Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign80 - back to list
Summary
./analyse_probe_search_results : Mon Nov 7 11:10:38 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign80 assembly : NCBIM34 bias : 5prime chromosome : 9 id : 71 strand : 1 ------------- Design window length: 1501bp All jobs for probe design are successful - total: 15 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 289 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 5prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 289/289 Putative probes that are unique : 0/289 No putative probes pass with the above criteria Now trying: score-ratio 2, and percent repetitive 40 Putative probes exceeding selection criteria : 140/289 (both unique and not unique) Putative probes with successfully-picked primers: 133/140 Identified 8 'redundant' probes exceeding selection criteria (but wholly contained by other probes, and higher repetitive DNA content)
Image
Unique (yellow), passed (green) and failed putative probes in the design window
![Chart](gfx/probedesign80.png)
Unique putative probes
No probes
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
67668 | 900 | 19.1 | 4500 | 24.0 | 540 | -28.9 |
67858 | 500 | 10.6 | 2500 | 19.8 | 400 | -29.0 |
67859 | 500 | 10.6 | 2500 | 19.8 | 425 | -29.0 |
67860 | 500 | 10.6 | 2500 | 19.8 | 450 | -29.0 |
67861 | 500 | 10.6 | 2500 | 19.8 | 475 | -29.0 |
67862 | 500 | 10.6 | 2500 | 20.0 | 500 | -29.4 |
67655 | 950 | 20.1 | 4750 | 24.9 | 517 | -29.8 |
67667 | 900 | 19.1 | 4500 | 24.4 | 495 | -29.8 |
67684 | 850 | 20.2 | 4250 | 25.4 | 588 | -30.6 |
67654 | 950 | 20.1 | 4750 | 25.8 | 470 | -31.5 |
67642 | 1000 | 21.2 | 5000 | 26.9 | 450 | -32.6 |
67682 | 850 | 18.0 | 4250 | 25.4 | 504 | -32.8 |
67683 | 850 | 18.0 | 4250 | 25.4 | 546 | -32.8 |
67643 | 1000 | 19.8 | 5000 | 27.0 | 500 | -34.2 |
67701 | 800 | 19.0 | 4000 | 27.0 | 600 | -35.0 |
67702 | 800 | 19.0 | 4000 | 27.0 | 640 | -35.0 |
67700 | 800 | 18.5 | 4000 | 27.0 | 560 | -35.5 |
67699 | 800 | 16.9 | 4000 | 27.0 | 520 | -37.1 |
67669 | 900 | 18.4 | 4500 | 28.3 | 585 | -38.3 |
67632 | 1050 | 22.2 | 5250 | 30.4 | 416 | -38.5 |
67857 | 500 | 10.6 | 2500 | 24.8 | 375 | -39.0 |
67863 | 500 | 10.6 | 2500 | 25.0 | 525 | -39.4 |
67720 | 750 | 17.9 | 3750 | 28.8 | 592 | -39.7 |
67721 | 750 | 17.9 | 3750 | 28.8 | 629 | -39.7 |
67722 | 750 | 17.9 | 3750 | 28.8 | 666 | -39.7 |
67666 | 900 | 19.1 | 4500 | 29.4 | 450 | -39.8 |
67685 | 850 | 17.7 | 4250 | 29.4 | 630 | -41.1 |
67653 | 950 | 20.1 | 4750 | 30.7 | 423 | -41.3 |
67719 | 750 | 16.2 | 3750 | 28.8 | 555 | -41.4 |
67681 | 850 | 18.0 | 4250 | 29.8 | 462 | -41.5 |
67723 | 750 | 17.9 | 3750 | 29.7 | 703 | -41.6 |
67718 | 750 | 15.9 | 3750 | 28.8 | 518 | -41.7 |
67698 | 800 | 16.9 | 4000 | 29.4 | 480 | -41.8 |
67641 | 1000 | 21.2 | 5000 | 31.5 | 400 | -41.8 |
67819 | 550 | 11.7 | 2750 | 27.1 | 351 | -42.5 |
67820 | 550 | 11.7 | 2750 | 27.1 | 378 | -42.5 |
67821 | 550 | 11.7 | 2750 | 27.1 | 405 | -42.5 |
67822 | 550 | 11.7 | 2750 | 27.1 | 432 | -42.5 |
67823 | 550 | 11.7 | 2750 | 27.1 | 459 | -42.5 |
67824 | 550 | 11.7 | 2750 | 27.1 | 486 | -42.5 |
67631 | 1050 | 22.2 | 5250 | 33.4 | 364 | -44.6 |
67623 | 1100 | 22.4 | 5500 | 33.5 | 385 | -44.6 |
67742 | 700 | 16.7 | 3500 | 30.9 | 595 | -45.0 |
67743 | 700 | 16.7 | 3500 | 30.9 | 630 | -45.0 |
67744 | 700 | 16.7 | 3500 | 30.9 | 665 | -45.0 |
67745 | 700 | 16.7 | 3500 | 30.9 | 700 | -45.0 |
67746 | 700 | 16.7 | 3500 | 30.9 | 735 | -45.0 |
67741 | 700 | 16.2 | 3500 | 30.9 | 560 | -45.5 |
67703 | 800 | 16.7 | 4000 | 31.2 | 680 | -45.8 |
67717 | 750 | 15.9 | 3750 | 31.2 | 481 | -46.5 |
67622 | 1100 | 23.3 | 5500 | 35.0 | 330 | -46.7 |
67740 | 700 | 14.8 | 3500 | 30.9 | 525 | -46.9 |
67825 | 550 | 11.7 | 2750 | 29.6 | 513 | -47.6 |
67856 | 500 | 10.6 | 2500 | 29.8 | 350 | -49.0 |
67864 | 500 | 10.6 | 2500 | 30.0 | 550 | -49.4 |
67739 | 700 | 14.8 | 3500 | 32.1 | 490 | -49.5 |
67665 | 900 | 19.1 | 4500 | 34.4 | 405 | -49.8 |
67615 | 1150 | 22.8 | 5750 | 36.4 | 342 | -50.1 |
67614 | 1150 | 24.4 | 5750 | 37.4 | 285 | -50.4 |
67766 | 650 | 15.5 | 3250 | 33.2 | 576 | -51.0 |
67767 | 650 | 15.5 | 3250 | 33.2 | 608 | -51.0 |
67768 | 650 | 15.5 | 3250 | 33.2 | 640 | -51.0 |
67769 | 650 | 15.5 | 3250 | 33.2 | 672 | -51.0 |
67770 | 650 | 15.5 | 3250 | 33.2 | 704 | -51.0 |
67771 | 650 | 15.5 | 3250 | 33.2 | 736 | -51.0 |
67772 | 650 | 15.5 | 3250 | 33.2 | 768 | -51.0 |
67652 | 950 | 20.1 | 4750 | 35.7 | 376 | -51.2 |
67680 | 850 | 18.0 | 4250 | 34.7 | 420 | -51.4 |
67697 | 800 | 16.9 | 4000 | 34.4 | 440 | -51.8 |
67640 | 1000 | 21.2 | 5000 | 36.5 | 350 | -51.8 |
67747 | 700 | 16.7 | 3500 | 34.3 | 770 | -51.9 |
67818 | 550 | 11.7 | 2750 | 31.8 | 324 | -52.0 |
67773 | 650 | 15.5 | 3250 | 33.8 | 800 | -52.2 |
67764 | 650 | 13.8 | 3250 | 33.2 | 512 | -52.7 |
67765 | 650 | 13.8 | 3250 | 33.2 | 544 | -52.7 |
67785 | 600 | 12.7 | 3000 | 33.2 | 300 | -53.6 |
67786 | 600 | 12.7 | 3000 | 33.2 | 330 | -53.6 |
67787 | 600 | 12.7 | 3000 | 33.2 | 360 | -53.6 |
67788 | 600 | 12.7 | 3000 | 33.2 | 390 | -53.6 |
67789 | 600 | 12.7 | 3000 | 33.2 | 420 | -53.6 |
67790 | 600 | 12.7 | 3000 | 33.2 | 450 | -53.6 |
67791 | 600 | 12.7 | 3000 | 33.2 | 480 | -53.6 |
67724 | 750 | 15.3 | 3750 | 34.7 | 740 | -54.0 |
67880 | 500 | 13.8 | 2500 | 34.0 | 950 | -54.2 |
67608 | 1200 | 23.8 | 6000 | 39.1 | 300 | -54.4 |
67630 | 1050 | 22.2 | 5250 | 38.4 | 312 | -54.5 |
67881 | 500 | 11.7 | 2500 | 34.0 | 975 | -56.3 |
67716 | 750 | 15.9 | 3750 | 36.1 | 444 | -56.4 |
67792 | 600 | 12.7 | 3000 | 35.0 | 510 | -57.3 |
67826 | 550 | 11.7 | 2750 | 34.5 | 540 | -57.4 |
67794 | 600 | 14.3 | 3000 | 36.0 | 570 | -57.7 |
67795 | 600 | 14.3 | 3000 | 36.0 | 600 | -57.7 |
67796 | 600 | 14.3 | 3000 | 36.0 | 630 | -57.7 |
67797 | 600 | 14.3 | 3000 | 36.0 | 660 | -57.7 |
67798 | 600 | 14.3 | 3000 | 36.0 | 690 | -57.7 |
67799 | 600 | 14.3 | 3000 | 36.0 | 720 | -57.7 |
67800 | 600 | 14.3 | 3000 | 36.0 | 750 | -57.7 |
67801 | 600 | 14.3 | 3000 | 36.0 | 780 | -57.7 |
67802 | 600 | 14.3 | 3000 | 36.0 | 810 | -57.7 |
67803 | 600 | 14.3 | 3000 | 36.0 | 840 | -57.7 |
67882 | 500 | 9.9 | 2500 | 34.0 | 1000 | -58.1 |
67865 | 500 | 11.9 | 2500 | 35.0 | 575 | -58.1 |
67763 | 650 | 13.8 | 3250 | 36.2 | 480 | -58.5 |
67855 | 500 | 10.6 | 2500 | 34.8 | 325 | -59.0 |
67793 | 600 | 12.7 | 3000 | 36.0 | 540 | -59.3 |
67738 | 700 | 14.8 | 3500 | 37.1 | 455 | -59.5 |
67664 | 900 | 19.1 | 4500 | 39.4 | 360 | -59.8 |
67607 | 1200 | 19.0 | 6000 | 39.6 | 240 | -60.2 |
67696 | 800 | 16.9 | 4000 | 39.4 | 400 | -61.8 |
67817 | 550 | 11.7 | 2750 | 36.7 | 297 | -61.8 |
67879 | 500 | 13.8 | 2500 | 38.2 | 925 | -62.6 |
67757 | 650 | 13.8 | 3250 | 38.3 | 288 | -62.8 |
67758 | 650 | 13.8 | 3250 | 38.3 | 320 | -62.8 |
67759 | 650 | 13.8 | 3250 | 38.3 | 352 | -62.8 |
67760 | 650 | 13.8 | 3250 | 38.3 | 384 | -62.8 |
67761 | 650 | 13.8 | 3250 | 38.3 | 416 | -62.8 |
67762 | 650 | 13.8 | 3250 | 38.3 | 448 | -62.8 |
67784 | 600 | 12.7 | 3000 | 38.2 | 270 | -63.6 |
67756 | 650 | 12.8 | 3250 | 38.3 | 256 | -63.8 |
67774 | 650 | 13.3 | 3250 | 38.8 | 832 | -64.3 |
67827 | 550 | 13.1 | 2750 | 39.3 | 567 | -65.5 |
67828 | 550 | 13.1 | 2750 | 39.3 | 594 | -65.5 |
67829 | 550 | 13.1 | 2750 | 39.3 | 621 | -65.5 |
67830 | 550 | 13.1 | 2750 | 39.3 | 648 | -65.5 |
67831 | 550 | 13.1 | 2750 | 39.3 | 675 | -65.5 |
67832 | 550 | 13.1 | 2750 | 39.3 | 702 | -65.5 |
67833 | 550 | 13.1 | 2750 | 39.3 | 729 | -65.5 |
67834 | 550 | 13.1 | 2750 | 39.3 | 756 | -65.5 |
67835 | 550 | 13.1 | 2750 | 39.3 | 783 | -65.5 |
67836 | 550 | 13.1 | 2750 | 39.3 | 810 | -65.5 |
67837 | 550 | 13.1 | 2750 | 39.3 | 837 | -65.5 |
67838 | 550 | 13.1 | 2750 | 39.3 | 864 | -65.5 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
67621 | 1100 | 23.3 | 5500 | 40.0 | 275 | -56.7 |
67679 | 850 | 18.0 | 4250 | 39.6 | 378 | -61.3 |
67839 | 550 | 14.5 | 2750 | 39.3 | 891 | -64.1 |
67840 | 550 | 15.2 | 2750 | 40.0 | 918 | -64.8 |
67804 | 600 | 14.3 | 3000 | 40.0 | 870 | -65.7 |
67866 | 500 | 11.9 | 2500 | 40.0 | 600 | -68.1 |
67854 | 500 | 10.6 | 2500 | 39.8 | 300 | -69.0 |
67841 | 550 | 10.9 | 2750 | 40.0 | 945 | -69.1 |
Overall score = score_ratio - 2 * repetitive DNA content