Markers + reference

Yushania

9 species · Poaceae · Poales

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Species 9
Genome length 140–140 kb
Candidate markers 268
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-UCC-trnT-GGU LSC 1972 0.0024 1.00 40.6 yes View details
rpoC1 LSC 2049 0.0008 1.00 41.5 yes View details
trnT-UGU-trnL-UAA LSC 818 0.0023 1.00 51.2 yes View details
rbcL-psaI LSC 1286 0.0019 1.00 48.2 yes View details
rps19 IRb 282 0.0000 1.00 25.9 no View details
rps15 SSC 273 0.0000 1.00 19.6 no View details
ndhF-rpl32 SSC 910 0.0017 0.98 52.1 yes View details
rpl32-trnL-UAG SSC 702 0.0040 1.00 52.1 yes View details
ndhA SSC 2088 0.0009 1.00 45.9 yes View details
rps15 SSC 273 0.0000 1.00 19.6 yes View details
rps19 IRa 282 0.0000 1.00 21.5 yes View details
rps16-trnQ-UUG LSC 1541 0.0007 0.99 51.5 yes View details
ycf3 LSC 2001 0.0001 1.00 49.8 yes View details
matK-trnK-UUU LSC 650 0.0017 1.00 48.0 yes View details
petA-psbJ LSC 991 0.0006 0.99 47.4 yes View details
trnD-GUC-psbM LSC 989 0.0009 1.00 47.3 yes View details
trnC-GCA-rpoB LSC 1179 0.0006 1.00 46.9 yes View details
rps19-psbA LSC 128 0.0129 1.00 46.5 no View details
atpI-atpH LSC 816 0.0008 1.00 45.1 yes View details
rps16 LSC 1087 0.0008 1.00 45.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2717–2760 1.000 73.6
trnK-UUU_p2 trnK-UUU ACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2716–2759 1.000 73.6
trnK-UUU_p3 trnK-UUU ATACCAATGTCAACCAAGCCA CGTGCGGTGTAATTCCATTG 2718–2761 1.000 69.6
trnK-UUU_p4 trnK-UUU TACCAATGTCAACCAAGCCAG CGTGCGGTGTAATTCCATTG 2717–2760 1.000 67.0
trnK-UUU_p5 trnK-UUU CAATGTCAACCAAGCCAGC CGTGCGGTGTAATTCCATTG 2714–2757 1.000 66.9
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 822–865 1.000 68.6
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG CGTGCGGTGTAATTCCATTG 822–865 1.000 66.8
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT CGTGCGGTGTAATTCCATTG 821–864 1.000 66.8
matK-trnK-UUU_p4 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT TGGGTTGCTAACTCAATGGT 763–806 1.000 62.3
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA CGTGCGGTGTAATTCCATTG 822–865 1.000 61.9
rps16_p1 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGA 1248–1252 1.000 51.2
rps16_p2 rps16 TGGCACGACATAAATCCAGT TCAATTCCCTATACCACTTTGCA 1253–1257 1.000 48.5
rps16_p3 rps16 TGGCACGACATAAATCCAGT TCCCTATACCACTTTGCAATGAA 1248–1252 1.000 48.5
rps16_p4 rps16 TGGCACGACATAAATCCAGT TTCCCTATACCACTTTGCAATGA 1249–1253 1.000 48.5
rps16_p5 rps16 TGGCACGACATAAATCCAGT CCCTATACCACTTTGCAATGA 1247–1251 1.000 47.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1607–1615 1.000 78.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1618–1626 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1611–1619 1.000 77.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1622–1630 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAAACCAGAAATGGGGCGT 1667–1675 1.000 77.1
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT GCGTTCAGACCAAAAATGCA 2941–2947 1.000 79.2
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU CATCGTTAGCTTGGAAGGCT TGCTTCGTTTAGCGTTCAGA 2952–2958 1.000 79.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU TTTCCACCGAGCTGAAACAA GCGTTCAGACCAAAAATGCA 2660–2666 1.000 79.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU TTTCCACCGAGCTGAAACAA TGCTTCGTTTAGCGTTCAGA 2671–2677 1.000 79.0
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU CGTTAGCTTGGAAGGCTAGG GCGTTCAGACCAAAAATGCA 2938–2944 1.000 79.0
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCA 1073–1075 1.000 48.4
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TGCGAGAATATTGACTTCCA 1105–1107 1.000 47.0
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATGCGAGAATATTGACTTCCA 1074–1076 1.000 45.3
trnD-GUC-psbM_p4 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TGCGAGAATATTGACTTCCAT 1073–1075 1.000 45.3
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC TGCGAGAATATTGACTTCCA 1074–1076 1.000 44.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Yushania brevipaniculata NC_043894.1 139568 View on NCBI ↗
Yushania confusa NC_043893.1 139601 View on NCBI ↗
Yushania glandulosa NC_043947.1 139621 View on NCBI ↗
Yushania maculata OR750784.1 139635 View on NCBI ↗
Yushania niitakayamensis NC_062890.1 139619 View on NCBI ↗
Yushania polytricha OR750783.1 139621 View on NCBI ↗
Yushania rubrovaginata PQ010623.1 139609 View on NCBI ↗
Yushania shuichengensis (nom. ined.) OR750781.1 139615 View on NCBI ↗
Yushania violascens NC_043946.1 139605 View on NCBI ↗