Markers + reference

Elymus

23 species · Poaceae · Poales

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Species 23
Genome length 135–138 kb
Candidate markers 269
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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0008 1.00 29.3 yes View details
trnT-GGU-trnE-UUC LSC 465 0.0029 1.00 43.5 yes View details
trnY-GUA-trnD-GUC LSC 361 0.0075 1.00 58.7 yes View details
trnC-GCA-rpoB LSC 1158 0.0025 1.00 46.6 yes View details
trnF-GAA-ndhJ LSC 587 0.0041 0.99 51.7 yes View details
rbcL-psaI LSC 1646 0.0053 1.00 58.9 yes View details
petA-psbJ LSC 822 0.0030 1.00 58.8 yes View details
ndhF-rpl32 SSC 908 0.0040 1.00 59.5 yes View details
rpl32-trnL-UAG SSC 702 0.0060 1.00 57.5 yes View details
rps19-psbA LSC 136 0.0184 1.00 60.0 no View details
trnT-UGU-trnL-UAA LSC 616 0.0021 1.00 54.3 yes View details
trnS-GCU-psbD LSC 980 0.0033 1.00 53.6 yes View details
rpl16 LSC 1462 0.0017 1.00 52.2 yes View details
rpoC2 LSC 4440 0.0012 1.00 51.6 yes View details
psaA-ycf3 LSC 706 0.0009 0.94 51.0 yes View details
psbE-petL LSC 1170 0.0023 1.00 50.6 yes View details
rps16 LSC 1070 0.0016 1.00 49.5 yes View details
rps8-rpl14 LSC 141 0.0045 1.00 46.7 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
psbA_p1 psbA TGCTAGAACAAGATATTGGGT AAATGCAAGCACGATTTGGG 1462 0.696 30.1
psbA_p2 psbA ACCCAATATCTTGCTAGAACAAG GCGCTAGAACTTTAGCTCGT 1892 0.652 28.6
psbA_p3 psbA ACCCAATATCTTGCTAGAACAAG TGCGCTAGAACTTTAGCTCG 1893 0.652 28.6
psbA_p4 psbA ACCCAATATCTTGCTAGAACAAG AAATGCAAGCACGATTTGGG 1473 0.652 28.5
psbA_p5 psbA ACCCAATATCTTGCTAGAACA AAATGCAAGCACGATTTGGG 1473 0.652 28.4
trnK_p1 trnK CAACCAAGTCAGCCCAAAGA AATGTTTTGACAGAAGCGCG 2750–2766 1.000 78.2
trnK_p2 trnK TCAACCAAGTCAGCCCAAAG AATGTTTTGACAGAAGCGCG 2751–2767 1.000 78.2
trnK_p3 trnK AATGTCAACCAAGTCAGCCC AATGTTTTGACAGAAGCGCG 2755–2771 1.000 77.6
trnK_p4 trnK GTCAACCAAGTCAGCCCAAA AATGTTTTGACAGAAGCGCG 2752–2768 1.000 75.9
trnK_p5 trnK ACCAAGTCAGCCCAAAGATT AATGTTTTGACAGAAGCGCG 2748–2764 1.000 75.2
rps16_p1 rps16 TGGCACGATATAAATCCAAATAGG TGCTCCATAGATAGCAAGTT 1287–1290 1.000 40.9
rps16_p2 rps16 TGGCACGATATAAATCCAAATAGG TCCATATTGCTCCATAGATAGCA 1294–1297 1.000 40.9
rps16_p3 rps16 TGGCACGATATAAATCCAAATAGG TGCTCCATAGATAGCAAGTTT 1287–1290 1.000 40.9
rps16_p4 rps16 TGGCACGATATAAATCCAAA TGCTCCATAGATAGCAAGTT 1287–1290 1.000 40.9
rps16_p5 rps16 TGGCACGATATAAATCCAAATAGG TGCTCCATAGATAGCAAGTTTT 1287–1290 1.000 40.9
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAGCAATAGGCCAGACCATC 1132–1154 1.000 80.9
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1110–1132 1.000 79.8
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CCCTTCGTAACCAGTCATCC 1094–1116 1.000 79.3
trnS-GCU-psbD_p4 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC GAGCAATAGGCCAGACCATC 1183–1205 1.000 79.2
trnS-GCU-psbD_p5 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA AGGCCAGACCATCCTACAAA 1125–1147 1.000 79.1
trnG_p1 trnG CAAACTGCTCTACTCCGCTC GGCTCAGTGTCATGAACCTT 974–975 1.000 76.5
trnG_p2 trnG AAACTGCTCTACTCCGCTCT GGCTCAGTGTCATGAACCTT 973–974 1.000 75.8
trnG_p3 trnG CAAACTGCTCTACTCCGCTC AGCCTTCTTGTCAAATGGCT 927–928 1.000 75.6
trnG_p4 trnG AAACTGCTCTACTCCGCTCT AGCCTTCTTGTCAAATGGCT 926–927 1.000 75.0
trnG_p5 trnG CAAACTGCTCTACTCCGCTC AACGGCTCAGTGTCATGAAC 977–978 1.000 74.1
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGTGGTAGAGTAATCTCGTGC GCTGCCTCCTTGAAAGAGAG 521–572 1.000 66.5
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC GTGGTAGAGTAATCTCGTGCT GCTGCCTCCTTGAAAGAGAG 520–571 1.000 66.5
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGTGGTAGAGTAATCTCGTGC TGTCCTGAACCACTAGACGA 500–551 1.000 66.4
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC GTGGTAGAGTAATCTCGTGCT TGTCCTGAACCACTAGACGA 499–550 1.000 66.4
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC GAGTAATCTCGTGCTAAGACGT GCTGCCTCCTTGAAAGAGAG 514–565 1.000 64.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Elymus atratus NC_061050.1 134991 View on NCBI ↗
[Elymus] breviaristatus PX795007.1 134972 View on NCBI ↗
Elymus ciliaris MK775252.1 134985 View on NCBI ↗
[Elymus] dahuricus var. violeus MT644149.1 135150 View on NCBI ↗
Elymus dentatus subsp. lachnophyllus PQ380099.1 135041 View on NCBI ↗
Elymus fedtschenkoi PQ385828.1 135038 View on NCBI ↗
Elymus grandis MN703669.1 135079 View on NCBI ↗
Elymus hystrix NC_058749.1 135051 View on NCBI ↗
Elymus jufinshanicus OL444889.1 135127 View on NCBI ↗
Elymus longearistatus PQ385829.1 135038 View on NCBI ↗
Elymus macrochaetus PQ385830.1 135022 View on NCBI ↗
Elymus nevskii PQ385831.1 135036 View on NCBI ↗
Elymus nodosus subsp. caespitosus MK775251.1 135094 View on NCBI ↗
Elymus praeruptus PV054326.1 135037 View on NCBI ↗
Elymus sibiricus NC_058919.1 135075 View on NCBI ↗
Elymus sinosubmuticus MT644146.1 134951 View on NCBI ↗
Elymus submuticus MT644143.1 135073 View on NCBI ↗
Elymus tauri MT385864.1 134959 View on NCBI ↗
Elymus transhyrcanus PQ385833.1 134968 View on NCBI ↗
Elymus tschimganicus PQ450446.1 134972 View on NCBI ↗
Elymus uralensis subsp. tianschanicus PV054327.1 135010 View on NCBI ↗
Elymus uzbekistanicus PQ362383.1 138328 View on NCBI ↗
Elymus virginicus NC_058750.1 135101 View on NCBI ↗