Markers + reference

Crucihimalaya

4 species · Brassicaceae · Brassicales

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Species 4
Genome length 155–155 kb
Candidate markers 266
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-CAC-psbA LSC 278 0.0546 1.00 74.9 yes View details
trnS-AGC-trnG-GGA LSC 678 0.0246 1.00 72.3 yes View details
trnC-UGC-petN LSC 665 0.0140 1.00 62.3 yes View details
psaA-ycf3 LSC 707 0.0229 1.00 61.6 yes View details
trnT-ACA-trnL-UUA LSC 766 0.0205 1.00 71.6 yes View details
trnL-UUA-trnF-UUC LSC 497 0.0335 0.86 70.4 yes View details
psbE-petL LSC 1388 0.0195 0.98 64.2 yes View details
ycf1 IRb 1032 0.0024 1.00 42.4 no View details
ndhF-rpl32 SSC 860 0.0297 1.00 68.5 yes View details
rpl32-trnL-CUA SSC 794 0.0347 1.00 72.2 yes View details
ycf1 SSC 5379 0.0131 1.00 47.2 yes View details
ndhK-ndhC LSC 65 0.0615 1.00 80.8 yes View details
psbZ-trnG-GGC LSC 478 0.0251 1.00 69.7 yes View details
ndhC-trnV-GUA LSC 891 0.0150 0.95 66.5 yes View details
rps16-trnQ-CAA LSC 418 0.0211 1.00 65.5 yes View details
accD-psaI LSC 672 0.0191 1.00 65.3 yes View details
ndhA SSC 2152 0.0101 1.00 65.3 yes View details
trnK-AAA-rps16 LSC 601 0.0200 1.00 65.2 yes View details
psbK-psbI LSC 381 0.0245 1.00 65.0 yes View details
trnE-GAA-trnT-ACC LSC 676 0.0137 0.99 64.6 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 95 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 ACTGAGTTTCCGTCTGGGTA 973–1021 1.000 82.0
trnH-CAC-psbA_p2 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT AGGTTACAGGTTTGGGCAAG 664–670 0.750 70.1
trnH-CAC-psbA_p3 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GAAGGTTACAGGTTTGGGCA 666–672 0.750 70.0
trnH-CAC-psbA_p4 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT GGTTACAGGTTTGGGCAAGA 663–669 0.750 70.0
trnH-CAC-psbA_p5 trnH-CAC-psbA CTGCCTTAATCCACTTGGCT TGAAGGTTACAGGTTTGGGC 667–668 0.500 59.6
trnK-AAA-rps16_p1 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG CCCAATGAGCCGTTTATCGA 963–1037 1.000 83.8
trnK-AAA-rps16_p2 trnK-AAA-rps16 CCTTTCAGGATCAGTCGTGG TCCCAATGAGCCGTTTATCG 964–1038 1.000 83.8
trnK-AAA-rps16_p3 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT CCCAATGAGCCGTTTATCGA 959–1033 1.000 83.4
trnK-AAA-rps16_p4 trnK-AAA-rps16 TCAGGATCAGTCGTGGTCTT TCCCAATGAGCCGTTTATCG 960–1034 1.000 83.4
trnK-AAA-rps16_p5 trnK-AAA-rps16 TTCAGGATCAGTCGTGGTCT CCCAATGAGCCGTTTATCGA 960–1034 1.000 83.4
rps16-trnQ-CAA_p1 rps16-trnQ-CAA AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 478–495 1.000 83.2
rps16-trnQ-CAA_p2 rps16-trnQ-CAA CCTTCAATTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 488–505 1.000 82.3
rps16-trnQ-CAA_p3 rps16-trnQ-CAA CCACAGCAGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 504–521 1.000 80.7
rps16-trnQ-CAA_p4 rps16-trnQ-CAA TCCACAGCAGATCATGTCCT GAGGTTCGAATCCTTCCGTC 505–522 1.000 80.7
rps16-trnQ-CAA_p5 rps16-trnQ-CAA ATCCACAGCAGATCATGTCC GAGGTTCGAATCCTTCCGTC 506–523 1.000 79.0
psbK-psbI_p1 psbK-psbI CAAGCCGCTGTAAGTTTTCG CCGGATTACGTCCTGGATCA 497–517 1.000 75.5
psbK-psbI_p2 psbK-psbI AGCCGCTGTAAGTTTTCGAT CCGGATTACGTCCTGGATCA 495–515 1.000 75.2
psbK-psbI_p3 psbK-psbI AAGCCGCTGTAAGTTTTCGA CCGGATTACGTCCTGGATCA 496–516 1.000 74.9
psbK-psbI_p4 psbK-psbI GCCGCTGTAAGTTTTCGATG CCGGATTACGTCCTGGATCA 494–514 1.000 74.7
psbK-psbI_p5 psbK-psbI CAAGCCGCTGTAAGTTTTCG CGGATTACGTCCTGGATCAT 496–516 1.000 74.4
trnS-AGC-trnG-GGA_p1 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTT 759–796 1.000 73.7
trnS-AGC-trnG-GGA_p2 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA ATCAAACCGAGAGACCCTTT 758–795 1.000 73.7
trnS-AGC-trnG-GGA_p3 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC AATCAAACCGAGAGACCCTT 757–794 1.000 73.4
trnS-AGC-trnG-GGA_p4 trnS-AGC-trnG-GGA AACGCTTTAGTCCACTCAGC ATCAAACCGAGAGACCCTTT 756–793 1.000 73.4
trnS-AGC-trnG-GGA_p5 trnS-AGC-trnG-GGA CCAACGCTTTAGTCCACTCA AATCAAACCGAGAGACCCTTT 759–796 1.000 71.7
trnC-UGC-petN_p1 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG AGCCCATGCGAGACTTACTA 709–722 1.000 81.7
trnC-UGC-petN_p2 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC AGCCCATGCGAGACTTACTA 765–778 1.000 81.2
trnC-UGC-petN_p3 trnC-UGC-petN TTCTATCGTTTTGGCGGCAT AGCCCATGCGAGACTTACTA 763–776 1.000 80.0
trnC-UGC-petN_p4 trnC-UGC-petN TTTCCCCAGTTCAAATCCGG CACACTACGAGAGAGAGGGA 753–766 1.000 80.0
trnC-UGC-petN_p5 trnC-UGC-petN GTTTCTATCGTTTTGGCGGC CACACTACGAGAGAGAGGGA 809–822 1.000 79.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Crucihimalaya himalaica NC_061290.1 155112 View on NCBI ↗
Crucihimalaya lasiocarpa NC_049612.1 155257 View on NCBI ↗
Crucihimalaya rupicola PQ878552.1 155020 View on NCBI ↗
Crucihimalaya wallichii NC_009271.1 155199 View on NCBI ↗