Markers + reference

Corchorus

2 species · Malvaceae · Malvales

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Species 2
Genome length 161–162 kb
Candidate markers 262
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-psaI LSC 2876 0.1740 0.86 79.1 yes View details
clpP LSC 2093 0.0844 0.93 80.5 yes View details
rpl23-trnI-CAU IRb 482 0.1327 0.81 80.9 yes View details
ycf1 SSC 5625 0.0703 0.96 72.3 yes View details
trnI-CAU-rpl23 IRa 482 0.1327 0.81 80.9 yes View details
rps11 LSC 417 0.0408 1.00 77.6 yes View details
rps12-clpP LSC 183 0.3312 0.87 75.3 yes View details
ycf2-trnI-CAU IRa 143 0.1557 0.85 75.0 yes View details
trnI-CAU-ycf2 IRb 143 0.1570 0.85 74.8 yes View details
psbN-psbH LSC 113 0.0442 1.00 74.3 yes View details
rpl2-trnH-GUG IRa 61 0.0164 0.98 73.1 no View details
trnW-CCA-trnP-UGG LSC 204 0.0410 0.96 72.6 yes View details
rps18 LSC 369 0.0813 1.00 72.1 yes View details
trnK-UUU-rps16 LSC 895 0.0157 0.93 71.8 yes View details
rpl20 LSC 366 0.0427 0.96 70.6 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CTGCCGATGGTATGAACGAA AAAAGGAGCTCAACCCACAG 1026–1087 1.000 84.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGGTCTTACAAACTCTGCCG AAAAGGAGCTCAACCCACAG 1040–1101 1.000 83.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAGGAGCTCAACCCACAG 962–1023 1.000 83.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAGGAGCTCAACCCACAG 961–1022 1.000 83.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAGGAGCTCAACCCACAG 971–1032 1.000 82.7
rbcL-psaI_p1 rbcL-psaI GAGGCTAGCAAATGGAGTCC AAAAATAGAGGGGAAGCCGC 2999 0.500 57.8
rbcL-psaI_p2 rbcL-psaI GAGGCTAGCAAATGGAGTCC AAGCCGCTGAAAGTTGTCAT 2986 0.500 56.6
rbcL-psaI_p3 rbcL-psaI GAGTCCTGAACTAGCTGCTG AAAAATAGAGGGGAAGCCGC 2985 0.500 55.8
rbcL-psaI_p4 rbcL-psaI GGCTAGCAAATGGAGTCCTG AAAAATAGAGGGGAAGCCGC 2997 0.500 55.5
rbcL-psaI_p5 rbcL-psaI AGGCTAGCAAATGGAGTCCT AAAAATAGAGGGGAAGCCGC 2998 0.500 54.8
trnW-CCA-trnP-UGG_p1 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT GTCACGGGTTCAAATCCTGT 264–272 1.000 83.9
trnW-CCA-trnP-UGG_p2 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT CACGGGTTCAAATCCTGTCA 262–270 1.000 83.9
trnW-CCA-trnP-UGG_p3 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT TGTCACGGGTTCAAATCCTG 265–273 1.000 83.9
trnW-CCA-trnP-UGG_p4 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT GGGTACAAAATGTCACGGGT 275–283 1.000 83.8
trnW-CCA-trnP-UGG_p5 trnW-CCA-trnP-UGG GTTTTGGAGACCCACGTTCT TGGGTACAAAATGTCACGGG 276–284 1.000 83.8
rps18_p1 rps18 ACCCTTCCCGAGAGTATGAG CTTTTTCTTCCCCAACCCGA 892–969 1.000 83.1
rps18_p2 rps18 ACCCTTCCCGAGAGTATGAG TCTTTTTCTTCCCCAACCCG 893–970 1.000 83.1
rps18_p3 rps18 AAAGGAGGTTCATGGCCAAG CTTTTTCTTCCCCAACCCGA 1127–1204 1.000 82.4
rps18_p4 rps18 AAAGGAGGTTCATGGCCAAG TCTTTTTCTTCCCCAACCCG 1128–1205 1.000 82.4
rps18_p5 rps18 AAAGGAGGTTCATGGCCAAG GGGTTCCCTCGAGAATGAAC 1248–1327 1.000 82.0
rpl20_p1 rpl20 AGACAATTCCTATTTGAGATAGCCA CTGAAAGAAAGAATTAGTTATTCATCA 446 0.500 20.0
rpl20_p2 rpl20 AGACAATTCCTATTTGAGATAGCCA ACTGAAAGAAAGAATTAGTTATTCATC 447 0.500 20.0
rpl20_p3 rpl20 TCCTATTTGAGATAGCCAAGT CTGAAAGAAAGAATTAGTTATTCATCA 439 0.500 20.0
rpl20_p4 rpl20 TCCTATTTGAGATAGCCAAGT ACTGAAAGAAAGAATTAGTTATTCATC 440 0.500 20.0
rpl20_p5 rpl20 TTCCTATTTGAGATAGCCAAGT CTGAAAGAAAGAATTAGTTATTCATCA 440 0.500 20.0
rps12-clpP_p1 rps12-clpP TGACCCTGTTAGTCCGTTCT TATAAAGCAACGGGGCCATC 1051–1097 1.000 91.1
rps12-clpP_p2 rps12-clpP TGACCCTGTTAGTCCGTTCT CGAAGACCTGGAAAGGGATG 680–719 1.000 90.9
rps12-clpP_p3 rps12-clpP CTAGTACATGTTCCTCGGCG TATAAAGCAACGGGGCCATC 746–792 1.000 90.8
rps12-clpP_p4 rps12-clpP TGACCCTGTTAGTCCGTTCT CCCATTTCAGCGTCACAAAC 1242 0.500 59.6
rps12-clpP_p5 rps12-clpP TGACCCTGTTAGTCCGTTCT TCCTCGCCATTCGTGAAAAA 750 0.500 59.0

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
Corchorus capsularis NC_044467.1 161088 View on NCBI ↗
Corchorus olitorius NC_044468.1 161766 View on NCBI ↗