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"conf": 100.0, "score": 163.15217230191863, "cscore": 154.5648159785869, "sscore": 8.587356323331726, "rscore": 0.6140893623422361, "uscore": 3.328711115221232, "tscore": 4.644555845768258, "upstream_window_seq": "GCGCTGCCAGGCTCGTCGCC", "start_codon_seq": "ATG", "n_terminal_aa": "MSTVTVIGAGTIGLGWIN", "start_node_ndx": 4322, "stop_node_ndx": 5243 }, { "id": "1_7", "seq_id": "NC_003888.3:5510001-5595000", "beg": 5246, "end": 6232, "strand": "+", "length_bp": 987, "length_aa": 328, "partial_5prime": false, "partial_3prime": false, "start_type": "ATG", "rbs_motif": "AGGAGG", "rbs_spacer": "5-10bp", "gc_cont": 0.7487335359675785, "conf": 99.99, "score": 194.62803419824508, "cscore": 174.61411974174715, "sscore": 20.013914456497933, "rscore": 13.255711862001958, "uscore": 0.8303967487277194, "tscore": 4.644555845768258, "upstream_window_seq": "CCCCAGGAGGAGACCAAGTG", "start_codon_seq": "ATG", "n_terminal_aa": "MRAVQFDRYGDPDVLYVA", "start_node_ndx": 5245, "stop_node_ndx": 6229 }, { "id": "1_8", "seq_id": "NC_003888.3:5510001-5595000", "beg": 6299, "end": 6943, "strand": "+", "length_bp": 645, "length_aa": 214, "partial_5prime": false, "partial_3prime": false, "start_type": "ATG", "rbs_motif": "AGGAG", "rbs_spacer": "5-10bp", "gc_cont": 0.6883720930232559, "conf": 100.0, "score": 170.84717616713073, "cscore": 150.58646936181097, "sscore": 20.260706805319764, "rscore": 11.134202914400612, "uscore": 4.481948045150893, "tscore": 4.644555845768258, "upstream_window_seq": "AGCCCGAAGGAGACCTTTCC", "start_codon_seq": "ATG", "n_terminal_aa": "MTSSLHHAIRLTTASAIA", "start_node_ndx": 6298, "stop_node_ndx": 6940 }, { "id": "1_9", "seq_id": "NC_003888.3:5510001-5595000", "beg": 6977, "end": 7897, "strand": "+", "length_bp": 921, "length_aa": 306, "partial_5prime": false, "partial_3prime": false, "start_type": "ATG", "rbs_motif": "GGAG/GAGG", "rbs_spacer": "5-10bp", "gc_cont": 0.748099891422367, "conf": 99.99, "score": 178.46443425848005, "cscore": 169.57600460583643, "sscore": 8.88842965264361, "rscore": 5.831994637140253, "uscore": -2.5016208302648995, "tscore": 4.644555845768258, "upstream_window_seq": "GGACGAACAATGGAGAACGC", "start_codon_seq": "ATG", "n_terminal_aa": "MPKAVAIHQFGGPDVLGL", "start_node_ndx": 6976, "stop_node_ndx": 7894 }, { "id": "1_10", "seq_id": "NC_003888.3:5510001-5595000", "beg": 7894, "end": 9495, "strand": "+", "length_bp": 1602, "length_aa": 533, "partial_5prime": false, "partial_3prime": false, "start_type": "GTG", "rbs_motif": "None", "rbs_spacer": "None", "gc_cont": 0.7297128589263421, "conf": 99.99, "score": 280.25709851492644, "cscore": 283.09727274216186, "sscore": -2.8401742272354316, "rscore": -4.796415836187606, "uscore": -0.3822703328072895, "tscore": -4.134299227235431, "upstream_window_seq": "CTCGTCCTGGTGCCGGACCT", "start_codon_seq": "GTG", "n_terminal_aa": "MTANPGRPGGPADQGHPR", "start_node_ndx": 7893, "stop_node_ndx": 9492 } ] } ], "eukaryotic_intron_horizon": { "locus_name": "Human APOE (Apolipoprotein E, Chr19q13.32)", "genomic_accession": "NC_000019.10:44890001-44950000", "mrna_accession": "NM_000041.4", "genomic_window_bp": 60000, "mrna_length_bp": 1166, "kozak_window_seq": "GGCAGGAAG [ATG] AAG", "kozak_consensus_match_score": 0.914, "reconstructed_exons": [ { "exon_number": 1, "genomic_beg": 44905796, "genomic_end": 44905841, "length_bp": 46, "phase_5prime": 0, "phase_3prime": 0, "splice_acceptor_3prime_ss": "5'-Cap (TSS)", "splice_donor_5prime_ss": "CCG|GTGAGA", "exon_gc_fraction": 0.6739130434782609 }, { "exon_number": 2, "genomic_beg": 44906602, "genomic_end": 44906667, "length_bp": 66, "phase_5prime": 0, "phase_3prime": 1, "splice_acceptor_3prime_ss": "CCCCAG|ACT", "splice_donor_5prime_ss": "CAG|GTATGG", "exon_gc_fraction": 0.5606060606060606 }, { "exon_number": 3, "genomic_beg": 44907760, "genomic_end": 44907952, "length_bp": 193, "phase_5prime": 1, "phase_3prime": 0, "splice_acceptor_3prime_ss": "ACACAG|GAT", "splice_donor_5prime_ss": "GAG|GTGAGT", "exon_gc_fraction": 0.6528497409326425 }, { "exon_number": 4, "genomic_beg": 44908533, "genomic_end": 44909393, "length_bp": 861, "phase_5prime": 0, "phase_3prime": 0, "splice_acceptor_3prime_ss": "CCGCAG|GGC", "splice_donor_5prime_ss": "Poly(A) / 3'-UTR", "exon_gc_fraction": 0.7096399535423926 } ], "spliced_cds_length_bp": 954, "spliced_polypeptide_aa": 317, "prokaryotic_caller_intron_fragment_count": 5, "longest_prokaryotic_orf_in_locus_bp": 555 }, "ascii_gc_frame_and_coding_track": "Coordinate (bp) : 1 1000 2000 3000 4000 5000 (E. coli K-12 NC_000913.3)\n |---------|---------|---------|---------|---------|\nOperon Architecture: [thrL] [====== thrA (2,463 bp) ======][=thrB=][==thrC==]\nCoordinates (bp) : 190..255 337.....................2799 2801..3733 3734..5020\nDicodon cscore : +10.7 ██████████████████████████████ +93.8 +142.3\n3rd-Codon GC Skew : 53% ▆▇▆▇▇▆▇▆▇▇▆▇▇▆▇▆▇▇▆▇▇▆▇▆▇▇▆▇▇▆ 56.4% 52.8%\nRBS + TIS sscore : +12.8 +12.3 (GGAG 6bp) +7.3 +13.9 (GGAG + -1bp coupling)", "ascii_rbs_initiation_alignment": "Locus / Organism Strand Upstream RBS Window (-20 .. -1) Start N-Term AA rscore tscore sscore cscore\n-------------------------- ------ ------------------------------- ----- ---------------- ------- ------- -------- -------\nE. coli thrL (190..255) + AysaCAGGTAACGGTGCGGG (GGAG 6bp) [ATG] MKRISTTITTTITITG +5.96 +3.83 +12.75 +10.71\nE. coli thrA (337..2799) + TTCGTTACCTGGTACGCGGA (GGAG 6bp) [ATG] MRVLKFGGTSVANAER +5.96 +3.83 +12.26 +283.14\nE. coli thrB (2801..3733) + CCTGACAGTGCGGGCTTTTT (GGA 9bp) [ATG] MVKVYAPASSANMSVG +2.64 +3.83 +7.30 +93.75\nE. coli thrC (3734..5020) + GCCGTGAAACTGGATAA (-1bp TA[ATG]) [ATG] MKLYNLKDHNEQVSFA +5.96 +3.83 +13.86 +142.33\nE. coli dnaK (12163..14079) + CAACCAGACGATAGCAATTC (AGGA 8bp) [ATG] MGKIIGIDLGTTNSCV +9.04 +3.83 +13.95 +329.40\nE. coli nhaA (17489..18655) + CTTAAGTAGCGAAGCGTTAC (AGGA 7bp) [GTG] MKHLHRFFSSDASGGI +9.04 -4.87 +5.41 +146.12\nS. aureus dnaA (517..1878) + AATTAAAGGAGTTTTTATT (AGGAGG 7) [ATG] MSEKEIWEKVLEIAQE +14.18 +3.46 +18.92 +194.60\nS. coelicolor SCO5087 (t1pks) + CGCCCGCCGGAGGACCCCGC (GGAGG 6bp) [GTG] MTRRVVVTGIGVVAPG +11.24 +1.12 +13.48 +318.75\nH. sapiens APOE Exon 2 (CDS) + AGGGGGAGCCCTATAATTGG (Kozak -3A) [ATG] MKVLWAALLVTFLAGC (Kozak 0.914 + GT..AG 4-Exon Splice)" }