Markers + reference

Viscum

6 species · Viscaceae · Santalales

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Species 6
Genome length 126–129 kb
Candidate markers 233
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 233 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
APQ78_gt002-APQ78_gp070 Genome 555 0.1679 0.82 77.4 yes View details
APQ78_gp070-APQ78_gt003 Genome 773 0.1548 0.92 81.6 yes View details
APQ78_gt004-APQ78_gt005 Genome 419 0.2574 0.91 77.4 yes View details
APQ78_gt011-APQ78_gp055 Genome 433 0.1403 0.96 81.9 yes View details
APQ78_gp032 Genome 57129 0.0382 0.98 71.2 yes View details
APQ78_gt009-APQ78_gt010 Genome 524 0.0805 0.99 85.7 yes View details
APQ78_gp033-APQ78_gp031 Genome 800 0.0488 0.97 84.5 yes View details
APQ78_gp018 Genome 1432 0.0705 0.99 84.5 yes View details
APQ78_gp025 Genome 1428 0.0501 0.98 84.3 yes View details
APQ78_gp038-APQ78_gp037 Genome 861 0.0862 0.99 84.0 yes View details
APQ78_gp066 Genome 1354 0.0520 0.97 83.9 yes View details
APQ78_gp051-APQ78_gt014 Genome 499 0.0953 0.99 83.6 yes View details
APQ78_gp048-APQ78_gp047 Genome 664 0.1022 0.98 83.6 yes View details
APQ78_gp030-APQ78_gp029 Genome 581 0.1042 0.92 83.1 yes View details
APQ78_gt010-APQ78_gp057 Genome 753 0.1001 0.92 82.6 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
APQ78_gt002-APQ78_gp070_p1 APQ78_gt002-APQ78_gp070 GGAGAACAAAAGCTCGTTGC AAGGCAGGGGTTTATCATCG 976–986 0.500 60.8
APQ78_gt002-APQ78_gp070_p2 APQ78_gt002-APQ78_gp070 AAAGCCGAGTACTCTACCGT AAGGCAGGGGTTTATCATCG 664–680 0.500 60.6
APQ78_gt002-APQ78_gp070_p3 APQ78_gt002-APQ78_gp070 AAGCCGAGTACTCTACCGTT AAGGCAGGGGTTTATCATCG 663–679 0.500 60.6
APQ78_gt002-APQ78_gp070_p4 APQ78_gt002-APQ78_gp070 AGCCGAGTACTCTACCGTTT AAGGCAGGGGTTTATCATCG 662–678 0.500 60.6
APQ78_gt002-APQ78_gp070_p5 APQ78_gt002-APQ78_gp070 CCGCACTTAAAAGCCGAGTA AAGGCAGGGGTTTATCATCG 673–689 0.500 59.6
APQ78_gp070-APQ78_gt003_p1 APQ78_gp070-APQ78_gt003 GCTAAGAGCACTTCCAGTCC CAAAGGTCTGATCCGGATGG 1491–1514 0.500 64.7
APQ78_gp070-APQ78_gt003_p2 APQ78_gp070-APQ78_gt003 GCTAAGAGCACTTCCAGTCC TGGTCCTGTTATTCGGAGGT 903–932 0.500 64.7
APQ78_gp070-APQ78_gt003_p3 APQ78_gp070-APQ78_gt003 GCTAAGAGCACTTCCAGTCC GAGGTTCGAATCCTTCCGTC 888–917 0.500 64.6
APQ78_gp070-APQ78_gt003_p4 APQ78_gp070-APQ78_gt003 CGAGCTAAGAGCACTTCCAG CAAAGGTCTGATCCGGATGG 1494–1517 0.500 64.1
APQ78_gp070-APQ78_gt003_p5 APQ78_gp070-APQ78_gt003 TTTCTACTCGAGCTCCACCA CAAAGGTCTGATCCGGATGG 1616–1639 0.500 64.1
APQ78_gt004-APQ78_gt005_p1 APQ78_gt004-APQ78_gt005 GGGATTTGAACCCTCGGTAC GAGTTGGATCTGCAGCTCAA 1214–2243 1.000 90.9
APQ78_gt004-APQ78_gt005_p2 APQ78_gt004-APQ78_gt005 GGGATTTGAACCCTCGGTAC CCATGAAACAAGTAGCCGGA 1187–2216 1.000 90.9
APQ78_gt004-APQ78_gt005_p3 APQ78_gt004-APQ78_gt005 GGGATTTGAACCCTCGGTAC AACTCAGGAAGATGAACGCC 868–1897 0.833 84.3
APQ78_gt004-APQ78_gt005_p4 APQ78_gt004-APQ78_gt005 CCATCCGGATCAGACCTTTG AACTCAGGAAGATGAACGCC 1387–1705 0.500 66.4
APQ78_gt004-APQ78_gt005_p5 APQ78_gt004-APQ78_gt005 CCATCCGGATCAGACCTTTG GAGTTGGATCTGCAGCTCAA 1733–2051 0.500 65.1
APQ78_gp066_p1 APQ78_gp066 ACCTAAAAACGCCTTGCTCA AGGCCAAGCTGTAGAAGGTA 2269–2308 0.833 84.8
APQ78_gp066_p2 APQ78_gp066 AACACGACCTAAAAACGCCT AGGCCAAGCTGTAGAAGGTA 2275–2314 0.833 84.6
APQ78_gp066_p3 APQ78_gp066 CACCCGCCATTACTTCATCA AGGCCAAGCTGTAGAAGGTA 1823–2144 0.667 75.5
APQ78_gp066_p4 APQ78_gp066 ACACGACCTAAAAACGCCTT AGGCCAAGCTGTAGAAGGTA 2281–2313 0.500 60.7
APQ78_gp066_p5 APQ78_gp066 TAGTATCCGTGGCTACTGCA AGGCCAAGCTGTAGAAGGTA 2508–2540 0.500 60.5
APQ78_gt009-APQ78_gt010_p1 APQ78_gt009-APQ78_gt010 TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 578–667 1.000 89.7
APQ78_gt009-APQ78_gt010_p2 APQ78_gt009-APQ78_gt010 TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 557–646 1.000 89.2
APQ78_gt009-APQ78_gt010_p3 APQ78_gt009-APQ78_gt010 TGTCCTGAACCACTAGACGA TGGCGTTACTCTACCACTGA 554–643 1.000 89.1
APQ78_gt009-APQ78_gt010_p4 APQ78_gt009-APQ78_gt010 TGTCCTGAACCACTAGACGA CCGATGACTTACGCCTTACC 575–664 1.000 88.5
APQ78_gt009-APQ78_gt010_p5 APQ78_gt009-APQ78_gt010 TGTCCTGAACCACTAGACGA TTGAACCGATGACTTACGCC 580–669 1.000 87.5
APQ78_gt010-APQ78_gp057_p1 APQ78_gt010-APQ78_gp057 ATGGGGGCATACTTATCCGA GGAACTGGCTAATCCATGGG 1535–1558 0.667 78.3
APQ78_gt010-APQ78_gp057_p2 APQ78_gt010-APQ78_gp057 ATGGGGGCATACTTATCCGA TGAACAGATCGAGCAAGCTC 1747–1770 0.667 77.8
APQ78_gt010-APQ78_gp057_p3 APQ78_gt010-APQ78_gp057 ATGGGGGCATACTTATCCGA AGCTTGGGTGGGGTTAAAAG 2057–2080 0.667 76.8
APQ78_gt010-APQ78_gp057_p4 APQ78_gt010-APQ78_gp057 ATGGGGGCATACTTATCCGA AGTTTCTTCAGCTTGGGTGG 2066–2089 0.667 76.8
APQ78_gt010-APQ78_gp057_p5 APQ78_gt010-APQ78_gp057 ATGGGGGCATACTTATCCGA GAACAGATCGAGCAAGCTCA 1746–1769 0.500 63.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Viscum album NC_028012.1 128921 View on NCBI ↗
Viscum coloratum NC_035414.1 128744 View on NCBI ↗
Viscum crassulae NC_027959.1 126064 View on NCBI ↗
Viscum liquidambaricola NC_048985.1 128601 View on NCBI ↗
Viscum ovalifolium NC_048986.1 129465 View on NCBI ↗
Viscum trachycarpum OR712485.1 128593 View on NCBI ↗