Markers + reference

Hydrostachys

3 species · Hydrostachyaceae · Cornales

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Species 3
Genome length 156–156 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1086 0.0738 0.97 86.2 yes View details
rps16-trnQ-UUG LSC 280 0.0860 1.00 78.5 yes View details
trnS-GCU-trnG-UCC LSC 675 0.0924 0.98 86.1 yes View details
rpoB-trnC-GCA LSC 1408 0.0436 0.99 76.5 yes View details
trnT-UGU-trnL-UAA LSC 931 0.0484 1.00 80.6 yes View details
atpB-rbcL LSC 900 0.0399 0.99 71.4 yes View details
trnP-GGG-psaJ LSC 536 0.0361 0.98 73.6 yes View details
ycf1 IRb 893 0.0022 1.00 36.9 no View details
ndhF-rpl32 SSC 647 0.0726 0.99 85.2 yes View details
rpl32-trnL-UAG SSC 730 0.0736 0.99 81.3 yes View details
ycf1 SSC 5553 0.0317 1.00 59.5 yes View details
trnG-UCC-trnR-UCU LSC 133 0.0758 0.99 84.9 yes View details
trnW-CCA-trnP-UGG LSC 202 0.1010 0.98 82.2 yes View details
trnS-GGA-rps4 LSC 344 0.0514 0.96 81.7 yes View details
atpH-atpI LSC 1144 0.0452 0.99 81.1 yes View details
trnE-UUC-trnT-GGU LSC 828 0.0431 1.00 79.5 yes View details
trnR-UCU-atpA LSC 160 0.0708 1.00 79.0 yes View details
psbI-trnS-GCU LSC 158 0.0743 0.99 78.8 yes View details
trnH-GUG-psbA LSC 158 0.1013 1.00 78.4 yes View details
psaA-ycf3 LSC 1149 0.0413 0.98 78.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 605–613 1.000 83.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 604–612 1.000 83.7
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 619–627 1.000 83.6
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 618–626 1.000 83.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 620–628 1.000 83.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCAAAGAGCATCAATTTAATCA 1146–1169 1.000 51.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA TCAAAGAGCATCAATTTAATCA 1147–1170 1.000 51.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGAGTCGCACTTAAAAGCC TCAAAGAGCATCAATTTAATCA 1149–1172 1.000 51.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TCAAAGAGCATCAATTTAATCAA 1146–1169 1.000 51.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG TTCAAAGAGCATCAATTTAATCA 1147–1170 1.000 51.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 360–404 1.000 87.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACCGGATCGTGTCTTTCAAG GAGGTTCGAATCCTTCCGTC 370–414 1.000 86.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCGGATCGTGTCTTTCAAGT GAGGTTCGAATCCTTCCGTC 369–413 1.000 86.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 353–397 1.000 86.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCGTGTCTTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 365–409 1.000 85.8
psbI-trnS-GCU_p1 psbI-trnS-GCU GCAATAAAAATGGCGCACCT TGGACTAAAGCGTCGGATTG 494–505 1.000 86.4
psbI-trnS-GCU_p2 psbI-trnS-GCU GCAATAAAAATGGCGCACCT GTGGACTAAAGCGTCGGATT 495–506 1.000 86.4
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 655–666 1.000 86.3
psbI-trnS-GCU_p4 psbI-trnS-GCU GTTTGGCAAGCTGCTGTAAG GTGGACTAAAGCGTCGGATT 656–667 1.000 86.3
psbI-trnS-GCU_p5 psbI-trnS-GCU GCAATAAAAATGGCGCACCT TAGGAGAGATGGCTGAGTGG 511–522 1.000 85.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 744–899 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 743–898 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 747–902 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 746–901 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 745–900 1.000 62.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTATGTCCT 219–247 1.000 52.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTATGTCCTATCCA 213–241 1.000 52.8
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTATGTCCT 222–250 1.000 52.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTATGTCCTATCCA 216–244 1.000 52.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG ACCAAAGGTTTAGAAGACCTATGT 224–252 1.000 52.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Hydrostachys goudotiana NC_044800.1 156122 View on NCBI ↗
Hydrostachys imbricata NC_044799.1 155653 View on NCBI ↗
Hydrostachys polymorpha NC_044847.1 156250 View on NCBI ↗