Markers + reference

Procris

3 species · Urticaceae · Rosales

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Species 3
Genome length 154–154 kb
Candidate markers 271
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 8 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0019 1.00 36.3 yes View details
trnK-UUU-rps16 LSC 673 0.0278 1.00 67.2 yes View details
trnS-GCU-trnG-UCC LSC 672 0.0186 0.99 64.2 yes View details
psbC-trnS-UGA LSC 240 0.0847 1.00 92.8 yes View details
trnS-UGA-psbZ LSC 274 0.0024 1.00 34.1 yes View details
clpP LSC 2057 0.0177 0.99 56.6 yes View details
rpl22 LSC 408 0.0229 1.00 54.6 yes View details
ndhF-rpl32 SSC 1094 0.0232 1.00 65.7 yes View details
rpl32-trnL-UAG SSC 913 0.0268 0.99 61.9 yes View details
ycf1 SSC 5484 0.0191 1.00 51.0 yes View details
psbI-trnS-GCU LSC 150 0.0467 1.00 79.0 yes View details
trnH-GUG-psbA LSC 210 0.0794 1.00 75.9 yes View details
petA-psbJ LSC 835 0.0216 1.00 71.3 yes View details
rps3-rpl22 LSC 128 0.0469 1.00 71.1 yes View details
ycf3-trnS-GGA LSC 712 0.0140 1.00 70.1 yes View details
rps4-trnT-UGU LSC 498 0.0295 1.00 69.9 yes View details
trnT-UGU-trnL-UAA LSC 653 0.0200 1.00 67.8 yes View details
trnY-GUA-trnE-UUC LSC 58 0.0345 1.00 66.0 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 276 1.000 85.7
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 279 1.000 85.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 290 1.000 85.3
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 289 1.000 85.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 291 1.000 85.3
psbA_p1 psbA TGCTCCTTTATTTTCAAGAACTCA ATTCATGTGCTTGGGAGTCC 1162 1.000 40.2
psbA_p2 psbA TTGCTCCTTTATTTTCAAGAACTCA ATTCATGTGCTTGGGAGTCC 1163 1.000 40.2
psbA_p3 psbA TGCTCCTTTATTTTCAAGAACTCAT ATTCATGTGCTTGGGAGTCC 1162 1.000 40.2
psbA_p4 psbA GCTCCTTTATTTTCAAGAACTCA ATTCATGTGCTTGGGAGTCC 1161 1.000 40.2
psbA_p5 psbA TGCTCCTTTATTTTCAAGAACTC ATTCATGTGCTTGGGAGTCC 1162 1.000 40.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAGGCGGGTGT 753–758 1.000 82.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAGGCGGGTGT 752–757 1.000 82.4
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ATTTCAAAGAAGGCGGGTGT 762–767 1.000 81.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAGAAGGCGGGTGTTTT 749–754 1.000 80.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGAAGGCGGGTGTTT 750–755 1.000 80.6
psbI-trnS-GCU_p1 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TGGACTAAAGCGTCGGATTG 226–247 1.000 79.8
psbI-trnS-GCU_p2 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA GTGGACTAAAGCGTCGGATT 227–248 1.000 79.8
psbI-trnS-GCU_p3 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTTTTCGTACCGAGGGTTCG 189–210 1.000 78.7
psbI-trnS-GCU_p4 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 226–247 1.000 77.5
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 227–248 1.000 77.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ATTAATCAACCCGAGGGACC 775–787 1.000 74.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ATTAATCAACCCGAGGGACC 774–786 1.000 74.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TTAATCAACCCGAGGGACCC 774–786 1.000 74.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TTAATCAACCCGAGGGACCC 773–785 1.000 74.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ATTAATCAACCCGAGGGACC 829–841 1.000 73.5
trnY-GUA-trnE-UUC_p1 trnY-GUA-trnE-UUC TGGATCGGCGAATTATTGGG AAGTATGCCCCCATCGTCTA 237 1.000 79.4
trnY-GUA-trnE-UUC_p2 trnY-GUA-trnE-UUC CATGGTGGATCGGCGAATTA AAGTATGCCCCCATCGTCTA 242 1.000 79.2
trnY-GUA-trnE-UUC_p3 trnY-GUA-trnE-UUC CCAGCGTAGACATATTGCCA AAGTATGCCCCCATCGTCTA 201 1.000 78.5
trnY-GUA-trnE-UUC_p4 trnY-GUA-trnE-UUC ACCAGCGTAGACATATTGCC AAGTATGCCCCCATCGTCTA 202 1.000 78.5
trnY-GUA-trnE-UUC_p5 trnY-GUA-trnE-UUC TGGATCGGCGAATTATTGGG CTCTCTTTCAAGGAGGCAGC 203 1.000 78.2

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
Procris crenata NC_056276.1 154124 View on NCBI ↗
Procris frutescens PQ676469.1 153727 View on NCBI ↗
Procris montana PQ676470.1 154077 View on NCBI ↗