Markers + reference

Crocus

3 species · Iridaceae · Asparagales

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Species 3
Genome length 151–151 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 588 0.0193 1.00 53.8 yes View details
rps16-trnQ-UUG LSC 586 0.0148 1.00 46.8 yes View details
trnS-GCU-trnG-UCC LSC 772 0.0190 1.00 50.9 yes View details
psbM-trnD-GUC LSC 1094 0.0116 1.00 44.1 yes View details
accD LSC 1395 0.0119 1.00 51.1 yes View details
ndhF-rpl32 SSC 567 0.0165 1.00 49.6 yes View details
rpl32-trnL SSC 693 0.0135 1.00 41.6 yes View details
psaC-ndhE SSC 345 0.0232 1.00 48.6 yes View details
ycf1 SSC 5421 0.0119 1.00 34.9 yes View details
trnR-UCU-atpA LSC 54 0.0494 1.00 69.3 yes View details
psbK-psbI LSC 159 0.0252 1.00 61.4 yes View details
trnG-UCC-trnfM-CAU LSC 129 0.0310 1.00 55.8 yes View details
rps7-rps12 IRb 58 0.0230 1.00 54.7 yes View details
rps12-rps7 IRa 58 0.0230 1.00 54.7 yes View details
rpl20-rps12 LSC 745 0.0089 1.00 52.6 yes View details
rps19-psbA LSC 111 0.0300 1.00 51.9 no View details
rpoB-trnC-GCA LSC 920 0.0109 1.00 51.8 yes View details
trnG-UCC-trnR-UCU LSC 139 0.0288 1.00 50.6 yes View details
rps15-ycf1 SSC 443 0.0166 1.00 50.5 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGCCAATGTCAACCAATCTCA GGAGTTGTGCAGTGCAATTC 2917–2929 1.000 72.3
trnK-UUU_p2 trnK-UUU TGCCAATGTCAACCAATCTCA ATGGAGTTGTGCAGTGCAAT 2919–2931 1.000 69.8
trnK-UUU_p3 trnK-UUU TGCCAATGTCAACCAATCTCA TGGAGTTGTGCAGTGCAATT 2918–2930 1.000 68.0
trnK-UUU_p4 trnK-UUU GCCAATGTCAACCAATCTCA GGAGTTGTGCAGTGCAATTC 2916–2928 1.000 67.8
trnK-UUU_p5 trnK-UUU TGCCAATGTCAACCAATCTC GGAGTTGTGCAGTGCAATTC 2917–2929 1.000 67.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AAAAAGGCGCTCAACCTACA 702–711 1.000 82.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AAAAAGGCGCTCAACCTACA 701–710 1.000 82.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CTTGAAAAAGGCGCTCAACC 706–715 1.000 80.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CCTTGAAAAAGGCGCTCAAC 706–715 1.000 80.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGCGCTCAACC 705–714 1.000 80.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 652–659 1.000 81.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGCTTTCTACCGCATCGTTT GAGGTTCGAATCCTTCCGTC 641–648 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TTGCTTTCTACCGCATCGTT GAGGTTCGAATCCTTCCGTC 642–649 1.000 80.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 663–670 1.000 80.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 656–663 1.000 79.9
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTACGTCCCGGATCGTTAGA 267–281 1.000 85.0
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGTCCCGGATCGTTAGATA 265–279 1.000 83.2
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TACGTCCCGGATCGTTAGAT 266–280 1.000 83.2
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT TTACGTCCCGGATCGTTAGA 264–278 1.000 83.0
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT TTACGTCCCGGATCGTTAGA 265–279 1.000 83.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 878–964 1.000 67.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCTGCCGCTTTAGTCCA AACCGAAAGACCCCTTAACT 879–965 1.000 67.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACCGAAAGACCCCTTAACT 932–1018 1.000 67.3
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GCTTTAGTCCACTCAGCCAT AACCGAAAGACCCCTTAACT 870–956 1.000 66.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 879–965 1.000 66.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 218–219 1.000 65.9
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 221–222 1.000 65.6
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 224–225 1.000 65.2
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 227–228 1.000 64.9
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 222–223 1.000 63.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Crocus cartwrightianus NC_041459.1 150819 View on NCBI ↗
Crocus sativus NC_041460.1 150820 View on NCBI ↗
Crocus vernus PP175360.1 151260 View on NCBI ↗