Markers + reference

Semiaquilegia

2 species · Ranunculaceae · Ranunculales

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Species 2
Genome length 162–164 kb
Candidate markers 269
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1135 0.0143 0.99 58.7 yes View details
ndhC-trnV-UAC LSC 971 0.0372 1.00 71.0 yes View details
rbcL-accD LSC 3415 0.0115 0.94 66.1 yes View details
rps12-clpP LSC 2624 0.0089 0.98 63.4 yes View details
rpl36-trnN-GUU LSC 710 0.0160 0.88 64.2 yes View details
trnN-GUU-infA LSC 428 0.0308 0.99 74.2 yes View details
rpl2 IRb 1479 0.0027 1.00 46.9 no View details
trnN-GUU-ycf1 IRb 708 0.0174 0.97 71.3 yes View details
ycf1 IRb 1155 0.0078 1.00 48.3 no View details
ndhF SSC 2220 0.0104 1.00 48.7 yes View details
ndhF-trnL-UAG SSC 1347 0.0230 0.94 65.0 yes View details
ycf1 SSC 5349 0.0109 1.00 47.8 yes View details
ycf1-trnR-ACG IRa 1377 0.0096 0.99 65.6 yes View details
rpl2 IRa 1479 NA 0.00 35.7 yes View details
psbL-psbF LSC 22 0.0455 1.00 78.6 yes View details
trnK-UUU-rps16 LSC 693 0.0212 0.95 75.6 yes View details
atpF-atpH LSC 469 0.0245 0.96 74.1 yes View details
ccsA-ndhD SSC 229 0.0263 1.00 68.0 yes View details
trnP-UGG-psaJ LSC 415 0.0196 0.98 67.8 yes View details
rps2 LSC 837 0.0131 1.00 66.3 yes View details
psaJ-rpl33 LSC 433 0.0164 0.99 66.0 yes View details
trnL-UAA-trnF-GAA LSC 351 0.0178 0.96 65.6 yes View details
psbE-petL LSC 1069 0.0095 0.99 65.4 yes View details
rps8-rpl14 LSC 229 0.0369 0.95 64.8 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGCATATTTTCATATGATAATGGA CGTATCTACGCACCATAATTTCA 2641–2654 1.000 40.9
trnK-UUU_p2 trnK-UUU TGCATATTTTCATATGATAATGGA CGTATCTACGCACCATAATTTCAT 2641–2654 1.000 40.9
trnK-UUU_p3 trnK-UUU TGCATATTTTCATATGATAATGGA CGTATCTACGCACCATAATTTC 2641–2654 1.000 40.9
trnK-UUU_p4 trnK-UUU TGCATATTTTCATATGATAATGGA CGTATCTACGCACCATAATT 2641–2654 1.000 40.9
trnK-UUU_p5 trnK-UUU TGCATATTTTCATATGATAATGGA CGTATCTACGCACCATAATTT 2641–2654 1.000 40.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCCTTGAAAAAGGCGCG 797–825 1.000 82.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCCTTGAAAAAGGCGCG 796–824 1.000 82.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTACCAACGGTATGGACGA ATTTCCTTGAAAAAGGCGCG 862–890 1.000 82.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC ATTTCCTTGAAAAAGGCGCG 811–839 1.000 82.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ATTTCCTTGAAAAAGGCGCG 806–834 1.000 81.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGAGCACCTCAGAATTCC GAGGTTCGAATCCTTCCGTC 1273–1277 1.000 80.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AGAACCCACAACCGATCATG GAGGTTCGAATCCTTCCGTC 1230–1234 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1225–1229 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1204–1208 1.000 80.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACCCACAACCGATCATGTC GAGGTTCGAATCCTTCCGTC 1228–1232 1.000 79.8
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA ATTTATGGACTGGTCGTGGC 548–564 1.000 83.8
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 576–592 1.000 83.0
atpF-atpH_p3 atpF-atpH AGTGACCCAAGGAAACGAAA ATTTATGGACTGGTCGTGGC 547–563 1.000 78.4
atpF-atpH_p4 atpF-atpH TGACCCAAGGAAACGAAAGA ATTTATGGACTGGTCGTGGC 545–561 1.000 76.1
atpF-atpH_p5 atpF-atpH GTGACCCAAGGAAACGAAAG ATTTATGGACTGGTCGTGGC 546–562 1.000 75.7
rps2_p1 rps2 ATTGTTCGGATACCCAGTCA TTTAACTAGCGGGTCCGTTC 988–993 1.000 63.9
rps2_p2 rps2 TGTTCGGATACCCAGTCATT TTTAACTAGCGGGTCCGTTC 986–991 1.000 63.9
rps2_p3 rps2 TTGTTCGGATACCCAGTCAT TTTAACTAGCGGGTCCGTTC 987–992 1.000 63.9
rps2_p4 rps2 TGTTCGGATACCCAGTCATT TAACTAGCGGGTCCGTTCTT 984–989 1.000 63.2
rps2_p5 rps2 TGTTCGGATACCCAGTCATT TTAACTAGCGGGTCCGTTCT 985–990 1.000 63.2
trnL-UAA-trnF-GAA_p1 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TTTGAACTGGTGACACGAGG 428–441 1.000 79.5
trnL-UAA-trnF-GAA_p2 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC CACATGCCAGGAACCAGATT 446–459 1.000 78.5
trnL-UAA-trnF-GAA_p3 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TACCAACTGAGCTATCCCGA 390–403 1.000 76.7
trnL-UAA-trnF-GAA_p4 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC GAACTGGTGACACGAGGATT 425–438 1.000 76.3
trnL-UAA-trnF-GAA_p5 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC ACCGGTCCATGTCGATTACT 485–498 1.000 75.3

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
Semiaquilegia guangxiensis NC_057495.1 164047 View on NCBI ↗
Semiaquilegia quelpaertensis PX987619.1 162312 View on NCBI ↗