Markers + reference

Aglaonema

2 species · Araceae · Alismatales

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Species 2
Genome length 165–166 kb
Candidate markers 270
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1559 0.0184 0.94 59.8 yes View details
trnQ-UUG-psbK LSC 383 0.0317 0.99 60.6 yes View details
trnS-GCU-trnG-UCC LSC 1680 0.0173 0.96 63.1 yes View details
atpH-atpI LSC 873 0.0218 1.00 71.5 yes View details
rpoB-trnC-GCA LSC 1465 0.0304 0.96 72.1 yes View details
trnE-UUC-trnT-GGU LSC 906 0.0199 0.94 74.2 yes View details
rps4-trnT-UGU LSC 705 0.0240 0.83 71.1 yes View details
trnT-UGU-trnL-UAA LSC 1033 0.0366 0.98 81.9 yes View details
trnF-GAA-ndhJ LSC 1029 0.0214 0.96 75.2 yes View details
accD-psaI LSC 1108 0.0163 0.94 72.6 yes View details
psaC-ndhE SSC 1169 0.0191 0.98 66.3 yes View details
rps15-ycf1 SSC 692 0.0261 0.89 62.3 yes View details
psbC-trnS-UGA LSC 123 0.0976 1.00 85.5 yes View details
rpl22-rps19 LSC 93 0.0323 1.00 71.0 yes View details
petA-psbJ LSC 1115 0.0156 0.98 69.7 yes View details
trnY-GUA-trnE-UUC LSC 166 0.0303 0.80 69.6 yes View details
rpoC1-rpoB LSC 26 0.0385 1.00 68.5 yes View details
ycf4-cemA LSC 1198 0.0086 0.97 66.2 yes View details
atpB-rbcL LSC 770 0.0059 0.88 65.0 yes View details
trnL-CAA-ndhB IRb 1064 0.0039 0.96 64.4 yes View details
ndhB-trnL-CAA IRa 1064 0.0039 0.96 64.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AAGAAAACGAGGGCAGATCC ATCAATTCCATCCCGGTTCG 2153–2209 1.000 83.9
rps16_p2 rps16 AAGAAAACGAGGGCAGATCC CAATTCCATCCCGGTTCGAA 2151–2207 1.000 82.1
rps16_p3 rps16 AGACTTGTGTTGGATTGGCA ATCAATTCCATCCCGGTTCG 1868–1948 1.000 82.0
rps16_p4 rps16 AATGCACGATCCCACCAAAA ATCAATTCCATCCCGGTTCG 2250–2305 1.000 81.8
rps16_p5 rps16 ATGCACGATCCCACCAAAAA ATCAATTCCATCCCGGTTCG 2249–2304 1.000 81.8
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATGGGTGCGGAAAGGAAAAT AACTGCTTGAAGAAAGGGCA 1163–1176 1.000 82.1
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ATGGGTGCGGAAAGGAAAAT CTTACAGCAGCTTGCCAAAC 1278–1291 1.000 82.0
trnQ-UUG-psbK_p3 trnQ-UUG-psbK ATGGGTGCGGAAAGGAAAAT GCGGACAAAAGGGAAAATGG 1468–1481 1.000 81.5
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ATGGGTGCGGAAAGGAAAAT GGCGGACAAAAGGGAAAATG 1469–1482 1.000 81.5
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CTTAATGGGTGCGGAAAGGA CTTACAGCAGCTTGCCAAAC 1282–1295 1.000 81.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGGACGAATCACACTTTTACCA 1723–1757 1.000 65.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CGCACAACGGATTAGCAATC AGGACGAATCACACTTTTACCA 1733–1767 1.000 64.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GGACGAATCACACTTTTACCAC 1722–1756 1.000 64.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGCACAACGGATTAGCAATC GGACGAATCACACTTTTACCAC 1732–1766 1.000 64.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCGCACAACGGATTAGCAAT AGGACGAATCACACTTTTACCA 1734–1768 1.000 63.4
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TCACAAGCGGTATTCAAGCT 983–994 1.000 77.1
atpH-atpI_p2 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCG 959–970 1.000 76.8
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG TCACAAGCGGTATTCAAGCT 993–1004 1.000 76.5
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC TCACAAGCGGTATTCAAGCT 1000–1011 1.000 76.2
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTTGCAACTTTAGCCGCG 969–980 1.000 76.2
rpoC1-rpoB_p1 rpoC1-rpoB TTACCTCTCCGACTACCTCC ACGATCTTTGGCTCTGGAAC 214 1.000 73.8
rpoC1-rpoB_p2 rpoC1-rpoB GACTACCTCCCCGTTAGGTA ACGATCTTTGGCTCTGGAAC 204 1.000 73.7
rpoC1-rpoB_p3 rpoC1-rpoB ACCTCCCCGTTAGGTAGAAT ACGATCTTTGGCTCTGGAAC 200 1.000 72.7
rpoC1-rpoB_p4 rpoC1-rpoB GTTGAGGAGAAACTGGTCCA ACGATCTTTGGCTCTGGAAC 157 1.000 72.3
rpoC1-rpoB_p5 rpoC1-rpoB TGTTGAGGAGAAACTGGTCC ACGATCTTTGGCTCTGGAAC 158 1.000 72.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG GCGACACCCAGATTTGAACT 1523–1557 1.000 80.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCATTTTCATCCCGGAGCA GCGACACCCAGATTTGAACT 1521–1555 1.000 80.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG TAAAGGATTTGCAGTCCCCC 1498–1532 1.000 80.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTTCATCCCGGAGCA TAAAGGATTTGCAGTCCCCC 1496–1530 1.000 80.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG TTTGTTGATCAGGCGACACC 1535–1569 1.000 78.6

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
Aglaonema commutatum OR068724.1 165052 View on NCBI ↗
Aglaonema modestum NC_070237.1 165626 View on NCBI ↗