Markers + reference

Fossombronia

2 species · Fossombroniaceae · Fossombroniales

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Species 2
Genome length 123–124 kb
Candidate markers 265
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

10 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
ndhB-trnL-CAA Genome 228 0.1963 0.96 77.2 yes View details
ycf2-trnG-GCC Genome 339 0.1238 0.95 78.1 yes View details
atpB-rbcL Genome 614 0.1117 0.86 84.3 yes View details
psbE-petL Genome 775 0.0932 0.97 84.7 yes View details
16rrn Genome 1490 0.0612 1.00 75.4 yes View details
23rrn Genome 2808 0.0210 1.00 54.1 no View details
rpl32-trnP Genome 1050 0.1376 0.87 82.2 yes View details
23rrn Genome 2808 0.0453 1.00 68.1 yes View details
16rrn Genome 1490 0.0423 1.00 69.6 no View details
trnV-rps12 Genome 793 0.1030 0.97 81.9 no View details
trnG-GCC-trnY-GUA Genome 154 0.1096 0.95 82.2 yes View details
trnL-UAA-trnF-GAA Genome 153 0.1156 0.96 81.9 yes View details
trnF-GAA-psbD Genome 724 0.0617 0.98 81.1 yes View details
trnE-UUC-trnF-GAA Genome 540 0.0633 0.99 80.5 yes View details
trnM-CAU-trnT Genome 375 0.0852 0.97 80.5 yes View details
trnW-trnP Genome 117 0.1197 1.00 79.0 yes View details
chlB-trnK-UUU Genome 628 0.0747 0.98 77.9 yes View details
trnS-GGA-rps4 Genome 243 0.0928 0.98 77.7 yes View details
psbL-psbF Genome 24 0.0476 0.88 77.1 yes View details
rpl23-trnM-CAU Genome 167 0.0783 0.99 76.7 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhB-trnL-CAA_p1 ndhB-trnL-CAA CACCTTGGGTTTTCTCACGA GATAACCTCCCTCCCCTACC 869 0.500 59.5
ndhB-trnL-CAA_p2 ndhB-trnL-CAA TCACCTTGGGTTTTCTCACG GATAACCTCCCTCCCCTACC 870 0.500 59.5
ndhB-trnL-CAA_p3 ndhB-trnL-CAA CACCTTGGGTTTTCTCACGA TGTTTTGACTAGCTGTGCGT 831 0.500 59.3
ndhB-trnL-CAA_p4 ndhB-trnL-CAA TCACCTTGGGTTTTCTCACG TGTTTTGACTAGCTGTGCGT 832 0.500 59.3
ndhB-trnL-CAA_p5 ndhB-trnL-CAA CACCTTGGGTTTTCTCACGA TAGTAATACGTCAGCCCGGT 651 0.500 59.2
chlB-trnK-UUU_p1 chlB-trnK-UUU AATCGCGGACCTGGTCTATA AGAGACGAACGAACGACATG 1065–1073 1.000 85.0
chlB-trnK-UUU_p2 chlB-trnK-UUU ATCGCGGACCTGGTCTATAA AGAGACGAACGAACGACATG 1064–1072 1.000 85.0
chlB-trnK-UUU_p3 chlB-trnK-UUU TCGCGGACCTGGTCTATAAT AGAGACGAACGAACGACATG 1063–1071 1.000 85.0
chlB-trnK-UUU_p4 chlB-trnK-UUU AAGCTGTGGTTTTCGGTGAT AGAGACGAACGAACGACATG 1411–1419 1.000 83.9
chlB-trnK-UUU_p5 chlB-trnK-UUU GTTGGAATCCTGAGAGCCAG AGAGACGAACGAACGACATG 951 0.500 59.4
ycf2-trnG-GCC_p1 ycf2-trnG-GCC GTTTGTTCCCACAGATCCGT CTTTCTATCTGGGTCGGTGC 1225–1232 1.000 85.7
ycf2-trnG-GCC_p2 ycf2-trnG-GCC GTTTGTTCCCACAGATCCGT CCCCCACGATCGATGATTTT 1647–1650 1.000 85.1
ycf2-trnG-GCC_p3 ycf2-trnG-GCC TAAGGGGGAGGAACGTACAG CCCCCACGATCGATGATTTT 1818–1821 1.000 84.4
ycf2-trnG-GCC_p4 ycf2-trnG-GCC GTTTGTTCCCACAGATCCGT GAGCTCCAAATGGTCCAGAG 1109 0.500 58.9
ycf2-trnG-GCC_p5 ycf2-trnG-GCC TAAGGGGGAGGAACGTACAG GAGCTCCAAATGGTCCAGAG 1280 0.500 58.6
trnG-GCC-trnY-GUA_p1 trnG-GCC-trnY-GUA TTGACAGGGCGGTACTCTAA CCTACGCTGGTTCAAATCCA 217–225 1.000 87.2
trnG-GCC-trnY-GUA_p2 trnG-GCC-trnY-GUA CTTGACAGGGCGGTACTCTA CCTACGCTGGTTCAAATCCA 218–226 1.000 83.6
trnG-GCC-trnY-GUA_p3 trnG-GCC-trnY-GUA CAACTTCCGTCTTGACAGGG CCTACGCTGGTTCAAATCCA 228–236 1.000 83.5
trnG-GCC-trnY-GUA_p4 trnG-GCC-trnY-GUA TTGACAGGGCGGTACTCTAA GACTGTAAATCCGCTGGCAA 239–247 1.000 82.9
trnG-GCC-trnY-GUA_p5 trnG-GCC-trnY-GUA TTGACAGGGCGGTACTCTAA ACTGTAAATCCGCTGGCAAC 238–246 1.000 80.7
trnE-UUC-trnF-GAA_p1 trnE-UUC-trnF-GAA CCGTCACCTCCTTGAAAGAG CCATGGCGTTACTCTACCAC 625–629 1.000 83.5
trnE-UUC-trnF-GAA_p2 trnE-UUC-trnF-GAA CCGTCACCTCCTTGAAAGAG TGGCGTTACTCTACCACTGA 622–626 1.000 83.4
trnE-UUC-trnF-GAA_p3 trnE-UUC-trnF-GAA CCGTCACCTCCTTGAAAGAG ACCAGATTTGAACCGGTGAC 655–659 1.000 83.0
trnE-UUC-trnF-GAA_p4 trnE-UUC-trnF-GAA CCGTCACCTCCTTGAAAGAG GACAAAGAGCCCCTTACCAG 670–674 1.000 82.8
trnE-UUC-trnF-GAA_p5 trnE-UUC-trnF-GAA CCGTCACCTCCTTGAAAGAG ACATGGATGACAAAGAGCCC 678 0.500 58.2
trnF-GAA-psbD_p1 trnF-GAA-psbD GTGGTAGAGTAACGCCATGG GAATACGAAACGGTCCCTCC 872–876 1.000 84.0
trnF-GAA-psbD_p2 trnF-GAA-psbD GTGGTAGAGTAACGCCATGG GCCTACGAATACGAAACGGT 878–882 1.000 83.8
trnF-GAA-psbD_p3 trnF-GAA-psbD TCAGTGGTAGAGTAACGCCA GAATACGAAACGGTCCCTCC 875–879 1.000 83.8
trnF-GAA-psbD_p4 trnF-GAA-psbD GTCACCGGTTCAAATCTGGT GAATACGAAACGGTCCCTCC 842–846 1.000 83.8
trnF-GAA-psbD_p5 trnF-GAA-psbD TCAGTGGTAGAGTAACGCCA GCCTACGAATACGAAACGGT 881–885 1.000 83.6

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
Fossombronia foveolata NC_080365.1 123443 View on NCBI ↗
Fossombronia wondraczekii PX421530.1 123576 View on NCBI ↗