Markers + reference

Didymocarpus

11 species · Gesneriaceae · Lamiales

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Species 11
Genome length 153–154 kb
Candidate markers 266
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 302 0.0495 1.00 78.3 yes View details
trnS-GCU-trnG-UCC LSC 901 0.0274 0.94 74.4 yes View details
ndhC-trnV-UAC LSC 1043 0.0198 1.00 70.9 yes View details
petA-psbJ LSC 1033 0.0195 1.00 71.8 yes View details
ndhF SSC 2286 0.0200 1.00 61.4 yes View details
ndhF-rpl32 SSC 793 0.0330 0.99 75.7 yes View details
rpl32-trnL-UAG SSC 902 0.0257 0.99 73.2 yes View details
ycf1 SSC 4824 0.0215 1.00 58.9 yes View details
rps4-trnT-UGU LSC 391 0.0236 0.98 78.2 yes View details
rps16-trnQ-UUG LSC 1089 0.0197 0.98 75.0 yes View details
atpA-atpF LSC 76 0.0861 0.87 72.9 yes View details
trnG-UCC-trnR-UCU LSC 182 0.0451 1.00 72.7 yes View details
atpB-rbcL LSC 771 0.0112 1.00 67.4 yes View details
trnT-UGU-trnL-UAA LSC 652 0.0135 1.00 66.4 yes View details
trnF-GAA-ndhJ LSC 636 0.0124 1.00 66.1 yes View details
psbA-trnK-UUU LSC 226 0.0238 1.00 65.9 yes View details
ycf3-trnS-GGA LSC 843 0.0142 1.00 65.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 748–799 1.000 87.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 762–813 1.000 87.6
trnH-GUG-psbA_p3 trnH-GUG-psbA TATTTGTAGGGCGAACGACG TCAGTGCTATGCATGGTTCC 813 0.091 42.6
trnH-GUG-psbA_p4 trnH-GUG-psbA TATTTGTAGGGCGAACGACG CAGTGCTATGCATGGTTCCT 812 0.091 42.5
trnH-GUG-psbA_p5 trnH-GUG-psbA TATTTGTAGGGCGAACGACG GGTGTAGCTGGTGTATTCGG 844 0.091 42.4
psbA-trnK-UUU_p1 psbA-trnK-UUU CCCCATAGGCTTTCGCTTTC CTAGTTCCGGGTTCGAATCC 285–308 1.000 80.0
psbA-trnK-UUU_p2 psbA-trnK-UUU TCGCGTCTCTCTAAAATTGCA CTAGTTCCGGGTTCGAATCC 267–290 1.000 79.8
psbA-trnK-UUU_p3 psbA-trnK-UUU CCCCATAGGCTTTCGCTTT CTAGTTCCGGGTTCGAATCC 285–308 1.000 78.2
psbA-trnK-UUU_p4 psbA-trnK-UUU CGCGTCTCTCTAAAATTGCAG CTAGTTCCGGGTTCGAATCC 266–289 1.000 77.8
psbA-trnK-UUU_p5 psbA-trnK-UUU CCCATAGGCTTTCGCTTTCG CTAGTTCCGGGTTCGAATCC 284–307 1.000 77.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1113–1201 1.000 88.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1096–1184 1.000 87.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1114–1202 1.000 87.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1111–1199 1.000 85.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1110–1198 1.000 85.9
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 824–970 1.000 62.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 823–969 1.000 62.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 827–973 1.000 61.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 826–972 1.000 61.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 825–971 1.000 61.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG TGTCCTATCCATTAGACAATG 252–279 1.000 52.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU ACCCTTAGCCTTCCAAGCTA TGTCCTATCCATTAGACAATG 258–285 1.000 52.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU CTAACGATGCGGGTTCGATT TGTCCTATCCATTAGACAATG 241–268 1.000 52.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU TAACGATGCGGGTTCGATTC TGTCCTATCCATTAGACAATG 240–267 1.000 52.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU TAACCCTTAGCCTTCCAAGC TGTCCTATCCATTAGACAATG 260–287 1.000 52.0
atpA-atpF_p1 atpA-atpF CACTTGAAGTACGGTACCGG ACATGTTGGGAGCGATGAAA 194–259 1.000 87.8
atpA-atpF_p2 atpA-atpF CCACTTGAAGTACGGTACCG ACATGTTGGGAGCGATGAAA 195–260 1.000 87.8
atpA-atpF_p3 atpA-atpF CAATACCATCGCCCACTTGA ACATGTTGGGAGCGATGAAA 207–272 1.000 87.3
atpA-atpF_p4 atpA-atpF CACTTGAAGTACGGTACCGG GACATGTTGGGAGCGATGAA 195–260 1.000 87.3
atpA-atpF_p5 atpA-atpF CCACTTGAAGTACGGTACCG GACATGTTGGGAGCGATGAA 196–261 1.000 87.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Didymocarpus cortusifolius NC_086896.1 153628 View on NCBI ↗
Didymocarpus dissectus NC_086892.1 153841 View on NCBI ↗
Didymocarpus glandulosus var. minor PP296632.1 153439 View on NCBI ↗
Didymocarpus heucherifolius NC_086895.1 153701 View on NCBI ↗
Didymocarpus heucherifolius var. gamosepalus PP296631.1 153588 View on NCBI ↗
Didymocarpus heucherifolius var. yinzhengii PP296621.1 153832 View on NCBI ↗
Didymocarpus lobulatus NC_086894.1 153580 View on NCBI ↗
Didymocarpus purpureobracteatus NC_086890.1 153263 View on NCBI ↗
Didymocarpus salviiflorus NC_086893.1 154046 View on NCBI ↗
Didymocarpus sinoprimulinus NC_086891.1 153652 View on NCBI ↗
Didymocarpus yuenlingensis NC_086889.1 153931 View on NCBI ↗