Markers + reference

Hellenia

2 species · Costaceae · Zingiberales

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Species 2
Genome length 168–168 kb
Candidate markers 277
Primer pairs 100

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 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1676 0.0031 0.97 62.9 yes View details
atpH-atpI LSC 1523 0.0014 0.97 62.8 yes View details
rpoC1 LSC 2899 0.0010 0.99 57.2 yes View details
petN-psbM LSC 1393 0.0051 0.98 63.3 yes View details
trnF-GAA-ndhJ LSC 755 0.0040 1.00 48.5 yes View details
petA-psbJ LSC 1024 0.0029 0.99 61.0 yes View details
rpl16 LSC 2235 0.0038 0.95 64.1 yes View details
ycf1 IRb 1240 0.0008 1.00 59.2 no View details
ccsA-ndhD SSC 916 0.0085 0.90 66.9 yes View details
ycf1 SSC 5535 0.0014 1.00 53.3 yes View details
matK-trnK-UUU LSC 825 0.0097 1.00 64.3 yes View details
psaC-ndhE SSC 1253 0.0008 0.96 63.4 yes View details
accD-psaI LSC 937 0.0022 0.97 63.1 yes View details
rpl32-trnL-UAG SSC 892 0.0000 0.92 62.9 yes View details
trnT-UGU-trnL-UAA LSC 1036 0.0010 0.98 61.3 yes View details
atpF-atpH LSC 529 0.0019 0.97 61.1 yes View details
ndhF-rpl32 SSC 934 0.0022 0.99 60.6 yes View details
rbcL-accD LSC 820 0.0000 0.99 60.2 yes View details
atpB-rbcL LSC 829 0.0024 1.00 60.1 yes View details
trnC-GCA-petN LSC 1127 0.0018 1.00 59.8 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU ACCAATCTCAACAGAACACACA GTAGGGTCGTGCAGTGTAAG 2976–2977 1.000 63.3
trnK-UUU_p2 trnK-UUU CCAATCTCAACAGAACACACAG GTAGGGTCGTGCAGTGTAAG 2975–2976 1.000 60.4
trnK-UUU_p3 trnK-UUU ACCAATCTCAACAGAACACACA TAGGGTCGTGCAGTGTAAGT 2975–2976 1.000 60.3
trnK-UUU_p4 trnK-UUU ACCAATCTCAACAGAACACACA GGTCGTGCAGTGTAAGTGTA 2972–2973 1.000 59.9
trnK-UUU_p5 trnK-UUU ACCAATCTCAACAGAACACACA ATGTTTTGGTAGGGTCGTGC 2984–2985 1.000 59.6
matK-trnK-UUU_p1 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA GTAGGGTCGTGCAGTGTAAG 996–997 1.000 78.0
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA AACGGTAGAGTACTCGGCTT 905–906 1.000 76.8
matK-trnK-UUU_p3 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA ACGGTAGAGTACTCGGCTTT 904–905 1.000 76.8
matK-trnK-UUU_p4 matK-trnK-UUU AAGTGTTGTTGCCGAGATCT GTAGGGTCGTGCAGTGTAAG 993–994 1.000 76.2
matK-trnK-UUU_p5 matK-trnK-UUU AGAAAGTGTTGTTGCCGAGA TAGGGTCGTGCAGTGTAAGT 995–996 1.000 75.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TTAGCAATCCGACGCCTTAG AACTGAGAGACCCCTTAACT 1776–1787 1.000 57.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC TTAGCAATCCGACGCCTTAG ACTGAGAGACCCCTTAACTT 1775–1786 1.000 57.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TTAGCAATCCGACGCCTTAG ACTGAGAGACCCCTTAACTTTTG 1775–1786 1.000 56.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACTGAGAGACCCCTTAACT 1825–1836 1.000 56.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA ACTGAGAGACCCCTTAACTT 1824–1835 1.000 56.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG AATTTACGGACTGGTCGTGG 638–653 1.000 80.3
atpF-atpH_p2 atpF-atpH AATGGCCCAAGGAAACGAAA AATTTACGGACTGGTCGTGG 609–624 1.000 79.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 624–639 1.000 78.9
atpF-atpH_p4 atpF-atpH AATGGCCCAAGGAAACGAAA TCGTGGCATTAGCGCTTTTA 595–610 1.000 77.6
atpF-atpH_p5 atpF-atpH GGCCCAAGGAAACGAAAGAA AATTTACGGACTGGTCGTGG 606–621 1.000 76.0
atpH-atpI_p1 atpH-atpI TACCTTCTACAGCTTGGCCT ATAGGGGAATCCATGGAGGG 1616–1668 1.000 81.7
atpH-atpI_p2 atpH-atpI TACCTTCTACAGCTTGGCCT ATTTTTGCAACCTTAGCCGC 1643–1695 1.000 81.6
atpH-atpI_p3 atpH-atpI AACAGAAGCGGCAGAAATCA ATAGGGGAATCCATGGAGGG 1531–1583 1.000 81.4
atpH-atpI_p4 atpH-atpI AACAGAAGCGGCAGAAATCA ATTTTTGCAACCTTAGCCGC 1558–1610 1.000 81.3
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG ATAGGGGAATCCATGGAGGG 1541–1593 1.000 80.9
rpoC1_p1 rpoC1 GCACGAACATCGCCTAATCT AGGAAGGAAGCTTGATCTGA 2971–2993 1.000 60.0
rpoC1_p2 rpoC1 GCACGAACATCGCCTAATCT AGGAAGGAAGCTTGATCTGAA 2971–2993 1.000 58.3
rpoC1_p3 rpoC1 GCACGAACATCGCCTAATCT AGGAAGGAAGCTTGATCTGAAT 2971–2993 1.000 54.4
rpoC1_p4 rpoC1 GCACGAACATCGCCTAATCT GGAAGGAAGCTTGATCTGAATG 2970–2992 1.000 54.1
rpoC1_p5 rpoC1 GCACGAACATCGCCTAATCT GGAAGGAAGCTTGATCTGAA 2970–2992 1.000 53.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Hellenia lacera NC_066959.1 168053 View on NCBI ↗
Hellenia speciosa NC_066960.1 167626 View on NCBI ↗