Markers + reference

Gironniera

2 species · Cannabaceae · Rosales

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Species 2
Genome length 158–168 kb
Candidate markers 264
Primer pairs 80

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 8 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC2-rpoB LSC 16537 0.0422 0.40 52.3 yes View details
ycf1 SSC 5646 0.3427 0.89 75.7 yes View details
ndhH SSC 1182 0.4753 0.91 82.4 yes View details
ndhA SSC 2310 0.4657 0.79 77.7 yes View details
ndhI SSC 504 0.4865 0.88 79.8 yes View details
ndhG SSC 531 0.4587 0.91 81.1 yes View details
psaC SSC 246 0.5000 0.93 76.9 yes View details
ndhD SSC 1503 0.4633 0.80 79.4 yes View details
rpl32-ndhF SSC 1234 0.4235 0.85 80.7 yes View details
ccsA SSC 966 0.4604 0.80 79.3 yes View details
trnL-UAG-rpl32 SSC 791 0.4035 0.80 79.3 yes View details
ycf1-rps15 SSC 419 0.4550 0.90 78.6 yes View details
ndhI-ndhG SSC 383 0.4258 0.93 78.6 yes View details
rps15 SSC 273 0.4397 0.94 77.2 yes View details
ndhF SSC 2259 0.4347 0.70 75.3 yes View details
rpl32 SSC 159 0.4317 0.87 75.2 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rpoC2-rpoB_p1 rpoC2-rpoB CCCTCCCTGTCATCGTATCT TGCCCCCTTATCTACTACGG 1822 0.500 59.9
rpoC2-rpoB_p2 rpoC2-rpoB TCCCTCCCTGTCATCGTATC TGCCCCCTTATCTACTACGG 1823 0.500 59.9
rpoC2-rpoB_p3 rpoC2-rpoB GTCTTGTCAACAACGCTTCG TGCCCCCTTATCTACTACGG 1227 0.500 59.9
rpoC2-rpoB_p4 rpoC2-rpoB CCCTCCCTGTCATCGTATCT GAACTACTGAAGCTGCTCCC 1664 0.500 59.8
rpoC2-rpoB_p5 rpoC2-rpoB CCCTCCCTGTCATCGTATCT GGAACTACTGAAGCTGCTCC 1665 0.500 59.8
ycf1_p1 ycf1 AATTTCCCGAATGGTCCGAG AGTTGTTTTCGGGGAGAACC 295 0.500 59.5
ycf1_p2 ycf1 GACGATTTGGAACACGAGGA AGTTGTTTTCGGGGAGAACC 908 0.500 59.2
ycf1_p3 ycf1 ACGATTTGGAACACGAGGAG AGTTGTTTTCGGGGAGAACC 907 0.500 59.2
ycf1_p4 ycf1 TCAAGCAAACGTACACTCCC AGTTGTTTTCGGGGAGAACC 642 0.500 58.8
ycf1_p5 ycf1 AGGAGGGAGAAATCGACGAA AGTTGTTTTCGGGGAGAACC 892 0.500 58.6
ycf1-rps15_p1 ycf1-rps15 ATGGAAGCGGGGTTTGATTT GATGAGTCGAAGAACGCCAT 1624 0.500 58.9
ycf1-rps15_p2 ycf1-rps15 ATGGAAGCGGGGTTTGATTT CTTCACCGTCGAGAGTAACG 1643 0.500 58.5
ycf1-rps15_p3 ycf1-rps15 ATGGAAGCGGGGTTTGATTT GGACCGAGCCATAACAGATG 1896 0.500 58.5
ycf1-rps15_p4 ycf1-rps15 ATGGAAGCGGGGTTTGATTT ACGGTTATTGCTTCGGTGAA 1785 0.500 58.1
ycf1-rps15_p5 ycf1-rps15 GCCCCTAGACGTCGTATAGA GATGAGTCGAAGAACGCCAT 1162 0.500 58.0
rps15_p1 rps15 GCCCCTAGACGTCGTATAGA AGCCATGAGGTAAATCAGCG 1586 0.500 58.3
rps15_p2 rps15 GCCCCTAGACGTCGTATAGA CATGAGGTAAATCAGCGGCT 1583 0.500 58.3
rps15_p3 rps15 AGCCCCTAGACGTCGTATAG AGCCATGAGGTAAATCAGCG 1587 0.500 58.2
rps15_p4 rps15 AGCCCCTAGACGTCGTATAG CATGAGGTAAATCAGCGGCT 1584 0.500 58.2
rps15_p5 rps15 GCCCCTAGACGTCGTATAGA GATGAGTCGAAGAACGCCAT 1162 0.500 58.0
ndhH_p1 ndhH CGCCAAAGGATGCTGTCTTA ACAAGGTGAGAGCCAAAAGG 1751 0.500 57.8
ndhH_p2 ndhH CGCCAAAGGATGCTGTCTTA GTTGTTGTATCCCTGCCGAT 1564 0.500 57.6
ndhH_p3 ndhH TTGGGAAAACGCCAAAGGAT ACAAGGTGAGAGCCAAAAGG 1760 0.500 57.6
ndhH_p4 ndhH GAAAACGCCAAAGGATGCTG ACAAGGTGAGAGCCAAAAGG 1756 0.500 57.5
ndhH_p5 ndhH CGCCAAAGGATGCTGTCTTA TGTCTTAACGAATCGCACGT 1954 0.500 57.5
ndhA_p1 ndhA TAGGGGATCAGAACGGGTTT ATTTCCAATCAACGACGGGT 2804 0.500 58.1
ndhA_p2 ndhA TAGGGGATCAGAACGGGTTT TAAACGACCCAGGGCAATTT 2986 0.500 57.3
ndhA_p3 ndhA ATAGGGGATCAGAACGGGTT ATTTCCAATCAACGACGGGT 2805 0.500 56.9
ndhA_p4 ndhA TCTAGAAGGAATTCCGGGGG ATTTCCAATCAACGACGGGT 2995 0.500 56.9
ndhA_p5 ndhA AACGGGTTTCCTTGGAGATG ATTTCCAATCAACGACGGGT 2793 0.500 56.8

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
Gironniera nervosa NC_084177.1 167688 View on NCBI ↗
Gironniera subaequalis NC_039729.1 157807 View on NCBI ↗