Markers + reference

Corethrodendron

2 species · Fabaceae · Fabales

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Species 2
Genome length 123–123 kb
Candidate markers 220
Primer pairs 80

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 6 remaining regions by MarkerSeek score (out of 220 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnV-GAC-rps12 Genome 1723 0.0006 1.00 58.6 yes View details
rpl14-rps8 Genome 625 0.0016 1.00 59.8 yes View details
psbE Genome 252 0.0000 1.00 22.9 yes View details
psbE-petL Genome 922 0.0011 1.00 59.4 yes View details
rps2 Genome 711 0.0000 1.00 36.5 yes View details
rps2-rpoC2 Genome 279 0.0036 1.00 54.9 yes View details
psaA-ycf3 Genome 908 0.0033 1.00 61.1 yes View details
ycf3 Genome 1993 0.0000 1.00 53.6 yes View details
rpl32-trnL-UAG Genome 586 0.0034 1.00 60.4 yes View details
atpF Genome 1264 0.0008 1.00 59.2 yes View details
trnT-UGU-trnL-UAA Genome 1151 0.0009 1.00 59.2 yes View details
ndhC-trnM-CAU Genome 1219 0.0008 1.00 59.2 yes View details
atpB-rbcL Genome 741 0.0000 1.00 58.9 yes View details
rpl20 Genome 363 0.0028 1.00 55.4 yes View details
rps15-trnN-GUU Genome 6244 0.0000 1.00 53.0 no 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
trnA-UGC_p1 trnA-UGC AGCATAGATCAAACTGCCGA TGATTTACTTCACGGGCGAG 1075 1.000 72.1
trnA-UGC_p2 trnA-UGC AGCATAGATCAAACTGCCGA GACTACTTCCTGCATGCTCC 994 1.000 71.7
trnA-UGC_p3 trnA-UGC AGCATAGATCAAACTGCCGA AGGTCTCTGGTTCAAGTCCA 1057 1.000 71.3
trnA-UGC_p4 trnA-UGC AGCATAGATCAAACTGCCGA TACTTCCTGCATGCTCCAAC 991 1.000 71.2
trnA-UGC_p5 trnA-UGC CGAATCGGAAAAATGGAGTGC TGATTTACTTCACGGGCGAG 1058 1.000 70.2
trnI_p1 trnI GGAGCATGCAGGAAGTAGTC GGTAAAGAGAGGGATGGGGT 1152 1.000 78.8
trnI_p2 trnI GGAGCATGCAGGAAGTAGTC AGAGAGGGATGGGGTTTCTC 1147 1.000 78.7
trnI_p3 trnI GGAGCATGCAGGAAGTAGTC AGAGGGATGGGGTTTCTCTC 1145 1.000 78.7
trnI_p4 trnI GGAGCATGCAGGAAGTAGTC GAGAGGGATGGGGTTTCTCT 1146 1.000 78.7
trnI_p5 trnI GGAGCATGCAGGAAGTAGTC GATGGGGTTTCTCTCGCTTT 1140 1.000 78.7
trnV-GAC-rps12_p1 trnV-GAC-rps12 GATGACTTCCACCACGTCAA GAGGTTAAGCGTACTCTGGC 1835 1.000 78.1
trnV-GAC-rps12_p2 trnV-GAC-rps12 AACTGATGACTTCCACCACG GAGGTTAAGCGTACTCTGGC 1839 1.000 78.1
trnV-GAC-rps12_p3 trnV-GAC-rps12 ATGACTTCCACCACGTCAAG GAGGTTAAGCGTACTCTGGC 1834 1.000 78.1
trnV-GAC-rps12_p4 trnV-GAC-rps12 GATGACTTCCACCACGTCAA GGTTAAGCGTACTCTGGCAA 1833 1.000 78.0
trnV-GAC-rps12_p5 trnV-GAC-rps12 ATGACTTCCACCACGTCAAG GGTTAAGCGTACTCTGGCAA 1832 1.000 78.0
rpl14-rps8_p1 rpl14-rps8 GCCCGAGAATTGAGACAGTT TCACGATGCTTTCTGACGTT 794–795 1.000 78.2
rpl14-rps8_p2 rpl14-rps8 GCCCGAGAATTGAGACAGTT TTCACGATGCTTTCTGACGT 795–796 1.000 78.2
rpl14-rps8_p3 rpl14-rps8 CGCAATAGCCCGAGAATTGA TCACGATGCTTTCTGACGTT 801–802 1.000 75.7
rpl14-rps8_p4 rpl14-rps8 CGCAATAGCCCGAGAATTGA TTCACGATGCTTTCTGACGT 802–803 1.000 75.7
rpl14-rps8_p5 rpl14-rps8 AGCCCGAGAATTGAGACAGT TCACGATGCTTTCTGACGTT 795–796 1.000 73.2
psbE_p1 psbE GAACAGCCAACCATCGTACT GGAATCGATCCCCCTTTGAC 358 1.000 79.0
psbE_p2 psbE AACAGCCAACCATCGTACTG GGAATCGATCCCCCTTTGAC 357 1.000 78.2
psbE_p3 psbE GTGAACAGCCAACCATCGTA GGAATCGATCCCCCTTTGAC 360 1.000 78.2
psbE_p4 psbE TGAACAGCCAACCATCGTAC GGAATCGATCCCCCTTTGAC 359 1.000 78.2
psbE_p5 psbE GAACAGCCAACCATCGTACT TCGATCCCCCTTTGACTGTA 354 1.000 77.3
psbE-petL_p1 psbE-petL TGACAAATAACCAACCCGCA ACTGATAAAAAGACCTGCGGT 1109 1.000 68.6
psbE-petL_p2 psbE-petL CAACCCGCAATGAATAGGGA ACTGATAAAAAGACCTGCGGT 1098 1.000 68.3
psbE-petL_p3 psbE-petL AGAACGTTCTCCTGTGCTTC ACTGATAAAAAGACCTGCGGT 1021 1.000 67.5
psbE-petL_p4 psbE-petL GTTCTCCTGTGCTTCCAGAC ACTGATAAAAAGACCTGCGGT 1016 1.000 67.1
psbE-petL_p5 psbE-petL ACCAACCCGCAATGAATAGG ACTGATAAAAAGACCTGCGGT 1100 1.000 66.8

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
Corethrodendron fruticosum NC_086598.1 123100 View on NCBI ↗
Corethrodendron scoparium PX508261.1 123115 View on NCBI ↗