Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign109 - back to list

Summary

./analyse_probe_search_results : Fri Feb 17 09:53:40 2006

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

Fetched probe design: ProbeDesign109
  assembly      : NCBIM34
  bias          : 3prime
  chromosome    : 5
  id            : 105
  strand        : 1
  -------------

Design window length: 2501bp

All jobs for probe design are successful - total: 35
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 700 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            : 700/700
Putative probes that are unique                 : 79/700
Putative probes exceeding selection criteria    : 503/700 (both unique and not unique)
Putative probes with successfully-picked primers: 497/503

Identified 3 '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
1001989504750-1551
1002349004500-1575
1002728504250-1554
1002738504250-1596
1002748504250-1638
1003148004000-1560
1003158004000-1600
1003168004000-1640
1003178004000-1680
1003607503750-1554
1003617503750-1591
1003627503750-1628
1003637503750-1665
1003647503750-1702
1003657503750-1739
1004107003500-1540
1004117003500-1575
1004127003500-1610
1004137003500-1645
1004147003500-1680
1004157003500-1715
1004167003500-1750
1004177003500-1785
1004676503250-1568
1004686503250-1600
1004696503250-1632
1004706503250-1664
1004716503250-1696
1004726503250-1728
1004736503250-1760
1004746503250-1792
1004756503250-1824
1005286003000-1560
1005296003000-1590
1005306003000-1620
1005316003000-1650
1005326003000-1680
1005336003000-1710
1005346003000-1740
1005356003000-1770
1005366003000-1800
1005376003000-1830
1005386003000-1860
1005396003000-1890
1005975502750-1539
1005985502750-1566
1005995502750-1593
1006005502750-1620
1006015502750-1647
1006025502750-1674
1006035502750-1701
1006045502750-1728
1006055502750-1755
1006065502750-1782
1006075502750-1809
1006085502750-1836
1006095502750-1863
1006105502750-1890
1006115502750-1917
1006125502750-1944
1006755002500-1550
1006765002500-1575
1006775002500-1600
1006785002500-1625
1006795002500-1650
1006805002500-1675
1006815002500-1700
1006825002500-1725
1006835002500-1750
1006845002500-1775
1006855002500-1800
1006865002500-1825
1006875002500-1850
1006885002500-1875
1006895002500-1900
1006905002500-1925
1006915002500-1950
1006925002500-1975
1006935002500-2000

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
100002130038.76500-52038.7
100003130038.76500-58538.7
100004130038.76500-65038.7
100005130038.76500-71538.7
100006130038.76500-78038.7
100007130038.76500-84538.7
100008130038.76500-91038.7
100009130038.76500-97538.7
100010130038.76500-104038.7
100011130038.76500-110538.7
100012130038.76500-117038.7
100022125037.26250-55837.2
100023125037.26250-62037.2
100024125037.26250-68237.2
100025125037.26250-74437.2
100026125037.26250-80637.2
100027125037.26250-86837.2
100028125037.26250-93037.2
100029125037.26250-99237.2
100030125037.26250-105437.2
100031125037.26250-111637.2
100032125037.26250-117837.2
100033125037.26250-124037.2
100021125037.262500.249636.7
100043120035.76000-54035.7
100044120035.76000-60035.7
100045120035.76000-66035.7
100046120035.76000-72035.7
100047120035.76000-78035.7
100048120035.76000-84035.7
100049120035.76000-90035.7
100050120035.76000-96035.7
100051120035.76000-102035.7
100052120035.76000-108035.7
100053120035.76000-114035.7
100054120035.76000-120035.7
100055120035.76000-126035.7
100065115034.25750-51334.2
100066115034.25750-57034.2
100067115034.25750-62734.2
100068115034.25750-68434.2
100069115034.25750-74134.2
100070115034.25750-79834.2
100071115034.25750-85534.2
100072115034.25750-91234.2
100073115034.25750-96934.2
100074115034.25750-102634.2
100075115034.25750-108334.2
100076115034.25750-114034.2
100077115034.25750-119734.2
100078115034.25750-125434.2
100079115034.25750-131134.2
100090110032.75500-55032.7
100091110032.75500-60532.7
100092110032.75500-66032.7
100093110032.75500-71532.7
100094110032.75500-77032.7
100095110032.75500-82532.7
100096110032.75500-88032.7
100097110032.75500-93532.7
100098110032.75500-99032.7
100099110032.75500-104532.7
100100110032.75500-110032.7
100101110032.75500-115532.7
100102110032.75500-121032.7
100103110032.75500-126532.7
100104110032.75500-132032.7
100105110032.75500-137532.7
100042120035.760001.648032.5
100089110032.755000.449532.0
100116105031.65250-52031.6
100117105031.25250-57231.2
100118105031.25250-62431.2
100119105031.25250-67631.2
100120105031.25250-72831.2
100121105031.25250-78031.2
100122105031.25250-83231.2
100123105031.25250-88431.2
100124105031.25250-93631.2
100125105031.25250-98831.2
100126105031.25250-104031.2
100127105031.25250-109231.2
100128105031.25250-114431.2
100129105031.25250-119631.2
100130105031.25250-124831.2
100131105031.25250-130031.2
100132105031.25250-135231.2
100133105031.25250-140431.2
100144100030.15000-50030.1
100145100030.15000-55030.1
100146100029.85000-60029.8
100147100029.85000-65029.8
100148100029.85000-70029.8
100149100029.85000-75029.8
100150100029.85000-80029.8
100151100029.85000-85029.8
100152100029.85000-90029.8
100153100029.85000-95029.8
100154100029.85000-100029.8
100155100029.85000-105029.8
100156100029.85000-110029.8
100157100029.85000-115029.8
100158100029.85000-120029.8
100159100029.85000-125029.8
100160100029.85000-130029.8
100161100029.85000-135029.8
100162100029.85000-140029.8
100163100029.85000-145029.8
100164100029.85000-150029.8
10017695028.64750-51728.6
10017795028.64750-56428.6
10017895028.64750-61128.6
10017995028.34750-65828.3
10018095028.34750-70528.3
10018195028.34750-75228.3
10018295028.34750-79928.3
10018395028.34750-84628.3
10018495028.34750-89328.3
10018595028.34750-94028.3
10018695028.34750-98728.3
10018795028.34750-103428.3
10018895028.34750-108128.3
10018995028.34750-112828.3
10019095028.34750-117528.3
10019195028.34750-122228.3
10019295028.34750-126928.3
10019395028.34750-131628.3
10019495028.34750-136328.3
10019595028.34750-141028.3
10019695028.34750-145728.3
10019795028.34750-150428.3
10021190027.14500-54027.1
10021290027.14500-58527.1
10021390027.14500-63027.1
10021490027.14500-67527.1
10021590026.84500-72026.8
10021690026.84500-76526.8
10021790026.84500-81026.8
10021890026.84500-85526.8
10021990026.84500-90026.8
10022090026.84500-94526.8
10022190026.84500-99026.8
10022290026.84500-103526.8
10022390026.84500-108026.8
10022490026.84500-112526.8
10022590026.84500-117026.8
10022690026.84500-121526.8
10022790026.84500-126026.8
10022890026.84500-130526.8
10022990026.84500-135026.8
10023090026.84500-139526.8
10023190026.84500-144026.8
10023290026.84500-148526.8
10023390026.84500-153026.8
10021090027.145000.449526.2
10024785025.64250-50425.6
10024885025.64250-54625.6
10024985025.64250-58825.6
10025085025.64250-63025.6
10025185025.64250-67225.6
10025285025.64250-71425.6
10025385025.34250-75625.3
10025485025.34250-79825.3
10025585025.34250-84025.3
10025685025.34250-88225.3
10025785025.34250-92425.3
10025885025.34250-96625.3
10025985025.34250-100825.3
10026085025.34250-105025.3
10026185025.34250-109225.3
10026285025.34250-113425.3
10026385025.34250-117625.3
10026485025.34250-121825.3
10026585025.34250-126025.3
10026685025.34250-130225.3
10026785025.34250-134425.3
10026885025.34250-138625.3
10026985025.34250-142825.3
10027085025.34250-147025.3
10027185025.34250-151225.3
10028880024.14000-52024.1
10028980024.14000-56024.1
10029080024.14000-60024.1
10029180024.14000-64024.1
10029280024.14000-68024.1
10029380024.14000-72024.1
10029480024.14000-76024.1
10029580023.84000-80023.8
10029680023.84000-84023.8
10029780023.84000-88023.8
10029880023.84000-92023.8
10029980023.84000-96023.8
10030080023.84000-100023.8
10030180023.84000-104023.8
10030280023.84000-108023.8
10030380023.84000-112023.8
10030480023.84000-116023.8
10030580023.84000-120023.8
10030680023.84000-124023.8
10030780023.84000-128023.8
10030880023.84000-132023.8
10030980023.84000-136023.8
10031080023.84000-140023.8
10031180023.84000-144023.8
10031280023.84000-148023.8
10031380023.84000-152023.8
10033275022.63750-51822.6
10033375022.63750-55522.6
10033475022.63750-59222.6
10033575022.63750-62922.6
10033675022.63750-66622.6
10033775022.63750-70322.6
10033875022.63750-74022.6
10033975022.63750-77722.6
10034075022.63750-81422.6
10034175022.33750-85122.3
10034275022.33750-88822.3
10034375022.33750-92522.3
10034475022.33750-96222.3
10034575022.33750-99922.3
10034675022.33750-103622.3
10034775022.33750-107322.3
10034875022.33750-111022.3
10034975022.33750-114722.3
10035075022.33750-118422.3
10035175022.33750-122122.3
10035275022.33750-125822.3
10035375022.33750-129522.3
10035475022.33750-133222.3
10035575022.33750-136922.3
10035675022.33750-140622.3
10035775022.33750-144322.3
10035875022.33750-148022.3
10035975022.33750-151722.3
100115105028.252503.046822.3
100001130028.065003.445521.2
10038170021.13500-52521.1
10038270021.13500-56021.1
10038370021.13500-59521.1
10038470021.13500-63021.1
10038570021.13500-66521.1
10038670021.13500-70021.1
10038770021.13500-73521.1
10038870021.13500-77021.1
10038970021.13500-80521.1
10039070021.13500-84021.1
10039170021.13500-87521.1
10039270020.83500-91020.8
10039370020.83500-94520.8
10039470020.83500-98020.8
10039570020.83500-101520.8
10039670020.83500-105020.8
10039770020.83500-108520.8
10039870020.83500-112020.8
10039970020.83500-115520.8
10040070020.83500-119020.8
10040170020.83500-122520.8
10040270020.83500-126020.8
10040370020.83500-129520.8
10040470020.83500-133020.8
10040570020.83500-136520.8
10040670020.83500-140020.8
10040770020.83500-143520.8
10040870020.83500-147020.8
10040970020.83500-150520.8
10043465020.23250-51220.2
10017595026.247503.147020.1
10043565019.63250-54419.6
10043665019.63250-57619.6
10043765019.63250-60819.6
10043865019.63250-64019.6
10043965019.63250-67219.6
10044065019.63250-70419.6
10044165019.63250-73619.6
10044265019.63250-76819.6
10044365019.63250-80019.6
10044465019.63250-83219.6
10044565019.63250-86419.6
10044665019.63250-89619.6
10044765019.63250-92819.6
10028780024.140002.448019.3
10044865019.33250-96019.3
10044965019.33250-99219.3
10045065019.33250-102419.3
10045165019.33250-105619.3
10045265019.33250-108819.3
10045365019.33250-112019.3
10045465019.33250-115219.3
10045565019.33250-118419.3
10045665019.33250-121619.3
10045765019.33250-124819.3
10045865019.33250-128019.3
10045965019.33250-131219.3
10046065019.33250-134419.3
10046165019.33250-137619.3
10046265019.33250-140819.3
10046365019.33250-144019.3
10046465019.33250-147219.3
10046565019.33250-150419.3
10046665019.33250-153619.3
10049360018.63000-51018.6
10049460018.63000-54018.6
10038070021.135001.349018.5
10049560018.13000-57018.1
10049660018.13000-60018.1
10049760018.13000-63018.1
10049860018.13000-66018.1
10049960018.13000-69018.1
10050060018.13000-72018.1
10050160018.13000-75018.1
10050260018.13000-78018.1
10050360018.13000-81018.1
10050460018.13000-84018.1
10050560018.13000-87018.1
10050660018.13000-90018.1
10050760018.13000-93018.1
10050860018.13000-96018.1
10050960018.13000-99018.1
10051060017.93000-102017.9
10051160017.93000-105017.9
10051260017.93000-108017.9
10051360017.93000-111017.9
10051460017.93000-114017.9
10051560017.93000-117017.9
10051660017.93000-120017.9
10051760017.93000-123017.9
10051860017.93000-126017.9
10051960017.93000-129017.9
10052060017.93000-132017.9
10052160017.93000-135017.9
10052260017.93000-138017.9
10052360017.93000-141017.9
10052460017.93000-144017.9
10052560017.93000-147017.9
10052660017.93000-150017.9
10052760017.93000-153017.9
10033175022.637502.448117.8
10055955017.12750-51317.1
10056055017.12750-54017.1
10056155017.12750-56717.1
10056255017.12750-59417.1
10056355016.62750-62116.6
10056455016.62750-64816.6
10056555016.62750-67516.6
10056655016.62750-70216.6
10056755016.62750-72916.6
10056855016.62750-75616.6
10056955016.62750-78316.6
10057055016.62750-81016.6
10057155016.62750-83716.6
10057255016.62750-86416.6
10057355016.62750-89116.6
10057455016.62750-91816.6
10057555016.62750-94516.6
10057655016.62750-97216.6
10057755016.62750-99916.6
10057855016.62750-102616.6
10057955016.42750-105316.4
10058055016.42750-108016.4
10058155016.42750-110716.4
10058255016.42750-113416.4
10058355016.42750-116116.4
10058455016.42750-118816.4
10058555016.42750-121516.4
10058655016.42750-124216.4
10058755016.42750-126916.4
10058855016.42750-129616.4
10058955016.42750-132316.4
10059055016.42750-135016.4
10059155016.42750-137716.4
10059255016.42750-140416.4
10059355016.42750-143116.4
10059455016.42750-145816.4
10059555016.42750-148516.4
10059655016.42750-151216.4
10063350015.52500-50015.5
10063450015.52500-52515.5
10063550015.52500-55015.5
10063650015.52500-57515.5
10063750015.52500-60015.5
10063850015.52500-62515.5
10063950015.52500-65015.5
10064050015.12500-67515.1
10064150015.12500-70015.1
10064250015.12500-72515.1
10064350015.12500-75015.1
10064450015.12500-77515.1
10064550015.12500-80015.1
10064650015.12500-82515.1
10064750015.12500-85015.1
10064850015.12500-87515.1
10064950015.12500-90015.1
10065050015.12500-92515.1
10065150015.12500-95015.1
10065250015.12500-97515.1
10065350015.12500-100015.1
10065450015.12500-102515.1
10065550015.12500-105015.1
10065650015.12500-107515.1
10065750014.92500-110014.9
10065850014.92500-112514.9
10065950014.92500-115014.9
10066050014.92500-117514.9
10066150014.92500-120014.9
10066250014.92500-122514.9
10066350014.92500-125014.9
10066450014.92500-127514.9
10066550014.92500-130014.9
10066650014.92500-132514.9
10066750014.92500-135014.9
10066850014.92500-137514.9
10066950014.92500-140014.9
10067050014.92500-142514.9
10067150014.92500-145014.9
10067250014.92500-147514.9
10067350014.92500-150014.9
10067450014.92500-152514.9
10043365020.132502.948014.2
10055855017.127502.448612.4
10049260018.530003.248012.2
100143100019.550004.94509.7

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
100064115025.357503.745617.9
10024685021.642504.446212.9
10063250014.825004.84755.2

Overall score = score_ratio - 2 * repetitive DNA content

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EUROSPIN (FP7-HEALTH-241498), SynSys (FP7-HEALTH-242167) and GENCODYS (FP7-HEALTH-241995).

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