Markers + reference

Nanocnide

2 species · Urticaceae · Rosales

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Species 2
Genome length 145–146 kb
Candidate markers 264
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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1233 0.0561 0.84 74.4 yes View details
petN-psbM LSC 410 0.0757 0.90 74.7 yes View details
rps4-trnT-UGU LSC 462 0.0670 0.97 75.6 yes View details
trnT-UGU-trnL-UAA LSC 540 0.0826 0.83 79.2 yes View details
petA-psbJ LSC 817 0.0465 0.97 79.3 yes View details
psbE-petL LSC 1007 0.0384 0.80 70.0 yes View details
psaJ-rpl33 LSC 424 0.0334 0.99 61.5 yes View details
rpl16 LSC 1358 0.0359 0.94 71.1 yes View details
ndhD SSC 1530 0.0131 1.00 51.5 yes View details
ycf1 SSC 5433 0.0302 0.99 55.7 yes View details
rpl33-rps18 LSC 239 0.1000 0.92 77.4 yes View details
trnW-CCA-trnP-UGG LSC 122 0.0796 0.93 77.0 yes View details
trnV-UAC-trnM-CAU LSC 165 0.0510 0.95 76.5 yes View details
atpE-atpB LSC 20 0.1000 1.00 76.2 yes View details
ccsA-ndhD SSC 192 0.1146 1.00 75.3 yes View details
psbI-trnS-GCU LSC 99 0.0659 0.92 74.9 yes View details
psbA-trnK-UUU LSC 296 0.0651 0.88 74.4 yes View details
trnF-GAA-ndhJ LSC 400 0.0596 0.96 73.8 yes View details
rpl36-rps8 LSC 387 0.0566 0.96 73.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGGCGGTTTTCAGTGCT ACTAGTTCCGGGTTCGAGTC 385–416 1.000 80.6
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGGCGGTTTTCAGTGCT GACTAGTTCCGGGTTCGAGT 386–417 1.000 80.6
psbA-trnK-UUU_p3 psbA-trnK-UUU GTAAAGGCGGTTTTCAGTGC ACTAGTTCCGGGTTCGAGTC 386–417 1.000 80.4
psbA-trnK-UUU_p4 psbA-trnK-UUU GTAAAGGCGGTTTTCAGTGC GACTAGTTCCGGGTTCGAGT 387–418 1.000 80.4
psbA-trnK-UUU_p5 psbA-trnK-UUU TAAAGGCGGTTTTCAGTGCT ATCCGACTAGTTCCGGGTTC 390–421 1.000 80.0
trnK-UUU_p1 trnK-UUU CAGTCTCCCCACCCATAGAT TATTTATCTCTGCGCGTCGG 2915 0.500 58.8
trnK-UUU_p2 trnK-UUU TTCCATGTCAACCAGTCTCC TATTTATCTCTGCGCGTCGG 2927 0.500 52.8
trnK-UUU_p3 trnK-UUU AGTCTCCCCACCCATAGATT TATTTATCTCTGCGCGTCGG 2914 0.500 52.4
trnK-UUU_p4 trnK-UUU TCCATGTCAACCAGTCTCCC TATTTATCTCTGCGCGTCGG 2926 0.500 51.5
trnK-UUU_p5 trnK-UUU CAGTCTCCCCACCCATAGAT GCGCGTCGGTTCATCTTTAT 2904 0.500 50.6
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AGTCGCGGTCTTACAAACTC AGCAGCTTGCCAAACAAAAG 1807–1950 1.000 86.3
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG GTCGCGGTCTTACAAACTCT AGCAGCTTGCCAAACAAAAG 1806–1949 1.000 86.3
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AGTCGCGGTCTTACAAACTC CTTACAGCAGCTTGCCAAAC 1812–1955 1.000 86.2
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG GTCGCGGTCTTACAAACTCT CTTACAGCAGCTTGCCAAAC 1811–1954 1.000 86.2
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG CCTTTCCCACATCAAGCACT AGCAGCTTGCCAAACAAAAG 2097–2236 1.000 85.9
psbI-trnS-GCU_p1 psbI-trnS-GCU CCTATCTAATGATCCGGGACG TGGACTAAAGCGTCGGATTG 212–235 1.000 70.7
psbI-trnS-GCU_p2 psbI-trnS-GCU CCTATCTAATGATCCGGGACG GTGGACTAAAGCGTCGGATT 213–236 1.000 70.7
psbI-trnS-GCU_p3 psbI-trnS-GCU CCTATCTAATGATCCGGGACG TTTTTCGTACCGAGGGTTCG 175–198 1.000 70.0
psbI-trnS-GCU_p4 psbI-trnS-GCU CCTATCTAATGATCCGGGACG GACTAAAGCGTCGGATTGCT 210–233 1.000 67.9
psbI-trnS-GCU_p5 psbI-trnS-GCU CCTATCTAATGATCCGGGACG CTGAGTGGACTAAAGCGTCG 217–240 1.000 67.6
petN-psbM_p1 petN-psbM AAAGGCCGGTTATGCGTATT ACCAATGGTAGGGCACTTTG 1164 0.500 59.0
petN-psbM_p2 petN-psbM AAGGCCGGTTATGCGTATTT ACCAATGGTAGGGCACTTTG 1163 0.500 59.0
petN-psbM_p3 petN-psbM AAGGCCGGTTATGCGTATTT CAACCAATGGTAGGGCACTT 1165 0.500 59.0
petN-psbM_p4 petN-psbM AGGCCGGTTATGCGTATTTT ACCAATGGTAGGGCACTTTG 1162 0.500 59.0
petN-psbM_p5 petN-psbM AGGCCGGTTATGCGTATTTT CAACCAATGGTAGGGCACTT 1164 0.500 59.0
rps4-trnT-UGU_p1 rps4-trnT-UGU TTTTCCGGCGATATGAACGT ACCAATTTCGCCATATCCCC 1292–1317 1.000 88.2
rps4-trnT-UGU_p2 rps4-trnT-UGU TGCTTTTCCGGCGATATGAA ACCAATTTCGCCATATCCCC 1295–1320 1.000 88.0
rps4-trnT-UGU_p3 rps4-trnT-UGU TTGCTTTTCCGGCGATATGA ACCAATTTCGCCATATCCCC 1296–1321 1.000 88.0
rps4-trnT-UGU_p4 rps4-trnT-UGU TTTTCCGGCGATATGAACGT TAGCGTCTACCAATTTCGCC 1300–1325 1.000 87.6
rps4-trnT-UGU_p5 rps4-trnT-UGU CCAACCGCATTTCAAGCAAT ACCAATTTCGCCATATCCCC 1344–1369 1.000 87.4

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
Nanocnide japonica NC_064934.1 145970 View on NCBI ↗
Nanocnide lobata NC_064935.1 145302 View on NCBI ↗