# STOCKHOLM 1.0
#  structure and alignment from [Brown99]
#  reference line imposes the E. coli RNase P RNA coordinate system


E.coli                    GAAGCUGACCAGACAGUCGCCGCUUCGUCGUCGUCCUC-------UUCG-
S.typhimurium             GAAGCUGACCAGACAGUCGCCGCUUCGUCGUCGUCCU--------UUCG-
Y.pestis                  GGAGUUGACUAGACAGUCGCCGCUUCACUGCCGUCCCU-------UUCG-
P.aeruginosa              AGAGUCGAUUGGACAGUCGCUGUCGCGC-----------------AAUA-
H.influenza               CGAGUUGGUUAGACAAUCGCUGGUUUAUUGAAGCCCUUAACCGUAUUUAU
#=GC SS_cons              <<<<<<<<<<<<<<<<<<-<<<<<<<<<<<<<-<<<<<<-<<<<------
#=GC RF                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-------xxxx-

E.coli                    -----GGGG-AGAC-GGGCGGAGGGGAGGAAAGUCCGGGCUCCAUAGGGC
S.typhimurium             ------GGG-AGAC-GGGCGGAGGGGAGGAAAGUCCGGGCUCCAUAGGGC
Y.pestis                  -----GGGG-AGAC-AGGUGGAGGGGAGGAAAGUCCGGGCUCCAUAGGGC
P.aeruginosa              -----------------GCGCGGUGGAGGAAAGUCCGGGCUCCAUAGGGC
H.influenza               ACGACCUAGUGGGACAAGUAAACGAGAGGAAAGUCCGAGCUACACAGGGC
#=GC SS_cons              >>>>>>>>>->>>>->->>>>>>>>>----AAA-AAAAA<<<<---BBBB
#=GC RF                   -----xxxx-xxxx-xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

E.coli                    AGGGUGCCAGGUAACGCCUGGGGGG-GAAA-CCCACGACCAGUGCAACAG
S.typhimurium             AGGGUGCCAGGUAACGCCUGGGGGG-GAAA-CCCACGACCAGUGCAACAG
Y.pestis                  AGGGUGCCAGGUAACGCCUGGGAGGCGCAAGCCUACGACAAGUGCAACAG
P.aeruginosa              AGAGUGCCAGGUAACGCCUGGGAGGCGCGAGCCUACGGAAAGUGCCACAG
H.influenza               AGAGUGCCGGAUAACGUCCGGGCGGCGUGAGCCGACGACCAGUGCAACAG
#=GC SS_cons              -<<<<<<<<<<----->>>>><<<<<---->>>>-><<---<<<<<----
#=GC RF                   xxxxxxxxxxxxxxxxxxxxxxxxx-xxxx-xxxxxxxxxxxxxxxxxxx

E.coli                    AGAGCAAACCGCC-GAUGGCCCGCGCAAGCGGGAUCA-GGUAAGGGUGAA
S.typhimurium             AGAGCAAACCGCC-GAUGGCCCACGUAAGUGGGAUCA-GGUAAGGGUGAA
Y.pestis                  AGAGCAAACCGCC-GAUGGCCCACGCAAGUGGGAUCA-GGUAAGGGUGAA
P.aeruginosa              AAAAUA-ACCGCCUAAGCGC----AACA----G-CGCCGGUAAGGGUGAA
H.influenza               AGAGCAGACCGCC---GU------GUAA-------AC-GGUAAGGGUGAA
#=GC SS_cons              --------<<<<<---<<<<<<<<---->>>>>->>>->>>-->>-----
#=GC RF                   xxxxxxxxxxxxx-xxxxxxxxxxxxxxxxxxxxxxx-xxxxxxxxxxxx

E.coli                    AGGGUGCGGUAAGAGCGCACCGCGCGGCUGGUAACAGUCCGUGGCACGGU
S.typhimurium             AGGGUGCGGUAAGAGCGCACCGCGCGGCUGGUAACAGUCCGUGGCACGGU
Y.pestis                  AGGGUGCGGUAAGAGCGCACCGCGCGGCUGGCAACAGUUCGUGGCAUGGU
P.aeruginosa              AAGGUGCGGUAAGAGCGCACCGCACGGCUGGCAACAGUGCGUGGCUAGGU
H.influenza               AGGGUGCGGUAAGAGCGCACCGUGCCGUUGGUAACAACGUGCAGCAGGGU
#=GC SS_cons              --<<<<<<------->>>>>><<<<<<<<<---->>>->>>>>->-->>>
#=GC RF                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

E.coli                    AAACUCCACCCGGAGCAAGGCCAAAUAGGGGUUCAUAAGGUACGGCCCGU
S.typhimurium             AAACUCCACCCGGAGCAAGGCCAAAUAGGGGUUCAUAAGGUACGGCCCGU
Y.pestis                  AAACUCCACCCGGAGCAAGGCCAAAUAGGGGUUCGCAUGGUACGGCCCGU
P.aeruginosa              AAACCCCACUCGGAGCAAGACCAAAUAGGAAUCCAU-UGGCGCGGCCCGC
H.influenza               AAACUCCACUCGUAGCAAGACCAAAUAGGAACUCA--AUGGGUGGCCCGU
#=GC SS_cons              -->>>>>>>>>>>>>---<<<<------<<<<<<----<<<<<-bbbb>>
#=GC RF                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

E.coli                    ACUGAACCCGGGUAGGCUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGAU
S.typhimurium             ACUGAACCCGGGUAGGCUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGAU
Y.pestis                  ACUGAACCCGGGUAGGCUGCUUGAGCCAGUGAGCGAUUGCUGGCCUAGAG
P.aeruginosa              GUUGGAUUCGGGUAGGUCGCUUGAGGCGUACAGUGAUGUGCGUCCCAGAG
H.influenza               CCAGAGUUCGGGUAGGUUGCUUGAGCGGCAGAGUAAUUUGUCGCCUAGAG
#=GC SS_cons              >>>>>>>>>----->>>>------<<<<<<<<---->>>>>>>>------
#=GC RF                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


E.coli                    GAAUGACUGUCCACGACAGAACCCGGCUUAUCGGUCAGUUUCACCU
S.typhimurium             GAAUGACUGUCCACGACAGAACCCGGCUUAUCGGUCAGUUUCACCU
Y.pestis                  GAAUGACUGUCCACGACAGAACCCGGCUUACCGGUCAACUCCAC..
P.aeruginosa              GAAUGGCUGUCCUCGACAGAACCCGGCUUAUAGAUCGACUCUCCCA
H.influenza               GAAUGAUUGUCCACGACAGAACUCGGCUUAUCGACCAACUCAAAAC
#=GC SS_cons              ---->>>>>>>----------aaaaaaaa->->>>>>>>>>>----
#=GC RF                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
//
