Markers + reference

Aletris

13 species · Nartheciaceae · Dioscoreales

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Species 13
Genome length 154–155 kb
Candidate markers 269
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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 355 0.0238 1.00 60.0 yes View details
trnS-GCU-trnG-UCC LSC 851 0.0192 1.00 69.7 yes View details
rps2-rpoC2 LSC 257 0.0499 0.99 70.3 yes View details
trnT-GGU-psbD LSC 930 0.0161 0.95 61.1 yes View details
ndhF SSC 2226 0.0084 1.00 43.4 yes View details
ndhF-rpl32 SSC 900 0.0279 0.98 72.5 yes View details
rpl32-trnL-UAG SSC 763 0.0175 0.97 57.7 yes View details
ycf1 SSC 5625 0.0116 1.00 46.1 yes View details
psbC-trnS-UGA LSC 127 0.0396 1.00 78.5 yes View details
trnH-GUG-psbA IRa 383 0.0215 1.00 75.6 no View details
psbA-trnK-UUU LSC 222 0.0274 0.99 69.6 yes View details
psbI-trnS-GCU LSC 102 0.0302 1.00 66.8 yes View details
trnG-UCC-trnR-UCU LSC 166 0.0307 0.96 66.3 yes View details
trnL-UAA-trnF-GAA LSC 358 0.0233 0.97 66.3 yes View details
petD-rpoA LSC 122 0.0180 1.00 66.0 yes View details
trnW-CCA-trnP-UGG LSC 183 0.0366 1.00 65.9 yes View details
rpoB-trnC-GCA LSC 1179 0.0153 1.00 65.0 yes View details
petN-psbM LSC 1052 0.0162 1.00 64.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AAAATGCAAGCACGGTTTGG 358–367 1.000 82.0
psbA-trnK-UUU_p2 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC ACTCCATCCGACTAGTTCCG 297–306 1.000 81.6
psbA-trnK-UUU_p3 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC TGAAAAATGCAAGCACGGTT 361–370 1.000 80.6
psbA-trnK-UUU_p4 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AAAGCCGTGTGCAATGAAAA 375–384 1.000 80.4
psbA-trnK-UUU_p5 psbA-trnK-UUU TAGGCTTGTACTTTCGCGTC AAGCCGTGTGCAATGAAAAA 374–383 1.000 80.4
trnK-UUU_p1 trnK-UUU TAGGCTTGTACTTTCGCGTC AATCCGATCTGCCCATTTTT 2952–2971 0.923 61.3
trnK-UUU_p2 trnK-UUU GCTTGTACTTTCGCGTCTCT AATCCGATCTGCCCATTTTT 2949–2968 0.923 59.0
trnK-UUU_p3 trnK-UUU AGGACTCCCAAGCACACATA AATCCGATCTGCCCATTTTT 2885–2904 0.846 55.4
trnK-UUU_p4 trnK-UUU GCCGTATATGTCAATGTCAACC TCCGTTTTGGTTATCCCACC 2990–2997 0.692 49.4
trnK-UUU_p5 trnK-UUU GCCGTATATGTCAATGTCAACC TATCCCACCCCATTTTCCCT 2986 0.077 23.3
trnQ-UUG-psbK_p1 trnQ-UUG-psbK CTGCCTTACCACTTGGCC GGGCAATTTGGCGAAGAAAA 461–483 1.000 70.2
trnQ-UUG-psbK_p2 trnQ-UUG-psbK CCTTACCACTTGGCCACG GGGCAATTTGGCGAAGAAAA 458–480 1.000 70.1
trnQ-UUG-psbK_p3 trnQ-UUG-psbK AAAACCCGCTGCCTTACC GGGCAATTTGGCGAAGAAAA 469–491 1.000 69.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK CCAAAACCCGCTGCCTTA GGGCAATTTGGCGAAGAAAA 471–493 1.000 69.3
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CTGCCTTACCACTTGGCC GGCATAAGACTCGGGCAATT 473–495 1.000 68.9
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA TAAAGCGGCGGATTGCTAAT 192–199 1.000 82.7
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA GGGTTCGAATCCCTCTCTCT 147–154 1.000 82.5
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA TTTTTCGTACCGAGGGTTCG 160–167 1.000 82.4
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA GGAATTGGGAGAGATGGCTG 219–226 1.000 82.0
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGGCGTGAAGAA ATTGGGAGAGATGGCTGAGT 216–223 1.000 81.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TACCACTAAACTATGCCCGC 879–938 1.000 85.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATAAGGAGCGGAGAGAGAGG TACCACTAAACTATGCCCGC 935–994 1.000 83.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA TACCACTAAACTATGCCCGC 927–986 1.000 82.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT TACCACTAAACTATGCCCGC 865–924 1.000 82.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGTCCACTCAGCCATCTCTC TACCACTAAACTATGCCCGC 860–919 1.000 81.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 240–246 1.000 70.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 243–249 1.000 70.6
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 246–252 1.000 70.1
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 249–255 1.000 69.8
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 244–250 1.000 68.4

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
Aletris alpestris PP988366.1 154551 View on NCBI ↗
Aletris fauriei NC_033412.1 154440 View on NCBI ↗
Aletris glabra PP988367.1 154201 View on NCBI ↗
Aletris glandulifera PP988368.1 155143 View on NCBI ↗
Aletris gracilis PP988369.1 154285 View on NCBI ↗
Aletris laxiflora PP988370.1 154468 View on NCBI ↗
Aletris megalantha NC_054333.1 154704 View on NCBI ↗
Aletris pauciflora var. khasiana PP988373.1 154309 View on NCBI ↗
Aletris pauciflora var. pauciflora PP988372.1 154205 View on NCBI ↗
Aletris pedicellata PP988374.1 154204 View on NCBI ↗
Aletris scopulorum PP988375.1 154167 View on NCBI ↗
Aletris spicata NC_033411.1 154999 View on NCBI ↗
Aletris stenoloba PP988377.1 154993 View on NCBI ↗