AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imalT_ecoli_bsub_100.orf -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 malP 300 maltodextrin phosphorylase #2 malS 300 alpha-amylase #3 malF 153 part of maltose permease, periplasmic #4 malE_malK 364 malE: periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis, malK: ATP-binding component of transport system for maltose #5 lamB 71 phage lambda receptor protein; maltose high-affinity receptor #6 malM 242 periplasmic protein of mal regulon #7 glgD 23 ADP-glucose pyrophosphorylase #8 glgB 300 1,4-alpha-glucan branching enzyme #9 yurJ 181 similar to multiple sugar ABC transporter (ATP-binding protein) #10 yurN 57 similar to sugar permease #11 yurO 80 similar to multiple sugar-binding protein #12 yurP 215 similar to opine catabolism #13 yvfL 39 similar to maltodextrin transport system permease #14 yvfK 140 similar to maltose/maltodextrin-binding protein #15 yvdH 39 similar to maltodextrin transport system permease #16 yvdG 95 similar to maltose/maltodextrin-binding protein #17 yvdF 112 similar to glucan 1,4-alpha-maltohydrolase #18 msmX 120 multiple sugar-binding transport ATP-binding protein Motif number 1 CTCATCCTGCGGGGGATTAGGCAGGGAGGAGT 1 209 0 GGGGATAGGC 0.993815 -92 GGCGGATGAGTCCTTATTGCTG 2 289 0 GCGGATAGTC 0.848364 -12 GCTGTGAAATGCCGGATGCGGCGTGAACGCCT 3 12 1 GCGGATCGGC 0.501295 -142 GGTTTTGTAGGCCGGACAAGGCGTTCACGCCG 3 30 0 GCGGACAGGC 0.892973 -124 ACGCTGACGCGTCTTATCAGGCCTACATACGT 3 65 0 GCTTATAGGC 0.598507 -89 ACGCGTCAGCGTCGCATCAGGCAGTTGTTGTC 3 85 1 GCGCATAGGC 0.724814 -69 GGCAGTTGTTGTCGGATAAGGCGTGAAAGCCT 3 104 1 GCGGATAGGC 0.927438 -50 CTCATTCCAGGACGGATAAGGCTTTCACGCCT 3 122 0 GCGGATAGGC 0.79222 -32 GCTTTTTTATGGGGGAGGAGGCGGGAGGATGA 4 107 1 GGGGAGAGGC 0.959929 -258 CAAAACCTGGGCCGGATAAGGCGTTTACGCCG 6 14 1 GCGGATAGGC 0.536743 -229 AGGCGTTTACGCCGCATTCGGCAACCAACGCC 6 32 1 GCGCATCGGC 0.527748 -211 ACGCGCAAGCGTCGCATCAGGCGTTGGTTGCC 6 51 0 GCGCATAGGC 0.724814 -192 ACGCTTGCGCGTCTTATCAGGCCTACAACGGC 6 71 1 GCTTATAGGC 0.598507 -172 TCAAATGTAGGCCGGATAAGGCGTTTACGCCG 6 105 1 GCGGATAGGC 0.536743 -138 CTGTTTTTATGCCGGATGCGGCGTAAACGCCT 6 123 0 GCGGATCGGC 0.501295 -120 * ***** **** Masking position 6 Map Score: 55.7041 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 144 Number in noncoding regions = 542 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 GGCTGAATTTTGCGATAACCCCCACATTTTCT 2 156 0 TGCGTACCCC 0.835058 -145 AGCAAGGGTGAGCGATCTCGCGCAAAAAACGG 2 186 0 AGCGTTCGCG 0.869133 -115 GGCCGGACAAGGCGTTCACGCCGCATCCGGCA 3 21 0 GGCGTACGCC 0.537677 -133 TGCCTGATGCGACGCTGACGCGTCTTATCAGG 3 76 0 GACGTACGCG 0.987014 -78 GGACGGATAAGGCTTTCACGCCTTATCCGACA 3 113 0 GGCTTACGCC 0.896897 -41 CACACAAAGCGACGGTGGGGCGTAGGGGCAAG 4 258 1 GACGTGGGCG 0.885636 -107 GGCCGGATAAGGCGTTTACGCCGCATTCGGCA 6 23 1 GGCGTACGCC 0.537677 -220 CGCCTGATGCGACGCTTGCGCGTCTTATCAGG 6 60 1 GACGTGCGCG 0.986218 -183 GGCCGGATAAGGCGTTTACGCCGCATCCGGCA 6 114 1 GGCGTACGCC 0.537677 -129 TAATCAGAGGGGCTTTCGCCCCTTTCAGATAA 6 162 0 GGCTTGCCCC 0.918517 -81 GCGGTAGCCAGGCAATAGCGCGCTAAACCCGA 6 194 0 GGCATGCGCG 0.936568 -49 GCCCTTTCACGGCGGTAACACGGGTTCGAATC 8 35 1 GGCGTACACG 0.960138 -266 TATTCTTCCGGACGCTATCCCGCCGTT 15 6 0 GACGTTCCCG 0.9022 -34 **** * ***** Masking position 6 Map Score: 23.49 Number of sites scoring better than the average of aligned sites = 1715 Number in coding regions = 1243 Number in noncoding regions = 472 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 GGGGGATTAGGCAGGGAGGAGTTGCGGGGA 1 201 0 GCAGGGAGGA 0.851098 -100 CCTAATCCCCCGCAGGATGAGGAAGGTCAA 1 220 1 CGCAGGATGA 0.876581 -81 AGGATGAGAAGCAAGGGTGAGCGATCTCGC 2 197 0 GCAAGGGTGA 0.97004 -104 GCGGTAAGTCCACAGGATGAGAAGCAAGGG 2 210 0 CACAGGATGA 0.906301 -91 CAGGTTGTTACAAAGGGAGAAGGGC 4 6 0 CAAAGGGAGA 0.779747 -359 CCATAAAAAAGCCAGGGGGTGGAGGATTTA 4 89 0 GCCAGGGGGT 0.803778 -276 TGGGGGAGGAGGCGGGAGGATGAGAACACG 4 116 1 GGCGGGAGGA 0.848465 -249 GGGCGTAGGGGCAAGGAGGATGGAAAGAGG 4 275 1 GCAAGGAGGA 0.958143 -90 TATGATGTCAGAAAGGATGATTAC 8 287 1 GAAAGGATGA 0.950948 -14 CGGGTCAAAAGATAGGGGGACTTTTCTG 9 164 1 GATAGGGGGA 0.900089 -18 ATCAAAGAAAAGGTGAAGCTTCGCAC 10 7 1 GAAAAGGTGA 0.686194 -51 CATTCCTACCGAAAGGGTGACAATCA 14 125 1 GAAAGGGTGA 0.977824 -16 TTTCGTAAATAGAAGGAGGAAAAGAG 16 80 1 AGAAGGAGGA 0.760795 -16 TGTTATCGGTAACAGGGTGAAAAGGATTGT 17 22 1 AACAGGGTGA 0.857167 -91 AAACGGAAATCAAAGGGGGAAAC 17 100 1 CAAAGGGGGA 0.973055 -13 CACGAAAAATGGCTGGGTGATTTTATGAAC 18 23 1 GGCTGGGTGA 0.743816 -98 TTTACAATAACAAAGGGGGATGTTAG 18 105 1 CAAAGGGGGA 0.973055 -16 ********** Masking position 6 Map Score: 18.4995 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 530 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 GGAGTTCCACTTTTCTTAGATTTTCAACACAA 1 278 0 TTTTCTTATT 0.746892 -23 AACCCCCACATTTTCTGCGATTTAGCGCCAAT 2 140 0 TTTTCTGATT 0.950382 -161 CGCTGGCAAACTGTCTGAAATCGCAGCAATAA 2 266 1 CTGTCTGATC 0.963759 -35 CCCACCGTCGCTTTGTGTGATCTCTGTTACAG 4 245 0 CTTTGTGATC 0.890011 -120 GTAATCATCCTTTCTGACATCATAGTTTTCA 8 280 0 CTTTCTGATC 0.985773 -21 ACAACTTGGTCTTTCTGTTATTTTTAGAGTAA 9 115 0 CTTTCTGATT 0.973284 -67 TATAGACCCTTTGTCTGTCATCCGAATAAATT 12 88 1 TTGTCTGATC 0.933253 -128 GTCAATATTATTTTCTGAAATTTCTCAATAAT 12 117 0 TTTTCTGATT 0.950382 -99 CATTCTGTTATCGGTAACAAAT 16 1 1 CATTCTGATC 0.945032 -95 GCGCCTTATTCTGTTATCGGTAACAGGG 17 7 1 TATTCTGATC 0.90039 -106 ATTGTAAACGCTTTCTTATATTGAGTGTAACA 18 81 0 CTTTCTTATT 0.848771 -40 ******* *** Masking position 10 Map Score: 12.122 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 189 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AAGGAGGATGGAAAGAGGTTGCCGTATAAA 4 287 1 GAAAGAGGTT 0.959355 -78 GCCCTTTCCTGAAAGCGCTTATACTTATAG 8 218 0 GAAAGCGCTT 0.994452 -83 GCGCTTTCAGGAAAGGGCTTTTTTTTATTT 8 230 1 GAAAGGGCTT 0.980753 -71 CGGTAGGAATGAAAGCGCTTTAAAGATAAT 14 106 0 GAAAGCGCTT 0.994452 -35 TTGTCCTATAGAAAGCGGTTACAACAACTT 16 36 0 GAAAGCGGTT 0.991942 -60 CTCAATATAAGAAAGCGTTTACAATAACAA 18 88 1 GAAAGCGTTT 0.978235 -33 ********** Masking position 4 Map Score: 9.89618 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 32 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 CCTGCGGGGGATTAGGCAGGGAGGAGTTGC 1 206 0 ATTAGGCAGG 0.687249 -95 GTTTCGGTTTTGTAGGCCGGACAAGGCGTT 3 37 0 TGTAGGCCGG 0.994567 -117 CCGAAACGTATGTAGGCCTGATAAGACGCG 3 60 1 TGTAGGCCTG 0.973007 -94 GGATAAGGCGTTTACGCCGCATTCGGCAAC 6 27 1 TTTACGCCGC 0.948119 -216 TGACAGCCGTTGTAGGCCTGATAAGACGCG 6 78 0 TGTAGGCCTG 0.973007 -165 GGCTGTCAAATGTAGGCCGGATAAGGCGTT 6 100 1 TGTAGGCCGG 0.994567 -143 GGATAAGGCGTTTACGCCGCATCCGGCATA 6 118 1 TTTACGCCGC 0.948119 -125 ACAACCTGTTTTTATGCCGGATGCGGCGTA 6 130 0 TTTATGCCGG 0.956516 -113 TTCCGTTTTATTGAAGCCGGCTCATAGTTT 17 78 0 TTGAAGCCGG 0.837119 -35 ********** Masking position 4 Map Score: 10.4509 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 155 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 7 TATCTAAGTGCAAAAAATGGCCGTTGCGTATT 1 80 0 CAAAAAAGCC 0.990768 -221 CGATCTCGCGCAAAAAACGGCTGAATTTTGCG 2 174 0 CAAAAAAGCT 0.960857 -127 CCTCCTCCCCCATAAAAAAGCCAGGGGGTGGA 4 96 0 CATAAAAGCC 0.985272 -269 GAGATGCGCACATAAAATCGCCACGATTTTTG 4 197 0 CATAAAAGCC 0.985272 -168 TTCGAAGAAATAAAAAAAAGCCCTTTCCTGAA 8 235 0 TAAAAAAGCC 0.922986 -66 GGTCTATATGCGAAAAAATGCCCAAATCAAAA 12 64 0 CGAAAAAGCC 0.983812 -152 GAAATATGCACGAAAAATGGCTGGGTGATTTT 18 15 1 CGAAAAAGCT 0.932888 -106 GGGCAGCGTTCATAAAATCACCCAGCCATTTT 18 28 0 CATAAAAACC 0.881945 -93 ******* *** Masking position 6 Map Score: 8.87485 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 130 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 TAATCATTCCAACACCTTATATTTTTCACAA 2 11 1 AAACCTTATA 0.874053 -290 ATAACGTCATAATACATTATAATATAAATAA 9 33 0 AAACATTATA 0.939043 -149 ATAATGTATTATGACGTTATAATACAAATTT 9 44 1 ATACGTTATA 0.96706 -138 ATAATGTTATATAACATTATAGTCTAATGCA 11 32 0 ATACATTATA 0.972537 -49 ATAATGTTATATAACATTATAGTCTAATGTC 11 43 1 ATACATTATA 0.972537 -38 ATAACGTTATATAACATTATATATTGTTATA 12 170 0 ATACATTATA 0.972537 -46 ATAATGTTATATAACGTTATATAATAAAAAC 12 181 1 ATACGTTATA 0.96706 -35 ** ******** Masking position 4 Map Score: 7.10644 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 12 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 AACTGTTTCACTCCTTTACTTAATTTATAG 1 29 1 CTCCTTTACT 0.703207 -272 CACTTAGATACAGATTTTCTGCGCTGTATT 1 102 1 CAGATTTTCT 0.726143 -199 TGGTTGAGATCACATTTCCTTGCTCATCCC 1 175 1 CACATTTCCT 0.979349 -126 AGGAGTTCCACTTTTCTTAGATTTTCAA 1 283 0 CACTTTTCTT 0.706927 -18 CGATAACCCCCACATTTTCTGCGATTTAGC 2 146 0 CACATTTTCT 0.96144 -155 TTTCTTTTTTCACATCACCTGTGACAGGCT 5 31 0 CACATCACCT 0.754345 -41 TGCGAAGCTTCACCTTTTCTTTGAT 10 6 0 CACCTTTTCT 0.964302 -52 TGAAGCTTCGCACCTTTTCTTTTTATAAAG 10 24 1 CACCTTTTCT 0.964302 -34 GGGTATCTCATCTCCTTTATAAAAAG 10 42 0 CTCATCTCCT 0.904083 -16 CGTTTTCACCTCTCTTACAATACAAA 13 24 0 CACCTCTCTT 0.799631 -16 AGTTTGTTTACACATTTTCTCAGGCATGCT 14 74 1 CACATTTTCT 0.96144 -67 CTCTTTTCCTCCTTCTATTT 16 86 0 CTCTTTTCCT 0.860575 -10 ********** Masking position 5 Map Score: 11.4142 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 207 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 10 CAAGGTTTTTTTGTTTTTATAAATCATGATAT 8 101 1 TTTTTTATAA 0.931879 -200 GATTTTGTTCTTTATTTTAAAAACAGACTACA 8 139 1 TTTTTTAAAA 0.710348 -162 TAACCTATTATTTATATTATAATGTATTATGA 9 26 1 TTTATTATAA 0.943876 -156 AAAATGTAAATTTGTATTATAACGTCATAATA 9 50 0 TTTATTATAA 0.943876 -132 ATTTACATTTTTTATTTTAGAAATATAGCAAA 9 71 1 TTTTTTAGAA 0.784239 -111 TTCGCACCTTTTCTTTTTATAAAGGAGATGAG 10 30 1 TTTTTTATAA 0.93175 -28 TCACTCCTCGTTTTTATTATATAACGTTATAT 12 189 0 TTTATTATAT 0.726536 -27 GAAAGCTAGATTTGTATTGTAAGAGAGGTGAA 13 14 1 TTTATTGTAA 0.891664 -26 ACATCCCCCTTTGTTATTGTAAACGCTTTCTT 18 96 0 TTTATTGTAA 0.891085 -25 ** ******** Masking position 7 Map Score: 3.57325 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 16 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 TTTGCACTTAGATACAGATTTTCTGCGCTGTAT 1 98 1 GTCAGATTTC 0.922708 -203 ACGTGACATAGTTTCAGATTTGGACTATTCCTT 2 94 0 GTCAGATTGG 0.976102 -207 TGTGATCTCTGTTACAGAATTGGCGGTAATGTG 4 229 0 GTCAGATTGG 0.976102 -136 CACATCACCTGTGACAGGCTTTGTGTGTTTTGT 5 18 0 GGCAGGTTTG 0.948453 -54 CGCCTTATCCGGCCCAGGTTTTGCTA 6 4 0 GCCAGGTTTG 0.980129 -239 CTACCGCTGAGCTCCAGATTTTGAGGTGAAAAC 6 219 1 GTCAGATTTG 0.986326 -24 ATCATGATATGTCTTAGATTTTGTTCTTTATTT 8 123 1 GCTAGATTTG 0.906775 -178 TATTGAAGCCGGCTCATAGTTTGAAAGTATCAT 17 67 0 GCCATATTTG 0.906775 -46 * * **** **** Masking position 6 Map Score: 3.53159 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 161 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 CGTATTTTCAAAAAGCGGAAGGTAACTCTATAAA 1 52 0 AAAAGGAAGA 0.952599 -249 TCCGGCCTACAAAACCGAAACGTATGTAGGCCTG 3 46 1 AAAAGAAAGA 0.967601 -108 AGGTGATGTGAAAAAAGAAAAGCAATGACTCAGG 5 41 1 AAAAGAAAGA 0.967601 -31 TTTTCTGAAGAAAAACGAAATATATGGAGATTTT 8 171 0 AAAAGAAAAA 0.882586 -130 AATAAATACTATAAATGAAAACTATGATGTCAGA 8 265 1 ATAAGAAACA 0.861115 -36 AAATATAGCAAAAATGGGAATCGATTACTCTAAA 9 91 1 AAAAGGAACA 0.952599 -91 CGGCTTCAATAAAACGGAAATCAAAGGGGGAAAC 17 89 1 AAAAGAAACA 0.967601 -24 **** **** * * Masking position 9 Map Score: 1.52998 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 79 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 GCGATAACCCCCACATTTTCTGCGATTTAGCG 2 145 0 CCCATTTCTG 0.822012 -156 CACGCCGCATCCGGCATTTCACAGCA 3 5 0 CCGCTTTCAC 0.964627 -149 GGTGTTTTCACGAGCACTTCACCAACAAGGAC 4 335 1 CGGCCTTCAC 0.820375 -30 GAGGGGCTTTCGCCCCTTTCAGATAATGACAA 6 156 0 CGCCTTTCAG 0.948681 -87 CCGCTGAGCTCCAGATTTTGAGGTGAAAACA 6 222 1 CCGATTTGAG 0.754762 -21 TGACTCTGCCCCCTCTTCAGTAA 7 4 0 CCCCCTTCAG 0.977426 -20 GGTTAAGACACCGCCCTTTCACGGCGGTAACA 8 23 1 CCCCTTTCAC 0.979077 -278 AGGGTAGCCTCCTTTTAACCTATTATTTA 9 8 1 CCCCTTTAAC 0.889983 -174 CATAATGGTTCTTCATTTTCAGA 11 2 0 CTCATTTCAG 0.780848 -79 AACAGCGAAGCCAGAGCTTAAGTCAAGTTCTG 12 30 1 CCGACTTAAG 0.69636 -186 AGGATTGTTCCCACAATTTCATCATGATACTT 17 44 1 CCCATTTCAT 0.82501 -69 ** ** ****** Masking position 8 Map Score: 3.32587 Number of sites scoring better than the average of aligned sites = 910 Number in coding regions = 841 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 14 ATGCAATACAGCGCAGAAAATCTGTATCTA 1 106 0 GCGCAGAAAA 0.872646 -195 CGATTCAGATTGGCGCTAAATCGCAGAAAA 2 132 1 TGGCGCTAAA 0.949458 -169 TGGCGCTAAATCGCAGAAAATGTGGGGGTT 2 142 1 TCGCAGAAAA 0.874854 -159 GTGAGCGATCTCGCGCAAAAAACGGCTGAA 2 181 0 TCGCGCAAAA 0.968318 -120 GTTACAGAATTGGCGGTAATGTGGAGATGC 4 222 0 TGGCGGTAAT 0.770986 -143 CCAGGCAATAGCGCGCTAAACCCGATAATC 6 189 0 GCGCGCTAAA 0.967698 -54 GAAGAATAGAGGGCGGAAAA 15 30 1 GGGCGGAAAA 0.948489 -10 AGCAATTCCCTCTCGCTAAAATGGGCAGCG 18 52 0 TCTCGCTAAA 0.773393 -69 ********** Masking position 8 Map Score: 2.97586 Number of sites scoring better than the average of aligned sites = 949 Number in coding regions = 889 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 15 CATTTCCTTGCTCATCCCCGCAACTCCTCC 1 187 1 CTCATCCCCG 0.97965 -114 ATCCCCGCAACTCCTCCCTGCCTAATCCCC 1 200 1 CTCCTCCCTG 0.975046 -101 CCAAACAAAACTCATCCCTGAGCGGTAAGT 2 231 0 CTCATCCCTG 0.990729 -70 TTTTGTTTGGCTTATCGCTGGCAAACTGTC 2 251 1 CTTATCGCTG 0.949681 -50 CGGATGAGTCCTTATTGCTGCGATTTCAGA 2 279 0 CTTATTGCTG 0.864449 -22 GGGGTTCTTCCTCATTCCAGGACGGATAAG 3 134 0 CTCATTCCAG 0.916494 -20 ********** Masking position 5 Map Score: 3.09508 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 93 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