Markers + reference

Iris

62 species · Iridaceae · Asparagales

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Species 62
Genome length 151–156 kb
Candidate markers 272
Primer pairs 85

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 9 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 877 0.0406 0.99 73.0 yes View details
rpoB-trnC-GCA LSC 1203 0.0389 1.00 76.6 yes View details
trnT-UGU-trnL-UAA LSC 996 0.0363 0.99 74.4 yes View details
petA-psbJ LSC 846 0.0445 0.99 78.4 yes View details
ycf1 IRb 900 0.0106 1.00 51.7 no View details
ndhF-rpl32 SSC 899 0.0452 0.99 73.7 yes View details
rpl32-trnL-UAG SSC 745 0.0406 0.99 74.7 yes View details
rps15-ycf1 SSC 496 0.0648 0.90 72.0 yes View details
ycf1 SSC 5361 0.0322 0.99 68.3 yes View details
psbM-trnD-GUC LSC 843 0.0308 0.99 75.8 yes View details
trnS-GCU-trnG-UCC LSC 889 0.0372 0.96 75.6 yes View details
petN-psbM LSC 897 0.0305 1.00 75.3 yes View details
psbE-petL LSC 1198 0.0286 0.98 74.4 yes View details
trnG-UCC-trnR-UCU LSC 137 0.0500 1.00 73.8 yes View details
trnD-GUC-trnY-GUA LSC 383 0.0446 1.00 73.2 yes View details
psbK-psbI LSC 386 0.0375 1.00 73.1 yes View details
trnL-UAA-trnF-GAA LSC 382 0.0326 1.00 72.6 yes View details
trnK-UUU-rps16 LSC 651 0.0385 0.97 72.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CTCTGCCGTTGAGTTAGCAA AGAGACAGGATTCCGGAACA 1055–1282 0.790 81.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 ATGGTCCACTCACAGGAGAA TCGATCCCGAAGAGAAGGAA 1105–1318 0.677 77.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 ATGGTCCACTCACAGGAGAA TCGAGCCGTATGAGGAGAAA 1207–1420 0.677 76.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 ATGGTCCACTCACAGGAGAA AGAGACAGGATTCCGGAACA 1506–1713 0.532 72.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 ATGGTCCACTCACAGGAGAA GGTGCTCAACCTACAGGAAC 1105–1212 0.548 72.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG ACCCTAGATTTTTCCCCCGA AACGGGGAAATAAGCGGATC 1658–1887 0.323 59.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG ACCCTAGATTTTTCCCCCGA GAACGGGGAAATAAGCGGAT 1659–1888 0.323 59.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ACCCTAGATTTTTCCCCCGA TCAGAACGGGGAAATAAGCG 1662–1891 0.306 59.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGTTCCGGAATCCTGTCTCT TCAGAACGGGGAAATAAGCG 1952–2191 0.306 59.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ACCCTAGATTTTTCCCCCGA CGGGGAAATAAGCGGATCAA 1656–1885 0.274 57.4
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACAAAGAGTTTGAGAGTAAGCA 120–460 1.000 56.4
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACAAAGAGTTTGAGAGTAAGCA 117–457 1.000 54.4
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACAAAGAGTTTGAGAGTAAGCA 118–458 1.000 54.4
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACAAAGAGTTTGAGAGTAAGCA 119–459 1.000 54.4
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACAAAGAGTTTGAGAGTAAGCA 121–461 1.000 54.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC ACGAATCACACTTTTACCACT 914–957 1.000 61.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCTGCCGCTTTAGTCCA ACGAATCACACTTTTACCACT 915–958 1.000 61.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA ACGAATCACACTTTTACCACT 968–1011 1.000 61.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC AGAACGAATCACACTTTTACCAC 917–960 1.000 60.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 916–959 1.000 60.6
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 209–222 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 212–225 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 215–228 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 218–231 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 213–226 1.000 72.9
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAATCCCGCGGGTA CGGGGCAAGAATTCGTCTAA 1237–1637 0.871 86.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCGAGGGCTCTACCAATTGA CGGGGCAAGAATTCGTCTAA 1215–1563 0.758 81.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCAAATTAATCCCGCGGGTA CCGAACTCCGACTTTCGTAG 1334–1902 0.742 80.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCAAATTAATCCCGCGGGTA ACCAAGATTTCCGAACTCCG 1344–1912 0.435 68.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCAAATTAATCCCGCGGGTA GGATTTGAACCGGGGATGAA 1524–1536 0.113 45.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (62)

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

Species Accession Length (bp) Link
Iris albomarginata PX505523.1 151296 View on NCBI ↗
Iris austrotschatkalica NC_068838.1 150887 View on NCBI ↗
Iris barbatula PX406250.1 153600 View on NCBI ↗
Iris bloudowii NC_086581.1 153322 View on NCBI ↗
Iris bostrensis NC_085776.1 153186 View on NCBI ↗
Iris bucharica PQ638941.1 151525 View on NCBI ↗
Iris bulleyana PX406251.1 152198 View on NCBI ↗
Iris confusa PP916053.1 152470 View on NCBI ↗
Iris dabashanensis PX752863.1 152807 View on NCBI ↗
Iris delavayi PX406253.1 152397 View on NCBI ↗
Iris dichotoma NC_056172.1 153573 View on NCBI ↗
Iris ensata NC_056173.1 153055 View on NCBI ↗
Iris flavissima NC_086580.1 153249 View on NCBI ↗
Iris glaucescens PX505513.1 153453 View on NCBI ↗
Iris halophila PX505514.1 152390 View on NCBI ↗
Iris hippolyti PX939352.1 151155 View on NCBI ↗
Iris hoogiana NC_085777.1 153269 View on NCBI ↗
Iris iberica NC_085774.1 153193 View on NCBI ↗
Iris imbricata NC_085779.1 153532 View on NCBI ↗
Iris khassanovii PQ639295.1 151422 View on NCBI ↗
Iris koreana NC_056174.1 150947 View on NCBI ↗
Iris kuschakewiczii PX505525.1 155046 View on NCBI ↗
Iris lactea NC_056175.1 152294 View on NCBI ↗
Iris lactea var. lactea MT740331.1 152409 View on NCBI ↗
Iris latistyla PX406254.1 155878 View on NCBI ↗
Iris loczyi MT254070.1 150940 View on NCBI ↗
Iris longnanensis OR839138.1 153839 View on NCBI ↗
Iris lutescens NC_085775.1 153544 View on NCBI ↗
Iris magnifica PQ639298.1 151346 View on NCBI ↗
Iris maracandica PQ639299.1 151170 View on NCBI ↗
Iris minutoaurea NC_056177.1 150955 View on NCBI ↗
Iris narbutii PQ639294.1 151167 View on NCBI ↗
Iris nicolai PQ639303.1 151095 View on NCBI ↗
Iris orchioides NC_088562.1 151622 View on NCBI ↗
Iris parvula PQ218628.1 151348 View on NCBI ↗
Iris proantha PX752861.1 153186 View on NCBI ↗
Iris probstii PX752860.1 151979 View on NCBI ↗
Iris pseudacorus NC_056179.1 152562 View on NCBI ↗
Iris pseudocapnoides NC_068839.1 151393 View on NCBI ↗
Iris pseudomeda NC_085781.1 153167 View on NCBI ↗
Iris pumila PX505517.1 153550 View on NCBI ↗
Iris rodionenkoi PQ639296.1 155021 View on NCBI ↗
Iris rossii NC_056180.1 153083 View on NCBI ↗
Iris rossii var. latifolia OR396998.1 153417 View on NCBI ↗
Iris rudolphii PQ639304.1 151156 View on NCBI ↗
Iris ruthenica NC_056181.1 152287 View on NCBI ↗
Iris sanguinea NC_029227.1 152408 View on NCBI ↗
Iris setosa NC_056182.1 152921 View on NCBI ↗
Iris sibirica PX505518.1 152396 View on NCBI ↗
Iris sichuanensis NC_085782.1 153752 View on NCBI ↗
Iris sofarana NC_085780.1 153176 View on NCBI ↗
Iris sogdiana PX505519.1 152410 View on NCBI ↗
Iris sprengeri NC_085778.1 153183 View on NCBI ↗
Iris subdecolorata PX915249.1 151365 View on NCBI ↗
Iris tectorum f. alba PX406258.1 153199 View on NCBI ↗
Iris tubergeniana PQ639301.1 151394 View on NCBI ↗
Iris typhifolia NC_067991.1 152405 View on NCBI ↗
Iris uniflora NC_056183.1 152281 View on NCBI ↗
Iris vicaria PQ639302.1 151483 View on NCBI ↗
Iris victoris NC_068840.1 151143 View on NCBI ↗
Iris warleyensis PQ639297.1 151151 View on NCBI ↗
Iris wattii PX171330.1 153867 View on NCBI ↗