Supplemental Table 7A. Pyrococcus abyssi sRNAs

Name
 
C Box
 
D' Box
 
C' Box
 
D Box
 
sR1 ATAAATGGCA ATGATGA AGCCTTCCGCAC CTGA ACGG TGAGGA GTGGACGGCTTC CTGA GCCTCACTCC
sR2 GAGAAAAGGG ATGATGA GTTTTTCCCTCACT CTGA GCCG TGATGA GGAGCCGATGCT CTGA CCTCTGCCAT
sR3 TATGAAGGCG ATGATGA GTAGCAAGCCAC CTGA CCTA TGATGA GGTGAACACCCC CTGA GCCAATTTCA
sR4 GAAGGATGGG ATGATGA AGGAGATTTCGG CCGA AAGG TGAGGA AACTCGCATGGG CTGA CCTTTCTCAG
sR5 AAGACAATAG ATGATGA GCGCCATCGATG CTGA GGAG TGATGA CCGGATTCCTGG CTGA TCTTTATTCT
sR6 CCAATGAGGA ATGATGA GATTTGCTACCA CTGA GCAG TGATGA GCCCTGCCGTTA CTGA CCTTTTACTA
sR7 ATTATAAGGG ATGATGA GCCTCCATCCAAG CTGA GCAAG TGATGA GTGCACATCAGG CTGA ACCTTTTTAT
sR8 TTGAAAGGCG ATGATGA GCTCCATCCCTAT CTGA GTTG TGATGA CTGTAGCGCGCT CTGA GCTACAGGCT
sR9 GCCTACAGTT ATGATGA ACTTTTGCTTTG CTGA TGTGG TGATGA GCACGCCCTTCG CTGA TACTCTCTCG
sR10 AACGGTAGCG ATGATGA ACTACTCCCGG CTGA GCTG TGATGA ACCACCTACCGG CTGA GGTGGAAACA
sR11 CTTTAATGGG ATGATGA CTTTGCCGAGTG CTGA GGAAG TGATGA GTAAACAGTCGC CTGA CCCCCTGCTT
sR12 ATCGGCTGGG ATGATGA GCGTTTACCGGT CTGA GCTG TGATGA CATCGGCACTGT CTGA CTAGTAGTCA
sR13 TATTACTTGA ATGATGA GATGGCGGATTG CTGA GCTG TGATGA AGACCTTAGGGT CTGA CTTCCCAAAA
sR14 AGACGATCCG ATGATGA TGGATCAACCGG CTGA GTGG TGATGA AGTCCGCATCAC CTGA GGCTCTCAAG
sR15 ATGTGTAGTG ATGATGA TTAAACCCGTTG CTGA GAGG TGATGA GGGGACCGACTAG CTGA ACAACACTTA
sR16 GTTTCCATAG ATGATGA GCCTTCCCCTCAC CTGA GTGG TGATGA GCACACCGGTAGG CTGA GGGTGATATT
sR17 ACGGTTTGCG ATGATGA AAGCGAACTGCA CTGA AAAG TGATGA GAGGGCCTCG CTGA GCGGTGATGT
sR18 TCTATTTTTG ATGATGA TACAGCCAGGACC CTGA TGGGA TGATGA GTGGTGGGCTTAG CTGA TGTTGCCGTT
sR19 TGGCGGGCAT ATGATGA GCTTTCCCTACGGC CCGA GCTCACG CGATGA GGAATACAGCCAGGG CTGA TTTCGGTGAT
sR20 GAGGACCGCG ATGATGA AGCCTCGATTGG CTGA ATCG CGATGA TTGGGAGGGACTTGG CCGA GCGGTGGTTA
sR21 TAGCTTGCCA ATGATGA GACCGGCACTAA CTGA GTTG TGATGA GCACTCGGTTGG CTGA GACTGAAAAC
sR22 GAAATGCCCG ATGATGC CAACAGGGTAGCTG CCGA GG CGATGA GGAAGCCGTTCCAGA CTGA GGGCGTAGCA
sR23 ATACTAAAAG ATGATGA ATCTGGAGCCCC CTGA GTGA TGATGA GCAGTCTGCGGAG CTGA TATCATGATT
sR24 AAGTGGCCCT ATGATGA GAGAGCTGTTAA ATGA T TGATGA TTAGAGGATGGCTGG CTGA GGGGATAATC
sR25 TGGGCCTGCG ATGATGA TAACTCCCTGAC CTGA AAGG TGATGA GGACCGGTTCA CTGA GCTTTGGATT
sR26 GGGCTTGGCG ATGATGA GTGATGGGCGAA CTGA GAAG TGATGA TGGTAGGTGATCT CTGA GCCAATCCGG
sR27 CTTGCCTCGA GTGATGA GCCCGCGCAGCG CTGA GCAAGA TGATGA AGATTTTAAGTG CTGA CGCCCAATAA
sR28 TAAACCTTGG ATGATGA CCGGTTTCGGGA CTGA GCTA TGATGA CACCAGCTATCG CTGA CTCCTCTTAC
sR29 GCTATGGCGG ATGACGA GCCTTGCCCAGC CTGA AAGG TGATGA TGTCGGTATTAG CTGA CGCCCAGGAG
sR30 ATAATCGTGG ATGATGA TTAGTCGGAAGG CTGA AGTG TGATGA AGGACGCCCATGG CTGA ACAAAGCATA
sR31 GAAGATGAAG ATGATGA GCTCGGCAGGTC CTGA GGAG TGATGA GGATCTTGAGTG CTGA TTCACCTTAC
sR32 AATCCGAGAA ATGATGA GCTTGGCCGCTAC CCGA T CGATGA GGGTTAAACTCCGGTG CTGA TCATAGGATG
sR34 ATCCCAGCCG ATGAGGA CCGTTAGCCACG CTGA GGA TGATGA TAAGAGGGTTAG CCGA GGCTTATTTT
sR35 ACAAAATAAA ATGATGA GTACGGGGCCAC CTGA ATGG TGATGA GGTTTCTCCCAAGG CTGA TTACCTTACC
sR36 GAATTGGTGG ATGAGGA GAGGGTAGGTAG CTGA GTTA TGATGA ACTAATCGGCCC CCGA CACCTATTGG
sR37 AAGCAAAGCG ATGATGT AGATTAGCCCCGA CTGA GTTG TGATGA GGCTGGCCCATCG CTGA GCTAGATGCT
sR38 AAAATAGGCG ATGATTT GACTCCGGAAAAG CTGA GCGA TGATGA AGTCCAGCCCGA ATGA GCCGAGGTGA
sR39 TAAGTAGGCG ATGAAGA AAATTTCGCTAG CTGA AAAG TGATGA GTACCCTCGCAA CTGA GCCTATTTGA
sR40 TCCAGAGGCC ATGAGGA CAGGCGGGTTTG CTGA CCTCGGGGCG TGATGA ACCTTTGGAGCC CCGA GGGCCGGA
sR41 ACCTTGGCGG ATGATGA GCTAGTAATT CTGA GCGA TGAAGA GCCCTATGAGCG CTGA CGCCTTGGAA
sR42 ATAAGCTATG GTGATGA TCTTCACGGTACC CTGA GAGACCCTCGA TGATGA GCCCCCTCTCAA CTGA CCTAAATTCT
sR43 AAGTAGGGAG ATGAAGA GAAAGCACCTCCA CTGA TTGA TGATGA AACGCCCACGGT CGGA TTTCCTTTCC
sR44 CAAGAAGGCA ATGATGA AATCGGTCTTGT CCGA GGAG TGATGA TAGTGGTCACCG CTGA GCCACCAACT
sR45 AAAAAACGGG ATGAGGA AGCCGAGGACAC CTGA ATTG TGATGA ATCTTCGCTTCG CCGA CCGAGGTGAT
sR46 CTCAAGGGCA ATGAGGA ATGAATCCAATG CTGA GCAAAGG CAATGA TTGACCCCAGAGTGG CCGA GCCTCTATAT
sR47 GAGTATTGGG ATGATGA AACTCCTTTCGGGCA CTGA TCCG TGATGA AGGCCCTCCTAT CTGA GCATCCCAAC
sR48 ATTTTTCTCG AGGATGA TCCCACCCTTGG CTGA AGTG TGATGA TGTCTCGTGGTT CTGA GAGAAGTTAG
sR49 TTCCTGGGCG ATGAAGA ACTGGATCCGAG CTGA GCTTA TGATGA TGGAGGTTTAAC CTGA GCCTTCATAA
sR50 ATAAGGAGGG ATGATGA GGCCTACCTCG CTGA GCTG TGATGA GTGGGTGAGCTGG CTGA CATTTCATTA
sR51 AACCTTGTTG ATGATGA ACTCGCTTGTTG CTGA AGGG TGATGA AGGGCATACTGG CTGA TTTGGAGGTT
sR52 AGGTAGGGGG AGGATGA AGAAAAAGTTCAAAGG CTGA AAGG TGATGA GAGGGGACCTCG CTGA TGTTGATCGG
sR53 GAGCAACCCG ATGACGA AGGTGGGCACTCT CCGA CT TGATGA GGATGTGGGGCGAGGAGC CAGA GGGTGGTGCG
sR54 TTAGATGGGA GTGATGA GGTTCGCTAGAG CTGA AGGAT TGATGA TGAGACCCAGGGTAT CTGA CCGCATTAGA
sR55 AAAACCACCG ATGATGA GTGTCATCCCTG CTGA AATCGGGGTCGA TGATGA CGTAAATTCCCCAC CTGA GGTGTTTAAT
sR56 TTAATATCCG ATGAGGA GCGAGCCCGGCC CTGA GCGA TGATGA GAGCTACCACTA CTGA GGTCACCCAA
sR57 ATAATTAGCG ATGATGA ATTCACGAAGG ATGA GG TGAAGA GCCTAATATGGGAGGCCTCG CTGA GGGTTCTCGG

None of the Pab 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 gap in numbering for sR33 is intentional (a Pab homolog was not found).