Automated design of genomic Southern blot probes
Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant
Design Case - ProbeDesign54 - back to list
Summary
./analyse_probe_search_results : Mon Sep 26 11:58:27 2005
Connected to host: host, as user: user Database : southern_blot_designs Fetched probe design: ProbeDesign54 assembly : NCBIM34 bias : 5prime chromosome : 6 id : 36 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 exceeding selection criteria: 193/907 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 |
---|---|---|---|---|---|---|
38802 | 1300 | 41.7 | 6500 | - | 1235 | 41.7 |
38803 | 1300 | 41.7 | 6500 | - | 1300 | 41.7 |
38804 | 1300 | 41.7 | 6500 | - | 1365 | 41.7 |
38805 | 1300 | 41.7 | 6500 | - | 1430 | 41.7 |
38806 | 1300 | 41.7 | 6500 | - | 1495 | 41.7 |
38807 | 1300 | 41.7 | 6500 | - | 1560 | 41.7 |
38808 | 1300 | 41.7 | 6500 | - | 1625 | 41.7 |
38830 | 1250 | 40.1 | 6250 | - | 1240 | 40.1 |
38831 | 1250 | 40.1 | 6250 | - | 1302 | 40.1 |
38832 | 1250 | 40.1 | 6250 | - | 1364 | 40.1 |
38833 | 1250 | 40.1 | 6250 | - | 1426 | 40.1 |
38834 | 1250 | 40.1 | 6250 | - | 1488 | 40.1 |
38835 | 1250 | 40.1 | 6250 | - | 1550 | 40.1 |
38836 | 1250 | 40.1 | 6250 | - | 1612 | 40.1 |
38860 | 1200 | 38.5 | 6000 | - | 1260 | 38.5 |
38861 | 1200 | 38.5 | 6000 | - | 1320 | 38.5 |
38862 | 1200 | 38.5 | 6000 | - | 1380 | 38.5 |
38863 | 1200 | 38.5 | 6000 | - | 1440 | 38.5 |
38864 | 1200 | 38.5 | 6000 | - | 1500 | 38.5 |
38865 | 1200 | 38.5 | 6000 | - | 1560 | 38.5 |
38866 | 1200 | 38.5 | 6000 | - | 1620 | 38.5 |
38892 | 1150 | 36.9 | 5750 | - | 1254 | 36.9 |
38893 | 1150 | 36.9 | 5750 | - | 1311 | 36.9 |
38894 | 1150 | 36.9 | 5750 | - | 1368 | 36.9 |
38895 | 1150 | 36.9 | 5750 | - | 1425 | 36.9 |
38896 | 1150 | 36.9 | 5750 | - | 1482 | 36.9 |
38897 | 1150 | 36.9 | 5750 | - | 1539 | 36.9 |
38898 | 1150 | 36.9 | 5750 | - | 1596 | 36.9 |
38859 | 1200 | 38.5 | 6000 | 0.8 | 1200 | 36.8 |
38801 | 1300 | 41.7 | 6500 | 3.1 | 1170 | 35.5 |
38925 | 1100 | 35.3 | 5500 | - | 1210 | 35.3 |
38926 | 1100 | 35.3 | 5500 | - | 1265 | 35.3 |
38927 | 1100 | 35.3 | 5500 | - | 1320 | 35.3 |
38928 | 1100 | 35.3 | 5500 | - | 1375 | 35.3 |
38929 | 1100 | 35.3 | 5500 | - | 1430 | 35.3 |
38930 | 1100 | 35.3 | 5500 | - | 1485 | 35.3 |
38931 | 1100 | 35.3 | 5500 | - | 1540 | 35.3 |
38932 | 1100 | 35.3 | 5500 | - | 1595 | 35.3 |
38829 | 1250 | 40.1 | 6250 | 2.6 | 1178 | 34.9 |
38891 | 1150 | 36.9 | 5750 | 1.1 | 1197 | 34.6 |
38962 | 1050 | 33.7 | 5250 | - | 1248 | 33.7 |
38963 | 1050 | 33.7 | 5250 | - | 1300 | 33.7 |
38964 | 1050 | 33.7 | 5250 | - | 1352 | 33.7 |
38965 | 1050 | 33.7 | 5250 | - | 1404 | 33.7 |
38966 | 1050 | 33.7 | 5250 | - | 1456 | 33.7 |
38967 | 1050 | 33.7 | 5250 | - | 1508 | 33.7 |
38968 | 1050 | 33.7 | 5250 | - | 1560 | 33.7 |
38969 | 1050 | 33.7 | 5250 | - | 1612 | 33.7 |
39001 | 1000 | 32.1 | 5000 | - | 1250 | 32.1 |
39002 | 1000 | 32.1 | 5000 | - | 1300 | 32.1 |
39003 | 1000 | 32.1 | 5000 | - | 1350 | 32.1 |
39004 | 1000 | 32.1 | 5000 | - | 1400 | 32.1 |
39005 | 1000 | 32.1 | 5000 | - | 1450 | 32.1 |
39006 | 1000 | 32.1 | 5000 | - | 1500 | 32.1 |
39007 | 1000 | 32.1 | 5000 | - | 1550 | 32.1 |
39008 | 1000 | 32.1 | 5000 | - | 1600 | 32.1 |
38961 | 1050 | 33.7 | 5250 | 1.3 | 1196 | 31.0 |
39043 | 950 | 30.4 | 4750 | - | 1222 | 30.4 |
39044 | 950 | 30.4 | 4750 | - | 1269 | 30.4 |
39045 | 950 | 30.4 | 4750 | - | 1316 | 30.4 |
39046 | 950 | 30.4 | 4750 | - | 1363 | 30.4 |
39047 | 950 | 30.4 | 4750 | - | 1410 | 30.4 |
39048 | 950 | 30.4 | 4750 | - | 1457 | 30.4 |
39049 | 950 | 30.4 | 4750 | - | 1504 | 30.4 |
39050 | 950 | 30.4 | 4750 | - | 1551 | 30.4 |
39051 | 950 | 30.4 | 4750 | - | 1598 | 30.4 |
39000 | 1000 | 32.1 | 5000 | 1.0 | 1200 | 30.1 |
39088 | 900 | 28.8 | 4500 | - | 1215 | 28.8 |
39089 | 900 | 28.8 | 4500 | - | 1260 | 28.8 |
39090 | 900 | 28.8 | 4500 | - | 1305 | 28.8 |
39091 | 900 | 28.8 | 4500 | - | 1350 | 28.8 |
39092 | 900 | 28.8 | 4500 | - | 1395 | 28.8 |
39093 | 900 | 28.8 | 4500 | - | 1440 | 28.8 |
39094 | 900 | 28.8 | 4500 | - | 1485 | 28.8 |
39095 | 900 | 28.8 | 4500 | - | 1530 | 28.8 |
39096 | 900 | 28.8 | 4500 | - | 1575 | 28.8 |
39097 | 900 | 28.8 | 4500 | - | 1620 | 28.8 |
39137 | 850 | 27.2 | 4250 | - | 1218 | 27.2 |
39138 | 850 | 27.2 | 4250 | - | 1260 | 27.2 |
39139 | 850 | 27.2 | 4250 | - | 1302 | 27.2 |
39140 | 850 | 27.2 | 4250 | - | 1344 | 27.2 |
39141 | 850 | 27.2 | 4250 | - | 1386 | 27.2 |
39142 | 850 | 27.2 | 4250 | - | 1428 | 27.2 |
39143 | 850 | 27.2 | 4250 | - | 1470 | 27.2 |
39144 | 850 | 27.2 | 4250 | - | 1512 | 27.2 |
39145 | 850 | 27.2 | 4250 | - | 1554 | 27.2 |
39146 | 850 | 27.2 | 4250 | - | 1596 | 27.2 |
39191 | 800 | 25.6 | 4000 | - | 1240 | 25.6 |
39192 | 800 | 25.6 | 4000 | - | 1280 | 25.6 |
39193 | 800 | 25.6 | 4000 | - | 1320 | 25.6 |
39194 | 800 | 25.6 | 4000 | - | 1360 | 25.6 |
39195 | 800 | 25.6 | 4000 | - | 1400 | 25.6 |
39196 | 800 | 25.6 | 4000 | - | 1440 | 25.6 |
39197 | 800 | 25.6 | 4000 | - | 1480 | 25.6 |
39198 | 800 | 25.6 | 4000 | - | 1520 | 25.6 |
39199 | 800 | 25.6 | 4000 | - | 1560 | 25.6 |
39200 | 800 | 25.6 | 4000 | - | 1600 | 25.6 |
38924 | 1100 | 35.3 | 5500 | 5.0 | 1155 | 25.3 |
39249 | 750 | 24.0 | 3750 | - | 1221 | 24.0 |
39250 | 750 | 24.0 | 3750 | - | 1258 | 24.0 |
39251 | 750 | 24.0 | 3750 | - | 1295 | 24.0 |
39252 | 750 | 24.0 | 3750 | - | 1332 | 24.0 |
39253 | 750 | 24.0 | 3750 | - | 1369 | 24.0 |
39254 | 750 | 24.0 | 3750 | - | 1406 | 24.0 |
39255 | 750 | 24.0 | 3750 | - | 1443 | 24.0 |
39256 | 750 | 24.0 | 3750 | - | 1480 | 24.0 |
39257 | 750 | 24.0 | 3750 | - | 1517 | 24.0 |
39258 | 750 | 24.0 | 3750 | - | 1554 | 24.0 |
39259 | 750 | 24.0 | 3750 | - | 1591 | 24.0 |
39260 | 750 | 24.0 | 3750 | - | 1628 | 24.0 |
39190 | 800 | 25.6 | 4000 | 1.2 | 1200 | 23.1 |
39312 | 700 | 22.4 | 3500 | - | 1225 | 22.4 |
39313 | 700 | 22.4 | 3500 | - | 1260 | 22.4 |
39314 | 700 | 22.4 | 3500 | - | 1295 | 22.4 |
39315 | 700 | 22.4 | 3500 | - | 1330 | 22.4 |
39316 | 700 | 22.4 | 3500 | - | 1365 | 22.4 |
39317 | 700 | 22.4 | 3500 | - | 1400 | 22.4 |
39318 | 700 | 22.4 | 3500 | - | 1435 | 22.4 |
39319 | 700 | 22.4 | 3500 | - | 1470 | 22.4 |
39320 | 700 | 22.4 | 3500 | - | 1505 | 22.4 |
39321 | 700 | 22.4 | 3500 | - | 1540 | 22.4 |
39322 | 700 | 22.4 | 3500 | - | 1575 | 22.4 |
39323 | 700 | 22.4 | 3500 | - | 1610 | 22.4 |
39381 | 650 | 20.8 | 3250 | - | 1216 | 20.8 |
39382 | 650 | 20.8 | 3250 | - | 1248 | 20.8 |
39383 | 650 | 20.8 | 3250 | - | 1280 | 20.8 |
39384 | 650 | 20.8 | 3250 | - | 1312 | 20.8 |
39385 | 650 | 20.8 | 3250 | - | 1344 | 20.8 |
39386 | 650 | 20.8 | 3250 | - | 1376 | 20.8 |
39387 | 650 | 20.8 | 3250 | - | 1408 | 20.8 |
39388 | 650 | 20.8 | 3250 | - | 1440 | 20.8 |
39389 | 650 | 20.8 | 3250 | - | 1472 | 20.8 |
39390 | 650 | 20.8 | 3250 | - | 1504 | 20.8 |
39391 | 650 | 20.8 | 3250 | - | 1536 | 20.8 |
39392 | 650 | 20.8 | 3250 | - | 1568 | 20.8 |
39393 | 650 | 20.8 | 3250 | - | 1600 | 20.8 |
39394 | 650 | 20.8 | 3250 | - | 1632 | 20.8 |
39458 | 600 | 19.2 | 3000 | - | 1230 | 19.2 |
39459 | 600 | 19.2 | 3000 | - | 1260 | 19.2 |
39460 | 600 | 19.2 | 3000 | - | 1290 | 19.2 |
39461 | 600 | 19.2 | 3000 | - | 1320 | 19.2 |
39462 | 600 | 19.2 | 3000 | - | 1350 | 19.2 |
39463 | 600 | 19.2 | 3000 | - | 1380 | 19.2 |
39464 | 600 | 19.2 | 3000 | - | 1410 | 19.2 |
39465 | 600 | 19.2 | 3000 | - | 1440 | 19.2 |
39466 | 600 | 19.2 | 3000 | - | 1470 | 19.2 |
39467 | 600 | 19.2 | 3000 | - | 1500 | 19.2 |
39468 | 600 | 19.2 | 3000 | - | 1530 | 19.2 |
39469 | 600 | 19.2 | 3000 | - | 1560 | 19.2 |
39470 | 600 | 19.2 | 3000 | - | 1590 | 19.2 |
39471 | 600 | 19.2 | 3000 | - | 1620 | 19.2 |
39543 | 550 | 17.6 | 2750 | - | 1215 | 17.6 |
39544 | 550 | 17.6 | 2750 | - | 1242 | 17.6 |
39545 | 550 | 17.6 | 2750 | - | 1269 | 17.6 |
39546 | 550 | 17.6 | 2750 | - | 1296 | 17.6 |
39547 | 550 | 17.6 | 2750 | - | 1323 | 17.6 |
39548 | 550 | 17.6 | 2750 | - | 1350 | 17.6 |
39549 | 550 | 17.6 | 2750 | - | 1377 | 17.6 |
39550 | 550 | 17.6 | 2750 | - | 1404 | 17.6 |
39551 | 550 | 17.6 | 2750 | - | 1431 | 17.6 |
39552 | 550 | 17.6 | 2750 | - | 1458 | 17.6 |
39553 | 550 | 17.6 | 2750 | - | 1485 | 17.6 |
39554 | 550 | 17.6 | 2750 | - | 1512 | 17.6 |
39555 | 550 | 17.6 | 2750 | - | 1539 | 17.6 |
39556 | 550 | 17.6 | 2750 | - | 1566 | 17.6 |
39557 | 550 | 17.6 | 2750 | - | 1593 | 17.6 |
39558 | 550 | 17.6 | 2750 | - | 1620 | 17.6 |
39311 | 700 | 22.4 | 3500 | 2.9 | 1190 | 16.7 |
39638 | 500 | 16.0 | 2500 | - | 1225 | 16.0 |
39639 | 500 | 16.0 | 2500 | - | 1250 | 16.0 |
39640 | 500 | 16.0 | 2500 | - | 1275 | 16.0 |
39641 | 500 | 16.0 | 2500 | - | 1300 | 16.0 |
39642 | 500 | 16.0 | 2500 | - | 1325 | 16.0 |
39643 | 500 | 16.0 | 2500 | - | 1350 | 16.0 |
39644 | 500 | 16.0 | 2500 | - | 1375 | 16.0 |
39645 | 500 | 16.0 | 2500 | - | 1400 | 16.0 |
39646 | 500 | 16.0 | 2500 | - | 1425 | 16.0 |
39647 | 500 | 16.0 | 2500 | - | 1450 | 16.0 |
39648 | 500 | 16.0 | 2500 | - | 1475 | 16.0 |
39649 | 500 | 16.0 | 2500 | - | 1500 | 16.0 |
39650 | 500 | 16.0 | 2500 | - | 1525 | 16.0 |
39651 | 500 | 16.0 | 2500 | - | 1550 | 16.0 |
39652 | 500 | 16.0 | 2500 | - | 1575 | 16.0 |
39653 | 500 | 16.0 | 2500 | - | 1600 | 16.0 |
39654 | 500 | 16.0 | 2500 | - | 1625 | 16.0 |
39457 | 600 | 19.2 | 3000 | 1.7 | 1200 | 15.9 |
39637 | 500 | 16.0 | 2500 | 2.0 | 1200 | 12.0 |
Overall score = score_ratio - 2 * repetitive DNA content
Redundant probes
Putative probe ID | Length | Score ratio | Actual | %rep DNA | Distance | Overall |
---|---|---|---|---|---|---|
39042 | 950 | 30.4 | 4750 | 3.7 | 1175 | 23.1 |
39087 | 900 | 28.8 | 4500 | 4.4 | 1170 | 20.0 |
39136 | 850 | 27.2 | 4250 | 4.0 | 1176 | 19.2 |
39248 | 750 | 24.0 | 3750 | 3.5 | 1184 | 17.1 |
39380 | 650 | 20.8 | 3250 | 4.0 | 1184 | 12.8 |
39542 | 550 | 17.6 | 2750 | 4.0 | 1188 | 9.6 |
Overall score = score_ratio - 2 * repetitive DNA content