Locus 4863

Sequence ID	X_DroMel_CAF1
Location	12,647,543 – 12,647,673
Length	130
Max. P	0.874274

overview

Window 0

Location	12,647,543 – 12,647,637
Length	94
Sequences	5
Columns	97
Reading direction	forward
Mean pairwise identity	91.49
Mean single sequence MFE	-24.54
Consensus MFE	-24.24
Energy contribution	-24.08
Covariance contribution	-0.16
Combinations/Pair	1.12
Mean z-score	-1.18
Structure conservation index	0.99
SVM decision value	0.59
SVM RNA-class probability	0.791993
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12647543 94 + 22224390
UUCAGAGUGAUUUCGGAAUUGCUUCCCUUCCAUUGGACGACAAAGGAGAGUUCCCAUCAAAGGACAUUCCUGGCC---GGCCCCUUUCAUUUGUCGU
....(((..(((....)))..))).((.......))((((((((.(((((...((.....(((.....)))....---))...))))).)))))))) ( -23.90)
>DroSec_CAF1 1431 94 + 1
UCCAGAGUGAUUUCGGAAUUGCUUCCCUUCCAUCGGACGACAAAGGAGAGUCCCCAUCUUAGGACAUUCCUGGCC---GACCCCUUUCAUUUGUCGC
(((.(((....)))((((.........))))...)))(((((((((((.((((........)))).)))))((..---....))......)))))). ( -23.70)
>DroSim_CAF1 3290 94 + 1
UCCAGAGUGAUUUCGGAAUUGCUUCCCUUCCAUCGGACGACAAAGGAGAGUCCCCAUCAAAGGACAUUCCUGGCC---GGCCCCUUUCAUUUGUCGC
(((.(((....)))((((.........))))...)))(((((((((((.((((........)))).)))))((..---..))........)))))). ( -24.80)
>DroEre_CAF1 1471 94 + 1
UUCAGAGUGAUUUCCGAAUUGCUUCCUUCCCAUCGGACGACAAAGGAAAGUCCCCAUCAAAGGACAUUCCUGGCC---GGCCCCUUUCAUUUGUCCU
....(((..(((....)))..)))..........((((((...(((((.((((........)))).)))))((..---..))........)))))). ( -24.10)
>DroYak_CAF1 3831 97 + 1
UCCAGAGUGAUUUCAGAAUUGCUUCCUUCCCAUCGAACGACAAAGGAAAGUCCCCAUCAAAGGACAUUCUUGGCCAUGGGCCCCUUUCAUUUGUCGU
....(((..(((....)))..)))............((((((((.((((((((........))))......((((...))))..)))).)))))))) ( -26.20)
>consensus
UCCAGAGUGAUUUCGGAAUUGCUUCCCUUCCAUCGGACGACAAAGGAGAGUCCCCAUCAAAGGACAUUCCUGGCC___GGCCCCUUUCAUUUGUCGU
....(((..(((....)))..))).............(((((((((((.((((........)))).)))))((((...))))........)))))). (-24.24 = -24.08 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	12,647,580 – 12,647,673
Length	93
Sequences	5
Columns	100
Reading direction	forward
Mean pairwise identity	87.16
Mean single sequence MFE	-27.91
Consensus MFE	-23.48
Energy contribution	-23.36
Covariance contribution	-0.12
Combinations/Pair	1.17
Mean z-score	-1.77
Structure conservation index	0.84
SVM decision value	0.88
SVM RNA-class probability	0.874274
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12647580 93 + 22224390
CGACAAAGGAGAGUUCCCAUCAAAGGACAUUCCUGGCC---GGCCCCUUUCAUUUGUCGUAUUUCCAAUUUCGAGGGCCAGUCCAGGUCC---AUGGAC-
(((((((.(((((...((.....(((.....)))....---))...))))).)))))))..........((((.(((((......)))))---.)))).- ( -27.50)
>DroSec_CAF1 1468 96 + 1
CGACAAAGGAGAGUCCCCAUCUUAGGACAUUCCUGGCC---GACCCCUUUCAUUUGUCGCAUUUCCAAUUUCGAGGGCCAGUCCAGGUCCAUCAUGGAC-
(((((((((((.((((........)))).)))))((..---....))......))))))....((((.....(((((((......))))).)).)))).- ( -27.90)
>DroSim_CAF1 3327 96 + 1
CGACAAAGGAGAGUCCCCAUCAAAGGACAUUCCUGGCC---GGCCCCUUUCAUUUGUCGCAUUUCCAAUUUCGAGGGCCAGUCCAGGUCCAUCAUGGAC-
(((((((((((.((((........)))).)))))((..---..))........))))))....((((.....(((((((......))))).)).)))).- ( -29.00)
>DroEre_CAF1 1508 92 + 1
CGACAAAGGAAAGUCCCCAUCAAAGGACAUUCCUGGCC---GGCCCCUUUCAUUUGUCCUAUUUCCAAUUCCUAG-GCCAGUCCAAGUCC---GUGAGC-
.(((..(((((.((((........)))).)))))(((.---((((........(((.........)))......)-))).)))...)))(---....).- ( -22.84)
>DroYak_CAF1 3868 92 + 1
CGACAAAGGAAAGUCCCCAUCAAAGGACAUUCUUGGCCAUGGGCCCCUUUCAUUUGUCGUAUUUCCAAUUUGGAG-----GUCCAGGUAC---AUGGACC
(((((((.((((((((........))))......((((...))))..)))).)))))))....(((.....)))(-----(((((.....---.)))))) ( -32.30)
>consensus
CGACAAAGGAGAGUCCCCAUCAAAGGACAUUCCUGGCC___GGCCCCUUUCAUUUGUCGUAUUUCCAAUUUCGAGGGCCAGUCCAGGUCC___AUGGAC_
(((((((((((.((((........)))).)))))((((...))))........)))))).....................(((((.........))))). (-23.48 = -23.36 +  -0.12)

alignment

secondary structure

dotplot

Window 2

Location	12,647,580 – 12,647,673
Length	93
Sequences	5
Columns	100
Reading direction	reverse
Mean pairwise identity	87.16
Mean single sequence MFE	-33.26
Consensus MFE	-23.54
Energy contribution	-24.02
Covariance contribution	0.48
Combinations/Pair	1.08
Mean z-score	-2.03
Structure conservation index	0.71
SVM decision value	0.43
SVM RNA-class probability	0.734581
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12647580 93 - 22224390
-GUCCAU---GGACCUGGACUGGCCCUCGAAAUUGGAAAUACGACAAAUGAAAGGGGCC---GGCCAGGAAUGUCCUUUGAUGGGAACUCUCCUUUGUCG
-......---((((((((.((((((((.....(((.........)))......))))))---)))))))....((((.....))))....)))....... ( -31.30)
>DroSec_CAF1 1468 96 - 1
-GUCCAUGAUGGACCUGGACUGGCCCUCGAAAUUGGAAAUGCGACAAAUGAAAGGGGUC---GGCCAGGAAUGUCCUAAGAUGGGGACUCUCCUUUGUCG
-......((..(((((((.((((((((.....(((.........)))......))))))---)))))))...(((((......))))).....))..)). ( -32.50)
>DroSim_CAF1 3327 96 - 1
-GUCCAUGAUGGACCUGGACUGGCCCUCGAAAUUGGAAAUGCGACAAAUGAAAGGGGCC---GGCCAGGAAUGUCCUUUGAUGGGGACUCUCCUUUGUCG
-......((..(((((((.((((((((.....(((.........)))......))))))---)))))))...((((((....)))))).....))..)). ( -35.70)
>DroEre_CAF1 1508 92 - 1
-GCUCAC---GGACUUGGACUGGC-CUAGGAAUUGGAAAUAGGACAAAUGAAAGGGGCC---GGCCAGGAAUGUCCUUUGAUGGGGACUUUCCUUUGUCG
-......---.(((.(((.(((((-((.....(((.........))).......)))))---)))))((((.((((((....)))))).))))...))). ( -31.60)
>DroYak_CAF1 3868 92 - 1
GGUCCAU---GUACCUGGAC-----CUCCAAAUUGGAAAUACGACAAAUGAAAGGGGCCCAUGGCCAAGAAUGUCCUUUGAUGGGGACUUUCCUUUGUCG
((((((.---.....)))))-----)(((.....)))....(((((((.(((((.((((...)))).......(((((....)))))))))).))))))) ( -35.20)
>consensus
_GUCCAU___GGACCUGGACUGGCCCUCGAAAUUGGAAAUACGACAAAUGAAAGGGGCC___GGCCAGGAAUGUCCUUUGAUGGGGACUCUCCUUUGUCG
.(((((.........)))))......................((((((.......((((...)))).(((..((((((....))))))..))))))))). (-23.54 = -24.02 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:48 2006