viral_seq 1.8.1.1 → 1.9.0
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/README.md +6 -0
- data/bin/tcs +7 -1
- data/bin/tcs_sdrm +87 -131
- data/lib/viral_seq/drm_region_config.rb +83 -0
- data/lib/viral_seq/drm_version.rb +120 -0
- data/lib/viral_seq/hivdr.rb +206 -2
- data/lib/viral_seq/sdrm.rb +34 -99
- data/lib/viral_seq/sequence.rb +26 -1
- data/lib/viral_seq/tcs_core.rb +1 -1
- data/lib/viral_seq/tcs_dr.rb +87 -5
- data/lib/viral_seq/util/drm_list.json +684 -0
- data/lib/viral_seq/util/drm_versions_config.json +114 -0
- data/lib/viral_seq/version.rb +2 -2
- data/lib/viral_seq.rb +3 -0
- metadata +7 -3
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"HCV_NS5A": [
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"wild-type": "H",
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"wild-type": "T",
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"wild-type": "R",
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"wild-type": "S",
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"wild-type": "T",
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"mutations": [
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386
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387
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388
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390
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392
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393
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394
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395
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397
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399
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400
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405
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407
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408
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409
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410
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412
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413
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414
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415
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416
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417
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418
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420
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423
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424
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425
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426
|
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|
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428
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429
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430
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431
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432
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433
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434
|
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436
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438
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439
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440
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441
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442
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443
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444
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446
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447
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452
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453
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455
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465
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469
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470
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472
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473
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474
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475
|
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476
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477
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478
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479
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480
|
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{
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481
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482
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483
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485
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487
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488
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489
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490
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491
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492
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493
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494
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495
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496
|
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{
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497
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498
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499
|
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500
|
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501
|
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502
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503
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504
|
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{
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505
|
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506
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507
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508
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509
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512
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513
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514
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515
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516
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517
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518
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519
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520
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522
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523
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524
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525
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527
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528
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529
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530
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531
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532
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533
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534
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535
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536
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537
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538
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539
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541
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542
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543
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544
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545
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546
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547
|
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548
|
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549
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550
|
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551
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552
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553
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554
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555
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556
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557
|
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{
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558
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559
|
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560
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561
|
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562
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563
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564
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565
|
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566
|
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567
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568
|
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569
|
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570
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571
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572
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573
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574
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575
|
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576
|
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577
|
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578
|
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579
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580
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581
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582
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|
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584
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585
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586
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587
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588
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589
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590
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591
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592
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593
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594
|
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596
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597
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598
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599
|
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600
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601
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602
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|
603
|
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604
|
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605
|
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606
|
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607
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609
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610
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611
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612
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613
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615
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616
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617
|
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618
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619
|
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620
|
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621
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622
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|
623
|
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624
|
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625
|
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626
|
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627
|
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628
|
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629
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630
|
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631
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632
|
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633
|
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634
|
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635
|
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636
|
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637
|
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638
|
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639
|
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640
|
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641
|
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642
|
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643
|
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644
|
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"K"
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645
|
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646
|
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|
647
|
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648
|
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649
|
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|
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650
|
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651
|
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652
|
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653
|
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654
|
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"S"
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655
|
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656
|
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|
657
|
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658
|
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659
|
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|
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660
|
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661
|
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662
|
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663
|
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664
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665
|
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|
666
|
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667
|
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668
|
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669
|
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670
|
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671
|
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"E"
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672
|
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673
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|
674
|
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|
675
|
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676
|
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677
|
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678
|
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679
|
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680
|
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681
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|
682
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|
683
|
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|
684
|
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