Markers + reference

Rorippa

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 155–156 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 IRb 951 0.0019 1.00 35.6 no View details
trnK-UUU-rps16 LSC 700 0.0252 0.98 67.2 yes View details
trnC-GCA-petN LSC 636 0.0236 1.00 66.2 yes View details
psbM-trnD-GUC LSC 1028 0.0230 1.00 63.3 yes View details
trnD-GUC-trnY-GUA LSC 428 0.0284 0.99 67.3 yes View details
trnL-UAA-trnF-GAA LSC 703 0.0278 0.72 67.6 yes View details
trnF-GAA-ndhJ LSC 585 0.0345 0.97 74.9 yes View details
rbcL-accD LSC 656 0.0264 0.97 64.0 yes View details
psbE-petL LSC 1388 0.0166 0.69 61.5 yes View details
ycf1 IRa 1029 0.0031 1.00 37.5 no View details
rpl32-trnL-UAG SSC 920 0.0375 0.94 79.2 yes View details
ycf1 SSC 4440 0.0171 1.00 50.1 yes View details
ndhK-ndhC LSC 70 0.0357 0.90 77.5 yes View details
trnH-GUG-psbA LSC 315 0.0414 1.00 70.0 yes View details
accD-psaI LSC 662 0.0166 0.96 69.7 yes View details
ccsA-ndhD SSC 221 0.0318 1.00 67.6 yes View details
trnS-GCU-trnT-CGU LSC 627 0.0145 0.99 67.3 yes View details
trnE-UUC-trnT-GGU LSC 821 0.0197 0.98 67.3 yes View details
rpl20-rps12 LSC 751 0.0110 0.91 66.4 yes View details
petA-psbJ LSC 1014 0.0222 0.98 65.9 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-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 373–391 1.000 83.9
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 374–392 1.000 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG GCTGTTGAGGCTCCATCTAC 366–384 1.000 82.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGCTGTTGAGGCTCCATCTA 374–392 1.000 80.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGCTGTTGAGGCTCCATCTA 375–393 1.000 80.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGCAGGGATTTTTACGGA 785–800 1.000 76.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGCAGGGATTTTTACGGAA 784–799 1.000 76.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGCAGGGATTTTTACGGA 784–799 1.000 76.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGCAGGGATTTTTACGGAA 783–798 1.000 76.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGCAGGGATTTTTACGGAA 784–799 1.000 73.8
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCA 695–736 1.000 58.1
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU AACGCTTTAGTCCACTCAGC GGAACGAATCACACTTTTACCA 693–734 1.000 57.8
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU CCAACGCTTTAGTCCACTCA AGGGATTAAAGGAACGAATCACA 705–746 1.000 57.3
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU AACGCTTTAGTCCACTCAGC AGGGATTAAAGGAACGAATCACA 703–744 1.000 57.0
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU CCAACGCTTTAGTCCACTCA GGAACGAATCACACTTTTACCAC 695–736 1.000 57.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 738–748 1.000 82.7
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 739–749 1.000 82.1
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CTTCCCCACACTACGAGAGA 734–744 1.000 81.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCACACTACGAGAG 735–745 1.000 81.5
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCCCCACACTACGAGAGAG 733–743 1.000 81.5
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1136–1140 1.000 56.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1137–1141 1.000 52.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC TCAATTGGTCAGAGCACCG 1135–1139 1.000 50.9
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC AGTTCAATTGGTCAGAGCACC 1138–1142 1.000 48.8
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAAGAGTGCAGTAGC AGCTACCCACTTGATTTCCA 1167–1171 1.000 48.1
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 493–498 1.000 79.6
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 492–497 1.000 79.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 514–519 1.000 78.5
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 513–518 1.000 78.3
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CGGACTGTAAATTCGTTGGC 509–514 1.000 77.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Rorippa cantoniensis NC_070424.1 155650 View on NCBI ↗
Rorippa curvipes NC_070419.1 154738 View on NCBI ↗
Rorippa dubia NC_070412.1 154740 View on NCBI ↗
Rorippa sinuata NC_070423.1 155717 View on NCBI ↗