Markers + reference

Cotoneaster

67 species · Rosaceae · Rosales

Back to catalogue

Species 67
Genome length 110–160 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

10 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
psbA LSC 1062 0.0001 1.00 32.9 yes View details
trnR-UCU-atpA LSC 639 0.0159 0.95 67.8 yes View details
rpoB-trnC-GCA LSC 1212 0.0042 1.00 41.0 yes View details
trnT-GGU-psbD LSC 1461 0.0057 0.97 52.2 yes View details
trnT-UGU-trnL-UAA LSC 1197 0.0064 1.00 51.3 yes View details
ndhC-trnV-UAC LSC 554 0.0097 0.97 53.6 yes View details
petL-petG LSC 158 0.0043 1.00 28.0 yes View details
rpl33-rps18 LSC 338 0.0217 0.68 56.7 yes View details
ndhF-rpl32 SSC 1046 0.0063 1.00 47.0 yes View details
rpl32-trnL-UAG SSC 1437 0.0052 1.00 48.2 yes View details
petG-trnW-CCA LSC 124 0.0365 1.00 63.5 yes View details
rps19-trnH-GUG LSC 63 0.0443 0.86 61.3 no View details
trnK-UUU-rps16 LSC 962 0.0054 0.99 55.5 yes View details
trnH-GUG-psbA LSC 230 0.0139 1.00 53.8 yes View details
petN-psbM LSC 1202 0.0023 0.99 52.6 yes View details
rpl22-rps19 LSC 61 0.0075 1.00 52.4 yes View details
psbM-trnD-GUC LSC 1235 0.0036 0.99 51.9 yes View details
atpH-atpI LSC 1167 0.0019 1.00 51.6 yes View details
psaA-ycf3 LSC 702 0.0021 1.00 49.5 yes View details
trnG-UCC-trnR-UCU LSC 198 0.0139 1.00 49.4 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 277–302 0.985 88.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 327–352 0.985 87.5
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 341–366 0.985 87.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 340–365 0.985 87.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 342–367 0.985 87.2
psbA_p1 psbA ATTCTGGGTTATGGGCGAAC GAAAGCCGTGTGCAATGAAA 1768–1795 0.985 82.6
psbA_p2 psbA ATTCTGGGTTATGGGCGAAC CGGTATTGGTTGACATGGGT 1509–1534 0.985 82.5
psbA_p3 psbA ATTCTGGGTTATGGGCGAAC AGAATTCGTGTGCTTGGGAG 1419–1444 0.985 82.3
psbA_p4 psbA ATTCTGGGTTATGGGCGAAC AGAGAATTCGTGTGCTTGGG 1421–1446 0.985 82.3
psbA_p5 psbA ATTCTGGGTTATGGGCGAAC GAGAATTCGTGTGCTTGGGA 1420–1445 0.985 82.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGGAACTTCGCCCTAATCAA 1004–1060 0.985 83.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGGAACTTCGCCCTAATCAA 1003–1059 0.985 83.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA CGGAACTTCGCCCTAATCAA 1013–1069 0.985 82.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 1059–1115 0.985 81.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 1058–1114 0.985 81.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 269–361 0.985 70.6
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 272–364 0.985 70.3
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 275–367 0.985 69.8
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 278–370 0.985 69.4
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 273–365 0.985 68.0
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 627–887 0.985 72.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 626–886 0.985 72.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 566–826 0.985 72.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGACGAAGCG 601–861 0.985 69.2
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 627–887 0.985 68.8
atpH-atpI_p1 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1257–1271 0.985 80.3
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1223–1237 0.985 80.2
atpH-atpI_p3 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1287–1301 0.985 79.4
atpH-atpI_p4 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1253–1267 0.985 79.4
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1224–1238 0.985 79.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (67)

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

Species Accession Length (bp) Link
Cotoneaster acuminatus NC_045340.1 159524 View on NCBI ↗
Cotoneaster acutifolius MK638990.1 159521 View on NCBI ↗
Cotoneaster acutifolius var. villosulus MK650048.1 159555 View on NCBI ↗
Cotoneaster adpressus var. praecox MK638986.1 159606 View on NCBI ↗
Cotoneaster affinis MK650051.1 159607 View on NCBI ↗
Cotoneaster argenteus PQ777082.1 159694 View on NCBI ↗
Cotoneaster astrophoros MK650065.1 159649 View on NCBI ↗
Cotoneaster brickellii PQ777085.1 159671 View on NCBI ↗
Cotoneaster bullatus MK614791.1 159570 View on NCBI ↗
Cotoneaster buxifolius NC_045356.1 159563 View on NCBI ↗
Cotoneaster buxifolius var. vellaeus MK614795.1 159707 View on NCBI ↗
Cotoneaster cf. chengkangensis KM-2021 MK605514.1 159548 View on NCBI ↗
Cotoneaster cochleatus MK524400.1 159754 View on NCBI ↗
Cotoneaster conspicuus MK638987.1 159582 View on NCBI ↗
Cotoneaster coriaceus PQ777073.1 159665 View on NCBI ↗
Cotoneaster dammeri PQ777069.1 159152 View on NCBI ↗
Cotoneaster dammeri subsp. songmingensis MK605511.1 159658 View on NCBI ↗
Cotoneaster delavayanus PQ777091.1 159660 View on NCBI ↗
Cotoneaster densiflorus NC_085347.1 159759 View on NCBI ↗
Cotoneaster dielsianus MZ475329.1 159898 View on NCBI ↗
Cotoneaster foveolatus MK650046.1 159611 View on NCBI ↗
Cotoneaster franchetii MK638985.1 159612 View on NCBI ↗
Cotoneaster franchetii var. cinerascens MK638991.1 159602 View on NCBI ↗
Cotoneaster frigidus NC_045341.1 159626 View on NCBI ↗
Cotoneaster gamblei MK650052.1 159596 View on NCBI ↗
Cotoneaster glaucophyllus PQ777071.1 159773 View on NCBI ↗
Cotoneaster glaucophyllus var. meiophyllus PQ777077.1 159723 View on NCBI ↗
Cotoneaster glaucophyllus var. serotinus PQ777084.1 159795 View on NCBI ↗
Cotoneaster harrysmithii MK544859.1 109969 View on NCBI ↗
Cotoneaster hebephyllus MZ475334.1 160016 View on NCBI ↗
Cotoneaster hebephyllus var. fulvidus PQ777075.1 159801 View on NCBI ↗
Cotoneaster horizontalis NC_045357.1 159548 View on NCBI ↗
Cotoneaster horizontalis var. perpusillus MK638994.1 159887 View on NCBI ↗
Cotoneaster huahongdongensis MK614796.1 159622 View on NCBI ↗
Cotoneaster insolitus PQ777086.1 159793 View on NCBI ↗
Cotoneaster integerrimus OP494722.1 159925 View on NCBI ↗
Cotoneaster langei MK605516.1 159624 View on NCBI ↗
Cotoneaster laxiflorus MK561977.1 159970 View on NCBI ↗
Cotoneaster leveillei MK544857.1 159614 View on NCBI ↗
Cotoneaster marginatus MK605510.1 159683 View on NCBI ↗
Cotoneaster microphyllus NC_045339.1 159662 View on NCBI ↗
Cotoneaster microphyllus var. microphyllus MK544856.1 159601 View on NCBI ↗
Cotoneaster mongolicus NC_060853.1 159797 View on NCBI ↗
Cotoneaster morrisonensis PQ777070.1 159569 View on NCBI ↗
Cotoneaster moupinensis MK614797.1 159727 View on NCBI ↗
Cotoneaster multiflorus NC_060854.1 159855 View on NCBI ↗
Cotoneaster obscurus MK614798.1 159509 View on NCBI ↗
Cotoneaster pannosus PQ777081.1 159649 View on NCBI ↗
Cotoneaster qungbixiensis MK605513.1 159579 View on NCBI ↗
Cotoneaster reticulatus MK650055.1 159573 View on NCBI ↗
Cotoneaster rockii MK605515.1 159668 View on NCBI ↗
Cotoneaster rosiflorus NC_069634.1 159449 View on NCBI ↗
Cotoneaster rotundifolius MK650063.1 159589 View on NCBI ↗
Cotoneaster rubens NC_045359.1 159525 View on NCBI ↗
Cotoneaster salicifolius var. henryanus MN577863.1 159746 View on NCBI ↗
Cotoneaster schantungensis NC_045840.1 159883 View on NCBI ↗
Cotoneaster sherriffii MK614794.1 159701 View on NCBI ↗
Cotoneaster silvestrii NC_045358.1 159796 View on NCBI ↗
Cotoneaster soongoricus MK650057.1 159808 View on NCBI ↗
Cotoneaster subadpressus MK650058.1 159706 View on NCBI ↗
Cotoneaster submultiflorus NC_060855.1 159614 View on NCBI ↗
Cotoneaster taylorii NC_045338.1 159607 View on NCBI ↗
Cotoneaster tenuipes NC_060856.1 159595 View on NCBI ↗
Cotoneaster turbinatus PQ742993.1 159674 View on NCBI ↗
Cotoneaster vandelaarii MK544858.1 159811 View on NCBI ↗
Cotoneaster verruculosus MK605512.1 159533 View on NCBI ↗
Cotoneaster zabelii MK650056.1 159856 View on NCBI ↗