Markers + reference

Scilla

2 species · Asparagaceae · Asparagales

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Species 2
Genome length 154–155 kb
Candidate markers 271
Primer pairs 115

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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 924 0.0418 0.49 64.2 yes View details
psbK-psbI LSC 406 0.0519 1.00 71.4 yes View details
trnS-GCU-trnG-UCC LSC 972 0.0507 0.95 79.0 yes View details
rpoB-trnC-GCA LSC 1202 0.0285 0.96 68.0 yes View details
psbM-trnD-GUC LSC 686 0.0838 0.99 79.1 yes View details
trnT-GGU-psbD LSC 1079 0.0362 1.00 65.5 yes View details
ndhC-trnV-UAC LSC 975 0.0432 0.97 71.6 yes View details
atpB-rbcL LSC 796 0.0506 0.99 73.8 yes View details
infA LSC 201 0.0647 1.00 68.2 yes View details
ndhF SSC 2259 0.0266 1.00 58.6 yes View details
ndhF-rpl32 SSC 703 0.0431 0.99 74.8 yes View details
ycf1 SSC 5472 0.0314 1.00 57.2 yes View details
trnL-UAG-ccsA SSC 78 0.0685 0.94 79.4 yes View details
trnW-CCA-trnP-UGG LSC 173 0.0539 0.97 78.9 yes View details
trnE-UUC-trnT-GGU LSC 488 0.0503 0.98 78.8 yes View details
petA-psbJ LSC 613 0.0425 1.00 77.9 yes View details
rpl14-rpl16 LSC 149 0.0429 0.94 77.4 yes View details
rps18-rpl20 LSC 267 0.0500 0.97 77.3 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0508 1.00 75.4 yes View details
petG-trnW-CCA LSC 115 0.0609 1.00 74.6 yes View details
trnM-CAU-atpE LSC 174 0.0632 1.00 73.2 yes View details
trnK-UUU-rps16 LSC 639 0.0460 0.99 71.9 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CGGAAGTTGGGTGAAAATCG GACAAATGATGGGTTTGCCG 2936 0.500 55.1
trnK-UUU_p2 trnK-UUU CGGAAGTTGGGTGAAAATCG TTGAGAAAATGGGCGGTCTC 2869 0.500 53.7
trnK-UUU_p3 trnK-UUU CGGAAGTTGGGTGAAAATCG TTTGAGAAAATGGGCGGTCT 2870 0.500 52.8
trnK-UUU_p4 trnK-UUU CGGAAGTTGGGTGAAAATCG GAAAATGGGCGGTCTCCTAA 2865 0.500 51.8
trnK-UUU_p5 trnK-UUU CGGAAGTTGGGTGAAAATCG AGAAAATGGGCGGTCTCCTA 2866 0.500 51.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAA TCGATCCCGAAGAGAAGGAA 863–875 1.000 81.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAA GCATGTTGCTGCCTTTTGAA 1336–1353 1.000 81.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTCTCCCTCCCCTTCTAT GCATGTTGCTGCCTTTTGAA 1937 0.500 58.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCTCTCCCTCCCCTTCTAT TCGATCCCGAAGAGAAGGAA 1464 0.500 58.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTCTCCCTCCCCTTCTAT GGTGCTCAACCTACAGGAAC 1358 0.500 58.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 557–1007 1.000 85.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 547–997 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG CTCGGAGGTTCGAATCCTTC 561–1011 1.000 84.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 551–1001 1.000 83.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TATGTCCTTCAAGTCGCACG TACTCGGAGGTTCGAATCCT 563–1013 1.000 82.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCA 459–465 1.000 48.2
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAGAGTTTGAGAGTAAGCA 456–462 1.000 46.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACAAAGAGTTTGAGAGTAAGCA 457–463 1.000 46.2
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACAAAGAGTTTGAGAGTAAGCA 458–464 1.000 46.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACAAAGAGTTTGAGAGTAAGCA 460–466 1.000 46.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TGAACGAATCACACTTTTACCAC 1035–1085 1.000 56.4
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TGAACGAATCACACTTTTACCAC 1030–1080 1.000 55.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT ACGAATCACACTTTTACCACT 1032–1082 1.000 55.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC ACGAATCACACTTTTACCACT 1027–1077 1.000 54.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT GAACGAATCACACTTTTACCACT 1034–1084 1.000 54.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA TAAAGGATTTGCAGTCCCCC 1278–1310 1.000 71.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC TAAAGGATTTGCAGTCCCCC 1279–1311 1.000 71.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTGGACATTCCCTCATTTCCA TTTGTTGATCAGGCGACACC 1315–1347 1.000 69.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TGTGGACATTCCCTCATTTCC TTTGTTGATCAGGCGACACC 1316–1348 1.000 69.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCAGGTATTGTGGACATTCCC TAAAGGATTTGCAGTCCCCC 1287–1319 1.000 69.7

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
Scilla messeniaca PQ210195.1 153640 View on NCBI ↗
Scilla siberica NC_061320.1 154943 View on NCBI ↗