Markers + reference

Boehmeria

8 species · Urticaceae · Rosales

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Species 8
Genome length 155–171 kb
Candidate markers 294
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 294 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 285 0.0424 0.84 69.6 yes View details
trnK-UUU-rps16 LSC 794 0.0227 1.00 72.6 yes View details
rps8 IRb 405 0.0202 1.00 52.3 no View details
rpl16 IRb 1449 0.0142 1.00 60.1 yes View details
ndhF-rpl32 SSC 1179 0.0252 1.00 66.0 yes View details
rpl32-trnL-UAG SSC 788 0.0237 0.98 71.1 yes View details
ccsA-ndhD SSC 289 0.0465 1.00 68.3 yes View details
ycf1 SSC 4125 0.0183 0.99 58.8 yes View details
rpl16 IRa 1449 0.0038 0.00 29.9 no View details
rps8 IRa 405 0.0214 0.00 30.1 yes View details
clpP-trnH-GUG LSC 1544 0.1634 0.01 67.2 no View details
trnE-UUC-trnT-GGU LSC 654 0.0109 1.00 66.2 yes View details
trnC-GCA-petN LSC 1196 0.0134 0.99 65.7 yes View details
trnT-GGU-psbD LSC 1410 0.0128 0.98 64.4 yes View details
psaA-ycf3 LSC 779 0.0123 1.00 63.4 yes View details
psbK-psbI LSC 490 0.0129 1.00 62.3 yes View details
rps4-trnT-UGU LSC 524 0.0092 1.00 62.0 yes View details
ndhC-trnV-UAC LSC 496 0.0159 1.00 61.9 yes View details
rpl36-rps8 IRb 515 0.0147 0.99 61.9 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TAGGCTGGTTCCTATAGGCC GAACTTAGCTTCCGTCTGGG 1428–1495 0.250 51.2
trnH-GUG-psbA_p2 trnH-GUG-psbA TAGGCTGGTTCCTATAGGCC GGAACTTAGCTTCCGTCTGG 1429–1496 0.250 51.2
trnH-GUG-psbA_p3 trnH-GUG-psbA GCCTTGACCTACTTGGCTAC GAACTTAGCTTCCGTCTGGG 981 0.125 44.7
trnH-GUG-psbA_p4 trnH-GUG-psbA GCCTTGACCTACTTGGCTAC GGAACTTAGCTTCCGTCTGG 982 0.125 44.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGACCTACTTGGCTAC GGGAACTTAGCTTCCGTCTG 983 0.125 44.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAGGCGGGTGT 865–942 1.000 87.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAGGCGGGTGT 864–941 1.000 87.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAGAAGGCGGGTGTTTT 861–938 1.000 85.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAGAAGGCGGGTGTTT 862–939 1.000 85.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCAAAGAAGGCGGGTGTT 863–940 1.000 85.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCCGGATCATTAGATA 594–619 1.000 85.8
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGCCCCGGATCATTAGAT 595–620 1.000 85.8
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT ACGCCCCGGATCATTAGATA 599–624 1.000 85.7
psbK-psbI_p4 psbK-psbI CTTTTGTTTGGCAAGCTGCT TACGCCCCGGATCATTAGAT 600–625 1.000 85.7
psbK-psbI_p5 psbK-psbI CTTTTGTTTGGCAAGCTGCT TTACGCCCCGGATCATTAGA 601–626 1.000 83.9
trnC-GCA-petN_p1 trnC-GCA-petN CCGGATTTGAACTGGGGAAA AGCCCAAGCGAGACTTACTA 1013–1366 1.000 85.2
trnC-GCA-petN_p2 trnC-GCA-petN CCGGATTTGAACTGGGGAAA AGAGTCCACTTCTTCCCCAT 1074–1427 1.000 83.5
trnC-GCA-petN_p3 trnC-GCA-petN AAAAGGATTTGCAGTCCCCC AGCCCAAGCGAGACTTACTA 995–1348 1.000 83.1
trnC-GCA-petN_p4 trnC-GCA-petN AAAAGGATTTGCAGTCCCCC AGAGTCCACTTCTTCCCCAT 1056–1409 1.000 81.3
trnC-GCA-petN_p5 trnC-GCA-petN TAATTAGGCGACACCCGGAT AGCCCAAGCGAGACTTACTA 1027–1380 1.000 81.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 723–758 1.000 85.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 721–756 1.000 85.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 777–812 1.000 84.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 702–737 1.000 84.8
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 700–735 1.000 84.8
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG AGTAGACCGGACCAACCTAC 1339–1579 1.000 84.9
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA AGTAGACCGGACCAACCTAC 1342–1582 1.000 84.7
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1321–1561 1.000 84.2
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1335–1575 1.000 84.0
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1324–1564 1.000 84.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Boehmeria clidemioides var. diffusa PQ766620.1 170741 View on NCBI ↗
Boehmeria japonica NC_062312.1 156266 View on NCBI ↗
Boehmeria pilosiuscula OP549684.1 169428 View on NCBI ↗
Boehmeria tricuspis OR643823.1 157765 View on NCBI ↗
Boehmeria tsaratananensis OP549685.1 154753 View on NCBI ↗
Boehmeria ulmifolia OQ183443.1 154946 View on NCBI ↗
Boehmeria virgata OQ183444.1 154793 View on NCBI ↗
Boehmeria virgata subsp. macrophylla PP866772.1 161166 View on NCBI ↗