Markers + reference

Amorphophallus

22 species · Araceae · Alismatales

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Species 22
Genome length 152–186 kb
Candidate markers 267
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 11 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 675 0.1549 0.82 77.9 yes View details
rps16 LSC 1712 0.0755 0.93 80.9 yes View details
trnT-UGU-trnL-UAA LSC 1754 0.1030 0.83 77.0 yes View details
accD LSC 1230 0.1096 0.94 81.1 yes View details
rpl16 LSC 2179 0.0806 0.93 79.9 yes View details
ycf1-ndhF IRb 1735 0.2844 0.40 69.0 yes View details
ndhG-ndhI SSC 869 0.1642 0.75 77.5 yes View details
rps15-ycf1 IRa 1715 0.2168 0.48 70.1 yes View details
ndhB-trnL-CAA IRa 1142 0.0614 0.91 91.3 yes View details
trnL-CAA-ndhB IRb 1142 0.0550 0.90 90.4 yes View details
trnS-GCU-trnG-UCC LSC 1908 0.0991 0.90 85.0 yes View details
rpoB-trnC-GCA LSC 1533 0.0361 0.99 81.1 yes View details
rps7 IRa 468 0.0525 1.00 81.1 yes View details
rps12 IRb 801 0.0484 1.00 80.7 yes View details
rps7 IRb 468 0.0540 1.00 79.7 yes View details
ndhB IRa 2210 0.0351 1.00 79.6 yes View details
trnE-UUC-trnT-GGU LSC 907 0.0750 0.96 79.5 yes View details
ndhB IRb 2210 0.0376 1.00 79.3 no View details
rps12 IRa 801 0.0370 1.00 76.7 no 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-GUG-psbA_p1 trnH-GUG-psbA CCACTTGGCTACATCCGC AGCTGCTGTTGAAGTTCCAT 358–952 0.909 68.6
trnH-GUG-psbA_p2 trnH-GUG-psbA CCACTTGGCTACATCCGC GCTGCTGTTGAAGTTCCATC 357–951 0.909 65.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CCACTTGGCTACATCCGC TAGCTGCTGTTGAAGTTCCA 359–953 0.909 63.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CCACTTGGCTACATCCGC TTAGCTGCTGTTGAAGTTCCA 360–954 0.909 61.2
trnH-GUG-psbA_p5 trnH-GUG-psbA CCACTTGGCTACATCCGC TAGCTGCTGTTGAAGTTCCAT 359–953 0.909 59.5
rps16_p1 rps16 TATGGGTGGGGATAAACGGA ATCAATTCCATCCCGGTTCG 2018–2395 0.500 70.2
rps16_p2 rps16 TATGGGTGGGGATAAACGGA GTTAATGTAGCGACTCGGGG 2624–2984 0.455 67.0
rps16_p3 rps16 AAAGCAAGAAAAGGTGCGTG ATCAATTCCATCCCGGTTCG 1755–2132 0.227 53.5
rps16_p4 rps16 CAAAGCAAGAAAAGGTGCGT ATCAATTCCATCCCGGTTCG 1756–2133 0.227 53.5
rps16_p5 rps16 AAAGCAAGAAAAGGTGCGTG GTTAATGTAGCGACTCGGGG 2371–2753 0.227 52.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GAGAAAGCGGAGAAAGAGGG AGGACGAATCACACTTTTACCA 1040–2954 0.955 71.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA AGGACGAATCACACTTTTACCA 985–2899 0.955 71.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GAGAAAGCGGAGAAAGAGGG GGACGAATCACACTTTTACCAC 1039–2953 0.955 70.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GGACGAATCACACTTTTACCAC 984–2898 0.955 70.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCAAGTGACCAGAGAAAGCG AGGACGAATCACACTTTTACCA 1051–2965 0.909 68.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG GCGACACCCAGATTTGAACT 1555–1987 0.955 86.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCATTTTCATCCCGGAGCA GCGACACCCAGATTTGAACT 1553–1985 0.955 86.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG CCTTACCACTTGGCCATGTC 1509–1941 0.955 85.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCCTCATTTTCATCCCGGAG TAAAGGATTTGCAGTCCCCC 1530–1840 0.909 83.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CTCATTTTCATCCCGGAGCA TAAAGGATTTGCAGTCCCCC 1528–1838 0.909 83.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA TCTACCACTGAGTTAAAAGGGC 270–1608 0.955 70.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA TCTACCACTGAGTTAAAAGGGC 268–1606 0.955 70.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC TCTACCACTGAGTTAAAAGGGC 267–1605 0.955 70.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TCTACCACTGAGTTAAAAGGGC 286–1624 0.955 69.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GAGATGTCCTGAACCGCTAG TCTACCACTGAGTTAAAAGGGC 269–1607 0.955 67.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 768–1906 0.955 89.1
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA AAGTTACCGCGGCATAACAT ACCAATTTCGCCATATCCCC 1176–2090 0.864 86.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA AAGTTACCGCGGCATAACAT TCCATACCAAGGCTCAATGC 1215–2129 0.864 85.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA AAGTTACCGCGGCATAACAT ACCAAGGCTCAATGCAATCA 1210–2124 0.864 85.7
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA AAGTTACCGCGGCATAACAT TAGCGTCTACCAATTTCGCC 1184–2098 0.727 80.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (22)

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

Species Accession Length (bp) Link
Amorphophallus albus NC_067990.1 175728 View on NCBI ↗
Amorphophallus allenii PX769913.1 170657 View on NCBI ↗
Amorphophallus atroviridis PX508299.1 175133 View on NCBI ↗
Amorphophallus coaetaneus NC_072945.1 175465 View on NCBI ↗
Amorphophallus fornicatus PZ226531.1 152492 View on NCBI ↗
Amorphophallus gigas PX852198.1 173034 View on NCBI ↗
Amorphophallus glaucophyllus PZ243066.1 184539 View on NCBI ↗
Amorphophallus hewitii PZ235491.1 171707 View on NCBI ↗
Amorphophallus josefbogneri PX804936.1 172957 View on NCBI ↗
Amorphophallus kachinensis NC_086583.1 173330 View on NCBI ↗
Amorphophallus kiusianus NC_086582.1 168269 View on NCBI ↗
Amorphophallus konjac NC_046702.1 161647 View on NCBI ↗
Amorphophallus krausei NC_082907.1 172418 View on NCBI ↗
Amorphophallus macrophyllus PZ250735.1 185810 View on NCBI ↗
Amorphophallus maxwellii PX833257.1 179466 View on NCBI ↗
Amorphophallus mossambicensis PX710723.1 168728 View on NCBI ↗
Amorphophallus myosuroides PX872556.1 171894 View on NCBI ↗
Amorphophallus ochroleucus PX683778.1 172779 View on NCBI ↗
Amorphophallus paeoniifolius NC_086625.1 176258 View on NCBI ↗
Amorphophallus pendulus PZ266516.1 176384 View on NCBI ↗
Amorphophallus titanum NC_056329.1 176835 View on NCBI ↗
Amorphophallus tonkinensis NC_086855.1 169341 View on NCBI ↗