Markers + reference

Atraphaxis

7 species · Polygonaceae · Caryophyllales

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Species 7
Genome length 164–164 kb
Candidate markers 264
Primer pairs 105

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 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl2 IRb 1490 NA 0.00 30.2 yes View details
petN-psbM LSC 1179 0.0057 0.98 62.6 yes View details
trnD-GUC-trnY-GUA LSC 377 0.0088 0.98 38.4 yes View details
rps4-trnT-UGU LSC 724 0.0067 1.00 63.7 yes View details
trnF-GAA-ndhJ LSC 689 0.0085 0.99 55.9 yes View details
petA-psbJ LSC 928 0.0107 1.00 52.6 yes View details
rpl2 IRa 1490 0.0002 1.00 28.6 no View details
ndhF-rpl32 SSC 1069 0.0065 1.00 47.7 yes View details
rpl32-trnL-UAG SSC 745 0.0091 1.00 43.5 yes View details
ndhE-ndhG SSC 242 0.0196 0.97 54.0 yes View details
rps15 SSC 264 0.0072 1.00 29.9 yes View details
trnR-UCU-atpA LSC 153 0.0322 0.99 62.8 yes View details
psbZ-trnG-UCC LSC 307 0.0076 0.98 55.5 yes View details
atpB-rbcL LSC 824 0.0014 0.98 54.8 yes View details
rpoB-trnC-GCA LSC 1437 0.0028 0.99 52.9 yes View details
rpl14-rpl16 LSC 118 0.0161 1.00 52.5 yes View details
trnT-GGU-psbD LSC 1575 0.0031 0.99 51.4 yes View details
trnE-UUC-trnT-GGU LSC 902 0.0028 0.99 51.3 yes View details
psbE-petL LSC 1279 0.0035 1.00 51.3 yes View details
clpP LSC 2168 0.0018 1.00 50.8 yes View details
rbcL-accD LSC 432 0.0073 1.00 50.1 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
rpl2_p1 rpl2 CGCTTCAACCGGGTTATTCT GTGAACGTGTCACGGTTAAT 1630–1635 1.000 69.1
rpl2_p2 rpl2 ATCATTACGCTTCAACCGGG GTGAACGTGTCACGGTTAAT 1637–1642 1.000 68.6
rpl2_p3 rpl2 CGCTTCAACCGGGTTATTCT GTGAACGTGTCACGGTTAATT 1630–1635 1.000 67.0
rpl2_p4 rpl2 ACGCTTCAACCGGGTTATTC GTGAACGTGTCACGGTTAAT 1631–1636 1.000 66.8
rpl2_p5 rpl2 ATCATTACGCTTCAACCGGG GTGAACGTGTCACGGTTAATT 1637–1642 1.000 66.4
trnG-UCC_p1 trnG-UCC CGTTGTTCGACAAAAGTTCCA TCGTGAATTAATGCATTTTTGA 850–868 1.000 40.8
trnG-UCC_p2 trnG-UCC CGTTGTTCGACAAAAGTTCCA TCGTGAATTAATGCATTTTTGAA 850–868 1.000 40.8
trnG-UCC_p3 trnG-UCC CGTTGTTCGACAAAAGTTCCA TTCGTGAATTAATGCATTTTTGA 851–869 1.000 40.8
trnG-UCC_p4 trnG-UCC TCGTTGTTCGACAAAAGTTCC TCGTGAATTAATGCATTTTTGA 851–869 1.000 40.8
trnG-UCC_p5 trnG-UCC CGTTGTTCGACAAAAGTTCCA TCGTGAATTAATGCATTTTTGAATG 850–868 1.000 40.8
trnR-UCU-atpA_p1 trnR-UCU-atpA ATGAGAAGCGTCCATTGTCT ACCAAGACACTCACTGAGGA 316–321 1.000 73.8
trnR-UCU-atpA_p2 trnR-UCU-atpA AATGAGAAGCGTCCATTGTCT ACCAAGACACTCACTGAGGA 317–322 1.000 71.6
trnR-UCU-atpA_p3 trnR-UCU-atpA ATGGTAATGAGAAGCGTCCA ACCAAGACACTCACTGAGGA 322–327 1.000 71.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGTAATGAGAAGCGTCCAT ACCAAGACACTCACTGAGGA 321–326 1.000 71.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGTAATGAGAAGCGTCCATT ACCAAGACACTCACTGAGGA 321–326 1.000 69.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CTTACCGCTCGGCCATGT 1442–1498 1.000 48.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG TTACCGCTCGGCCATGTC 1441–1497 1.000 48.4
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CTTACCGCTCGGCCATGTC 1442–1498 1.000 47.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC CTTACCGCTCGGCCATGT 1444–1500 1.000 44.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC TTACCGCTCGGCCATGTC 1443–1499 1.000 44.2
petN-psbM_p1 petN-psbM CCCTTTCACTCGTCGTATGG TGCTACTGCACTCTTCATTCT 1268–1296 1.000 66.4
petN-psbM_p2 petN-psbM CCTTTCACTCGTCGTATGGG TGCTACTGCACTCTTCATTCT 1267–1295 1.000 66.4
petN-psbM_p3 petN-psbM CTTTCACTCGTCGTATGGGG TGCTACTGCACTCTTCATTCT 1266–1294 1.000 66.4
petN-psbM_p4 petN-psbM GTATGGGGGAGAAGTGGACT TGCTACTGCACTCTTCATTCT 1254–1282 1.000 66.1
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTCTTCATTCT 1313–1341 1.000 65.7
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 439–463 1.000 79.7
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 438–462 1.000 79.7
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 460–484 1.000 78.7
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 459–483 1.000 78.5
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CGGACTGTAAATTCGTTGGC 455–479 1.000 77.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Atraphaxis bracteata NC_059952.1 164264 View on NCBI ↗
Atraphaxis decipiens NC_070100.1 164187 View on NCBI ↗
Atraphaxis frutescens PQ523294.1 164230 View on NCBI ↗
Atraphaxis frutescens var. papillosa ON229542.1 164233 View on NCBI ↗
Atraphaxis irtyschensis NC_070099.1 164216 View on NCBI ↗
Atraphaxis pungens PQ523295.1 164065 View on NCBI ↗
Atraphaxis spinosa NC_070098.1 164106 View on NCBI ↗