Markers + reference

Nothoscordum

2 species · Amaryllidaceae · Asparagales

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Species 2
Genome length 157–157 kb
Candidate markers 270
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 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 590 0.0051 1.00 52.2 yes View details
trnS_UGA-psbZ LSC 332 0.0030 1.00 54.9 yes View details
ndhC-trnV_UAC LSC 1830 0.0033 1.00 49.7 yes View details
petA-psbJ LSC 1122 0.0098 1.00 64.4 yes View details
rpl33 LSC 201 0.0000 1.00 22.1 yes View details
rpl20-rps12 LSC 744 0.0054 1.00 55.3 yes View details
rpl16 LSC 1464 0.0062 1.00 62.4 yes View details
ndhF-rpl32 SSC 989 0.0062 0.98 57.0 yes View details
rps15-ycf1 SSC 510 0.0118 1.00 52.4 yes View details
rpl33-rps18 LSC 171 0.0240 0.98 68.5 yes View details
matK-trnK-UUU LSC 779 0.0039 0.98 63.2 yes View details
trnH_GUG-psbA LSC 134 0.0080 0.93 61.4 no View details
rps14-psaB LSC 133 0.0150 1.00 61.1 yes View details
rbcL-accD LSC 806 0.0037 1.00 60.9 yes View details
trnT_UGU-trnL_UAA LSC 938 0.0032 1.00 60.6 yes View details
atpF LSC 1453 0.0007 0.99 60.4 yes View details
psaA-ycf3 LSC 620 0.0016 0.99 60.3 yes View details
ndhD SSC 1503 0.0027 1.00 60.3 yes View details
rpoA LSC 1020 0.0020 1.00 59.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU GTGTTGTTGCCGGGATCTAT TCTGGGTTGCTAACTCAACG 852–870 1.000 80.3
matK-trnK-UUU_p2 matK-trnK-UUU GTGTTGTTGCCGGGATCTAT AACGGTAGAGTACTCGGCTT 836–854 1.000 80.3
matK-trnK-UUU_p3 matK-trnK-UUU GTGTTGTTGCCGGGATCTAT ACGGTAGAGTACTCGGCTTT 835–853 1.000 80.3
matK-trnK-UUU_p4 matK-trnK-UUU ATAGGAAGTGTTGTTGCCGG TCTGGGTTGCTAACTCAACG 859–877 1.000 79.2
matK-trnK-UUU_p5 matK-trnK-UUU ATAGGAAGTGTTGTTGCCGG ACGGTAGAGTACTCGGCTTT 842–860 1.000 79.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 696–698 1.000 77.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 695–697 1.000 77.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 682–684 1.000 75.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGGAAC 707–709 1.000 74.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 705–707 1.000 73.1
atpF_p1 atpF TCTTTTTCGGAAACAAAGGGA AAAAAGGGCGAGTCAAGTGA 1569–1586 1.000 53.6
atpF_p2 atpF TCTTTTTCGGAAACAAAGGGA GGGCGAGTCAAGTGATACAA 1564–1581 1.000 53.3
atpF_p3 atpF ACTAATTTCGTCAGCTCGAA AAAAAGGGCGAGTCAAGTGA 1613–1630 1.000 53.1
atpF_p4 atpF ACTAATTTCGTCAGCTCGAA GGGCGAGTCAAGTGATACAA 1608–1625 1.000 52.8
atpF_p5 atpF TCTTTTTCGGAAACAAAGGGA AGGGCGAGTCAAGTGATACA 1565–1582 1.000 52.8
trnS_UGA-psbZ_p1 trnS_UGA-psbZ CAACCACTCAGCCATCTCTC ACCAACCATCAGAAGAAGCA 453–459 1.000 72.3
trnS_UGA-psbZ_p2 trnS_UGA-psbZ GAGCTATCAACCACTCAGCC ACCAACCATCAGAAGAAGCA 460–466 1.000 72.1
trnS_UGA-psbZ_p3 trnS_UGA-psbZ GGAGCTATCAACCACTCAGC ACCAACCATCAGAAGAAGCA 461–467 1.000 72.1
trnS_UGA-psbZ_p4 trnS_UGA-psbZ CAACCACTCAGCCATCTCTC TGCAAAAACAGCCAATTGGA 386–392 1.000 72.1
trnS_UGA-psbZ_p5 trnS_UGA-psbZ CAAGACCGGAGCTATCAACC ACCAACCATCAGAAGAAGCA 468–474 1.000 72.0
rps14-psaB_p1 rps14-psaB TGTCGCTTCTTCTCCCTTTG CCAGTGGCTCTTTCCATTGT 291 1.000 78.5
rps14-psaB_p2 rps14-psaB TGTCGCTTCTTCTCCCTTTG GCAGCTTTCTTGATTGCCTC 216 1.000 77.2
rps14-psaB_p3 rps14-psaB TCTGTCGCTTCTTCTCCCTT CCAGTGGCTCTTTCCATTGT 293 1.000 76.9
rps14-psaB_p4 rps14-psaB TTCTGTCGCTTCTTCTCCCT CCAGTGGCTCTTTCCATTGT 294 1.000 76.9
rps14-psaB_p5 rps14-psaB TGTCGCTTCTTCTCCCTTTG GCTCTTTCCATTGTGCAAGC 285 1.000 76.9
psaA-ycf3_p1 psaA-ycf3 GTTCTTGAAAAATGGCCGGG CAGAGGCTTGGTTCGATCAA 833–837 1.000 79.1
psaA-ycf3_p2 psaA-ycf3 CCCATTCCTCGAAAGACGTT CAGAGGCTTGGTTCGATCAA 808–812 1.000 78.9
psaA-ycf3_p3 psaA-ycf3 GTTCTTGAAAAATGGCCGGG TTGAAGATCACGAGGCGTTT 747–751 1.000 78.6
psaA-ycf3_p4 psaA-ycf3 CCCATTCCTCGAAAGACGTT TTGAAGATCACGAGGCGTTT 722–726 1.000 78.5
psaA-ycf3_p5 psaA-ycf3 GTTCTTGAAAAATGGCCGGG TTGGTTGAAGATCACGAGGC 751–755 1.000 78.4

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
Nothoscordum bonariense NC_057582.1 156559 View on NCBI ↗
Nothoscordum felipponei PP853216.1 156561 View on NCBI ↗