Markers + reference

Symphoricarpos

2 species · Caprifoliaceae · Dipsacales

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Species 2
Genome length 156–156 kb
Candidate markers 267
Primer pairs 60

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 339 0.0000 1.00 34.6 yes View details
psbA LSC 1062 0.0000 1.00 40.0 yes View details
rpl2 LSC 1488 0.0081 1.00 49.1 yes View details
rpl23 LSC 285 0.0140 1.00 46.2 yes View details
trnN-GUU-ndhF IRb 1056 0.0064 0.89 65.4 yes View details
rpl2-rpl23 LSC 18 0.0556 1.00 68.9 yes View details
trnI-CAU-trnH-GUG IRa 286 0.0000 1.00 68.7 no View details
ycf1-trnN-GUU IRa 1611 0.0000 0.91 62.3 yes View details
ycf1 SSC 5460 0.0000 0.98 54.7 yes View details
matK LSC 1515 0.0000 1.00 40.0 yes View details
matK-trnK-UUU LSC 721 0.0000 1.00 40.0 yes View details
rps16 LSC 1121 0.0000 1.00 40.0 yes View details
trnS-GCU-trnG-UCC LSC 730 0.0000 1.00 40.0 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 60 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTCTAGACCTAGCCGCTCTT 405 1.000 78.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTCTAGACCTAGCCGCTCTT 419 1.000 78.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTCTAGACCTAGCCGCTCTT 418 1.000 78.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTCTAGACCTAGCCGCTCTT 420 1.000 78.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTTCCCTCTAGACCTAGCCG 410 1.000 78.4
psbA_p1 psbA CAATGGCGCCCTCTTGATAA TGGGAGTCCCTGAGAATTCA 1183 1.000 74.7
psbA_p2 psbA AATGGCGCCCTCTTGATAAA TGGGAGTCCCTGAGAATTCA 1182 1.000 73.8
psbA_p3 psbA ATGGCGCCCTCTTGATAAAA TGGGAGTCCCTGAGAATTCA 1181 1.000 73.8
psbA_p4 psbA CAATGGCGCCCTCTTGATAA AATTCGTGTGCTTGGGAGTC 1195 1.000 73.6
psbA_p5 psbA GGCGCCCTCTTGATAAAACA TGGGAGTCCCTGAGAATTCA 1179 1.000 72.9
matK_p1 matK CCATGCTACATCAACGTTTCAG CCCCCAACCCTCTACTTTTT 1672 1.000 56.0
matK_p2 matK CCATGCTACATCAACGTTTCA CCCCCAACCCTCTACTTTTT 1672 1.000 55.3
matK_p3 matK CCATGCTACATCAACGTTTCAG CCCTGTTTTGACTGTATCGC 1712 1.000 54.5
matK_p4 matK CCATGCTACATCAACGTTTCAG CCCCAACCCTCTACTTTTTGT 1671 1.000 54.0
matK_p5 matK CCATGCTACATCAACGTTTCAG TGACTGTATCGCACTATGCA 1704 1.000 54.0
matK-trnK-UUU_p1 matK-trnK-UUU TGAGACCCATCTAGCTCGAA AACGGTAGAGTACTCGGCTT 786 1.000 75.2
matK-trnK-UUU_p2 matK-trnK-UUU TGAGACCCATCTAGCTCGAA ACGGTAGAGTACTCGGCTTT 785 1.000 75.2
matK-trnK-UUU_p3 matK-trnK-UUU TTGAGACCCATCTAGCTCGA AACGGTAGAGTACTCGGCTT 787 1.000 75.2
matK-trnK-UUU_p4 matK-trnK-UUU TTGAGACCCATCTAGCTCGA ACGGTAGAGTACTCGGCTTT 786 1.000 75.2
matK-trnK-UUU_p5 matK-trnK-UUU GTTGAGACCCATCTAGCTCG ACGGTAGAGTACTCGGCTTT 787 1.000 74.6
rps16_p1 rps16 GTGTTGGATTGGCACTACAT TGGACAGCTGAACCAATGAC 1318 1.000 63.3
rps16_p2 rps16 AGGTTTAGGTGGGGAAATCA TGGACAGCTGAACCAATGAC 1288 1.000 63.2
rps16_p3 rps16 GTGTTGGATTGGCACTACAT GGACAGCTGAACCAATGACT 1317 1.000 62.6
rps16_p4 rps16 AGGTTTAGGTGGGGAAATCA GGACAGCTGAACCAATGACT 1287 1.000 62.5
rps16_p5 rps16 AGGTTTAGGTGGGGAAATCAA TGGACAGCTGAACCAATGAC 1288 1.000 61.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA TGAATCAAACCGAAAGATCCCT 849 1.000 61.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC GCTCGTACAACGGATTAGCA TGAATCAAACCGAAAGATCCCT 862 1.000 60.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACCGAAAGATCCCT 898 1.000 60.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCTCGTACAACGGATTAGC TGAATCAAACCGAAAGATCCCT 863 1.000 59.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TGGAAACGGAAAGAGAGGGA TGAATCAAACCGAAAGATCCCT 903 1.000 59.4

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
Symphoricarpos orbiculatus NC_047443.1 156044 View on NCBI ↗
Symphoricarpos sinensis NC_054265.1 155738 View on NCBI ↗