Markers + reference

Frullania

2 species · Frullaniaceae · Porellales

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Species 2
Genome length 120–120 kb
Candidate markers 271
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnE-UUC-trnT-GGU Genome 817 0.0327 0.97 69.3 yes View details
rps14 Genome 303 0.0099 1.00 43.6 yes View details
cemA Genome 1005 0.0149 1.00 53.0 yes View details
trnP-UGG-psaJ Genome 218 0.0642 1.00 77.0 yes View details
rpl32-trnP-GGG Genome 795 0.0303 0.99 62.7 yes View details
rps15 Genome 267 0.0150 1.00 46.3 yes View details
ycf1-2 Genome 1410 0.0184 1.00 56.1 yes View details
ycf1-1 Genome 3156 0.0171 1.00 51.4 yes View details
trnS-GGA-rps4 Genome 75 0.0704 0.95 80.1 yes View details
cemA-petA Genome 208 0.0493 0.98 74.3 yes View details
rps15-ycf1-2 Genome 155 0.0694 0.93 74.0 yes View details
rpl2-rpl23 Genome 31 0.1290 1.00 73.8 yes View details
trnM-CAU-rps14 Genome 93 0.1290 1.00 72.9 yes View details
trnD-GUC-trnY-GUA Genome 157 0.0536 0.71 72.5 yes View details
rpl22-rps19 Genome 17 0.0588 1.00 71.4 yes View details
rps7-ndhB Genome 183 0.0391 0.98 70.1 yes View details
petA-psbJ Genome 143 0.0350 1.00 70.0 yes View details
atpB-rbcL Genome 680 0.0165 0.98 69.9 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps7-ndhB_p1 rps7-ndhB TGAACTGATAGATGCAGCCA AAAAAGGATGTACCAAGTTCT 315–316 1.000 42.8
rps7-ndhB_p2 rps7-ndhB TGAACTGATAGATGCAGCCA AGGATGTACCAAGTTCTAATTTCA 311–312 1.000 42.8
rps7-ndhB_p3 rps7-ndhB TGAACTGATAGATGCAGCCAA AAAAAGGATGTACCAAGTTCT 315–316 1.000 42.8
rps7-ndhB_p4 rps7-ndhB TGAACTGATAGATGCAGCCAA AGGATGTACCAAGTTCTAATTTCA 311–312 1.000 42.8
rps7-ndhB_p5 rps7-ndhB TGAACTGATAGATGCAGCCA AAGGATGTACCAAGTTCTAATTTCA 312–313 1.000 42.8
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA GGCGGTGCTCTAACCTATTG CTGGTTCAAATCCAGCTCGA 169–213 1.000 82.4
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA GGCGGTGCTCTAACCTATTG CCTACGCTGGTTCAAATCCA 175–219 1.000 82.2
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA GGCGGTGCTCTAACCTATTG TGGTTCAAATCCAGCTCGAC 168–212 1.000 81.7
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CAACTTCCGTCTTGACAGGG CTGGTTCAAATCCAGCTCGA 187–231 1.000 81.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CAACTTCCGTCTTGACAGGG CCTACGCTGGTTCAAATCCA 193–237 1.000 81.5
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GTCGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 920–925 1.000 84.2
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GTCGCCTCCTTGAAAGAGAG CCATGGCGTTACTCTACCAC 899–904 1.000 83.8
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TCGCCTCCTTGAAAGAGAGA GAACCGATGACTTACGCCTT 919–924 1.000 83.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GTCGCCTCCTTGAAAGAGAG TGGCGTTACTCTACCACTGA 896–901 1.000 83.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCGCCTCCTTGAAAGAGAGA CCATGGCGTTACTCTACCAC 898–903 1.000 83.2
trnM-CAU-rps14_p1 trnM-CAU-rps14 AAGGTTATGAGCCTTGCGAG CAGTGCACCTAGTCGTCTTC 281 1.000 83.6
trnM-CAU-rps14_p2 trnM-CAU-rps14 AAGGTTATGAGCCTTGCGAG AGTCGTCTTCATCGTCGTTG 271 1.000 83.3
trnM-CAU-rps14_p3 trnM-CAU-rps14 CGTTATGGATCGGGTTGGTT CAGTGCACCTAGTCGTCTTC 661–674 1.000 82.2
trnM-CAU-rps14_p4 trnM-CAU-rps14 GCTTCGTTATGGATCGGGTT CAGTGCACCTAGTCGTCTTC 665–678 1.000 82.1
trnM-CAU-rps14_p5 trnM-CAU-rps14 TACCAGACTGCTCTACTCCG CAGTGCACCTAGTCGTCTTC 260 0.500 59.6
rps14_p1 rps14 AAGGTTATGAGCCTTGCGAG CTCACGAGCGTACTCCTCTA 641–643 1.000 81.9
rps14_p2 rps14 AAGGTTATGAGCCTTGCGAG TCACGAGCGTACTCCTCTAG 640–642 1.000 81.9
rps14_p3 rps14 CGTTATGGATCGGGTTGGTT CTCACGAGCGTACTCCTCTA 1023–1034 1.000 81.5
rps14_p4 rps14 CGTTATGGATCGGGTTGGTT TCACGAGCGTACTCCTCTAG 1022–1033 1.000 81.5
rps14_p5 rps14 TACCAGACTGCTCTACTCCG TCACGAGCGTACTCCTCTAG 621 0.500 59.2
trnS-GGA-rps4_p1 trnS-GGA-rps4 TTTTGTCTACCGAGGGTTCG ACACAGTTGCAAGGTTCTGT 210–213 1.000 78.8
trnS-GGA-rps4_p2 trnS-GGA-rps4 GGGTTCGAATCCCTCTCTTT ACACAGTTGCAAGGTTCTGT 197–200 1.000 73.9
trnS-GGA-rps4_p3 trnS-GGA-rps4 GGGTTCGAATCCCTCTCTTTC ACACAGTTGCAAGGTTCTGT 197–200 1.000 73.9
trnS-GGA-rps4_p4 trnS-GGA-rps4 GGTTCGAATCCCTCTCTTTCC ACACAGTTGCAAGGTTCTGT 196–199 1.000 73.9
trnS-GGA-rps4_p5 trnS-GGA-rps4 TTTTTGTCTACCGAGGGTTCG ACACAGTTGCAAGGTTCTGT 211–214 1.000 72.4

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
Frullania amplicrania MT762134.1 120259 View on NCBI ↗
Frullania muscicola NC_079849.1 120444 View on NCBI ↗