Markers + reference

Koeleria

4 species · Poaceae · Poales

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Species 4
Genome length 136–136 kb
Candidate markers 265
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 395 0.0101 1.00 56.1 yes View details
rbcL-psaI LSC 1458 0.0058 1.00 48.1 yes View details
petA-psbJ LSC 807 0.0064 1.00 63.4 yes View details
trnP-UGG-psaJ LSC 337 0.0475 1.00 62.4 yes View details
rpl16 LSC 1409 0.0079 1.00 64.3 yes View details
trnN-GUU-rps15 IRb 1549 0.0037 1.00 61.2 yes View details
ndhF-rpl32 SSC 861 0.0058 1.00 63.7 yes View details
rpl32-trnL-UAG SSC 617 0.0081 1.00 49.5 yes View details
ccsA SSC 945 0.0011 1.00 36.1 yes View details
ccsA-ndhD SSC 152 0.0362 1.00 69.2 yes View details
psbT-psbN LSC 48 0.0521 1.00 67.9 yes View details
rps16-trnQ-UUG LSC 794 0.0060 0.98 64.7 yes View details
ycf3-trnS-GGA LSC 615 0.0035 1.00 61.1 yes View details
rps15-trnN-GUU IRa 1549 0.0032 1.00 60.9 yes View details
atpI-atpH LSC 568 0.0035 1.00 60.5 yes View details
petB LSC 1413 0.0019 1.00 60.1 yes View details
atpB LSC 1497 0.0013 1.00 59.7 yes View details
rps15-ndhF SSC 387 0.0052 1.00 59.4 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 858–882 1.000 80.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC AGTGTCGCATAAAACCCGAA 927–951 1.000 79.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 862–886 1.000 79.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TACTCGGAGGTTCGAATCCT 864–888 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC ACTCGGAGGTTCGAATCCTT 863–887 1.000 77.2
psbK-psbI_p1 psbK-psbI CGTGGATGTTATGCCTGTCA TTCCGTCCTGGGTCATTAGA 566 1.000 78.9
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCCGTCCTGGGTCATTAGA 517 1.000 78.7
psbK-psbI_p3 psbK-psbI CGTGGATGTTATGCCTGTCA GAATTTTTACTCCTCGCGCC 591 1.000 77.1
psbK-psbI_p4 psbK-psbI CGTGGATGTTATGCCTGTCA GGAATTTTTACTCCTCGCGC 592 1.000 77.1
psbK-psbI_p5 psbK-psbI CGTGGATGTTATGCCTGTCA TCCGTCCTGGGTCATTAGAT 565 1.000 77.0
atpI-atpH_p1 atpI-atpH TTTTGCAACATTAGCCGCAG GCAATAACAGAAGCAGCAGC 658–680 1.000 79.2
atpI-atpH_p2 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGCAATAACAGAAGCAGC 661–683 1.000 79.2
atpI-atpH_p3 atpI-atpH TTTTGCAACATTAGCCGCAG GCAGTACCTTGACCAACTCC 715–737 1.000 78.4
atpI-atpH_p4 atpI-atpH TTTTGCAACATTAGCCGCAG AAGCAGCAGCAATTAGTGGA 648–670 1.000 78.3
atpI-atpH_p5 atpI-atpH TAGGTGAATCCATGGAGGGG GCAATAACAGAAGCAGCAGC 632–654 1.000 78.3
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT ACGGAAAGAGAGGGATTCGA 798–802 1.000 78.7
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT TTCCAATGCTACGCCTTCAA 748–752 1.000 78.4
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TCTCCTGAGGTTGTCGGAAT AGTTCCAATGCTACGCCTTC 750–754 1.000 77.8
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTCTCCTGAGGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 799–803 1.000 76.9
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTTCTCCTGAGGTTGTCGGA ACGGAAAGAGAGGGATTCGA 800–804 1.000 76.9
atpB_p1 atpB GTGGTTTGGTAATACGCCGA TTTTTGGATTTGATTTGGCA 1683–1684 1.000 40.2
atpB_p2 atpB GTGGTTTGGTAATACGCCGA GGATTTGATTTGGCATTATTCAACA 1678–1679 1.000 40.2
atpB_p3 atpB GTGGTTTGGTAATACGCCGA TGGATTTGATTTGGCATTATTCAAC 1679–1680 1.000 40.2
atpB_p4 atpB GTGGTTTGGTAATACGCCGA TGGATTTGATTTGGCATTATTCA 1679–1680 1.000 40.2
atpB_p5 atpB GTGGTTTGGTAATACGCCGA TGATTTGGCATTATTCAACAAGA 1673–1674 1.000 40.2
rbcL-psaI_p1 rbcL-psaI GATCATATCCACGCCGGTAC CCCGCAATTCCGTAGAAAGA 2591–2597 1.000 80.7
rbcL-psaI_p2 rbcL-psaI ATATCCACGCCGGTACAGTA CCCGCAATTCCGTAGAAAGA 2587–2593 1.000 80.6
rbcL-psaI_p3 rbcL-psaI TCTTCACATTCACCGTGCAA CCCGCAATTCCGTAGAAAGA 2691–2697 1.000 80.4
rbcL-psaI_p4 rbcL-psaI TTCTTCACATTCACCGTGCA CCCGCAATTCCGTAGAAAGA 2692–2698 1.000 80.4
rbcL-psaI_p5 rbcL-psaI GCATGACTACATCACTGGGG CCCGCAATTCCGTAGAAAGA 2763–2769 1.000 80.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Koeleria glauca NC_059965.1 136051 View on NCBI ↗
Koeleria macrantha NC_072345.1 136065 View on NCBI ↗
Koeleria nitidula NC_042404.1 136085 View on NCBI ↗
Koeleria spicata NC_065056.1 136262 View on NCBI ↗