Markers + reference

Anubias

3 species · Araceae · Alismatales

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Species 3
Genome length 170–170 kb
Candidate markers 270
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnF(GAA)-ndhJ LSC 1396 0.0114 0.96 63.7 yes View details
accD-psaI LSC 2138 0.0124 0.96 55.7 yes View details
trnL(CAA)-ndhB IRb 1087 0.0480 1.00 86.9 yes View details
rrn4.5-rrn5 IRb 232 0.0460 1.00 66.6 yes View details
rrn5-trnR(ACG) IRb 250 0.0093 1.00 58.7 yes View details
ycf1 IRb 714 0.0037 1.00 33.7 yes View details
rps15-ycf1 SSC 1080 0.0162 0.96 70.3 yes View details
ycf1 SSC 5685 0.0043 1.00 46.2 no View details
trnR(ACG)-rrn5 IRa 250 0.0080 1.00 58.1 yes View details
rrn5-rrn4.5 IRa 232 0.0460 1.00 66.6 yes View details
ndhB-trnL(CAA) IRa 1087 0.0408 0.99 82.1 yes View details
psbC-trnS(UGA) LSC 123 0.0650 1.00 72.7 yes View details
psaA-ycf3 LSC 687 0.0039 1.00 66.3 yes View details
ndhD-psaC SSC 113 0.0177 1.00 63.8 yes View details
trnK(UUU)-rps16 LSC 710 0.0020 0.96 63.6 yes View details
ycf4-cemA LSC 1226 0.0078 0.98 62.9 yes View details
trnT(UGU)-trnL(UAA) LSC 1227 0.0087 0.99 62.5 yes View details
rpl16-rps3 LSC 156 0.0171 1.00 62.3 yes View details
ndhE-ndhG SSC 373 0.0089 1.00 62.3 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK(UUU)-rps16_p1 trnK(UUU)-rps16 CCGCACTTAAAAGCCGAGTA AAAGGAGCTCAACCCACAAG 794–817 1.000 80.6
trnK(UUU)-rps16_p2 trnK(UUU)-rps16 CCGCACTTAAAAGCCGAGTA AGCTCAACCCACAAGAACTG 789–812 1.000 80.5
trnK(UUU)-rps16_p3 trnK(UUU)-rps16 CATAGCCGCACTTAAAAGCC AAAGGAGCTCAACCCACAAG 799–822 1.000 79.1
trnK(UUU)-rps16_p4 trnK(UUU)-rps16 CATAGCCGCACTTAAAAGCC AGCTCAACCCACAAGAACTG 794–817 1.000 79.0
trnK(UUU)-rps16_p5 trnK(UUU)-rps16 CCGCACTTAAAAGCCGAGTA GAGCTCAACCCACAAGAACT 790–813 1.000 78.6
psbC-trnS(UGA)_p1 psbC-trnS(UGA) CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 230 1.000 82.4
psbC-trnS(UGA)_p2 psbC-trnS(UGA) CCTGTTCTTTCCATGACCCC GGGTTCGAATCCCTCTCTCT 176 1.000 82.4
psbC-trnS(UGA)_p3 psbC-trnS(UGA) CCTGTTCTTTCCATGACCCC GATGGCCGAGTGGTTGATAG 241 1.000 81.7
psbC-trnS(UGA)_p4 psbC-trnS(UGA) TTCCATGACCCCTCTTAGCT GGTTGATAGCTCCGGTCTTG 222 1.000 81.7
psbC-trnS(UGA)_p5 psbC-trnS(UGA) TTGTGGGTCATTTGTGGCAT GGTTGATAGCTCCGGTCTTG 310 1.000 80.3
psaA-ycf3_p1 psaA-ycf3 GTCTGGCCCATTCCTCAAAA TGGTTGAAGATAACGAGGCG 727–802 1.000 83.8
psaA-ycf3_p2 psaA-ycf3 TGGCCCATTCCTCAAAAGAC TGGTTGAAGATAACGAGGCG 724–799 1.000 83.8
psaA-ycf3_p3 psaA-ycf3 GTCTGGCCCATTCCTCAAAA GTTGAAGATAACGAGGCGGT 725–800 1.000 83.8
psaA-ycf3_p4 psaA-ycf3 TGGCCCATTCCTCAAAAGAC GTTGAAGATAACGAGGCGGT 722–797 1.000 83.8
psaA-ycf3_p5 psaA-ycf3 CTGGCCCATTCCTCAAAAGA TGGTTGAAGATAACGAGGCG 725–800 1.000 82.6
trnT(UGU)-trnL(UAA)_p1 trnT(UGU)-trnL(UAA) GGAAAAAGCCAGCTATCGGA ACCAATTTCGCCATATCCCC 1326–1375 1.000 82.3
trnT(UGU)-trnL(UAA)_p2 trnT(UGU)-trnL(UAA) AGGGAAAAAGCCAGCTATCG ACCAATTTCGCCATATCCCC 1328–1377 1.000 82.3
trnT(UGU)-trnL(UAA)_p3 trnT(UGU)-trnL(UAA) GGAAAAAGCCAGCTATCGGA TCCATACCAAGGCTCAATGC 1365–1414 1.000 81.8
trnT(UGU)-trnL(UAA)_p4 trnT(UGU)-trnL(UAA) AGGGAAAAAGCCAGCTATCG TCCATACCAAGGCTCAATGC 1367–1416 1.000 81.8
trnT(UGU)-trnL(UAA)_p5 trnT(UGU)-trnL(UAA) GGAAAAAGCCAGCTATCGGA TAGCGTCTACCAATTTCGCC 1334–1383 1.000 81.8
trnF(GAA)-ndhJ_p1 trnF(GAA)-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGCTGGC 1506–1538 1.000 83.7
trnF(GAA)-ndhJ_p2 trnF(GAA)-ndhJ CGATGCATGGAAAATGGTCG TGAAAGTTGGATAGGCTGGC 1561–1593 1.000 83.2
trnF(GAA)-ndhJ_p3 trnF(GAA)-ndhJ GCGATGCATGGAAAATGGTC TGAAAGTTGGATAGGCTGGC 1562–1594 1.000 82.8
trnF(GAA)-ndhJ_p4 trnF(GAA)-ndhJ AATGGTCGGGATAGCTCAGT TGAAAGTTGGATAGGCTGGC 1549–1581 1.000 82.4
trnF(GAA)-ndhJ_p5 trnF(GAA)-ndhJ ATGGTCGGGATAGCTCAGTT TGAAAGTTGGATAGGCTGGC 1548–1580 1.000 82.4
accD-psaI_p1 accD-psaI TCACAAGCGGCTGAGTATTC ATGATCCCCCTTTGACCAGA 2501–2574 1.000 85.1
accD-psaI_p2 accD-psaI TCACAAGCGGCTGAGTATTC CCATTGCAATTGCCGGAAAT 2255–2328 1.000 85.0
accD-psaI_p3 accD-psaI TCACAAGCGGCTGAGTATTC TTCGCAAGGAGCCACATATC 2406–2479 1.000 84.8
accD-psaI_p4 accD-psaI TCACAAGCGGCTGAGTATTC TTGTTTTTCGAGACCCCGTT 2721–2794 1.000 84.6
accD-psaI_p5 accD-psaI GCGAGAAAATCACCCGTTTG ATGATCCCCCTTTGACCAGA 2821–2894 1.000 84.4

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
Anubias barteri NC_068131.1 169910 View on NCBI ↗
Anubias hastifolia NC_062430.1 169841 View on NCBI ↗
Anubias heterophylla MN046884.1 170037 View on NCBI ↗