AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jarcA.reg -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 = 181 Input sequences: #1 lpdA 300 bp lpdA 474 1-1425 CDS #2 gltA 300 bp gltA 427 1-1284 CDS #3 sdhC 300 bp sdhC 129 1-390 CDS #4 cydA 300 bp cydA 523 1-1572 CDS #5 focA 300 bp focA 285 1-858 CDS #6 icdA 201 bp icdA 416 1-1251 CDS #7 aldA 196 bp aldA 479 1-1440 CDS #8 glcD_glcC 250 bp glcD 499 1-1500 CDS glcC 254 1-765 CDS #9 lldP 300 bp lldP 551 1-1656 CDS #10 sodA 284 bp sodA 206 1-621 CDS Motif number 1 CGTTTGTTGTTTAAAAATTGTTAACAATTTTGTAAA 1 72 1 TAAGTTAACA 0.869179 -229 AGTCGGTATTTCACCTAAGATTAACTTATGTAACAG 2 15 1 TACATTAACT 0.795037 -286 CGTCTCCAGGTAACAGAAAGTTAACCTCTGTGCCCG 3 233 1 TACGTTAACC 0.982267 -68 GGGATCAATTTGAGTTTTTATTAACATGTTTGCAAC 4 142 1 TAGATTAACA 0.716532 -159 TAAATACAAATTACCGATATTTAACCTTATAATTAC 5 11 0 TACTTTAACC 0.860836 -290 GACAAGCCAATTACAAATCATTAACAAAAAATTGCT 6 92 1 TACATTAACA 0.95584 -110 GCCCGTTTGCAAACAAGTGGTTCACAAACGGGCAAT 7 13 0 AACGTTCACA 0.788882 -184 TGATGTTAATTAACAATGTATTCACCGAAAACAAAC 7 149 1 TACATTCACC 0.948484 -48 AAAAGCCCGCTTAATAACTGTTCACAGAAGCAGCGC 8 55 0 TAAGTTCACA 0.829894 -196 TACATCAATTTAACATTGAGTTAACCAAGACAAGGT 8 146 0 TACGTTAACC 0.982267 -105 TTCGCTTATCTGACCTCTGGTTCACAATTTCCCAAT 9 114 1 TACGTTCACA 0.972309 -187 TGCCAATACATAACATTTAGTTAACCATTCATTGTC 9 168 1 TACGTTAACC 0.982267 -133 AACCAACTGCTTACGCGGCATTAACAATCGGCCGCC 10 239 1 TACATTAACA 0.95584 -46 * ** ******* Masking position 3 Map Score: 12.1732 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 77 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 TAAGGCGCTAAGGAGACCTTAA 2 289 1 AGGAGACCTT 0.766482 -12 CAGGGTGTTCCGGAGACCTGGCGGCAGTAT 3 78 0 CGGAGACCTG 0.97602 -223 TTTATTAAGTCGGCGACGAGATACTAACAA 5 269 0 CGGCGACGAG 0.906593 -32 TAGCGCTCGAAGGAGAGGTGA 6 191 1 AGGAGAGGTG 0.960079 -11 ATAATCACTTACGTGATGTGCGTGTTTTGC 8 184 1 ACGTGATGTG 0.821435 -67 ACGTGTGACAAGGAGATGAGCAACAGACTC 9 246 1 AGGAGATGAG 0.967514 -55 CGTGGACTCCAGGAGACCTGCA 9 289 1 AGGAGACCTG 0.974073 -12 CTCATCTCGTCGGAGATGTGACGCGACGAA 10 30 0 CGGAGATGTG 0.98616 -255 CACATCTCCGACGAGATGAGTGTAAAAATC 10 40 1 ACGAGATGAG 0.929644 -245 AGGAAAATGCCCGAGATGTGAAGCAAATCA 10 139 0 CCGAGATGTG 0.969339 -146 ********** Masking position 6 Map Score: 8.78563 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 257 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 ACATCAACCTGGCTTTACCCGTTTTTTATTTGGCTC 2 217 0 GGTCCTTTTT 0.966143 -84 TTGGGGCATGCGTGTGACCCTTTCTAACGGGGTTCA 4 242 1 CGGCCTTCTA 0.958562 -59 TTTAGCTACCGGTCAGACCATTTTTTTTCCAGCTCT 8 107 1 GGGCCTTTTT 0.993147 -144 CTCGTGCACAGGTAGGACCAATTTTTCTGTTCTTAA 8 217 0 GGGCCTTTTT 0.993147 -34 TCTCTGATGAGGATTGCCCTTTTCTTTACCAGACAT 9 47 1 GGGCCTTCTT 0.993009 -254 GCGAAGAATTGGTAGGGCCAATTCTTGTGGGGGGAG 9 83 0 GGGCCTTCTT 0.993009 -218 CAACACAATTGGCAGTGCCACTTTTACACAACGTGT 9 216 1 GGTCCTTTTA 0.900175 -85 AAAGGTTAATCGACAGCACGATTTTTACACTCATCT 10 53 0 CGGACTTTTT 0.879829 -232 CCAGTATTGTCGGGCGGCCGATTGTTAATGCCGCGT 10 251 0 CGGCCTTGTT 0.964673 -34 ** * ** ***** Masking position 12 Map Score: 9.18078 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 69 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TCCTGGGGATTCTGGCGCTTGCTACCTTGCTGCACC 1 173 0 TGCGTTGCCC 0.983798 -128 GGCGTGAAGCTAACGCCGCTGCGGCCTGAAAGACGA 1 237 1 TCCCCTGCCC 0.941032 -64 AATGGATCCTTTACCTGCAAGCGCCCAGAGCTCTGT 2 150 1 TCTGAAGCCC 0.905309 -151 GGACGCTGTCTGACCCGCAAGCAGACCGGAGGAAGG 3 188 1 TCCGAAGCAC 0.937671 -113 GAGTTTTTATTAACATGTTTGCAACCTTTCTTTACG 4 153 1 TCTGTTGCCC 0.960848 -148 TTAGAAAGGGTCACACGCATGCCCCAATAGAAATTT 4 233 0 TCCGATGCCA 0.9149 -68 TGTTACTTTATTCGCCTGATGCTCCCTTTTAATTAA 5 64 1 TGCTATGCCC 0.942796 -237 TAACAAAAAATTGCTCTAAAGCATCCGTATCGCAGG 6 113 1 TCCTAAGCCC 0.960585 -89 CGCTACTGGTTTGCTCGTCTGCCACCACGTTGCATA 6 160 0 TCCGCTGCCC 0.990977 -42 AAATTGCCCGTTTGTGAACCACTTGTTTG 7 4 1 TCCGTTGTAC 0.717791 -193 GTCAGGAGTCATGCCCGTTTGCAAACAAGTGGTTCA 7 25 0 ACCGTTGCAC 0.804284 -172 CGTTTTCGTCTATCTCTTTAGCTACCGGTCAGACCA 8 91 1 TCCTTAGCCC 0.966625 -160 CGATTAACCTTTCGCCTGTTGCCGCCGTTGTCGATT 10 77 1 TGCTTTGCCC 0.951419 -208 * * ** **** ** Masking position 11 Map Score: 10.0867 Number of sites scoring better than the average of aligned sites = 664 Number in coding regions = 625 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CGGTATTTCACCTAAGATTAACTTATGTAACAG 2 18 1 CTAGTTAACT 0.750628 -283 TCACAAAATCATTACAATTAACCTACATATAGT 3 38 0 ATAATTAACC 0.635648 -263 CTCCAGGTAACAGAAAGTTAACCTCTGTGCCCG 3 236 1 CGAATTAACC 0.974949 -65 GGCTGAAAGGCGGTAATTTAGCTATAAATTGAT 4 35 1 CGTATTAGCT 0.74784 -266 CATGAAGACTCCGAGAGTGAACCCCGTTAGAAA 4 262 0 CGAATGAACC 0.930978 -39 ATACAAATTACCGATATTTAACCTTATAATTAC 5 11 0 CGAATTAACC 0.974949 -290 CTGATGCTCCCTTTTAATTAACTGTTTTAGCGG 5 79 1 CTTATTAACT 0.915208 -222 AAATTGCCCGTTTGTGAACCACTTGTTTGC 7 8 1 CGTTTGAACC 0.723203 -189 ATCAATTTAACATTGAGTTAACCAAGACAAGGT 8 146 0 CTTATTAACC 0.970987 -105 CAATACATAACATTTAGTTAACCATTCATTGTC 9 171 1 CTTATTAACC 0.970987 -130 AAAAATCGTGCTGTCGATTAACCTTTCGCCTGT 10 63 1 CGTGTTAACC 0.953624 -222 TTTTCAATATCATTTAATTAACTATAATGAACC 10 210 1 CTTATTAACT 0.915208 -75 * ** * ****** Masking position 10 Map Score: 8.41227 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 246 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TATGTAAGCTCCTGGGGATTCTGGCGCTTGCTAC 1 184 0 CCTGGGGTGG 0.943251 -117 TAAGTAAGTGACTGGGGTGAGGGCGTGAAGCTAA 1 216 1 ACTGGGGGGC 0.8785 -85 GAGGGGAAAACCTGGGTACAGAGCTCTGGGCGCT 2 169 0 CCTGGGTAGC 0.903169 -132 CGCACATCAACCTGGCTTTACCCGTTTTTTATTT 2 222 0 CCTGGCTCCG 0.910731 -79 GCTCGGGATTGCAGGGTGTTCCGGAGACCTGGCG 3 85 0 GCAGGGTCGG 0.879251 -216 ACGTTACAACGCTGGGTGGCTCGGGATTGCAGGG 3 103 0 GCTGGGTCGG 0.984209 -198 TAGAAAGGACGCTGTCTGACCCGCAAGCAGACCG 3 182 1 GCTGTCTCGC 0.687859 -119 CTTTCTGTTACCTGGAGACGTCGGGATTTCCTTC 3 219 0 CCTGGAGCGG 0.977436 -82 CTTATTATTCCCTGGGGACTACGGGCACAGAGGT 3 256 0 CCTGGGGCGG 0.994671 -45 TCATATCTCGCCTGGCTTATAGGCCCGTAACTCG 5 207 0 CCTGGCTGGC 0.948774 -94 TGCAGGTCTCCTGGAGTCCACGCACATCGTGTA 9 278 0 CCTGGAGCGC 0.968614 -23 TTGTCGATTTACTGGCAATCACGGCATTAAGTGG 10 104 1 ACTGGCACGG 0.796832 -181 ******* *** Masking position 2 Map Score: 6.71136 Number of sites scoring better than the average of aligned sites = 1464 Number in coding regions = 1400 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 CGTTCTATCCGTCGGTATTTTACAAAATTG 1 96 0 GTCGGTATTT 0.979098 -205 ATGAAGTCGGTATTTCACCTAAGAT 2 6 1 GTCGGTATTT 0.979098 -295 CATATAGTTTGTCGGGTTTTATCCTGAACA 3 16 0 GTCGGGTTTT 0.915307 -285 CGCTGGGTGGCTCGGGATTGCAGGGTGTTC 3 98 0 CTCGGGATTG 0.896486 -203 ACCTGGAGACGTCGGGATTTCCTTCCTCCG 3 214 0 GTCGGGATTT 0.983689 -87 TTGGCTGAAAGGCGGTAATTTAGCTATAAA 4 33 1 GGCGGTAATT 0.851656 -268 AAGGTTAAATATCGGTAATTTGTATTTAAT 5 19 1 ATCGGTAATT 0.791724 -282 CAAATATTTACTCCGTATTTGCATAAAAAC 5 173 1 CTCCGTATTT 0.807075 -128 TGCTTCACATCTCGGGCATTTTCCTGCAAA 10 144 1 CTCGGGCATT 0.83778 -141 ********** Masking position 9 Map Score: 4.78986 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 206 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GTATTTTACAAAATTGTTAACAATTTTTAAACA 1 79 0 AAATTGTCAA 0.926163 -222 CCGGAACTTAAATTTGCCTTCGCACATCAACCT 2 243 0 AATTTGCCGC 0.695518 -58 AGATAAATTGTTCTCGATCAAATTGGC 4 5 1 AAATTGTCGA 0.887085 -296 GTTCTCGATCAAATTGGCTGAAAGGCGGTAATT 4 20 1 AAATTGCAAA 0.816294 -281 GAAAAATGCAAATTTGCTTCAACAAAAACCTGT 4 75 1 AATTTGTAAC 0.897657 -226 ATAAAAACTCAAATTGATCCCACGTATATATTA 4 130 0 AAATTGTCAC 0.95977 -171 CCCCAATAGAAATTTGTTTGAACACTTTCATCA 4 215 0 AATTTGTAAC 0.897657 -86 TATAGATGAGAAATTGATATAGATCATATCTCG 5 231 0 AAATTGTAGA 0.878808 -70 CATTAACAAAAAATTGCTCTAAAGCATCCGTAT 6 110 1 AAATTGTAAA 0.920494 -92 ACTCAATGTTAAATTGATGTAACATAATCACTT 8 161 1 AAATTGTAAC 0.95656 -90 AAGAACAGAAAAATTGGTCCTACCTGTGCACGA 8 219 1 AAATTGTTAC 0.820518 -32 ****** * *** Masking position 2 Map Score: 5.97792 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 132 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 CCTTTCTATAACTGCGCGTCATGCAAAACACTGC 3 156 0 ACTGCGCGTC 0.948035 -145 AGTTAACCTCTGTGCCCGTAGTCCCCAGGGAATA 3 251 1 TGTGCCCGTC 0.980399 -50 AAGAACAGCATGTGGGCGTTATTC 3 287 1 TGTGGGCGTC 0.989253 -14 ACTTACGTGATGTGCGTGTTTTGCGAGTTAAGAA 8 190 1 TGTGCGTGTC 0.990621 -61 TGGTCCTACCTGTGCACGAGGTCCGGGA 8 233 1 TGTGCACGTC 0.97122 -18 CATTACACGATGTGCGTGGACTCCAGGAGACCTG 9 275 1 TGTGCGTGTC 0.990621 -26 CACGGCATTAAGTGGGTGATTTGCTTCACATCTC 10 123 1 AGTGGGTGTC 0.950953 -162 ******** * * Masking position 3 Map Score: 4.30208 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 103 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 TCAGGCCGCAGCGGCGTTAGCTTCACGCCC 1 236 0 GCGGCGTTAG 0.895948 -65 CTTACGCAATAAGGCGCTAAGGAGACCTTA 2 280 1 AAGGCGCTAA 0.746368 -21 CGGAGACCTGGCGGCAGTATAGGCTGTTCA 3 68 0 GCGGCAGTAT 0.812616 -233 AATTGGCTGAAAGGCGGTAATTTAGCTATA 4 31 1 AAGGCGGTAA 0.911982 -270 TAAGGATTTTGCGGCGTAATATATACGTGG 4 114 1 GCGGCGTAAT 0.857958 -187 GCACACAAAAACGGCGTAAAGAAAGGTTGC 4 173 0 ACGGCGTAAA 0.967311 -128 TTATGCAAATACGGAGTAAATATTTGATTA 5 169 0 ACGGAGTAAA 0.67982 -132 AAAGGAATAAAAGGCAGAAATAAAAGTCAG 7 56 0 AAGGCAGAAA 0.734413 -141 TAAATCGACAACGGCGGCAACAGGCGAAAG 10 85 0 ACGGCGGCAA 0.925741 -200 ACTGGCAATCACGGCATTAAGTGGGTGATT 10 114 1 ACGGCATTAA 0.957837 -171 TACGAAAAGTACGGCATTGATAATCATTTT 10 184 1 ACGGCATTGA 0.795916 -101 AACTGCTTACGCGGCATTAACAATCGGCCG 10 243 1 GCGGCATTAA 0.94921 -42 ********** Masking position 4 Map Score: 6.17742 Number of sites scoring better than the average of aligned sites = 2454 Number in coding regions = 2325 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 11 TTTTGTAAAATACCGACGGATAGAACGACC 1 99 1 TACCGACGGA 0.932005 -202 CGACGGGTATGACCGCCGGAGATAAATATA 1 270 1 GACCGCCGGA 0.993518 -31 TATTGCGTAAGACTGCCGGAACTTAAATTT 2 261 0 GACTGCCGGA 0.952103 -40 CCCGCAAGCAGACCGGAGGAAGGAAATCCC 3 201 1 GACCGGAGGA 0.970525 -100 TTAACTGTTTTAGCGGAGGATGCGGAAAAA 5 96 1 TAGCGGAGGA 0.792447 -205 AAAGCATCCGTATCGCAGGACGCAAACGCA 6 130 1 TATCGCAGGA 0.76837 -72 TCAATCATCAGAGAGACGGAATCGTGAAAG 7 122 0 GAGAGACGGA 0.77192 -75 AAGGTTAATCGACAGCACGATTTTTACACT 10 58 0 GACAGCACGA 0.844632 -227 ATTAACAATCGGCCGCCCGACAATACTGGA 10 258 1 GGCCGCCCGA 0.916041 -27 ********** Masking position 10 Map Score: 3.16874 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 714 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 12 TTCCCCTCTTTCACAGAGCGGCGAGCCAAAT 2 195 1 TCACAGAGGG 0.955243 -106 ATGAAGCCCTTCACAGAATTGTCCTTTCACG 7 99 1 TCACAGAATG 0.967877 -98 ACATCAATCATCAGAGAGACGGAATCGTGAA 7 124 0 TCAGAGAGCG 0.977558 -73 TAATAACTGTTCACAGAAGCAGCGCGCAAAA 8 49 0 TCACAGAACA 0.860051 -202 CAAGACAAGGTCACAGAGCTGGAAAAAAAAT 8 126 0 TCACAGAGTG 0.973252 -125 GCAATCCTCATCAGAGAATTGCCCTTAGGTT 9 33 0 TCAGAGAATG 0.958228 -268 GAACCAGAGGTCAGATAAGCGAAGAATTGGT 9 106 0 TCAGATAACG 0.823905 -195 ******** ** Masking position 5 Map Score: 2.91147 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 71 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 ATACATTCATGAGATTACCAGAAAAAAGC 1 9 0 GAGATTCCAG 0.824184 -292 TGCGGCCTGAAAGACGACGGGTATGACCGCC 1 256 1 AAGACGCGGG 0.974642 -45 CTTATTGCGTAAGACTGCCGGAACTTAAATT 2 262 0 AAGACTCCGG 0.953478 -39 TGGGTGGCTCGGGATTGCAGGGTGTTCCGGA 3 94 0 GGGATTCAGG 0.809703 -207 CTGTTACCTGGAGACGTCGGGATTTCCTTCC 3 218 0 GAGACGCGGG 0.989932 -83 TTATTCCCTGGGGACTACGGGCACAGAGGTT 3 255 0 GGGACTCGGG 0.982701 -46 TCATCGCATGAAGACTCCGAGAGTGAACCCC 4 270 0 AAGACTCGAG 0.899687 -31 CTTGTGGGGGGAGATGTCTGGTAAAGAAAAG 9 65 0 GAGATGCTGG 0.880455 -236 ****** **** Masking position 4 Map Score: 2.41471 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 211 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 ACGAATAAATGGCGAATCAAGTACTTAGCA 2 116 0 GGCGAATCAA 0.958664 -185 ATCCATTGATGACGAATAAATGGCGAATCA 2 127 0 GACGAATAAA 0.903659 -174 TTCACAGAGCGGCGAGCCAAATAAAAAACG 2 204 1 GGCGAGCCAA 0.98286 -97 GGGAGCATCAGGCGAATAAAGTAACAATAT 5 60 0 GGCGAATAAA 0.936504 -241 GGGTAGTATTGACAAGCCAATTACAAATCA 6 82 1 GACAAGCCAA 0.849433 -120 CGTGGTGGCAGACGAGCAAACCAGTAGCGC 6 167 1 GACGAGCAAA 0.958664 -35 ********** Masking position 5 Map Score: 1.77262 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 189 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 GCCAAATAAAAAACGGGTAAAGCCAGGTTG 2 219 1 AAACGGGTAA 0.778396 -82 TATAGGCCCGTAACTCGCATGGTTTTTATG 5 194 0 TAACTCGCAT 0.906656 -107 TATAGCCTAATAACGCGCATCTTTCATGAC 6 41 1 TAACGCGCAT 0.949748 -161 AGTGGTTCACAAACGGGCAATTT 7 4 0 AAACGGGCAA 0.972879 -193 ACTTGTTTGCAAACGGGCATGACTCCTGAC 7 31 1 AAACGGGCAT 0.966796 -166 TTTCTGTTCTTAACTCGCAAAACACGCACA 8 200 0 TAACTCGCAA 0.92288 -51 TCTGGTAAAGAAAAGGGCAATCCTCATCAG 9 50 0 AAAAGGGCAA 0.778676 -251 TTCCCAATTAAAACTCACATCAATGTTGCC 9 142 1 AAACTCACAT 0.539899 -159 CGTTGTCGATTTACTGGCAATCACGGCATT 10 102 1 TTACTGGCAA 0.700337 -183 ********** Masking position 3 Map Score: 3.32431 Number of sites scoring better than the average of aligned sites = 671 Number in coding regions = 604 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675