Locus 3909

Sequence ID 3L_DroMel_CAF1
Location 11,324,399 – 11,324,491
Length 92
Max. P 0.998949
window6086 window6087

overview

Window 6

Location 11,324,399 – 11,324,491
Length 92
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 76.54
Mean single sequence MFE -34.10
Consensus MFE -16.75
Energy contribution -17.75
Covariance contribution 1.00
Combinations/Pair 1.17
Mean z-score -4.20
Structure conservation index 0.49
SVM decision value 3.30
SVM RNA-class probability 0.998949
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11324399 92 + 23771897
GCUCCAAGCCGAGUUGGUAUACUAAU----AUGCAU----AUAU-----UGUAGUAUAGUAUACUACUAUGCUAU---GUACAUGGUAUAUGGGCUC---CGAGGUCUGGG
...(((..(((((((.((((((((..----.(((((----((((-----.(((((((...))))))).))).)))---)))..)))))))).)))))---...))..))). ( -33.30)
>DroSec_CAF1 45060 87 + 1
GCUCCAAGCCGAGUUGGUAUACUACU----AUGUAU----AU----------AGUAUAGUAUACUA---CGCUAU---GUACAUGGUAUAUGGACUCGGCUGAGGUCUGGG
.(((..(((((((((.(((((((...----((((((----((----------((..(((....)))---..))))---))))))))))))).))))))))))))....... ( -42.10)
>DroSim_CAF1 52163 87 + 1
GCUCCAAGCCGAGUUGGUAUACUACU----AUGUAU----AU----------AGUAUAGUAUACUA---CGCUAU---GUACACGGUAUAUGGGCUCAGCUGAGGUCUGGG
.(((..(((.(((((.(((((((...----.(((((----((----------((..(((....)))---..))))---))))).))))))).))))).))))))....... ( -33.90)
>DroYak_CAF1 37358 105 + 1
GCUCCAAGCCGACUUGGUAUACUACUUACUUUGUGUAUAUAUAGGUAUAUAUAGUAUGGUGUUCUA---UGGUGUAUGGUGUAUGGUAUAUGGGCUC---UGAGGUCUGGG
.(((..((((.(..(.((((((((..(((.((((((((((....))))))))))(((((....)))---)))))..)))))))).)....).)))).---.)))....... ( -27.10)
>consensus
GCUCCAAGCCGAGUUGGUAUACUACU____AUGUAU____AU__________AGUAUAGUAUACUA___CGCUAU___GUACAUGGUAUAUGGGCUC___UGAGGUCUGGG
...(((..(((((((.((((((((.......(((((..............(((((((...)))))))...........))))))))))))).)))))......))..))). (-16.75 = -17.75 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 11,324,399 – 11,324,491
Length 92
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 76.54
Mean single sequence MFE -22.68
Consensus MFE -9.34
Energy contribution -10.21
Covariance contribution 0.87
Combinations/Pair 1.10
Mean z-score -3.15
Structure conservation index 0.41
SVM decision value 1.09
SVM RNA-class probability 0.913961
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11324399 92 - 23771897
CCCAGACCUCG---GAGCCCAUAUACCAUGUAC---AUAGCAUAGUAGUAUACUAUACUACA-----AUAU----AUGCAU----AUUAGUAUACCAACUCGGCUUGGAGC
.......(((.---(((((....(((.((((..---...)))).)))((((((((.....((-----....----.))...----..))))))))......))))).))). ( -23.20)
>DroSec_CAF1 45060 87 - 1
CCCAGACCUCAGCCGAGUCCAUAUACCAUGUAC---AUAGCG---UAGUAUACUAUACU----------AU----AUACAU----AGUAGUAUACCAACUCGGCUUGGAGC
......((..((((((((...(((((.(((((.---((((..---(((....)))..))----------))----.)))))----....)))))...)))))))).))... ( -28.50)
>DroSim_CAF1 52163 87 - 1
CCCAGACCUCAGCUGAGCCCAUAUACCGUGUAC---AUAGCG---UAGUAUACUAUACU----------AU----AUACAU----AGUAGUAUACCAACUCGGCUUGGAGC
......((..(((((((....(((((.(((((.---((((..---(((....)))..))----------))----.)))))----....)))))....))))))).))... ( -24.80)
>DroYak_CAF1 37358 105 - 1
CCCAGACCUCA---GAGCCCAUAUACCAUACACCAUACACCA---UAGAACACCAUACUAUAUAUACCUAUAUAUACACAAAGUAAGUAGUAUACCAAGUCGGCUUGGAGC
.......(((.---(((((.((.....((((..(.(((....---..(.....)....(((((((....)))))))......))).)..)))).....)).))))).))). ( -14.20)
>consensus
CCCAGACCUCA___GAGCCCAUAUACCAUGUAC___AUAGCA___UAGUAUACUAUACU__________AU____AUACAU____AGUAGUAUACCAACUCGGCUUGGAGC
.......(((....((((((((.....))).................(((((((((..............................)))))))))......))))).))). ( -9.34 = -10.21 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:46 2006