Markers + reference

Viola

42 species · Violaceae · Malpighiales

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Species 42
Genome length 156–159 kb
Candidate markers 260
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 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0031 1.00 35.8 yes View details
trnK-UUU-trnQ-UUG LSC 704 0.0433 0.85 77.4 yes View details
trnG-UCC-trnR-UCU LSC 592 0.0527 0.88 77.7 yes View details
petN-psbM LSC 1272 0.0242 0.94 66.1 yes View details
trnE-UUC-trnT-GGU LSC 939 0.0273 0.97 76.5 yes View details
psbZ-trnG-GCC LSC 1029 0.0343 0.85 70.2 yes View details
ndhC-trnV-UAC LSC 863 0.0279 0.88 75.7 yes View details
rpl33-rps18 LSC 362 0.0612 0.79 72.6 yes View details
ndhF-trnL-UAG SSC 1725 0.0367 0.97 74.0 yes View details
petA-psbJ LSC 1119 0.0265 0.98 71.5 yes View details
rpl2-trnH-GUG LSC 184 0.0981 0.74 70.3 no View details
trnD-GUC-trnY-GUA LSC 388 0.0321 0.97 70.1 yes View details
clpP-psbB LSC 739 0.0205 0.95 69.6 yes View details
psbM-trnD-GUC LSC 1212 0.0154 0.98 67.7 yes View details
ycf4-cemA LSC 438 0.0225 0.93 67.1 yes View details
trnS-GCU-trnG-UCC LSC 642 0.0164 0.94 67.0 yes View details
psaI-ycf4 LSC 456 0.0205 1.00 67.0 yes View details
rpoB-trnC-GCA LSC 1157 0.0117 0.99 66.7 yes View details
trnL-UAG-ccsA SSC 151 0.0326 0.87 66.1 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA CATGGTGGATTCACAACCCA AAAGGGCGGGTTTGGTATTT 1995–2208 0.976 87.7
psbA_p2 psbA CATGGTGGATTCACAACCCA AAGGGCGGGTTTGGTATTTT 1994–2207 0.976 87.7
psbA_p3 psbA GATCCACTTGGCTACATCCG AAAGGGCGGGTTTGGTATTT 1968–2181 0.976 87.3
psbA_p4 psbA GATCCACTTGGCTACATCCG AAGGGCGGGTTTGGTATTTT 1967–2180 0.976 87.3
psbA_p5 psbA CATGGTGGATTCACAACCCA AATTCGTGTGCTTGGGAGTT 1350–1581 1.000 86.3
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CGTTAGCCGCACTTAAAAGC GAGGTTCGAATCCTTCCGTC 616–787 1.000 90.4
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG GTTAGCCGCACTTAAAAGCC GAGGTTCGAATCCTTCCGTC 615–786 1.000 89.3
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG CCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 610–781 1.000 89.1
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAAAGACGTTAGCCGCACTT GAGGTTCGAATCCTTCCGTC 622–793 1.000 88.1
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG AGACGTTAGCCGCACTTAAA GAGGTTCGAATCCTTCCGTC 619–790 1.000 87.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGCCGAAGATCCCTTAACTT 650–756 1.000 80.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TGCCGAAGATCCCTTAACTT 649–755 1.000 80.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATGCCGAAGATCCCTTAACT 651–757 1.000 78.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATGCCGAAGATCCCTTAACT 650–756 1.000 78.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TGCCGAAGATCCCTTAACTTT 650–756 1.000 78.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 533–789 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 536–792 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 539–795 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 542–798 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 537–793 1.000 72.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTCCATCCCCAAG CCGGATTTGAACTGGGGAAA 1113–1285 1.000 90.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CTCATTTCCATCCCCAAGCA CCGGATTTGAACTGGGGAAA 1111–1283 1.000 89.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTCCATCCCCAA CCGGATTTGAACTGGGGAAA 1114–1286 1.000 88.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCCCTCATTTCCATCCCCA CCGGATTTGAACTGGGGAAA 1115–1287 1.000 88.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTCCATCCCCAAG AAAAGGATTTGCAGTCCCCC 1095–1267 1.000 88.1
petN-psbM_p1 petN-psbM AGTATGGGGAAGAAGTGGACT TGCTACTGCACTGTTTATTCT 884–1385 1.000 52.3
petN-psbM_p2 petN-psbM AGTATGGGGAAGAAGTGGACT ACTGCACTGTTTATTCTAGTTCCT 880–1381 1.000 52.0
petN-psbM_p3 petN-psbM AGTATGGGGAAGAAGTGGAC TGCTACTGCACTGTTTATTCT 884–1385 1.000 52.0
petN-psbM_p4 petN-psbM GTATGGGGAAGAAGTGGACT TGCTACTGCACTGTTTATTCT 883–1384 1.000 52.0
petN-psbM_p5 petN-psbM AGTATGGGGAAGAAGTGGACT TGCTACTGCACTGTTTATTCTAGT 884–1376 0.952 50.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (42)

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

Species Accession Length (bp) Link
Viola acuminata NC_064999.1 158940 View on NCBI ↗
Viola albida NC_069576.1 157542 View on NCBI ↗
Viola arcuata NC_061694.1 157870 View on NCBI ↗
Viola belophylla NC_065004.1 156580 View on NCBI ↗
Viola betonicifolia NC_065257.1 156395 View on NCBI ↗
Viola biflora NC_068138.1 158070 View on NCBI ↗
Viola canina PP622712.1 158035 View on NCBI ↗
Viola chaerophylloides NC_065000.1 157113 View on NCBI ↗
Viola collina NC_065001.1 157890 View on NCBI ↗
Viola diffusa PP952083.1 157904 View on NCBI ↗
Viola dissecta NC_065002.1 157113 View on NCBI ↗
Viola faurieana PZ127156.1 158237 View on NCBI ↗
Viola grypoceras NC_061911.1 158357 View on NCBI ↗
Viola inconspicua NC_065003.1 156624 View on NCBI ↗
Viola japonica NC_057486.1 156504 View on NCBI ↗
Viola jordanii PZ127157.1 158489 View on NCBI ↗
Viola kunawurensis NC_060866.1 156837 View on NCBI ↗
Viola kusanoana NC_068137.1 158644 View on NCBI ↗
Viola labradorica NC_080538.1 158751 View on NCBI ↗
Viola mandshurica PZ316350.1 156476 View on NCBI ↗
Viola mirabilis NC_041582.1 158162 View on NCBI ↗
Viola mongolica NC_065005.1 156870 View on NCBI ↗
Viola orientalis NC_068136.1 157774 View on NCBI ↗
Viola patrinii NC_065006.1 156508 View on NCBI ↗
Viola phalacrocarpa NC_041583.1 157842 View on NCBI ↗
Viola philippica NC_052919.1 156469 View on NCBI ↗
Viola prionantha NC_057663.1 156501 View on NCBI ↗
Viola raddeana NC_041584.1 157597 View on NCBI ↗
Viola ramiflora NC_068135.1 156717 View on NCBI ↗
Viola rostrata PZ127158.1 158179 View on NCBI ↗
Viola selkirkii NC_059909.1 157451 View on NCBI ↗
Viola seoulensis NC_026986.1 156507 View on NCBI ↗
Viola suavis NC_066026.1 158145 View on NCBI ↗
Viola takesimana NC_080347.1 158287 View on NCBI ↗
Viola thomasiana PP622713.1 158125 View on NCBI ↗
Viola vaginata LC802718.2 158056 View on NCBI ↗
Viola variegata NC_065007.1 156582 View on NCBI ↗
Viola verecunda MW586692.1 157843 View on NCBI ↗
Viola websteri NC_041585.1 158111 View on NCBI ↗
Viola woosanensis NC_068134.1 157809 View on NCBI ↗
Viola yezoensis NC_065008.1 156537 View on NCBI ↗
Viola yunnanfuensis NC_065009.1 156974 View on NCBI ↗