Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign104 - back to list
Summary
./analyse_probe_search_results : Tue Jan 31 11:12:10 2006
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign104 assembly : NCBIM34 bias : 5prime chromosome : 13 id : 97 strand : 1 ------------- Design window length: 3001bp All jobs for probe design are successful - total: 46 Fetched conf : Exonerate mouse_NCBIM34 (id: 1) Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted Fetched 907 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 : 907/907 Putative probes that are unique : 244/907 Putative probes exceeding selection criteria : 255/907 (both unique and not unique) Putative probes with successfully-picked primers: 255/255 Identified 7 '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/probedesign104.png)
Unique putative probes
Putative probe ID | Length | Actual | %rep DNA | Distance |
---|---|---|---|---|
92637 | 1250 | 6250 | - | 0 |
92666 | 1200 | 6000 | - | 0 |
92667 | 1200 | 6000 | - | 60 |
92697 | 1150 | 5750 | - | 0 |
92698 | 1150 | 5750 | - | 57 |
92699 | 1150 | 5750 | - | 114 |
92730 | 1100 | 5500 | - | 0 |
92731 | 1100 | 5500 | - | 55 |
92732 | 1100 | 5500 | - | 110 |
92733 | 1100 | 5500 | - | 165 |
92765 | 1050 | 5250 | - | 0 |
92766 | 1050 | 5250 | - | 52 |
92767 | 1050 | 5250 | - | 104 |
92768 | 1050 | 5250 | - | 156 |
92769 | 1050 | 5250 | - | 208 |
92803 | 1000 | 5000 | - | 0 |
92804 | 1000 | 5000 | - | 50 |
92805 | 1000 | 5000 | - | 100 |
92806 | 1000 | 5000 | - | 150 |
92807 | 1000 | 5000 | - | 200 |
92808 | 1000 | 5000 | - | 250 |
92844 | 950 | 4750 | - | 0 |
92845 | 950 | 4750 | - | 47 |
92846 | 950 | 4750 | - | 94 |
92847 | 950 | 4750 | - | 141 |
92848 | 950 | 4750 | - | 188 |
92849 | 950 | 4750 | - | 235 |
92850 | 950 | 4750 | - | 282 |
92851 | 950 | 4750 | - | 329 |
92888 | 900 | 4500 | - | 0 |
92889 | 900 | 4500 | - | 45 |
92890 | 900 | 4500 | - | 90 |
92891 | 900 | 4500 | - | 135 |
92892 | 900 | 4500 | - | 180 |
92893 | 900 | 4500 | - | 225 |
92894 | 900 | 4500 | - | 270 |
92895 | 900 | 4500 | - | 315 |
92896 | 900 | 4500 | - | 360 |
92935 | 850 | 4250 | - | 0 |
92936 | 850 | 4250 | - | 42 |
92937 | 850 | 4250 | - | 84 |
92938 | 850 | 4250 | - | 126 |
92939 | 850 | 4250 | - | 168 |
92940 | 850 | 4250 | - | 210 |
92941 | 850 | 4250 | - | 252 |
92942 | 850 | 4250 | - | 294 |
92943 | 850 | 4250 | - | 336 |
92944 | 850 | 4250 | - | 378 |
92945 | 850 | 4250 | - | 420 |
92987 | 800 | 4000 | - | 0 |
92988 | 800 | 4000 | - | 40 |
92989 | 800 | 4000 | - | 80 |
92990 | 800 | 4000 | - | 120 |
92991 | 800 | 4000 | - | 160 |
92992 | 800 | 4000 | - | 200 |
92993 | 800 | 4000 | - | 240 |
92994 | 800 | 4000 | - | 280 |
92995 | 800 | 4000 | - | 320 |
92996 | 800 | 4000 | - | 360 |
92997 | 800 | 4000 | - | 400 |
92998 | 800 | 4000 | - | 440 |
92999 | 800 | 4000 | - | 480 |
93043 | 750 | 3750 | - | 0 |
93044 | 750 | 3750 | - | 37 |
93045 | 750 | 3750 | - | 74 |
93046 | 750 | 3750 | - | 111 |
93047 | 750 | 3750 | - | 148 |
93048 | 750 | 3750 | - | 185 |
93049 | 750 | 3750 | - | 222 |
93050 | 750 | 3750 | - | 259 |
93051 | 750 | 3750 | - | 296 |
93052 | 750 | 3750 | - | 333 |
93053 | 750 | 3750 | - | 370 |
93054 | 750 | 3750 | - | 407 |
93055 | 750 | 3750 | - | 444 |
93056 | 750 | 3750 | - | 481 |
93057 | 750 | 3750 | - | 518 |
93104 | 700 | 3500 | - | 0 |
93105 | 700 | 3500 | - | 35 |
93106 | 700 | 3500 | - | 70 |
93107 | 700 | 3500 | - | 105 |
93108 | 700 | 3500 | - | 140 |
93109 | 700 | 3500 | - | 175 |
93110 | 700 | 3500 | - | 210 |
93111 | 700 | 3500 | - | 245 |
93112 | 700 | 3500 | - | 280 |
93113 | 700 | 3500 | - | 315 |
93114 | 700 | 3500 | - | 350 |
93115 | 700 | 3500 | - | 385 |
93116 | 700 | 3500 | - | 420 |
93117 | 700 | 3500 | - | 455 |
93118 | 700 | 3500 | - | 490 |
93119 | 700 | 3500 | - | 525 |
93120 | 700 | 3500 | - | 560 |
93170 | 650 | 3250 | - | 0 |
93171 | 650 | 3250 | - | 32 |
93172 | 650 | 3250 | - | 64 |
93173 | 650 | 3250 | - | 96 |
93174 | 650 | 3250 | - | 128 |
93175 | 650 | 3250 | - | 160 |
93176 | 650 | 3250 | - | 192 |
93177 | 650 | 3250 | - | 224 |
93178 | 650 | 3250 | - | 256 |
93179 | 650 | 3250 | - | 288 |
93180 | 650 | 3250 | - | 320 |
93181 | 650 | 3250 | - | 352 |
93182 | 650 | 3250 | - | 384 |
93183 | 650 | 3250 | - | 416 |
93184 | 650 | 3250 | - | 448 |
93185 | 650 | 3250 | - | 480 |
93186 | 650 | 3250 | - | 512 |
93187 | 650 | 3250 | - | 544 |
93188 | 650 | 3250 | - | 576 |
93189 | 650 | 3250 | - | 608 |
93244 | 600 | 3000 | - | 0 |
93245 | 600 | 3000 | - | 30 |
93246 | 600 | 3000 | - | 60 |
93247 | 600 | 3000 | - | 90 |
93248 | 600 | 3000 | - | 120 |
93249 | 600 | 3000 | - | 150 |
93250 | 600 | 3000 | - | 180 |
93251 | 600 | 3000 | - | 210 |
93252 | 600 | 3000 | - | 240 |
93253 | 600 | 3000 | - | 270 |
93254 | 600 | 3000 | - | 300 |
93255 | 600 | 3000 | - | 330 |
93256 | 600 | 3000 | - | 360 |
93257 | 600 | 3000 | - | 390 |
93258 | 600 | 3000 | - | 420 |
93259 | 600 | 3000 | - | 450 |
93260 | 600 | 3000 | - | 480 |
93261 | 600 | 3000 | - | 510 |
93262 | 600 | 3000 | - | 540 |
93263 | 600 | 3000 | - | 570 |
93264 | 600 | 3000 | - | 600 |
93265 | 600 | 3000 | - | 630 |
93266 | 600 | 3000 | - | 660 |
93325 | 550 | 2750 | - | 0 |
93326 | 550 | 2750 | - | 27 |
93327 | 550 | 2750 | - | 54 |
93328 | 550 | 2750 | - | 81 |
93329 | 550 | 2750 | - | 108 |
93330 | 550 | 2750 | - | 135 |
93331 | 550 | 2750 | - | 162 |
93332 | 550 | 2750 | - | 189 |
93333 | 550 | 2750 | - | 216 |
93334 | 550 | 2750 | - | 243 |
93335 | 550 | 2750 | - | 270 |
93336 | 550 | 2750 | - | 297 |
93337 | 550 | 2750 | - | 324 |
93338 | 550 | 2750 | - | 351 |
93339 | 550 | 2750 | - | 378 |
93340 | 550 | 2750 | - | 405 |
93341 | 550 | 2750 | - | 432 |
93342 | 550 | 2750 | - | 459 |
93343 | 550 | 2750 | - | 486 |
93344 | 550 | 2750 | - | 513 |
93345 | 550 | 2750 | - | 540 |
93346 | 550 | 2750 | - | 567 |
93347 | 550 | 2750 | - | 594 |
93348 | 550 | 2750 | - | 621 |
93349 | 550 | 2750 | - | 648 |
93350 | 550 | 2750 | - | 675 |
93351 | 550 | 2750 | - | 702 |
93352 | 550 | 2750 | - | 729 |
93416 | 500 | 2500 | - | 0 |
93417 | 500 | 2500 | - | 25 |
93418 | 500 | 2500 | - | 50 |
93419 | 500 | 2500 | - | 75 |
93420 | 500 | 2500 | - | 100 |
93421 | 500 | 2500 | - | 125 |
93422 | 500 | 2500 | - | 150 |
93423 | 500 | 2500 | - | 175 |
93424 | 500 | 2500 | - | 200 |
93425 | 500 | 2500 | - | 225 |
93426 | 500 | 2500 | - | 250 |
93427 | 500 | 2500 | - | 275 |
93428 | 500 | 2500 | - | 300 |
93429 | 500 | 2500 | - | 325 |
93430 | 500 | 2500 | - | 350 |
93431 | 500 | 2500 | - | 375 |
93432 | 500 | 2500 | - | 400 |
93433 | 500 | 2500 | - | 425 |
93434 | 500 | 2500 | - | 450 |
93435 | 500 | 2500 | - | 475 |
93436 | 500 | 2500 | - | 500 |
93437 | 500 | 2500 | - | 525 |
93438 | 500 | 2500 | - | 550 |
93439 | 500 | 2500 | - | 575 |
93440 | 500 | 2500 | - | 600 |
93441 | 500 | 2500 | - | 625 |
93442 | 500 | 2500 | - | 650 |
93443 | 500 | 2500 | - | 675 |
93444 | 500 | 2500 | - | 700 |
93445 | 500 | 2500 | - | 725 |
93446 | 500 | 2500 | - | 750 |
93447 | 500 | 2500 | - | 775 |
93505 | 500 | 2500 | 0.2 | 2225 |
93190 | 650 | 3250 | 1.1 | 640 |
93267 | 600 | 3000 | 1.2 | 690 |
92610 | 1300 | 6500 | 1.3 | 0 |
92809 | 1000 | 5000 | 1.7 | 300 |
93121 | 700 | 3500 | 1.7 | 595 |
93504 | 500 | 2500 | 2.0 | 2200 |
93448 | 500 | 2500 | 3.4 | 800 |
93506 | 500 | 2500 | 5.2 | 2250 |
93406 | 550 | 2750 | 6.5 | 2187 |
93407 | 550 | 2750 | 7.3 | 2214 |
93507 | 500 | 2500 | 10.2 | 2275 |
93408 | 550 | 2750 | 12.2 | 2241 |
93317 | 600 | 3000 | 14.3 | 2190 |
93508 | 500 | 2500 | 15.2 | 2300 |
93318 | 600 | 3000 | 16.0 | 2220 |
93409 | 550 | 2750 | 17.1 | 2268 |
93509 | 500 | 2500 | 20.2 | 2325 |
93239 | 650 | 3250 | 20.9 | 2208 |
93319 | 600 | 3000 | 21.0 | 2250 |
93042 | 800 | 4000 | 21.9 | 2200 |
93103 | 750 | 3750 | 22.0 | 2220 |
93410 | 550 | 2750 | 22.0 | 2295 |
93168 | 700 | 3500 | 23.6 | 2240 |
93169 | 700 | 3500 | 23.6 | 2275 |
93167 | 700 | 3500 | 24.3 | 2205 |
93510 | 500 | 2500 | 25.2 | 2350 |
93240 | 650 | 3250 | 25.4 | 2240 |
93241 | 650 | 3250 | 25.4 | 2272 |
93242 | 650 | 3250 | 25.4 | 2304 |
93243 | 650 | 3250 | 25.4 | 2336 |
93320 | 600 | 3000 | 26.0 | 2280 |
93411 | 550 | 2750 | 26.9 | 2322 |
93321 | 600 | 3000 | 27.5 | 2310 |
93322 | 600 | 3000 | 27.5 | 2340 |
93323 | 600 | 3000 | 27.5 | 2370 |
93324 | 600 | 3000 | 27.5 | 2400 |
93412 | 550 | 2750 | 30.0 | 2349 |
93413 | 550 | 2750 | 30.0 | 2376 |
93414 | 550 | 2750 | 30.0 | 2403 |
93415 | 550 | 2750 | 30.0 | 2430 |
93511 | 500 | 2500 | 30.2 | 2375 |
93512 | 500 | 2500 | 33.0 | 2400 |
93513 | 500 | 2500 | 33.0 | 2425 |
93514 | 500 | 2500 | 33.0 | 2450 |
93515 | 500 | 2500 | 33.0 | 2475 |
93516 | 500 | 2500 | 33.0 | 2500 |
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
92638 | 1250 | 33.2 | 6250 | 2.3 | 62 | 28.6 |
92668 | 1200 | 26.3 | 6000 | 3.1 | 120 | 20.1 |
92700 | 1150 | 24.7 | 5750 | 3.3 | 171 | 18.1 |
92852 | 950 | 19.1 | 4750 | 4.5 | 376 | 10.0 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
92770 | 1050 | 28.1 | 5250 | 2.6 | 260 | 22.9 |
92897 | 900 | 27.1 | 4500 | 2.4 | 405 | 22.2 |
92734 | 1100 | 24.1 | 5500 | 3.4 | 220 | 17.4 |
93058 | 750 | 22.6 | 3750 | 2.9 | 555 | 16.7 |
92946 | 850 | 22.6 | 4250 | 3.4 | 462 | 15.8 |
93000 | 800 | 17.5 | 4000 | 4.6 | 520 | 8.3 |
93353 | 550 | 16.1 | 2750 | 4.2 | 756 | 7.7 |
Overall score = score_ratio - 2 * repetitive DNA content