Markers + reference

Jatropha

2 species · Euphorbiaceae · Malpighiales

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Species 2
Genome length 164–170 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 354 0.2831 0.94 78.9 yes View details
trnS-GCU-trnG-GCC LSC 1339 0.0736 0.75 87.4 yes View details
trnG-GCC-trnR-UCU LSC 811 0.1013 0.66 81.5 yes View details
trnR-UCU-atpA LSC 588 0.0521 0.55 71.6 yes View details
psbM-trnD-GUC LSC 1346 0.0238 0.97 66.9 yes View details
psbZ-trnG-GCC LSC 849 0.0419 0.93 77.1 yes View details
ndhC-trnV-UAC LSC 975 0.0528 0.74 75.6 yes View details
rpl16 LSC 1803 0.0177 0.97 58.8 yes View details
rpl32-trnL-UAG SSC 1019 0.0353 0.86 76.7 yes View details
atpA-atpF LSC 58 0.0526 0.98 83.1 yes View details
trnE-UUC-trnT_GGU LSC 1141 0.0214 0.90 74.1 yes View details
rpl16-rps3 LSC 208 0.0632 0.91 73.8 yes View details
rpl2-trnH-GUG LSC 69 0.2029 1.00 72.7 no View details
petD-rpoA LSC 211 0.0429 1.00 71.8 yes View details
rps12-clpP LSC 202 0.0396 1.00 70.8 yes View details
clpP-psbB LSC 524 0.0268 1.00 70.8 yes View details
trnI-GAU-trnA_UGC IRb 64 0.0312 1.00 70.5 yes View details
trnA-UGC-trnI-GAU IRa 64 0.0312 1.00 70.5 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 807–1039 1.000 88.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 821–1053 1.000 88.5
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 806–1038 1.000 88.5
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 820–1052 1.000 88.5
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 822–1054 1.000 88.5
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAATATGAACCGAGGGATCCC 1172–1465 1.000 77.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GGAATATGAACCGAGGGATCC 1173–1466 1.000 77.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAATATGAACCGAGGGATCCC 1171–1464 1.000 77.8
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GGAATATGAACCGAGGGATCC 1172–1465 1.000 77.8
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AAATTCCAAGTCATCGCCGA GAATATGAACCGAGGGATCCC 1248–1541 1.000 76.7
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTAGCGAT AGAAGACCTCTGTCCTATCCA 617–892 1.000 68.6
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTAGCGAT AGGTTTAGAAGACCTCTGTCCT 623–898 1.000 67.9
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU CGTCGACTATAACCCCTAGC AGAAGACCTCTGTCCTATCCA 633–908 1.000 65.3
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCCCTAGCCTTCCAAGCTA AGAAGACCTCTGTCCTATCCA 621–896 1.000 64.7
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU CGTCGACTATAACCCCTAGC AGGTTTAGAAGACCTCTGTCCT 639–914 1.000 64.6
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCACCGAAGAAGCAGAAAGC 450–690 1.000 68.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGGAACTGAAGGAGCGTTTT 411–651 1.000 67.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACATTCACCGAAGAAGCAGA 454–694 1.000 66.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TCACCGAAGAAGCAGAAAGC 485–725 1.000 65.9
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAACTGAAGGAGCGTTTTC 410–650 1.000 65.3
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC CAACGGGTTTTCCAACAAGC 261–302 1.000 76.9
atpA-atpF_p2 atpA-atpF TACTAATCTCGTCGGCTCGA CAACGGGTTTTCCAACAAGC 179–220 1.000 76.3
atpA-atpF_p3 atpA-atpF TTGTTCAATACGTTCGCGGA CAACGGGTTTTCCAACAAGC 205–246 1.000 76.2
atpA-atpF_p4 atpA-atpF CGTCGGCTCGAATAGTTACC CAACGGGTTTTCCAACAAGC 170–211 1.000 76.2
atpA-atpF_p5 atpA-atpF ATCTCGTCGGCTCGAATAGT CAACGGGTTTTCCAACAAGC 174–215 1.000 74.9
psbM-trnD-GUC_p1 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA TCCCCGGGATTGTAGTTCAA 1483–1594 1.000 64.2
psbM-trnD-GUC_p2 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA TTCCCCGGGATTGTAGTTCA 1484–1595 1.000 64.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCCCCGGGATTGTAGTTCAA 1471–1582 1.000 63.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCCCCGGGATTGTAGTTCA 1472–1583 1.000 63.3
psbM-trnD-GUC_p5 psbM-trnD-GUC GCGGTAGGAACTAGAATGAACA TTCAATTGGTCAGAGCACCG 1468–1579 1.000 63.1

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
Jatropha curcas NC_012224.1 163856 View on NCBI ↗
Jatropha multifida PX316413.1 169759 View on NCBI ↗