Markers + reference

Scapania

2 species · Scapaniaceae · Jungermanniales

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Species 2
Genome length 118–118 kb
Candidate markers 267
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

4 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-ycf2 Genome 799 0.0940 0.98 80.6 yes View details
ycf2 Genome 6069 0.0700 1.00 69.7 yes View details
trnE-UUC-trnT-GGU Genome 836 0.1127 1.00 80.1 yes View details
rpl32-trnL-UAG Genome 836 0.1090 0.95 83.2 yes View details
atpB-rbcL Genome 562 0.0588 0.97 83.0 yes View details
trnR-UCU-trnG-UCC Genome 77 0.1067 0.97 81.4 yes View details
trnV-GAC-rps12 Genome 353 0.0680 0.99 81.1 no View details
chlB-trnK-UUU Genome 507 0.0655 0.93 80.1 yes View details
trnL-UAA-trnF-GAA Genome 69 0.1014 1.00 80.1 yes View details
psaC-ndhE Genome 155 0.1143 0.90 79.8 yes View details
trnT-UGU-trnL-UAA Genome 266 0.1188 0.98 79.0 yes View details
psbM-ycf66 Genome 123 0.1017 0.96 78.4 yes View details
rps12-rps7 Genome 50 0.1064 0.94 78.2 yes View details
trnT-GGU-psbD Genome 609 0.0643 0.97 78.0 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 65 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps12-rps7_p1 rps12-rps7 AATCGGATGTACGGTTTGGG ATTGGATCAGGCTTCGCAAT 167–171 1.000 85.4
rps12-rps7_p2 rps12-rps7 AATCGGATGTACGGTTTGGG CGTGACGTTCGGAGTTACTT 339–343 1.000 83.6
rps12-rps7_p3 rps12-rps7 AATCGGATGTACGGTTTGGG GATCCACCTATACGACGTGC 365–369 1.000 83.3
rps12-rps7_p4 rps12-rps7 AATCGGATGTACGGTTTGGG GCAGCCATATTTCCACCTGA 470–474 1.000 83.0
rps12-rps7_p5 rps12-rps7 AATCGGATGTACGGTTTGGG TTACTGATGGCTTGACGTGG 324 0.500 59.0
psbM-ycf66_p1 psbM-ycf66 TGTACGAACAGCTGGTCAAA AGTACTGGGGCCTAATTCCA 176–181 1.000 80.5
psbM-ycf66_p2 psbM-ycf66 ATGTACGAACAGCTGGTCAA AGTACTGGGGCCTAATTCCA 177–182 1.000 78.7
psbM-ycf66_p3 psbM-ycf66 TGTACGAACAGCTGGTCAAAA AGTACTGGGGCCTAATTCCA 176–181 1.000 76.6
psbM-ycf66_p4 psbM-ycf66 ATGTACGAACAGCTGGTCAAA AGTACTGGGGCCTAATTCCA 177–182 1.000 76.4
psbM-ycf66_p5 psbM-ycf66 TGTACGAACAGCTGGTCAAA AGTACTGGGGCCTAATTCCAT 176–181 1.000 73.1
trnR-UCU-trnG-UCC_p1 trnR-UCU-trnG-UCC ATCCTTTAGACGATGGACGC ACCCTTAGCCTTCCAAGCTA 145–147 1.000 81.1
trnR-UCU-trnG-UCC_p2 trnR-UCU-trnG-UCC ATCCTTTAGACGATGGACGC TTTGCATGTTCGGTTCTGGA 203–205 1.000 79.6
trnR-UCU-trnG-UCC_p3 trnR-UCU-trnG-UCC ATCCTTTAGACGATGGACGC TTCCAAGCTAATGATGCGGG 135–137 1.000 79.2
trnR-UCU-trnG-UCC_p4 trnR-UCU-trnG-UCC ATCCTTTAGACGATGGACGC TCGGTTCTGGAGTAGAGACG 194–196 1.000 77.9
trnR-UCU-trnG-UCC_p5 trnR-UCU-trnG-UCC ATCCTTTAGACGATGGACGC GCATGTTCGGTTCTGGAGTA 200–202 1.000 76.9
chlB-trnK-UUU_p1 chlB-trnK-UUU GACAAAACGGTGTTGCCAAA CAAGTCGCACTTAAAAGCCG 587–622 1.000 87.7
chlB-trnK-UUU_p2 chlB-trnK-UUU GACAAAACGGTGTTGCCAAA AAGTCGCACTTAAAAGCCGA 586–621 1.000 87.1
chlB-trnK-UUU_p3 chlB-trnK-UUU CGGAAAAATTTGCCCGACAA CAAGTCGCACTTAAAAGCCG 602–637 1.000 86.5
chlB-trnK-UUU_p4 chlB-trnK-UUU CGGAAAAATTTGCCCGACAA AAGTCGCACTTAAAAGCCGA 601–636 1.000 85.9
chlB-trnK-UUU_p5 chlB-trnK-UUU GACAAAACGGTGTTGCCAAA CCAAGTCGCACTTAAAAGCC 588–623 1.000 85.4
trnH-GUG-ycf2_p1 trnH-GUG-ycf2 GCGCTAACCTTGGTATGGAA AACCCGAGTAAACTGCGTTT 1202–1207 1.000 85.9
trnH-GUG-ycf2_p2 trnH-GUG-ycf2 GCGCTAACCTTGGTATGGAA ACCCGAGTAAACTGCGTTTT 1201–1206 1.000 85.9
trnH-GUG-ycf2_p3 trnH-GUG-ycf2 TGTTGCAGCTCACGGTTATT ACCCGAGTAAACTGCGTTTT 1425–1430 1.000 84.4
trnH-GUG-ycf2_p4 trnH-GUG-ycf2 TGGGTGTTGCTGGTGTATTC AACCCGAGTAAACTGCGTTT 1571–1576 1.000 84.0
trnH-GUG-ycf2_p5 trnH-GUG-ycf2 TGGGTGTTGCTGGTGTATTC ACCCGAGTAAACTGCGTTTT 1570–1575 1.000 84.0
ycf2_p1 ycf2 TTTCCCTTTAACCGCGCATA CCCACCATTCCCATGTAAAGA 1519 0.500 48.1
ycf2_p2 ycf2 TTTCCCTTTAACCGCGCATA TCCCACCATTCCCATGTAAAG 1520 0.500 48.1
ycf2_p3 ycf2 TTCCCTTTAACCGCGCATAT CCCACCATTCCCATGTAAAGA 1518 0.500 46.3
ycf2_p4 ycf2 TTCCCTTTAACCGCGCATAT TCCCACCATTCCCATGTAAAG 1519 0.500 46.3
ycf2_p5 ycf2 TTTCCCTTTAACCGCGCATA TCCCACCATTCCCATGTAAA 1520 0.500 46.2

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
Scapania ampliata NC_051002.1 118026 View on NCBI ↗
Scapania undulata NC_061219.1 117651 View on NCBI ↗