Automated design of genomic Southern blot probes

Mike DR Croning, David G Fricker, Noboru H Komiyama and Seth GN Grant

Design Case - ProbeDesign64 - back to list

Summary

./analyse_probe_search_results : Fri Oct 7 10:39:48 2005

Connected to host: host, as user: user
Database       : southern_blot_designs

Fetched probe design: ProbeDesign64
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 7
  id            : 59
  strand        : 1
  -------------

Design window length: 2701bp

All jobs for probe design are successful - total: 40
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 785 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            : 785/785
Putative probes that are unique                 : 141/785
Putative probes exceeding selection criteria    : 107/785 (but not unique)
Putative probes with successfully-picked primers: 248/248

Identified 2 '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

Unique putative probes

Putative probe IDLengthActual%rep DNADistance
5773910505250-1404
5777210005000-1400
5777310005000-1450
578099504750-1410
578109504750-1457
578119504750-1504
578489004500-1395
578499004500-1440
578509004500-1485
578519004500-1530
578529004500-1575
578918504250-1386
578928504250-1428
578938504250-1470
578948504250-1512
578958504250-1554
578968504250-1596
578978504250-1638
579388004000-1400
579398004000-1440
579408004000-1480
579418004000-1520
579428004000-1560
579438004000-1600
579448004000-1640
579458004000-1680
579897503750-1406
579907503750-1443
579917503750-1480
579927503750-1517
579937503750-1554
579947503750-1591
579957503750-1628
579967503750-1665
579977503750-1702
579987503750-1739
580447003500-1400
580457003500-1435
580467003500-1470
580477003500-1505
580487003500-1540
580497003500-1575
580507003500-1610
580517003500-1645
580527003500-1680
580537003500-1715
580547003500-1750
580557003500-1785
581066503250-1408
581076503250-1440
581086503250-1472
581096503250-1504
581106503250-1536
581116503250-1568
581126503250-1600
581136503250-1632
581146503250-1664
581156503250-1696
581166503250-1728
581176503250-1760
581186503250-1792
581196503250-1824
581746003000-1410
581756003000-1440
581766003000-1470
581776003000-1500
581786003000-1530
581796003000-1560
581806003000-1590
581816003000-1620
581826003000-1650
581836003000-1680
581846003000-1710
581856003000-1740
581866003000-1770
581876003000-1800
581886003000-1830
581896003000-1860
581906003000-1890
582095502750-297
582505502750-1404
582515502750-1431
582525502750-1458
582535502750-1485
582545502750-1512
582555502750-1539
582565502750-1566
582575502750-1593
582585502750-1620
582595502750-1647
582605502750-1674
582615502750-1701
582625502750-1728
582635502750-1755
582645502750-1782
582655502750-1809
582665502750-1836
582675502750-1863
582685502750-1890
582695502750-1917
582705502750-1944
582895002500-275
582905002500-300
582915002500-325
582925002500-350
583345002500-1400
583355002500-1425
583365002500-1450
583375002500-1475
583385002500-1500
583395002500-1525
583405002500-1550
583415002500-1575
583425002500-1600
583435002500-1625
583445002500-1650
583455002500-1675
583465002500-1700
583475002500-1725
583485002500-1750
583495002500-1775
583505002500-1800
583515002500-1825
583525002500-1850
583535002500-1875
583545002500-1900
583555002500-1925
583565002500-1950
583575002500-1975
5817360030000.31380
57707110055000.61375
5824955027500.91377
5810565032500.91376
5833350025001.41375
5798875037501.71369
5780895047502.01363
5804370035002.41365
5793780040002.81360
57738105052502.91352
5821055027503.5324
5829350025004.0375

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
57627125036.86250-142636.8
57603130038.265001.3136535.6
57652120035.36000-144035.3
57653120035.36000-150035.3
57651120035.360000.2138035.0
57740105034.15250-145634.1
57626125036.862501.4136433.9
57679115033.85750-142533.8
57680115033.85750-148233.8
57681115033.85750-153933.8
57774100033.35000-150033.3
57678115035.357501.2136832.8
57708110032.45500-143032.4
57709110032.45500-148532.4
57710110032.45500-154032.4
57711110032.45500-159532.4
57741105030.95250-150830.9
57742105030.95250-156030.9
57743105030.95250-161230.9
5781295030.84750-155130.8
57775100029.45000-155029.4
57776100029.45000-160029.4
57777100029.45000-165029.4
57778100029.45000-170029.4
5781395027.94750-159827.9
5781495027.94750-164527.9
5781595027.94750-169227.9
5781695027.94750-173927.9
5785390027.44500-162027.4
5785490026.54500-166526.5
5785590026.54500-171026.5
5785690026.54500-175526.5
5785790026.54500-180026.5
57771100032.350003.2135025.9
5789885025.04250-168025.0
5789985025.04250-172225.0
5790085025.04250-176425.0
5790185025.04250-180625.0
5790285025.04250-184825.0
5794680024.44000-172024.4
5794780023.54000-176023.5
5794880023.54000-180023.5
5794980023.54000-184023.5
5795080023.54000-188023.5
5799975022.13750-177622.1
5800075022.13750-181322.1
5800175022.13750-185022.1
5800275022.13750-188722.1
5800375022.13750-192422.1
5805670021.33500-182021.3
5812065021.13250-185621.1
5805770020.63500-185520.6
5805870020.63500-189020.6
5805970020.63500-192520.6
5806070020.63500-196020.6
5806170020.63500-199520.6
5812165019.13250-188819.1
5812265019.13250-192019.1
5812365019.13250-195219.1
5812465019.13250-198419.1
5812565019.13250-201619.1
5812665019.13250-204819.1
5819160018.33000-192018.3
5806865017.93250-19217.9
5820855017.72750-27017.7
5819260017.63000-195017.6
5819360017.63000-198017.6
5819460017.63000-201017.6
5819560017.63000-204017.6
5819660017.63000-207017.6
5819760017.63000-210017.6
5813560017.23000-24017.2
5835850016.72500-200016.7
5813360016.53000-18016.5
5813460016.53000-21016.5
5827155016.32750-197116.3
5827255016.22750-199816.2
5827355016.22750-202516.2
5827455016.22750-205216.2
5827555016.22750-207916.2
5827655016.22750-210616.2
5827755016.22750-213316.2
5828850016.12500-25016.1
5820755015.82750-24315.8
5806765017.932501.216015.4
5820555015.12750-18915.1
5820655015.12750-21615.1
5835950014.72500-202514.7
5836050014.72500-205014.7
5836150014.72500-207514.7
5836250014.72500-210014.7
5836350014.72500-212514.7
5836450014.72500-215014.7
5836550014.72500-217514.7
5836650014.72500-220014.7
5789085023.642504.5134414.7
5813660019.430002.527014.4
5828550013.72500-17513.7
5828650013.72500-20013.7
5828750013.72500-22513.7
5800970019.235002.917513.5
5820455015.127501.116212.9
5800870019.235004.014011.2
5813260016.530003.015010.5
5828450013.725003.61506.5

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
5784790029.045003.6135021.9
5806965017.932502.922412.0

Overall score = score_ratio - 2 * repetitive DNA content

© G2C 2014. The Genes to Cognition Programme received funding from The Wellcome Trust and the EU FP7 Framework Programmes:
EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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