Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign15 - back to list

Summary

./analyse_probe_search_results : Tue Feb 20 17:43:19 2007

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

Fetched probe design: ProbeDesign15
  assembly      : NCBIM36
  bias          : 3prime
  chromosome    : 16
  id            : 10
  strand        : 1
  -------------

Design window length: 2460bp

All jobs for probe design are successful - total: 35
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 683 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            : 683/683
Putative probes that are unique                 : 7/683
Putative probes exceeding selection criteria    : 299/683 (both unique and not unique)
Putative probes with successfully-picked primers: 294/299

Identified 7 '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
87545502750-1512
87555502750-1539
87565502750-1566
88305002500-1525
88315002500-1550
88325002500-1575
88335002500-1600

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
8224120038.76000-126038.7
8247115037.15750-125437.1
8271110035.55500-126535.5
8272110035.55500-132035.5
8223120038.760001.7120035.4
8297105033.95250-124833.9
8298105033.95250-130033.9
8299105033.95250-135233.9
8300105033.95250-140433.9
8270110035.555000.9121033.7
8246115037.157502.0119733.1
8326100032.35000-125032.3
8327100032.35000-130032.3
8328100032.35000-135032.3
8329100032.35000-140032.3
8330100032.35000-145032.3
836395031.54750-150431.5
8301100030.95000-030.9
835795030.64750-122230.6
835895030.64750-126930.6
835995030.64750-131630.6
836095030.64750-136330.6
836195030.64750-141030.6
836295030.64750-145730.6
8202125036.862503.4117830.0
839890029.84500-153029.8
833195029.34750-029.3
833295029.34750-4729.3
8296105033.952502.3119629.3
839290029.04500-126029.0
839390029.04500-130529.0
839490029.04500-135029.0
839590029.04500-139529.0
839690029.04500-144029.0
839790029.04500-148529.0
8325100032.350002.0120028.3
843585028.14250-151228.1
843685028.14250-155428.1
843785028.14250-159628.1
839190029.045000.6121527.9
836490027.84500-027.8
836590027.84500-4527.8
836690027.84500-9027.8
842985027.44250-126027.4
843085027.44250-130227.4
843185027.44250-134427.4
843285027.44250-138627.4
843385027.44250-142827.4
843485027.44250-147027.4
842885027.442500.2121826.9
847680026.54000-152026.5
847780026.54000-156026.5
847880026.54000-160026.5
847980026.54000-164026.5
839985026.24250-026.2
840085026.24250-4226.2
840185026.24250-8426.2
840285026.24250-12626.2
840385026.242500.116826.0
846980025.84000-124025.8
847080025.84000-128025.8
847180025.84000-132025.8
847280025.84000-136025.8
847380025.84000-140025.8
847480025.84000-144025.8
847580025.84000-148025.8
852175024.83750-151724.8
852275024.83750-155424.8
852375024.83750-159124.8
852475024.83750-162824.8
852575024.83750-166524.8
852675024.83750-170224.8
843880024.74000-024.7
843980024.74000-4024.7
844080024.74000-8024.7
844180024.74000-12024.7
844280024.74000-16024.7
844380024.74000-20024.7
851375024.23750-122124.2
851475024.23750-125824.2
851575024.23750-129524.2
851675024.23750-133224.2
851775024.23750-136924.2
851875024.23750-140624.2
851975024.23750-144324.2
852075024.23750-148024.2
836790027.845002.013523.8
857070023.23500-150523.2
857170023.23500-154023.2
857270023.23500-157523.2
857370023.23500-161023.2
857470023.23500-164523.2
857570023.23500-168023.2
857670023.23500-171523.2
857770023.23500-175023.2
848075023.13750-023.1
848175023.13750-3723.1
848275023.13750-7423.1
848375023.13750-11123.1
848475023.13750-14823.1
848575023.13750-18523.1
848675023.13750-22223.1
848775023.13750-25923.1
8273105029.052503.1022.7
856270022.63500-122522.6
856370022.63500-126022.6
856470022.63500-129522.6
856570022.63500-133022.6
856670022.63500-136522.6
856770022.63500-140022.6
856870022.63500-143522.6
856970022.63500-147022.6
852770021.63500-021.6
852870021.63500-3521.6
852970021.63500-7021.6
853070021.63500-10521.6
853170021.63500-14021.6
853270021.63500-17521.6
853370021.63500-21021.6
853470021.63500-24521.6
853570021.63500-28021.6
853670021.63500-31521.6
862565021.53250-150421.5
862665021.53250-153621.5
862765021.53250-156821.5
862865021.53250-160021.5
862965021.53250-163221.5
863065021.53250-166421.5
863165021.53250-169621.5
863265021.53250-172821.5
863365021.53250-176021.5
863465021.53250-179221.5
861765021.03250-124821.0
861865021.03250-128021.0
861965021.03250-131221.0
862065021.03250-134421.0
862165021.03250-137621.0
862265021.03250-140821.0
862365021.03250-144021.0
862465021.03250-147221.0
846880025.840002.5120020.8
833395026.247502.89420.6
857865020.13250-020.1
857965020.13250-3220.1
858065020.13250-6420.1
858165020.13250-9620.1
858265020.13250-12820.1
858365020.13250-16020.1
858465020.13250-19220.1
858565020.13250-22420.1
858665020.13250-25620.1
858765020.13250-28820.1
858865020.13250-32020.1
858965020.13250-35220.1
868660019.93000-153019.9
868760019.93000-156019.9
868860019.93000-159019.9
868960019.93000-162019.9
869060019.93000-165019.9
869160019.93000-168019.9
869260019.93000-171019.9
869360019.93000-174019.9
869460019.93000-177019.9
869560019.93000-180019.9
869660019.93000-183019.9
869760019.93000-186019.9
861665021.032500.6121619.7
867660019.43000-123019.4
867760019.43000-126019.4
867860019.43000-129019.4
867960019.43000-132019.4
868060019.43000-135019.4
868160019.43000-138019.4
868260019.43000-141019.4
868360019.43000-144019.4
868460019.43000-147019.4
868560019.43000-150019.4
863560018.53000-018.5
863660018.53000-3018.5
863760018.53000-6018.5
863860018.53000-9018.5
863960018.53000-12018.5
864060018.53000-15018.5
864160018.53000-18018.5
864260018.53000-21018.5
864360018.53000-24018.5
864460018.53000-27018.5
864560018.53000-30018.5
864660018.53000-33018.5
864760018.53000-36018.5
864860018.53000-39018.5
864960019.530000.542018.5
875755018.22750-159318.2
875855018.22750-162018.2
875955018.22750-164718.2
876055018.22750-167418.2
876155018.22750-170118.2
876255018.22750-172818.2
876355018.22750-175518.2
876455018.22750-178218.2
876555018.22750-180918.2
876655018.22750-183618.2
876755018.22750-186318.2
876855018.22750-189018.2
871355017.92750-40517.9
871455017.92750-43217.9
871555017.92750-45917.9
874455017.72750-124217.7
874555017.72750-126917.7
874655017.72750-129617.7
874755017.72750-132317.7
874855017.72750-135017.7
874955017.72750-137717.7
875055017.72750-140417.7
875155017.72750-143117.7
875255017.72750-145817.7
875355017.72750-148517.7
869855017.02750-017.0
869955017.02750-2717.0
870055017.02750-5417.0
870155017.02750-8117.0
870255017.02750-10817.0
870355017.02750-13517.0
870455017.02750-16217.0
870555017.02750-18917.0
870655017.02750-21617.0
870755017.02750-24317.0
870855017.02750-27017.0
870955017.02750-29717.0
871055017.02750-32417.0
871155017.02750-35117.0
871255017.02750-37817.0
883450016.72500-162516.7
844480022.340002.924016.6
883550016.62500-165016.6
883650016.62500-167516.6
883750016.62500-170016.6
883850016.62500-172516.6
883950016.62500-175016.6
884050016.62500-177516.6
884150016.62500-180016.6
884250016.62500-182516.6
884350016.62500-185016.6
884450016.62500-187516.6
884550016.62500-190016.6
884650016.62500-192516.6
884750016.62500-195016.6
878550016.22500-40016.2
878650016.22500-42516.2
878750016.22500-45016.2
878850016.22500-47516.2
878950016.22500-50016.2
835695025.747504.7117516.2
881850016.12500-122516.1
881950016.12500-125016.1
882050016.12500-127516.1
882150016.12500-130016.1
882250016.12500-132516.1
882350016.12500-135016.1
882450016.12500-137516.1
882550016.12500-140016.1
882650016.12500-142516.1
882750016.12500-145016.1
882850016.12500-147516.1
882950016.12500-150016.1
874355017.727500.9121515.9
876950015.42500-015.4
877050015.42500-2515.4
877150015.42500-5015.4
877250015.42500-7515.4
877350015.42500-10015.4
877450015.42500-12515.4
877550015.42500-15015.4
877650015.42500-17515.4
877750015.42500-20015.4
877850015.42500-22515.4
877950015.42500-25015.4
878050015.42500-27515.4
878150015.42500-30015.4
878250015.42500-32515.4
878350015.42500-35015.4
878450015.42500-37515.4
859065020.132502.638414.8
879050016.225001.652513.0
867560019.430003.3120012.7

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
8302100027.650003.35021.0
856170022.635004.3119014.0
851275023.037504.8118413.4
848875020.737503.929613.0
871655017.227503.548610.3
853770019.335004.73509.9
881750016.125004.012008.1

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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