Markers + reference

Reaumuria

2 species · Tamaricaceae · Caryophyllales

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Species 2
Genome length 155–156 kb
Candidate markers 269
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 704 0.0468 0.94 77.1 yes View details
rps16-trnQ-UUG LSC 1026 0.0541 0.97 77.8 yes View details
trnS-GCU-trnG-UCC LSC 908 0.0295 0.93 73.7 yes View details
psbM-trnD-GUC LSC 1022 0.0327 0.99 70.4 yes View details
trnD-GUC-trnY-GUA LSC 393 0.0308 0.99 68.7 yes View details
trnT-GGU-psbD LSC 1304 0.0261 0.85 68.6 yes View details
accD-psaI LSC 636 0.0411 0.96 72.2 yes View details
psbE-petL LSC 1223 0.0275 0.77 62.9 yes View details
trnR-ACG-trnN-GUU IRb 577 0.0355 0.98 80.7 yes View details
ndhF SSC 2226 0.0175 1.00 54.9 yes View details
ycf1 SSC 5385 0.0210 1.00 52.1 yes View details
trnN-GUU-trnR-ACG IRa 577 0.0355 0.98 80.7 yes View details
petL-petG LSC 191 0.0628 1.00 79.7 yes View details
psbT-psbN LSC 60 0.0667 1.00 76.7 yes View details
trnG-GCC-trnfM-CAU LSC 174 0.0575 1.00 74.1 yes View details
rpl33-rps18 LSC 525 0.0251 0.99 72.9 yes View details
psbA-trnK-UUU LSC 238 0.0588 1.00 71.6 yes View details
trnH-GUG-psbA LSC 227 0.0284 0.93 70.5 yes View details
rps4-trnT-UGU LSC 541 0.0301 0.92 69.7 yes View details
atpH-atpI LSC 630 0.0181 0.97 69.2 yes View details
trnC-GCA-petN LSC 878 0.0182 0.94 69.1 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 105 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 TGGGCTGACATCATTAACCG 347–362 1.000 83.6
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GGGCTGACATCATTAACCGT 346–361 1.000 83.6
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TGGGCTGACATCATTAACCG 361–376 1.000 83.4
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GGGCTGACATCATTAACCGT 360–375 1.000 83.4
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TGGGCTGACATCATTAACCG 360–375 1.000 83.4
psbA-trnK-UUU_p1 psbA-trnK-UUU TACAGAAGCGACCCCATAGG ACTCCATCCGACTAGTTCCG 335 1.000 73.7
psbA-trnK-UUU_p2 psbA-trnK-UUU ATCCAGTTACAGAAGCGACC ACTCCATCCGACTAGTTCCG 342 1.000 73.0
psbA-trnK-UUU_p3 psbA-trnK-UUU AGTTACAGAAGCGACCCCAT ACTCCATCCGACTAGTTCCG 338 1.000 72.7
psbA-trnK-UUU_p4 psbA-trnK-UUU TACAGAAGCGACCCCATAGG ACTAGTTCCGGGTTCGAGTC 325 1.000 72.1
psbA-trnK-UUU_p5 psbA-trnK-UUU TACAGAAGCGACCCCATAGG GACTAGTTCCGGGTTCGAGT 326 1.000 72.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTACCGATGATGTGGACGA TTTCCTTGAAAGGGGTGCTC 868–912 1.000 86.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT TTTCCTTGAAAGGGGTGCTC 895–939 1.000 86.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTACCGATGATGTGGACGA GCCGTACGAGGAGAAAACTT 1058–1102 1.000 85.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTACCGATGATGTGGACGA AAAAGGGTATGTTGCTGCCA 1464–1500 1.000 85.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAAGGGTATGTTGCTGCCA 1491–1527 1.000 84.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCCGCACGATAGACTTTTGA GAACAGCGGTATAACTGGCA 1967–1990 1.000 84.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCCCGCACGATAGACTTTTG GAACAGCGGTATAACTGGCA 1968–1991 1.000 84.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCCGCACGATAGACTTTTGA CGAAAACTTACCGCAGCTTG 2011–2034 1.000 84.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGCAGCAACATACCCTTTT GAACAGCGGTATAACTGGCA 2026 0.500 59.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AACCCTAGATTCTTGCCCCT GAACAGCGGTATAACTGGCA 1811 0.500 59.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACAAATGACTCGTACACCGG AATCAAACCGAAAGACCCCT 1027–1044 1.000 77.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACAAATGACTCGTACACCGG ATCAAACCGAAAGACCCCTT 1026–1043 1.000 77.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCCTCGGTACAAATGACTCG AATCAAACCGAAAGACCCCT 1035–1052 1.000 77.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CCCTCGGTACAAATGACTCG ATCAAACCGAAAGACCCCTT 1034–1051 1.000 77.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GACTCGTACACCGGATTAGC ATCAAACCGAAAGACCCCTT 1020–1037 1.000 77.2
atpH-atpI_p1 atpH-atpI GCCAACTCCAGGTCCAATAG TTTGCAACTTTAGCTGCAGC 743–765 1.000 82.0
atpH-atpI_p2 atpH-atpI GCCAACTCCAGGTCCAATAG CCCGTCATGTTCCTTGGATT 791–813 1.000 81.9
atpH-atpI_p3 atpH-atpI GCCAACTCCAGGTCCAATAG CGAATCCATGGAGGGTCATC 714–736 1.000 81.9
atpH-atpI_p4 atpH-atpI CAGCAGCAATAACAGAAGCG TTTGCAACTTTAGCTGCAGC 702–724 1.000 81.2
atpH-atpI_p5 atpH-atpI CAGCAGCAATAACAGAAGCG CCCGTCATGTTCCTTGGATT 750–772 1.000 81.1

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
Reaumuria songarica NC_041273.1 155596 View on NCBI ↗
Reaumuria trigyna NC_041265.1 154533 View on NCBI ↗