Markers + reference

Vallisneria

2 species · Hydrocharitaceae · Alismatales

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Species 2
Genome length 157–159 kb
Candidate markers 205
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 205 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-UGU-rps4 LSC 494 0.4466 0.95 81.5 yes View details
trnS-GGA-ycf3 LSC 788 0.4695 0.81 79.7 yes View details
ycf3 LSC 2063 0.4807 0.80 78.3 yes View details
ycf3-trnF-GAA LSC 571 0.4690 0.93 82.5 yes View details
psbE-petG LSC 1321 0.1752 0.87 83.6 yes View details
trnP-UGG-rps18 LSC 1461 0.2355 0.92 83.4 yes View details
trnL-UAA-trnM-CAU LSC 1070 0.1317 0.91 83.0 yes View details
trnW-CCA-trnP-UGG LSC 212 0.2359 0.92 81.3 yes View details
rpl14-rps3 LSC 742 0.1277 0.98 80.8 yes View details
rps18-rps12 LSC 1761 0.1754 0.85 80.4 yes View details
trnM-CAU-rps14 LSC 138 0.1716 0.97 80.2 yes View details
rps3 LSC 657 0.1796 1.00 78.9 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnM-CAU-rps14_p1 trnM-CAU-rps14 GAACCCGTGACTTCAAGGTT GCGCAACAAGATCAAGTTGG 218–247 1.000 86.5
trnM-CAU-rps14_p2 trnM-CAU-rps14 GAACCCGTGACTTCAAGGTT GGCGCAACAAGATCAAGTTG 219–248 1.000 86.5
trnM-CAU-rps14_p3 trnM-CAU-rps14 TTGAACCCGTGACTTCAAGG GCGCAACAAGATCAAGTTGG 220–249 1.000 86.4
trnM-CAU-rps14_p4 trnM-CAU-rps14 TTGAACCCGTGACTTCAAGG GGCGCAACAAGATCAAGTTG 221–250 1.000 86.4
trnM-CAU-rps14_p5 trnM-CAU-rps14 GGGATTTGAACCCGTGACTT GCGCAACAAGATCAAGTTGG 225–254 1.000 85.8
trnT-UGU-rps4_p1 trnT-UGU-rps4 GAGAAACCCCTTTTCCTGCA ACTAATTGCCTGGCGTTAGG 1206 0.500 59.7
trnT-UGU-rps4_p2 trnT-UGU-rps4 CCGCCAATAGCCAAGTTTTG ACTAATTGCCTGGCGTTAGG 1416 0.500 59.7
trnT-UGU-rps4_p3 trnT-UGU-rps4 TGAACTCAAATGCCTGTGCT ACTAATTGCCTGGCGTTAGG 943 0.500 59.6
trnT-UGU-rps4_p4 trnT-UGU-rps4 GTGAACTCAAATGCCTGTGC ACTAATTGCCTGGCGTTAGG 944 0.500 59.2
trnT-UGU-rps4_p5 trnT-UGU-rps4 GAGAAACCCCTTTTCCTGCA CCTGGCGTTAGGAATTGTCA 1198 0.500 59.1
trnS-GGA-ycf3_p1 trnS-GGA-ycf3 CTACACCTTCAACCACTCGG ATGCTTGTTGTCCCAACCAT 1330 0.500 59.2
trnS-GGA-ycf3_p2 trnS-GGA-ycf3 GATCGGTCAGATTGGCGAAT ATGCTTGTTGTCCCAACCAT 1429 0.500 58.9
trnS-GGA-ycf3_p3 trnS-GGA-ycf3 TGGCGAATTCGATGGATGAG ATGCTTGTTGTCCCAACCAT 1417 0.500 58.8
trnS-GGA-ycf3_p4 trnS-GGA-ycf3 GGCGAATTCGATGGATGAGA ATGCTTGTTGTCCCAACCAT 1416 0.500 58.6
trnS-GGA-ycf3_p5 trnS-GGA-ycf3 CTACACCTTCAACCACTCGG TCAACGCCTCTGATTTCCAG 1415 0.500 58.6
ycf3_p1 ycf3 AGGAAGGGGGATCTTCATGT ATCCTCTCCTTCCGGGTTTT 2949 0.500 55.0
ycf3_p2 ycf3 ATGTTTGTCAAGACCGACGG ATCCTCTCCTTCCGGGTTTT 2933 0.500 53.4
ycf3_p3 ycf3 AGGAAGGGGGATCTTCATGT TATCCTCTCCTTCCGGGTTT 2950 0.500 53.1
ycf3_p4 ycf3 AGGAAGGGGGATCTTCATGT TTATCCTCTCCTTCCGGGTT 2951 0.500 53.1
ycf3_p5 ycf3 AGGAAGGGGGATCTTCATGT TTTATCCTCTCCTTCCGGGT 2952 0.500 53.1
ycf3-trnF-GAA_p1 ycf3-trnF-GAA GAATGGATTGCTGAGCCGTA CCGTCGACTTGAGAAATCGT 1301 0.500 59.5
ycf3-trnF-GAA_p2 ycf3-trnF-GAA CAGAATTTTGGAAACGCGCT CCGTCGACTTGAGAAATCGT 1158 0.500 59.4
ycf3-trnF-GAA_p3 ycf3-trnF-GAA AGGGCACAGAATTGGTTGAG CCGTCGACTTGAGAAATCGT 1111 0.500 59.1
ycf3-trnF-GAA_p4 ycf3-trnF-GAA GGGCACAGAATTGGTTGAGA CCGTCGACTTGAGAAATCGT 1110 0.500 59.1
ycf3-trnF-GAA_p5 ycf3-trnF-GAA GTTTGGTTCGATCATGCTGC CCGTCGACTTGAGAAATCGT 1177 0.500 59.0
trnL-UAA_p1 trnL-UAA GGGACAGGGACTCAAAAAGG TGAATCAGAGCACATGGAGC 1589 0.500 59.0
trnL-UAA_p2 trnL-UAA AAGAAAGGGACAGGGACTCA TGAATCAGAGCACATGGAGC 1595 0.500 58.8
trnL-UAA_p3 trnL-UAA AGAAAGGGACAGGGACTCAA TGAATCAGAGCACATGGAGC 1594 0.500 58.8
trnL-UAA_p4 trnL-UAA CATGCCACCAAAAACTTGGG TGAATCAGAGCACATGGAGC 1415 0.500 58.8
trnL-UAA_p5 trnL-UAA GAGCTATCCTGACTCAACGC TGAATCAGAGCACATGGAGC 1654 0.500 58.5

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
Vallisneria denseserrulata x Vallisneria spiralis NC_068656.1 156576 View on NCBI ↗
Vallisneria natans NC_069975.1 159131 View on NCBI ↗