Markers + reference

Xylia

2 species · Fabaceae · Fabales

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Species 2
Genome length 176–178 kb
Candidate markers 290
Primer pairs 85

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 7 remaining regions by MarkerSeek score (out of 290 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 861 0.0300 0.97 74.6 yes View details
accD-psaI LSC 589 0.0348 0.83 68.4 yes View details
psbJ-clpP LSC 911 0.0730 0.98 77.4 yes View details
clpP LSC 690 0.2445 0.98 80.4 yes View details
clpP-psbB LSC 733 0.1367 0.98 81.8 yes View details
rps11-rpl36 LSC 295 0.0272 1.00 53.9 yes View details
ycf1 IRb 5493 0.0134 0.99 46.9 yes View details
trnL-UAG-ndhF IRb 431 0.0932 0.92 79.0 yes View details
ndhF-rpl32 SSC 911 0.0432 0.99 69.8 yes View details
rpl32-trnL-UAG IRa 487 0.0409 0.85 66.7 yes View details
ycf1 IRa 5493 0.0134 0.99 46.9 no View details
psbE-psbF LSC 9 0.1111 1.00 77.0 yes View details
rbcL-accD LSC 979 0.0193 0.95 74.4 yes View details
ndhI-ndhG IRb 619 0.0217 0.97 74.1 yes View details
ndhG-ndhI IRa 619 0.0217 0.97 74.1 yes View details
ndhC-trnV-UAC LSC 625 0.0175 0.82 69.7 yes View details
rpl32 SSC 168 0.0595 1.00 68.3 yes View details
rpl36 LSC 114 0.0439 1.00 66.4 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGGATCCC 973–1279 1.000 78.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGGATCCC 972–1278 1.000 78.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAGGGATCCC 1027–1333 1.000 76.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TGGAAACGGAAAGAGAGGGA TGAATCAAACGAGGGATCCC 1032–1338 1.000 75.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 941–1247 1.000 75.6
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CTGGCCCTTTACTAATCGGG AGAAGGTCTACGGTTCGAGT 668–773 1.000 81.4
ndhC-trnV-UAC_p2 ndhC-trnV-UAC CTGGCCCTTTACTAATCGGG AAATGCACGTTGGGTCTGTA 736–841 1.000 80.8
ndhC-trnV-UAC_p3 ndhC-trnV-UAC CTGGCCCTTTACTAATCGGG AATGCACGTTGGGTCTGTAA 735–840 1.000 80.8
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CTGGCCCTTTACTAATCGGG ATGCACGTTGGGTCTGTAAA 734–839 1.000 80.8
ndhC-trnV-UAC_p5 ndhC-trnV-UAC CTGGCCCTTTACTAATCGGG ACGTTGGGTCTGTAAAGCAA 730–835 1.000 80.2
rbcL-accD_p1 rbcL-accD AGTCCTGAATTAGCTGCTGC TGGGTCTTCACTTACACTGG 1135–1174 1.000 74.4
rbcL-accD_p2 rbcL-accD AGTCCTGAATTAGCTGCTGC GGGTCTTCACTTACACTGGT 1134–1173 1.000 74.4
rbcL-accD_p3 rbcL-accD GAGGCTAGCAAATGGAGTCC TGGGTCTTCACTTACACTGG 1150–1189 1.000 74.4
rbcL-accD_p4 rbcL-accD GAGGCTAGCAAATGGAGTCC GGGTCTTCACTTACACTGGT 1149–1188 1.000 74.3
rbcL-accD_p5 rbcL-accD TTCGTGAGGCTAGCAAATGG TGGGTCTTCACTTACACTGG 1155–1194 1.000 72.6
accD-psaI_p1 accD-psaI GCTCCATGCTTTCTTTCCTT CCATTGCAATTGCCGGAAAT 597–696 1.000 72.3
accD-psaI_p2 accD-psaI GCTCCATGCTTTCTTTCCTT AAGAAGCCATTGCAATTGCC 603–702 1.000 71.6
accD-psaI_p3 accD-psaI GCTCCATGCTTTCTTTCCTTT CCATTGCAATTGCCGGAAAT 597–696 1.000 70.3
accD-psaI_p4 accD-psaI GCTCCATGCTTTCTTTCCTTT AAGAAGCCATTGCAATTGCC 603–702 1.000 69.7
accD-psaI_p5 accD-psaI GTGAGTTATTTCAGCTCCATGC CCATTGCAATTGCCGGAAAT 610–709 1.000 67.6
psbE-psbF_p1 psbE-psbF AACTGGCCGTTTTGATCCTT GAACAGCCAACCATCGTACT 116 1.000 79.9
psbE-psbF_p2 psbE-psbF ACTGGCCGTTTTGATCCTTT GAACAGCCAACCATCGTACT 115 1.000 79.9
psbE-psbF_p3 psbE-psbF AACTGGCCGTTTTGATCCTT AACAGCCAACCATCGTACTG 115 1.000 79.1
psbE-psbF_p4 psbE-psbF ACTGGCCGTTTTGATCCTTT AACAGCCAACCATCGTACTG 114 1.000 79.1
psbE-psbF_p5 psbE-psbF ACTGGCCGTTTTGATCCTTT TGAACAGCCAACCATCGTAC 116 1.000 79.1
psbJ-clpP_p1 psbJ-clpP AACTGGCCGTTTTGATCCTT TATCGACTCAACTTGCTGGC 2051 0.500 59.9
psbJ-clpP_p2 psbJ-clpP ACTGGCCGTTTTGATCCTTT TATCGACTCAACTTGCTGGC 2050 0.500 59.9
psbJ-clpP_p3 psbJ-clpP AACTGGCCGTTTTGATCCTT CCTGGGGAAGAAGATGCATC 2142 0.500 59.8
psbJ-clpP_p4 psbJ-clpP ACTGGCCGTTTTGATCCTTT CCTGGGGAAGAAGATGCATC 2141 0.500 59.8
psbJ-clpP_p5 psbJ-clpP ACTGGCCGTTTTGATCCTTT TGCTGTATCCGAACACATGG 1677 0.500 59.8

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
Xylia hoffmannii PV870689.1 175547 View on NCBI ↗
Xylia xylocarpa var. kerrii PX666091.1 178282 View on NCBI ↗