Markers + reference

Galega

2 species · Fabaceae · Fabales

Back to catalogue

Species 2
Genome length 125–125 kb
Candidate markers 229
Primer pairs 85

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 229 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf1-trnN-GUU Genome 461 0.1064 0.98 82.9 yes View details
trnE-UUC-rrn16 Genome 306 0.1399 0.96 77.9 yes View details
trnM-CAU-rpl23 Genome 726 0.0924 0.92 90.8 yes View details
rps19 Genome 285 0.0394 0.98 63.6 yes View details
rps19-rpl22 Genome 322 0.1156 0.91 78.1 yes View details
clpP Genome 1189 0.0823 0.96 80.3 yes View details
trnC-GCA-petN Genome 977 0.0582 0.99 78.3 yes View details
trnT-UGU-trnL-UAA Genome 1018 0.0658 0.93 83.0 yes View details
trnL-UAA-trnF-GAA Genome 133 0.0902 1.00 82.8 yes View details
trnQ-UUG-psbK Genome 701 0.0541 0.92 82.2 yes View details
psbC-trnS-UGA Genome 215 0.0846 0.93 79.9 yes View details
ndhC-trnI-AAU Genome 416 0.0373 0.97 79.5 yes View details
trnL-CAA-ycf2 Genome 521 0.0465 0.95 78.8 yes View details
psaJ-trnP-UGG Genome 577 0.0396 0.96 78.0 yes View details
trnG-GCC-trnM-CAU Genome 56 0.1071 1.00 77.0 yes View details
clpP-rps12 Genome 76 0.1831 0.93 76.9 yes View details
rpl14-rps8 Genome 518 0.0699 0.99 75.9 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf1-trnN-GUU_p1 ycf1-trnN-GUU TCAGGCATAACACTAGTAGA ACCACTGAGCTACTGAGGAA 530–708 1.000 47.5
ycf1-trnN-GUU_p2 ycf1-trnN-GUU TTCAGGCATAACACTAGTAGA ACCACTGAGCTACTGAGGAA 531–709 1.000 47.5
ycf1-trnN-GUU_p3 ycf1-trnN-GUU TTTCAGGCATAACACTAGTAGA ACCACTGAGCTACTGAGGAA 532–710 1.000 47.5
ycf1-trnN-GUU_p4 ycf1-trnN-GUU TCAGGCATAACACTAGTAGAT ACCACTGAGCTACTGAGGAA 530–708 1.000 47.5
ycf1-trnN-GUU_p5 ycf1-trnN-GUU GCTGAATTAACTATTTTCAGGCA ACCACTGAGCTACTGAGGAA 546–724 1.000 47.3
trnE-UUC-rrn16_p1 trnE-UUC-rrn16 TGAATCGCCCCATCTATCCT CCGCGAATCCTCTTGAAAGA 1051–1064 1.000 84.2
trnE-UUC-rrn16_p2 trnE-UUC-rrn16 ATTGTACTGCGCTCTCCAAG CCTGTCCTCAGTTCGGATTG 1260–1268 1.000 83.9
trnE-UUC-rrn16_p3 trnE-UUC-rrn16 TGCTTGTTCCACCTTCTTCC CCTGTCCTCAGTTCGGATTG 1238–1246 1.000 83.9
trnE-UUC-rrn16_p4 trnE-UUC-rrn16 ATTGTACTGCGCTCTCCAAG CCGCGAATCCTCTTGAAAGA 1550–1558 1.000 83.2
trnE-UUC-rrn16_p5 trnE-UUC-rrn16 TGCTTGTTCCACCTTCTTCC CCGCGAATCCTCTTGAAAGA 1528–1536 1.000 83.2
trnL-CAA-ycf2_p1 trnL-CAA-ycf2 GGTGGTGGAATGGTAGACAC CCGGACGAGATGGTTGTTAC 628–653 1.000 82.3
trnL-CAA-ycf2_p2 trnL-CAA-ycf2 CCTTGGTGGTGGAATGGTAG CCGGACGAGATGGTTGTTAC 632–657 1.000 82.1
trnL-CAA-ycf2_p3 trnL-CAA-ycf2 GGTGGTGGAATGGTAGACAC AAAGATGGCTTTTCCCGGAC 642–667 1.000 81.5
trnL-CAA-ycf2_p4 trnL-CAA-ycf2 CCTTGGTGGTGGAATGGTAG AAAGATGGCTTTTCCCGGAC 646–671 1.000 81.3
trnL-CAA-ycf2_p5 trnL-CAA-ycf2 TGGTGGTGGAATGGTAGACA CCGGACGAGATGGTTGTTAC 629–654 1.000 81.1
trnM-CAU-rpl23_p1 trnM-CAU-rpl23 ATTGGCGAAGTCGTAGGTTC CGACCCAACGTTTTATTTCTGT 865–881 1.000 69.8
trnM-CAU-rpl23_p2 trnM-CAU-rpl23 GGCGAAGTCGTAGGTTCAAT CGACCCAACGTTTTATTTCTGT 862–878 1.000 69.8
trnM-CAU-rpl23_p3 trnM-CAU-rpl23 GAATGGTTAAAGCGCCCAAC CGACCCAACGTTTTATTTCTGT 890–906 1.000 69.6
trnM-CAU-rpl23_p4 trnM-CAU-rpl23 GGTAGTAGGATCCCCACGAA CGACCCAACGTTTTATTTCTGT 922–938 1.000 68.9
trnM-CAU-rpl23_p5 trnM-CAU-rpl23 GGCGAAGTCGTAGGTTCAAT TCGACCCAACGTTTTATTTCTG 863–879 1.000 67.8
rps19_p1 rps19 TGGAAAGGGTGGACAATTGG CAATTCCCTCGACACCAGAG 1562 0.500 59.8
rps19_p2 rps19 AACCCTGTAGACCATCCACA CAATTCCCTCGACACCAGAG 1330 0.500 59.6
rps19_p3 rps19 GGGTGGACAATTGGCTAGAG CAATTCCCTCGACACCAGAG 1556 0.500 59.5
rps19_p4 rps19 GCGGTAGCGAAACTTATTGC CAATTCCCTCGACACCAGAG 1528 0.500 59.2
rps19_p5 rps19 GTTGGACAAGTCGGGAATGT CAATTCCCTCGACACCAGAG 1432 0.500 59.0
rps19-rpl22_p1 rps19-rpl22 AACCCTGTAGACCATCCACA AGTCTGAAACCAAGCGGATG 1105–1184 1.000 86.3
rps19-rpl22_p2 rps19-rpl22 AACCCTGTAGACCATCCACA ATCCATTCCACACGTGCAAT 1606–1685 1.000 85.5
rps19-rpl22_p3 rps19-rpl22 AACCCTGTAGACCATCCACA CAATTCCCTCGACACCAGAG 1330 0.500 59.6
rps19-rpl22_p4 rps19-rpl22 CCGCACTTGGAAGAAGAAGT CAATTCCCTCGACACCAGAG 1248 0.500 58.9
rps19-rpl22_p5 rps19-rpl22 AGGGAAGCGTCCTGTAGTAA CAATTCCCTCGACACCAGAG 1364 0.500 58.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Galega officinalis NC_051885.1 125086 View on NCBI ↗
Galega orientalis NC_069214.1 125280 View on NCBI ↗