# STOCKHOLM 1.0
#=GF ID MH_s7
#=GF AC RF02878
#=GF DE Mesorhizobail RNA 7
#=GF AU Argasinska J; 0000-0003-2678-2824
#=GF GA 221.0
#=GF NC 85.0
#=GF TC 235.5
#=GF SE Argasinska J
#=GF SS Predicted; RNAfold;
#=GF TP Gene; sRNA;
#=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; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 28943874
#=GF RT A Genome-Wide Prediction and Identification of Intergenic Small RNAs by
#=GF RT Comparative Analysis in Mesorhizobium huakuii 7653R.
#=GF RA Fuli X, Wenlong Z, Xiao W, Jing Z, Baohai H, Zhengzheng Z, Bin-Guang M,
#=GF RA Youguo L
#=GF RL Front Microbiol. 2017;8:1730.
#=GF CC Existence predicted via genome wide comparisons with 4 related strains.
#=GF CC Analysed further by deep sequencing and Northern blot under various stress
#=GF CC conditions. Expressed only under rare growth conditions: symbiosis,
#=GF CC micro-oxygen stress, and alkali stress. 
#=GF WK Mesorhizobium
#=GF SQ 3

BA000012.4/4551188-4550877         UGGUUUUCCCUGCCU-CCGCUCGCGGUCCGCUGGCAUUUGCCAGCAACCCGUCAAGCGUCAUAACAUAUACCACUUGCGGUAUAGCAACCAUCAAAGAUCGCAUUUGACAGUUAUGGCAAAAGGACGGCAACGUCAGCGCGUUCCGAGACGCAACGGUCGCCGACGAU-AAAAUCGUAUCGAUUGAAAUCAGCGGCUCGG
#=GR BA000012.4/4551188-4550877 PP ***************.******************************************************************************************************6157899999***************************************9.8888***************************
CP002447.1/6190604-6190914         UCGCUUUCCCUGCCUUCUGCUCGUGU-ACGACCGACAUCGGGGUCAGCCCGUCACGUCGCAAUACAUAUACCAACCAUGAUAUAGCAACCAUCAAAGAUCGCAUUUGACAGUUAUGGCA-AAGACCCACACCCUCCGCGCGUUCCAAGACGUGACGGUCGCCGACGAGAAAAAUCGUAUCGAUUGA-AUCAGCGUCUCGG
#=GR CP002447.1/6190604-6190914 PP 9999*****9***95499******96.899999999999********************************************************************************.******************************************************************.9************
AGSN01000165.1/5606-5295           GAUUUCGCAAUGCCG-CCAUGAGUGUCGCCUGUUCGCGUCGAAGGAUCGA-UC-UGUUUUCGAUCAUAUAUCAGUUUCGGUAUAGCAAUCAUCAAAGAUCGCAUUUGACAGUUAUGUCA-AAGGGACACACCCUUCGCGCGUCCUGGGGCGUGCCAGUCGAUGACGAGGAAAAUCGUAUCGAUUGAAAUCUGCGUCCCGG
#=GR AGSN01000165.1/5606-5295   PP ***************.**********999999999999888887777665.44.999**************************************************************.********************************************************************************
#=GC SS_cons                       :::::::::<____>.<<<<-<-<<___________________________>>>>>------>>::::::::::<<<------<<<<<--<<<<<_______>>>>>-->>>--->>-.--->>>:::::::::::<<<<<<____>>>>>>:<<<<<<----<<<______>>>--->>>>>>:::::::[<<<____
#=GC RF                            uaguUuuCccUGCCg.ccgcucGcGuuaCguuugcauuuggaagcAaCccGUCgggcuucaaagcAUAUAcCAauuccGgUAUAGcaacCAuCaaaGAUCGCAuuuGaCAguuAUGgCA.AAGggacaCAcCcUccGcgCGucCcgagaCGcgaCaguCGccGACGagaAAAAuCGUAUCGauuGAAAUCaGcGcCuCGG

BA000012.4/4551188-4550877         GGCCA--UGGGAGGAUACCGGAGAUCGAUAUGACGGCAGCAGUGCCUUGGCGCUUCUGCACGAUUGCGCGGCCCGCGACCCCC-GGGGUGCUGCGUCCAUCAACCAGGGAGAGUUAC
#=GR BA000012.4/4551188-4550877 PP *****..****************************************************************************.*********************************
CP002447.1/6190604-6190914         GGCCA--UGGGAGGAUACCGGAGAUCGAUAUGACGGCAGCGGUGCCUUGGCGCUUCUGCACGAUUGCGCGGCCCGCGACCCCC-GGGGUGCCGCGUCCAUCAAACAGGGAGAGUUAA
#=GR CP002447.1/6190604-6190914 PP *****..****************************************************************************.*********************************
AGSN01000165.1/5606-5295           GGCCGAUUGGGAGGAUACCGGAGAUCGAUA-GACGACAGCAGCGCGCUUGCGCUUCUGCUCGACUGCGCGGCCCGCGAAGCCCCGAGGUGUCGCGUCCAUCAACCAGGGAGAGUUAC
#=GR AGSN01000165.1/5606-5295   PP ******************************.*************************************************6544*********************************
#=GC SS_cons                       >>>,(..-(((----------------------(((,,<<_______>>,,<<____>>,,,,)))-----)))----)]<<<.<<<<<<_______>>>>-->>->>>::::::::
#=GC RF                            GgCCg..UGGGAGGAUACCGGAGAUCGAUAUGACggCAgcaGuGCcuucGCGCUUCUGCaCGAcuGCGCGGCCCGCGAcgCCC.GgGguGccGCGUCCauCAAcCAGGGAGAGUUAc
//
