General
The grID is a unique number given to a specific location in the genome.
The grID Score is an exponential scale indicating the "uniqueness" of the gRNA. The higher the score the more unique the target site in the genome. The scale is from 0-1000.
Summary
Genomic Context
gRNA location:
Gene: Exonic
Gene: Intronic
Intergenic
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Sequence Analysis
The target sequence is the 20 nucleotide ribonucleotide sequence that is incorporated into the gRNA.
Target Sequence Occurence:
Target Sequence Occurence can be either unique or non-unique.
PAM motif:
The PAM (Protospacer Adjacent Motif) sequence refers to the nucleotides adjacent to the target sequence, typically where high-affinity binding of Cas9 occurs. For S. pyogenes, the most commonly used Cas9, the connonical PAM Motif is 5'-NGG-3'; it has also been reported that 5'-NAG-3' can be targeted, albeit with lower efficiency, and can contribute to off-target hits.
Sequence Complexity:
Homopolymeric Runs:
This detects the presence of low-complexity sequences due to runs of nucleotides.
Pol III Terminator:
This detects the presence of a potential pol III terminator sequence.
Thermodynamic Properties
GC Content Scoring:
0 to 20: very low
20 to 40: low
40 to 60: moderate
60 to 80: high
80 to 100: very high
Tm Scoring:
0 to 20: very low
20 to 40: low
40 to 60: moderate
60 to 80: high
80 to 100: very high
RNA Secondary Structure:
0 to -2: very low secondary structure
-2 to -4: low secondary structure
-4 to -6: medium secondary structure
-6 to -8: high secondary structure
< -8: very high secondary structure
Offtarget Analysis
References