Markers + reference

Salsola

9 species · Amaranthaceae · Caryophyllales

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Species 9
Genome length 151–153 kb
Candidate markers 270
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 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-rps16 LSC 601 0.0501 1.00 74.3 yes View details
rpoB-trnC-GCA LSC 1146 0.0433 1.00 71.3 yes View details
trnN-GUU-ycf1 IRb 515 0.0494 0.88 71.8 yes View details
ycf1 IRb 1533 0.0393 1.00 65.2 no View details
ycf1 SSC 5361 0.0572 1.00 74.1 yes View details
ycf1-trnN-GUU IRa 515 0.0493 0.88 71.6 yes View details
rps4-trnT-UGU LSC 434 0.0527 0.99 78.9 yes View details
rps16-trnQ-UUG LSC 558 0.0556 1.00 77.6 yes View details
ndhF-rpl32 SSC 1113 0.0462 1.00 77.2 yes View details
trnE-UUC-trnT-GGU LSC 420 0.0331 1.00 75.0 yes View details
trnD-GUC-trnY-GUA LSC 403 0.0494 1.00 74.6 yes View details
trnT-UGU-trnL-UAA LSC 697 0.0336 0.99 73.4 yes View details
trnT-GGU-psbD LSC 1300 0.0297 1.00 71.7 yes View details
psbE-petL LSC 1147 0.0338 0.99 71.2 yes View details
trnF-GAA-ndhJ LSC 671 0.0332 1.00 70.7 yes View details
ndhC-trnV-UAC LSC 750 0.0365 1.00 70.7 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCTATCCCAATGAGCCGTCT 938–1066 1.000 90.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGCCGTCTATCGAATCGTTG 926–1054 1.000 90.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT TCTATCCCAATGAGCCGTCT 934–1062 1.000 89.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TTGCGGCCATTTTTGAAAGG 1407–1529 1.000 89.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TCCGTTGTTCGCATGATTCT 1462–1476 0.667 66.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 628–669 1.000 90.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 639–680 1.000 89.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 658–699 1.000 89.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC TAAGGCATCGGGTTTTGGTC 669–710 1.000 89.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTAAGGCATCGGGTTTTGGT 659–700 1.000 87.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CACGAGCCCATATTCTTGCT CCGGATTTGAACTGGGGAAA 1684–1749 1.000 89.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GAAAATACCGGGTCTCCACC CCGGATTTGAACTGGGGAAA 1889–1954 1.000 88.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCGGGCTTTGCAATATTTG ATAGGAATGGGGAGGTCTCG 1798–1857 0.889 84.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CACGAGCCCATATTCTTGCT ATAGGAATGGGGAGGTCTCG 1920–1979 0.889 83.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GAAAATACCGGGTCTCCACC ATAGGAATGGGGAGGTCTCG 2125–2184 0.889 83.2
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA TGGCAATATGTCTACGCTGG 451–474 1.000 85.7
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGCAATATGTCTACGCTGGT 450–473 1.000 85.7
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGGGACGGACTGTAAATTCG 472–495 1.000 84.8
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA GGGACGGACTGTAAATTCGT 471–494 1.000 84.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA GCGGTGCTCTAACCAATTGA CGGACTGTAAATTCGTTGGC 467–490 1.000 83.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 507–537 1.000 88.9
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 505–535 1.000 88.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 486–516 1.000 88.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 484–514 1.000 88.9
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GATGTCCTGAACCGCTAGAC GAACCGATGACTTACGCCTT 504–534 1.000 88.4
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CGTAACCAGTCATCCATAACA 1438–1483 1.000 60.5
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CGTAACCAGTCATCCATAACA 1441–1486 1.000 60.4
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA CGTAACCAGTCATCCATAACA 1415–1460 1.000 58.9
trnT-GGU-psbD_p4 trnT-GGU-psbD CCGATAAGGGGCTTTTGAGG CGTAACCAGTCATCCATAACA 1393–1438 1.000 58.7
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CGTAACCAGTCATCCATAACATC 1438–1483 1.000 57.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Salsola collina NC_066995.1 152923 View on NCBI ↗
Salsola foliosa ON929866.1 151508 View on NCBI ↗
Salsola junatovii ON929856.1 152510 View on NCBI ↗
Salsola monoptera PP234571.1 152828 View on NCBI ↗
Salsola paulsenii ON929855.1 152890 View on NCBI ↗
Salsola pellucida ON929859.1 152890 View on NCBI ↗
Salsola rosacea ON929864.1 151239 View on NCBI ↗
Salsola tragus ON929869.1 152882 View on NCBI ↗
Salsola zaidamica ON149859.1 152933 View on NCBI ↗