Markers + reference

Heteropolygonatum

5 species · Asparagaceae · Asparagales

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Species 5
Genome length 156–156 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

10 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
trnS-GCU-trnG-UCC LSC 1332 0.0065 0.98 60.2 yes View details
rpoB-trnC-GCA LSC 1254 0.0069 0.99 50.3 yes View details
trnC-GCA-petN LSC 882 0.0098 1.00 56.3 yes View details
petA-psbJ LSC 1048 0.0069 1.00 63.5 yes View details
ycf2 IRb 6753 0.0013 1.00 54.4 yes View details
ycf1 IRb 897 0.0007 1.00 35.9 no View details
ccsA SSC 972 0.0039 1.00 37.1 yes View details
ndhG-ndhI SSC 380 0.0137 1.00 42.7 yes View details
ycf1 SSC 5439 0.0047 1.00 43.9 yes View details
ycf2 IRa 6753 0.0011 1.00 54.3 no View details
rps19-psbA LSC 104 0.0064 1.00 74.0 no View details
ndhC-trnV-UAC LSC 1663 0.0046 1.00 63.2 yes View details
ccsA-ndhD SSC 222 0.0279 1.00 61.4 yes View details
psbE-petL LSC 961 0.0019 1.00 61.1 yes View details
rps16-trnQ-UUG LSC 1280 0.0048 0.96 58.9 yes View details
psaI-ycf4 LSC 348 0.0103 1.00 58.9 yes View details
atpF-atpH LSC 499 0.0024 1.00 58.6 yes View details
rpoC1 LSC 2788 0.0021 1.00 57.7 yes View details
ndhF-rpl32 SSC 991 0.0067 1.00 56.9 yes View details
psbI-trnS-GCU LSC 115 0.0157 1.00 56.3 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1242–1353 1.000 83.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1253–1364 1.000 82.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1246–1357 1.000 78.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1272–1383 1.000 78.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1254–1365 1.000 77.9
psbI-trnS-GCU_p1 psbI-trnS-GCU CTTATCTAACGATCCGGGCC ATTGGGAGAGATGGCTGAGT 250–254 1.000 77.5
psbI-trnS-GCU_p2 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GGGTTCGAATCCCTCTCTCT 181–185 1.000 77.1
psbI-trnS-GCU_p3 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GTGGACTAAAGCGGCAGATT 232–236 1.000 76.4
psbI-trnS-GCU_p4 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TGGACTAAAGCGGCAGATTG 231–235 1.000 76.3
psbI-trnS-GCU_p5 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TTCGAATCCCTCTCTCTCCG 178–182 1.000 76.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCACT 531–1466 1.000 74.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AAGTGATCAGAGGGAACGGA ACGAATCGCACTTTTACCACT 535–1470 1.000 74.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATCAGAGGGAACGGAGAGAG ACGAATCGCACTTTTACCACT 530–1465 1.000 74.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCAC 530–1466 1.000 74.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AAGTGATCAGAGGGAACGGA ACGAATCGCACTTTTACCAC 534–1470 1.000 74.7
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 621–622 1.000 79.3
atpF-atpH_p2 atpF-atpH CAGTGGCCTAAGGAAACGAA ATTTATGGACTGGTCGTGGC 593–594 1.000 78.8
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 608–609 1.000 77.4
atpF-atpH_p4 atpF-atpH CAGTGGCCTAAGGAAACGAA TCGTGGCATTAGCGCTTTTA 580–581 1.000 76.9
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CGTGGCATTAGCGCTTTTAT 607–608 1.000 73.5
rpoC1_p1 rpoC1 GGCACCGGTATCGTCTAATC TTGCTCGTTCGAGAACTACG 1848–2939 1.000 79.7
rpoC1_p2 rpoC1 GCACCGGTATCGTCTAATCG TTGCTCGTTCGAGAACTACG 1847–2938 1.000 77.7
rpoC1_p3 rpoC1 GGCACCGGTATCGTCTAATC GCTCGTTCGAGAACTACGAT 1847–2937 1.000 76.4
rpoC1_p4 rpoC1 TTGGATAGACCCGTCTTCCC TTGCTCGTTCGAGAACTACG 1871–2962 1.000 76.1
rpoC1_p5 rpoC1 GCACCGGTATCGTCTAATCG GCTCGTTCGAGAACTACGAT 1846–2936 1.000 74.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CGCCAAGCCCTGATTAATGA TAAAGGATTTGCAGTCCCCC 1385–1394 1.000 75.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATTCCGGA TAAAGGATTTGCAGTCCCCC 1313–1322 1.000 74.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCCCTCATTTCCATTCCGG TAAAGGATTTGCAGTCCCCC 1314–1323 1.000 74.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGCCAAGCCCTGATTAATGA TTTGTTGATCAGGCGACACC 1422–1431 1.000 73.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGCCAAGCCCTGATTAATGA GACACCCGGATTTGAACTGG 1408–1417 1.000 72.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Heteropolygonatum alternicirrhosum NC_058552.1 155944 View on NCBI ↗
Heteropolygonatum binatifolium NC_088740.1 155510 View on NCBI ↗
Heteropolygonatum ginfushanicum NC_057220.1 155508 View on NCBI ↗
Heteropolygonatum ogisui NC_058553.1 155665 View on NCBI ↗
Heteropolygonatum pendulum PV087152.1 155943 View on NCBI ↗