Your Settings:
Query File: firstRNA.struct
Subject File: secondRNA.struct
Dissimilarity Threshold: 0.1
#====================== Query RNA ======================#
>firstRNA	
1   UGAAAAAAAAUAUAAUAUAAUUACGUGUCCCCGCGAAACCCCCGCCGCGG 50
    .(((....(((........))).((((....)))).((((........))
51  UUAAGGUUGUUACCAAAAUUC 71
    ))..(((....)))....)))

#===================== Subject RNA =====================#
>secondRNA	
1   UGAAAAAAAAUAUAAUAUAAUUAAAACCCCCGCCGCGGUUAAAAAAUUC 49
    .(((....(((........)))..((((........))))......)))

#################### Common Patterns (1) ###################
#=============== Pattern Found in Query RNA ===============#
>firstRNA 
1                                                           
U   G   A   A   A   A   A   A   A   A   U   A   U   A   A   
.   (   (   (   .   .   .   .   (   (   (   .   .   .   .   
                            23  36                          
U   A   U   A   A   U   U   A   A   A   A   C   C   C   C   
.   .   .   .   )   )   )   .   .   (   (   (   (   .   .   
                                            54  65          
C   G   C   C   G   C   G   G   U   U   A   A   A   A   A   
.   .   .   .   .   .   )   )   )   )   .   .   .   .   .   
            71 
A   U   U   C   
.   )   )   )   

#============== Pattern Found in Subject RNA ==============#
>secondRNA 
1                                                           
U   G   A   A   A   A   A   A   A   A   U   A   U   A   A   
.   (   (   (   .   .   .   .   (   (   (   .   .   .   .   
                                                            
U   A   U   A   A   U   U   A   A   A   A   C   C   C   C   
.   .   .   .   )   )   )   .   .   (   (   (   (   .   .   
                                                            
C   G   C   C   G   C   G   G   U   U   A   A   A   A   A   
.   .   .   .   .   .   )   )   )   )   .   .   .   .   .   
            49 
A   U   U   C   
.   )   )   )