AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_ctra_reg_100.orf -o00530_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 htrB 131 Acyltransferase #2 glgX 117 Glycogen Hydrolase (debranching) #3 leuS 196 Leucyl tRNA Synthetase #4 yaeT 300 Omp85 Analog #5 CT242 68 (OmpH-Like Outer Membrane Protein) #6 lpxD 27 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase #7 dut 36 dUTP Nucleotidohydrolase #8 accD 71 AcCoA Carboxylase/Transferase Beta #9 sodM 131 Superoxide Dismutase (Mn) #10 pcnB_1 214 PolyA Polymerase #11 lpxB 60 Lipid A Disaccharide Synthase #12 murA 211 UDP-N-Acetylglucosamine Transferase #13 lpxC 100 UDP-3-O-Acyl GlcNAc Deacetylase #14 cutE 63 Apolipoprotein N-Acetyltransferase #15 yciA 135 Acyl-CoA Thioester Hydrolase #16 glmU 52 UDP-GlcNAc Pyrophosphorylase #17 cpxR 178 HTH Transcriptional Regulatory Protein and Receiver Domain #18 mrsA 245 Phosphoglucomutase #19 murB 132 UDP-N-Acetylenolpyruvoylglucosamine Reductase Motif number 1 ATCCATCATCTTTTTTTTAATGCGATCCTG 3 54 0 TTTTTTTTAA 0.865347 -143 TAACCTGTTGTTATTTTTAAGGTTTTCTCT 3 171 0 TTATTTTTAA 0.925804 -26 CTTTTTTTCGTTGTTTTCAAAGTTCTCTCT 4 74 1 TTGTTTTCAA 0.75499 -227 CCTATTGGTTATATTTTTATAGGAAAGAAT 5 48 1 ATATTTTTAT 0.789527 -21 TTTATTGTAATTTTTTTTAACCAATCAATA 8 17 0 TTTTTTTTAA 0.865347 -55 GATAGTAACCTTATTTTTTAGGATGGCT 9 114 1 TTATTTTTTA 0.843319 -18 AAATCGGCTGTTGTTTTTATTTAATTTGTA 12 14 0 TTGTTTTTAT 0.938201 -198 TTTTAAAAAGTTGTTTTTATTATTTGCTAC 12 51 1 TTGTTTTTAT 0.938201 -161 GCTACAAAGTTTATTTTTATTTGTTTTTAA 12 76 1 TTATTTTTAT 0.948676 -136 TTATTTTTATTTGTTTTTAAAAACAAACAA 12 86 1 TTGTTTTTAA 0.911098 -126 TGTTAATAAGATGTTTTTTTTAGAAAAATA 12 125 1 ATGTTTTTTT 0.570631 -87 CACGAAAACTTTATTTTTCTAAAAAAAACA 12 136 0 TTATTTTTCT 0.886559 -76 CGGTATGCTGTTATTTTTCACGAAAACTTT 12 154 0 TTATTTTTCA 0.840655 -58 TATTATCCTTTTTTTTTTTTAGCAAGCAAG 13 54 0 TTTTTTTTTT 0.80417 -47 ATCTTCAGACTTTTTTTCAAGTTTAGACTA 17 79 0 TTTTTTTCAA 0.658972 -100 AAGATATCGGTTTTTTTTCTGAGGCTCTTT 17 104 1 TTTTTTTTCT 0.800998 -75 ACTAAATGATTTATTTTTTTTGTTTTT 18 8 0 TTATTTTTTT 0.888557 -238 TTTTCGATAATTATTTTCTTACTTCTTATT 18 37 1 TTATTTTCTT 0.705655 -209 TAAATATTCCCTATTTTTATCAAAATCTTT 18 167 0 CTATTTTTAT 0.687537 -79 ATACCTATATTTTTATCTTTAGCATT 19 7 1 ATATTTTTAT 0.789527 -126 ********** Masking position 5 Map Score: 20.8508 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 227 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 2 TCATACAACAAAAGGAAGAGGGTCTCTCTT 2 22 1 AAAGGAAGAG 0.989269 -96 CTTAAACACAAAAGGAAGAGAGACCCTCTT 2 37 0 AAAGGAAGAG 0.989269 -81 CTAACCGAAGAAATGAAGAGAAGAGAGGGG 2 67 0 AAATGAAGAG 0.858599 -51 AGATTGGGGAAAGGGAAGTGTATACCAGGA 3 29 1 AAGGGAAGTG 0.968407 -168 CCCTACAAATATAGGAAGAAAAGAGAACAG 4 102 0 ATAGGAAGAA 0.881702 -199 TCCCCACATATTAGGAAGAGACTACTCAAG 4 174 0 TTAGGAAGAG 0.882143 -127 CTTACTCTTTCTGGGAAGAGCACCATTCTT 4 232 0 CTGGGAAGAG 0.937466 -69 TTTTCTAGATAAAGGAAGTAATA 4 288 1 AAAGGAAGTA 0.840804 -13 TTTTTCTATTATAGGAAGAGCTTTCCTGGA 10 127 1 ATAGGAAGAG 0.983308 -88 GATAGCAAGTGTTTTAGAACT 13 2 1 ATAGCAAGTG 0.839236 -99 TTTTTTTTAGCAAGCAAGCGATATCAAAAA 13 42 0 CAAGCAAGCG 0.816585 -59 ATGACAGAGTAAGGGAAGCGACTCCGTCCA 19 55 1 AAGGGAAGCG 0.979674 -78 TTGACTGTTCAAGGGAAGCGACACAAGCCC 19 94 0 AAGGGAAGCG 0.979674 -39 ********** Masking position 6 Map Score: 18.9581 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 212 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 3 GGAAGAGAGACCCTCTTCCTTTTGTTGTATGA 2 22 0 CCCTCTTCTT 0.747583 -96 GGAAGAGGGTCTCTCTTCCTTTTGTGTTTAAG 2 35 1 CTCTCTTCTT 0.709042 -83 GTGTTTAAGCCCCTCTCTTCTCTTCATTTCTT 2 58 1 CCCTCTCTTC 0.972719 -60 ATACACTTCCCTTTCCCCAATCTTTACAGAGA 3 20 0 CTTTCCCCTC 0.930695 -177 CGAAATCAAGTCCTCTCCAGTCTGCGAATCCA 3 79 0 TCCTCTCCTC 0.969489 -118 ATTTTTAAGGTTTTCTCTCCTTACAACCGCCT 3 157 0 TTTTCTCTTT 0.83317 -40 GTTTTCAAAGTTCTCTCTGTTCTCTTTTCTTC 4 86 1 TTCTCTCTTC 0.942061 -215 AGGATGCTCTCCTTCTCCTTTCGGATT 5 6 0 CCTTCTCCTC 0.969489 -63 AGGAGAGCATCCTTCTCCTTTCACCTATTGGT 5 25 1 CCTTCTCCTC 0.969489 -44 ATCCTCGCCACCTTCTCTATTTTCTACAGGCT 9 85 0 CCTTCTCTTT 0.91633 -47 AGCTTTATGACTCTCTCTCCTT 10 1 0 CTCTCTCTTT 0.942061 -214 GGGAAAATTCTTCTCCCCTATCGATTACTACA 11 29 1 TTCTCCCCTC 0.930695 -32 AGGGGATTCTTTTTCTCTCATCTTGAATGTAA 14 21 1 TTTTCTCTTC 0.900112 -43 GGCCCACCTCTACTCCCCAGTCATCTCTGTAA 15 59 0 TACTCCCCTC 0.842493 -77 TTTCTCTCAAATTTTTCGATCAA 17 2 1 TTCTCTCATT 0.586869 -177 ATAAACAGCTCATTCTCTGCTTTATCTAGTTT 17 34 0 CATTCTCTTT 0.782102 -145 CAGAGATAAATATTCCCTATTTTTATCAAAAT 18 171 0 TATTCCCTTT 0.505371 -75 ******** ** Masking position 4 Map Score: 17.4925 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 403 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 AAGCAGAGATCTCTGTAAAGATTG 3 5 1 AGAGATCTCT 0.410164 -192 GAGAACTCAGAGGGGGTGCTGGTCACTAGC 4 12 0 AGGGGGTGCT 0.921437 -289 AACCTGCTAGAGGGGTTGCTTTTCGGGCTT 4 47 1 AGGGGTTGCT 0.91001 -254 ATAGGTCTTGAGTAGTCTCTTCCTAATATG 4 168 1 AGTAGTCTCT 0.734927 -133 CCAAGTAAGAATGGTGCTCTTCCCAGAAAG 4 226 1 ATGGTGCTCT 0.72947 -75 TGAAAGGAGAAGGATGCTCTCCTTCTCCTT 5 18 0 AGGATGCTCT 0.934827 -51 AAGATCATAGGAGGCTCTTCAAAAAGAG 7 9 1 AGGAGGCTCT 0.978119 -28 GAAGGCTTTTAGAGTTCTCTCCAGGAAAGC 10 146 0 AGAGTTCTCT 0.565327 -69 GGATAATATACGGGGTCTCTTTGTCAGGGT 13 76 1 CGGGGTCTCT 0.96618 -25 GTAACTTCTAAGGGGATTCTTTTTCTCTCA 14 11 1 AGGGGATTCT 0.872681 -53 TCCTCCAAGGAATTTCTTGATTTTCTT 15 8 1 AGGAATTTCT 0.697646 -128 GGTTTTTTTTCTGAGGCTCTTTGAAAAAAC 17 112 1 CTGAGGCTCT 0.705665 -67 TTTGAGCCAAAGGATATTCTTAGGGATAGA 18 223 1 AGGATATTCT 0.580145 -23 ATATCTTGGACGGAGTCGCTTCCCTTACTC 19 61 0 CGGAGTCGCT 0.891308 -72 ********** Masking position 10 Map Score: 7.64327 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 363 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 5 TTCGCAGACTGGAGAGGACTTGATTTCGAT 3 83 1 GGAGAGGACT 0.917095 -114 TATTGTAATTGGATAGGTCTTGAGTAGTCT 4 156 1 GGATAGGTCT 0.975551 -145 TCCTTTATCTAGAAAAGTCTGCGCTAGGGA 4 274 0 AGAAAAGTCT 0.869122 -27 GTAAAGATGTGGATAGCTCTTGACAGTGAA 9 20 1 GGATAGCTCT 0.968104 -112 GTTCTCTCCAGGAAAGCTCTTCCTATAATA 10 133 0 GGAAAGCTCT 0.98253 -82 GCTTTCCTGGAGAGAACTCTAAAAGCCTTC 10 146 1 AGAGAACTCT 0.796276 -69 TTTGAAATTGGGAAAATTCTTCTCCCCTAT 11 20 1 GGAAAATTCT 0.847818 -41 TGATGTTTGAGGAAAGGTCTTAAGAAGGCG 18 131 1 GGAAAGGTCT 0.986736 -115 ********** Masking position 5 Map Score: 6.36082 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 57 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 AAAAACTAGAACAAGTAAGTTTAATAAAA 2 99 0 AGAAAGTAAG 0.984794 -19 GATTGGCTTCTGACCAAGTAAGAATGGTGCTC 4 213 1 TGACAGTAAG 0.920568 -88 TGCTCTTCCCAGAAAGAGTAAGAATAAAACTT 4 240 1 AGAAAGTAAG 0.984794 -61 AGACTTTTCTAGATAAAGGAAGTAATA 4 284 1 AGATAGGAAG 0.86794 -17 CAAGTGTTTTAGAACTAGGTAGTAATTTTTTG 13 16 1 AGAAAGGTAG 0.909063 -85 CACTTTTTAAATAAGAAGTAAGAAAATAATTA 18 44 0 ATAAAGTAAG 0.927289 -202 TTGTTTGGTTATAAATAGTAAGCTATTGATAC 18 93 1 ATAAAGTAAG 0.927287 -153 CTGAAAATCAAGGATCAGTTAGTTTTGAGCCA 18 200 1 AGGAAGTTAG 0.827043 -46 CACATTAGAATGACAGAGTAAGGGAAGCGACT 19 46 1 TGACAGTAAG 0.920568 -87 **** ****** Masking position 7 Map Score: 5.1823 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 77 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 7 TTCTTCGGTTAGATTTTTATTAAACTTACT 2 85 1 AGATTTTTAT 0.888987 -33 CCTATTGGTTATATTTTTATAGGAAAGAAT 5 48 1 ATATTTTTAT 0.66483 -21 CAGTACGTAAAGATGTGGATAGCTCTTGAC 9 14 1 AGATGTGGAT 0.763952 -118 AGAGTCATAAAGCTGTTGATGATCAAAAAG 10 19 1 AGCTGTTGAT 0.938314 -196 CTAGGTAGTAATTTTTTGATATCGCTTGCT 13 30 1 ATTTTTTGAT 0.770931 -71 TGCTTTATCTAGTTTTTGATCGAAAAATTT 17 19 0 AGTTTTTGAT 0.931444 -160 GCAGAGAATGAGCTGTTTATCACAGAACAA 17 46 1 AGCTGTTTAT 0.848223 -133 TAAATCATTTAGTTTTCGATAATTATTTTC 18 25 1 AGTTTTCGAT 0.73914 -221 ATAAATAGTAAGCTATTGATACCCAGATTG 18 103 1 AGCTATTGAT 0.792881 -143 CGAATTGCAAAGATTTTGATAAAAATAGGG 18 159 1 AGATTTTGAT 0.956133 -87 ATACCTATATTTTTATCTTTAGCATT 19 7 1 ATATTTTTAT 0.66483 -126 ********** Masking position 9 Map Score: 4.71855 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 151 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 8 CTACGTAAAAGCTTCTTTATATAAAACGCT 1 40 0 GCTTCTTTAT 0.908962 -92 CGATCACAAAGCTTCTTTCTGTAACTACTA 1 79 1 GCTTCTTTCT 0.93055 -53 GGAAGAGAGACCCTCTTCCTTTTGTTGTAT 2 24 0 CCCTCTTCCT 0.821068 -94 TATGTTTGACGCTTATTTCTCTCTAAGTGC 3 126 1 GCTTATTTCT 0.776461 -71 AGAAGGCCCTCTTTTTGAAGAGCCTC 7 21 0 CCCTCTTTTT 0.912652 -16 CTAGATAGATCCCTCTAGATTATCAATAAA 9 53 0 CCCTCTAGAT 0.800837 -79 ATCCTCGCCACCTTCTCTATTTTCTACAGG 9 87 0 CCTTCTCTAT 0.83651 -45 AGGATAGTAACCTTATTTTTTAGGATGGCT 9 112 1 CCTTATTTTT 0.748615 -20 AAAAGACGTGCCTTATATATGGTCCTCTAA 10 44 1 CCTTATATAT 0.783903 -171 ACTCTAAAAGCCTTCTTGCTCAAGGACAAA 10 161 1 CCTTCTTGCT 0.902767 -54 TTCTTGATTTTCTTCTATATCGAGACTACT 15 24 1 TCTTCTATAT 0.550066 -112 GAGTCTAATAGCCTCTATCTTGACTAGTCT 15 101 0 GCCTCTATCT 0.8862 -35 ATCACCCTTCTATATGAGTCTAATA 15 121 0 CCTTCTATAT 0.933303 -15 GATAAATATTCCCTATTTTTATCAAAATCT 18 169 0 CCCTATTTTT 0.730357 -77 ********** Masking position 6 Map Score: 8.63055 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 382 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 TGTGTTCCGTAAGGCTAGTATGACTTTGCT 1 108 0 AAGGCTAGTA 0.934827 -24 CTATATTTGTAGGGCTAGTCAAATTATCCT 4 118 1 AGGGCTAGTC 0.868151 -183 ATATTAGGAAGAGACTACTCAAGACCTATC 4 167 0 GAGACTACTC 0.93611 -134 AAGATCATAGGAGGCTCTTCAAAAAGAGGG 7 11 1 GAGGCTCTTC 0.905493 -26 AGAAGGTGGCGAGGATAGTAACCTTATTTT 9 101 1 GAGGATAGTA 0.895993 -31 CTTCTATATCGAGACTACTATCCATTACAG 15 35 1 GAGACTACTA 0.882304 -101 CTGTAACTCTGAGACTAGTCAAGATAGAGG 15 90 1 GAGACTAGTC 0.965725 -46 AGTCAAGATAGAGGCTATTAGACTCATATA 15 106 1 GAGGCTATTA 0.954934 -30 TTTTGAGCCAAAGGATATTCTTAGGGATAG 18 222 1 AAGGATATTC 0.728731 -24 ********** Masking position 6 Map Score: 3.46334 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 101 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 10 CCCTCTTCCTTTTGTTGTATGATAGCAAAA 2 14 0 TTTGTTGTAT 0.525934 -104 TTCGGTTAGATTTTTATTAAACTTACTTGT 2 88 1 TTTTTATTAA 0.7528 -30 ATCCATCATCTTTTTTTTAATGCGATCCTG 3 54 0 TTTTTTTTAA 0.711546 -143 TGGTTATATTTTTATAGGAAAGAATT 5 53 1 TTTATAGGAA 0.480193 -16 TTTATTGTAATTTTTTTTAACCAATCAATA 8 17 0 TTTTTTTTAA 0.711546 -55 GAGCAATAATTTTATTGTAATTTTTTTTAA 8 27 0 TTTATTGTAA 0.634218 -45 TATTGCTCAATTTTTTGTAAAGAGGATGGT 8 49 1 TTTTTTGTAA 0.902342 -23 GTAACCTTATTTTTTAGGATGGCT 9 118 1 TTTTTAGGAT 0.515897 -14 CCCTTGAAAATTTTTAGAAACATATAGGTG 10 75 1 TTTTTAGAAA 0.847762 -140 AACAACTCATTGTAGTAATCGATAGGGG 11 43 0 ATTGTAGTAA 0.325145 -18 AAAAATAAACTTTGTAGCAAATAATAAAAA 12 64 0 TTTGTAGCAA 0.839644 -148 TTTTTATTTGTTTTTAAAAACAAACAAATG 12 89 1 TTTTTAAAAA 0.241818 -123 TAAGATGTTTTTTTTAGAAAAATAAAGTTT 12 131 1 TTTTTAGAAA 0.847762 -81 TAGGTAGTAATTTTTTGATATCGCTTGCTT 13 31 1 TTTTTTGATA 0.266152 -70 TCCTTTTTTTTTTTTAGCAAGCAAGCGATA 13 49 0 TTTTTAGCAA 0.90398 -52 ATCTTCAGACTTTTTTTCAAGTTTAGACTA 17 79 0 TTTTTTTCAA 0.669893 -100 AAAAACTATTTTTGTTGTATTAGGTAATCT 17 136 1 TTTGTTGTAT 0.525934 -43 ATATTCCCTATTTTTATCAAAATCTTTGCA 18 164 0 TTTTTATCAA 0.714851 -82 ********** Masking position 5 Map Score: 6.02956 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 302 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 11 TTCGGGGGAGAACTCAGAGGGGGTGCTGGTCA 4 17 0 AACTAGAGGG 0.946091 -284 TCAGAAGCCAATCTCATAGGCGTCCCCACATA 4 194 0 ATCTATAGGG 0.954282 -107 AATCCGAAAGGAGAAGGAGAGCA 5 2 1 ATCCAAAGGG 0.934477 -67 ATAAAAATATAACCAATAGGTGAAAGGAGAAG 5 36 0 AACCATAGGG 0.982389 -33 AATTTTTAGAAACATATAGGTGATTTTGCCCT 10 83 1 AACAATAGGG 0.952842 -132 TCATTGTAGTAATCGATAGGGGAGAAGAATTT 11 33 0 AATCATAGGG 0.931396 -28 **** ***** * Masking position 6 Map Score: 0.291809 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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: -4.64452e-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: -4.64452e-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 ACTTCCCTTTCCCCAATCTTTACAGAGATC 3 18 0 CCCCAATCTT 0.91319 -179 TTGATTTCGATCTCAGACATAGTGTATGTT 3 102 1 TCTCAGACAT 0.753057 -95 GAGAAATAAGCGTCAAACATACACTATGTC 3 117 0 CGTCAAACAT 0.797882 -80 GGACAAAATCCTCCAGACTTTTTAACTTTC 10 184 1 CTCCAGACTT 0.879546 -31 CACCTCTACTCCCCAGTCATCTCTGTAATG 15 57 0 CCCCAGTCAT 0.943456 -79 AGTCTAATAGCCTCTATCTTGACTAGTCTC 15 100 0 CCTCTATCTT 0.657917 -36 AAACCGATATCTTCAGACTTTTTTTCAAGT 17 87 0 CTTCAGACTT 0.881652 -92 TAAGACCTTTCCTCAAACATCAATCTGGGT 18 123 0 CCTCAAACAT 0.945106 -123 ********** Masking position 10 Map Score: 0.175091 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 82 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: -4.64452e-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