Markers + reference

Deschampsia

2 species · Poaceae · Poales

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Species 2
Genome length 135–135 kb
Candidate markers 278
Primer pairs 105

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 8 remaining regions by MarkerSeek score (out of 278 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-psbD LSC 963 0.0031 1.00 58.8 yes View details
psbC LSC 1422 0.0014 1.00 52.3 yes View details
trnY-trnD LSC 312 0.0064 1.00 56.4 yes View details
rpoB LSC 3231 0.0009 1.00 55.8 yes View details
atpH-atpF LSC 468 0.0065 0.99 61.0 yes View details
trnT-UGU-trnL LSC 765 0.0026 1.00 60.4 yes View details
trnL-trnF LSC 351 0.0028 1.00 49.8 yes View details
rpl23-accD LSC 426 0.0047 0.99 58.8 yes View details
ndhF SSC 2220 0.0018 1.00 48.2 yes View details
ndhF-rpl32 SSC 847 0.0071 1.00 62.8 yes View details
psaC-ndhE SSC 509 0.0040 0.99 60.3 yes View details
atpB-rbcL LSC 852 0.0013 0.93 63.8 yes View details
rpl32-trnL SSC 676 0.0044 1.00 61.3 yes View details
trnC-rpoB LSC 1018 0.0029 1.00 60.4 yes View details
rps16-trnQ LSC 778 0.0026 1.00 60.2 yes View details
petN-trnC LSC 835 0.0024 1.00 60.2 yes View details
petD LSC 1220 0.0025 1.00 60.2 yes View details
petB LSC 1408 0.0014 1.00 59.6 yes View details
atpB LSC 1497 0.0013 1.00 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ_p1 rps16-trnQ AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 852 1.000 78.5
rps16-trnQ_p2 rps16-trnQ TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 863 1.000 77.9
rps16-trnQ_p3 rps16-trnQ AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 856 1.000 77.4
rps16-trnQ_p4 rps16-trnQ TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 867 1.000 76.9
rps16-trnQ_p5 rps16-trnQ AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 858 1.000 75.6
trnS-psbD_p1 trnS-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1108 1.000 78.5
trnS-psbD_p2 trnS-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1095 1.000 77.9
trnS-psbD_p3 trnS-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1079 1.000 77.4
trnS-psbD_p4 trnS-psbD GAGCGGAAAGAGAGGGATTC GCCGGACCATCCTACAAAAA 1159 1.000 77.0
trnS-psbD_p5 trnS-psbD GAGCGGAAAGAGAGGGATTC ACAAAAACGAAACGGTCCCT 1146 1.000 76.4
psbC_p1 psbC TGTTTCCCAGGAAATCCGTG TGGCTCGGCTAGATGGAATA 1612 1.000 79.3
psbC_p2 psbC GCAGCGGAAGATCCTGAATT TGGCTCGGCTAGATGGAATA 1593 1.000 77.4
psbC_p3 psbC TGTTTCCCAGGAAATCCGTG AACCGAGCCAGAACAGAAAA 1593 1.000 76.6
psbC_p4 psbC TGTTTCCCAGGAAATCCGTG ACCGAGCCAGAACAGAAAAA 1592 1.000 76.6
psbC_p5 psbC TGTTTCCCAGGAAATCCGTG GGAATAACCGAGCCAGAACA 1598 1.000 76.2
trnY-trnD_p1 trnY-trnD AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 436 1.000 76.2
trnY-trnD_p2 trnY-trnD GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 403 1.000 73.8
trnY-trnD_p3 trnY-trnD GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 402 1.000 73.6
trnY-trnD_p4 trnY-trnD AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 435 1.000 72.0
trnY-trnD_p5 trnY-trnD TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 404 1.000 70.4
petN-trnC_p1 petN-trnC AGTCCACTCCTTCCCCATAC TTTCTCGATTTTCGCTCGGA 1018 1.000 76.4
petN-trnC_p2 petN-trnC GTCCACTCCTTCCCCATACT TTTCTCGATTTTCGCTCGGA 1017 1.000 76.4
petN-trnC_p3 petN-trnC AGCCCAAGCGAGACTTACTA TTTCTCGATTTTCGCTCGGA 959 1.000 76.2
petN-trnC_p4 petN-trnC GAGTCCACTCCTTCCCCATA TTTCTCGATTTTCGCTCGGA 1019 1.000 76.0
petN-trnC_p5 petN-trnC CTAGAGTCCACTCCTTCCCC TTTCTCGATTTTCGCTCGGA 1022 1.000 75.6
trnC-rpoB_p1 trnC-rpoB AAAGGATTTGCAGTCCCCTG ATTCCCTCGTTTCCATTCCG 1087–1187 1.000 79.3
trnC-rpoB_p2 trnC-rpoB AAAGGATTTGCAGTCCCCTG TGTGGACATTCCCTCGTTTC 1094–1194 1.000 78.2
trnC-rpoB_p3 trnC-rpoB AAAGGATTTGCAGTCCCCTG TGTCAAGTTCTTCTGCCAGG 1170–1270 1.000 77.5
trnC-rpoB_p4 trnC-rpoB AAAGGATTTGCAGTCCCCTG CCGGGTATTGTGGACATTCC 1102–1202 1.000 77.0
trnC-rpoB_p5 trnC-rpoB AAAGGATTTGCAGTCCCCTG CGGGTATTGTGGACATTCCC 1101–1201 1.000 77.0

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
Deschampsia antarctica NC_023533.1 135362 View on NCBI ↗
Deschampsia cespitosa NC_040999.1 135340 View on NCBI ↗