Markers + reference

Urophysa

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 158–159 kb
Candidate markers 269
Primer pairs 75

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 8 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps4 LSC 582 0.0292 1.00 68.8 yes View details
rps4-trnT-UGU LSC 337 0.0090 0.99 49.2 yes View details
ycf2 IRb 6876 0.0134 1.00 45.4 no View details
rps12-trnV-GAC IRb 1858 0.0114 0.99 65.2 yes View details
ycf1 IRb 1081 0.0167 1.00 54.7 yes View details
ycf1 SSC 5340 0.0054 1.00 42.0 no View details
trnV-GAC-rps12 IRa 1858 0.0114 0.99 65.2 yes View details
ycf2 IRa 6876 0.0134 1.00 45.4 yes View details
rps14-psaB LSC 129 0.0431 0.90 80.2 yes View details
trnI-CAU IRb 69 0.0870 1.00 72.0 yes View details
trnI-CAU IRa 69 0.0870 1.00 72.0 yes View details
rrn23-rrn4.5 IRb 98 0.0306 1.00 70.1 yes View details
rrn4.5-rrn23 IRa 98 0.0306 1.00 70.1 yes View details
ycf4-cemA LSC 797 0.0154 0.97 70.0 yes View details
trnR-UCU-atpA LSC 136 0.0242 0.91 69.9 yes View details
trnS-GCU-trnG-UCC LSC 753 0.0135 0.98 68.2 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGAACCCTTAACT 849–860 1.000 54.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGAACCCTTAACT 848–859 1.000 54.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 811–822 1.000 53.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 810–821 1.000 53.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCAGAAGAGGCGGAAAGAGA AACCGAAAGAACCCTTAACT 912–923 1.000 53.3
trnR-UCU-atpA_p1 trnR-UCU-atpA AAATGAAGGGCGTCCATTGT GAACAGACGGAGCGGTTTAT 244–256 1.000 84.1
trnR-UCU-atpA_p2 trnR-UCU-atpA AGGGCGTCCATTGTCTAATG GAACAGACGGAGCGGTTTAT 238–250 1.000 82.2
trnR-UCU-atpA_p3 trnR-UCU-atpA AAATGAAGGGCGTCCATTGT CGAAGAAGCGGAAGTCCTTT 281–293 1.000 81.9
trnR-UCU-atpA_p4 trnR-UCU-atpA AAATGAAGGGCGTCCATTGT CGACCAAGACATTCACCGAA 297–309 1.000 81.7
trnR-UCU-atpA_p5 trnR-UCU-atpA AAATGAAGGGCGTCCATTGT TTCGACCAAGACATTCACCG 299–311 1.000 81.6
rps14-psaB_p1 rps14-psaB CACTCACCGACGAAACTCTT GTGGCTCTATCCATTGTGCA 345–358 1.000 82.7
rps14-psaB_p2 rps14-psaB CACTCACCGACGAAACTCTT GCAGCTTTCTTGATTGCCTC 273–286 1.000 81.9
rps14-psaB_p3 rps14-psaB TTTGTCACTCACCGACGAAA GTGGCTCTATCCATTGTGCA 350–363 1.000 81.3
rps14-psaB_p4 rps14-psaB CACTCACCGACGAAACTCTT AGTGGCTCTATCCATTGTGC 346–359 1.000 80.3
rps14-psaB_p5 rps14-psaB TTGTCACTCACCGACGAAAC GTGGCTCTATCCATTGTGCA 349–362 1.000 80.2
rps4_p1 rps4 GAAAAATCCAGACCAAGCGC TGGATTTAGCTTCGTTTATCGT 766 0.500 27.2
rps4_p2 rps4 GAAAAATCCAGACCAAGCGC GCTTCGTTTATCGTTTAGTTCAGT 758 0.500 26.7
rps4_p3 rps4 GAAAAATCCAGACCAAGCGC TGGATTTAGCTTCGTTTATCGTT 766 0.500 24.8
rps4_p4 rps4 CGCCTTCCCTTTACCTTAGG TGGATTTAGCTTCGTTTATCGT 749 0.500 24.7
rps4_p5 rps4 GAAAAATCCAGACCAAGCGC AGCTTCGTTTATCGTTTAGTTCAG 759 0.500 24.7
rps4-trnT-UGU_p1 rps4-trnT-UGU TAGTCCCGGTAAAACACCCA CTCAGAGGTTAGAGCATCGC 462–463 1.000 77.8
rps4-trnT-UGU_p2 rps4-trnT-UGU TAGTCCCGGTAAAACACCCA ATGGTCATCGGTTCGATTCC 430–431 1.000 77.0
rps4-trnT-UGU_p3 rps4-trnT-UGU TAGTCCCGGTAAAACACCCA CAGAGGTTAGAGCATCGCAT 460–461 1.000 74.7
rps4-trnT-UGU_p4 rps4-trnT-UGU TAGTCCCGGTAAAACACCCA TCAGAGGTTAGAGCATCGCA 461–462 1.000 74.7
rps4-trnT-UGU_p5 rps4-trnT-UGU TAGTCCCGGTAAAACACCCA AAGTCCTATGCACAGCACAA 506–507 1.000 74.2
trnL-UAA_p1 trnL-UAA TGGCATCCTAACGAGATCCT TGGAATGGAACCGCTGAAAA 683 0.500 59.2
trnL-UAA_p2 trnL-UAA TGGCATCCTAACGAGATCCT TTGGAATGGAACCGCTGAAA 684 0.500 59.2
trnL-UAA_p3 trnL-UAA CCATGTAAACGGCTCCAGAA TGGAATGGAACCGCTGAAAA 726 0.500 59.0
trnL-UAA_p4 trnL-UAA CCATGTAAACGGCTCCAGAA TTGGAATGGAACCGCTGAAA 727 0.500 59.0
trnL-UAA_p5 trnL-UAA TTCCATGTAAACGGCTCCAG TGGAATGGAACCGCTGAAAA 728 0.500 59.0

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
Urophysa henryi NC_039744.1 158303 View on NCBI ↗
Urophysa rockii NC_039742.1 158512 View on NCBI ↗