Markers + reference

Aponogeton

3 species · Aponogetonaceae · Alismatales

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Species 3
Genome length 155–155 kb
Candidate markers 268
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 381 0.0595 1.00 88.6 yes View details
trnK-UUU-rps16 LSC 733 0.0332 0.99 68.5 yes View details
rps16-trnQ-UUG LSC 1187 0.0319 0.99 70.1 yes View details
psbK-psbI LSC 259 0.0425 1.00 69.0 yes View details
atpH-atpI LSC 803 0.0399 1.00 73.6 yes View details
trnE-UUC-trnT-GGU LSC 501 0.0293 1.00 68.1 yes View details
trnS-UGA-psbZ LSC 355 0.0254 1.00 61.3 yes View details
trnT-UGU-trnL-UAA LSC 881 0.0302 0.98 73.1 yes View details
trnF-GAA-ndhJ LSC 693 0.0269 1.00 66.8 yes View details
trnN-GUU-ndhF IRb 629 0.0360 0.93 72.3 yes View details
ndhF SSC 2217 0.0141 1.00 52.3 yes View details
ndhF-rpl32 SSC 1211 0.0254 1.00 64.3 yes View details
ycf1 SSC 5508 0.0227 1.00 53.3 yes View details
psbC-trnS-UGA LSC 127 0.0907 0.98 82.9 yes View details
psaJ-rpl33 LSC 453 0.0316 1.00 75.3 yes View details
rrn4.5-rrn5 IRb 227 0.0499 1.00 71.8 yes View details
rrn5-rrn4.5 IRa 227 0.0499 1.00 71.8 yes View details
rps4-trnT-UGU LSC 392 0.0376 0.99 71.7 yes View details
ycf3-trnS-GGA LSC 346 0.0344 0.98 71.2 yes View details
psbI-trnS-GCU LSC 115 0.0464 1.00 71.1 yes View details
trnS-GCU-trnG-UCC LSC 907 0.0256 0.99 70.0 yes View details
accD-psaI LSC 846 0.0221 1.00 69.4 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 427–514 1.000 88.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 430–517 1.000 87.9
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 482–569 1.000 86.5
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 484–571 1.000 86.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTGCTGTTGAAGTTCCAT 416–503 1.000 86.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 ATCCGCTCACAGGAAAATCC TATCCCAATGGGCCGTCTAT 1398–1417 0.667 70.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 ATCCGCTCACAGGAAAATCC TATCTATCCCAATGGGCCGT 1402–1421 0.667 70.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 ACACATCCATCTCCACCTCA TATCCCAATGGGCCGTCTAT 1452–1455 0.667 68.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 ACACATCCATCTCCACCTCA TATCTATCCCAATGGGCCGT 1456–1459 0.667 68.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACACATCCATCTCCACCTCA CAATTGATGCTCGATCCCGA 1422–1425 0.667 67.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGGTCCTGTTATTCGGAGGT 1255–1379 1.000 83.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1240–1364 1.000 83.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1244–1368 1.000 79.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TGGTCCTGTTATTCGGAGGT 1247–1371 1.000 78.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1232–1356 1.000 78.6
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCA 311–313 1.000 48.8
psbK-psbI_p2 psbK-psbI AATCGTAGACGTTATGCCCG ACAAAGAGTTTGAGAGTAAGCA 363–365 1.000 47.6
psbK-psbI_p3 psbK-psbI CGTTATGCCCGTCATACCTC ACAAAGAGTTTGAGAGTAAGCA 354–356 1.000 46.9
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAGAGTTTGAGAGTAAGCA 308–310 1.000 46.8
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACAAAGAGTTTGAGAGTAAGCA 309–311 1.000 46.8
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGACCCAGGGCGTA TGGACTAAAGCGTCGGATTG 228 1.000 82.0
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGACCCAGGGCGT TGGACTAAAGCGTCGGATTG 229 1.000 82.0
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGACCCAGGGCGTA GTGGACTAAAGCGTCGGATT 229 1.000 82.0
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGACCCAGGGCGT GTGGACTAAAGCGTCGGATT 230 1.000 82.0
psbI-trnS-GCU_p5 psbI-trnS-GCU TCTAATGACCCAGGGCGTAA TGGACTAAAGCGTCGGATTG 227 1.000 81.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 917–976 1.000 58.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 916–975 1.000 58.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 920–979 1.000 57.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 919–978 1.000 57.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 918–977 1.000 57.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Aponogeton abyssinicus NC_053910.1 154562 View on NCBI ↗
Aponogeton desertorum NC_053911.1 154590 View on NCBI ↗
Aponogeton rehmannii NC_053913.1 154528 View on NCBI ↗