Markers + reference

Baphia

2 species · Fabaceae · Fabales

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Species 2
Genome length 156–162 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1 SSC 5271 0.3830 0.84 74.2 yes View details
ndhH SSC 1182 0.4828 0.84 80.4 yes View details
ndhA SSC 2303 0.4560 0.82 78.4 yes View details
ndhI-ndhG SSC 450 0.4739 0.90 79.1 yes View details
psaC SSC 246 0.5158 0.90 76.0 yes View details
ndhD SSC 1500 0.4809 0.80 79.4 yes View details
ccsA SSC 975 0.4701 0.82 80.1 yes View details
ndhF SSC 2238 0.4776 0.91 80.9 yes View details
ndhJ-trnF-GAA LSC 806 0.0851 0.93 86.0 yes View details
psbK-trnQ-UUG LSC 736 0.1219 0.93 84.7 yes View details
psbE-petL LSC 1201 0.1243 0.95 83.9 yes View details
trnL-UAA-trnT-UGU LSC 1032 0.0679 0.96 83.7 yes View details
trnG-UCC-trnS-GCU LSC 565 0.0788 0.94 82.5 yes View details
trnG-GCC-psbZ LSC 789 0.0896 0.93 81.9 yes View details
trnS-GGA-ycf3 LSC 267 0.0951 0.99 81.2 yes View details
rps3-rps19 LSC 519 0.1240 0.99 81.0 yes View details
petA-psbJ LSC 1129 0.0683 0.99 80.9 yes View details
trnL-UAG-rpl32 SSC 694 0.4327 0.86 80.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ndhJ-trnF-GAA_p1 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC GGGATAGCTCAGCTGGTAGA 929–946 1.000 88.9
ndhJ-trnF-GAA_p2 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CCTCGTGTCACCAGTTCAAA 893–910 1.000 88.7
ndhJ-trnF-GAA_p3 ndhJ-trnF-GAA TTGGATAGGATGGCCTTTGC CTGGTAGAGCAGAGGACTGA 917–934 1.000 87.9
ndhJ-trnF-GAA_p4 ndhJ-trnF-GAA ATGCCCGAAAGTTGGATAGG GGGATAGCTCAGCTGGTAGA 940–957 1.000 86.6
ndhJ-trnF-GAA_p5 ndhJ-trnF-GAA ATGCCCGAAAGTTGGATAGG CCTCGTGTCACCAGTTCAAA 904–921 1.000 86.4
trnL-UAA-trnT-UGU_p1 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GCGATGCTCTAACCTCTGAG 1082–1217 1.000 86.7
trnL-UAA-trnT-UGU_p2 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GCGATGCTCTAACCTCTGAG 1090–1225 1.000 86.1
trnL-UAA-trnT-UGU_p3 trnL-UAA-trnT-UGU ACCAATTTCGCCATATCCCC GGAATCGAACCGATGACCAT 1114–1249 1.000 85.6
trnL-UAA-trnT-UGU_p4 trnL-UAA-trnT-UGU TAGCGTCTACCAATTTCGCC GGAATCGAACCGATGACCAT 1122–1257 1.000 85.1
trnL-UAA-trnT-UGU_p5 trnL-UAA-trnT-UGU AGTCCGTAGCGTCTACCAAT GCGATGCTCTAACCTCTGAG 1096–1231 1.000 84.7
trnS-GGA-ycf3_p1 trnS-GGA-ycf3 TTCCAATGCTACGCCTTGAA TTCTCCTGAAGTTGTCGGAA 397–401 1.000 71.6
trnS-GGA-ycf3_p2 trnS-GGA-ycf3 TTCCAATGCTACGCCTTGAA TTTCTCCTGAAGTTGTCGGA 398–402 1.000 71.6
trnS-GGA-ycf3_p3 trnS-GGA-ycf3 TTCCAATGCTACGCCTTGAA TCTCCTGAAGTTGTCGGAAT 396–400 1.000 69.8
trnS-GGA-ycf3_p4 trnS-GGA-ycf3 GTGCGGAAAGAGAGGGATTC TTCTCCTGAAGTTGTCGGAA 450–454 1.000 69.7
trnS-GGA-ycf3_p5 trnS-GGA-ycf3 GTGCGGAAAGAGAGGGATTC TTTCTCCTGAAGTTGTCGGA 451–455 1.000 69.7
trnG-GCC-psbZ_p1 trnG-GCC-psbZ CGCCGATCCTCAAAAGAAGA TGGGCTCGGCTATATTACCA 2171 0.500 59.8
trnG-GCC-psbZ_p2 trnG-GCC-psbZ TCGCCGATCCTCAAAAGAAG TGGGCTCGGCTATATTACCA 2172 0.500 59.8
trnG-GCC-psbZ_p3 trnG-GCC-psbZ CGCCGATCCTCAAAAGAAGA CAACCACTCAGCCATCTCTC 2009 0.500 59.7
trnG-GCC-psbZ_p4 trnG-GCC-psbZ TCGCCGATCCTCAAAAGAAG CAACCACTCAGCCATCTCTC 2010 0.500 59.7
trnG-GCC-psbZ_p5 trnG-GCC-psbZ CGTTGTTTTTCGACCGGAAG TGGGCTCGGCTATATTACCA 2057 0.500 59.7
trnG-UCC-trnS-GCU_p1 trnG-UCC-trnS-GCU ACGAATCACACTTTTACCACT CAATCCGACGCTTTAGTCCA 634–826 1.000 59.8
trnG-UCC-trnS-GCU_p2 trnG-UCC-trnS-GCU ACGAATCACACTTTTACCACT AATCCGACGCTTTAGTCCAC 633–825 1.000 59.8
trnG-UCC-trnS-GCU_p3 trnG-UCC-trnS-GCU AGAACGAATCACACTTTTACCAC CAATCCGACGCTTTAGTCCA 637–829 1.000 58.7
trnG-UCC-trnS-GCU_p4 trnG-UCC-trnS-GCU GAACGAATCACACTTTTACCACT CAATCCGACGCTTTAGTCCA 636–828 1.000 58.7
trnG-UCC-trnS-GCU_p5 trnG-UCC-trnS-GCU GAACGAATCACACTTTTACCACT AATCCGACGCTTTAGTCCAC 635–827 1.000 58.7
psbK-trnQ-UUG_p1 psbK-trnQ-UUG GGTCCGGGTTTTTCTTGTCT GTCTTTCAAGTCGCACGTTG 1623 0.500 59.8
psbK-trnQ-UUG_p2 psbK-trnQ-UUG GGTCCGGGTTTTTCTTGTCT CCCTCTTCCTGTCCCCTAAA 1750 0.500 59.6
psbK-trnQ-UUG_p3 psbK-trnQ-UUG AGCAGCTTGCCAAACAAAAG GTCTTTCAAGTCGCACGTTG 1454 0.500 59.5
psbK-trnQ-UUG_p4 psbK-trnQ-UUG CTTACAGCAGCTTGCCAAAC GTCTTTCAAGTCGCACGTTG 1459 0.500 59.5
psbK-trnQ-UUG_p5 psbK-trnQ-UUG GGTCCGGGTTTTTCTTGTCT ACCTCCGAATAACAGGACCA 1129 0.500 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
Baphia leptostemma PV870744.1 161681 View on NCBI ↗
Baphia racemosa NC_047397.1 156237 View on NCBI ↗