Markers + reference

Myricaria

7 species · Tamaricaceae · Caryophyllales

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Species 7
Genome length 155–155 kb
Candidate markers 276
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 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 920 0.0137 1.00 64.8 yes View details
trnS-GCU-trnG-UCC LSC 899 0.0178 1.00 70.4 yes View details
trnC-GCA-petN LSC 748 0.0115 0.99 54.3 yes View details
trnE-UUC-trnT-GGU LSC 834 0.0171 1.00 68.5 yes View details
psbZ-trnG-GCC LSC 325 0.0105 1.00 50.1 yes View details
trnT-UGU-trnL-UAA LSC 893 0.0126 0.99 63.5 yes View details
trnF-GAA-ndhJ LSC 745 0.0142 1.00 62.4 yes View details
clpP LSC 2041 0.0080 1.00 49.3 yes View details
ndhF-rpl32 SSC 705 0.0185 1.00 65.0 yes View details
rpl32-trnL-UAG SSC 1394 0.0186 1.00 70.0 yes View details
ndhC-trnV-UAC LSC 832 0.0124 1.00 71.8 yes View details
petN-psbM LSC 875 0.0115 1.00 69.2 yes View details
psaA-ycf3 LSC 850 0.0102 1.00 67.7 yes View details
rpl2-trnH-GUG IRa 274 0.0000 1.00 65.7 no View details
psbE-petL LSC 728 0.0092 1.00 64.1 yes View details
ycf3-trnS-GGA LSC 705 0.0113 1.00 63.7 yes View details
rpoB-trnC-GCA LSC 1257 0.0104 0.99 61.5 yes View details
rps4-trnT-UGU LSC 433 0.0139 1.00 61.4 yes View details
psbK-psbI LSC 409 0.0129 0.99 61.2 yes View details
trnM-CAU-atpE LSC 287 0.0156 1.00 60.2 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 981–1003 1.000 82.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 992–1014 1.000 81.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTGTCGAATAGAAGTGGGGC 1043–1065 1.000 79.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGAATAGAAGTGGGGC 1054–1076 1.000 79.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 985–1007 1.000 77.4
psbK-psbI_p1 psbK-psbI CAAGCTGCGGTAAGTTTTCG AGGATTACGCCCTGGATCAT 516–530 1.000 81.9
psbK-psbI_p2 psbK-psbI AGCTGCGGTAAGTTTTCGAT AGGATTACGCCCTGGATCAT 514–528 1.000 81.6
psbK-psbI_p3 psbK-psbI AAGCTGCGGTAAGTTTTCGA AGGATTACGCCCTGGATCAT 515–529 1.000 81.3
psbK-psbI_p4 psbK-psbI GCAAGCTGCGGTAAGTTTTC AGGATTACGCCCTGGATCAT 517–531 1.000 79.8
psbK-psbI_p5 psbK-psbI CAAGCTGCGGTAAGTTTTCG GGATTACGCCCTGGATCATT 515–529 1.000 79.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCCTCGGTACAAATGACTCG AATCAAACCGAAAGACCCCT 1016–1056 1.000 78.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCCTCGGTACAAATGACTCG ATCAAACCGAAAGACCCCTT 1015–1055 1.000 78.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AATCAAACCGAAAGACCCCT 1037–1077 1.000 78.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATCAAACCGAAAGACCCCTT 1036–1076 1.000 78.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCCTCGGTACAAATGACTCG ACCGAAAGACCCCTTAACTC 1010–1050 1.000 77.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTTCATCCGGGAG CCGGATTTGAACTGGGGAAT 1321–1351 1.000 82.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCATTTTCATCCGGGAGCA CCGGATTTGAACTGGGGAAT 1319–1349 1.000 82.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCTCATTTTCATCCGGGAG ATTTGCAATCCTCCGCCTTA 1296–1326 1.000 80.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCATTTTCATCCGGGAGCA ATTTGCAATCCTCCGCCTTA 1294–1324 1.000 80.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCCCTCATTTTCATCCGGGA CCGGATTTGAACTGGGGAAT 1322–1352 1.000 79.6
trnC-GCA-petN_p1 trnC-GCA-petN ATTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 796–808 1.000 80.7
trnC-GCA-petN_p2 trnC-GCA-petN ATTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 857–869 1.000 78.9
trnC-GCA-petN_p3 trnC-GCA-petN TAAGGCGGAGGATTGCAAAT AGCCCAAGCGAGACTTACTA 821–833 1.000 78.3
trnC-GCA-petN_p4 trnC-GCA-petN GTAAGGCGGAGGATTGCAAA AGCCCAAGCGAGACTTACTA 822–834 1.000 77.5
trnC-GCA-petN_p5 trnC-GCA-petN TAAGGCGGAGGATTGCAAAT AGAGTCCACTTCTTCCCCAT 882–894 1.000 76.5
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT ACGTAAAAACGGTCAGCCAA 986–997 1.000 79.1
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT ACGTAAAAACGGTCAGCCAA 925–936 1.000 77.7
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TACGTAAAAACGGTCAGCCA 987–998 1.000 77.6
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TACGTAAAAACGGTCAGCCA 926–937 1.000 76.2
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT CGTAAAAACGGTCAGCCAAA 985–996 1.000 75.7

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
Myricaria bracteata NC_088075.1 154709 View on NCBI ↗
Myricaria germanica PQ898998.1 154749 View on NCBI ↗
Myricaria laxiflora NC_072270.1 154897 View on NCBI ↗
Myricaria paniculata NC_041270.1 154651 View on NCBI ↗
Myricaria rosea NC_072271.1 155300 View on NCBI ↗
Myricaria squamosa NC_060684.1 154689 View on NCBI ↗
Myricaria wardii NC_072272.1 155284 View on NCBI ↗