Hotspot

ccsA-trnL-UAG

SSC · 122672-122787 · 116 bp

Back to Orthosiphon

Pi 0.476

MarkerSeek score 76.20

Primer available yes

Label ccsA-trnL-UAG

Feature Metadata

label_name: ccsA-trnL-UAG
feature_type: igs
region: SSC
length_bp: 116
variable_sites: 50
pi: 0.476
unique_haplotype_count: 2
primer_available: yes
alignment_reliability: 0.91
markerseek_score: 76.20

Pi Curve

Haplotype Network

Species Separation

Primer Ranking

Primer ID	fwd_seq	rev_seq	fwd_gc	rev_gc	fwd_tm	rev_tm	amplicon_size	cross_species_success_rate	primer_score
ccsA-trnL-UAG_p1	AACCACTCGGATTGAAGAGC	TAGACACGCTGCTCTTAGGA	50.0	50.0	57.9	57.9	584 bp	0.5	58.2
ccsA-trnL-UAG_p2	AACCACTCGGATTGAAGAGC	ACAAGCCGCTATGGTGAAAT	50.0	45.0	57.9	57.9	607 bp	0.5	58.2
ccsA-trnL-UAG_p3	AACCACTCGGATTGAAGAGC	AAATTGGTAGACACGCTGCT	50.0	45.0	57.9	57.8	591 bp	0.5	57.7
ccsA-trnL-UAG_p4	AACCACTCGGATTGAAGAGC	GGTAGACACGCTGCTCTTAG	50.0	55.0	57.9	57.8	586 bp	0.5	57.6
ccsA-trnL-UAG_p5	AACCACTCGGATTGAAGAGC	GTAGACACGCTGCTCTTAGG	50.0	55.0	57.9	57.8	585 bp	0.5	57.6