Markers + reference

Gyrotaenia

2 species · Urticaceae · Rosales

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Species 2
Genome length 154–154 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 772 0.0232 0.95 69.4 yes View details
psbC-trnS-UGA LSC 241 0.0456 1.00 77.0 yes View details
trnT-UGU-trnL-UAA LSC 609 0.0219 0.90 69.9 yes View details
ndhC-trnV-UAC LSC 558 0.0167 0.96 70.9 yes View details
psbE-petL LSC 1137 0.0160 0.99 69.1 yes View details
clpP LSC 2015 0.0085 1.00 48.9 yes View details
rpl22 LSC 378 0.0159 1.00 50.4 yes View details
ycf1 IRb 846 0.0000 1.00 38.8 no View details
ndhF-rpl32 SSC 1141 0.0123 1.00 55.3 yes View details
rpl32-trnL-UAG SSC 770 0.0117 1.00 58.3 yes View details
ccsA-ndhD SSC 278 0.0755 1.00 71.2 yes View details
ndhE SSC 306 0.0065 1.00 41.6 yes View details
ycf1 SSC 5442 0.0103 0.99 45.5 yes View details
petG-trnW-CCA LSC 123 0.0325 1.00 71.2 yes View details
rpl2-trnH-GUG IRa 258 0.0078 1.00 70.0 no View details
trnK-UUU-rps16 LSC 833 0.0087 0.97 66.6 yes View details
psbK-psbI LSC 495 0.0088 0.92 65.6 yes View details
trnH-GUG-psbA LSC 205 0.0343 0.85 65.5 yes View details
psaA-ycf3 LSC 734 0.0082 1.00 63.6 yes View details
atpH-atpI LSC 676 0.0074 1.00 63.0 yes View details
rps19-rpl2 IRb 119 0.0169 0.99 63.0 yes View details
trnG-GCC-trnfM-CAU LSC 174 0.0119 0.97 62.6 yes View details
accD LSC 1662 0.0043 0.98 62.6 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 245–275 1.000 84.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 259–289 1.000 84.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 258–288 1.000 84.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 260–290 1.000 84.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCCTCTAGACCTAGCTGCTC 243–273 1.000 81.8
trnK-UUU_p1 trnK-UUU GGACTCCCAAGCACAAGAAT TTGATTGCGCCGTACAATTT 2944 0.500 50.4
trnK-UUU_p2 trnK-UUU GGACTCCCAAGCACAAGAAT TTTGATTGCGCCGTACAATT 2945 0.500 50.4
trnK-UUU_p3 trnK-UUU GGACTCCCAAGCACAAGAAT ATTTGATTGCGCCGTACAAT 2946 0.500 48.6
trnK-UUU_p4 trnK-UUU GGACTCCCAAGCACAAGAAT TTTGATTGCGCCGTACAATTT 2945 0.500 48.0
trnK-UUU_p5 trnK-UUU TCCCATGTCAACCATTCTCA TGGATGCGCGAAGTCTTTAA 2996 0.500 46.7
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAGGCGGGTGT 998–1069 1.000 81.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAGGCGGGTGT 997–1068 1.000 81.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAGGCGGGTGT 915–986 1.000 81.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAGGCGGGTGT 914–985 1.000 81.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT ATTTCAAAGAAGGCGGGTGT 999–1070 1.000 80.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 806–845 1.000 83.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 821–860 1.000 81.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 820–859 1.000 81.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGGTGTAAGAATCCACAGC GAGGTTCGAATCCTTCCGTC 840–879 1.000 80.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 827–866 1.000 79.9
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT GGATTACGTCCCGGATCATT 592–625 1.000 77.4
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG GGATTACGTCCCGGATCATT 587–620 1.000 77.4
psbK-psbI_p3 psbK-psbI CTTTTGTTTGGCAAGCTGCT TCTTCACGTCCAGGATTACG 604–637 1.000 76.6
psbK-psbI_p4 psbK-psbI GTTTGGCAAGCTGCTGTAAG TCTTCACGTCCAGGATTACG 599–632 1.000 76.6
psbK-psbI_p5 psbK-psbI TGGCAAGCTGCTGTAAGTTT GGATTACGTCCCGGATCATT 584–617 1.000 75.4
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCTGCGG 761 1.000 78.6
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 819 1.000 78.5
atpH-atpI_p3 atpH-atpI GTCCAATAGAAGCAAGCCCA TTTTGCAACTTTAGCTGCGG 801 1.000 78.4
atpH-atpI_p4 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTGCAACTTTAGCTGCGG 778 1.000 77.7
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA ACAAGTGGCATTCAAGCTCT 784 1.000 77.4

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
Gyrotaenia microcarpa NC_064743.1 153911 View on NCBI ↗
Gyrotaenia myriocarpa NC_064744.1 153979 View on NCBI ↗