Markers + reference

Triumfetta

7 species · Malvaceae · Malvales

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Species 7
Genome length 160–160 kb
Candidate markers 268
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 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
trnS-GCU-trnS-CGA LSC 777 0.0076 0.99 58.1 yes View details
atpF-atpH LSC 615 0.0116 1.00 67.8 yes View details
psbD LSC 1062 0.0048 1.00 44.5 yes View details
psbZ-trnG-GCC LSC 734 0.0099 0.99 66.3 yes View details
trnF-GAA-ndhJ LSC 710 0.0087 1.00 57.0 yes View details
petA-psbJ LSC 1132 0.0092 1.00 48.0 yes View details
psbE-petL LSC 854 0.0059 1.00 53.5 yes View details
rpl33-rps18 LSC 619 0.0131 0.95 55.3 yes View details
rps8 LSC 405 0.0049 1.00 40.2 yes View details
ndhD SSC 1503 0.0027 1.00 44.3 yes View details
trnL-UAG-rpl32 SSC 1217 0.0065 1.00 42.1 yes View details
rpl2-trnH-GUG IRa 165 0.0044 1.00 64.9 no View details
clpP1 LSC 2169 0.0026 1.00 61.3 yes View details
ndhD-ccsA SSC 317 0.0143 1.00 58.6 yes View details
ndhC-trnC-ACA LSC 1064 0.0064 0.99 57.4 yes View details
psaC-ndhD SSC 146 0.0398 1.00 57.3 yes View details
atpH-atpI LSC 1198 0.0047 1.00 57.1 yes View details
rbcL-accD LSC 711 0.0031 1.00 56.5 yes View details
rps16-trnQ-UUG LSC 610 0.0056 1.00 56.4 yes View details
trnL-CAA-ndhB IRb 634 0.0032 1.00 55.0 yes View details
ndhB-trnL-CAA IRa 634 0.0032 1.00 55.0 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC GAGGTTCGAATCCTTCCGTC 704–731 1.000 82.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 683–710 1.000 82.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 681–708 1.000 82.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AGTGGTGGGTTTTGACATCC TAAGGCATCGGGTTTTGGTC 734–761 1.000 81.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA TAAGGCATCGGGTTTTGGTC 713–740 1.000 81.6
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA GCTCGGAATATGAATCAAACCG 892–916 1.000 65.0
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC GCTCGGAATATGAATCAAACCG 891–915 1.000 65.0
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA GAAAGAGGGGGATTCGAACC GCTCGGAATATGAATCAAACCG 943–967 1.000 64.6
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA GGAAAGAGGGGGATTCGAAC GCTCGGAATATGAATCAAACCG 944–968 1.000 64.6
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CGCACAACGGATTAGCAATC GCTCGGAATATGAATCAAACCG 907–931 1.000 64.3
atpF-atpH_p1 atpF-atpH CCAGTGACCCAAAGAAACGA TGGTTGTAGCATTGGCACTT 689–715 1.000 85.4
atpF-atpH_p2 atpF-atpH CCAGTGACCCAAAGAAACGA TTGGTTGTAGCATTGGCACT 690–716 1.000 85.4
atpF-atpH_p3 atpF-atpH CCAGTGACCCAAAGAAACGA GTTGGTTGTAGCATTGGCAC 691–717 1.000 85.0
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TGGTTGTAGCATTGGCACTT 716–742 1.000 84.6
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG TTGGTTGTAGCATTGGCACT 717–743 1.000 84.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1255–1257 1.000 79.2
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 1311–1313 1.000 78.6
atpH-atpI_p3 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1256–1258 1.000 78.1
atpH-atpI_p4 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 1315–1317 1.000 78.0
atpH-atpI_p5 atpH-atpI GGCAGTACCTTGACCAACTC CGAATCCATGGAGGGTCATC 1316–1318 1.000 78.0
psbD_p1 psbD ATTATAAGGGGCAGTGCACG ACGACCGGCTAAAGCTAAAG 1201 1.000 80.9
psbD_p2 psbD ATTATAAGGGGCAGTGCACG CGACCGGCTAAAGCTAAAGT 1200 1.000 80.9
psbD_p3 psbD CCAAACGCCCCCATAACATA ACGACCGGCTAAAGCTAAAG 1150 1.000 80.7
psbD_p4 psbD CCAAACGCCCCCATAACATA CGACCGGCTAAAGCTAAAGT 1149 1.000 80.7
psbD_p5 psbD TGCTCGGAAATGGTTGAAGT CGACCGGCTAAAGCTAAAGT 1126 1.000 79.1
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 891–993 1.000 81.9
psbZ-trnG-GCC_p2 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTT CGTCTTCTCCTTGGCAAAGA 889–991 1.000 81.9
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG TACATTGACCTGGGCGGATA 927–1029 1.000 81.5
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTT TACATTGACCTGGGCGGATA 925–1027 1.000 81.5
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG AAATACATTGACCTGGGCGG 930–1032 1.000 81.2

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
Triumfetta appendiculata BK065791.1 160237 View on NCBI ↗
Triumfetta chaetocarpa BK065792.1 160201 View on NCBI ↗
Triumfetta clementii BK065793.1 160114 View on NCBI ↗
Triumfetta johnstonii BK065794.1 160165 View on NCBI ↗
Triumfetta leptacantha BK065795.1 160334 View on NCBI ↗
Triumfetta maconochieana BK064973.1 160075 View on NCBI ↗
Triumfetta ramosa BK065796.1 160241 View on NCBI ↗