Locus 5211

Sequence ID 2R_DroMel_CAF1
Location 16,962,263 – 16,962,382
Length 119
Max. P 0.999822
window8325 window8326

overview

Window 5

Location 16,962,263 – 16,962,354
Length 91
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 82.23
Mean single sequence MFE -21.75
Consensus MFE -14.79
Energy contribution -14.97
Covariance contribution 0.19
Combinations/Pair 1.22
Mean z-score -2.02
Structure conservation index 0.68
SVM decision value 0.79
SVM RNA-class probability 0.850772
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16962263 91 + 20766785
AAAUAUUUU--UUCGCGUGUGUGGUCCAUGUUUGCCAUCGGCAGACAUCGGAUAAUGUCUAAUAUAUUAUAUCCUAUUAACUGGAAAUACAAG
.........--......(((((.(((((((((((((...))))))))).))))..................(((........))).))))).. ( -22.20)
>DroSim_CAF1 63079 90 + 1
AAAUAUUUUUCUUAGCGUGUGUGGACCAUGUUUGCCAUCGGCAGACAUCGGAUGAUAUGUAAUAUAUUAUAUCCUAUUAACUGGAAAUAC---
.......(((((.((...(((.((((((((((((((...))))))))).))((((((((...)))))))).))))))...)))))))...--- ( -21.90)
>DroEre_CAF1 60587 91 + 1
ACUUAU-UUUCUUCUAGUGUGUGAGCCAUAUUUGCCAUCGGCAGACAUUUGAUGAUGUGUAAUAUAUUGUAUCCUAUUAACUGGAAAUACCA-
......-....((((((((((.((((.(((((((((((((.(((....))).))))).)))).)))).)).)).)))..)))))))......- ( -17.00)
>DroYak_CAF1 62636 93 + 1
CCUUGUGUUUUUUCUUGUGUAUGGGCCAUGUUUGCCAUCGGCAGACAUUUGAUUAUGUGUUUCAUAUUACAUCCUAUUAACUGGAAAUACAAG
.(((((((((((....((..(((((..(((((((((...)))))))))......(((((........))))))))))..)).))))))))))) ( -25.90)
>consensus
AAAUAUUUUUCUUCGCGUGUGUGGGCCAUGUUUGCCAUCGGCAGACAUCGGAUGAUGUGUAAUAUAUUAUAUCCUAUUAACUGGAAAUACAA_
..................((((...(((((((((((...))))))))....((((((((...))))))))...........)))..))))... (-14.79 = -14.97 +   0.19)

alignment

Postscript

secondary structure

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dotplot

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Window 6

Location 16,962,285 – 16,962,382
Length 97
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 72.23
Mean single sequence MFE -20.85
Consensus MFE -12.60
Energy contribution -12.97
Covariance contribution 0.37
Combinations/Pair 1.20
Mean z-score -2.89
Structure conservation index 0.60
SVM decision value 4.17
SVM RNA-class probability 0.999822
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16962285 97 + 20766785
UCCAUGUUUGCCAUCGGCAGACAUCGGAUAAUGUCUAAUAUAUUAUAUCCUAUUAACUGGAAAUACAAGCUUCCAACUAAG-----------GCUAACAAGCCUAACA
((((((((((((...))))))))).)))((((((.....))))))............(((((........)))))....((-----------(((....))))).... ( -25.30)
>DroSim_CAF1 63103 85 + 1
ACCAUGUUUGCCAUCGGCAGACAUCGGAUGAUAUGUAAUAUAUUAUAUCCUAUUAACUGGAAAUAC------------AAG-----------GCUAACAAGCCUAACA
.(((((((((((...))))))))).))((((((((...)))))))).(((........))).....------------.((-----------(((....))))).... ( -24.90)
>DroEre_CAF1 60610 76 + 1
GCCAUAUUUGCCAUCGGCAGACAUUUGAUGAUGUGUAAUAUAUUGUAUCCUAUUAACUGGAAAUACCA--------------------------------GCCCAACA
((.(((((((((((((.(((....))).))))).)))).)))).))..........((((.....)))--------------------------------)....... ( -13.30)
>DroYak_CAF1 62660 108 + 1
GCCAUGUUUGCCAUCGGCAGACAUUUGAUUAUGUGUUUCAUAUUACAUCCUAUUAACUGGAAAUACAAGCUUUAUACUAACCCUAUGUAUCAUCUAAAAAGCCUAACA
...(((((((((...))))))))).......((((((((...(((........)))...)))))))).(((((((((.........)))).......)))))...... ( -19.91)
>consensus
GCCAUGUUUGCCAUCGGCAGACAUCGGAUGAUGUGUAAUAUAUUAUAUCCUAUUAACUGGAAAUACAA__________AAG___________GCUAACAAGCCUAACA
...(((((((((...)))))))))...((((((((...)))))))).(((........)))............................................... (-12.60 = -12.97 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:14 2006