Markers + reference

Pristimera

3 species · Celastraceae · Celastrales

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Species 3
Genome length 157–159 kb
Candidate markers 273
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 670 0.0866 0.83 81.8 yes View details
trnK-UUU-trnQ-UUG LSC 1970 0.0291 0.94 66.1 yes View details
trnS-GCU-trnG-UCC LSC 844 0.0300 0.99 70.6 yes View details
rpoB-trnC-GCA LSC 1016 0.0216 0.97 67.4 yes View details
trnD-GUC-trnY-GUA LSC 443 0.0610 0.96 84.3 yes View details
psbZ-trnG-GCC LSC 797 0.0483 0.90 75.5 yes View details
trnN-GUU-ndhF IRb 2152 0.0281 0.99 66.8 yes View details
ndhF-rpl32 SSC 927 0.0411 0.99 76.6 yes View details
rps15-ycf1 SSC 450 0.0418 0.92 69.0 yes View details
ycf1 SSC 5658 0.0225 0.99 53.2 yes View details
petD-rpoA LSC 191 0.0456 0.99 83.8 yes View details
trnM-CAU-atpE LSC 278 0.0566 0.97 83.5 yes View details
trnC-GCA-petN LSC 883 0.0316 0.99 76.5 yes View details
rpl32-trnL-UAG SSC 493 0.0407 0.98 72.6 yes View details
trnF-GAA-ndhJ LSC 853 0.0233 0.95 71.7 yes View details
rps12-clpP LSC 209 0.0408 0.98 69.3 yes View details
trnT-UGU-trnL-UAA LSC 1070 0.0294 0.98 68.6 yes View details
psbI-trnS-GCU LSC 229 0.0393 1.00 68.4 yes View details
trnT-GGU-psbD LSC 1495 0.0259 0.98 68.2 yes View details
rps18-rpl20 LSC 249 0.0321 1.00 67.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CTGTCGAAACTCCATCCACA 585–721 1.000 87.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACTGTCGAAACTCCATCCAC 586–722 1.000 87.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTGTCGAAACTCCATCCACA 599–735 1.000 87.3
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTGTCGAAACTCCATCCACA 598–734 1.000 87.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CTGTCGAAACTCCATCCACA 600–736 1.000 87.3
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG CGCGATCTTCCCAACTCTAC GAGGTTCGAATCCTTCCGTC 2006–2108 1.000 85.3
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG CGCGATCTTCCCAACTCTAC CTAACAGCAGCTTGCCAAAC 2616–2682 1.000 85.2
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT CTAACAGCAGCTTGCCAAAC 2536–2602 0.667 71.0
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT CTAACAGCAGCTTGCCAAAC 2535–2601 0.667 71.0
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1925–2027 0.667 70.9
psbI-trnS-GCU_p1 psbI-trnS-GCU GTTTGGCAAGCTGCTGTTAG TGGACTAAAGCGTCGGATTG 897–927 1.000 86.6
psbI-trnS-GCU_p2 psbI-trnS-GCU GTTTGGCAAGCTGCTGTTAG GTGGACTAAAGCGTCGGATT 898–928 1.000 86.6
psbI-trnS-GCU_p3 psbI-trnS-GCU GTTTGGCAAGCTGCTGTTAG GTTCTTCGTACCGAGGGTTC 861–891 1.000 86.6
psbI-trnS-GCU_p4 psbI-trnS-GCU GTTTGGCAAGCTGCTGTTAG AGTTTGTGTTGACCGATGCT 1586 0.333 52.6
psbI-trnS-GCU_p5 psbI-trnS-GCU GTTTGGCAAGCTGCTGTTAG TGCTACTGGCCAAAACTGTT 1570 0.333 52.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 913–977 1.000 57.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 912–976 1.000 57.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 915–979 1.000 56.8
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 916–980 1.000 56.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 914–978 1.000 56.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTACATCCCCCAGC CCGGATTTGAACTGGGGAAA 1030–1100 1.000 85.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATTTACATCCCCCAGC AAAAGGATTTGCAGTCCCCC 1012–1082 1.000 83.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCCTCATTTACATCCCCCA CCGGATTTGAACTGGGGAAA 1032–1102 1.000 83.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCCTCATTTACATCCCCCA AAAAGGATTTGCAGTCCCCC 1014–1084 1.000 81.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTACATCCCCCAG CCGGATTTGAACTGGGGAAA 1031–1101 1.000 80.3
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 917–986 1.000 84.9
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 978–1047 1.000 82.9
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 935–1004 1.000 82.6
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 996–1065 1.000 80.6
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 916–985 1.000 79.0

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
Pristimera arborea NC_065721.1 158774 View on NCBI ↗
Pristimera cambodiana NC_065722.1 157414 View on NCBI ↗
Pristimera indica NC_065719.1 157903 View on NCBI ↗