Markers + reference

Thalictrum

23 species · Ranunculaceae · Ranunculales

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Species 23
Genome length 155–156 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 571 0.0191 0.98 64.7 yes View details
atpF-atpH LSC 455 0.0246 1.00 67.8 yes View details
petN-psbM LSC 1205 0.0139 0.99 75.5 yes View details
trnT-UGU-trnL-UAA LSC 693 0.0181 0.99 73.9 yes View details
ndhC-trnV-UAC LSC 944 0.0230 0.98 80.7 yes View details
trnP-UGG-psaJ LSC 443 0.0224 0.96 64.3 yes View details
ndhF-trnL-UAG SSC 741 0.0331 0.96 81.3 yes View details
ndhG-ndhI SSC 409 0.0273 0.98 73.4 yes View details
ycf1 SSC 5571 0.0135 1.00 57.8 yes View details
ccsA-ndhD SSC 236 0.0354 0.92 73.2 yes View details
psbA-trnK-UUU LSC 247 0.0264 1.00 73.1 yes View details
trnS-UGA-psbZ LSC 354 0.0223 1.00 71.7 yes View details
rps16-trnQ-UUG LSC 1030 0.0147 0.99 71.3 yes View details
psbM-trnD-GUC LSC 1141 0.0095 0.99 70.5 yes View details
psbE-petL LSC 1080 0.0082 0.99 69.5 yes View details
trnT-GGU-psbD LSC 1228 0.0092 0.98 68.4 yes View details
trnW-CCA-trnP-UGG LSC 192 0.0191 1.00 66.8 yes View details
ycf3-trnS-GGA LSC 566 0.0097 0.98 65.8 yes View details
rps4-trnT-UGU LSC 384 0.0153 1.00 65.7 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 AACACCGAACCATCCAATGT ACTCCATCCGACTAGTTCCG 329–414 1.000 83.3
psbA-trnK-UUU_p2 psbA-trnK-UUU ACGGTTTTCAGTGCTGGTTA ACTCCATCCGACTAGTTCCG 305–390 1.000 83.3
psbA-trnK-UUU_p3 psbA-trnK-UUU TCAAAACACCGAACCATCCA ACTCCATCCGACTAGTTCCG 333–418 1.000 82.7
psbA-trnK-UUU_p4 psbA-trnK-UUU AACACCGAACCATCCAATGT ACTAGTTCCGGGTTCGAGTC 319–404 1.000 81.7
psbA-trnK-UUU_p5 psbA-trnK-UUU AACACCGAACCATCCAATGT GACTAGTTCCGGGTTCGAGT 320–405 1.000 81.7
trnK-UUU_p1 trnK-UUU GCTCGTGTCAACCGATATCA TGGGACCAGTCTCTCTTGTT 2731–2816 1.000 85.7
trnK-UUU_p2 trnK-UUU GGACTCCCAAGCACACAAAT TGGGACCAGTCTCTCTTGTT 2813–2898 1.000 84.1
trnK-UUU_p3 trnK-UUU TTATACGCTCGTGTCAACCG TGGGACCAGTCTCTCTTGTT 2770–2822 0.913 80.2
trnK-UUU_p4 trnK-UUU ACGGTTTTCAGTGCTGGTTA TGGGACCAGTCTCTCTTGTT 2923–2997 0.522 63.9
trnK-UUU_p5 trnK-UUU TTATACGCTCGTGTCAACCG ATACCCGCCCCAATAAGTTG 2904 0.043 38.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG TCGATCCCGAAGAGAAGGAA 1245–1437 1.000 87.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TCGATCCCGAAGAGAAGGAA 873–1066 1.000 87.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG ATTCTTTCTCGAGCCGTACG 1358–1549 1.000 86.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGGATAGGGGATTTCTCGGG TCGATCCCGAAGAGAAGGAA 1510–1679 0.913 81.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 CACATTCGTCTCCACTCAGG TGAAATGCCAAGGACTCAGG 1559–1737 0.783 74.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1068–1160 1.000 89.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1047–1139 1.000 89.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACCGATCATGTCCTT CTCGGAGGTTCGAATCCTTC 1072–1164 1.000 88.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1051–1143 1.000 88.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1058–1150 0.957 86.8
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TCGTGGCATTAGCGCTTTTA 488–553 1.000 88.8
atpF-atpH_p2 atpF-atpH CAGTGACCCAAGGAAACGAA CGTGGCATTAGCGCTTTTAT 487–552 1.000 85.0
atpF-atpH_p3 atpF-atpH AGTGACCCAAGGAAACGAAA TCGTGGCATTAGCGCTTTTA 487–552 1.000 83.4
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA CGTGGCATTAGCGCTTTTATT 487–552 1.000 82.5
atpF-atpH_p5 atpF-atpH TGACCCAAGGAAACGAAAGA TCGTGGCATTAGCGCTTTTA 485–550 1.000 81.1
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA ATTGCTACTGCGCTGTTCAT 1328–1370 1.000 87.7
petN-psbM_p2 petN-psbM TCTTGCTTGGGCTGCTTTAA TATTGCTACTGCGCTGTTCA 1329–1371 1.000 86.7
petN-psbM_p3 petN-psbM TCTTGCTTGGGCTGCTTTAA TTGCTACTGCGCTGTTCATT 1327–1369 1.000 85.9
petN-psbM_p4 petN-psbM AGTAAGTCTTGCTTGGGCTG ATTGCTACTGCGCTGTTCAT 1334–1376 0.957 84.3
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TATTGCTACTGCGCTGTTCA 1335–1377 0.957 83.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (23)

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

Species Accession Length (bp) Link
Thalictrum alpinum PP234509.1 155311 View on NCBI ↗
Thalictrum aquilegiifolium NC_058830.1 156253 View on NCBI ↗
Thalictrum aquilegiifolium subsp. aquilegiifolium PP622696.1 155839 View on NCBI ↗
Thalictrum aquilegiifolium var. sibiricum LC661621.1 156074 View on NCBI ↗
Thalictrum atriplex PX686334.1 155984 View on NCBI ↗
Thalictrum baicalense MZ962406.1 156196 View on NCBI ↗
Thalictrum cirrhosum NC_061927.1 155969 View on NCBI ↗
Thalictrum coreanum NC_026103.1 155088 View on NCBI ↗
Thalictrum elegans NC_085600.1 155864 View on NCBI ↗
Thalictrum fargesii NC_070058.1 155929 View on NCBI ↗
Thalictrum finetii PX682254.1 156009 View on NCBI ↗
Thalictrum foeniculaceum NC_053570.1 155923 View on NCBI ↗
Thalictrum foetidum subsp. foetidum PP622697.1 155935 View on NCBI ↗
Thalictrum foliolosum NC_058920.1 155764 View on NCBI ↗
Thalictrum lucidum PP622698.1 156182 View on NCBI ↗
Thalictrum minus NC_041544.1 156217 View on NCBI ↗
Thalictrum minus var. hypoleucum OM501079.1 156258 View on NCBI ↗
Thalictrum petaloideum MK253449.1 155876 View on NCBI ↗
Thalictrum przewalskii PX686327.1 155922 View on NCBI ↗
Thalictrum simplex NC_068627.1 156211 View on NCBI ↗
Thalictrum tenue MK253448.1 156103 View on NCBI ↗
Thalictrum thalictroides NC_039433.1 154924 View on NCBI ↗
Thalictrum viscosum NC_058831.1 155984 View on NCBI ↗