Input sequences :

>AB013372
GCGCCCGUAGCUCAAUUGGAUAGAGCGUUUGACUACGGAUCAAAAGGUUAGGGGUUCGACUCCUCUCGGGCGCG
(((((((..((((.........)))).((((((....).))))).....(((((.....)))))..))))))).
>AB013373
GCGGAAGUAGUUCAGUGGUAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCU
(((((((..((((.......)))).((((((.....)))))).....(((((.......)))))))))))).
>AE000930
GGCCCGUAGCUCAGACUGGGAGAGCGCCGCCCUUGCAAGGCGGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA
(((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))..
>AB067577
GGGCUAUUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCCCUGGUUCAAGUCCAGGAUGGCCCA
((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
>AF034440
GUUGAUGUAGCUUAACCCAAAGCAAGGCACUGAAAAUGCCUAGAUGAGUCUCCCAACUCCAUAAACA
(((.(((..((((......)))).(((((.(....))))))....((((......))))))).))).

Scores used :

base deletion (w_d) = 2
base mismatch (w_m) = 1
arc  removing (w_r) = 2
arc  breaking (w_b) = 1.5
arc  mismatch (w_am)= 1.8

Alignment : 
AB013372    GCGCCCGUAGCUCAAUUGGAUAGAGCGUUUGACUACGGAUCAAAAGGUUAGGGGUUCGACUCCUCUCGGGCGCG
AB013373    GCGGAAGUAGUUCAGU-GG-UAGAACACCACCUUGCCAAGGUGGGGGUCGCGGGUUCGAAUCCCGUCUUCCGCU
AE000930    -GGCCCGUAGCUCAGACUGGGAGAGCGCCGCCCUUGCAAGGCGGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA
AB067577    GGGCUAUUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCCCUGGUUCAAGUCCAGGAUGGCCCA
AF034440    GUUGAUGUAGCUUAACC---CAAAGCAAGGCACUGAAAAUGCCUAGAUGAGUCUCCCAACUCCAUAA----ACA
Seq         gNgcNNgUAGcUcAgNNggNuAgAgCgcNNcccUgNNaAggNNgaGgucNcggguuCaANUCCNgNNNggcNCa


AB013372    (((((((..((((.........)))).((((((....).))))).....(((((.....)))))..))))))).
AB013373    (((((((..((((...-..-..)))).((((((.....)))))).....(((((.......)))))))))))).
AE000930    -(((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))..
AB067577    ((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
AF034440    (((.(((..((((....---..)))).(((((.(....))))))....((((......))))))).)----)).
Str(50%)    ((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
Str(60%)    ((((((...((((.........)))).(((((.......))))).....(((((.......))))).)))))).
Str(70%)    ((((((...((((.........)))).(((((.......))))).......................)))))).
Str(80%)    ((((((...((((.........)))).(((((.......))))).......................)))))).
Str(90%)    .(.......((((.........)))).(((((.......)))))...........................)..
Str(100%)   .(.......((((.........)))).(((((.......)))))...........................)..
A row with stars characterizes the ambigous assignment of multiple structures to a sequence.
The consensus sequence(in blue) is successively constructed column by column. A capital letter indicates 
the full conservation of a nucleotide. A lowercase letter indicates a nucleotide conservation in at least 
50% of all sequences. The consensus structures reflect the conservation of base-pairs in per cent 
occurring in all structures.