Markers + reference

Styphnolobium

4 species · Fabaceae · Fabales

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Species 4
Genome length 159–159 kb
Candidate markers 265
Primer pairs 85

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 879 0.0028 1.00 52.8 yes View details
clpP LSC 2028 0.0012 1.00 49.2 yes View details
rps11-rpl36 LSC 512 0.0010 1.00 32.8 yes View details
trnV-GAC-rrn16S IRb 222 0.0225 1.00 42.6 yes View details
rrn16S IRb 1491 0.0007 1.00 30.4 no View details
ycf1 IRb 357 0.0000 1.00 22.2 yes View details
ndhA SSC 2325 0.0022 1.00 44.5 yes View details
ycf1 SSC 5490 0.0009 1.00 43.7 no View details
rrn16S IRa 1491 0.0007 1.00 30.4 yes View details
trnC-GCA-petN LSC 1217 0.0014 0.99 52.2 yes View details
rbcL-accD LSC 971 0.0005 1.00 51.8 yes View details
trnS-GCU-trnT-CGU LSC 620 0.0016 1.00 50.7 yes View details
atpB-rbcL LSC 753 0.0009 1.00 50.1 yes View details
trnT-GGU-psbD LSC 1485 0.0003 1.00 49.8 yes View details
rps15-ycf1 SSC 321 0.0000 0.99 49.6 yes View details
trnP-GGG-psaJ LSC 743 0.0000 1.00 49.4 yes View details
rpl16 LSC 1534 0.0000 1.00 49.4 yes View details
psbE-petL LSC 1373 0.0004 1.00 46.9 yes View details
atpH-atpI LSC 1374 0.0004 1.00 46.8 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTACCGATGGTATGGACGA AACAAGGCGCTCAACCTAC 1065–1075 1.000 67.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCTACCGATGGTATGGACGA GAACAAGGCGCTCAACCTAC 1066–1076 1.000 66.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTACCGATGGTATGGACGA GAACAAGGCGCTCAACCTA 1066–1076 1.000 66.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCA AACAAGGCGCTCAACCTAC 1061–1071 1.000 66.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 ACCGATGGTATGGACGAATC AACAAGGCGCTCAACCTAC 1062–1072 1.000 66.2
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA GGGGTCCATAGAACGAATCG 703–713 1.000 79.1
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC GGGGTCCATAGAACGAATCG 702–712 1.000 79.1
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA GGTCCATAGAACGAATCGCA 701–711 1.000 78.6
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC GGTCCATAGAACGAATCGCA 700–710 1.000 78.5
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU ACGGAAAGAGAGGGATTCGA GGGGTCCATAGAACGAATCG 756–766 1.000 77.9
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ACAAGCGGTATTCAAGCTCT 1465–1485 1.000 74.8
atpH-atpI_p2 atpH-atpI GATCCCTTCTACAGCTTGCC ACAAGCGGTATTCAAGCTCT 1550–1570 1.000 74.7
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA ACAAGCGGTATTCAAGCTCT 1466–1486 1.000 73.6
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TAGGTGAATCCATGGAAGGC 1416–1436 1.000 72.7
atpH-atpI_p5 atpH-atpI GATCCCTTCTACAGCTTGCC TAGGTGAATCCATGGAAGGC 1501–1521 1.000 72.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC TTAAAGCAGCCCAAGCAAGA 1314–1336 1.000 81.0
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 1258–1280 1.000 80.9
trnC-GCA-petN_p3 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC CAGCCCAAGCAAGACTTACT 1308–1330 1.000 79.6
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 1252–1274 1.000 79.4
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 1276–1298 1.000 78.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CACAAAAACGAAACGGTCCC 1635–1636 1.000 78.3
trnT-GGU-psbD_p2 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCACAAAAACGAAACGGTCC 1636–1637 1.000 78.3
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCCACAAAAACGAAACGGTC 1637–1638 1.000 78.3
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CACAAAAACGAAACGGTCCC 1638–1639 1.000 78.1
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCACAAAAACGAAACGGTCC 1639–1640 1.000 78.1
atpB-rbcL_p1 atpB-rbcL CCTGGGGGAAAAGCTACATC AACACCAGCTTTGAACCCAA 938 1.000 78.6
atpB-rbcL_p2 atpB-rbcL CTGGGGGAAAAGCTACATCC AACACCAGCTTTGAACCCAA 937 1.000 78.6
atpB-rbcL_p3 atpB-rbcL GGGGGAAAAGCTACATCCAG AACACCAGCTTTGAACCCAA 935 1.000 78.6
atpB-rbcL_p4 atpB-rbcL AAGCTACATCCAGTACCGGA AACACCAGCTTTGAACCCAA 928 1.000 77.8
atpB-rbcL_p5 atpB-rbcL ATTTGAGCGATACGTCCCAG AACACCAGCTTTGAACCCAA 902 1.000 77.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Styphnolobium japonicum f. oligophyllum ON571618.1 158739 View on NCBI ↗
Styphnolobium japonicum f. pendulum ON571617.1 158645 View on NCBI ↗
Styphnolobium japonicum f. violaceum KY872756.1 158837 View on NCBI ↗
Styphnolobium japonicum var. japonicum NC_045071.1 158738 View on NCBI ↗