Markers + reference

Trichomanes

5 species · Hymenophyllaceae · Hymenophyllales

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Species 5
Genome length 147–147 kb
Candidate markers 270
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 8 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 Genome 5485 0.0230 1.00 55.8 yes View details
psbA-matK Genome 684 0.0355 1.00 70.7 yes View details
psbM-trnD-GTC Genome 606 0.0432 1.00 78.3 yes View details
trnY-GTA-trnE-TTC Genome 399 0.0498 0.86 73.6 yes View details
trnE-TTC-trnG-GCC Genome 682 0.0306 1.00 71.7 yes View details
psbD-trnT-GGT Genome 1376 0.0294 1.00 71.4 yes View details
rps4-trnL-CAA Genome 775 0.0329 1.00 69.9 yes View details
trnL-CAA-trnF-GAA Genome 368 0.0342 0.98 67.2 yes View details
trnF-GAA-ndhJ Genome 222 0.0523 1.00 73.0 yes View details
ndhC-trnV-TAC Genome 472 0.0362 1.00 62.1 yes View details
trnH-GTG-psbA Genome 451 0.0361 1.00 74.4 yes View details
clpP-psbB Genome 404 0.0262 1.00 71.8 yes View details
trnS-GGA-rps4 Genome 355 0.0293 0.96 68.9 yes View details
infA-rps8 Genome 72 0.0500 1.00 68.1 yes View details
rps12-clpP Genome 297 0.0392 1.00 67.2 yes View details
trnT-GGT-trnfM-CAT Genome 409 0.0311 1.00 66.7 yes View details
atpB-rbcL Genome 678 0.0222 0.99 66.6 yes View details
rpl16-rps3 Genome 127 0.0383 1.00 66.6 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf2_p1 ycf2 GTATGCCTGTCTTCGTCTCG TCTTCTGGGCCCAATTCAAG 1369–1378 1.000 82.7
ycf2_p2 ycf2 GTATGCCTGTCTTCGTCTCG ATCTATCCGTTAGCTGGGCA 1207–1216 1.000 82.4
ycf2_p3 ycf2 GTATGCCTGTCTTCGTCTCG AGTTCTATCTTCTGGGCCCA 1376–1385 1.000 82.3
ycf2_p4 ycf2 CCAGAAGATCCAACGAACCC TCTTCTGGGCCCAATTCAAG 1439–1448 1.000 82.0
ycf2_p5 ycf2 CCAGAAGATCCAACGAACCC AGTTCTATCTTCTGGGCCCA 1446–1455 1.000 81.6
trnH-GTG-psbA_p1 trnH-GTG-psbA TAATCCACTTGGCTACGTCC TGAAGCTCCTTCTGTAAACGG 478–508 1.000 73.1
trnH-GTG-psbA_p2 trnH-GTG-psbA TAATCCACTTGGCTACGTCC GAAGCTCCTTCTGTAAACGGA 477–507 1.000 70.9
trnH-GTG-psbA_p3 trnH-GTG-psbA TTAATCCACTTGGCTACGTCC TGAAGCTCCTTCTGTAAACGG 479–509 1.000 70.8
trnH-GTG-psbA_p4 trnH-GTG-psbA CCTTAATCCACTTGGCTACGT TGAAGCTCCTTCTGTAAACGG 481–511 1.000 70.7
trnH-GTG-psbA_p5 trnH-GTG-psbA TAATCCACTTGGCTACGTCC AAGCTCCTTCTGTAAACGGA 476–506 1.000 69.3
psbA-matK_p1 psbA-matK CGGAAGCTAAGTTCCCACTC GTTGGCTCCATTGCTATCGA 1664–1676 1.000 83.8
psbA-matK_p2 psbA-matK CGGAAGCTAAGTTCCCACTC TCGTTGGCTCCATTGCTATC 1666–1678 1.000 83.8
psbA-matK_p3 psbA-matK CGGAAGCTAAGTTCCCACTC TTACGTCCTAAAATCCGCCG 1699–1711 1.000 83.5
psbA-matK_p4 psbA-matK CTACAGGAGGAGCTGCAATG GTTGGCTCCATTGCTATCGA 1434–1444 0.800 73.7
psbA-matK_p5 psbA-matK CTACAGGAGGAGCTGCAATG TCGTTGGCTCCATTGCTATC 1436–1446 0.800 73.7
psbM-trnD-GTC_p1 psbM-trnD-GTC CAATTAATGCTCCGGGACCA CTCTCTTTCAAGGAGCCGAC 1599–1734 1.000 89.5
psbM-trnD-GTC_p2 psbM-trnD-GTC AAATGAGAAAAGCTGCCGGA CTCTCTTTCAAGGAGCCGAC 1466–1601 1.000 89.2
psbM-trnD-GTC_p3 psbM-trnD-GTC CAATTAATGCTCCGGGACCA TTTGACAGGAGACGGACTCT 1444–1550 0.800 81.5
psbM-trnD-GTC_p4 psbM-trnD-GTC AAATGAGAAAAGCTGCCGGA TTTGACAGGAGACGGACTCT 1311–1417 0.800 81.3
psbM-trnD-GTC_p5 psbM-trnD-GTC CAATTAATGCTCCGGGACCA GTTTGACAGGAGACGGACTC 1445–1551 0.800 81.0
trnY-GTA-trnE-TTC_p1 trnY-GTA-trnE-TTC TGGATTTGAACCAGCGTAGG CTCTCTTTCAAGGAGCCGAC 381–516 1.000 89.7
trnY-GTA-trnE-TTC_p2 trnY-GTA-trnE-TTC ATTTGAACCAGCGTAGGCAT CTCTCTTTCAAGGAGCCGAC 378–513 1.000 89.5
trnY-GTA-trnE-TTC_p3 trnY-GTA-trnE-TTC TGGATTTGAACCAGCGTAGG TCTCTCTTTCAAGGAGCCGA 382–517 1.000 89.1
trnY-GTA-trnE-TTC_p4 trnY-GTA-trnE-TTC GTCGAGCTGGATTTGAACCA CTCTCTTTCAAGGAGCCGAC 388–523 1.000 88.9
trnY-GTA-trnE-TTC_p5 trnY-GTA-trnE-TTC GAAACACAACGAAGCAACCC CTCTCTTTCAAGGAGCCGAC 733–868 0.800 79.5
trnE-TTC-trnG-GCC_p1 trnE-TTC-trnG-GCC GTCGGCTCCTTGAAAGAGAG TCTTTGCCAAGGAGAAGACG 772–784 1.000 84.3
trnE-TTC-trnG-GCC_p2 trnE-TTC-trnG-GCC TCGGCTCCTTGAAAGAGAGA TCTTTGCCAAGGAGAAGACG 771–783 1.000 83.7
trnE-TTC-trnG-GCC_p3 trnE-TTC-trnG-GCC ATGTCCTAGGCCTCTAGACG TCTTTGCCAAGGAGAAGACG 752–764 1.000 82.2
trnE-TTC-trnG-GCC_p4 trnE-TTC-trnG-GCC CCTAGGCCTCTAGACGATGG TCTTTGCCAAGGAGAAGACG 748–760 1.000 80.8
trnE-TTC-trnG-GCC_p5 trnE-TTC-trnG-GCC CTAGGCCTCTAGACGATGGG TCTTTGCCAAGGAGAAGACG 747–759 1.000 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Trichomanes nipponicum PQ874240.1 146998 View on NCBI ↗
Trichomanes quelpaertense PQ874241.1 147128 View on NCBI ↗
Trichomanes speciosum NC_041000.1 146874 View on NCBI ↗
Trichomanes stenosiphon PQ874237.1 146846 View on NCBI ↗
Trichomanes striatum NC_060609.1 147014 View on NCBI ↗