Locus 1006

Sequence ID	X_DroMel_CAF1
Location	2,908,663 – 2,908,760
Length	97
Max. P	0.933341

overview

Window 8

Location	2,908,663 – 2,908,760
Length	97
Sequences	4
Columns	100
Reading direction	forward
Mean pairwise identity	89.00
Mean single sequence MFE	-37.17
Consensus MFE	-28.17
Energy contribution	-27.42
Covariance contribution	-0.75
Combinations/Pair	1.20
Mean z-score	-2.60
Structure conservation index	0.76
SVM decision value	1.23
SVM RNA-class probability	0.933341
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2908663 97 + 22224390
CCUUGUCCUCGUCCUAAUUUUCGUCCUGCAAAGGAG---GCGGACGCUCUGGACAUGACCAGUCGCCUGGUUGUGUUUACCUUUCCGGCUCGUUGGACAG
...(((((.((............((((....))))(---.((((.....((((((..(((((....)))))..))))))....)))).).))..))))). ( -33.90)
>DroSim_CAF1 264388 100 + 1
CCUUGUCCUCGUCCCAAUUUUCGUCCUGCGAAGGAGGAGGAGGACGCUCUGGACAUGGCCAGUCGCCUGGUUGUGUUUACCUUUCCGGCUCGUUGGACAG
...(((((.((..((..(((((.((((....)))).)))))(((.....((((((..(((((....)))))..))))))....)))))..))..))))). ( -40.50)
>DroEre_CAF1 319340 97 + 1
CCUUGUUCACGUCCUAAUUUUCCUUCUGAGAAGGAG---GAGAAUGCUCUGGACAUGACCAGUCGCCUGGUUGUGUUUACCUUUCCGGCUCGUUGGACAG
...((((((((.((..(((((((((((....)))))---))))))....((((((..(((((....)))))..)))))).......))..)).)))))). ( -37.10)
>DroYak_CAF1 303876 92 + 1
--UUGUCCUCGUCCUAAAUUUCCUCCUGAGCAGGAG---G---AUGCUCUGGACAUGGCCAGUCGCCUGGUUGUGUUUACCUUUCCGGCUCGUUGGACAG
--.(((((.((.((......(((((((....)))))---)---).....((((((..(((((....)))))..)))))).......))..))..))))). ( -37.20)
>consensus
CCUUGUCCUCGUCCUAAUUUUCCUCCUGAGAAGGAG___GAGGACGCUCUGGACAUGACCAGUCGCCUGGUUGUGUUUACCUUUCCGGCUCGUUGGACAG
...(((((...............((((....)))).......((((..(((((((..(((((....)))))..))........)))))..))))))))). (-28.17 = -27.42 +  -0.75)

alignment

secondary structure

dotplot

Window 9

Location	2,908,663 – 2,908,760
Length	97
Sequences	4
Columns	100
Reading direction	reverse
Mean pairwise identity	89.00
Mean single sequence MFE	-32.80
Consensus MFE	-22.93
Energy contribution	-23.93
Covariance contribution	1.00
Combinations/Pair	1.04
Mean z-score	-2.22
Structure conservation index	0.70
SVM decision value	0.48
SVM RNA-class probability	0.752939
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2908663 97 - 22224390
CUGUCCAACGAGCCGGAAAGGUAAACACAACCAGGCGACUGGUCAUGUCCAGAGCGUCCGC---CUCCUUUGCAGGACGAAAAUUAGGACGAGGACAAGG
.(((((.....(((.....))).......(((((....)))))..(((((.((.(((((((---.......)).)))))....)).))))).)))))... ( -33.60)
>DroSim_CAF1 264388 100 - 1
CUGUCCAACGAGCCGGAAAGGUAAACACAACCAGGCGACUGGCCAUGUCCAGAGCGUCCUCCUCCUCCUUCGCAGGACGAAAAUUGGGACGAGGACAAGG
(((..((....(((.....)))........((((....))))...))..)))...((((((.((((..((((.....))))....)))).)))))).... ( -31.90)
>DroEre_CAF1 319340 97 - 1
CUGUCCAACGAGCCGGAAAGGUAAACACAACCAGGCGACUGGUCAUGUCCAGAGCAUUCUC---CUCCUUCUCAGAAGGAAAAUUAGGACGUGAACAAGG
((.(((........))).))..........((((....))))((((((((.(((....)))---.((((((...))))))......))))))))...... ( -29.40)
>DroYak_CAF1 303876 92 - 1
CUGUCCAACGAGCCGGAAAGGUAAACACAACCAGGCGACUGGCCAUGUCCAGAGCAU---C---CUCCUGCUCAGGAGGAAAUUUAGGACGAGGACAA--
.(((((.....(((.....)))........((((....))))...(((((.(((..(---(---(((((....)))))))..))).))))).))))).-- ( -36.30)
>consensus
CUGUCCAACGAGCCGGAAAGGUAAACACAACCAGGCGACUGGCCAUGUCCAGAGCAUCCUC___CUCCUUCGCAGGACGAAAAUUAGGACGAGGACAAGG
.(((((.....(((.....)))........((((....))))...(((((.((.(((((...............)))))....)).))))).)))))... (-22.93 = -23.93 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:12 2006