Markers + reference

Colocasia

4 species · Araceae · Alismatales

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Species 4
Genome length 162–163 kb
Candidate markers 269
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-psbA LSC 623 0.0154 0.96 67.5 yes View details
tRNA-Lys(UUU)-rps16 LSC 758 0.0062 1.00 67.5 yes View details
tRNA-Ser(GCU)-tRNA-Gly(UCC) LSC 1569 0.0093 0.98 62.8 yes View details
rpoB-tRNA-Cys(GCA) LSC 1431 0.0052 0.99 62.7 yes View details
accD-psaI LSC 992 0.0056 1.00 63.7 yes View details
tRNA-Asn(GUU)-ndhF SSC 1069 0.0140 0.78 58.7 yes View details
ndhD SSC 1503 0.0017 1.00 47.7 yes View details
rps15 SSC 279 0.0018 1.00 25.6 yes View details
ndhD-psaC SSC 133 0.0677 1.00 66.9 yes View details
tRNA-Tyr(GUA)-tRNA-Glu(UUC) LSC 160 0.0167 1.00 66.1 yes View details
psbE-petL LSC 1229 0.0025 0.98 62.6 yes View details
petA-psbJ LSC 896 0.0050 1.00 62.3 yes View details
tRNA-Thr(UGU)-tRNA-Leu(UAA) LSC 1142 0.0031 1.00 62.1 yes View details
petN-psbM LSC 1225 0.0037 1.00 61.4 yes View details
ndhE-ndhG SSC 362 0.0028 1.00 61.3 yes View details
atpF LSC 1370 0.0018 1.00 60.9 yes View details
psbA-tRNA-Lys(UUU) LSC 261 0.0045 1.00 60.7 yes View details
rbcL-accD LSC 772 0.0019 1.00 60.4 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-psbA_p1 trnH-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 537–745 1.000 83.6
trnH-psbA_p2 trnH-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 551–759 1.000 83.5
trnH-psbA_p3 trnH-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 550–758 1.000 83.5
trnH-psbA_p4 trnH-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 552–760 1.000 83.5
trnH-psbA_p5 trnH-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 539–747 1.000 83.5
psbA-tRNA-Lys(UUU)_p1 psbA-tRNA-Lys(UUU) TAGGCTTGTACTTTCGCGTC TCGTGTGCAATGAAAACTGC 406–424 1.000 83.3
psbA-tRNA-Lys(UUU)_p2 psbA-tRNA-Lys(UUU) TAGGCTTGTACTTTCGCGTC AATGAAAACTGCAAGCACGG 398–416 1.000 83.2
psbA-tRNA-Lys(UUU)_p3 psbA-tRNA-Lys(UUU) TAGGCTTGTACTTTCGCGTC CGTGTGCAATGAAAACTGCA 405–423 1.000 83.0
psbA-tRNA-Lys(UUU)_p4 psbA-tRNA-Lys(UUU) ATGTAAAGGCGGTTTTCGGT TCGTGTGCAATGAAAACTGC 456–474 1.000 82.2
psbA-tRNA-Lys(UUU)_p5 psbA-tRNA-Lys(UUU) ATGTAAAGGCGGTTTTCGGT AATGAAAACTGCAAGCACGG 448–466 1.000 82.1
tRNA-Lys(UUU)-rps16_p1 tRNA-Lys(UUU)-rps16 AAAGCCGAGTACTCTACCGT AAAGGAGCTCAACCCACAAG 836–855 1.000 82.1
tRNA-Lys(UUU)-rps16_p2 tRNA-Lys(UUU)-rps16 AAGCCGAGTACTCTACCGTT AAAGGAGCTCAACCCACAAG 835–854 1.000 82.1
tRNA-Lys(UUU)-rps16_p3 tRNA-Lys(UUU)-rps16 AAAGCCGAGTACTCTACCGT AGCTCAACCCACAAGAACTG 831–850 1.000 82.0
tRNA-Lys(UUU)-rps16_p4 tRNA-Lys(UUU)-rps16 AAGCCGAGTACTCTACCGTT AGCTCAACCCACAAGAACTG 830–849 1.000 82.0
tRNA-Lys(UUU)-rps16_p5 tRNA-Lys(UUU)-rps16 CCGCACTTAAAAGCCGAGTA AAAGGAGCTCAACCCACAAG 845–864 1.000 81.2
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p1 tRNA-Ser(GCU)-tRNA-Gly(UCC) GAGAAAGCGGAGAAAGAGGG AGGACGAATCACACTTTTACCA 1679–1743 1.000 66.4
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p2 tRNA-Ser(GCU)-tRNA-Gly(UCC) ATTAGCAATCCGCCGCTTTA AGGACGAATCACACTTTTACCA 1624–1688 1.000 66.2
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p3 tRNA-Ser(GCU)-tRNA-Gly(UCC) GAGAAAGCGGAGAAAGAGGG GGACGAATCACACTTTTACCAC 1678–1742 1.000 65.9
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p4 tRNA-Ser(GCU)-tRNA-Gly(UCC) ATTAGCAATCCGCCGCTTTA GGACGAATCACACTTTTACCAC 1623–1687 1.000 65.8
tRNA-Ser(GCU)-tRNA-Gly(UCC)_p5 tRNA-Ser(GCU)-tRNA-Gly(UCC) TCAAGTGACCAGAGAAAGCG AGGACGAATCACACTTTTACCA 1690–1754 1.000 65.3
atpF_p1 atpF ACTAATTTCGTCGGCTCGAA TCAATCAAAAAGGGGAGGGC 1544–1554 1.000 75.1
atpF_p2 atpF ACTAATTTCGTCGGCTCGAA GAGGGCGAAGTGATCCAAAA 1530–1540 1.000 74.2
atpF_p3 atpF ACTAATTTCGTCGGCTCGAA AGGGCGAAGTGATCCAAAAA 1529–1539 1.000 73.4
atpF_p4 atpF AATTTCGTCGGCTCGAATGG TCAATCAAAAAGGGGAGGGC 1541–1551 1.000 72.3
atpF_p5 atpF AATTTCGTCGGCTCGAATGG GAGGGCGAAGTGATCCAAAA 1527–1537 1.000 71.4
rpoB-tRNA-Cys(GCA)_p1 rpoB-tRNA-Cys(GCA) CCCTCATTTTCATCCCGGAG GCGACACCCAGATTTGAACT 1523–1568 1.000 79.3
rpoB-tRNA-Cys(GCA)_p2 rpoB-tRNA-Cys(GCA) CTCATTTTCATCCCGGAGCA GCGACACCCAGATTTGAACT 1521–1566 1.000 79.2
rpoB-tRNA-Cys(GCA)_p3 rpoB-tRNA-Cys(GCA) CCCTCATTTTCATCCCGGAG TAAAGGATTTGCAGTCCCCC 1498–1543 1.000 79.0
rpoB-tRNA-Cys(GCA)_p4 rpoB-tRNA-Cys(GCA) CCCTCATTTTCATCCCGGAG CCTTACCACTTGGCCATGTC 1477–1522 1.000 78.9
rpoB-tRNA-Cys(GCA)_p5 rpoB-tRNA-Cys(GCA) CTCATTTTCATCCCGGAGCA TAAAGGATTTGCAGTCCCCC 1496–1541 1.000 78.8

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
Colocasia esculenta NC_016753.1 162424 View on NCBI ↗
Colocasia formosana PP817742.1 162158 View on NCBI ↗
Colocasia lihengiae PP817743.1 162557 View on NCBI ↗
Colocasia spongifolia PP817747.1 162388 View on NCBI ↗