Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign62 - back to list

Summary

./analyse_probe_search_results : Fri Oct 7 10:47:37 2005

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

Fetched probe design: ProbeDesign62
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 1
  id            : 53
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 25
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 494 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            : 494/494
Putative probes that are unique                 : 13/494
Putative probes exceeding selection criteria    : 209/494 (but not unique)
Putative probes with successfully-picked primers: 202/222

Identified 32 '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
526096003000-390
526106003000-420
526575502750-378
526585502750-405
526595502750-432
526605502750-459
527125002500-375
527135002500-400
527145002500-425
527155002500-450
527165002500-475
527175002500-500
527185002500-525

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
52304115030.957501.711427.4
52358100026.95000-25026.9
52268130034.965004.326026.3
52269130034.965004.332526.3
52270130034.965004.339026.3
52271130034.965004.345526.3
52272130034.965004.352026.3
52273130034.965004.358526.3
52274130034.965004.365026.3
52319110029.655001.811025.9
52320110029.655001.816525.9
52338105028.252501.320825.6
5237995025.54750-23525.5
5238095025.54750-28225.5
5238195025.54750-32925.5
5248775025.03750-22225.0
5248875025.03750-25925.0
52279125033.662504.524824.6
52287125033.662504.574424.6
52337105028.252501.915624.4
5240290024.24500-22524.2
5240390024.24500-27024.2
5240490024.24500-31524.2
5240590024.24500-36024.2
52336105028.252502.410423.5
5252270023.33500-24523.3
5252370023.33500-28023.3
5252470023.33500-31523.3
52359100026.950001.930023.1
52292120032.360004.724022.9
52356100026.950002.015022.9
52357100026.950002.020022.9
5242885022.84250-25222.8
5242985022.84250-29422.8
5243085022.84250-33622.8
5243185022.84250-37822.8
5243285022.84250-42022.8
52339105028.252502.826022.7
52290120032.360004.912022.4
5245680022.24000-24022.2
52321110029.655003.722022.1
5256065021.73250-22421.7
5256165021.73250-25621.7
5256265021.73250-28821.7
5256365021.73250-32021.7
5256465021.73250-35221.7
5245780021.54000-28021.5
5245880021.54000-32021.5
5245980021.54000-36021.5
5246080021.54000-40021.5
5246180021.54000-44021.5
5246280021.54000-48021.5
5245580026.540002.520021.5
5237795025.547502.114121.3
5237895025.547502.118821.3
52306115030.957504.922821.2
5240090025.645002.213521.1
52355100026.950002.910021.1
5248975020.83750-29620.8
5249075020.23750-33320.2
5249175020.23750-37020.2
5249275020.23750-40720.2
5249375020.23750-44420.2
5249475020.23750-48120.2
5249575020.23750-51820.2
5242785022.842501.421020.0
5260460020.03000-24020.0
5260560020.03000-27020.0
5260660020.03000-30020.0
5260760020.03000-33020.0
5260860020.03000-36020.0
5252170023.335001.721019.9
5242685024.642502.416819.9
5240190024.245002.218019.7
5242585024.442502.412619.7
5237695026.447503.79419.0
5240690024.245002.740518.9
5252570018.83500-35018.8
5252670018.83500-38518.8
5252770018.83500-42018.8
5252870018.83500-45518.8
5252970018.83500-49018.8
5253070018.83500-52518.8
5253170018.83500-56018.8
5256565018.53250-38418.5
5265255018.32750-24318.3
5265355018.32750-27018.3
5265455018.32750-29718.3
5265555018.32750-32418.3
5265655018.32750-35118.3
5245480023.140002.516018.1
5245380023.040002.512018.0
5259565017.63250-134417.6
5256665017.53250-41617.5
5256765017.53250-44817.5
5256865017.53250-48017.5
5256965017.53250-51217.5
5257065017.53250-54417.5
5257165017.53250-57617.5
5257265017.53250-60817.5
5239990025.945004.39017.2
5270650016.72500-22516.7
5270750016.72500-25016.7
5270850016.72500-27516.7
5270950016.72500-30016.7
5271050016.72500-32516.7
5271150016.72500-35016.7
5248675021.837502.718516.5
5275750016.22500-150016.2
5248575021.637502.714816.2
5264160016.23000-135016.2
5264260016.23000-138016.2
5265155018.327501.121616.2
5261160016.13000-45016.1
5261260016.13000-48016.1
5261360016.13000-51016.1
5261460016.13000-54016.1
5261560016.13000-57016.1
5261660016.13000-60016.1
5261760016.13000-63016.1
5261860016.13000-66016.1
5275650016.12500-147516.1
5260360020.030002.021016.0
5266155015.62750-48615.6
5243385022.842503.646215.6
5269355014.92750-135014.9
5269455014.92750-137714.9
5269555014.92750-140414.9
5269655014.92750-143114.9
5253270018.835002.059514.8
5275550014.82500-145014.8
5266255014.82750-51314.8
5266355014.82750-54014.8
5266455014.82750-56714.8
5266555014.82750-59414.8
5266655014.82750-62114.8
5266755014.82750-64814.8
5266855014.82750-67514.8
5266955014.82750-70214.8
5267055014.82750-72914.8
5257365017.532501.464014.7
5252070020.335002.917514.6
5251970020.135002.914014.4
5249675020.237503.255513.8
5275150013.52500-135013.5
5275250013.52500-137513.5
5275350013.52500-140013.5
5275450013.52500-142513.5
5271950013.42500-55013.4
5272050013.42500-57513.4
5272150013.42500-60013.4
5272250013.42500-62513.4
5272350013.42500-65013.4
5272450013.42500-67513.4
5272550013.42500-70013.4
5272650013.42500-72513.4
5272750013.42500-75013.4
5272850013.42500-77513.4
5255965019.532503.119213.3
5261960016.130001.569013.1
5255865018.832503.116012.6
5255765018.732503.112812.5
5260260017.430003.318010.8
5260060017.230003.312010.6
5260160017.230003.315010.6
5264060016.230002.8132010.5
5259465017.632503.813129.9
5269255014.927502.513239.8
5265055016.027503.61898.7
5275050013.525002.413258.7
5264955015.927503.61628.6
5270550016.625004.02008.6
5264855015.827503.61358.5
5270450014.525004.01756.5
5270250014.425004.01256.4
5270350014.425004.01506.4
5272950013.425003.88005.8

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
52280125033.662504.531024.6
52281125033.662504.537224.6
52282125033.662504.543424.6
52283125033.662504.549624.6
52284125033.662504.555824.6
52285125033.662504.562024.6
52286125033.662504.568224.6
52293120032.360004.730022.9
52294120032.360004.736022.9
52295120032.360004.742022.9
52296120032.360004.748022.9
52297120032.360004.754022.9
52298120032.360004.760022.9
52299120032.360004.766022.9
52300120032.360004.772022.9
52301120032.360004.778022.9
52307115030.957504.928521.2
52308115030.957504.934221.2
52309115030.957504.939921.2
52310115030.957504.945621.2
52311115030.957504.951321.2
52312115030.957504.957021.2
52313115030.957504.962721.2
52314115030.957504.968421.2
52315115030.957504.974121.2
52316115030.957504.979821.2
5248475021.637502.711116.2
5238295025.547504.737616.1
5251870020.135003.410513.3
5246380021.540004.952011.8
5264755015.827503.81088.2
5267155014.827504.57565.7

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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