better than the average of aligned sites = 5152 Number in coding regions = 4558 Number in noncoding regions = 594 Number of orfs with sites within 600 bp upstream = 520 Fraction of orfs with sites within 600 bp upstream = 0.0835207 Motif number 2 GTTTTGGCGCGGTGTTCCCCCTCCACCAAT 1 120 0 GGTGTTCCCC 0.736929 -181 TCATGGATTATTCGATCGCCACACTT 1 285 1 TTCGATCGCC 0.884688 -16 GCGGGGCAAAGGTGATAGCCA 14 2 0 GGTGATAGCC 0.838339 -105 GTTAATGAATGGCGATAGCGT 16 2 0 GGCGATAGCG 0.637006 -39 CAGGAATTGCGGTCATCCCCCTTTTGTGCC 21 43 1 GGTCATCCCC 0.890148 -258 TCAGGAGGATGGCGATCGCCTAGGGTCTAA 22 37 1 GGCGATCGCC 0.499977 -71 TTACCAGGGGGGCGATACCCCCAGA 23 6 0 GGCGATACCC 0.938878 -104 CTTCAGCCCCGGCGATCGCCAAGGGGCATT 25 175 1 GGCGATCGCC 0.499977 -72 ACCCCAAGGAGGTGAAACCCGA 25 235 1 GGTGAAACCC 0.60941 -12 CCGCGGTGGGTTTGATCGCCGTTAATTCAC 27 48 1 TTTGATCGCC 0.687865 -54 CTGGATTGCCGGCAATCCCCCCAGTCAATA 28 242 1 GGCAATCCCC 0.868737 -38 GGTTGCGGAGGGCCGTCCCCCATGGTAACA 30 19 1 GGCCGTCCCC 0.796687 -169 ATTGCTCCCTGGCGATCGCCAATTTTGGCG 30 87 1 GGCGATCGCC 0.499977 -101 TTTCTGACTGGGCCAGCCCCACTGACTATT 32 65 1 GGCCAGCCCC 0.817068 -83 CTTGTTTTTGGTCGAACCCCCGGTTAGGAG 34 179 1 GTCGAACCCC 0.891834 -28 TGGTCGTTAGTTCGATCGCCGGAGGTGAGC 37 23 0 TTCGATCGCC 0.884688 -179 CACGGAGGGATTCGAACCCCCGACCCTCAG 39 103 0 TTCGAACCCC 0.674064 -123 AGGAAAAGTATGCGATCGCCATTTAAAAGT 40 251 1 TGCGATCGCC 0.605035 -50 ********** Masking position 9 Map Score: 23.8181 Number of sites scoring better than the average of aligned sites = 7051 Number in coding regions = 6404 Number in noncoding regions = 647 Number of orfs with sites within 600 bp upstream = 413 Fraction of orfs with sites within 600 bp upstream = 0.0663347 Motif number 3 TTGTCGAGGTTTGCCATTGACCATGAAGTTTGTA 1 205 0 TTCCATTGCT 0.839462 -96 CATTAATTTTTTACCTTTGCCACCGTCAAATTAA 6 14 0 TTCCTTTGCC 0.879184 -124 AGTAATTTCCTTGGATGTTAATGGGTTTG 11 21 0 TTCCTTGGTT 0.800047 -19 TGTGCTCGAGTTCCCTTCGTCCATCTACTCTCTG 14 56 1 TTCCTTCGCT 0.921153 -51 GCCCCCTTAATTGCCTTGCCCCCTAATCTCAATC 22 74 1 TTCCTTGCCT 0.816904 -34 TACTGCCCAATAAGCTTTGACTTTCTTTCGATAG 28 42 1 TAGCTTTGCT 0.28892 -238 ACCAAAAGCCTGTCCATGGACTGCAATACCCCTC 29 53 0 TGCCATGGCC 0.663597 -228 GCTAGTTCAGTTGCCATGGAAGACACTGTTATTC 29 196 0 TTCCATGGAC 0.671859 -85 GGAGCAATTTTTACCTGGGGCAATGGACAGAAAG 30 61 0 TTCCTGGGCT 0.878589 -127 TGTTGCCATGGAAATTTAACTCAGAA 32 132 0 TTCCATGGAT 0.830071 -16 GCCTCCCGTTTTCCCTTGGGAAAGAGAGAGCTTG 34 149 1 TTCCTTGGAG 0.658783 -58 GGAACATACTTTGGCTTGGTCGTTAGTTCGATCG 37 35 0 TTGCTTGGCT 0.929948 -167 ATCTCTAGGTTTTGCTTGGACAATGGGGTATAAT 38 100 1 TTGCTTGGCT 0.929948 -65 AATTTCTACTTAACCTTGGCCGCTTGAAAAGTAC 40 132 0 TACCTTGGCT 0.909924 -169 ATAAATTTTTTTACCTTTGACCATGGGAAGAAAA 40 191 1 TTCCTTTGCT 0.945538 -110 AGTTGCCTTTGACGGTGCATAGTTGT 41 3 1 TTCCTTTGCT 0.945538 -155 AACTCAATTTTTTCCTTCGAAATCAGAACTTATG 43 78 0 TTCCTTCGAC 0.511995 -223 GGACAAAATCTGCCCCTGGTCATTGGCCG 45 6 0 TGCCCTGGCT 0.850372 -89 TTTCCCTGGTCTGTGAACATTTTC 46 1 1 TTCCCTGGCT 0.964952 -96 AAAGTGAATTTTTCCCTGGGCAGTCAGTCTAGGG 47 127 1 TTCCCTGGCT 0.964952 -75 CATAAAAATCTTTCCTTGGGATCTTGAAGATTTT 49 80 0 TTCCTTGGAT 0.941923 -27 ** ****** * * Masking position 1 Map Score: 18.1205 Number of sites scoring better than the average of aligned sites = 1110 Number in coding regions = 987 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 4 TCTTCCCCCCATCCCTGTCCTGTTTATTGA 4 10 1 CACCCTGTCC 0.843311 -99 CTGATTGATGCAACTCTGCCCGTAAAAATAG 8 17 0 CACTCTGCCC 0.961102 -91 TGGCTATCACCTTTGCCCCGCAAGCAAT 14 8 1 CACTTTGCCC 0.923347 -99 CTTGAGAGACCACCTTCGGCCCTAGCGGTAG 21 92 0 CACTTCGGCC 0.973233 -209 ATTCAGGCTTCAACCTCGGCAGGTTAATTAA 25 92 0 CACCTCGGCA 0.915366 -155 TCCTCTGCTTCAGCCCCGGCGATCGCCAAGG 25 168 1 CACCCCGGCG 0.948432 -79 TTTTATTTCTCAGCTACGCCCTCGATATTTT 28 131 1 CACTACGCCC 0.881266 -149 GTAACCCATCCAACATTGCCCAAAGTTTAGA 29 18 1 CACATTGCCC 0.628935 -263 TTACTTTCGGCAACCCAGCCCGAAACGTTTG 35 79 1 CACCCAGCCC 0.884803 -72 AGCAATGGCTCACCTCCGGCGATCGAACTAA 37 16 1 CACTCCGGCG 0.935881 -186 TAACTCCAGTCAACTCCGGCCATTCTGTTAA 37 157 0 CACTCCGGCC 0.986769 -45 TGGAGTTATTTATCTCCGCCCCCCCACTTTC 37 180 1 TACTCCGCCC 0.887871 -22 AATTTCTACTTAACCTTGGCCGCTTGAAAAG 40 135 0 TACCTTGGCC 0.553965 -166 TTGAACATCACATCCCCGCCATGGGACAGTG 41 56 1 CACCCCGCCA 0.961934 -102 CCTATCAAGTCATCTTCGCTAATCTCC 46 80 1 CACTTCGCTA 0.476797 -17 AATTCACTTTCAACCCCGGTCAAGAAGTTTT 47 106 0 CACCCCGGTC 0.897532 -96 GTCAAACCTCCATCTTCGTCATCTCAATTTA 49 15 0 CACTTCGTCA 0.62828 -92 ** ******** Masking position 2 Map Score: 16.1699 Number of sites scoring better than the average of aligned sites = 1029 Number in coding regions = 964 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 CCATGGCTCACCCACTTTCCAGGGATTGGT 1 96 1 CCCACTTTCC 0.968167 -205 TCTTCCCCCCATCCCTGTCCTGTTT 4 6 1 CCCCCATCCC 0.874684 -103 AGGGTCTAATCCTCCTGCCCCCTTAATTGC 22 58 1 CCTCCTGCCC 0.929059 -50 TCAGATTTAACCTACTTACCTATAGGAGTC 24 62 1 CCTACTTACC 0.930119 -26 GGAGAAGTTCCCTACTTCGCCAGTACCCAA 26 52 1 CCTACTTCGC 0.877873 -59 CCTAAGGGTCTCCACTTCCCCCCAGACATT 31 95 1 TCCACTTCCC 0.885508 -206 CTTTCCCAACTTTCCATTAGCCTAG 35 6 1 CCAACTTTCC 0.892437 -145 GGAGAACGATCCTAATTCCCACTATATTTA 36 73 1 CCTAATTCCC 0.829059 -24 TCTCCGCCCCCCCACTTTCC 37 192 1 CCCACTTTCC 0.968167 -10 TTTGGTTTGTCCAACTGCCCTGCTGTACTG 40 53 1 CCAACTGCCC 0.910642 -248 AAATCCATATCCCCCTTCCCCCCAGAGGGT 40 99 1 CCCCCTTCCC 0.983676 -202 TGTCAGTCTCCCTACTTACCCCTTGAACAT 41 34 1 CCTACTTACC 0.930119 -124 ********** Masking position 2 Map Score: 11.9898 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 381 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 GCAGCAGTAATCAAACCCATTGAGCTTG 2 9 0 TCAAACCCAT 0.856002 -96 CCGGTCTGTCTTAAACCCTACTCCATAAAT 5 34 1 TTAAACCCTA 0.772422 -49 CAACGTTAACCAAACCCATTAACATCCAA 11 10 1 CCAAACCCAT 0.893524 -30 GCAAGCAATGCTAGACCCTAACCCGATGTG 14 30 1 CTAGACCCTA 0.838649 -77 TAACTGTTATCTAAACCCATGGGTATTCGT 19 42 1 CTAAACCCAT 0.856002 -32 GGCAGGAGGATTAGACCCTAGGCGATCGCC 22 47 0 TTAGACCCTA 0.786412 -61 CCGGCCTTCCCTAACCCCAACCACCGCAAA 23 43 1 CTAACCCCAA 0.88427 -67 GCTTGCTATCCCAACCCCAAGGAGGTGAAA 25 222 1 CCAACCCCAA 0.915157 -25 GTTTGAGGGCCTAGACCCAATAAGTTTTCC 26 11 1 CTAGACCCAA 0.909844 -100 TTAACGGCGATCAAACCCACCGCGGGGAGC 27 43 0 TCAAACCCAC 0.800006 -59 GACTATGGGATTAACCCCTAGCTCCCCGGC 29 95 1 TTAACCCCTA 0.735985 -186 GTATAAGAAATTAGACCCATTGATTGACCC 31 221 1 TTAGACCCAT 0.820404 -80 ACAAAAAATTTCAGACCCTTCATTGTACGA 31 278 0 TCAGACCCTT 0.768586 -23 TCTGACTGGGCCAGCCCCACTGACTATTCA 32 67 1 CCAGCCCCAC 0.834197 -81 TGGGGGCAACTCAACCCCAAACCTGTATCA 34 30 0 TCAACCCCAA 0.88427 -177 ********** Masking position 3 Map Score: 11.2776 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 652 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 TCCACCAATCCCTGGAAAGTGGGTGAGCCATG 1 97 0 CTGGAAATGG 0.691439 -204 TTACAAACTTCATGGTCAATGGCAAACCTCGA 1 204 1 CTGGTCATGG 0.979759 -97 ATCTGTGTCGCATGGTAACTGAACTCCTAAAA 2 69 0 CTGGTAATGA 0.82822 -36 GGTCTCTGGGCTTGGTCAGAGAGTAGATGGAC 14 74 0 CTGGTCAAGA 0.935679 -33 GGTATTTACAGGGTCTCTGGGCTTGGTCAG 14 87 0 CGGGTCTTGG 0.779081 -20 GGCCGTCCCCCATGGTAACAGAGTAACTTTGC 30 29 1 CTGGTAAAGA 0.675297 -159 CATACTTTGGCTTGGTCGTTAGTTCGATCGCC 37 33 0 CTGGTCGTAG 0.708764 -169 CTGCCACTTTCATGGACTGTAACCTCTACAAC 37 88 1 CTGGACTTAA 0.640854 -114 CTAGGTTTTGCTTGGACAATGGGGTATAATGG 38 104 1 CTGGACATGG 0.940026 -61 GTTTTCTTCCCATGGTCAAAGGTAAAAAAATT 40 194 0 CTGGTCAAGG 0.954294 -107 TTTAAAAGTGGGTGGTCTTTAGTATCATTGCT 40 272 1 GTGGTCTTAG 0.532775 -29 GGGTGTCACTGCTGGTCATAGATTCTCAAGGG 42 68 0 GTGGTCAAGA 0.677137 -45 GAAAATTGTACTTGGACTATAAACACATAAGT 43 53 1 CTGGACTTAA 0.640854 -248 ATTAAAATGGCATGGTCACAGATGTGAAATAG 43 215 1 CTGGTCAAGA 0.935679 -86 AAAATCTGCCCCTGGTCATTGGCCG 45 4 0 CTGGTCATGG 0.979759 -91 TTTCCCTGGTCTGTGAACATTTTCCT 46 5 1 CTGGTCTTGA 0.953789 -92 AAACTTGGTCTTTAACCTAGTCCGA 47 4 1 CTGGTCTTAA 0.846401 -198 * ****** *** Masking position 5 Map Score: 14.8169 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 781 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 CCATGAAGTTTGTAATGGAAATCCGCCCTC 1 189 0 TGTAATGGAA 0.558663 -112 ATCGTGGCCGTGTCATGGCAAATATTAAAT 6 71 0 TGTCATGGCA 0.575827 -67 CTTGCAGTGTTGCCAAAGAAAATCAGGC 6 120 1 TGCCAAAGAA 0.71127 -18 AAAAAAAGACGGTCAAGGAAGCAGCTTTGT 8 79 0 GGTCAAGGAA 0.750896 -29 GATCAAAAGCTGTCAAGGAAGCAAATCCCC 25 140 0 TGTCAAGGAA 0.950168 -107 CTAGTTCAGTTGCCATGGAAGACACTGTTA 29 199 0 TGCCATGGAA 0.891344 -82 TGTTGCCATGGAAATTTAACTCA 32 135 0 TGCCATGGAA 0.891344 -13 GCTCTCTCTTTCCCAAGGGAAAACGGGAGG 34 150 0 TCCCAAGGGA 0.813142 -57 CCTGCTGTACTGTCAAGAAATAATGGTTAA 40 71 1 TGTCAAGAAA 0.537732 -230 ATCACATCCCCGCCATGGGACAGTGAACTC 41 62 1 CGCCATGGGA 0.70757 -96 GGTCATAGATTCTCAAGGGAATTTAGATGG 42 57 0 TCTCAAGGGA 0.794631 -56 AATTCTCCTTTGCAAAGGAATTCCGATAGA 47 71 0 TGCAAAGGAA 0.824562 -131 CTAGACTGACTGCCCAGGGAAAAATTCACT 47 129 0 TGCCCAGGGA 0.811059 -73 ATCTTCAAGATCCCAAGGAAAGATTTTTAT 49 83 1 TCCCAAGGAA 0.914159 -24 ********** Masking position 10 Map Score: 6.3093 Number of sites scoring better than the average of aligned sites = 999 Number in coding regions = 889 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 9 GGTGAGCCATGGCAGAGGGCAAATAAACTAGT 1 76 0 GGCAGGGCAA 0.85545 -225 CGGGGTGAAGGGAAGCGTTAGAATTGTCGAGG 1 230 0 GGAAGGTAGA 0.770419 -71 GGAGATATAAGGGAGGTCGCGTCA 3 95 1 GGGAGTGCGT 0.695811 -14 ATTTGACGGTGGCAAAGGTAAAAAATTAATGC 6 17 1 GGCAAGTAAA 0.471283 -121 CCCCTCAGTGGGGAGAGTTAATTTAATATTTG 6 51 1 GGGAGGTAAT 0.898081 -87 CCCATAGCCTGGGAGAGAGCGATAATAGGTTA 9 32 1 GGGAGGGCGA 0.963882 -70 CCTAGCGGTAGGGAGAGTTAGTCCTACATAGG 21 71 0 GGGAGGTAGT 0.925592 -230 ACCCACCGCGGGGAGCGAGAATTTACTTCCAA 27 27 0 GGGAGGGAAT 0.941547 -75 AGCAAGACTGGGCAGAGTGAATGTTGGGGATT 28 199 0 GGCAGGGAAT 0.834508 -81 AATGTCTGGGGGGAAGTGGAGACCCTTAGGGG 31 93 0 GGGAATGAGA 0.550125 -208 GTTTTCCCTTGGGAAAGAGAGAGCTTGTTTTT 34 156 1 GGGAAGGAGA 0.880207 -51 CGAAAGTAAGGGGAGTGGTAAAGCCAGCTACA 35 56 0 GGGAGGTAAA 0.944779 -95 TGATATGATGGGGAGTGCTCAATTTTTAGACT 39 182 1 GGGAGGTCAA 0.911829 -44 AGACCAATGGGGAAGCTCGAAACTTCT 40 6 0 GGAAGTGAAA 0.419678 -295 AGTCAGTCTAGGGTGTGATAGAGAGAAAAGGC 47 148 1 GGGTGGTAGA 0.688573 -54 ***** * **** Masking position 2 Map Score: 7.24621 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 548 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 10 TTCCAACGAATAAAAACAAAAATAG 18 4 0 TAAAAAAAAA 0.718698 -29 AATCTGATTAGACAAACCAAAAACAAATGACT 24 37 0 GACAAAAAAA 0.939008 -51 GGGCGTAGCTGAGAAATAAAAATCTTATTTTA 28 120 0 GAGAAAAAAA 0.893227 -160 CAACAGGATCGAAAAAATAAAAAATATCGAGG 28 150 0 GAAAAAAAAA 0.958122 -130 AGGGCAGTTGGACAAACCAAAAGTTATTTAAA 40 42 0 GACAAAAAAA 0.939008 -259 TTCAACATTGGAAAAATTAAAAGCACAATTTC 40 160 0 GAAAAAAAAA 0.958122 -141 CTCTTACTGTGAAAAATCAAAAGATATGGCTG 41 124 0 GAAAAAAAAA 0.958122 -34 ATGCAAGCCAGAAAAAAGAAAAGACACGAGGA 43 140 1 GAAAAAAAAA 0.958122 -161 ****** **** Masking position 6 Map Score: 4.81637 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 71 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 11 TTGGCGCGGTGTTCCCCCTCCACCAATCCC 1 117 0 GTTCCCCCTC 0.912908 -184 CAATTCTAACGCTTCCCTTCACCCCGTAAG 1 236 1 GCTTCCCTTC 0.842483 -65 GTTGATTTTCCTCTAAATAAGTT 5 70 0 GATTTTCCTC 0.695228 -13 AAAAATTAATGCTTCCCCTCAGTGGGGAGA 6 37 1 GCTTCCCCTC 0.982001 -101 AGCTTTGTAAGCTTTCCCTAACCGCAGTGT 8 57 0 GCTTTCCCTA 0.564249 -51 CCTGCTGGTAGATTCTCCTAAGGGATGATG 13 68 0 GATTCTCCTA 0.695228 -24 TCGGGTTTCACCTCCTTGGGGTTG 25 233 0 GTTTCACCTC 0.878342 -14 TTGACTAGAAGTTTCTCATCAGCTATCGAA 28 68 0 GTTTCTCATC 0.804163 -212 CCTAGTTCCAGATTCTCCTCCAAACAAGTT 31 152 1 GATTCTCCTC 0.936736 -149 GATTGACCCGGTTTCCCATCCAGGGGCCGA 31 242 1 GTTTCCCATC 0.905857 -59 AGGGTAACTAGTTTCCCCTCTCCT 44 12 1 GTTTCCCCTC 0.982351 -14 ********** Masking position 3 Map Score: 6.38939 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 240 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 12 CCGTGTAAATAGCTTGACCGACGCTATCTC 3 67 0 AGCTTGACCG 0.811393 -42 TTTTAGGAGGTCATTAACCGC 7 109 1 TCATTAACCG 0.736841 -11 TTGTAAGCTTTCCCTAACCGCAGTGTTTAA 8 53 0 TCCCTAACCG 0.810136 -55 CAAAGCTGCTTCCTTGACCGTCTTTTTTTG 8 80 1 TCCTTGACCG 0.982878 -28 GGGATTTGCTTCCTTGACAGCTTTTGATCC 25 141 1 TCCTTGACAG 0.908454 -106 TAACCATTATTTCTTGACAGTACAGCAGGG 40 70 0 TTCTTGACAG 0.661484 -231 TTTCTACTTAACCTTGGCCGCTTGAAAAGT 40 134 0 ACCTTGGCCG 0.948736 -167 GAACAACAAAACACTGGCCGCA 42 101 1 ACACTGGCCG 0.691865 -12 CTGCCCCTGGTCATTGGCCG 45 1 0 TCATTGGCCG 0.920206 -94 TTCACAAAACTTCTTGACCGGGGTTGAAAG 47 101 1 TTCTTGACCG 0.918724 -101 ********** Masking position 5 Map Score: 2.91155 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 429 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 13 ATCAGGAATTGCGGTCATCCCCCTTTTGTG 21 41 1 GCGGTCATCC 0.835717 -260 ACCGATAGACACGGTAACCCTCTACCTAAA 21 260 0 ACGGTAACCC 0.855115 -41 TAACCTCTCCCCGGCCTTCCCTAACCCCAA 23 33 1 CCGGCCTTCC 0.933737 -77 GCCTGGATTGCCGGCAATCCCCCCAGTCAA 28 240 1 CCGGCAATCC 0.971062 -40 GGGGACGGTAACCCATCCAACATT 29 5 1 ACGGTAACCC 0.855115 -276 CCCTAGCTCCCCGGCCACCCTAACGAGTAT 29 110 1 CCGGCCACCC 0.992088 -171 ACCATGGGGGACGGCCCTCCGCAACCAGAT 30 15 0 ACGGCCCTCC 0.937593 -173 CCCCTTACTTTCGGCAACCCAGCCCGAAAC 35 75 1 TCGGCAACCC 0.892224 -76 CCAGTCAACTCCGGCCATTCTGTTAATCTT 37 153 0 CCGGCCATTC 0.872932 -49 TTATTTATCTCCGCCCCCCCACTTTCC 37 185 1 CCGCCCCCCC 0.888103 -17 ********** Masking position 2 Map Score: 5.34372 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 327 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 TGTTGTTAATTTTTTAGGAGTTCAGTTACC 2 58 1 TTTTTAGGAG 0.949706 -47 TTCCGCTTTATTTTTAGGAGGTCATTAACC 7 98 1 TTTTTAGGAG 0.949706 -22 TCCGATTTTTTTAGGAAAACGCC 15 8 1 TTTTTAGGAA 0.923106 -16 GTCTATCGGTATTTTAGGAACAAAGCTGGG 21 280 1 ATTTTAGGAA 0.747647 -21 TCCCGTTAGTTTTTCAGGAGGATGGCGATC 22 24 1 TTTTCAGGAG 0.939959 -84 CCTGGGTTAGTTTTCAGGAAAATTCCCCCT 34 66 1 TTTTCAGGAA 0.908726 -141 ********** Masking position 6 Map Score: 2.02421 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 11 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 CAAGCTCAATGGGTTTGATTACTG 2 3 1 ACTCATGGGT 0.977237 -102 TTAATGCTTCCCCTCAGTGGGGAGAGTTAATT 6 42 1 CCTCATGGGG 0.903889 -96 AGTAATTTCCTTGGATGTTAATGGGT 11 24 0 ATTCCTGGAT 0.639745 -16 TCGGGTTTCACCTCCTTGGGGTTGGGATAGC 25 226 0 ACTCCTGGGG 0.97853 -21 ATAAATGGAAAACTTATTGGGTCTAGGCCCTC 26 15 0 ACTTATGGGT 0.80801 -96 TGGATTTGGTAACTCCTTGGGTACTGGCGAAG 26 66 0 ACTCCTGGGT 0.982228 -45 CGAACTCAGTGGAGCCAAGGGGTC 28 3 1 ACTCATGGAG 0.920669 -277 TTGCCCCCACGCCTCCCTGGGTTAGTTTTCAG 34 51 1 GCTCCTGGGT 0.936225 -156 CTGGACACGTAGCTCAGTGGATAGAGCATCAG 39 62 1 ACTCATGGAT 0.933642 -164 * **** ***** Masking position 8 Map Score: 3.30033 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 139 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789