Markers + reference

Sisyrinchium

2 species · Iridaceae · Asparagales

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Species 2
Genome length 151–151 kb
Candidate markers 272
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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 999 0.0147 0.95 65.3 yes View details
trnF-GAA-ndhJ LSC 624 0.0920 0.98 89.5 yes View details
rbcL LSC 1461 0.0068 1.00 52.6 yes View details
accD-psaI LSC 343 0.0289 0.91 73.3 yes View details
petA-psbJ LSC 907 0.0146 0.98 68.8 yes View details
petD LSC 1208 0.0043 0.96 45.5 yes View details
rpl16 LSC 1380 0.0165 0.96 57.4 yes View details
ycf1 IRb 1161 0.0018 0.98 60.6 no View details
ycf1 SSC 5427 0.0102 1.00 54.6 yes View details
petD-rpoA LSC 178 0.0412 0.96 78.2 yes View details
rps3-rpl22 LSC 71 0.0588 0.96 78.0 yes View details
psbT-pbf1 LSC 68 0.0294 1.00 66.5 yes View details
rpl32-trnL-UAG SSC 826 0.0085 1.00 64.1 yes View details
ndhF-rpl32 SSC 946 0.0074 1.00 63.2 yes View details
psaI-ycf4 LSC 347 0.0122 0.94 62.8 yes View details
ycf4-cemA LSC 769 0.0078 1.00 62.7 yes View details
rpl23-trnI-CAU IRb 165 0.0125 0.97 62.6 yes View details
trnI-CAU-rpl23 IRa 165 0.0125 0.97 62.6 yes View details
rps7-rps12 IRb 58 0.0172 1.00 62.4 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 ATGCCAATGTCAACCAACCT CGTTTTGATGGAGTTGTGCA 2606–2887 1.000 78.2
trnK-UUU_p2 trnK-UUU ATGCCAATGTCAACCAACCT ACGTTTTGATGGAGTTGTGC 2607–2888 1.000 78.2
trnK-UUU_p3 trnK-UUU TTTCAAGGACTCCCAAGCAC CGTTTTGATGGAGTTGTGCA 2698–2979 1.000 78.1
trnK-UUU_p4 trnK-UUU TTTCAAGGACTCCCAAGCAC ACGTTTTGATGGAGTTGTGC 2699–2980 1.000 78.1
trnK-UUU_p5 trnK-UUU ATGCCAATGTCAACCAACCT CGTTTTGATGGAGTTGTGCAA 2606–2887 1.000 75.7
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GCAACGGATTAGCAATCTGC AACCGAAAGACCCCTTAACT 1089–1118 1.000 70.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCTGCCGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 1076–1105 1.000 69.4
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCTGCCGCTTTAGTCCA AACCGAAAGACCCCTTAACT 1077–1106 1.000 69.4
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CGGAGAGAGAGGGATTCGAA AACCGAAAGACCCCTTAACT 1130–1159 1.000 68.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC GCAACGGATTAGCAATCTGC AAACCGAAAGACCCCTTAACT 1090–1119 1.000 68.6
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ TGTCACCAGTTCAAACCTGG TGAAAGTTGGATAGGCTGGC 729–783 1.000 86.1
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGCTGGC 734–788 1.000 86.0
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ TGTCACCAGTTCAAACCTGG ATAGGCTGGCCCTTACGTAA 719–773 1.000 85.6
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATAGGCTGGCCCTTACGTAA 724–778 1.000 85.5
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ TAGGATAATGCGCGGTAAGC TGAAAGTTGGATAGGCTGGC 794–848 1.000 85.3
rbcL_p1 rbcL TCAAAGGTTTCATTCACGCC TGGGCCGAGATTAATTGCAA 1587 1.000 70.8
rbcL_p2 rbcL TCAAAGGTTTCATTCACGCC TTGGGCCGAGATTAATTGCA 1588 1.000 70.8
rbcL_p3 rbcL CAAAGGTTTCATTCACGCCT TGGGCCGAGATTAATTGCAA 1586 1.000 70.7
rbcL_p4 rbcL CAAAGGTTTCATTCACGCCT TTGGGCCGAGATTAATTGCA 1587 1.000 70.7
rbcL_p5 rbcL GTCAAAGGTTTCATTCACGCC TGGGCCGAGATTAATTGCAA 1588 1.000 68.7
accD-psaI_p1 accD-psaI GGTTCACAAGTGGCTGAGTA CCATTGCAATTGCCGGAAAT 511–533 1.000 80.8
accD-psaI_p2 accD-psaI GGTTCACAAGTGGCTGAGTA AAGAAGCCATTGCAATTGCC 517–539 1.000 80.2
accD-psaI_p3 accD-psaI GGTTCACAAGTGGCTGAGTAT CCATTGCAATTGCCGGAAAT 511–533 1.000 76.7
accD-psaI_p4 accD-psaI GGTTCACAAGTGGCTGAGTAT AAGAAGCCATTGCAATTGCC 517–539 1.000 76.1
accD-psaI_p5 accD-psaI GGTTCACAAGTGGCTGAGTA CCGGAAATACTAGGCCCACT 499–521 1.000 74.1
psaI-ycf4_p1 psaI-ycf4 ATTTCCGGCAATTGCAATGG ATGTTCTGATCGCCAGTTCA 429–435 1.000 78.1
psaI-ycf4_p2 psaI-ycf4 ATTTCCGGCAATTGCAATGG TGTTCTGATCGCCAGTTCAT 428–434 1.000 78.1
psaI-ycf4_p3 psaI-ycf4 GGCAATTGCAATGGCTTCTT ATGTTCTGATCGCCAGTTCA 423–429 1.000 77.5
psaI-ycf4_p4 psaI-ycf4 GGCAATTGCAATGGCTTCTT TGTTCTGATCGCCAGTTCAT 422–428 1.000 77.5
psaI-ycf4_p5 psaI-ycf4 GGCCTAGTATTTCCGGCAAT TGTTCTGATCGCCAGTTCAT 436–442 1.000 76.1

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
Sisyrinchium angustifolium NC_056184.1 151305 View on NCBI ↗
Sisyrinchium idahoense NC_072581.1 151006 View on NCBI ↗