Markers + reference

Convallaria

3 species · Asparagaceae · Asparagales

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Species 3
Genome length 162–163 kb
Candidate markers 276
Primer pairs 90

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 276 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1312 0.0046 1.00 53.4 yes View details
trnE-UUC-trnT-GGU LSC 496 0.0067 1.00 52.2 yes View details
trnT-GGU-psbD LSC 762 0.0052 1.00 62.1 yes View details
petA-psbJ LSC 1099 0.0067 1.00 50.6 yes View details
ycf2-rpl10 IRb 1233 0.0070 1.00 51.3 yes View details
ndhF-rpl32 SSC 946 0.0056 1.00 53.5 yes View details
ccsA SSC 996 0.0000 1.00 25.8 yes View details
rpl10-ycf2 IRa 1233 0.0070 1.00 51.3 yes View details
ccsA-ndhD SSC 207 0.0386 1.00 77.1 yes View details
psbE-petL LSC 1316 0.0025 1.00 66.0 yes View details
atpB LSC 1488 0.0031 1.00 60.7 yes View details
atpB-rbcL LSC 787 0.0025 1.00 60.5 yes View details
petB LSC 1397 0.0024 1.00 60.4 yes View details
ndhC-trnV-UAC LSC 1493 0.0022 1.00 60.3 yes View details
psaA-ycf3 LSC 639 0.0000 0.99 60.1 yes View details
rpl16 LSC 1436 0.0019 1.00 60.1 yes View details
atpF-atpH LSC 498 0.0040 1.00 59.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT GAGGTTCGAATCCTTCCGTC 1374–1376 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT GAGGTTCGAATCCTTCCGTC 1375–1377 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1385–1387 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1396–1398 1.000 78.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GCTTTCTACCACAGCGTTTC GAGGTTCGAATCCTTCCGTC 1373–1375 1.000 75.1
trnG-GCC_p1 trnG-GCC TGCTCATTCCTTTGTTCGACA AGGGGATTGCATGGAAAATCT 922–925 1.000 59.8
trnG-GCC_p2 trnG-GCC GCTCATTCCTTTGTTCGACA AGGGGATTGCATGGAAAATCT 921–924 1.000 56.0
trnG-GCC_p3 trnG-GCC TGCTCATTCCTTTGTTCGAC AGGGGATTGCATGGAAAATCT 922–925 1.000 56.0
trnG-GCC_p4 trnG-GCC TGCTCATTCCTTTGTTCGACA AGGGGATTGCATGGAAAATC 922–925 1.000 55.3
trnG-GCC_p5 trnG-GCC TGCTCATTCCTTTGTTCGACA GGGGATTGCATGGAAAATCT 921–924 1.000 55.3
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG ATTTATGGACTGGTCGTGGC 621–622 1.000 79.5
atpF-atpH_p2 atpF-atpH CAGTGGCCTAAGGAAACGAA ATTTATGGACTGGTCGTGGC 593–594 1.000 79.1
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG TCGTGGCATTAGCGCTTTTA 608–609 1.000 77.7
atpF-atpH_p4 atpF-atpH CAGTGGCCTAAGGAAACGAA TCGTGGCATTAGCGCTTTTA 580–581 1.000 77.2
atpF-atpH_p5 atpF-atpH ATTAAACCCGAAACTCCCGG CGTGGCATTAGCGCTTTTAT 607–608 1.000 73.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 600 1.000 79.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCATGGCGTTACTCTACCAC 579 1.000 78.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TGGCGTTACTCTACCACTGA 576 1.000 78.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 597 1.000 78.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TTGAACCGATGACTTACGCC 602 1.000 77.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 922–925 1.000 79.1
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 925–928 1.000 78.9
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 899–902 1.000 77.4
trnT-GGU-psbD_p4 trnT-GGU-psbD GGCCCTTTTAACTCAGTGGT GGACCAGCCTACAAAAACGA 937–940 1.000 77.3
trnT-GGU-psbD_p5 trnT-GGU-psbD TGGTAGAGTAACGCCATGGT GGACCAGCCTACAAAAACGA 921–924 1.000 76.1
psaA-ycf3_p1 psaA-ycf3 CCCATTCCTCGAAAGACGTT TTGAAGATCACGAGGCGTTT 737–745 1.000 78.9
psaA-ycf3_p2 psaA-ycf3 CCCATTCCTCGAAAGACGTT TTGGTTGAAGATCACGAGGC 741–749 1.000 78.7
psaA-ycf3_p3 psaA-ycf3 CCCATTCCTCGAAAGACGTT TGAAGATCACGAGGCGTTTC 736–744 1.000 77.9
psaA-ycf3_p4 psaA-ycf3 CCCATTCCTCGAAAGACGTT TCACGAGGCGTTTCGAATAA 730–738 1.000 77.4
psaA-ycf3_p5 psaA-ycf3 CCCATTCCTCGAAAGACGTT GCTATAGCGCTTACTCCAGG 782–790 1.000 77.3

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
Convallaria keiskei NC_042228.1 162109 View on NCBI ↗
Convallaria majalis NC_063623.1 162198 View on NCBI ↗
Convallaria pseudomajalis NC_063624.1 162987 View on NCBI ↗