AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_fla_operon_tpal_reg_300.orf -o259_tpal_300.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP01136 83 AE000520 #2 RTP01045 27 AE000520 #3 RTP00239 45 AE000520 #4 RTP00117 32 AE000520 #5 RTP00119 147 AE000520 #6 RTP00120 84 AE000520 #7 RTP00121 55 AE000520 #8 RTP00124 116 AE000520 #9 RTP00126 47 AE000520 #10 RTP00129 27 AE000520 #11 RTP00531 65 AE000520 #12 RTP00530 55 AE000520 #13 RTP00526 34 AE000520 #14 RTP00978 18 AE000520 #15 RTP00518 21 AE000520 #16 RTP00514 57 AE000520 #17 RTP00513 70 AE000520 #18 RTP00512 75 AE000520 #19 RTP00725 75 AE000520 #20 RTP00726 85 AE000520 #21 RTP00727 110 AE000520 #22 RTP00730 24 AE000520 #23 RTP00731 46 AE000520 #24 RTP01206 21 AE000520 #25 RTP00735 155 AE000520 #26 RTP00736 87 AE000520 Motif number 1 ACAGACACGGCTGCCTCGGGG 4 22 1 CTGCCTCGGG 0.928927 -11 GCGTAAAGGCCTGCCCCGGCCTGGGGGATT 5 114 1 CTGCCCCGGC 0.991261 -34 CGCGCCCCCACCCCCCTGTCT 6 2 0 CCCCCCTGTC 0.956055 -83 CGATACAAAACTCCCTCTGCGCACTGAGAA 6 44 0 CTCCCTCTGC 0.822022 -41 AGTTTTGTATCGCCCCGTGCGCCGCGCGCT 6 62 1 CGCCCCGTGC 0.963914 -23 GCCCCGTGCGCCGCGCGCTGCA 6 73 1 CCGCGCGCTG 0.739979 -12 ACCCCGCCCTCTGCCCGGGGGACACCACGA 7 30 1 CTGCCCGGGG 0.984396 -26 GGTTGCAGGGCTGCGCGTGGAATCCTACCT 8 19 1 CTGCGCGTGG 0.936632 -98 GGAATCCTACCTGAGCGCGCTCAATGAGGC 8 37 1 CTGAGCGCGC 0.686246 -80 GAGCCTGCGCCGGCAAGGATAAGA 8 103 0 CTGCGCCGGC 0.99109 -14 TGTCACCGTCCCCCGTGGTCG 9 2 0 CCCCGTGGTC 0.969039 -46 CAGGGTGCATCTCCCTGGGGAACTGG 10 12 1 CTCCCTGGGG 0.926494 -16 CCGCATGTGCCTGTGCCGTC 11 1 1 CCGCATGTGC 0.71662 -65 CCGCATGTGCCTGTGCCGTCTGCATCCGAC 11 11 1 CTGTGCCGTC 0.712498 -55 CCGTCTGCATCCGACCCGTCGCGTGACGCT 11 26 1 CCGACCCGTC 0.866333 -40 CATCGGCAACCGGCACGCGCCAGC 12 5 0 CGGCACGCGC 0.852647 -51 ACAAGAAGGCCTCCGCTGTCCGAGCTCTAC 17 12 1 CTCCGCTGTC 0.936179 -59 ACCGGCCCGGTGATCTTTGGAG 19 64 0 CGGCCCGGTG 0.980279 -12 ACGTTCGCGGCCGCGCGGTTTTTGTTATCG 20 26 1 CCGCGCGGTT 0.920348 -60 ATGCGCCGGGCGGTGTTGCCGTTCT 20 71 0 CCGGGCGGTG 0.821316 -15 AAGACGTACACGGCGTTGTCATCTATGTCG 21 74 0 CGGCGTTGTC 0.885312 -37 TGAGCAAGAACTCGCCTGGCTGG 23 4 0 CTCGCCTGGC 0.794285 -43 TGCTCAGAAACGCCCTCCTCCTCAAGGAG 23 28 1 CGCCCTCCTC 0.75524 -19 CGTACACGCACGCGCCCTTCGAAACAATGC 25 16 0 CGCGCCCTTC 0.657117 -140 CCCGTTCTTCCGGCGCCGTTGCTGGTGTAC 25 74 0 CGGCGCCGTT 0.84412 -82 CGTCGTGGTCCCTCCCGTTCTTCCGGCGCC 25 87 0 CCTCCCGTTC 0.752406 -69 CGGTTGAAGGCGTCGTGGTCCCTCCCGTTC 25 97 0 CGTCGTGGTC 0.749305 -59 ATGGGGCAATCCGCATTGGCGGGT 25 142 1 CCGCATTGGC 0.696027 -14 CACGGGGCTGCCGCCCGTGCTCAGGGCATT 26 34 0 CCGCCCGTGC 0.983412 -54 CGGGCGGCAGCCCCGTGGGGTTCAGGAGAC 26 47 1 CCCCGTGGGG 0.510693 -41 AGTTCAAAGACTCGGCCGTCTCCTGAACCC 26 64 0 CTCGGCCGTC 0.888334 -24 ********** Masking position 1 Map Score: 42.5324 Number of sites scoring better than the average of aligned sites = 3764 Number in coding regions = 3393 Number in noncoding regions = 371 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 2 CATGAGGGGTGCCTTTTTTAAC 1 3 1 TGAGGGGTGC 0.534961 -81 AAGCAGTTCGGGTCCTTGCCAATGGTCAGG 5 32 1 GGTCCTTGCC 0.730777 -116 TTGTAGCAGTGGAGCGTTGCTTCAAAAGAC 5 68 1 GGAGCGTTGC 0.728484 -80 GAATCCCCCAGGCCGGGGCAGGCCTTTACG 5 115 0 GGCCGGGGCA 0.752795 -33 AGACAGGGGGGTGGGGGCGCGCTATACTT 6 10 1 GGTGGGGGCG 0.504263 -75 CAGCGCGCGGCGCACGGGGCGATACAAAAC 6 63 0 CGCACGGGGC 0.7896 -22 CCCCGTGCGCCGCGCGCTGCA 6 74 1 CGCGCGCTGC 0.971531 -11 GGGGTAGTCGCGCGCTTTGCGCTC 7 5 0 CGCGCTTTGC 0.937465 -51 GCGACTACCCCGCCCTCTGCCCGGGGGACA 7 24 1 CGCCCTCTGC 0.934884 -32 AGATGCTCGTGGTGTCCCCCGGGCAGA 7 39 0 CGTGGTGTCC 0.631029 -17 GTTGCAGGGCTGCGCGTGGAATCCTACCTG 8 20 1 TGCGCGTGGA 0.868673 -97 CGCCTCATTGAGCGCGCTCAGGTAGGATTC 8 38 0 AGCGCGCTCA 0.497299 -79 CGCAGCGTCAGGCCGTTTGCCATTATGGCA 8 66 1 GGCCGTTTGC 0.922495 -51 AAGGATAAGAAGCGGGCTGCCATAATGGCA 8 83 0 AGCGGGCTGC 0.840553 -34 TTCTTATCCTTGCCGGCGCAGGCTC 8 102 1 TGCCGGCGCA 0.770395 -15 CATGTGCCTGTGCCGTCTGCATCCGACCCG 11 14 1 TGCCGTCTGC 0.838587 -52 GCTGGCGCGTGCCGGTTGCCGAT 12 4 1 GGCGCGTGCC 0.554075 -52 CCGAGCATTGTGTGCGTGGCAGTTGGGGAC 13 15 0 TGTGCGTGGC 0.78704 -20 CCATTGCGGTGGCCATCGCGTGGT 18 5 1 TGCGGTGGCC 0.903937 -71 AAAATATGTACGCCGTTGGAGGGA 18 62 1 CGCCGTTGGA 0.832511 -14 ACCGGCCCGGTGATCTTTGGAGA 19 63 0 GGCCCGGTGA 0.897322 -13 ACGGCAACACCGCCCGGCGCAT 20 74 1 CGCCCGGCGC 0.868177 -12 TGTTTCGAAGGGCGCGTGCGTGTACGCCTG 25 20 1 GGCGCGTGCG 0.517486 -136 GTTCTTCCGGCGCCGTTGCTGGTGTACGTG 25 71 0 CGCCGTTGCT 0.609851 -85 ACGGGGCTGCCGCCCGTGCTCAGGGCATTC 26 33 0 CGCCCGTGCT 0.763639 -55 TCAAAGACTCGGCCGTCTCCTGAACCCCAC 26 61 0 GGCCGTCTCC 0.913149 -27 ********** Masking position 2 Map Score: 21.5385 Number of sites scoring better than the average of aligned sites = 5810 Number in coding regions = 5380 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 3 CTTCAAAAGACGCTTTGGGTTTTTTGAGCGTA 5 87 1 CGCTGGGTTT 0.625117 -61 GCCGGGGCAGGCCTTTACGCTCAAAAAACCCA 5 102 0 GCCTACGCTC 0.798007 -46 AGACAGGGGGGTGGGGGCGCGCTATACTTG 6 9 1 GGGTGGGCGC 0.70823 -76 ATACAAAACTCCCTCTGCGCACTGAGAATTGC 6 40 0 CCCTGCGCAC 0.984653 -45 TGCAGCGCGCGGCGCACGGGGCGATAC 6 68 0 CGCGGCGCAC 0.992588 -17 GGTAGTCGCGCGCTTTGCGCTC 7 1 0 CGCTGCGCTC 0.992739 -55 CCGCCCTCTGCCCGGGGGACACCACGAGCATC 7 33 1 CCCGGGACAC 0.866585 -23 TAGGATTCCACGCGCAGCCCTGCAACCGAAAA 8 14 0 CGCGGCCCTG 0.60201 -103 TTATCCTTGCCGGCGCAGGCTC 8 105 1 CGGCAGGCTC 0.891208 -12 CGGATGCAGACGGCACAGGCACATGCGG 11 7 0 CGGCAGGCAC 0.891382 -59 TCCGACCCGTCGCGTGACGCTCCAGAGGAGGA 11 35 1 CGCGACGCTC 0.975166 -31 TGCCGATGAGCCCTATGGGCTCTCGTGCAATG 12 27 1 CCCTGGGCTC 0.986138 -29 AAATGAACCACGCGATGGCCACCGCAATGG 18 9 0 CGCGGGCCAC 0.955376 -67 CTGGGACAAACGGTCAGCACTCGTTCTACCAA 19 29 0 CGGTGCACTC 0.823342 -47 ACGGCAACACCGCCCGGCGCAT 20 74 1 CGCCGCGCAT 0.90213 -12 TTCTTACTTTCGCTGCAGGCACGACCCAAAGA 21 11 0 CGCTAGGCAC 0.977997 -100 CGAAACACAGGCGTACACGCACGCGCCCTTCG 25 25 0 GCGTACGCAC 0.590978 -131 CTGCCGCCCGTGCTCAGGGCATTCAAACTCTT 26 25 0 TGCTGGGCAT 0.516942 -63 GGGCGGCAGCCCCGTGGGGTTCAGGAGACGGC 26 48 1 CCCGGGGTTC 0.851625 -40 **** ****** Masking position 10 Map Score: 23.0346 Number of sites scoring better than the average of aligned sites = 2727 Number in coding regions = 2538 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 AGTGGAGCGTTGCTTCAAAAGACGCTTTGGG 5 75 1 TGCTTCAAAG 0.969078 -73 GCGACGGGTCGGATGCAGACGGCACAGGCAC 11 17 0 GGATGCAGAG 0.80962 -49 CGTCGCGTGACGCTCCAGAGGAGGAGTCAGA 11 42 1 CGCTCCAGAG 0.86803 -24 CGCTGGATGATGTTGCGAAGG 16 1 0 TGTTGCGAAG 0.971395 -57 AGCTCTACCGTGCTTCAGATGAGCCCTTTTC 17 34 1 TGCTTCAGAG 0.971396 -37 AGAATCGTCTTGTTCCAAATGAACCACGCGA 18 26 0 TGTTCCAAAG 0.942444 -50 TGTTCCTTGATGCAAATGTTGGTAGAAC 19 8 1 TGATGCAAAG 0.943821 -68 GGGTCGTGCCTGCAGCGAAAGTAAGAAGTGA 21 16 1 TGCAGCGAAG 0.883443 -95 TACCAGCATTGTTTCGAAGGGCGCGTGCGT 25 10 1 TGTTTCGAAG 0.955354 -146 TGTACGCCTGTGTTTCGGGGGAAGGTGTGTA 25 40 1 TGTTTCGGGG 0.828694 -116 ********* * Masking position 6 Map Score: 5.85922 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 194 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CACGCAGTGCAAGATATACCGTGAA 3 5 1 CAGGCAAGAT 0.683111 -41 CACAGCTGCGCAAAGTTAATAAAGCA 5 6 1 CTGGCAAAGT 0.962295 -142 GATGCCTCGCCAAAAAGAGAACTACC 9 32 0 CTCCCAAAAA 0.917974 -16 CGAACTACTGAGAAAAGAAAAGGGCTCA 17 53 0 CTGGAAAAGA 0.900008 -18 TTGTCCCAGGCTCTCCAAAGATCACCGGGCC 19 52 1 CTCCCAAAGA 0.963268 -24 CGGTGTATATCTGTGGAAAGACGTACACGGC 21 90 0 CTGGGAAAGA 0.930266 -21 GAGGGCGTTTCTGAGCAAGAACTCGCCTGGC 23 14 0 CTGGCAAGAA 0.965395 -33 AAACGCCCTCCTCCTCAAGGAG 23 35 1 CTCTCAAGGA 0.945344 -12 GGCATTCAAACTCTTCAAAAAACTGATTC 26 9 0 CTCTCAAAAA 0.911996 -79 AGACAGTTCAAAGACTCGGCCGTC 26 74 0 CAGTCAAAGA 0.908894 -14 *** ******* Masking position 7 Map Score: 5.19541 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 306 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 CTTTTGTTTGCCGTTAAAAAAGGCACCCCTCATG 1 5 0 CCGAGCCCCT 0.942417 -79 CGCAAGTTCCTCGAACTTTCTGGACACCCCATTAAACTTT 1 41 0 TCGTGAACCC 0.975047 -43 CCCCGAGGCAGCCGTGTCTGTATACGCTGCGC 4 5 0 CAGTGAACCT 0.8877 -28 GACCGTTGATTTTGAATCCCCCAGGCCGGGGC 5 126 0 CCGAGACCCC 0.990092 -22 TGAGAATTGCAAGTATAGCGCGCCCCCACCCCCCTGTCT 6 10 0 AAGAGCCCCC 0.72537 -75 AAGAAGCGGGCTGCCATAATGGCAAACGGCCTGACGCTGC 8 67 0 CTGTGAACGC 0.834629 -50 ACGAGACGTATTGCTTAGTATGCATACCCCAAGAACGCTG 16 27 0 TTGAGAACCC 0.950783 -31 GGTGAGCACCTCGACCAGAACGGCAACACCGCCCGGCGCA 20 55 1 TCGAGCACCC 0.973849 -31 TTTTGCTTTACCGACATAGATGACAACGCCGTGTACGTCT 21 63 1 CCGTGCACCC 0.990066 -48 CCCCGAAACACAGGCGTACACGCACGCGCCCTTCGAAACA 25 20 0 CAGTGAGCCC 0.965835 -136 GGCGCCGTTGCTGGTGTACGTGTACACACCTTCCCCCGAA 25 53 0 CTGTGAACCC 0.981024 -103 ACCCGCCAATGCGGATTGCCCCATTTGTTTTG 25 134 0 CCGAGTGCCC 0.940308 -22 AATCAGTTTTTTGAAGAGTTTGAATGCCCTGAGCACGGGC 26 12 1 TTGAGAGCCT 0.732503 -76 *** * * * ** ** Masking position 17 Map Score: 12.5889 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 324 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 AGACACTCAGCCAGATACGGAGTGA 2 6 0 CCAGATACGG 0.68681 -22 CGCAGCGTATACAGACACGGCTGCCTCGGG 4 12 1 ACAGACACGG 0.914843 -21 ACGCTCCACTGCTACAACGCGTACCTGACC 5 55 0 GCTACAACGC 0.744663 -93 AGCGTAAAGGCCTGCCCCGGCCTGGGGGAT 5 113 1 CCTGCCCCGG 0.925823 -35 AAAGCGCGCGACTACCCCGCCCTCTGCCCG 7 17 1 ACTACCCCGC 0.763539 -39 CACGCGCAGCCCTGCAACCGAAAACTG 8 8 0 CCTGCAACCG 0.757531 -109 CTCATCGGCAACCGGCACGCGCCAGC 12 7 0 ACCGGCACGC 0.910581 -49 CCTGTCCCCAACTGCCACGCACACAATGCT 13 12 1 ACTGCCACGC 0.970481 -23 TATGCATACCCCAAGAACGCTGGATGATGT 16 19 0 CCAAGAACGC 0.935314 -39 GACAAGAAGGCCTCCGCTGTC 17 2 1 ACAAGAAGGC 0.5328 -69 TCCCTCCAACGGCGTACATATT 18 64 0 CCTCCAACGG 0.910146 -12 GAGCACCTCGACCAGAACGGCAACACCGCC 20 58 1 ACCAGAACGG 0.751926 -28 CCAGCCAGGCGAGTTCTTGC 23 1 1 CCAGCCAGGC 0.90783 -46 GAGTTCTTGCTCAGAAACGCCCTCCTCCTC 23 21 1 TCAGAAACGC 0.631601 -26 ACACAGGCGTACACGCACGCGCCCTTCGAA 25 23 0 ACACGCACGC 0.849488 -133 TACACGTACACCAGCAACGGCGCCGGAAGA 25 69 1 CCAGCAACGG 0.979724 -87 ATTTGTTTTGCCTAAAACGGTTGAAGGCGT 25 114 0 CCTAAAACGG 0.852278 -42 ********** Masking position 2 Map Score: 11.8562 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 1035 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 CTACCTGTCACCGTCCCCCGTGGTCG 9 7 0 CCGTCCCCCG 0.929311 -41 TGCATCCGACCCGTCGCGTGACGCTCCAGA 11 31 1 CCGTCGCGTG 0.993902 -35 GCTGGCGCGTGCCGGTTGCCG 12 2 1 CTGGCGCGTG 0.93555 -54 ACTAAGCAATACGTCTCGTT 16 48 1 ACGTCTCGTT 0.86874 -10 ATTGCGGTGGCCATCGCGTGGTTCATTTGG 18 13 1 CCATCGCGTG 0.959197 -63 ATTGTTTCGAAGGGCGCGTGCGTGTACGCC 25 18 1 AGGGCGCGTG 0.898801 -138 TACACCAGCAACGGCGCCGGAAGAACGGGA 25 75 1 ACGGCGCCGG 0.505161 -81 GCGTCGTGGTCCCTCCCGTTCTTCCGGCGC 25 88 0 CCCTCCCGTT 0.777054 -68 GGGAGGGACCACGACGCCTTCAACCGTTTT 25 101 1 ACGACGCCTT 0.80132 -55 AAAGACTCGGCCGTCTCCTGAACCCCACGG 26 59 0 CCGTCTCCTG 0.973581 -29 ********** Masking position 5 Map Score: 6.14867 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 533 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 GGGTCCTTGCCAATGGTCAGGTACGCGTTG 5 41 1 CAATGGTCAG 0.937335 -107 GCTATACTTGCAATTCTCAGTGCGCAGAGG 6 31 1 CAATTCTCAG 0.946797 -54 TGCAGCGCGCGGCGCACGGGGC 6 73 0 CAGCGCGCGG 0.744249 -12 CAGTTTTCGGTTGCAGGGCT 8 1 1 CAGTTTTCGG 0.89396 -116 GCCACGCACACAATGCTCGG 13 25 1 CAATGCTCGG 0.987776 -10 GGGCTGCCGCCCGTGCTCAGGGCATTCAAA 26 30 0 CCGTGCTCAG 0.944205 -58 ********** Masking position 8 Map Score: 0.45159 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 162 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 TAGGATTCCACGCGCAGCCCTGCAACCGAA 8 16 0 CGCGCAGCCC 0.870518 -101 AACGGCCTGACGCTGCGCCTCATTGAGCGC 8 53 0 CGCTGCGCCT 0.823015 -64 TTCCCCAGGGAGATGCACCCTGG 10 4 0 AGATGCACCC 0.565724 -24 TGCCGGTTGCCGATGAGCCCTATGGGCTCT 12 20 1 CGATGAGCCC 0.991948 -36 ACTGCATTGCACGAGAGCCCATAGGGCTCA 12 33 0 ACGAGAGCCC 0.664581 -23 ACCGTGCTTCAGATGAGCCCTTTTCTTTTC 17 40 1 AGATGAGCCC 0.968269 -31 ATGAACCACGCGATGGCCACCGCAATGG 18 9 0 CGATGGCCAC 0.768923 -67 CTGGGACAAACGGTCAGCACTCGTTCTACC 19 31 0 CGGTCAGCAC 0.924698 -45 TTTTTGTTATCGGTGAGCACCTCGACCAGA 20 44 1 CGGTGAGCAC 0.980963 -42 AGCATTGTTTCGAAGGGCGCGTGCGTGTAC 25 15 1 CGAAGGGCGC 0.762919 -141 AGTTTGAATGCCCTGAGCACGGGCGGCAGC 26 28 1 CCCTGAGCAC 0.924698 -60 ********** Masking position 8 Map Score: 3.88527 Number of sites scoring better than the average of aligned sites = 875 Number in coding regions = 801 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 11 ********** No masking Map Score: 2.8375e-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 12 ********** No masking Map Score: 2.8375e-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 13 ********** No masking Map Score: 2.8375e-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