Markers + reference

Satureja

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 152–152 kb
Candidate markers 274
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 342 0.0398 0.96 65.7 yes View details
rps16-trnQ-UUG LSC 975 0.0105 0.98 57.7 yes View details
rps14 LSC 303 0.0066 1.00 56.4 yes View details
petA-psbJ LSC 1025 0.0128 0.99 66.7 yes View details
petL-petG LSC 170 0.0294 1.00 69.4 yes View details
ycf1 IRb 1131 0.0000 1.00 27.5 no View details
ndhF SSC 2232 0.0094 1.00 48.4 yes View details
rpl32-trnL-UAG SSC 741 0.0123 0.99 66.8 yes View details
ccsA SSC 978 0.0041 1.00 47.0 yes View details
ndhD SSC 1503 0.0027 1.00 48.5 yes View details
rps15-ycf1 SSC 419 0.0170 0.98 51.7 yes View details
ycf1 SSC 5547 0.0074 1.00 42.1 yes View details
trnG-GCC-trnM-CAU LSC 158 0.0446 0.99 78.7 yes View details
rpl2-rps19 IRa 60 0.0333 1.00 71.7 yes View details
rpl14-rpl16 LSC 131 0.0305 1.00 70.1 yes View details
psbT-psbN LSC 63 0.0635 1.00 69.7 yes View details
ndhD-psaC SSC 120 0.0588 0.99 69.1 yes View details
rps19-rpl2 IRb 60 0.0333 1.00 68.5 yes View details
ccsA-ndhD SSC 238 0.0256 0.98 64.0 yes View details
atpI LSC 744 0.0067 1.00 62.6 yes View details
ycf3-trnS-GGA LSC 848 0.0060 0.98 62.3 yes View details
trnS-UGA-psbZ LSC 344 0.0118 0.98 61.9 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGTTGCGTATTCAGCTCCT 977–992 1.000 81.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 1020–1035 1.000 81.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GAGTGGGAGCTTAGTTTCCG 1034–1049 1.000 81.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GAGTGGGAGCTTAGTTTCCG 1033–1048 1.000 81.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GAGTGGGAGCTTAGTTTCCG 1035–1050 1.000 81.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1032–1049 1.000 80.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCAAGAGCACCTCATTTCT GAGGTTCGAATCCTTCCGTC 1103–1120 1.000 80.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCTCGCTATTCGGAGGTTC 1045–1062 1.000 80.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCCAAGAGCACCTCATTTCT GTCTCGCTATTCGGAGGTTC 1116–1133 1.000 80.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAAAATCCACAACGGGTCGT GAGGTTCGAATCCTTCCGTC 1059–1076 1.000 79.3
atpI_p1 atpI ACATATGCGTTGCTTTGCAC TCCGATTCAAGTAGACAAAGAGA 858–859 1.000 48.5
atpI_p2 atpI CACATATGCGTTGCTTTGCA TCCGATTCAAGTAGACAAAGAGA 859–860 1.000 48.5
atpI_p3 atpI CATATGCGTTGCTTTGCACT TCCGATTCAAGTAGACAAAGAGA 857–858 1.000 46.5
atpI_p4 atpI ATGCGTTGCTTTGCACTAAG TCCGATTCAAGTAGACAAAGAGA 854–855 1.000 46.0
atpI_p5 atpI TCTTGAGCCACATATGCGTT TCCGATTCAAGTAGACAAAGAGA 867–868 1.000 45.4
trnS-UGA-psbZ_p1 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC CCAACCATCAGGAGAAGCAA 458–464 1.000 79.9
trnS-UGA-psbZ_p2 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GACCAACCATCAGGAGAAGC 460–466 1.000 79.5
trnS-UGA-psbZ_p3 trnS-UGA-psbZ GTTTTCAAGACCGGGGCTAT CCAACCATCAGGAGAAGCAA 478–484 1.000 79.0
trnS-UGA-psbZ_p4 trnS-UGA-psbZ CAACCACTCAGCCATCTCTC GCAAATACGACAGGTACGCT 442–448 1.000 78.7
trnS-UGA-psbZ_p5 trnS-UGA-psbZ GTTTTCAAGACCGGGGCTAT GACCAACCATCAGGAGAAGC 480–486 1.000 78.6
trnG-GCC-trnM-CAU_p1 trnG-GCC-trnM-CAU AGAAGATGCGGGTTCGATTC CTTGAGGTCACGGGTTCAAA 225–226 1.000 82.1
trnG-GCC-trnM-CAU_p2 trnG-GCC-trnM-CAU GAGAAGATGCGGGTTCGATT CTTGAGGTCACGGGTTCAAA 226–227 1.000 82.1
trnG-GCC-trnM-CAU_p3 trnG-GCC-trnM-CAU AGAAGATGCGGGTTCGATTC GGGTAGAGCAGTTTGGTAGC 261–262 1.000 81.8
trnG-GCC-trnM-CAU_p4 trnG-GCC-trnM-CAU GAGAAGATGCGGGTTCGATT GGGTAGAGCAGTTTGGTAGC 262–263 1.000 81.8
trnG-GCC-trnM-CAU_p5 trnG-GCC-trnM-CAU ATGCGGATATGGTCGAATGG GGGTAGAGCAGTTTGGTAGC 302–303 1.000 81.1
rps14_p1 rps14 AAAGAACGATTGAATGCGCC TTTTTCGATGGGGAGAAGGC 506 1.000 76.9
rps14_p2 rps14 CGCCCCTCTACCATATCTGT TTTTTCGATGGGGAGAAGGC 490 1.000 76.1
rps14_p3 rps14 ACAGAATGGTAAAGAGGCCG TTTTTCGATGGGGAGAAGGC 448 1.000 75.8
rps14_p4 rps14 CAGAATGGTAAAGAGGCCGT TTTTTCGATGGGGAGAAGGC 447 1.000 75.8
rps14_p5 rps14 AATGCGCCCCTCTACCATAT TTTTTCGATGGGGAGAAGGC 494 1.000 73.9

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
Satureja hortensis PP316497.1 151777 View on NCBI ↗
Satureja montana NC_066034.1 151858 View on NCBI ↗