Locus 3552

Sequence ID	2L_DroMel_CAF1
Location	10,353,626 – 10,353,784
Length	158
Max. P	0.583184

overview

Window 2

Location	10,353,626 – 10,353,744
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.94
Mean single sequence MFE	-31.30
Consensus MFE	-19.84
Energy contribution	-21.09
Covariance contribution	1.25
Combinations/Pair	1.10
Mean z-score	-2.50
Structure conservation index	0.63
SVM decision value	0.04
SVM RNA-class probability	0.553246
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10353626 118 + 22407834
UCCAUUAUCCUUGGCUUGGGUAAACAAAUAAAUGCCGUUGCUUUUUU--AUGCGUUCGAGCAUAAGUUGCUGUAACGAAACUAAGCUGCCGACUAUUUUAUAGUCAACACCAAUGGCAUU
....((((((.......)))))).......(((((((((((((....--...((((..((((.....))))..)))).....))))....((((((...))))))......))))))))) ( -31.40)
>DroSim_CAF1 6325 118 + 1
UCCAUUAUCCUUGGCUUGGGUAAACAAAUAAAUGCCGCUGCUUUUUU--AUGCGUUCGAGCAUAAGUUGCUGUAACGAAACUAAGCUGCCGACUAUUUUAUAGUCAACACCAAUGGCAAU
....((((((.......)))))).........((((((.((((....--...((((..((((.....))))..)))).....)))).)).((((((...)))))).........)))).. ( -30.60)
>DroYak_CAF1 6341 118 + 1
UCCAUUAUCCUUGGCUUGGGUAAAUAAAUAAAUGCCGCUGCUUUUUU--AUGCGUUCGAGCAUAAGUUGCUGUAAGGAAACUAAGCUGCCGACUAUUUUAUAGUCAACACCAAUGGCAUU
....((((((.......)))))).......((((((((.((((.(((--((((......)))))))........((....)))))).)).((((((...)))))).........)))))) ( -32.30)
>DroAna_CAF1 6014 118 + 1
UCCAUA--CUUUUGCUAAAAUAAAUAAAUAAUCGCGGCAGAUUUUUUCGCUGCGUUGGAGCAUAAGUUGCUGUAACGGAACUUAGUUGCCGACUAUUUUAUAGUCAACACCAAUAGCAUU
......--....(((((...............((((((.((.....))))))))((((((((.....))))(((((........))))).((((((...))))))....))))))))).. ( -30.90)
>consensus
UCCAUUAUCCUUGGCUUGGGUAAACAAAUAAAUGCCGCUGCUUUUUU__AUGCGUUCGAGCAUAAGUUGCUGUAACGAAACUAAGCUGCCGACUAUUUUAUAGUCAACACCAAUGGCAUU
....((((((.......))))))..........(((((.((((.........((((..((((.....))))..)))).....)))).)).((((((...)))))).........)))... (-19.84 = -21.09 +   1.25)

alignment

secondary structure

dotplot

Window 3

Location	10,353,626 – 10,353,744
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.94
Mean single sequence MFE	-29.09
Consensus MFE	-20.24
Energy contribution	-20.55
Covariance contribution	0.31
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.70
SVM decision value	0.09
SVM RNA-class probability	0.577891
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10353626 118 - 22407834
AAUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCGUUACAGCAACUUAUGCUCGAACGCAU--AAAAAAGCAACGGCAUUUAUUUGUUUACCCAAGCCAAGGAUAAUGGA
((((((.....((((((((((...))))))))))((((..((.((((..((((.....))))..))))...--))..))))...))))))...........(((..(....)....))). ( -29.30)
>DroSim_CAF1 6325 118 - 1
AUUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCGUUACAGCAACUUAUGCUCGAACGCAU--AAAAAAGCAGCGGCAUUUAUUUGUUUACCCAAGCCAAGGAUAAUGGA
....((((((.((((((((((...)))))))))).(((.((((.(.((.(((((...((((.((...((..--......))..))))))....))))))).).)))).)))..)))))). ( -28.50)
>DroYak_CAF1 6341 118 - 1
AAUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCCUUACAGCAACUUAUGCUCGAACGCAU--AAAAAAGCAGCGGCAUUUAUUUAUUUACCCAAGCCAAGGAUAAUGGA
....((((((.((((((((((...)))))))))).)......(((((...((...((((((......))))--))....))...(((..................)))))))).))))). ( -30.77)
>DroAna_CAF1 6014 118 - 1
AAUGCUAUUGGUGUUGACUAUAAAAUAGUCGGCAACUAAGUUCCGUUACAGCAACUUAUGCUCCAACGCAGCGAAAAAAUCUGCCGCGAUUAUUUAUUUAUUUUAGCAAAAG--UAUGGA
..(((((((((((((((((((...))))))))))..((((((.(......).))))))....))))(((.(((........))).)))...............)))))....--...... ( -27.80)
>consensus
AAUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCGUUACAGCAACUUAUGCUCGAACGCAU__AAAAAAGCAGCGGCAUUUAUUUAUUUACCCAAGCCAAGGAUAAUGGA
..((((...(.((((((((((...)))))))))).).......((((..((((.....))))..))))................))))................................ (-20.24 = -20.55 +   0.31)

alignment

secondary structure

dotplot

Window 4

Location	10,353,666 – 10,353,784
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.12
Mean single sequence MFE	-33.23
Consensus MFE	-26.12
Energy contribution	-26.62
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.93
Structure conservation index	0.79
SVM decision value	0.10
SVM RNA-class probability	0.583184
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10353666 118 - 22407834
CGCAGCAAUAAAGAGCCAACUGAGGUGAUUAGGCACGCCGAAUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCGUUACAGCAACUUAUGCUCGAACGCAU--AAAAAAG
.((.((........))....(((.(.((((((((..(((((......)))))(((((((((...))))))))).)))))))).).)))..))...((((((......))))--))..... ( -31.40)
>DroSim_CAF1 6365 118 - 1
CGCAGCAAUAAAGAGCCAACUGAGGUGAUUAGGCACGCCGAUUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCGUUACAGCAACUUAUGCUCGAACGCAU--AAAAAAG
.((.((........)).((((((((..(((.((....)))))..))...(.((((((((((...)))))))))).)))))))........))...((((((......))))--))..... ( -32.20)
>DroYak_CAF1 6381 118 - 1
CGCAGCAAUAAAGAGCCAACUGAGGUGAUUAGGCACGCCGAAUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCCUUACAGCAACUUAUGCUCGAACGCAU--AAAAAAG
.((.((........))....(((((.((((((((..(((((......)))))(((((((((...))))))))).)))))))).)))))..))...((((((......))))--))..... ( -35.80)
>DroAna_CAF1 6052 120 - 1
CGCAGCGAUAAAGAGCCAAGUGAAGUGAUUAGGCACGCCGAAUGCUAUUGGUGUUGACUAUAAAAUAGUCGGCAACUAAGUUCCGUUACAGCAACUUAUGCUCCAACGCAGCGAAAAAAU
(((.(((.....((((.(((((..(((((..((.(((((((......)))))(((((((((...)))))))))......)).)))))))..).))))..))))...))).)))....... ( -33.50)
>consensus
CGCAGCAAUAAAGAGCCAACUGAGGUGAUUAGGCACGCCGAAUGCCAUUGGUGUUGACUAUAAAAUAGUCGGCAGCUUAGUUUCGUUACAGCAACUUAUGCUCGAACGCAU__AAAAAAG
....((......((((....((..(((((.((((..(((((......)))))(((((((((...)))))))))......)))).)))))..))......))))....))........... (-26.12 = -26.62 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:22 2006