Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign26 - back to list

Summary

./analyse_probe_search_results : Mon Sep 5 11:54:51 2005

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

Fetched probe design: ProbeDesign26
  assembly      : NCBIM33
  bias          : 5prime
  chromosome    : 3
  id            : 3
  strand        : 1
  -------------

Design window length: 2001bp

All jobs for probe design are successful - total: 41
Fetched conf : Exonerate mouse_NCBI33 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM33/genome/masked_dusted
Fetched 405 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        : 405/405
Putative probes exceeding selection criteria: 249/405

PASSED (GREEN) AND FAILED PUTATIVE PROBES IN THE DESIGN WINDOW
--------------------------------------------------------------

Image

Unique (yellow), passed (green) and failed putative probes in the design window

Chart

Unique putative probes

No probes

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
811100031.85000-031.8
812100031.85000-5031.8
83295030.34750-030.3
83395030.34750-4730.3
83495030.34750-9430.3
813100029.95000-10029.9
814100029.95000-15029.9
815100029.95000-20029.9
816100029.95000-25029.9
817100029.95000-30029.9
818100029.95000-35029.9
819100029.95000-40029.9
820100029.95000-45029.9
821100029.95000-50029.9
822100029.95000-55029.9
83595029.34750-14129.3
85590028.74500-028.7
85690028.74500-4528.7
85790028.74500-9028.7
85890028.74500-13528.7
85990028.74500-18028.7
83695028.44750-18828.4
83795028.44750-23528.4
83895028.44750-28228.4
83995028.44750-32928.4
84095028.44750-37628.4
84195028.44750-42328.4
84295028.44750-47028.4
84395028.44750-51728.4
84495028.44750-56428.4
88185028.34250-4228.3
84595027.34750-61127.3
88285027.14250-8427.1
88385027.14250-12627.1
88485027.14250-16827.1
88585027.14250-21027.1
86090026.94500-22526.9
86190026.94500-27026.9
86290026.94500-31526.9
86390026.94500-36026.9
86490026.94500-40526.9
86590026.94500-45026.9
86690026.94500-49526.9
86790026.94500-54026.9
86890026.94500-58526.9
86990026.94500-63026.9
91180025.54000-12025.5
91280025.54000-16025.5
91380025.54000-20025.5
91480025.54000-24025.5
91580025.54000-28025.5
88685025.44250-25225.4
88785025.44250-29425.4
88885025.44250-33625.4
88985025.44250-37825.4
89085025.44250-42025.4
89185025.44250-46225.4
89285025.44250-50425.4
89385025.44250-54625.4
89485025.44250-58825.4
89585025.44250-63025.4
89685025.44250-67225.4
91680024.04000-32024.0
91780024.04000-36024.0
91880024.04000-40024.0
91980024.04000-44024.0
92080024.04000-48024.0
92180024.04000-52024.0
92280024.04000-56024.0
92380024.04000-60024.0
92480024.04000-64024.0
92580024.04000-68024.0
92680024.04000-72024.0
94375023.93750-14823.9
94475023.93750-18523.9
94575023.93750-22223.9
94675023.93750-25923.9
94775023.93750-29623.9
94875023.93750-33323.9
92780023.74000-76023.7
89785022.54250-71422.5
94975022.53750-37022.5
95075022.53750-40722.5
95175022.53750-44422.5
95275022.53750-48122.5
95375022.53750-51822.5
95475022.53750-55522.5
95575022.53750-59222.5
95675022.53750-62922.5
95775022.53750-66622.5
95875022.53750-70322.5
95975022.53750-74022.5
96075022.53750-77722.5
97970022.33500-21022.3
98070022.33500-24522.3
98170022.33500-28022.3
98270022.33500-31522.3
98370022.33500-35022.3
98470022.33500-38522.3
98570021.03500-42021.0
98670021.03500-45521.0
98770021.03500-49021.0
98870021.03500-52521.0
98970021.03500-56021.0
99070021.03500-59521.0
99170021.03500-63021.0
99270021.03500-66521.0
99370021.03500-70021.0
99470021.03500-73521.0
99570021.03500-77021.0
99670021.03500-80521.0
99770021.03500-84021.0
101965020.73250-25620.7
102065020.73250-28820.7
102165020.73250-32020.7
102265020.73250-35220.7
102365020.73250-38420.7
102465020.73250-41620.7
87090019.94500-67519.9
96175019.83750-81419.8
102565019.53250-44819.5
102665019.53250-48019.5
102765019.53250-51219.5
102865019.53250-54419.5
102965019.53250-57619.5
103065019.53250-60819.5
103165019.53250-64019.5
103265019.53250-67219.5
103365019.53250-70419.5
103465019.53250-73619.5
103565019.53250-76819.5
103665019.53250-80019.5
103765019.53250-83219.5
103865019.53250-86419.5
103965019.53250-89619.5
106460019.13000-30019.1
106560019.13000-33019.1
106660019.13000-36019.1
106760019.13000-39019.1
106860019.13000-42019.1
106960019.13000-45019.1
107060019.13000-48019.1
107160018.03000-51018.0
107260018.03000-54018.0
107360018.03000-57018.0
107460018.03000-60018.0
107560018.03000-63018.0
107660018.03000-66018.0
107760018.03000-69018.0
107860018.03000-72018.0
107960018.03000-75018.0
108060018.03000-78018.0
108160018.03000-81018.0
108260018.03000-84018.0
108360018.03000-87018.0
108460018.03000-90018.0
108560018.03000-93018.0
108660017.83000-96017.8
113855017.72750-99917.7
111455017.52750-35117.5
111555017.52750-37817.5
111655017.52750-40517.5
111755017.52750-43217.5
111855017.52750-45917.5
111955017.52750-48617.5
112055017.52750-51317.5
112155017.52750-54017.5
112255016.52750-56716.5
112355016.52750-59416.5
112455016.52750-62116.5
112555016.52750-64816.5
112655016.52750-67516.5
112755016.52750-70216.5
112855016.52750-72916.5
112955016.52750-75616.5
113055016.52750-78316.5
113155016.52750-81016.5
113255016.52750-83716.5
113355016.52750-86416.5
113455016.52750-89116.5
113555016.52750-91816.5
113655016.52750-94516.5
113755016.52750-97216.5
823100016.15000-60016.1
119550016.12500-100016.1
117150015.92500-40015.9
117250015.92500-42515.9
117350015.92500-45015.9
117450015.92500-47515.9
117550015.92500-50015.9
117650015.92500-52515.9
117750015.92500-55015.9
117850015.92500-57515.9
99870015.53500-87515.5
117950015.02500-60015.0
118050015.02500-62515.0
118150015.02500-65015.0
118250015.02500-67515.0
118350015.02500-70015.0
118450015.02500-72515.0
118550015.02500-75015.0
118650015.02500-77515.0
118750015.02500-80015.0
118850015.02500-82515.0
118950015.02500-85015.0
119050015.02500-87515.0
119150015.02500-90015.0
119250015.02500-92515.0
119350015.02500-95015.0
119450015.02500-97515.0
84695014.94750-65814.9
824100013.55000-65013.5
825100013.55000-70013.5
826100013.55000-75013.5
104065013.53250-92813.5
89885013.44250-75613.4
92880012.94000-80012.9
84795012.84750-70512.8
84895012.84750-75212.8
84995012.84750-79912.8
87190012.54500-72012.5
87290012.24500-76512.2
87390012.24500-81012.2
87490012.24500-85512.2
96275012.13750-85112.1
113955011.92750-102611.9
85095012.847500.684611.6
827100013.550001.080011.5
89985011.54250-79811.5
90085011.54250-84011.5
90185011.54250-88211.5
90285011.54250-92411.5
119850011.12500-107511.1
99970010.93500-91010.9
92980010.84000-84010.8
93080010.84000-88010.8
93180010.84000-92010.8
93280010.84000-96010.8
108760010.63000-99010.6
104165010.23250-96010.2
96375010.13750-88810.1
96475010.13750-92510.1
96575010.13750-96210.1
96675010.13750-99910.1
96775010.13750-103610.1
90385011.542503.19665.4
96875010.137504.410731.3

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
87590012.245001.19009.9
93380010.840001.210008.3

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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