Locus 4768

Sequence ID 2L_DroMel_CAF1
Location 13,583,406 – 13,583,606
Length 200
Max. P 0.684648
window7548 window7549

overview

Window 8

Location 13,583,406 – 13,583,526
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -25.73
Consensus MFE -23.70
Energy contribution -23.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.89
Structure conservation index 0.92
SVM decision value 0.31
SVM RNA-class probability 0.684648
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13583406 120 - 22407834
CGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGCAGCAGACAAUGCCAAUAACAAUAAACGAAAAUAAAGUUUAUGACCGUGCUAAACACAGCGGCGAGCCGGAAAAUGCCCAACA
(((..(((.(((..........))).((......(((((........)))))......((((((.........))))))....))(((......))))))...))).............. ( -25.60)
>DroSec_CAF1 16534 120 - 1
CGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGCAGCAGACAAUGCCAAUAACAAUAAACGAAAAUAAAGUUUAUGACCGUGCUAAACACAGCGGCGAGCCGGAGAAUGCCCAACA
(((..(((.(((..........))).((......(((((........)))))......((((((.........))))))....))(((......))))))...))).............. ( -25.60)
>DroYak_CAF1 13609 120 - 1
CGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGGAGCAGACAAUGCCAAUAACAAUAAACGAAAAUAAAGUUUAUGACCGUGCUAAACACAGCGGCGAGCCGGAAAAUGCCCAACA
(((..(((..((((..(((((.(....)))))).)))).((.................((((((.........))))))....(((.....))).)))))...))).............. ( -26.00)
>consensus
CGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGCAGCAGACAAUGCCAAUAACAAUAAACGAAAAUAAAGUUUAUGACCGUGCUAAACACAGCGGCGAGCCGGAAAAUGCCCAACA
(((..(((.(((..........)))........((((..(((.....)))........((((((.........))))))..))))(((......))))))...))).............. (-23.70 = -23.70 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 13,583,486 – 13,583,606
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -26.88
Consensus MFE -21.56
Energy contribution -22.88
Covariance contribution 1.31
Combinations/Pair 1.03
Mean z-score -2.22
Structure conservation index 0.80
SVM decision value 0.29
SVM RNA-class probability 0.670307
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13583486 120 - 22407834
UGGCAAACAACAACAAAACCAUUAACAUGAAAUUACAAGGAAUAAAUAAAGUACAUUCCUGUUUCGGCCUUUCUUGGCUUCGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGCAG
((((........................(((((....((((((...........)))))))))))((((......))))......))))(((....(((((.(....))))))..))).. ( -24.60)
>DroSec_CAF1 16614 120 - 1
UGGCAAACAACAACAAAACCAUUAACAUGAAAUUACAAGGAAUAAAUAAAGUAGAUUCCUGUUUCGGCCUUCCAUGGCUUCGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGCAG
((((........................(((((....((((((...........)))))))))))((((......))))......))))(((....(((((.(....))))))..))).. ( -24.90)
>DroEre_CAF1 16814 120 - 1
UGGCAAACAACAACAAAACCAUUAACAUGAAAUUACAAGGAAUAAAUAAAGUAGAUUCCUGUUUUGGGCUUUCUUGGGCUCGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGGAG
((((.................................((((((...........)))))).((((((((((....)))))))))))))).((((..(((((.(....)))))).)))).. ( -28.00)
>DroYak_CAF1 13689 120 - 1
UGGCAAACAACAACAAAACCAUUAACAUGAAAUUACAAGGAAUAAAUAAGGAAGAUUCCUGUUUCGGGCUUUCUUGGGCUCGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGGAG
((((.................................((((((...........)))))).((((((((((....)))))))))))))).((((..(((((.(....)))))).)))).. ( -30.00)
>consensus
UGGCAAACAACAACAAAACCAUUAACAUGAAAUUACAAGGAAUAAAUAAAGUAGAUUCCUGUUUCGGCCUUUCUUGGCCUCGGAAGCCAGCCCAAAUUUAUAGGCAACAUAAAAUGGCAG
((((.................................((((((...........)))))).((((((((((....)))))))))))))).((((..(((((.(....)))))).)))).. (-21.56 = -22.88 +   1.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:53 2006