Markers + reference

Trichocladus

2 species · Hamamelidaceae · Saxifragales

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Species 2
Genome length 159–159 kb
Candidate markers 271
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 877 0.0068 1.00 54.5 yes View details
trnS-GCU-trnS-CGA LSC 896 0.0056 0.99 62.8 yes View details
petN-psbM LSC 1179 0.0051 1.00 61.7 yes View details
psbC LSC 1422 0.0007 1.00 50.5 yes View details
psbC-trnS-UGA LSC 216 0.0370 1.00 65.1 yes View details
atpB-rbcL LSC 751 0.0054 0.98 58.6 yes View details
psbE-petL LSC 896 0.2122 0.97 81.3 yes View details
petL-petG LSC 222 0.1055 0.90 75.5 yes View details
rpoA LSC 1014 0.0010 1.00 47.3 yes View details
ycf1 IRb 1020 0.0000 1.00 34.2 no View details
ccsA SSC 978 0.0010 1.00 50.9 yes View details
ndhD SSC 1530 0.0026 1.00 47.1 yes View details
ycf1 SSC 5595 0.0041 1.00 54.9 yes View details
ccsA-ndhD SSC 245 0.0449 1.00 67.8 yes View details
petL LSC 108 0.4364 0.51 66.4 yes View details
psbM-trnD-GUC LSC 1158 0.0018 0.99 61.1 yes View details
petB LSC 1440 0.0035 1.00 60.7 yes View details
rbcL-accD LSC 617 0.0032 1.00 60.6 yes View details
rpl16-rps3 LSC 145 0.0138 1.00 60.4 yes View details
trnT-GGU-psbD LSC 1387 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGAAGGCGGAGGTTTTTACG 1025–1031 1.000 78.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGAAGGCGGAGGTTTTTACG 964–970 1.000 77.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGAGGTTTTTACG 963–969 1.000 77.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GGTTTTTACGGAACTTCGCC 1015–1021 1.000 77.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TCAAAGAAGGCGGAGGTTTT 1029–1035 1.000 77.0
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA GAATTAAACCGAGGGACCCC 1002–1009 1.000 80.6
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC GAATTAAACCGAGGGACCCC 1001–1008 1.000 80.6
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA GAATTAAACCGAGGGACCCC 1056–1063 1.000 79.4
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA TGGAAACGGAAAGAGAGGGA GAATTAAACCGAGGGACCCC 1061–1068 1.000 78.4
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC GAATTAAACCGAGGGACCCC 1004–1011 1.000 77.8
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT GCTACGGCACTGTTCATTCT 1340–1343 1.000 77.0
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT GCTACGGCACTGTTCATTCT 1279–1282 1.000 75.4
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACGGCACTGTTCATTC 1341–1344 1.000 74.7
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACGGCACTGTTCATTC 1280–1283 1.000 73.1
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC GCTACGGCACTGTTCATTCT 1341–1344 1.000 71.0
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCCGTAGC TTCAATTGGTCAGAGCACCG 1253–1269 1.000 75.1
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCCGTAGC GTTCAATTGGTCAGAGCACC 1254–1270 1.000 71.0
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCCGTAGC TCAATTGGTCAGAGCACCG 1252–1268 1.000 69.1
psbM-trnD-GUC_p4 psbM-trnD-GUC TAGAATGAACAGTGCCGTAGC TTCAATTGGTCAGAGCACCG 1254–1270 1.000 68.4
psbM-trnD-GUC_p5 psbM-trnD-GUC ACTAGAATGAACAGTGCCGT TTCAATTGGTCAGAGCACCG 1256–1272 1.000 68.3
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1551–1558 1.000 77.5
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GACCGGACCAACCTACAAAA 1565–1572 1.000 77.4
trnT-GGU-psbD_p3 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA TAGACCGGACCAACCTACAA 1567–1574 1.000 77.0
trnT-GGU-psbD_p4 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA CCCTTCGTAACCAGTCATCC 1535–1542 1.000 76.9
trnT-GGU-psbD_p5 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GAGCAATAGACCGGACCAAC 1573–1580 1.000 76.7
psbC_p1 psbC GTGCAGCAGAAGATCCTGAA ACCTGATCCGGATCCGAATA 1588 1.000 76.8
psbC_p2 psbC AAATCCGTGCAGCAGAAGAT ACCTGATCCGGATCCGAATA 1594 1.000 76.7
psbC_p3 psbC TTCGTTTCCCAGGAAATCCG ACCTGATCCGGATCCGAATA 1607 1.000 76.1
psbC_p4 psbC GTGCAGCAGAAGATCCTGAA TATGACCTGATCCGGATCCG 1592 1.000 75.6
psbC_p5 psbC AAATCCGTGCAGCAGAAGAT TATGACCTGATCCGGATCCG 1598 1.000 75.5

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
Trichocladus crinitus ON729361.1 158787 View on NCBI ↗
Trichocladus ellipticus ON729360.1 158856 View on NCBI ↗