Markers + reference

Brocchinia

6 species · Bromeliaceae · Poales

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Species 6
Genome length 159–162 kb
Candidate markers 273
Primer pairs 110

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 10 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 712 0.0238 1.00 56.1 yes View details
rps16-trnQ-UUG LSC 1537 0.0177 0.97 67.4 yes View details
trnS-GCU-trnG-UCC LSC 1404 0.0229 0.80 56.7 yes View details
trnE-UUC-trnT-GGU LSC 272 0.0445 1.00 71.1 yes View details
trnT-UGU-trnL-UAA LSC 813 0.0267 1.00 63.4 yes View details
rbcL-accD LSC 771 0.0219 1.00 66.0 yes View details
accD-psaI LSC 815 0.0254 0.99 59.0 yes View details
ycf4-cemA LSC 821 0.0209 1.00 63.0 yes View details
petA-psbJ LSC 1116 0.0165 1.00 54.2 yes View details
psbE-petL LSC 1576 0.0203 0.98 63.1 yes View details
rpl22 LSC 420 0.0165 1.00 46.8 yes View details
ndhF-rpl32 SSC 1086 0.0384 0.99 74.1 yes View details
psaC-ndhE SSC 801 0.0561 0.97 72.5 yes View details
rpl22-rps19 IRb 111 0.0595 0.96 71.8 yes View details
rps3-rpl22 LSC 51 0.0520 0.94 70.0 yes View details
rps19-psbA IRa 175 0.0519 0.90 67.7 no View details
psaA-ycf3 LSC 639 0.0171 1.00 65.8 yes View details
psbC-trnS-UGA LSC 137 0.0384 1.00 64.9 yes View details
atpH-atpI LSC 1009 0.0139 1.00 64.1 yes View details
rpl20-rps12 LSC 716 0.0090 1.00 64.0 yes View details
rpl36-infA LSC 105 0.0419 1.00 62.7 yes View details
rps8-rpl14 LSC 190 0.0381 0.97 62.7 yes View details
atpB-rbcL LSC 795 0.0179 1.00 61.7 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT AAAAGGGTATGTTGCTGCCA 1488–1495 1.000 82.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT GATCCCCGGGGTAATGTCTA 1452–1455 0.833 75.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT GAATAAGGATCCCCGGGGTA 1459–1462 0.833 74.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCACAGGAGAACCCACTCTT AAAAGGGTATGTTGCTGCCA 1852–1856 0.833 74.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCACAGGAGAACCCACTCTT GATCCCCGGGGTAATGTCTA 1816–1819 0.833 74.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1572–1628 1.000 85.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1570–1626 1.000 85.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1578–1634 1.000 85.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1554–1610 1.000 85.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1565–1621 1.000 84.6
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG ACGAATCACACTTTTACCACT 813–1548 1.000 59.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 758–1493 1.000 59.2
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG AGAACGAATCACACTTTTACCAC 816–1551 1.000 58.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC GAGAAAGCGGAAAGAGAGGG GAACGAATCACACTTTTACCACT 815–1550 1.000 58.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 760–1495 1.000 58.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CGAATCCATGGAGGGTCATC 1066–1169 1.000 81.6
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT CGAATCCATGGAGGGTCATC 1122–1225 1.000 80.8
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA CGAATCCATGGAGGGTCATC 1082–1185 1.000 80.7
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA CGAATCCATGGAGGGTCATC 1067–1170 1.000 80.4
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC CGAATCCATGGAGGGTCATC 1126–1229 1.000 80.2
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 354–845 1.000 84.3
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 375–866 1.000 84.2
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA CCATGGCGTTACTCTACCAC 333–824 1.000 84.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 354–845 1.000 84.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 351–842 1.000 83.9
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 244–260 1.000 81.8
psbC-trnS-UGA_p2 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GGTTGATAGCTCCGGTCTTG 283–299 1.000 81.5
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GATGGCCGAGTGGTTGATAG 255–271 1.000 81.1
psbC-trnS-UGA_p4 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GGGTTCGAATCCCTCTCTCT 229–245 1.000 81.0
psbC-trnS-UGA_p5 psbC-trnS-UGA GCAGCAGGGTTTGAAAAAGG GATGGCCGAGTGGTTGATAG 294–310 1.000 80.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Brocchinia acuminata NC_069195.1 160622 View on NCBI ↗
Brocchinia hechtioides NC_069197.1 159675 View on NCBI ↗
Brocchinia micrantha NC_081906.1 161108 View on NCBI ↗
Brocchinia paniculata NC_085608.1 159445 View on NCBI ↗
Brocchinia reducta NC_085609.1 159677 View on NCBI ↗
Brocchinia tatei NC_085613.1 161864 View on NCBI ↗