Locus 556

Sequence ID X_DroMel_CAF1
Location 1,606,748 – 1,606,868
Length 120
Max. P 0.774340
window874 window875

overview

Window 4

Location 1,606,748 – 1,606,868
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.96
Mean single sequence MFE -39.33
Consensus MFE -28.79
Energy contribution -29.57
Covariance contribution 0.78
Combinations/Pair 1.03
Mean z-score -2.09
Structure conservation index 0.73
SVM decision value 0.24
SVM RNA-class probability 0.648207
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1606748 120 + 22224390
AUUUGGACAACUUUGUGAGUGAUUUCCAAAGGAGUCGAGCCCUCGUUCGCAAAUCCAUAGUGCUAAGACAACGGUGGAUGCCAUGGGUUUGCACGGUAAUCGCGGGGAGCUGUCCAUGAU
...((((((.((((....((((((.((....(((.(((....))))))((((((((((.((......))...(((....)))))))))))))..)).))))))..)))).)))))).... ( -41.20)
>DroSec_CAF1 2508 102 + 1
AUUUGGACACCUUUGUGAGUGAUUUCCAAAGGAGUCGAGCCCUCGUUAGCAAAUCCAUGGCGCUAAGACACCGGUGGAUGCCAUGG------------------GGGAGCUGUCCAUGAU
...((((((((((((.(((....)))))))))....(..(((((((..(((..(((((((.(......).)).)))))))).))))------------------)))..))))))).... ( -37.20)
>DroSim_CAF1 18509 102 + 1
AUUUGGACACCUUUGUGAGUGAUUUCCAAAGGAGUCGAGCCCUCGUUCGCAAAUCCACGGCGCUAAGACACCGGUGGAUGCCAUGG------------------GGGAGCUGUCCAUGAU
...((((((((((((.(((....)))))))))....(..(((((((..(((..(((((((.(......).)).)))))))).))))------------------)))..))))))).... ( -39.60)
>consensus
AUUUGGACACCUUUGUGAGUGAUUUCCAAAGGAGUCGAGCCCUCGUUCGCAAAUCCAUGGCGCUAAGACACCGGUGGAUGCCAUGG__________________GGGAGCUGUCCAUGAU
...((((((((((((.(((....)))))))))....(..(((..(....)....(((((((((((.(....)..))).))))))))..................)))..))))))).... (-28.79 = -29.57 +   0.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 1,606,748 – 1,606,868
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.96
Mean single sequence MFE -34.87
Consensus MFE -26.56
Energy contribution -26.57
Covariance contribution 0.01
Combinations/Pair 1.10
Mean z-score -2.26
Structure conservation index 0.76
SVM decision value 0.54
SVM RNA-class probability 0.774340
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1606748 120 - 22224390
AUCAUGGACAGCUCCCCGCGAUUACCGUGCAAACCCAUGGCAUCCACCGUUGUCUUAGCACUAUGGAUUUGCGAACGAGGGCUCGACUCCUUUGGAAAUCACUCACAAAGUUGUCCAAAU
....(((((((((.............((((.((..(((((......))).))..)).))))....(((((.((((.(((.......))).)))).)))))........)))))))))... ( -33.20)
>DroSec_CAF1 2508 102 - 1
AUCAUGGACAGCUCCC------------------CCAUGGCAUCCACCGGUGUCUUAGCGCCAUGGAUUUGCUAACGAGGGCUCGACUCCUUUGGAAAUCACUCACAAAGGUGUCCAAAU
....((((((((((.(------------------...(((((((((..(((((....))))).))))..)))))..).))))......((((((((......)).))))))))))))... ( -35.10)
>DroSim_CAF1 18509 102 - 1
AUCAUGGACAGCUCCC------------------CCAUGGCAUCCACCGGUGUCUUAGCGCCGUGGAUUUGCGAACGAGGGCUCGACUCCUUUGGAAAUCACUCACAAAGGUGUCCAAAU
....((((((((((.(------------------...(.((((((((.(((((....))))))))))..))).)..).))))......((((((((......)).))))))))))))... ( -36.30)
>consensus
AUCAUGGACAGCUCCC__________________CCAUGGCAUCCACCGGUGUCUUAGCGCCAUGGAUUUGCGAACGAGGGCUCGACUCCUUUGGAAAUCACUCACAAAGGUGUCCAAAU
....((((((.((......................(((((......))(((((....))))))))(((((.((((.(((.......))).)))).)))))........)).))))))... (-26.56 = -26.57 +   0.01)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:39 2006