Markers + reference

Ruscus

2 species · Asparagaceae · Asparagales

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Species 2
Genome length 154–154 kb
Candidate markers 276
Primer pairs 90

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 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1687 0.0006 1.00 58.7 yes View details
atpA LSC 1524 0.0000 1.00 27.9 yes View details
rpoB-trnC-GCA LSC 1241 0.0146 1.00 67.6 yes View details
petD LSC 1259 0.0016 1.00 59.7 yes View details
rpl2 IRb 1480 0.0000 1.00 25.2 yes View details
rpl23 IRb 282 0.0000 1.00 20.2 no View details
ndhD SSC 1506 0.0013 1.00 59.5 yes View details
rpl23 IRa 282 0.0000 1.00 20.2 yes View details
rpl2 IRa 1480 0.0000 1.00 25.2 no View details
rpl2-rpl23 IRb 24 0.0833 1.00 85.4 yes View details
rpl23-rpl2 IRa 24 0.0833 1.00 85.4 yes View details
petA-psbJ LSC 1063 0.0000 0.97 61.9 yes View details
atpA-atpF LSC 74 0.0135 1.00 60.3 yes View details
trnT-GGU-psbD LSC 763 0.0013 1.00 59.5 yes View details
rps12 IRb 800 0.0013 1.00 59.5 yes View details
rps12 IRa 800 0.0013 1.00 59.5 yes View details
trnC-GCA-petN LSC 920 0.0011 1.00 59.4 yes View details
ycf3-trnS-GGA LSC 573 0.0017 1.00 59.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGAAGCGAGCTAAAACTCAA ACGTAGTTGTACAGTGCAAT 2776 1.000 40.0
trnK-UUU_p2 trnK-UUU TTGAAGCGAGCTAAAACTCA ACGTAGTTGTACAGTGCAAT 2777 1.000 40.0
trnK-UUU_p3 trnK-UUU TGAAGCGAGCTAAAACTCAA CGTAGTTGTACAGTGCAATTCA 2775 1.000 40.0
trnK-UUU_p4 trnK-UUU TTGAAGCGAGCTAAAACTCA CGTAGTTGTACAGTGCAATTCA 2776 1.000 40.0
trnK-UUU_p5 trnK-UUU TGAAGCGAGCTAAAACTCAA ACGTAGTTGTACAGTGCAATTC 2776 1.000 40.0
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1745 1.000 78.1
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1744 1.000 78.1
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 1731 1.000 75.8
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AGTCGCACTTAAAAGCCGAG GAGGTTCGAATCCTTCCGTC 1756 1.000 74.9
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 1754 1.000 73.6
atpA_p1 atpA GGCGATACCAAGAAACCCTT TTTACCTTTGTTTCCGAAAAA 1649 1.000 40.0
atpA_p2 atpA GGCGATACCAAGAAACCCTT TTTTACCTTTGTTTCCGAAAA 1650 1.000 40.0
atpA_p3 atpA GGCGATACCAAGAAACCCTT TTTTTACCTTTGTTTCCGAAA 1651 1.000 40.0
atpA_p4 atpA GGCGATACCAAGAAACCCTT TTTTACCTTTGTTTCCGAAAAA 1650 1.000 40.0
atpA_p5 atpA GGCGATACCAAGAAACCCTT TTTTTACCTTTGTTTCCGAAAA 1651 1.000 40.0
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC CGGGGCCATGGAAGAAATAA 215 1.000 79.1
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG CGGGGCCATGGAAGAAATAA 213 1.000 79.1
atpA-atpF_p3 atpA-atpF CCGTCGCCTACTTGAAGTAC AGCCTTACAGGGAGCTCTAG 302 1.000 78.9
atpA-atpF_p4 atpA-atpF GTCGCCTACTTGAAGTACGG AGCCTTACAGGGAGCTCTAG 300 1.000 78.9
atpA-atpF_p5 atpA-atpF GTCGCCTACTTGAAGTACGG GCGAGTTACATCTCCGTACC 256 1.000 78.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGACAAGCCCTG TAAAGGATTTGCAGTCCCCC 1389 1.000 75.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA AATTCTTCCGACAAGCCCTG TTTGTTGATCAGGCGACACC 1426 1.000 73.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGACAAGCCCTG GACACCCGGATTTGAACTGG 1412 1.000 73.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AAATTCTTCCGACAAGCCCT TAAAGGATTTGCAGTCCCCC 1390 1.000 72.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AATTCTTCCGACAAGCCCTG CCGGATTTGAACTGGGGATA 1407 1.000 71.8
trnC-GCA-petN_p1 trnC-GCA-petN ATTTTGGACCGAATTTGGCG TTAAAGCAGCCCAAGCAAGA 1041 1.000 77.1
trnC-GCA-petN_p2 trnC-GCA-petN ATTTTGGACCGAATTTGGCG AGCAATTAGTAGTGCCCAGC 1118 1.000 76.8
trnC-GCA-petN_p3 trnC-GCA-petN ATTTTGGACCGAATTTGGCG AGTCCACTCCTTCCCCATAC 1093 1.000 76.2
trnC-GCA-petN_p4 trnC-GCA-petN ATTTTGGACCGAATTTGGCG GTCCACTCCTTCCCCATACT 1092 1.000 76.2
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTA TTAAAGCAGCCCAAGCAAGA 1001 1.000 75.8

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
Ruscus aculeatus NC_070130.1 153883 View on NCBI ↗
Ruscus hypophyllum PV087168.1 154089 View on NCBI ↗