Markers + reference

Ostryopsis

2 species · Betulaceae · Fagales

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Species 2
Genome length 159–159 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCT-trnG-UCC LSC 874 0.0059 0.96 61.9 yes View details
trnG-UCC-trnR-TCT LSC 311 0.0043 0.75 52.5 yes View details
trnR-TCT-atpA LSC 263 0.0266 1.00 67.8 yes View details
trnE-TTC-trnT-GGT LSC 912 0.0103 0.96 68.3 yes View details
trnF-GAA-ndhJ LSC 820 0.0073 1.00 63.0 yes View details
petA-psbJ LSC 1139 0.0053 0.99 62.7 yes View details
rrn4.5 IRb 276 0.0580 1.00 82.2 yes View details
rpl32-trnL-TAG SSC 980 0.0092 1.00 63.9 yes View details
ycf1 SSC 5739 0.0044 1.00 50.2 yes View details
trnR-ACG-rrn5 IRa 261 0.0000 1.00 33.8 yes View details
rrn4.5 IRa 271 0.0590 1.00 82.4 yes View details
atpA-atpF LSC 63 0.0635 1.00 82.9 yes View details
psbI-trnS-GCT LSC 152 0.0211 0.93 68.9 yes View details
psbM-trnD-GTC LSC 1183 0.0052 0.98 63.2 yes View details
petD-rpoA LSC 168 0.0179 1.00 62.8 yes View details
psbZ-trnG-GCC LSC 321 0.0128 0.98 62.7 yes View details
trnQ-TTG-psbK LSC 494 0.0045 0.90 62.6 yes View details
petL-petG LSC 180 0.0115 0.97 62.3 yes View details
accD-psaI LSC 907 0.0023 0.98 62.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnQ-TTG-psbK_p1 trnQ-TTG-psbK ATAGGTATGCTCTGGGACGG TAGGCTTCGGGTAATTTGGC 618–666 1.000 80.9
trnQ-TTG-psbK_p2 trnQ-TTG-psbK GAATACCGGGACCAAAACCC TAGGCTTCGGGTAATTTGGC 582–630 1.000 79.6
trnQ-TTG-psbK_p3 trnQ-TTG-psbK ATAGGTATGCTCTGGGACGG GCGTAGGCTTCGGGTAATTT 621–669 1.000 78.6
trnQ-TTG-psbK_p4 trnQ-TTG-psbK GACCAAAACCCGTTGCCTTA TAGGCTTCGGGTAATTTGGC 573–621 1.000 78.5
trnQ-TTG-psbK_p5 trnQ-TTG-psbK ATAGGTATGCTCTGGGACGG TCGGGTAATTTGGCGAAGAA 612–660 1.000 77.5
psbI-trnS-GCT_p1 psbI-trnS-GCT CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 240–249 1.000 76.7
psbI-trnS-GCT_p2 psbI-trnS-GCT CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 241–250 1.000 76.7
psbI-trnS-GCT_p3 psbI-trnS-GCT CGTAATCCTGGACGTGAAGA GGTTTTTCGTACCGAGGGTT 205–214 1.000 76.6
psbI-trnS-GCT_p4 psbI-trnS-GCT CGTAATCCTGGACGTGAAGA TTTTTCGTACCGAGGGTTCG 203–212 1.000 75.8
psbI-trnS-GCT_p5 psbI-trnS-GCT CGTAATCCTGGACGTGAAGA GGAGATGGCTGAGTGGACTA 253–262 1.000 74.8
trnS-GCT-trnG-UCC_p1 trnS-GCT-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 931–943 1.000 54.8
trnS-GCT-trnG-UCC_p2 trnS-GCT-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 930–942 1.000 54.8
trnS-GCT-trnG-UCC_p3 trnS-GCT-trnG-UCC ACAAAAGCGGAAAGAGAGGG ACGAATCACACTTTTACCACT 991–1003 1.000 53.9
trnS-GCT-trnG-UCC_p4 trnS-GCT-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 934–946 1.000 53.8
trnS-GCT-trnG-UCC_p5 trnS-GCT-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 933–945 1.000 53.8
trnG-UCC-trnR-TCT_p1 trnG-UCC-trnR-TCT AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 319–391 1.000 67.6
trnG-UCC-trnR-TCT_p2 trnG-UCC-trnR-TCT CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 322–394 1.000 67.3
trnG-UCC-trnR-TCT_p3 trnG-UCC-trnR-TCT AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 325–397 1.000 66.9
trnG-UCC-trnR-TCT_p4 trnG-UCC-trnR-TCT CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 328–400 1.000 66.7
trnG-UCC-trnR-TCT_p5 trnG-UCC-trnR-TCT ACCAAAGTTTCACGTTCGGT AGAAGACCTCTGTCCTATCCA 389–461 1.000 65.7
trnR-TCT-atpA_p1 trnR-TCT-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCAGAAGCCCTTTT 360–366 1.000 67.3
trnR-TCT-atpA_p2 trnR-TCT-atpA GGTTCAAATCCTATTGGACGC TTCACTGAGGAAGCAGAAGC 366–372 1.000 66.6
trnR-TCT-atpA_p3 trnR-TCT-atpA GGTTCAAATCCTATTGGACGC AGGAAGCAGAAGCCCTTTTG 359–365 1.000 65.0
trnR-TCT-atpA_p4 trnR-TCT-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 358–364 1.000 65.0
trnR-TCT-atpA_p5 trnR-TCT-atpA TGGATAGGACAGAGGTCTTCT GAGGAAGCAGAAGCCCTTTT 395–401 1.000 64.3
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC TGTTTGGGACGCTGAAAGAA 208 1.000 80.4
atpA-atpF_p2 atpA-atpF GTCGCCTACTTGAAGTACGG TGTTTGGGACGCTGAAAGAA 206 1.000 80.4
atpA-atpF_p3 atpA-atpF CCGTCGCCTACTTGAAGTAC ATGTTTGGGACGCTGAAAGA 209 1.000 78.6
atpA-atpF_p4 atpA-atpF GTCGCCTACTTGAAGTACGG ATGTTTGGGACGCTGAAAGA 207 1.000 78.6
atpA-atpF_p5 atpA-atpF ACTTGAAGTACGGTACCGGT TGTTTGGGACGCTGAAAGAA 199 1.000 78.2

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
Ostryopsis davidiana NC_039130.1 159280 View on NCBI ↗
Ostryopsis intermedia NC_040000.1 159213 View on NCBI ↗