Markers + reference

Karpatiosorbus

2 species · Rosaceae · Rosales

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Species 2
Genome length 160–160 kb
Candidate markers 259
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 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 278 0.0000 1.00 33.4 yes View details
rps16-trnQ-UUG LSC 799 0.0075 1.00 63.0 yes View details
trnR-UCU-atpA LSC 749 0.0176 0.91 72.4 yes View details
petN-psbM LSC 1256 0.0048 1.00 61.5 yes View details
trnT-GGU-psbD LSC 1454 0.0014 0.98 61.4 yes View details
trnT-UGU-trnL-UAA LSC 1236 0.0008 0.99 60.6 yes View details
ndhC-trnV-UAC LSC 723 0.0086 0.97 66.9 yes View details
petL-petG LSC 158 0.0000 1.00 31.7 yes View details
rpl36-infA LSC 270 0.0037 1.00 54.6 yes View details
ndhF SSC 2244 0.0009 1.00 57.7 yes View details
petG-trnW-CCA LSC 124 0.0847 0.95 89.8 yes View details
accD-psaI LSC 802 0.0000 0.97 61.9 yes View details
ndhF-rpl32 SSC 1104 0.0000 0.98 60.5 yes View details
rpl32-trnL-UAG SSC 1471 0.0000 0.99 59.9 yes View details
rps16 LSC 1136 0.0000 0.99 59.8 yes View details
atpI LSC 744 0.0013 1.00 59.5 yes View details
clpP LSC 2070 0.0000 0.98 59.3 yes View details
rbcL LSC 1428 0.0007 1.00 59.2 yes View details
petD LSC 1207 0.0008 1.00 59.2 yes View details
ycf3-trns-GGA LSC 616 0.0000 1.00 59.1 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 ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 455–456 1.000 79.1
trnH-GUG-psbA_p2 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 405–406 1.000 78.9
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 408–409 1.000 78.8
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 394–395 1.000 78.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 408–409 1.000 78.7
rps16_p1 rps16 AGAAACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1261–1273 1.000 40.8
rps16_p2 rps16 AGAAACAAAAAGGTTATACAAGGCT CCGACCGAACCGATGATTAT 1255–1267 1.000 40.8
rps16_p3 rps16 ACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1257–1269 1.000 40.8
rps16_p4 rps16 AGAAACAAAAAGGTTATACAAGGCT ATTATGTACCGACCGAACCG 1263–1275 1.000 40.8
rps16_p5 rps16 GGAAATAGCAAAGAAACAAAAAGGT TATGTACCGACCGAACCGAT 1272–1284 1.000 40.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 883–900 1.000 78.3
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 893–910 1.000 76.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 860–877 1.000 76.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 894–911 1.000 76.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 945–962 1.000 76.1
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 917–918 1.000 69.5
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 916–917 1.000 69.4
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 856–857 1.000 68.6
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 891–892 1.000 65.7
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 917–918 1.000 65.4
atpI_p1 atpI CATTGCGTCAGGCTAAGACT ACAATTCAAGTAGGCAAGTCA 855 1.000 51.4
atpI_p2 atpI TTACCTTGAGTCGCGCATAC ACAATTCAAGTAGGCAAGTCA 874 1.000 50.8
atpI_p3 atpI CATTGCGTCAGGCTAAGACT ACAATTCAAGTAGGCAAGTCAA 855 1.000 49.5
atpI_p4 atpI ACATTGCGTCAGGCTAAGAC ACAATTCAAGTAGGCAAGTCA 856 1.000 49.3
atpI_p5 atpI TTACCTTGAGTCGCGCATAC ACAATTCAAGTAGGCAAGTCAA 874 1.000 49.0
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG AAAACAGTCAGCCAAGGTGA 1362–1365 1.000 76.6
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC AAAACAGTCAGCCAAGGTGA 1305–1308 1.000 75.9
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT AAAACAGTCAGCCAAGGTGA 1304–1307 1.000 75.9
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC AAAACAGTCAGCCAAGGTGA 1303–1306 1.000 75.5
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG AAAACAGTCAGCCAAGGTGA 1300–1303 1.000 75.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Karpatiosorbus bakonyensis NC_085571.1 160377 View on NCBI ↗
Karpatiosorbus semi-incisa NC_085648.1 160197 View on NCBI ↗