Markers + reference

Cuphea

7 species · Lythraceae · Myrtales

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Species 7
Genome length 159–160 kb
Candidate markers 266
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 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 424 0.1281 0.91 79.3 yes View details
trnK-UUU-rps16 LSC 882 0.0750 0.93 82.1 yes View details
rps16-trnQ-UUG LSC 1126 0.0754 0.98 84.4 yes View details
atpH-atpI LSC 1051 0.0706 1.00 84.3 yes View details
petN-psbM LSC 954 0.0661 0.99 83.6 yes View details
trnE-UUC-trnT-GGU LSC 1004 0.0770 0.96 82.9 yes View details
trnT-GGU-psbD LSC 1452 0.0532 0.98 85.1 yes View details
psbZ-trnG-GCC LSC 420 0.0797 0.88 76.9 yes View details
ycf1 IRb 1272 0.0158 0.99 60.6 no View details
ndhF-rpl32 SSC 1034 0.0880 0.97 87.2 yes View details
ycf1 SSC 5583 0.0507 1.00 73.5 yes View details
trnC-GCA-petN LSC 913 0.0491 0.97 88.4 yes View details
psbM-trnD-GUC LSC 1079 0.0534 0.99 88.4 yes View details
trnS-GCU-trnG-UCC LSC 777 0.0595 0.94 85.3 yes View details
ndhC-trnV-UAC LSC 1304 0.0520 0.98 85.0 yes View details
atpF-atpH LSC 545 0.0639 0.99 84.8 yes View details
rbcL-accD LSC 795 0.0513 0.99 84.5 yes View details
accD-psaI LSC 693 0.0533 0.98 84.2 yes View details
trnT-UGU-trnL-UAA LSC 713 0.0594 0.98 84.0 yes View details
trnF-GAA-ndhJ LSC 734 0.0487 0.99 83.9 yes View details
trnP-UGG-psaJ LSC 443 0.0754 1.00 83.8 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 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 TCGAAGCTCCATCTACAAATGG 429–584 1.000 73.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCGAAGCTCCATCTACAAATGG 443–598 1.000 73.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCGAAGCTCCATCTACAAATGG 442–597 1.000 73.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCGAAGCTCCATCTACAAATGG 444–599 1.000 73.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGAAGCTCCATCTACAAATGG 428–583 1.000 73.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CTTCCCCTTACCGGTCACTA GCAATTGATGTGCGATCTCG 1411–1504 0.857 85.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCAATTGATGTGCGATCTCG 1042–1138 0.857 84.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCAATTGATGTGCGATCTCG 1041–1137 0.857 84.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 GAAAACCCTTCCCCTTACCG GCAATTGATGTGCGATCTCG 1418–1511 0.857 84.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGGAAAACCCTTCCCCTTAC GCAATTGATGTGCGATCTCG 1420–1513 0.429 64.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 1194–1553 1.000 89.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GGGTTTTGGTCCCGGTATTC 1215–1574 1.000 86.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA TTCGGAGGTTCGAATCCTTC 1198–1557 1.000 85.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA TAAGGCAACGGGTTTTGGTC 1224–1583 1.000 85.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGCACGTTGCTTTTTACCAC GAGGTTCGAATCCTTCCGTC 1195–1554 1.000 84.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 815–861 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 814–860 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTCGTACAACGGATTAGCA ACGAATCACACTTTTACCACT 833–879 1.000 63.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCTCGTACAACGGATTAGC ACGAATCACACTTTTACCACT 834–880 1.000 62.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACGAATCACACTTTTACCACT 816–862 1.000 61.8
atpF-atpH_p1 atpF-atpH GAAAGAATCGGTTACATTTTTCA ATTTGCGAATCCTTTTGTGT 590–643 1.000 52.0
atpF-atpH_p2 atpF-atpH AAAGAATCGGTTACATTTTTCA ATTTGCGAATCCTTTTGTGT 589–642 1.000 52.0
atpF-atpH_p3 atpF-atpH GAAAGAATCGGTTACATTTTTCAT ATTTGCGAATCCTTTTGTGT 590–643 1.000 52.0
atpF-atpH_p4 atpF-atpH AAGAATCGGTTACATTTTTCAT ATTTGCGAATCCTTTTGTGT 588–641 1.000 52.0
atpF-atpH_p5 atpF-atpH GAAAGAATCGGTTACATTTTTCA TTGCGAATCCTTTTGTGTAA 588–641 1.000 52.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TCATGGGGAATTAGCTGCAC 1406–1593 1.000 91.2
atpH-atpI_p2 atpH-atpI GAAGCAAGTCCGACAGCTAA TCATGGGGAATTAGCTGCAC 1436–1623 1.000 90.9
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TCATGGGGAATTAGCTGCAC 1462–1649 1.000 90.6
atpH-atpI_p4 atpH-atpI TCCAGGTCCGATAGAAGCAA TCATGGGGAATTAGCTGCAC 1449–1636 1.000 90.4
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT AATTAGCTGCACCCACGAAT 1398–1585 0.857 84.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Cuphea arenarioides NC_082004.1 158528 View on NCBI ↗
Cuphea curiosa NC_081999.1 159799 View on NCBI ↗
Cuphea fruticosa NC_082003.1 158984 View on NCBI ↗
Cuphea hyssopifolia NC_046574.1 158821 View on NCBI ↗
Cuphea palustris NC_082001.1 159450 View on NCBI ↗
Cuphea spruceana NC_082000.1 158994 View on NCBI ↗
Cuphea tarapotensis NC_082002.1 159420 View on NCBI ↗