Markers + reference

Ziziphora

6 species · Lamiaceae · Lamiales

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Species 6
Genome length 152–152 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 314 0.0214 1.00 53.1 yes View details
rps16-trnQ-UUG LSC 890 0.0079 1.00 56.4 yes View details
rpoB-trnC-GCA LSC 1102 0.0068 1.00 65.1 yes View details
ndhC-trnV-UAC LSC 964 0.0069 1.00 48.5 yes View details
rbcL-accD LSC 759 0.0087 0.99 46.4 yes View details
psaI-ycf4 LSC 450 0.0070 1.00 45.6 yes View details
rpl32-trnL-UAG SSC 760 0.0092 1.00 52.5 yes View details
ndhD SSC 1530 0.0029 1.00 40.6 yes View details
ycf1 SSC 5616 0.0068 1.00 45.7 yes View details
rps2-rpoC2 LSC 227 0.0106 0.98 65.3 yes View details
petN-psbM LSC 958 0.0068 1.00 58.1 yes View details
trnT-GGU-psbD LSC 1371 0.0047 1.00 56.6 yes View details
psbB-psbT LSC 197 0.0186 0.99 56.1 yes View details
petD-rpoA LSC 199 0.0047 0.99 55.0 yes View details
psbI-trnS-GCU LSC 131 0.0112 1.00 54.4 yes View details
ndhG-ndhI SSC 387 0.0110 1.00 52.0 yes View details
trnS-GCU-trnG-UCC LSC 718 0.0036 0.97 51.8 yes View details
psaJ-rpl33 LSC 452 0.0062 1.00 51.7 yes View details
rpl20-rps12 LSC 805 0.0017 1.00 51.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 432–450 1.000 81.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 434–452 1.000 81.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 446–464 1.000 80.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 445–463 1.000 80.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 447–465 1.000 80.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1021–1108 1.000 84.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 963–1050 1.000 83.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCTCGCTATTCGGAGGTTC 976–1063 1.000 83.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAAAATCCACAACGGGTCGT GAAATTGAAATGGGGCGTGG 1048–1135 1.000 82.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAAAATCCACAACGGGTCGT GAGGTTCGAATCCTTCCGTC 990–1077 1.000 82.0
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 239–279 1.000 82.3
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 240–280 1.000 82.3
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 240–280 1.000 82.2
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 241–281 1.000 82.2
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA ATTGGGAGAGATGGCTGAGT 258–298 1.000 81.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 761–787 1.000 73.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 760–786 1.000 73.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 761–787 1.000 73.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 760–786 1.000 73.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 815–841 1.000 72.1
rps2-rpoC2_p1 rps2-rpoC2 CATGGCCAAAATGAACTCCC TTCGAGGGGGAAATGAGAGA 400–414 1.000 76.3
rps2-rpoC2_p2 rps2-rpoC2 CCATGGCCAAAATGAACTCC TTCGAGGGGGAAATGAGAGA 401–415 1.000 76.3
rps2-rpoC2_p3 rps2-rpoC2 ATGGCCAAAATGAACTCCCG TTCGAGGGGGAAATGAGAGA 399–413 1.000 75.2
rps2-rpoC2_p4 rps2-rpoC2 CATGGCCAAAATGAACTCCC TCGAGGGGGAAATGAGAGAT 399–413 1.000 74.5
rps2-rpoC2_p5 rps2-rpoC2 CCATGGCCAAAATGAACTCC TCGAGGGGGAAATGAGAGAT 400–414 1.000 74.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG TTTTGGTGATTCAGGCGACA 1289–1331 1.000 81.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA TTTTGGTGATTCAGGCGACA 1288–1330 1.000 81.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGTTCTTCTGCCAAACCCTG CCGGATTTGAACTGGGGAAA 1268–1310 1.000 81.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTTCTTCTGCCAAACCCTGA CCGGATTTGAACTGGGGAAA 1267–1309 1.000 81.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAAACCCTGATCGATGAA TTTTGGTGATTCAGGCGACA 1280–1322 1.000 79.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Ziziphora capitata PV226239.1 151725 View on NCBI ↗
Ziziphora clinopodioides PV116304.1 151728 View on NCBI ↗
Ziziphora pamiroalaica PV138186.1 151725 View on NCBI ↗
Ziziphora pedicellata PV138187.1 151750 View on NCBI ↗
Ziziphora persica PV116306.1 151693 View on NCBI ↗
Ziziphora tenuior PV116305.1 151610 View on NCBI ↗