Markers + reference

Zygia

2 species · Fabaceae · Fabales

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Species 2
Genome length 164–177 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1060 0.0525 0.99 74.4 yes View details
rps16-trnQ-UUG LSC 702 0.0608 0.94 82.1 yes View details
trnQ-UUG-psbK LSC 592 0.0550 0.98 76.1 yes View details
trnS-GCU-trnG-UCC LSC 766 0.1472 0.99 86.7 yes View details
trnT-UGU-trnL-UAA LSC 1242 0.0726 0.99 88.1 yes View details
accD LSC 2313 0.0398 0.74 64.3 yes View details
rps12-clpP LSC 298 0.0917 0.81 70.0 yes View details
clpP LSC 2081 0.0639 0.99 73.9 yes View details
trnN-GUU-ccsA IRb 2355 0.0399 0.89 68.2 yes View details
rps8-rpl14 LSC 297 0.0505 1.00 81.3 yes View details
trnL-UAG-rpl32 SSC 451 0.0690 0.93 77.2 yes View details
ndhD-psaC SSC 119 0.0513 0.98 76.6 yes View details
atpF-atpH LSC 708 0.0284 0.99 75.0 yes View details
rpl22-rps19 LSC 170 0.0701 0.92 73.2 yes View details
ndhC-trnV-UAC LSC 931 0.0325 0.96 73.0 yes View details
trnR-UCU-atpA LSC 524 0.0547 0.52 72.6 yes View details
psbL-psbF LSC 22 0.0455 1.00 72.6 yes View details
rpl2-rpl23 IRb 18 0.0556 1.00 72.5 yes View details
rpl23-rpl2 IRa 18 0.0556 1.00 72.5 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 1295–1610 1.000 83.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 1433–1748 1.000 83.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 1434–1749 1.000 83.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG AAGCTAACGGATCGTGGAAC 1844–2160 1.000 83.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCTGGATCAGTCGTGG TGGGTATGTTGCTGCCATTT 1917–2233 1.000 82.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 782–784 1.000 87.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 770–772 1.000 86.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 783–785 1.000 84.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG AAATAAAAATGGGGCGTGGC 839–841 1.000 84.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTTTAC GAGGTTCGAATCCTTCCGTC 774–776 1.000 84.5
trnQ-UUG-psbK_p1 trnQ-UUG-psbK ATATGCTCTCTCTGGGACGG AGCAGCTTGCCAAACAAAAG 846 0.500 56.6
trnQ-UUG-psbK_p2 trnQ-UUG-psbK ATATGCTCTCTCTGGGACGG CTTACAGCAGCTTGCCAAAC 851 0.500 56.6
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CTCTCTGGGACGGAAGGATT AGCAGCTTGCCAAACAAAAG 839 0.500 55.5
trnQ-UUG-psbK_p4 trnQ-UUG-psbK CTCTCTGGGACGGAAGGATT CTTACAGCAGCTTGCCAAAC 844 0.500 55.5
trnQ-UUG-psbK_p5 trnQ-UUG-psbK TCTCTGGGACGGAAGGATTC AGCAGCTTGCCAAACAAAAG 838 0.500 55.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGGATCCC 878–1271 1.000 82.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGGATCCC 877–1270 1.000 82.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAGGGATCCC 932–1325 1.000 81.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 846–1239 1.000 80.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 845–1238 1.000 80.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CATTCACTCGGGAAGCAGAA 388–638 1.000 72.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AAGACATTCACTCGGGAAGC 392–642 1.000 72.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCAGAAGCCCTTTTGA 378–628 1.000 69.8
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ATTCACTCGGGAAGCAGAAG 387–637 1.000 69.7
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT CATTCACTCGGGAAGCAGAA 423–673 1.000 69.0
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGGCTGGTTGTAGCATTAG 826–842 1.000 78.0
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AGGCAGAGGGAAAAATACGG 893–909 1.000 77.8
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATACGGGG 891–907 1.000 76.3
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCAGAGGGAAAAATACGGG 892–908 1.000 76.3
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CCGAGGCAGAGGGAAAAATA 896–912 1.000 75.5

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
Zygia conzattii PV870700.1 164298 View on NCBI ↗
Zygia longifolia PV870728.1 177302 View on NCBI ↗