Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign20 - back to list

Summary

./analyse_probe_search_results : Tue Dec 19 12:00:58 2006

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

Fetched probe design: ProbeDesign20
  assembly      : NCBIM36
  bias          : 5prime
  chromosome    : 16
  id            : 2
  strand        : 1
  -------------

Design window length: 3171bp

All jobs for probe design are successful - total: 49
Fetched conf : Exonerate mouse_NCBIM36 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM36/genome/softmasked_dusted
Fetched 974 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            : 974/974
Putative probes that are unique                 : 49/974
Putative probes exceeding selection criteria    : 581/974 (both unique and not unique)
Putative probes with successfully-picked primers: 500/581

Identified 301 '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
17707003500-1260
17717003500-1295
18086503250-96
18096503250-128
18456503250-1280
18466503250-1312
18476503250-1344
18876003000-90
18886003000-120
18896003000-150
18906003000-180
19266003000-1260
19276003000-1290
19286003000-1320
19296003000-1350
19306003000-1380
19735502750-81
19745502750-108
19755502750-135
19765502750-162
19775502750-189
19785502750-216
20175502750-1269
20185502750-1296
20195502750-1323
20205502750-1350
20215502750-1377
20225502750-1404
20235502750-1431
20725002500-100
20735002500-125
20745002500-150
20755002500-175
20765002500-200
20775002500-225
20785002500-250
20795002500-275
21185002500-1250
21195002500-1275
21205002500-1300
21215002500-1325
21225002500-1350
21235002500-1375
21245002500-1400
21255002500-1425
21265002500-1450
21275002500-1475
21285002500-1500
21745002500-2650

Putative probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
145595028.84750-9428.8
150390028.54500-9028.5
150490027.34500-13527.3
150590027.345000.118027.1
155485026.94250-8426.9
155585026.94250-12626.9
155685026.94250-16826.9
1410100026.35000-5026.3
145695028.847501.314126.3
1368105026.05250-026.0
1201130029.065001.5025.9
1202130029.065001.56525.9
1203130029.065001.513025.9
1204130029.065001.519525.9
1205130029.065001.526025.9
1206130029.065001.532525.9
1207130029.065001.539025.9
1208130029.065001.545525.9
1209130029.065001.552025.9
1210130029.065001.558525.9
1211130029.065001.565025.9
1212130029.065001.571525.9
155785025.84250-21025.8
161080025.34000-8025.3
161180025.34000-12025.3
161280025.34000-16025.3
161380025.34000-20025.3
145495025.04750-4725.0
1409100024.85000-024.8
1231125027.962501.66224.7
1232125027.962501.612424.7
1233125027.962501.618624.7
1234125027.962501.624824.7
161480024.24000-24024.2
170275024.03750-125824.0
161580024.240000.128024.0
167075023.73750-7423.7
167175023.73750-11123.7
167275023.73750-14823.7
167375023.73750-18523.7
167475023.73750-22223.7
167575023.73750-25923.7
145395023.54750-023.5
150290023.44500-4523.4
167675022.73750-29622.7
150190022.34500-022.3
173770022.23500-10522.2
173870022.23500-14022.2
173970022.23500-17522.2
174070022.23500-21022.2
174170022.23500-24522.2
174270022.23500-28022.2
174370022.23500-31522.2
155385022.14250-4222.1
173670021.73500-7021.7
184465021.73250-124821.7
167775022.737500.533321.7
174470021.23500-35021.2
155285021.04250-021.0
181065020.63250-16020.6
181165020.63250-19220.6
181265020.63250-22420.6
181365020.63250-25620.6
181465020.63250-28820.6
181565020.63250-32020.6
181665020.63250-35220.6
160980020.44000-4020.4
173375020.33750-240520.3
152690020.14500-112520.1
160880019.84000-019.8
181765019.73250-38419.7
181865019.73250-41619.7
174570021.235000.938519.5
193160019.23000-141019.2
166975019.13750-3719.1
189160019.03000-21019.0
189260019.03000-24019.0
189360019.03000-27019.0
189460019.03000-30019.0
189560019.03000-33019.0
189660019.03000-36019.0
189760019.03000-39019.0
189860019.03000-42019.0
157985019.04250-113419.0
158085019.04250-117619.0
180370018.93500-241518.9
180470018.93500-245018.9
166875018.63750-018.6
1213130021.665001.578018.5
180765018.33250-6418.3
189960018.23000-45018.2
197955018.12750-24318.1
173570017.93500-3517.9
163680017.94000-112017.9
163780017.94000-116017.9
163880017.94000-120017.9
190060018.230000.248017.8
180270018.935000.6238017.8
176970017.83500-122517.8
202455017.62750-145817.6
188065017.63250-240017.6
188165017.63250-243217.6
188265017.63250-246417.6
188365017.63250-249617.6
198055017.42750-27017.4
198155017.42750-29717.4
198255017.42750-32417.4
198355017.42750-35117.4
198455017.42750-37817.4
198555017.42750-40517.4
198655017.42750-43217.4
198755017.42750-45917.4
173470017.33500-017.3
157885019.042500.8109217.3
170175017.33750-122117.3
188660017.13000-6017.1
192560017.13000-123017.1
169875016.73750-111016.7
169975016.73750-114716.7
170075016.73750-118416.7
198855016.72750-48616.7
198955016.72750-51316.7
1431100016.65000-110016.6
1276120019.960001.790016.6
180665016.63250-3216.6
207150016.42500-7516.4
201655016.42750-124216.4
196460016.23000-240016.2
196560016.23000-243016.2
196660016.23000-246016.2
196760016.23000-249016.2
196860016.23000-252016.2
196960016.23000-255016.2
180565016.13250-016.1
173275020.337502.1236816.0
208050015.92500-30015.9
208150015.82500-32515.8
208250015.82500-35015.8
208350015.82500-37515.8
208450015.82500-40015.8
208550015.82500-42515.8
208650015.82500-45015.8
208750015.82500-47515.8
208850015.82500-50015.8
147795015.84750-112815.8
208950015.72500-52515.7
176670015.63500-112015.6
176770015.63500-115515.6
176870015.63500-119015.6
188560015.33000-3015.3
209050015.22500-55015.2
209150015.22500-57515.2
163980015.04000-124015.0
152790015.04500-117015.0
197255014.92750-5414.9
205955014.92750-240314.9
206055014.92750-243014.9
206155014.92750-245714.9
206255014.92750-248414.9
206355014.92750-251114.9
206455014.92750-253814.9
206555014.92750-256514.9
206655014.92750-259214.9
206755014.92750-261914.9
188460014.93000-014.9
184865014.83250-137614.8
1244125020.862503.086814.7
177270014.63500-133014.6
1348110018.355001.899014.6
184065014.53250-112014.5
184165014.53250-115214.5
184265014.53250-118414.5
184365014.53250-121614.5
158185014.14250-121814.1
197155014.02750-2714.0
1388105017.452501.9104013.6
197055013.62750-013.6
217350013.62500-262513.6
216450013.52500-240013.5
216550013.52500-242513.5
216650013.52500-245013.5
216750013.52500-247513.5
216850013.52500-250013.5
216950013.52500-252513.5
217050013.52500-255013.5
217150013.52500-257513.5
217250013.52500-260013.5
192160013.43000-111013.4
192260013.43000-114013.4
192360013.43000-117013.4
192460013.43000-120013.4
164080013.34000-128013.3
207050013.22500-5013.2
170375013.03750-129513.0
166780018.840003.0236012.8
206950012.82500-2512.8
211750012.72500-122512.7
187965017.632502.5236812.6
170475012.53750-133212.5
206850012.42500-012.4
1311115019.157503.496912.3
201155012.32750-110712.3
201255012.32750-113412.3
201355012.32750-116112.3
201455012.32750-118812.3
201555012.32750-121512.3
205855014.927501.5237612.0
158285014.142501.2126011.8
212950011.72500-152511.7
177370011.63500-136511.6
177470011.63500-140011.6
152890015.045001.7121511.6
1214130021.665005.084511.6
196360016.230002.3237011.5
193260011.33000-144011.3
211250011.22500-110011.2
211350011.22500-112511.2
211450011.22500-115011.2
211550011.22500-117511.2
211650011.22500-120011.2
184965010.83250-140810.8
185065010.83250-144010.8
202555010.62750-148510.6
147895015.847502.6117510.5
216350013.525001.823759.9
164180013.340002.513208.3
1389105017.452504.710928.1
170575012.537502.513697.4
1432100016.650005.011506.6
185165010.832503.414724.0
177570011.635005.014351.6

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
1262120031.960001.76028.6
1230125030.962501.6027.7
1295115030.657501.75727.1
1296115030.657501.711427.1
1261120029.760001.7026.4
1411100030.350002.010026.3
1331110029.355001.85525.6
1332110029.355001.811025.6
1333110029.355001.816525.6
1294115028.557501.7025.0
1235125027.962501.631024.7
1236125027.962501.637224.7
1237125027.962501.643424.7
1238125027.962501.649624.7
1239125027.962501.655824.7
1240125027.962501.662024.7
1241125027.962501.668224.7
1242125027.962501.674424.7
1370105027.952501.910424.1
1371105027.952501.915624.1
1372105027.952501.920824.1
1369105027.652501.95223.8
1330110027.255001.8023.6
1263120026.860001.712023.5
1264120026.860001.718023.5
1265120026.860001.724023.5
1266120026.860001.730023.5
1267120026.860001.736023.5
1268120026.860001.742023.5
1269120026.860001.748023.5
1270120026.860001.754023.5
1271120026.860001.760023.5
1272120026.860001.766023.5
1273120026.860001.772023.5
1274120026.860001.778023.5
1412100026.650002.015022.6
1413100026.650002.020022.6
1414100026.650002.025022.6
1297115025.757501.717122.2
1298115025.757501.722822.2
1299115025.757501.728522.2
1300115025.757501.734222.2
1301115025.757501.739922.2
1302115025.757501.745622.2
1303115025.757501.751322.2
1304115025.757501.757022.2
1305115025.757501.762722.2
1306115025.757501.768422.2
1307115025.757501.774122.2
1308115025.757501.779822.2
1309115025.757501.785522.2
145795026.147502.118821.9
150690025.645002.222521.1
145895025.347502.123521.1
145995025.347502.128221.1
155885025.842502.425221.1
1334110024.655001.822020.9
1335110024.655001.827520.9
1336110024.655001.833020.9
1337110024.655001.838520.9
1338110024.655001.844020.9
1339110024.655001.849520.9
1340110024.655001.855020.9
1341110024.655001.860520.9
1342110024.655001.866020.9
1343110024.655001.871520.9
1344110024.655001.877020.9
1345110024.655001.882520.9
1346110024.655001.888020.9
1373105023.452501.926019.6
1374105023.452501.931219.6
1375105023.452501.936419.6
1376105023.452501.941619.6
1377105023.452501.946819.6
1378105023.452501.952019.6
1379105023.452501.957219.6
1380105023.452501.962419.6
1381105023.452501.967619.6
1382105023.452501.972819.6
1383105023.452501.978019.6
1384105023.452501.983219.6
1385105023.452501.988419.6
1386105023.452501.993619.6
150790023.945002.227019.5
150890023.945002.231519.5
150990023.945002.236019.5
1275120022.660001.784019.2
161680023.440002.532018.4
1415100022.350002.030018.3
1416100022.350002.035018.3
1417100022.350002.040018.3
1418100022.350002.045018.3
1419100022.350002.050018.3
1420100022.350002.055018.3
1421100022.350002.060018.3
1422100022.350002.065018.3
1423100022.350002.070018.3
1424100022.350002.075018.3
1425100022.350002.080018.3
1426100022.350002.085018.3
1427100022.350002.090018.3
1428100022.350002.095018.3
1429100022.350002.0100018.3
155985022.642502.429417.9
156085022.642502.433617.9
156185022.642502.437817.9
1347110021.255001.893517.6
146095021.847502.132917.6
1243125020.862501.680617.6
156285021.842502.442017.1
146195021.247502.137617.0
146295021.247502.142317.0
146395021.247502.147017.0
146495021.247502.151717.0
146595021.247502.156417.0
146695021.247502.161117.0
146795021.247502.165817.0
146895021.247502.170517.0
146995021.247502.175217.0
147095021.247502.179917.0
147195021.247502.184617.0
147295021.247502.189317.0
147395021.247502.194017.0
147495021.247502.198717.0
147595021.247502.1103417.0
167875021.937502.737016.6
161780021.340002.536016.3
161880021.340002.540016.3
161980021.340002.544016.3
1387105019.852501.998816.0
152590020.145002.1108015.9
147695019.547501.9108115.7
151090020.145002.240515.6
151190020.145002.245015.6
151290020.145002.249515.6
151390020.145002.254015.6
151490020.145002.258515.6
151590020.145002.263015.6
151690020.145002.267515.6
151790020.145002.272015.6
151890020.145002.276515.6
151990020.145002.281015.6
152090020.145002.285515.6
152190020.145002.290015.6
152290020.145002.294515.6
152390020.145002.299015.6
152490020.145002.2103515.6
1310115019.157501.791215.6
174670020.535002.942014.8
167975019.937502.740714.6
168075019.937502.744414.6
168175019.937502.748114.6
168275019.737502.751814.4
156385019.042502.446214.3
156485019.042502.450414.3
156585019.042502.454614.3
156685019.042502.458814.3
156785019.042502.463014.3
156885019.042502.467214.3
156985019.042502.471414.3
157085019.042502.475614.3
157185019.042502.479814.3
157285019.042502.484014.3
157385019.042502.488214.3
157485019.042502.492414.3
157585019.042502.496614.3
157685019.042502.4100814.3
157785019.042502.4105014.3
181965019.732502.944813.9
162080018.340002.548013.3
163580017.940002.4108013.1
174770018.635002.945512.9
174870018.635002.949012.9
174970018.635002.952512.9
175070018.635002.956012.9
162180017.940002.552012.9
162280017.940002.556012.9
162380017.940002.560012.9
162480017.940002.564012.9
162580017.940002.568012.9
162680017.940002.572012.9
162780017.940002.576012.9
162880017.940002.580012.9
162980017.940002.584012.9
163080017.940002.588012.9
163180017.940002.592012.9
163280017.940002.596012.9
163380017.940002.5100012.9
163480017.940002.5104012.9
1430100016.750002.0105012.7
199055016.727502.054012.7
176570015.635002.0108511.6
182065017.632503.148011.4
168375016.737502.755511.4
168475016.737502.759211.4
168575016.737502.762911.4
168675016.737502.766611.4
168775016.737502.770311.4
168875016.737502.774011.4
168975016.737502.777711.4
169075016.737502.781411.4
169175016.737502.785111.4
169275016.737502.788811.4
169375016.737502.792511.4
169475016.737502.796211.4
169575016.737502.799911.4
169675016.737502.7103611.4
169775016.737502.7107311.4
182165017.332503.151211.1
182265017.332503.154411.1
182365017.332503.157611.1
182465017.332503.160811.1
183965014.532501.7108811.1
190160017.630003.351011.0
175170015.635002.95959.9
175270015.635002.96309.9
175370015.635002.96659.9
175470015.635002.97009.9
175570015.635002.97359.9
175670015.635002.97709.9
175770015.635002.98059.9
175870015.635002.98409.9
175970015.635002.98759.9
176070015.635002.99109.9
176170015.635002.99459.9
176270015.635002.99809.9
176370015.635002.910159.9
176470015.635002.910509.9
190260016.530003.35409.8
190360016.030003.35709.3
190460016.030003.36009.3
190560016.030003.36309.3
190660016.030003.36609.3
199155016.127503.65678.8
182565014.532503.16408.4
182665014.532503.16728.4
182765014.532503.17048.4
182865014.532503.17368.4
182965014.532503.17688.4
183065014.532503.18008.4
183165014.532503.18328.4
183265014.532503.18648.4
183365014.532503.18968.4
183465014.532503.19288.4
183565014.532503.19608.4
183665014.532503.19928.4
183765014.532503.110248.4
183865014.532503.110568.4
199255014.627503.65947.4
199355014.627503.66217.4
199455014.627503.66487.4
199555014.627503.66757.4
199655014.627503.67027.4
209250015.225004.06007.2
192060013.430003.210807.1
190760013.430003.36906.7
190860013.430003.37206.7
190960013.430003.37506.7
191060013.430003.37806.7
191160013.430003.38106.7
191260013.430003.38406.7
191360013.430003.38706.7
191460013.430003.39006.7
191560013.430003.39306.7
191660013.430003.39606.7
191760013.430003.39906.7
191860013.430003.310206.7
191960013.430003.310506.7
209350014.225004.06256.2
201055012.327503.510805.4
199755012.627503.67295.3
209450013.325004.06505.3
209550013.325004.06755.3
209650013.325004.07005.3
209750013.325004.07255.3
209850013.325004.07505.3
199855012.327503.67565.0
199955012.327503.67835.0
200055012.327503.68105.0
200155012.327503.68375.0
200255012.327503.68645.0
200355012.327503.68915.0
200455012.327503.69185.0
200555012.327503.69455.0
200655012.327503.69725.0
200755012.327503.69995.0
200855012.327503.610265.0
200955012.327503.610535.0
209950012.425004.07754.4
210050011.225004.08003.2
210150011.225004.08253.2
210250011.225004.08503.2
210350011.225004.08753.2
210450011.225004.09003.2
210550011.225004.09253.2
210650011.225004.09503.2
210750011.225004.09753.2
210850011.225004.010003.2
210950011.225004.010253.2
211050011.225004.010503.2
211150011.225004.010753.2

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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