Markers + reference

Sinogentiana

2 species · Gentianaceae · Gentianales

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Species 2
Genome length 134–144 kb
Candidate markers 254
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 254 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 742 0.0634 0.89 77.6 yes View details
trnS-GCU-trnG-UCC LSC 444 0.1111 0.89 80.5 yes View details
trnR-ACG-trnN-GUU IRb 325 0.1648 0.84 76.0 yes View details
trnN-GUU-ndhF IRb 2537 0.1576 0.95 85.5 yes View details
ndhA SSC 1305 0.0278 0.99 60.8 yes View details
ycf1 SSC 5205 0.0271 0.99 56.9 yes View details
trnN-GUU-trnR-ACG IRa 325 0.1648 0.84 76.0 yes View details
ycf15 IRb 117 0.0660 0.91 82.3 yes View details
ycf15 IRa 117 0.0660 0.91 82.3 yes View details
trnC-GCA-petN LSC 692 0.0423 0.92 81.6 yes View details
trnT-UGU-trnL-UAA LSC 630 0.0556 0.91 81.5 yes View details
trnF-GAA-trnV-UAC LSC 734 0.0463 0.97 80.0 yes View details
trnY-GUA-trnE-UUC LSC 55 0.1273 1.00 79.2 yes View details
petA-psbJ LSC 463 0.0552 0.94 79.1 yes View details
rrn4.5-rrn5 IRb 187 0.1647 0.91 77.2 yes View details
rrn5-rrn4.5 IRa 187 0.1647 0.91 77.2 yes View details
trnL-UAA-trnF-GAA LSC 292 0.0498 0.89 76.0 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
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CGAATCCCTTGCTTCATCCA AGCAGCTTGCCAAACAAAAG 1381–1417 1.000 86.8
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CGAATCCCTTGCTTCATCCA CTTACAGCAGCTTGCCAAAC 1386–1422 1.000 86.7
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG ACGAATCCCTTGCTTCATCC AGCAGCTTGCCAAACAAAAG 1382–1418 1.000 86.7
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG ATGGACGAATCCCTTGCTTC AGCAGCTTGCCAAACAAAAG 1386–1422 1.000 86.7
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG GGACGAATCCCTTGCTTCAT AGCAGCTTGCCAAACAAAAG 1384–1420 1.000 86.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 498–586 1.000 57.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATCCACTCAGCCATCTCTCC GGGTTAGAAAAACGAATCACACT 509–597 1.000 56.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ATCCACTCAGCCATCTCTCC AACGAATCACACTTTTACCACT 499–587 1.000 55.7
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ATCCACTCAGCCATCTCTCC TACCACTAAACTATACCCGC 484–572 1.000 54.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC TCCACTCAGCCATCTCTCC ACGAATCACACTTTTACCACT 497–585 1.000 53.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 733–755 1.000 86.2
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 727–749 1.000 84.7
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 751–773 1.000 83.9
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TAGTCCACTTCTTCCCCACA 786–808 1.000 82.8
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TCCACTTCTTCCCCACACTA 783–805 1.000 82.8
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC CCAGCGTAGACTTATTGCCA CTCTCTTTCAAGGAGGCAGC 164–171 1.000 78.8
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC ACCAGCGTAGACTTATTGCC CTCTCTTTCAAGGAGGCAGC 165–172 1.000 78.7
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CCAGCGTAGACTTATTGCCA TCGTCTAGTGGTTCAGGACA 185–192 1.000 78.2
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC ACCAGCGTAGACTTATTGCC TCGTCTAGTGGTTCAGGACA 186–193 1.000 78.2
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC CCAGCGTAGACTTATTGCCA AAGTAGCCCCCATCGTCTAG 197–204 1.000 78.0
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 655–680 1.000 86.7
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 663–688 1.000 86.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 687–712 1.000 85.7
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT TAGCGTCTACCAATTTCGCC 695–720 1.000 85.1
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG AGTCCGTAGCGTCTACCAAT 669–694 1.000 84.8
trnL-UAA-trnF-GAA_p1 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TCTACCAGCTGAGCTATCCC 346–407 1.000 82.9
trnL-UAA-trnF-GAA_p2 trnL-UAA-trnF-GAA AATCGTGAGGGTTCAAGTCC TTTGAACTGGTGACACGAGG 382–443 1.000 82.3
trnL-UAA-trnF-GAA_p3 trnL-UAA-trnF-GAA GTCCCGTTCTGCATGTCAAT TCTACCAGCTGAGCTATCCC 415–476 1.000 81.9
trnL-UAA-trnF-GAA_p4 trnL-UAA-trnF-GAA TCCCGTTCTGCATGTCAATG TCTACCAGCTGAGCTATCCC 414–475 1.000 81.9
trnL-UAA-trnF-GAA_p5 trnL-UAA-trnF-GAA GTCCCGTTCTGCATGTCAAT TTTGAACTGGTGACACGAGG 451–512 1.000 81.4

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
Sinogentiana souliei MN234138.1 134336 View on NCBI ↗
Sinogentiana striata MN199149.1 144282 View on NCBI ↗