Markers + reference

Liparis

19 species · Orchidaceae · Asparagales

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Species 19
Genome length 144–159 kb
Candidate markers 272
Primer pairs 100

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 476 0.1058 0.97 74.3 yes View details
rps16 LSC 1089 0.0431 0.99 81.3 yes View details
trnS-GCU-trnG-UCC LSC 954 0.0810 0.97 85.7 yes View details
ndhC-trnV-UAC LSC 889 0.0664 0.95 80.8 yes View details
clpP-psbB LSC 741 0.0663 0.96 82.6 yes View details
ycf1 IRb 1039 0.0149 1.00 50.3 no View details
ndhF SSC 2247 0.0393 0.99 73.4 yes View details
ndhF-rpl32 SSC 788 0.0944 0.96 81.1 yes View details
psaC-ndhE SSC 582 0.0782 0.89 79.6 yes View details
ycf1 SSC 5400 0.0449 0.99 76.3 yes View details
trnE-UUC-trnT-GGU LSC 982 0.0532 0.98 88.3 yes View details
trnT-UGU-trnL-UAA LSC 602 0.0555 0.99 85.1 yes View details
trnC-GCA-petN LSC 599 0.0574 0.98 84.2 yes View details
matK-trnK-UUU LSC 1070 0.0612 0.96 83.9 yes View details
petA-psbJ LSC 929 0.0599 0.97 83.6 yes View details
rpl32-trnL-UAG SSC 584 0.0610 0.99 82.3 yes View details
trnT-GGU-psbD LSC 973 0.0437 0.97 81.5 yes View details
trnF-GAA-ndhJ LSC 592 0.0571 0.93 81.4 yes View details
psbE-petL LSC 1096 0.0420 0.99 80.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TCGCGACGAGAATGGAATTT GCAACGAGCTTCCCTTCTTA 922–1149 0.579 74.4
trnK-UUU_p2 trnK-UUU AAATCGCGACGAGAATGGAA GCAACGAGCTTCCCTTCTTA 925–1146 0.316 62.2
trnK-UUU_p3 trnK-UUU AAATCGCGACGAGAATGGAA TTGCGGATTGTAGACGGATG 994 0.053 41.5
trnK-UUU_p4 trnK-UUU TCGCGACGAGAATGGAATTT TTGCGGATTGTAGACGGATG 991 0.053 41.5
trnK-UUU_p5 trnK-UUU ACCTAAAATTTCCGCGGGTT TTGCGGATTGTAGACGGATG 793 0.053 40.9
matK-trnK-UUU_p1 matK-trnK-UUU TCGCGACGAGAATGGAATTT ATCCGGGTTGCTAACTCAAC 1278–1481 0.684 78.5
matK-trnK-UUU_p2 matK-trnK-UUU TCGCGACGAGAATGGAATTT TCGATCCCGAAGAGAAGGAA 1968–2163 0.684 78.2
matK-trnK-UUU_p3 matK-trnK-UUU TCGCGACGAGAATGGAATTT ACGGTAGAGTACTCGGCTTT 1260–1463 0.684 78.0
matK-trnK-UUU_p4 matK-trnK-UUU AAATCGCGACGAGAATGGAA ATCCGGGTTGCTAACTCAAC 1281–1477 0.368 64.3
matK-trnK-UUU_p5 matK-trnK-UUU AAATCGCGACGAGAATGGAA TCGATCCCGAAGAGAAGGAA 1971–2166 0.368 64.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCGATCCCGAAGAGAAGGAA 640–794 1.000 89.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCGATCCCGAAGAGAAGGAA 639–793 1.000 89.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 TAAGAAGGGAAGCTCGTTGC TCGATCCCGAAGAGAAGGAA 946–1112 0.947 88.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CATCCGTCTACAATCCGCAA TCGATCCCGAAGAGAAGGAA 1192 0.053 40.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 CATCCGTCTACAATCCGCAA GCTCAACCCACAGGAATTGT 1083 0.053 38.5
rps16_p1 rps16 GTTGAGTTAGCAACCCGGAT GACCAAATCAAAATGGGGCG 1996–2208 0.947 88.9
rps16_p2 rps16 AAAGCCGAGTACTCTACCGT GACCAAATCAAAATGGGGCG 2014–2226 0.947 88.5
rps16_p3 rps16 AAGCCGAGTACTCTACCGTT GACCAAATCAAAATGGGGCG 2013–2225 0.947 88.5
rps16_p4 rps16 GTTGAGTTAGCAACCCGGAT GAGGTTCGAATCCTTCCGTC 1935–2147 0.947 88.4
rps16_p5 rps16 GTTGAGTTAGCAACCCGGAT AAATCCCAGCGACAACATGT 2108–2271 0.421 67.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 929–1247 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 931–1249 1.000 62.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 930–1248 0.947 61.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 933–1251 0.947 60.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 932–1250 0.947 60.5
trnC-GCA-petN_p1 trnC-GCA-petN TTGGATGGAATTTGGCGACA GCTCTAAAGCCCACTCCTTC 747–1072 0.842 84.8
trnC-GCA-petN_p2 trnC-GCA-petN AAGTTTTTAAGCGACGCGTG GCTCTAAAGCCCACTCCTTC 999–1375 0.789 83.2
trnC-GCA-petN_p3 trnC-GCA-petN AAGTTTTTAAGCGACGCGTG AGGAAGAAGAGTACGGGCAT 1263–1671 0.789 82.4
trnC-GCA-petN_p4 trnC-GCA-petN AAGTTTTTAAGCGACGCGTG GGGGGCCCATCGAAATAATT 1288–1387 0.263 60.7
trnC-GCA-petN_p5 trnC-GCA-petN TTGGATGGAATTTGGCGACA GGGGGCCCATCGAAATAATT 1036–1409 0.263 59.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Liparis auriculata NC_046800.1 153460 View on NCBI ↗
Liparis bootanensis NC_047433.1 158325 View on NCBI ↗
Liparis brunnea PQ571150.1 150365 View on NCBI ↗
Liparis campylostalix PQ571151.1 153831 View on NCBI ↗
Liparis ferruginea NC_072702.1 158298 View on NCBI ↗
Liparis gigantea NC_088741.1 158462 View on NCBI ↗
Liparis kumokiri MN687902.1 153556 View on NCBI ↗
Liparis luteola NC_064069.1 156405 View on NCBI ↗
Liparis makinoana NC_046803.1 153093 View on NCBI ↗
Liparis nervosa NC_045896.1 158787 View on NCBI ↗
Liparis odorata PQ571148.1 158622 View on NCBI ↗
Liparis pauliana MN686022.1 153800 View on NCBI ↗
Liparis petiolata PQ571152.1 154344 View on NCBI ↗
Liparis pingtaoi NC_047432.1 157052 View on NCBI ↗
Liparis resupinata PQ571157.1 144232 View on NCBI ↗
Liparis sootenzanensis PQ571149.1 158275 View on NCBI ↗
Liparis tsii PQ571153.1 151687 View on NCBI ↗
Liparis viridiflora NC_063587.1 157354 View on NCBI ↗
Liparis vivipara MK862100.1 158329 View on NCBI ↗