Markers + reference

Sarmentypnum

2 species · Amblystegiaceae · Hypnales

Back to catalogue

Species 2
Genome length 125–125 kb
Candidate markers 260
Primer pairs 90

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 9 remaining regions by MarkerSeek score (out of 260 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
atpI Genome 747 0.0000 1.00 27.0 yes View details
atpA Genome 1524 0.0007 1.00 46.6 yes View details
chlB Genome 1533 0.0000 1.00 27.9 yes View details
chlB-trnK-UUU Genome 744 0.0054 1.00 61.8 yes View details
ndhJ Genome 519 0.0019 1.00 48.3 yes View details
ndhC Genome 372 0.0027 1.00 44.1 yes View details
rbcL Genome 1428 0.0014 1.00 59.6 yes View details
ycf4 Genome 555 0.0018 1.00 50.4 yes View details
ndhI Genome 552 0.0018 1.00 57.1 yes View details
ndhH Genome 1176 0.0008 1.00 51.1 yes View details
trnS-GCU-psbI Genome 106 0.0101 0.93 62.6 yes View details
rpl16 Genome 1284 0.0000 0.98 60.9 yes View details
trnV-GAC-rps12 Genome 1397 0.0000 0.98 60.3 no View details
chlL Genome 876 0.0023 1.00 60.1 yes View details
rps4 Genome 609 0.0016 1.00 59.7 yes View details
ndhG Genome 603 0.0017 1.00 59.7 yes View details
trnT-GGU-psbD Genome 651 0.0015 1.00 59.6 yes View details
petA-psbJ Genome 895 0.0011 1.00 59.4 yes View details
ycf66 Genome 1026 0.0010 1.00 59.3 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
ycf66_p1 ycf66 TTAAAGCGTGGAGGTTCGAG AAGTGGTAAGGCAGAGGACT 2133–2135 1.000 79.2
ycf66_p2 ycf66 TTAAAGCGTGGAGGTTCGAG GCGATATGGCCAAGTGGTAA 2144–2146 1.000 79.1
ycf66_p3 ycf66 TTAAAGCGTGGAGGTTCGAG CAAGTGGTAAGGCAGAGGAC 2134–2136 1.000 78.6
ycf66_p4 ycf66 GTTCGAGTCCTCTTCAAGGC AAGTGGTAAGGCAGAGGACT 2120–2122 1.000 77.5
ycf66_p5 ycf66 GTTCGAGTCCTCTTCAAGGC GCGATATGGCCAAGTGGTAA 2131–2133 1.000 77.5
atpI_p1 atpI GCAAATGATGATGCTCGAGC TACCTTGACCAATCCCAGGT 1582 1.000 79.5
atpI_p2 atpI AAATCAAAAGTGGCTTGGCG TACCTTGACCAATCCCAGGT 1910 1.000 78.5
atpI_p3 atpI GCAAATGATGATGCTCGAGC GCAGCAGTACCTTGACCAAT 1589 1.000 78.5
atpI_p4 atpI TTGCAGGTCGTTGTAATCCC TACCTTGACCAATCCCAGGT 1521 1.000 78.3
atpI_p5 atpI GCAAATGATGATGCTCGAGC GCAGTACCTTGACCAATCCC 1586 1.000 77.9
atpA_p1 atpA AGCGAGAAAGCCGAATGAAT ACCCTTAGCCTTCCAAGCTA 2443–2452 1.000 79.6
atpA_p2 atpA AGCGAGAAAGCCGAATGAAT CCCACTACCCGCCTTTATTC 2406–2415 1.000 79.6
atpA_p3 atpA AGCGAGAAAGCCGAATGAAT CGCCGACTATAACCCTTAGC 2454–2463 1.000 79.4
atpA_p4 atpA AGCGAGAAAGCCGAATGAAT GCGCCGACTATAACCCTTAG 2455–2464 1.000 79.4
atpA_p5 atpA GGGGCAGGCTTAGTTTTTCT ACCCTTAGCCTTCCAAGCTA 2468–2477 1.000 79.2
trnS-GCU-psbI_p1 trnS-GCU-psbI GGGTTCGAATCCCTCTCTCT AATGATCCTGGCCGTAATCC 157–164 1.000 77.7
trnS-GCU-psbI_p2 trnS-GCU-psbI GAGATGGCCGAGTGGTTTAA AATGATCCTGGCCGTAATCC 219–226 1.000 75.2
trnS-GCU-psbI_p3 trnS-GCU-psbI AGAGATGGCCGAGTGGTTTA AATGATCCTGGCCGTAATCC 220–227 1.000 74.9
trnS-GCU-psbI_p4 trnS-GCU-psbI GGGTTCGAATCCCTCTCTCT TCAAATGATCCTGGCCGTAA 160–167 1.000 73.5
trnS-GCU-psbI_p5 trnS-GCU-psbI GGGTTCGAATCCCTCTCTCT AAATGATCCTGGCCGTAATCC 158–165 1.000 73.1
chlB_p1 chlB GAGGTTCGAATCCTTCCGTC TGGGATTCATAAACTTTTCCTACA 2019 1.000 40.2
chlB_p2 chlB ATCTATTTATGGGGCGTCGC TGGGATTCATAAACTTTTCCTACA 2076 1.000 40.2
chlB_p3 chlB GAGGTTCGAATCCTTCCGTC AATTCTTTTTGTCAATGCTGT 2329 1.000 40.2
chlB_p4 chlB ATCTATTTATGGGGCGTCGC AATTCTTTTTGTCAATGCTGT 2386 1.000 40.2
chlB_p5 chlB GGTAAGGCAGCAGGTTTTGA TGGGATTCATAAACTTTTCCTACA 2051 1.000 40.2
chlB-trnK-UUU_p1 chlB-trnK-UUU ACTGAAAAATTTGCGCGTCA AGTCGCACTTAAAAGCCGAG 873 1.000 71.9
chlB-trnK-UUU_p2 chlB-trnK-UUU ACTGAAAAATTTGCGCGTCA TAGTCGCACTTAAAAGCCGA 874 1.000 70.7
chlB-trnK-UUU_p3 chlB-trnK-UUU ACTGAAAAATTTGCGCGTCA TCGCACTTAAAAGCCGAGTA 871 1.000 70.7
chlB-trnK-UUU_p4 chlB-trnK-UUU ACTGAAAAATTTGCGCGTCA CGCACTTAAAAGCCGAGTAC 870 1.000 70.2
chlB-trnK-UUU_p5 chlB-trnK-UUU ACTGAAAAATTTGCGCGTCA GTCGCACTTAAAAGCCGAGT 872 1.000 69.7

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
Sarmentypnum exannulatum NC_049076.1 124787 View on NCBI ↗
Sarmentypnum sarmentosum NC_049071.1 124819 View on NCBI ↗