AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icrp_tpal_opreg_100.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #2 TP0076 39 sugar ABC transporter, permease protein (y4oR) #3 TP0077 40 capsular polysaccharide biosynthesis protein (cap5D) #4 TP0255 118 ribosomal protein L31 (rpmE) #5 TP0256 44 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (pgsA) #6 TP0257 96 glycerophosphoryldiester phosphodiesterase (glpQ) #7 TP0261 114 catabolite gene activator, putative #8 TP0418 26 galactokinase #9 TP0652 175 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #10 TP0681 88 alanine racemase (alr) #11 TP0682 92 cell division protein (ftsJ) #12 TP0734 81 purine nucleoside phosphorylase (deoD) #13 TP0736 233 hydrogenase, gamma chain (hydG) #14 TP0802 45 T. pallidum predicted coding region TP0802 #15 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) #16 TP0840 104 conserved hypothetical integral membrane protein #17 TP0949 275 membrane protein #18 TP0979 169 conserved hypothetical protein #19 TP0981 59 sensory transduction histidine kinase, putative Motif number 1 TCTATCTGTGGAGCGCGTTACGTTGGGTAGC 1 82 1 GAGCGCGTTC 0.911119 -37 GATAAACACTCTGCGCGGGTGAGTACGTGCA 3 14 1 CTGCGCGGGG 0.895029 -27 CGGTTACACCCGGCGTGTACGAGCCTTCTGG 4 33 1 CGGCGTGTAG 0.977015 -86 ACCTTTTTAAGGGCGCGGCGCGCTGTAGAAT 4 79 1 GGGCGCGGCC 0.930776 -40 TGGAGATATGCGGCGTGCTACTATGCACGGT 6 36 1 CGGCGTGCTC 0.95344 -61 CTCTGCAGGTGTGCGCGCAGGAGCGCGTGAC 7 42 1 GTGCGCGCAG 0.987548 -73 GGCGCGAGAAGTGCGCATGAGGAAGAAAGGA 9 30 0 GTGCGCATGG 0.846121 -146 TCTCGCGCCAGCGAGCGTAACACGCCAGCGG 9 52 1 GCGAGCGTAC 0.8689 -124 GGTAAGAATAGGGAGCGTAGGCGCCTGTGGC 10 13 1 GGGAGCGTAG 0.941141 -76 TACCGTTATACGGCGTGTTTGCCTTTTGTGC 11 13 1 CGGCGTGTTG 0.968975 -80 TTTGCCTTTTGTGCGAGCACGATGTGTGGGA 11 30 1 GTGCGAGCAG 0.94442 -63 ATAGCATGGGGGGCGTGTAGGAAGGT 11 77 1 GGGCGTGTAG 0.984479 -16 CGGTAACCTCGCGCGTGTACGCTCAGCGCAT 12 21 0 GCGCGTGTAG 0.981165 -61 AAGCAGCGGTCGGCGCGTTAGTTGCCTTGTG 13 120 1 CGGCGCGTTG 0.986856 -114 ATCCATCCCTCCGAGAGTTTGGTCGAAGGAG 13 205 1 CCGAGAGTTG 0.580779 -29 TTTGAAACACGGGTGCGCAACACACTACTTT 15 42 0 GGGTGCGCAC 0.761136 -36 TGCGCGCGATTGTACTGATGCG 16 93 0 GCGCGCGATG 0.887294 -12 AGACAGCTTGCGGCGTATCAGCGGCTGCTGT 17 38 1 CGGCGTATCG 0.762468 -238 TTGTGTGATCGCGCGCGTCTGTTCTCTGAAT 17 74 1 GCGCGCGTCG 0.989447 -202 GGAATAGGCCGTGAGTGTGCGTCGCTTGTGT 17 121 1 GTGAGTGTGG 0.703986 -155 AAACGGATCAGCGCGAGCAACAATCCACTAA 17 162 0 GCGCGAGCAC 0.946211 -114 TGAGGGGAAAGAGCGCGCTGGTAAAAACGGA 17 186 0 GAGCGCGCTG 0.963485 -90 CATAGGCATACTGCGAGCAACTCGGATAATA 17 236 0 CTGCGAGCAC 0.85179 -40 ATGCCTATGAGAGCGTGCGAGTACATGG 17 258 1 GAGCGTGCGG 0.930265 -18 AGCTGGGCCGTGCGCGCATGTCCGCGTCGG 18 10 1 GTGCGCGCAG 0.987548 -160 TCCGCAAATACCGCGCGTGTGTGCCGCGCGT 18 87 1 CCGCGCGTGG 0.986831 -83 CGCGTGTGTGCCGCGCGTTGCGCTTCCGGCG 18 100 1 CCGCGCGTTC 0.968866 -70 GTTGCGCTTCCGGCGTACCAGGGCGGTACGC 18 116 1 CGGCGTACCG 0.806581 -54 AGGGCGGTACGCGCGAGCGCCTCACAGCACT 18 135 1 GCGCGAGCGC 0.940149 -35 CGTACGCTTCCGGCGTACCCCAACTTACT 19 41 1 CGGCGTACCC 0.677905 -19 ********* * Masking position 5 Map Score: 49.2462 Number of sites scoring better than the average of aligned sites = 4102 Number in coding regions = 3808 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 2 CTTTTCTGCCCTCTCTTCCCCCAAGAAGAAGA 1 17 0 CTCCTCCCCC 0.885709 -102 CCCAACGTAACGCGCTCCACAGATAGAACACG 1 77 0 CGCCCCACAG 0.807928 -42 CACTCCCCCTCTTACGCTACCCAACGTAACGC 1 96 0 CTTCCTACCC 0.82497 -23 TTATCTAACCCGTACGCAACCC 2 1 0 CGTCCAACCC 0.925493 -39 ATCTGCTGCACGTACTCACCCGCGCAGAGTGT 3 19 0 CGTCCACCCG 0.953024 -22 CATTCTACAGCGCGCCGCGCCCTTAAAAAGGT 4 79 0 CGCCGCGCCC 0.842417 -40 TGAATCGCTCCTTTCCCCATTCTACAGCGCGC 4 96 0 CTTCCCATTC 0.397199 -23 CTGCAGAGATCGTTCGCACGCCTTTTCCAGGA 7 18 0 CGTCCACGCC 0.951345 -97 ATTCACGTCACGCGCTCCTGCGCGCACACCTG 7 47 0 CGCCCCTGCG 0.941988 -68 AACTTTCCCCTGCCAGAAAAGCAT 8 3 1 CTTCCCTGCC 0.856398 -24 GTGGTCCTTTCTTCCTCATGCGCACTTCTCGC 9 26 1 CTTCCATGCG 0.572847 -150 ATGCGCACTTCTCGCGCCAGCGAGCGTAACAC 9 43 1 CTCCCCAGCG 0.929014 -133 CCAGCAAGGACACACGGACGCCTTGCGTACCC 9 91 1 CACCGACGCC 0.697404 -85 GGACGCCTTGCGTACCCCAACCGCGAGCCTTG 9 106 1 CGTCCCAACC 0.904385 -70 CAGGCGCCTACGCTCCCTATTCTTACCCA 10 8 0 CGCCCTATTC 0.412967 -81 ACACTGACAGCTCCCACACATCGTGCTCGCAC 11 40 0 CTCCCACATC 0.592702 -53 ACGCTCAGCGCATGCAGCACCCG 12 2 0 CATCGCACCC 0.742167 -80 ATGCGCTGAGCGTACACGCGCGAGGTTACCGA 12 21 1 CGTCCGCGCG 0.714265 -61 CGTCACTCCCTCCCTTCGTGGGGCCTA 12 65 0 CTCCCCCTTC 0.708743 -17 GTAAACCTCCCCGACACGTATATCTGTT 13 7 1 CTCCGACACG 0.638095 -227 GCAGGTTTTGCGTGCAGTCCTCATTCAAGCAA 13 69 0 CGTCGTCCTC 0.806474 -165 GCTGTACTATCATCCATCCCTCCGAGAGTTTG 13 194 1 CATCTCCCTC 0.325984 -40 TTCCTCTCCATACCCTCGTGGGGGATGCCC 14 9 1 CATCCTCGTG 0.349881 -37 CACTACTTTCCTTACGCAAACGGGAGGTGGTG 15 19 0 CTTCCAAACG 0.474799 -59 TTTCTCCCCCTCACCTATTTCTCCT 16 4 1 CTCCCTCACC 0.806124 -101 TCTGTAGAGCCTTTCCTCCGTCCTTAAACTGA 16 35 1 CTTCTCCGTC 0.507948 -70 TCACACAACACGCACAGCAGCCGCTGATACGC 17 50 0 CGCCGCAGCC 0.959057 -226 ACACAAGCGACGCACACTCACGGCCTATTCCT 17 120 0 CGCCCTCACG 0.874803 -156 GATTGTTGCTCGCGCTGATCCGTTTTTACCAG 17 168 1 CGCCGATCCG 0.796202 -108 TTTACCAGCGCGCTCTTTCCCCTCATCTTTTG 17 192 1 CGCCTTCCCC 0.836184 -84 CGGACATGCGCGCACGGCCCAGCT 18 3 0 CGCCGCCCAG 0.83499 -167 TTCTAGTTCGCGTGCCCCTGTGCCCGCAATGG 18 44 1 CGTCCCTGTG 0.758073 -126 GGAAGCGCAACGCGCGGCACACACGCGCGGTA 18 95 0 CGCCGCACAC 0.756022 -75 GGCGCTCGCGCGTACCGCCCTGGTACGCCGGA 18 124 0 CGTCGCCCTG 0.914301 -46 GCGCGAGCGCCTCACAGCACTCAGGATATTAG 18 145 1 CTCCGCACTC 0.818216 -25 GCGTGAAAAACGTACGCTTCCGGCGTACCCCA 19 31 1 CGTCCTTCCG 0.802903 -29 *** * ****** Masking position 5 Map Score: 36.4683 Number of sites scoring better than the average of aligned sites = 4968 Number in coding regions = 4412 Number in noncoding regions = 556 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 3 TCCCCCAAGAAGAAGAGACTTT 1 2 0 AGAAGAGCTT 0.822889 -117 AAGAGAGGGCAGAAAAGATGCTGGATATGAG 1 32 1 AGAAAAGTGC 0.919245 -87 CTGTAGAATGGGGAAAGGAGCGATTCAG 4 101 1 GGGAAAGAGC 0.941362 -18 ACTCACCTAGGGGAAAGACGTAATGGTACAC 5 24 0 GGGAAAGCGT 0.972071 -21 ATAACAGGGGAGGAGAGAAGTTT 6 84 1 AGGAGAGAGT 0.907915 -13 CGCCTTTTCCAGGAAAGGTGG 7 1 0 AGGAAAGTGG 0.760309 -114 CACCTTTCCTGGAAAAGGCGTGCGAACGATC 7 12 1 GGAAAAGCGT 0.96626 -103 TTCCCCTGCCAGAAAAGCATTT 8 15 1 AGAAAAGATT 0.869397 -12 AACAATGATGAGAAAAGCAGCGGTCGGCGCG 13 106 1 AGAAAAGAGC 0.96319 -128 GATTTGTCAAAGAAAAGCCTTTCTTCAGCTC 13 156 0 AGAAAAGCTT 0.936332 -78 CGTTTGCGTAAGGAAAGTAGTGTGTTGCGCA 15 29 1 AGGAAAGAGT 0.968952 -49 TTAAGGACGGAGGAAAGGCTCTACAGAGGAG 16 31 0 AGGAAAGCTC 0.947951 -74 GTAAATTCAGAGAACAGACGCGCGCGATCAC 17 78 0 AGAACAGCGC 0.908457 -198 TCACGCGGTTTGAAAAGCCGTGCAAC 19 6 0 TGAAAAGCGT 0.87817 -54 ******* *** Masking position 6 Map Score: 16.5127 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 189 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 TCCAGCATCTTTTCTGCCCTCTCTTCCCCC 1 27 0 TTTCTGCCCT 0.916551 -92 CGTCATTCTGTTTCCGCTCATATCCAGCAT 1 49 0 TTTCCGCTCA 0.881797 -70 GCACTCCCCCTCTTACGCTACCC 1 106 0 CTCCCCCTCT 0.985455 -13 GCTATCTGCTCCTGCTCTTATCTAACCC 2 22 0 CTCCTGCTCT 0.977004 -18 AAACTTCTCTCCTCCCCTGTTATAGAAT 6 79 0 CTCCTCCCCT 0.97545 -18 CGTCACTCCCTCCCTTCGTGGGGCC 12 67 0 CTCCCTCCCT 0.907426 -15 AAAAGCCTTTCTTCAGCTCTGTCGCACAAG 13 145 0 CTTCAGCTCT 0.846409 -89 TTTCTCCCCCTCACCTATTTCTC 16 4 1 CTCCCCCTCA 0.964269 -101 CCCTCACCTATTTCTCCTCTGTAGAGCCTT 16 18 1 TTTCTCCTCT 0.921535 -87 TCACGGCCTATTCCTGCCTTTCAGCGGTAA 17 105 0 TTCCTGCCTT 0.622072 -171 CAGCGCGCTCTTTCCCCTCATCTTTTGCCT 17 197 1 TTTCCCCTCA 0.881797 -79 ********** Masking position 2 Map Score: 12.246 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 253 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 GTTACATCCACCCTCTTCCAGAAGGCTCGTACACGC 4 45 0 CTCTCAAAGC 0.991773 -74 TTCTCTCCTCCCCTGTTATAGAATGCACAGATCGTC 6 67 0 CTGTTAAAGC 0.936038 -30 TGCAATCAGGCATTGATCCATTTAGCAAACTTGCGT 10 45 1 CTGACATTGC 0.816044 -44 TGGGAGCTGTCAGTGTAACACATAGCATGGGGGGCG 11 56 1 CTGTCAATGC 0.979249 -37 GTGCAGTCCTCATTCAAGCAAAACGCCATCGGCGCC 13 54 0 CTCACAAAGC 0.984433 -180 CTTTCTTCAGCTCTGTCGCACAAGGCAACTAACGCG 13 133 0 CTGTCAAAGC 0.993348 -101 TGTTGCGCACCCGTGTTTCAAAAGGAATGTAAACGC 15 51 1 CTGTCAAAGA 0.943317 -27 ACGCCGCAAGCTGTCTTCCACAACGGAAACCAAGAG 17 18 0 CTCTCAAAGG 0.952274 -258 CAGACGCGCGCGATCACACAACACGCACAGCAGCCG 17 59 0 CTCACACAGC 0.94381 -217 * *** ** ** ** Masking position 10 Map Score: 6.54668 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 48 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GAGTACACCTGTGGTGTACCATTAC 5 6 1 CACCTGTGGT 0.796072 -39 GAGCGTAACACGCCAGCGGTAATCTGTCCA 9 64 1 CGCCAGCGGT 0.981416 -112 CCAAATACCGCACCATCGGCCTCCGCAATG 9 149 1 CACCATCGGC 0.935093 -27 GGAGCGTAGGCGCCTGTGGCATGCAATCAG 10 24 1 CGCCTGTGGC 0.990165 -65 GTACGCTCAGCGCATGCAGCACCCG 12 6 0 CGCATGCAGC 0.885767 -76 TCAAGCAAAACGCCATCGGCGCCGAGAAGG 13 47 0 CGCCATCGGC 0.986516 -187 TGTGGAAGACAGCTTGCGGCGTATCAGCGG 17 32 1 AGCTTGCGGC 0.951438 -244 CCGCGCGTTGCGCTTCCGGCGTACCAGGGC 18 110 1 CGCTTCCGGC 0.988281 -60 GAAAAACGTACGCTTCCGGCGTACCCCAAC 19 35 1 CGCTTCCGGC 0.988281 -25 ********** Masking position 3 Map Score: 11.1442 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 360 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 CCCTCTCTTCCCCCAAGAAGAAGAGACTTT 1 11 0 CCCCAAGAAG 0.974543 -108 GCACGTACTCACCCGCGCAGAGTGTTTATC 3 14 0 ACCCGCGCAG 0.930919 -27 ACGCTCGCTGGCGCGAGAAGTGCGCATGAG 9 40 0 GCGCGAGAAG 0.909933 -136 CTGAGCGTACACGCGCGAGGTTACCGAAAC 12 26 1 ACGCGCGAGG 0.916921 -56 TGGGTCTAGGCCCCACGAAGGGAGGGAGTG 12 59 1 CCCCACGAAG 0.988888 -23 ACGCCATCGGCGCCGAGAAGGGTCCGATGA 13 38 0 CGCCGAGAAG 0.942276 -196 GGGGGGCATCCCCCACGAGGGTATGGAGAG 14 14 0 CCCCACGAGG 0.97694 -32 CGCTGATACGCCGCAAGCTGTCTTCCACAA 17 31 0 CCGCAAGCTG 0.871733 -245 CGGATAATAACGGCACGAAGGCAAAAGATG 17 215 0 CGGCACGAAG 0.959899 -61 CGCGTGTGTGCCGCGCGTTGCGCTTCCGGC 18 100 1 CCGCGCGTTG 0.875335 -70 ********** Masking position 4 Map Score: 10.4832 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 315 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 GCACTCCCCCTCTTACGCTACCCAA 1 104 0 CCCCCTCTTA 0.970233 -15 GCTATCTGCTCCTGCTCTTATCTAACCCGT 2 20 0 CCTGCTCTTA 0.802767 -20 ACGCCGCATATCTCCACTGAGCGCTGATCC 6 22 0 TCTCCACTGA 0.680471 -75 AAACTTCTCTCCTCCCCTGTTATAGAATGC 6 77 0 CCTCCCCTGT 0.973692 -20 GAAAGGACCACCCCGTCTTACGCATT 9 7 0 CCCCGTCTTA 0.843618 -169 TGGGGGATGCCCCCCTGTGTACGCTTC 14 29 1 CCCCCTGTGT 0.90909 -17 GACAACACCACCTCCCGTTTGCGTAAGGAA 15 14 1 CCTCCCGTTT 0.890601 -64 TTTCTCCCCCTCACCTATTTCTCCTCTG 16 9 1 CCTCACCTAT 0.666791 -96 CTCACCTATTTCTCCTCTGTAGAGCCTTTC 16 20 1 TCTCCTCTGT 0.873622 -85 CGCTCTTTCCCCTCATCTTTTGCCTTCGTG 17 202 1 CCTCATCTTT 0.921172 -74 TTCCGGCGTACCCCAACTTACT 19 48 1 CCCCAACTTA 0.770998 -12 ********** Masking position 8 Map Score: 3.77318 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 325 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 TCTCCACTGAGCGCTGATCCTACCTTCAGT 6 12 0 GCGCTGATCC 0.981321 -85 GTTATAGAATGCACAGATCGTCACCGTGCA 6 59 0 GCACAGATCG 0.950919 -38 GCGCACACCTGCAGAGATCGTTCGCACGCC 7 28 0 GCAGAGATCG 0.929225 -87 TGCGTAAGACGGGGTGGTCCTTTCTTCCTC 9 13 1 GGGGTGGTCC 0.816433 -163 CCTTCTCATTGCGGAGGCCGATGGTGCGGT 9 155 0 GCGGAGGCCG 0.947628 -21 ATGCAATCAGGCATTGATCCATTTAGCAAA 10 44 1 GCATTGATCC 0.797204 -45 GGTGCTGCATGCGCTGAGCGTACACGCGCG 12 13 1 GCGCTGAGCG 0.939215 -69 ACCCTTCTCGGCGCCGATGGCGTTTTGCTT 13 45 1 GCGCCGATGG 0.882852 -189 GATGAGAAAAGCAGCGGTCGGCGCGTTAGT 13 112 1 GCAGCGGTCG 0.948246 -122 ATTGTTGCTCGCGCTGATCCGTTTTTACCA 17 169 1 GCGCTGATCC 0.981321 -107 TGGGCCGTGCGCGCATGTCCGCGTCGGCCG 18 14 1 GCGCATGTCC 0.77908 -156 GCGCATGTCCGCGTCGGCCGTTCTAGTTCG 18 24 1 GCGTCGGCCG 0.877637 -146 ********** Masking position 1 Map Score: 10.8965 Number of sites scoring better than the average of aligned sites = 621 Number in coding regions = 576 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 10 TCTGTTTCCGCTCATATCCAGCATCTTTTCTG 1 41 0 CCATATCCGC 0.974588 -78 ACAGAACATACCCAAATACCGCACCATCGGCC 9 138 1 CCAAATACGC 0.979131 -38 ACATCGTGCTCGCACAAAAGGCAAACACGCCG 11 23 0 CCACAAAAGC 0.95036 -70 TGACAGCTCCCACACATCGTGCTCGCACAAAA 11 36 0 CCACATCGGC 0.977414 -57 GAGGACTGCACGCAAAACCTGCCAGGAAACAA 13 79 1 CCAAAACCGC 0.986741 -155 CGCGCGCGATCACACAACACGCACAGCAGCCG 17 59 0 CCACAACAGC 0.975334 -217 CTTTGTTCTCCGCAAATACCGCGCGTGTGTGC 18 79 1 CCAAATACGC 0.979131 -91 * ******* ** Masking position 6 Map Score: 6.25866 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 75 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ********** No masking Map Score: 9.90086e-13 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: 9.90086e-13 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: 9.90086e-13 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