Supplemental Table 6A. Pyrococcus furiosus sRNAs

Name		C Box		D' Box		C' Box		D Box
sR1	`AGGTAAGGCG`	`ATGATGA`	`TGCCTTCCGCAC`	`CTGA`	`TTGG`	`TGAGGA`	`GTGGACGGCTTC`	`CTGA`	`GCCTACTCCT`
sR2	`GAAATGGGGG`	`ATGATGA`	`GTTTTTCCCTCACT`	`CTGA`	`TTAG`	`TGATGA`	`GGAGCCGATGCA`	`CTGA`	`CCTCGAGCAT`
sR3	`ACCTCCGGCG`	`ATGATGA`	`ATAGCAAGCCAC`	`CTGA`	`AGAG`	`TGATGA`	`GGTGAACACCCC`	`CTGA`	`GCCTATTCCA`
sR4	`AGCATAAGGG`	`ATGATGA`	`AGGAGATTTCGG`	`CAGA`	`GGTG`	`TGAAGA`	`GACTCGCATGGG`	`CTGA`	`CCACCACCTT`
sR5	`CTTATTTTGA`	`ATGATGA`	`GCGCCATCCGATA`	`CTGA`	`GGGCA`	`TGATGA`	`CCGGATTCCTGG`	`CTGA`	`TCTCATTTTC`
sR6	`AAAAATAGGG`	`ATGATGA`	`GATTTGCTACCT`	`CTGA`	`AAATAA`	`TGATGA`	`ACCCTGCCGTTA`	`CTGA`	`CCGTTTAACT`
sR7	`GAGATTTTCG`	`ATGATGA`	`GCCTCCATCCCATG`	`CTGA`	`AGGG`	`TGATGA`	`GTGCACATCAGG`	`CTGA`	`GCTTTATAAC`
sR8	`TCAATGAGCA`	`ATGATGA`	`GCTCTATCCCTAT`	`CTGA`	`CCCA`	`TGATGA`	`CTGTAGCGCGCG`	`CTGA`	`GCTACTCCTT`
sR9	`CCACAATGGG`	`ATGATGA`	`CCTTTTGCTTTA`	`CTGA`	`ACACA`	`TGATGA`	`CCACGCCCTTCG`	`CTGA`	`CCTAAATATT`
sR10	`ATTATGGCAG`	`ATGATGA`	`GCTACTCCCGG`	`CTGA`	`AAGA`	`TGATGA`	`ACCACCTACCGG`	`CTGA`	`GGTTATGGAA`
sR11	`GCAGGAGGGG`	`ATGATGA`	`GTTTGCCGAGTG`	`CTGA`	`GCTAG`	`TGATGA`	`ATAAACAGTCGC`	`CTGA`	`CTTCCCCTCT`
sR12	`AAGAAAGGGG`	`ATGATGA`	`GCGTTTACCGGT`	`CTGA`	`GTTG`	`TGATGA`	`TACTGGCACTGT`	`CTGA`	`CCTTAGTAGT`
sR13	`TCCTACTGGT`	`GTGATGA`	`AAAGGCGGATTG`	`CTGA`	`GAGGA`	`TGATGA`	`AGACCTTAGGGG`	`CTGA`	`TCACACCTCA`
sR14	`CTATCACCCA`	`ATGATGA`	`TGGATCAACCGG`	`CTGA`	`AGTA`	`TGATGA`	`GGTCCGCATCAC`	`CTGA`	`GGGGATGGAT`
sR15	`TATGCATGAG`	`ATGATGA`	`ATAAACCCGTTG`	`CTGA`	`AAAA`	`TGATGA`	`GAGGATCGACTAG`	`CTGA`	`CTACAGCTCA`
sR16	`TGTATATCTG`	`ATGATGA`	`TCCTTCCCCTCAA`	`CTGA`	`GAGG`	`TGATGA`	`GCACACCGGTAGG`	`CTGA`	`GGTGATAGTA`
sR17	`AAGATGCGCG`	`ATGAAGA`	`AAGCGAACTGCT`	`CTGA`	`GAGA`	`TGATGA`	`AAAGGGCCTAA`	`CAGA`	`GCGTGAGAGG`
sR18	`TTAATTTTTG`	`ATGATGA`	`AACAGCCAGGACC`	`CTGA`	`TGAGA`	`TGATGA`	`ATGGTGGGCTTAG`	`CTGA`	`CGTAGCTGTT`
sR19	`TGGCGGGCTT`	`ATGATGA`	`ACTTTCCCTACGGC`	`CTGA`	`GCGTCACG`	`CGATGA`	`GGAATACAGCCAGGG`	`CTGA`	`TGAAGGTGAT`
sR20	`TAGAGGAGCA`	`ATGATGA`	`AGCCTCGATTGG`	`CTGA`	`TT`	`TGATGA`	`TTGGGAGGGACTTGG`	`CTGA`	`GCGGTGATTA`
sR21	`TTGTCTGTCG`	`ATGACGA`	`AACCGGCACTAT`	`CTGA`	`ATGA`	`TGATGA`	`GCACTCGGTTGT`	`CTGA`	`GACTACTAAA`
sR22	`TAATTGCCCG`	`ATGATGG`	`GAACAGGGTAGCTG`	`CCGA`	`GC`	`TGATGA`	`GGAAGCCGTTCCAGA`	`CTGA`	`GGGAAAAGTT`
sR23	`GTAAAGTTGA`	`ATGATGA`	`ATCTGGAGCCCA`	`CTGA`	`TTTAA`	`TGATGA`	`CCTGTTCGCGGGG`	`CTGA`	`TGCTGTGATA`
sR24	`AAATTTCCCT`	`ATGATGA`	`GAGAGCTGTTAA`	`ATGA`	`G`	`TGGTGA`	`TTAGAGGATGGCTGG`	`CTGA`	`GGGTGAGAGA`
sR25	`CAACGATGAG`	`ATGATGA`	`GAACTCCCTGAT`	`CTGA`	`GCGG`	`TGATGA`	`GGACCGGTGAT`	`CTGA`	`AAAATAGTAA`
sR26	`AAAAGAGGCA`	`ATGATGA`	`GTGATGGGCGAA`	`CTGA`	`AATAG`	`TGATGA`	`CGGTAGGTGATCT`	`CTGA`	`GCCAACTTAC`
sR27	`TGTGGTAAAG`	`ATGATGA`	`ACCCGCGCAGCT`	`CTGA`	`AGGGA`	`TGATGA`	`GGATCTTAAGTG`	`CTGA`	`TCTCTACCAA`
sR28	`AAGCGCAGAG`	`ATGATGA`	`CCGGTTTCGGAT`	`CCGA`	`TGGA`	`TGAGGA`	`CATCAGCTATCG`	`CTGA`	`TCTCTCATTC`
sR29	`GGATTAGCGG`	`ATGATGT`	`GCCTTGCCCAGC`	`CTGA`	`AAGG`	`TGATGA`	`TGTCGGTATTAG`	`CTGA`	`CGCTTTTCCG`
sR30	`ATTATTGTGG`	`ATGATGA`	`GTAGTCAGAAGG`	`CTGA`	`GTTGA`	`TGATGA`	`AGGACGCCCACGC`	`CTGA`	`CTCTTTTCTA`
sR31	`TTGGGTTGAG`	`ATGATGA`	`ACTCGGCAGGTC`	`CTGA`	`AGGA`	`TGATGA`	`GGATCTTGAGTG`	`CTGA`	`TCACCTAACT`
sR32	`AAGGAGTGAG`	`ATGATGA`	`GCTTGGCCGCTTC`	`CCGA`	`G`	`TGGTGA`	`GGGTCTAAACTCCGGTG`	`CTGA`	`TGAAGTCAAA`
sR34	`TATATGACCG`	`ATGAGGA`	`GCGTTAGCCACG`	`CTGA`	`AGA`	`TGATGA`	`CAAGAGGGTTAG`	`CCGA`	`GGTCTTCTCT`
sR36	`GAATAGGTGG`	`ATGAAGA`	`AAGGGTAGGTAG`	`CTGA`	`GCGG`	`TGATGA`	`TCTAATCGGCCC`	`CTGA`	`CACCGCATAA`
sR37	`AAGCTAGGCG`	`ATGATGT`	`AGATTAGCCCCGA`	`CTGA`	`GCGG`	`TGATGA`	`AGCTGGCCCATCG`	`CTGA`	`GTCTTTAAGA`
sR38	`TAGGGAGGCG`	`ATGATTT`	`GACTCCGGAAAAT`	`CTGA`	`TCGA`	`TGATGA`	`AGTCCAGCCCGA`	`ATGA`	`GCCGAGGTGA`
sR39	`AAAATGGGCG`	`ATGAAGA`	`TAATTTCGCTAG`	`CCGA`	`AAAATA`	`AGATGA`	`GGAGTACCCTCGCAA`	`CTGA`	`GCCTTACTTA`
sR40	`TCCAGAGGCC`	`ATGAGGA`	`TAGGCGGGTTTG`	`CTGA`	`CCTCGGGGCG`	`TGATGA`	`ACCTTTGGAGCC`	`CCGA`	`GGGCCGGAGA`
sR41	`GCACCGACGG`	`ATGATGA`	`AATGTAAAGA`	`CGGA`	`AAGA`	`TGAAGA`	`GCCCTATGAGCG`	`CTGA`	`CGCCCTTTCT`
sR42	`TTATAGCTTG`	`ATGATGA`	`ACTTCACGGTACC`	`CTGA`	`GTTCTAAAAACGA`	`TGATGA`	`GCCCCCTCTCGT`	`CTGA`	`TTACCTTTTT`
sR43	`TTGAGGGACG`	`ATGAAGA`	`GAAAGCACCTCCA`	`CGGA`	`TAGA`	`TGAAGA`	`AACGCCCACGGA`	`CTGA`	`GTCTTCACTC`
sR44	`AAATTTGGCT`	`ATGAGGA`	`AATCGGTCTTAG`	`CTGA`	`GCTTA`	`TGATGA`	`AAGTGGTCACCG`	`CCGA`	`GCCAAGTATA`
sR45	`AAAAGGCGGG`	`ATGAGGA`	`AGCCGAGGACAC`	`CTGA`	`TGGA`	`TGATGA`	`CTCTTCGCTTCG`	`CCGA`	`CCGGTGGTGA`
sR46	`CACTTAGGCG`	`ATGACGA`	`CTGAATCCAATG`	`CTGA`	`GCAAAGG`	`CGATGA`	`TTGGCCCCAGAGTGG`	`CTGA`	`GCCCTAATTT`
sR48	`CTTTCTCTTC`	`TTGATGT`	`GGAACCCACCCTTGG`	`CTGA`	`ATGA`	`TGATGA`	`GGCCTCGTGGGTT`	`CCGA`	`AGTTTTTATA`
sR50	`CCTATTGTAG`	`ATGATGA`	`GGCCATCCCCT`	`CTGA`	`TCTG`	`TGATGA`	`GTGGGTGAGCTGG`	`CTGA`	`TACTTTATTC`
sR51	`TATAGCTCCG`	`ATGATGA`	`GTCTCGCTCGG`	`CTGA`	`TAGA`	`TGATGT`	`AGGGCATACTGG`	`CTGA`	`GGTGATAGTA`
sR52	`TAAGGAGAAG`	`AGGATGA`	`AAAAGAAGAAAAGG`	`CTGA`	`ATAGA`	`TGATGA`	`GAGGGGACCTCT`	`CTGA`	`TGAAAGTTGG`
sR53	`TAGCGGGCCG`	`ATGATGA`	`TGGTGGGCACTCG`	`CCGA`	`T`	`TGGTGA`	`GGTAAGGGGCGAGGAGA`	`CAGA`	`GGCCCAAATA`
sR54	`AATAAAAGGG`	`ATGATGA`	`AGTTCGCTAGAC`	`CTGA`	`GGAG`	`TGATGA`	`GCCCTAGGGTAT`	`CTGA`	`CCACAAACTT`
sR55	`TTAGTAACCG`	`ATGAAGA`	`GTGTCATCCCTG`	`CTGA`	`AACGGGGTCGA`	`TGATGA`	`GGTATAGTCCCCAC`	`CTGA`	`GGTGTTTCCA`
sR56	`GTTTGGGCCG`	`ATGAAGA`	`GCGAGCCCGGCC`	`CTGA`	`GGAGA`	`TGATGA`	`AAGCTACCACTT`	`CTGA`	`GGTCATCAAC`

None of the Pfu predictions have been verified as RNA transcripts by primer extension. Exceptions to consensus box features shown in red. Predicted methylation guide regions with Watson-Crick/G-U base pairings to target RNAs shown in green (only those not found in Pho are shown in this alignment). Predicted terminal stem pairings shown in blue. 5' and 3' ends of sRNAs were not determined experimentally (an invariant 10 nucleotides of sequence flanking the C box and D boxes is displayed). The gaps in numbering for sR33, sR35, sR47, and sR49 are intentional (no Pfu homologs were found).