Markers + reference

Spatholobus

2 species · Fabaceae · Fabales

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Species 2
Genome length 151–152 kb
Candidate markers 256
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 10 remaining regions by MarkerSeek score (out of 256 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-psbZ LSC 802 0.0503 0.94 78.6 yes View details
psbD-trnT-GGU LSC 1401 0.0476 0.96 76.8 yes View details
psbM-petN LSC 741 0.0410 0.99 69.0 yes View details
petN-trnC-GCA LSC 1079 0.0393 0.97 76.3 yes View details
atpI-atpH LSC 1252 0.0347 0.97 70.2 yes View details
trnG-UCC-trnS-GCU LSC 458 0.1142 0.96 81.4 yes View details
accD-psaI LSC 329 0.0568 0.96 77.3 yes View details
petA-psbL LSC 1025 0.0339 0.98 70.1 yes View details
ycf2 IRb 6912 0.0122 0.99 49.6 yes View details
ycf1 SSC 5394 0.0327 1.00 56.6 yes View details
trnL-UAG-rpl32 SSC 469 0.0649 0.99 73.4 yes View details
ycf1 IRa 489 0.0143 1.00 52.7 no View details
ycf2 IRa 6912 0.0089 0.99 47.6 no View details
rps4-trnS-GGA LSC 219 0.0639 1.00 78.9 yes View details
trnH-GUG-psbA LSC 293 0.0636 0.97 76.8 yes View details
trnP-UGG-psaJ LSC 217 0.0691 1.00 76.2 yes View details
trnE-UUC-trnY-GUA LSC 64 0.0781 1.00 75.5 yes View details
cemA-petA LSC 193 0.0737 0.98 73.9 yes View details
psaI-ycf4 LSC 199 0.0754 1.00 73.6 yes View details
trnS-GGA-ycf3 LSC 258 0.0412 0.94 73.2 yes View details
trnT-UGU-rps4 LSC 283 0.0471 0.98 73.1 yes View details
psaC-ndhD SSC 121 0.0579 1.00 73.0 yes View details
psbI-psbK LSC 480 0.0390 0.96 72.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGAGCTAACCTTGGTATGG 411–412 1.000 82.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGAGCTAACCTTGGTATGG 425–426 1.000 82.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGAGCTAACCTTGGTATGG 424–425 1.000 82.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGAGCTAACCTTGGTATGG 426–427 1.000 82.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GATTTAGCTGCGATCGAAGC 353–354 1.000 80.8
trnT-UGU-rps4_p1 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC AGGTCCTCTGTAACGTGACA 362–368 1.000 83.3
trnT-UGU-rps4_p2 trnT-UGU-rps4 ATGGTCATCGGTTCGAATCC AGGTCCTCTGTAACGTGACA 330–336 1.000 82.8
trnT-UGU-rps4_p3 trnT-UGU-rps4 CCGCTTAGCTCAGAGGTTAG AGGTCCTCTGTAACGTGACA 370–376 1.000 80.2
trnT-UGU-rps4_p4 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC AACGAGGTCCTCTGTAACGT 366–372 1.000 80.2
trnT-UGU-rps4_p5 trnT-UGU-rps4 CTCAGAGGTTAGAGCATCGC AGTCCTGGTAAAGACCCCAG 403–409 1.000 80.1
rps4-trnS-GGA_p1 rps4-trnS-GGA TGACTCTTCACCCATTCCAA GTAGGAAAGATGGCCGAGTG 426–431 1.000 69.4
rps4-trnS-GGA_p2 rps4-trnS-GGA TTGACTCTTCACCCATTCCA GTAGGAAAGATGGCCGAGTG 427–432 1.000 69.4
rps4-trnS-GGA_p3 rps4-trnS-GGA TGACTCTTCACCCATTCCAA CCGGTTTCTGGGCATCATTA 447 0.500 46.5
rps4-trnS-GGA_p4 rps4-trnS-GGA TTGACTCTTCACCCATTCCA CCGGTTTCTGGGCATCATTA 448 0.500 46.5
rps4-trnS-GGA_p5 rps4-trnS-GGA TTGACTCTTCACCCATTCCAA CCGGTTTCTGGGCATCATTA 448 0.500 44.6
trnS-GGA-ycf3_p1 trnS-GGA-ycf3 TTCCAATGCTACGCCTTGAA TTCTCCTGAAGTTGTCGGAA 377–392 1.000 71.0
trnS-GGA-ycf3_p2 trnS-GGA-ycf3 TTCCAATGCTACGCCTTGAA TTTCTCCTGAAGTTGTCGGA 378–393 1.000 71.0
trnS-GGA-ycf3_p3 trnS-GGA-ycf3 TCGGAAAGAGAGGGATTCGA TTCTCCTGAAGTTGTCGGAA 428–443 1.000 70.8
trnS-GGA-ycf3_p4 trnS-GGA-ycf3 TCGGAAAGAGAGGGATTCGA TTTCTCCTGAAGTTGTCGGA 429–444 1.000 70.8
trnS-GGA-ycf3_p5 trnS-GGA-ycf3 TCGGAAAGAGAGGGATTCGA TCTCCTGAAGTTGTCGGAAT 427–442 1.000 69.0
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CTTGAGGTCACGGGTTCAAA CAACCACTCAGCCATCTCTC 1565–1584 1.000 85.5
trnG-GCC-psbZ_p2 trnG-GCC-psbZ CGATCATAGGAGGGTCCCTT CAACCACTCAGCCATCTCTC 1725–1744 1.000 85.1
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGTTGTTTTTCGACCGGAAG CCTCGATCCATGCCTCAAAA 1696–1715 1.000 85.1
trnG-GCC-psbZ_p4 trnG-GCC-psbZ CGTTGTTTTTCGACCGGAAG TCGATCCATGCCTCAAAAGG 1694–1713 1.000 85.1
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTTGTTTTTCGACCGGAAG CAACCACTCAGCCATCTCTC 1899–1917 1.000 84.8
psbD-trnT-GGU_p1 psbD-trnT-GGU AATTTACCAAGAGCTATAGTCA GGCGTAAGTCATCGGTTCAA 1432–1460 1.000 46.7
psbD-trnT-GGU_p2 psbD-trnT-GGU AATTTACCAAGAGCTATAGTCA GTGGTAGAGTAACGCCATGG 1455–1483 1.000 46.6
psbD-trnT-GGU_p3 psbD-trnT-GGU AATTTACCAAGAGCTATAGTCA TCAGTGGTAGAGTAACGCCA 1458–1486 1.000 46.6
psbD-trnT-GGU_p4 psbD-trnT-GGU AAATTTACCAAGAGCTATAGTCA GTGGTAGAGTAACGCCATGG 1456–1484 1.000 46.6
psbD-trnT-GGU_p5 psbD-trnT-GGU AAATTTACCAAGAGCTATAGTCA TCAGTGGTAGAGTAACGCCA 1459–1487 1.000 46.6

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
Spatholobus pulcher NC_049094.1 151099 View on NCBI ↗
Spatholobus suberectus NC_048966.1 152173 View on NCBI ↗