AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_synecho_ctra_300.orf -o197_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 RCY45080 251 Synechocystis #2 RCY05296 114 Synechocystis #3 RCY44021 99 Synechocystis #4 RCY07858 90 Synechocystis #5 RCY25948 41 Synechocystis #6 RCY21190 133 Synechocystis #7 RCY39030 187 Synechocystis #8 RCY14244 51 Synechocystis #9 RCY52400 142 Synechocystis #10 RCT00074 279 Chlamydia_trachomatis #11 RCT00181 62 Chlamydia_trachomatis #12 RCT00182 300 Chlamydia_trachomatis #13 RCT00239 76 Chlamydia_trachomatis #14 RCT00240 300 Chlamydia_trachomatis #15 RCT00261 277 Chlamydia_trachomatis #16 RCT00263 242 Chlamydia_trachomatis Motif number 1 CATTTATCGCCTCCTCCTCCTCCA 1 5 0 CTCCTCCTCC 0.980813 -247 GTTTCTTTCCCCCCTTTTCCCGTGCGTAT 3 81 1 CCCCTTTTCC 0.823158 -19 AAGGCTGATTCTCCTCCCCACTTTGCCGGG 4 20 0 CTCCTCCCCA 0.98437 -71 AGTTCCCATTCCCCACCCCCTGGAACAGTA 6 65 1 CCCCACCCCC 0.991198 -69 GCCGGTTAACCCCCACCCTCTAACATTTAA 9 13 0 CCCCACCCTC 0.957302 -130 GAACCGTATGCCCCTCTCTCCTTAAAAGGA 10 66 1 CCCCTCTCTC 0.977589 -214 TTCCTCTTCAAGATTTTTAG 11 53 0 TTCCTCTTCA 0.640542 -10 ATAACCATCCCCCCTCTCTACATCAAAAAG 14 55 0 CCCCTCTCTA 0.945457 -246 GAACGAGGCTTCCCTCCCCATAGGGAGAAC 14 266 1 TCCCTCCCCA 0.979744 -35 TTTACGTTCTCCCCTCTACCATACTTGACT 15 207 1 CCCCTCTACC 0.955516 -71 CTTGACTTTTTCCCTCCCCCGATTATGATT 15 230 1 TCCCTCCCCC 0.991851 -48 AGACTTTTTGCTTCTCCCCAGGATGAAATG 16 13 0 CTTCTCCCCA 0.80576 -230 TCGGTAATGCACCCTCCTCCTGGAGAAAAT 16 190 0 ACCCTCCTCC 0.939532 -53 ********** Masking position 4 Map Score: 18.1513 Number of sites scoring better than the average of aligned sites = 1832 Number in coding regions = 1652 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 2 AGGAGGAGGAGGCGATAAATGGTAGCACCAAAGCTAG 1 14 1 GGGAAAGAGA 0.982945 -238 GACCCATGGAGCTGATTATGGTCAATGTTAGGCTAAG 1 55 1 GCGATAGAAG 0.892109 -197 CTGTTTTACCGCTGACAAGGGCCAAAGTATAAACAGA 1 107 1 GCGAAAGAAG 0.924241 -145 GGAACTTTAGGGAAATTATGGCAAGGAA 2 2 0 GGAATAGAGA 0.902168 -113 CTTGACCAATGGTAAAAATTGAGGGCAACGCTGGCCC 3 15 0 GGAAAAGGGA 0.785066 -85 AACTAAACGGGGCAAAAATTGGCAATATTTTCTAGC 5 10 0 GGAAAAGAAA 0.943071 -32 CCAGTAACAGGGCGAGAACAGGAAGCATCATCCCAAT 6 26 1 GGGAAAGAGA 0.982945 -108 ATCAAACTGTGCAGACTATTGGGAAAAATTGCCCAAA 7 20 1 GCGATAGAAA 0.951353 -168 CGGCGATCGTGGCGGATAATGAGAATATTTCCCTAAC 7 101 1 GGGGTAGAAA 0.952627 -87 GGCAATAACTGTGGGAAACTGAGAAAAACCAGATCCC 9 45 0 GTGGAAGAAA 0.700398 -98 CCAGAGCTGAGGGGGCAATAGGCAATAACTGTGGGAA 9 65 0 GGGGAAGAAA 0.967394 -78 TAAAAACTAAGGAGAGTATAGCAAAAAGGGCTTCTTC 10 23 1 GGGATAGAAA 0.979407 -257 GAACTACCATGCTAAATAAAGAAGAAATCATCGTCCC 11 17 1 GCAATAGGAA 0.553447 -46 GTATGGTAGAGGGGAGAACGTAAAGCAAAGGTTTTTA 15 194 0 GGGAAATAGA 0.76532 -84 CCCTCCTCCTGGAGAAAATCGCAAATGTAGCATTGCT 16 172 0 GGGAAAGAAG 0.967394 -71 ** ** ** * ** * Masking position 8 Map Score: 13.113 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 615 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 GTCCTTCCTAGCTTTGGTGCTACCATTTAT 1 28 0 GCTTTGGTGC 0.780035 -224 ATCTGTTTATACTTTGGCCCTTGTCAGCGG 1 115 0 ACTTTGGCCC 0.969225 -137 GTTTGGTGGCGCTTTGGTCAATTGGGATCA 2 65 1 GCTTTGGTCA 0.86352 -50 GTTCCGGAGCACTTCGGTCCAGTTGATCCC 2 88 0 ACTTCGGTCC 0.910001 -27 GGACCGAAGTGCTCCGGAACACTCATA 2 98 1 GCTCCGGAAC 0.73794 -17 ATTGAGGGCAACGCTGGCCCCTAC 3 5 0 ACGCTGGCCC 0.905747 -95 GGACTAAATTACGTCGGGAAAAGAACCCCG 6 113 0 ACGTCGGGAA 0.550817 -21 GGTAGGCTGGGCTTTGGGCAATTTTTCCCA 7 39 0 GCTTTGGGCA 0.941814 -149 CAGCCTACCATCGTTGGCCCTGTAAGCCGA 7 60 1 TCGTTGGCCC 0.841415 -128 TGCCCCCTCAGCTCTGGGACAAATACCTGG 9 85 1 GCTCTGGGAC 0.942695 -58 AAGCCCAGAGACTTTGGACAATATGACCAG 9 111 0 ACTTTGGACA 0.733957 -32 AAGTCTCTGGGCTTTGGGCCTTTTGC 9 127 1 GCTTTGGGCC 0.984237 -16 CAAAACATTTTCTCCGGGACCATTTGTCTC 12 34 1 TCTCCGGGAC 0.713816 -267 TATCTCTTTAACTTTGGCACCGGGAACTGC 12 261 0 ACTTTGGCAC 0.926009 -40 ********** Masking position 2 Map Score: 9.94487 Number of sites scoring better than the average of aligned sites = 1222 Number in coding regions = 1124 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 GGCTAAGGGAAGGAAATTAACCCTGTTTTACCG 1 85 1 AGGAAAACCC 0.868074 -167 TGTAATCGACGGGAAAATCGTCCGTGGTTAATC 1 217 0 GGGAAAGTCC 0.912915 -35 AAGTTCCGTCGGCTAAACCGCCCGATCTCCCAA 2 32 1 GGCTAAGCCC 0.838798 -83 GGGAAAAGGGGGGAAAGAAACCCTACCATTTTA 3 69 0 GGGAAAACCC 0.962734 -31 AAATTACGTCGGGAAAAGAACCCCGTTGATTCT 6 105 0 GGGAAAACCC 0.962734 -29 CAGACTATTGGGAAAAATTGCCCAAAGCCCAGC 7 31 1 GGAAAAGCCC 0.884724 -157 AGCGGTGTTAGGGAAATATTCTCATTATCCGCC 7 111 0 GGGAAATCTC 0.834653 -77 CCTCAGCTCTGGGACAAATACCTGGTCATATTG 9 90 1 GGGACAACCT 0.753404 -53 GAATGAATTCGGGATATCAACTCTTTTTGAGAG 12 227 0 GGGATAACTC 0.814246 -74 CCAAGTGCATGGAAAAGATACCCTCTATAAAAT 14 88 1 GGAAAAACCC 0.954054 -213 ATTAAGGATTCGGTAATGCACCCTCCTCCTGGA 16 196 0 CGGTAAACCC 0.866236 -47 ****** **** Masking position 6 Map Score: 8.42117 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 681 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 TCCTAGCTTTGGTGCTACCATTTATCGCCT 1 23 0 GGTGCTACCA 0.830357 -229 CAGCTCCATGGGTCCTTCCTAGCTTTGGTG 1 39 0 GGTCCTTCCT 0.859429 -213 TGGAAAGGCTGATTCTCCTCCCCACTTTGC 4 24 0 GATTCTCCTC 0.831064 -67 CCATTGGGATGATGCTTCCTGTTCTCGCCC 6 35 0 GATGCTTCCT 0.912168 -99 GAACCCCGTTGATTCTACCAAAATGTTACT 6 91 0 GATTCTACCA 0.913098 -43 AGGGGCATACGGTTCTTTCAAGAAGAAGCC 10 51 0 GGTTCTTTCA 0.625962 -229 TCCTTAAAAGGATTCTTCCTTTGTCATTGA 10 84 1 GATTCTTCCT 0.960243 -196 AACAGATTCTCCCATTAAGCATGC 12 5 1 GATTCTCCCA 0.974694 -296 ATCCGAGGTGGGTTCTCCCTATGGGGAGGG 14 277 0 GGTTCTCCCT 0.98092 -24 GAGACTTTTTGCTTCTCCCCAGGATGAAAT 16 14 0 GCTTCTCCCC 0.907625 -229 CTTCTTGAGAGATTCTCCTTCTATTATTGA 16 43 1 GATTCTCCTT 0.879672 -200 ********** Masking position 6 Map Score: 8.2279 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 439 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 TGACCATAATCAGCTCCATGGGTCCTTCCTAG 1 47 0 CGCTCCAGGG 0.982919 -205 TTGGCGATCGCCGCTTGACCGGGGGAATGGTA 1 145 1 CGCTTGACGG 0.842794 -107 TTCTCCTCCCCACTTTGCCGGGTACAGTTTT 4 10 0 CCTTTGCGGG 0.909088 -81 CAAAATGTTACTGTTCCAGGGGGTGGGGAATG 6 71 0 CGTTCCAGGG 0.971449 -63 ATAGTCTGCACAGTTTGATGGGTTTGCT 7 7 0 CGTTTGAGGG 0.97718 -181 TCAGTTGCATCGGCTTACAGGGCCAACGATGG 7 67 0 CGCTTACGGG 0.952821 -121 TGTGAATTTCCGCCTTCATGGGGCTTTTTCAA 10 139 1 CCCTTCAGGG 0.957461 -141 AATGTTTTGCATGCTTAATGGGAGAATCTGTT 12 11 0 AGCTTAAGGG 0.714365 -290 ATTCATTCAGCAGTTCCCGGTGCCAAAGTTAA 12 252 1 CGTTCCCGTG 0.82266 -49 TAATAAGTTGCTGTTTGAGGTGTATTGAAGAG 15 150 0 CGTTTGAGTG 0.887535 -128 * ****** *** Masking position 5 Map Score: 6.05675 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 639 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 CATACGGTTCTTTCAAGAAGAAGCCCTTTTTGCTATACT 10 37 0 TTAGACCTTT 0.858658 -243 CAAATCCGTCTTTTGTCAAGATATTTTTTACTAAAGCTA 10 168 1 TTAGATTTTT 0.907071 -112 ATATCAACTCTTTTTGAGAGCTTTGTTTTAATACAGCAT 12 208 0 TTAGCGTTTT 0.968529 -93 CCGGTGCCAAAGTTAAAGAGATACGCTTTTTATTAGGAT 12 268 1 ATAGAGCTTT 0.796172 -33 TAGTACTGTTTTTTAATTAGAATAGTTTTATCAAAACTA 13 30 1 TTAGAGTTTT 0.963725 -47 CATCAAAAAGTTTAATGTAGAGTCGCTTTCAGATGTGGA 14 26 0 TTAGAGCTTT 0.973479 -275 CTTGGCGTCATTTTATAGAGGGTATCTTTTCCATGCACT 14 91 0 TTAGGTCTTT 0.781748 -210 CCTCTCCACTTCTTGTCGAGAATCGTCTTTTGCTTACAA 14 174 0 TTAGAGTCTT 0.807333 -127 GGAGAGGTTTTGTCTTTCTGCAAAGTTTTTTTGATTAGG 14 206 1 TTTGCGTTTT 0.766086 -95 ACAAGGGAATTTTTTGAAAGCTGTACTTTCGCAGCTAAG 15 62 0 TTAGCACTTT 0.826031 -216 GTTTGAGGTGTATTGAAGAGCTGTGCTTTTAACTAAACA 15 131 0 TTAGCGCTTT 0.977022 -147 AAGGAGAATCTCTCAAGAAGAGACTTTTTGCTTCTCCCC 16 24 0 TTAGATTTTT 0.907071 -219 AAAAACTTCTTGTCCTTAAGCGTATTTTTGAACGAAATG 16 115 1 TTAGCTTTTT 0.918745 -128 * * *** ***** Masking position 3 Map Score: 6.46509 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 74 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 CCCTAAAGTTCCGTCGGCTAAACCGCCCGA 2 27 1 CCGTCGGCTA 0.84349 -88 ATAGTTAAGGCCGTCTGCTTTTAAGCGGTG 7 137 0 CCGTCTGCTT 0.970195 -51 AGAAGAAGCCCTTTTTGCTATACTCTCCTT 10 31 0 CTTTTTGCTA 0.84556 -249 TCGAGAATCGTCTTTTGCTTACAAGAGATT 14 168 0 TCTTTTGCTT 0.715033 -133 GAGGTTTTGTCTTTCTGCAAAGTTTTTTTG 14 209 1 CTTTCTGCAA 0.836804 -92 GGGGAACCTTCTGCATAAAAGTTATT 15 7 1 CCTTCTGCAT 0.954636 -271 TACACTGCAACCTTCTGCTTTAGCTACAAG 15 96 0 CCTTCTGCTT 0.982901 -182 CAAGAAGAGACTTTTTGCTTCTCCCCAGGA 16 20 0 CTTTTTGCTT 0.897783 -223 ********** Masking position 4 Map Score: 3.71778 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 239 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 CGTCTTTTGTCAAGATATTTTTTACTAAAGC 10 174 1 CAAGAATTTT 0.896618 -106 TTCCTCTTCAAGATTTTTAGGGACGATGA 11 44 0 CAAGATTTTA 0.803835 -19 ATTAAGCATGCAAAACATTTTCTCCGGGACC 12 24 1 CAAAAATTTT 0.865785 -277 GGCTTGCCCGCAAGAATTTTTCGCAAATGAG 12 61 0 CAAGATTTTT 0.942752 -240 ATAGTTTTATCAAAACTATTTAGCTGAGATA 13 51 1 CAAAATATTT 0.753263 -26 CTCTCTACATCAAAAAGTTTAATGTAGAGTC 14 41 0 CAAAAGTTTA 0.633691 -260 TGTCTTTCTGCAAAGTTTTTTTGATTAGGGA 14 216 1 CAAAGTTTTT 0.884979 -85 GCTTTAGCTACAAGGGAATTTTTTGAAAGCT 15 79 0 CAAGGAATTT 0.574087 -199 GAACGTAAAGCAAAGGTTTTTAAGGTATTAG 15 185 0 CAAAGTTTTT 0.884979 -93 AAATCAGAAACAAAAATTATTAATACTCAAT 16 68 0 CAAAATTATT 0.610102 -175 CGCTTAAGGACAAGAAGTTTTTCTATTAATT 16 106 0 CAAGAGTTTT 0.903496 -137 ***** ***** Masking position 3 Map Score: 4.53713 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 280 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 AGACGGCCTTAACTATTATATTTAACTGCCCCTA 7 151 1 AACTTATATA 0.753692 -37 TCACCAATAGAGTTTTCCTACTAAGTATATTTGT 8 22 1 AGTTTCTATA 0.929429 -30 TGTCATTGATAATAATCCTAATCAGCAAGTACCA 10 105 1 AATATCTATA 0.842919 -175 AACTATCCTAATAAAAAGCGTATC 12 287 0 AACTTCTATA 0.968957 -14 CTAATTAAAAAACAGTACTACTTACCTTTTCGGT 13 16 0 AACATCTATA 0.94244 -61 GTTTTGATAAAACTATTCTAATTAAAAAACAGTA 13 33 0 AACTTCTATA 0.968957 -44 TGTATTGAAGAGCTGTGCTTTTAACTAAACATGC 15 128 0 AGCTTCTTTA 0.863664 -150 AAGGACAAGAAGTTTTTCTATTAATTTTTCCTGA 16 98 0 AGTTTCTATA 0.929429 -145 TCGCAAATGTAGCATTGCTATTGATAAGCAATCA 16 157 0 AGCATCTATA 0.954709 -86 **** * *** * * Masking position 6 Map Score: 4.27331 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 21 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 GTCAGCGGTAAAACAGGGTTAATTTCCTTC 1 93 0 AAACAGGGTT 0.960724 -159 GCCAAAGTATAAACAGATTTGGCGATCGCC 1 127 1 AAACAGATTT 0.66768 -125 ATTAAAGTTAAAATAGGGTTTTCTGTGGAT 1 190 1 AAATAGGGTT 0.926113 -62 AGCATCATCCCAATGGAGTTCCCATTCCCC 6 49 1 CAATGGAGTT 0.786325 -85 TTGGTAGAATCAACGGGGTTCTTTTCCCGA 6 100 1 CAACGGGGTT 0.906565 -34 TCACGCTCACCAATAGAGTTTTCCTACTAA 8 16 1 CAATAGAGTT 0.854555 -36 AAATATACAAATATACTTAGTAGGAAAA 8 34 0 AAATATACTT 0.388995 -18 GAGTATAGCAAAAAGGGCTTCTTCTTGAAA 10 36 1 AAAAGGGCTT 0.65217 -244 CCATGTCACAAAACATGGTTATTCATTCCA 10 232 1 AAACATGGTT 0.783122 -48 TATTCATTCCAAACAGACTTACATGATTAC 10 251 1 AAACAGACTT 0.890839 -29 CAAAGCTCTCAAAAAGAGTTGATATCCCGA 12 222 1 AAAAAGAGTT 0.834099 -79 ********** Masking position 3 Map Score: 3.24463 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 432 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 12 TAACTTTAATAGTGGGCGAGAGATACCATTC 1 169 0 AGGGGCGAGA 0.970932 -83 GTAGGGGCCAGCGTTGCCCTCA 3 2 1 TAGGGCCAGC 0.892439 -98 TTCCAACTAAACGGGGCAAAAATTGGCAATA 5 20 0 ACGGGCAAAA 0.917366 -22 GGACCCAGTAACAGGGCGAGAACAGGAAGCA 6 22 1 ACGGGCGAGA 0.977706 -112 GCATCGGCTTACAGGGCCAACGATGGTAGGC 7 62 0 ACGGGCCAAC 0.950016 -126 CCCAGAGCTGAGGGGGCAATAGGCAATAACT 9 72 0 AGGGGCAATA 0.827386 -71 AAGTCGTCTCTCGGGGCTAGCTTTAGTAAAA 10 193 0 TCGGGCTAGC 0.940867 -87 GAAAAATTCTTGCGGGCAAGCCACAAGAGGT 12 70 1 TGGGGCAAGC 0.968387 -231 ** ******** Masking position 9 Map Score: 1.42703 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 244 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 13 TTATGGTCAATGTTAGGCTAAGGGAAGGAAATTAACCCTG 1 70 1 TTGTGGAAAA 0.981182 -182 AGAGGCGTGGTATGAAATTCTAGGAAAGAAGTATAATGGG 12 104 1 TTATGGAAAA 0.963688 -197 TGACTCAGGCTATAGGGCTTAAGGATGGAATTTTATCGAT 12 145 1 TTGTGGATAA 0.976917 -156 TTGAGAGCTTTGTTTTAATACAGCATATAACGAAGCATTA 12 194 0 TTATGCATAA 0.757842 -107 TCTGCAAAGTTTTTTTGATTAGGGAATTAAAGCAACCTTG 14 222 1 TTGTGGAAAA 0.981176 -79 CTAAGCGGCTTATTGTAGTAGTGGATGGATAATAACTTTT 15 27 0 TTATGGATAT 0.871913 -251 AAGCAAAGGTTTTTAAGGTATTAGATGTAATAAGTTGCTG 15 169 0 TTGTAGATAA 0.80579 -109 ATAATTTTTGTTTCTGATTTCAGGAAAAATTAATAGAAAA 16 79 1 TTATGGAAAT 0.893461 -164 CGCGTTCTCTTTATCGCTTGAGGAATTAAGGATTCGGTA 16 214 0 TTGTGGAAAA 0.980881 -29 * * * * **** ** Masking position 9 Map Score: 2.09156 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 68 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 ********** No masking Map Score: 5.74362e-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: 5.74362e-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