Markers + reference

Disporopsis

4 species · Asparagaceae · Asparagales

Back to catalogue

Species 4
Genome length 156–156 kb
Candidate markers 268
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 637 0.0068 1.00 63.8 yes View details
trnC-GCA-petN LSC 882 0.0057 1.00 49.1 yes View details
ycf3 LSC 1995 0.0021 1.00 58.2 yes View details
rbcL LSC 1440 0.0007 1.00 41.7 yes View details
rbcL-accD LSC 675 0.0059 1.00 53.3 yes View details
accD-psaI LSC 376 0.0151 1.00 65.1 yes View details
petA-psbJ LSC 1081 0.0051 1.00 53.3 yes View details
rpl16 LSC 1456 0.0025 1.00 38.8 yes View details
rrn4.5S-rrn5S IRb 221 0.0226 1.00 54.3 yes View details
rpl32-trnL-UAG SSC 937 0.0045 0.99 54.4 yes View details
trnR-ACG-rrn5S IRa 256 0.0000 1.00 33.8 yes View details
rrn5S-rrn4.5S IRa 221 0.0226 1.00 54.3 yes View details
trnT-UGU-trnL LSC 969 0.0034 0.97 65.9 yes View details
ycf4-cemA LSC 773 0.0037 1.00 61.8 yes View details
petG-trnW-CCA LSC 124 0.0040 0.99 59.9 yes View details
ndhA SSC 2173 0.0015 1.00 58.4 yes View details
rrn16S-trnI-GAU IRb 301 0.0050 1.00 56.0 yes View details
trnI-GAU-rrn16S IRa 301 0.0050 1.00 56.0 yes View details
atpH-atpI LSC 500 0.0010 1.00 53.8 yes View details
trnS-GCU-trnG-UCC LSC 1310 0.0025 0.99 52.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 746–749 1.000 78.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 745–748 1.000 78.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 732–735 1.000 76.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGGAAC 757–760 1.000 75.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 755–758 1.000 73.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCACT 1432–1444 1.000 71.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AAGTGATCAGAGGGAACGGA ACGAATCGCACTTTTACCACT 1436–1448 1.000 71.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATCAGAGGGAACGGAGAGAG ACGAATCGCACTTTTACCACT 1431–1443 1.000 71.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GATCAGAGGGAACGGAGAGA ACGAATCGCACTTTTACCAC 1432–1444 1.000 71.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AAGTGATCAGAGGGAACGGA ACGAATCGCACTTTTACCAC 1436–1448 1.000 71.1
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 531–564 1.000 83.3
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT ATAGGGGAATCCATGGAGGG 619–652 1.000 82.9
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 587–620 1.000 82.7
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 532–565 1.000 82.1
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 591–624 1.000 82.1
trnC-GCA-petN_p1 trnC-GCA-petN ATTTTGGACCGAATTTGGCG TTAAAGCAGCCCAAGCAAGA 1000–1003 1.000 78.1
trnC-GCA-petN_p2 trnC-GCA-petN ATTTTGGACCGAATTTGGCG AGCAATTAGTAGTGCCCAGC 1077–1080 1.000 77.7
trnC-GCA-petN_p3 trnC-GCA-petN ATTTTGGACCGAATTTGGCG CACCCCTTCCCCATACTACA 1048–1051 1.000 77.2
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTA TTAAAGCAGCCCAAGCAAGA 960–963 1.000 76.8
trnC-GCA-petN_p5 trnC-GCA-petN ATTTTGGACCGAATTTGGCG CAGCCCAAGCAAGACTTACT 994–997 1.000 76.6
ycf3_p1 ycf3 TGTCATGGTCATGGTAATGGT CCGAGGGGGTAATGAGAAGA 2118–2120 1.000 62.5
ycf3_p2 ycf3 TGTCATGGTCATGGTAATGGTC CCGAGGGGGTAATGAGAAGA 2118–2120 1.000 61.7
ycf3_p3 ycf3 GTCATGGTCATGGTAATGGTCT CCGAGGGGGTAATGAGAAGA 2117–2119 1.000 61.4
ycf3_p4 ycf3 TCATGGTCATGGTAATGGTCTC CCGAGGGGGTAATGAGAAGA 2116–2118 1.000 59.3
ycf3_p5 ycf3 CATGGTCATGGTAATGGTCTCT CCGAGGGGGTAATGAGAAGA 2115–2117 1.000 59.2
trnT-UGU-trnL_p1 trnT-UGU-trnL GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 1014–1072 1.000 82.2
trnT-UGU-trnL_p2 trnT-UGU-trnL GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 1022–1080 1.000 81.6
trnT-UGU-trnL_p3 trnT-UGU-trnL AAATGCGATGCTCTAACCCC ACCAATTTCGCCATATCCCC 986–1044 1.000 81.6
trnT-UGU-trnL_p4 trnT-UGU-trnL AAATGCGATGCTCTAACCCC TAGCGTCTACCAATTTCGCC 994–1052 1.000 81.1
trnT-UGU-trnL_p5 trnT-UGU-trnL GGAATCGAACCGATGACCAT ATCCAATCAAGTCCGTAGCG 1037–1095 1.000 80.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Disporopsis aspersa NC_065353.1 156110 View on NCBI ↗
Disporopsis fuscopicta NC_056913.1 155963 View on NCBI ↗
Disporopsis longifolia NC_065354.1 156088 View on NCBI ↗
Disporopsis pernyi NC_065359.1 156072 View on NCBI ↗