OligoArray Design Parameters


This design was done using OligoArray version 3.1.0.


Option Usage Value
-aAuto parameters modeTrue
-ANot used
-bBlast database nameCP000733
-BNot used
-cUse complexity filterTrue
-CDNA concentration1e-06
-dFiles used to generate the blast databaseCP000733.gbk,CP000735.gbk
-DSearch space size3000
-eNot used
-ENot used
-fForward modeTrue
-FNot used
-gMinimum distance between probes 5' ends69
-GGrid-computation modeTrue
-hHelp availableYES
-HNot used
-iInput sequence fileCP000733.gbk,CP000735.gbk
-INot used
-jNot used
-JNot used
-kGenbank feature annotation requested3
-KGenbank feature requested1
-lMinimum probe length45
-LMaximum probe length47
-mProhibited sequencesGGGGG;CCCCC;TTTTT;AAAAA
-MMismatch modeFalse
-nMaximum number of probes requested per input sequence3
-NNumber of process to run in parallel1
-oOutput fileCoxiella_burnetii_Dugway_7E9-12_oligo.txt
-ONot used
-pMinimum probe %GC content34
-PMaximum probe %GC content50
-qNot used
-QNot used
-rRejected sequence fileCoxiella_burnetii_Dugway_7E9-12_rejected.fas
-RLog fileCoxiella_burnetii_Dugway_7E9-12.log
-sTemperature to fold a probe to detect secondary structures60
-SSodium concentration1
-tMinimum probe Tm80
-TMaximum probe Tm88
-uTranscript specific modeFalse
-UGene specific modeFalse
-vNot used
-VNot used
-wNot used
-WNot used
-xTemperature to start to consider cross-hybridization60
-XNot used
-yRequested length for the 5' linker sequence15
-YRequested length for the 3' linker sequence15
-zNot used
-ZNot used