Markers + reference

Stemona

5 species · Stemonaceae · Pandanales

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Species 5
Genome length 154–155 kb
Candidate markers 274
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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1119 0.0135 0.99 56.8 yes View details
psbI-trnS-GCU LSC 145 0.0124 1.00 41.5 yes View details
trnS-GCU-trnG-UCC LSC 515 0.0116 1.00 65.1 yes View details
rpoB-trnC-GCA LSC 1220 0.0086 0.99 60.4 yes View details
trnC-GCA-petN LSC 459 0.0249 1.00 61.7 yes View details
petN-psbM LSC 924 0.0111 1.00 64.6 yes View details
trnT-UGU-trnL-UAA LSC 855 0.0096 1.00 55.5 yes View details
ndhC-trnV-UAC LSC 1289 0.0117 0.98 58.5 yes View details
cemA-psbJ LSC 927 0.0181 1.00 70.8 yes View details
psaJ-rpl33 LSC 500 0.0105 1.00 51.4 yes View details
ycf1-rps15 SSC 305 0.0273 1.00 60.2 yes View details
trnL-UAG-rpl32 SSC 784 0.0154 0.99 70.7 yes View details
rpl33-rps18 LSC 167 0.0557 1.00 78.2 yes View details
rpl32-ndhF SSC 850 0.0107 0.99 71.4 yes View details
trnE-UUC-trnT-GGU LSC 594 0.0125 0.99 64.3 yes View details
rps16-trnQ-UUG LSC 521 0.0111 1.00 61.4 yes View details
psbM-trnD-GUC LSC 967 0.0056 1.00 60.6 yes View details
psbC-trnS-UGA LSC 128 0.0328 1.00 60.0 yes View details
petD-rpoA LSC 154 0.0198 0.99 59.4 yes View details
atpB-rbcL LSC 603 0.0108 1.00 59.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 TGCCCGAGGTGAAAGAAAAA GAGGTTCGAATCCTTCCGTC 2065–2095 1.000 83.2
rps16_p2 rps16 TTGCCCGAGGTGAAAGAAAA GAGGTTCGAATCCTTCCGTC 2066–2096 1.000 83.2
rps16_p3 rps16 TTTGCCCGAGGTGAAAGAAA GAGGTTCGAATCCTTCCGTC 2067–2097 1.000 83.2
rps16_p4 rps16 AAGGGCAAATTGGGGGAAAT GAGGTTCGAATCCTTCCGTC 1741–1770 0.800 75.2
rps16_p5 rps16 CCTTTCAGGATCAGTCGTGG GAGGTTCGAATCCTTCCGTC 2319–2349 0.800 74.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 605–615 1.000 84.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 603–613 1.000 84.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 611–621 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 587–597 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 598–608 1.000 82.8
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TAAAGCGGCGGATTGCTAAT 237–245 1.000 73.6
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 261–269 1.000 72.9
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GGGTTCGAATCCCTCTCTCT 192–200 1.000 72.4
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTCGAATCCCTCTCTCTCCG 189–197 1.000 71.6
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TAAAGCGGCGGATTGCTAAT 237–245 1.000 71.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCACT 572–609 1.000 74.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCGCACTTTTACCAC 572–609 1.000 74.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC TCGAACCCTCGGTACCAATA ACGAATCGCACTTTTACCACT 605–642 1.000 73.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TCGAACCCTCGGTACCAATA ACGAATCGCACTTTTACCAC 605–642 1.000 73.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA ACGAATCGCACTTTTACCACT 620–657 1.000 72.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TAAAGGATTTGCAGTCCCCC 1354–1387 1.000 77.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTGTGTACATTCCATCCCGC TAAAGGATTTGCAGTCCCCC 1284–1317 1.000 76.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG TTTGTTGATCAGGCGACACC 1391–1424 1.000 75.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AATTCTTCCGTCAAGCCCTG GACACCCGGATTTGAACTGG 1377–1410 1.000 74.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTGTGTACATTCCATCCCGC TTTGTTGATCAGGCGACACC 1321–1354 1.000 74.5
trnC-GCA-petN_p1 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGTCCACTCCTTCCCCATAC 553–652 1.000 81.7
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTA GTCCACTCCTTCCCCATACT 552–651 1.000 81.7
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTA AGCCCAAGCGAGACTTACTA 494–593 1.000 81.7
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTA GAGTCCACTCCTTCCCCATA 554–653 1.000 81.2
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTA CTAGAGTCCACTCCTTCCCC 557–656 1.000 80.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Stemona japonica NC_039675.1 154224 View on NCBI ↗
Stemona mairei NC_039676.1 154307 View on NCBI ↗
Stemona parviflora NC_064125.1 154552 View on NCBI ↗
Stemona sessilifolia NC_065767.1 154038 View on NCBI ↗
Stemona tuberosa NC_056376.1 154374 View on NCBI ↗