Locus 3593

Sequence ID	2R_DroMel_CAF1
Location	11,968,541 – 11,968,650
Length	109
Max. P	0.929465

overview

Window 6

Location	11,968,541 – 11,968,650
Length	109
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	79.25
Mean single sequence MFE	-27.47
Consensus MFE	-18.88
Energy contribution	-19.43
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.71
Structure conservation index	0.69
SVM decision value	0.78
SVM RNA-class probability	0.848791
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11968541 109 + 20766785
UGAAUGUUAUAAUGACAAAUCGAUAUAUUUUCGCUCAGUGUAUGUACCCCUUUCCCAC--GGCACUCGUGAGCGGCUGACUUAUGCAUUCAUCCAUCCAGUCAGCCGCCAG
....((((.....)))).............((((..(((((.(((...........))--)))))).))))((((((((((.(((........)))..))))))))))... ( -27.10)
>DroSec_CAF1 19802 109 + 1
UGAAUGUUAUAAUGACAAAUCGGAAUAUUUUCCCUCAGUGUUUGUACCCCUUUUCCAC--GGCACUCGUGAGCGGCUGACUUAUGCAUUCAUCCAUCCAGCCAGCCGCCAG
.(((.........((((....((((....)))).....))))..........)))(((--(.....)))).(((((((.((.(((........)))..)).)))))))... ( -23.31)
>DroSim_CAF1 23303 109 + 1
UGAAUGUUAUAAUGACAAAUGGGAAUAUUUUCCCUCAGUGUAUGUACCCCUUUUCCAC--GGCACUCGUGAGCGGCUGACUUAUGCAUUCAUCCAUCCAGCCAGCCGCCAG
.......((((...(((...(((((....)))))....))).)))).........(((--(.....)))).(((((((.((.(((........)))..)).)))))))... ( -26.70)
>DroEre_CAF1 19897 103 + 1
UGAAUUCUUU--UGGUAUAU----GUAUAUUCGCCCAGUGUACGUACCCCUUUCCCAC--GGCACUCGUGAGCGGCUGACUUAUGCAUUCAUCCAUCCAGUCAGCCGCCAG
..........--.((..(((----(((((((.....))))))))))..)).....(((--(.....)))).((((((((((.(((........)))..))))))))))... ( -33.10)
>DroYak_CAF1 20148 101 + 1
UGCAUUCAUU--GGGAGUA------UAUUUUCGCUCAGUGUACGUACCCCUUUCCCAC--GGCACUCGUGAGCGGCUGACUUAUGCAUUCAUCCAUCCAGUCAGCCGCCAG
(((...((((--(((.(..------......).)))))))...))).........(((--(.....)))).((((((((((.(((........)))..))))))))))... ( -30.70)
>DroAna_CAF1 21155 88 + 1
--------------------UG---UAUUAUUUUUCAUAGUGUUUACCCCUUUUGCAAGCAUCACUGGUGAGCGGCUGACUUAUGCAUUCAUCCAUCCAGUCAGCCGCCAG
--------------------..---((((((.....)))))).(((((.....((....)).....)))))((((((((((.(((........)))..))))))))))... ( -23.90)
>consensus
UGAAUGUUAU__UGACAAAU_G__AUAUUUUCGCUCAGUGUAUGUACCCCUUUCCCAC__GGCACUCGUGAGCGGCUGACUUAUGCAUUCAUCCAUCCAGUCAGCCGCCAG
....................................(((((..((...........))...)))))..((.((((((((((.(((........)))..)))))))))))). (-18.88 = -19.43 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	11,968,541 – 11,968,650
Length	109
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	79.25
Mean single sequence MFE	-32.28
Consensus MFE	-25.79
Energy contribution	-25.77
Covariance contribution	-0.03
Combinations/Pair	1.10
Mean z-score	-1.91
Structure conservation index	0.80
SVM decision value	1.20
SVM RNA-class probability	0.929465
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11968541 109 - 20766785
CUGGCGGCUGACUGGAUGGAUGAAUGCAUAAGUCAGCCGCUCACGAGUGCC--GUGGGAAAGGGGUACAUACACUGAGCGAAAAUAUAUCGAUUUGUCAUUAUAACAUUCA
.((((((((((((..(((........))).))))))))(((((...(((((--.(......).)))))......)))))................))))............ ( -32.90)
>DroSec_CAF1 19802 109 - 1
CUGGCGGCUGGCUGGAUGGAUGAAUGCAUAAGUCAGCCGCUCACGAGUGCC--GUGGAAAAGGGGUACAAACACUGAGGGAAAAUAUUCCGAUUUGUCAUUAUAACAUUCA
..(((((((((((..(((........))).))))))))))).(((((((((--.(......).)))))..........((((....))))...)))).............. ( -32.80)
>DroSim_CAF1 23303 109 - 1
CUGGCGGCUGGCUGGAUGGAUGAAUGCAUAAGUCAGCCGCUCACGAGUGCC--GUGGAAAAGGGGUACAUACACUGAGGGAAAAUAUUCCCAUUUGUCAUUAUAACAUUCA
..(((((((((((..(((........))).))))))))))).(((((((((--.(......).))))).........(((((....)))))..)))).............. ( -36.30)
>DroEre_CAF1 19897 103 - 1
CUGGCGGCUGACUGGAUGGAUGAAUGCAUAAGUCAGCCGCUCACGAGUGCC--GUGGGAAAGGGGUACGUACACUGGGCGAAUAUAC----AUAUACCA--AAAGAAUUCA
.(((.((((((((..(((........))).))))))))(((((...(((((--.(......).)))))......)))))........----.....)))--.......... ( -31.80)
>DroYak_CAF1 20148 101 - 1
CUGGCGGCUGACUGGAUGGAUGAAUGCAUAAGUCAGCCGCUCACGAGUGCC--GUGGGAAAGGGGUACGUACACUGAGCGAAAAUA------UACUCCC--AAUGAAUGCA
...((((((((((..(((........))).))))))))(((((...(((((--.(......).)))))......))))).......------.......--.......)). ( -32.80)
>DroAna_CAF1 21155 88 - 1
CUGGCGGCUGACUGGAUGGAUGAAUGCAUAAGUCAGCCGCUCACCAGUGAUGCUUGCAAAAGGGGUAAACACUAUGAAAAAUAAUA---CA--------------------
...((((((((((..(((........))).))))))))))(((..((((.(((((.......)))))..)))).))).........---..-------------------- ( -27.10)
>consensus
CUGGCGGCUGACUGGAUGGAUGAAUGCAUAAGUCAGCCGCUCACGAGUGCC__GUGGAAAAGGGGUACAUACACUGAGCGAAAAUAU__C_AUUUGUCA__AUAACAUUCA
..(((((((((((..(((........))).))))))))))).....(((((...(....)...)))))........................................... (-25.79 = -25.77 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:28 2006