Locus 3250

Sequence ID	3L_DroMel_CAF1
Location	9,506,801 – 9,506,938
Length	137
Max. P	0.991775

overview

Window 4

Location	9,506,801 – 9,506,912
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-32.08
Consensus MFE	-28.42
Energy contribution	-28.62
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.29
Structure conservation index	0.89
SVM decision value	2.29
SVM RNA-class probability	0.991775
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9506801 111 + 23771897
AGGGCCACGACUGCCACGCCCACCUGCUGUUCAGGAAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAA
.((((............))))...(((.((((((((........((((........)))).((((.....)))).((((((((....)))))))).))))))))))).... ( -30.00)
>DroSec_CAF1 23275 108 + 1
AGGGC---GACUGCCACGCCCACCUGCUGUUCAGGAAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAA
.((((---(.......)))))...(((.((((((((........((((........)))).((((.....)))).((((((((....)))))))).))))))))))).... ( -33.40)
>DroSim_CAF1 25483 108 + 1
AGGGC---GACUGCCACGCCCACCUGCUGUUCAGGAAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAA
.((((---(.......)))))...(((.((((((((........((((........)))).((((.....)))).((((((((....)))))))).))))))))))).... ( -33.40)
>DroEre_CAF1 23339 108 + 1
CGGGC---GACUGCCACGCCCACCUGCUGUUCAGGAAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAA
.((((---(.......)))))...(((.((((((((........((((........)))).((((.....)))).((((((((....)))))))).))))))))))).... ( -33.50)
>DroYak_CAF1 25907 108 + 1
AGGGC---GACUGCCACGCCCACCUGCUGUUCAGCAAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAA
.((((---(.......)))))...((((....))))...((...((((........))))...)).....(((((((((((((....))))))......)))))))..... ( -30.10)
>consensus
AGGGC___GACUGCCACGCCCACCUGCUGUUCAGGAAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAA
.((((...(....)...))))...(((.((((((((........((((........)))).((((.....)))).((((((((....)))))))).))))))))))).... (-28.42 = -28.62 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	9,506,836 – 9,506,938
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	97.84
Mean single sequence MFE	-23.56
Consensus MFE	-22.46
Energy contribution	-22.70
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.95
SVM decision value	1.57
SVM RNA-class probability	0.964853
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9506836 102 + 23771897
AAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAAUGUAGGGAAACUUUUAGGACAGCAUU
((((((((.((((........))))..((((....(((((((((((((....))))))......))))))).....))))...))))))))........... ( -23.70)
>DroSec_CAF1 23307 102 + 1
AAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAAUGUAGGGAAACUUUUAGGACAGCAUU
((((((((.((((........))))..((((....(((((((((((((....))))))......))))))).....))))...))))))))........... ( -23.70)
>DroSim_CAF1 25515 102 + 1
AAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAAUGUAGGGAAACUUUUAGGACAGCAUU
((((((((.((((........))))..((((....(((((((((((((....))))))......))))))).....))))...))))))))........... ( -23.70)
>DroEre_CAF1 23371 101 + 1
AAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAAUGUAGGAAAACU-UUAGGACAACAUU
.(((((((.((((........))))..((((....(((((((((((((....))))))......))))))).....))))...)))))-))........... ( -23.00)
>DroYak_CAF1 25939 101 + 1
AAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAAUGUGGAGAAACU-UUAGGACAGCAUU
.(((((((..((((....((((.((...)).))))(((((((((((((....))))))......)))))))......))))..)))))-))........... ( -23.70)
>consensus
AAAAGUUUAGCCAUUCAACUUUGGCCAUGCAGAAGGCAUUCAACAUUUAUUCAGAUGUUGCUCUUGAAUGCAACAAUGUAGGGAAACUUUUAGGACAGCAUU
((((((((.((((........))))..((((....(((((((((((((....))))))......))))))).....))))...))))))))........... (-22.46 = -22.70 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:53:01 2006