Markers + reference

Androsace

30 species · Primulaceae · Ericales

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Species 30
Genome length 149–154 kb
Candidate markers 270
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 716 0.0839 0.89 81.2 yes View details
rps16-trnQ-UUG LSC 1007 0.0603 0.78 79.7 yes View details
trnS-GCU-trnG-UCC LSC 685 0.0810 0.95 83.9 yes View details
rpoB-trnC-GCA LSC 1157 0.0569 0.97 83.5 yes View details
ycf1 IRb 1035 0.0222 0.98 69.6 no View details
ndhF-rpl32 SSC 685 0.0640 0.77 77.5 yes View details
rpl32-trnL-UAG SSC 725 0.0989 0.41 71.8 yes View details
ycf1 SSC 5445 0.0489 0.98 77.3 yes View details
trnF-GAA-ndhJ LSC 658 0.0492 0.98 87.1 yes View details
trnT-GGU-psbD LSC 1282 0.0446 0.97 86.1 yes View details
ndhC-trnV-UAC LSC 1093 0.0584 0.95 85.0 yes View details
trnT-UGU-trnL-UAA LSC 758 0.0481 0.97 84.5 yes View details
trnL-UAA-trnF-GAA LSC 392 0.0578 0.99 83.4 yes View details
psbE-petL LSC 1275 0.0534 0.96 83.2 yes View details
psaA-pafI LSC 686 0.0445 0.98 82.1 yes View details
rps16 LSC 1126 0.0445 0.97 81.3 yes View details
trnH-GUG-psbA LSC 234 0.0956 1.00 80.7 yes View details
trnG-UCC-trnR-UCU LSC 249 0.0690 1.00 80.6 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCGAT 228–486 1.000 90.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CTGCGATTGAAGCTCCATCT 215–473 0.967 89.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 231–489 0.967 89.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CTGCGATTGAAGCTCCATCT 216–474 0.967 89.0
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTCCCTCTAGACCTAGCTGC 232–490 0.967 88.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCGTGGCCTTTCAAACGTTA AAAAGGGTATGTTGCTGCCA 1428–1534 0.200 55.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGTGGCCTTTCAAACGTTAC CCCAATGAGCCGTTTATCGA 951–1063 0.167 54.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGTGGCCTTTCAAACGTTAC TCCCAATGAGCCGTTTATCG 952–1064 0.167 54.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGTGGCCTTTCAAACGTTAC AAAAGGGTATGTTGCTGCCA 1427–1533 0.167 54.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGGCCTTTCAAACGTTACCA AAAAGGGTATGTTGCTGCCA 1425–1531 0.167 54.0
rps16_p1 rps16 ACCACGCAATCCAAACATTG AGGGGTTGAAAGAATTGCGA 2380–2421 0.100 42.8
rps16_p2 rps16 TACCGTTGAGTTAGCAACCC AGGGGTTGAAAGAATTGCGA 2444–2485 0.100 42.6
rps16_p3 rps16 CCACGCAATCCAAACATTGA AGGGGTTGAAAGAATTGCGA 2379–2420 0.100 40.5
rps16_p4 rps16 ACTCATGTTGGATTGGCACT AGGGGTTGAAAGAATTGCGA 2066–2080 0.100 39.9
rps16_p5 rps16 CGTTGAGTTAGCAACCCGAA AGGGGTTGAAAGAATTGCGA 2481–2482 0.067 38.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 759–1085 0.967 83.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 762–1088 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 763–1089 0.967 79.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TGATCTCGGTATTCGGAGGT 774–1087 0.900 78.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA TGATCTCGGTATTCGGAGGT 777–1090 0.900 76.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TACCACTAAACTATACCCGC 568–763 1.000 54.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GATTCGAACCCTCGGTACAA TACCACTAAACTATACCCGC 619–814 1.000 54.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TTACCACTAAACTATACCCGC 569–764 1.000 53.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATTCGAACCCTCGGTACAA TTACCACTAAACTATACCCGC 620–815 1.000 53.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAAAGAGAGGGATTCGAA TACCACTAAACTATACCCGC 631–826 1.000 52.2
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 324–349 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 327–352 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 330–355 0.967 73.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 333–358 0.967 73.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 328–353 1.000 72.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (30)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Androsace axillaris NC_080505.1 151013 View on NCBI ↗
Androsace bulleyana NC_034641.1 152110 View on NCBI ↗
Androsace ciliifolia OM948749.1 152455 View on NCBI ↗
Androsace delavayi OM948774.1 153337 View on NCBI ↗
Androsace erecta NC_057637.1 153547 View on NCBI ↗
Androsace forrestiana OM948755.1 152382 View on NCBI ↗
Androsace geraniifolia OM948776.1 150825 View on NCBI ↗
Androsace globifera OM948773.1 153111 View on NCBI ↗
Androsace gmelinii var. geophila OM948771.1 149323 View on NCBI ↗
Androsace henryi NC_080506.1 149456 View on NCBI ↗
Androsace incana OM948764.1 153737 View on NCBI ↗
Androsace integra OM948752.1 152087 View on NCBI ↗
Androsace kouytchensis NC_080504.1 150792 View on NCBI ↗
Androsace laxa NC_039347.1 151942 View on NCBI ↗
Androsace limprichtii OM948753.1 152491 View on NCBI ↗
Androsace longifolia OM948766.1 152063 View on NCBI ↗
Androsace mariae NC_051991.1 151958 View on NCBI ↗
Androsace minor OM948751.1 153231 View on NCBI ↗
Androsace paxiana NC_034640.1 150528 View on NCBI ↗
Androsace rigida OM948758.1 151542 View on NCBI ↗
Androsace robusta OM948781.1 152656 View on NCBI ↗
Androsace selago OM948778.1 152156 View on NCBI ↗
Androsace spinulifera OM948754.1 153074 View on NCBI ↗
Androsace strigillosa OM948777.1 152499 View on NCBI ↗
Androsace sublanata OM948757.1 152136 View on NCBI ↗
Androsace tanggulashanensis OM948750.1 152606 View on NCBI ↗
Androsace tapete OM948760.1 152585 View on NCBI ↗
Androsace wardii OM948748.1 152108 View on NCBI ↗
Androsace yargongensis PP234566.1 152851 View on NCBI ↗
Androsace zambalensis OM948759.1 152727 View on NCBI ↗