Numbering refers to original rRNA sequences used in searches. The sequences have since been updated to be more accurate, thus nucleotide numbers may have shifted in some cases by as much as 4 nucleotides. Primer sequences themselves are unchanged.
Yeast - 5.8 S primers =====================5.8S-R62
(85-62) 5'- CGGAATTCTGCAATTCACATTACG Len: 24 Tm: 62.5 GC: 41.0 dG: -45.4 Covers no known meth sites -------------------------------5.8S-R137
(158-137) 5'- AAATGACGCTCAAACAGGCATG Len: 22 Tm: 61.3 GC: 45.0 dG: -42.5 Covers no known meth sites Yeast - 18S primers ======================SSU-R130
(130-154) 5'- CCACGGTTATACCATGTAGTAAAGG Len: 25 Tm: 58.5 GC: 44.0 dG: -44.3 Covers: Am28 Am100 -------------------------------SSU-R186
(210-186) 5'- TAAATACATCTCTTCCAAAGGGTCG Len: 25 Tm: 60.2 GC: 40% dG: -45.1 Covers: Am100 -------------------------------SSU-R224
(249-224) 5'- AATCATCAAAGAGTCCGAAGACATTG Len: 26 Tm: 61.9 GC: 38% dG: -45.6 Covers no know meth sites ---------------------------------SSU-R455
(480-455) 5'- CGTTATTTATTGTCACTACCTCCCTG Len: 26 Tm: 59.9 GC: 42% dG: -45.6 Covers: Am414 Am420 Am436 ----------------------------------SSU-R589
(614-589) 5'- GCAACAACTTTAATATACGCTATTGG Len: 26 Tm: 58.6 GC: 34% dG: -46.0 Covers: Am541 Am578 ----------------------------------SSU-R655
(678-655) 5'- TCCAGTACACGAAAAAATCGGACC Len: 24 Tm: 63.2 GC: 45% dG: -45.8 Covers: Am619 -----------------------------------SSU-R823
(848-823) 5'- GTCCTAGAAACCAACAAAATAGAACC Len: 26 Tm: 58.5 GC: 38% dG: -45.0 Covers: Am796 -----------------------------------SSU-R1020
(1044-1020) 5'- CCGATCTAGTCGGCATAGTTTATGG Len: 25 Tm: 62.5 GC: 48% dG: -46.9 Covers: Cm1006 (1008) Am973 (975) -----------------------------------SSU-R1170
(1193-1170) 5'- GTGTTGAGTCAAATTAGCCGCAGG Len: 24 Tm: 63.9 GC: 50% dG: -46.0 Covers: Gm1123 (1127) -----------------------------------SSU-R1291
(1315-1291) 5'- CGCAATTAAGCAGACAAATCACTCC Len: 25 Tm: 63.3 GC: 44% dG: -46.6 Covers: Um1265 (1267) Gm1267 (1269) -----------------------------------SSU-R1465
(1486-1465) 5'- CTCGCTGGCTCCGTCAGTGTAG Len: 22 Tm: 63.3 GC: 63% dG: -43.2 Covers: Gm1425 -----------------------------------SSU-R1582
(1604-1582) 5'- GCAAGCTGATGACTTGCGCTTAC Len: 23 Tm: 62.9 GC: 52% dG: -44.5 Covers: Gm1570 -----------------------------------SSU-R1652
(1675-1652) 5'- GAGGCCTCACTAAGCCATTCAATC Len: 24 Tm: 62.3 GC: 50 dG: -45.1 Covers: Gm1570 Cm1637 -----------------------------------SSU-R1776
(1797-1776) 5'- AATGATCCTTCCGCAGGTTCAC Len: 22 Tm: 61.6 GC: 50% dG: -42.8 Covers no known methylation sites ============================================= Yeast - 25S primers ======LSU-R198
(220-198) 5'- TGCTCACCCTCTATGACGTCCTG Len: 23 Tm: 62.6 GC: 56% dG: -42.9 Covers no known methylation sites ---------------------------------------LSU-R331
(355-331) 5'- TGTACTTGTTCGCTATCGGTCTCTC Len: 25 Tm: 60.9 GC: 48% dG: -44.3 Covers no known methylation sites --------------------------------------LSU-R419
(444-419) (lower strand, as ordered): 5'-ACACCATGTCTGATCAAATGCCCTTC Len: 26 Tm: 66.2 GC: 46% dG: -47.8 Covers no known methylation sites --------------------------------------LSU-R684
(707-684) 5'- TCATTACGCGTATGGGTTTTACAC Len: 24 Tm: 60.1 GC: 41% dG: -44.3 Covers: Cm661 Am647 Cm648 -----------------------------------------------LSU-R755
(777-755) 5'- CAAATCCATCCGAAGACATCAGG Len: 23 Tm: 62.0 GC: 47% dG: -43.3 Covers no known methylation sites ------------------------------------------------LSU-R842
(863-842) 5'- ACGAGCCTCCACCAGAGTTTCC Len: 22 Tm: 63.0 GC: 59% dG: -43.5 -----------------------------LSU-R914
(939-914) 5'-CCAGCTACTAGATGGTTCGATTAGTC Len: 26 Tm: 59.3 GC: 46% dG= -44.8 Covers: Gm906 Gm865 Am815 Am805 Gm803 snR39b ------------------------------LSU-R947
(968-947) 5'-TGCTATCCTGAGGGAAACTTCG Len: 22 Tm: 59.9 GC: 50% dG: -42.2 Covers: Gm906 Gm865 -------------------------------LSU-R1150
(1173-1150) 5'- GCACCTTAACTCTACGTTCGGTTC Len: 24 Tm: 60.5 GC: 50% dG: -44.4 covers: Am1131 -------------------------------LSU-R1572
(1591-1572) 5'- TCCCTTTCGATGGTGGCCTG Len: 20 Tm: 63.8 GC: 60% dG: -42.6 Covers no known methyl sites -------------------------------LSU-R1637
(1659-1637) 5'- CCGACGTCTCCACATTCAGTTAC Len: 23 Tm: 59.9 GC: 52% dG: -41.8 Covers no known methyl sites -------------------------------LSU-R1764
(1783-1764) 5'- CACAAGCGCACCGGAGCCAG Len: 20 Tm: 67.8 GC: 70% dG: -44.7 Covers no known methyl sites -------------------------------------------LSU-R1899
(1924-1899) 5'-CGAAGTTACGGATCTATTTTGCCGAC Len: 26 Tm: 65.6 GC: 46.0 dG= -50.2 Covers: Um1886 ----------------LSU-R1954
(1973-1954) 5'-CGTCTGACCAAGGCCCTCAC Len: 20 Tm: 61.1 GC: 65% dG: -40.4 -----------------LSU-R2031
(2050-2031) 5'- GCCGTCTACAACAAGGCACG Len: 20 Tm: 60.1 GC: 60% dG: -40.5 Covers no known methyl sites ----------------LSU-R2305
(2328-2305) 5'- GGAATCTCGTTAATCCATTCATGC Len: 24 Tm: 60.8 GC: 41% dG: -44.2 Covers: Am2218 Am2254 Am2278 Am2279 Gm2286 ---------------------------LSU-R2368
(2387-2368) 5'- GATTCTGCCAAGCCCGTTCC Len: 20 Tm: 62.7 GC: 60% dG: -42.6 Covers: Cm2335 Um2345 ----------------------------LSU-R2429
(2454-2429) 5'- TACACCCTCTATGTCTCTTCACAATG Len: 26 Tm: 58.5 GC: 42% dG: -42.7 Covers: Um2415 Um2345 Cm2335 ------------------------------LSU-R2628
(2652-2628) 5'- GGACATCTGCGTTATCGTTTAACAG Len: 25 Tm: 61.2 GC: 44% dG: -45.2 Covers: Gm2616 (pred meth & sno) ------------------------------LSU-R2661
(2684-2661) 5'- TGGAGATTTCTGTTCTCCATGAGC Len: 24 Tm: 61.1 GC: 45% dG: -43.1 Covers: Am2637 ------------------------------LSU-R2746
(2768-2746) 5'- GGACTAAAGGATCGATAGGCCAC Len: 23 Tm: 60.0 GC: 50% dG: -43.5 Covers: Um2721 Um2726 ------------------------------LSU-R2827
(2848-2827) 5'- TGTCGCTATGAACGCTTGACTG Len: 22 Tm: 60.1 GC: 50% dG: -41.2 Covers: Gm2812 Gm2788 Gm2790 ------------------------------LSU-R2956
(2981-2956) 5'- AGGGTAAAACTAACCTGTCTCACGAC Len: 26 Tm: 60.7 GC: 46% dG: -45.6 covers: Cm2945 Am2943 Gm2919 Um2918 --------------------------------------LSU-R2980
(3005-2980) 5'- CTATTGCTGGTAACATTCATCAGTAG Len: 26 Tm: 56.7 GC: 38% dG: -42.7 covers: Cm2956 Cm2945 Am2943 Gm2919 Um2918