Markers + reference

Nigella

18 species · Ranunculaceae · Ranunculales

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Species 18
Genome length 154–156 kb
Candidate markers 262
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnT-UGU-trnF-GAA LSC 1802 0.0175 1.00 64.5 yes View details
rpl16 LSC 1469 0.0188 1.00 58.1 yes View details
ndhF-trnL-UAG SSC 871 0.0269 1.00 64.5 yes View details
ycf1 SSC 5085 0.0386 1.00 63.4 yes View details
petN-psbM LSC 1181 0.0151 0.99 66.4 yes View details
rpl2-trnH-GUG IRa 100 0.0397 1.00 65.6 no View details
atpF-atpH LSC 478 0.0264 1.00 65.3 yes View details
rpl33-rps18 LSC 211 0.0297 0.95 65.2 yes View details
trnD-GUC-trnY-GUA LSC 390 0.0313 1.00 62.7 yes View details
ndhG-ndhI SSC 381 0.0286 0.99 62.7 yes View details
trnY-GUA-trnE-UUC LSC 68 0.0444 1.00 62.4 yes View details
ndhC-trnV-UAC LSC 1087 0.0143 1.00 62.3 yes View details
rpl22-rps19 LSC 94 0.0492 0.88 61.9 yes View details
rps12-clpP LSC 165 0.0354 1.00 60.9 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
atpF-atpH_p1 atpF-atpH CAGTGACCCAAGGAAACGAA TTTGCAAATCCCTTTGTTTAA 533–568 1.000 49.7
atpF-atpH_p2 atpF-atpH AGTGACCCAAGGAAACGAAA ATTTGCAAATCCCTTTGTTT 533–568 1.000 49.7
atpF-atpH_p3 atpF-atpH CAGTGACCCAAGGAAACGAA ATTTGCAAATCCCTTTGTTT 534–569 1.000 49.6
atpF-atpH_p4 atpF-atpH CAGTGACCCAAGGAAACGAA ATTTGCAAATCCCTTTGTTTA 534–569 1.000 49.6
atpF-atpH_p5 atpF-atpH CAGTGACCCAAGGAAACGAA CTTTTATTTGCAAATCCCTTTGT 539–574 1.000 49.5
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 1285–1336 1.000 76.6
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 1291–1342 1.000 75.1
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1231–1282 1.000 74.0
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTC 1285–1336 1.000 72.4
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTC 1291–1342 1.000 71.0
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA ATACTAGGTCGGGACTGACG TGGCAATATGTCTACGCTGG 502–513 1.000 85.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA ATACTAGGTCGGGACTGACG GGCAATATGTCTACGCTGGT 501–512 1.000 85.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA ATACTAGGTCGGGACTGACG GGGGACGGACTGTAAATTCG 523–534 1.000 84.1
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA ATACTAGGTCGGGACTGACG GGGACGGACTGTAAATTCGT 522–533 1.000 84.0
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CATCGGATACTAGGTCGGGA TGGCAATATGTCTACGCTGG 508–519 1.000 84.0
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CCAGCGTAGACATATTGCCA CTCTCTTTCAAGGAGGCAGC 177–200 1.000 81.8
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACCAGCGTAGACATATTGCC CTCTCTTTCAAGGAGGCAGC 178–201 1.000 81.7
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CGAATTTACAGTCCGTCCCC CTCTCTTTCAAGGAGGCAGC 156–179 1.000 81.1
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC ACGAATTTACAGTCCGTCCC CTCTCTTTCAAGGAGGCAGC 157–180 1.000 80.9
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC GCCAACGAATTTACAGTCCG CTCTCTTTCAAGGAGGCAGC 161–184 1.000 79.6
trnT-UGU-trnF-GAA_p1 trnT-UGU-trnF-GAA GCGATGCTCTAACCTCTGAG TTTGAACTGGTGACACGAGG 1813–1950 1.000 86.8
trnT-UGU-trnF-GAA_p2 trnT-UGU-trnF-GAA GCGATGCTCTAACCTCTGAG TTAACCACATGCCAGGAACC 1836–1973 1.000 86.6
trnT-UGU-trnF-GAA_p3 trnT-UGU-trnF-GAA GCGATGCTCTAACCTCTGAG CACATGCCAGGAACCAGATT 1831–1968 1.000 86.0
trnT-UGU-trnF-GAA_p4 trnT-UGU-trnF-GAA GGAATCGAACCGATGACCAT TTTGAACTGGTGACACGAGG 1845–1982 1.000 85.9
trnT-UGU-trnF-GAA_p5 trnT-UGU-trnF-GAA GGAATCGAACCGATGACCAT TTAACCACATGCCAGGAACC 1868–2005 1.000 85.6
ndhC-trnV-UAC_p1 ndhC-trnV-UAC CCTTCGTTAATTGGGGCCAA AGTGCATGTTGGGTCTTTGA 1282–1318 1.000 79.0
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TAATTGGGGCCAAAACTCCG AGTGCATGTTGGGTCTTTGA 1275–1311 1.000 79.0
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TGGTCCTTCGTTAATTGGGG AGTGCATGTTGGGTCTTTGA 1286–1322 1.000 78.6
ndhC-trnV-UAC_p4 ndhC-trnV-UAC CCTTCGTTAATTGGGGCCAA AGAAGGTCTACGGTTCGAGA 1215–1251 1.000 78.3
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TAATTGGGGCCAAAACTCCG AGAAGGTCTACGGTTCGAGA 1208–1244 1.000 78.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (18)

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

Species Accession Length (bp) Link
Nigella arvensis subsp. aristata ON897798.1 154293 View on NCBI ↗
Nigella arvensis subsp. arvensis ON897799.1 154281 View on NCBI ↗
Nigella arvensis subsp. brevifolia ON897800.1 154360 View on NCBI ↗
Nigella arvensis subsp. glauca ON897801.1 154377 View on NCBI ↗
Nigella carpatha ON897805.1 154223 View on NCBI ↗
Nigella ciliaris ON897806.1 155585 View on NCBI ↗
Nigella damascena NC_041537.1 155218 View on NCBI ↗
Nigella degenii subsp. barbro ON897804.1 154334 View on NCBI ↗
Nigella degenii subsp. degenii ON897802.1 154275 View on NCBI ↗
Nigella degenii subsp. jenny ON897803.1 154259 View on NCBI ↗
Nigella doerfleri ON897808.1 154279 View on NCBI ↗
Nigella elata ON897809.1 154834 View on NCBI ↗
Nigella fumariifolia ON897810.1 153979 View on NCBI ↗
Nigella icarica ON897811.1 154313 View on NCBI ↗
Nigella orientalis ON897814.1 155585 View on NCBI ↗
Nigella papillosa ON897815.1 153952 View on NCBI ↗
Nigella sativa NC_083219.1 154120 View on NCBI ↗
Nigella stricta ON897817.1 154158 View on NCBI ↗