Markers + reference

Cyclea

2 species · Menispermaceae · Ranunculales

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Species 2
Genome length 160–160 kb
Candidate markers 267
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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 603 0.0138 0.96 64.1 yes View details
psbI-trnS-GCU LSC 156 0.0513 1.00 77.7 yes View details
petN-psbM LSC 1193 0.0085 0.99 54.1 yes View details
trnD-GUC-trnY-GUA LSC 536 0.0174 0.97 70.6 yes View details
psbZ-trnG-GCC LSC 726 0.0139 0.99 67.7 yes View details
trnN-GUU-ndhF SSC 867 0.0314 0.96 67.5 yes View details
ndhF-rpl32 SSC 996 0.0121 0.99 62.4 yes View details
rpl32-trnL-UAG SSC 1068 0.0132 1.00 60.3 yes View details
ndhD SSC 1530 0.0046 1.00 47.4 yes View details
ndhA SSC 2270 0.0080 0.99 63.1 yes View details
psbT-psbN LSC 59 0.0508 1.00 77.2 yes View details
rps8-rpl14 LSC 193 0.0363 1.00 73.4 yes View details
ndhD-psaC SSC 96 0.0625 1.00 67.8 yes View details
rpl14-rpl16 LSC 148 0.0203 1.00 64.2 yes View details
ndhC-trnV-UAC LSC 1243 0.0041 0.97 63.8 yes View details
trnK-UUU-rps16 LSC 884 0.0079 1.00 63.3 yes View details
atpB-rbcL LSC 820 0.0073 1.00 63.3 yes View details
psbA-trnK-UUU LSC 436 0.0161 1.00 62.8 yes View details
rpoB-trnC-GCA LSC 1299 0.0100 1.00 62.7 yes View details
trnE-UUC-trnT-GGU LSC 1018 0.0069 1.00 62.7 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 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 CTGCCTTAATCCACTTGGCT CAACCGTGCTAACCTTGGTA 711–732 1.000 81.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT ATCAACCGTGCTAACCTTGG 713–734 1.000 80.9
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CAACCGTGCTAACCTTGGTA 712–733 1.000 80.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC ATCAACCGTGCTAACCTTGG 714–735 1.000 80.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 708–729 1.000 79.7
psbA-trnK-UUU_p1 psbA-trnK-UUU TGTACAGACGGTTTTCGGTG GTTTGGGGAGGGGTTTTTCT 626–628 1.000 79.2
psbA-trnK-UUU_p2 psbA-trnK-UUU TGTACAGACGGTTTTCGGTG CTAGTTCCGGGTTCGAATCC 554–555 1.000 78.2
psbA-trnK-UUU_p3 psbA-trnK-UUU TGTACAGACGGTTTTCGGTG TTTGGGGAGGGGTTTTTCTC 625–627 1.000 76.9
psbA-trnK-UUU_p4 psbA-trnK-UUU TGTACAGACGGTTTTCGGTG AAAATGCAAGCACGGTTTGG 640–642 1.000 76.6
psbA-trnK-UUU_p5 psbA-trnK-UUU TTTTCGGTGCTGGTTATCCA GTTTGGGGAGGGGTTTTTCT 615–617 1.000 75.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGTACGGACGAATCCATTGC TCCTTGAAAAAGGTGCCCAA 1093–1117 1.000 78.7
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGTACGGACGAATCCATTGC TTCCTTGAAAAAGGTGCCCA 1094–1118 1.000 78.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 GTACGGACGAATCCATTGCT TCCTTGAAAAAGGTGCCCAA 1092–1116 1.000 78.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 GTACGGACGAATCCATTGCT TTCCTTGAAAAAGGTGCCCA 1093–1117 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTACGGACGAATCCATTGCT CCTTGAAAAAGGTGCCCAAC 1091–1115 1.000 78.1
psbI-trnS-GCU_p1 psbI-trnS-GCU AATCCTGGGCGTGAGGAATA TAAAGCGGCGGATTGCTAAT 245 1.000 78.4
psbI-trnS-GCU_p2 psbI-trnS-GCU ATCCTGGGCGTGAGGAATAA TAAAGCGGCGGATTGCTAAT 244 1.000 78.4
psbI-trnS-GCU_p3 psbI-trnS-GCU TAATCCTGGGCGTGAGGAAT TAAAGCGGCGGATTGCTAAT 246 1.000 78.4
psbI-trnS-GCU_p4 psbI-trnS-GCU AATCCTGGGCGTGAGGAATA AAACTGGGAGAGATGGCTGA 271 1.000 75.7
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCCTGGGCGTGAGGAATAA AAACTGGGAGAGATGGCTGA 270 1.000 75.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AAGTTCTTCGATCAAGCCCC CCGGATTTGAACTGGGGAAA 1466–1480 1.000 79.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCAATGAACCCACGGAATCC CCGGATTTGAACTGGGGAAA 1444–1458 1.000 79.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCCACGGAATCCCTCAAATT CCGGATTTGAACTGGGGAAA 1436–1450 1.000 79.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCAAGCCCCGATCAATGAAC CCGGATTTGAACTGGGGAAA 1455–1469 1.000 78.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GATCAAGCCCCGATCAATGA CCGGATTTGAACTGGGGAAA 1457–1471 1.000 78.1
petN-psbM_p1 petN-psbM TTCACTCGTAGTATGGGGGC AGCTACTGCGCTGTTCATTC 1296–1306 1.000 69.1
petN-psbM_p2 petN-psbM TTCACTCGTAGTATGGGGGC GCTACTGCGCTGTTCATTCT 1295–1305 1.000 69.1
petN-psbM_p3 petN-psbM TTCACTCGTAGTATGGGGGC TAGCTACTGCGCTGTTCATT 1297–1307 1.000 68.8
petN-psbM_p4 petN-psbM TTCACTCGTAGTATGGGGGC ACTGCGCTGTTCATTCTAGT 1292–1302 1.000 68.2
petN-psbM_p5 petN-psbM TTCACTCGTAGTATGGGGGC ATAGCTACTGCGCTGTTCAT 1298–1308 1.000 67.0

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
Cyclea hypoglauca OR166992.1 159727 View on NCBI ↗
Cyclea sutchuenensis OR166993.1 159761 View on NCBI ↗