Locus 1987

Sequence ID 3R_DroMel_CAF1
Location 5,619,067 – 5,619,162
Length 95
Max. P 0.898756
window3248

overview

Window 8

Location 5,619,067 – 5,619,162
Length 95
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 75.14
Mean single sequence MFE -21.07
Consensus MFE -9.03
Energy contribution -8.87
Covariance contribution -0.16
Combinations/Pair 1.44
Mean z-score -2.28
Structure conservation index 0.43
SVM decision value 1.00
SVM RNA-class probability 0.898756
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5619067 95 + 27905053
CAAGAA-----AAUAUUAGCUAA-----GCGAAAAGUUUAAAAAGUUAAUAUA----UAUAUGUGCAGCGGUCGGUG--CCAGCGCUUUAUGGGUACAUAGUGCAUAUGUA
......-----.(((((((((((-----((.....))))....)))))))))(----((((((..(((((.(.(...--.)).)))).((((....)))))..))))))). ( -24.20)
>DroPse_CAF1 5425 93 + 1
CAAGAAGAAAAAGUCUUAACGUA-----ACAAAAAGUAU-------UAGCAU------UGAUGUAUAGUAAAUAGUGGAAAAGUGUUUAAUGGGUACAUAGUGCAUAUGUA
....((((.....)))).(((((-----((.....))..-------..((((------((.(((((..((((((.(.....).))))))....))))))))))).))))). ( -16.60)
>DroSim_CAF1 1781 99 + 1
CAAGAA-----AAUAUUAGCUAA-----GCGAAAAGUUUAAAAAGUUAAUAUAUAUAUAUAUGUGCAGCGGUCGGUG--CAAGUGCUUUAUGGGUACAUAGUGCAUAUGUA
......-----.(((((((((((-----((.....))))....)))))))))...((((((((..(.(((.....))--)..(((((.....)))))...)..)))))))) ( -24.80)
>DroEre_CAF1 1808 89 + 1
CAAGAA-----AAUAUUAGCUAA-----GCGAAAAGUU------GUUAAAAUA----UAUAUGUGCAGCGGUCGGUG--CAAGUGCUUUAUGGGUACAUAGUGCAUAUGUA
......-----....(((((..(-----((.....)))------)))))..((----((((((..(.(((.....))--)..(((((.....)))))...)..)))))))) ( -19.70)
>DroYak_CAF1 1803 89 + 1
CAAGAA-----AAUAUUAGCUAA-----GCGAAAAGUU------GUUAACAUA----UAUAUGUGCAGCGGUCGAUG--CAAGUGCUUUAUGGGUACAUAGUGCAUAUGUA
......-----............-----.(((...(((------((..((((.----...)))))))))..))).((--((.((((.(((((....))))).)))).)))) ( -20.90)
>DroAna_CAF1 2220 91 + 1
AAAUAA-----AAUAAUAGCUUAGCUCUGCGAAAAAUAU-------U-AAAUA----CAUAAGUACAGCAGCCAGUG--CUGGUGCU-AAUGGGUACAUAGUGCGUAUGUA
......-----.......((........)).........-------.-...((----((((.((((..((((....)--)))(((((-....)))))...)))).)))))) ( -20.20)
>consensus
CAAGAA_____AAUAUUAGCUAA_____GCGAAAAGUUU_____GUUAAAAUA____UAUAUGUGCAGCGGUCGGUG__CAAGUGCUUUAUGGGUACAUAGUGCAUAUGUA
.........................................................(((((((((((((.(.........).)))).((((....))))))))))))).. ( -9.03 =  -8.87 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:24 2006