# STOCKHOLM 1.0
#=GF ID SQ2397
#=GF AC RF03532
#=GF DE Cis-regulator of HTH transcription factor
#=GF AU SANGARANE V
#=GF GA 100.0
#=GF NC 95.2
#=GF TC 101.8
#=GF SE Published; PMID:23675309
#=GF SS Predicted; LocARNA;
#=GF TP Cis-reg;
#=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 SO; 0005836; regulatory_region;
#=GF RN [1]
#=GF RM 23675309
#=GF RT Genome-wide identification of regulatory RNAs in the human pathogen
#=GF RT Clostridium difficile.
#=GF RA Soutourina OA, Monot M, Boudry P, Saujet L, Pichon C, Sismeiro O, Semenova
#=GF RA E, Severinov K, Le Bouguenec C, Coppee JY, Dupuy B, Martin-Verstraete I
#=GF RL PLoS Genet. 2013;9:e1003493.
#=GF CC This element was identified by RNA deep sequencing of Clostridioides
#=GF CC difficile 630 [1] where it is located immediately upstream of an
#=GF CC uncharacterized HTH-type Transcriptional regulator. Homologues are found
#=GF CC widely across firmicutes, consistently located 5’ of transcriptional
#=GF CC regulators of similar size and sequence, which strongly supports a
#=GF CC cis-regulatory function. RNA is referred to as CD630_SQ2397 in ref [1].
#=GF CC Note: the sequence is highly conserved and shows no evidence for
#=GF CC covariation as per R-scape analysis. The proposed secondary structure is
#=GF CC therefore purely hypothetical.
#=GF WK SQ2397
#=GF SQ 57

AM180355.1/3894182-3893938     CUUUUUUACGCAUAAUACACCACCUCCAUACAUUUUACUGUUCCUGUUAUAAUAGUGACAGGUAUAGAAAAACGUAUUGUAUAGUU-GUACAGUUCCUAUUAUGC---GUAUC------AAAGA----UAAAACU--AUGCUGCUGAAACGG-AAAUAAAA-AAAA-CCGUUA-U-UUGGCAGUACACU---UUUCUUGC
FP929062.1/366277-366033       CUUUUUUACGCAUAAUACACCACCUCUGUACAUUUUACUGUUCCUGUUAUAAUAGUGACAGGUAUAGAAAAACGUAUUGUACAGUU-GUACAGUUCCUAUUAUGU---GUACC------AAAGA----UAAAACU--AUGCUGCUGAAACGG-AAAUAAAA-AAAC-CCGUUA-U-UUGGCAGUACACU---UUUCUUGC
KE992698.1/111149-110907       CUUUUUUACGCAUAAUAAACCACCUAUUUACAUUUUACUGUUCCUGUUCAAUAAGUGACAGGUAUAGAAAAACGUAUUAUAAGGUU-UUAUAGUUCCUAUUAUGC---GAUUU------AUACA----AAAAAAU--AUACUGCCAGA-CGGCAAAUAAAA-AAAA-CCGUUU-U-CUGGCAGCAUGAU---UUUCUUGC
DS264285.1/97081-96846         CUUUUUUACGCAUAUUUAAUCACCUCACUACAUUUUACUGUUCCUGUUGAUUUUCUAACAGGUAUAGAAAAACGUAUAGUAUGGUU-UGUCAGUUCCUAUUAUGC---GUAU-------AAAGG----UGAAAAU--GUACUGCCU-AGCGGCAAAUAAAA-AAAA-CCGCUA-U-C-AACAGUACCGU---UUUUGCAU
MNRE01000078.1/16408-16642     CUUUUUUACGCAUAUGUAAUCACCUCACUAUAUUUUACUGUUCCUGUUGAUUUUCUGACAGGUACAGUAAAACGUAUAGUAUGGUU-UGUCAGUUCCUAUUAUGC---GUAUA------AAAGC----AAAAA-G--GUACUGCCU-AGCGG-UAAAUAAA-AAAA-CCGUUA-U-U-AACAGUACCAU---UUUUGCGU
MNRD01000115.1/2449-2213       CUUUUUUACGCAUAUGUAAUCACCUCACUAUAUUUUACUGUUCCUGUUGAUUUUCUAACAGGUAUAGAAAAACGUAUAGUAUGGUUUGU-GAGUUCCUAUUAUGC---GUAUA------AAACC----AAAAAAG--GUACUGCCUA-GCGG-UAAAUAAA-AAAA-CCGUUA-U-U-AACAGUAUCAU---UUUUGCGU
FP929061.1/407509-407745       CUUUUUUACGCAUAUGUAAUCAUCUCAAUACAUUUUACUGUUCCUGUUGAUUUUCUGACAGGUAUAGAAAAACGUAUUAUAUGGUU-CAUCAGUUCCUA--GUGU---GUAA-------AAAGA----ACAAAAU---UACUGUU-AUACGGUAAAUAAAA-AAAA-CCGUUA---UCGGCAGUAACCU---UUUUGCAU
JXKD01000002.1/184641-184393   CCUUUUUACGCAUAAUAAACCACCUCUAUACAUUUUACUGUUCCUAUUCUGUUAGAAACAGGUAUUGAAAAACACAUCGUAAGGUU-UAUUAGUUCCUAUUAUGC---GUGCGGU--AUAAUGA----AAAAUAC--UGUUAGUUAGAA-GG-UAAUAAAA-AAAA-CCGUUA-U-CUAACAGUUCUUU---UUCUAUGC
LTFS01000184.1/14022-14259     CCUUUUUACGCAUAAUAAACCACCUAUAUAUAUUUUACUGUUCCUAUUUAAUUAGAAACAGGUAUAUAAAAACGUGCUACAUGGUU-UAUUAGUUCCUAUUAAAC---AGACU------AAAAU----ACAAAUA--AUACUACCAAAA-GG-UUAUAAAA-AAAA-CCGUAG-U-UUGGUAGUAUCCU----UUCAUGC
KE159795.1/73212-72975         CUUUUUUACGCAUAGCAAAUCACCUCACUACAUUCUAUAGUUCCUAUAGAAGAAUGAACAGGUAUGGAAAGACGUGUUAUAUAGUC-UCACAGUUCCUAUUGUGU---GUAAA------AAGGU----ACGAAUC--ACGCUGCAAAUGCGG-UUAAU-AA-AAAA-CCGUU--G-UUUACAGCUC--U---UUUUGGGA
MNRC01000346.1/5084-5321       CUUUUUUACGCAUAUGUAAUCACCUCACUACAUUUUACUGUUCCUGUUGAUUUUCUAACAGGUAUAGAAAAACGCAUAGUAUGGUU--UGUAAGUUCCUAUCUGC---GUAA-------AAGGAACAUUAAAAAA--GUGCUG-CAUUGCGGUAAAUAAAA-AAAA-CCGCU--A-UUGUCAGUAGCAU---UUUUGCAU
MNRC01000333.1/3967-4191       GUUUUAC--GCAUAAUUAAUCACCUCACUACAUUUUACUGUUCCUAAAGAAUUUGUGACAGGUACAGUAAAACGUAUUGCAAGGUU-UAUCAGUUCCUAUAAAC-----AGGU------AAAUA----ACAAUAU--AUGCUGCUUG-GCGG-UAA--AAA-AAAA-CCGUUG---UCAGCAGUAAUGC---UUUUAUAC
LGPD01000047.1/115341-115101   CUUUUUUACGCAUAAUAAACCACCUCUAUACAUUCUACUGUUCCUGUUAAACUAGAAACAGGUAUAGAAAAACGUACUAUAUGUUU-AGACAGUUCCUGUU--GC---GUUAUU----UAUACA----ACAAAAG--AUACUGCCAG-ACGG-CAAUAAAA-AAAA-UCGUUA-U-CUGGCAGUGCUCU---UUUCAUGC
GG666045.1/47521-47758         CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUACUGUUCCUAUUGAAUUAGAAACAGGUAUAGAAAAACAUGUUAUAUAGUU-UAUAGGUUCAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUAUGCUG
AFUH01000001.1/1892352-1892116 CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUACUGUUCCUAUUGAAUUAGAAACAGGUAUAGAAAAACAUGUUAUAUAGUU-UAUAGGUUCAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUA-AA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUAUGCUG
AENN01000009.1/2656-2885       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAAAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
MRAE01000009.1/40166-39937     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGC-U
LVZN01000020.1/25806-26035     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
LTBB01000003.1/122875-122646   CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
LOJO01000001.1/352240-352469   CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
LFIL01000020.1/44798-44569     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
KQ965586.1/7397-7168           CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
KQ960172.1/48023-47794         CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
KQ959663.1/149493-149264       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
KQ959572.1/20027-20256         CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
JRNL01000095.1/4174-3945       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
JH932300.1/691392-691621       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
JH932292.1/1198118-1197889     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
GL878519.1/1142950-1143179     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
FRCP01000008.1/78866-78637     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
FRAD01000012.1/90104-89875     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
FQXP01000004.1/150572-150343   CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
FR903009.1/14104-13875         CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
FQUF01000011.1/68529-68300     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
FMKA01000006.1/144830-145059   CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
AEUY02000005.1/37265-37494     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
AE009948.1/926768-926539       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
JPMD01000046.1/12052-11822     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAAAAAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
FOOE01000042.1/7895-7652       CUUUCUUACGCAUAAUAGACCACCUCUAUACAUUUUACUGUUCCUGUUGAAUUUGAAACAGGUAUAGAAAAACGUGUUAAAUAGUU-UUUCAGUUCCUAUUA-------AAUU------ACAUU----CUUAAAA--GCACUACUCA-ACUU-CAAUAA-A-AAAA-CCGUUG-U-UUGGAAAUGCUAU---UCGUGCU-
CM002129.1/64389-64161         CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUA-AA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
AM180355.1/602643-602886       CUUUCUUACGCAUAAUAGACCACCUCUAUACAUUUUACUGUUCCUGUUGAAUUUGAAACAGGUAUAGAAAAACGUGUUAAAUAGUU-UUUCAGUUCCUAUUA-------AAUU------ACAUU----CUUAAAA--GCACUACUCA-ACUU-CAAUAA-A-AAAA-CCGUUG-U-UUGGAAAUGCUAU---UCGUGCU-
CP015626.1/2262752-2262523     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
CP015626.1/346461-346232       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
CP014159.1/1490015-1490244     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
CP003025.1/1544877-1545106     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
CP000407.1/891553-891324       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
CP001850.2/553003-553232       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
GL520133.1/18718-18947         CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
GL397071.1/1628829-1628600     CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
JRMZ01000033.1/3606-3377       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
AENP01000025.1/2678-2907       CUUUUUUACGCAUAGUAGACCACCUCUAUACAUUUUAUUGUUCCUACUGAAUUAAAAACAGGUAUAGAAAAACGUGUUAUAUGGUU-UAUAGGUUUAUAUU--------UAAU------AAAAA-------------GCACUACUAA-ACGC-CAAUAAAA-AAAA-CCGUUA-U-AUGGUAGUGCUAU---UUACGCUG
CP002390.1/1250390-1250152     CUUUUUUACGCAUAAUAGACCACCUCUAUACAUUUUACUGUUCCUAUUAAAUUUGAAACAGGUAUAGAAAAACGUGUUAUAUAGUU-UGUGAGUUCCUA--AGG----UUUAU------AUAUU----AAUACAA--GCACUACUCA-ACUC-CAAUAAAA-AAAAGCCGUUG-U-UUGGUAGUGCUAU---UUGUGCU-
FQZB01000017.1/29570-29813     CUUUGUUACGCAUAUCUAAUCACCUAAGUACAAUCUACAGUUCCUAAUAAUUGUGUAACAGGUAUAGAAAAACGUAUUAUUAGGUU-UUAUAAUUCUGAUUAUG-----UAUUGU-UUGAAAA--------AAAU--AUACUGUUGU-ACGG-UAAAUAAA-AAAA-CCGCUAUU-ACAGCAGUAUCCU---UUUCUUGC
CM001240.1/6241145-6240902     CUUUGUUACGCAUAUUUAAUCACCUAAGUAUAUUCUA-GGUUCCUAAUAAUUGUGUAACAGGUAUAGAAAAACGUAUUGUUAGGUU-UUAUAAUUCUUAUUAU-----CUAUUGUCUAUAAA---------AAAU--AUACUGCUGU-GCGGUAAAUAAAA-AAAA-CCGCUA-UUGCAGCAGUAUUCU---UUUCUUGC
JXKM01000007.1/155156-155413   CUUUUUUACGCAUAAUAAACCACCUCUAUACAUUUUACUGUUCCUAUCCAAGUGGAAACAGGUAUAGAAAAACGUGUUAUGUAGUU-UGUGAGUUC-UUUUAAGAGCGCUAUU------AUGCU----UAUGAAUGUGAUAAAUCCA-AUCU-CAAAU----AGAA-AGGUCG-C-UGAUUUUAUUUACCCAUACAACUA
CP019433.1/226380-226123       CUUUUUUACGCAUAAUAAACCACCUCUAUACAUUUUACUGUUCCUAUCCAAGUGGAAACAGGUAUAGAAAAACGUGUUAUGUAGUU-UGUGAGUUC-UUUUAAGAGCGCUAUU------AUGCU----UAUGAAUGUGAUAAAUCCA-AUCU-CAAAU----AGAA-AGGUCG-C-UGAUUUUAUUUACCCAUACAACUA
CP016318.1/3851403-3851159     CUUUUUUACGCAUAAUACACCACCUCCAUACAUUUUACUGUUCCUGUUAUAAUAGUGACAGGUAUAGAAAAACGUAUUGUAUAGUU-GUACAGUUCCUAUUAUGC---GUAUC------AAAGA----UAAAACU--AUGCUGCUGAAACGG-AAAUAAAA-AAAA-CCGUUA-U-UUGGCAGUACACU---UUUCUUGC
#=GC SS_cons                   ((((--((--(-(((((,,,,,,,,,,<<<<-<<<<-<<<<-<<<<<<<<____>>>>>>>>->>>>->>>>->>>><<<<<____.>>>>>,,,,,)))))-)....-))--......)))):....:::::::..:<<<<<<<<<.<<<<.________.____.>>>>--.-.>>>>>>>>>::::...::::::::
#=GC RF                        cuUUUUuACGCAuAauaaACCACCUCuauACAUUUUAcuGUUCCUguuccAUUaggaacAGGUAUagAAAAACGUguuguccGGUU.ggacaGUUcauauUauG....gUaaU......AAaga....aaaAAau..gcaCugccag.aCGg.cAAUAAAA.AAAA.cCGuUA.U.cuggcaGugcUaU...UUucgcug

AM180355.1/3894182-3893938     GUCAAAAUCUCAUAAAU-------------CUUUCCAGACGACGGUUU-GAC------AAAAGCCGCCGUCUUUCUUUUUUCCAGAAUA
FP929062.1/366277-366033       GUCAAAAUCACAUAAGC-------------CUUUCCAGACGACGGUUU-AAU------AAAAGCCGCCGUCUUUCUUUUUUCCAGAACA
KE992698.1/111149-110907       GUCAAAAUCAGUUU--U-------------AAAUCCAGACGACGGUUU-GAA------GAAAGCCGUCGUCUUUUUGAUUGUUAAAUGA
DS264285.1/97081-96846         GUCACAA---AAUAUCU-------------UUUUCCAGAUGGCGGUUG----------AAAAGCCGCCUU-UUUCUUUUCCCAUCAAUA
MNRE01000078.1/16408-16642     GUCAAAAAAU-AUCAUU-------------ACUUCA--AUGGCGGUUU-GA--------AAAGCCGCCUU--UUCUUUUUCCACCAAUA
MNRD01000115.1/2449-2213       GUCAAAAAAUAUCAUUA-------------CU-U-CAA-UGGCGGUUU-GAU--------AAGCCGCC-UUUUUCUUUUUCCAUCAAAA
FP929061.1/407509-407745       AUCCAAA---AAUAUUU-------------CUGAUUUGAUGGCGGUCA-AGA------UAAAGCCGCCGUUUUUCUUUUUCCUCAAUUC
JXKD01000002.1/184641-184393   UUUAAAUUAACAUUAGAACC-------CCAUUUGAUUGAUGACGGUUU-GA-------AAAAGCCGUCUUCUUUCUUUUA-CGACA---
LTFS01000184.1/14022-14259     AAUAAAUUAUCA--AUU-------------ACUUUCAAACGACGGUUC----------AAGAGCCGUCGUUUUAUAUAUUUUAUAAACA
KE159795.1/73212-72975         UACGGACUUUGAUAUAU-------------UCUCUCGAACGACGGUUG----------AAAAGCCGUCGUUUUUUCUUUUUCCUCACGG
MNRC01000346.1/5084-5321       GUUAAAAAUUU---UCU-------------UUGUUUAGAUGGCGGUU--GAC------A--AGCCGCCUUUUUUCCAUCCCCGAAAA--
MNRC01000333.1/3967-4191       GUCCU-----UUUAGA------------------UAGAACGACGGUUC--AU------AC-AGCCGCCGUUUUAUUUUUGUCCAACGGU
LGPD01000047.1/115341-115101   GUUAAAAUGAUAUUC-C-------------CUUUCCAGACGACGGUUU-A--------AAUAGCCGCCGUCUUUCUUUUUAUACAGAAU
GG666045.1/47521-47758         UUAAAAUAUUGUAUCUU-------------ACUUCCAAAUGGCGGUUU-GUUGGAGGUCAAAGUCGCCAUGAAGUAUAUCACAUACAAU
AFUH01000001.1/1892352-1892116 UUAAAAUAUUGUAUCUU-------------ACUUCCAAAUGGCGGUUU-GUUGGAGGUCAAAGUCGCCAUGAAGUAUAUCACAUACAAU
AENN01000009.1/2656-2885       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
MRAE01000009.1/40166-39937     GUCAAAAUAUUGUAUAU------------UACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
LVZN01000020.1/25806-26035     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
LTBB01000003.1/122875-122646   UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
LOJO01000001.1/352240-352469   UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
LFIL01000020.1/44798-44569     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
KQ965586.1/7397-7168           UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
KQ960172.1/48023-47794         UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
KQ959663.1/149493-149264       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
KQ959572.1/20027-20256         UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
JRNL01000095.1/4174-3945       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
JH932300.1/691392-691621       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
JH932292.1/1198118-1197889     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
GL878519.1/1142950-1143179     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
FRCP01000008.1/78866-78637     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
FRAD01000012.1/90104-89875     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
FQXP01000004.1/150572-150343   UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
FR903009.1/14104-13875         UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
FQUF01000011.1/68529-68300     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
FMKA01000006.1/144830-145059   UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
AEUY02000005.1/37265-37494     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
AE009948.1/926768-926539       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
JPMD01000046.1/12052-11822     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
FOOE01000042.1/7895-7652       GUAAAAAUAUAAAUCUC-------------ACUUUCAAAUGGCGGUUU-AAUGGAGAUAAACGUCGCCAUGAGAUAUAUUACAUAUAGU
CM002129.1/64389-64161         UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
AM180355.1/602643-602886       GUAAAAAUAUAAAUCUC-------------ACUUUCAAAUGGCGGUUU-AAUGGAGAUAAACGUCGCCAUGAGAUAUAUUACAUAUAGU
CP015626.1/2262752-2262523     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
CP015626.1/346461-346232       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
CP014159.1/1490015-1490244     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
CP003025.1/1544877-1545106     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
CP000407.1/891553-891324       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
CP001850.2/553003-553232       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
GL520133.1/18718-18947         UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
GL397071.1/1628829-1628600     UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
JRMZ01000033.1/3606-3377       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
AENP01000025.1/2678-2907       UUAAAAUAUUGUAUAUU-------------ACUUCCAAAUGGCGGUUU-GUU------GGAGGUCAACGUCGCC--AUGAAGUACAUCA
CP002390.1/1250390-1250152     GUAAAAACGUAAUUCUC-------------ACUUUCAAAUGGCGGUUC-GUU------GGAGGUCGAAGUUGCC--AUGAGAUAUAUUA
FQZB01000017.1/29570-29813     GCUCA-----UUUAAAU-------------AUAGUUAUACGGCGGUUUU-GAAU-AAUUGAAGCUGUCGUAUUUUUUUCUUGAAAUUCG
CM001240.1/6241145-6240902     UCUCA-----UUUAAAU-------------AUAGCUAUACGGCGGUUUU-GAAU-AAUCAAAGCUGUCGUAUUUUUUCAAAUUCAGAAA
JXKM01000007.1/155156-155413   UAUAAAAUUUAGUUAU-GCUGCUAAAAAGUAGAUAAAAUUGGCGACUG-AAU------GGAGGUCACAGUCGCC--AUGAAAAAGAUAC
CP019433.1/226380-226123       UAUAAAAUUUAGUUAU-GCUGCUAAAAAGUAGAUAAAAUUGGCGACUG-AAU------GGAGGUCACAGUCGCC--AUGAAAAAGAUAC
CP016318.1/3851403-3851159     GUCAAAAUCUCAUAAAU-------------CUUUCCAGACGACGGUUU-GAC------AAAAGCCGCCGUCUUUCUUUUUUCCAGAAUA
#=GC SS_cons                   :::::::::::::::::.............::::::<<<<<-<<<<<<.___......__>>>>>>->>>>>:::::::::::::::::
#=GC RF                        uUaAAAuauUguuuauU.............acUUccagAcGGcGgUuu.GuU......gaaaGcCgaCgUcuuuuuuUuaacuaaAuca
//
