Markers + reference

Tofieldia

3 species · Tofieldiaceae · Alismatales

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Species 3
Genome length 155–158 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 994 0.0181 1.00 64.2 yes View details
psbI-trnS-GCU LSC 242 0.0565 0.98 75.6 yes View details
psbZ-trnG-GCC LSC 582 0.0235 1.00 63.6 yes View details
trnT-UGU-trnL-UAA LSC 1285 0.0137 0.97 62.1 yes View details
rbcL-accD LSC 994 0.0272 1.00 67.7 yes View details
accD-psaI LSC 1094 0.0260 0.90 75.3 yes View details
clpP1 LSC 2003 0.0127 1.00 56.2 yes View details
infA LSC 234 0.0057 1.00 30.3 yes View details
ndhF-rpl32 SSC 577 0.0277 1.00 58.4 yes View details
rpl32-trnL-UAG SSC 760 0.0217 0.97 65.9 yes View details
ndhD SSC 1505 0.0078 1.00 50.5 yes View details
psbT-pbf1 LSC 64 0.0938 1.00 86.9 yes View details
rpl2-trnH-GUG IRa 43 0.0465 1.00 80.0 no View details
ccsA-ndhD SSC 189 0.0741 1.00 79.5 yes View details
rpl22-rps19 LSC 72 0.0463 1.00 72.0 yes View details
petA-psbJ LSC 988 0.0135 1.00 66.2 yes View details
rpl36-infA LSC 109 0.2752 1.00 66.2 yes View details
atpH-atpI LSC 1020 0.0073 0.98 65.1 yes View details
trnH-GUG-psbA LSC 340 0.0338 0.99 63.4 yes View details
pafI-trnS-GGA LSC 278 0.0242 0.99 61.8 yes View details
trnT-GGU-psbD LSC 1123 0.0110 1.00 61.5 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 GATCCACTTGGCTACATCCG TAGTTGACAGTCAGGGTCGT 388–521 1.000 86.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TAGTTGACAGTCAGGGTCGT 402–535 1.000 86.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TAGTTGACAGTCAGGGTCGT 401–534 1.000 86.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TAGTTGACAGTCAGGGTCGT 403–536 1.000 86.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TGCATGGTTCCTTGGTAACC 664–797 1.000 84.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1072–1085 1.000 82.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1070–1083 1.000 82.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1078–1091 1.000 82.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1054–1067 1.000 81.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA CTCGGAGGTTCGAATCCTTC 1076–1089 1.000 81.5
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TAAAGCGGCGGATTGCTAAT 227–406 1.000 85.4
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GGGTTCGAATCCCTCTCTCT 182–361 1.000 84.6
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA ATTGGGAGAGATGGCTGAGT 251–430 1.000 84.5
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TTCGAATCCCTCTCTCTCCG 179–358 1.000 83.8
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA ATGGCTGAGTGGACTAAAGC 241–420 1.000 82.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1071–1108 1.000 80.4
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT TTTTTGCAACTTTAGCCGCG 1159–1196 1.000 80.1
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAGGGT 1044–1081 1.000 79.8
atpH-atpI_p4 atpH-atpI TACCTTGACCAACTCCAGGT TTTTTGCAACTTTAGCCGCG 1127–1164 1.000 79.7
atpH-atpI_p5 atpH-atpI CGCAATACCTTCTACGGCTT TAGGTGAATCCATGGAGGGT 1132–1169 1.000 79.6
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1224–1277 1.000 81.8
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCTCCGTAACCAATCATCC 1208–1261 1.000 81.8
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GTCCGGACCAACCTACAAAA 1238–1291 1.000 81.6
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1227–1280 1.000 81.6
trnT-GGU-psbD_p5 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG ACAAAAACGAAACGGTCCCT 1292–1296 0.667 64.0
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTGGTAGCTATCCTTAATTCTCTCA AATCGAACCCGCATCTTCTC 499–710 1.000 46.3
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CTGGTAGCTATCCTTAATTCTCTCA GAATCGAACCCGCATCTTCT 500–711 1.000 46.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TGGTAGCTATCCTTAATTCTCTCA AATCGAACCCGCATCTTCTC 498–709 1.000 46.3
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TGGTAGCTATCCTTAATTCTCTCA GAATCGAACCCGCATCTTCT 499–710 1.000 46.3
psbZ-trnG-GCC_p5 psbZ-trnG-GCC CTGGTAGCTATCCTTAATTCTCTCA TACTTCACCATGGGCGGATA 524–735 1.000 46.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Tofieldia coccinea var. kondoi OM678460.1 157803 View on NCBI ↗
Tofieldia ulleungensis NC_068654.1 158407 View on NCBI ↗
Tofieldia yoshiiana var. kanwonensis OM640091.1 155060 View on NCBI ↗