Markers + reference

Salix

59 species · Salicaceae · Malpighiales

Back to catalogue

Species 59
Genome length 155–160 kb
Candidate markers 258
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 258 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbK-psbI LSC 457 0.0072 1.00 47.6 yes View details
trnS-GCU-trnT-CGU LSC 619 0.0071 1.00 53.8 yes View details
rpoB-trnC-GCA LSC 1201 0.0085 1.00 55.6 yes View details
psbZ-trnG-GCC LSC 525 0.0125 1.00 60.2 yes View details
ndhC-trnV-UAC LSC 1312 0.0071 1.00 47.8 yes View details
petA-psbJ LSC 862 0.0089 1.00 63.3 yes View details
ndhF SSC 2355 0.0082 0.96 49.4 yes View details
ndhF-trnL-UAG SSC 518 0.0138 1.00 53.3 yes View details
ccsA SSC 963 0.0063 1.00 35.2 yes View details
ndhA SSC 2203 0.0072 1.00 47.5 yes View details
rps15-ycf1 IRa 414 0.0257 1.00 57.9 yes View details
psbI-trnS-GCU LSC 149 0.0207 0.99 59.9 yes View details
trnH-GUG-psbA LSC 221 0.0110 1.00 58.9 yes View details
rps4-trnT-UGU LSC 230 0.0137 1.00 57.8 yes View details
trnN-GUU-trnR-ACG IRa 726 0.0044 1.00 56.4 yes View details
ccsA-ndhD SSC 199 0.0220 0.99 56.2 yes View details
trnR-ACG-trnN-GUU IRb 726 0.0044 1.00 55.9 yes View details
psbM-trnD-GUC LSC 1170 0.0044 0.99 54.3 yes View details
trnT-CGU-trnR-UCU LSC 233 0.0122 1.00 54.1 yes View details
petN-psbM LSC 1313 0.0045 1.00 53.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA TCACAATCCACTGCCTTGAG CCTCTAGACCTAGCTGCTGT 300–328 1.000 85.3
trnH-GUG-psbA_p2 trnH-GUG-psbA TCACAATCCACTGCCTTGAG TTCCCTCTAGACCTAGCTGC 303–331 1.000 85.2
trnH-GUG-psbA_p3 trnH-GUG-psbA GCGAATGACGGGAATTGAAC CCTCTAGACCTAGCTGCTGT 335–363 1.000 84.7
trnH-GUG-psbA_p4 trnH-GUG-psbA GCGAATGACGGGAATTGAAC TTCCCTCTAGACCTAGCTGC 338–366 1.000 84.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GCGAATGACGGGAATTGAAC TAGACCTAGCTGCTGTCGAA 331–359 1.000 84.3
psbK-psbI_p1 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGATTACGCCCTGGATCAT 542–581 1.000 82.2
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGCCCTGGATCAT 574–584 0.932 79.9
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGATTACGCCCTGGATCAT 572–582 0.932 77.9
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGATTACGCCCTGGATCAT 573–583 0.932 77.9
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGCCCTGGATCATT 573–583 0.932 77.5
psbI-trnS-GCU_p1 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT TGGACTAAAGCGTCGGATTG 251–272 1.000 85.6
psbI-trnS-GCU_p2 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT GTGGACTAAAGCGTCGGATT 252–273 1.000 85.6
psbI-trnS-GCU_p3 psbI-trnS-GCU ATGATCCAGGGCGTAATCCT ATTGGGAGAGATGGCTGAGT 270–291 1.000 84.3
psbI-trnS-GCU_p4 psbI-trnS-GCU AATGATCCAGGGCGTAATCC TGGACTAAAGCGTCGGATTG 252–273 1.000 83.1
psbI-trnS-GCU_p5 psbI-trnS-GCU AATGATCCAGGGCGTAATCC GTGGACTAAAGCGTCGGATT 253–274 1.000 83.1
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CAATCCGACGCTTTAGTCCA GCCGACGGATCCCTTAACTA 721–749 1.000 79.7
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU AATCCGACGCTTTAGTCCAC GCCGACGGATCCCTTAACTA 720–748 1.000 79.7
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU ATCAACGGAACCGGAAAGAG GCCGACGGATCCCTTAACTA 785–813 1.000 78.7
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU CATCAACGGAACCGGAAAGA GCCGACGGATCCCTTAACTA 786–814 1.000 77.9
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU TCATCAACGGAACCGGAAAG GCCGACGGATCCCTTAACTA 787–815 1.000 77.9
trnT-CGU-trnR-UCU_p1 trnT-CGU-trnR-UCU TTCCAAGCTAATGATGCGGG AGGTTTAGAAGACCTTTGTCCT 295–337 1.000 61.5
trnT-CGU-trnR-UCU_p2 trnT-CGU-trnR-UCU TTCCAAGCTAATGATGCGGG AGAAGACCTTTGTCCTATCCA 289–331 0.983 59.6
trnT-CGU-trnR-UCU_p3 trnT-CGU-trnR-UCU TTCCAAGCTAATGATGCGGG TCTGGAAAAATATTGCGTCCA 338–380 0.949 58.5
trnT-CGU-trnR-UCU_p4 trnT-CGU-trnR-UCU GCTAATGATGCGGGTTCGAT TCTGGAAAAATATTGCGTCCA 332–374 0.949 57.3
trnT-CGU-trnR-UCU_p5 trnT-CGU-trnR-UCU TTCCAAGCTAATGATGCGGG TCTGGAAAAATATTGCGTCCAA 338–380 0.949 56.5
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCATTTCCATCCCCAAGCAT CCGGATTTGAACTGGGGAAA 1256–1310 1.000 85.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CATTCCCCCATTTCCATCCC CCGGATTTGAACTGGGGAAA 1263–1317 1.000 84.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCATTTCCATCCCCAAGCAT AAAAGGATTTGCAGTCCCCC 1238–1292 1.000 83.1
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACATTCCCCCATTTCCATCC CCGGATTTGAACTGGGGAAA 1264–1318 1.000 83.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTCCCCCATTTCCATCCC AAAAGGATTTGCAGTCCCCC 1245–1299 1.000 82.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (59)

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

Species Accession Length (bp) Link
Salix acutifolia MW435413.1 159546 View on NCBI ↗
Salix appendiculata MW435416.1 155610 View on NCBI ↗
Salix argyracea NC_056250.1 155605 View on NCBI ↗
Salix bicolor MW435419.1 160369 View on NCBI ↗
Salix breviserrata PP622677.1 155577 View on NCBI ↗
Salix caesia MW435422.1 159760 View on NCBI ↗
Salix caprea MW435423.1 155562 View on NCBI ↗
Salix chaenomeloides NC_037422.1 156154 View on NCBI ↗
Salix cheilophila MN495628.1 155322 View on NCBI ↗
Salix cinerea PP622678.1 155592 View on NCBI ↗
Salix cupularis NC_057535.1 155518 View on NCBI ↗
Salix daphnoides MW435427.1 158667 View on NCBI ↗
Salix dasyclados NC_056251.1 155763 View on NCBI ↗
Salix elaeagnos MW435428.1 155596 View on NCBI ↗
Salix eriocephala NC_056252.1 155552 View on NCBI ↗
Salix floderusii NC_064995.1 155540 View on NCBI ↗
Salix foetida MW435429.1 160129 View on NCBI ↗
Salix fragilis MW435430.1 159546 View on NCBI ↗
Salix glabra MW435431.1 155604 View on NCBI ↗
Salix glaucosericea MW435432.1 156892 View on NCBI ↗
Salix gordejevii NC_058001.1 155491 View on NCBI ↗
Salix hastata PP622679.1 155550 View on NCBI ↗
Salix helvetica MW435434.1 156868 View on NCBI ↗
Salix hypoleuca NC_037423.1 155126 View on NCBI ↗
Salix integra NC_056253.1 155538 View on NCBI ↗
Salix kochiana OL339478.1 155657 View on NCBI ↗
Salix lapponum MW435437.1 155599 View on NCBI ↗
Salix lindleyana NC_063129.1 155304 View on NCBI ↗
Salix linearistipularis MZ018223.1 155564 View on NCBI ↗
Salix magnifica NC_037424.1 154977 View on NCBI ↗
Salix maizhokunggarensis MN952983.1 155093 View on NCBI ↗
Salix matsudana NC_059039.1 155672 View on NCBI ↗
Salix matsudana f. tortuosa MT872638.1 155673 View on NCBI ↗
Salix mielichhoferi MW435438.1 155414 View on NCBI ↗
Salix minjiangensis NC_037425.1 155038 View on NCBI ↗
Salix myrsinifolia MW435439.1 155549 View on NCBI ↗
Salix myrtilloides MW435441.1 160386 View on NCBI ↗
Salix oreinoma NC_035743.1 155531 View on NCBI ↗
Salix paraplesia NC_037426.1 155553 View on NCBI ↗
Salix pentandra MW435442.1 155584 View on NCBI ↗
Salix pierotii PQ842549.1 155688 View on NCBI ↗
Salix psammophila NC_051969.1 155278 View on NCBI ↗
Salix pseudolasiogyne PQ842553.1 155689 View on NCBI ↗
Salix rehderiana NC_037427.1 155051 View on NCBI ↗
Salix reticulata PP622680.1 155574 View on NCBI ↗
Salix retusa MW435446.1 155693 View on NCBI ↗
Salix rorida NC_037428.1 155144 View on NCBI ↗
Salix rosmarinifolia PP622681.1 155593 View on NCBI ↗
Salix serpyllifolia MW435448.1 158597 View on NCBI ↗
Salix silesiaca MW435449.1 155574 View on NCBI ↗
Salix sitchensis MW435450.1 155626 View on NCBI ↗
Salix taoensis NC_037429.1 155085 View on NCBI ↗
Salix tetrasperma NC_035744.1 155671 View on NCBI ↗
Salix triandra NC_069592.1 155657 View on NCBI ↗
Salix triandra subsp. triandra PP622682.1 155677 View on NCBI ↗
Salix triandroides NC_058986.1 155683 View on NCBI ↗
Salix udensis NC_068758.1 155530 View on NCBI ↗
Salix viminalis NC_068759.1 155566 View on NCBI ↗
Salix waldsteiniana MW435453.1 159465 View on NCBI ↗