Markers + reference

Nassella

3 species · Poaceae · Poales

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Species 3
Genome length 138–138 kb
Candidate markers 267
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbZ-trnG-GCC LSC 217 0.0031 1.00 40.2 yes View details
trnG-UCC-trnT-GGU LSC 1529 0.0009 1.00 46.4 yes View details
atpI LSC 744 0.0009 1.00 32.4 yes View details
rbcL LSC 1431 0.0014 1.00 47.1 yes View details
rbcL-psaI LSC 1592 0.0013 1.00 59.4 yes View details
ycf4-cemA LSC 434 0.0031 1.00 57.7 yes View details
rpl32-trnL-UAG SSC 723 0.0028 1.00 60.5 yes View details
ndhD SSC 1503 0.0009 1.00 56.2 yes View details
atpF LSC 1380 0.0005 1.00 64.3 yes View details
trnD-GUC-psbM LSC 772 0.0009 1.00 62.4 yes View details
rpl14-rpl16 LSC 112 0.0119 1.00 60.1 yes View details
psbE-petL LSC 1260 0.0016 1.00 60.0 yes View details
petA-psbJ LSC 840 0.0016 1.00 59.8 yes View details
ndhF-rpl32 SSC 903 0.0015 1.00 59.7 yes View details
trnT-UGU-trnL-UAA LSC 808 0.0008 1.00 59.6 yes View details
trnF-GAA-ndhJ LSC 595 0.0011 1.00 59.6 yes View details
petN-trnC-GCA LSC 897 0.0007 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 876 0.0000 0.99 59.5 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-UUU_p1 trnK-UUU CAACCAAGTCAGCCCAAAGA CGTGCGGTGTAATTCCATTG 2735 1.000 76.2
trnK-UUU_p2 trnK-UUU TCAACCAAGTCAGCCCAAAG CGTGCGGTGTAATTCCATTG 2736 1.000 76.2
trnK-UUU_p3 trnK-UUU GTCAACCAAGTCAGCCCAAA CGTGCGGTGTAATTCCATTG 2737 1.000 73.9
trnK-UUU_p4 trnK-UUU AACCAAGTCAGCCCAAAGAT CGTGCGGTGTAATTCCATTG 2734 1.000 73.2
trnK-UUU_p5 trnK-UUU ACCAAGTCAGCCCAAAGATT CGTGCGGTGTAATTCCATTG 2733 1.000 73.2
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TATTCCATCTAGCCGAGCCA GTTTCCAGTACTCCAGAGCG 1598 1.000 80.2
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TATTCCATCTAGCCGAGCCA GCAGTTTGCCAGTTGTTTGT 1257 1.000 80.1
psbZ-trnG-GCC_p3 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC GTTTCCAGTACTCCAGAGCG 1430 1.000 80.1
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TATTCCATCTAGCCGAGCCA GGGTGCAAAGGAAGGGTAAA 1162 0.667 66.7
psbZ-trnG-GCC_p5 psbZ-trnG-GCC CAACCACTCAGCCATCTCTC GGGTGCAAAGGAAGGGTAAA 994 0.667 66.6
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGACTTACGTCTTACCACGC 1679 1.000 49.1
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGACTTACGTCTTACCACGC 1682 1.000 48.1
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGACTTACGTCTTACCACGC 1681 1.000 48.1
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AACGAATCACACTTTTACCACT TGACTTACGTCTTACCACGC 1680 1.000 47.2
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GACTTACGTCTTACCACGCT 1678 1.000 46.8
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 863–883 1.000 60.4
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG AGAATGAACAGTGCAGTAGC 895–915 1.000 58.9
trnD-GUC-psbM_p3 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC AGAATGAACAGTGCAGTAGC 864–884 1.000 56.2
trnD-GUC-psbM_p4 trnD-GUC-psbM CGCGGGGATTGTAGTTCAA AGAATGAACAGTGCAGTAGC 877–897 1.000 55.0
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTCAGAGCACCG AGAATGAACAGTGCAGTAGC 862–882 1.000 54.3
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 944–946 1.000 70.6
petN-trnC-GCA_p2 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 946–948 1.000 70.2
petN-trnC-GCA_p3 petN-trnC-GCA CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1000–1002 1.000 69.6
petN-trnC-GCA_p4 petN-trnC-GCA CCACTCCTCCCCCATACTAC CCAGTTCAAATCTGGGTGCC 1002–1004 1.000 69.1
petN-trnC-GCA_p5 petN-trnC-GCA TCCACTCCTCCCCCATACTA AGTTCAAATCTGGGTGCCG 1001–1003 1.000 68.8
atpI_p1 atpI GAGGGCCGTTCTCTCTCTAT TTCTGGCTGTCTCGCAATAC 1688–1694 1.000 80.2
atpI_p2 atpI GAGGGCCGTTCTCTCTCTAT AACCCGCACAAAAGATGACT 1275–1281 1.000 80.2
atpI_p3 atpI ATCAGCTGCAATAAGGGCTC TTCTGGCTGTCTCGCAATAC 2112–2118 1.000 80.0
atpI_p4 atpI AATTGTGACCCAGATCTCGC TTCTGGCTGTCTCGCAATAC 1787–1793 1.000 80.0
atpI_p5 atpI ATCAGCTGCAATAAGGGCTC AACCCGCACAAAAGATGACT 1699–1705 1.000 80.0

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
Nassella hyalina NC_036696.1 137710 View on NCBI ↗
Nassella neesiana MF480752.1 137700 View on NCBI ↗
Nassella tenuissima PQ585797.1 137546 View on NCBI ↗