Markers + reference

Gymnosporia

2 species · Celastraceae · Celastrales

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Species 2
Genome length 159–159 kb
Candidate markers 276
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnQ-UUG-psbK LSC 357 0.0056 1.00 44.9 yes View details
trnS-GCU-trnG-UCC LSC 840 0.0024 1.00 53.4 yes View details
rpoB-trnC-GCA LSC 973 0.0041 1.00 61.1 yes View details
psbC-trnS-UGA LSC 242 0.0000 1.00 26.7 yes View details
ycf3-trnS-GGA LSC 931 0.0043 1.00 57.4 yes View details
trnM-CAU-atpE LSC 296 0.0101 1.00 54.6 yes View details
psbE-petL LSC 1134 0.0053 1.00 61.9 yes View details
rpl16 LSC 1516 0.0046 1.00 47.0 yes View details
rrn16-trnI-GAU IRb 295 0.0305 1.00 70.0 yes View details
trnI-GAU-rrn16 IRa 295 0.0305 1.00 70.0 yes View details
ndhJ-ndhK LSC 127 0.0157 1.00 61.6 yes View details
psaA-ycf3 LSC 684 0.0029 1.00 60.7 yes View details
trnH-GUG-psbA LSC 533 0.0038 0.99 60.6 no View details
psbZ-trnG-GCC LSC 692 0.0029 1.00 60.4 yes View details
trnT-UGU LSC 73 0.0137 1.00 60.4 yes View details
rpl20-rps12 LSC 765 0.0026 1.00 60.3 yes View details
ndhD SSC 1500 0.0027 1.00 60.3 yes View details
atpH-atpI LSC 1266 0.0024 1.00 60.1 yes View details
petN-psbM LSC 847 0.0024 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACAGATCCAGATCAAACTAAAGA 428 1.000 40.4
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AAACAGATCCAGATCAAACT 430 1.000 40.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AAAACAGATCCAGATCAAACT 431 1.000 40.4
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC ACAGATCCAGATCAAACTAAAGA 437 1.000 40.4
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GAATAGCGGGACCAAAACCC AAACAGATCCAGATCAAACT 439 1.000 40.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CCCAGGGACCCCTTAACTAT 945–946 1.000 78.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CCCAGGGACCCCTTAACTAT 944–945 1.000 78.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA CCCAGGGACCCCTTAACTAT 999–1000 1.000 77.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC CCCAGGGACCCCTTAACTAT 947–948 1.000 75.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGACGCTTTAGTCCACTCAG CCCAGGGACCCCTTAACTAT 940–941 1.000 75.6
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1352 1.000 75.2
atpH-atpI_p2 atpH-atpI CAGCAGCAATAACAGAAGCG TTTTTGCAACTTTAGCCGCG 1362 1.000 74.7
atpH-atpI_p3 atpH-atpI AACAGAAGCGGCAGAAATCA TAGGTGAATCCATGGAGGGT 1325 1.000 74.7
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TAGGTGAATCCATGGAGGGT 1335 1.000 74.1
atpH-atpI_p5 atpH-atpI AATAGAAGCAAGACCGACGG TTTTTGCAACTTTAGCCGCG 1388 1.000 73.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC GCTTTTGTTGATCAGGCGAC 1083 1.000 79.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC CCGGATTTGAACTGGGGAAA 1061 1.000 79.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GTTCCCTCATTTCCATCCCC AGCTTTTGTTGATCAGGCGA 1084 1.000 78.9
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CGTTCCCTCATTTCCATCCC GCTTTTGTTGATCAGGCGAC 1084 1.000 77.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CGTTCCCTCATTTCCATCCC CCGGATTTGAACTGGGGAAA 1062 1.000 77.1
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT CGATCAGTCAAAGTCAGGGC 965 1.000 73.9
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT GATCAGTCAAAGTCAGGGCG 964 1.000 73.9
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT CAGTCAAAGTCAGGGCGATA 961 1.000 73.6
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGATCAGTCAAAGTCAGGG 966 1.000 72.9
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT GATCAGTCAAAGTCAGGGCG 903 1.000 72.3
psbC-trnS-UGA_p1 psbC-trnS-UGA AGCCTGTTCTCTCCATGACT GGTTGATAGCTCCGGTCTTG 351 1.000 79.1
psbC-trnS-UGA_p2 psbC-trnS-UGA TGAGCCTGTTCTCTCCATGA GGTTGATAGCTCCGGTCTTG 353 1.000 79.1
psbC-trnS-UGA_p3 psbC-trnS-UGA AGCCTGTTCTCTCCATGACT GATGGCCGAGTGGTTGATAG 362 1.000 78.6
psbC-trnS-UGA_p4 psbC-trnS-UGA TGAGCCTGTTCTCTCCATGA GATGGCCGAGTGGTTGATAG 364 1.000 78.5
psbC-trnS-UGA_p5 psbC-trnS-UGA AGCCTGTTCTCTCCATGACT GGGTTCGAATCCCTCTCTCT 297 1.000 77.9

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
Gymnosporia graciliramula NC_065704.1 158697 View on NCBI ↗
Gymnosporia orbiculata NC_065705.1 158748 View on NCBI ↗