Markers + reference

Aristida

8 species · Poaceae · Poales

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Species 8
Genome length 137–138 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1478 0.0185 0.70 59.8 yes View details
trnG-UCC-trnT-GGU LSC 655 0.0250 0.99 75.2 yes View details
trnD-GUC-psbM LSC 1046 0.0172 0.98 62.9 yes View details
psbM-petN LSC 451 0.0212 1.00 62.2 yes View details
trnC-GCA-rpoB LSC 1177 0.0165 0.98 63.0 yes View details
trnT-UGU-trnL-UAA LSC 771 0.0218 0.98 66.8 yes View details
petA-psbJ LSC 939 0.0173 0.99 61.5 yes View details
petB LSC 1460 0.0104 0.97 57.1 yes View details
rpl16 LSC 1425 0.0132 1.00 57.4 yes View details
ndhF SSC 2217 0.0112 1.00 53.5 yes View details
ndhF-rpl32 SSC 743 0.0204 0.99 66.1 yes View details
rpl32-trnL-UAG SSC 475 0.0312 1.00 72.8 yes View details
ndhC-trnV-UAC LSC 580 0.0184 0.99 71.5 yes View details
petN-trnC-GCA LSC 953 0.0173 0.98 69.8 yes View details
trnS-GCU-psbD LSC 1012 0.0108 1.00 67.2 yes View details
atpB-rbcL LSC 774 0.0107 0.99 66.2 yes View details
psbE-petL LSC 1234 0.0103 1.00 66.2 yes View details
rpl14-rpl16 LSC 113 0.0344 0.96 65.2 yes View details
trnT-GGU-trnE-UUC LSC 479 0.0129 0.97 65.0 yes View details
psaJ-rpl33 LSC 501 0.0211 1.00 65.0 yes View details
atpI-atpH LSC 730 0.0127 1.00 64.9 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-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 566–1610 1.000 86.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 577–1621 1.000 85.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 570–1614 1.000 85.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 581–1625 1.000 84.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GCATAAAACCAAATGGGGCG 627–1671 1.000 84.1
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1134–1158 1.000 84.4
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1121–1145 1.000 83.8
trnS-GCU-psbD_p3 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT GCCGGACCATCCTACAAAAA 1120–1144 1.000 81.5
trnS-GCU-psbD_p4 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GAAACGGTCCCTTCGTAACC 1113–1137 1.000 81.3
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACAAAAACGAAACGGTCCCT 1107–1131 1.000 81.0
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 402–793 1.000 50.0
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT CCGATGACTTATGCCTTACCA 402–789 1.000 49.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT ACCGATGACTTATGCCTTACC 403–790 1.000 49.3
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC TGAACCGATGACTTATGCCT 405–796 1.000 49.3
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 404–795 1.000 49.3
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA TGTCCTGAACCACTAGACGA 538–836 1.000 72.8
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT TGTCCTGAACCACTAGACGA 575–836 1.000 72.7
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC AGGCATAAGTCATCGGTTCA GCTGCCTCCTTGAAAGAGAG 559–857 1.000 72.7
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC AGCCCTTTTAACTCAGTGGT GCTGCCTCCTTGAAAGAGAG 596–857 1.000 72.6
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC TGGTAAGGCATAAGTCATCGG GCTGCCTCCTTGAAAGAGAG 564–856 1.000 71.9
trnD-GUC-psbM_p1 trnD-GUC-psbM CGCTATCGTCTAGTGATGCC TAGTAAGTCTCGCTTGGGCT 2324–2361 1.000 84.7
trnD-GUC-psbM_p2 trnD-GUC-psbM GGCGCTATCGTCTAGTGATG TAGTAAGTCTCGCTTGGGCT 2326–2363 1.000 84.7
trnD-GUC-psbM_p3 trnD-GUC-psbM AATTCTTCCTGGGTCGATGC TAGGGCCGAATCACCTTTTG 2289–2328 0.875 79.5
trnD-GUC-psbM_p4 trnD-GUC-psbM CGCTATCGTCTAGTGATGCC TAGGGCCGAATCACCTTTTG 2430–2461 0.875 79.3
trnD-GUC-psbM_p5 trnD-GUC-psbM GGCGCTATCGTCTAGTGATG TAGGGCCGAATCACCTTTTG 2432–2463 0.875 79.3
psbM-petN_p1 psbM-petN TGGATGTCTATGTGACCCGT CGGATTCTGTCGAGAACCAG 1358–1505 1.000 86.0
psbM-petN_p2 psbM-petN TGGATGTCTATGTGACCCGT TCTCTCTATTCCCGCGTCTT 1258–1276 1.000 83.2
psbM-petN_p3 psbM-petN TGGATGTCTATGTGACCCGT TCTCTATTCCCGCGTCTTCT 1256–1274 1.000 83.1
psbM-petN_p4 psbM-petN TGGATGTCTATGTGACCCGT TAGGGCCGAATCACCTTTTG 1099–1117 0.875 77.1
psbM-petN_p5 psbM-petN TGGATGTCTATGTGACCCGT GGACATCCTCCTACCCCTTT 1231–1249 0.875 76.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Aristida adscensionis NC_060728.1 137947 View on NCBI ↗
Aristida behriana NC_046729.1 137074 View on NCBI ↗
Aristida diffusa NC_046732.1 137542 View on NCBI ↗
Aristida pruinosa NC_042836.1 137353 View on NCBI ↗
Aristida purpurea NC_025228.1 138423 View on NCBI ↗
Aristida rufescens NC_036130.1 137659 View on NCBI ↗
Aristida stipitata NC_046730.1 138226 View on NCBI ↗
Aristida triseta PZ161599.1 138428 View on NCBI ↗