Markers + reference

Stachyurus

5 species · Stachyuraceae · Crossosomatales

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Species 5
Genome length 162–163 kb
Candidate markers 274
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 407 0.0025 1.00 34.1 yes View details
psbK-psbI LSC 321 0.0037 1.00 36.9 yes View details
psbI-trnS-GCU LSC 186 0.0213 0.99 59.8 yes View details
trnC-GCA-petN LSC 997 0.0020 0.97 57.0 yes View details
trnS-UGA-psbZ LSC 331 0.0036 1.00 42.3 yes View details
psbZ-trnG-UCC LSC 433 0.0122 0.98 61.3 yes View details
trnG-UCC-trnfM-CAU LSC 241 0.0243 0.87 69.9 yes View details
rpl16 LSC 1520 0.0046 0.98 57.0 yes View details
ndhF SSC 2241 0.0023 1.00 30.3 yes View details
rpl32-trnL-UAG SSC 1051 0.0065 1.00 59.7 yes View details
ccsA SSC 960 0.0000 1.00 32.4 yes View details
ccsA-ndhD SSC 273 0.0256 1.00 70.0 yes View details
rps15-ycf1 SSC 395 0.0062 1.00 40.9 yes View details
ycf1 SSC 5640 0.0017 1.00 35.6 yes View details
rpl2-trnH-GUG LSC 201 0.0438 0.86 77.8 no View details
infA-rps8 LSC 127 0.0110 0.98 63.4 yes View details
rps4-trnT-UGU LSC 409 0.0073 0.98 57.1 yes View details
psbE-petL LSC 1352 0.0019 0.99 54.7 yes View details
ndhF-rpl32 SSC 1134 0.0009 1.00 54.0 yes View details
trnR-UCU-atpA LSC 387 0.0015 1.00 53.4 yes View details
rps16-trnQ-UUG LSC 1153 0.0009 1.00 52.9 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 100 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 CCTCTAGACCTAGCTGCTGT 472–473 1.000 78.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 486–487 1.000 78.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 485–486 1.000 78.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 487–488 1.000 78.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 475–476 1.000 78.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1216–1230 1.000 79.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACATCGCTTCAAACGAAG GAGGTTCGAATCCTTCCGTC 1196–1210 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGCGGATGTAAGAATCCACA GAGGTTCGAATCCTTCCGTC 1252–1266 1.000 77.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGCGGATGTAAGAATCCAC GAGGTTCGAATCCTTCCGTC 1253–1267 1.000 77.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1230–1244 1.000 77.3
psbK-psbI_p1 psbK-psbI CCAAATTACCCGAGGCCTAC TTCTTCACGCCCAGGATTAC 544–545 1.000 77.0
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTTCACGCCCAGGATTAC 458–459 1.000 76.9
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTCTTCACGCCCAGGATTAC 455–456 1.000 74.9
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTCTTCACGCCCAGGATTAC 456–457 1.000 74.9
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT TTCTTCACGCCCAGGATTAC 457–458 1.000 74.9
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA TGGACTAAAGCGTCGGATTG 273–288 1.000 81.3
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA GTGGACTAAAGCGTCGGATT 274–289 1.000 81.3
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA ATTGGGAGAGATGGCTGAGT 292–307 1.000 80.2
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA GACTAAAGCGTCGGATTGCT 271–286 1.000 78.5
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA CTGAGTGGACTAAAGCGTCG 278–293 1.000 78.3
trnR-UCU-atpA_p1 trnR-UCU-atpA ATCGGAATGAAAAGCGTCCA GGACCGCTTTCTACTTCAGG 490–510 1.000 83.2
trnR-UCU-atpA_p2 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT GGACCGCTTTCTACTTCAGG 489–509 1.000 83.2
trnR-UCU-atpA_p3 trnR-UCU-atpA ATCGGAATGAAAAGCGTCCA GAGGAAGCAGAAGCCCTTTT 534–554 1.000 82.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT GAGGAAGCAGAAGCCCTTTT 533–553 1.000 82.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT CATTCACCGAGGAAGCAGAA 541–561 1.000 82.1
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1031–1080 1.000 80.0
trnC-GCA-petN_p2 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGCCCAAGCGAGACTTACTA 1006–1055 1.000 79.1
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 1092–1141 1.000 78.2
trnC-GCA-petN_p4 trnC-GCA-petN AGTTCAAATCTGGGTGTCGC AGAGTCCACTTCTTCCCCAT 1067–1116 1.000 77.3
trnC-GCA-petN_p5 trnC-GCA-petN TTCAAATCTGGGTGTCGCC AGCCCAAGCGAGACTTACTA 1004–1053 1.000 74.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Stachyurus chinensis var. cuspidatus PX223373.1 162700 View on NCBI ↗
Stachyurus cordatulus PX223375.1 162297 View on NCBI ↗
Stachyurus obovatus PX223374.1 162688 View on NCBI ↗
Stachyurus praecox PX229811.1 162425 View on NCBI ↗
Stachyurus praecox var. matsuzakii PX229822.1 161624 View on NCBI ↗