Markers + reference

Cercidiphyllum

2 species · Cercidiphyllaceae · Saxifragales

Back to catalogue

Species 2
Genome length 160–160 kb
Candidate markers 264
Primer pairs 110

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 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-trnD-GUC LSC 2452 0.0012 1.00 57.5 yes View details
trnE-UUC-trnT-GGU LSC 857 0.0036 0.97 64.1 yes View details
psbZ-trnG-UCC LSC 485 0.0104 0.99 62.9 yes View details
rps4-trnT-UGU LSC 345 0.0058 1.00 56.8 yes View details
trnT-UGU-trnL-UAA LSC 1073 0.0037 1.00 60.9 yes View details
ycf4-cemA LSC 846 0.0024 1.00 53.1 yes View details
petA-psbJ LSC 942 0.0032 1.00 60.6 yes View details
rpoA LSC 1014 0.0039 1.00 61.0 yes View details
ycf1 SSC 1069 0.0000 1.00 38.4 no View details
rpl32-trnL-UAG SSC 1191 0.0017 1.00 49.4 yes View details
ccsA SSC 960 0.0010 1.00 56.3 yes View details
ycf1 SSC 5637 0.0018 1.00 51.9 yes View details
DR679_pgr001-trnI-GAU IRb 1132 1.0000 0.00 68.9 no View details
psaA-ycf3 LSC 682 0.0000 0.98 60.7 yes View details
accD-psaI LSC 749 0.0027 1.00 60.3 yes View details
atpB-rbcL LSC 757 0.0013 0.99 60.2 yes View details
ycf3-trnS-GGA LSC 837 0.0000 0.99 60.0 yes View details
matK-trnK-UUU LSC 714 0.0014 1.00 59.7 yes View details
rps16-trnQ-UUG LSC 1580 0.0013 1.00 59.7 yes View details
trnR-ACG-trnN-GUU SSC 598 0.0017 1.00 59.7 yes View details
trnN-GUU-trnR-ACG SSC 598 0.0017 1.00 59.7 yes View details
rbcL LSC 1428 0.0014 1.00 59.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGTGAATGAATGAAGTGAGTTACA GCGACTGTATCTACACACCC 2673–2674 1.000 40.2
trnK-UUU_p2 trnK-UUU TGTGAATGAATGAAGTGAGTTACA ATGTTTTGATTGCGTCGTGC 2724–2725 1.000 40.2
trnK-UUU_p3 trnK-UUU TGTGAATGAATGAAGTGAGTTACA CGTCGTGCAATCCAATCTCT 2712–2713 1.000 40.2
trnK-UUU_p4 trnK-UUU TGTGAATGAATGAAGTGAGT GCGACTGTATCTACACACCC 2673–2674 1.000 40.2
trnK-UUU_p5 trnK-UUU TGTGAATGAATGAAGTGAGTT GCGACTGTATCTACACACCC 2673–2674 1.000 40.2
matK-trnK-UUU_p1 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT AACGGTAGAGTACTCGGCTT 792–793 1.000 78.6
matK-trnK-UUU_p2 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT ACGGTAGAGTACTCGGCTTT 791–792 1.000 78.6
matK-trnK-UUU_p3 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT GCGACTGTATCTACACACCC 854–855 1.000 78.3
matK-trnK-UUU_p4 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT GGGTTGCTAACTCAACGGTA 805–806 1.000 76.3
matK-trnK-UUU_p5 matK-trnK-UUU GGAAGTCATGTTGCCGAGAT TTCGGGTTGCTAACTCAACG 808–809 1.000 76.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1647–1653 1.000 78.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1658–1664 1.000 78.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1668–1674 1.000 76.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1669–1675 1.000 76.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1670–1676 1.000 74.7
trnG-GCC_p1 trnG-GCC CCTGTCTTGATTACGTCCGA GAGAATTTCGGGAATTGCGT 933–942 1.000 63.1
trnG-GCC_p2 trnG-GCC TCCTGTCTTGATTACGTCCG GAGAATTTCGGGAATTGCGT 934–943 1.000 63.1
trnG-GCC_p3 trnG-GCC CCTGTCTTGATTACGTCCGA AGAGAATTTCGGGAATTGCGT 934–943 1.000 62.4
trnG-GCC_p4 trnG-GCC TCCTGTCTTGATTACGTCCG AGAGAATTTCGGGAATTGCGT 935–944 1.000 62.4
trnG-GCC_p5 trnG-GCC CCTGTCTTGATTACGTCCGA GAGAGAATTTCGGGAATTGCG 935–944 1.000 62.1
petN-trnD-GUC_p1 petN-trnD-GUC TAGTAAGTCTCGCTTGGGCT TTCAATTGGTCAGAGCACCG 2599–2600 1.000 75.1
petN-trnD-GUC_p2 petN-trnD-GUC ATGGGGAAGAAGTGGACTCT TTCAATTGGTCAGAGCACCG 2538–2539 1.000 73.5
petN-trnD-GUC_p3 petN-trnD-GUC TAGTAAGTCTCGCTTGGGCT GTTCAATTGGTCAGAGCACC 2600–2601 1.000 70.9
petN-trnD-GUC_p4 petN-trnD-GUC ATGGGGAAGAAGTGGACTCT GTTCAATTGGTCAGAGCACC 2539–2540 1.000 69.3
petN-trnD-GUC_p5 petN-trnD-GUC ATAGTAAGTCTCGCTTGGGC TTCAATTGGTCAGAGCACCG 2600–2601 1.000 69.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 969–998 1.000 81.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TACCGCTGAGTTAAAAGGGC 934–963 1.000 80.6
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 931–960 1.000 80.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 910–939 1.000 80.5
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 966–995 1.000 80.1

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
Cercidiphyllum japonicum NC_037940.1 159854 View on NCBI ↗
Cercidiphyllum magnificum NC_046692.1 159899 View on NCBI ↗