Markers + reference

Genista

3 species · Fabaceae · Fabales

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Species 3
Genome length 153–153 kb
Candidate markers 250
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 9 remaining regions by MarkerSeek score (out of 250 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbB-clpP LSC 471 0.0297 1.00 71.8 yes View details
trnT-trnL LSC 675 0.0174 0.97 60.8 yes View details
trnL-trnF LSC 398 0.0201 1.00 59.3 yes View details
trnF-ndhJ LSC 595 0.0202 1.00 63.9 yes View details
psbA-trnH LSC 344 0.0282 0.89 63.8 yes View details
ycf1 SSC 5331 0.0161 1.00 48.6 yes View details
ycf1-rps15 SSC 429 0.0241 1.00 64.6 yes View details
ndhI-ndhG SSC 361 0.0369 1.00 66.3 yes View details
rpl32-ndhF SSC 750 0.0160 1.00 58.7 yes View details
rps4-trnT LSC 270 0.0370 1.00 66.9 yes View details
trnH-rpl2 LSC 115 0.0232 1.00 66.2 yes View details
rpoC2-rps2 LSC 204 0.0196 1.00 66.1 yes View details
trnY-trnD LSC 414 0.0242 1.00 64.5 yes View details
ndhC-trnV LSC 455 0.0224 0.98 62.9 yes View details
rps12-rpl20 LSC 741 0.0063 1.00 62.8 yes View details
rbcL-trnK LSC 853 0.0166 0.99 62.6 yes View details
atpF LSC 1289 0.0044 1.00 62.0 yes View details
trnG-trnS LSC 839 0.0115 1.00 60.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbB-clpP_p1 psbB-clpP AAACGGCCGGGATCATTTAA CTTTTGGAACACCAATGGGC 548–549 1.000 80.8
psbB-clpP_p2 psbB-clpP AACGGCCGGGATCATTTAAA CTTTTGGAACACCAATGGGC 547–548 1.000 80.8
psbB-clpP_p3 psbB-clpP ACGGCCGGGATCATTTAAAA CTTTTGGAACACCAATGGGC 546–547 1.000 80.8
psbB-clpP_p4 psbB-clpP AACGGCCGGGATCATTTAAA TTTGGAACACCAATGGGCAT 545–546 1.000 80.0
psbB-clpP_p5 psbB-clpP ACGGCCGGGATCATTTAAAA TTTGGAACACCAATGGGCAT 544–545 1.000 80.0
rps12-rpl20_p1 rps12-rpl20 ACAGCCAATCCGAAATGTCA TTTTGTCCTCCGTTTCCGAG 868–893 1.000 78.0
rps12-rpl20_p2 rps12-rpl20 ACAAGACAGCCAATCCGAAA TTTTGTCCTCCGTTTCCGAG 873–898 1.000 77.5
rps12-rpl20_p3 rps12-rpl20 AGGAACGTGTACTAGGGTGT TTTTGTCCTCCGTTTCCGAG 811–836 1.000 77.3
rps12-rpl20_p4 rps12-rpl20 ACAGCCAATCCGAAATGTCA TTTTTGTCCTCCGTTTCCGA 869–894 1.000 76.4
rps12-rpl20_p5 rps12-rpl20 ACAAGACAGCCAATCCGAAA TTTTTGTCCTCCGTTTCCGA 874–899 1.000 75.8
trnY-trnD_p1 trnY-trnD TGGCAATATGTCTACGCTGG TATCTATCGGGACTGACGGG 525–535 1.000 80.3
trnY-trnD_p2 trnY-trnD GGCAATATGTCTACGCTGGT TATCTATCGGGACTGACGGG 524–534 1.000 80.3
trnY-trnD_p3 trnY-trnD GGGGACGGACTGTAAATTCG TATCTATCGGGACTGACGGG 546–556 1.000 79.2
trnY-trnD_p4 trnY-trnD GGGACGGACTGTAAATTCGT TATCTATCGGGACTGACGGG 545–555 1.000 79.1
trnY-trnD_p5 trnY-trnD TGGCAATATGTCTACGCTGG CGGTGCTCTGACCAATTGAA 474–484 1.000 78.4
rpoC2-rps2_p1 rpoC2-rps2 TGTTCCACCACAGAGAAGTT AATGAACTCCCGCTTCCATC 324–327 1.000 70.9
rpoC2-rps2_p2 rpoC2-rps2 TTGTTCCACCACAGAGAAGT AATGAACTCCCGCTTCCATC 325–328 1.000 70.9
rpoC2-rps2_p3 rpoC2-rps2 TGTTCCACCACAGAGAAGTT CCCGCTTCCATCATCTCTTC 316–319 1.000 70.4
rpoC2-rps2_p4 rpoC2-rps2 TGTTCCACCACAGAGAAGTT CCGCTTCCATCATCTCTTCC 315–318 1.000 70.4
rpoC2-rps2_p5 rpoC2-rps2 TTGTTCCACCACAGAGAAGT CCGCTTCCATCATCTCTTCC 316–319 1.000 70.4
atpF_p1 atpF AGCACTTTTATTTGCGAATCCT CACGAATGCTTACCATGAGT 1463–1470 1.000 40.9
atpF_p2 atpF AGCATTAGCACTTTTATTTGCGA CACGAATGCTTACCATGAGT 1469–1476 1.000 40.9
atpF_p3 atpF AGCACTTTTATTTGCGAATCCTT CACGAATGCTTACCATGAGT 1463–1470 1.000 40.9
atpF_p4 atpF AGCACTTTTATTTGCGAATCC CACGAATGCTTACCATGAGT 1463–1470 1.000 40.9
atpF_p5 atpF GCACTTTTATTTGCGAATCCT CACGAATGCTTACCATGAGT 1462–1469 1.000 40.9
trnG-trnS_p1 trnG-trnS TGAATCAAACGAGGGATCCC CAATCCGACGCTTTAGTCCA 747–953 1.000 79.6
trnG-trnS_p2 trnG-trnS TGAATCAAACGAGGGATCCC AATCCGACGCTTTAGTCCAC 746–952 1.000 79.5
trnG-trnS_p3 trnG-trnS TGAATCAAACGAGGGATCCC AGCAATCCGACGCTTTAGTC 749–955 1.000 76.7
trnG-trnS_p4 trnG-trnS TGAATCAAACGAGGGATCCC CGACGCTTTAGTCCACTCAG 742–948 1.000 76.5
trnG-trnS_p5 trnG-trnS TGAATCAAACGAGGGATCCC GCTTTAGTCCACTCAGCCAT 738–944 1.000 76.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Genista canariensis PQ469249.1 152876 View on NCBI ↗
Genista monspessulana PQ474196.1 153021 View on NCBI ↗
Genista splendens PQ484034.1 152852 View on NCBI ↗