diff --git a/README.md b/README.md index 9867293a30a586031d31f0effd634ef7a3ddc92a..e4ff80808d75395e25120365b950b343d8c676c6 100644 --- a/README.md +++ b/README.md @@ -11,9 +11,9 @@ pretty_name: PDB --- # PDB - upload_date: 2023-11-22 14:34:34 + upload_date: 2023-11-24 11:40:55 user: alberic - source: `CT_files_pdbee` (CT files format) + source: `bpSEQ_files_pdbee` (BPSEQ files format) Data types: - structure (Read from source.) diff --git a/data.json b/data.json index 2a93d214dbe52bcf69cbfa7e4f04ed58c9cee781..eadcc5cd115022034fc5f9c00857774c5dae1fff 100644 --- a/data.json +++ b/data.json @@ -1,355 +1,355 @@ { -"1OSU-2D":{"sequence": "UUCGCG", "paired_bases": []}, -"2BE0-2D":{"sequence": "CGCGUCACACCGGUGAAGUCGCCGCGUCACACCGGUGAAGUCGC", "paired_bases": [[1, 43], [2, 42], [3, 41], [5, 39], [7, 36], [8, 35], [9, 34], [10, 33], [11, 32], [12, 31], [13, 30], [14, 29], [17, 27], [19, 25], [20, 24], [21, 23]]}, -"6C8N-2D":{"sequence": "CCCGACUUAAGUCGGCCCGACUUAAGUCGG", "paired_bases": [[1, 29], [2, 28], [3, 27], [4, 26], [5, 25], [6, 24], [7, 23], [8, 22], [9, 21], [10, 20], [11, 19], [12, 18], [13, 17], [14, 16]]}, -"4F8V-2D":{"sequence": "GCGUCACACCGGUGAAGUCGCGCGUCACACCGGUGAAGUCGC", "paired_bases": [[0, 41], [1, 40], [2, 39], [4, 37], [6, 34], [7, 33], [8, 32], [9, 31], [10, 30], [11, 29], [12, 28], [13, 27], [16, 25], [18, 23], [19, 22], [20, 21]]}, -"5FJ0-2D":{"sequence": "GGCGAAGAACCGGGGAGCCGGCGAAGAACCGGGGAGCC", "paired_bases": [[0, 37], [1, 36], [2, 35], [9, 31], [10, 30], [11, 29], [12, 28], [16, 21], [17, 20], [18, 19]]}, -"4NXH-2D":{"sequence": "UGCUCCUAGUACGAGAGGACCGGAGUG", "paired_bases": [[1, 25], [2, 24], [3, 23], [4, 22], [5, 21], [11, 16]]}, -"406D-2D":{"sequence": "CACCGGAUGGUUCGGUGCACCGGAUGGUUCGGUG", "paired_bases": [[0, 33], [1, 32], [2, 31], [3, 30], [4, 29], [5, 28], [6, 27], [7, 26], [9, 24], [10, 23], [11, 22], [12, 21], [13, 20], [14, 19], [15, 18], [16, 17]]}, -"4FNJ-2D":{"sequence": "CUGCUGGCUAAGGCAUGAAAGUGCUAUGCCUGCUG", "paired_bases": [[0, 34], [2, 32], [3, 31], [5, 29], [6, 28], [7, 27], [10, 26], [11, 24], [12, 23], [13, 22], [14, 21], [15, 20]]}, -"8SX6-2D":{"sequence": "UCCGACUUAAGUCGUCCGACUUAAGUCGGAG", "paired_bases": [[1, 30], [2, 27], [3, 26], [4, 25], [5, 24], [6, 23], [7, 22], [8, 21], [9, 20], [10, 19], [11, 18], [12, 17], [13, 16], [15, 28]]}, -"2HOM-2D":{"sequence": "GCGACUCGGGGUGCCCUUCUGCGUGAAGGCUGAGAAAUACCCGUAUCACCUGAUCUGGAUAAUGCCAGCGUAGGGAAGUCGCA", "paired_bases": [[0, 81], [1, 80], [2, 79], [3, 78], [4, 77], [5, 76], [6, 42], [7, 41], [8, 40], [9, 39], [11, 36], [12, 29], [13, 28], [14, 27], [48, 73], [49, 72], [50, 71], [54, 67], [55, 66], [56, 65], [57, 64]]}, -"3DJ0-2D":{"sequence": "GGCCGACGGAGGCGCGCCCGAGAUGAGUAGGCUGUCCCAUCAGGGGAGGAAUCGGGGACGGCUGAAAGGCGAGGGCGCCGAAGGGUGCAGAGUUCCUCCCGCUCUGCAUGCCUGGGGGUAUGGGGAAUACCCAUACCACUGUCACGGAGGUCUCUCCGUGGAGAGCCGUCGGUC", "paired_bases": [[0, 173], [1, 172], [2, 171], [3, 170], [4, 169], [5, 168], [6, 167], [7, 166], [8, 165], [11, 78], [13, 77], [14, 76], [15, 75], [16, 74], [17, 73], [18, 72], [21, 69], [29, 62], [30, 61], [31, 60], [32, 59], [33, 58], [34, 57], [35, 56], [36, 55], [37, 54], [40, 53], [43, 99], [44, 98], [45, 97], [46, 96], [47, 95], [48, 94], [81, 112], [82, 111], [83, 110], [84, 108], [85, 107], [86, 106], [87, 105], [88, 104], [89, 103], [90, 102], [91, 101], [92, 100], [113, 139], [114, 138], [116, 136], [117, 135], [118, 134], [119, 133], [120, 132], [121, 131], [122, 130], [123, 129], [141, 160], [142, 159], [143, 158], [144, 157], [145, 156], [146, 155], [147, 154], [148, 153]]}, -"1KD4-2D":{"sequence": "GGUCACAGCCCGGUCACAGCCC", "paired_bases": [[0, 20], [1, 19], [2, 18], [7, 13], [8, 12], [9, 11]]}, -"469D-2D":{"sequence": "CGCGAAUUCGCGCGCGAAUUCGCG", "paired_bases": [[0, 23], [1, 22], [2, 21], [3, 20], [4, 19], [5, 18], [6, 17], [7, 16], [8, 15], [9, 14], [10, 13], [11, 12]]}, -"4P43-2D":{"sequence": "UUGCGUCUCGUCGACGAAGUCGCUUGCGUCUCGUCGACGAAGUCGC", "paired_bases": [[2, 45], [3, 44], [4, 43], [6, 41], [7, 39], [8, 38], [9, 37], [10, 36], [11, 35], [12, 34], [13, 33], [14, 32], [15, 31], [16, 30], [18, 29], [20, 27], [21, 26], [22, 25]]}, +"4FRG-2D":{"sequence": "GGCCUAAAAGCAUAGUGGGAAAGUGACGUGAAAUUCGUCCAGAUGCGAAAGCAUACGGUUAUACUCCGAAUGCCACCUAGGCCAGGCCUAAAAGCAUAGUGGGAAAGUGACGUGAAAUUCGUCCAGAUGCGAAAGCAUACGGUUAUACUCCGAAUGCCACCUAGGCCA", "paired_bases": [[0, 82], [1, 81], [2, 80], [3, 79], [4, 78], [5, 77], [10, 71], [14, 75], [15, 74], [16, 73], [17, 72], [22, 39], [24, 38], [25, 37], [26, 36], [27, 35], [40, 64], [41, 63], [42, 53], [43, 52], [44, 51], [45, 50], [55, 67], [56, 66], [57, 65], [84, 166], [85, 165], [86, 164], [87, 163], [88, 162], [89, 161], [94, 155], [98, 159], [99, 158], [100, 157], [101, 156], [106, 123], [108, 122], [109, 121], [110, 120], [111, 119], [124, 148], [125, 147], [126, 137], [127, 136], [128, 135], [129, 134], [139, 151], [140, 150], [141, 149]]}, +"4YAZ-2D":{"sequence": "GGUACACGACAAUACUAAACCAUCCGCGAGGAUGGGGCGGAAAGCCUAAGGGUCUCCCUGAGACAGCCGGGCUGCCGAAAUAUCGGUACACGACAAUACUAAACCAUCCGCGAGGAUGGGGCGGAAAGCCUAAGGGUCUCCCUGAGACAGCCGGGCUGCCGAAAUAUCAA", "paired_bases": [[0, 83], [1, 82], [2, 81], [3, 80], [6, 76], [7, 75], [14, 39], [15, 38], [19, 34], [20, 33], [21, 32], [22, 31], [23, 30], [24, 29], [37, 65], [43, 71], [44, 70], [45, 69], [46, 68], [49, 67], [50, 66], [51, 63], [52, 62], [53, 61], [54, 60], [55, 59], [84, 167], [85, 166], [86, 165], [87, 164], [90, 160], [91, 159], [98, 123], [99, 122], [103, 118], [104, 117], [105, 116], [106, 115], [107, 114], [108, 113], [121, 149], [127, 155], [128, 154], [129, 153], [130, 152], [133, 151], [134, 150], [135, 147], [136, 146], [137, 145], [138, 144], [139, 143]]}, +"8SWG-2D":{"sequence": "CCCGACUUAAGUCGCCCGACUUAAGUCG", "paired_bases": [[2, 27], [3, 26], [4, 25], [5, 24], [6, 23], [7, 22], [8, 21], [9, 20], [10, 19], [11, 18], [12, 17], [13, 16]]}, +"3Q3Z-2D":{"sequence": "GCGCGGAAACAAUGAUGAAUGGGUUUAAAUUGGGCACUUGACUCAUUUUGAGUUAGUAGUGCAACCGACCGUGCUGCGCGGAAACAAUGAUGAAUGGGUUUAAAUUGGGCACUUGACUCAUUUUGAGUUAGUAGUGCAACCGACCGUGCUGGGG", "paired_bases": [[0, 73], [1, 72], [2, 71], [3, 70], [4, 69], [5, 68], [8, 52], [9, 51], [16, 47], [17, 46], [18, 45], [19, 44], [20, 43], [21, 42], [22, 41], [23, 40], [24, 39], [30, 62], [31, 65], [32, 64], [33, 61], [34, 60], [35, 59], [36, 58], [37, 57], [75, 148], [76, 147], [77, 146], [78, 145], [79, 144], [80, 143], [83, 127], [84, 126], [91, 122], [92, 121], [93, 120], [94, 119], [95, 118], [96, 117], [97, 116], [98, 115], [99, 114], [105, 137], [106, 140], [107, 139], [108, 136], [109, 135], [110, 134], [111, 133], [112, 132]]}, +"1F1T-2D":{"sequence": "GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC", "paired_bases": [[0, 37], [1, 36], [2, 35], [3, 34], [4, 33], [5, 32], [6, 28], [7, 27], [9, 22], [10, 21], [11, 20], [12, 19], [13, 18]]}, +"4RBZ-2D":{"sequence": "CGCGAAUUAGCG", "paired_bases": []}, +"4JRD-2D":{"sequence": "AAAAAAAAAAAAAAAAAAAAAA", "paired_bases": []}, +"2XO1-2D":{"sequence": "GAACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUC", "paired_bases": [[2, 64], [3, 63], [4, 62], [5, 61], [6, 60], [7, 37], [10, 30], [12, 28], [13, 27], [14, 26], [15, 25], [16, 24], [22, 46], [23, 45], [31, 38], [39, 57], [40, 56], [41, 55], [42, 54], [43, 53], [44, 52]]}, +"7KGA-2D":{"sequence": "GGGGGCCAGAUGUCAUGUCUCUCAAGCCUAGGAGACACUAGACACUCUGGACUAUCGGUUAGAGGAAACCCCCCCAAAAAUGUAUAGGCUGGGGGCCAGAUGUCAUGUCUCUCAAGCCUAGGAGACACUAGACACUCUGGACUAUCGGUUAGAGGAAACCCCCCCAAAAAUGUAUAGGCU", "paired_bases": [[0, 74], [1, 73], [2, 72], [3, 71], [4, 70], [5, 49], [6, 48], [7, 47], [8, 46], [9, 45], [10, 43], [11, 42], [12, 41], [13, 40], [14, 38], [15, 36], [16, 35], [17, 34], [18, 33], [19, 32], [20, 31], [21, 30], [25, 88], [26, 87], [27, 86], [28, 85], [50, 144], [51, 64], [52, 63], [54, 140], [56, 159], [57, 158], [58, 157], [66, 149], [67, 148], [68, 147], [69, 146], [90, 164], [91, 163], [92, 162], [93, 161], [94, 160], [95, 139], [96, 138], [97, 137], [98, 136], [99, 135], [100, 133], [101, 132], [102, 131], [103, 130], [104, 128], [105, 126], [106, 125], [107, 124], [108, 123], [109, 122], [110, 121], [111, 120], [115, 178], [116, 177], [117, 176], [118, 175], [119, 174], [141, 154], [142, 153]]}, +"6QIQ-2D":{"sequence": "GCAGCAGCGCAGCAGC", "paired_bases": [[0, 15], [1, 14], [6, 9], [7, 8]]}, +"205D-2D":{"sequence": "GGACUUUGGUCCGGACUUUGGUCC", "paired_bases": [[0, 23], [1, 22], [2, 21], [3, 20], [4, 19], [7, 16], [8, 15], [9, 14], [10, 13], [11, 12]]}, +"7EEM-2D":{"sequence": "UGCUCCUAGUACGAGAGGACCGGAGU", "paired_bases": [[1, 25], [2, 24], [3, 23], [4, 22], [5, 21], [11, 16]]}, +"5V0K-2D":{"sequence": "CCCGACUUAAGUC", "paired_bases": []}, +"5V0J-2D":{"sequence": "CCAGACUUAAGUCUCCAGACUUAAGUCU", "paired_bases": [[2, 27], [3, 26], [4, 25], [5, 24], [6, 23], [7, 22], [8, 21], [9, 20], [10, 19], [11, 18], [12, 17], [13, 16]]}, +"2O3X-2D":{"sequence": "UUGCGUCACACCGGUGAAGUCGCUUGCGUCACACCGGUGAAGUCGC", "paired_bases": [[2, 45], [3, 44], [4, 43], [6, 41], [8, 38], [9, 37], [10, 36], [11, 35], [12, 34], [13, 33], [14, 32], [15, 31], [18, 29], [20, 27], [21, 26], [22, 25]]}, "2O3Y-2D":{"sequence": "UUGCGUCGCUCCGGAAAAGUCGCUUGCGUCGCUCCGGAAAAGUCGC", "paired_bases": [[2, 45], [3, 44], [4, 43], [6, 41], [9, 37], [10, 36], [11, 35], [12, 34], [13, 33], [14, 32], [18, 29], [20, 27], [21, 26], [22, 25]]}, -"5LR3-2D":{"sequence": "GCCGGAUGGCGCCGGAUGGC", "paired_bases": [[0, 19], [1, 18], [2, 17], [7, 12], [8, 11], [9, 10]]}, -"310D-2D":{"sequence": "CGCGCGCGCGCG", "paired_bases": [[0, 11], [1, 10], [2, 9], [3, 8], [4, 7], [5, 6]]}, -"5NZ3-2D":{"sequence": "CCGGACGAGGUGCGCCGUACCCGGUCAGGACAAGACGGCGC", "paired_bases": [[0, 23], [1, 22], [2, 21], [3, 20], [11, 40], [12, 39], [13, 38], [14, 37], [15, 36], [16, 35], [17, 34], [19, 28]]}, +"1MWL-2D":{"sequence": "CGCGUCACACCGGUGAAGUCGCCGCGUCACACCGGUGAAGUCGC", "paired_bases": [[1, 43], [2, 42], [3, 41], [5, 39], [7, 36], [8, 35], [9, 34], [10, 33], [11, 32], [12, 31], [13, 30], [14, 29], [17, 27], [19, 25], [20, 24], [21, 23]]}, +"8D2B-2D":{"sequence": "GGCGAUACCAGCCGAAAGGCCCUUGGCAGCGCC", "paired_bases": [[0, 32], [1, 31], [2, 30], [3, 29], [7, 25], [8, 24], [10, 19], [11, 18], [12, 17]]}, +"5DA6-2D":{"sequence": "AGAGAAGAAAGGGAAAUUUUUUUUUUUUUUUU", "paired_bases": []}, +"6U89-2D":{"sequence": "CUGUACACUGUACAGG", "paired_bases": [[0, 15], [1, 13], [2, 12], [3, 11], [4, 10], [5, 9], [6, 8], [7, 14]]}, +"4WFL-2D":{"sequence": "UGCCGUGCUAAGCGGGGAGGUAGCGGUGCCCUGUACCUGCAAUCCGCUCUAGCAGGGCCGAAUCCCUUCUCGAGGUUCGGUAACGAAUCGACAGAAGGUGCACGGUC", "paired_bases": [[1, 105], [2, 104], [3, 103], [4, 102], [5, 101], [6, 100], [7, 99], [11, 57], [12, 56], [13, 31], [14, 30], [15, 29], [16, 28], [21, 47], [22, 46], [23, 45], [24, 44], [25, 43], [35, 55], [36, 54], [37, 53], [38, 52], [39, 51], [64, 97], [65, 96], [66, 95], [67, 94], [68, 93], [69, 92], [73, 88], [74, 87], [75, 86], [76, 85], [77, 84], [78, 83]]}, +"2EES-2D":{"sequence": "GGACAUUUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACAAUGUCC", "paired_bases": [[1, 65], [2, 64], [3, 63], [4, 62], [5, 61], [6, 60], [7, 37], [10, 30], [12, 28], [13, 27], [14, 26], [15, 25], [16, 24], [22, 46], [23, 45], [31, 38], [39, 57], [40, 56], [41, 55], [42, 54], [43, 53], [44, 52]]}, +"283D-2D":{"sequence": "GGCCGAAAGGCC", "paired_bases": []}, +"1ZEV-2D":{"sequence": "CUGCUGCUGCUGCUGCUGCUGCUGCUGCUGCUGCUG", "paired_bases": [[0, 35], [2, 33], [3, 32], [5, 30], [6, 29], [8, 27], [9, 26], [11, 24], [12, 23], [14, 21], [15, 20], [17, 18]]}, +"7UR5-2D":{"sequence": "GGAGGGGAACUUCUAUCUGGUGAUAGACGGGAACUCUAAAUUCCUUGAAAUGCCUCGCCGCAUUGGGUUCGAUUCCCUUCCCCUCCGCCA", "paired_bases": [[0, 85], [1, 84], [2, 83], [3, 82], [4, 81], [5, 80], [6, 79], [7, 78], [8, 77], [11, 26], [12, 25], [13, 24], [14, 23], [15, 22], [16, 21], [19, 69], [27, 46], [28, 44], [29, 43], [30, 42], [31, 41], [32, 40], [48, 63], [49, 62], [50, 61], [51, 60], [52, 59], [64, 76], [65, 75], [66, 74]]}, +"6V9D-2D":{"sequence": "AUCGAGGGAGUGGUGAGGAUGAGGCGAUAUCGAGGGAGUGGUGAGGAUGAGGCGA", "paired_bases": [[1, 32], [2, 31], [3, 30], [4, 29]]}, +"1XJR-2D":{"sequence": "GGAGUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUU", "paired_bases": [[2, 46], [3, 45], [4, 44], [5, 43], [6, 42], [7, 41], [8, 40], [12, 38], [13, 36], [14, 35], [15, 34], [17, 31], [18, 30], [19, 27], [20, 26]]}, +"3D2G-2D":{"sequence": "GGGACCAGGGGUGCUUGUUCACAGGCUGAGAAAGUCCCUUUGAACCUGAACAGGGUAAUGCCUGCGCAGGGAGUGUC", "paired_bases": [[2, 76], [3, 75], [4, 74], [5, 72], [6, 38], [7, 37], [8, 36], [9, 35], [12, 25], [13, 24], [14, 23], [15, 22], [16, 21], [44, 69], [45, 68], [46, 67], [50, 63], [51, 62], [52, 61], [53, 60]]}, +"3NJ6-2D":{"sequence": "GGCAGCAGCC", "paired_bases": []}, +"4NLF-2D":{"sequence": "UGCUCCUAGUACGAGAGGACCGGAGUG", "paired_bases": [[1, 25], [2, 24], [3, 23], [4, 22], [5, 21], [11, 16]]}, +"3NJ7-2D":{"sequence": "GGCAGCAGCCGGCAGCAGCC", "paired_bases": [[0, 19], [1, 18], [2, 17], [4, 15], [5, 14], [7, 12], [8, 11], [9, 10]]}, +"6UGI-2D":{"sequence": "GGAGCGGGCGGGUUCGAGUCCCGUCCGUUCC", "paired_bases": [[0, 30], [1, 29], [2, 28], [3, 27], [4, 26], [5, 25], [6, 24], [7, 23], [8, 22], [9, 21], [10, 20], [11, 19]]}, +"6N5S-2D":{"sequence": "GGUUGCCGAAUCCAAAGUUGGUACGGAGGAACCGCUUUUUGGGGUUAAUCUGCAGUGAAGCUGCAGUAGGGAUACCUUCUGUCCCGCACCCGACAGCUAACUCCGGAGGCAAUAAAGGAAGGAGAA", "paired_bases": [[3, 110], [4, 109], [5, 108], [6, 107], [11, 20], [12, 19], [13, 18], [23, 104], [24, 103], [25, 102], [26, 101], [27, 100], [32, 95], [38, 92], [40, 93], [41, 90], [42, 89], [43, 88], [44, 87], [49, 65], [50, 64], [51, 63], [52, 62], [53, 61], [54, 60], [68, 84], [69, 83], [70, 82], [71, 81], [72, 80], [74, 121], [75, 120], [76, 119], [77, 118], [78, 117], [79, 116]]}, +"3JXR-2D":{"sequence": "CGCGCGCGCGCG", "paired_bases": [[0, 11], [1, 10], [2, 9], [3, 8], [4, 7], [5, 6]]}, +"4GPY-2D":{"sequence": "UUGCGUCACGCCGGCGAAGUCGCUUGCGUCACGCCGGCGAAGUCGC", "paired_bases": [[2, 45], [3, 44], [4, 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[[2, 45], [3, 44], [4, 43], [6, 41], [8, 38], [9, 37], [10, 36], [11, 35], [12, 34], [13, 33], [14, 32], [15, 31], [18, 29], [20, 27], [21, 26], [22, 25]]}, -"2GRB-2D":{"sequence": "GGGGUGGGGUUGGGGUUGGGGU", "paired_bases": []}, -"6PRV-2D":{"sequence": "GCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGU", "paired_bases": [[0, 57], [1, 56], [2, 55], [3, 54], [4, 53], [6, 30], [7, 29], [8, 28], [11, 25], [12, 24], [13, 23], [36, 51], [39, 50], [40, 49], [41, 48]]}, -"4JF2-2D":{"sequence": "GGAACCGCGAAAGCGGUUCCACGACGAUACUUAUUUCCUUUGAUCGUCGUUAUUACUGGCUUCGGCCACAAAGGAGA", "paired_bases": [[0, 19], [1, 18], [2, 17], [3, 16], [4, 15], [5, 14], [6, 13], [7, 12], [20, 49], [21, 48], [22, 47], [23, 46], [24, 45], [25, 44], [26, 43], [27, 42], [35, 74], [36, 73], [37, 72], [38, 71], [39, 70], [56, 67], [57, 66], [58, 65], [59, 64]]}, -"5Z71-2D":{"sequence": "UGCGUCGCUCCGGAAAAGUCGCUGCGUCGCUCCGGAAAAGUCGC", "paired_bases": [[1, 43], [2, 42], [3, 41], [5, 39], [8, 35], [9, 34], [10, 33], [11, 32], [12, 31], [13, 30], [17, 27], [19, 25], [20, 24], [21, 23]]}, -"6QN3-2D":{"sequence": "CGUUCACCCUUCGGGGCGCAUGAAAUGGGAGUAGGGAACGGGAUUCUCAUCGUUCACCCUUCGGGGCGCAUGAAAUGGGAGUAGGGAACGGGAUUCUCAU", "paired_bases": [[0, 89], [1, 88], [2, 87], [3, 86], [4, 85], [6, 15], [7, 14], [8, 13], [18, 90], [24, 49], [25, 48], [26, 47], [27, 46], [28, 45], [29, 44], [30, 43], [31, 42], [35, 54], [36, 53], [37, 52], [38, 51], [39, 50], [40, 68], [56, 65], [57, 64], [58, 63], [74, 99], [75, 98], [76, 97], [77, 96], [78, 95], [79, 94], [80, 93], [81, 92]]}, -"8TJV-2D":{"sequence": "GGGCGAUGAGGCCCGCCCAAACUGCCCUAUAUGGAUGCAGUUCACAGACUAAAUGUCGGUCGGGGAAGAUGUAUUCUUCUCAUAAGAUAUAGUCGGACCUCUCCUUAAUGGGAGCUAGCGGAUGAAGUGAUGCAACACUGGAGCCGCUGGGAACUAAUUUGUAUGCGAAAGUAUAUUGAUUAGUUUUGGAGGAGGGAAAAGUUAUCAGGCAUGCACCUGGUAGCUAGUCUUUAAACCAAUAGAUUGCAUCGGUUUAAAAGGCAAGACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUAGGGCUGAUGGCCUCUACUG", "paired_bases": [[1, 16], [2, 15], [3, 14], [4, 13], [7, 411], [8, 410], [9, 409], [10, 408], [11, 407], [12, 406], [23, 401], [24, 400], [25, 399], [26, 398], [27, 397], [28, 396], [29, 395], [32, 391], [33, 390], [34, 389], [35, 388], [39, 384], [40, 383], [44, 94], [46, 93], [47, 92], [48, 91], [49, 90], [50, 89], [54, 270], [56, 268], [57, 267], [58, 266], [59, 265], [60, 264], [62, 80], [63, 79], [64, 78], [65, 77], [66, 76], [67, 75], [68, 74], [97, 188], [98, 187], [100, 113], [101, 112], [102, 111], [103, 110], [104, 109], [114, 149], [115, 148], [116, 147], [117, 146], [118, 145], [119, 144], [120, 143], [125, 138], [126, 137], [127, 136], [128, 135], [129, 248], [130, 247], [131, 246], [132, 245], [133, 244], [134, 243], [151, 184], [152, 183], [153, 182], [154, 181], [155, 180], [156, 179], [157, 178], [161, 174], [162, 173], [163, 172], [164, 171], [165, 170], [199, 224], [200, 223], [201, 222], [202, 221], [203, 220], [204, 219], [205, 218], [206, 217], [207, 216], [208, 215], [211, 340], [212, 338], [213, 337], [226, 261], [227, 260], [228, 259], [229, 258], [230, 257], [231, 255], [232, 254], [233, 253], [234, 252], [235, 251], [236, 250], [241, 249], [275, 382], [276, 381], [277, 380], [278, 379], [279, 377], [280, 376], [284, 373], [285, 372], [286, 371], [287, 370], [288, 369], [289, 368], [295, 363], [296, 362], [297, 361], [299, 360], [300, 359], [301, 358], [302, 357], [304, 350], [305, 349], [306, 348], [309, 330], [310, 329], [311, 328], [312, 327], [313, 326], [314, 325], [315, 324], [316, 323], [317, 322], [333, 343], [334, 342]]}, -"8FZA-2D":{"sequence": "UUGGGUUCCCUCACCCCAAUCAUAAAAAGG", "paired_bases": [[1, 17], [2, 16], [3, 15], [4, 14], [8, 29], [9, 28], [10, 27]]}, +"1Q96-2D":{"sequence": "GGUGCUCAGUAUGAGAAGAACCGCACCGGUGCUCAGUAUGAGAAGAACCGCACC", "paired_bases": [[0, 26], [1, 25], [2, 24], [3, 23], [4, 22], [11, 16], [27, 53], [28, 52], [29, 51], [30, 50], [31, 49], [38, 43]]}, +"5L4O-2D":{"sequence": "AGCGGGGCGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCUACC", "paired_bases": [[1, 71], [2, 70], [3, 69], [4, 68], [5, 67], [6, 66], [9, 25], [10, 24], [11, 23], [12, 22], [19, 56], [27, 43], [28, 42], [29, 41], [30, 40], [31, 39], [49, 65], [50, 64], [51, 63], [52, 62], [53, 61]]}, +"5FK2-2D":{"sequence": "GGCUUAUCAAGAGAGGGGGAGCGACUGGCGCGAAGAGCCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCGA", "paired_bases": [[0, 92], [1, 91], [2, 90], [3, 89], [4, 88], [5, 87], [6, 86], [7, 85], [12, 40], [14, 39], [15, 38], [16, 37], [20, 30], [21, 29], [22, 28], [24, 67], [26, 65], [27, 64], [41, 59], [42, 58], [43, 57], [46, 55], [47, 54], [48, 53], [63, 84], [68, 81], [69, 80], [70, 79], [71, 78], [72, 77]]}, +"5FK3-2D":{"sequence": "GGCUUAUCAAGAGAGGGCGAGCGACUGGCGCGAAGACCCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCGA", "paired_bases": [[0, 92], [1, 91], [2, 90], [3, 89], [4, 88], [5, 87], [6, 86], [7, 85], [12, 40], [14, 39], [15, 38], [16, 37], [20, 30], [21, 29], [22, 28], [24, 67], [26, 65], [27, 64], [41, 59], [42, 58], [43, 57], [46, 55], [47, 54], [48, 53], [63, 84], [68, 81], [69, 80], [70, 79], [71, 78], [72, 77]]}, +"2ZY6-2D":{"sequence": "GCCCGGAUAGUGUCCUUGGGAAACCGAGUCCGGGCACC", "paired_bases": [[0, 34], [1, 33], [2, 32], [3, 31], [4, 30], [5, 29], [6, 28], [9, 24], [11, 23]]}, +"7EDN-2D":{"sequence": "UUGCGUCGCGUCGACGAAGUCGC", "paired_bases": []}, +"3GX7-2D":{"sequence": "GGCUUCGCAAGAGAGGUGGAGGGACUGGCCCGACGAAACCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGCGGAGCCGA", "paired_bases": [[0, 92], [1, 91], [2, 90], [3, 89], [5, 87], [6, 86], [7, 85], [12, 40], [14, 39], [15, 38], [16, 37], [20, 30], [21, 29], [22, 28], [24, 67], [26, 65], [27, 64], [41, 59], [42, 58], [43, 57], [46, 55], [47, 54], [48, 53], [63, 84], [68, 81], [69, 80], [70, 79], [71, 78], [72, 77]]}, +"8SX5-2D":{"sequence": "CUCGACUUAAGUCGCUCGACUUAAGUCG", "paired_bases": [[2, 27], [3, 26], [4, 25], [5, 24], [6, 23], [7, 22], [8, 21], [9, 20], [10, 19], [11, 18], [12, 17], [13, 16]]}, +"1Y27-2D":{"sequence": "GGAUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGGUC", "paired_bases": [[1, 67], [2, 66], [3, 65], [4, 64], [5, 63], [6, 62], [7, 61], [8, 38], [11, 31], [13, 29], [14, 28], [15, 27], [16, 26], [17, 25], [23, 47], [24, 46], [32, 39], [40, 58], [41, 57], [42, 56], [43, 55], [44, 54], [45, 53]]}, "1Y26-2D":{"sequence": "CGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUGA", "paired_bases": [[0, 70], [1, 69], [2, 68], [3, 67], [4, 66], [5, 65], [6, 64], [7, 63], [8, 62], [9, 39], [12, 32], [13, 31], [14, 30], [15, 29], [16, 28], [17, 27], [24, 48], [25, 47], [33, 40], [41, 59], [42, 58], [43, 57], [44, 56], [45, 55], [46, 54], [61, 71]]}, -"5FJC-2D":{"sequence": "GGCUUAUCAAGAGAGGGGGAGUGACUGGCGCGAAGAACCCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCGA", "paired_bases": [[0, 92], [1, 91], [2, 90], [3, 89], [4, 88], [5, 87], [6, 86], [7, 85], [12, 40], [14, 39], [15, 38], [16, 37], [20, 30], [21, 29], [22, 28], [24, 67], [26, 65], [27, 64], [41, 59], [42, 58], [43, 57], [46, 55], [47, 54], [48, 53], [63, 84], [68, 81], [69, 80], [70, 79], [71, 78], [72, 77]]}, -"4FEN-2D":{"sequence": "GGACAUAUAUACGCGUGGAUAUGGCACGCGAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGUCC", "paired_bases": [[0, 66], [1, 65], [2, 64], [3, 63], [4, 62], [5, 61], [6, 60], [7, 37], [11, 29], [12, 28], [13, 27], [14, 26], [15, 25], [16, 24], [22, 46], [23, 45], [31, 38], [39, 57], [40, 56], [41, 55], [42, 54], [43, 53], [44, 52]]}, +"3SYW-2D":{"sequence": "UUGGGCCUGCUGCUGGUCCUUGGGCCUGCUGCUGGUCC", "paired_bases": [[2, 37], [3, 36], [4, 35], [5, 34], [6, 33], [8, 31], [9, 30], [11, 28], [12, 27], [14, 25], [15, 24], [16, 23], [17, 22], [18, 21]]}, +"1GID-2D":{"sequence": "GAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUCGAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUC", "paired_bases": [[0, 114], [4, 111], [5, 110], [6, 109], [7, 108], [8, 106], [9, 105], [13, 102], [14, 101], [15, 100], [16, 99], [17, 98], [18, 97], [24, 92], [25, 91], [26, 90], [28, 89], [29, 88], [30, 87], [31, 86], [33, 79], [34, 78], [35, 77], [38, 59], [39, 58], [40, 57], [41, 56], [42, 55], [43, 54], [44, 53], [45, 52], [46, 51], [62, 72], [63, 71], [66, 310], [67, 309], [117, 150], [118, 149], [119, 148], [120, 147], [123, 146], [124, 144], [125, 143], [126, 142], [127, 141], [128, 140], [129, 139], [130, 138], [131, 137], [132, 136], [151, 225], [152, 224], [158, 272], [162, 269], [163, 268], [164, 267], [165, 266], [166, 264], [167, 263], [171, 260], [172, 259], [173, 258], [174, 257], [175, 256], [176, 255], [182, 250], [183, 249], [184, 248], [186, 247], [187, 246], [188, 245], [189, 244], [191, 237], [192, 236], [193, 235], [196, 217], [197, 216], [198, 215], [199, 214], [200, 213], [201, 212], [202, 211], [203, 210], [204, 209], [220, 230], [221, 229], [275, 308], [276, 307], [277, 306], [278, 305], [281, 304], [282, 302], [283, 301], [284, 300], [285, 299], [286, 298], [287, 297], [288, 296], [289, 295], [290, 294]]}, +"4JF2-2D":{"sequence": "GGAACCGCGAAAGCGGUUCCACGACGAUACUUAUUUCCUUUGAUCGUCGUUAUUACUGGCUUCGGCCACAAAGGAGA", "paired_bases": [[0, 19], [1, 18], [2, 17], [3, 16], [4, 15], [5, 14], [6, 13], [7, 12], [20, 49], [21, 48], [22, 47], [23, 46], [24, 45], [25, 44], [26, 43], [27, 42], [35, 74], [36, 73], [37, 72], [38, 71], [39, 70], [56, 67], [57, 66], [58, 65], [59, 64]]}, +"7LO9-2D":{"sequence": "CGCGAUUAGCGCGCGAUUAGCG", "paired_bases": [[0, 21], [1, 20], [2, 19], [4, 16], [5, 15], [8, 13], [9, 12], [10, 11]]}, +"3RG5-2D":{"sequence": "GCCCGGAUGAUCCUCAGUGGUCUGGGGUGCAGGCUUCAAACCUGUAGCUGUUUAGCGACAGAGUGGUUCAAUUCCACCUUUCGGGC", "paired_bases": [[0, 85], [1, 84], [2, 83], [3, 82], [4, 81], [5, 80], [6, 79], [8, 77], [11, 26], [12, 25], [13, 24], [14, 23], [15, 22], [16, 21], [19, 68], [27, 45], [28, 44], [29, 43], [30, 42], [31, 41], [32, 40], [47, 60], [48, 59], [49, 58], [50, 57], [51, 56], [62, 76], [63, 75], [64, 74], [65, 73]]}, +"4FEJ-2D":{"sequence": "GGACAUAUAUUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGUCC", "paired_bases": [[0, 66], [1, 65], [2, 64], [3, 63], [4, 62], [5, 61], [6, 60], [7, 37], [10, 30], [12, 28], [13, 27], [14, 26], [15, 25], [16, 24], [22, 46], [23, 45], [31, 38], [39, 57], [40, 56], [41, 55], [42, 54], [43, 53], [44, 52]]}, "7QUA-2D":{"sequence": "CGCGGAUUAGCG", "paired_bases": []}, -"6E8T-2D":{"sequence": "GUACGAAGGAAGGUUUGGUAUGUGGUAUAUUCGUAC", "paired_bases": [[0, 35], [1, 34], [2, 33], [3, 32], [4, 31], [5, 30], [6, 29]]}, -"2G3S-2D":{"sequence": "GGCGUGCCGGCGUGCC", "paired_bases": [[0, 15], [1, 14], [2, 13], [3, 12], [4, 11], [5, 10], [6, 9], [7, 8]]}, -"5DUN-2D":{"sequence": "UUUUUAAUGAAGCCACAGGCUGUGAGGGUCCUAAGCCCCUAAUUCAGAAGGGAA", "paired_bases": [[1, 53], [2, 52], [7, 45], [8, 44], [9, 43], [10, 42], [11, 35], [12, 34], [13, 23], [14, 22], [15, 21], [16, 20], [17, 19], [25, 38], [26, 37], [27, 36], [29, 50], [30, 49], [31, 48]]}, -"5DHB-2D":{"sequence": "CUGUACACUGUACAG", "paired_bases": [[1, 13], [2, 12], [3, 11], [4, 10], [5, 9], [6, 8], [7, 14]]} +"3GLP-2D":{"sequence": "GCUGCUGCGCUGCUGC", "paired_bases": [[0, 15], [1, 14], [3, 12], [4, 11], [6, 9], [7, 8]]}, +"3IQP-2D":{"sequence": "GGCUUAUCAAGAGAGGUGGAGGGACUGGCCCGAUGAAACCCGGCAACCAGAAAUGGUGCCAAUUCCUGCAGCGGAAACGUUGAAAGAUGAGCCG", "paired_bases": [[0, 92], [1, 91], [2, 90], [3, 89], [4, 88], [5, 87], [6, 86], [7, 85], [12, 40], [14, 39], [15, 38], [16, 37], [20, 30], [21, 29], [22, 28], [24, 67], [26, 65], [27, 64], [41, 59], [42, 58], [43, 57], [45, 56], [46, 55], [47, 54], [48, 53], [63, 84], [68, 81], [69, 80], [70, 79], [71, 78], [72, 77]]}, +"3SD3-2D":{"sequence": "GGAGAGUAGAUGAUUCGCGUUAAGCGUGUGUGAAUGGGAUGUCGUCACACAACGAAGCGAGAGCGCGGUGAAUCAUUGCAUCCGCUCCA", "paired_bases": [[0, 87], [1, 86], [2, 85], [3, 84], [8, 76], [9, 75], [10, 74], [11, 73], [12, 72], [13, 71], [14, 70], [15, 69], [16, 68], [17, 66], [18, 65], [19, 64], [26, 50], [27, 49], [28, 48], [29, 47], [30, 46], [31, 45], [32, 44], [36, 82], [37, 81], [38, 80], [39, 79], [40, 78], [56, 63], [57, 62]]}, +"3NPN-2D":{"sequence": "GGACGAGGAGCGUUGCAAGCGAAAGCCCAGGCUAGUCCGUUCAAACGGCGCUCAA", "paired_bases": [[3, 34], [5, 32], [6, 31], [7, 52], [8, 51], [9, 50], [10, 49], [11, 48], [15, 30], [18, 25], [19, 24], [29, 45]]}, +"6QN3-2D":{"sequence": "CGUUCACCCUUCGGGGCGCAUGAAAUGGGAGUAGGGAACGGGAUUCUCAUCGUUCACCCUUCGGGGCGCAUGAAAUGGGAGUAGGGAACGGGAUUCUCAU", "paired_bases": [[0, 89], [1, 88], [2, 87], [3, 86], [4, 85], [6, 15], [7, 14], [8, 13], [18, 90], [24, 49], [25, 48], [26, 47], [27, 46], [28, 45], [29, 44], [30, 43], [31, 42], [35, 54], [36, 53], [37, 52], [38, 51], [39, 50], [40, 68], [56, 65], [57, 64], [58, 63], [74, 99], [75, 98], [76, 97], [77, 96], [78, 95], [79, 94], [80, 93], [81, 92]]} } diff --git a/info.json b/info.json index 20a3f9c8510285ab7b6b01c01090f065bb82b938..658993510d395c0aec03176da8767c577df1a4e3 100644 --- a/info.json +++ b/info.json @@ -1,8 +1,8 @@ { "name": "PDB", - "upload_date": "2023-11-22 14:34:34", + "upload_date": "2023-11-24 11:40:55", "user": "alberic", - "source": "`CT_files_pdbee` (CT files format)", + "source": "`bpSEQ_files_pdbee` (BPSEQ files format)", "structure": "source", "about structure": "Read from source.", "filtering_report": "Over a total of 702 datapoints, there are:\n - 353 valid datapoints\n - 0 invalid datapoints (ex: sequence with non-regular characters)\n - 0 datapoints with the same reference\n - 302 duplicate sequences with the same structure / dms\n - 47 duplicate sequences with different structure / dms" diff --git a/source/bpSEQ_files_pdbee/157D-2D.bpseq b/source/bpSEQ_files_pdbee/157D-2D.bpseq new file mode 100644 index 0000000000000000000000000000000000000000..c1a2a6d50e90bcab0dd43d84325522ffc1d149ce --- /dev/null +++ b/source/bpSEQ_files_pdbee/157D-2D.bpseq @@ -0,0 +1,24 @@ +1 c 24 +2 G 23 +3 C 22 +4 G 0 +5 A 20 +6 A 19 +7 U 18 +8 U 17 +9 A 0 +10 G 15 +11 C 14 +12 G 13 +13 c 12 +14 G 11 +15 C 10 +16 G 0 +17 A 8 +18 A 7 +19 U 6 +20 U 5 +21 A 0 +22 G 3 +23 C 2 +24 G 1 diff --git a/source/bpSEQ_files_pdbee/165D-2D.bpseq b/source/bpSEQ_files_pdbee/165D-2D.bpseq new file mode 100644 index 0000000000000000000000000000000000000000..50ec10ff2d917968203c459e014a66e5bde473d3 --- /dev/null +++ b/source/bpSEQ_files_pdbee/165D-2D.bpseq @@ -0,0 +1,18 @@ +1 g 17 +2 C 16 +3 U 15 +4 U 0 +5 C 0 +6 G 12 +7 G 11 +8 C 10 +9 u 0 +10 g 8 +11 C 7 +12 U 6 +13 U 0 +14 C 0 +15 G 3 +16 G 2 +17 C 1 +18 u 0 diff --git a/source/bpSEQ_files_pdbee/1DUH-2D.bpseq b/source/bpSEQ_files_pdbee/1DUH-2D.bpseq new file mode 100644 index 0000000000000000000000000000000000000000..92f186f8d87f3a05d691cf414646a798bb7bae39 --- /dev/null +++ b/source/bpSEQ_files_pdbee/1DUH-2D.bpseq @@ -0,0 +1,45 @@ +1 c 0 +2 U 0 +3 C 0 +4 U 0 +5 G 0 +6 U 0 +7 U 0 +8 U 0 +9 A 0 +10 C 0 +11 C 0 +12 A 0 +13 G 0 +14 G 0 +15 U 0 +16 C 0 +17 A 0 +18 G 0 +19 G 0 +20 U 0 +21 C 0 +22 C 0 +23 G 0 +24 G 0 +25 A 0 +26 A 0 +27 G 0 +28 G 0 +29 A 0 +30 A 0 +31 G 0 +32 C 0 +33 A 0 +34 G 0 +35 C 0 +36 C 0 +37 A 0 +38 A 0 +39 G 0 +40 G 0 +41 C 0 +42 A 0 +43 G 0 +44 A 0 +45 g 0 diff --git a/source/bpSEQ_files_pdbee/1EHZ-2D.bpseq b/source/bpSEQ_files_pdbee/1EHZ-2D.bpseq new file mode 100644 index 0000000000000000000000000000000000000000..d9f258f87127644004679f1c351c212b3963d894 --- /dev/null +++ b/source/bpSEQ_files_pdbee/1EHZ-2D.bpseq @@ -0,0 +1,76 @@ +1 g 72 +2 C 71 +3 G 70 +4 G 69 +5 A 68 +6 U 67 +7 U 66 +8 U 0 +9 A 0 +10 g 25 +11 C 24 +12 U 23 +13 C 22 +14 A 0 +15 G 0 +16 u 0 +17 u 0 +18 G 0 +19 G 56 +20 G 0 +21 A 0 +22 G 13 +23 A 12 +24 G 11 +25 C 10 +26 g 0 +27 C 43 +28 C 42 +29 A 41 +30 G 40 +31 A 0 +32 c 0 +33 U 0 +34 g 0 +35 A 0 +36 A 0 +37 g 0 +38 A 0 +39 u 0 +40 c 30 +41 U 29 +42 G 28 +43 G 27 +44 A 0 +45 G 0 +46 g 0 +47 U 0 +48 C 0 +49 c 65 +50 U 64 +51 G 63 +52 U 62 +53 G 61 +54 u 0 +55 u 0 +56 C 19 +57 G 0 +58 a 0 +59 U 0 +60 C 0 +61 C 53 +62 A 52 +63 C 51 +64 A 50 +65 G 49 +66 A 7 +67 A 6 +68 U 5 +69 U 4 +70 C 3 +71 G 2 +72 C 1 +73 A 0 +74 C 0 +75 C 0 +76 A 0 diff --git a/source/bpSEQ_files_pdbee/1ET4-2D.bpseq b/source/bpSEQ_files_pdbee/1ET4-2D.bpseq new file mode 100644 index 0000000000000000000000000000000000000000..74129fa196b344bfb9f86ed43b709bcaed1b512f --- /dev/null +++ b/source/bpSEQ_files_pdbee/1ET4-2D.bpseq @@ -0,0 +1,70 @@ +1 g 0 +2 G 0 +3 A 0 +4 A 0 +5 C 0 +6 C 0 +7 G 22 +8 G 21 +9 U 20 +10 G 0 +11 C 30 +12 G 33 +13 C 32 +14 A 0 +15 U 0 +16 A 0 +17 A 0 +18 C 28 +19 C 26 +20 A 9 +21 C 8 +22 C 7 +23 U 0 +24 C 0 +25 A 0 +26 G 19 +27 U 0 +28 G 18 +29 C 0 +30 G 11 +31 A 0 +32 G 13 +33 C 12 +34 A 0 +35 A 0 +36 g 0 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