Markers + reference

Ascarina

2 species · Chloranthaceae · Chloranthales

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Species 2
Genome length 158–158 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1804 0.0105 1.00 51.3 yes View details
psbK-psbI LSC 403 0.0100 0.99 55.8 yes View details
trnS-GCU-trnG-UCC LSC 1144 0.0205 0.98 71.2 yes View details
trnC-GCA-petN LSC 900 0.0114 0.98 66.8 yes View details
trnT-UGU-trnL-UAA LSC 756 0.0127 0.94 61.4 yes View details
cemA LSC 744 0.0067 1.00 50.5 yes View details
ycf1 SSC 5628 0.0089 1.00 44.9 yes View details
ndhD SSC 1503 0.0040 1.00 53.8 yes View details
ndhD-ccsA SSC 269 0.0706 1.00 76.0 yes View details
rpl32-ndhF SSC 1188 0.0129 0.98 64.6 yes View details
psbA-trnK-UUU LSC 243 0.0247 1.00 66.7 yes View details
trnT-GGU-psbD LSC 1445 0.0078 0.97 65.7 yes View details
petG-trnW-CCA LSC 144 0.0147 0.94 65.5 yes View details
accD-psaI LSC 595 0.0118 1.00 65.4 yes View details
ndhC-trnV-UAC LSC 1619 0.0076 0.98 64.6 yes View details
trnF-GAA-ndhJ LSC 675 0.0133 1.00 64.1 yes View details
trnL-UAG-rpl32 SSC 1067 0.0122 1.00 63.4 yes View details
ycf3-trnS-GGA LSC 844 0.0083 1.00 63.3 yes View details
trnR-ACG-trnN-GUU IRb 580 0.0086 1.00 63.3 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
psbA-trnK-UUU_p1 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA GAAAGCCGTGTGCAATGAAA 395 1.000 80.0
psbA-trnK-UUU_p2 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC GAAAGCCGTGTGCAATGAAA 424 1.000 79.2
psbA-trnK-UUU_p3 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA ACGGTTTGGGGAGAGATCTT 366 1.000 78.4
psbA-trnK-UUU_p4 psbA-trnK-UUU GTGCTTTCGCGTCTCTCTAA AAAATGCAAGCACGGTTTGG 377 1.000 77.7
psbA-trnK-UUU_p5 psbA-trnK-UUU TCCAGTTACAAAAGCGACCC ACGGTTTGGGGAGAGATCTT 395 1.000 77.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1894–1895 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1892–1893 1.000 80.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1900–1901 1.000 79.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1876–1877 1.000 79.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1887–1888 1.000 78.6
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCCTCACGTCCAGGATTACG 535–540 1.000 73.7
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT TCCTCACGTCCAGGATTACG 532–537 1.000 71.7
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT TCCTCACGTCCAGGATTACG 533–538 1.000 71.7
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT TCCTCACGTCCAGGATTACG 534–539 1.000 71.7
psbK-psbI_p5 psbK-psbI TGCCAGTCATACCTGTGTTC TCCTCACGTCCAGGATTACG 573–578 1.000 70.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AACCGAAAGACCCCTTAACT 1253–1256 1.000 69.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AAACCGAAAGACCCCTTAACT 1254–1257 1.000 67.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACCGAAAGACCCCTTAACT 1301–1304 1.000 67.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AACCGAAAGACCCCTTAACT 1239–1242 1.000 66.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC AACCGAAAGACCCCTTAACT 1234–1237 1.000 65.8
trnG-UCC_p1 trnG-UCC AACACGTCAGCACTCCAATT TGCATGTTCAAATCAATGATGCA 925–926 1.000 55.1
trnG-UCC_p2 trnG-UCC ACACGTCAGCACTCCAATTT TGCATGTTCAAATCAATGATGCA 924–925 1.000 55.1
trnG-UCC_p3 trnG-UCC GTCTCACTCCCTTGTTCGAC TGCATGTTCAAATCAATGATGCA 877–878 1.000 54.9
trnG-UCC_p4 trnG-UCC TCTCACTCCCTTGTTCGACA TGCATGTTCAAATCAATGATGCA 876–877 1.000 53.0
trnG-UCC_p5 trnG-UCC ACACGTCAGCACTCCAATTT GCATGTTCAAATCAATGATGCA 923–924 1.000 52.8
trnC-GCA-petN_p1 trnC-GCA-petN CTGCAAATCCTTTCTCCCCA AGCGAGACTGACTGTATCCA 950–962 1.000 79.8
trnC-GCA-petN_p2 trnC-GCA-petN TGCAAATCCTTTCTCCCCAG AGCGAGACTGACTGTATCCA 949–961 1.000 79.8
trnC-GCA-petN_p3 trnC-GCA-petN ACTGCAAATCCTTTCTCCCC AGCGAGACTGACTGTATCCA 951–963 1.000 79.8
trnC-GCA-petN_p4 trnC-GCA-petN GCAAATCCTTTCTCCCCAGT AGCGAGACTGACTGTATCCA 948–960 1.000 79.8
trnC-GCA-petN_p5 trnC-GCA-petN GGGGACTGCAAATCCTTTCT AGCGAGACTGACTGTATCCA 955–967 1.000 79.8

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
Ascarina rubricaulis PQ728875.1 158415 View on NCBI ↗
Ascarina swamyana PQ728876.1 158381 View on NCBI ↗