Markers + reference

Casearia

10 species · Salicaceae · Malpighiales

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Species 10
Genome length 156–159 kb
Candidate markers 270
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 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 2634 0.0332 0.97 73.7 yes View details
trnS-GCU-trnG-UCC LSC 348 0.0529 0.94 91.1 yes View details
trnR-UCU-atpA LSC 355 0.0445 0.99 74.8 yes View details
psbZ-trnG-GCC LSC 509 0.0488 0.94 78.1 yes View details
ndhC-trnV-UAC LSC 1405 0.0353 0.89 74.9 yes View details
rbcL-accD LSC 779 0.0385 0.98 79.3 yes View details
petA-psbJ LSC 1084 0.0357 0.98 79.8 yes View details
infA LSC 291 0.0246 0.99 65.0 yes View details
rps19 IRb 279 0.0105 1.00 31.8 no View details
ndhF SSC 2271 0.0190 1.00 59.5 yes View details
rps19 IRa 279 0.0714 0.70 57.5 yes View details
rps8-rpl14 LSC 259 0.0533 0.95 83.2 yes View details
trnT-GGU-psbD LSC 1602 0.0244 0.99 80.7 yes View details
rpl22-rps19 LSC 174 0.0640 0.93 77.5 yes View details
rpoB-trnC-GCA LSC 1037 0.0259 0.98 77.2 yes View details
trnH-GUG-psbA LSC 152 0.0469 1.00 77.0 yes View details
psbE-petL LSC 1151 0.0289 0.98 76.3 yes View details
rps12-clpP LSC 194 0.0336 1.00 75.6 yes View details
atpB-rbcL LSC 761 0.0211 0.99 75.5 yes View details
psaJ-rpl33 LSC 491 0.0313 0.98 73.8 yes View details
psbA-trnK-UUU LSC 267 0.0318 0.98 73.7 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 100 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 CGTGCTAACCTTGGTATGGA 262–289 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGTGCTAACCTTGGTATGGA 276–303 1.000 85.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGTGCTAACCTTGGTATGGA 275–302 1.000 85.0
trnH-GUG-psbA_p4 trnH-GUG-psbA TAGGCGAATGACGGGAATTG GACCTAGCTGTTGTCGAAGT 260–285 0.800 73.6
trnH-GUG-psbA_p5 trnH-GUG-psbA TAGGCGAATGACGGGAATTG CGTGCTAACCTTGGTATGGA 317–342 0.800 73.3
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT AAAATGCAAGCACGGTTTGG 450–497 1.000 82.3
psbA-trnK-UUU_p2 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC AAAATGCAAGCACGGTTTGG 451–498 1.000 81.8
psbA-trnK-UUU_p3 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT TGAAAAATGCAAGCACGGTT 453–500 1.000 80.9
psbA-trnK-UUU_p4 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT AAAGCCGTGTGCAATGAAAA 467–514 1.000 80.7
psbA-trnK-UUU_p5 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT AAGCCGTGTGCAATGAAAAA 466–513 1.000 80.7
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG TGTAAAAGCTGTTAGCCGCA GAGGTTCGAATCCTTCCGTC 1275–2744 1.000 90.5
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAAGCTGTTAGCCGCACTTA GAGGTTCGAATCCTTCCGTC 1271–2740 1.000 90.0
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAGCTGTTAGCCGCACTTAA GAGGTTCGAATCCTTCCGTC 1270–2739 1.000 90.0
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AGCTGTTAGCCGCACTTAAA GAGGTTCGAATCCTTCCGTC 1269–2738 1.000 90.0
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG TAAAAGCTGTTAGCCGCACT GAGGTTCGAATCCTTCCGTC 1273–2742 1.000 90.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATGCACCGAGAGATCCCTTA 430–521 0.900 87.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TATGCACCGAGAGATCCCTT 431–522 0.900 87.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATGCACCGAGAGATCCCTTA 429–520 0.900 87.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TATGCACCGAGAGATCCCTT 430–521 0.900 87.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGCACCGAGAGATCCCTTAA 429–520 0.900 86.8
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGTTTTCTACTTCAGGAACAGG 394–430 1.000 54.5
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGTTTTCTACTTCAGGAACAGG 395–431 1.000 52.0
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC CGTTTTCTACTTCAGGAACAGGT 394–430 1.000 52.0
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC ACGTTTTCTACTTCAGGAACAG 395–431 1.000 52.0
trnR-UCU-atpA_p5 trnR-UCU-atpA GTTCAAATCCTATTGGACGCA CGTTTTCTACTTCAGGAACAGG 393–429 1.000 52.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCCATTTCCATCCCTAAGC AAAAGGATTTGCAGTCCCCC 1086–1131 1.000 86.8
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCCATTTCCATCCCTAAGC GCGACACCCAGATTTGAACT 1111–1156 1.000 85.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CATTCCCCCATTTCCATCCC AAAAGGATTTGCAGTCCCCC 1091–1136 1.000 84.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCCCATTTCCATCCCTAA AAAAGGATTTGCAGTCCCCC 1088–1133 1.000 84.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTCCCCCATTTCCATCCCTA AAAAGGATTTGCAGTCCCCC 1089–1134 1.000 84.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Casearia aculeata PV276164.1 158160 View on NCBI ↗
Casearia arborea PV276169.1 158687 View on NCBI ↗
Casearia comocladifolia PV276170.1 157302 View on NCBI ↗
Casearia decandra MN078142.1 156809 View on NCBI ↗
Casearia glomerata NC_059787.1 156224 View on NCBI ↗
Casearia kurzii PQ400062.1 157998 View on NCBI ↗
Casearia nitida PV276167.1 156648 View on NCBI ↗
Casearia spinescens PV276166.1 158368 View on NCBI ↗
Casearia sylvestris PV276165.1 157934 View on NCBI ↗
Casearia velutina MN078141.1 156008 View on NCBI ↗