Markers + reference

Arisaema

13 species · Araceae · Alismatales

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Species 13
Genome length 161–176 kb
Candidate markers 246
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 246 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 786 0.1147 0.79 81.5 yes View details
trnS-GCU-trnS-CGA LSC 2498 0.1080 0.75 75.5 yes View details
atpF LSC 1869 0.0623 0.93 84.4 yes View details
rpoB-trnC-GCA LSC 1772 0.0691 0.96 85.3 yes View details
rps4-trnT-UGU LSC 1198 0.0893 0.66 74.7 yes View details
trnT-UGU-trnL-UAA LSC 1519 0.0849 0.91 84.7 yes View details
trnN-GUU-ndhF IRb 1152 0.0903 0.91 78.7 yes View details
ndhE-ndhG SSC 967 0.0934 0.69 79.0 yes View details
ndhG-ndhI SSC 698 0.1230 0.75 77.0 yes View details
rps15-ycf1 SSC 1225 0.1134 0.72 75.2 yes View details
trnF-GAA-ndhJ LSC 1121 0.0556 0.90 90.5 yes View details
psbE-petL LSC 1708 0.0445 0.84 85.5 yes View details
rpl33-rps18 LSC 574 0.1052 0.72 84.0 yes View details
atpB-rbcL LSC 1094 0.0673 0.85 82.3 yes View details
psaC-ndhE SSC 843 0.0475 0.93 82.1 yes View details
rpl16-rps3 LSC 1286 0.0309 0.95 76.2 yes View details
ycf1-trnN-GUU IRa 2016 0.0425 0.92 76.0 yes View details
psbK-psbI LSC 480 0.0213 1.00 75.8 yes View details
psaJ-rpl33 LSC 450 0.0203 1.00 75.6 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 696–1168 1.000 89.6
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 695–1167 1.000 89.5
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 697–1169 1.000 89.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ATCAACCGTGCTAACCTTGG 698–1170 1.000 89.5
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ATCAACCGTGCTAACCTTGG 697–1169 1.000 89.5
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGGTTACGTCCTGGATCAT 589–621 1.000 87.2
psbK-psbI_p2 psbK-psbI GTGGACATTATGCCCGTCAT AGGGTTACGTCCTGGATCAT 637–669 1.000 86.9
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGGTTACGTCCTGGATCAT 586–618 1.000 85.3
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGGTTACGTCCTGGATCAT 587–619 1.000 85.3
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGGTTACGTCCTGGATCAT 588–620 1.000 85.2
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA GAGAAAGCGGAGAAAGAGGG TACCACTAAACTATACCCGC 1486–2613 1.000 59.8
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA TACCACTAAACTATACCCGC 1431–2558 1.000 59.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA GAGAAAGCGGAGAAAGAGGG TTACCACTAAACTATACCCGC 1487–2614 1.000 58.7
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA ATTAGCAATCCGCCGCTTTA TTACCACTAAACTATACCCGC 1432–2559 1.000 58.5
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA AGAAAGCGGAGAAAGAGGGA TACCACTAAACTATACCCGC 1485–2612 1.000 57.1
atpF_p1 atpF CCTACTTGAAGTACGGTGCC CCTCTCGCTTTCTTCCTTCC 1903–2992 1.000 91.8
atpF_p2 atpF CCTACTTGAAGTACGGTGCC CTCTCGCTTTCTTCCTTCCC 1902–2991 1.000 91.8
atpF_p3 atpF CCTACTTGAAGTACGGTGCC ATTTATGGACTGGTCGTGGC 2114–2850 0.923 88.6
atpF_p4 atpF CCTACTTGAAGTACGGTGCC CGGGAAGGACGGATTTTAGG 1940–2675 0.923 88.5
atpF_p5 atpF ATACGAGCAATTCCGTCACC CTCTCGCTTTCTTCCTTCCC 1920–2655 0.923 88.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG GCGACACCCAGATTTGAACT 1485–2110 1.000 88.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCATTTTCATCCCGGAGCA GCGACACCCAGATTTGAACT 1483–2108 1.000 87.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG TAAAGGATTTGCAGTCCCCC 1460–2085 1.000 87.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG CCTTACCACTTGGCCATGTC 1439–2064 1.000 87.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCATTTTCATCCCGGAGCA TAAAGGATTTGCAGTCCCCC 1458–2083 1.000 87.5
rps4-trnT-UGU_p1 rps4-trnT-UGU AGTCAAATGTTTCGGCACCT GCACGAGCTTGAGATGAGAA 1142–1876 0.923 88.8
rps4-trnT-UGU_p2 rps4-trnT-UGU ATCCGACCCTTCCCTTGTTA GCACGAGCTTGAGATGAGAA 1284–2018 0.923 88.6
rps4-trnT-UGU_p3 rps4-trnT-UGU TCCGACCCTTCCCTTGTTAT GCACGAGCTTGAGATGAGAA 1283–2017 0.923 88.6
rps4-trnT-UGU_p4 rps4-trnT-UGU TGTGATCTTTTACCGGAGCG GCACGAGCTTGAGATGAGAA 775–1509 0.846 85.8
rps4-trnT-UGU_p5 rps4-trnT-UGU ATCTTTTACCGGAGCGCAAT GCACGAGCTTGAGATGAGAA 771–1505 0.846 85.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Arisaema amurense NC_085264.1 171454 View on NCBI ↗
Arisaema bockii MZ380241.1 175537 View on NCBI ↗
Arisaema decipiens NC_064687.1 167792 View on NCBI ↗
Arisaema erubescens NC_051541.1 167607 View on NCBI ↗
Arisaema flavum NC_065735.1 167582 View on NCBI ↗
Arisaema franchetianum MN046885.1 169443 View on NCBI ↗
Arisaema heterophyllum NC_063965.1 170554 View on NCBI ↗
Arisaema lackneri PV068279.1 169523 View on NCBI ↗
Arisaema nepenthoides MW338731.1 166390 View on NCBI ↗
Arisaema prazeri NC_072165.1 167954 View on NCBI ↗
Arisaema ringens NC_044118.1 160792 View on NCBI ↗
Arisaema sinii PV067999.1 168126 View on NCBI ↗
Arisaema takesimense PQ651946.1 174361 View on NCBI ↗