Markers + reference

Dipelta

2 species · Caprifoliaceae · Dipsacales

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Species 2
Genome length 155–155 kb
Candidate markers 263
Primer pairs 85

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 8 remaining regions by MarkerSeek score (out of 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 1730 0.0568 0.98 90.0 yes View details
accD LSC 2151 0.0098 1.00 57.6 yes View details
petA-psbJ LSC 1007 0.0321 0.99 78.0 yes View details
psbJ-psbL LSC 266 0.0494 0.99 67.4 yes View details
rps18 LSC 615 0.0217 0.98 64.0 yes View details
rpl16 LSC 411 0.0000 1.00 22.6 yes View details
rpl16-rps3 LSC 1243 0.0154 0.99 68.5 yes View details
trnI-CAU-ycf2 IRb 184 0.1050 0.98 74.1 yes View details
ycf2 IRb 6774 0.0012 0.99 39.9 no View details
ycf2 IRa 6774 0.0012 0.99 39.9 yes View details
ycf2-trnI-CAU IRa 184 0.1050 0.98 74.1 yes View details
rpl32-trnL-UAG SSC 794 0.0052 0.97 64.3 yes View details
clpP-psbB LSC 631 0.0017 0.92 63.7 yes View details
psbM-trnD-GUC LSC 869 0.0047 0.98 63.6 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 yes View details
trnS-GCU-trnG-GCC LSC 782 0.0026 0.97 63.2 yes View details
rpl20-rps12 LSC 800 0.0013 0.97 62.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA TGAATCAAACCGAAAGATCCCT 886–901 1.000 63.6
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TGAATCAAACCGAAAGATCCCT 899–914 1.000 63.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA TGAATCAAACCGAAAGATCCCT 935–950 1.000 62.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AGCTCGTACAACGGATTAGC TGAATCAAACCGAAAGATCCCT 900–915 1.000 62.2
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC TAGTCCACTCAGCCATCTCC TGAATCAAACCGAAAGATCCCT 868–883 1.000 62.2
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAAAGGCGGTAGGGACTAG TTCAATTGGTCAGAGCACCG 987–998 1.000 76.3
psbM-trnD-GUC_p2 psbM-trnD-GUC GAAAGGCGGTAGGGACTAGA TTCAATTGGTCAGAGCACCG 986–997 1.000 76.2
psbM-trnD-GUC_p3 psbM-trnD-GUC AAAGGCGGTAGGGACTAGAA TTCAATTGGTCAGAGCACCG 985–996 1.000 76.1
psbM-trnD-GUC_p4 psbM-trnD-GUC AAGTAGAAAGGCGGTAGGGA TTCAATTGGTCAGAGCACCG 991–1002 1.000 76.1
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCGGTAGC TTCAATTGGTCAGAGCACCG 969–980 1.000 75.9
rbcL-accD_p1 rbcL-accD TAAACAGCTGTCTGGGGGTA TCAAGGATGGATCTAGGGGG 615–633 1.000 84.5
rbcL-accD_p2 rbcL-accD CATTCGGAGTTGCGATGAGA TCAAGGATGGATCTAGGGGG 243–261 1.000 84.3
rbcL-accD_p3 rbcL-accD GCTGCTTGTGAGGTATGGAA AAAGAGGACTCCACTTCGGA 2960–2969 1.000 83.5
rbcL-accD_p4 rbcL-accD GCTGCTTGTGAGGTATGGAA GGACTCCACTTCGAAATCCC 2919–2928 1.000 83.5
rbcL-accD_p5 rbcL-accD AATGAGGGACGTGATCTTGC GGACTCCACTTCGAAATCCC 2994 0.500 59.6
accD_p1 accD ACACGACATAGCAGAAATGAGA CGGGAGGAGGAAATTCGTTT 2344 0.500 39.5
accD_p2 accD ACACGACATAGCAGAAATGAGA TAAGGCGGGAGGAGGAAATT 2349 0.500 37.1
accD_p3 accD CGATGTTTAACACGACATAGCA CGGGAGGAGGAAATTCGTTT 2353 0.500 36.5
accD_p4 accD ACACGACATAGCAGAAATGAG CGGGAGGAGGAAATTCGTTT 2344 0.500 35.8
accD_p5 accD ACACGACATAGCAGAAATGAGAT CGGGAGGAGGAAATTCGTTT 2344 0.500 35.0
petA-psbJ_p1 petA-psbJ GGCCTTTTGTTCTTCTTGGC GGGTCATATTCCGGATTGGG 1133–1142 1.000 80.0
petA-psbJ_p2 petA-psbJ GGCCTTTTGTTCTTCTTGGC ATTCCGGATTGGGTTCATCC 1126–1135 1.000 78.7
petA-psbJ_p3 petA-psbJ CGTCCAAGGCCTTTTGTTCT GGGTCATATTCCGGATTGGG 1140–1149 1.000 75.8
petA-psbJ_p4 petA-psbJ GATCCATTACGCGTCCAAGG GGGTCATATTCCGGATTGGG 1151–1160 1.000 75.0
petA-psbJ_p5 petA-psbJ CGTCCAAGGCCTTTTGTTCT ATTCCGGATTGGGTTCATCC 1133–1142 1.000 74.5
psbJ-psbL_p1 psbJ-psbL TCCTAGCCTTCGTCACAAGA ACGACACAATCAAACCCGAA 1125–1132 1.000 83.2
psbJ-psbL_p2 psbJ-psbL TCCTAGCCTTCGTCACAAGA AACTGCCCGTTTTGATCCTT 1331–1338 1.000 82.9
psbJ-psbL_p3 psbJ-psbL TCCTAGCCTTCGTCACAAGA ACTGCCCGTTTTGATCCTTT 1330–1337 1.000 82.9
psbJ-psbL_p4 psbJ-psbL TCCTAGCCTTCGTCACAAGA TCCCTATTCATTGCGGGTTG 1444–1451 1.000 82.3
psbJ-psbL_p5 psbJ-psbL TCCTAGCCTTCGTCACAAGA GCACTGGCTTAGCTTACGAT 1413–1420 1.000 82.2

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
Dipelta floribunda NC_037955.1 155370 View on NCBI ↗
Dipelta yunnanensis NC_042201.1 155359 View on NCBI ↗