Markers + reference

Aesculus

10 species · Sapindaceae · Sapindales

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Species 10
Genome length 155–156 kb
Candidate markers 277
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 7 remaining regions by MarkerSeek score (out of 277 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 785 0.0106 0.99 53.7 yes View details
psbZ-trnG-GCC LSC 503 0.0514 0.99 78.8 yes View details
accD-psaI LSC 690 0.0132 1.00 62.4 yes View details
rps19 LSC 282 0.0119 0.99 45.8 yes View details
ycf1 IRb 1164 0.0181 0.94 60.0 yes View details
ndhF SSC 2223 0.0042 1.00 45.3 yes View details
ndhF-rpl32 SSC 1039 0.0070 0.98 57.0 yes View details
rpl32-trnL-UAG SSC 1040 0.0111 0.99 60.4 yes View details
ndhD SSC 1533 0.0043 1.00 38.6 yes View details
ycf1 SSC 5619 0.0066 1.00 46.3 yes View details
trnE-UUC-trnT-GGU LSC 879 0.0061 0.95 68.6 yes View details
ndhC-trnV-UAC LSC 968 0.0068 0.95 65.2 yes View details
ycf3-trnS-GGA LSC 855 0.0043 1.00 60.1 yes View details
trnM-CAU-psbD LSC 1418 0.0080 1.00 59.7 yes View details
trnT-UGU-trnL-UAA LSC 752 0.0071 1.00 57.4 yes View details
atpF-atpH LSC 364 0.0095 1.00 56.4 yes View details
trnF-GAA-ndhJ LSC 687 0.0070 1.00 56.0 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CTTATAGCCCCGTGTCAACC GGGTTCGCTGGATTTACTGT 2836–2872 1.000 81.7
trnK-UUU_p2 trnK-UUU CTTATAGCCCCGTGTCAACC ATTCAAATGACGGGTTCGCT 2847–2883 1.000 81.2
trnK-UUU_p3 trnK-UUU TGACTTATAGCCCCGTGTCA GGGTTCGCTGGATTTACTGT 2839–2875 1.000 80.9
trnK-UUU_p4 trnK-UUU TGACTTATAGCCCCGTGTCA ATTCAAATGACGGGTTCGCT 2850–2886 1.000 80.4
trnK-UUU_p5 trnK-UUU GGGACTCCCAAGCATACAAC GGGTTCGCTGGATTTACTGT 2905–2941 1.000 80.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TGAATGAAACTGAAGGACCCC 892–905 1.000 74.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCACT 847–860 1.000 73.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCAC 847–860 1.000 73.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTCGTACAACGGATTAGCA TGAATGAAACTGAAGGACCCC 914–927 1.000 73.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCTCGTACAACGGATTAGCA ACGAATCGCACTTTTACCACT 869–882 1.000 72.9
atpF-atpH_p1 atpF-atpH GCGAACCAAGGAAACGAAAG CGAGGCGGAGGGAAAAATAC 513–521 1.000 78.7
atpF-atpH_p2 atpF-atpH GCGAACCAAGGAAACGAAAG GAGGCGGAGGGAAAAATACG 512–520 1.000 78.7
atpF-atpH_p3 atpF-atpH ATTAAACCCGAAACTCCCGG CGAGGCGGAGGGAAAAATAC 543–551 1.000 77.8
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG GAGGCGGAGGGAAAAATACG 542–550 1.000 77.8
atpF-atpH_p5 atpF-atpH AGCGAACCAAGGAAACGAAA GAGGCGGAGGGAAAAATACG 513–521 1.000 76.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 976–1020 1.000 83.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCATGGCGTTACTCTACCAC 955–999 1.000 83.3
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TGGCGTTACTCTACCACTGA 952–996 1.000 83.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 938–982 1.000 83.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 917–961 1.000 83.0
trnM-CAU-psbD_p1 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG TCTCCGTAACCAGTCATCCA 1544–1562 1.000 80.1
trnM-CAU-psbD_p2 trnM-CAU-psbD TCAGTGGTAGAGTAACGCCA TCTCCGTAACCAGTCATCCA 1547–1565 1.000 79.9
trnM-CAU-psbD_p3 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1575–1593 1.000 79.7
trnM-CAU-psbD_p4 trnM-CAU-psbD TCAGTGGTAGAGTAACGCCA GACCGGACCAACCTACAAAA 1578–1596 1.000 79.6
trnM-CAU-psbD_p5 trnM-CAU-psbD GTGGTAGAGTAACGCCATGG TAGACCGGACCAACCTACAA 1577–1595 1.000 79.4
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CTTCTCCTGATGGTTGGTCG CGTCTTCTCCTTGGCAAAGA 618–694 1.000 88.9
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG CGTCTTCTCCTTGGCAAAGA 621–697 1.000 87.3
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TCCTGATGGTTGGTCGAGTA CGTCTTCTCCTTGGCAAAGA 614–690 1.000 87.2
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC CGTCTTCTCCTTGGCAAAGA 619–695 1.000 86.9
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTCTCCTGATGGTTGGTCGA CGTCTTCTCCTTGGCAAAGA 617–693 1.000 86.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Aesculus assamica NC_056237.1 155431 View on NCBI ↗
Aesculus chinensis NC_046788.1 155528 View on NCBI ↗
Aesculus chinensis var. chekiangensis PP809760.1 155516 View on NCBI ↗
Aesculus chinensis var. wilsonii PP809769.1 155783 View on NCBI ↗
Aesculus hippocastanum NC_066015.1 156100 View on NCBI ↗
Aesculus pavia PX251891.1 156394 View on NCBI ↗
Aesculus polyneura PP809764.1 155291 View on NCBI ↗
Aesculus tsiangii PP809765.1 155270 View on NCBI ↗
Aesculus turbinata PP809766.1 156251 View on NCBI ↗
Aesculus wangii NC_035955.1 155871 View on NCBI ↗