Markers + reference

Isatis

9 species · Brassicaceae · Brassicales

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Species 9
Genome length 153–157 kb
Candidate markers 270
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 568 0.0936 0.88 73.0 yes View details
trnS-GCU-trnT-CGU LSC 668 0.0279 0.99 72.8 yes View details
ndhC-trnV-UAC LSC 683 0.0296 1.00 66.1 yes View details
petA-psbJ LSC 956 0.0218 1.00 62.4 yes View details
ycf1 IRb 1032 0.0010 1.00 34.7 no View details
ndhF-rpl32 SSC 809 0.0257 0.99 62.0 yes View details
rpl32-trnL-UAG SSC 714 0.0474 0.98 79.7 yes View details
ycf1 SSC 5310 0.0198 1.00 45.9 yes View details
psaJ-rpl33 LSC 441 0.0291 1.00 70.0 yes View details
trnT-CGU-trnR-UCU LSC 161 0.0393 0.99 65.4 yes View details
trnE-trnT-GGU LSC 822 0.0219 1.00 65.2 yes View details
rpl36-rps8 LSC 469 0.0268 0.98 63.1 yes View details
trnM-CAU-atpE LSC 137 0.0328 1.00 61.1 yes View details
psbE-petL LSC 1364 0.0168 1.00 60.9 yes View details
trnT-UGU-trnL-UAA LSC 761 0.0182 0.99 60.5 yes View details
psbI-trnS-GCU LSC 85 0.0261 1.00 59.9 yes View details
rps16-trnQ-UUG LSC 452 0.0191 1.00 58.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 341–673 1.000 90.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 356–688 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTCCCTCTAGACCTAGCTGC 359–691 1.000 90.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GCTGTTGAGGCTCCATCTAC 342–674 1.000 90.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTAGACCTAGCTGCTGT 357–689 1.000 90.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTTACAGCTGCTTGCCAAAC 1067–1099 1.000 83.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAACGCTTGATTCACGCATG GAGGTTCGAATCCTTCCGTC 867–899 0.889 81.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAAACGCTTGATTCACGCAT GAGGTTCGAATCCTTCCGTC 868–900 0.889 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAACGCTTGATTCACGCATG CTTACAGCTGCTTGCCAAAC 1431–1466 0.889 79.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAAACGCTTGATTCACGCAT CTTACAGCTGCTTGCCAAAC 1432–1467 0.889 79.8
psbI-trnS-GCU_p1 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT TAGGAGAGATGGCTGAGTGG 209–224 1.000 61.6
psbI-trnS-GCU_p2 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT TGAGTGGACTAAAGCGTTGG 196–211 1.000 61.3
psbI-trnS-GCU_p3 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT GCTGAGTGGACTAAAGCGTT 198–213 1.000 61.0
psbI-trnS-GCU_p4 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT CGAGTTAATCGTACCGAGGG 159–174 1.000 60.2
psbI-trnS-GCU_p5 psbI-trnS-GCU TCCTATCTAATGATCCAGGACGT ATGGCTGAGTGGACTAAAGC 201–216 1.000 59.2
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CCAACGCTTTAGTCCACTCA AGGGGTTAAAGGAACGAATCA 691–840 1.000 72.0
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU CCAACGCTTTAGTCCACTCA GGGGTTAAAGGAACGAATCAC 690–839 1.000 71.8
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU AACGCTTTAGTCCACTCAGC AGGGGTTAAAGGAACGAATCA 689–838 1.000 71.7
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU AACGCTTTAGTCCACTCAGC GGGGTTAAAGGAACGAATCAC 688–837 1.000 71.5
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU CCAACGCTTTAGTCCACTCA AGGGGTTAAAGGAACGAATCAC 691–840 1.000 70.1
trnT-CGU-trnR-UCU_p1 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTATGTCCT 245–251 1.000 50.6
trnT-CGU-trnR-UCU_p2 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTATGTCCTATCCA 239–245 1.000 50.5
trnT-CGU-trnR-UCU_p3 trnT-CGU-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTATGTCCT 251–257 1.000 50.4
trnT-CGU-trnR-UCU_p4 trnT-CGU-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGAAGACCTATGTCCTATCCA 245–251 1.000 50.3
trnT-CGU-trnR-UCU_p5 trnT-CGU-trnR-UCU CGACGTCGACTAAAACCCTT AGGTTTAGAAGACCTATGTCCT 265–271 1.000 50.0
trnE-trnT-GGU_p1 trnE-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 899–929 1.000 86.3
trnE-trnT-GGU_p2 trnE-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 878–908 1.000 86.2
trnE-trnT-GGU_p3 trnE-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 878–908 1.000 85.9
trnE-trnT-GGU_p4 trnE-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 857–887 1.000 85.9
trnE-trnT-GGU_p5 trnE-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 875–905 1.000 85.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

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

Species Accession Length (bp) Link
Isatis cappadocica NC_061905.1 153800 View on NCBI ↗
Isatis costata NC_072555.1 153818 View on NCBI ↗
Isatis gymnocarpa NC_081128.1 153161 View on NCBI ↗
Isatis indigotica PX118598.1 153823 View on NCBI ↗
Isatis minima NC_072727.1 153643 View on NCBI ↗
Isatis multicaulis PQ059879.1 153609 View on NCBI ↗
Isatis oblongata NC_081129.1 153643 View on NCBI ↗
Isatis tinctoria NC_028415.1 156670 View on NCBI ↗
Isatis violascens NC_072728.1 153262 View on NCBI ↗