Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign11 - back to list

Summary

./analyse_probe_search_results : Mon Mar 12 15:53:06 2007

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

Fetched probe design: ProbeDesign11
  assembly      : NCBIM36
  bias          : 5prime
  chromosome    : X
  id            : 14
  strand        : 1
  -------------

Design window length: 16430bp

All jobs for probe design are successful - total: 161
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 3207 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            : 3207/3207
Putative probes that are unique                 : 214/3207
Putative probes exceeding selection criteria    : 502/3207 (both unique and not unique)
Putative probes with successfully-picked primers: 487/502

Identified 79 '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
1930613006500-8580
1930713006500-8710
1942612506250-8625
1942712506250-8750
1942812506250-8875
1955112006000-8640
1955212006000-8760
1955312006000-8880
1968111505750-8625
1968211505750-8740
1968311505750-8855
1968411505750-8970
1981711005500-8580
1981811005500-8690
1981911005500-8800
1982011005500-8910
1982111005500-9020
1996110505250-8610
1996210505250-8715
1996310505250-8820
1996410505250-8925
1996510505250-9030
2011210005000-8600
2011310005000-8700
2011410005000-8800
2011510005000-8900
2011610005000-9000
2011710005000-9100
202729504750-8645
202739504750-8740
202749504750-8835
202759504750-8930
202769504750-9025
202779504750-9120
204409004500-8640
204419004500-8730
204429004500-8820
204439004500-8910
204449004500-9000
204459004500-9090
204469004500-9180
206188504250-8585
206198504250-8670
206208504250-8755
206218504250-8840
206228504250-8925
206238504250-9010
206248504250-9095
206258504250-9180
206268504250-9265
208098004000-8640
208108004000-8720
208118004000-8800
208128004000-8880
208138004000-8960
208148004000-9040
208158004000-9120
208168004000-9200
208178004000-9280
210127503750-8625
210137503750-8700
210147503750-8775
210157503750-8850
210167503750-8925
210177503750-9000
210187503750-9075
210197503750-9150
210207503750-9225
210217503750-9300
210227503750-9375
212307003500-8610
212317003500-8680
212327003500-8750
212337003500-8820
212347003500-8890
212357003500-8960
212367003500-9030
212377003500-9100
212387003500-9170
212397003500-9240
212407003500-9310
212417003500-9380
214646503250-8580
214656503250-8645
214666503250-8710
214676503250-8775
214686503250-8840
214696503250-8905
214706503250-8970
214716503250-9035
214726503250-9100
214736503250-9165
214746503250-9230
214756503250-9295
214766503250-9360
214776503250-9425
216046003000-1740
217186003000-8580
217196003000-8640
217206003000-8700
217216003000-8760
217226003000-8820
217236003000-8880
217246003000-8940
217256003000-9000
217266003000-9060
217276003000-9120
217286003000-9180
217296003000-9240
217306003000-9300
217316003000-9360
217326003000-9420
217336003000-9480
217486003000-10380
218715502750-1760
219955502750-8580
219965502750-8635
219975502750-8690
219985502750-8745
219995502750-8800
220005502750-8855
220015502750-8910
220025502750-8965
220035502750-9020
220045502750-9075
220055502750-9130
220065502750-9185
220075502750-9240
220085502750-9295
220095502750-9350
220105502750-9405
220115502750-9460
220125502750-9515
220135502750-9570
220285502750-10395
220295502750-10450
221635002500-1750
221645002500-1800
221655002500-1850
222445002500-5800
222735002500-7250
222865002500-7900
222875002500-7950
223005002500-8600
223015002500-8650
223025002500-8700
223035002500-8750
223045002500-8800
223055002500-8850
223065002500-8900
223075002500-8950
223085002500-9000
223095002500-9050
223105002500-9100
223115002500-9150
223125002500-9200
223135002500-9250
223145002500-9300
223155002500-9350
223165002500-9400
223175002500-9450
223185002500-9500
223195002500-9550
223205002500-9600
223355002500-10350
223365002500-10400
223375002500-10450
223385002500-10500
19308130065000.28840
2194455027500.45775
2147865032500.59490
2080880040000.58560
2173460030000.59540
19309130065001.18970
19429125062501.19000
19554120060001.29000
19685115057501.29085
19822110055001.39130
19966105052501.39135
20118100050001.49200
2027895047501.59215
2027995047501.59310
2135865032501.51690
2044790045001.69270
2044890045001.69360
2062785042501.69350
2160360030001.71680
2081880040001.89360
2081980040001.89440
2187055027501.81705
2124270035001.99450
2102375037501.99450
2102475037501.99525
2124370035002.09520
2216250025002.01700
2147965032502.29555
2148065032502.29620
2198355027502.27920
2173560030002.39600
2173660030002.39660
2201455027502.59625
2201555027502.59680
2232150025002.69650
2232250025002.89700
2232350025002.89750
2197055027503.57205
2224550025003.65850
2234750025005.010950
2186955027505.31650
2216150025005.81650
2235750025006.811450
2135765032508.31625
2228850025008.48000
22216500250022.24400

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
19669115032.55750-724532.5
20130100032.55000-1040032.5
19805110031.15500-726031.1
2029095030.84750-1035530.8
2029195030.84750-1045030.8
19978105034.152501.91039530.3
19833110032.955001.41034030.2
19539120033.960002.0720029.9
19948105029.75250-724529.7
19949105029.75250-735029.7
2045990029.24500-1035029.2
2046090029.24500-1044029.2
19806110031.155001.1737028.9
19320130037.865004.51040028.7
19321130037.865004.51053028.7
19322130037.865004.51066028.7
19415125035.362503.4725028.6
20099100028.25000-730028.2
20100100028.25000-740028.2
2046190029.245000.61053028.1
2063985027.64250-1037027.6
2064085027.64250-1045527.6
2064185027.64250-1054027.6
19440125036.362504.71037526.9
19441125036.362504.71050026.9
19442125036.362504.71062526.9
2025895026.84750-731526.8
2025995026.84750-741026.8
2026095026.84750-750526.8
2025795026.847500.4722026.0
2083180026.04000-1040026.0
2083280026.04000-1048026.0
2083380026.04000-1056026.0
2042590025.44500-729025.4
2042690025.44500-738025.4
2042790025.44500-747025.4
2027195028.347501.5855025.3
2042890025.445000.2756025.0
2103575024.43750-1035024.4
2103675024.43750-1042524.4
2103775024.43750-1050024.4
2103875024.43750-1057524.4
2103975024.43750-1065024.4
2060285024.04250-722524.0
2060385024.04250-731024.0
2060485024.04250-739524.0
2060585024.04250-748024.0
2060685024.04250-756524.0
2043990026.845001.6855023.7
2072280026.140001.2168023.6
19670115032.557504.5736023.4
19550120030.860003.7852023.4
2113270022.93500-175022.9
2125570022.73500-1036022.7
2125670022.73500-1043022.7
2125770022.73500-1050022.7
2125870022.73500-1057022.7
2125970022.73500-1064022.7
2126070022.73500-1071022.7
2079280022.64000-728022.6
2079380022.64000-736022.6
2079480022.64000-744022.6
2079580022.64000-752022.6
2079680022.64000-760022.6
2083480026.040001.91064022.2
2135965021.23250-175521.2
2136065021.23250-182021.2
2099475021.23750-727521.2
2099575021.23750-735021.2
2099675021.23750-742521.2
2099775021.23750-750021.2
2099875021.23750-757521.2
2099975021.23750-765021.2
2149265021.13250-1040021.1
2149365021.13250-1046521.1
2149465021.13250-1053021.1
2149565021.13250-1059521.1
2149665021.13250-1066021.1
2149765021.13250-1072521.1
19950105029.752504.5745520.7
2144465019.93250-728019.9
2121170019.83500-728019.8
2121270019.83500-735019.8
2121370019.83500-742019.8
2121470019.83500-749019.8
2121570019.83500-756019.8
2121670019.83500-763019.8
2121770019.83500-770019.8
2160560019.63000-180019.6
2160660019.63000-186019.6
2174960019.53000-1044019.5
2175060019.53000-1050019.5
2175160019.53000-1056019.5
2175260019.53000-1062019.5
2175360019.53000-1068019.5
2175460019.53000-1074019.5
2175560019.53000-1080019.5
20129100019.55000-1030019.5
2083080018.84000-1032018.8
2101175022.337501.9855018.6
2169660018.43000-726018.4
2169760018.43000-732018.4
2144565018.43250-734518.4
2144665018.43250-741018.4
2144765018.43250-747518.4
2144865018.43250-754018.4
2144965018.43250-760518.4
2145065018.43250-767018.4
2145165018.43250-773518.4
2145265018.43250-780018.4
2187255018.02750-181518.0
2187355018.02750-187018.0
2187455018.02750-192518.0
19977105017.95250-1029017.9
2203055017.92750-1050517.9
2203155017.92750-1056017.9
2203255017.92750-1061517.9
2203355017.92750-1067017.9
2203455017.92750-1072517.9
2203555017.92750-1078017.9
2203655017.92750-1083517.9
2121070021.535002.0721017.5
19680115026.757504.7851017.4
2144365019.932501.4721517.2
2079780022.640002.8768017.1
2169860016.93000-738016.9
2169960016.93000-744016.9
2170060016.93000-750016.9
2170160016.93000-756016.9
2170260016.93000-762016.9
2170360016.93000-768016.9
2170460016.93000-774016.9
2170560016.93000-780016.9
2149165016.93250-1033516.9
2197155016.92750-726016.9
2197255016.92750-731516.9
2197355016.92750-737016.9
2091975024.537503.9165016.8
2100075021.237502.3772516.7
2202755016.52750-1034016.5
2121870019.835001.7777016.3
2216650016.32500-190016.3
2216750016.32500-195016.3
2170660016.930000.3786016.3
2233950016.22500-1055016.2
2234050016.22500-1060016.2
2234150016.22500-1065016.2
2234250016.22500-1070016.2
2234350016.22500-1075016.2
2234450016.22500-1080016.2
2234550016.22500-1085016.2
2234650016.22500-1090016.2
2197455015.52750-742515.5
2197555015.52750-748015.5
2197655015.52750-753515.5
2197755015.52750-759015.5
2197855015.52750-764515.5
2197955015.52750-770015.5
2198055015.52750-775515.5
2198155015.52750-781015.5
2198255015.52750-786515.5
2220150015.32500-365015.3
2227450015.32500-730015.3
2227550015.32500-735015.3
2227650015.32500-740015.3
2227750014.12500-745014.1
2227850014.12500-750014.1
2227950014.12500-755014.1
2228050014.12500-760014.1
2228150014.12500-765014.1
2228250014.12500-770014.1
2228350014.12500-775014.1
2228450014.12500-780014.1
2228550014.12500-785014.1
2174760014.13000-1032014.1
2063885013.54250-1028513.5
2122970019.735003.4854012.8
19695115012.55750-1023512.5
19564120012.56000-1020012.5
2028995012.14750-1026012.1
19832110012.05500-1023012.0
2125470011.93500-1029011.9
2216850016.325002.2200011.9
2045890011.44500-1026011.4
19310130013.565001.1910011.4
19311130013.565001.1923011.4
19312130013.565001.1936011.4
19313130013.565001.1949011.4
19314130013.565001.1962011.4
19315130013.565001.1975011.4
19316130013.565001.1988011.4
19317130013.565001.11001011.4
19976105010.95250-1018510.9
19436125013.062501.1987510.8
19437125013.062501.11000010.8
19438125013.062501.11012510.8
2103475010.63750-1027510.6
20128100010.45000-1020010.4
19558120012.560001.2948010.1
19559120012.560001.2960010.1
2220050015.225002.836009.6
19318130013.565002.0101409.5
2142165017.232503.857859.5
2113370018.235004.418209.4
2229950014.925002.885509.3
2190555016.827503.836309.1
19319130017.565004.5102708.4
19439125015.062504.7102505.6
2224750013.225005.059503.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
19967105029.352501.3924026.7
19566120034.960004.91044025.1
19567120034.960004.91056025.1
19568120034.960004.91068025.1
2062885027.642501.6943524.3
20098100028.250002.4720023.4
19555120024.360001.2912022.0
2092075024.537501.3172521.8
2042490025.445002.7720020.1
2113170022.935001.4168020.0
20119100022.750001.4930019.9
20101100028.250004.2750019.8
19565120028.260004.91032018.3
19823110019.955001.3924017.4
2079180022.640003.0720016.6
2149865021.132502.31079016.5
2124470019.635002.0959015.6
2099375021.237503.2720014.8
2060785024.042504.9765014.1
19686115015.757501.2920013.3
2201655017.927502.5973512.8
2082080016.240001.8952012.7
2203755017.927502.71089012.4
19430125013.762501.1912511.5
19431125013.062501.1925010.8
19432125013.062501.1937510.8
19433125013.062501.1950010.8
19434125013.062501.1962510.8
19435125013.062501.1975010.8
2169560018.430004.0720010.4
19556120012.560001.2924010.1
19557120012.560001.2936010.1
19560120012.560001.2972010.1
19561120012.560001.2984010.1
19562120012.560001.2996010.1
19563120012.560001.21008010.1
19687115012.057501.293159.5
19688115012.057501.294309.5
19689115012.057501.295459.5
19690115012.057501.296609.5
19691115012.057501.297759.5
19692115012.057501.298909.5
19693115012.057501.2100059.5
19694115012.057501.2101209.5
2028095012.147501.594059.2
2044990012.345001.694509.2
19824110011.455001.393508.9
19825110011.455001.394608.9
19826110011.455001.395708.9
19827110011.455001.396808.9
19828110011.455001.397908.9
19829110011.455001.399008.9
19830110011.455001.3100108.9
19831110011.455001.3101208.9
19968105010.952501.393458.2
19969105010.952501.394508.2
19970105010.952501.395558.2
19971105010.952501.396608.2
19972105010.952501.397658.2
19973105010.952501.398708.2
19974105010.952501.399758.2
19975105010.952501.3100808.2
2148165012.232502.296857.9
20120100010.450001.494007.6
20121100010.450001.495007.6
20122100010.450001.496007.6
20123100010.450001.497007.6
20124100010.450001.498007.6
20125100010.450001.499007.6
20126100010.450001.4100007.6
20127100010.450001.4101007.6
2167260015.930004.258207.5
2173760012.130002.397207.5
2102575010.237501.996006.5
2194555015.227504.558306.1
2227250015.425004.872005.8
2232450011.425002.898005.8
2194655014.627504.558855.5
2224650013.225005.059003.2

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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