Locus 778

Sequence ID 2R_DroMel_CAF1
Location 3,741,191 – 3,741,425
Length 234
Max. P 0.645964
window1362 window1363

overview

Window 2

Location 3,741,191 – 3,741,305
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.53
Mean single sequence MFE -39.60
Consensus MFE -31.75
Energy contribution -32.75
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.27
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.645964
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3741191 114 - 20766785
CCUGGACGAGCCCUCGUCCAAGAAAUUCCUAGCUGGCGCCAUCGAAAAGUCGAGCUCCGCUUGGAGGCCGUGGUAGAUCAAC------CGCACAGGCCACUUCUAUGUUACGUUUAUACA
..(((((((....)))))))((((..(((.(((.((.((..((((....)))))).))))).)))(((((((((......))------)))...))))..))))................ ( -40.20)
>DroSim_CAF1 3883 114 - 1
CCUGGACGAACCCUCGUCCAAGAAAUUCCUAGCAGGCGCCAUCGAAAAGUCGAGCUCCGCUUGGAGGCCGUGGUAGAUCAAC------UGCAUAGGCCACUGCUAUGUUACGUUUAUACA
..(((((((....))))))).........(((((((((...((((....))))....))).....((((...((((.....)------)))...)))).))))))............... ( -38.30)
>DroYak_CAF1 3801 120 - 1
CUUGGACGAACCCUCGUCCAAGAAAUUCCUAGCAGGCGCCAUCGAAAAGUCAAGCUCCGCUUGGAGGCCGUGGUAGAUCAUCUGCAUCUGCAUAGGCCACUUCUACGUUACGUUUAUACA
(((((((((....)))))))))....(((.(((.((.((...(.....)....)).))))).)))((((...(((((((....).))))))...))))...................... ( -40.30)
>consensus
CCUGGACGAACCCUCGUCCAAGAAAUUCCUAGCAGGCGCCAUCGAAAAGUCGAGCUCCGCUUGGAGGCCGUGGUAGAUCAAC______UGCAUAGGCCACUUCUAUGUUACGUUUAUACA
..(((((((....)))))))((((..(((.(((.((.((..((((....)))))).))))).)))((((...(((.............)))...))))..))))................ (-31.75 = -32.75 +   1.00)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 3

Location 3,741,305 – 3,741,425
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -57.20
Consensus MFE -53.92
Energy contribution -53.70
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.51
Structure conservation index 0.94
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3741305 120 + 20766785
GAGCAGUCGCUGGACUCGGCCUCCGCCUCCCUGUCGCGCUUGGCGAUUCCGCUGGUGGAGCUCACUUGCUGUUGCUGCAAGUGGGCCAGCGGUCGCGAGCAUCCGCUGCUGUCGUGGCUU
.......((((((.......(((((((.....(((((.....)))))......)))))))(((((((((.......)))))))))))))))((((((((((.....)))..))))))).. ( -54.20)
>DroSim_CAF1 3997 120 + 1
GAGCAGUCGCUGGACUCGGCCUCCGCCUCCCUGUCGCGCUUGGCGAUUCCGCUGGUGGAGCUCACUUGCUGUUGCUGCAAGUGGGCCAGCGGUCGCGAGCAUCCGCUGCUGUCGUGGCUG
...(((((((..(((..((((((((((.....(((((.....)))))......))))))...(((((((.......)))))))))))(((((.(....)...)))))...)))))))))) ( -54.90)
>DroYak_CAF1 3921 120 + 1
GAGCAGUCGCUGGACUCGGCCUCCGCCUCCCUGUCGCGCUUGGCGAUUCCGCUGGUGGAGGUCACUUGCUGUUGCUGCAAGUGGGCCAGCGAUCGCGAGCAUCCGCUGCUGUCGUGGCUU
((((.((((((((.(((((((((((((.....(((((.....)))))......))))))))))((((((.......)))))))))))))))))((((((((.....)))..))))))))) ( -62.50)
>consensus
GAGCAGUCGCUGGACUCGGCCUCCGCCUCCCUGUCGCGCUUGGCGAUUCCGCUGGUGGAGCUCACUUGCUGUUGCUGCAAGUGGGCCAGCGGUCGCGAGCAUCCGCUGCUGUCGUGGCUU
..((..(((((((.(((((.(((((((.....(((((.....)))))......))))))).))((((((.......))))))))))))))))..))........((..(....)..)).. (-53.92 = -53.70 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:06 2006