Locus 410

Sequence ID 2L_DroMel_CAF1
Location 1,233,346 – 1,233,504
Length 158
Max. P 0.545073
window657 window658

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

Postscript

secondary structure

Postscript

dotplot

Postscript

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

Postscript

secondary structure

Postscript

dotplot

Postscript


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