Markers + reference

Aphanocalyx

2 species · Fabaceae · Fabales

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Species 2
Genome length 160–160 kb
Candidate markers 266
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR-UCU-atpA LSC 421 0.0214 1.00 59.8 yes View details
atpH-atpI LSC 1010 0.0099 1.00 64.6 yes View details
rps4-trnT-UGU LSC 446 0.0115 0.97 64.7 yes View details
trnT-UGU-trnL-UAA LSC 657 0.0122 1.00 65.8 yes View details
trnF-GAA-ndhJ LSC 733 0.0109 1.00 58.7 yes View details
rbcL-accD LSC 981 0.0227 0.99 71.3 yes View details
rps3 LSC 663 0.0060 1.00 51.3 yes View details
rps3-rps19 LSC 646 0.0140 0.99 61.2 yes View details
rpl32-trnL-UAG SSC 1371 0.0135 0.97 56.5 yes View details
ndhG-ndhI SSC 482 0.0145 1.00 51.9 yes View details
trnN-GUU-trnR-ACG IRa 679 0.0151 0.97 70.0 yes View details
trnR-ACG-trnN-GUU IRb 679 0.0151 0.97 70.0 yes View details
ndhI-ndhA SSC 76 0.0263 1.00 67.6 yes View details
atpF-atpH LSC 616 0.0052 0.94 66.2 yes View details
trnK-UUU-rps16 LSC 930 0.0088 0.98 65.8 yes View details
ndhC-trnV-UAC LSC 611 0.0056 0.87 64.5 yes View details
psaA-ycf3 LSC 730 0.0082 1.00 63.5 yes View details
clpP-psbB LSC 525 0.0076 1.00 61.6 yes View details
psbN LSC 132 0.0152 1.00 61.2 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 TGGGTGTATATTACTTCGAGATGA TTCCGTTCCATATCCATAGT 2778–2779 1.000 40.4
trnK-UUU_p2 trnK-UUU TGGGTGTATATTACTTCGAGATGA TTTCCGTTCCATATCCATAGT 2779–2780 1.000 40.4
trnK-UUU_p3 trnK-UUU TGGGTGTATATTACTTCGAGATG TTCCGTTCCATATCCATAGT 2778–2779 1.000 40.4
trnK-UUU_p4 trnK-UUU TGGGTGTATATTACTTCGAGATG TTTCCGTTCCATATCCATAGT 2779–2780 1.000 40.4
trnK-UUU_p5 trnK-UUU TGGGTGTATATTACTTCGAGATGA ATTTCCGTTCCATATCCATAGT 2780–2781 1.000 40.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGCTGGTATGAACGAATCCA CAAAAAGGGCGGGTGTTTTT 1082–1102 1.000 81.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCGCTGGTATGAACGAATCC CAAAAAGGGCGGGTGTTTTT 1083–1103 1.000 80.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGCTGGTATGAACGAATCCA GGCGGGTGTTTTTATCGAAC 1075–1095 1.000 79.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCGCTGGTATGAACGAATCC GGCGGGTGTTTTTATCGAAC 1076–1096 1.000 78.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CAAAAAGGGCGGGTGTTTTT 1034–1054 1.000 77.3
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTTACCGGGGAAGCAGAA 535–556 1.000 66.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTTACCGGGGAAGC 539–560 1.000 66.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 525–546 1.000 64.9
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTTACCGGGGAAGCAGAAG 534–555 1.000 64.6
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CATTTACCGGGGAAGCAGAA 570–591 1.000 64.0
atpF-atpH_p1 atpF-atpH TTAAACCCGAAACTCCCAGC AGGCAGAGGGAAAAATACGG 766–800 1.000 80.1
atpF-atpH_p2 atpF-atpH CGTATGGCCAGTAACCCAAA AGGCAGAGGGAAAAATACGG 747–781 1.000 80.0
atpF-atpH_p3 atpF-atpH TTAAACCCGAAACTCCCAGC CCTGAGGCAGAGGGAAAAAT 770–804 1.000 79.3
atpF-atpH_p4 atpF-atpH CGTATGGCCAGTAACCCAAA CCTGAGGCAGAGGGAAAAAT 751–785 1.000 79.2
atpF-atpH_p5 atpF-atpH TTAAACCCGAAACTCCCAGC GCAGAGGGAAAAATACGGGG 764–798 1.000 78.6
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1131–1291 1.000 79.5
atpH-atpI_p2 atpH-atpI CGCAATCCCTTCTACAGCTT TTTTGCAACTTTAGCTGCGG 1185–1345 1.000 79.5
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1097–1257 1.000 79.4
atpH-atpI_p4 atpH-atpI AATAGAAGCAAGCCCGACAG TCCCTGTCATGTTCCTTGGA 1180–1340 1.000 78.5
atpH-atpI_p5 atpH-atpI CGCAATCCCTTCTACAGCTT TCCCTGTCATGTTCCTTGGA 1234–1394 1.000 78.4
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TTGGTTGAAGATCACAGGGC 841 1.000 78.9
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT AGCGCAGAATTGGTTGAAGA 850 1.000 78.8
psaA-ycf3_p3 psaA-ycf3 GAAAAATGACCGGGTTTGGC TTGGTTGAAGATCACAGGGC 859 1.000 78.2
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TGAAGATCACAGGGCGTTTC 836 1.000 78.1
psaA-ycf3_p5 psaA-ycf3 GAAAAATGACCGGGTTTGGC AGCGCAGAATTGGTTGAAGA 868 1.000 78.0

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
Aphanocalyx microphyllus PV870709.1 159748 View on NCBI ↗
Aphanocalyx obscurus PV870738.1 159772 View on NCBI ↗