Markers + reference

Adinandra

3 species · Pentaphylacaceae · Ericales

Back to catalogue

Species 3
Genome length 156–156 kb
Candidate markers 262
Primer pairs 115

Genome-wide nucleotide diversity

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

Candidate markers

14 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1011 0.0053 1.00 59.3 yes View details
rps2-rpoC1 LSC 4557 0.0022 1.00 54.9 yes View details
petN-psbM LSC 1106 0.0066 1.00 55.2 yes View details
psaA-ycf3 LSC 733 0.0073 1.00 50.6 yes View details
rbcL LSC 1428 0.0033 1.00 56.3 yes View details
accD-psaI LSC 787 0.0068 1.00 63.1 yes View details
psbE-petL LSC 1216 0.0071 1.00 63.3 yes View details
psaJ-rpl33 LSC 455 0.0059 1.00 49.4 yes View details
rpl16 LSC 1506 0.0040 0.99 50.1 yes View details
trnR-ACG-trnN-GUU IRb 583 0.0069 1.00 62.8 yes View details
ndhF-rpl32 SSC 955 0.0056 1.00 62.3 yes View details
ndhD SSC 1500 0.0027 1.00 47.9 yes View details
ndhH-trnN-GUU SSC 6665 0.0026 1.00 46.2 yes View details
trnN-GUU-trnR-ACG IRa 583 0.0069 1.00 62.8 yes View details
trnK-UUU-rps16 LSC 866 0.0038 1.00 63.3 yes View details
trnH-GUG-psbA LSC 373 0.0054 0.99 62.1 yes View details
trnT-GGU-psbD LSC 1057 0.0038 1.00 61.4 yes View details
ndhC-trnM-CAU LSC 1150 0.0023 1.00 60.3 yes View details
petB LSC 1423 0.0023 1.00 60.2 yes View details
matK LSC 1527 0.0013 1.00 59.5 yes View details
psbB LSC 1527 0.0013 1.00 59.5 yes View details
psbC-trnS-UGA LSC 259 0.0056 0.92 59.4 yes View details
clpP LSC 2063 0.0019 1.00 59.3 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 115 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCTCTGGACCTAGCTGCTAT 435–446 1.000 82.3
trnH-GUG-psbA_p2 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CCTCTGGACCTAGCTGCTAT 436–447 1.000 82.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTTGGCTACATCCG CCTCTGGACCTAGCTGCTAT 428–439 1.000 80.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CGCATGGTGGATTCACAATC CCTCTGGACCTAGCTGCTAT 457–468 1.000 79.4
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 487–498 1.000 79.3
matK_p1 matK ACATGCTACATGAACATTTCAGA CCTTGTTTTGACTGTATCGCA 1712 1.000 40.1
matK_p2 matK ACATGCTACATGAACATTTCAGA ACCTTGTTTTGACTGTATCGC 1713 1.000 40.1
matK_p3 matK ACATGCTACATGAACATTTCAGA CCTTGTTTTGACTGTATCGCAC 1712 1.000 40.1
matK_p4 matK ACATGCTACATGAACATTTCAGAA CCTTGTTTTGACTGTATCGCA 1712 1.000 40.1
matK_p5 matK ACATGCTACATGAACATTTCAGAA ACCTTGTTTTGACTGTATCGC 1713 1.000 40.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC TTTCCTTGAAAGGGGTGCTC 1040–1056 1.000 81.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT TTTCCTTGAAAGGGGTGCTC 1038–1054 1.000 81.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGACGAATCCCTTGCTTC AGAAGGCGGGGGTTTTTAAG 990–1006 1.000 80.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 GGACGAATCCCTTGCTTCAT AGAAGGCGGGGGTTTTTAAG 988–1004 1.000 80.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 986–1002 1.000 80.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1159–1200 1.000 80.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1142–1183 1.000 79.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1101–1142 1.000 79.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTCGAGTCAAGAGCACCTTT GAAATTGAAATGGGGCGTGG 1213–1254 1.000 79.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1084–1125 1.000 79.1
rps2-rpoC1_p1 rps2-rpoC1 CCCCATAATGGCCATGAACA CCCGATCCATGCAGTAACAT 253–254 1.000 78.8
rps2-rpoC1_p2 rps2-rpoC1 CATGAACAGTTGCTCCTGGA CCCGATCCATGCAGTAACAT 241–242 1.000 78.1
rps2-rpoC1_p3 rps2-rpoC1 AATGGCCATGAACAGTTGCT CCCGATCCATGCAGTAACAT 247–248 1.000 76.6
rps2-rpoC1_p4 rps2-rpoC1 CCCCATAATGGCCATGAACA ATCCCGATCCATGCAGTAAC 255–256 1.000 76.5
rps2-rpoC1_p5 rps2-rpoC1 TCCCCATAATGGCCATGAAC CCCGATCCATGCAGTAACAT 254–255 1.000 76.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1268–1284 1.000 68.2
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1207–1223 1.000 66.7
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTC 1268–1284 1.000 64.0
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTC 1207–1223 1.000 62.5
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTCT 1269–1285 1.000 62.3

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
Adinandra bockiana MW699853.1 156284 View on NCBI ↗
Adinandra glischroloma NC_087777.1 156277 View on NCBI ↗
Adinandra megaphylla MW697901.1 156298 View on NCBI ↗