Markers + reference

Bergenia

3 species · Saxifragaceae · Saxifragales

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Species 3
Genome length 156–156 kb
Candidate markers 269
Primer pairs 90

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1453 0.0117 1.00 63.9 yes View details
trnR-UCU-atpA LSC 235 0.0426 1.00 69.4 yes View details
petA-psbJ LSC 723 0.0231 1.00 75.8 yes View details
rps18 LSC 306 0.0044 1.00 30.9 yes View details
ycf1 IRb 1161 0.0052 1.00 47.0 no View details
ndhF SSC 2235 0.0063 1.00 46.3 yes View details
ndhF-rpl32 SSC 1117 0.0114 1.00 56.7 yes View details
ccsA-ndhD SSC 304 0.0322 0.95 62.7 yes View details
ycf1 SSC 5538 0.0081 1.00 44.8 yes View details
ycf1-ndhF SSC 38 0.1930 1.00 72.6 yes View details
trnT-UGU-trnL-UAA LSC 1012 0.0083 0.99 67.1 yes View details
rpl33-rps18 LSC 172 0.0504 1.00 66.8 yes View details
ycf3-trnS-GGA LSC 870 0.0084 1.00 66.4 yes View details
petB-petD LSC 841 0.0040 1.00 64.0 yes View details
atpH-atpI LSC 1065 0.0069 1.00 63.8 yes View details
psbM-trnD-GUC LSC 1159 0.0046 1.00 61.8 yes View details
trnS-GCU-trnG-UCC LSC 768 0.0091 1.00 60.8 yes View details
rps12-trnV-GAC IRb 1519 0.0022 1.00 60.1 yes View details
trnV-GAC-rps12 IRa 1519 0.0022 1.00 60.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1028–1727 1.000 83.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1039–1738 1.000 82.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1049–1748 1.000 81.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1050–1749 1.000 81.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1051–1750 1.000 79.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 700–855 1.000 56.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 699–854 1.000 56.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 703–858 1.000 55.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 702–857 1.000 55.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 701–856 1.000 55.6
trnR-UCU-atpA_p1 trnR-UCU-atpA ATCGGAATGAAAAGCGTCCA GTTTTCTACTTCAGGAACAAGCA 320–361 1.000 55.9
trnR-UCU-atpA_p2 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT GTTTTCTACTTCAGGAACAAGCA 319–360 1.000 55.9
trnR-UCU-atpA_p3 trnR-UCU-atpA ATCGGAATGAAAAGCGTCCA TTCTACTTCAGGAACAAGCA 317–358 1.000 55.7
trnR-UCU-atpA_p4 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT TTCTACTTCAGGAACAAGCA 316–357 1.000 55.7
trnR-UCU-atpA_p5 trnR-UCU-atpA TCGGAATGAAAAGCGTCCAT TTTCTACTTCAGGAACAAGCA 317–358 1.000 54.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCAGCGG 1152–1244 1.000 79.8
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCAGCGG 1144–1236 1.000 79.6
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCAGCGG 1208–1300 1.000 79.1
atpH-atpI_p4 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCAGCGG 1145–1237 1.000 78.8
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCAGCGG 1153–1245 1.000 78.6
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 1269–1280 1.000 58.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AGGAACTAGAATGAACAGTGCA TTCAATTGGTCAGAGCACCG 1276–1287 1.000 55.8
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC GTTCAATTGGTCAGAGCACC 1270–1281 1.000 54.8
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAGAATGAACAGTGCAG TTCAATTGGTCAGAGCACCG 1275–1286 1.000 53.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TCAATTGGTCAGAGCACCG 1268–1279 1.000 52.9
ycf3-trnS-GGA_p1 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 768–971 1.000 75.7
ycf3-trnS-GGA_p2 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTGAA 739–942 1.000 75.0
ycf3-trnS-GGA_p3 ycf3-trnS-GGA CATTTATCCGCGATCTAGGCA ACCCTCGGTAAACAAAAGCC 769–972 1.000 73.4
ycf3-trnS-GGA_p4 ycf3-trnS-GGA ATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 767–970 1.000 72.7
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTTATCCGCGATCTAGGCAT CCCTCGGTAAACAAAAGCCT 766–969 1.000 72.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Bergenia ciliata OR668896.1 155949 View on NCBI ↗
Bergenia crassifolia PQ591706.1 156378 View on NCBI ↗
Bergenia scopulosa NC_036061.1 156041 View on NCBI ↗