Markers + reference

Sasamorpha

3 species · Poaceae · Poales

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Species 3
Genome length 139–140 kb
Candidate markers 276
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpF LSC 1411 0.0034 0.99 35.6 yes View details
rbcL-accD LSC 537 0.0087 1.00 36.3 yes View details
psaI-ycf4 LSC 370 0.0055 0.98 44.1 yes View details
clpP LSC 651 0.0061 1.00 50.2 yes View details
petD LSC 1232 0.0011 1.00 36.0 yes View details
petD-rpoA LSC 241 0.0313 0.88 61.6 yes View details
ndhF-rpl32 SSC 864 0.0108 1.00 47.8 yes View details
ndhG-ndhI SSC 246 0.0298 1.00 59.0 yes View details
ndhA SSC 2115 0.0028 1.00 37.2 yes View details
psbT-psbN LSC 48 0.0694 1.00 75.0 yes View details
rps16-trnQ LSC 1525 0.0031 1.00 60.6 yes View details
matK-trnK LSC 690 0.0039 1.00 59.4 yes View details
rpl14-rpl16 LSC 111 0.0183 0.98 54.9 yes View details
trnC-rpoB LSC 1160 0.0034 1.00 54.3 yes View details
clpP-psbB LSC 494 0.0027 1.00 52.9 yes View details
trnT-trnL LSC 826 0.0041 0.99 50.0 yes View details
trnK-rps16 LSC 556 0.0060 1.00 49.2 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK_p1 trnK TACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2754–2760 1.000 73.6
trnK_p2 trnK ACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2753–2759 1.000 73.6
trnK_p3 trnK ATACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2755–2761 1.000 69.6
trnK_p4 trnK TACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2754–2760 1.000 67.1
trnK_p5 trnK CAATGTCAACCAAGCCAGC CGTGCGGTGTAATTCCATTG 2751–2757 1.000 66.9
matK-trnK_p1 matK-trnK ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 859–865 1.000 68.6
matK-trnK_p2 matK-trnK ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 859–865 1.000 66.7
matK-trnK_p3 matK-trnK CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 858–864 1.000 66.7
matK-trnK_p4 matK-trnK ACTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 800–806 1.000 62.2
matK-trnK_p5 matK-trnK ACTCCTGAAAGAGAAGTGGGTA CGTGCGGTGTAATTCCATTG 859–865 1.000 61.9
trnK-rps16_p1 trnK-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 690 1.000 67.0
trnK-rps16_p2 trnK-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 691 1.000 65.7
trnK-rps16_p3 trnK-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 688 1.000 65.7
trnK-rps16_p4 trnK-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 687 1.000 65.3
trnK-rps16_p5 trnK-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 689 1.000 64.7
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1599–1607 1.000 78.6
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1610–1618 1.000 78.1
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1603–1611 1.000 77.5
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1614–1622 1.000 77.0
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1659–1667 1.000 76.9
trnG_p1 trnG CAAACTGCTCTACTCCGCTC CTCGAATGGCTACCCTTGAC 906 1.000 77.0
trnG_p2 trnG CAAACTGCTCTACTCCGCTC CGAATGGCTACCCTTGACAA 904 1.000 76.7
trnG_p3 trnG TGGTGGACGAAAAAGGTTGA CTCGAATGGCTACCCTTGAC 871 1.000 76.6
trnG_p4 trnG AACTGGTGGACGAAAAAGGT CTCGAATGGCTACCCTTGAC 874 1.000 76.5
trnG_p5 trnG ACTGGTGGACGAAAAAGGTT CTCGAATGGCTACCCTTGAC 873 1.000 76.5
trnC-rpoB_p1 trnC-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1244–1263 1.000 77.2
trnC-rpoB_p2 trnC-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1243–1262 1.000 77.2
trnC-rpoB_p3 trnC-rpoB AAAGGATTTGCAGTCCCCTG AAGTTCTTCTGCCAAGCCTT 1308–1327 1.000 76.8
trnC-rpoB_p4 trnC-rpoB AAAGGATTTGCAGTCCCCTG AGTTCTTCTGCCAAGCCTTG 1307–1326 1.000 76.7
trnC-rpoB_p5 trnC-rpoB AAAGGATTTGCAGTCCCCTG CAAGTTCTTCTGCCAAGCCT 1309–1328 1.000 76.7

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
Sasamorpha borealis PP545473.1 139032 View on NCBI ↗
Sasamorpha hubeiensis PP681297.1 139698 View on NCBI ↗
Sasamorpha qingyuanensis PP590241.1 139663 View on NCBI ↗