Markers + reference

Pachira

2 species · Malvaceae · Malvales

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Species 2
Genome length 158–158 kb
Candidate markers 263
Primer pairs 80

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 6 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2211 0.4782 0.87 80.1 yes View details
ndhD SSC 1503 0.4747 0.80 79.4 yes View details
psaC-ndhE SSC 247 0.5169 0.84 74.2 yes View details
ndhG SSC 531 0.5088 0.96 81.3 yes View details
ndhG-ndhI SSC 423 0.4607 0.84 76.9 yes View details
ndhI SSC 504 0.5147 0.81 77.6 yes View details
ndhA SSC 2221 0.4680 0.79 77.8 yes View details
ndhH SSC 1182 0.4914 0.84 80.4 yes View details
ycf1 SSC 5685 0.4614 0.86 74.9 yes View details
ycf1-trnN-GUU SSC 317 0.4746 0.56 67.4 yes View details
ndhF-rpl32 SSC 1255 0.4616 0.90 82.3 yes View details
ccsA SSC 972 0.4536 0.76 78.4 yes View details
trnN-GUU-trnR-ACG SSC 611 0.4733 0.74 77.6 yes View details
ccsA-ndhD SSC 299 0.4507 0.95 77.4 yes View details
rpl32-trnL-UAG SSC 867 0.4384 0.72 77.3 yes View details
psaC SSC 246 0.5175 0.93 76.7 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhF_p1 ndhF CCTTGTTCCTACATGACCCG AGAGCCGGTGAATCAGAAAC 2733 0.500 59.0
ndhF_p2 ndhF GGTGACGATACTGTAGGGGA AGACAATCGATCAGTTCCGC 2850 0.500 58.9
ndhF_p3 ndhF TGTCCCCTCCAGTCAAGAAT AGAGCCGGTGAATCAGAAAC 2591 0.500 58.8
ndhF_p4 ndhF GTCAAGTGGAAGTGCAGTGA AGAGCCGGTGAATCAGAAAC 2794 0.500 58.8
ndhF_p5 ndhF CAGCTGAGGCATCCTAACAG AGAGCCGGTGAATCAGAAAC 2768 0.500 58.8
ndhF-rpl32_p1 ndhF-rpl32 GGGAAGTGGCACAAAAGGTA GGTTGAAAGCAAGGGAAGGA 1836 0.500 59.9
ndhF-rpl32_p2 ndhF-rpl32 GCCCACATACGACGAAGATT GGTTGAAAGCAAGGGAAGGA 1907 0.500 59.5
ndhF-rpl32_p3 ndhF-rpl32 GGGAAGTGGCACAAAAGGTA TGGGCGATGGGGAAAATAAG 1581 0.500 59.4
ndhF-rpl32_p4 ndhF-rpl32 GGGAAGTGGCACAAAAGGTA TGCTCCGCTATGGCTATAGT 1711 0.500 59.3
ndhF-rpl32_p5 ndhF-rpl32 GCCCACATACGACGAAGATT TGGGCGATGGGGAAAATAAG 1652 0.500 59.0
rpl32-trnL-UAG_p1 rpl32-trnL-UAG CGGCGTTGAAAGCTTTTTCA AGCGTGTCTACCGATTTCAC 982 0.500 58.6
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CGGCGTTGAAAGCTTTTTCA CAGCGTGTCTACCGATTTCA 983 0.500 58.6
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CGGCGTTGAAAGCTTTTTCA TCCTAAGAGCAGCGTGTCTA 992 0.500 57.7
rpl32-trnL-UAG_p4 rpl32-trnL-UAG CGGCGTTGAAAGCTTTTTCA CCTAAGAGCAGCGTGTCTAC 991 0.500 57.1
rpl32-trnL-UAG_p5 rpl32-trnL-UAG CGGCGTTGAAAGCTTTTTCA CTAAGAGCAGCGTGTCTACC 990 0.500 57.1
ccsA_p1 ccsA TCCTTCCCTTGCTTTCAACC CGAAATGGGCGGAATGTCTA 2390 0.500 59.5
ccsA_p2 ccsA TCCTTCCCTTGCTTTCAACC TGGGCGGAATGTCTATTTCG 2385 0.500 59.5
ccsA_p3 ccsA GTGAAATCGGTAGACACGCT CGAAATGGGCGGAATGTCTA 1859 0.500 59.5
ccsA_p4 ccsA GTGAAATCGGTAGACACGCT TGGGCGGAATGTCTATTTCG 1854 0.500 59.5
ccsA_p5 ccsA TGAAATCGGTAGACACGCTG TGGGCGGAATGTCTATTTCG 1853 0.500 59.5
ccsA-ndhD_p1 ccsA-ndhD TTGGACCGTATTCGCGATTT CGAAATGGGCGGAATGTCTA 892 0.500 59.5
ccsA-ndhD_p2 ccsA-ndhD TTGGACCGTATTCGCGATTT TGGGCGGAATGTCTATTTCG 887 0.500 59.5
ccsA-ndhD_p3 ccsA-ndhD GTAAATTCCGCACTTGTGGC CGAAATGGGCGGAATGTCTA 837 0.500 59.4
ccsA-ndhD_p4 ccsA-ndhD GTAAATTCCGCACTTGTGGC TGGGCGGAATGTCTATTTCG 832 0.500 59.4
ccsA-ndhD_p5 ccsA-ndhD TTACTTGGACCGTATTCGCG TGGGCGGAATGTCTATTTCG 891 0.500 58.9
ndhD_p1 ndhD TTGGACCGTATTCGCGATTT CAAATTGCTTCCGCTCCAAG 2242 0.500 59.8
ndhD_p2 ndhD GTAAATTCCGCACTTGTGGC CAAATTGCTTCCGCTCCAAG 2187 0.500 59.7
ndhD_p3 ndhD TTGGACCGTATTCGCGATTT AGATGTGAATCCGCTTGTCC 2197 0.500 59.7
ndhD_p4 ndhD GTAAATTCCGCACTTGTGGC AGATGTGAATCCGCTTGTCC 2142 0.500 59.6
ndhD_p5 ndhD TTACTTGGACCGTATTCGCG CAAATTGCTTCCGCTCCAAG 2246 0.500 59.2

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
Pachira aquatica MT053008.1 157936 View on NCBI ↗
Pachira macrocarpa NC_057439.1 157936 View on NCBI ↗