Markers + reference

Disporum

4 species · Colchicaceae · Liliales

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Species 4
Genome length 157–157 kb
Candidate markers 261
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 617 0.0054 1.00 39.1 yes View details
trnC-GCA-petN LSC 1195 0.0078 0.99 51.0 yes View details
ndhC-trnV-UAC LSC 1289 0.0104 1.00 56.9 yes View details
rbcL LSC 1446 0.0091 1.00 45.5 yes View details
rrn16S IRb 1491 0.0000 1.00 40.0 yes View details
ndhF SSC 2199 0.0041 1.00 35.8 yes View details
ndhF-rpl32 SSC 800 0.0098 1.00 42.2 yes View details
rpl32-trnL-UAG SSC 809 0.0130 1.00 61.9 yes View details
rps15-trnN-GUU SSC 6247 0.0052 1.00 56.5 yes View details
rrn16S IRa 1491 0.0000 1.00 40.0 no View details
trnE-UUC-trnT-GGU LSC 684 0.0032 1.00 61.2 yes View details
clpP LSC 2094 0.0037 1.00 60.7 yes View details
trnH-GUG-psbA IRa 229 0.0199 0.95 60.2 no View details
rps12-trnV-GAC IRb 1806 0.0013 1.00 59.0 yes View details
trnV-GAC-rps12 IRa 1806 0.0013 1.00 59.0 yes View details
trnL-UAA-trnF-GAA LSC 424 0.0083 0.97 57.9 yes View details
ndhG-ndhI SSC 408 0.0045 1.00 57.7 yes View details
trnT-UGU-trnL-UAA LSC 602 0.0061 0.98 56.5 yes View details
rps16-trnQ-UUG LSC 1211 0.0043 0.99 55.7 yes View details
rpoB LSC 3213 0.0015 1.00 53.6 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAGTGGGGTTTTACGATCCG 901–903 1.000 79.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGAGCCGTATGAGGAGAAAG 1034–1039 1.000 79.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCGATCCCGAAGAGAAGGAA 933–935 1.000 79.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GAGCCGTATGAGGAGAAAGC 1033–1038 1.000 79.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAGTGGGGTTTTACGATCCG 897–899 1.000 79.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGGCAGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1281–1302 1.000 81.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC GAGGTTCGAATCCTTCCGTC 1251–1272 1.000 81.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACGGCAGATCATGTC GAGGTTCGAATCCTTCCGTC 1287–1308 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACGGCAGATCATGT GAGGTTCGAATCCTTCCGTC 1288–1309 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1274–1295 1.000 80.1
rpoB_p1 rpoB ATCCTCGGGGTTAGGTACTG TGATAAAATCCACGGGCGTT 238 1.000 79.1
rpoB_p2 rpoB CATCCTCGGGGTTAGGTACT TGATAAAATCCACGGGCGTT 239 1.000 79.1
rpoB_p3 rpoB CCTCCAATGATCGTAGCACC TGATAAAATCCACGGGCGTT 216 1.000 78.8
rpoB_p4 rpoB ATCCTCGGGGTTAGGTACTG ATGATAAAATCCACGGGCGT 239 1.000 77.3
rpoB_p5 rpoB CATCCTCGGGGTTAGGTACT ATGATAAAATCCACGGGCGT 240 1.000 77.3
trnC-GCA-petN_p1 trnC-GCA-petN TCATTTTGGGTCGGATTGGG CCATTAAAACAGCCCAAGCG 1307–1321 1.000 80.8
trnC-GCA-petN_p2 trnC-GCA-petN TCATTTTGGGTCGGATTGGG AGTCCACTCCTTCCCCATAC 1356–1370 1.000 79.8
trnC-GCA-petN_p3 trnC-GCA-petN TCATTTTGGGTCGGATTGGG GTCCACTCCTTCCCCATACT 1355–1369 1.000 79.8
trnC-GCA-petN_p4 trnC-GCA-petN TCATTTTGGGTCGGATTGGG AGCCCAAGCGAGACTTACTA 1297–1311 1.000 79.6
trnC-GCA-petN_p5 trnC-GCA-petN TCATTTTGGGTCGGATTGGG GAGTCCACTCCTTCCCCATA 1357–1371 1.000 79.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 785–787 1.000 78.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 764–766 1.000 78.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TACCGCTGAGTTAAAAGGGC 750–752 1.000 77.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA TACCGCTGAGTTAAAAGGGC 729–731 1.000 77.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCGATGACTTACGCCTTACC 782–784 1.000 77.3
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 652–682 1.000 81.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 660–690 1.000 81.1
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 684–714 1.000 80.7
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 692–722 1.000 80.1
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 666–696 1.000 79.7

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
Disporum cantoniense NC_065360.1 156562 View on NCBI ↗
Disporum megalanthum NC_065355.1 156583 View on NCBI ↗
Disporum uniflorum NC_065356.1 156588 View on NCBI ↗
Disporum viridescens NC_062144.1 156645 View on NCBI ↗