Markers + reference

Chlorophytum

2 species · Asparagaceae · Asparagales

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Species 2
Genome length 154–154 kb
Candidate markers 267
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1165 0.0493 0.98 80.0 yes View details
atpA LSC 1524 0.0184 1.00 58.5 yes View details
ycf3-trnS-GGA LSC 548 0.0310 1.00 68.8 yes View details
ndhC-trnV-UAC LSC 1595 0.0382 0.97 71.2 yes View details
accD LSC 1671 0.0810 0.78 74.4 yes View details
ccsA-ndhD SSC 244 0.1073 0.95 78.4 yes View details
ndhD SSC 1503 0.0226 1.00 58.7 yes View details
ycf1 SSC 5139 0.0286 1.00 61.1 yes View details
trnH-GUG-psbA LSC 163 0.0909 0.94 82.5 no View details
trnH-GUG-rpl2 IRb 43 0.0698 1.00 79.7 yes View details
rpl2-trnH-GUG IRa 43 0.0698 1.00 79.7 yes View details
rrn4.5-rrn5 IRb 221 0.0505 0.99 79.2 yes View details
rrn5-rrn4.5 IRa 221 0.0505 0.99 79.2 yes View details
ndhF-rpl32 SSC 931 0.0431 0.95 75.0 yes View details
ycf4-cemA LSC 639 0.0341 0.87 74.2 yes View details
trnW-CCA-trnP-UGG LSC 148 0.0676 1.00 74.2 yes View details
trnS-GCU-trnG-UCC LSC 1063 0.0321 1.00 72.2 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 80 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 1221–1238 1.000 83.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1232–1249 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1225–1242 1.000 79.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1233–1250 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1213–1230 1.000 78.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TGATCAGAGAGAGCGGAGAG AAAGTTTTTGGGGACGGGAA 1264–1355 1.000 80.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AAGTGATCAGAGAGAGCGGA AAAGTTTTTGGGGACGGGAA 1267–1358 1.000 79.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC AAAGTTTTTGGGGACGGGAA 1197–1288 1.000 79.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATCAGAGAGAGCGGAGAGA AAAGTTTTTGGGGACGGGAA 1263–1354 1.000 79.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATCAGAGAGAGCGGAGAGAG AAAGTTTTTGGGGACGGGAA 1262–1353 1.000 78.9
atpA_p1 atpA TGATCTTGTACTAAGAAATGATCT TTTTCCTTTGTTTCCGAAAAA 1614 0.500 20.0
atpA_p2 atpA TGATCTTGTACTAAGAAATGATCT TTTTTCCTTTGTTTCCGAAAA 1615 0.500 20.0
atpA_p3 atpA TGATCTTGTACTAAGAAATGATCT TTTTTCCTTTGTTTCCGAAAAA 1615 0.500 20.0
atpA_p4 atpA ATGATCTTGTACTAAGAAATGATCT TTTTCCTTTGTTTCCGAAAAA 1615 0.500 20.0
atpA_p5 atpA ATGATCTTGTACTAAGAAATGATCT TTTTTCCTTTGTTTCCGAAAA 1616 0.500 20.0
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CCATTTATCCGGGATCTAGGC ACGGAAAGAGAGGGATTCGA 660 1.000 70.7
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CCATTTATCCGGGATCTAGGC TTCCAATGCTACGCCTTCAA 609 1.000 70.5
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CCATTTATCCGGGATCTAGGC AGTTCCAATGCTACGCCTTC 611 1.000 70.0
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 733 1.000 68.0
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA ACGGAAAGAGAGGGATTCGA 734 1.000 68.0
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CGTATTCGTGAAGCAGAAACA AGAAGGTCTACGGTTCGAGT 1623–1650 1.000 67.4
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TCGTATTCGTGAAGCAGAAAC AGAAGGTCTACGGTTCGAGT 1624–1651 1.000 65.2
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TCGTATTCGTGAAGCAGAAACA AGAAGGTCTACGGTTCGAGT 1624–1651 1.000 65.0
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CGTATTCGTGAAGCAGAAACA GAAGGTCTACGGTTCGAGTC 1622–1649 1.000 64.7
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CGTATTCGTGAAGCAGAAACA GTTCGAGTCCGTATAGCCCT 1611–1638 1.000 63.6
accD_p1 accD CTATCCCGCAGTTTCAGACC AAAGAAGCCATTGCAATCGC 2152–2520 1.000 87.5
accD_p2 accD CTATCCCGCAGTTTCAGACC CCGGGCCTTTTTAACCAGAT 2389–2757 1.000 86.2
accD_p3 accD GGATCGTTTTCTATCCCGCA AAAGAAGCCATTGCAATCGC 2162–2530 1.000 86.1
accD_p4 accD ACTCGGCTCAATCCTTTTCC AAAGAAGCCATTGCAATCGC 2736 0.500 59.1
accD_p5 accD CTATCCCGCAGTTTCAGACC TATTCGCCGGGCCTTTTTAA 2763 0.500 58.5

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
Chlorophytum comosum NC_053844.1 154248 View on NCBI ↗
Chlorophytum laxum NC_081044.1 153678 View on NCBI ↗