AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0682 300 ketol-acid reductoisomerase (ilvC) #2 HI0737 247 acetohydroxy acid synthase II, putative #3 HI0738 71 dihydroxyacid dehydratase (ilvD) #4 HI0986 300 2-isopropylmalate synthase (leuA) #5 HI0987 85 3-isopropylmalate dehydrogenase (beta-IPM dehydrogenase) (leuB) #6 HI0988 175 3-isopropylmalate dehydratase, alpha subunit (leuC) #7 HI0989 23 3-isopropylmalate dehydratase small subunit (leuD) #8 HI1585 266 acetolactate synthase III large subunit (ilvI) #9 HI1586 300 conserved hypothetical integral membrane protein Motif number 1 TAAATCGCTGTTCTTTGCTTTGTTTCAATTTTCTT 1 41 0 TTCTTTTTTT 0.854886 -260 AATGTTGCGATTTGTGCAATTATTTTTTTTTGTGA 1 159 0 TTTGTTTTTT 0.944725 -142 TTTGCATATTTTTTTGTTGTGGTTTGATTATAGGA 1 231 0 TTTTTTGTTT 0.921468 -70 TTTTTGTCCTTAATTGTGTAAGGTT 1 286 0 TTTTTTTATT 0.88778 -15 ATATTGAAACTCTTTTCATTTTTTTACATAGGATA 2 15 0 TCTTTTTTTT 0.969439 -233 TTTTTACCGCTCTTTTGGCTTATTTATTGACTGAT 2 64 0 TCTTTTTTTT 0.969439 -184 TCACCGCACTTTTTTTCGTTTTTTTCTCTCCAAGC 2 150 1 TTTTTTTTTT 0.987628 -98 GGTGTTTGTTTCCTGTTGTTTTTATTTTGGG 2 227 0 TGTTTTTTTT 0.87913 -21 TTAGGGTTCGTTTGTATGATTAATTTCTTCGTTAA 3 25 0 TTTGTTTATT 0.628769 -47 GTCAAACTATTTTTTGGCATTTTATATTAAAAATA 4 52 0 TTTTTTTTAT 0.950001 -249 ACACAGAGGATTTTTATTTATGTTTCGTATTGTTT 4 122 1 TTTTTATTTT 0.950001 -179 TGCGGTGCGTTTTTCCTGTATTTTTTAGATAAAAA 4 268 0 TTTTCATTTT 0.802681 -33 GTGCGGTTAGTTTTTTTGTATTTTTCCCCTCTTTG 5 33 0 TTTTTATTTT 0.950001 -53 ATTATTTTTCCTATTTTTTACTTCAAAAG 5 67 0 TTTTTTTTTT 0.987628 -19 AATATTTTTCTCTATTCGTTAAGGGAAGTG 6 156 0 TTTTCTTGTT 0.723751 -20 TTTTCTTTTTCCTCTTTTGAGCC 7 6 0 TCTTTTCTTT 0.716997 -18 AAAAATAATATTTTTACTATTTTATAAAATGCGGC 8 40 1 TTTTTTTTAT 0.950001 -227 TTTTGTCGCATTTTTTTATTTTTATTGATGGAAAA 8 76 1 TTTTTTTTAT 0.950001 -191 AAAATTTAGTTTTTTATAAATTTTTCCATCAATAA 8 97 0 TTTTTATTTT 0.950001 -170 AAAAACTAAATTTTCATTTATATTTGGTTTTTTAT 8 118 1 TTTTCATTTT 0.802681 -149 TATATTTGGTTTTTTATATTTTTTTAATTGATTTT 8 136 1 TTTTTTTTTT 0.987628 -131 TTTTAATTGATTTTTTTGTTGTTTTAGTGGCTAGA 8 157 1 TTTTTTGTTT 0.921468 -110 TAGACAAATTTTTTTTACTTTGTATTATGTGAAAC 8 188 1 TTTTTTTTAT 0.950001 -79 ATTGACATAATCTGTTCGTTTTTTTAAAAGTGCGG 8 223 1 TCTGTTTTTT 0.871656 -44 ATATATTTTTTTGTGTTTATTTTCTTTATATT 9 8 1 TTTTTTTTTT 0.987628 -293 GTGTTTATTTTCTTTATATTTTTATTAAAGTTTAT 9 23 1 TCTTTTTTAT 0.883042 -278 ATTCCTTTCTTTTTTCTTCTTCGTTATCCACTCTG 9 153 0 TTTTTTTGTT 0.924454 -148 ***** ** *** Masking position 1 Map Score: 48.9489 Number of sites scoring better than the average of aligned sites = 696 Number in coding regions = 478 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 2 ATCGCTGTTCTTTGCTTTGTTTCAATTTTCTT 1 41 0 TTTGTTGTTT 0.695369 -260 TGTGCAATTATTTTTTTTTGTGAATTGGCATC 1 150 0 TTTTTTTGTG 0.84572 -151 GATTATAGGATTTTTTGTTGTTGCGTAAAGTG 1 209 0 TTTTTTTGTT 0.959179 -92 GTTTGCATATTTTTTTGTTGTGGTTTGATTAT 1 235 0 TTTTTTTGTG 0.84572 -66 TTGAAACTCTTTTCATTTTTTTACATAGGATA 2 15 0 TTTCTTTTTT 0.950434 -233 CCGCACTTTTTTTCGTTTTTTTCTCTCCAAGC 2 153 1 TTTCTTTTTT 0.950434 -95 GGTGTTTGTTTCCTGTTGTTTTTATTTTGG 2 228 0 TTTCTTTGTT 0.95062 -20 TTTAGGGTTCGTTTGTATGATTAATTTCTTCG 3 29 0 GTTTTTGATT 0.538038 -43 TTTATTTATGTTTCGTATTGTTTCTTTATCTC 4 134 1 TTTCTTTGTT 0.95062 -167 GCGGTGCGTTTTTCCTGTATTTTTTAGATAAA 4 270 0 TTTCTTATTT 0.60632 -31 CGGTTAGTTTTTTTGTATTTTTCCCCTCTTTG 5 33 0 TTTTTTTTTT 0.959024 -53 ATTATTTTTCCTATTTTTTACTTCAAAA 5 68 0 TTTCTTTTTT 0.950434 -18 TTTTCTTTTTCCTCTTTTGAGCC 7 5 0 TTTCTTTTTG 0.817299 -19 TTTGTCGCATTTTTTTATTTTTATTGATGGAA 8 77 1 TTTTTTTTTT 0.959024 -190 AAATTTTCATTTATATTTGGTTTTTTATATTT 8 125 1 TTATTTGGTT 0.509175 -142 ATATTTGGTTTTTTATATTTTTTTAATTGATT 8 137 1 TTTTTTTTTT 0.959024 -130 TTTAATTGATTTTTTTGTTGTTTTAGTGGCTA 8 158 1 TTTTTTTGTT 0.959179 -109 GACATAATCTGTTCGTTTTTTTAAAAGTGCGG 8 226 1 GTTCTTTTTT 0.824047 -41 ATATATTTTTTTGTGTTTATTTTCTTTA 9 7 1 TTTTTTGTTT 0.950434 -294 TGTTTATTTTCTTTATATTTTTATTAAAGTTT 9 24 1 CTTTTTTTTT 0.680759 -277 TCTGTTGGCATTTTGTTTGTTTTACGGTAATC 9 73 1 TTTTTTGTTT 0.950434 -228 TATTCCTTTCTTTTTTCTTCTTCGTTATCCAC 9 157 0 TTTTTTTCTT 0.773455 -144 ACAAAACGACTTTTATTTGATTTCGGCAACTA 9 187 0 TTTTTTGATT 0.826648 -114 ATAAAAGTCGTTTTGTTTGGTTGGTGGCGTGC 9 203 1 TTTTTTGGTT 0.95062 -98 CACTGTCATAGTTTTTCTGATTAACTATGGAG 9 248 1 GTTTTTGATT 0.538038 -53 **** * ***** Masking position 6 Map Score: 44.2587 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 306 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 3 AATTTTCTTAACGGCAATTTGCTGAACTCG 1 20 0 ACGGCAATTT 0.911186 -281 GTGAATTTTTACCGCTCTTTTGGCTTATTT 2 74 0 ACCGCTCTTT 0.98475 -174 GCCAATTTTCACCGCACTTTTTTTCGTTTT 2 142 1 ACCGCACTTT 0.998036 -106 CAATTTTAAACCCGCACTTTATAAGTTGCG 4 235 1 CCCGCACTTT 0.995445 -66 AGATAAAAAACCCGCAACTTATAAAGTGCG 4 247 0 CCCGCAACTT 0.876752 -54 GGAAAAACGCACCGCACTTTTGGA 4 287 1 ACCGCACTTT 0.998036 -14 AAAAAAACTAACCGCACTTTTGAAGTAAAA 5 51 1 ACCGCACTTT 0.998036 -35 GTGTTTTTCAACCGCACTTTAAATACTTTG 6 111 0 ACCGCACTTT 0.998036 -65 TCGAATTTTAACCGCACTTCCCTTAACGAA 6 142 1 ACCGCACTTC 0.989659 -34 GCGACAAAATGCCGCATTTTATAAAATAGT 8 55 0 GCCGCATTTT 0.920888 -212 CCTTAAATTCACCGCACTTTTAAAAAAACG 8 239 0 ACCGCACTTT 0.998036 -28 ********** Masking position 9 Map Score: 33.9206 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 806 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 295 Fraction of orfs with sites within 600 bp upstream = 0.0473819 Motif number 4 ATAAGCCAAAAGAGCGGTAAAAATTCACTA 2 76 1 AGAGCGGTAA 0.904726 -172 AACGAAAAAAAGTGCGGTGAAAATTGGCTT 2 140 0 AGTGCGGTGA 0.995839 -108 TCACATTTTGTGTGCGGCTAAGTTGTGGAT 4 180 1 TGTGCGGCTA 0.910903 -121 CAACTTATAAAGTGCGGGTTTAAAATTGGG 4 233 0 AGTGCGGGTT 0.930863 -68 TCCAAAAGTGCGGTGCGTTTTTCCTG 4 285 0 AGTGCGGTGC 0.986603 -16 TTACTTCAAAAGTGCGGTTAGTTTTTTTGT 5 49 0 AGTGCGGTTA 0.995921 -37 AAGTATTTAAAGTGCGGTTGAAAAACACAT 6 113 1 AGTGCGGTTG 0.986865 -63 CGTTAAGGGAAGTGCGGTTAAAATTCGATG 6 140 0 AGTGCGGTTA 0.995921 -36 TTTTTTTAAAAGTGCGGTGAATTTAAGGAG 8 241 1 AGTGCGGTGA 0.995839 -26 ********** Masking position 5 Map Score: 19.8773 Number of sites scoring better than the average of aligned sites = 881 Number in coding regions = 546 Number in noncoding regions = 335 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 5 CTCTTTTGGCTTATTTATTGACTGATGATTA 2 59 0 TTATTTATTA 0.753348 -189 GAATATTTTATCAATTAACGAAGA 3 4 1 TATTTTATCA 0.763986 -68 TTTTTTGGCATTTTATATTAAAAATAAACCT 4 47 0 TTTTATATTA 0.753349 -254 TGACAGCCAGTTTTTTATTCGTAATATGGAA 4 83 1 TTTTTTATTG 0.819066 -218 TACACAGAGGATTTTTATTTATGTTTCGTAT 4 121 1 ATTTTTATTA 0.945006 -180 ATCTGACTGTTTTTTTATCCACAACTTAGCC 4 195 0 TTTTTTATCA 0.949115 -106 AAGTTGCGGGTTTTTTATCTAAAAAATACAG 4 257 1 TTTTTTATCA 0.949114 -44 AAAAATATTATTTTTTATTCAAATTTTTGAA 8 24 0 TTTTTTATTA 0.970899 -243 ATATTTTTACTATTTTATAAAATGCGGCATT 8 47 1 TATTTTATAA 0.672743 -220 GCATTTTTTTATTTTTATTGATGGAAAAATT 8 83 1 ATTTTTATTA 0.945006 -184 GAAAATTTAGTTTTTTATAAATTTTTCCATC 8 102 0 TTTTTTATAA 0.921811 -165 AAAAAACTAAATTTTCATTTATATTTGGTTT 8 117 1 ATTTTCATTA 0.714829 -150 TTTTTATATTTTTTTAATTGATTTTTTTGTT 8 146 1 TTTTTAATTA 0.766555 -121 TTTTCTTTATATTTTTATTAAAGTTTATAAA 9 30 1 ATTTTTATTA 0.945005 -271 AGTTTATAAAATTTTTATAAAATCTGTTGGC 9 51 1 ATTTTTATAA 0.859332 -250 ********* * Masking position 7 Map Score: 17.1593 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 183 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 TCTTTGCTAAAAAGGGGAACTCGATAAA 5 6 0 AAAGGGGACG 0.902704 -80 TTTTTAGCAAAGAGGGGAAAAATACAAAAAAAC 5 26 1 AGAGGGGAAT 0.928181 -60 TCCTCCGTTTACGGGGGAAGGTGCCTGAAGGGC 6 20 1 ACGGGGGAGG 0.965749 -156 AGGTGCCTGAAGGGCGGAAGGGGGCAATCTCCA 6 38 1 AGGGCGGAGG 0.971122 -138 TAAATAACTAAGGGTGGAGATTGCCCCCTTCCG 6 52 0 AGGGTGGAAG 0.986044 -124 CCCAATAAACAGGGGGGACAAAGTATTTAAAGT 6 93 1 AGGGGGGAAG 0.996154 -83 GGCTCAAAAGAGGAAAAAGAAAA 7 7 1 AAAGAGGAAG 0.823467 -17 GTATTTTTTCAGAGTGGATAACGAAGAAGAAAA 9 144 1 AGAGTGGAAG 0.972946 -157 CGTGCTCGAAAGGGGCGACACTGTCATAGTTTT 9 230 1 AGGGGCGAAG 0.974116 -71 ******** * * Masking position 8 Map Score: 6.97536 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 22 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 GAAAATTGAAACAAAGCAAAGAACAGCGAT 1 43 1 ACAAAGCAAA 0.843282 -258 CGAGCGAAATACGATGCCAATTCACAAAAA 1 138 1 ACGATGCCAA 0.758983 -163 ACAACAAAAAAATATGCAAACACAACATCA 1 246 1 AATATGCAAA 0.926482 -55 CCTATGTAAAAAAATGAAAAGAGTTTCAAT 2 18 1 AAAATGAAAA 0.767054 -230 TCAGTCAATAAATAAGCCAAAAGAGCGGTA 2 65 1 AATAAGCCAA 0.936109 -183 GAATATTCAAAATAAGCCAATTTTCACCGC 2 127 1 AATAAGCCAA 0.936109 -121 TTTTTAATATAAAATGCCAAAAAATAGTTT 4 54 1 AAAATGCCAA 0.971599 -247 TTTTATTCGTAATATGGAAAACGTTTTACA 4 95 1 AATATGGAAA 0.620036 -206 AAAGAGGGGAAAAATACAAAAAAACTAACC 5 34 1 AAAATACAAA 0.748092 -52 TCAAAAGAGGAAAAAGAAAA 7 14 1 AAAAAGAAAA 0.705183 -10 AAAAAAATATAAAAAACCAAATATAAATGA 8 131 0 AAAAAACCAA 0.775417 -136 TAAAACAAACAAAATGCCAACAGATTTTAT 9 67 0 AAAATGCCAA 0.971599 -234 ********** Masking position 4 Map Score: 11.7054 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 468 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 TTGGTAGGGCTTGGAGAGAAAAAAACGAAA 2 163 0 TTGGAGAGAA 0.968507 -85 TGTTTTTATTTTGGGGATAAGTTCAGCATT 2 212 0 TTGGGGATAA 0.983015 -36 TAAATTTTACTCGGAGAGATTATTT 3 57 1 TCGGAGAGAT 0.918336 -15 TGCGGCTAAGTTGTGGATAAAAAAACAGTC 4 192 1 TTGTGGATAA 0.899512 -109 CCCCTGTTTATTGGGGATATTTCTAAATAA 6 78 0 TTGGGGATAT 0.983017 -98 TTTGTAGTGATTGGGGAGATTACCGTAAAA 9 92 0 TTGGGGAGAT 0.989132 -209 ********** Masking position 7 Map Score: 5.18024 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 24 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ATTGTGTAAGGTTGATAATTGTATGATGTTG 1 268 0 GTTATAATTG 0.888474 -33 CCAAAAGAGCGGTAAAAATTCACTAAATTTT 2 81 1 GGTAAAATTC 0.942709 -167 AAAAAAGTGCGGTGAAAATTGGCTTATTTTG 2 134 0 GGTAAAATTG 0.974997 -114 TTGGGGATAAGTTCAGCATTGTAGCGAAATT 2 201 0 GTTAGCATTG 0.88821 -47 TAAAGTGCGGGTTTAAAATTGGGTATTTACA 4 225 0 GTTAAAATTG 0.969963 -76 AGGGAAGTGCGGTTAAAATTCGATGTGTTTT 6 134 0 GGTAAAATTC 0.942709 -42 TTTGTATTATGTGAAACATTGACATAATCTG 8 206 1 GTGAACATTG 0.869896 -61 *** ******* Masking position 5 Map Score: 2.0204 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 48 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TATGATTAATTTCTTCGTTAATTGATAAAA 3 16 0 TTCTTCGTTA 0.973903 -56 TTTATTAGTTAAATGTATATT 4 2 1 TTATTAGTTA 0.897298 -299 AGCCAGTTTTTTATTCGTAATATGGAAAAC 4 87 1 TTATTCGTAA 0.78945 -214 GCAATCTCCACCCTTAGTTATTTAGAAATA 6 61 1 CCCTTAGTTA 0.891089 -115 ATATTTTTCTCTATTCGTTAAGGGAAGTGC 6 155 0 CTATTCGTTA 0.924005 -21 TTCTTTTTTCTTCTTCGTTATCCACTCTGA 9 152 0 TTCTTCGTTA 0.973903 -149 ACCGTAGCACTCCATAGTTAATCAGAAAAA 9 259 0 TCCATAGTTA 0.716251 -42 ********** Masking position 10 Map Score: 1.97547 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 80 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 GAACAGCGATTTAACTGGGGCGTGTTTTCT 1 63 1 TTAACTGGGG 0.875902 -238 GAAAACGTTTTACACAGAGGATTTTTATTT 4 111 1 TACACAGAGG 0.786893 -190 AGTGCGGGTTTAAAATTGGGTATTTACATC 4 223 0 TAAAATTGGG 0.713615 -78 CCGCAACTTATAAAGTGCGGGTTTAAAATT 4 236 0 TAAAGTGCGG 0.959139 -65 CCCTCTTTGCTAAAAAGGGGAACTCGATAA 5 12 0 TAAAAAGGGG 0.969348 -74 CCCTTTTTAGCAAAGAGGGGAAAAATACAA 5 23 1 CAAAGAGGGG 0.877928 -63 CCTTCCCCCGTAAACGGAGGAAGGCAAGTA 6 11 0 TAAACGGAGG 0.877592 -165 ATATCCCCAATAAACAGGGGGGACAAAGTA 6 88 1 TAAACAGGGG 0.980454 -88 ACAAAGTATTTAAAGTGCGGTTGAAAAACA 6 110 1 TAAAGTGCGG 0.959139 -66 GGCTCAAAAGAGGAAAAAGAAAA 7 4 1 TCAAAAGAGG 0.720514 -20 TACTATTTTATAAAATGCGGCATTTTGTCG 8 54 1 TAAAATGCGG 0.951071 -213 ********** Masking position 4 Map Score: 8.9367 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 203 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 12 TAAGAAAATTGAAACAAAGCAAAGAACAGCGA 1 40 1 GAAAAAGCAA 0.694288 -261 TAAAAGAAAGTAGGCAAAGAAAACACGCCCCA 1 78 0 TAGAAAGAAA 0.930872 -223 TCTTTTACTCGTGTAAAAGAAAGTAGGCAAAG 1 91 0 GTGAAAGAAA 0.939755 -210 TCTTTTACACGAGTAAAAGAAAGTAGGTCGTT 1 103 1 GAGAAAGAAA 0.988642 -198 GTAGGGCTTGGAGAGAAAAAAACGAAAAAAAG 2 158 0 GAGAAAAAAA 0.944874 -90 AGTAGGTTGAGAGATAAAGAAACAATACGAAA 4 144 0 GAGAAAGAAA 0.988642 -157 GGCTCAAAAGAGGAAAAAGAAAA 7 11 1 AGGAAAGAAA 0.90037 -13 ACATAATACAAAGTAAAAAAAATTTGTCTAGC 8 186 0 AAGAAAAAAA 0.870128 -81 CTTTAATAAAAATATAAAGAAAATAAACACAA 9 21 0 AATAAAGAAA 0.791645 -280 *** ******* Masking position 6 Map Score: 5.59384 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 158 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 ********** No masking Map Score: 6.80943e-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 14 ********** No masking Map Score: 6.80943e-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: 6.80943e-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