Markers + reference

Klebsormidium

2 species · Klebsormidiaceae · Klebsormidiales

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Species 2
Genome length 194–212 kb
Candidate markers 313
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 313 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
orf337 Genome 1014 0.4644 0.94 83.4 yes View details
orf337-trnG(gcc) Genome 3380 0.4861 0.94 79.6 yes View details
orf441 Genome 1326 0.4741 0.74 78.0 yes View details
orf441-orf489 Genome 371 0.5017 0.79 74.3 yes View details
orf342 Genome 1029 0.4681 0.88 81.7 yes View details
trnF(gaa)-rrs Genome 498 0.3497 0.69 76.1 yes View details
chlN-ycf1 Genome 2207 0.4489 0.74 76.4 yes View details
ycf20 Genome 384 0.4372 0.48 67.8 no View details
ycf20 Genome 384 0.4890 0.95 79.0 yes View details
ycf1-chlN Genome 2207 0.4487 0.74 76.3 yes View details
trnF(gaa)-ycf4 Genome 1558 0.4201 0.42 71.5 yes View details
psaA-orf337 Genome 1693 0.4311 0.81 79.2 no View details
trnQ(uug)-rps12 Genome 541 0.3074 0.95 84.5 yes View details
rps12-rps4 Genome 599 0.2379 0.93 83.7 yes View details
odpB-psaI Genome 637 0.2748 0.95 83.7 yes View details
psaI-odpB Genome 637 0.2748 0.95 83.7 yes View details
trnS(uga)-psbZ Genome 591 0.2667 0.91 83.4 yes View details
psbJ-orf342 Genome 687 0.4266 0.94 83.4 yes View details
orf342-psaA Genome 1758 0.3846 0.95 83.2 yes View details
rps14-psbA Genome 1099 0.4128 0.90 83.2 yes View details
psbA-rps14 Genome 1099 0.4128 0.90 83.2 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
orf337_p1 orf337 GGCGTAAACCCCGTCATAAT TCACCATTTGCCTCTTGCTT 1706 0.500 59.7
orf337_p2 orf337 GGCGTAAACCCCGTCATAAT TAGCGGGTATGGTCTAGTGG 1562 0.500 59.6
orf337_p3 orf337 GGCGTAAACCCCGTCATAAT TTGGGTCGTTTGTTTTTGGC 1407 0.500 59.6
orf337_p4 orf337 GGCGTAAACCCCGTCATAAT CAAGAGCTCCCCATCATTCC 1244 0.500 59.5
orf337_p5 orf337 GGCGTAAACCCCGTCATAAT AGCGGGGTACTAAAAGACCT 1359 0.500 59.2
orf337-trnG(gcc)_p1 orf337-trnG(gcc) ACACGTCGTTTTCAAGGTGA CGTCGACTTGGATACGGATC 1012 0.500 59.6
orf337-trnG(gcc)_p2 orf337-trnG(gcc) TCACACGTCGTTTTCAAGGT CGTCGACTTGGATACGGATC 1014 0.500 59.6
orf337-trnG(gcc)_p3 orf337-trnG(gcc) ACACGTCGTTTTCAAGGTGA ATACGGATCTTGGTGAACGC 1001 0.500 59.4
orf337-trnG(gcc)_p4 orf337-trnG(gcc) TCACACGTCGTTTTCAAGGT ATACGGATCTTGGTGAACGC 1003 0.500 59.4
orf337-trnG(gcc)_p5 orf337-trnG(gcc) ACACGTCGTTTTCAAGGTGA AGCGTTCCGACTCATTGATC 1148 0.500 59.3
orf441_p1 orf441 AAAAGGACACTGTGACCACC TGTTCAGAGGCTCAGTCTCA 2288 0.500 59.6
orf441_p2 orf441 AGACCATACCCGCCTCTATC TGTTCAGAGGCTCAGTCTCA 2083 0.500 59.4
orf441_p3 orf441 ACCATACCCGCCTCTATCAA TGTTCAGAGGCTCAGTCTCA 2081 0.500 59.2
orf441_p4 orf441 AAAAGGACACTGTGACCACC TGAGCTATTATCTGCGACGC 2403 0.500 59.2
orf441_p5 orf441 AATGACAGAGCGTAAACCCC TGTTCAGAGGCTCAGTCTCA 1922 0.500 59.1
orf441-orf489_p1 orf441-orf489 GACGAGCAGAGACCATTTGT TGTTCAGAGGCTCAGTCTCA 831 0.500 59.3
orf441-orf489_p2 orf441-orf489 GACGAGCAGAGACCATTTGT CGGTCGAGTTAACAGGACTG 1214 0.500 59.1
orf441-orf489_p3 orf441-orf489 AAACTGGACGCTCTTCTTGG TGTTCAGAGGCTCAGTCTCA 498 0.500 59.1
orf441-orf489_p4 orf441-orf489 AAACTGGACGCTCTTCTTGG CGGTCGAGTTAACAGGACTG 881 0.500 58.9
orf441-orf489_p5 orf441-orf489 GACGAGCAGAGACCATTTGT TGAGCTATTATCTGCGACGC 946 0.500 58.9
rps12-rps4_p1 rps12-rps4 TTGATCAGGTAGTCGCAAGC TGACCTGTACCAGCTCTTGA 1163 0.500 59.8
rps12-rps4_p2 rps12-rps4 TTGATCAGGTAGTCGCAAGC GGCGAGGAATGTCTTGCATA 1399 0.500 59.5
rps12-rps4_p3 rps12-rps4 TTGATCAGGTAGTCGCAAGC TCTTTGCAGAGAGTTCGACG 1024 0.500 59.5
rps12-rps4_p4 rps12-rps4 ATCAGGTAGTCGCAAGCATG TGACCTGTACCAGCTCTTGA 1160 0.500 59.5
rps12-rps4_p5 rps12-rps4 TTGATCAGGTAGTCGCAAGC GGTAGGCGAGGAATGTCTTG 1403 0.500 59.4
trnK(uuu)_p1 trnK(uuu) TTTCTTGGCGGAGAAAGCTT GCGCTCCTACCTGATCAAAA 1879 0.500 59.7
trnK(uuu)_p2 trnK(uuu) CCATACCGCTAGTGATCGTG GCGCTCCTACCTGATCAAAA 1956 0.500 59.4
trnK(uuu)_p3 trnK(uuu) CGGAGAAAGCTTGCTTTTGG GCGCTCCTACCTGATCAAAA 1871 0.500 59.4
trnK(uuu)_p4 trnK(uuu) CGAGACAAACATTCGTGTGC GCGCTCCTACCTGATCAAAA 1510 0.500 59.3
trnK(uuu)_p5 trnK(uuu) GCGAGACAAACATTCGTGTG GCGCTCCTACCTGATCAAAA 1511 0.500 59.3

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
Klebsormidium crenulatum NC_082069.1 211508 View on NCBI ↗
Klebsormidium elegans NC_082071.1 194140 View on NCBI ↗