Markers + reference

Urtica

20 species · Urticaceae · Rosales

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Species 20
Genome length 146–148 kb
Candidate markers 264
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 1449 0.0554 0.99 82.2 yes View details
rpoB-trnC-GCA LSC 1053 0.0424 0.97 78.1 yes View details
rps19 LSC 219 0.1001 0.95 64.5 yes View details
ndhF-rpl32 SSC 765 0.0599 0.98 77.2 yes View details
rps15-ycf1 SSC 367 0.0535 0.99 73.7 yes View details
ycf1 SSC 5487 0.0359 1.00 67.4 yes View details
psbZ-trnG-GCC LSC 378 0.0492 1.00 81.1 yes View details
rpl2-trnH-GUG IRa 166 0.0456 1.00 78.1 no View details
trnE-UUC-trnT-GGU LSC 564 0.0329 0.99 77.6 yes View details
trnT-UGU-trnL-UAA LSC 715 0.0399 1.00 75.9 yes View details
psbE-petL LSC 1071 0.0300 1.00 75.9 yes View details
trnD-GUC-trnY-GUA LSC 384 0.0428 0.99 75.4 yes View details
rpl32-trnL-UAG SSC 462 0.0424 0.99 74.5 yes View details
trnC-GCA-petN LSC 786 0.0386 0.99 74.1 yes View details
psaA-ycf3 LSC 677 0.0271 1.00 73.0 yes View details
rbcL-accD LSC 718 0.0344 0.98 72.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 1239–1528 1.000 90.0
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 1238–1527 1.000 90.0
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG CCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 1248–1537 1.000 89.1
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG TACCGTTGAGTTAGCAACCC GAGGTTCGAATCCTTCCGTC 1225–1514 1.000 87.7
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG GTGTAAAAGATGCTAGCCGC GAGGTTCGAATCCTTCCGTC 1264–1553 1.000 85.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TTCATTTCCACTCCCAAGCA CCGGATTTGAACTGGGGAAA 1075–1165 1.000 86.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCATTTCCACTCCCAAGCAT CCGGATTTGAACTGGGGAAA 1074–1164 1.000 84.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCATTTCCACTCCCAAGCA AAAAGGATTTGCAGTCCCCC 1057–1147 1.000 83.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTCATTTCCACTCCCAAGCAT CCGGATTTGAACTGGGGAAA 1075–1165 1.000 82.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TCATTTCCACTCCCAAGCAT AAAAGGATTTGCAGTCCCCC 1056–1146 1.000 81.9
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 841–865 1.000 88.8
trnC-GCA-petN_p2 trnC-GCA-petN GGTGTCGCCTGATAACCAAA AGCCCAAGCGAGACTTACTA 822–846 1.000 88.1
trnC-GCA-petN_p3 trnC-GCA-petN TTAGATCGTTTTGGCGGCAT AGCCCAAGCGAGACTTACTA 895–919 1.000 87.3
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 902–926 1.000 87.1
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 859–883 1.000 86.6
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 408–458 1.000 86.3
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 407–457 1.000 86.3
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 429–479 1.000 85.4
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 428–478 1.000 85.2
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA CGGACTGTAAATTCGTTGGC 424–474 1.000 84.0
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 613–672 1.000 90.8
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 611–670 1.000 90.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 667–726 1.000 90.7
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 592–651 1.000 90.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 590–649 1.000 90.3
psbZ-trnG-GCC_p1 psbZ-trnG-GCC CCGGTACATCATTATGGATTGGA AATCGAACCCGCATCTTCTC 499–523 1.000 66.8
psbZ-trnG-GCC_p2 psbZ-trnG-GCC CCGGTACATCATTATGGATTGGA GAATCGAACCCGCATCTTCT 500–524 1.000 66.8
psbZ-trnG-GCC_p3 psbZ-trnG-GCC TCCGGTACATCATTATGGATTGG AATCGAACCCGCATCTTCTC 500–524 1.000 66.8
psbZ-trnG-GCC_p4 psbZ-trnG-GCC TCCGGTACATCATTATGGATTGG GAATCGAACCCGCATCTTCT 501–525 1.000 66.8
psbZ-trnG-GCC_p5 psbZ-trnG-GCC CCGGTACATCATTATGGATTGG AATCGAACCCGCATCTTCTC 499–523 1.000 65.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (20)

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

Species Accession Length (bp) Link
Urtica angustifolia NC_064944.1 146703 View on NCBI ↗
Urtica ardens NC_064945.1 146795 View on NCBI ↗
Urtica atrichocaulis NC_064946.1 146717 View on NCBI ↗
Urtica cannabina PQ846489.1 147958 View on NCBI ↗
Urtica chamaedryoides NC_064947.1 146455 View on NCBI ↗
Urtica dioica NC_064948.1 147799 View on NCBI ↗
Urtica dioica subsp. xingjiangensis NC_062305.1 147935 View on NCBI ↗
Urtica domingensis NC_064949.1 146125 View on NCBI ↗
Urtica fissa MZ313540.1 146837 View on NCBI ↗
Urtica hyperborea NC_064950.1 147898 View on NCBI ↗
Urtica kioviensis NC_064951.1 146725 View on NCBI ↗
Urtica lobatifolia NC_056314.1 146848 View on NCBI ↗
Urtica macrorrhiza NC_062304.1 146747 View on NCBI ↗
Urtica magellanica NC_064952.1 146606 View on NCBI ↗
Urtica mairei NC_064953.1 146790 View on NCBI ↗
Urtica mairei var. mairei OM877284.1 146819 View on NCBI ↗
Urtica morifolia NC_064955.1 146755 View on NCBI ↗
Urtica radicans NC_064979.1 146667 View on NCBI ↗
Urtica rupestris NC_064956.1 146751 View on NCBI ↗
Urtica thunbergiana NC_064957.1 146846 View on NCBI ↗