Automated design of genomic Southern blot probes

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

Design Case - ProbeDesign54 - back to list

Summary

./analyse_probe_search_results : Mon Sep 26 11:58:27 2005

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

Fetched probe design: ProbeDesign54
  assembly      : NCBIM34
  bias          : 5prime
  chromosome    : 6
  id            : 36
  strand        : 1
  -------------

Design window length: 3001bp

All jobs for probe design are successful - total: 46
Fetched conf : Exonerate mouse_NCBIM34 (id: 1)
  Genome file(s) at: /blastdb/Mouse/NCBIM34/softmasked_dusted
Fetched 907 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        : 907/907
Putative probes exceeding selection criteria: 193/907

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
38802130041.76500-123541.7
38803130041.76500-130041.7
38804130041.76500-136541.7
38805130041.76500-143041.7
38806130041.76500-149541.7
38807130041.76500-156041.7
38808130041.76500-162541.7
38830125040.16250-124040.1
38831125040.16250-130240.1
38832125040.16250-136440.1
38833125040.16250-142640.1
38834125040.16250-148840.1
38835125040.16250-155040.1
38836125040.16250-161240.1
38860120038.56000-126038.5
38861120038.56000-132038.5
38862120038.56000-138038.5
38863120038.56000-144038.5
38864120038.56000-150038.5
38865120038.56000-156038.5
38866120038.56000-162038.5
38892115036.95750-125436.9
38893115036.95750-131136.9
38894115036.95750-136836.9
38895115036.95750-142536.9
38896115036.95750-148236.9
38897115036.95750-153936.9
38898115036.95750-159636.9
38859120038.560000.8120036.8
38801130041.765003.1117035.5
38925110035.35500-121035.3
38926110035.35500-126535.3
38927110035.35500-132035.3
38928110035.35500-137535.3
38929110035.35500-143035.3
38930110035.35500-148535.3
38931110035.35500-154035.3
38932110035.35500-159535.3
38829125040.162502.6117834.9
38891115036.957501.1119734.6
38962105033.75250-124833.7
38963105033.75250-130033.7
38964105033.75250-135233.7
38965105033.75250-140433.7
38966105033.75250-145633.7
38967105033.75250-150833.7
38968105033.75250-156033.7
38969105033.75250-161233.7
39001100032.15000-125032.1
39002100032.15000-130032.1
39003100032.15000-135032.1
39004100032.15000-140032.1
39005100032.15000-145032.1
39006100032.15000-150032.1
39007100032.15000-155032.1
39008100032.15000-160032.1
38961105033.752501.3119631.0
3904395030.44750-122230.4
3904495030.44750-126930.4
3904595030.44750-131630.4
3904695030.44750-136330.4
3904795030.44750-141030.4
3904895030.44750-145730.4
3904995030.44750-150430.4
3905095030.44750-155130.4
3905195030.44750-159830.4
39000100032.150001.0120030.1
3908890028.84500-121528.8
3908990028.84500-126028.8
3909090028.84500-130528.8
3909190028.84500-135028.8
3909290028.84500-139528.8
3909390028.84500-144028.8
3909490028.84500-148528.8
3909590028.84500-153028.8
3909690028.84500-157528.8
3909790028.84500-162028.8
3913785027.24250-121827.2
3913885027.24250-126027.2
3913985027.24250-130227.2
3914085027.24250-134427.2
3914185027.24250-138627.2
3914285027.24250-142827.2
3914385027.24250-147027.2
3914485027.24250-151227.2
3914585027.24250-155427.2
3914685027.24250-159627.2
3919180025.64000-124025.6
3919280025.64000-128025.6
3919380025.64000-132025.6
3919480025.64000-136025.6
3919580025.64000-140025.6
3919680025.64000-144025.6
3919780025.64000-148025.6
3919880025.64000-152025.6
3919980025.64000-156025.6
3920080025.64000-160025.6
38924110035.355005.0115525.3
3924975024.03750-122124.0
3925075024.03750-125824.0
3925175024.03750-129524.0
3925275024.03750-133224.0
3925375024.03750-136924.0
3925475024.03750-140624.0
3925575024.03750-144324.0
3925675024.03750-148024.0
3925775024.03750-151724.0
3925875024.03750-155424.0
3925975024.03750-159124.0
3926075024.03750-162824.0
3919080025.640001.2120023.1
3931270022.43500-122522.4
3931370022.43500-126022.4
3931470022.43500-129522.4
3931570022.43500-133022.4
3931670022.43500-136522.4
3931770022.43500-140022.4
3931870022.43500-143522.4
3931970022.43500-147022.4
3932070022.43500-150522.4
3932170022.43500-154022.4
3932270022.43500-157522.4
3932370022.43500-161022.4
3938165020.83250-121620.8
3938265020.83250-124820.8
3938365020.83250-128020.8
3938465020.83250-131220.8
3938565020.83250-134420.8
3938665020.83250-137620.8
3938765020.83250-140820.8
3938865020.83250-144020.8
3938965020.83250-147220.8
3939065020.83250-150420.8
3939165020.83250-153620.8
3939265020.83250-156820.8
3939365020.83250-160020.8
3939465020.83250-163220.8
3945860019.23000-123019.2
3945960019.23000-126019.2
3946060019.23000-129019.2
3946160019.23000-132019.2
3946260019.23000-135019.2
3946360019.23000-138019.2
3946460019.23000-141019.2
3946560019.23000-144019.2
3946660019.23000-147019.2
3946760019.23000-150019.2
3946860019.23000-153019.2
3946960019.23000-156019.2
3947060019.23000-159019.2
3947160019.23000-162019.2
3954355017.62750-121517.6
3954455017.62750-124217.6
3954555017.62750-126917.6
3954655017.62750-129617.6
3954755017.62750-132317.6
3954855017.62750-135017.6
3954955017.62750-137717.6
3955055017.62750-140417.6
3955155017.62750-143117.6
3955255017.62750-145817.6
3955355017.62750-148517.6
3955455017.62750-151217.6
3955555017.62750-153917.6
3955655017.62750-156617.6
3955755017.62750-159317.6
3955855017.62750-162017.6
3931170022.435002.9119016.7
3963850016.02500-122516.0
3963950016.02500-125016.0
3964050016.02500-127516.0
3964150016.02500-130016.0
3964250016.02500-132516.0
3964350016.02500-135016.0
3964450016.02500-137516.0
3964550016.02500-140016.0
3964650016.02500-142516.0
3964750016.02500-145016.0
3964850016.02500-147516.0
3964950016.02500-150016.0
3965050016.02500-152516.0
3965150016.02500-155016.0
3965250016.02500-157516.0
3965350016.02500-160016.0
3965450016.02500-162516.0
3945760019.230001.7120015.9
3963750016.025002.0120012.0

Overall score = score_ratio - 2 * repetitive DNA content

Redundant probes

Putative probe IDLengthScore ratioActual%rep DNADistanceOverall
3904295030.447503.7117523.1
3908790028.845004.4117020.0
3913685027.242504.0117619.2
3924875024.037503.5118417.1
3938065020.832504.0118412.8
3954255017.627504.011889.6

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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