Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign124 - back to list
Summary
./analyse_probe_search_results : Thu Jun 29 10:00:49 2006
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign124 assembly : NCBIM36 bias : 3prime chromosome : 11 id : 118 strand : 1 ------------- Design window length: 5001bp All jobs for probe design are successful - total: 87 Fetched conf : Exonerate mouse_NCBIM36 (id: 2) Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted Fetched 1729 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 : 1729/1729 Putative probes that are unique : 111/1729 Putative probes exceeding selection criteria : 264/1729 (both unique and not unique) Putative probes with successfully-picked primers: 263/264 Identified 119 '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
Unique putative probes
Putative probe ID | Length | Actual | %rep DNA | Distance |
---|---|---|---|---|
110097 | 900 | 4500 | - | 2565 |
110193 | 850 | 4250 | - | 2562 |
110194 | 850 | 4250 | - | 2604 |
110295 | 800 | 4000 | - | 2560 |
110296 | 800 | 4000 | - | 2600 |
110297 | 800 | 4000 | - | 2640 |
110298 | 800 | 4000 | - | 2680 |
110407 | 750 | 3750 | - | 2590 |
110408 | 750 | 3750 | - | 2627 |
110409 | 750 | 3750 | - | 2664 |
110410 | 750 | 3750 | - | 2701 |
110411 | 750 | 3750 | - | 2738 |
110526 | 700 | 3500 | - | 2590 |
110527 | 700 | 3500 | - | 2625 |
110528 | 700 | 3500 | - | 2660 |
110529 | 700 | 3500 | - | 2695 |
110530 | 700 | 3500 | - | 2730 |
110531 | 700 | 3500 | - | 2765 |
110655 | 650 | 3250 | - | 2560 |
110656 | 650 | 3250 | - | 2592 |
110657 | 650 | 3250 | - | 2624 |
110658 | 650 | 3250 | - | 2656 |
110659 | 650 | 3250 | - | 2688 |
110660 | 650 | 3250 | - | 2720 |
110661 | 650 | 3250 | - | 2752 |
110662 | 650 | 3250 | - | 2784 |
110663 | 650 | 3250 | - | 2816 |
110745 | 600 | 3000 | - | 1020 |
110746 | 600 | 3000 | - | 1050 |
110797 | 600 | 3000 | - | 2580 |
110798 | 600 | 3000 | - | 2610 |
110799 | 600 | 3000 | - | 2640 |
110800 | 600 | 3000 | - | 2670 |
110801 | 600 | 3000 | - | 2700 |
110802 | 600 | 3000 | - | 2730 |
110803 | 600 | 3000 | - | 2760 |
110804 | 600 | 3000 | - | 2790 |
110805 | 600 | 3000 | - | 2820 |
110806 | 600 | 3000 | - | 2850 |
110807 | 600 | 3000 | - | 2880 |
110895 | 550 | 2750 | - | 999 |
110896 | 550 | 2750 | - | 1026 |
110897 | 550 | 2750 | - | 1053 |
110898 | 550 | 2750 | - | 1080 |
110899 | 550 | 2750 | - | 1107 |
110953 | 550 | 2750 | - | 2565 |
110954 | 550 | 2750 | - | 2592 |
110955 | 550 | 2750 | - | 2619 |
110956 | 550 | 2750 | - | 2646 |
110957 | 550 | 2750 | - | 2673 |
110958 | 550 | 2750 | - | 2700 |
110959 | 550 | 2750 | - | 2727 |
110960 | 550 | 2750 | - | 2754 |
110961 | 550 | 2750 | - | 2781 |
110962 | 550 | 2750 | - | 2808 |
110963 | 550 | 2750 | - | 2835 |
110964 | 550 | 2750 | - | 2862 |
110965 | 550 | 2750 | - | 2889 |
110966 | 550 | 2750 | - | 2916 |
111040 | 500 | 2500 | - | 425 |
111063 | 500 | 2500 | - | 1000 |
111064 | 500 | 2500 | - | 1025 |
111065 | 500 | 2500 | - | 1050 |
111066 | 500 | 2500 | - | 1075 |
111067 | 500 | 2500 | - | 1100 |
111068 | 500 | 2500 | - | 1125 |
111069 | 500 | 2500 | - | 1150 |
111126 | 500 | 2500 | - | 2575 |
111127 | 500 | 2500 | - | 2600 |
111128 | 500 | 2500 | - | 2625 |
111129 | 500 | 2500 | - | 2650 |
111130 | 500 | 2500 | - | 2675 |
111131 | 500 | 2500 | - | 2700 |
111132 | 500 | 2500 | - | 2725 |
111133 | 500 | 2500 | - | 2750 |
111134 | 500 | 2500 | - | 2775 |
111135 | 500 | 2500 | - | 2800 |
111136 | 500 | 2500 | - | 2825 |
111137 | 500 | 2500 | - | 2850 |
111138 | 500 | 2500 | - | 2875 |
111139 | 500 | 2500 | - | 2900 |
111140 | 500 | 2500 | - | 2925 |
111141 | 500 | 2500 | - | 2950 |
111142 | 500 | 2500 | - | 2975 |
110607 | 650 | 3250 | 0.2 | 1024 |
110606 | 650 | 3250 | 0.3 | 992 |
111070 | 500 | 2500 | 0.4 | 1175 |
110744 | 600 | 3000 | 0.7 | 990 |
110967 | 550 | 2750 | 0.9 | 2943 |
110195 | 850 | 4250 | 0.9 | 2646 |
110747 | 600 | 3000 | 1.2 | 1080 |
110664 | 650 | 3250 | 1.5 | 2848 |
110532 | 700 | 3500 | 1.7 | 2800 |
110900 | 550 | 2750 | 2.0 | 1134 |
111039 | 500 | 2500 | 2.0 | 400 |
111143 | 500 | 2500 | 2.4 | 3000 |
110098 | 900 | 4500 | 2.4 | 2610 |
110808 | 600 | 3000 | 3.7 | 2910 |
110856 | 600 | 3000 | 12.3 | 4350 |
110857 | 600 | 3000 | 12.3 | 4380 |
111019 | 550 | 2750 | 13.5 | 4347 |
111020 | 550 | 2750 | 13.5 | 4374 |
111021 | 550 | 2750 | 13.5 | 4401 |
111022 | 550 | 2750 | 13.5 | 4428 |
111197 | 500 | 2500 | 14.8 | 4350 |
111198 | 500 | 2500 | 14.8 | 4375 |
111199 | 500 | 2500 | 14.8 | 4400 |
111200 | 500 | 2500 | 14.8 | 4425 |
111201 | 500 | 2500 | 14.8 | 4450 |
111202 | 500 | 2500 | 14.8 | 4475 |
111203 | 500 | 2500 | 14.8 | 4500 |
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
109514 | 1300 | 41.1 | 6500 | 2.1 | 2535 | 37.0 |
109515 | 1300 | 41.1 | 6500 | 2.6 | 2600 | 35.9 |
109574 | 1250 | 39.6 | 6250 | 2.2 | 2604 | 35.2 |
109637 | 1200 | 38.0 | 6000 | 2.2 | 2640 | 33.5 |
109705 | 1150 | 36.4 | 5750 | 2.3 | 2736 | 31.7 |
109575 | 1250 | 39.6 | 6250 | 4.0 | 2666 | 31.6 |
110007 | 950 | 31.0 | 4750 | - | 2538 | 31.0 |
109775 | 1100 | 34.8 | 5500 | 2.5 | 2750 | 29.9 |
109771 | 1100 | 34.8 | 5500 | 2.8 | 2530 | 29.2 |
109850 | 1050 | 33.2 | 5250 | 2.6 | 2808 | 28.1 |
109776 | 1100 | 34.8 | 5500 | 3.5 | 2805 | 27.7 |
109635 | 1200 | 33.1 | 6000 | 3.4 | 2520 | 26.3 |
110406 | 750 | 25.0 | 3750 | - | 2553 | 25.0 |
110525 | 700 | 23.3 | 3500 | - | 2555 | 23.3 |
110096 | 900 | 24.9 | 4500 | 1.6 | 2520 | 21.8 |
110192 | 850 | 23.5 | 4250 | 1.6 | 2520 | 20.2 |
110796 | 600 | 20.0 | 3000 | - | 2550 | 20.0 |
110654 | 650 | 21.2 | 3250 | 0.9 | 2528 | 19.4 |
110294 | 800 | 22.1 | 4000 | 1.8 | 2520 | 18.6 |
110952 | 550 | 18.0 | 2750 | - | 2538 | 18.0 |
110480 | 700 | 23.0 | 3500 | 3.0 | 980 | 17.0 |
111125 | 500 | 16.7 | 2500 | - | 2550 | 16.7 |
109701 | 1150 | 25.8 | 5750 | 4.6 | 2508 | 16.6 |
110524 | 700 | 19.3 | 3500 | 2.0 | 2520 | 15.3 |
110405 | 750 | 18.7 | 3750 | 2.4 | 2516 | 13.9 |
111124 | 500 | 16.3 | 2500 | 1.8 | 2525 | 12.7 |
110795 | 600 | 16.6 | 3000 | 2.3 | 2520 | 11.9 |
109922 | 1000 | 19.0 | 5000 | 4.6 | 2500 | 9.8 |
111041 | 500 | 15.8 | 2500 | 3.4 | 450 | 9.0 |
110894 | 550 | 16.4 | 2750 | 4.0 | 972 | 8.4 |
111062 | 500 | 15.6 | 2500 | 3.8 | 975 | 8.0 |
110006 | 950 | 15.9 | 4750 | 4.5 | 2491 | 6.8 |
110873 | 550 | 15.0 | 2750 | 4.9 | 405 | 5.2 |
110951 | 550 | 12.7 | 2750 | 4.2 | 2511 | 4.3 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
109573 | 1250 | 39.6 | 6250 | 2.2 | 2542 | 35.2 |
109636 | 1200 | 38.0 | 6000 | 2.2 | 2580 | 33.5 |
109638 | 1200 | 38.0 | 6000 | 2.8 | 2700 | 32.3 |
109702 | 1150 | 36.4 | 5750 | 2.3 | 2565 | 31.7 |
109703 | 1150 | 36.4 | 5750 | 2.3 | 2622 | 31.7 |
109704 | 1150 | 36.4 | 5750 | 2.3 | 2679 | 31.7 |
109772 | 1100 | 34.8 | 5500 | 2.5 | 2585 | 29.9 |
109773 | 1100 | 34.8 | 5500 | 2.5 | 2640 | 29.9 |
109774 | 1100 | 34.8 | 5500 | 2.5 | 2695 | 29.9 |
109845 | 1050 | 33.2 | 5250 | 2.6 | 2548 | 28.1 |
109846 | 1050 | 33.2 | 5250 | 2.6 | 2600 | 28.1 |
109847 | 1050 | 33.2 | 5250 | 2.6 | 2652 | 28.1 |
109848 | 1050 | 33.2 | 5250 | 2.6 | 2704 | 28.1 |
109849 | 1050 | 33.2 | 5250 | 2.6 | 2756 | 28.1 |
109923 | 1000 | 31.6 | 5000 | 2.7 | 2550 | 26.2 |
109924 | 1000 | 31.6 | 5000 | 2.7 | 2600 | 26.2 |
109925 | 1000 | 31.6 | 5000 | 2.7 | 2650 | 26.2 |
109926 | 1000 | 31.6 | 5000 | 2.7 | 2700 | 26.2 |
109927 | 1000 | 31.6 | 5000 | 2.7 | 2750 | 26.2 |
109928 | 1000 | 31.6 | 5000 | 2.7 | 2800 | 26.2 |
109929 | 1000 | 31.6 | 5000 | 2.7 | 2850 | 26.2 |
109851 | 1050 | 33.2 | 5250 | 4.2 | 2860 | 24.8 |
109930 | 1000 | 31.6 | 5000 | 3.4 | 2900 | 24.8 |
110008 | 950 | 30.1 | 4750 | 2.8 | 2585 | 24.4 |
110009 | 950 | 30.1 | 4750 | 2.8 | 2632 | 24.4 |
110010 | 950 | 30.1 | 4750 | 2.8 | 2679 | 24.4 |
110011 | 950 | 30.1 | 4750 | 2.8 | 2726 | 24.4 |
110012 | 950 | 30.1 | 4750 | 2.8 | 2773 | 24.4 |
110013 | 950 | 30.1 | 4750 | 2.8 | 2820 | 24.4 |
110014 | 950 | 30.1 | 4750 | 2.8 | 2867 | 24.4 |
110015 | 950 | 30.1 | 4750 | 2.8 | 2914 | 24.4 |
110099 | 900 | 28.5 | 4500 | 3.0 | 2655 | 22.5 |
110100 | 900 | 28.5 | 4500 | 3.0 | 2700 | 22.5 |
110101 | 900 | 28.5 | 4500 | 3.0 | 2745 | 22.5 |
110102 | 900 | 28.5 | 4500 | 3.0 | 2790 | 22.5 |
110103 | 900 | 28.5 | 4500 | 3.0 | 2835 | 22.5 |
110104 | 900 | 28.5 | 4500 | 3.0 | 2880 | 22.5 |
110105 | 900 | 28.5 | 4500 | 3.0 | 2925 | 22.5 |
110106 | 900 | 28.5 | 4500 | 3.0 | 2970 | 22.5 |
110016 | 950 | 30.1 | 4750 | 4.7 | 2961 | 20.6 |
110196 | 850 | 26.9 | 4250 | 3.2 | 2688 | 20.5 |
110197 | 850 | 26.9 | 4250 | 3.2 | 2730 | 20.5 |
110198 | 850 | 26.9 | 4250 | 3.2 | 2772 | 20.5 |
110199 | 850 | 26.9 | 4250 | 3.2 | 2814 | 20.5 |
110200 | 850 | 26.9 | 4250 | 3.2 | 2856 | 20.5 |
110201 | 850 | 26.9 | 4250 | 3.2 | 2898 | 20.5 |
110202 | 850 | 26.9 | 4250 | 3.2 | 2940 | 20.5 |
110203 | 850 | 26.9 | 4250 | 3.2 | 2982 | 20.5 |
110204 | 850 | 26.9 | 4250 | 3.2 | 3024 | 20.5 |
110299 | 800 | 25.3 | 4000 | 3.4 | 2720 | 18.6 |
110300 | 800 | 25.3 | 4000 | 3.4 | 2760 | 18.6 |
110301 | 800 | 25.3 | 4000 | 3.4 | 2800 | 18.6 |
110302 | 800 | 25.3 | 4000 | 3.4 | 2840 | 18.6 |
110303 | 800 | 25.3 | 4000 | 3.4 | 2880 | 18.6 |
110304 | 800 | 25.3 | 4000 | 3.4 | 2920 | 18.6 |
110305 | 800 | 25.3 | 4000 | 3.4 | 2960 | 18.6 |
110306 | 800 | 25.3 | 4000 | 3.4 | 3000 | 18.6 |
110307 | 800 | 25.3 | 4000 | 3.4 | 3040 | 18.6 |
110308 | 800 | 25.3 | 4000 | 3.4 | 3080 | 18.6 |
110412 | 750 | 23.7 | 3750 | 3.6 | 2775 | 16.5 |
110413 | 750 | 23.7 | 3750 | 3.6 | 2812 | 16.5 |
110414 | 750 | 23.7 | 3750 | 3.6 | 2849 | 16.5 |
110415 | 750 | 23.7 | 3750 | 3.6 | 2886 | 16.5 |
110416 | 750 | 23.7 | 3750 | 3.6 | 2923 | 16.5 |
110417 | 750 | 23.7 | 3750 | 3.6 | 2960 | 16.5 |
110418 | 750 | 23.7 | 3750 | 3.6 | 2997 | 16.5 |
110419 | 750 | 23.7 | 3750 | 3.6 | 3034 | 16.5 |
110420 | 750 | 23.7 | 3750 | 3.6 | 3071 | 16.5 |
110421 | 750 | 23.7 | 3750 | 3.6 | 3108 | 16.5 |
110422 | 750 | 23.7 | 3750 | 3.9 | 3145 | 16.0 |
110533 | 700 | 22.2 | 3500 | 3.9 | 2835 | 14.4 |
110534 | 700 | 22.2 | 3500 | 3.9 | 2870 | 14.4 |
110535 | 700 | 22.2 | 3500 | 3.9 | 2905 | 14.4 |
110536 | 700 | 22.2 | 3500 | 3.9 | 2940 | 14.4 |
110537 | 700 | 22.2 | 3500 | 3.9 | 2975 | 14.4 |
110538 | 700 | 22.2 | 3500 | 3.9 | 3010 | 14.4 |
110539 | 700 | 22.2 | 3500 | 3.9 | 3045 | 14.4 |
110540 | 700 | 22.2 | 3500 | 3.9 | 3080 | 14.4 |
110541 | 700 | 22.2 | 3500 | 3.9 | 3115 | 14.4 |
110542 | 700 | 22.2 | 3500 | 3.9 | 3150 | 14.4 |
110543 | 700 | 22.2 | 3500 | 3.9 | 3185 | 14.4 |
110665 | 650 | 20.6 | 3250 | 4.2 | 2880 | 12.3 |
110666 | 650 | 20.6 | 3250 | 4.2 | 2912 | 12.3 |
110667 | 650 | 20.6 | 3250 | 4.2 | 2944 | 12.3 |
110668 | 650 | 20.6 | 3250 | 4.2 | 2976 | 12.3 |
110669 | 650 | 20.6 | 3250 | 4.2 | 3008 | 12.3 |
110670 | 650 | 20.6 | 3250 | 4.2 | 3040 | 12.3 |
110671 | 650 | 20.6 | 3250 | 4.2 | 3072 | 12.3 |
110672 | 650 | 20.6 | 3250 | 4.2 | 3104 | 12.3 |
110673 | 650 | 20.6 | 3250 | 4.2 | 3136 | 12.3 |
110674 | 650 | 20.6 | 3250 | 4.2 | 3168 | 12.3 |
110675 | 650 | 20.6 | 3250 | 4.2 | 3200 | 12.3 |
110676 | 650 | 20.6 | 3250 | 4.2 | 3232 | 12.3 |
110809 | 600 | 19.0 | 3000 | 4.5 | 2940 | 10.0 |
110810 | 600 | 19.0 | 3000 | 4.5 | 2970 | 10.0 |
110811 | 600 | 19.0 | 3000 | 4.5 | 3000 | 10.0 |
110812 | 600 | 19.0 | 3000 | 4.5 | 3030 | 10.0 |
110813 | 600 | 19.0 | 3000 | 4.5 | 3060 | 10.0 |
110814 | 600 | 19.0 | 3000 | 4.5 | 3090 | 10.0 |
110815 | 600 | 19.0 | 3000 | 4.5 | 3120 | 10.0 |
110816 | 600 | 19.0 | 3000 | 4.5 | 3150 | 10.0 |
110817 | 600 | 19.0 | 3000 | 4.5 | 3180 | 10.0 |
110818 | 600 | 19.0 | 3000 | 4.5 | 3210 | 10.0 |
110819 | 600 | 19.0 | 3000 | 4.5 | 3240 | 10.0 |
110820 | 600 | 19.0 | 3000 | 4.5 | 3270 | 10.0 |
110968 | 550 | 17.4 | 2750 | 4.9 | 2970 | 7.6 |
110969 | 550 | 17.4 | 2750 | 4.9 | 2997 | 7.6 |
110970 | 550 | 17.4 | 2750 | 4.9 | 3024 | 7.6 |
110971 | 550 | 17.4 | 2750 | 4.9 | 3051 | 7.6 |
110972 | 550 | 17.4 | 2750 | 4.9 | 3078 | 7.6 |
110973 | 550 | 17.4 | 2750 | 4.9 | 3105 | 7.6 |
110974 | 550 | 17.4 | 2750 | 4.9 | 3132 | 7.6 |
110975 | 550 | 17.4 | 2750 | 4.9 | 3159 | 7.6 |
110976 | 550 | 17.4 | 2750 | 4.9 | 3186 | 7.6 |
110977 | 550 | 17.4 | 2750 | 4.9 | 3213 | 7.6 |
110978 | 550 | 17.4 | 2750 | 4.9 | 3240 | 7.6 |
110979 | 550 | 17.4 | 2750 | 4.9 | 3267 | 7.6 |
110980 | 550 | 17.4 | 2750 | 4.9 | 3294 | 7.6 |
110981 | 550 | 17.4 | 2750 | 4.9 | 3321 | 7.6 |
Overall score = score_ratio - 2 * repetitive DNA content