Markers + reference

Aframomum

4 species · Zingiberaceae · Zingiberales

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Species 4
Genome length 161–161 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1344 0.0051 1.00 38.1 yes View details
atpF-atpH LSC 516 0.0158 1.00 51.9 yes View details
trnG-GCC-trnfM-CAU LSC 273 0.0159 1.00 53.0 yes View details
ndhC-trnV-UAC LSC 1620 0.0086 1.00 56.0 yes View details
accD-psaI LSC 515 0.0129 0.96 48.0 yes View details
ycf1 IRb 1770 0.0014 1.00 35.8 no View details
ccsA SSC 978 0.0039 1.00 38.8 yes View details
psaC-ndhE SSC 670 0.0153 0.97 61.2 yes View details
ndhE SSC 306 0.0033 1.00 28.3 yes View details
ndhA SSC 2132 0.0040 1.00 49.8 yes View details
rps15-ycf1 SSC 441 0.0113 1.00 50.7 yes View details
ycf1 SSC 5481 0.0061 1.00 42.1 yes View details
trnH-GUG-rpl2 IRb 50 0.0600 1.00 75.6 yes View details
rpl2-trnH-GUG IRa 50 0.0600 1.00 75.6 yes View details
trnS-GCU-trnG-UCC LSC 955 0.0044 0.99 64.7 yes View details
trnT-UGU-trnL-UAA LSC 1098 0.0067 0.95 61.5 yes View details
psaA-pafI LSC 642 0.0062 1.00 61.1 yes View details
rps11-rpl36 LSC 122 0.0219 1.00 60.6 yes View details
clpP1-psbB LSC 459 0.0033 1.00 58.6 yes View details
psbE-petL LSC 1192 0.0043 1.00 58.4 yes View details
trnD-GUC-trnY-GUA LSC 413 0.0036 1.00 57.7 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
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 760–1027 1.000 56.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 759–1026 1.000 56.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AGTATCAAGCGGGTCGAGTA ACGAATCACACTTTTACCACT 844–1111 1.000 55.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 763–1030 1.000 55.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 762–1029 1.000 55.3
atpF_p1 atpF CAATTCCGTCGCCTACTTGA TATTGCGAGACAACCGGAAG 2175 1.000 81.0
atpF_p2 atpF CAATTCCGTCGCCTACTTGA TGGTTGTGGCATTAGCACTT 2086 1.000 81.0
atpF_p3 atpF CCGTTTCGGCTACCACAATA TATTGCGAGACAACCGGAAG 2742 1.000 80.9
atpF_p4 atpF CCGTTTCGGCTACCACAATA TGGTTGTGGCATTAGCACTT 2653 1.000 80.8
atpF_p5 atpF CAATTCCGTCGCCTACTTGA AGGAATTACCGCATTCGCTT 1878 1.000 80.6
atpF-atpH_p1 atpF-atpH AGTGGCCCAAGTAAACGAAA TGGTTGTGGCATTAGCACTT 600 1.000 79.3
atpF-atpH_p2 atpF-atpH CAGTGGCCCAAGTAAACGAA TGGTTGTGGCATTAGCACTT 601 1.000 78.9
atpF-atpH_p3 atpF-atpH TGGCCCAAGTAAACGAAAGA TGGTTGTGGCATTAGCACTT 598 1.000 77.0
atpF-atpH_p4 atpF-atpH GTGGCCCAAGTAAACGAAAG TGGTTGTGGCATTAGCACTT 599 1.000 76.5
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTTCCGGC TGGTTGTGGCATTAGCACTT 628 1.000 75.9
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA AATTCTTCCTGGGTCGATGC 591–615 1.000 79.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GATCGGATCCTAGTTCGGGA AATTCTTCCTGGGTCGATGC 595–619 1.000 79.4
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGGACGGACTGTAAATTCG 558–582 1.000 77.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATCGGATCCTAGTTCGGGAC AATTCTTCCTGGGTCGATGC 594–618 1.000 77.1
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GGATCCTAGTTCGGGACTGA GGGACGGACTGTAAATTCGT 557–581 1.000 77.0
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU CGGATTGTGAGGCCCATTAA CTTGAGGTCACGGGTTCAAA 510–541 1.000 84.8
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU TGTGTGGACATATGCATGCA CTTGAGGTCACGGGTTCAAA 386–417 1.000 84.4
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU TGTGTGGACATATGCATGCA GTCACGGGTTCAAATCCTGT 380–411 1.000 83.9
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU CGGATTGTGAGGCCCATTAA CTTCGTCCATAAGTTCCCGG 578–609 0.750 74.3
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU TGTGTGGACATATGCATGCA CTTCGTCCATAAGTTCCCGG 454–485 0.750 74.0
psaA-pafI_p1 psaA-pafI TGTTCTTGAGAAATGGCCGG AAGATCACGAGGCGTTTTGA 764–771 1.000 76.7
psaA-pafI_p2 psaA-pafI TGTTCTTGAGAAATGGCCGG AGATCACGAGGCGTTTTGAA 763–770 1.000 76.7
psaA-pafI_p3 psaA-pafI TGTTCTTGAGAAATGGCCGG TGAAGATCACGAGGCGTTTT 766–773 1.000 76.7
psaA-pafI_p4 psaA-pafI TGTTCTTGAGAAATGGCCGG TTGAAGATCACGAGGCGTTT 767–774 1.000 76.7
psaA-pafI_p5 psaA-pafI TGTTCTTGAGAAATGGCCGG TTGGTTGAAGATCACGAGGC 771–778 1.000 76.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Aframomum angustifolium PV600844.1 161252 View on NCBI ↗
Aframomum daniellii PV600846.1 161295 View on NCBI ↗
Aframomum melegueta PV600845.1 161101 View on NCBI ↗
Aframomum sceptrum PV600847.1 161224 View on NCBI ↗