Markers + reference

Gillenia

2 species · Rosaceae · Rosales

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Species 2
Genome length 159–160 kb
Candidate markers 267
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 253 0.0279 0.99 56.9 yes View details
trnK-UUU-rps16 LSC 775 0.0251 0.98 64.1 yes View details
psbK-psbl LSC 257 0.0558 0.98 69.9 yes View details
trnR-UCU-atpA LSC 523 0.0299 0.96 65.3 yes View details
psbZ-trnG-GCC LSC 496 0.0357 0.90 73.5 yes View details
rps4-trnT-UGU LSC 400 0.0347 0.94 66.4 yes View details
trnT-UGU-trnL-UAA LSC 1052 0.0193 0.98 63.2 yes View details
trnF-GAA-ndhJ LSC 734 0.0236 0.98 59.6 yes View details
rpl32-trnL-UAG SSC 1166 0.1941 0.95 88.6 yes View details
ycf1 SSC 5616 0.0155 1.00 50.6 yes View details
rps16-trnQ-UUG LSC 842 0.0213 0.95 70.9 yes View details
ndhF-rpl32 SSC 1093 0.0172 0.96 70.0 yes View details
atpH-atpI LSC 1132 0.0168 1.00 68.7 yes View details
psaA-ycf3 LSC 704 0.0170 1.00 68.6 yes View details
atpF-atpH LSC 461 0.0197 0.99 68.0 yes View details
trnD-GUC-trnY-GUA LSC 441 0.0147 0.93 67.9 yes View details
rps8-rpl14 LSC 162 0.0370 1.00 67.3 yes View details
ndhE-ndhG SSC 251 0.0206 0.97 67.3 yes View details
rpl2-trnH-GUG LSC 331 0.0481 0.63 66.7 no 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 GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 309–313 1.000 79.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 323–327 1.000 78.9
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 322–326 1.000 78.9
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 324–328 1.000 78.9
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCTGCTGTTGAAGTTCCATC 308–312 1.000 76.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGGTTTTTACGGAACTTCGC 856–869 1.000 79.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTTTTTACGGAACTTCGCC 855–868 1.000 79.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGGTTTTTACGGAACTTCGC 855–868 1.000 79.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTTTTTACGGAACTTCGCC 854–867 1.000 79.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTTTTTACGGAACTTCGCC 864–877 1.000 78.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 886–926 1.000 83.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 863–903 1.000 81.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 896–936 1.000 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 897–937 1.000 81.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 948–988 1.000 80.5
psbK-psbl_p1 psbK-psbl GTTTGGCAAGCTGCTGTAAG TGGACTAAAGCGTCGGATTG 613–619 1.000 83.0
psbK-psbl_p2 psbK-psbl CGTGGGTCAGGTATGTTCTG TGGACTAAAGCGTCGGATTG 1253–1260 1.000 81.7
psbK-psbl_p3 psbK-psbl CGTGGGTCAGGTATGTTCTG GTGGACTAAAGCGTCGGATT 1254–1261 1.000 81.7
psbK-psbl_p4 psbK-psbl CGTGGGTCAGGTATGTTCTG TTTGGAGGAGAGATGGCTGA 1274–1281 1.000 81.6
psbK-psbl_p5 psbK-psbl CGTGGGTCAGGTATGTTCTG GCCGTGGAACTAAAAAGCAC 1374 0.500 59.5
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 616–631 1.000 68.2
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCCCTTTTGAAAGAAGC 597–612 1.000 63.1
trnR-UCU-atpA_p3 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA AGACATTTACCGACGAAGCG 615–630 1.000 62.6
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACCAAGACATTTACCGACGA 620–635 1.000 62.3
trnR-UCU-atpA_p5 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAACAGATGGAACGTT 573–588 1.000 61.8
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CTGGTTGTCGCATTAGCTCT 575–609 1.000 80.7
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGACTGGTTGTCGCATTAG 579–613 1.000 80.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG ACTGGTTGTCGCATTAGCTC 576–610 1.000 78.6
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GACTGGTTGTCGCATTAGCT 577–611 1.000 78.6
atpF-atpH_p5 atpF-atpH GATGGCCAATAACCCAAGGA CTGGTTGTCGCATTAGCTCT 553–587 1.000 78.1

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
Gillenia stipulata NC_045321.1 159575 View on NCBI ↗
Gillenia trifoliata NC_045311.1 159400 View on NCBI ↗