Markers + reference

Mitella

2 species · Saxifragaceae · Saxifragales

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Species 2
Genome length 155–155 kb
Candidate markers 265
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 327 0.0536 0.97 71.1 yes View details
rps16-trnQ-UUG LSC 1351 0.0249 0.98 75.0 yes View details
atpH-atpI LSC 1125 0.0235 0.98 66.0 yes View details
trnF-GAA-ndhJ LSC 656 0.0276 1.00 71.4 yes View details
psbE-petL LSC 1280 0.0210 0.48 51.1 yes View details
rpl20-rps12 LSC 775 0.0469 0.99 73.5 yes View details
rpl16 LSC 1436 0.0191 0.98 56.8 yes View details
rpl32-trnL-UAG SSC 457 0.0504 1.00 72.9 yes View details
ccsA-psaC SSC 1874 0.0211 0.99 64.5 yes View details
rpl22-rps19 LSC 54 0.0370 1.00 73.8 yes View details
petN-psbM LSC 693 0.0231 1.00 72.2 yes View details
trnR-UCU-atpA LSC 197 0.0383 0.93 70.8 yes View details
petA-psbJ LSC 730 0.0140 0.98 69.0 yes View details
atpB-rbcL LSC 767 0.0175 0.97 68.6 yes View details
ndhF-rpl32 SSC 1122 0.0209 0.85 66.2 yes View details
trnD-GUC-trnY-GUA LSC 399 0.0258 0.97 65.8 yes View details
rbcL-accD LSC 593 0.0135 1.00 65.8 yes View details
trnY-GUA-trnE-UUC LSC 59 0.0339 1.00 65.3 yes View details
rpl14-rpl16 LSC 140 0.0299 0.96 65.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CCACTGCCTTATCCACTTGG CCTCTAGACCTAGCTGCTGT 394–402 1.000 83.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CCACTGCCTTATCCACTTGG TCAGTGCTATGCATGGTTCC 780–788 1.000 80.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CCACTGCCTTATCCACTTGG CAGTGCTATGCATGGTTCCT 779–787 1.000 80.5
trnH-GUG-psbA_p4 trnH-GUG-psbA CCACTGCCTTATCCACTTGG CTGCGACTGCTGTTTTCTTG 954–962 1.000 80.3
trnH-GUG-psbA_p5 trnH-GUG-psbA CCACTGCCTTATCCACTTGG ATATTCAGCTCCCGTTGCAG 974–982 1.000 80.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1424–1692 1.000 81.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1435–1703 1.000 80.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1445–1713 1.000 79.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1446–1714 1.000 79.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGAAAGCTAAATGGGGCGTG 1483–1751 1.000 77.6
trnR-UCU-atpA_p1 trnR-UCU-atpA ACAATCGGAATGAAAGGCGT GAGGAAGCAGAAGCCCTTTT 360–364 1.000 82.5
trnR-UCU-atpA_p2 trnR-UCU-atpA ACAATCGGAATGAAAGGCGT CATTCACCGAGGAAGCAGAA 368–372 1.000 82.3
trnR-UCU-atpA_p3 trnR-UCU-atpA ACAATCGGAATGAAAGGCGT AAGACATTCACCGAGGAAGC 372–376 1.000 82.3
trnR-UCU-atpA_p4 trnR-UCU-atpA CAATCGGAATGAAAGGCGTC GAGGAAGCAGAAGCCCTTTT 359–363 1.000 80.3
trnR-UCU-atpA_p5 trnR-UCU-atpA ACAATCGGAATGAAAGGCGT AGGAAGCAGAAGCCCTTTTG 359–363 1.000 80.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 1202–1212 1.000 81.5
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 1194–1204 1.000 81.3
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 1258–1268 1.000 80.8
atpH-atpI_p4 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCTGCGG 1195–1205 1.000 80.5
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 1203–1213 1.000 80.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 855–863 1.000 69.1
petN-psbM_p2 petN-psbM GGGGACACAATTCACATGGA TGCTACTGCACTGTTCATTCT 877–885 1.000 68.6
petN-psbM_p3 petN-psbM AGGGGACACAATTCACATGG TGCTACTGCACTGTTCATTCT 878–886 1.000 68.5
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 794–802 1.000 67.6
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 855–863 1.000 64.9
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA AGTATTTATTGGGTCCGCCG TGGCAATATGTCTACGCTGG 525–531 1.000 79.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA AGTATTTATTGGGTCCGCCG GGCAATATGTCTACGCTGGT 524–530 1.000 79.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA AGTATTTATTGGGTCCGCCG GGGGACGGACTGTAAATTCG 546–552 1.000 78.2
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA AGTATTTATTGGGTCCGCCG GGGACGGACTGTAAATTCGT 545–551 1.000 78.1
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 463–469 1.000 77.9

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
Mitella diphylla NC_042925.1 155445 View on NCBI ↗
Mitella yamatoensis (nom. nud.) PQ064095.1 154540 View on NCBI ↗