Markers + reference

Strombocarpa

3 species · Fabaceae · Fabales

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Species 3
Genome length 161–162 kb
Candidate markers 264
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1344 0.0179 1.00 46.6 yes View details
rps16-trnQ-UUG LSC 782 0.0196 1.00 56.0 yes View details
trnT-GGU-psbD LSC 1539 0.0091 1.00 52.6 yes View details
psbZ-trnG-UCC LSC 598 0.0167 1.00 62.4 yes View details
trnT-UGU-trnL-UAA LSC 1250 0.0080 1.00 51.6 yes View details
trnL-UAA-trnF-GAA LSC 405 0.0181 1.00 54.3 yes View details
ndhC-trnV-UAC LSC 999 0.0160 1.00 60.0 yes View details
accD-psaI LSC 565 0.0224 1.00 54.5 yes View details
clpP LSC 2006 0.0063 1.00 40.4 yes View details
ndhA SSC 2526 0.0048 1.00 48.2 yes View details
ycf1 SSC 5568 0.0077 0.98 49.7 yes View details
trnC-GCA-petN LSC 1296 0.0077 1.00 62.7 yes View details
atpH-atpI LSC 1406 0.0043 1.00 58.9 yes View details
trnM-CAU-atpE LSC 265 0.0226 1.00 57.0 yes View details
petN-psbM LSC 1199 0.0095 1.00 55.8 yes View details
ycf2 IRb 5591 0.0004 1.00 55.2 yes View details
ycf2 IRa 5591 0.0004 1.00 55.2 yes View details
petA-psbJ LSC 1319 0.0045 1.00 53.2 yes View details
trnQ-UUG-psbK LSC 677 0.0108 1.00 52.8 yes View details
psbI-trnS-GCU LSC 272 0.0245 1.00 52.7 yes View details
ycf4-cemA LSC 419 0.0095 1.00 52.4 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 CCTTTCTGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1585–1624 1.000 82.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAGCTAACGGATCGTGGAAC 2130–2168 1.000 82.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG TGAGGTTGCGAATACGAGTG 1932–1971 1.000 82.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1723–1762 1.000 82.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGGCCAAGGATCGAAGATTT AAGCTAACGGATCGTGGAAC 2744–2788 1.000 81.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 831–862 1.000 85.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 833–864 1.000 84.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 819–850 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 834–865 1.000 83.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 832–863 1.000 82.7
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG AGGCTTCAGGTAATTTCGCG 834–845 1.000 75.4
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG GGCTTCAGGTAATTTCGCGA 833–844 1.000 75.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA AGGCTTCAGGTAATTTCGCG 792–803 1.000 73.7
trnQ-UUG-psbK_p4 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA GGCTTCAGGTAATTTCGCGA 791–802 1.000 73.7
trnQ-UUG-psbK_p5 trnQ-UUG-psbK AATGGATATGCTCTGGGACG AGGCTTCAGGTAATTTCGCG 838–849 1.000 72.2
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 339–368 1.000 80.9
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 340–369 1.000 80.9
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA TTTTTCGTACCGAGGGTTCG 302–331 1.000 79.5
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA GACTAAAGCGTCGGATTGCT 337–366 1.000 78.1
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCCGGACGTGAAGAA CTGAGTGGACTAAAGCGTCG 344–373 1.000 77.9
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTGCAACTTTAGCTGCGG 1518–1527 1.000 81.2
atpH-atpI_p2 atpH-atpI CAATAGAAGCAAGCCCGACA TTTTGCAACTTTAGCTGCGG 1519–1528 1.000 79.3
atpH-atpI_p3 atpH-atpI CCTTCTACAGCTTGACCTGC TTTTGCAACTTTAGCTGCGG 1565–1574 1.000 79.2
atpH-atpI_p4 atpH-atpI TCCCTTCTACAGCTTGACCT TTTTGCAACTTTAGCTGCGG 1567–1576 1.000 78.7
atpH-atpI_p5 atpH-atpI CCCTTCTACAGCTTGACCTG TTTTGCAACTTTAGCTGCGG 1566–1575 1.000 78.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1336–1362 1.000 83.0
trnC-GCA-petN_p2 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGCCCAAGCGAGACTTACTA 1388–1414 1.000 82.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 1397–1423 1.000 81.4
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCATACTACGAGGG 1387–1413 1.000 81.2
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG AGAGTCCACTTCTTCCCCAT 1449–1475 1.000 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Strombocarpa burkartii PP646452.1 162104 View on NCBI ↗
Strombocarpa strombulifera OP672366.1 160569 View on NCBI ↗
Strombocarpa tamarugo NC_060845.1 161575 View on NCBI ↗