# STOCKHOLM 1.0
#=GF ID Magnesium
#=GF AC RF00380
#=GF DE M-box riboswitch aptamer (ykoK leader)
#=GF AU Ontiveros-Palacios N; 0000-0001-8457-4455
#=GF GA 44.0
#=GF NC 36.5
#=GF TC 45.2
#=GF PI ykoK;; M-box
#=GF SE Barrick JE, Breaker RR
#=GF SS Predicted; Barrick JE, Breaker RR
#=GF TP Cis-reg; riboswitch;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR GO; 0010468; regulation of gene expression;
#=GF DR GO; 0032026; response to magnesium ion;
#=GF DR SO; 0000035; riboswitch;
#=GF RN [1]
#=GF RM 15096624
#=GF RT New RNA motifs suggest an expanded scope for riboswitches in bacterial
#=GF RT genetic control.
#=GF RA Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M,
#=GF RA Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR
#=GF RL Proc Natl Acad Sci U S A 2004;101:6421-6426.
#=GF RN [2]
#=GF RM 17803910
#=GF RT Structure and mechanism of a metal-sensing regulatory RNA.
#=GF RA Dann CE 3rd, Wakeman CA, Sieling CL, Baker SC, Irnov I, Winkler WC
#=GF RL Cell. 2007;130:878-892.
#=GF RN [3]
#=GF RM 21315082
#=GF RT Insights into metalloregulation by M-box riboswitch RNAs via structural
#=GF RT analysis of manganese-bound complexes.
#=GF RA Ramesh A, Wakeman CA, Winkler WC
#=GF RL J Mol Biol. 2011;407:556-570
#=GF RN [4]
#=GF RM 20023416
#=GF RT Magnesium-sensing riboswitches in bacteria.
#=GF RA Ramesh A, Winkler WC
#=GF RL RNA Biol. 2010;7:77-83.
#=GF CC M-box riboswitch, also know as ykoK leader is described as a
#=GF CC metaloregulatory RNA that sense divalent metals and function as a genetic
#=GF CC control element of genes related to divalent metal transport in bacteria.
#=GF CC It was first reported upstream of the B.subtilis ykoK gene and genes with
#=GF CC related functions in other bacteria [1]. The structure of the M-box was
#=GF CC first reported in PDB 2QBZ [2], as a structure of three parallel helices,
#=GF CC where P3 and P4 helixes form a coaxial stack that folds alongside P2 and
#=GF CC P5. Six Mg2+ recognition sites were reported in 2QBZ, while in a second
#=GF CC structure report in PDB 3PDR, the authors report another three sites of
#=GF CC Mn2+ bound that been predicted from phosphorothioate substitution
#=GF CC experiments and six more additional Mn2+ proposed from the analysis of the
#=GF CC anomalous density in the sequence [3]. Phylogenetic analysis of the
#=GF CC distribution of M-box RNAs across bacterial genomes revealed that M-box
#=GF CC riboswitches are most often employed for the regulation of Mg2+
#=GF CC transporter genes [4]
#=GF WK ykoK_leader
#=GF ** seedtax: Bacteria; unclassified sequences
#=GF SQ 159

BX571871.1/238808-238637                      GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUGCUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGAUAU-AUCGAA---CCAAGGU--A-U-AUCCCCAUGUAACU-UUCU------------
AY129558.1/14501-14670                        GCAACAUCU-C-GUUA-GG-C-GAGGCU-CCUGUA-U-AA-AC----------A-----------------------------AAGGCCACUGAUCUCACGACG-UCGAGAGA-CGCCCA-----AG-CU-C-AGGACA-GUUUUC-AUCGGA---UUAAGGU---GU-AAACCCAAGUGGCU-UCCG------------
BX842577.1/4252-4421                          UAAGCACCU-C-GUUA-GG-U-GAGGCG-GCUACA-C-GA-AC----------A-----------------------------UAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCG------------
X90691.1/1632-1461                            GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------AAGGUUGCUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGUUAU-AUCGAA--CAGAAGGU--A-U-AACCCGAAGUAACU-UCCCGC----------
AL596173.1/245334-245167                      AGUUUUGCC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCCACUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGGAUU-GUCGGA---UUAAGGC---UU-UCCAUAAUGUGGCU-AAGA------------
AL035300.1/11215-11044                        CAAGCACCU-C-GGUA-GG-U-GAGGCU-UCUGCA-U-GG-AU----------A-----------------------------UAGGCCACCGAUCC-CGGACG-UCGAGAGA-UGCAUC-----GG-GU-C-AAGACA-ACU---CCCAGGG---UU--GGG---UCCAAGUCCAAGUGGUU-UCUGG-----------
AL591984.1/47104-46938                        AGUUUUGCC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCCACUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGGAUU-GUCGGA---UUAAGGC---UU-UCCAUAAUGUGGCU-AAGA------------
AJ250603.1/195-363                            UAAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUAUUGCCCA-GAAACG-UCGAAAGU-CGCCAA-----UG-GG-U-AAAACA-GAAACU-GUCGGA---UUAAGGC---UU-UUUCCAA--UAGCU-AAGA------------
AB089921.1/2048-2202                          AUGGAAAAU-C-GGUA-GG-U-GAGGCUUACCAUA-A-GG-AU----------A-----------------------------CGGAUGACUACCGC-AAAGCAGUGGAGACACUACUCG-----UU-GG-U--CAACA-GUCCU-GAUCG-----CCAAGGU---CA-AGACUAUGCUCAUU-----------------
AL583922.1/170727-170556                      CAAGUGCCU-C-GUUA-GG-U-GAGGGU-UCUGCA-C-GG-AU----------A-----------------------------UAGGCCACUG--------ACG-UCGAACGA-UGCCCA-----GG-AG-C-AGGACA-GUUCCU-CCCAGA---UUAAGGAG-UUU-GAGCCUAAAUUGUU-UCCGGCU---------
AF031552.1/1396-1226                          ACAGCAUCU-C-GUUA-GG-C-GAGGCU-CCUGUA-C-AA-AC----------A-----------------------------UAGGCCACUGAUCUCACGACA-UCCAGAGA-UGCCCA-----AG-AU-C-AGGACA-GUUUUC-AUCGGA---UUAAGGU---GU-UAACCCAAGUGGCU-UUCG------------
AF117609.1/346-514                            UAAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUGUUGCCCA-GAAACG-UCGAAAGU-CGCCAA-----UG-GG-U-AAAACA-GAAACU-GUCGGA---UUAAGGC---UU-UUUCCAA--UAGCU-AAGA------------
AAFX01011285.1/689-521                        AAUAAAGCU-U-GUUA-GG-U-GAGGUU-ACUGGU-U-GA-AC----------A-----------------------------GAGGCUGCUGCCCG-GAAAUG-UCGAAAGA-CACCAA-----UG-GG-U-AGAGCA-GGCGUA-GUCGGA---UUAAGGC---UU-CGCAUAAGGCAGCU-UUCC------------
AE017194.1/1660591-1660756                    AUAAGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-AUCGAA---UUAAGGU---UU-UUCUUAACGUAGCU-GGUA------------
CP000717.1/2055847-2056021                    CAAGCACCU-C-GCUA-GG-U-GAGGCG-UCUGCG-C-GG-AU----------A-----------------------------UAGGCCACUGACCU-CGAACG-UCGAAAGA-CGCCCA-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAAGUGGCU-UCCGGCU---------
CP000412.1/281461-281624                      CAAAUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GAAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAAUA-GAAAUU-GUCGAA---AUAAGGC---AC-UUUC-CAGGUAGCU-AGCA------------
AE016822.1/2178766-2178596                    AGAGCACUU-C-GUUA-GG-U-GAGGCU-CCUGCG-U-GA-AC----------A-----------------------------CAGGCCACUGAUCUGACGACG-UCGAGAGA-UGCCCA-----AG-AU-C-AGGACA-GGUCUC-CCCGGC---CUAAGGG---GU-GACCCCAGGUGGCU-UCCCG-----------
CP000416.1/2122885-2122722                    AUAAAUUGC-A-AUUA-GG-U-GAGGUU-ACUUUA-A-GA-AC----------A-----------------------------UAGGUUGUUGCCCA-GAAAUG-UCGAGAGA-CAGGAA-----UG-AG-U-AAAGCA-GAAACU-GCCGAA---UUAAGGC---UU-UUUC-AAAACAACU-AGAC------------
CP000728.1/236297-236462                      UAAUAAUGUAC-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UACGCUACUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CACCA-GGUAUU-ACCGAA---GUAAGGU---UU-UACUUAAUGUAGCU-GGCU------------
AASN01000027.1/80343-80511                    UAAGCACCU-C-GUUA-GG-U-GAGGCG-GCUACA-C-GA-AC----------A-----------------------------UAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCG------------
AE016830.1/3116366-3116533                    AAAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUC-C-AA-AC----------A-----------------------------UAGGCUAUUGCGCA-GAAAUG-UCGAAAGA-CACCAA-----UG-UG-U-AAAACA-GGAAUG-GUCGAA---UUAAGGC---UC-UUCUAAAAAUAGCU-AAGA------------
CP000482.1/1208117-1207951                    GUCGUUCCU-C-GUUA-GAAU-GAGGCG-UUUGCA-C-AA-AC----------A-----------------------------CAGGCUGCUACCCA-GAAACG-UCGAAAGA-CGCCAA-----UG-CG-G-UCAACA-GGUUCU-GCCGGA---UUAAGGC---UU-AACCUAAUGCAGCU-GGCC------------
ABDV01000005.1/84537-84695                    AAUAUUAAU-C-GGUA-GG-U-GAGGUU-ACCACC-G-GG-AU----------A-----------------------------CGGAUUGCUGCCGC-AAAAUAGUGGAGACACUAUGAG-----AA-GG-U--UAGCA-GGCUAU-GUCGAGA-AACAAGGC---AU-AAUCUAAUGCAAUU-----------------
AARF01000169.1/465-629                        GCUAGUCUC-C-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-GUCGAA--AAGAAGGC---CC-CUCUUAAUGUAGCU-GGUU------------
BA000004.3/3341002-3340838                    AGUUGUCUU-C-GUUA-GG-U-GAGGCU-CCUGUG-CUGG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAACG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGUAGCU-GGAU------------
CP000673.1/3641499-3641330                    UUUUUGUUA-U-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UAUGCUACUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CAACA-GGUAUU-ACCGAA---UUAAGGU---UU-UACUUAAUGUAGCU-GGACA-----------
AAAK03000021.1/12650-12476                    AAUAAGAUU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUACUGCCCA-AAAACG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGAG---AUAAGGC---UU-UUCAUAAGGUAGCU-AAAAGCA---------
ABDQ01000001.1/467807-467647                  UAAGUACCU-C-GGUA-GG-U-GAGGUU-ACUACA-A-GG-AU----------A-----------------------------CGGGUUGCUACCGUGAAAGAG-UGGAAACA-UUCUAA-----AC-AG-G-UUAGCA-GGUUUU-GCCGAACAAAGAAGGC---UU-AAUCUAAUGCAACU-----------------
BA000004.3/2041941-2042105                    AAUCAUCCU-C-GUUA-GG-U-GAGGCU-CCUGUG-CUGG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAACG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAACC-AUCGAC---AUAAGGU---GG-UUUUUAACGUAGCU-GGCU------------
AAWL01000016.1/43438-43265                    GUACUUCCU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-AA-AC----------A-----------------------------UAGGCCACUGCCCG-GAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGUAUU-ACCGGC---AUAAGGU---UU-UACUUAAGGUGGCU-GAGCAU----------
CP000480.1/5735476-5735649                    ACCGCGCUU-C-GUUA-GG-U-GAGGCU-CCUACA-C-GA-AC----------A-----------------------------CAGGCCACUGAUCCGACGACG-UCGAGAGA-CGCCCA-----GG-GU-U-AGGACA-GAUCUU-CCCGGC---CUAAGGG---AU-GAUCCGAAGUGGCU-UCCCAC----------
AP009389.1/428061-428228                      UAUGUUCUU-C-GUUA-GG-U-GAGGCU-UCUACA-C-AG-AC----------A-----------------------------UAUGCCACUGCCCG-GAAAUG-UCGAGAGA-CGCCUA-----CG-GG-U--UAACA-GGUACU-GCCGGA---UUAAGGU---UU-UACUUAAUGUGGCU-GGGA------------
CP000679.1/1386114-1386270                    GAAAUAUCU-C-GGUA-GG-C-GAGGCU-CCUACA-G-GG-AU----------A-----------------------------UAGGCUGCUGCCGCGAAAGAU-UGGAGACA-AUCUGA-----GC-UG-G-UAAACA-GGUUUU-GCCGAA--UCCAAGGC---AU-AACCUAAUGCAGCU-----------------
AE016958.1/3916507-3916677                    CAAGCACCU-C-GGUA-GG-U-GAGGCG-UCUGCA-U-GG-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGA--CCCAAGGG---UU-GAGCCCAAGUGGCU-UCCG------------
CP000647.1/4212343-4212524                    UAACGAUCU-C-GUUAUGG-C-GAGGCU-CCUGCA-U-AA-AU----------A-----------------------------CAAGUUACCGCCCUGUUGGUA-UCGAGAGA-GACCACU---CAG-GG-A-AAUACA-GGCUUCCAUCGAA---UCAAGGU---GU-UGCC-AAGGUAACU-UCUGGCGGU-------
CP000568.1/2645160-2644994                    GAAUAUUUU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AG-AA----------A-----------------------------GACGCUGCUGCCCG-GAAACG-UCGAAAGA-CGCCAA-----UG-GG-U--AAACA-GGCACU-ACCGGA---UUAAGGU---UU-UGCUUAAUGCAGCU-GGU-------------
AE017198.1/1073421-1073588                    CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UAUGCUGAUGCCCA-GGAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGAACU-GUCGAG---UUAAGUC---UU-UUCC-CAGUCAGCU-AGUU------------
CP000413.1/234944-235115                      CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------UAUGCUGUCGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGGAUC-GUCGAU---AUAAGGC---CC-UCCC-CAGCCAGCU-AGUU------------
AE016958.1/1663674-1663849                    CAAGCACCU-C-GCUA-GG-U-GAGGCG-UCUGCA-C-GG-AC----------A-----------------------------CAGGCCACUGACCU-CGAACG-UCGAAAGA-CGCCCA-----GG-GU-C-AGGACA-GCUCCU-CCCGGA---UUAAGGG---UU-GAGCCCAAGUGGCU-UCCGGCU---------
CP000325.1/5326076-5325906                    CAAGCACCU-C-GGUA-GG-C-GAGGCG-UCUGCA-U-GG-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAGAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCUU-CCCGGC---CUAAGGG---UU-GAGCCCAAGUGGCU-UCCG------------
AE016830.1/1024864-1024697                    UUUGUAAUA-A-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUAUUGCUCA-GAAAUG-UCGAGAGA-CACCAA-----UG-AG-U-AGAACA-AGACUG-GUCGAG--GAGAAGGC---UU-UUCUCAAAAUAGCU-AAGA------------
CP000724.1/3301490-3301319                    AAAAUAACU-U-GUUA-GG-A-GAGGCU-CCUAAA-U-GA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGCAUG-AUCGGA---UUAAGGU----C-UGCUUAAGAUAGCU-GAUUCA----------
AP006627.1/810916-810751                      UAUAUUCCU-C-GUUA-GG-U-GAGGCU-CCUGUG-CAGG-AG----------A-----------------------------UACGCUGCUACCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAACC-AUCGAC---AUAAGGU---GG-UUUUUAAUGUAGCU-GGCA------------
CP000423.1/1285762-1285925                    GGUGCUUUC-C-GUUA-GG-U-GAGGCU-CCUAUA-C-G--AA----------C-----------------------------AAUGCUGCUGCUCA-GAAACA-UCGAGAGA-UGCCAA----UUG-AG-U--CAACU-GCGUCU-GCCC-A---UUAAGGC---UU-ACGCUAAUGCAGCU-GAAG------------
CP000544.1/1425650-1425831                    AGCGAGUCC-C-GUUA-GG-U-GAGGCU-CCUGUG-C-CG-AC----------A-----------------------------AGGUGUGCUGCCCA-GAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-UGAACA-GGCCCU-GCCGAA---CGAAGGC---UU-GGUCUAAUGCACAC-CGCGGCCC--------
CP000141.1/329676-329842                      UAUUUUCUU-C-GUUA-GG-U-GAGGCU-ACUUCC-U-GG-AU----------A-----------------------------UAGGCUACUGCCCG-GAAAUG-UCGAGAGA-CACCAA-----CG-GG-U--AAACA-GGUAUU-ACCGGC---UUAAGGU---UU-UACCUAAUGUAGCU-GAGG------------
CP000413.1/962812-962978                      CAAAUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UACGCUGAUGCCCA-GCAACA-UCUAGAGA-UGCCAA-----CG-GG-U-UAAACA-GGAAUU-GUCAAC---UUAAGGC---UU-UUCC-CAGUCAGCU-AGUU------------
AE017198.1/231904-232076                      CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CAUGCUGUCGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGGAUC-GUCGAU---AUAAGGC---CC-UCCC-CAGCCAGCU-AGUUAUA---------
AAXV01000059.1/1758-1594                      GACUCCCUU-C-GUUA-GG-U-GAGGCU-CCUAUG-U-GG-AG----------A-----------------------------UACGCUACUACCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAA---AUAAGGU---GU-UUUUUAACGUAGCU-GGAU------------
CR936503.1/1082354-1082189                    UCGCUUUUC-C-GUUA-GG-U-GAGGCU-CCUAUA-U-GA-AC----------A-----------------------------UACGCUGCUACUCA-GAAACA-UCGAGAGA-UGCCAA----UUG-AG-U--CAACA-AAAACU-GCC-AA---UGAAGGC---UU-UUUCUAACGUAGCU-GAAC------------
CP000232.1/409831-409996                      GCAAACCUU-C-GUUA-GG-U-GAGGCU-UCUGCA-U-AG-AC----------A-----------------------------GACGCCACUGCCCG-GAAACG-UCGAAAGA-CGCCAA-----UG-GG-U--CAACA-GGUAUU-ACCGGC---UUAAGGU---UU-UACCUAAUGUGGCU-GAGA------------
BA000004.3/3340549-3340386                    CAACCACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UAUGCUGCUGCCCA-AAAACG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGUAGCU-GGCA------------
AE001437.1/789407-789580                      AAAAGUUUU-A-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UACGCUACUGCCCA-GAAACA-UCGAGAGA-UGCCAAA---UUG-GG-U--CAGCA-GAUAUU-ACCGAA---UCAAGGU---UC-UAUCUAAUGUAGCUGGAUUUA----------
CP000479.1/3338383-3338199                    UAAGCACCU-C-GUUA-GG-U-GAGGCG-UCUACA-C-GA-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAAAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCCU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCGGCUCGGA-----
AE001437.1/3501846-3501683                    AUAAUGUAU-U-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UAUGCUACUGCCCA-AAAAUA-UCGAAAGA-UGCCAA-----UG-GG-U--UAACA-GGUACU-ACCGAA---UUAAGGU---UU-UACUUAAUGUAGCU-GGGA------------
AAJM01000138.1/1999-1823                      UGCUGAACC-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGG---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUGAUG--------
AE016830.1/1027779-1027612                    AUAGAAUCA-U-AUUA-GG-U-GAGGUU-ACUCUGAA-GA-AC----------A-----------------------------CAGGUUAUCGCUCG-GAAAUG-UCGAGAGA-CAGUAA-----CG-AG-U-AAAGCA-GGGAUU-GUCGAA---UUAAGGC----U-UUCCUAAGAUAACU-AGAA------------
AE016830.1/1323290-1323457                    CUGAAUAAU-U-GUUA-GG-U-GAGGCU-CCUAUU-U-GG-AC----------A-----------------------------AAUGCUGCUGCCGC-GAAAGGAUCGAGAGACCCUUAG-----UU-GG-U-UGAACA-GGAAUA-AUCG-----UGAAGGU---UA-UUCAUAAUGUAGCU-GAUA------------
CP000325.1/3411572-3411396                    CAAGCACUU-C-GCUA-GG-U-GAGGCG-UCUGGA-C-GG-AU----------A-----------------------------CAGGCCACUGACCU-CGAACG-UCGAAAGA-CGCCAC----CGG-GU-C-AGGACA-GCUCUU-CCCGGC---UUAAGGG---UU-GAGCCCAAGUGGCU-UCCGGCU---------
CP000721.1/3911114-3911286                    UAAAAACUU-U-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------CAUGCUGCUGCCCG-GAAACG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGUAUU-GCCGGA---UUAAGGU---UC-UACUUAAUGUAGCC-GAAAAC----------
AE017333.1/1420164-1420328                    ACAGCUCUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAU---CUAAGGU---GA-UUUUUAAUGCAGCU-GGCA------------
CP000698.1/2388949-2388777                    GUAAUUCCU-C-GUUA-GG-AAGAGGCG-UUUGCA-C-AA-AC----------A-----------------------------AAAGCUACUGCCCA-GAAACG-UCGAAAGA-CGCCAA-----UGCGG-U-AGACCA-GGUUUA-GUCGGA---UUAAGGC---UU-UAUCUAAUGUAGCU-GGUUGU----------
CP000686.1/5712317-5712483                    GUUGCUCCC-U-GGUA-GG-C-GCGGCU-U-CACA-C-AA-AC----------A-----------------------------CAGGUUACUGCUCC-GGCCCG-UCGAAAGA-CGCUCA-----GG-GG-C--GCACA-GCAGG--CUCGGC---UUAAGGG---CU-UUGCCAAGGUAACU-ACGG------------
CP000416.1/93409-93243                        AAUAGAAGC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-GG-A-----------A-----------------------------AAUGCUACUGCUCA-GAAACG-UCGAGAAA-CGCCAA-----UG-AG-U--CAGCU-GUUCAG-GUCAAU---CGAAGGC---CU-GAUCUAACGUAGCU-GUUA------------
CP000612.1/2523319-2523491                    CAUUUUCUU-C-GUUA-GG-U-GAGGCU-UCUACA-U-AG-AC----------A-----------------------------GAUGCCACUGCCCG-GAAAUG-UCGAGAGA-CUCUAA-----CG-GG-U--UAACA-GGUAUU-ACCGGA---UUAAGGU---UU-UACCUAAUGUGGCU-GGGACA----------
CP000478.1/2034435-2034257                    UCGAUCCUC-A-GGUA-GG-U-GAGGCU-CCCGUG-UGAC-AC----------A-----------------------------CAGGCCGCUGCCCA-GAAGUA-UCCAAAGA-UACGGCGCAACAG-GG-U-AGAACA-GGCACU-CCCGGA---UUAAGGG---UU-UGCCUAAGGCGGCU-GAGGC-----------
CP000478.1/2956592-2956762                    AAAAUUCCU-C-GUUA-GC-AUGAGGCG-UUUGCA-C-AA-AC----------A-----------------------------CAGGCUGCUGCCCA-GAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGACAA-GGUAUG-GUCGGC---AUAAGGC---UU-UACCCGAGGUAGCU-GGUUC-----------
AACY022501423.1/463-646                       UACCGAUCU-C-GUUAUGG-C-GAGGCU-CCUGUA-C-AA-AU----------A-----------------------------CAAGUUACCGCCCUGCUGGUA-UCGAGAGA-GACCACU---CAG-GG-A-AAUACA-GGCAUCCAUCGAA---UCAAGGU---GU-UGCC-AAGGUAACU-UCUGACGAUU------
AP008232.1/1074084-1073916                    GCAGUAUCU-C-GUUU-GG-C-GAGGCU-CCUAUA-C-AA-AU----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-GU-U-AGGACA-GGCUUU-AUCGGA---UUAAGGU---UU-AGCCCAAAGUAACU-UCUG------------
AB271060.1/1350-1503                          AUGAAAAAU-C-GGUA-GG-U-GAGGCU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUGACUACCGCAAAGUAG-UGGAGACA-CUAUGC-----GC-UG-G-UUAGCA-GUUGAG-AUCG-----CUAAGGU---UU-UGACUAAUGUCAUU-----------------
AE016825.1/3525127-3525291                    GCAGUGUCU-C-GUUC-GG-C-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGUCACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-GU-U-AGGACA-GGCUUU-AUCGGA---UUAAGGU---UU-AGCCCAAAGUGACU-UCCA------------
AE016830.1/1268265-1268435                    AAUAAGAUU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U-AGAACA-GGAACU-GUCGAA---UGAAGGC---UU-UUCUUAAGGUAGCU-AAAA------------
AAJM01000138.1/2313-2480                      AAUAAUCUU-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAACG-GUCGGA---UUAAGGC---CC-UUCUUAAUGUAGCU-GGUU------------
AARF01000550.1/280-107                        AGAUAUCCU-C-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------AAAGCCACUGCCCG-GAAAUA-UCGAGAGA-UACCUA-----CG-GG-U-AGAACA-GAAAUU-GUCGGA---UUAAGGC---UU-UUUCUAAGGUGGCU-AAGAGAU---------
CP000804.1/127786-127952                      GUUGCUCCC-U-GGUA-GG-C-GCGGCU-U-CACG-C-AA-AC----------A-----------------------------CAGGUUACUGCUCC-GGCCCG-UCGAAAGA-CGCUCA-----GG-GG-C--GCACA-GCAGG--CUCGGC---UUAAGGG---CU-UUGCCAAAGUAACU-GCGG------------
AE008691.1/2398115-2397950                    UUAAUACCU-C-GUUA-GG-U-GAGGCU-CCUAUA-C-AG-AU----------A-----------------------------CAGGCUGCUGCCCG-GAAACA-UCGAGAGA-UGGUAA-----CG-GG-U--GAACA-GGCAUU-ACCGAA---UCAAGGU---UU-UGCCUAAUGCAGCU-GGAG------------
AJ002571.1/47742-47907                        UAGGAACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGCAGCU-GGAU------------
CP001175.1/2843327-2843491                    AGUUUUGCC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCCACUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGGAUU-GUCGGA---UUAAGGC---UU-UCCAUAAUGUGGCU-AAGA------------
CP001124.1/3732610-3732441                    ACUGUUCCU-C-GUUA-GC-AUGAGGCG-UUUGCA-C-AA-AC----------A-----------------------------GAGGCUACUGCCCA-AAAACG-UCGAAAGA-CGCCAA-----UG-GG-U-AGACCA-GGGCUU-GCCGGA---UUAAGGC---UU-GACCUAAGGUAGCU-GGUU------------
AE005176.1/1288920-1288763                    -CAUAGCCG-UCGGUA-GG-U-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------CGGGUUGCUGCCGC-AGAGUCGUGGAGACACGAUGAG-----AG-GG-C--CAACA-GUUCAC-GUCGAAA-AACAAGGC---GU-GAAAUAGUGCAACA-----------------
CP000962.1/3124853-3124692                    AAUAAACCU-C-GGUA-GG-U-GAGGUU-ACUACA-A-GG-AU----------A-----------------------------CGGGUUGUUGCCGUAAAAGAA-UGGAAACA-UUCUUA-----AC-UG-G-UUAGCA-GGUUUU-GCCGAACAAAGAAGGC---AU-AAUCUAAUACAGCU-----------------
CP001186.1/4113904-4114071                    UAUGGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAAG-GUCGGA--AUGAAGGC---CU-UUUUUAACGUAGCU-GGUU------------
ACOM01000001.1/624108-624271                  AAAUAAAUU-U-GUUA-GG-U-GAGGCU-CCUAUA-A-AG-AU----------A-----------------------------UAUGCCGCUACCCA-GAAAAA-UCGAGAGA-UUCCAA-----CG-GG-U--UAACA-GAAAUU-AUCG-----CAAAGGU---AA-UUUUUAAUGUGGCU-GACU------------
CP001390.1/3327040-3327209                    GAAAUUCCU-C-GUUA-GG-AAGAGGCG-UUAGCA-C-AA-AC----------A-----------------------------GAAGCUACUGCCCA-GAAACG-UCGAAAGA-CGCCAA-----UGCGG-U-AGACCA-GAUUCA-GUCGGA---UUAAGGC---UU-UAUCUAAGGUAGCU-GGUG------------
AE005176.1/907250-907410                      CUAAC-CAU-C-GGUA-GG-U-GAGGCU-ACCACA-G-GG-AU----------A-----------------------------CGGGUUGCUGCCGC-AGAGUCGUGGAGACACGAUGAG-----AG-GG-C--CAACA-GUUCAC-GUCGAAAAAAGAAGGC---GU-GAAAUAGUGCAACA-----------------
CP001124.1/511763-511594                      CGGGUUCCU-C-GUUA-CG-AUGAGGCG-UUUGCU-C-AA-AC----------A-----------------------------CAGGCUACUGCCCG-GAAACG-UCGAAAGA-CGCCAA-----CG-GG-U-AGACCA-GGUCUU-GCCGGC---UUAAGGC---UU-GACCCAAGGUAGCU-GGUC------------
CP001348.1/2365884-2365715                    CUAAAUAUU-C-GUUA-GG-U-GAGGUU-CCUAUA-C-AG-AU----------A-----------------------------AAUGCUGCUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CAACA-GGUAUU-ACCGAA---AUAAGGU---UU-UACUUAAUGUAGCU-GGAG------------
CP000885.1/3684636-3684463                    AUUAAACUU-C-GGUA-GG-U-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGAUUGCUACCGC-GAAAUAAUGGAGACACUAUUAG-----UU-GG-U--UAGCA-GGUUGU-GUCGAA---UCAAGGC---AU-AACCUAAUGCAAUU-UCAAGGC---------
CP001176.1/2412253-2412418                    AAUAAACUU-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAACG-GUCGGA---UUAAGGC---CC-UUCUUAAUGUAGCU-GGUU------------
CP000924.1/241045-241209                      UUAAUACAA-UCGUUA-GG-U-GAGGCU-CCUAUA-C-AG-AU----------A-----------------------------CACGCUGCUGCCCG-GAAACA-UCGAGAGA-UGCUAA-----CG-GG-U--CAACA-AGUAUU-ACCGAA---UUAAGGU---UU-UACUUAAUGCAGCU-GGAG------------
CP000033.3/206473-206636                      UAUAAAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GAAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAAUA-GGUGUC-GUCGAC---UUAAGGC---GA-GAUC-CAGAUAGCU-AGCA------------
ACMS01000077.1/22055-22218                    AUAAGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-AUCGAA---UUAAGGU---UU-UUCUUAACGUAGCU-GGUA------------
ACAO01000024.1/41200-41025                    AUAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAAGCUAUUGCGCA-GAAACG-UCGAAAGA-CGCCAA-----UG-UG-U-AAAACA-GGAAUU-GUCGGA---UUAAGGC---UU-UUCAUAAAAUAGCU-AAGAGAGC--------
ACLX01000114.1/2858-3034                      UUUAUAACC-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUA-UCGAAAGA-UGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUGAUG--------
CP000813.1/1287638-1287801                    AUGAGACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGCAGCU-GGAU------------
ABDP01000004.1/121407-121244                  AAUAGUGUA-C-GUUA-GG-U-GAGGCU-CCUAUA-U-AG-AU----------A-----------------------------UAUGCUACUGCCCG-GAAACA-UCGAGAGA-UGCCAA-----UG-GG-U--CACCA-GGUAUU-ACCGAA---GUAAGGU---UU-UACUUAAUGUAGCU-GGCU------------
CP000560.1/1275022-1275187                    UAAGAACUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUC-AUCGAC---AUAAGGU---GA-UUCUUAACGCAGCU-GGAU------------
ACMP01000214.1/1800-1624                      UGCUAAACC-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUAAUC--------
ACAJ01000014.1/157903-157714                  GGAUAACCU-U-GUUA-GG-U-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAAGCUAUUGCGCA-GAAACG-UCGAAAGA-CGCCAA-----UG-UG-U-AAAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCAUAAAAUAGCU-AAGAAGAAAUAAAUA-
ACND01000068.1/9860-9684                      UGCUUAACC-U-GUUA-GG-U-GAGGCU-CCUAUG-C-AA-AC----------A-----------------------------CAGGCUAUUGCCCA-AAAAUG-UCGAAAGA-CGCCAA-----UG-GG-U-AGAACA-GGAAUU-GUCGGA---UUAAGGC---UC-UUCUUAAGAUAGCU-AAGUAAUG--------
ACMV01000122.1/63091-63256                    AUAUGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------GACGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAAG-GUCGGA--AUGAAGGU---CU-UUUUUAACGUAGCU-GGUU------------
ACNO01000010.1/64597-64770                    GCAGUACCU-C-GUUA-GG-U-GAGGCU-UCUGCA-C-GA-AC----------A-----------------------------CAGGCCACUGAUCUCACGACG-UCGAGAGA-CGCCCA-----AG-GU-U-AGGACA-GAUCUC-CCCGGC---UUAAGGG---GU-GAUCCAAAGUGGCU-UCCCGG----------
ACBV01000002.1/67696-67865                    UAAGCACCU-C-GUUA-GG-U-GAGGCG-GCUACA-C-GA-AC----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAAAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCCU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCG------------
CP001034.1/3063723-3063914                    UUAUAAACU-C-GUUA-GG-U-GAGGCU-CCUGGG-U-GG-AU----------A-----------------------------UAAGCUGCUGCCCA-AAAACG-UCGAGAGA-CGCCAA-----UG-GG-U-AUAACA-GACAGU-GUCGGC---UUAAGGC----C-UGUCUAAUGCAGCU-GGUCCUCUUCUACCUU
ABJD02000101.1/1953821-1953650                GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-C-AGGACA-GGAUAU-AUCGAA---CGAAGGU---AU-AUCCCCAUGUAACU-UCCAA-----------
CP000826.1/2785644-2785471                    GCAGUAUCU-C-GUUU-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACA-UCGAGAGA-UGCCCA-----AG-GU-U-AAGACA-GGCUUU-AUCGGA---UUAAGGU---UC-AGCCCAAGGUAACU-UCUGAU----------
CU458896.1/4831187-4831017                    UCAGCACCU-C-GCUA-GG-C-GAGGCU-CCUGCA-C-GA-AC----------A-----------------------------CAGGCCACUGAUCCGACGACG-UCGAGAGA-CGCCCA-----GG-GU-U-AGGACA-GAUCUC-CCCGGC---UUAAGGG---GU-GAUCCGAGGUGGCU-UCCC------------
ACGH01000107.1/2043-1878                      AAUAGAAGC-U-GUUA-GG-U-GAGGCU-CCUAUG-U-GA-A-----------A-----------------------------AAUGCUACUGCUCA-GAAACG-UCGAAAAA-CGCCAA-----UG-AG-U--CAGCU-GUUCUA-GUCAAA---GUAAGGC---UU-GAACUAACGUAGCU-GUUA------------
ABIN01000151.1/583-766                        UAAGCACCU-C-GUUA-GG-U-GAGGCG-UCUACA-C-GA-AU----------A-----------------------------CAGGCCACUGACCC-CGAACG-UCGAAAGA-CGCCCC-----GG-GU-C-AGGACA-GCUCCU-CCCGGC---UUAAGGG---UU-GAGCCCAGGUGGCU-UCCGGUUUGGA-----
ACGU01000110.1/97211-97378                    CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UACGCUGACGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAACG-GGAACU-GUCGAA---UUAAGGC---UU-UUCC-CAGUCAGCU-AGUU------------
ABVP01000024.1/147149-146978                  GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGAUAU-AUCGAC---CGAAGGU---AU-AUCCCCAUGUAACU-UCCAG-----------
ACLM01000103.1/132-299                        CAAAUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-AA-AU----------A-----------------------------UACGCUGACGCCCA-GCAACA-UCCAGAGA-UGCCGA-----UG-GG-U-UAAACA-GGAACU-GUCGAA---UUAAGGC---UU-UGCC-CAGUCAGCU-AGUU------------
ACEC01000025.1/21421-21256                    AAAGAACAC-C-GUUA-GG-U-GAGGUU-ACUUUA-C-GG-AU----------A-----------------------------U-GGCUAUUGCCCG-GAAAUG-UCGAGAGA-CGCCAA-----CG-GG-U--CAGUU-GACACU-AUCGAA---UCAAGGU---UU-UGUCUAAUAUAGCU-GACA------------
BABE01005974.1/721-547                        AAUAAGAUU-U-GUUA-GG-U-GAGCUU-CCUAUA-C-AA-AC----------A-----------------------------UAGGCUACUGCCCA-AAAACG-UCGAGAGA-CGCCAU-----NN-GG-U-AGA-CAGGGAAUN-GUCGAG---AUAAGGC---UU-UUCAUAAGGUAGCU-AAAAGCA---------
ACLN01000004.1/169541-169717                  AAUUUGAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AA----------A-----------------------------UAUGCUGUUGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAACA-GGGAUC-GUCGAU---UUAAGGC---CC-UCCC-CAGACAGCU-GGUUACUA--------
CP000517.1/232404-232566                      AAGUAAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GAAACA-UCUAGAGA-UGCCAA-----CG-GG-U-UAAAUA-GGUGUC-GUCGAC---UUAAGGC---GA-GAUC-CAGAUAGCU-AGCA------------
ACKR01000005.1/5717-5880                      CAAAUAAAC-U-GUUA-GG-U-GAGGCU-CCUACG-U-GA-AC----------A-----------------------------CAAGCUAUCGCCCG-GAAACA-UCCAGAGA-UGCCAA-----CG-AG-U-AAAAUA-GUUCUU-GUCGAG---AUAAGGC---GA-GAUC-CAGAUAGCU-AGCC------------
CP001364.1/587050-586882                      UUCGCUCCU-U-GGUA-GG-C-GCGGUC-UGCAUA-C-AA-AC----------A-----------------------------CAGGUUGCUGCUCC-GACCCG-UCGAAAGA-CGCUUA-----GG-GG-U--AUACA-GUAUAG-CUCGGC---UUAAGGG---UU-AUGCUAAAGCAACU-GUAG------------
CP001393.1/739372-739528                      AAGAUAUCU-C-GGUA-GG-C-GAGGCU-CCUACA-G-GG-AU----------A-----------------------------UAGGCUGCUGCCGCGAAAGAU-UGGAGACA-AUCUGA-----GC-UG-G-UGAACA-GGUUUU-GCCGAA--ACCAAGGC---AU-AACCUAAUGCAGCU-----------------
CP000910.1/746842-747026                      GCAGCACCU-C-GUUA-GG-C-GAGGCU-CCUGCG-C-GA-AC----------A-----------------------------CAGGCCACUGAUCUGACGACA-UCGAGAGA-UGCCCA-----AG-AU-C-AGGACA-GGCCGC-CUCGGC---UUAAGGG---GC-GGUCCCAAGUGGCU-UCCGGUGCCAGU----
AB385841.1/13217-13047                        CACGCACCU-C-GUUC-GG-U-GAGGCG-UCGUCA-C-GG-AC----------A-----------------------------CAGGCCACUGAUCC-CACCCG-UCGAGAGA-CGCUCC-----GG-AU-C-AGGACA-GGUCUC-CCCGGC---CCAAGGG---GU-GACUCCAAGUGGCU-GCCC------------
ACNB01000463.1/4534-4369                      AUAUGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AACGCUGCUACCCA-AAAAUG-UCGAGAUA-CGCCAA-----UC-GG-U--CAACA-GGAACG-GUCCAA---UUAAGGCCCUUC-UUCUUAAUGUAGAU-GGUU------------
ABQP01000004.1/146576-146420                  UGAGAGCGU-C-GGUA-GG-C-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-UAACAG-UGGAGACA-CUGCAC-----GC-AG-G-UCAGCA-GUUCUU-GUCGGA---UUAAGGC---AU-GAACUAACGCAACU-----------------
CP001095.1/485733-485576                      UGGGAGCGU-C-GGUA-GG-C-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-UAACAG-UGGAGACA-CUGCAC-----GC-AG-G-UCAGCA-GUUCUU-GUCGGA---UCAAGGC---AU-GAACUAACGCAAUU-----------------
CP001078.1/1435636-1435795                    UAAUAUUCU-C-GGUA-GG-U-GAGGUU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUUGCUGCCGC-AAAAUAAUGGAGACAUUAUUAG-----UU-GG-U--UAGCA-GGAUAC-GUCGAAA-AAUAAGGC---GU-AUCUUAAUGCAAUU-----------------
ACDH01000013.1/27326-27487                    AAAUAGAUC-C-GGUA-GG-U-AAGGCU-ACUACA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-AAAAUAGUGGAGACACUAUGCG-----UU-GGUU-UGAACA-GGCGAU-AUCGAA--ACCAAGGU---AU-CAUCUAAUGCAACU-----------------
ACDK01000064.1/73825-73664                    UUAAUAUUU-C-GGUA-GG-U-GAGGUU-ACCACA-A-GG-AU----------A-----------------------------AGGGUUGCUGCCGCAAAAUAG-UGGAGACA-CUAUGA----GAA-GG-U--UAGCA-GUCUAU-GUCGAA--GCCAAGGC---AU-AGACUAAUGCAAUU-----------------
CP001056.1/1473093-1473254                    UAAUAUUCU-C-GGUA-GG-U-GAGGUU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUUGCUGCCGC-AAAAUAAUGGAGACAUUAUUAG-----UU-GG-U--UAGCA-GGAUAC-GUCGAAA-AAUAAGGC---GU-AUUUUAAUGCAAUU-----------------
ABWO01000186.1/16693-16863                    AAUAAGAUU-C-GGUA-GG-U-GAGGCU-ACCACA-G-GG-AU----------UUGGAU------------------UUUCCUAAGAUUGCUGCCGCAACAACG-UGGAGACA-CGAUUC-----GC-UG-G-UUAGCA-GGAUAU-GUCGCA--GAUAAGGC---AU-AUCUUAAUGCAAUU-----------------
ACIL02000005.1/103424-103269                  GGUGCAAUU-C-GGUA-GG-U-GAGACU-ACCAUA-G-GG-AU----------A-----------------------------CGGAUGACUACCGCAAAGAAG-UGGAGACA-CUUCGC----GUU-GG-U--UAGCA-GUUGCU-GUCG-----AGAAGGC---GG-CGACUAACGUCAUU-----------------
ACKZ01000007.1/32791-32946                    AUAGUAAAU-C-GGUA-GG-U-GAGACU-ACCAUG-G-AG-AU----------A-----------------------------CGGAUGACUACCGC-AAAAUAGUGGAGACACUAUUCG-----UU-GG-U--CAGCA-GCCUCU-GUCG-----UGAAGGC---AG-AGACUAAUGUCAUU-----------------
ABFX02000002.1/189276-189122                  UAAAAGAAU-C-GGUA-GG-U-GAGACU-ACCAUA-G-GG-AU----------A-----------------------------CGGGUUGCUACCGCAAAGCA-GUGGAGACAC-UGUGC-----GC-UG-G-UCAACA-GUUCUU-GUCG-----UGAAGGC---AA-AAACUAAUGCAAUU-----------------
AAVL02000037.1/263157-262991                  CUACUUUAU-C-GGUA-GG-U-GAGGUU-ACCAUA-G-GG-AUUCGG--UUUA-AU------------------------CCUAAGAUUGCUGCCGCGAGAUUG-UGGAGACA-CAAUUA-----GU-UG-G-UUAGCA-GGAUGU-GUCG-----UUAAGGC---AU-AACCUAAUGCAAUU-----------------
ABYT01000060.1/16817-16983                    AAAGAUAUA-C-GGUA-GG-U-GAGGUU-ACCGCA-G-GG-AU----------UUGGAU-------------------UUCCUAAGAUUACUGCCGCAAAGUUG-UGGAGACA-CGACUC----GUU-GG-U--CAGCA-GGCAAA-GUCG-----CAAAGGC---UU-GGCUUAAUGUAAUU-----------------
CP000764.1/1422391-1422554                    UAAAGUCUC-U-GUUA-GG-U-GAGGCU-CCUGUA-U-AG-AG----------A-----------------------------AAUGCUACUGCCCA-AAAAUG-UCGAGAGA-CGCCAA-----UG-GG-U--CAACA-GGAAUG-AUCGAA---UUAAGGU---UU-UUCUUAAUGUAGCU-GGUA------------
CP000822.1/4527413-4527596                    UAUCGAUCU-C-GUUAUGG-C-GAGGCU-CCUGCA-C-AA-AU----------A-----------------------------UAAGUUACCGCCCUGCUGGUA-UCGAGAGA-GACCACU---CAG-GG-A-AAUACA-GGCAUCCAUCGAA---UCAAGGU---GU-UGCC-AAGGUAACU-UCUGACGAUA------
ABOU02000050.1/75054-74870                    ACAUCAUUU-C-GGUA-GG-U-GAGGUU-ACCACA-G-GG-AU----------UGGAUGAUUCGGCUUAUGUCGUUAAAUCCGAAGAUUGCUACCGCGGAAUUG-UGGAGACA-CGAUGA-----GC-UG-G-UUAGCA-GGCUGC-GUCG-----CGAAGGC---GC-AACUUAAUGCAAUU-----------------
CP001727.1/2253817-2253654                    UGCGUUCCU-C-GUUA-GG-C-GAGGCU-ACUAUA-C-GA-AC----------A-----------------------------CAAGCCACUGCCCG-GAAACG-UGGAGACA-CGCCAA-----UG-GG-U-AGAACA-GGUAUG-GCCGGC---UUAAGGC---UU-UACCUAACGUGGCU-GGGU------------
ACCI02000061.1/145679-145508                  GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGUUACUGAUCUGACGACG-UCGAGAGA-CGCCCA-----AG-AU-U-AGGACA-GGAUAU-AUCGAC---CGAAGGU---AU-AUCCCCAUGUAACU-UCCUG-----------
ABYU02000030.1/155655-155490                  GAGAAAAAU-C-GGUA-GG-U-GAGGUU-ACCACA-G-GG-AUUUGGGAGACCU-----------------------------AAGAUUGCUGCCGCAGAUUUG-UGGAGACA-CAAUGC-----GC-UG-G-UUAGCA-GGCUAU-GUCG-U---GGAAGGC---AU-AACCUAAUGCAAUU-----------------
CP001700.1/1972480-1972312                    AGGACACCU-C-GUUC-GG-U-GAGGCG-UCUUCA-C-GG-AC----------A-----------------------------AAGGCCACUGAUCC-CAUCGG-UCGAGAGA-CCCUCC-----GG-AU-C-AGGACA-GAUCUC-CUCGGC---UUAAGGG---GU-GAUCCCAAGUGGCU-GCGC------------
CP002743.1/503463-503307                      UGGGAGCGU-C-GGUA-GG-C-GAGGCU-ACCGCA-G-GG-AU----------A-----------------------------UGGGUUGCUGCCGC-UAACAG-UGGAGACA-CUGCAU-----GC-UG-G-UCAACA-GUUCUU-GUCGGA---UCAAGGC---AU-GAACUAAUGCAAUU-----------------
ACDB02000044.1/535177-535016                  UAAUAGUUC-C-GGUA-AG-U-AAGGCU-ACUAUA-G-GG-AU----------A-----------------------------UGGGUUACUGCCGCAAAAUAG-UGGAGACA-CUAUGC----GCU-GGUU-UGAACA-GGCAAC-AUCGAA--ACCAAGGU---GU-UAUCUAAUGUAACU-----------------
ABWM02000004.1/570492-570323                  CAACGAUCU-C-GUUAUGG-C-GAGGCU-CCUGUA-C-AA-AU----------A-----------------------------CACGUUAUCGCUCUGGUGGGU-UCGAGAGA-ACCGGCA---CAG-GG-U-AAAACA-GGCACU-GUCGAA---UCAAGGC---UU-UGUC-AGUAUAACU-UCCC------------
CP001720.1/1833967-1834136                    AUAAUUCCU-C-GUUA-GG-U-GAGGCU-UCUGCA-U-AGAAC----------A-----------------------------UAUGCCACUGCCCG-GAUAGG-UCGAAAGA-CCGUAA-----CG-GG-U--UAACA-GGUAUU-ACCGGA---UUAAGGU---UU-UAUCUAAUGUGGCU-GAGA------------
AL935263.2/1874649-1874486                    AUCAGUUGC-A-AUUA-GG-U-GAGGUU-ACUUUA-A-GA-AU----------A-----------------------------UAGGUUAUCGCCCA-GAAAUG-UCGAGAGA-CAGGAA-----UG-AG-U-AAAGCA-GAAUUU-GCCGAA---UUAAGGC---UC-UUUC-AAGAUAACU-AGA-------------
CP001706.1/2088420-2088246                    UAGGUGUCU-C-GUUA-GG-U-GAGGCU-CCAUCG-C-GA-AC----------A-----------------------------UAGGCCACUCAUCUGACGACA-UCGAGAGA-UGCCCA-----AG-AU-G-AGGACA-AAUCCU-CCCGGC---UUAAGGG---UU-GAUUCCAAGUGGCU-UCCUACG---------
ACCD01000002.1/42362-42531                    GCAGUAUCU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------CAGGUUACUGAUCUGACGACG-UCCAGAGA-CGCCCA-----AG-GU-U-AGGACA-GGUUAU-AUCGGA---UUAAGGU---AU-AACCCAAAGUAACU-UCUG------------
CP001739.1/2726594-2726752                    GAGAAAAAU-C-GGUA-GG-U-GAGGCU-AACAUA-A-GG-AU----------A-----------------------------AGGAUUGCUGCCGCGAAAAGA-UGGAGACA-UUUUUA-----GCAGG-UCUGAACA-GUCUGG-GUCG-A---AUAAGGC---UC-AGAAUAAUGCAAUU-----------------
ABXV02000030.1/100107-99935                   GCAGUAACU-C-GUUA-GG-C-GAGGCU-CCUAUA-C-AA-AC----------A-----------------------------UAGGUUACUGAUCUGACGACG-UCUAGAGA-CGCCCA-----AG-AU-C-AGGACA-GGAUAU-AUCGAC---CGAAGGU---AU-AUCCCCAUGUAACU-UCCUGC----------
CP001834.1/1924075-1923906                    AACUAAUCA-U-AUUA-GG-U-GAGGUU-ACUCUG-AAGA-AC----------A-----------------------------UAGGUUAUCGCUCA-AAACUG-UCGAGAGA-CAAUAA-----UG-GG-U-AAAGCA-GGACUA-GUCGAA---UCAAGGC---UU-UUCC-AAGAUAACU-AGAAA-----------
ABWG02000004.1/102839-102676                  CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------CACGCUAUCGCCCA-GGAACA-UCCAGAGA-UGCCAA-----CG-GG-U-UAAACA-GGUAUU-GUCGAG---UUAAGGC---AC-UAUC-CAGAUAGCU-AGCA------------
CP001966.1/2592315-2592145                    UCAGUACCU-C-GCUA-GG-U-GAGGCU-CCUGCG-C-GA-AC----------A-----------------------------CAGGCCACUGAUCCGACGACG-UCGAGAGA-CGCCCA-----GG-GU-U-AGGACA-GAUCCU-CCCGGA---UUAAGGG---UU-GAUCCGAAGUGGCU-UCCC------------
ACGO02000002.1/246026-245855                  CAAAUAAAC-U-GUUA-GG-U-GAGACU-CCUACG-U-GA-AC----------A-----------------------------UAUGCUGUCGCCCA-GCAACA-UCCAGAGA-UGCCAA-----CG-GG-U-CAAACA-GGGAUC-GUCGAU---AUAAGGC---CC-UCCC-CAGCCAGCU-AGUUAU----------
CP001791.1/527842-527676                      UGAAUCCCU-C-GUUA-GG-U-GAGGCU-CCUGCA-GUGG-AG----------A-----------------------------CAUGCUGAUGCCCA-ACAACG-UCCAAAGA-CGCCAA-----UG-GG-U-UGAACA-GGAACC-AUCGAC---AUAAGGU---GG-UUUUUAACGCAGCU-GAGC------------
CP002104.1/1491224-1491064                    GAGCACGGU-C-GGUA-GG-U-AAGGCU-ACCACG-G-GG-AU----------A-----------------------------CGGGUUGCUGCCGCAACACA-GUGGAGACAC-UGCAA----GUU-GG-U--CAACA-GUCGUU-GUCGAU--UUCAAGGC---UU-CGACUAAUGCAACA-----------------
ACFX02000041.1/21421-21266                    AAGAACAUU-C-GGUA-GG-U-GAGGCU-ACCACA-G-GG-AU----------A-----------------------------AGGGUUACUGCCGGUUAAAGG-UGGAGACA-CCUCUAA---UCA-GG-U--CAGCA-GUCUGU-GUCGCU---GUAAGGC---GC-AGAAUAAUGUAAUU-----------------
URS000080E29A_32630/1-161                     ---GGGCUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGCAGCU-GGAU------------
#=GR URS000080E29A_32630/1-161      2QBZ_X_SS ...((((((.(.(({..((.(...((((..(((((.(.((..............................................(((((.(((((......(.((....)).)..........)).)).)........((((((.(((.........})))...)).))))....)))))..(...............
URS000080E29A_1423/1-161                      ---GGGCUU-C-GUUA-GG-U-GAGGCU-CCUGUA-U-GG-AG----------A-----------------------------UACGCUGCUGCCCA-AAAAUG-UCCAAAGA-CGCCAA-----UG-GG-U--CAACA-GAAAUC-AUCGAC---AUAAGGU---GA-UUUUUAAUGCAGCU-GGAU------------
#=GR URS000080E29A_1423/1-161       3PDR_X_SS ...((((((.(.(({..((.(...((((..(((((.(.((..............................................(((((.(((((.....((.((....)).)).........)).)).)........((((((.(((.........})))...)).))))....)))))..((..............
#=GR URS000080E29A_1423/1-161       3PDR_A_SS ...((((((.(.(({..((.(...((((..(((((.(.((..............................................(((((.(((((......(.((....)).)..........)).)).)........((((((.(((.........})))...)).))))....)))))..((..............
#=GC SS_cons                                  ::::[[[[[.[.[[A-.[[.[.--[[[-.-[[[[[.[.[[.,,..........,.............................,,,(((((,<<<<<.----<<.<<____>>.>>----.....>>.>>.>.,,,,,,.<<<<--.<<<___...___a>>>...--.>>>>,,,,))))),.<<<_............
#=GC RF                                       aaaauaccc.c.GuUA.gG.u.GAgGCU.ccugcg.c.Gg.Au..........A.............................uAgGcugcUgCccc.aAAAcg.UcGAGAgA.cgCcaA.....gg.gG.c.agAACA.Ggucuu.guCGaa...uUAAGgc...uU.gacCUAAugcagCU.ggcu............
#=GC RNA_structural_elements                  ===[==P1=5p==]=[==========P2=5p==========]============================================[=P3]=[==================P4==================]=[J4/5]=[==============P5===============]=X[==P3=]==[===============

BX571871.1/238808-238637                      ------------GAUAAUU---CAGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGUA---GAGAUAGUCG
AY129558.1/14501-14670                        -------------GCAUG----CCGGA-----UACGUUAUACA-G-UGCUAAAGCUGGU-ACGUG---GGGAUGAUGA
BX842577.1/4252-4421                          ------------GCUUAC-----CGGA-----CACGUCGUGUG-G-UGCCGAAGCUCUG-ACGAGA--GGGGUGCGGA
X90691.1/1632-1461                            -----------AGUCUGC-----GGGA-----UACGUUGUAUA-G-UGCUAAACCGA-G-ACGU----GAGAUAGCCU
AL596173.1/245334-245167                      -------------GUAAU-----UCUU-----UACGUUGUAUA-G-UGCCAAAACUUUA-GCGAG---GGGAGUCUGU
AL035300.1/11215-11044                        -----------ACGUUGGU---CCAGA-----UAUGCUGUGCA-G-UGCCUAAGCUCCG-GCGAUG-AGGGGAUGCGU
AL591984.1/47104-46938                        -------------GUAU------UCUU-----UACGUUGCAUA-G-UGCCAAAACUUUA-GCGAG---GGGAGUCUGU
AJ250603.1/195-363                            -------------AUGUU----UUCUU-----UACGUUGUAUA-G-UGCUAAAACUCGG-ACGAUG-AGAUGAUGCUA
AB089921.1/2048-2202                          -------------UCA-----------------UUGCCUUAUG-G-AGUUAAAGCUUGA-ACG-----GUAAAUACUU
AL583922.1/170727-170556                      ----------CUCAUUGAG---CUGUA-----CAUGUCGUUUG-G-UGCCAAAGCUCUG-ACGAUA--GGGAGGCCGU
AF031552.1/1396-1226                          ------------CGUGAG-----CGAA-----UACGUUGUGCA-G-UGCUGAAGCUGGG-ACUCGG--GGAAUGAAGU
AF117609.1/346-514                            -------------AUGUU----UUCUU-----UACGUUGUAUA-G-UGCUAAAACUCGG-ACGAUG-AGAUGAUGCUA
AAFX01011285.1/689-521                        -------------GGAAUC---CGGAA-----UAAGUCAACCU-G-AACUAAAACUC-U-ACGAG---GAGCUUCAUG
AE017194.1/1660591-1660756                    -------------AUGU-------ACC-----UAUGCUAUACA-G-UGCUAAAACUC-G-GCGAGG-GAGAGGUCCGU
CP000717.1/2055847-2056021                    ----------GGACCGGC-----CGGA-----UACGCCGUGUG-G-UGCCAAAGCUCUG-ACGAGA--GGGGUGCCGA
CP000412.1/281461-281624                      -------------UGU--------GCU-----UACGUCACGUA-G-UGUUAAAGCUG-A-GCGAUU--AGUCAAUAGC
AE016822.1/2178766-2178596                    ------------CCCGGC-----GGGA-----CACGUCGCGCA-G-UGCCGAAACUCUU-ACGUG---GAAGUGCCGA
CP000416.1/2122885-2122722                    -------------UAGU-------UCU-----UACGUCUUAAA-G-UGCUAAAACUC-A-AUGAA---UGCGUCGAUA
CP000728.1/236297-236462                      -------------GUGG-------UCC-----AAAGCUAUAUA-G-UGCUAAAACUC-A-ACGAUU--GAUGUUAAAG
AASN01000027.1/80343-80511                    -------------GCUUA----CCGGA-----CAGGUCGUGUG-G-UGCGAAAGCCU-G-ACAGAA--GGGGUCGGUU
AE016830.1/3116366-3116533                    -------------GAAA------UCUU-----UACGUUGGAUA-G-UGCUAAAGCUCAG-ACGAUG--AGAACCGAUU
CP000482.1/1208117-1207951                    -------------CCAG-------GCC-----UACGUUGUGCU-C-UGCCAAAAUCC-A-ACCAGA--GGGGAAUUGG
ABDV01000005.1/84537-84695                    -----------------U-----C--------AUUGCCCAGUG-A-AGCUAAAACUUGA-ACGA----UAUUAUACUU
AARF01000169.1/465-629                        -------------UUAA-------ACC-----UAUGCUGUACA-G-UGCUAAAACUC-A-ACGAA---GGAGAGGUUA
BA000004.3/3341002-3340838                    -------------GAU--------UCC-----UAUGCCGCACA-G-UGCUAAAGCUC-U-ACGAAU--GGGGGACAGU
CP000673.1/3641499-3641330                    -----------AAAUUUA-----GUCU-----AAAGCUAUAUA-G-UGCUAAAACUCAG-ACGAU---UUAAAAGUUU
AAAK03000021.1/12650-12476                    ---------GGUAUCUGC-----UUUU-----UACGUUGUACA-G-UGUCAAAACUC-A-ACGAUG--AGAUCUGAGA
ABDQ01000001.1/467807-467647                  -----------------A-----C--------AUUGCCUUGCA-G-AGCCAAAACUUGA-ACGAG---AAAGUAUAGA
BA000004.3/2041941-2042105                    -------------UCG--------UCC-----UAUGCCGCACA-G-UGCUAAAGCUC-U-ACGAAU--GGAGGAGUUU
AAWL01000016.1/43438-43265                    ----------UUUGUUUG-----ACUC-----UACGUUAUACA-G-UGCCAAAGCUCAA-ACGAGU--GGGGAGGUUA
CP000480.1/5735476-5735649                    ----------CUCAAGGU-----GGGA-----CACGUCGUGCA-G-UGCCAAAGCUCUG-AUGAG---GAAGUGCUCG
AP009389.1/428061-428228                      -------------UCUUU-----UCCC------UAGCUGUGUAUG-UGUCAAAGCUUUG-ACGAGU--GGAGAAGGUU
CP000679.1/1386114-1386270                    -------------UUU----------------UAUGCCGUGUA-G-UGCCAAAGCUUGU-AC------GAGGUAGCUA
AE016958.1/3916507-3916677                    -------------GAGCC----CCGGA-----UACGCCGUGCA-G-UGCCGAAGCUCCG-ACGAGA--GGGGUGCGAC
CP000647.1/4212343-4212524                    --------CAUGACCGUU-----CAGA-----UACGUUAUGCA-G-UGCUAAAACCAGG-ACGUA---GGGAUCUGCC
CP000568.1/2645160-2644994                    -------------GUUGC-----AGCC-----UAAGCUGUAUA-G-UGCCAAAGCUC-A-ACGAGG-GAAAGAUAUAA
AE017198.1/1073421-1073588                    -------------GAAAA-----AACU----UUACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUUAAAU
CP000413.1/234944-235115                      -------------AUUUUUAAUAACCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAAA
AE016958.1/1663674-1663849                    ---------UUUGACGGC-----CGGA-----UACGCCGUGUG-G-UGCCGAAGCUCUG-ACGAGA--GGGGUGCCGC
CP000325.1/5326076-5325906                    -------------GAUAGU---CCGGA-----UACGCCGUGCA-G-UGCCGAAGCUCCC-ACGAGA--GGGGUGCGUU
AE016830.1/1024864-1024697                    -------------GUGA------UCUU-----UACGUUGUAUA-G-UGCUAAAGCUC-A-ACGUUC--AUGUUGAUGU
CP000724.1/3301490-3301319                    ----------AUUACUUG-----AAUC-----UACGUCAUUUA-G-UGCUAAAACCAGU-ACGAG---GAGUUAAUAG
AP006627.1/810916-810751                      -------------AUA--------GCC-----UAUGCCGCACA-G-UGCUAAAGCUC-U-ACGAAU-GGAGGCUAUUU
CP000423.1/1285762-1285925                    -------------CUCG------CUUC-----UAGG-CGUAUA-G-UGCUAAAACUA-A-ACGAUU--GGGAUGCUUU
CP000544.1/1425650-1425831                    --------GCGCCCUGCG-----CGCGGCCUUUGAGUCGCACA-G-UGCCGAAGCUC-U-ACGAAG--GGGACUUGGU
CP000141.1/329676-329842                      -------------GUUU------CCUC-----UAAGCCAGGUU-G-AGCUAAAGCUUUG-ACGAGU--GGAGAAGGUU
CP000413.1/962812-962978                      -------------AAAAA-----ACUU-----CACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAUC
AE017198.1/231904-232076                      ----------UUUUUAUA-----ACCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAAA
AAXV01000059.1/1758-1594                      -------------AAUU-------UCC-----UAUGCCGCAUA-G-UGCUAAAACUC-A-ACGUUU--GAAGGUAACA
CR936503.1/1082354-1082189                    -------------AUGG------UUUC-----UACGUCAUAUA-G-UGCUAAAACUG-A-ACGAUU--GGGAACGCCA
CP000232.1/409831-409996                      -------------AAAU------UCUC------UAGCUAUGCACG-UGCCAAAGCUC-A-ACGAGU--GGGGGUUAAU
BA000004.3/3340549-3340386                    -------------AUG--------UCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAAU--GAAGGGAAUC
AE001437.1/789407-789580                      -----------UAGUUUU-----AAUC-----UAAGCUAUAUA-G-UGCUAAAGCUC-U-ACUGUC--UAAUUUCGUA
CP000479.1/3338383-3338199                    ------UUGUCGUUCGGGC---CAGGA-----CACGUCGUGUG-G-UGUCAAAGCUCUG-ACGAGA--GGGGUGCGGA
AE001437.1/3501846-3501683                    -------------UUA--------CCC-----AAAGCUAUAUA-G-UGCUAAAGCUC-A-ACGAAA--GAUAGUGUAU
AAJM01000138.1/1999-1823                      --------AAUUUUCAUU-----ACUU-----UACGUUGUAUA-G-UGCCAAAGCUC-U-ACUAGG--GGGAAAAGCC
AE016830.1/1027779-1027612                    -------------UUUUU-----UUCU-----UACGUCUCAGA-A-AGCCAAAGCUC-A-AUUAUU--GUGAUUACCC
AE016830.1/1323290-1323457                    -------------CAUGU-----UAUC-----UACGCCCUAUA-G-UGCUAAAGCUC-A-ACGAUA--GAGAAUCUUA
CP000325.1/3411572-3411396                    ---------UGAAAGCGU-----CGGA-----UACGCCGUGUG-G-UGCCAAAGCUCUG-ACGAGA--GGGGUGCCGC
CP000721.1/3911114-3911286                    ----------CAUAUGGU-----UUUC-----UAUGCUCUAUA-G-UGCUAAAACUC-A-ACGAGU-GAAGGUUAAUA
AE017333.1/1420164-1420328                    -------------UGCU-------GCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUG--GAAGGCGUUA
CP000698.1/2388949-2388777                    -----------CAUUUUC-----GACC-----UACGUUGUGCA-C-UGCUGAAACUCAA-ACCA----GGGGAAAGUC
CP000686.1/5712317-5712483                    -------------UUCAA-----CCGU-----UACGUUGUGUG-AAAGCUUAAGAUCAA-CCGGAG--GGGGAGCGUU
CP000416.1/93409-93243                        ------------AGUGAU-----UAAC-----UACGCCGUAUA-G-UGCUAAAACUC-A-ACGACU--AGCUAGACAC
CP000612.1/2523319-2523491                    ----------UUCCCAAU-----GCCC------UAGCUAUGUAUG-UGCUAAAGCUUGU-ACGAGU--GGGGAGGCCA
CP000478.1/2034435-2034257                    ------------GAUAAGC---GUCUC----UUACGGUGCACG-G-UGCUGAAGCUUGA-ACGAG---UGGGGGAAUC
CP000478.1/2956592-2956762                    ------------UUCGAA-----AACC-----UACGUUGUGCA-C-UGCCGAAAGUC-U-ACGAGU--GGGGAAAUGA
AACY022501423.1/463-646                       -------UCACCAUCGGA-----CAGA-----UACGUUGUUCA-G-UGCUAAAACCAGG-ACGUA---GGGAUCUGCC
AP008232.1/1074084-1073916                    -------------UUGUA-----CAGA-----UACGUUGUAUA-G-UGCCAAAACCGUG-ACGUG---GAGAUAGGCU
AB271060.1/1350-1503                          -----------------U-----C--------ACUGCCCUACG-G-AGUUAAAGCUUGA-ACG-----GAACACAAGA
AE016825.1/3525127-3525291                    -------------AC---------GGA-----UACGUUGCAUA-G-UGCCAAAACCUAG-ACGCG---GAGAUCGCUU
AE016830.1/1268265-1268435                    -------------GCAAUC--GCUUUU-----UACGUUGUAUA-G-UGCUAAAGCUC-A-ACGAUA--AGAACGAUUA
AAJM01000138.1/2313-2480                      -------------AUAAA-----AACC-----UAUGCUAUACA-G-UGCUAAAACUC-A-ACGAGG-GAGUGGUAUAC
AARF01000550.1/280-107                        ----------GCUUCUAC-----UCUU-----UACGUUGUAUA-G-UGCUAAAAC-CAG-ACCAGG--GGGAACGGAC
CP000804.1/127786-127952                      -------------CGCUG-----CCGC-----UACGUUGUGUG-ACAGCUUAAGCUCAA-CCGGAG--GGGGAGUGUU
AE008691.1/2398115-2397950                    -------------UUUU------CUCC-----AAAGCUGUAUA-G-UGCCAAAGCUC-A-ACGAAG--GAAAUUGGAU
AJ002571.1/47742-47907                        -------------GCUU------GUCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GAAGGCGCCC
CP001175.1/2843327-2843491                    -------------GUAU------UCUU-----UACGUUGCAUA-G-UGCCAAAACUUUA-GCGAG---GGGAG-UCU-
CP001124.1/3732610-3732441                    -------------CUUCC----UGACC-----UACGUUGUGCA-C-UGCUGAAAACC-U-ACGAGU--GGGGAACCAC
AE005176.1/1288920-1288763                    -------------ACA-----------------UCGCCCUGCG-G-AGCUAAAGCUUGA-ACG-----AUAGCUUGUA
CP000962.1/3124853-3124692                    -----------------U-----C--------AUUGCCUUGCA-G-AGCCAAAACUUGA-ACGAGA--AAGUGUUGUU
CP001186.1/4113904-4114071                    -------------UCAG------UACC-----UAUGCUAUACA-G-UGCUAAAACUC-A-ACGAGG-GAGAGGUGCAU
ACOM01000001.1/624108-624271                  -------------AGAA------AGUC-----AAAGCUCUAUA-G-UGCUAAAGCUC-U-ACAACU--AAGUAAUUAU
CP001390.1/3327040-3327209                    -------------GUGGU----UCACC-----UACGUUGUGCU-C-UGCUAAAACUCAA-ACCA----GGGGAAAAUG
AE005176.1/907250-907410                      -------------ACA-----------------UCGCCCUGCG-G-AGCUAAAGCUUGA-ACGAUA-CUGGGUACUU-
CP001124.1/511763-511594                      ------------CCCCGG-----GACC-----UACGUUGCGCA-C-UGCCGAAAACC-U-ACGAGA--GGGGAAUCCG
CP001348.1/2365884-2365715                    -------------AUAAAG--UGGUCC-----AAAGCUGUAUA-G-UGCUAAAACUC-A-ACGAGU--GAAGGGUUUU
CP000885.1/3684636-3684463                    ---------GUCAAAUGU-----ACGC-----CAUGCCCUGCG-A-UGCUAAAGCUUGA-ACG-----GUUAAUUGCU
CP001176.1/2412253-2412418                    -------------AUAAA-----AACC-----UAUGCUAUACA-G-UGCUAAAACUC-A-ACGAG---GGAGUGGUAU
CP000924.1/241045-241209                      -------------GAUG------CUCC-----AAAGCUGUAUA-G-UGCCAAAGCUC-A-ACGA----AUUGAAAUGU
CP000033.3/206473-206636                      -------------UGU--------GCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAACGG
ACMS01000077.1/22055-22218                    -------------AUGA-------ACC-----UAUGCUAUACA-G-UGCUAAAACUC-G-ACGAG---GGAGAGGUCU
ACAO01000024.1/41200-41025                    ---------AAAUGACUU-----UCUU-----UACGUUGUAUA-G-UGCUAAAACUCGG-ACGAU---GAGAUUGCUG
ACLX01000114.1/2858-3034                      --------AAUGAUUCAU-----CCUU-----UACGUUGUAUA-G-UGCCAAAACUC-A-ACUAGG--GGGGAAUGAG
CP000813.1/1287638-1287801                    -------------UUU--------UCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GAAGGAGCAA
ABDP01000004.1/121407-121244                  -------------GUAG-------UCC-----AAAGCUAUAUA-G-UGCUAAAACUC-A-ACGAUU--G-AUGUUAAA
CP000560.1/1275022-1275187                    -------------GGCU------GUCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GGAGGCCCCG
ACMP01000214.1/1800-1624                      --------AAUUUCCAUU-----ACUU-----UACGUUGUAUA-G-UGCCAAAGCUC-U-ACUAGG--GGGAGGAAAG
ACAJ01000014.1/157903-157714                  --CUACUAAUUUGCUUCU-----UCUU-----UACGUUGUAUA-G-UGCCAAAACUCGG-ACGAU---GAGAUUGCUU
ACND01000068.1/9860-9684                      --------AAUUUUCAUU-----ACUU-----UACGUUGUAUA-G-UGCCAAAGCUC-U-ACUAGG--GGGGAAAAGC
ACMV01000122.1/63091-63256                    -------------UGA--------ACC-----UAUGCUAUACA-G-UGCUAAAGCUC-A-ACGAGG-GAGAGGUACGA
ACNO01000010.1/64597-64770                    ----------UCUUGAUC-----GGGA-----CACGUCGUGCA-G-UGCCAAAACUCGG-ACGUG---GAGGUGUUUU
ACBV01000002.1/67696-67865                    ------------GAUUAC-----CGGA-----CACGUCGUGUG-G-UGCCAAAGCUCUG-ACGAGA--GGGGUGCGGG
CP001034.1/3063723-3063914                    AUUAGAUAUUAAAUUUCG-----GAUC-----UACGUCACCCA-G-UGCCAAAGCUAAG-ACGAG---GAGUGCGUAA
ABJD02000101.1/1953821-1953650                -----------UGUAAGU-----UGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGUA---GAGAUAGCCA
CP000826.1/2785644-2785471                    ----------GAAUACAU-----CAGA-----UACGUUGUAUA-G-UGCUAAAACCUGG-ACGCG---GAGAUAGGCU
CU458896.1/4831187-4831017                    -------------GUCCA-----GGGA----UUACGUCGUGCA-G-UGCCGAAGCUCUG-ACGAGA--GAGGUGGUCG
ACGH01000107.1/2043-1878                      -------------UUGAA-----UAAC-----UACAUCACAUA-G-UGCUAAAGCUC-A-ACGACU--GGCUAAAGCU
ABIN01000151.1/583-766                        -----UUUUUUCCAGGCC-----AGGA-----CACGUCGUGUG-G-UGCCGAAGCUCUG-ACGAGA--GGGGUGCGGA
ACGU01000110.1/97211-97378                    -------------AAACA-----GACU----UCACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAAAAUCG
ABVP01000024.1/147149-146978                  -----------UAUUCAU-----CGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGUG---UAGAUAGCUU
ACLM01000103.1/132-299                        -------------GAACA-----GACU----UCACGUUACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAGAAAUC
ACEC01000025.1/21421-21256                    -------------GUUC------UGUC-----UAUGCCGUAGA-G-AGCCAAAGCUC-G-ACGAAC-AGGGGUGUGGC
BABE01005974.1/721-547                        ---------GGUAUCUGC-----UUUU-----UACGUUGUACA-G-UGUCAAAACUC-A-ACGAUG--AGAUCUGAGA
ACLN01000004.1/169541-169717                  --------ACUUUGUAGU-----AACG----UUACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUGAAUUAA
CP000517.1/232404-232566                      -------------U---------UGCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUGACAA
ACKR01000005.1/5717-5880                      -------------UGU--------GCU-----UACGUCACGUA-G-UGUCAAAACUG-A-ACGACG--AGGAAACAUC
CP001364.1/587050-586882                      -------------CGCUG-----CUAC-----UACGUUGUAUG-CGGGCUUAAGCUCAA-CCGAAG--AGGGAGCAAA
CP001393.1/739372-739528                      ----------------UU-----U--------UAUGCCGUGUA-G-UGCCAAAGCUU-GUAC------GAGGUAGCUU
CP000910.1/746842-747026                      ----AAAUAUUGCCAGCC-----CAGA-----UACGUCGCGCA-G-CGCCGAAGCUC-U-ACGUG---GGGGUGACUC
AB385841.1/13217-13047                        ------------CACCCG-----GGGC-----UACGCCGUGAC-G-UGCCAAAGCUCUG-ACGAGU-GGGGGUGAGCC
ACNB01000463.1/4534-4369                      -------------UUAA-------ACC-----UAUACUGUACA-G-UGCUAAAACUC-A-AUGA----GGGGGCUUUU
ABQP01000004.1/146576-146420                  -----------------C-----C--------ACCGCCCUGCG-A-UGCUGAAGCUUGA-ACGAU---GACACGACCA
CP001095.1/485733-485576                      -----------------C-----C--------ACCGCCCUGCG-A-UGCUGAAGCUUGA-ACGAUG--GCCGAAUCGG
CP001078.1/1435636-1435795                    -----------------U-----C--------AUUGCCCUACG-A-AGCUGAAGCUUGA-ACGAG---GAGAUAGUAA
ACDH01000013.1/27326-27487                    -----------------U-----C--------ACCGCCCUGUA-G-AGUUAAAGCUCAA-ACGGUG--GCGUAAAUCA
ACDK01000064.1/73825-73664                    -----------------U-----C--------AUCGCCUUGUG-A-AGCUGAAGCUUGU-ACGAUGAUGAAGCAGUUU
CP001056.1/1473093-1473254                    -----------------U-----C--------AUUGCCCUACG-A-AGCUGAAGCUUGA-ACGAGC-AGAUAAUAAGA
ABWO01000186.1/16693-16863                    -----------------U-----A--------UAUGCCCUGUG-A-UGCUAAAGCUUGA-ACGAUG--UUGUCACGGA
ACIL02000005.1/103424-103269                  -----------------U-----C--------AUCGCCCUAUG-A-UGUUAAAGCUUGG-ACGAU---GAAUGAGAAA
ACKZ01000007.1/32791-32946                    -----------------U-----C--------AUCGCUCCAUG-A-UGUUAAAGCUUGG-ACGAG---AAUAUAAGAA
ABFX02000002.1/189276-189122                  -----------------A-----C--------AUGGCCCUAUG-A-UGUUGAAGCUUGA-ACGA----GAUAAAGUUA
AAVL02000037.1/263157-262991                  ---------------AAU-----A--------UACGCCCUAUG-A-UGCUAAAGCUUGA-AC------GGUGAUUUUA
ABYT01000060.1/16817-16983                    -----------------U-----A--------UAUGCCCUGUG-A-UACUAAAGCUUGA-ACGGUG--AUACUAGAUU
CP000764.1/1422391-1422554                    -------------AUGU-------ACC-----UAUGCUAUACA-G-UGCUAAAGCUC-G-GCGAG---GGAGAGGUUC
CP000822.1/4527413-4527596                    -------UCACUAUCGGG-----CAGA-----UACGUUGUGCA-G-UGCUAAAACCAGG-ACGUA---GGGAUCUGCC
ABOU02000050.1/75054-74870                    -----------------U-----A--------UAUGCCCUGUG-A-UGCUAAAGCUUGA-ACGGU---GCUAUUAUUU
CP001727.1/2253817-2253654                    -------------UUU--------CCC-----UACGUCGUAUA-G-UGCCAAAGCUC-A-ACCAG---GGGGAUGUGC
ACCI02000061.1/145679-145508                  -----------CUAAGUC-----AGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGAA---GAGAUAGCUU
ABYU02000030.1/155655-155490                  -----------------U-----A--------UAUGCCCUGUG-A-UACUAAAGCUUGU-ACGU----GGCACUCAGA
CP001700.1/1972480-1972312                    -------------AGCUG-----ACGC-----UACGCCGUGAA-G-UGCCGAAGCUCUG-ACGAGA--GAGGUGGCCG
CP002743.1/503463-503307                      -----------------C-----C--------ACCGCCCUGCG-A-UGCUGAAGCUUGA-ACGAU---GGCUCGAAUC
ACDB02000044.1/535177-535016                  -----------------U-----C--------ACCGCCCUACA-G-AGUUAAAGCUCAA-ACGGUG--GUAAAAAAUA
ABWM02000004.1/570492-570323                  -------------UUGC------GGGA-----UACGGUGUACA-G-UGCUGAACCCAGG-ACGUG---GGGAUCUCUU
CP001720.1/1833967-1834136                    -------------UUUAU----GUCUC-----U-AGCUGUGCAUG-UGCCAAAACUCGU-ACGAGU--GGGGAAUGGG
AL935263.2/1874649-1874486                    -------------CUAG------UUCU-----UACGUCUUAAA-G-UGCUAAAACUC-A-AUGAA---UGCGUCGAUG
CP001706.1/2088420-2088246                    ----------UUUGGCGU-----AGGA-----CACGUCGCGGU-G-UGUCAAAGCUCUU-ACGUG---GACGCGCCAC
ACCD01000002.1/42362-42531                    -------------AGAAA----UCAGA-----UACGUUGUAUA-G-UGCUAAAACUUAG-ACACG---GAGAUAGCCA
CP001739.1/2726594-2726752                    -----------------U-----C--------AUUGCCUUAUG-A-AGUUAAAACUUGA-ACGAU---GAUUACAUUU
ABXV02000030.1/100107-99935                   -----------UUUAUUC-----AGGA-----UACGUUGUAUA-G-UGCUAAAACCGAG-ACGAA---GAGAUAGCGA
CP001834.1/1924075-1923906                    ------------UAUCAU-----UUCU-----UACGUCUCAGA-A-AGCCAAAACUCAA-AUGUC---GUGAUUAAAU
ABWG02000004.1/102839-102676                  -------------UGU--------GCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGAUU--GGUUAUAACG
CP001966.1/2592315-2592145                    ------------GGACAC-----GGGA----UCACGUCGCGCA-G-UGCCGAAGCCC-G-ACGAGA--GGGGUGCGAG
ACGO02000002.1/246026-245855                  ----------GUUAAAUA-----ACCU-----UACGUCACGUA-G-UGUUAAAACUG-A-ACGACG--AGUAUAAAAA
CP001791.1/527842-527676                      -------------GCCG-------CUC-----UAUGCCCUGCA-G-UGCUAAAGCUC-A-ACGAAU--GGAGGAAAAA
CP002104.1/1491224-1491064                    -----------------C-----C--------ACCGCCCUGCG-A-AGCUGAAGCUUGA-ACGACA-AGAUUAAGGUU
ACFX02000041.1/21421-21266                    -----------------------U--------CACGCCCUGUG-A-AGCUAAAGCUUGA-ACG-----GAUUGGAUAC
URS000080E29A_32630/1-161                     -------------GCU-U-----GUCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GAAGCCCA--
#=GR URS000080E29A_32630/1-161      2QBZ_X_SS ..........................)........)))))))).).))))...)))....))......)))))))...
URS000080E29A_1423/1-161                      -------------GCU-U-----GUCC-----UAUGCCAUACA-G-UGCUAAAGCUC-U-ACGAUU--GAAGCCCA--
#=GR URS000080E29A_1423/1-161       3PDR_X_SS .........................))........)))))))).).))))...)))....))......)))))))...
#=GR URS000080E29A_1423/1-161       3PDR_A_SS .........................))........)))))))).).))))...)))....))......)))))))...
#=GC SS_cons                                  ............._____....._>>>.....,,,,]]]]]]].].-]]]---]]]---.]]----..]]]]]]::::
#=GC RF                                       .............uuuuu.....ugcc.....UAcGcCgcgca.g.UGCcAAAaCucga.aCGAuu..gggguaauuu
#=GC RNA_structural_elements                  =======P6==================]=======[============P2=3p========]======[==P1=]===
//
