Markers + reference

Monstera

2 species · Araceae · Alismatales

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Species 2
Genome length 163–164 kb
Candidate markers 268
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Ser(GCU)-tRNA-Ser (CGA) LSC 784 0.0174 0.95 67.3 yes View details
tRNA-Glu(UUC)-tRNA-Thr(GGU) LSC 936 0.0178 0.90 71.0 yes View details
rps4-tRNA-Thr(UGU) LSC 546 0.0278 0.99 74.6 yes View details
accD-psaI LSC 1146 0.0189 0.88 72.2 yes View details
rpl16 LSC 1766 0.0122 0.97 54.9 yes View details
tRNA-Asn(GUU)-ndhF SSC 823 0.0275 0.93 77.2 yes View details
rpl32-tRNA-Leu(UAG) SSC 987 0.0356 0.91 80.3 yes View details
psaC-ndhE SSC 1040 0.0214 0.77 70.1 yes View details
ndhG-ndhI SSC 477 0.0388 0.92 77.0 yes View details
rps15-ycf1 SSC 618 0.0295 0.82 75.6 yes View details
ycf1 SSC 5715 0.0082 1.00 45.1 yes View details
rpl2-tRNA-GUG IRa 49 0.1522 0.94 79.0 no View details
rps19-rpl2 IRb 59 0.1186 1.00 76.9 yes View details
ndhF-rpl32 SSC 1303 0.0132 0.99 67.3 yes View details
ycf1-tRNA-Asn(GUU) IRa 423 0.0202 0.94 66.4 yes View details
psbM-tRNA-Asp(GUC) LSC 1080 0.0094 0.98 65.9 yes View details
atpH-atpI LSC 890 0.0102 0.99 65.5 yes View details
petN-psbM LSC 1198 0.0085 0.98 65.5 yes View details
psbI-tRNA-Ser(GCU) LSC 142 0.0352 1.00 64.9 yes View details
tRNA-Thr(GGU)-psbD LSC 1141 0.0071 0.99 64.3 yes View details
tRNA-Lys(UUU)-rps16 LSC 665 0.0105 1.00 63.6 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
tRNA-Lys(UUU)-rps16_p1 tRNA-Lys(UUU)-rps16 AAAGCCGAGTACTCTACCGT AAAGGAGCTCAACCCACAAG 763–767 1.000 79.3
tRNA-Lys(UUU)-rps16_p2 tRNA-Lys(UUU)-rps16 AAGCCGAGTACTCTACCGTT AAAGGAGCTCAACCCACAAG 762–766 1.000 79.3
tRNA-Lys(UUU)-rps16_p3 tRNA-Lys(UUU)-rps16 AAAGCCGAGTACTCTACCGT AGCTCAACCCACAAGAACTG 758–762 1.000 79.2
tRNA-Lys(UUU)-rps16_p4 tRNA-Lys(UUU)-rps16 AAGCCGAGTACTCTACCGTT AGCTCAACCCACAAGAACTG 757–761 1.000 79.2
tRNA-Lys(UUU)-rps16_p5 tRNA-Lys(UUU)-rps16 CCGCACTTAAAAGCCGAGTA AAAGGAGCTCAACCCACAAG 772–776 1.000 78.4
psbI-tRNA-Ser(GCU)_p1 psbI-tRNA-Ser(GCU) AATCCTGGGCGTGAGGAATA TAAAGCGGCGGATTGCTAAT 231 1.000 77.5
psbI-tRNA-Ser(GCU)_p2 psbI-tRNA-Ser(GCU) ATCCTGGGCGTGAGGAATAA TAAAGCGGCGGATTGCTAAT 230 1.000 77.5
psbI-tRNA-Ser(GCU)_p3 psbI-tRNA-Ser(GCU) TAATCCTGGGCGTGAGGAAT TAAAGCGGCGGATTGCTAAT 232 1.000 77.5
psbI-tRNA-Ser(GCU)_p4 psbI-tRNA-Ser(GCU) AATCCTGGGCGTGAGGAATA TAGGAGAGATGGCTGAGTGG 253 1.000 77.0
psbI-tRNA-Ser(GCU)_p5 psbI-tRNA-Ser(GCU) ATCCTGGGCGTGAGGAATAA TAGGAGAGATGGCTGAGTGG 252 1.000 77.0
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p1 tRNA-Ser(GCU)-tRNA-Ser (CGA) ATTAGCAATCCGCCGCTTTA AGGACGAATCACACTTTTACCA 861–905 1.000 65.5
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p2 tRNA-Ser(GCU)-tRNA-Ser (CGA) ATTAGCAATCCGCCGCTTTA GGACGAATCACACTTTTACCAC 860–904 1.000 65.1
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p3 tRNA-Ser(GCU)-tRNA-Ser (CGA) AAAGCGGAGAGAGAGGGATT AGGACGAATCACACTTTTACCA 913–957 1.000 64.6
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p4 tRNA-Ser(GCU)-tRNA-Ser (CGA) CAAGTGACCAGAGAAAGCGA AGGACGAATCACACTTTTACCA 932–976 1.000 64.3
tRNA-Ser(GCU)-tRNA-Ser (CGA)_p5 tRNA-Ser(GCU)-tRNA-Ser (CGA) TCAAGTGACCAGAGAAAGCG AGGACGAATCACACTTTTACCA 933–977 1.000 64.3
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TCACAAGCGGTATTCAAGCT 997–1000 1.000 76.8
atpH-atpI_p2 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCG 973–976 1.000 76.4
atpH-atpI_p3 atpH-atpI CAGCAGCAATAACAGAAGCG TCACAAGCGGTATTCAAGCT 1007–1010 1.000 76.2
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTTGCAACTTTAGCCGCG 983–986 1.000 75.9
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TCACAAGCGGTATTCAAGCT 1014–1017 1.000 75.8
petN-psbM_p1 petN-psbM CTCGTAGTATGGGGGAGGAG TGCTACTGCACTGTTCATTCT 1289–1307 1.000 70.1
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1342–1360 1.000 69.5
petN-psbM_p3 petN-psbM GTAGTATGGGGGAGGAGTGG TGCTACTGCACTGTTCATTCT 1286–1304 1.000 68.5
petN-psbM_p4 petN-psbM ACGTTTTCCCTTTCACTCGT TGCTACTGCACTGTTCATTCT 1304–1322 1.000 68.2
petN-psbM_p5 petN-psbM TCACTCGTAGTATGGGGGAG TGCTACTGCACTGTTCATTCT 1292–1310 1.000 67.9
psbM-tRNA-Asp(GUC)_p1 psbM-tRNA-Asp(GUC) AGAATGAACAGTGCAGTAGC AGTTCAATCGGTCAGAGCAC 1193–1209 1.000 63.5
psbM-tRNA-Asp(GUC)_p2 psbM-tRNA-Asp(GUC) AGAATGAACAGTGCAGTAGC CCGCTGGGATTGTAGTTCAA 1206–1222 1.000 63.3
psbM-tRNA-Asp(GUC)_p3 psbM-tRNA-Asp(GUC) AGAATGAACAGTGCAGTAGC ATGTATGCTGTACATCCCGC 1222–1238 1.000 62.8
psbM-tRNA-Asp(GUC)_p4 psbM-tRNA-Asp(GUC) AGGAACTAGAATGAACAGTGCA AGTTCAATCGGTCAGAGCAC 1200–1216 1.000 60.3
psbM-tRNA-Asp(GUC)_p5 psbM-tRNA-Asp(GUC) AGAATGAACAGTGCAGTAGC GTATGCTGTACATCCCGCTG 1220–1236 1.000 60.1

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
Monstera adansonii NC_047234.1 163643 View on NCBI ↗
Monstera deliciosa NC_082227.1 163499 View on NCBI ↗