Locus 5472

Sequence ID	2L_DroMel_CAF1
Location	15,615,074 – 15,615,196
Length	122
Max. P	0.999747

overview

Window 3

Location	15,615,074 – 15,615,185
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	94.79
Mean single sequence MFE	-33.35
Consensus MFE	-28.63
Energy contribution	-29.30
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.86
SVM decision value	0.41
SVM RNA-class probability	0.724884
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15615074 111 + 22407834
UAGUCAGACAUGAAUGCUG---------CGCUUUGUUGCCCUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCA
...(((....)))..((.(---------.((......)).).))...(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).))))). ( -33.70)
>DroVir_CAF1 164966 110 + 1
UAGUCAGACAUGAAUGCUG---------CGCUUUGUUGCUGUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGGCAAG-CA
...(((....))).(((((---------(((.........))))...(((((...........(((...)))((((((((..(((((........))))).))))))))))))).))-)) ( -30.90)
>DroSec_CAF1 121911 111 + 1
UAGUCAGACAUGAAUGCUG---------CGCUUUGUUGCCCUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGUCUUUACGAGCCAAGGCA
...(((....)))..((.(---------.((......)).).))...(((((.(((((((((((((....))))))......(((((........)))))......))))))).))))). ( -32.10)
>DroWil_CAF1 173741 120 + 1
UAGUCAGACAUGAAUGCUGUUGCUGCAGUGCUUUGUUGCUCUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCA
(((.((((((.((..(((((....)))))..))...)).))))))).(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).))))). ( -41.50)
>DroYak_CAF1 120202 111 + 1
UAGUCAGACAUGAAUGCUG---------AGCUUUGUUGCCCUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCA
...((((.((....)))))---------)((......))........(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).))))). ( -34.00)
>DroMoj_CAF1 161563 110 + 1
UAGUCAGACAUGAAUGCUG---------CGCUUUGUUGCUGUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAG-CA
(((((((..(..((.((..---------.))))..)..))).)))).((.((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).)))-). ( -27.90)
>consensus
UAGUCAGACAUGAAUGCUG_________CGCUUUGUUGCCCUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCA
(((((((.((....)))))..........((......))...)))).(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).))))). (-28.63 = -29.30 +   0.67)

alignment

secondary structure

dotplot

Window 4

Location	15,615,105 – 15,615,196
Length	91
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	93.10
Mean single sequence MFE	-29.25
Consensus MFE	-26.85
Energy contribution	-27.35
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.92
SVM decision value	3.99
SVM RNA-class probability	0.999747
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15615105 91 + 22407834
CUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCAA-AAGCCAAAAA-----
..(((..(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).)))))..-.)))......----- ( -30.80)
>DroVir_CAF1 164997 95 + 1
GUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGGCAAG-CAA-AAGCCAAAACCCAGC
.......((.(((((((((....(((...)))((((((((..(((((........))))).))))))))...)))))-)))-).))........... ( -27.50)
>DroPse_CAF1 177218 91 + 1
CUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCAA-AAGCCGAAUU-----
..(((..(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).)))))..-.)))......----- ( -30.80)
>DroWil_CAF1 173781 94 + 1
CUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCAAAAAGCCAAAAA---AC
..(((..(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).)))))....)))......---.. ( -30.10)
>DroMoj_CAF1 161594 95 + 1
GUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAG-CAA-AAGCCAAAACCCAGC
.......((.((((((((..((.(((...)))((((((((..(((((........))))).))))))))))..))))-)))-).))........... ( -25.50)
>DroPer_CAF1 176423 91 + 1
CUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCAA-AAGCCGAAUU-----
..(((..(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).)))))..-.)))......----- ( -30.80)
>consensus
CUGCUACGCCUUUGUUUGUAUUGCCCUCAGGGGUAAAGUUUUUAGGAUAAUAACUUCCUGCGACUUUACGAGCCAAGGCAA_AAGCCAAAAA_____
..(((..(((((.(((((((((((((....))))))((((..(((((........))))).)))).))))))).)))))....)))........... (-26.85 = -27.35 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:58 2006