Markers + reference

Salicornia

5 species · Amaranthaceae · Caryophyllales

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Species 5
Genome length 153–153 kb
Candidate markers 269
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ACI62_gt001-rps16 LSC 571 0.0279 0.97 64.4 yes View details
ACI62_gt003-ACI62_gt004 LSC 1139 0.0409 0.98 82.2 yes View details
rpoB-ACI62_gt006 LSC 1182 0.0235 0.97 71.9 yes View details
psbM-ACI62_gt007 LSC 821 0.0127 0.98 64.2 yes View details
psaA-ycf3 LSC 758 0.0245 1.00 57.5 yes View details
ACI62_gt015-ACI62_gt016 LSC 578 0.0197 0.87 56.1 yes View details
rpl33-rps18 LSC 376 0.0247 0.95 61.1 yes View details
ycf1 IRb 1350 0.0080 0.99 41.6 yes View details
ndhF-rpl32 SSC 1094 0.0204 0.99 62.2 yes View details
ycf1 SSC 5670 0.0107 1.00 46.4 no View details
ACI62_gt017-ndhJ LSC 704 0.0118 1.00 65.8 yes View details
petA-psbJ LSC 1010 0.0121 0.96 65.6 yes View details
ndhC-ACI62_gt018 LSC 678 0.0121 1.00 63.5 yes View details
ACI62_gt010-psbD LSC 1324 0.0070 1.00 62.4 yes View details
rps16-ACI62_gt002 LSC 595 0.0177 0.97 62.2 yes View details
psbE-petL LSC 1341 0.0096 0.98 61.3 yes View details
accD-psaI LSC 684 0.0140 0.98 60.4 yes View details
ACI62_gt008-ACI62_gt009 LSC 64 0.0375 1.00 60.2 yes View details
rpl20-rps12 LSC 798 0.0093 0.98 60.1 yes View details
ycf4-cemA LSC 735 0.0142 0.97 59.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ACI62_gt001-rps16_p1 ACI62_gt001-rps16 AAAGCCGAGTACTCTACCGT AGAAGGCGGGGGTTTTTAAC 628–677 1.000 83.7
ACI62_gt001-rps16_p2 ACI62_gt001-rps16 AAAGCCGAGTACTCTACCGT GAAGGCGGGGGTTTTTAACT 627–676 1.000 83.7
ACI62_gt001-rps16_p3 ACI62_gt001-rps16 AAGCCGAGTACTCTACCGTT AGAAGGCGGGGGTTTTTAAC 627–676 1.000 83.7
ACI62_gt001-rps16_p4 ACI62_gt001-rps16 AAGCCGAGTACTCTACCGTT GAAGGCGGGGGTTTTTAACT 626–675 1.000 83.7
ACI62_gt001-rps16_p5 ACI62_gt001-rps16 AAGCCGAGTACTCTACCGTT AAGAAGGCGGGGGTTTTTAA 628–677 1.000 83.6
rps16-ACI62_gt002_p1 rps16-ACI62_gt002 AAGAAATCCGGGTTCGAGTG TAGGCTTCCGGTAATTTGGC 1195–1226 1.000 84.8
rps16-ACI62_gt002_p2 rps16-ACI62_gt002 AAGAAATCCGGGTTCGAGTG CTTACAGCAGCTTGCCAAAC 1282–1313 1.000 84.7
rps16-ACI62_gt002_p3 rps16-ACI62_gt002 CCACAACGGATCATGTCCTT TAGGCTTCCGGTAATTTGGC 1113–1144 1.000 84.7
rps16-ACI62_gt002_p4 rps16-ACI62_gt002 CTAGACCCCTTCCCCCTAAG TAGGCTTCCGGTAATTTGGC 1280–1311 0.800 74.1
rps16-ACI62_gt002_p5 rps16-ACI62_gt002 CTAGACCCCTTCCCCCTAAG CTTACAGCAGCTTGCCAAAC 1367–1398 0.800 73.8
ACI62_gt003-ACI62_gt004_p1 ACI62_gt003-ACI62_gt004 ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 1262–1384 1.000 60.8
ACI62_gt003-ACI62_gt004_p2 ACI62_gt003-ACI62_gt004 ACGGAAAGAGAGGGATTCGA AGAACGAATCACACTTTTACCAC 1265–1387 1.000 59.7
ACI62_gt003-ACI62_gt004_p3 ACI62_gt003-ACI62_gt004 ACGGAAAGAGAGGGATTCGA GAACGAATCACACTTTTACCACT 1264–1386 1.000 59.7
ACI62_gt003-ACI62_gt004_p4 ACI62_gt003-ACI62_gt004 ACGGAAAGAGAGGGATTCGA AACGAATCACACTTTTACCACT 1263–1385 1.000 58.9
ACI62_gt003-ACI62_gt004_p5 ACI62_gt003-ACI62_gt004 ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 1248–1370 1.000 57.1
rpoB-ACI62_gt006_p1 rpoB-ACI62_gt006 ATTCCCTCATTTCCATCCCG CCGGATTTGAACTGGGGAAA 1245–1282 1.000 81.8
rpoB-ACI62_gt006_p2 rpoB-ACI62_gt006 TTCCCTCATTTCCATCCCGT CCGGATTTGAACTGGGGAAA 1244–1281 1.000 81.5
rpoB-ACI62_gt006_p3 rpoB-ACI62_gt006 ATTCCCTCATTTCCATCCCG AAAGGATTTGCAGTCCTCCG 1226–1263 1.000 81.1
rpoB-ACI62_gt006_p4 rpoB-ACI62_gt006 TTCCCTCATTTCCATCCCGT AAAGGATTTGCAGTCCTCCG 1225–1262 1.000 80.8
rpoB-ACI62_gt006_p5 rpoB-ACI62_gt006 CCTCATTTCCATCCCGTCG CCGGATTTGAACTGGGGAAA 1241–1278 1.000 79.0
psbM-ACI62_gt007_p1 psbM-ACI62_gt007 AGAATGAATAGCGCAGTAGCA TCAATTGGTTAGAGCACCGC 930–935 1.000 69.7
psbM-ACI62_gt007_p2 psbM-ACI62_gt007 GAATGAATAGCGCAGTAGCA TCAATTGGTTAGAGCACCGC 929–934 1.000 65.6
psbM-ACI62_gt007_p3 psbM-ACI62_gt007 AGAATGAATAGCGCAGTAGCA AATTGGTTAGAGCACCGCC 928–933 1.000 65.0
psbM-ACI62_gt007_p4 psbM-ACI62_gt007 AGAATGAATAGCGCAGTAGCAA TCAATTGGTTAGAGCACCGC 930–935 1.000 63.7
psbM-ACI62_gt007_p5 psbM-ACI62_gt007 GAATGAATAGCGCAGTAGCAA TCAATTGGTTAGAGCACCGC 929–934 1.000 63.6
ACI62_gt008-ACI62_gt009_p1 ACI62_gt008-ACI62_gt009 GATGAGCGAATTTTTGGGCC TAGCGGTTCAGGACATCTCT 223 1.000 80.0
ACI62_gt008-ACI62_gt009_p2 ACI62_gt008-ACI62_gt009 GATGAGCGAATTTTTGGGCC TCTAGCGGTTCAGGACATCT 225 1.000 80.0
ACI62_gt008-ACI62_gt009_p3 ACI62_gt008-ACI62_gt009 GATGAGCGAATTTTTGGGCC GTCTAGCGGTTCAGGACATC 226 1.000 79.5
ACI62_gt008-ACI62_gt009_p4 ACI62_gt008-ACI62_gt009 GATGAGCGAATTTTTGGGCC CAAGGAGACAACGGGGATTC 199 1.000 79.3
ACI62_gt008-ACI62_gt009_p5 ACI62_gt008-ACI62_gt009 CCAGCGTAGACATATTGCCA TAGCGGTTCAGGACATCTCT 189 1.000 79.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Salicornia bigelovii NC_027226.1 153076 View on NCBI ↗
Salicornia brachiata NC_027224.1 153324 View on NCBI ↗
Salicornia europaea NC_027225.1 153232 View on NCBI ↗
Salicornia fruticosa NC_066030.1 153005 View on NCBI ↗
Salicornia ramosissima NC_066032.1 153308 View on NCBI ↗