Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign25 - back to list
Summary
./analyse_probe_search_results : Mon Sep 5 11:47:24 2005
Connected to host: host, as user: user Database : gene_targeting_production Fetched probe design: ProbeDesign25 assembly : NCBIM33 bias : 3prime chromosome : 12 id : 2 strand : 1 ------------- Design window length: 2001bp All jobs for probe design are successful - total: 41 Fetched conf : Exonerate mouse_NCBI33 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM33/genome/masked_dusted Fetched 405 putative probes to analyse Selection criteria to rank probes: Minimum score ratio : 10 (i.e. self-hit must score at least 10 times higher than the next best hit) Maximum percent repetitive bases: 5 Favour probes to the 3prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 405/405 Putative probes exceeding selection criteria: 217/405 PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW --------------------------------------------------------------
Image
Unique (yellow), passed (green) and failed putative probes in the design window
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
424 | 1000 | 32.9 | 5000 | - | 900 | 32.9 |
425 | 1000 | 32.9 | 5000 | - | 950 | 32.9 |
426 | 1000 | 32.9 | 5000 | - | 1000 | 32.9 |
423 | 1000 | 32.9 | 5000 | 0.5 | 850 | 31.9 |
446 | 950 | 31.2 | 4750 | - | 893 | 31.2 |
447 | 950 | 31.2 | 4750 | - | 940 | 31.2 |
448 | 950 | 31.2 | 4750 | - | 987 | 31.2 |
449 | 950 | 31.2 | 4750 | - | 1034 | 31.2 |
469 | 900 | 29.6 | 4500 | - | 855 | 29.6 |
470 | 900 | 29.6 | 4500 | - | 900 | 29.6 |
471 | 900 | 29.6 | 4500 | - | 945 | 29.6 |
472 | 900 | 29.6 | 4500 | - | 990 | 29.6 |
473 | 900 | 29.6 | 4500 | - | 1035 | 29.6 |
445 | 950 | 31.2 | 4750 | 0.9 | 846 | 29.4 |
496 | 850 | 28.0 | 4250 | - | 882 | 28.0 |
497 | 850 | 28.0 | 4250 | - | 924 | 28.0 |
498 | 850 | 28.0 | 4250 | - | 966 | 28.0 |
499 | 850 | 28.0 | 4250 | - | 1008 | 28.0 |
500 | 850 | 28.0 | 4250 | - | 1050 | 28.0 |
525 | 800 | 26.3 | 4000 | - | 880 | 26.3 |
526 | 800 | 26.3 | 4000 | - | 920 | 26.3 |
527 | 800 | 26.3 | 4000 | - | 960 | 26.3 |
528 | 800 | 26.3 | 4000 | - | 1000 | 26.3 |
529 | 800 | 26.3 | 4000 | - | 1040 | 26.3 |
563 | 750 | 24.8 | 3750 | - | 1073 | 24.8 |
558 | 750 | 24.7 | 3750 | - | 888 | 24.7 |
559 | 750 | 24.7 | 3750 | - | 925 | 24.7 |
560 | 750 | 24.7 | 3750 | - | 962 | 24.7 |
561 | 750 | 24.7 | 3750 | - | 999 | 24.7 |
562 | 750 | 24.7 | 3750 | - | 1036 | 24.7 |
495 | 850 | 28.0 | 4250 | 1.8 | 840 | 24.4 |
557 | 750 | 24.7 | 3750 | 0.5 | 851 | 23.6 |
593 | 700 | 23.0 | 3500 | - | 875 | 23.0 |
594 | 700 | 23.0 | 3500 | - | 910 | 23.0 |
595 | 700 | 23.0 | 3500 | - | 945 | 23.0 |
596 | 700 | 23.0 | 3500 | - | 980 | 23.0 |
597 | 700 | 23.0 | 3500 | - | 1015 | 23.0 |
598 | 700 | 23.0 | 3500 | - | 1050 | 23.0 |
524 | 800 | 26.3 | 4000 | 1.9 | 840 | 22.6 |
569 | 700 | 22.4 | 3500 | - | 35 | 22.4 |
534 | 750 | 21.7 | 3750 | - | 0 | 21.7 |
633 | 650 | 21.4 | 3250 | - | 864 | 21.4 |
634 | 650 | 21.4 | 3250 | - | 896 | 21.4 |
635 | 650 | 21.4 | 3250 | - | 928 | 21.4 |
636 | 650 | 21.4 | 3250 | - | 960 | 21.4 |
637 | 650 | 21.4 | 3250 | - | 992 | 21.4 |
638 | 650 | 21.4 | 3250 | - | 1024 | 21.4 |
639 | 650 | 21.4 | 3250 | - | 1056 | 21.4 |
608 | 650 | 21.1 | 3250 | - | 64 | 21.1 |
609 | 650 | 20.7 | 3250 | - | 96 | 20.7 |
678 | 600 | 19.7 | 3000 | - | 870 | 19.7 |
679 | 600 | 19.7 | 3000 | - | 900 | 19.7 |
680 | 600 | 19.7 | 3000 | - | 930 | 19.7 |
681 | 600 | 19.7 | 3000 | - | 960 | 19.7 |
682 | 600 | 19.7 | 3000 | - | 990 | 19.7 |
683 | 600 | 19.7 | 3000 | - | 1020 | 19.7 |
684 | 600 | 19.7 | 3000 | - | 1050 | 19.7 |
653 | 600 | 19.4 | 3000 | - | 120 | 19.4 |
503 | 800 | 18.9 | 4000 | - | 0 | 18.9 |
592 | 700 | 23.0 | 3500 | 2.1 | 840 | 18.7 |
702 | 550 | 18.1 | 2750 | - | 162 | 18.1 |
728 | 550 | 18.1 | 2750 | - | 864 | 18.1 |
729 | 550 | 18.1 | 2750 | - | 891 | 18.1 |
730 | 550 | 18.1 | 2750 | - | 918 | 18.1 |
731 | 550 | 18.1 | 2750 | - | 945 | 18.1 |
732 | 550 | 18.1 | 2750 | - | 972 | 18.1 |
733 | 550 | 18.1 | 2750 | - | 999 | 18.1 |
734 | 550 | 18.1 | 2750 | - | 1026 | 18.1 |
735 | 550 | 18.1 | 2750 | - | 1053 | 18.1 |
535 | 750 | 17.7 | 3750 | - | 37 | 17.7 |
703 | 550 | 17.6 | 2750 | - | 189 | 17.6 |
654 | 600 | 17.3 | 3000 | - | 150 | 17.3 |
570 | 700 | 17.3 | 3500 | - | 70 | 17.3 |
793 | 500 | 16.6 | 2500 | - | 1075 | 16.6 |
571 | 700 | 16.5 | 3500 | - | 105 | 16.5 |
785 | 500 | 16.4 | 2500 | - | 875 | 16.4 |
786 | 500 | 16.4 | 2500 | - | 900 | 16.4 |
787 | 500 | 16.4 | 2500 | - | 925 | 16.4 |
788 | 500 | 16.4 | 2500 | - | 950 | 16.4 |
789 | 500 | 16.4 | 2500 | - | 975 | 16.4 |
790 | 500 | 16.4 | 2500 | - | 1000 | 16.4 |
791 | 500 | 16.4 | 2500 | - | 1025 | 16.4 |
792 | 500 | 16.4 | 2500 | - | 1050 | 16.4 |
536 | 750 | 17.7 | 3750 | 0.8 | 74 | 16.1 |
759 | 500 | 16.0 | 2500 | - | 225 | 16.0 |
610 | 650 | 15.3 | 3250 | - | 128 | 15.3 |
611 | 650 | 15.3 | 3250 | - | 160 | 15.3 |
677 | 600 | 19.7 | 3000 | 2.5 | 840 | 14.7 |
760 | 500 | 14.5 | 2500 | - | 250 | 14.5 |
784 | 500 | 16.4 | 2500 | 1.0 | 850 | 14.4 |
632 | 650 | 21.4 | 3250 | 3.5 | 832 | 14.3 |
655 | 600 | 14.2 | 3000 | - | 180 | 14.2 |
656 | 600 | 14.2 | 3000 | - | 210 | 14.2 |
704 | 550 | 13.6 | 2750 | - | 216 | 13.6 |
422 | 1000 | 20.8 | 5000 | 3.7 | 800 | 13.4 |
504 | 800 | 18.9 | 4000 | 2.8 | 40 | 13.4 |
705 | 550 | 13.0 | 2750 | - | 243 | 13.0 |
406 | 1000 | 19.7 | 5000 | 3.7 | 0 | 12.3 |
407 | 1000 | 19.7 | 5000 | 3.7 | 50 | 12.3 |
408 | 1000 | 19.7 | 5000 | 3.7 | 100 | 12.3 |
409 | 1000 | 19.7 | 5000 | 3.7 | 150 | 12.3 |
410 | 1000 | 19.7 | 5000 | 3.7 | 200 | 12.3 |
411 | 1000 | 19.7 | 5000 | 3.7 | 250 | 12.3 |
412 | 1000 | 19.7 | 5000 | 3.7 | 300 | 12.3 |
413 | 1000 | 19.7 | 5000 | 3.7 | 350 | 12.3 |
414 | 1000 | 19.7 | 5000 | 3.7 | 400 | 12.3 |
415 | 1000 | 19.7 | 5000 | 3.7 | 450 | 12.3 |
416 | 1000 | 19.7 | 5000 | 3.7 | 500 | 12.3 |
417 | 1000 | 19.7 | 5000 | 3.7 | 550 | 12.3 |
418 | 1000 | 19.7 | 5000 | 3.7 | 600 | 12.3 |
419 | 1000 | 19.7 | 5000 | 3.7 | 650 | 12.3 |
420 | 1000 | 19.7 | 5000 | 3.7 | 700 | 12.3 |
421 | 1000 | 19.7 | 5000 | 3.7 | 750 | 12.3 |
706 | 550 | 13.0 | 2750 | 0.4 | 270 | 12.2 |
761 | 500 | 11.8 | 2500 | - | 275 | 11.8 |
762 | 500 | 11.8 | 2500 | - | 300 | 11.8 |
727 | 550 | 18.1 | 2750 | 3.3 | 837 | 11.5 |
572 | 700 | 16.5 | 3500 | 3.1 | 140 | 10.2 |
763 | 500 | 11.8 | 2500 | 1.4 | 325 | 9.0 |
612 | 650 | 15.3 | 3250 | 3.7 | 192 | 7.9 |
657 | 600 | 14.2 | 3000 | 3.7 | 240 | 6.8 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
468 | 900 | 20.1 | 4500 | 4.1 | 810 | 11.9 |
444 | 950 | 19.4 | 4750 | 3.9 | 799 | 11.6 |
475 | 850 | 18.5 | 4250 | 3.8 | 0 | 10.9 |
427 | 950 | 18.7 | 4750 | 3.9 | 0 | 10.9 |
428 | 950 | 18.7 | 4750 | 3.9 | 47 | 10.9 |
429 | 950 | 18.7 | 4750 | 3.9 | 94 | 10.9 |
430 | 950 | 18.7 | 4750 | 3.9 | 141 | 10.9 |
431 | 950 | 18.7 | 4750 | 3.9 | 188 | 10.9 |
432 | 950 | 18.7 | 4750 | 3.9 | 235 | 10.9 |
433 | 950 | 18.7 | 4750 | 3.9 | 282 | 10.9 |
434 | 950 | 18.7 | 4750 | 3.9 | 329 | 10.9 |
435 | 950 | 18.7 | 4750 | 3.9 | 376 | 10.9 |
436 | 950 | 18.7 | 4750 | 3.9 | 423 | 10.9 |
437 | 950 | 18.7 | 4750 | 3.9 | 470 | 10.9 |
438 | 950 | 18.7 | 4750 | 3.9 | 517 | 10.9 |
439 | 950 | 18.7 | 4750 | 3.9 | 564 | 10.9 |
440 | 950 | 18.7 | 4750 | 3.9 | 611 | 10.9 |
441 | 950 | 18.7 | 4750 | 3.9 | 658 | 10.9 |
442 | 950 | 18.7 | 4750 | 3.9 | 705 | 10.9 |
443 | 950 | 18.7 | 4750 | 3.9 | 752 | 10.9 |
450 | 900 | 17.7 | 4500 | 4.1 | 0 | 9.5 |
451 | 900 | 17.7 | 4500 | 4.1 | 45 | 9.5 |
452 | 900 | 17.7 | 4500 | 4.1 | 90 | 9.5 |
453 | 900 | 17.7 | 4500 | 4.1 | 135 | 9.5 |
454 | 900 | 17.7 | 4500 | 4.1 | 180 | 9.5 |
455 | 900 | 17.7 | 4500 | 4.1 | 225 | 9.5 |
456 | 900 | 17.7 | 4500 | 4.1 | 270 | 9.5 |
457 | 900 | 17.7 | 4500 | 4.1 | 315 | 9.5 |
458 | 900 | 17.7 | 4500 | 4.1 | 360 | 9.5 |
459 | 900 | 17.7 | 4500 | 4.1 | 405 | 9.5 |
460 | 900 | 17.7 | 4500 | 4.1 | 450 | 9.5 |
461 | 900 | 17.7 | 4500 | 4.1 | 495 | 9.5 |
462 | 900 | 17.7 | 4500 | 4.1 | 540 | 9.5 |
463 | 900 | 17.7 | 4500 | 4.1 | 585 | 9.5 |
464 | 900 | 17.7 | 4500 | 4.1 | 630 | 9.5 |
465 | 900 | 17.7 | 4500 | 4.1 | 675 | 9.5 |
466 | 900 | 17.7 | 4500 | 4.1 | 720 | 9.5 |
467 | 900 | 17.7 | 4500 | 4.1 | 765 | 9.5 |
494 | 850 | 17.0 | 4250 | 4.4 | 798 | 8.3 |
476 | 850 | 16.7 | 4250 | 4.4 | 42 | 8.0 |
477 | 850 | 16.7 | 4250 | 4.4 | 84 | 8.0 |
478 | 850 | 16.7 | 4250 | 4.4 | 126 | 8.0 |
479 | 850 | 16.7 | 4250 | 4.4 | 168 | 8.0 |
480 | 850 | 16.7 | 4250 | 4.4 | 210 | 8.0 |
481 | 850 | 16.7 | 4250 | 4.4 | 252 | 8.0 |
482 | 850 | 16.7 | 4250 | 4.4 | 294 | 8.0 |
483 | 850 | 16.7 | 4250 | 4.4 | 336 | 8.0 |
484 | 850 | 16.7 | 4250 | 4.4 | 378 | 8.0 |
485 | 850 | 16.7 | 4250 | 4.4 | 420 | 8.0 |
486 | 850 | 16.7 | 4250 | 4.4 | 462 | 8.0 |
487 | 850 | 16.7 | 4250 | 4.4 | 504 | 8.0 |
488 | 850 | 16.7 | 4250 | 4.4 | 546 | 8.0 |
489 | 850 | 16.7 | 4250 | 4.4 | 588 | 8.0 |
490 | 850 | 16.7 | 4250 | 4.4 | 630 | 8.0 |
491 | 850 | 16.7 | 4250 | 4.4 | 672 | 8.0 |
492 | 850 | 16.7 | 4250 | 4.4 | 714 | 8.0 |
493 | 850 | 16.7 | 4250 | 4.4 | 756 | 8.0 |
523 | 800 | 16.7 | 4000 | 4.6 | 800 | 7.4 |
556 | 750 | 16.8 | 3750 | 4.9 | 814 | 6.9 |
505 | 800 | 15.7 | 4000 | 4.6 | 80 | 6.5 |
506 | 800 | 15.7 | 4000 | 4.6 | 120 | 6.5 |
507 | 800 | 15.7 | 4000 | 4.6 | 160 | 6.5 |
508 | 800 | 15.7 | 4000 | 4.6 | 200 | 6.5 |
509 | 800 | 15.7 | 4000 | 4.6 | 240 | 6.5 |
510 | 800 | 15.7 | 4000 | 4.6 | 280 | 6.5 |
511 | 800 | 15.7 | 4000 | 4.6 | 320 | 6.5 |
512 | 800 | 15.7 | 4000 | 4.6 | 360 | 6.5 |
513 | 800 | 15.7 | 4000 | 4.6 | 400 | 6.5 |
514 | 800 | 15.7 | 4000 | 4.6 | 440 | 6.5 |
515 | 800 | 15.7 | 4000 | 4.6 | 480 | 6.5 |
516 | 800 | 15.7 | 4000 | 4.6 | 520 | 6.5 |
517 | 800 | 15.7 | 4000 | 4.6 | 560 | 6.5 |
518 | 800 | 15.7 | 4000 | 4.6 | 600 | 6.5 |
519 | 800 | 15.7 | 4000 | 4.6 | 640 | 6.5 |
520 | 800 | 15.7 | 4000 | 4.6 | 680 | 6.5 |
521 | 800 | 15.7 | 4000 | 4.6 | 720 | 6.5 |
522 | 800 | 15.7 | 4000 | 4.6 | 760 | 6.5 |
537 | 750 | 14.8 | 3750 | 4.9 | 111 | 4.9 |
538 | 750 | 14.8 | 3750 | 4.9 | 148 | 4.9 |
539 | 750 | 14.8 | 3750 | 4.9 | 185 | 4.9 |
540 | 750 | 14.8 | 3750 | 4.9 | 222 | 4.9 |
541 | 750 | 14.8 | 3750 | 4.9 | 259 | 4.9 |
542 | 750 | 14.8 | 3750 | 4.9 | 296 | 4.9 |
543 | 750 | 14.8 | 3750 | 4.9 | 333 | 4.9 |
544 | 750 | 14.8 | 3750 | 4.9 | 370 | 4.9 |
545 | 750 | 14.8 | 3750 | 4.9 | 407 | 4.9 |
546 | 750 | 14.8 | 3750 | 4.9 | 444 | 4.9 |
547 | 750 | 14.8 | 3750 | 4.9 | 481 | 4.9 |
548 | 750 | 14.8 | 3750 | 4.9 | 518 | 4.9 |
549 | 750 | 14.8 | 3750 | 4.9 | 555 | 4.9 |
550 | 750 | 14.8 | 3750 | 4.9 | 592 | 4.9 |
551 | 750 | 14.8 | 3750 | 4.9 | 629 | 4.9 |
552 | 750 | 14.8 | 3750 | 4.9 | 666 | 4.9 |
553 | 750 | 14.8 | 3750 | 4.9 | 703 | 4.9 |
554 | 750 | 14.8 | 3750 | 4.9 | 740 | 4.9 |
555 | 750 | 14.8 | 3750 | 4.9 | 777 | 4.9 |
Overall score = score_ratio - 2 * repetitive DNA content