Markers + reference

Driessenia

3 species · Melastomataceae · Myrtales

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Species 3
Genome length 157–157 kb
Candidate markers 264
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0031 1.00 46.5 yes View details
rps16-trnQ-UUG LSC 994 0.0218 0.98 62.9 yes View details
atpF LSC 1372 0.0112 1.00 54.8 yes View details
atpH-atpI LSC 957 0.0201 0.99 61.5 yes View details
trnE-UUC-trnT-GGU LSC 953 0.0231 0.99 64.5 yes View details
petA-psbJ LSC 900 0.0359 0.99 82.5 yes View details
psbE-petL LSC 1155 0.0205 0.99 58.6 yes View details
rpl20-rps12 LSC 846 0.0150 1.00 57.6 yes View details
psbB-psbT LSC 186 0.0179 1.00 55.4 yes View details
ycf1 IRb 1899 0.0025 1.00 45.8 no View details
ndhF-rpl32 SSC 902 0.0312 0.98 69.2 yes View details
rps15-ycf1 SSC 351 0.0533 1.00 77.1 yes View details
ycf1 SSC 5613 0.0103 0.98 47.6 yes View details
rps12-clpP1 LSC 187 0.0517 1.00 80.0 yes View details
psbT-pbf1 LSC 72 0.1019 1.00 73.2 yes View details
trnT-UGU-trnL-UAA LSC 859 0.0170 0.96 72.6 yes View details
trnH-GUG-psbA LSC 228 0.0585 1.00 71.5 yes View details
rpoA-rps11 LSC 65 0.0410 1.00 69.3 yes View details
ndhB-trnL-CAA IRa 613 0.0074 0.95 67.8 yes View details
petG-trnW-CCA LSC 135 0.0207 0.96 65.8 yes View details
ccsA-ndhD SSC 321 0.0355 0.97 65.5 yes View details
psbZ-trnG-UCC LSC 315 0.0341 0.99 65.3 yes View details
trnW-CCA-trnP-UGG LSC 193 0.0227 0.99 64.8 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 110 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 GCGCTAACCTTGGTATGGAA 344–361 1.000 83.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 358–375 1.000 83.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 357–374 1.000 83.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 359–376 1.000 83.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 680–697 1.000 81.3
psbA_p1 psbA GATCCACTTGGCTACATCCG AACACAAAACTACTGGCCGT 2048–2070 1.000 80.2
psbA_p2 psbA GATCCACTTGGCTACATCCG ACAAAACTACTGGCCGTGTT 2045–2067 1.000 80.2
psbA_p3 psbA CAATCCACTGCCTTGATCCA AACACAAAACTACTGGCCGT 2062–2084 1.000 80.2
psbA_p4 psbA CAATCCACTGCCTTGATCCA ACAAAACTACTGGCCGTGTT 2059–2081 1.000 80.2
psbA_p5 psbA AATCCACTGCCTTGATCCAC ACAAAACTACTGGCCGTGTT 2058–2080 1.000 80.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1045–1059 1.000 77.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 1049–1063 1.000 72.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 1047–1061 1.000 71.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GGGTTTTGGTCCCGCTATTC 1066–1080 1.000 70.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCTTTCTACCACAT GAGGTTCGAATCCTTCCGTC 1047–1061 1.000 70.3
atpF_p1 atpF GCCTACTTGCAGGACAGTAC TTAGCTGTCGGACTTGCTTC 2248–2264 1.000 81.3
atpF_p2 atpF GCCTACTTGCAGGACAGTAC TGATTTCTGCCGCTTCTGTT 2280–2296 1.000 81.1
atpF_p3 atpF GTATCATCAAACCGTCCCCC TTAGCTGTCGGACTTGCTTC 2390–2406 1.000 81.0
atpF_p4 atpF GAAATCTCACCCCGACCATC TTAGCTGTCGGACTTGCTTC 2508–2524 1.000 80.8
atpF_p5 atpF GTATCATCAAACCGTCCCCC TGATTTCTGCCGCTTCTGTT 2422–2438 1.000 80.8
atpH-atpI_p1 atpH-atpI GAAGCAAGTCCGACAGCTAA CCATGGAGGGTCATCATTGA 1039–1069 1.000 75.3
atpH-atpI_p2 atpH-atpI GAAGCAAGTCCGACAGCTAA TCCATGGAGGGTCATCATTG 1040–1070 1.000 75.3
atpH-atpI_p3 atpH-atpI AACAGAAGCGGCAGAAATCA CCATGGAGGGTCATCATTGA 1007–1037 1.000 75.3
atpH-atpI_p4 atpH-atpI AACAGAAGCGGCAGAAATCA TCCATGGAGGGTCATCATTG 1008–1038 1.000 75.3
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG CCATGGAGGGTCATCATTGA 1017–1047 1.000 74.7
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGGATCAGGGAATTCTTGGG GAACCGATGACTTACGCCTT 1240–1281 1.000 84.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TCATTTCATGGCGGATCAGG GAACCGATGACTTACGCCTT 1251–1292 1.000 84.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGGATCAGGGAATTCTTGGG CCATGGCGTTACTCTACCAC 1219–1260 1.000 84.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TCATTTCATGGCGGATCAGG CCATGGCGTTACTCTACCAC 1230–1271 1.000 84.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGGATCAGGGAATTCTTGGG TAAACCCTTCTCTGCGAACG 1677–1731 1.000 83.9

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
Driessenia axantha NC_068187.1 156790 View on NCBI ↗
Driessenia glanduligera MK994879.1 156509 View on NCBI ↗
Driessenia phasmolacuna MK994923.1 156620 View on NCBI ↗