Markers + reference

Alocasia

2 species · Araceae · Alismatales

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Species 2
Genome length 165–166 kb
Candidate markers 261
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnS-CGA LSC 1830 0.1468 0.80 80.8 yes View details
trnF-GAA-ndhJ LSC 1355 0.1036 0.61 77.3 yes View details
rpl16 LSC 1869 0.1195 0.90 82.5 yes View details
trnL-CAA-ndhB IRb 1274 0.0465 0.64 68.4 yes View details
trnN-GUU-ndhF IRb 1204 0.3582 0.80 80.0 yes View details
rps15-ycf1 SSC 843 0.1876 0.95 83.9 yes View details
ndhB-trnL-CAA IRa 1274 0.0428 0.64 66.4 yes View details
rpl2-trnH-GUG IRa 47 0.0652 0.97 86.1 no View details
petA-psbJ LSC 1130 0.0785 0.94 85.4 yes View details
rps16-trnQ-UUG LSC 735 0.0924 0.93 84.6 yes View details
trnE-UUC-trnT-GGU LSC 798 0.0684 0.92 83.7 yes View details
psaC-ndhE SSC 836 0.0987 0.85 83.2 yes View details
rps4-trnT-UGU LSC 503 0.1202 0.98 83.0 yes View details
trnH-GUG-psbA LSC 489 0.1000 0.98 81.8 yes View details
ndhG-ndhI SSC 396 0.1230 0.94 80.9 yes View details
trnK-UUU-rps16 LSC 804 0.0947 0.89 80.7 yes View details
accD-psaI LSC 602 0.0935 0.98 80.7 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTGCTGTTGAAGTTCCAT 552–690 1.000 84.0
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTGTTGAAGTTCCAT 551–689 1.000 84.0
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTGTTGAAGTTCCAT 553–691 1.000 84.0
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCTGCTGTTGAAGTTCCATC 551–689 1.000 81.3
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCTGCTGTTGAAGTTCCATC 550–688 1.000 81.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGCTCAACCCACAAGAACTG 951–991 1.000 89.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGAGATCTTCGGAGAGTGGG 1040–1080 1.000 89.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AGCTCAACCCACAAGAACTG 947–987 1.000 89.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTCTTTCTTGCTTGAGCCGT 1166–1211 1.000 88.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1196 0.500 59.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 808–1476 1.000 86.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGATCACGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 822–1490 1.000 84.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 812–1480 1.000 81.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 800–1468 1.000 81.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 807–1475 1.000 80.6
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA GCTTTAGTCCACTCAGCCAT AGGACGAATCACACTTTTACCA 1776–1893 1.000 70.0
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA GCTTTAGTCCACTCAGCCAT GGACGAATCACACTTTTACCAC 1775–1892 1.000 69.5
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA AGTCCACTCAGCCATCTCTC AGGACGAATCACACTTTTACCA 1771–1888 1.000 69.1
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGTCCACTCAGCCATCTCTC GGACGAATCACACTTTTACCAC 1770–1887 1.000 68.7
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA TAGTCCACTCAGCCATCTCT AGGACGAATCACACTTTTACCA 1772–1889 1.000 66.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 851–885 1.000 87.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 849–883 1.000 87.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 828–862 1.000 87.1
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 830–864 1.000 87.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 848–882 1.000 86.9
rps4-trnT-UGU_p1 rps4-trnT-UGU CCCCAGACGGCGTATTTTT GATGGTCATCGGTTCGACTC 583–741 1.000 78.2
rps4-trnT-UGU_p2 rps4-trnT-UGU CCCCAGACGGCGTATTTTT CTCAGAGGTTAGAGCATCGC 614–772 1.000 78.0
rps4-trnT-UGU_p3 rps4-trnT-UGU CCCCAGACGGCGTATTTTT CCGCTTAGCTCAGAGGTTAG 622–780 1.000 75.0
rps4-trnT-UGU_p4 rps4-trnT-UGU CCCCAGACGGCGTATTTTT CAGAGGTTAGAGCATCGCAT 612–770 1.000 74.9
rps4-trnT-UGU_p5 rps4-trnT-UGU CCCCAGACGGCGTATTTTT TCAGAGGTTAGAGCATCGCA 613–771 1.000 74.9

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
Alocasia cucullata NC_060696.1 164520 View on NCBI ↗
Alocasia fornicata MK636779.1 166052 View on NCBI ↗