Markers + reference

Rohdea

4 species · Asparagaceae · Asparagales

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Species 4
Genome length 157–157 kb
Candidate markers 276
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1292 0.0120 1.00 51.6 yes View details
psbK-psbI LSC 405 0.0091 1.00 51.7 yes View details
trnS-GCU-trnG-UCC LSC 1331 0.0048 0.99 65.5 yes View details
ycf3 LSC 1995 0.0020 1.00 42.3 yes View details
petA-psbJ LSC 1092 0.0055 1.00 53.2 yes View details
rps12-trnV-GAC IRb 1841 0.0206 1.00 62.3 yes View details
ycf1 IRb 894 0.0011 1.00 37.8 no View details
ccsA SSC 996 0.0000 1.00 28.0 yes View details
ycf1 SSC 5460 0.0026 1.00 41.9 yes View details
trnV-GAC-rps12 IRa 1841 0.0206 1.00 62.3 yes View details
ccsA-ndhD SSC 231 0.0281 1.00 70.6 yes View details
ndhF-rpl32 SSC 1015 0.0041 1.00 61.9 yes View details
trnR-UCU-atpA LSC 118 0.0127 1.00 60.3 yes View details
rpoB-trnC-GCA LSC 1193 0.0027 1.00 59.8 yes View details
psbA-trnK-UUU LSC 244 0.0075 1.00 57.4 yes View details
trnT-UGU-trnL-UAA LSC 956 0.0018 0.98 55.9 yes View details
trnQ-UUG LSC 72 0.0139 1.00 52.8 yes View details
rbcL-accD LSC 689 0.0015 0.98 52.2 yes View details
trnF-GAA-ndhJ LSC 720 0.0016 1.00 51.4 yes View details
trnT-GGU-psbD LSC 759 0.0022 1.00 51.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU GGGGATCATCAAAACACCGA GGTTTGGGAAGGGGTCTTTT 451 1.000 78.8
psbA-trnK-UUU_p2 psbA-trnK-UUU TGGGGATCATCAAAACACCG GGTTTGGGAAGGGGTCTTTT 452 1.000 78.4
psbA-trnK-UUU_p3 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GGTTTGGGAAGGGGTCTTTT 420 1.000 77.8
psbA-trnK-UUU_p4 psbA-trnK-UUU AACACCGAACCATCCAATGT GGTTTGGGAAGGGGTCTTTT 439 1.000 77.5
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTGTACTTTCGCGTCTCT GGTTTGGGAAGGGGTCTTTT 370 1.000 77.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGTTCGAATCCTTCCGTCC 1363–1367 1.000 71.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTTCGAATCCTTCCGTCCC 1362–1366 1.000 71.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GGTTCGAATCCTTCCGTCC 1374–1378 1.000 71.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTTCGAATCCTTCCGTCCC 1373–1377 1.000 71.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGAATCCTTCCGTCCCA 1361–1365 1.000 69.8
trnQ-UUG_p1 trnQ-UUG AACAAAGAAGGGGTTGGGTC TATTTGGGCTGGGATTGACG 246 1.000 79.6
trnQ-UUG_p2 trnQ-UUG GAACAAAGAAGGGGTTGGGT TATTTGGGCTGGGATTGACG 247 1.000 79.6
trnQ-UUG_p3 trnQ-UUG AGAACAAAGAAGGGGTTGGG TATTTGGGCTGGGATTGACG 248 1.000 77.2
trnQ-UUG_p4 trnQ-UUG AACAAAGAAGGGGTTGGGTC CTGGGATTGACGAATGACCA 238 1.000 76.8
trnQ-UUG_p5 trnQ-UUG GAACAAAGAAGGGGTTGGGT CTGGGATTGACGAATGACCA 239 1.000 76.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGCCCGGATCGTTAGATAAG 521–523 1.000 77.9
psbK-psbI_p2 psbK-psbI CTTTTGTTTGGCAAGCTGCT GGCCCGGATCGTTAGATAAG 526–528 1.000 77.8
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGCCCGGATCGTTAGATAAG 518–520 1.000 75.8
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT GGCCCGGATCGTTAGATAAG 519–521 1.000 75.8
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT GGCCCGGATCGTTAGATAAG 520–522 1.000 75.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCACT 1448–1490 1.000 72.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AAGTGATCAGAGGGAACGGA ACGAATCGCACTTTTACCACT 1452–1494 1.000 72.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATCAGAGGGAACGGAGAGAG ACGAATCGCACTTTTACCACT 1447–1489 1.000 72.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCAC 1448–1490 1.000 72.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA CGAACGAATCGCACTTTTACC 1451–1493 1.000 72.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT ACTGAGGAAGCAGAAACCCT 278 1.000 63.5
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT CTGAGGAAGCAGAAACCCTT 277 1.000 63.4
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACTGAGGAAGCAGAAACCCT 218 1.000 62.7
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CTGAGGAAGCAGAAACCCTT 217 1.000 62.6
trnR-UCU-atpA_p5 trnR-UCU-atpA AGGAATGAAAAGCGTCCATTG ACTGAGGAAGCAGAAACCCT 279 1.000 61.2

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
Rohdea aurantiaca NC_070120.1 156927 View on NCBI ↗
Rohdea chinensis NC_070132.1 157102 View on NCBI ↗
Rohdea delavayi NC_070122.1 156855 View on NCBI ↗
Rohdea japonica NC_070119.1 156907 View on NCBI ↗