Markers + reference

Cheniella

15 species · Fabaceae · Fabales

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Species 15
Genome length 157–157 kb
Candidate markers 270
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 375 0.0166 1.00 52.8 yes View details
trnQ-UUG-psbK LSC 446 0.0035 1.00 47.9 yes View details
trnT-GGU-psbD LSC 1378 0.0063 0.99 63.9 yes View details
psbE-petL LSC 1326 0.0041 0.99 60.2 yes View details
petD-rpoA LSC 241 0.0182 0.99 55.2 yes View details
ycf1 IRb 370 0.0048 0.99 28.9 no View details
ndhF SSC 2244 0.0013 1.00 32.4 yes View details
ndhF-rpl32 SSC 1046 0.0091 1.00 69.6 yes View details
rpl32-trnL-UAG SSC 564 0.0127 0.99 75.0 yes View details
ycf1 SSC 5157 0.0042 0.99 44.0 yes View details
ycf1-ndhF SSC 116 0.0857 0.68 68.3 yes View details
ndhG-ndhI SSC 519 0.0074 1.00 67.6 yes View details
trnK-UUU-rps16 LSC 985 0.0027 1.00 63.8 yes View details
trnT-UGU-trnL-UAA LSC 1017 0.0026 0.99 63.5 yes View details
rps16-trnQ-UUG LSC 641 0.0056 1.00 62.3 yes View details
atpF-atpH LSC 528 0.0037 0.98 61.6 yes View details
clpP LSC 2050 0.0036 1.00 61.5 yes View details
trnC-GCA-petN LSC 1301 0.0034 0.99 60.5 yes View details
psbZ-trnG-GCC LSC 619 0.0050 1.00 59.4 yes View details
rps3-rps19 LSC 956 0.0027 1.00 58.7 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 443–464 1.000 83.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 457–478 1.000 82.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 456–477 1.000 82.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 458–479 1.000 82.8
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGGTCGAGGCTCCATCTATA 424–445 1.000 82.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG AAAAAGGCGCTCAACCTACA 1110–1137 1.000 79.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA AAAAAGGCGCTCAACCTACA 1111–1138 1.000 79.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA AAAAAGGCGCTCAACCTACA 1108–1135 1.000 77.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG CTTGAAAAAGGCGCTCAACC 1114–1141 1.000 77.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 GAGTCGCACTTAAAAGCCGA CTTGAAAAAGGCGCTCAACC 1115–1142 1.000 77.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCACACGTTGCTTTCTACCC AAGGTTCGAATCCTTCCGTC 655–728 1.000 81.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCACACGTTGCTTTCTACCC TTGGTCCCGTTATTCGAAGG 671–744 1.000 81.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TCACACGTTGCTTTCTACCC GGTCCCGTTATTCGAAGGTT 669–742 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG ACACGTTGCTTTCTACCCAA AAGGTTCGAATCCTTCCGTC 653–726 1.000 79.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACACGTTGCTTTCTACCCAA TTGGTCCCGTTATTCGAAGG 669–742 1.000 79.6
trnQ-UUG-psbK_p1 trnQ-UUG-psbK TGGATATGTTCTGGGACGGA AGGCTTCAGGTAATTTCGCG 616–625 1.000 75.4
trnQ-UUG-psbK_p2 trnQ-UUG-psbK TGGATATGTTCTGGGACGGA GGCTTCAGGTAATTTCGCGA 615–624 1.000 75.4
trnQ-UUG-psbK_p3 trnQ-UUG-psbK CCTTCGAATAACGGGACCAA AGGCTTCAGGTAATTTCGCG 586–595 1.000 73.7
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AACCTTCGAATAACGGGACC AGGCTTCAGGTAATTTCGCG 588–597 1.000 73.7
trnQ-UUG-psbK_p5 trnQ-UUG-psbK CCTTCGAATAACGGGACCAA GGCTTCAGGTAATTTCGCGA 585–594 1.000 73.7
atpF-atpH_p1 atpF-atpH GGATGTCCAGTAAGCCAAGG AGAGGGAAAAATCCGGGGTA 669–688 1.000 84.0
atpF-atpH_p2 atpF-atpH GGATGTCCAGTAAGCCAAGG GAGGGAAAAATCCGGGGTAC 668–687 1.000 83.8
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG AGAGGGAAAAATCCGGGGTA 690–709 1.000 83.3
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GAGGGAAAAATCCGGGGTAC 689–708 1.000 83.1
atpF-atpH_p5 atpF-atpH GGATGTCCAGTAAGCCAAGG AGGGAAAAATCCGGGGTACT 667–686 1.000 81.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC AGCCCAAGCGAGACTTACTA 1394–1426 1.000 81.8
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 1337–1369 1.000 81.7
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 1356–1388 1.000 79.5
trnC-GCA-petN_p4 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC GCCCAAGCGAGACTTACTAT 1393–1425 1.000 75.9
trnC-GCA-petN_p5 trnC-GCA-petN TTTTGTATCGTTTTGGCGGC ATTAAAGCAGCCCAAGCGAG 1402–1434 1.000 75.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

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

Species Accession Length (bp) Link
Cheniella clemensiorum OQ701641.1 157207 View on NCBI ↗
Cheniella corymbosa OQ701642.1 157251 View on NCBI ↗
Cheniella damiaoshanensis OQ701646.1 157163 View on NCBI ↗
Cheniella didyma NC_060991.1 157186 View on NCBI ↗
Cheniella glauca OQ701649.1 157266 View on NCBI ↗
Cheniella hechiensis OQ701650.1 157231 View on NCBI ↗
Cheniella lakhonensis OQ701654.1 157181 View on NCBI ↗
Cheniella longipes OQ701655.1 156737 View on NCBI ↗
Cheniella longistaminea OQ701658.1 157041 View on NCBI ↗
Cheniella ovatifolia OQ701662.1 157256 View on NCBI ↗
Cheniella pubicarpa OQ701664.1 157194 View on NCBI ↗
Cheniella quinnanensis OQ701665.1 157217 View on NCBI ↗
Cheniella quinnanensis subsp. villosa OQ701674.1 157359 View on NCBI ↗
Cheniella tenuiflora OQ701666.1 157123 View on NCBI ↗
Cheniella tianlinensis OQ701670.1 157214 View on NCBI ↗