Markers + reference

Jaltomata

2 species · Solanaceae · Solanales

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Species 2
Genome length 155–156 kb
Candidate markers 272
Primer pairs 95

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 6 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpH-atpI LSC 1171 0.0051 1.00 61.7 yes View details
ycf3-trnS-GGA LSC 837 0.0048 1.00 61.5 yes View details
accD-psaI LSC 735 0.0082 1.00 63.4 yes View details
psbB LSC 1527 0.0026 0.99 55.5 yes View details
psbB-psbT LSC 197 0.0152 1.00 61.3 yes View details
ycf15-ndhB IRb 968 0.0041 1.00 61.1 yes View details
trnR-ACG-trnN-GUU SSC 578 0.0069 1.00 62.3 yes View details
rps15-ycf1 SSC 3940 0.0013 1.00 54.9 yes View details
ycf1-trnN-GUU SSC 328 0.0000 1.00 26.2 yes View details
trnN-GUU-trnR-ACG SSC 578 0.0069 1.00 62.3 yes View details
ndhB-trnL-CAA IRa 539 0.0000 1.00 34.5 yes View details
trnL-CAA-ycf15 IRa 348 0.0115 1.00 60.1 yes View details
rpl32-sprA SSC 43 0.0233 1.00 65.9 yes View details
trnK-rps16 LSC 699 0.0043 1.00 61.2 yes View details
rbcL-accD LSC 756 0.0026 1.00 60.3 yes View details
petA-psbJ LSC 1091 0.0027 1.00 60.3 yes View details
atpB-rbcL LSC 810 0.0025 1.00 60.2 yes View details
trnE-UUC-trnT-GGU LSC 842 0.0024 1.00 60.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-rps16_p1 trnK-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGGGCTCAACCT 831–834 1.000 75.2
trnK-rps16_p2 trnK-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGGGCTCAACCT 830–833 1.000 75.2
trnK-rps16_p3 trnK-rps16 TCAGTCGTGGTCTTCCAAAC TTGAAAAAGGGGCTCAACCT 916–919 1.000 74.6
trnK-rps16_p4 trnK-rps16 CAGTCGTGGTCTTCCAAACT TTGAAAAAGGGGCTCAACCT 915–918 1.000 74.6
trnK-rps16_p5 trnK-rps16 AAAAGACACTAGCCGCACTT TTGAAAAAGGGGCTCAACCT 852–855 1.000 74.5
atpH-atpI_p1 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1390–1397 1.000 78.8
atpH-atpI_p2 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1322–1329 1.000 78.3
atpH-atpI_p3 atpH-atpI TCCAGCAGCAATAACGGAAG TACCTGTCATGCTCCTTGGA 1317–1324 1.000 77.9
atpH-atpI_p4 atpH-atpI AATCCAGCAGCAATAACGGA TACCTGTCATGCTCCTTGGA 1319–1326 1.000 76.6
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TACCTGTCATGCTCCTTGGA 1318–1325 1.000 76.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 983–1024 1.000 78.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 962–1003 1.000 78.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 959–1000 1.000 78.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 945–986 1.000 78.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 980–1021 1.000 77.7
ycf3-trnS-GGA_p1 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA GCGAAGGTACGGAAAGAGAG 1029 1.000 66.9
ycf3-trnS-GGA_p2 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA GCGAAGGTACGGAAAGAGAG 1030 1.000 66.9
ycf3-trnS-GGA_p3 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA CCCTCGGTAAACAAAAGCCT 1000 1.000 66.9
ycf3-trnS-GGA_p4 ycf3-trnS-GGA TTTCTCCTGAAGTTGTCGGA CCCTCGGTAAACAAAAGCCT 1001 1.000 66.9
ycf3-trnS-GGA_p5 ycf3-trnS-GGA TTCTCCTGAAGTTGTCGGAA ACGGAAAGAGAGGGATTCGA 1021 1.000 66.4
trnV-UAC_p1 trnV-UAC ATCTGCTTAAACGATTGCCG TGTTGATGTTGGATCATGGA 824–844 1.000 44.2
trnV-UAC_p2 trnV-UAC ATCTGCTTAAACGATTGCCG TGTTGATGTTGGATCATGGAA 824–844 1.000 43.0
trnV-UAC_p3 trnV-UAC ATCTGCTTAAACGATTGCCG TTGTTGATGTTGGATCATGGA 825–845 1.000 43.0
trnV-UAC_p4 trnV-UAC CATCTGCTTAAACGATTGCCG TGTTGATGTTGGATCATGGA 825–845 1.000 42.8
trnV-UAC_p5 trnV-UAC CATCTGCTTAAACGATTGCCG TGTTGATGTTGGATCATGGAA 825–845 1.000 41.6
atpB-rbcL_p1 atpB-rbcL GACCGATGATTTGGACGACA CACCAGCTTTGAATCCAACAC 944–951 1.000 72.0
atpB-rbcL_p2 atpB-rbcL GACCGATGATTTGGACGACA ACCAGCTTTGAATCCAACACT 943–950 1.000 71.7
atpB-rbcL_p3 atpB-rbcL GACCGATGATTTGGACGACA CCTTGGTTTGGTACTCAGGAG 992–999 1.000 71.6
atpB-rbcL_p4 atpB-rbcL GGAAACCCCAGAACCAGAAG CACCAGCTTTGAATCCAACAC 898–905 1.000 71.3
atpB-rbcL_p5 atpB-rbcL GGAAACCCCAGAACCAGAAG ACCAGCTTTGAATCCAACACT 897–904 1.000 71.1

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
Jaltomata bicolor NC_062862.1 155459 View on NCBI ↗
Jaltomata sinuosa NC_062863.1 156163 View on NCBI ↗