Locus 478

Sequence ID	3R_DroMel_CAF1
Location	1,792,635 – 1,792,743
Length	108
Max. P	0.822052

overview

Window 4

Location	1,792,635 – 1,792,743
Length	108
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	80.58
Mean single sequence MFE	-28.98
Consensus MFE	-21.04
Energy contribution	-22.43
Covariance contribution	1.39
Combinations/Pair	1.06
Mean z-score	-1.75
Structure conservation index	0.73
SVM decision value	0.68
SVM RNA-class probability	0.822052
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1792635 108 + 27905053
GUGCUCCUGCGAUGACGACAGGUGAGUUCGU---UGAG-----UACCUGUACCUGGUCAAAGUCUAUAAUUAACAAAUGAUUAAUUAUGCAUGACUUUGGCGCCUUCGCUCGUUAU
.(((....)))(((((((((((((.((.(..---...)-----.))...))))))(((((((((((((((((((....).)))))))))...)))))))))........))))))) ( -31.10)
>DroPse_CAF1 92871 99 + 1
------------UGACGACAGGUGAGUCCGAGUCCGAG-----UACCUGUACUUGGUCAAAGUCUAUAAUUAACAAAUGAUUAAUUAUGCAUGACUCUGGCGCGUUCGCUCGUUAU
------------((((((...(((((..((...(((((-----((....)))))))(((.((((((((((((((....).)))))))))...)))).)))))..))))))))))). ( -27.60)
>DroSec_CAF1 103373 108 + 1
UUGCUCCUGCGAUGACGACAGGUGAGUCCGU---UGAG-----UACCUGUACCUGGUCAAAGUCUAUAAUUAACAAAUGAUUAAUUAUGCAUGACUUUGGCGCCUUCGUUCGUUAU
((((....))))((((((((((((.((.(..---...)-----.))...))))))(((((((((((((((((((....).)))))))))...)))))))))........)))))). ( -31.50)
>DroWil_CAF1 102230 88 + 1
GUGC-CCU--------GCCUGGUAU------------G-----UAC--GUACUUGGUCAAAGUCUAUAAUUAACAGAUGAUUAAUUAUGCAUGACUUUGGCGCCUUCGCUUGUUAU
((((-(..--------(((.(((((------------.-----...--))))).))).((((((((((((((((....).)))))))))...)))))))))))............. ( -23.10)
>DroAna_CAF1 93989 107 + 1
-UGUUCUUAGGAUGACGACAGGUGAGUCCGU---UGAG-----UACCUGUACCCGGUCAAAGUCUAUAAUUAACAAAUGAUUAAUUAUGCAUGACUUUGGCGCCUUCGCUCGUUAU
-.........((((((((((((((..((...---.)).-----))))))).....(((((((((((((((((((....).)))))))))...))))))))).....)).))))).. ( -29.00)
>DroPer_CAF1 95455 104 + 1
------------UGACGACAGGUGAGUCCGAGUCGGAGUCCUGUACCUGUACUUGGUCAAAGUCUAUAAUUAACAAAUGAUUAAUUAUGCAUGACUCUGGCGCGUUCGCUCGUUAU
------------((((((...(((((..((.(((((((((.((((((.......)))........(((((((((....).))))))))))).))))))))).))))))))))))). ( -31.60)
>consensus
_UGC_CCU____UGACGACAGGUGAGUCCGU___UGAG_____UACCUGUACCUGGUCAAAGUCUAUAAUUAACAAAUGAUUAAUUAUGCAUGACUUUGGCGCCUUCGCUCGUUAU
............((((((((((((....(........).....))))))).....(((((((((((((((((((....).)))))))))...))))))))).........))))). (-21.04 = -22.43 +   1.39)

alignment

secondary structure

dotplot

Window 5

Location	1,792,635 – 1,792,743
Length	108
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	80.58
Mean single sequence MFE	-24.55
Consensus MFE	-16.22
Energy contribution	-17.17
Covariance contribution	0.95
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.66
SVM decision value	0.10
SVM RNA-class probability	0.585253
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1792635 108 - 27905053
AUAACGAGCGAAGGCGCCAAAGUCAUGCAUAAUUAAUCAUUUGUUAAUUAUAGACUUUGACCAGGUACAGGUA-----CUCA---ACGAACUCACCUGUCGUCAUCGCAGGAGCAC
.......((((.((((.(((((((....(((((((((.....))))))))).)))))))..(((((...(((.-----(...---..).))).))))).)))).))))........ ( -28.10)
>DroPse_CAF1 92871 99 - 1
AUAACGAGCGAACGCGCCAGAGUCAUGCAUAAUUAAUCAUUUGUUAAUUAUAGACUUUGACCAAGUACAGGUA-----CUCGGACUCGGACUCACCUGUCGUCA------------
....((((.........(((((((....(((((((((.....))))))))).))))))).((.((((....))-----)).)).))))(((......)))....------------ ( -24.60)
>DroSec_CAF1 103373 108 - 1
AUAACGAACGAAGGCGCCAAAGUCAUGCAUAAUUAAUCAUUUGUUAAUUAUAGACUUUGACCAGGUACAGGUA-----CUCA---ACGGACUCACCUGUCGUCAUCGCAGGAGCAA
........(((.((((.(((((((....(((((((((.....))))))))).))))))).......((((((.-----.((.---...))...)))))))))).)))......... ( -24.40)
>DroWil_CAF1 102230 88 - 1
AUAACAAGCGAAGGCGCCAAAGUCAUGCAUAAUUAAUCAUCUGUUAAUUAUAGACUUUGACCAAGUAC--GUA-----C------------AUACCAGGC--------AGG-GCAC
.......((....))(((((((((....(((((((((.....))))))))).))))))(.((..(((.--...-----.------------.)))..)))--------..)-)).. ( -19.50)
>DroAna_CAF1 93989 107 - 1
AUAACGAGCGAAGGCGCCAAAGUCAUGCAUAAUUAAUCAUUUGUUAAUUAUAGACUUUGACCGGGUACAGGUA-----CUCA---ACGGACUCACCUGUCGUCAUCCUAAGAACA-
.......((....))..(((((((....(((((((((.....))))))))).)))))))...((((((((((.-----.((.---...))...))))))....))))........- ( -24.60)
>DroPer_CAF1 95455 104 - 1
AUAACGAGCGAACGCGCCAGAGUCAUGCAUAAUUAAUCAUUUGUUAAUUAUAGACUUUGACCAAGUACAGGUACAGGACUCCGACUCGGACUCACCUGUCGUCA------------
...(((((((....)))(((((((....(((((((((.....))))))))).)))))))........(((((....((.((((...)))).)))))))))))..------------ ( -26.10)
>consensus
AUAACGAGCGAAGGCGCCAAAGUCAUGCAUAAUUAAUCAUUUGUUAAUUAUAGACUUUGACCAAGUACAGGUA_____CUCA___ACGGACUCACCUGUCGUCA____AGG_GCA_
...((((((....))..(((((((....(((((((((.....))))))))).)))))))........(((((.....................))))))))).............. (-16.22 = -17.17 +   0.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:12 2006