Markers + reference

Xylosalsola

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 151–151 kb
Candidate markers 273
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1130 0.0027 1.00 59.7 yes View details
psbK-psbI LSC 421 0.0024 1.00 56.4 yes View details
atpF LSC 1354 0.0037 0.99 61.4 yes View details
psaA-ycf3 LSC 733 0.0027 1.00 60.5 yes View details
psbE-petL LSC 1145 0.0026 1.00 60.3 yes View details
trnP-UGG-psaJ LSC 432 0.0048 0.96 59.6 yes View details
trnN-GUU-ndhF IRb 740 0.0191 0.99 66.1 yes View details
ndhF-rpl32 SSC 1117 0.0063 1.00 62.8 yes View details
matK-trnK-UUU LSC 721 0.0014 0.99 60.1 yes View details
accD-psaI LSC 677 0.0000 0.99 60.0 yes View details
petA-psbJ LSC 987 0.0020 1.00 59.9 yes View details
rps4 LSC 606 0.0016 1.00 59.7 yes View details
trnR-ACG-trnN-GUU IRb 605 0.0017 1.00 59.7 yes View details
trnN-GUU-trnR-ACG IRa 605 0.0017 1.00 59.7 yes View details
trnT-UGU-trnL-UAA LSC 668 0.0015 1.00 59.6 yes View details
ndhK LSC 684 0.0015 1.00 59.6 yes View details
rps3 LSC 657 0.0015 1.00 59.6 yes View details
atpI LSC 744 0.0013 1.00 59.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TCAAGTTATGTTGCCAAGACCT AACGGTAGAGTACTCGGCTT 796–800 1.000 62.4
matK-trnK-UUU_p2 matK-trnK-UUU TCAAGTTATGTTGCCAAGACCT ACGGTAGAGTACTCGGCTTT 795–799 1.000 62.4
matK-trnK-UUU_p3 matK-trnK-UUU TCAAGTTATGTTGCCAAGACCT GGGTTGCTAACTCAACGGTA 809–813 1.000 60.0
matK-trnK-UUU_p4 matK-trnK-UUU TCAAGTTATGTTGCCAAGACCT TTCGGGTTGCTAACTCAACG 812–816 1.000 59.7
matK-trnK-UUU_p5 matK-trnK-UUU TCAAGTTATGTTGCCAAGACC ACGGTAGAGTACTCGGCTTT 795–799 1.000 58.7
rps16_p1 rps16 CAAACTACAACACTACAACCACA CGTGTATTGACTGTTCTGGC 1300 1.000 40.4
rps16_p2 rps16 ACTACAACACTACAACCACA CGTGTATTGACTGTTCTGGC 1297 1.000 40.2
rps16_p3 rps16 CAAACTACAACACTACAACCACA CGTGTATTGACTGTTCTGGCT 1300 1.000 40.2
rps16_p4 rps16 CAAACTACAACACTACAACCACA TCCGTGTATTGACTGTTCTGG 1302 1.000 40.2
rps16_p5 rps16 AACTACAACACTACAACCACA CGTGTATTGACTGTTCTGGC 1298 1.000 40.2
psbK-psbI_p1 psbK-psbI GCCAAATTACCGGAAGCCTA TTTTATTCTTCGCGCCCAGG 651 1.000 72.5
psbK-psbI_p2 psbK-psbI GCCAAATTACCGGAAGCCTA TTTTTATTCTTCGCGCCCAG 652 1.000 72.5
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTATTCTTCGCGCCCAGG 564 1.000 72.4
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTTTTATTCTTCGCGCCCAG 565 1.000 72.4
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTTTATTCTTCGCGCCCAGG 561 1.000 70.4
atpF_p1 atpF TGCTAATTTCGTCTGCTCGA GGAATTGGGGAATCTCAATT 1568–1573 1.000 40.6
atpF_p2 atpF TGCTAATTTCGTCTGCTCGAA GGAATTGGGGAATCTCAATT 1568–1573 1.000 40.6
atpF_p3 atpF TTGCTAATTTCGTCTGCTCGA GGAATTGGGGAATCTCAATT 1569–1574 1.000 40.6
atpF_p4 atpF CGTCTGCTCGAATAGTTACCA GGAATTGGGGAATCTCAATT 1559–1564 1.000 40.6
atpF_p5 atpF TTGCTAATTTCGTCTGCTCG GGAATTGGGGAATCTCAATT 1569–1574 1.000 40.6
atpI_p1 atpI AGACTATCTTGAGCCACACA AGGTCGAGGAAGAGATGGTT 894 1.000 61.2
atpI_p2 atpI AGACTATCTTGAGCCACACA GGTCGAGGAAGAGATGGTTG 893 1.000 60.7
atpI_p3 atpI AGACTATCTTGAGCCACACA ACAGGTCGAGGAAGAGATGG 896 1.000 59.0
atpI_p4 atpI AGACTATCTTGAGCCACACA CAGGTCGAGGAAGAGATGGT 895 1.000 59.0
atpI_p5 atpI AGACTATCTTGAGCCACACAT AGGTCGAGGAAGAGATGGTT 894 1.000 57.7
psaA-ycf3_p1 psaA-ycf3 TGAAAAATGACCGGGTCTGG ATCAAGCCGCTGAGTATTGG 929–930 1.000 79.2
psaA-ycf3_p2 psaA-ycf3 TGAAAAATGACCGGGTCTGG TTGGTTGAAGATCACAGGGC 862–863 1.000 78.8
psaA-ycf3_p3 psaA-ycf3 TGAAAAATGACCGGGTCTGG CAGAGGCTTGGTTCGATCAA 944–945 1.000 78.7
psaA-ycf3_p4 psaA-ycf3 TGAAAAATGACCGGGTCTGG CGATCAAGCCGCTGAGTATT 931–932 1.000 78.4
psaA-ycf3_p5 psaA-ycf3 TGAAAAATGACCGGGTCTGG TGAAGATCACAGGGCGTTTC 857–858 1.000 78.0

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
Xylosalsola arbuscula ON929861.1 151288 View on NCBI ↗
Xylosalsola richteri PP754488.1 151177 View on NCBI ↗