Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign50 - back to list

Summary

./analyse_probe_search_results : Mon Sep 26 11:52:39 2005

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

Fetched probe design: ProbeDesign50
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 6
  id            : 32
  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 699 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        : 699/699
Putative probes exceeding selection criteria: 384/699

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
34012130042.26500-78042.2
34013130042.26500-84542.2
34014130042.26500-91042.2
34015130042.26500-97542.2
34016130042.26500-104042.2
34017130042.26500-110542.2
34018130042.26500-117042.2
34031125040.66250-74440.6
34032125040.66250-80640.6
34033125040.66250-86840.6
34034125040.66250-93040.6
34035125040.66250-99240.6
34036125040.66250-105440.6
34037125040.66250-111640.6
34038125040.66250-117840.6
34039125040.66250-124040.6
34008130039.46500-52039.4
34009130039.46500-58539.4
34010130039.46500-65039.4
34011130039.46500-71539.4
34053120039.06000-78039.0
34054120039.06000-84039.0
34055120039.06000-90039.0
34056120039.06000-96039.0
34057120039.06000-102039.0
34058120039.06000-108039.0
34059120039.06000-114039.0
34060120039.06000-120039.0
34061120039.06000-126039.0
34027125037.96250-49637.9
34028125037.96250-55837.9
34029125037.96250-62037.9
34030125037.96250-68237.9
34076115037.35750-79837.3
34077115037.35750-85537.3
34078115037.35750-91237.3
34079115037.35750-96937.3
34080115037.35750-102637.3
34081115037.35750-108337.3
34082115037.35750-114037.3
34083115037.35750-119737.3
34084115037.35750-125437.3
34085115037.35750-131137.3
34049120036.46000-54036.4
34050120036.46000-60036.4
34051120036.46000-66036.4
34052120036.46000-72036.4
34075115036.25750-74136.2
34100110035.75500-77035.7
34101110035.75500-82535.7
34102110035.75500-88035.7
34103110035.75500-93535.7
34104110035.75500-99035.7
34105110035.75500-104535.7
34106110035.75500-110035.7
34107110035.75500-115535.7
34108110035.75500-121035.7
34109110035.75500-126535.7
34110110035.75500-132035.7
34111110035.75500-137535.7
34048120036.460000.448035.5
34071115034.85750-51334.8
34072115034.85750-57034.8
34073115034.85750-62734.8
34074115034.85750-68434.8
34007130039.465002.345534.8
34127105034.15250-78034.1
34128105034.15250-83234.1
34129105034.15250-88434.1
34130105034.15250-93634.1
34131105034.15250-98834.1
34132105034.15250-104034.1
34133105034.15250-109234.1
34134105034.15250-114434.1
34135105034.15250-119634.1
34136105034.15250-124834.1
34137105034.15250-130034.1
34138105034.15250-135234.1
34139105034.15250-140434.1
34095110033.35500-49533.3
34096110033.35500-55033.3
34097110033.35500-60533.3
34098110033.35500-66033.3
34099110033.35500-71533.3
34155100032.55000-75032.5
34156100032.55000-80032.5
34157100032.55000-85032.5
34158100032.55000-90032.5
34159100032.55000-95032.5
34160100032.55000-100032.5
34161100032.55000-105032.5
34162100032.55000-110032.5
34163100032.55000-115032.5
34164100032.55000-120032.5
34165100032.55000-125032.5
34166100032.55000-130032.5
34167100032.55000-135032.5
34168100032.55000-140032.5
34169100032.55000-145032.5
34170100032.55000-150032.5
34122105031.85250-52031.8
34123105031.85250-57231.8
34124105031.85250-62431.8
34125105031.85250-67631.8
34126105031.85250-72831.8
3418795030.84750-75230.8
3418895030.84750-79930.8
3418995030.84750-84630.8
3419095030.84750-89330.8
3419195030.84750-94030.8
3419295030.84750-98730.8
3419395030.84750-103430.8
3419495030.84750-108130.8
3419595030.84750-112830.8
3419695030.84750-117530.8
3419795030.84750-122230.8
3419895030.84750-126930.8
3419995030.84750-131630.8
3420095030.84750-136330.8
3420195030.84750-141030.8
3420295030.84750-145730.8
3420395030.84750-150430.8
34150100030.35000-50030.3
34151100030.35000-55030.3
34152100030.35000-60030.3
34153100030.35000-65030.3
34154100030.35000-70030.3
34026125037.962504.143429.7
3422290029.24500-81029.2
3422390029.24500-85529.2
3422490029.24500-90029.2
3422590029.24500-94529.2
3422690029.24500-99029.2
3422790029.24500-103529.2
3422890029.24500-108029.2
3422990029.24500-112529.2
3423090029.24500-117029.2
3423190029.24500-121529.2
3423290029.24500-126029.2
3423390029.24500-130529.2
3423490029.24500-135029.2
3423590029.24500-139529.2
3423690029.24500-144029.2
3423790029.24500-148529.2
3423890029.24500-153029.2
3423990029.24500-157529.2
3418295028.84750-51728.8
3418395028.84750-56428.8
3418495028.84750-61128.8
3418595028.84750-65828.8
3418695028.84750-70528.8
34121105031.852501.646828.6
3426185027.64250-88227.6
3426285027.64250-92427.6
3426385027.64250-96627.6
3426485027.64250-100827.6
3426585027.64250-105027.6
3426685027.64250-109227.6
3426785027.64250-113427.6
3426885027.64250-117627.6
3426985027.64250-121827.6
3427085027.64250-126027.6
3427185027.64250-130227.6
3427285027.64250-134427.6
3427385027.64250-138627.6
3427485027.64250-142827.6
3427585027.64250-147027.6
3427685027.64250-151227.6
3427785027.64250-155427.6
3427885027.64250-159627.6
3427985027.64250-163827.6
3421590027.34500-49527.3
3421690027.34500-54027.3
3421790027.34500-58527.3
3421890027.34500-63027.3
3421990027.34500-67527.3
3422090027.34500-72027.3
3430380026.04000-92026.0
3430480026.04000-96026.0
3430580026.04000-100026.0
3430680026.04000-104026.0
3430780026.04000-108026.0
3430880026.04000-112026.0
3430980026.04000-116026.0
3431080026.04000-120026.0
3431180026.04000-124026.0
3431280026.04000-128026.0
3431380026.04000-132026.0
3431480026.04000-136026.0
3431580026.04000-140026.0
3431680026.04000-144026.0
3431780026.04000-148026.0
3431880026.04000-152026.0
3431980026.04000-156026.0
3432080026.04000-160026.0
3432180026.04000-164026.0
3425285025.84250-50425.8
3425385025.84250-54625.8
3425485025.84250-58825.8
3425585025.84250-63025.8
3425685025.84250-67225.8
3425785025.84250-71425.8
3418195028.847501.647025.6
3434975024.43750-96224.4
3435075024.43750-99924.4
3435175024.43750-103624.4
3435275024.43750-107324.4
3435375024.43750-111024.4
3435475024.43750-114724.4
3435575024.43750-118424.4
3435675024.43750-122124.4
3435775024.43750-125824.4
3435875024.43750-129524.4
3435975024.43750-133224.4
3436075024.43750-136924.4
3436175024.43750-140624.4
3436275024.43750-144324.4
3436375024.43750-148024.4
3436475024.43750-151724.4
3436575024.43750-155424.4
3436675024.43750-159124.4
3436775024.43750-162824.4
3429380024.24000-52024.2
3429480024.24000-56024.2
3429580024.24000-60024.2
3429680024.24000-64024.2
3429780024.24000-68024.2
3429880024.24000-72024.2
3434375023.63750-74023.6
34149100030.350003.545023.3
3441870023.03500-164523.0
3429280024.240000.648023.0
3433775022.73750-51822.7
3433875022.73750-55522.7
3433975022.73750-59222.7
3434075022.73750-62922.7
3434175022.73750-66622.7
3434275022.73750-70322.7
3440070022.73500-101522.7
3440170022.73500-105022.7
3440270022.73500-108522.7
3440370022.73500-112022.7
3440470022.73500-115522.7
3440570022.73500-119022.7
3440670022.73500-122522.7
3440770022.73500-126022.7
3440870022.73500-129522.7
3440970022.73500-133022.7
3441070022.73500-136522.7
3441170022.73500-140022.7
3441270022.73500-143522.7
3441370022.73500-147022.7
3441470022.73500-150522.7
3441570022.73500-154022.7
3441670022.73500-157522.7
3441770022.73500-161022.7
3433675022.737500.548121.7
3439270021.33500-73521.3
3438570021.23500-49021.2
3438670021.23500-52521.2
3438770021.23500-56021.2
3438870021.23500-59521.2
3438970021.23500-63021.2
3439070021.23500-66521.2
3439170021.23500-70021.2
3445665021.13250-105621.1
3445765021.13250-108821.1
3445865021.13250-112021.1
3445965021.13250-115221.1
3446065021.13250-118421.1
3446165021.13250-121621.1
3446265021.13250-124821.1
3446365021.13250-128021.1
3446465021.13250-131221.1
3446565021.13250-134421.1
3446665021.13250-137621.1
3446765021.13250-140821.1
3446865021.13250-144021.1
3446965021.13250-147221.1
3447065021.13250-150421.1
3447165021.13250-153621.1
3447265021.13250-156821.1
3447365021.13250-160021.1
3447465021.13250-163221.1
3444665019.93250-73619.9
3443965019.73250-51219.7
3444065019.73250-54419.7
3444165019.73250-57619.7
3444265019.73250-60819.7
3444365019.73250-64019.7
3444465019.73250-67219.7
3444565019.73250-70419.7
3421490027.345003.945019.5
3451860019.53000-111019.5
3451960019.53000-114019.5
3452060019.53000-117019.5
3452160019.53000-120019.5
3452260019.53000-123019.5
3452360019.53000-126019.5
3452460019.53000-129019.5
3452560019.53000-132019.5
3452660019.53000-135019.5
3452760019.53000-138019.5
3452860019.53000-141019.5
3452960019.53000-144019.5
3453060019.53000-147019.5
3453160019.53000-150019.5
3453260019.53000-153019.5
3453360019.53000-156019.5
3453460019.53000-159019.5
3453560019.53000-162019.5
3460655018.22750-164718.2
3449860018.23000-51018.2
3449960018.23000-54018.2
3450060018.23000-57018.2
3450160018.23000-60018.2
3450260018.23000-63018.2
3450360018.23000-66018.2
3450460018.23000-69018.2
3450560018.23000-72018.2
3443865019.732500.848018.2
3458855017.92750-116117.9
3458955017.92750-118817.9
3459055017.92750-121517.9
3459155017.92750-124217.9
3459255017.92750-126917.9
3459355017.92750-129617.9
3459455017.92750-132317.9
3459555017.92750-135017.9
3459655017.92750-137717.9
3459755017.92750-140417.9
3459855017.92750-143117.9
3459955017.92750-145817.9
3460055017.92750-148517.9
3460155017.92750-151217.9
3460255017.92750-153917.9
3460355017.92750-156617.9
3460455017.92750-159317.9
3460555017.92750-162017.9
3456355016.72750-48616.7
3456455016.72750-51316.7
3456555016.72750-54016.7
3456655016.72750-56716.7
3456755016.72750-59416.7
3456855016.72750-62116.7
3456955016.72750-64816.7
3457055016.72750-67516.7
3457155016.72750-70216.7
3457255016.72750-72916.7
3449760018.230000.848016.5
3466650016.22500-120016.2
3466750016.22500-122516.2
3466850016.22500-125016.2
3466950016.22500-127516.2
3467050016.22500-130016.2
3467150016.22500-132516.2
3467250016.22500-135016.2
3467350016.22500-137516.2
3467450016.22500-140016.2
3467550016.22500-142516.2
3467650016.22500-145016.2
3467750016.22500-147516.2
3467850016.22500-150016.2
3467950016.22500-152516.2
3468050016.22500-155016.2
3468150016.22500-157516.2
3468250016.22500-160016.2
3468350016.22500-162516.2
3463850015.22500-50015.2
3463950015.22500-52515.2
3464050015.22500-55015.2
3464150015.22500-57515.2
3464250015.22500-60015.2
3464350015.22500-62515.2
3464450015.22500-65015.2
3464550015.22500-67515.2
3464650015.22500-70015.2
3464750015.22500-72515.2
3463750015.225002.047511.2

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
34070115034.857502.545629.8
34094110033.355004.144025.2
3425185025.842502.746220.3
3438470021.235004.345512.6
3456255016.727504.74597.2

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).

Cookies Policy | Terms and Conditions. This site is hosted by Edinburgh University and the Genes to Cognition Programme.