Markers + reference

Symplocos

7 species · Symplocaceae · Ericales

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Species 7
Genome length 157–157 kb
Candidate markers 272
Primer pairs 105

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1130 0.0071 1.00 46.6 yes View details
rps16-trnQ-UUG LSC 1438 0.0096 1.00 60.9 yes View details
trnE-UUC-trnT-GGU LSC 778 0.0139 1.00 58.7 yes View details
trnT-GGU-psbD LSC 1521 0.0074 1.00 55.0 yes View details
ycf3-trnS-GGA LSC 821 0.0097 1.00 57.6 yes View details
ycf4 LSC 555 0.0077 1.00 44.1 yes View details
petA-psbJ LSC 976 0.0167 0.98 53.8 yes View details
rpl20 LSC 354 0.0073 1.00 31.9 yes View details
rpl16 LSC 1453 0.0087 1.00 49.0 yes View details
ycf1 IRb 1054 0.0030 1.00 46.6 no View details
ndhF SSC 2253 0.0073 1.00 42.3 yes View details
ndhF-rpl32 SSC 775 0.0127 0.98 57.6 yes View details
ycf1 SSC 5622 0.0089 1.00 49.4 yes View details
trnS-GCU-trnG-GCC LSC 668 0.0098 0.99 66.5 yes View details
petN-psbM LSC 1151 0.0082 1.00 64.8 yes View details
ccsA-ndhD SSC 234 0.0122 1.00 63.0 yes View details
trnR-ACG-trnN-GUU IRb 590 0.0099 1.00 61.0 yes View details
trnN-GUU-trnR-ACG IRa 590 0.0099 1.00 61.0 yes View details
trnT-UGU-trnL-UAA LSC 875 0.0079 0.98 59.8 yes View details
trnF-GAA-ndhJ LSC 699 0.0108 1.00 58.4 yes View details
trnK-UUU-rps16 LSC 814 0.0088 1.00 55.6 yes View details
trnG-GCC-trnR-UCU LSC 260 0.0092 0.95 55.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAGGCGGAGGTTTTTAAGGA 703–909 1.000 76.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGCGGAGGTTTTTAAGGAA 702–908 1.000 76.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAGGCGGAGGTTTTTAAGGA 702–908 1.000 76.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGCGGAGGTTTTTAAGGAA 701–907 1.000 76.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC AGGCGGAGGTTTTTAAGGAA 717–923 1.000 75.7
rps16_p1 rps16 TACGAATCATCACTCCCCCG TGTACCGACTGAACCGATGA 1240–1246 1.000 70.0
rps16_p2 rps16 CATCACTCCCCCGCTTTTT TGTACCGACTGAACCGATGA 1233–1239 1.000 69.4
rps16_p3 rps16 TACGAATCATCACTCCCCCG ATGTACCGACTGAACCGATG 1241–1247 1.000 69.1
rps16_p4 rps16 CATCACTCCCCCGCTTTTT ATGTACCGACTGAACCGATG 1234–1240 1.000 68.5
rps16_p5 rps16 TACGAATCATCACTCCCCCG GTACCGACTGAACCGATGAT 1239–1245 1.000 66.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1341–1709 1.000 84.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1324–1692 1.000 83.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1342–1710 1.000 83.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1339–1707 1.000 82.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1338–1706 1.000 82.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACCGAAAGACCCTTTAACT 777–781 1.000 53.8
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 739–743 1.000 53.8
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 742–746 1.000 52.7
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 741–745 1.000 52.7
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AAACCGAAAGACCCTTTAACT 778–782 1.000 52.6
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG TCTGGAAAAATTTGCGTCCA 388–411 1.000 68.8
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG TCTGGAAAAATTTGCGTCCA 391–414 1.000 68.5
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 340–363 1.000 67.7
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 343–366 1.000 67.4
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU AGCCTTCCAAGCTAACGATG TCTGGAAAAATTTGCGTCCAA 388–411 1.000 66.9
petN-psbM_p1 petN-psbM CGTAGTATGGGGAAGAAGCG TGCTACTGCACTGTTCATTCT 1257–1258 1.000 69.1
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1312–1313 1.000 68.9
petN-psbM_p3 petN-psbM TAGTATGGGGAAGAAGCGGA TGCTACTGCACTGTTCATTCT 1255–1256 1.000 66.4
petN-psbM_p4 petN-psbM GTAGTATGGGGAAGAAGCGG TGCTACTGCACTGTTCATTCT 1256–1257 1.000 65.9
petN-psbM_p5 petN-psbM CGTAGTATGGGGAAGAAGCG TGCTACTGCACTGTTCATTC 1257–1258 1.000 64.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Symplocos chinensis f. pilosa MW307951.1 156961 View on NCBI ↗
Symplocos coreana NC_058287.1 157365 View on NCBI ↗
Symplocos ovatilobata NC_036489.1 157417 View on NCBI ↗
Symplocos prunifolia NC_058288.1 157204 View on NCBI ↗
Symplocos stellaris PP056251.1 157083 View on NCBI ↗
Symplocos tanakana NC_058289.1 156971 View on NCBI ↗
Symplocos tetragona NC_066798.1 157271 View on NCBI ↗