Markers + reference

Sanguisorba

12 species · Rosaceae · Rosales

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Species 12
Genome length 154–156 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 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
trnH-GUG-psbA LSC 316 0.0645 0.92 76.2 yes View details
trnK-UUU-rps16 LSC 799 0.0242 0.99 73.2 yes View details
rps16-trnQ-UUG LSC 944 0.0235 1.00 75.6 yes View details
trnR-UCU-atpA LSC 505 0.0348 0.98 70.8 yes View details
trnC-GCA-petN LSC 787 0.0228 0.98 66.2 yes View details
trnT-UGU-trnL-UAA LSC 1092 0.0232 0.94 80.3 yes View details
ndhC-trnV-UAC LSC 668 0.0368 0.97 73.8 yes View details
ycf1 IRb 1110 0.0044 1.00 39.1 no View details
ycf1-ndhF SSC 315 0.2493 0.35 65.6 yes View details
ndhF-rpl32 SSC 1176 0.0199 0.95 64.5 yes View details
ccsA-ndhD SSC 287 0.0486 0.94 70.0 yes View details
ycf1 SSC 5715 0.0166 1.00 59.6 yes View details
rpl22-rps19 LSC 99 0.0532 0.96 74.5 yes View details
petN-psbM LSC 1228 0.0164 1.00 71.9 yes View details
rpoB-trnC-GCA LSC 1072 0.0171 0.97 71.6 yes View details
psaJ-rpl33 LSC 470 0.0192 1.00 71.4 yes View details
rps18-rpl20 LSC 296 0.0124 0.98 70.6 yes View details
atpH-atpI LSC 745 0.0138 1.00 70.3 yes View details
ycf3-trnS-GGA LSC 886 0.0149 1.00 69.2 yes View details
rpl32-trnL-UAG SSC 670 0.0199 1.00 68.9 yes View details
trnL-UAA-trnF-GAA LSC 414 0.0254 0.95 68.7 yes View details
atpF-atpH LSC 480 0.0138 1.00 68.3 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 105 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 CCTCTAGACCTAGCTGCTGT 353–421 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 367–435 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 366–434 1.000 90.4
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 368–436 1.000 90.4
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 356–424 1.000 90.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 903–970 1.000 90.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 902–969 1.000 90.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 912–979 1.000 89.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 907–974 1.000 88.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 906–973 1.000 88.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 877–1088 1.000 89.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCACAGTCGATCATGTCCT GAGGTTCGAATCCTTCCGTC 899–1110 1.000 89.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 888–1099 1.000 89.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CTCCACAGTCGATCATGTCC GAGGTTCGAATCCTTCCGTC 900–1111 1.000 88.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CCACAGTCGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 898–1109 1.000 85.1
trnR-UCU-atpA_p1 trnR-UCU-atpA ATTGGAGTGAAAAGCGTCCA GACCAGATGGACCGTTTTCT 599–629 1.000 86.0
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT GACCAGATGGACCGTTTTCT 597–627 1.000 86.0
trnR-UCU-atpA_p3 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT GACCAGATGGACCGTTTTCT 598–628 1.000 86.0
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT GGACCAGATGGACCGTTTTC 598–628 1.000 85.4
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT GGACCAGATGGACCGTTTTC 599–629 1.000 85.4
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG CGGAAGGAAAAATACGGGGT 643–667 1.000 86.6
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG CCAGAGGCGGAAGGAAAAAT 650–674 1.000 86.2
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG AGGCGGAAGGAAAAATACGG 646–670 1.000 85.5
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGGGCTGGTTGTAGCATTAG 579–603 1.000 84.7
atpF-atpH_p5 atpF-atpH GATGGCCAATAACCCAAGGA CGGAAGGAAAAATACGGGGT 621–645 1.000 83.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGGGAATCCATGGAAGGT 786–808 1.000 83.3
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA TAGGGGAATCCATGGAAGGT 787–809 1.000 82.2
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT ATTTTTGCAACCCTAGCTGC 814–836 1.000 82.0
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGGGAATCCATGGAAGGTC 785–807 1.000 82.0
atpH-atpI_p5 atpH-atpI ATAACGGAAGCGGCAGAAAT ACAAGCGGTATTCAAGCTCT 835–857 1.000 81.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Sanguisorba alpina NC_072253.1 155730 View on NCBI ↗
Sanguisorba applanata NC_080264.1 155454 View on NCBI ↗
Sanguisorba diandra NC_080346.1 154839 View on NCBI ↗
Sanguisorba filiformis NC_044693.1 154282 View on NCBI ↗
Sanguisorba hakusanensis NC_056804.1 155645 View on NCBI ↗
Sanguisorba minor subsp. minor PP622683.1 153785 View on NCBI ↗
Sanguisorba officinalis NC_044694.1 155479 View on NCBI ↗
Sanguisorba sitchensis NC_044691.1 155127 View on NCBI ↗
Sanguisorba stipulata NC_056805.1 155328 View on NCBI ↗
Sanguisorba tenuifolia NC_042223.1 155403 View on NCBI ↗
Sanguisorba tenuifolia var. alba NC_044692.1 155457 View on NCBI ↗
Sanguisorba tenuifolia var. tenuifolia ON360979.1 155426 View on NCBI ↗