Locus 4700

Sequence ID	X_DroMel_CAF1
Location	12,236,271 – 12,236,406
Length	135
Max. P	0.980575

overview

Window 0

Location	12,236,271 – 12,236,373
Length	102
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	90.62
Mean single sequence MFE	-29.13
Consensus MFE	-26.75
Energy contribution	-26.75
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.92
SVM decision value	0.62
SVM RNA-class probability	0.803303
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12236271 102 + 22224390
GUUGCCCCACAAACCAAU-CCCAUCCAGA------GCCAGACUGGAGAGCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUCGCC
............((((((-....(((((.------......)))))..(((((((((((.(((....((........))....)))))))..))))))))))))).... ( -27.50)
>DroSim_CAF1 59953 102 + 1
GUUGCCCCACAAACCAAU-CCCAUCCAGA------ACCAGACUGGAGAGCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUCGCC
............((((((-....(((((.------......)))))..(((((((((((.(((....((........))....)))))))..))))))))))))).... ( -27.50)
>DroYak_CAF1 43903 105 + 1
----CAACACAAACCAAUACCCAUCCAGAUGCAUGGGCAGACUGGAGAGCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUCGCC
----........((((((.....(((((.(((....)))..)))))..(((((((((((.(((....((........))....)))))))..))))))))))))).... ( -32.40)
>consensus
GUUGCCCCACAAACCAAU_CCCAUCCAGA______GCCAGACUGGAGAGCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUCGCC
............((((((.....(((((.............)))))..(((((((((((.(((....((........))....)))))))..))))))))))))).... (-26.75 = -26.75 +  -0.00)

alignment

secondary structure

dotplot

Window 1

Location	12,236,304 – 12,236,406
Length	102
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.33
Mean single sequence MFE	-33.88
Consensus MFE	-23.25
Energy contribution	-22.62
Covariance contribution	-0.62
Combinations/Pair	1.21
Mean z-score	-2.77
Structure conservation index	0.69
SVM decision value	1.87
SVM RNA-class probability	0.980575
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12236304 102 + 22224390
ACUGGAGA-----GCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUC------GCCAAAACGCGGCC-CUACA---AAUUGUUUCUCCUCUC---C
...(((((-----(((((((((((.(((....((........))....)))))))..)))))))((.((((------((......))))))-..)).---.......)))))....---. ( -34.70)
>DroVir_CAF1 29804 119 + 1
-CUGGAGCUGCACUCCGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCGAGUGUUUGCCUUGGUCAGCGCUGCCCAAGCCCGGCACCGACAUUUAAUUUUUGUUUUUUUCCUCU
-..((((.....))))((((((((.(((.............))))))).((((((((((((.((....)).))))))((....)).))))))..............)))).......... ( -30.52)
>DroSim_CAF1 59986 102 + 1
ACUGGAGA-----GCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUC------GCCAAAACGCGGCC-CUACA---AAUUGUUUCUCCUCUC---C
...(((((-----(((((((((((.(((....((........))....)))))))..)))))))((.((((------((......))))))-..)).---.......)))))....---. ( -34.70)
>DroYak_CAF1 43939 105 + 1
ACUGGAGA-----GCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUC------GCCAAAACGCGGCC-CUACA---AAUUGUUUCUCCUCUCCACC
..((((((-----(((((((((((.(((....((........))....)))))))..)))))))((.((((------((......))))))-..)).---............)))))).. ( -35.60)
>consensus
ACUGGAGA_____GCAGACAUGGCCACUAACAACAUCAAAAAGUGCCAAGUGCCAAGUGUUUGCGUUGGUC______GCCAAAACGCGGCC_CUACA___AAUUGUUUCUCCUCUC___C
...(((((.....(((((((((((.(((....((........))....)))))))..))))))).............(((.......))).................)))))........ (-23.25 = -22.62 +  -0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:18 2006