Markers + reference

Reseda

2 species · Resedaceae · Brassicales

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Species 2
Genome length 152–154 kb
Candidate markers 272
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 947 0.0584 0.98 77.7 yes View details
rps16-trnQ-UUG LSC 438 0.0594 1.00 73.0 yes View details
trnS-GCU-trnG-UCC LSC 486 0.0557 1.00 76.3 yes View details
rpoB-trnC-GCA LSC 996 0.0383 1.00 66.6 yes View details
trnC-GCA-petN LSC 751 0.0511 0.96 81.6 yes View details
psbM-trnD-GUC LSC 965 0.0754 0.92 84.5 yes View details
trnD-GUC-trnY-GUA LSC 451 0.0622 0.96 81.3 yes View details
trnE-UUC-trnT-GGU LSC 382 0.0707 1.00 70.5 yes View details
trnT-GGU-psbD LSC 1357 0.0422 1.00 73.7 yes View details
ycf1 IRb 1188 0.0152 1.00 53.3 no View details
rpl32-trnL-UAG SSC 583 0.1257 0.98 81.1 yes View details
rps15-ycf1 SSC 414 0.0793 0.94 77.6 yes View details
ycf1 SSC 5205 0.0390 1.00 61.2 yes View details
petN-psbM LSC 797 0.0442 0.96 86.7 yes View details
atpF-atpH LSC 562 0.0486 0.99 84.9 yes View details
trnT-UGU-trnL-UAA LSC 779 0.0496 0.96 79.3 yes View details
trnR-UCU-atpA LSC 151 0.0993 1.00 77.0 yes View details
trnY-GUA-trnE-UUC LSC 48 0.0833 1.00 76.9 yes View details
psbI-trnS-GCU LSC 72 0.0571 0.97 76.7 yes View details
rps19-trnH-GUG LSC 31 0.1600 0.81 75.9 no View details
petB-petD LSC 198 0.0969 0.99 75.8 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCCGGATCAGTCATGG AAAAAGGCGCTCAACCTACA 1149–1170 1.000 85.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCCGGATCAGTCATGG CCCAATGAGCCGTTTATCGA 1287–1308 1.000 84.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCCGGATCAGTCATGG TCCCAATGAGCCGTTTATCG 1288–1309 1.000 84.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCGGATCAGTCATGGTCTT AAAAAGGCGCTCAACCTACA 1145–1166 1.000 84.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCCGGATCAGTCATGG AGTAAGGGCTTGTTGCTGTC 1800 0.500 58.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 511–512 1.000 82.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 521–522 1.000 81.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCAATTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 518–519 1.000 78.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 515–516 1.000 77.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 503–504 1.000 77.2
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 169–170 1.000 75.3
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 170–171 1.000 75.3
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA AGTTAGTCGTACCGAGGGTT 134–135 1.000 74.4
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA ATTGGGAGAGATGGCTGAGT 188–189 1.000 74.2
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GAGTTAGTCGTACCGAGGGT 135–136 1.000 74.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGACCCCTTAACTATTCAGGG 587–604 1.000 68.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGGACCCCTTAACTATTCAGG 588–605 1.000 68.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGACCCCTTAACTATTCAGGG 586–603 1.000 68.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGGACCCCTTAACTATTCAGG 587–604 1.000 68.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC GGACCCCTTAACTATTCAGGG 589–606 1.000 66.0
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGAGCAAATGGAACGTT 216–228 1.000 69.7
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGAGCAAATGGAACGT 217–229 1.000 69.7
trnR-UCU-atpA_p3 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TCAGGAGCAAATGGAACGTT 251–263 1.000 66.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT TTCAGGAGCAAATGGAACGT 252–264 1.000 66.1
trnR-UCU-atpA_p5 trnR-UCU-atpA ACTAGAAAAGCGTCCATTGTCT TCAGGAGCAAATGGAACGTT 275–287 1.000 63.9
atpF-atpH_p1 atpF-atpH CGGATGTCCAGTGATCCAAG AGGCAGAAGGAAAAATCCGA 727–749 1.000 76.2
atpF-atpH_p2 atpF-atpH TTAAATCCGAAACTCCCGGC AGGCAGAAGGAAAAATCCGA 746–768 1.000 74.5
atpF-atpH_p3 atpF-atpH GGATGTCCAGTGATCCAAGG AGGCAGAAGGAAAAATCCGA 726–748 1.000 73.9
atpF-atpH_p4 atpF-atpH CGGATGTCCAGTGATCCAAG GCAGAAGGAAAAATCCGAGG 725–747 1.000 73.6
atpF-atpH_p5 atpF-atpH CGGATGTCCAGTGATCCAAG GGCAGAAGGAAAAATCCGAG 726–748 1.000 73.5

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
Reseda lutea subsp. lutea PP541881.1 151907 View on NCBI ↗
Reseda luteola PP541882.1 154142 View on NCBI ↗