AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_hpyl_reg_100.orf -o00190_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0031 108 H. pylori predicted coding region HP0031 #2 HP0032 30 conserved hypothetical protein #3 HP0144 300 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound (fixN) #4 HP0193 214 fumarate reductase, cytochrome b subunit (frdC) #5 HP0620 300 inorganic pyrophosphatase (ppa) #6 HP0828 121 ATP synthase F0, subunit a (atpB) #7 HP1010 300 polyphosphate kinase (ppk) #8 HP1067 290 chemotaxis protein (cheY) #9 HP1132 22 ATP synthase F1, subunit beta (atpD) #10 HP1137 110 ATP synthase F0, subunit b' (atpF') #11 HP1212 132 ATP synthase F0, subunit c (atpE) #12 HP1260 101 NADH-ubiquinone oxidoreductase, NQO7 subunit (NQO7) #13 HP1422 24 isoleucyl-tRNA synthetase (ileS) #14 HP1423 101 conserved hypothetical protein Motif number 1 GTATAATACCAAAACTTCATTTAAGGTTGGTTCT 1 84 1 AAAACTTTAA 0.966385 -25 GGCTAAAGGTTAAACATGATTAAACAAACCCTCA 3 123 0 TAAACTTTAA 0.86753 -178 ATTTGGCTTAAAAATGCCATTCAAATGGGATTGA 3 170 1 AAAATCTTAA 0.788338 -131 ACAATGTTACAGAAAAAGATTAAAAATTAAGCTT 3 210 1 AGAAAATTAA 0.650038 -91 TCAACAAAGATAAACATAATTATAAAATTTTATC 3 253 0 TAAACTTTTA 0.461278 -48 AAATTGAGAAAAAATTCAATTCAAAGGGGCTATT 4 87 0 AAAATCTTAA 0.788338 -128 TGTTTATAAGAAAAATTATTTCAAATGTAGTAGA 4 127 1 AAAAATTTAA 0.973848 -88 ATTAAACACTAGAAAGTGCTTAAAAGCCTTTCAC 5 178 1 AGAAATTTAA 0.939493 -123 CTTTGAATAAAAAGACTTATTCTAACATAAAGCC 5 268 0 AAAGATTTTA 0.687962 -33 CAAATCGTTAAAAAACTCGTTAAAAAGCTTGGTT 6 30 1 AAAAATTTAA 0.97385 -92 ATTAAGTTTTAAAAACTCATTAAACCAAGCTTTT 6 52 0 AAAAATTTAA 0.97385 -70 AAAGTTTCTCTAAGCCTTATTGAAAATTTCCTTA 6 95 0 TAAGCTTTAA 0.747769 -27 TTTAACCCTAAAAGATCGCTTAAAATTTTTTTAG 7 16 0 AAAGACTTAA 0.89814 -285 TTTTTTGAATAAAACTTCATTTAACCCTAAAAGA 7 35 0 AAAACTTTAA 0.966385 -266 GTTTTACAAAAAAGAGTTTTTAAACAACAACTAA 7 73 1 AAAGATTTAA 0.944005 -228 CATGACTTTTTAAAAAAGCTTCAATGATTATCAT 7 216 1 TAAAAATTAA 0.503638 -85 TAGAAATCCTTTAAATCATCATGTT 7 286 0 AGAAACTTAA 0.890362 -15 TATCGCACTCAAAGAGTTATTTTATTACTTTTAA 8 61 1 AAAGATTTTA 0.687951 -230 CTGTTTAAAAAGAGCCTAATTTAAATGCAATCTT 8 252 1 AGAGCTTTAA 0.844383 -39 TATCTTAACAAAAAATCGCTTAAAATTTGAGAAT 10 20 0 AAAAACTTAA 0.951166 -91 CTAAAATCCTACAAAATATTTGAAACTCGCATTT 10 73 0 ACAAATTTAA 0.905155 -38 ACGCTTTTAAAAAACGCTTTTTAAAATT 11 5 0 AAAACCTTAA 0.93764 -128 AAACTAGCTTAAAAACGCTTTTAAAAAACGCTTT 11 19 0 AAAAAGTTAA 0.789215 -114 AATACAAGCAAGAATTTATTTTAATACAAACTAG 11 46 0 AGAATTTTAA 0.748051 -87 CTGAAAAAATAAAAATTATTTTAACATTTC 12 7 0 AAAAATTTAA 0.97367 -95 ACGATTAGCAAAAACATGGTTTAATTGGCTTTGT 12 44 1 AAAACTTTAA 0.966384 -58 CAGACTCTCAAACTCCTTTAATTACTAGCAA 12 81 0 TCAAATTTAA 0.684833 -21 ACAAATTCCTTAAAAAGAGTGGTG 14 1 1 ACAAATTTAA 0.905156 -101 ***** * ** ** Masking position 10 Map Score: 38.6956 Number of sites scoring better than the average of aligned sites = 1563 Number in coding regions = 1233 Number in noncoding regions = 330 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 2 GTAGCAATTTGGCTTAAAAATGCCATTCAA 3 164 1 GGCTTAAAAA 0.893341 -137 AATTTTATCTTTTTCAAAAAGCTTAATTTT 3 232 0 TTTTCAAAAA 0.696615 -69 TATCTAATAGCGTTTAAAAAATGTAAATTT 4 52 1 CGTTTAAAAA 0.947794 -163 AAGGGGCTATTGTTTAAAATTTACATTTTT 4 68 0 TGTTTAAAAT 0.819811 -147 AAAGCATGCTTGTTTAAAGAAACAGGGCAA 5 61 0 TGTTTAAAGA 0.547475 -240 CACTAGAAAGTGCTTAAAAGCCTTTCACAA 5 184 1 TGCTTAAAAG 0.651983 -117 GCTTAAAAGCCTTTCACAAATACAGCAGAC 5 195 1 CTTTCACAAA 0.593633 -106 ACGATACGCTCCTTTAAAAACCCCTAAAGA 5 223 1 CCTTTAAAAA 0.732372 -78 CCCCTAAAGAGGTTTAAAAAGAGCGGGCTT 5 243 1 GGTTTAAAAA 0.951292 -58 GTCTTGTTTTCTTTTACAAT 6 1 0 CTTTTACAAT 0.531332 -121 CAAGACAAATCGTTAAAAAACTCGTTAAAA 6 25 1 CGTTAAAAAA 0.835088 -97 TTAAAAAACTCGTTAAAAAGCTTGGTTTAA 6 37 1 CGTTAAAAAG 0.541715 -85 TAGCAATTAAGTTTTAAAAACTCATTAAAC 6 61 0 GTTTTAAAAA 0.813581 -61 AAACGCTAAAAAAATTTTAAGCG 7 4 1 CGCTAAAAAA 0.678156 -297 CCTAAAAGATCGCTTAAAATTTTTTTAGCG 7 14 0 CGCTTAAAAT 0.771699 -287 AAAAAATGAAGTTTTACAAAAAAGAGTTTT 7 63 1 GTTTTACAAA 0.736662 -238 GCTTAGTTGTTGTTTAAAAACTCTTTTTTG 7 79 0 TGTTTAAAAA 0.865453 -222 CATTGAAGCTTTTTTAAAAAGTCATGGTCG 7 212 0 TTTTTAAAAA 0.49618 -89 TAAATCATCATGTTTAAAAATCAGTTTGTT 7 270 0 TGTTTAAAAA 0.865453 -31 TCATTGGATGGTTTGAAAAAAGAAAGACAA 8 26 0 GTTTGAAAAA 0.484458 -265 CTATGATAATCGTTTAAAAGTAATAAAATA 8 78 0 CGTTTAAAAG 0.851865 -213 AAACTGAATTTTTTTACAAATAAGAACGCT 8 113 1 TTTTTACAAA 0.666704 -178 ACGCTTTGGCTGTTTAAAAAGAGCCTAATT 8 243 1 TGTTTAAAAA 0.865453 -48 AACAAAAAATCGCTTAAAATTTGAGAATAT 10 18 0 CGCTTAAAAT 0.771699 -93 ACTCGCATTTGTTATAAAAACATTAACTCT 10 53 0 GTTATAAAAA 0.325589 -58 TAAAAAACGCTTTTTAAAATT 11 2 0 TTTTTAAAAT 0.592129 -131 CTTAAAAACGCTTTTAAAAAACGCTTTTTA 11 16 0 CTTTTAAAAA 0.563628 -117 CGTTCCTCTACTTTCAAAAATACAAGCAAG 11 68 0 CTTTCAAAAA 0.829011 -65 TTCGCACTCCGTTTCAAAAATTAGGCTTGA 11 112 0 GTTTCAAAAA 0.767287 -21 ACAAATTCCTTAAAAAGAGTGGTGGC 14 7 1 TCCTTAAAAA 0.534245 -95 ********** Masking position 6 Map Score: 33.6165 Number of sites scoring better than the average of aligned sites = 2198 Number in coding regions = 1776 Number in noncoding regions = 422 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 3 TATTATACCAAATAAACCCTAATGACCCGCTG 1 60 0 AAAAACCTAA 0.963915 -49 TTGGTATAATACCAAAACTTCATTTAAGGTTG 1 81 1 ACAAACTTCA 0.849484 -28 AAGAACCAACCTTAAATGAAGTTTT 1 94 0 AACAACTTAA 0.955926 -15 AACATGATTAAACAAACCCTCATCATTCTTGC 3 113 0 AAAAACCTCA 0.922648 -188 ACAGAAAAAGATTAAAAATTAAGCTTTTTGAA 3 218 1 ATAAAATTAA 0.434018 -83 TTTTCTTATAAACAAAACCTAAATTGAGAAAA 4 109 0 AAAAACCTAA 0.963915 -106 GCTCCTAAAAACTCAAAATTAACCTAAAATCG 4 186 0 ACCAAATTAA 0.582622 -29 TTCAAAATGCAAAAAAGCCTGACATTTCATTA 5 102 1 AAAAACCTGA 0.772086 -199 ACGCTCCTTTAAAAACCCCTAAAGAGGTTTAA 5 228 1 AAAACCCTAA 0.728695 -73 AAACGCTAAAAAAATTTTAAGCGATCTTTT 7 9 1 AAAAATTTAA 0.549628 -292 TCATTTTTTGAATAAAACTTCATTTAACCCTA 7 40 0 AAAAACTTCA 0.916585 -261 ATGACTTTTTAAAAAAGCTTCAATGATTATCA 7 217 1 AAAAACTTCA 0.916585 -84 TTATCATAGCAAACAAACTGAATTTTTTTACA 8 99 1 AACAACTGAA 0.685613 -192 TGGCTGTTTAAAAAGAGCCTAATTTAAATGCA 8 249 1 AAAGACCTAA 0.749764 -42 CCTAATTTAAATGCAATCTTAAAAGGAGAAGC 8 266 1 ATCAACTTAA 0.843597 -25 AAAAACATTAACTCTATCTTAACAAAAAATCG 10 36 0 ACCTACTTAA 0.597848 -75 ATTTTAATACAAACTAGCTTAAAAACGCTTTT 11 31 0 AACTACTTAA 0.74322 -102 TCGAAATGAAAATCAAGCCTAATTTTTGAAAC 11 100 1 AACAACCTAA 0.959256 -33 AGACAAAAGACTAAGGATTAATCA 13 3 1 ACAAAACTAA 0.632248 -22 TAAGTTATGGATAAAAACTTAAAGAATAGGGT 14 69 1 ATAAACTTAA 0.859545 -33 ** *** ***** Masking position 1 Map Score: 16.4952 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 641 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 4 GCTGAAAGCTCAAAGATAAAGCGCTACAAT 1 34 0 CAAAGATAAA 0.785487 -75 GGTATAATACCAAAACTTCATTTAAGGTTG 1 83 1 CAAAACTTCA 0.842178 -26 CATGAAAATACAAAAATAAAGCCAAGCGTT 3 25 1 CAAAAATAAA 0.828348 -276 CGGTGCGCCTAAAAAATACAACAGCGTTGC 3 70 1 AAAAAATACA 0.861461 -231 ATGTTACAGAAAAAGATTAAAAATTAAGCT 3 213 1 AAAAGATTAA 0.864384 -88 ATCTTTTTCAAAAAGCTTAATTTTTAATCT 3 226 0 AAAAGCTTAA 0.885884 -75 AGCTTTTTGAAAAAGATAAAATTTTATAAT 3 239 1 AAAAGATAAA 0.851974 -62 GTAAATTCAACAAAGATAAACATAATTATA 3 263 0 CAAAGATAAA 0.785487 -38 CTAAATTGAGAAAAAATTCAATTCAAAGGG 4 93 0 AAAAAATTCA 0.873195 -122 TCTTATAAACAAAACCTAAATTGAGAAAAA 4 108 0 AAAACCTAAA 0.71267 -107 AACTGCTCCTAAAAACTCAAAATTAACCTA 4 192 0 AAAAACTCAA 0.658331 -23 AATGAGTTTTTAAAACTTAATTGCTACAAT 6 65 1 TAAAACTTAA 0.717859 -57 ATTTTTTGAATAAAACTTCATTTAACCCTA 7 40 0 TAAAACTTCA 0.675935 -261 AGTTTTATTCAAAAAATGAAGTTTTACAAA 7 53 1 AAAAAATGAA 0.612685 -248 GACTTTTTAAAAAAGCTTCAATGATTATCA 7 219 1 AAAAGCTTCA 0.864205 -82 CTTATTTGTAAAAAAATTCAGTTTGTTTGC 8 107 0 AAAAAATTCA 0.873195 -184 ATTTGTTATAAAAACATTAACTCTATCTTA 10 47 0 AAAACATTAA 0.692783 -64 CCTCTACTTTCAAAAATACAAGCAAGAATT 11 64 0 CAAAAATACA 0.798227 -69 TCGTTAGCTGAAAAAATAAAAATTATTTTA 12 18 0 AAAAAATAAA 0.883521 -84 GCTAACATGCTAAAACTAAAACCCTTATAA 14 42 1 TAAAACTAAA 0.696753 -60 AGTTATGGATAAAAACTTAAAGAATAGGGT 14 71 1 AAAAACTTAA 0.910965 -31 ********** Masking position 7 Map Score: 23.7251 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 567 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 5 TAAAGCGCTACAATCTCGCTTAGAAAAAGGA 1 17 0 CAATCTCCTT 0.981934 -92 TGTAATAACTCAATCCCATTTGAATGGCATT 3 182 0 CAATCCCTTT 0.958215 -119 TTCATAAACAACCCCACTTACCATGATGT 5 9 1 CAACCCCCTT 0.96229 -292 TGCAATCTCCTTTGAATAAAAAG 5 288 0 CAATCTCTTT 0.965112 -13 ACTCGCGCTACAATCTCCCTTTTTGATTGCG 7 111 1 CAATCTCCTT 0.981935 -190 GCTACTCCGACCATGACTTTTTAAAAAAGCT 7 205 1 CCATGACTTT 0.759781 -96 TCAAACCATCCAATGACCCTTTATCGCACTC 8 40 1 CAATGACCTT 0.927079 -251 CAGACTCTCAAACTCCTTTAATTACTAGC 12 83 0 CAAACTCTTT 0.851711 -19 TAGCATTCAGCCACCACTCTTTTTAAGGAAT 14 15 0 CCACCACCTT 0.920349 -87 ******* *** Masking position 3 Map Score: 7.13489 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 232 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 TTTGTGTCCTTTTTCTAAGCGAGATTGT 1 8 1 CCTTTTTTAA 0.815962 -101 CATTCTTGCCCCTTTTTTTATCGCAACGCTG 3 91 0 CCTTTTTTAT 0.951896 -210 GCAATACTCCTATTTGTAGTAAATTCAAC 3 282 0 CCTATTTTAG 0.760474 -19 TGAACGATCCTTATTTTATAGGTGGTAAC 4 9 1 CCTTATTTAT 0.937601 -206 GGTAACTATCCCTTATTATATCTAATAGCGT 4 34 1 CCTTATTTAT 0.937601 -181 TTTGCCTTGCCCTGTTTCTTTAAACAAGCAT 5 55 1 CCTGTTTTTT 0.701826 -246 CCTAGAAAATCCTATTTTGATAATCTTTTTT 5 140 1 CCTATTTGAT 0.858645 -161 GCTACAATCTCCCTTTTTGATTGCGGAGTAT 7 117 1 CCCTTTTGAT 0.79204 -184 GTCTCTAACGCCTTATAATAATAAATCGTTC 8 214 0 CCTTATATAA 0.496291 -77 AGTGCTTCTCCTTTTAAGATTGCATTTAAA 8 271 0 CCTTTTAGAT 0.793391 -20 AACCTATTTCTTTCCTAAAATCC 10 98 0 CCTATTTTTT 0.839356 -13 GAAAATCAAGCCTAATTTTTGAAACGGAGTG 11 107 1 CCTAATTTTG 0.578948 -26 AAACTAAAACCCTTATAAGTTATGGATAAAA 14 54 1 CCTTATAGTT 0.624494 -48 GTTTATTTTACCCTATTCTTTAAGTTTTTAT 14 79 0 CCCTATTTTT 0.713268 -23 ******* *** Masking position 6 Map Score: 6.17434 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 482 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 7 CTTATCCATGCTATTTGGCTACTTGG 2 7 0 CTATTTGGCT 0.976667 -24 AATTGCTACTATCTTTGGCTAAAGGTTAAA 3 143 0 ATCTTTGGCT 0.930283 -158 AAGATAGTAGCAATTTGGCTTAAAAATGCC 3 158 1 CAATTTGGCT 0.963089 -143 CCACTTACCATGATGTGGCTAATTTTACCT 5 24 1 TGATGTGGCT 0.678224 -277 CTAATTTTACCTATTTGCCTTGCCCTGTTT 5 42 1 CTATTTGCCT 0.844241 -259 AGTTTTTTAACGATTTGTCTTGTTTTCTTT 6 17 0 CGATTTGTCT 0.781876 -105 ACCGACAATAATCATTGGCTAAATGGAGCG 8 150 0 ATCATTGGCT 0.768028 -141 GCGTTAGAGACGCTTTGGCTGTTTAAAAAG 8 234 1 CGCTTTGGCT 0.962541 -57 GATTGCATTTAAATTAGGCTCTTTTTAAAC 8 254 0 AAATTAGGCT 0.767179 -37 TCCGTTTCAAAAATTAGGCTTGATTTTCAT 11 105 0 AAATTAGGCT 0.767179 -28 AAAACATGGTTTAATTGGCTTTGTCATTTG 12 54 1 TTAATTGGCT 0.739123 -48 ********** Masking position 10 Map Score: 5.85733 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 370 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 CTTTAGCCAAAGATAGTAGCAATTTGGCTTAA 3 149 1 AGTATAGCAA 0.79871 -152 TGATCATAAAAAAGATTATCAAAATAGGATTT 5 146 0 AAGATATCAA 0.950066 -155 AAAAAGCTTCAATGATTATCATTTCATTATAT 7 228 1 AAGATATCAT 0.908931 -73 ATTACTTTTAAACGATTATCATAGCAAACAAA 8 84 1 AAGATATCAT 0.908931 -207 AAATCGTTCCAAATAATAGCATGTTTTGATTA 8 191 0 AATATAGCAT 0.908931 -100 GCAATCTTAAAAGGAGAAGCACT 8 278 1 AAGAAAGCAC 0.861339 -13 CTACTTTCAAAAATACAAGCAAGAATTTATTT 11 59 0 AATAAAGCAA 0.895999 -74 AACGATTCGAAATGAAAATCAAGCCTAATTTT 11 94 1 AAGAAATCAA 0.895999 -39 TTTTTCAGCTAACGATTAGCAAAAACATGGTT 12 33 1 AAGATAGCAA 0.978063 -69 AAACTCCTTTAATTACTAGCAAATGACAAAGC 12 71 0 AATATAGCAA 0.950066 -31 ** ** ****** Masking position 5 Map Score: 7.79674 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 110 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ATACCAAATAAACCCTAATGACCCGCTGAAAGCTCA 1 52 0 AACCCAACGC 0.989673 -57 GTTAGGTCTTAACCCATCCGGTGCGCCTAAAAAATA 3 52 1 AACCCCGCGC 0.995581 -249 AACTTCATTTAACCCTAAAAGATCGCTTAAAATTTT 7 21 0 AACCCAGCGC 0.998004 -280 CGACCTCACCCACCCCAAGGGTGCGCGCTAATCAGG 7 155 0 CACCCAGCGC 0.995581 -146 TACAAATAAGAACGCTCATTGAACGCTCCATTTAGC 8 127 1 AACGCAGCGC 0.993009 -164 ***** * * *** Masking position 2 Map Score: 2.17136 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 12 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 GCAATACTCCTATTTGTAGTAA 3 289 0 AATACTCCTA 0.870707 -12 CATTTCATTAAAACCCCCTAGAAAATCCTA 5 124 1 AAACCCCCTA 0.981937 -177 CGCTCCTTTAAAAACCCCTAAAGAGGTTTA 5 229 1 AAAACCCCTA 0.980529 -72 CGTGGGTTTGAATCCCGCTACTCCGACCAT 7 189 1 AATCCCGCTA 0.915072 -112 TGCTAAAACTAAAACCCTTATAAGTTATGG 14 49 1 AAAACCCTTA 0.9061 -53 ********** Masking position 2 Map Score: 0.181558 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 293 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 ********** No masking Map Score: -5.29822e-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: -5.29822e-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: -5.29822e-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