AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_synecho_ctra_300.orf -o012_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 Input sequences: #1 RCY07904 223 Synechocystis #2 RCY30559 209 Synechocystis #3 RCY21950 300 Synechocystis #4 RCY37124 170 Synechocystis #5 RCY13687 97 Synechocystis #6 RCY53785 100 Synechocystis #7 RCY18495 300 Synechocystis #8 RCY24628 300 Synechocystis #9 RCY41085 203 Synechocystis #10 RCY02891 259 Synechocystis #11 RCY43113 224 Synechocystis #12 RCY36036 64 Synechocystis #13 RCY10807 253 Synechocystis #14 RCY40708 300 Synechocystis #15 RCT00084 37 Chlamydia_trachomatis #16 RCT00085 17 Chlamydia_trachomatis #17 RCT00086 191 Chlamydia_trachomatis #18 RCT00237 155 Chlamydia_trachomatis #19 RCT00465 300 Chlamydia_trachomatis #20 RCT00764 300 Chlamydia_trachomatis #21 RCT00827 300 Chlamydia_trachomatis Motif number 1 GGCCAAGGGGCGATCGCCACCGGAAATTAAA 1 95 0 CGATCGCCCC 0.990244 -129 ACAATCAACTCGATCGCCGTCGAGCCGAAGT 1 175 1 CGATCGCCTC 0.988168 -49 GAAACAAGGGCGATCGCCCTTGTCATCGCCG 4 102 0 CGATCGCCTT 0.97527 -69 TAACCACTGGCGATCGCCGCTTCT 8 4 0 CGATCGCCCT 0.979562 -297 ACTAATCTGCCCTTTGCCATCAATTTCTAAT 8 61 0 CCTTTGCCTC 0.867941 -240 TACAGAAGCCCGATCGCCTTCTATAACCACC 8 218 0 CGATCGCCTC 0.988168 -83 CGTGGACTATCCATTGCCGGCCGGTGGCATG 9 41 0 CCATTGCCGC 0.904877 -163 ACGCCATGATCGATCGCCTTTTGTACGTTCG 10 42 0 CGATCGCCTT 0.97527 -218 TCTCACCCTACCAGTGCCCCAACGCCATGAT 10 63 0 CCAGTGCCCA 0.769848 -197 GCAGGTTTCTCCATTTCCCCC 13 243 1 CCATTTCCCC 0.723413 -11 CCAGATTTGCCCAGCGCCCCAGCAATGGGGG 14 28 1 CCAGCGCCCA 0.872792 -273 CAGTTTCCGACCTTTGCCATTTCGGTTATCC 14 102 1 CCTTTGCCTT 0.756309 -199 ATCCCAACGGCGATCGCCATTCTTGCTTGGG 14 167 1 CGATCGCCTT 0.97527 -134 GCAGACCTCTCGATTGCCAACAACACACTTC 14 278 0 CGATTGCCAC 0.865199 -23 GATCATTTTGCCATTGCCTCCAGCTATGGTG 17 126 1 CCATTGCCCC 0.980191 -66 AAAACTCCCAGCGCCTTTGTACTATCCT 21 283 0 CCAGCGCCTT 0.939103 -18 ******** ** Masking position 7 Map Score: 26.8688 Number of sites scoring better than the average of aligned sites = 4320 Number in coding regions = 4014 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 2 AGAATTCCCCTGGCCAAGGGGCGATCGCCAC 1 106 0 TGCCAAGGGG 0.955901 -118 CGCAAAACTTTCCCCAAGGGGTCGTGATGTC 2 117 0 TCCCAAGGGG 0.984226 -93 CGGGCTGTCTTCCCCGTGGGTCGGGGTAATA 3 37 1 TCCCGTGGGT 0.931632 -264 TTTTAAGGGGTCACCGTTTGGGATAGAACCT 7 142 1 TCCCGTTTGG 0.936952 -159 TCCTTAACAATGCCCGATGGGGTAGGTGTAG 8 113 1 TGCCGATGGG 0.955901 -188 TTAATTACTCTCTCCGATGGGTAACCACCAC 9 117 1 TCCCGATGGG 0.984239 -87 AACCCGATTTTCCCCATTGGG 10 1 0 TCCCATTGGG 0.974945 -259 AATGTTCAAATCACTGTGCGGTGTGATGCTT 11 16 1 TCCTGTGCGG 0.875865 -209 AGTTGTCAGATCACTGTGGGGGTACGGATAA 14 127 0 TCCTGTGGGG 0.963482 -174 AGAATGGCGATCGCCGTTGGGATTCGGAGCT 14 159 0 TCCCGTTGGG 0.988501 -142 GACCTGATCCTCGCCATGTGGATGTTAGGCG 17 85 1 TCCCATGTGG 0.936952 -107 CATTGGGGTGTGGCCAAGCGGTAAGGCAGCG 20 55 0 TGCCAAGCGG 0.852859 -246 ** ******** Masking position 1 Map Score: 16.6367 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 675 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 TTTTGGGTCATGGGCCTGGCTTTTTTTAGC 1 25 0 TGGGCCTGGC 0.909531 -199 TGGAGGAGAATTCCCCTGGCCAAGGGGCGA 1 113 0 TTCCCCTGGC 0.894034 -111 ACCGGCAATATTACCCCGACCCACGGGGAA 3 46 0 TTACCCCGAC 0.813529 -255 TCCGGATAATTTTGCCTGACTGCACGTAAC 3 77 0 TTTGCCTGAC 0.670119 -224 GAGCACTTGGTCACCCCGGCGCACCCGCAG 3 115 0 TCACCCCGGC 0.958907 -186 AAAGTTAGTTTAGCCCTGGCAAGTAAAAGG 4 52 0 TAGCCCTGGC 0.780959 -119 TTGGACTAGCTCTCCCAGGAGTTGCCACAC 7 59 1 TCTCCCAGGA 0.431911 -242 ATCGCTGTTGTGAGCCTGGATTGCCGGAGT 8 181 1 TGAGCCTGGA 0.638901 -120 CCACCATTAGTTACTCCGGCAATCCAGGCT 8 193 0 TTACTCCGGC 0.78043 -108 CGGGGTGACATCACCCAGGCTAGCCGACGC 8 259 0 TCACCCAGGC 0.842204 -42 CTGGGTGATGTCACCCCGACTTTTTCATCA 8 271 1 TCACCCCGAC 0.782092 -30 ACTCTGGCTTTGTCCCTGGACTCAAGAAAA 10 232 0 TGTCCCTGGA 0.846137 -28 ATTTTTTGACTCTGGCTTTGTCCCTG 10 244 0 TGACTCTGGC 0.828694 -16 TTTTTGCAGTTTTCCCTGGCTCACTGTATT 11 51 0 TTTCCCTGGC 0.973054 -174 CTGCAAGGGGTTTGCCCGCCCAAAGCTAGG 11 173 0 TTTGCCCGCC 0.740418 -52 GCCCGATAATTTGCCCTGCCCATGATCTTC 13 215 0 TTGCCCTGCC 0.845438 -39 CTGAGTAAACTGTCCCTGGCTTCGTATGAT 14 69 0 TGTCCCTGGC 0.977722 -232 TACAGTTTTGTTTGTCTGGCTTTTTTAATA 19 241 1 TTTGTCTGGC 0.623349 -60 CTGTCCCCGCCACCATAAAAA 19 290 0 TGTCCCCGCC 0.904561 -11 ********** Masking position 1 Map Score: 17.6885 Number of sites scoring better than the average of aligned sites = 2381 Number in coding regions = 2179 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 4 CAGTGATTTAAAGGTGGTAGGGAAGCCTCGT 2 24 1 AGGTGGTAGG 0.842851 -186 TATCTCAAAAGTAGGGGAAGTTTTTTTTCTT 2 168 1 GAGGGGAAGT 0.935757 -42 TAAGGAGGACGTGCGGGAAGTTAATGCTGGC 3 177 1 GGCGGGAAGT 0.868166 -124 GTTTTTTCCCGTGGTGGAAAGTTAGTTTAGC 4 68 0 GGGTGGAAAG 0.917681 -103 AGGCAGAAGAGAAGTGGAAGTTGGCGACAAA 6 11 1 GAGTGGAAGT 0.900759 -90 AACAATGCCCGATGGGGTAGGTGTAGAGTCT 8 118 1 GTGGGGTAGG 0.932713 -183 TAACTTTAGAGTAGTGTAAGGTCTCTGCCAA 8 148 0 GAGTGTAAGG 0.69753 -153 TGGCGTTGGGGCACTGGTAGGGTGAGATCAG 10 67 1 GACTGGTAGG 0.862829 -193 TTGTGAGTAAGTGGGGGTAGTCCCTCCCGTT 10 99 0 GGGGGGTAGT 0.973443 -161 CGATTGTAAAGAGGGGCTAGGTT 12 3 0 GGGGGCTAGG 0.932447 -62 ATCCCTAGGTGTAGGGGAAGGTGAAGATCAT 13 193 1 GAGGGGAAGG 0.982514 -61 TCAGATCACTGTGGGGGTACGGATAACCGAA 14 122 0 GGGGGGTACG 0.937643 -179 CTGGGGTGGAAGGATTCGAACCT 20 3 1 GGGTGGAAGG 0.988778 -298 GAAGGTCGTTGTGGTGGTAAGATGCCCCTTA 20 160 0 GGGTGGTAAG 0.917681 -141 * ********* Masking position 9 Map Score: 15.7512 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 929 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 GTGGCGATCGCCCCTTGGCCAGGGGAATTC 1 106 1 CCCCTTGGCC 0.82024 -118 GACATCACGACCCCTTGGGGAAAGTTTTGC 2 117 1 CCCCTTGGGG 0.588433 -93 TATTACCCCGACCCACGGGGAAGACAGCCC 3 38 0 ACCCACGGGG 0.888848 -263 ATTTAACATATCCAACGGGCCAAGAAATGA 5 48 0 TCCAACGGGC 0.890073 -50 CTACACCTACCCCATCGGGCATTGTTAAGG 8 114 0 CCCATCGGGC 0.979897 -187 GTGGTGGTTACCCATCGGAGAGAGTAATTA 9 118 0 CCCATCGGAG 0.961061 -86 CCCAATGGGGAAAATCGGGT 10 1 1 CCCAATGGGG 0.717662 -259 CCAGCGCCCCAGCAATGGGGGTAACCCCAT 14 38 1 AGCAATGGGG 0.719629 -263 AGCTCCGAATCCCAACGGCGATCGCCATTC 14 159 1 CCCAACGGCG 0.962009 -142 TTTGGTACCGCGCATCGGAGGTTCGAATCC 20 22 0 CGCATCGGAG 0.854807 -279 CTCGGTCTCTTCCATTGGGGTGTGGCCAAG 20 68 0 TCCATTGGGG 0.927782 -233 ********** Masking position 3 Map Score: 9.0073 Number of sites scoring better than the average of aligned sites = 1553 Number in coding regions = 1423 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 6 GAGAATTCCCCTGGCCAAGGGGCGATCGCC 1 108 0 CTGGCCAAGG 0.833484 -116 TCCTCCAGTGCTTGCAAGGGAGGGGCAATA 1 136 1 CTTGCAAGGG 0.659886 -88 CTTTAAATCACTGCTTTTGGGACGAT 2 7 0 CTGCTTTTGG 0.751159 -203 CATTCCATTTCTGGCTAGGATTGAGTACGA 2 51 0 CTGGCTAGGA 0.82777 -159 AGTCTTCCCTGGGAACAGCGGAA 3 4 1 CTTCCCTGGG 0.898143 -297 GAAGTTAATGCTGGCTATGAGTGCGGCATT 3 193 1 CTGGCTATGA 0.843316 -108 ACTCCTTTTACTTGCCAGGGCTAAACTAAC 4 49 1 CTTGCCAGGG 0.91819 -122 AATGACTTTACTGGTTTTGGCGGCGCTACT 5 23 0 CTGGTTTTGG 0.856004 -75 TTTGTTCCTTCTGGACTTGGACTAGCTCTC 7 43 1 CTGGACTTGG 0.790934 -258 GAAAACTAATCTGCCCTTTGCCATCAATTT 8 66 0 CTGCCCTTTG 0.613274 -235 CTAGCGTCGGCTAGCCTGGGTGATGTCACC 8 256 1 CTAGCCTGGG 0.883098 -45 TTTTTTGACTCTGGCTTTGTCCCTGGACTC 10 239 0 CTGGCTTTGT 0.7168 -21 CTTCCTACTCCTGGCTATGACTGCGGAGAA 11 117 0 CTGGCTATGA 0.843316 -108 TTGTCTTCCCCTAGCTTTGGGCGGGCAAAC 11 164 1 CTAGCTTTGG 0.840279 -61 ATAATTTGCCCTGCCCATGATCTTCACCTT 13 210 0 CTGCCCATGA 0.814638 -44 GATCGCCATTCTTGCTTGGGGCATTAAAAC 14 178 1 CTTGCTTGGG 0.915246 -123 GGTGAGGAATCTGCTCTTGGATAGGTATGC 19 67 1 CTGCTCTTGG 0.829177 -234 CACTCGGTCTCTTCCATTGGGGTGTGGCCA 20 70 0 CTTCCATTGG 0.630591 -231 ********** Masking position 2 Map Score: 10.7966 Number of sites scoring better than the average of aligned sites = 2883 Number in coding regions = 2641 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 7 CGTCGAGCCGAAGTCGAGTAAAAACCGCTATCAGGAGC 1 192 1 AATAGAAACC 0.85244 -32 CAACGACTGGAAGGAAGGAGACATCATCGAAGCCTATG 3 237 1 AAGGGGACCC 0.957139 -64 TTGGCGACAAAAATTTGGCAGAACCGCCCATCAACCAT 6 31 1 AATGGAGACC 0.775181 -70 ACAGCGGATGAAGTGTGGCAACTCCTGGGAGAGCTAGT 7 63 0 AATGGAACCG 0.790457 -238 AATCCTAAGTAATTATGGCGACAACAGCGGATGAAGTG 7 86 0 AATGGGACCC 0.964526 -215 CGCTAGCTCAAAGTACAGAAGCCCGATCGCCTTCTATA 8 224 0 AATAGAGCGC 0.922042 -77 ATTGAGCGGAAAGTATGGCAACCAGGCCCTGAACTCAA 9 157 1 AATGGAACGC 0.975302 -47 TGAGATCAGCAACGGGAGGGACTACCCCCACTTACTCA 10 89 1 AAGAGGACCC 0.940544 -171 GGGGGAAATGGAGAAACCTGCCCGATAATTTGC 13 231 0 AATAGAACGC 0.965486 -23 GCGCCCCAGCAATGGGGGTAACCCCATCATCATACGAA 14 41 1 AAGGGAACCC 0.973643 -260 CGAAATGGCAAAGGTCGGAAACTGCCGCTGAGTAAACT 14 88 0 AAGGGAACCC 0.973646 -213 TCTACTGACAAAGTTGAGTAGCTTGTTCA 17 2 0 AATAGAGCGC 0.922042 -190 TATGATAAACAAGTCCAGTGACCTGATCCTCGCCATGT 17 66 1 AATAGGACGC 0.944161 -126 ATTCGGTAAAAAATCAAGTAAAATGTTCGCCTTTTTTA 18 25 0 AATAGAAAGC 0.835297 -131 GAGGAGGTTCAAGGTGAGGAATCTGCTCTTGGATAGGT 19 55 1 AAGAGAATGC 0.622434 -246 ** * ** *** * * Masking position 2 Map Score: 12.1264 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 195 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 GGCTCCTGATAGCGGTTTTTACTCGACTTCGGC 1 198 0 AGCGGTTTTT 0.979299 -26 AGAGGCTCCTGATAGCGGTTTTT 1 211 0 AGAGGTCCTT 0.910481 -13 TCTGCAACCTAGCGGTTTGTTATTTTTTCGGTG 7 178 1 AGCGGTTGTT 0.935718 -123 GACTGCGGAGAAAGGATTTTGATTCAAGTTAAA 11 96 0 AAAGGTTTTT 0.782717 -129 CCGGCTAACCAGCGGGTTTTAATGCCCCAAGCA 14 190 0 AGCGGTTTTT 0.979299 -111 ACGATACTGCAGAGGGTCTTGATATTCGGTAAA 18 53 0 AGAGGTCTTT 0.947261 -103 AGAGGCTTCTCATGTAAAGAGTT 18 143 0 AGAGGTTCTT 0.954145 -13 GCGGTAAGGCAGCGGTTTTTGGTACCGCGCATC 20 36 0 AGCGGTTTTT 0.979299 -265 AAAATAATCAAGATGTTTTTGTTATATTTAATT 20 222 0 AGATGTTTTT 0.782717 -79 ***** **** * Masking position 7 Map Score: 5.13879 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 56 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 TGTTCAGATTCTTTCCCTTAAAACTAGCAA 4 147 0 CTTTCCCTTA 0.922728 -24 TCGTTGAGCCCTTTCTCTCACC 6 89 1 CTTTCTCTCA 0.922728 -12 AATGCTGTGCCTTTCCCTTATAGTGTCGGA 7 265 0 CTTTCCCTTA 0.922728 -36 ATCCCTATACCTTTTTCTTAGTGCTTTGTC 9 72 0 CTTTTTCTTA 0.708141 -132 CGCCGCTTTAATTTCTCCTAATGTC 13 6 0 ATTTCTCCTA 0.771131 -248 GAATAGAAATCTTTCTTTTAATATTAATAT 18 93 1 CTTTCTTTTA 0.945696 -63 CTCATTAATTATTTCTTTTAACAAAAATAA 20 248 0 ATTTCTTTTA 0.830902 -53 AGGAAATACGCTTTCTTCTATTCTAAAAAT 21 122 0 CTTTCTTCTA 0.882188 -179 ACAAAATAAGATTTCTTTTAATTACGAGTG 21 156 1 ATTTCTTTTA 0.830902 -145 ATTTAATCATCTTTCTTTCAGTAGGATGGA 21 240 0 CTTTCTTTCA 0.882188 -61 ********** Masking position 4 Map Score: 5.57651 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 79 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 TTTGGGTCATGGGCCTGGCTTTTTTTAGCC 1 24 0 GGGCCTGGCT 0.944342 -200 GGAGGAGAATTCCCCTGGCCAAGGGGCGAT 1 112 0 TCCCCTGGCC 0.843797 -112 CCGGATAATTTTGCCTGACTGCACGTAACA 3 76 0 TTGCCTGACT 0.558011 -225 TCGCTGTTGTGAGCCTGGATTGCCGGAGTA 8 182 1 GAGCCTGGAT 0.760944 -119 TTAGTGCTTTGTCCGTGGACTATCCATTGC 9 55 0 GTCCGTGGAC 0.838563 -149 ATGGCAACCAGGCCCTGAACTCAATTAGTG 9 171 1 GGCCCTGAAC 0.914439 -33 CTCTGGCTTTGTCCCTGGACTCAAGAAAAT 10 231 0 GTCCCTGGAC 0.956295 -29 TTTTGCAGTTTTCCCTGGCTCACTGTATTT 11 50 0 TTCCCTGGCT 0.928987 -175 TGAGTAAACTGTCCCTGGCTTCGTATGATG 14 68 0 GTCCCTGGCT 0.980915 -233 GGGGAGATGCGGCCCTGAATATGATAAACA 17 47 1 GGCCCTGAAT 0.889398 -145 CGAGGATCAGGTCACTGGACTTGTTTATCA 17 68 0 GTCACTGGAC 0.805921 -124 ********** Masking position 6 Map Score: 5.59725 Number of sites scoring better than the average of aligned sites = 1399 Number in coding regions = 1311 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 11 GTTTTTTTTCTTGTCAAGATACATACTGTC 2 187 1 TTGTCAAGAT 0.658844 -23 GGCGGCGCTACTGTCAAGATGTGC 5 5 0 CTGTCAAGAT 0.945337 -93 AGGAAAATCTCTTTCCAGATTTAACATATC 5 66 0 CTTTCCAGAT 0.937303 -32 TGTAAGGTCTCTGCCAAGACTCTACACCTA 8 135 0 CTGCCAAGAC 0.847224 -166 ACCTAGTCAGCTCCCCAGATTTGCCCAGCG 14 14 1 CTCCCCAGAT 0.929051 -287 GCCGGAATTTCCGTCCAGATTCCCTTTCCA 14 218 1 CCGTCCAGAT 0.921576 -83 TCCAGATTCCCTTTCCAGATGTCCCCCTCG 14 231 1 CTTTCCAGAT 0.937303 -70 TTGTACTATCCTCTCCAGACCTTATATTTA 21 265 0 CTCTCCAGAC 0.929028 -36 ********** Masking position 7 Map Score: 2.41486 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 80 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 GAAAGGGCTCAACGATCAACACTGTCCCTGT 6 73 0 AACGATCACA 0.92869 -28 AAAAGTTAGCAATGGTAACCAAATTTTAATT 7 230 1 AATGGTAACA 0.703369 -71 ACAGATTGTCCATGATAACCACTGGCGATCG 8 19 0 CATGATAACA 0.865564 -282 AATAGGGAGGAACGATCAGCAGGGAAGAAAT 12 39 1 AACGATCACA 0.92869 -26 TTGCCCTGCCCATGATCTTCACCTTCCCCTA 13 204 0 CATGATCTCA 0.703997 -50 CGGCCCTGAATATGATAAACAAGTCCAGTGA 17 56 1 TATGATAACA 0.806292 -136 GCAATGGCAAAATGATCATCAAGACCACGCC 17 112 0 AATGATCACA 0.963824 -80 TGGTGGACTTTATGATCACCATTAACTTGGC 17 152 1 TATGATCACA 0.907008 -40 CATAAAAAGAAATGATCCGCAGAGGAGGTTC 19 34 1 AATGATCCCA 0.861591 -267 AATTTTTTATAAGGATAAACATTTTTAGAAT 21 102 1 AAGGATAACA 0.75124 -199 ******** ** Masking position 6 Map Score: 2.68114 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 94 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 GAAGCCTCGTACTCAATCCTAGCCAGAAATGGAA 2 45 1 ACTCACTACC 0.864081 -165 GCAAAATTATCCGGAATCGTAACCTGCGGGTGCG 3 92 1 CCGGACTACC 0.988952 -209 ACAGCCAATGCCGCACTCATAGCCAGCATTAACT 3 195 0 CCGCACTACC 0.993181 -106 AGCCTCTTGACGCATTCGTGCCGATTCTTCTCT 7 10 1 ACGCACTGCG 0.951737 -291 CCATTGCCGGCCGGTGGCATGGCCTAAGTATTCC 9 28 0 CCGGTCTGCC 0.969808 -176 AATCCTTTCTCCGCAGTCATAGCCAGGAGTAGGA 11 111 1 CCGCACTACC 0.993181 -114 TTGACAAAAAACGGACCCATGCCCTTTATAGAGA 19 143 0 ACGGACTGCC 0.971669 -158 GTACCAAAAACCGCTGCCTTACCGCTTGGCCACA 20 44 1 CCGCTCTACG 0.949656 -257 ***** * ** ** Masking position 10 Map Score: 3.86828 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 156 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 ACGGGTATTTAGCGTGGTTGACATCACGAC 2 98 1 AGCGTGGTTG 0.86729 -112 CCTGCGGGTGCGCCGGGGTGACCAAGTGCT 3 114 1 CGCCGGGGTG 0.816243 -187 GTTTGAGGGAATCGATGTTGCCTTCAAAGA 3 143 0 ATCGATGTTG 0.45697 -158 AATAACAAACCGCTAGGTTGCAGAGATACA 7 172 0 CGCTAGGTTG 0.892513 -129 AGCGTCGGCTAGCCTGGGTGATGTCACCCC 8 258 1 AGCCTGGGTG 0.91295 -43 TTGAGTTCAGGGCCTGGTTGCCATACTTTC 9 165 0 GGCCTGGTTG 0.893772 -39 GATCGATCATGGCGTTGGGGCACTGGTAGG 10 58 1 GGCGTTGGGG 0.763303 -202 ATTGCACTTTGGCGTTGGTGATTACTTGGG 10 190 0 GGCGTTGGTG 0.917423 -70 TCGGCTATGGTGATTTTTTGAC 11 213 0 GGCTATGGTG 0.898494 -12 TATTGCGCCTCTCTTGGGTGCCATACACTG 13 130 0 CTCTTGGGTG 0.736753 -124 ACCTGATCCTCGCCATGTGGATGTTAGGCG 17 86 1 CGCCATGTGG 0.682349 -106 CATTGCCTCCAGCTATGGTGGACTTTATGA 17 137 1 AGCTATGGTG 0.873022 -55 GCTATTCCACATCTTTGTTGGCATACCTAT 19 87 0 ATCTTTGTTG 0.473637 -214 TGTAGGAGGTCGCTATGTTGATAATAACGT 21 184 1 CGCTATGTTG 0.872322 -117 ********** Masking position 3 Map Score: 4.80704 Number of sites scoring better than the average of aligned sites = 1744 Number in coding regions = 1652 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 15 GGAAGACAGCCCGCACTTCCGCTGTTCCCAGG 3 18 0 CCGCACTCCC 0.995902 -283 CATTAACTTCCCGCACGTCCTCCTTAATCCGT 3 171 0 CCGCACTCCC 0.995905 -130 AATTTTTGTCGCCAACTTCCACTTCTCTTCTG 6 14 0 GCCAACTCCC 0.864598 -87 TTTGGCAGAACCGCCCATCAACCATTAAAACA 6 44 1 CCGCCCTCAC 0.86449 -57 CCAGGAGTTGCCACACTTCATCCGCTGTTGTC 7 73 1 CCACACTCAC 0.768573 -228 TCCCTGTAACCCGATTTTCCCCATTGGG 10 7 0 CCGATTTCCC 0.658658 -253 GAGGGACTACCCCCACTTACTCACAATTGTAA 10 104 1 CCCCACTACC 0.82388 -156 TTTCGGTTATCCGTACCCCCACAGTGATCTGA 14 121 1 CCGTACCCCC 0.891798 -180 AATAAAAAGAGCGCACTTCCTTT 15 25 1 GCGCACTCCT 0.858608 -13 ATATTCAGGGCCGCATCTCCCCCGAATGTTCT 17 37 0 CCGCATTCCC 0.981759 -155 CAAGACCACGCCTAACATCCACATGGCGAGGA 17 92 0 CCTAACTCCC 0.870872 -100 ATAGAAGAAAGCGTATTTCCTCCTGACAAAAT 21 131 1 GCGTATTCCC 0.786234 -170 ****** *** * Masking position 2 Map Score: 6.21458 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 489 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344