Markers + reference

Sisymbrium

6 species · Brassicaceae · Brassicales

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Species 6
Genome length 154–155 kb
Candidate markers 270
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 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-CAC-psbA LSC 295 0.0643 0.93 71.5 yes View details
rps16-trnQ-CAA LSC 447 0.0267 1.00 65.4 yes View details
trnS-AGC-trnG-GGA LSC 626 0.0252 0.98 68.0 yes View details
trnD-GAC-trnY-UAC LSC 439 0.0243 1.00 58.3 yes View details
trnE-GAA-trnT-ACC LSC 785 0.0229 0.99 66.6 yes View details
atpB-rbcL LSC 785 0.0216 1.00 58.6 yes View details
petA-psbJ LSC 974 0.0220 1.00 62.6 yes View details
psbE-petL LSC 1091 0.0254 0.99 63.8 yes View details
rpl36-rps8 LSC 478 0.0307 0.97 64.1 yes View details
ycf1 IRb 1041 0.0019 1.00 34.2 no View details
ndhF-rpl32 SSC 853 0.0258 0.89 59.4 yes View details
rpl32-trnL-CUA SSC 639 0.0307 0.99 69.8 yes View details
ycf1 SSC 5289 0.0162 1.00 46.3 yes View details
ndhE-ndhG SSC 96 0.0437 1.00 67.3 yes View details
trnR-CGU-trnN-AAC IRb 617 0.0087 1.00 62.4 yes View details
trnN-AAC-trnR-CGU IRa 617 0.0084 1.00 62.3 yes View details
psbK-psbI LSC 292 0.0331 0.98 61.6 yes View details
ycf3-trnS-UCC LSC 1090 0.0107 0.99 61.0 yes View details
trnL-CUA-ccsA SSC 112 0.0274 1.00 61.0 yes View details
trnT-ACA-trnL-UUA LSC 745 0.0165 0.99 60.0 yes View details
trnF-UUC-ndhJ LSC 613 0.0174 0.95 58.6 yes View details
trnC-UGC-petN LSC 606 0.0164 1.00 57.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-CAC-psbA_p1 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GCTGTTGAGGCTCCATCTAC 338–353 1.000 90.5
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT CCTCTAGACCTAGCTGCTGT 353–368 1.000 90.4
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GGTGTAGCTGGTGTATTCGG 770–785 1.000 86.7
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GTTGATAGTCAAGGACGCGT 467 0.167 45.5
trnH-CAC-psbA_p5 trnH-CAC-psbA ACTGCCTTAATCCACTTGGC GTTGATAGTCAAGGACGCGT 468 0.167 45.3
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGGTGGCGGATCAAAACAT GAGGTTCGAATCCTTCCGTC 566–596 1.000 83.5
rps16-trnQ-CAA_p2 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 520–550 1.000 83.4
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 530–560 1.000 82.5
rps16-trnQ-CAA_p4 rps16-trnQ-CAA AAAGGTGGCGGATCAAAACA GAGGTTCGAATCCTTCCGTC 567–597 1.000 81.7
rps16-trnQ-CAA_p5 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 546–576 1.000 80.9
psbK-psbI_p1 psbK-psbI CAAGCAGCTGTCAGTTTTCG ACGGTGTATACAAAAAGTTTGAGA 347–354 1.000 47.1
psbK-psbI_p2 psbK-psbI CAAGCAGCTGTCAGTTTTCG ACGGTGTATACAAAAAGTTTGAGAG 347–354 1.000 47.1
psbK-psbI_p3 psbK-psbI CAAGCAGCTGTCAGTTTTCG CGGTGTATACAAAAAGTTTGAGAGT 346–353 1.000 47.1
psbK-psbI_p4 psbK-psbI AAGCAGCTGTCAGTTTTCGA ACGGTGTATACAAAAAGTTTGAGA 346–353 1.000 47.1
psbK-psbI_p5 psbK-psbI AAGCAGCTGTCAGTTTTCGA CGGTGTATACAAAAAGTTTGAGAGT 345–352 1.000 47.1
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 734–769 1.000 73.2
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 733–768 1.000 73.2
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 732–767 1.000 72.9
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 731–766 1.000 72.9
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 734–769 1.000 71.2
trnC-UGC-petN_p1 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 707–743 1.000 83.2
trnC-UGC-petN_p2 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 708–744 1.000 82.6
trnC-UGC-petN_p3 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CTTCCCCACACTACGAGAGA 703–739 1.000 81.9
trnC-UGC-petN_p4 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG TCTTCCCCACACTACGAGAG 704–740 1.000 81.9
trnC-UGC-petN_p5 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG TTCCCCACACTACGAGAGAG 702–738 1.000 81.9
trnD-GAC-trnY-UAC_p1 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 509–533 1.000 78.2
trnD-GAC-trnY-UAC_p2 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 508–532 1.000 78.2
trnD-GAC-trnY-UAC_p3 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 530–554 1.000 77.2
trnD-GAC-trnY-UAC_p4 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 529–553 1.000 77.0
trnD-GAC-trnY-UAC_p5 trnD-GAC-trnY-UAC CGGTGCTCTGACCAATTGAA CGGACTGTAAATTCGTTGGC 525–549 1.000 75.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Sisymbrium aculeolatum MK637787.1 153595 View on NCBI ↗
Sisymbrium altissimum NC_059802.1 154042 View on NCBI ↗
Sisymbrium irio NC_037838.1 154001 View on NCBI ↗
Sisymbrium loeselii NC_081131.1 154600 View on NCBI ↗
Sisymbrium officinale PP175359.1 154067 View on NCBI ↗
Sisymbrium polymorphum NC_081132.1 154469 View on NCBI ↗