Markers + reference

Sesamum

2 species · Pedaliaceae · Lamiales

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Species 2
Genome length 153–153 kb
Candidate markers 275
Primer pairs 90

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 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Lys (UUU)-rps16 LSC 889 0.0147 1.00 60.0 yes View details
ycf3-tRNA-Ser (GGA) LSC 864 0.0162 1.00 63.3 yes View details
rpl20 LSC 387 0.0103 1.00 53.6 yes View details
ycf1 IRb 1012 0.0010 0.98 46.3 yes View details
ndhF-rpl32 SSC 517 0.0252 1.00 69.2 yes View details
rpl32-tRNA-Leu (UAG) SSC 883 0.0114 0.99 52.2 yes View details
ndhD SSC 1503 0.0027 1.00 47.4 yes View details
rps15-ycf1 SSC 367 0.0227 0.96 57.5 yes View details
ycf1 SSC 5370 0.0111 0.99 46.3 no View details
ycf1-ndhF SSC 70 0.2667 0.64 74.7 yes View details
ndhD-psaC SSC 124 0.0726 1.00 72.4 yes View details
ccsA-ndhD SSC 252 0.0286 0.97 71.5 yes View details
psbH-petB LSC 124 0.0323 1.00 71.0 yes View details
tRNA-Phe (GAA)-ndhJ LSC 671 0.0076 0.97 65.6 yes View details
psaA-ycf3 LSC 742 0.0028 0.95 64.8 yes View details
tRNA-His (GUG)-psbA LSC 292 0.0205 1.00 64.3 yes View details
rps2-rpoC2 LSC 207 0.0194 1.00 64.1 yes View details
rbcL LSC 1434 0.0077 1.00 63.2 yes View details
petA-psbJ LSC 1004 0.0080 1.00 63.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
tRNA-His (GUG)-psbA_p1 tRNA-His (GUG)-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 359–363 1.000 79.7
tRNA-His (GUG)-psbA_p2 tRNA-His (GUG)-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 373–377 1.000 79.6
tRNA-His (GUG)-psbA_p3 tRNA-His (GUG)-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 372–376 1.000 79.6
tRNA-His (GUG)-psbA_p4 tRNA-His (GUG)-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 374–378 1.000 79.6
tRNA-His (GUG)-psbA_p5 tRNA-His (GUG)-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 411–415 1.000 78.7
tRNA-Lys (UUU)-rps16_p1 tRNA-Lys (UUU)-rps16 AAAGCCGAGTACTCTACCGT GGAACTTCCGTCTTCCGTC 944–945 1.000 71.0
tRNA-Lys (UUU)-rps16_p2 tRNA-Lys (UUU)-rps16 AAGCCGAGTACTCTACCGTT GGAACTTCCGTCTTCCGTC 943–944 1.000 71.0
tRNA-Lys (UUU)-rps16_p3 tRNA-Lys (UUU)-rps16 TCTAGCCGCACTTAAAAGCC GGAACTTCCGTCTTCCGTC 958–959 1.000 70.2
tRNA-Lys (UUU)-rps16_p4 tRNA-Lys (UUU)-rps16 CCGCACTTAAAAGCCGAGTA GGAACTTCCGTCTTCCGTC 953–954 1.000 70.0
tRNA-Lys (UUU)-rps16_p5 tRNA-Lys (UUU)-rps16 AAGCCGAGTACTCTACCGTT AGGAACTTCCGTCTTCCGT 944–945 1.000 69.9
rps2-rpoC2_p1 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG TATTCGAGGGGGAAACGAGA 371–372 1.000 77.3
rps2-rpoC2_p2 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG CGAGGGGGAAACGAGAGATA 367–368 1.000 76.0
rps2-rpoC2_p3 rps2-rpoC2 AAATGAACTCCTGCCTCCAG TATTCGAGGGGGAAACGAGA 384–385 1.000 75.8
rps2-rpoC2_p4 rps2-rpoC2 AAATGAACTCCTGCCTCCAG CGAGGGGGAAACGAGAGATA 380–381 1.000 74.5
rps2-rpoC2_p5 rps2-rpoC2 CCATGGCCAAAATGAACTCC TATTCGAGGGGGAAACGAGA 393–394 1.000 74.4
psaA-ycf3_p1 psaA-ycf3 TGAGAAATGACCCGGTTTGG ATCAAGCCGCTGAGTATTGG 919–939 1.000 82.0
psaA-ycf3_p2 psaA-ycf3 TGAGAAATGACCCGGTTTGG GGAAACAGGCTATAGCGCTT 901–921 1.000 82.0
psaA-ycf3_p3 psaA-ycf3 TGAGAAATGACCCGGTTTGG TTGAAGATCACGAGGCGTTT 848–868 1.000 81.3
psaA-ycf3_p4 psaA-ycf3 TGAGAAATGACCCGGTTTGG TTGGTTGAAGATCACGAGGC 852–872 1.000 81.0
psaA-ycf3_p5 psaA-ycf3 TGAGAAATGACCCGGTTTGG AGCCGCTGAGTATTGGAAAC 915–935 1.000 80.3
ycf3-tRNA-Ser (GGA)_p1 ycf3-tRNA-Ser (GGA) TGCCTCCTTTTCTCCTGAAG CCCTCGGTAAACAAAAGCCT 1036–1061 1.000 73.4
ycf3-tRNA-Ser (GGA)_p2 ycf3-tRNA-Ser (GGA) GCCTCCTTTTCTCCTGAAGT CCCTCGGTAAACAAAAGCCT 1035–1060 1.000 73.4
ycf3-tRNA-Ser (GGA)_p3 ycf3-tRNA-Ser (GGA) TGCCTCCTTTTCTCCTGAAG ACGGAAAGAGAGGGATTCGA 1057–1082 1.000 72.9
ycf3-tRNA-Ser (GGA)_p4 ycf3-tRNA-Ser (GGA) GCCTCCTTTTCTCCTGAAGT ACGGAAAGAGAGGGATTCGA 1056–1081 1.000 72.9
ycf3-tRNA-Ser (GGA)_p5 ycf3-tRNA-Ser (GGA) TGCCTCCTTTTCTCCTGAAG TTCCAATGCTACGCCTTGAA 1007–1032 1.000 72.6
tRNA-Phe (GAA)-ndhJ_p1 tRNA-Phe (GAA)-ndhJ GGGATAGCTCAGCTGGTAGA AGTTGGATAGGATGGCCCTT 796–813 1.000 81.5
tRNA-Phe (GAA)-ndhJ_p2 tRNA-Phe (GAA)-ndhJ GGATGCTACATTGGGACTGG AGTTGGATAGGATGGCCCTT 818–835 1.000 81.2
tRNA-Phe (GAA)-ndhJ_p3 tRNA-Phe (GAA)-ndhJ GGGATGCTACATTGGGACTG AGTTGGATAGGATGGCCCTT 819–836 1.000 81.2
tRNA-Phe (GAA)-ndhJ_p4 tRNA-Phe (GAA)-ndhJ CCTCGTGTCACCAGTTCAAA AGTTGGATAGGATGGCCCTT 760–777 1.000 81.2
tRNA-Phe (GAA)-ndhJ_p5 tRNA-Phe (GAA)-ndhJ CTGGTAGAGCAGAGGACTGA AGTTGGATAGGATGGCCCTT 784–801 1.000 80.4

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
Sesamum indicum NC_016433.2 153324 View on NCBI ↗
Sesamum schinzianum PZ173272.1 153121 View on NCBI ↗