Markers + reference

Agrostis

4 species · Poaceae · Poales

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Species 4
Genome length 137–137 kb
Candidate markers 270
Primer pairs 100

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 11 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 786 0.0127 1.00 56.5 yes View details
trnG-UCC-trnT-GGU LSC 1202 0.0141 1.00 59.2 yes View details
petN-trnC-GCA LSC 909 0.0109 0.99 60.6 yes View details
trnC-GCA-rpoB LSC 1163 0.0093 1.00 59.2 yes View details
ndhC-trnV-UAC LSC 915 0.0151 0.99 62.9 yes View details
rbcL-psaI LSC 1551 0.0133 1.00 53.0 yes View details
petA-psbJ LSC 803 0.0118 1.00 57.7 yes View details
psbE-petL LSC 1287 0.0120 1.00 61.8 yes View details
rpl16 LSC 1433 0.0076 0.98 53.9 yes View details
ndhF SSC 2220 0.0062 1.00 46.7 yes View details
rpl32-trnL-UAG SSC 662 0.0166 0.99 58.4 yes View details
psbT-psbN LSC 48 0.0694 1.00 68.8 yes View details
trnS-GCU-psbD LSC 965 0.0100 1.00 65.8 yes View details
trnY-GUA-trnD-GUC LSC 399 0.0149 0.87 63.9 yes View details
matK-trnK-UUU LSC 666 0.0090 1.00 63.8 yes View details
rps19-psbA LSC 127 0.0328 0.96 63.7 no View details
trnT-GGU-trnE-UUC LSC 533 0.0122 1.00 63.1 yes View details
rpl14-rpl16 LSC 120 0.0140 0.98 61.8 yes View details
trnT-UGU-trnL-UAA LSC 809 0.0087 1.00 61.6 yes View details
trnF-GAA-ndhJ LSC 579 0.0115 1.00 61.5 yes View details
rpl2 IRb 1485 0.0011 1.00 59.5 yes View details
rpl2 IRa 1485 0.0011 1.00 59.5 no 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGT AATGTTTTGACAGAAGCGCG 857–875 1.000 70.4
matK-trnK-UUU_p2 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGG AATGTTTTGACAGAAGCGCG 857–875 1.000 68.5
matK-trnK-UUU_p3 matK-trnK-UUU CTCCTGAAAGAGAAGTGGGT AATGTTTTGACAGAAGCGCG 856–874 1.000 68.5
matK-trnK-UUU_p4 matK-trnK-UUU TCCTGAAAGAGAAGTGGGTAGA AATGTTTTGACAGAAGCGCG 855–873 1.000 63.8
matK-trnK-UUU_p5 matK-trnK-UUU ACTCCTGAAAGAGAAGTGGGTA AATGTTTTGACAGAAGCGCG 857–875 1.000 63.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 856–860 1.000 80.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 867–871 1.000 80.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 860–864 1.000 79.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 871–875 1.000 79.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 862–866 1.000 78.0
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GACAAAAACGAAACGGTCCC 1095–1104 1.000 80.3
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1094–1103 1.000 79.2
trnS-GCU-psbD_p3 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CCGACAAAAACGAAACGGTC 1097–1106 1.000 79.0
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CGACAAAAACGAAACGGTCC 1096–1105 1.000 79.0
trnS-GCU-psbD_p5 trnS-GCU-psbD GAGCGGAAAGAGAGGGATTC GACAAAAACGAAACGGTCCC 1146–1155 1.000 78.7
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCACTGAGTTAAAAGGGCT 1256–1270 1.000 43.2
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 1293–1307 1.000 43.0
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT ACCACTGAGTTAAAAGGGCT 1258–1272 1.000 42.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 1289–1303 1.000 42.2
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 1290–1304 1.000 42.2
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT AAATACTCCCTACCCCCAGG 686–691 1.000 69.4
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA AAATACTCCCTACCCCCAGG 649–654 1.000 69.3
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 651–656 1.000 69.1
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 630–635 1.000 69.0
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 614–619 1.000 69.0
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC CGGTGCTCTGACCAATTGAA 419–524 1.000 81.3
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG CGGTGCTCTGACCAATTGAA 386–491 1.000 79.0
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT CGGTGCTCTGACCAATTGAA 385–490 1.000 78.8
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGTGCTCTGACCAATTGAAC 418–523 1.000 77.2
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC CGGTGCTCTGACCAATTGAA 387–492 1.000 75.6

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
Agrostis alpina PP316507.1 136553 View on NCBI ↗
Agrostis gigantea NC_037162.1 136705 View on NCBI ↗
Agrostis schraderiana PP316506.1 136514 View on NCBI ↗
Agrostis stolonifera NC_008591.1 136584 View on NCBI ↗