Markers + reference

Ziziphus

10 species · Rhamnaceae · Rosales

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Species 10
Genome length 161–162 kb
Candidate markers 266
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 1075 0.0310 0.92 63.9 yes View details
trnG-UCC-trnR-UCU LSC 345 0.0413 0.94 71.9 yes View details
trnR-UCU-atpA LSC 422 0.0620 0.92 79.2 yes View details
trnC-GCA-petN LSC 1112 0.0197 0.96 65.8 yes View details
psbZ-trnG-GCC LSC 566 0.0259 0.86 65.2 yes View details
ycf3 LSC 2202 0.0121 0.99 54.6 yes View details
accD-psaI LSC 906 0.0265 0.95 65.4 yes View details
psbE-petL LSC 1395 0.0212 0.99 68.4 yes View details
ndhF SSC 2250 0.0109 1.00 42.1 yes View details
ndhF-rpl32 SSC 1297 0.0226 0.96 62.5 yes View details
ndhA SSC 2386 0.0143 0.98 54.6 yes View details
rps15-ycf1 SSC 375 0.0372 0.99 64.5 yes View details
ycf1 SSC 5745 0.0152 1.00 49.5 yes View details
rbcL-accD LSC 792 0.0215 0.97 74.1 yes View details
atpH-atpI LSC 1093 0.0192 0.99 72.5 yes View details
rps2-rpoC2 LSC 223 0.0434 1.00 72.2 yes View details
trnF-GAA-ndhJ LSC 730 0.0150 0.97 67.8 yes View details
trnH-GUG-psbA LSC 345 0.0353 0.93 67.5 yes View details
atpF-atpH LSC 473 0.0204 0.96 67.5 yes View details
petD-rpoA LSC 199 0.0218 1.00 64.7 yes View details
trnS-GGA-rps4 LSC 295 0.0215 1.00 64.1 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 105 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 CGAAGTTCCGTCTACAAACG 352–391 1.000 81.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CGAAGTTCCGTCTACAAACG 366–405 1.000 80.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CGAAGTTCCGTCTACAAACG 365–404 1.000 80.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CGAAGTTCCGTCTACAAACG 367–406 1.000 80.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCGAAGTTCCGTCTACAAACG 353–392 1.000 79.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 1109–1266 1.000 57.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTACCACTAAACTATACCCGC 1110–1267 1.000 56.0
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TTTACCACTAAACTATACCCGC 1111–1268 1.000 54.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CTTTCGTCCACTCAGCCATC TACCACTAAACTATACCCGC 1045–1202 1.000 53.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AACGGAAAGAGAGGGATTCG TACCACTAAACTATACCCGC 1110–1267 1.000 52.9
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 387–461 1.000 74.5
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 390–464 1.000 74.2
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 393–467 1.000 73.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 396–470 1.000 73.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 391–465 1.000 72.0
trnR-UCU-atpA_p1 trnR-UCU-atpA TGCAAAGCGTCCATTGTCTA AGGAACAGCTGGAACGTTTT 451–678 1.000 90.2
trnR-UCU-atpA_p2 trnR-UCU-atpA TGCAAAGCGTCCATTGTCTA GAGGAAGCAGAAGCCCTTTT 485–712 1.000 89.9
trnR-UCU-atpA_p3 trnR-UCU-atpA TGCAAAGCGTCCATTGTCTA TTTACCGAGGAAGCAGAAGC 491–718 1.000 89.8
trnR-UCU-atpA_p4 trnR-UCU-atpA TGCAAAGCGTCCATTGTCTA ATTCAGGAACAGCTGGAACG 455–682 1.000 89.1
trnR-UCU-atpA_p5 trnR-UCU-atpA AATGCAAAGCGTCCATTGTC AGGAACAGCTGGAACGTTTT 453–680 1.000 88.8
atpF-atpH_p1 atpF-atpH ATTAAACCCGAAACTCCCGG GTTGTGGCATTAGCGCTTTT 561–584 1.000 86.0
atpF-atpH_p2 atpF-atpH ATTAAACCCGAAACTCCCGG TGGACTGGTTGTGGCATTAG 568–591 1.000 84.8
atpF-atpH_p3 atpF-atpH TGGCCAATAACCCAAGGAAA GTTGTGGCATTAGCGCTTTT 537–560 1.000 81.6
atpF-atpH_p4 atpF-atpH ATTAAACCCGAAACTCCCGG TTTATGGACTGGTTGTGGCA 572–595 1.000 81.0
atpF-atpH_p5 atpF-atpH TGGCCAATAACCCAAGGAAA TGGACTGGTTGTGGCATTAG 544–567 1.000 80.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1136–1151 1.000 85.6
atpH-atpI_p2 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1170–1185 1.000 85.5
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1166–1181 1.000 84.6
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA GCGAATCCATGGAAGGTCAT 1152–1167 1.000 84.6
atpH-atpI_p5 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1200–1215 1.000 84.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Ziziphus attopensis NC_057063.1 161342 View on NCBI ↗
Ziziphus hajarensis MZ475300.1 162162 View on NCBI ↗
Ziziphus incurva NC_050251.1 160920 View on NCBI ↗
Ziziphus jujuba NC_030299.1 161466 View on NCBI ↗
Ziziphus jujuba var. spinosa NC_083084.1 161626 View on NCBI ↗
Ziziphus mairei NC_069299.1 161546 View on NCBI ↗
Ziziphus mauritiana NC_037151.1 161543 View on NCBI ↗
Ziziphus nummularia PZ168344.1 161549 View on NCBI ↗
Ziziphus oxyphylla PZ168345.1 161739 View on NCBI ↗
Ziziphus spina-christi NC_037152.1 161615 View on NCBI ↗