Markers + reference

Equisetum

11 species · Equisetaceae · Equisetales

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Species 11
Genome length 131–134 kb
Candidate markers 265
Primer pairs 50

Genome-wide nucleotide diversity

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

Candidate markers

1 hotspot label from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnY-GUA-trnE-UUC Genome 4573 0.1887 0.86 70.0 yes View details
trnV-GAC-rps12 Genome 732 0.1384 0.97 89.0 no View details
rps12-clpP Genome 991 0.0734 0.86 79.5 yes View details
psbH-petB Genome 920 0.0488 0.99 78.1 yes View details
atpB-rbcL Genome 540 0.0764 0.96 77.5 yes View details
trnK-UUU-chlB Genome 970 0.1042 0.94 77.3 yes View details
psaA-trnS-GGA Genome 2415 0.0514 0.98 77.2 yes View details
psbD-trnT-GGU Genome 904 0.0952 0.99 77.1 yes View details
petA-psbJ Genome 1115 0.0853 1.00 76.9 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 50 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU GCCAAAGCTTGTTGTCAACC TCCAGGGTTTTTCATTTTGTTGT 2887–2952 0.364 31.2
trnK-UUU_p2 trnK-UUU GCCAAAGCTTGTTGTCAACC CCAGGGTTTTTCATTTTGTTGT 2886–2951 0.364 27.9
trnK-UUU_p3 trnK-UUU GCCAAAGCTTGTTGTCAACC ATCCAGGGTTTTTCATTTTGTTGT 2888–2953 0.364 26.6
trnK-UUU_p4 trnK-UUU GCTGGTAATCCAATCGCAGA TGGGGAAACTCTTTTGTAAGA 2851–2900 0.182 15.5
trnK-UUU_p5 trnK-UUU GACGGTTTTCAGTGCTGGTA TGGGGAAACTCTTTTGTAAGA 2864–2913 0.182 14.9
trnK-UUU-chlB_p1 trnK-UUU-chlB GATTCAAGCCTCACAAGCCT CGTCATATTGGTAAGCGCCT 1661–1727 1.000 89.6
trnK-UUU-chlB_p2 trnK-UUU-chlB AACCCTTCTGAATTGGGCTG CGTCATATTGGTAAGCGCCT 1453–1461 0.364 60.5
trnK-UUU-chlB_p3 trnK-UUU-chlB AACCCTTCTGAATTGGGCTG TCATATTGGTAAGCGCCTCG 1451–1459 0.364 60.4
trnK-UUU-chlB_p4 trnK-UUU-chlB CTCGTTCCTCCGGTTTCTTT CGTCATATTGGTAAGCGCCT 1721–1732 0.364 60.3
trnK-UUU-chlB_p5 trnK-UUU-chlB CTCGTTCCTCCGGTTTCTTT TCATATTGGTAAGCGCCTCG 1719–1730 0.364 60.2
trnG-UCC_p1 trnG-UCC TGGGTTCGGAATCGGAAATC TTTCCTCCTCCATTCTCGGT 1150–1165 0.364 59.0
trnG-UCC_p2 trnG-UCC TGGGTTCGGAATCGGAAATC CGCTTTCCTCCTCCATTCTC 1153–1168 0.364 58.9
trnG-UCC_p3 trnG-UCC TGGGTTCGGAATCGGAAATC GCTTTCCTCCTCCATTCTCG 1152–1167 0.364 58.9
trnG-UCC_p4 trnG-UCC TGGGTTCGGAATCGGAAATC TCCTCCTCCATTCTCGGTAC 1148–1163 0.364 58.8
trnG-UCC_p5 trnG-UCC ATTGCTCTACTGGCATCACG TTTCCTCCTCCATTCTCGGT 1267–1282 0.364 58.8
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC GTCCAGAAATCGTACCACCA GGTTGTGGGTACGACTTCTG 747–909 0.273 53.2
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC GTCCAGAAATCGTACCACCA GTTGTGGGTACGACTTCTGG 746–908 0.273 53.2
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC GTCCAGAAATCGTACCACCA CCATAGGTTGCAGGTACGAC 586–743 0.182 47.5
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC TGTCCAGAAATCGTACCACC CCATAGGTTGCAGGTACGAC 587–744 0.182 47.5
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC GTCCAGAAACTGTACGGTCA CCATAGGTTGCAGGTACGAC 710–862 0.182 46.9
psbD-trnT-GGU_p1 psbD-trnT-GGU TGTAGCACCGTGAATAGCAC GGGTAGAGCAGTTTGGTAGC 1853–1927 0.818 81.8
psbD-trnT-GGU_p2 psbD-trnT-GGU TGTAGCACCGTGAATAGCAC CTTGAGGTCACGGGTTCAAA 1817–1891 0.818 81.7
psbD-trnT-GGU_p3 psbD-trnT-GGU ACCGATTAGACCGAAAGCAC GGGTAGAGCAGTTTGGTAGC 1574–1648 0.636 74.3
psbD-trnT-GGU_p4 psbD-trnT-GGU GATTAGACCGAAAGCACCGT GGGTAGAGCAGTTTGGTAGC 1571–1645 0.636 74.3
psbD-trnT-GGU_p5 psbD-trnT-GGU GATTAGACCGAAAGCACCGT CTTGAGGTCACGGGTTCAAA 1535–1609 0.636 74.2
psaA-trnS-GGA_p1 psaA-trnS-GGA AATCTTGACTTCCGGTTCCG ATTCGAACCCTCGGTAAACG 2501–2635 1.000 89.6
psaA-trnS-GGA_p2 psaA-trnS-GGA TGACCCACTATTGGCCAAAC ATTCGAACCCTCGGTAAACG 2827–2961 1.000 89.4
psaA-trnS-GGA_p3 psaA-trnS-GGA GTTATTCCAGATGCTCGCCA CTACACCTTCAACCACTCGG 2872–2973 0.909 85.4
psaA-trnS-GGA_p4 psaA-trnS-GGA GTTATTCCAGATGCTCGCCA ATTCGAACCCTCGGTAAACG 2917–3000 0.455 67.5
psaA-trnS-GGA_p5 psaA-trnS-GGA TGGTGCAGCTTTGTGGTAAT CTACACCTTCAACCACTCGG 2969–2994 0.273 53.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Equisetum diffusum NC_088038.1 133450 View on NCBI ↗
Equisetum fluviatile PP103315.1 132501 View on NCBI ↗
Equisetum hyemale NC_020146.1 131760 View on NCBI ↗
Equisetum palustre NC_088053.1 132986 View on NCBI ↗
Equisetum ramosissimum NC_062377.1 131150 View on NCBI ↗
Equisetum ramosissimum subsp. debile PP471256.1 131760 View on NCBI ↗
Equisetum scirpoides NC_088041.1 130896 View on NCBI ↗
Equisetum sylvaticum NC_088054.1 133633 View on NCBI ↗
Equisetum variegatum NC_088040.1 131436 View on NCBI ↗
Equisetum x moorei PP103313.1 131517 View on NCBI ↗
Equisetum xylochaetum NC_065985.1 132400 View on NCBI ↗