Markers + reference

Krascheninnikovia

2 species · Amaranthaceae · Caryophyllales

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Species 2
Genome length 152–152 kb
Candidate markers 261
Primer pairs 80

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 9 remaining regions by MarkerSeek score (out of 261 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps19 LSC 315 0.0060 0.53 50.0 no View details
trnK-UUU-rps16 LSC 684 0.0044 0.99 62.1 yes View details
trnT-GGU-psbD LSC 838 0.0048 1.00 61.5 yes View details
rbcL LSC 1428 0.0035 1.00 60.8 yes View details
psaJ-rpl33 LSC 425 0.0048 0.99 46.4 yes View details
rps19 LSC 279 0.0072 1.00 43.9 yes View details
ycf2 IRb 4548 0.0011 1.00 53.8 yes View details
ycf1 IRb 1419 0.0007 1.00 57.6 no View details
ycf1 SSC 6735 0.0086 0.97 60.6 yes View details
ycf2 IRa 4548 0.0011 1.00 53.8 no View details
trnN-GUU-ycf1 IRb 528 0.0041 0.91 63.4 yes View details
rps16-trnQ-UUG LSC 609 0.0049 1.00 61.6 yes View details
trnI-CAU-rpl2 IRa 1178 0.0000 0.98 60.6 no View details
rpl2-trnI-CAU IRb 809 0.0000 0.98 60.3 yes View details
trnT-UGU-trnL-UAA LSC 786 0.0013 0.99 60.1 yes View details
rpoB-trnC-GCA LSC 1140 0.0009 0.99 59.9 yes View details
trnF-GAA-ndhJ LSC 596 0.0017 1.00 59.8 yes View details
psbE-petL LSC 1211 0.0017 1.00 59.7 yes View details
atpH-atpI LSC 777 0.0013 1.00 59.5 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GGTGCTCAACCTACAGAAACT 783–789 1.000 69.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TTAAAAAGGGCGGACGTTTT 750–756 1.000 66.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TTTAAAAAGGGCGGACGTTT 751–757 1.000 66.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC TTTTAAAAAGGGCGGACGTT 752–758 1.000 66.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCTAGCCGCACTTAAAAGCC GGTGCTCAACCTACAGAAAC 783–789 1.000 65.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GGAACCTGTATGCGGTTGAT GAGGTTCGAATCCTTCCGTC 679–680 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGAACCTGTATGCGGTTGAT TAAGGCATCGGGTTTTGGTC 709–710 1.000 78.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 745–746 1.000 78.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCATCGGGTTTTGGTC 775–776 1.000 77.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTTGGAACCTGTATGCGGTT GAGGTTCGAATCCTTCCGTC 682–683 1.000 77.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCCGCAG 864 1.000 78.7
atpH-atpI_p2 atpH-atpI GCCAACTCCAGGTCCAATAG TTTTGCAACTTTAGCCGCAG 913 1.000 78.7
atpH-atpI_p3 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCCGCAG 856 1.000 78.5
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 880 1.000 77.8
atpH-atpI_p5 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCCGCAG 857 1.000 77.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ACATTCCCTCGTTTCGATCC GGCGTCGATAAGTGAGTTGT 1279–1287 1.000 78.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCCCTGATCAATGAACCTCC GGCGTCGATAAGTGAGTTGT 1341–1349 1.000 78.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ACATTCCCTCGTTTCGATCC CGGATTTGAACTGGGGAACA 1221–1229 1.000 77.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GCCCTGATCAATGAACCTCC CGGATTTGAACTGGGGAACA 1283–1291 1.000 77.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTCCCTCGTTTCGATCCC GGCGTCGATAAGTGAGTTGT 1278–1286 1.000 77.2
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 988–991 1.000 77.8
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 991–994 1.000 77.7
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CAAAAACGAAACGGTCCCTC 987–990 1.000 76.7
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CAAAAACGAAACGGTCCCTC 990–993 1.000 76.5
trnT-GGU-psbD_p5 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA ACAAAAACGAAACGGTCCCT 965–968 1.000 76.1
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA CAAATGCGAGGCTCTAACCT AGCCAATTAAGTCCGTAGCG 860–865 1.000 79.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCATTACAAATGCGAGGCTC AGCCAATTAAGTCCGTAGCG 866–871 1.000 79.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GACTCGAACCGATGACCATC AGCCAATTAAGTCCGTAGCG 886–891 1.000 78.8
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA CAAATGCGAGGCTCTAACCT CCGTAGCGTCTACCGATTTC 848–853 1.000 78.3
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA ACAAATGCGAGGCTCTAACC AGCCAATTAAGTCCGTAGCG 861–866 1.000 78.0

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
Krascheninnikovia arborescens PX969667.1 152039 View on NCBI ↗
Krascheninnikovia ceratoides NC_084261.1 151968 View on NCBI ↗