Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign65 - back to list
Summary
./analyse_probe_search_results : Fri Oct 7 10:40:22 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign65 assembly : NCBIM34 bias : 3prime chromosome : 7 id : 60 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 3prime end of design window ------------------------ Putative probes without hits : 0 Putative probes with single_self_hit : 907/907 Putative probes that are unique : 108/907 Putative probes exceeding selection criteria : 180/907 (but not unique) Putative probes with successfully-picked primers: 280/288 Identified 29 '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 |
---|---|---|---|---|
58645 | 900 | 4500 | - | 0 |
58692 | 850 | 4250 | - | 0 |
58693 | 850 | 4250 | - | 42 |
58694 | 850 | 4250 | - | 84 |
58744 | 800 | 4000 | - | 0 |
58745 | 800 | 4000 | - | 40 |
58746 | 800 | 4000 | - | 80 |
58747 | 800 | 4000 | - | 120 |
58800 | 750 | 3750 | - | 0 |
58801 | 750 | 3750 | - | 37 |
58802 | 750 | 3750 | - | 74 |
58803 | 750 | 3750 | - | 111 |
58804 | 750 | 3750 | - | 148 |
58805 | 750 | 3750 | - | 185 |
58861 | 700 | 3500 | - | 0 |
58862 | 700 | 3500 | - | 35 |
58863 | 700 | 3500 | - | 70 |
58864 | 700 | 3500 | - | 105 |
58865 | 700 | 3500 | - | 140 |
58866 | 700 | 3500 | - | 175 |
58867 | 700 | 3500 | - | 210 |
58892 | 700 | 3500 | - | 1085 |
58927 | 650 | 3250 | - | 0 |
58928 | 650 | 3250 | - | 32 |
58929 | 650 | 3250 | - | 64 |
58930 | 650 | 3250 | - | 96 |
58931 | 650 | 3250 | - | 128 |
58932 | 650 | 3250 | - | 160 |
58933 | 650 | 3250 | - | 192 |
58934 | 650 | 3250 | - | 224 |
58935 | 650 | 3250 | - | 256 |
58936 | 650 | 3250 | - | 288 |
58961 | 650 | 3250 | - | 1088 |
58962 | 650 | 3250 | - | 1120 |
58963 | 650 | 3250 | - | 1152 |
59001 | 600 | 3000 | - | 0 |
59002 | 600 | 3000 | - | 30 |
59003 | 600 | 3000 | - | 60 |
59004 | 600 | 3000 | - | 90 |
59005 | 600 | 3000 | - | 120 |
59006 | 600 | 3000 | - | 150 |
59007 | 600 | 3000 | - | 180 |
59008 | 600 | 3000 | - | 210 |
59009 | 600 | 3000 | - | 240 |
59010 | 600 | 3000 | - | 270 |
59011 | 600 | 3000 | - | 300 |
59012 | 600 | 3000 | - | 330 |
59037 | 600 | 3000 | - | 1080 |
59038 | 600 | 3000 | - | 1110 |
59039 | 600 | 3000 | - | 1140 |
59040 | 600 | 3000 | - | 1170 |
59041 | 600 | 3000 | - | 1200 |
59082 | 550 | 2750 | - | 0 |
59083 | 550 | 2750 | - | 27 |
59084 | 550 | 2750 | - | 54 |
59085 | 550 | 2750 | - | 81 |
59086 | 550 | 2750 | - | 108 |
59087 | 550 | 2750 | - | 135 |
59088 | 550 | 2750 | - | 162 |
59089 | 550 | 2750 | - | 189 |
59090 | 550 | 2750 | - | 216 |
59091 | 550 | 2750 | - | 243 |
59092 | 550 | 2750 | - | 270 |
59093 | 550 | 2750 | - | 297 |
59094 | 550 | 2750 | - | 324 |
59095 | 550 | 2750 | - | 351 |
59096 | 550 | 2750 | - | 378 |
59122 | 550 | 2750 | - | 1080 |
59123 | 550 | 2750 | - | 1107 |
59124 | 550 | 2750 | - | 1134 |
59125 | 550 | 2750 | - | 1161 |
59126 | 550 | 2750 | - | 1188 |
59127 | 550 | 2750 | - | 1215 |
59128 | 550 | 2750 | - | 1242 |
59173 | 500 | 2500 | - | 0 |
59174 | 500 | 2500 | - | 25 |
59175 | 500 | 2500 | - | 50 |
59176 | 500 | 2500 | - | 75 |
59177 | 500 | 2500 | - | 100 |
59178 | 500 | 2500 | - | 125 |
59179 | 500 | 2500 | - | 150 |
59180 | 500 | 2500 | - | 175 |
59181 | 500 | 2500 | - | 200 |
59182 | 500 | 2500 | - | 225 |
59183 | 500 | 2500 | - | 250 |
59184 | 500 | 2500 | - | 275 |
59185 | 500 | 2500 | - | 300 |
59186 | 500 | 2500 | - | 325 |
59187 | 500 | 2500 | - | 350 |
59188 | 500 | 2500 | - | 375 |
59189 | 500 | 2500 | - | 400 |
59190 | 500 | 2500 | - | 425 |
59216 | 500 | 2500 | - | 1075 |
59217 | 500 | 2500 | - | 1100 |
59218 | 500 | 2500 | - | 1125 |
59219 | 500 | 2500 | - | 1150 |
59220 | 500 | 2500 | - | 1175 |
59221 | 500 | 2500 | - | 1200 |
59222 | 500 | 2500 | - | 1225 |
59223 | 500 | 2500 | - | 1250 |
59224 | 500 | 2500 | - | 1275 |
59225 | 500 | 2500 | - | 1300 |
58960 | 650 | 3250 | 2.0 | 1056 |
58891 | 700 | 3500 | 2.7 | 1050 |
59121 | 550 | 2750 | 2.9 | 1053 |
59036 | 600 | 3000 | 3.2 | 1050 |
59215 | 500 | 2500 | 3.8 | 1050 |
58828 | 750 | 3750 | 4.4 | 1036 |
Putative probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
58367 | 1300 | 41.7 | 6500 | 4.5 | 0 | 32.7 |
58368 | 1300 | 41.7 | 6500 | 4.5 | 65 | 32.7 |
58369 | 1300 | 41.7 | 6500 | 4.5 | 130 | 32.7 |
58370 | 1300 | 41.7 | 6500 | 4.5 | 195 | 32.7 |
58371 | 1300 | 41.7 | 6500 | 4.5 | 260 | 32.7 |
58372 | 1300 | 41.7 | 6500 | 4.5 | 325 | 32.7 |
58373 | 1300 | 41.7 | 6500 | 4.5 | 390 | 32.7 |
58374 | 1300 | 41.7 | 6500 | 4.5 | 455 | 32.7 |
58375 | 1300 | 41.7 | 6500 | 4.5 | 520 | 32.7 |
58376 | 1300 | 41.7 | 6500 | 4.5 | 585 | 32.7 |
58377 | 1300 | 41.7 | 6500 | 4.5 | 650 | 32.7 |
58378 | 1300 | 41.7 | 6500 | 4.5 | 715 | 32.7 |
58379 | 1300 | 41.7 | 6500 | 4.5 | 780 | 32.7 |
58582 | 1000 | 32.5 | 5000 | - | 1100 | 32.5 |
58560 | 1000 | 32.1 | 5000 | - | 0 | 32.1 |
58543 | 1050 | 34.1 | 5250 | 1.4 | 1092 | 31.2 |
58624 | 950 | 30.8 | 4750 | - | 1081 | 30.8 |
58625 | 950 | 30.8 | 4750 | - | 1128 | 30.8 |
58626 | 950 | 30.8 | 4750 | - | 1175 | 30.8 |
58395 | 1250 | 40.1 | 6250 | 4.6 | 62 | 30.8 |
58396 | 1250 | 40.1 | 6250 | 4.6 | 124 | 30.8 |
58397 | 1250 | 40.1 | 6250 | 4.6 | 186 | 30.8 |
58398 | 1250 | 40.1 | 6250 | 4.6 | 248 | 30.8 |
58408 | 1250 | 40.1 | 6250 | 4.6 | 868 | 30.8 |
58601 | 950 | 30.4 | 4750 | - | 0 | 30.4 |
58602 | 950 | 30.4 | 4750 | - | 47 | 30.4 |
58669 | 900 | 29.2 | 4500 | - | 1080 | 29.2 |
58670 | 900 | 29.2 | 4500 | - | 1125 | 29.2 |
58671 | 900 | 29.2 | 4500 | - | 1170 | 29.2 |
58672 | 900 | 29.2 | 4500 | - | 1215 | 29.2 |
58646 | 900 | 29.0 | 4500 | - | 45 | 29.0 |
58647 | 900 | 28.8 | 4500 | - | 90 | 28.8 |
58581 | 1000 | 32.5 | 5000 | 1.9 | 1050 | 28.7 |
58542 | 1050 | 34.1 | 5250 | 2.8 | 1040 | 28.6 |
58506 | 1100 | 35.7 | 5500 | 3.8 | 1045 | 28.1 |
58583 | 1000 | 32.5 | 5000 | 2.3 | 1150 | 27.9 |
58718 | 850 | 27.6 | 4250 | - | 1092 | 27.6 |
58719 | 850 | 27.6 | 4250 | - | 1134 | 27.6 |
58720 | 850 | 27.6 | 4250 | - | 1176 | 27.6 |
58721 | 850 | 27.6 | 4250 | - | 1218 | 27.6 |
58722 | 850 | 27.6 | 4250 | - | 1260 | 27.6 |
58695 | 850 | 27.2 | 4250 | - | 126 | 27.2 |
58522 | 1050 | 33.7 | 5250 | 3.7 | 0 | 26.2 |
58771 | 800 | 26.0 | 4000 | - | 1080 | 26.0 |
58772 | 800 | 26.0 | 4000 | - | 1120 | 26.0 |
58773 | 800 | 26.0 | 4000 | - | 1160 | 26.0 |
58774 | 800 | 26.0 | 4000 | - | 1200 | 26.0 |
58775 | 800 | 26.0 | 4000 | - | 1240 | 26.0 |
58776 | 800 | 26.0 | 4000 | - | 1280 | 26.0 |
58777 | 800 | 26.0 | 4000 | - | 1320 | 26.0 |
58748 | 800 | 25.6 | 4000 | - | 160 | 25.6 |
58749 | 800 | 25.6 | 4000 | - | 200 | 25.6 |
58696 | 850 | 27.2 | 4250 | 0.8 | 168 | 25.6 |
58829 | 750 | 24.4 | 3750 | - | 1073 | 24.4 |
58830 | 750 | 24.4 | 3750 | - | 1110 | 24.4 |
58831 | 750 | 24.4 | 3750 | - | 1147 | 24.4 |
58832 | 750 | 24.4 | 3750 | - | 1184 | 24.4 |
58833 | 750 | 24.4 | 3750 | - | 1221 | 24.4 |
58834 | 750 | 24.4 | 3750 | - | 1258 | 24.4 |
58835 | 750 | 24.4 | 3750 | - | 1295 | 24.4 |
58836 | 750 | 24.4 | 3750 | - | 1332 | 24.4 |
58837 | 750 | 24.4 | 3750 | - | 1369 | 24.4 |
58561 | 1000 | 32.1 | 5000 | 3.9 | 50 | 24.3 |
58806 | 750 | 24.0 | 3750 | - | 222 | 24.0 |
58807 | 750 | 24.0 | 3750 | - | 259 | 24.0 |
58648 | 900 | 28.8 | 4500 | 2.7 | 135 | 23.5 |
58603 | 950 | 30.4 | 4750 | 3.5 | 94 | 23.5 |
58623 | 950 | 30.8 | 4750 | 3.7 | 1034 | 23.5 |
58717 | 850 | 27.6 | 4250 | 2.2 | 1050 | 23.1 |
58893 | 700 | 22.7 | 3500 | - | 1120 | 22.7 |
58894 | 700 | 22.7 | 3500 | - | 1155 | 22.7 |
58895 | 700 | 22.7 | 3500 | - | 1190 | 22.7 |
58896 | 700 | 22.7 | 3500 | - | 1225 | 22.7 |
58897 | 700 | 22.7 | 3500 | - | 1260 | 22.7 |
58898 | 700 | 22.7 | 3500 | - | 1295 | 22.7 |
58899 | 700 | 22.7 | 3500 | - | 1330 | 22.7 |
58900 | 700 | 22.7 | 3500 | - | 1365 | 22.7 |
58901 | 700 | 22.7 | 3500 | - | 1400 | 22.7 |
58868 | 700 | 22.6 | 3500 | - | 245 | 22.6 |
58869 | 700 | 22.4 | 3500 | - | 280 | 22.4 |
58673 | 900 | 29.2 | 4500 | 3.7 | 1260 | 21.9 |
58723 | 850 | 27.6 | 4250 | 2.9 | 1302 | 21.7 |
58668 | 900 | 29.2 | 4500 | 3.8 | 1035 | 21.7 |
58627 | 950 | 30.8 | 4750 | 4.7 | 1222 | 21.4 |
58870 | 700 | 22.4 | 3500 | 0.6 | 315 | 21.3 |
58964 | 650 | 21.1 | 3250 | - | 1184 | 21.1 |
58965 | 650 | 21.1 | 3250 | - | 1216 | 21.1 |
58966 | 650 | 21.1 | 3250 | - | 1248 | 21.1 |
58967 | 650 | 21.1 | 3250 | - | 1280 | 21.1 |
58968 | 650 | 21.1 | 3250 | - | 1312 | 21.1 |
58969 | 650 | 21.1 | 3250 | - | 1344 | 21.1 |
58970 | 650 | 21.1 | 3250 | - | 1376 | 21.1 |
58971 | 650 | 21.1 | 3250 | - | 1408 | 21.1 |
58972 | 650 | 21.1 | 3250 | - | 1440 | 21.1 |
58973 | 650 | 21.1 | 3250 | - | 1472 | 21.1 |
58937 | 650 | 20.8 | 3250 | - | 320 | 20.8 |
58938 | 650 | 20.8 | 3250 | - | 352 | 20.8 |
58902 | 700 | 22.7 | 3500 | 1.1 | 1435 | 20.4 |
59042 | 600 | 19.5 | 3000 | - | 1230 | 19.5 |
59043 | 600 | 19.5 | 3000 | - | 1260 | 19.5 |
59044 | 600 | 19.5 | 3000 | - | 1290 | 19.5 |
59045 | 600 | 19.5 | 3000 | - | 1320 | 19.5 |
59046 | 600 | 19.5 | 3000 | - | 1350 | 19.5 |
59047 | 600 | 19.5 | 3000 | - | 1380 | 19.5 |
59048 | 600 | 19.5 | 3000 | - | 1410 | 19.5 |
59049 | 600 | 19.5 | 3000 | - | 1440 | 19.5 |
59050 | 600 | 19.5 | 3000 | - | 1470 | 19.5 |
59051 | 600 | 19.5 | 3000 | - | 1500 | 19.5 |
59013 | 600 | 19.2 | 3000 | - | 360 | 19.2 |
59014 | 600 | 19.2 | 3000 | - | 390 | 19.2 |
58770 | 800 | 26.0 | 4000 | 3.6 | 1040 | 18.7 |
59052 | 600 | 19.5 | 3000 | 0.5 | 1530 | 18.5 |
58750 | 800 | 25.6 | 4000 | 3.6 | 240 | 18.4 |
59129 | 550 | 17.9 | 2750 | - | 1269 | 17.9 |
59130 | 550 | 17.9 | 2750 | - | 1296 | 17.9 |
59131 | 550 | 17.9 | 2750 | - | 1323 | 17.9 |
59132 | 550 | 17.9 | 2750 | - | 1350 | 17.9 |
59133 | 550 | 17.9 | 2750 | - | 1377 | 17.9 |
59134 | 550 | 17.9 | 2750 | - | 1404 | 17.9 |
59135 | 550 | 17.9 | 2750 | - | 1431 | 17.9 |
59136 | 550 | 17.9 | 2750 | - | 1458 | 17.9 |
59137 | 550 | 17.9 | 2750 | - | 1485 | 17.9 |
59138 | 550 | 17.9 | 2750 | - | 1512 | 17.9 |
59139 | 550 | 17.9 | 2750 | - | 1539 | 17.9 |
59140 | 550 | 17.9 | 2750 | - | 1566 | 17.9 |
58778 | 800 | 26.0 | 4000 | 4.1 | 1360 | 17.7 |
59097 | 550 | 17.6 | 2750 | - | 405 | 17.6 |
59098 | 550 | 17.6 | 2750 | - | 432 | 17.6 |
59099 | 550 | 17.6 | 2750 | - | 459 | 17.6 |
58838 | 750 | 24.4 | 3750 | 3.9 | 1406 | 16.6 |
59226 | 500 | 16.2 | 2500 | - | 1325 | 16.2 |
59227 | 500 | 16.2 | 2500 | - | 1350 | 16.2 |
59228 | 500 | 16.2 | 2500 | - | 1375 | 16.2 |
59229 | 500 | 16.2 | 2500 | - | 1400 | 16.2 |
59230 | 500 | 16.2 | 2500 | - | 1425 | 16.2 |
59231 | 500 | 16.2 | 2500 | - | 1450 | 16.2 |
59232 | 500 | 16.2 | 2500 | - | 1475 | 16.2 |
59233 | 500 | 16.2 | 2500 | - | 1500 | 16.2 |
59234 | 500 | 16.2 | 2500 | - | 1525 | 16.2 |
59235 | 500 | 16.2 | 2500 | - | 1550 | 16.2 |
59236 | 500 | 16.2 | 2500 | - | 1575 | 16.2 |
59237 | 500 | 16.2 | 2500 | - | 1600 | 16.2 |
59238 | 500 | 16.2 | 2500 | - | 1625 | 16.2 |
59015 | 600 | 19.2 | 3000 | 1.5 | 420 | 16.2 |
59191 | 500 | 16.0 | 2500 | - | 450 | 16.0 |
59192 | 500 | 16.0 | 2500 | - | 475 | 16.0 |
59193 | 500 | 16.0 | 2500 | - | 500 | 16.0 |
58939 | 650 | 20.8 | 3250 | 3.5 | 384 | 13.8 |
58974 | 650 | 21.1 | 3250 | 4.2 | 1504 | 12.8 |
59141 | 550 | 17.9 | 2750 | 2.9 | 1593 | 12.0 |
59194 | 500 | 16.0 | 2500 | 2.8 | 525 | 10.4 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
58394 | 1250 | 40.1 | 6250 | 4.6 | 0 | 30.8 |
58399 | 1250 | 40.1 | 6250 | 4.6 | 310 | 30.8 |
58400 | 1250 | 40.1 | 6250 | 4.6 | 372 | 30.8 |
58401 | 1250 | 40.1 | 6250 | 4.6 | 434 | 30.8 |
58402 | 1250 | 40.1 | 6250 | 4.6 | 496 | 30.8 |
58403 | 1250 | 40.1 | 6250 | 4.6 | 558 | 30.8 |
58404 | 1250 | 40.1 | 6250 | 4.6 | 620 | 30.8 |
58405 | 1250 | 40.1 | 6250 | 4.6 | 682 | 30.8 |
58406 | 1250 | 40.1 | 6250 | 4.6 | 744 | 30.8 |
58407 | 1250 | 40.1 | 6250 | 4.6 | 806 | 30.8 |
58423 | 1200 | 38.5 | 6000 | 4.8 | 0 | 28.8 |
58424 | 1200 | 38.5 | 6000 | 4.8 | 60 | 28.8 |
58425 | 1200 | 38.5 | 6000 | 4.8 | 120 | 28.8 |
58426 | 1200 | 38.5 | 6000 | 4.8 | 180 | 28.8 |
58427 | 1200 | 38.5 | 6000 | 4.8 | 240 | 28.8 |
58428 | 1200 | 38.5 | 6000 | 4.8 | 300 | 28.8 |
58429 | 1200 | 38.5 | 6000 | 4.8 | 360 | 28.8 |
58430 | 1200 | 38.5 | 6000 | 4.8 | 420 | 28.8 |
58431 | 1200 | 38.5 | 6000 | 4.8 | 480 | 28.8 |
58432 | 1200 | 38.5 | 6000 | 4.8 | 540 | 28.8 |
58433 | 1200 | 38.5 | 6000 | 4.8 | 600 | 28.8 |
58434 | 1200 | 38.5 | 6000 | 4.8 | 660 | 28.8 |
58435 | 1200 | 38.5 | 6000 | 4.8 | 720 | 28.8 |
58436 | 1200 | 38.5 | 6000 | 4.8 | 780 | 28.8 |
58437 | 1200 | 38.5 | 6000 | 4.8 | 840 | 28.8 |
58438 | 1200 | 38.5 | 6000 | 4.8 | 900 | 28.8 |
58808 | 750 | 24.0 | 3750 | 4.7 | 296 | 14.7 |
59100 | 550 | 17.6 | 2750 | 4.5 | 486 | 8.5 |
59239 | 500 | 16.2 | 2500 | 4.6 | 1650 | 7.0 |
Overall score = score_ratio - 2 * repetitive DNA content