Markers + reference

Widdringtonia

2 species · Cupressaceae · Cupressales

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Species 2
Genome length 123–123 kb
Candidate markers 235
Primer pairs 50

Genome-wide nucleotide diversity

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

Candidate markers

1 hotspot label from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 235 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA Genome 1062 0.0000 1.00 40.0 yes View details
accD-ycf1 Genome 1091 0.0000 0.94 63.4 yes View details
trnI-CAU-psbA Genome 108 0.0000 1.00 58.7 no View details
matK Genome 1521 0.0000 1.00 40.0 yes View details
matK-trnK-UUU Genome 642 0.0000 1.00 40.0 yes View details
trnK-UUU-chlB Genome 1392 0.0000 1.00 40.0 yes View details
rps4 Genome 606 0.0000 1.00 40.0 yes View details
psbC Genome 1422 0.0000 1.00 40.0 yes View details
psbD Genome 1062 0.0000 1.00 40.0 yes View details
psbD-trnT-GGU Genome 968 0.0000 1.00 40.0 yes View details
trnD-GUC-psbM Genome 680 0.0000 1.00 40.0 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 50 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGCCAAGCAGCTAAAAAGA TCCCTACCCTATTGACTGCA 725 1.000 75.5
psbA_p2 psbA TGGCCAAGCAGCTAAAAAGA ACCCTATTGACTGCAACCTC 720 1.000 73.6
psbA_p3 psbA ACTGGCCAAGCAGCTAAAAA TCCCTACCCTATTGACTGCA 727 1.000 73.1
psbA_p4 psbA GCCATAGTGCTAATGCCCAA TCCCTACCCTATTGACTGCA 769 1.000 73.0
psbA_p5 psbA CTATTACTGGCCAAGCAGCT TCCCTACCCTATTGACTGCA 732 1.000 72.8
matK_p1 matK TGTAGGGATTGATCCTGGCA ATAATCCAAGAGGGGTCCGG 1598 1.000 74.6
matK_p2 matK TTTCATTGCACACGGCTTTC ATAATCCAAGAGGGGTCCGG 1672 1.000 74.4
matK_p3 matK GCACACGGCTTTCTCCATAT ATAATCCAAGAGGGGTCCGG 1665 1.000 72.8
matK_p4 matK CTGTAGGGATTGATCCTGGC ATAATCCAAGAGGGGTCCGG 1599 1.000 71.0
matK_p5 matK TTTTCATTGCACACGGCTTT ATAATCCAAGAGGGGTCCGG 1673 1.000 70.7
matK-trnK-UUU_p1 matK-trnK-UUU TGCGTAAAGATCTTCCCGAA TCAATGGTAGAGTACTCGGCT 752 1.000 63.5
matK-trnK-UUU_p2 matK-trnK-UUU TTGCGTAAAGATCTTCCCGA TCAATGGTAGAGTACTCGGCT 753 1.000 63.5
matK-trnK-UUU_p3 matK-trnK-UUU TGCGTAAAGATCTTCCCGAA AGGGTTGCTAACTCAATGGT 764 1.000 61.5
matK-trnK-UUU_p4 matK-trnK-UUU TTGCGTAAAGATCTTCCCGA AGGGTTGCTAACTCAATGGT 765 1.000 61.5
matK-trnK-UUU_p5 matK-trnK-UUU TGCGTAAAGATCTTCCCGAAA TCAATGGTAGAGTACTCGGCT 752 1.000 61.3
trnK-UUU-chlB_p1 trnK-UUU-chlB AGTCGCACTTAAAAGCCGAG TTGCACGACAAAAGGGGATT 1511 1.000 73.0
trnK-UUU-chlB_p2 trnK-UUU-chlB AGTCGCACTTAAAAGCCGAG TTTGCACGACAAAAGGGGAT 1512 1.000 73.0
trnK-UUU-chlB_p3 trnK-UUU-chlB TAGTCGCACTTAAAAGCCGA TTGCACGACAAAAGGGGATT 1512 1.000 71.8
trnK-UUU-chlB_p4 trnK-UUU-chlB TCGCACTTAAAAGCCGAGTA TTGCACGACAAAAGGGGATT 1509 1.000 71.8
trnK-UUU-chlB_p5 trnK-UUU-chlB TCGCACTTAAAAGCCGAGTA TTTGCACGACAAAAGGGGAT 1510 1.000 71.8
rps4_p1 rps4 TCCTCTTTCCAACATTATTTGTTCT ACAGAGGAACAGATGTGCAT 698 1.000 40.0
rps4_p2 rps4 TCCTCTTTCCAACATTATTTGTTC ACAGAGGAACAGATGTGCAT 698 1.000 40.0
rps4_p3 rps4 TCCTCTTTCCAACATTATTTGT ACAGAGGAACAGATGTGCAT 698 1.000 40.0
rps4_p4 rps4 CCTCTTTCCAACATTATTTGTTCT ACAGAGGAACAGATGTGCAT 697 1.000 40.0
rps4_p5 rps4 TCCTCTTTCCAACATTATTTGTTCTT ACAGAGGAACAGATGTGCAT 698 1.000 40.0
psbC_p1 psbC CCGAGCACCAAAGATTCAGT GAGATTCGTGCAGCAGAAGA 1595 1.000 78.5
psbC_p2 psbC CCGAGCACCAAAGATTCAGT GTGCAGCAGAAGATCCTGAA 1588 1.000 77.7
psbC_p3 psbC CCGAGCACCAAAGATTCAGT AGGTATTCGTGCTTGGATGG 1530 1.000 75.9
psbC_p4 psbC CCGAGCACCAAAGATTCAGT ATTCGTGCAGCAGAAGATCC 1592 1.000 75.8
psbC_p5 psbC CCGAGCACCAAAGATTCAGT TGTTTCCCAGGAGATTCGTG 1605 1.000 74.7

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
Widdringtonia nodiflora MW470997.1 123221 View on NCBI ↗
Widdringtonia schwarzii LC500584.1 123190 View on NCBI ↗