Locus 410

Sequence ID	2L_DroMel_CAF1
Location	1,233,346 – 1,233,504
Length	158
Max. P	0.545073

overview

Window 7

Location	1,233,346 – 1,233,464
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	92.58
Mean single sequence MFE	-42.02
Consensus MFE	-30.06
Energy contribution	-31.13
Covariance contribution	1.06
Combinations/Pair	1.03
Mean z-score	-2.21
Structure conservation index	0.72
SVM decision value	-0.05
SVM RNA-class probability	0.506431
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1233346 118 + 22407834
AAAGAUGCGAGAACAGCUCAAUGUUAAUGGCCAAGAUUAAGGGUCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG--GCCUUAGCUCCGAGCUUAGCGCCUUCCCGUCUGC
..(((((.(((..((((((...(((((.(((((......((((..((((..((((((((....)))))))).))))..))))))--))))))))...)))))....)..))).))))).. ( -46.20)
>DroSec_CAF1 10678 118 + 1
AAAGCUGCGCGAACAACUCAAUGUUAAUGGCCAAGAUUAAGGGGCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG--GCCUUAGCUCCGAGCUUAGCGCCUUCCCGUCUGC
......((((......(((...(((((.(((((......(((((.((((..((((((((....)))))))).)))).)))))))--))))))))...)))....))))............ ( -44.00)
>DroSim_CAF1 6496 118 + 1
AAAGCUGCGAGAACAACUCAAUGUUAAUGGCCAAGAUUAAGGGGCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG--GCCUUAGCUCCGAGCUUAACGCCUUCCCGUCUGC
.(((((.((((.....)))...(((((.(((((......(((((.((((..((((((((....)))))))).)))).)))))))--))))))))...))))))................. ( -41.40)
>DroYak_CAF1 6620 118 + 1
-AAGGUGUGAGAACAACUCAAUGUUAAUGGCCAAGAUUAAGGGGCUGGGCAAGACGUCCUCCAGCAGGACUCGCCAUUUCCUUGCUGCCUUAGCUGCAAGCUUAGCGCCU-CCCGUCUGC
-..(((.....((((......))))....))).((((..(((.(((((((..((.(((((.....))))))).........((((.((....)).))))))))))).)))-...)))).. ( -36.50)
>consensus
AAAGCUGCGAGAACAACUCAAUGUUAAUGGCCAAGAUUAAGGGGCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG__GCCUUAGCUCCGAGCUUAGCGCCUUCCCGUCUGC
......(((..((...(((...(((((.(((......(((((((.(((...((((((((....))))))))..))).)))))))..))))))))...))).))..)))............ (-30.06 = -31.13 +   1.06)

alignment

secondary structure

dotplot

Window 8

Location	1,233,386 – 1,233,504
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.96
Mean single sequence MFE	-33.60
Consensus MFE	-26.33
Energy contribution	-27.20
Covariance contribution	0.87
Combinations/Pair	1.07
Mean z-score	-2.06
Structure conservation index	0.78
SVM decision value	0.02
SVM RNA-class probability	0.545073
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1233386 118 + 22407834
GGGUCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG--GCCUUAGCUCCGAGCUUAGCGCCUUCCCGUCUGCUUUCAGCACAAUAAACAAAAAGUAAUUUUCACAAAUUUGC
(((....((..((((((((....))))))))..))........(--((((.(((.....))).)).)))..)))(((((....))).))............................... ( -33.10)
>DroSec_CAF1 10718 118 + 1
GGGGCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG--GCCUUAGCUCCGAGCUUAGCGCCUUCCCGUCUGCUUUCAGCACAAUAAACAAAAAGUAAUUUUCACAAAUUUGC
((((((((((.((((((((....))))))))...((......))--))).)))))))((((...(((......)))..))))...(((.(((.....((((....)))).....)))))) ( -35.70)
>DroSim_CAF1 6536 118 + 1
GGGGCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG--GCCUUAGCUCCGAGCUUAACGCCUUCCCGUCUGCUUUCAGCACAAUAAACAAAAAGUAAUUUUCACAAAUUUGC
((((((((((.((((((((....))))))))...((......))--))).)))))))((((...(((......)))..))))...(((.(((.....((((....)))).....)))))) ( -35.40)
>DroYak_CAF1 6659 119 + 1
GGGGCUGGGCAAGACGUCCUCCAGCAGGACUCGCCAUUUCCUUGCUGCCUUAGCUGCAAGCUUAGCGCCU-CCCGUCUGCUUUCAGCACAAUAAACAAAAAGUAAUUUUCACAAAUUUGC
((.(((((((..((.(((((.....))))))).........((((.((....)).))))))))))).)).-...(((((....))).))............................... ( -30.20)
>consensus
GGGGCUGGGCAAGUCCUGCUCCUGCAGGACUCUCCAUUUCCUUG__GCCUUAGCUCCGAGCUUAGCGCCUUCCCGUCUGCUUUCAGCACAAUAAACAAAAAGUAAUUUUCACAAAUUUGC
((((((((((.((((((((....))))))))...((......))..))).)))))))((((...(((......)))..))))...................................... (-26.33 = -27.20 +   0.87)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:23 2006