Markers + reference

Cajanus

2 species · Fabaceae · Fabales

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Species 2
Genome length 152–154 kb
Candidate markers 253
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rbcL LSC 1051 0.0509 0.97 76.5 yes View details
trnL-UAA-trnT(tgt) LSC 1116 0.0729 0.72 85.0 yes View details
trnG(gcc)-psbZ LSC 745 0.0678 0.63 75.4 yes View details
accD-psaI LSC 412 0.0987 0.54 71.8 yes View details
psbE-petL LSC 1242 0.0255 0.73 71.1 yes View details
rps11-rpl36 LSC 382 0.0896 0.88 89.3 yes View details
rps3-rps19 LSC 517 0.0719 0.65 81.6 yes View details
ycf1 SSC 5355 0.0208 1.00 52.8 yes View details
ycf1 IRa 543 0.0000 0.89 60.7 no View details
atpA-trnR(tct) LSC 232 0.0942 0.96 87.2 yes View details
psaI-ycf4 LSC 171 0.2083 0.42 78.7 yes View details
psbD-trnT(ggt) LSC 1160 0.0237 0.94 76.9 yes View details
rpoA-rps11 LSC 90 0.0345 0.97 75.4 yes View details
trnL(tag)-ndhF SSC 947 0.0219 0.92 75.0 yes View details
psbA-trnK-UUU LSC 281 0.0370 0.96 73.7 yes View details
trnH(gtg)-psbA LSC 328 0.0332 0.73 69.9 yes View details
trnV-UAC LSC 35 0.0286 1.00 68.9 yes View details
trnW(cca)-trnP(tgg) LSC 192 0.0417 1.00 68.7 yes View details
trnT(ggt)-trnE(ttc) LSC 760 0.0158 1.00 67.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH(gtg)-psbA_p1 trnH(gtg)-psbA CTGCCTTAATCCACTTGGCT CCGAGCTAACCTTGGTATGG 372–453 1.000 82.5
trnH(gtg)-psbA_p2 trnH(gtg)-psbA ACTGCCTTAATCCACTTGGC CCGAGCTAACCTTGGTATGG 373–454 1.000 82.3
trnH(gtg)-psbA_p3 trnH(gtg)-psbA AATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 365–446 1.000 81.0
trnH(gtg)-psbA_p4 trnH(gtg)-psbA CGCATGGTGGATTCACAATC CCGAGCTAACCTTGGTATGG 394–475 1.000 79.7
trnH(gtg)-psbA_p5 trnH(gtg)-psbA ATATGAATGGGCGAACGACG CCGAGCTAACCTTGGTATGG 508 0.500 54.1
psbA-trnK-UUU_p1 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA CGGCTTGGGGAGAGATTTTT 402–413 1.000 78.5
psbA-trnK-UUU_p2 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CGGCTTGGGGAGAGATTTTT 427–438 1.000 77.9
psbA-trnK-UUU_p3 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC CGGCTTGGGGAGAGATTTTT 434–445 1.000 77.1
psbA-trnK-UUU_p4 psbA-trnK-UUU AGTTACAGAAGCGACCCCAT CGGCTTGGGGAGAGATTTTT 430–441 1.000 76.8
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTCTCGCGTCTCTCTAAAA CTTCATCCGACTAGTTCCGG 341–352 1.000 76.5
trnK-UUU-rbcL_p1 trnK-UUU-rbcL ACCATTGAGTTAGCAACCC AGTCCTGAATTAGCTGCTGC 1145–1198 1.000 53.7
trnK-UUU-rbcL_p2 trnK-UUU-rbcL ACCATTGAGTTAGCAACCC GAGGCTAGCAAATGGAGTCC 1160–1213 1.000 53.6
trnK-UUU-rbcL_p3 trnK-UUU-rbcL ACCATTGAGTTAGCAACCC GGCTAGCAAATGGAGTCCTG 1158–1211 1.000 51.4
trnK-UUU-rbcL_p4 trnK-UUU-rbcL ACCATTGAGTTAGCAACCC GTGAGGCTAGCAAATGGAGT 1162–1215 1.000 50.7
trnK-UUU-rbcL_p5 trnK-UUU-rbcL ACCATTGAGTTAGCAACCC AGGCTAGCAAATGGAGTCCT 1159–1212 1.000 50.7
trnV-UAC_p1 trnV-UAC GCAATAAAAATGCACGTTGGG AGTATTAGTAATGAGATAGATTCGA 164 1.000 40.5
trnV-UAC_p2 trnV-UAC GCAATAAAAATGCACGTTGGG AGTATTAGTAATGAGATAGATTCGAT 164 1.000 40.5
trnV-UAC_p3 trnV-UAC TGCACGTTGGGTTTTTAAAC AGTATTAGTAATGAGATAGATTCGA 154 1.000 40.5
trnV-UAC_p4 trnV-UAC AAAAATGCACGTTGGGTTTT AGTATTAGTAATGAGATAGATTCGA 159 1.000 40.5
trnV-UAC_p5 trnV-UAC AAAATGCACGTTGGGTTTTT AGTATTAGTAATGAGATAGATTCGA 158 1.000 40.5
trnL-UAA-trnT(tgt)_p1 trnL-UAA-trnT(tgt) CTCAGGATTGCCCATTGTGA GCGATGCTCTAACCTCTGAG 935–1234 1.000 86.2
trnL-UAA-trnT(tgt)_p2 trnL-UAA-trnT(tgt) AGGATTTGGCTCAGGATTGC GCGATGCTCTAACCTCTGAG 944–1243 1.000 85.4
trnL-UAA-trnT(tgt)_p3 trnL-UAA-trnT(tgt) CCCATTGTGAATTCCAGGGT GCGATGCTCTAACCTCTGAG 925–1224 1.000 85.4
trnL-UAA-trnT(tgt)_p4 trnL-UAA-trnT(tgt) CTCAGGATTGCCCATTGTGA GGATTCGAACCGATGACCAT 967–1266 1.000 85.2
trnL-UAA-trnT(tgt)_p5 trnL-UAA-trnT(tgt) TCGGAAAACAGGATTTGGCT GCGATGCTCTAACCTCTGAG 953–1252 1.000 84.9
trnG(gcc)-psbZ_p1 trnG(gcc)-psbZ CGTCTTCTCCTTGGCAAAGA CGAAGGTTGGTCGAGTAACA 677–892 1.000 82.5
trnG(gcc)-psbZ_p2 trnG(gcc)-psbZ CGTCTTCTCCTTGGCAAAGA CGAAGGTTGGTCGAGTAACAA 677–892 1.000 75.9
trnG(gcc)-psbZ_p3 trnG(gcc)-psbZ ACATAACTAAGTGGAGGCGG CGAAGGTTGGTCGAGTAACA 716–931 1.000 75.8
trnG(gcc)-psbZ_p4 trnG(gcc)-psbZ CGTCTTCTCCTTGGCAAAGA TGTTGTATTTGCTTCTCCCGA 695–910 1.000 74.5
trnG(gcc)-psbZ_p5 trnG(gcc)-psbZ CGGATAGCGGGAATCGAAC CGAAGGTTGGTCGAGTAACA 699–914 1.000 74.2

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
Cajanus cajan NC_031429.1 153841 View on NCBI ↗
Cajanus scarabaeoides KU729878.1 152201 View on NCBI ↗