Markers + reference

Cassia

2 species · Fabaceae · Fabales

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Species 2
Genome length 160–162 kb
Candidate markers 267
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1142 0.0265 0.99 69.8 yes View details
rps16-trnQ-UUG LSC 1068 0.0549 0.66 79.9 yes View details
trnQ-UUG-psbK LSC 733 0.0237 0.92 64.4 yes View details
trnS-GCU-trnG-UCC LSC 840 0.0225 0.95 68.8 yes View details
trnG-UCC-trnR-UCU LSC 421 0.0556 0.94 80.8 yes View details
trnS-UGA-psbZ LSC 347 0.0116 0.99 51.3 yes View details
trnT-UGU-trnL-UAA LSC 1470 0.0388 1.00 72.7 yes View details
ndhC-trnV-UAC LSC 544 0.0323 0.97 79.2 yes View details
accD-psaI LSC 619 0.0441 0.92 83.2 yes View details
ycf1 IRb 802 0.0312 1.00 76.7 yes View details
ycf1 SSC 5430 0.0140 1.00 55.4 no View details
psbC-trnS-UGA LSC 241 0.0581 1.00 78.0 yes View details
rpl16-rps3 LSC 155 0.0387 1.00 74.8 yes View details
ndhG-ndhI SSC 389 0.0315 0.98 74.4 yes View details
rps8-rpl14 LSC 535 0.0270 0.97 72.8 yes View details
psaA-ycf3 LSC 786 0.0171 0.97 71.6 yes View details
atpF-atpH LSC 513 0.0216 0.99 69.9 yes View details
ndhE-ndhG SSC 236 0.0297 1.00 69.6 yes View details
rps3-rps19 LSC 624 0.0263 0.98 69.4 yes View details
rbcL-accD LSC 838 0.0135 0.97 68.9 yes View details
trnT-GGU-psbD LSC 1452 0.0166 0.99 67.2 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AAAAAGGCGCTCAACCTACA 1334–1354 1.000 81.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CCTTGAAAAAGGCGCTCAAC 1339–1359 1.000 80.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC CTTGAAAAAGGCGCTCAACC 1338–1358 1.000 80.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGATGGTATGGACGAATCC TGAAAAAGGCGCTCAACCTA 1336–1356 1.000 79.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGCGGGTGTTTTTATGGAA 1289–1309 1.000 79.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 927–1148 1.000 86.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 929–1150 1.000 85.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCACGTTGCTTTTTACCACA GAGGTTCGAATCCTTCCGTC 915–1136 1.000 84.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 930–1151 1.000 84.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 928–1149 1.000 83.6
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG ACAGACCAAACTAAAGATATTAAGCA 800–840 1.000 45.6
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACAGACCAAACTAAAGATATTAAGCA 758–798 1.000 45.6
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA ACAAATACAGACCAAACTAAAGA 764–804 1.000 45.6
trnQ-UUG-psbK_p4 trnQ-UUG-psbK AATGGATATGCTCTGGGACG ACAGACCAAACTAAAGATATTAAGCA 804–844 1.000 45.6
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GATATGCTCTGGGACGGAAG ACAAATACAGACCAAACTAAAGA 806–846 1.000 45.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGAATCAAACGAGGGATCCC 952–1001 1.000 79.0
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGAATCAAACGAGGGATCCC 951–1000 1.000 78.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TGAATCAAACGAGGGATCCC 1006–1055 1.000 77.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GGATCCATAGAACGAATCGCA 920–969 1.000 76.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GGATCCATAGAACGAATCGCA 919–968 1.000 76.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 501–515 1.000 70.8
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 504–518 1.000 70.5
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 507–521 1.000 70.0
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 510–524 1.000 69.7
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 505–519 1.000 68.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG TGGGCTGGTTGTAGCATTAG 631–634 1.000 77.5
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG AGGCAGAGGGAAAAATACGG 698–701 1.000 77.3
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG GCAGAGGGAAAAATACGGGG 696–699 1.000 75.8
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GGCAGAGGGAAAAATACGGG 697–700 1.000 75.8
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CCGAGGCAGAGGGAAAAATA 701–704 1.000 75.0

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
Cassia brewsteri NC_047376.1 160114 View on NCBI ↗
Cassia fistula NC_065246.1 161724 View on NCBI ↗