Locus 5836

Sequence ID 2L_DroMel_CAF1
Location 16,555,668 – 16,555,764
Length 96
Max. P 0.995291
window9259 window9260

overview

Window 9

Location 16,555,668 – 16,555,764
Length 96
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 70.40
Mean single sequence MFE -33.34
Consensus MFE -12.25
Energy contribution -13.25
Covariance contribution 1.00
Combinations/Pair 1.11
Mean z-score -2.49
Structure conservation index 0.37
SVM decision value 2.56
SVM RNA-class probability 0.995291
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16555668 96 + 22407834
UUGACGCCAUCGCC------AGUGACAAAUGUUAAUGGAAAUAUAGCACAGGCAGCAGCAGCAG---------CAGCUUCAGCGCCUAGAUUGCUGCUGCAACUGGACGCA
.((.(((((..(((------.(((....(((((......)))))..))).))).((((((((((---------(.((....))))......)))))))))...))).)))) ( -32.40)
>DroVir_CAF1 8053 93 + 1
UUGACACCGUCGGUGGCCGUUGUGACAAAUGUUAAUGGAAAUAUCGGCCAGGCAGCGG------------------CAACAGCGCCGCAAUUGCUGCUGCAACUGGACGCG
.......((((..((((((.(((..((........))...))).)))))).(((((((------------------(((..((...))..)))))))))).....)))).. ( -35.70)
>DroEre_CAF1 10070 93 + 1
UUGACGCCAUCGCC------UGUGACAAAUGUUAAUGGAAACAUAGCACAGGCAGCCGCA------------GCAGCUUCAGCGCCUAGAUUGCUGCUGCAACUGGACGCA
.((.(((((..(((------((((....(((((......)))))..)))))))....(((------------(((((.((........))..))))))))...))).)))) ( -37.30)
>DroWil_CAF1 12490 87 + 1
UC---------AGC------AGUGACAAAUGUUAAUGGAAAUCUGGUCCAGGCUGGGCAAGCAGCAA-CACAGCA--------GCCUCGUUUAUUGCUGCAACUGGACGCA
..---------.((------..((((....))))...........((((((((((......))))..-....(((--------((..........)))))..)))))))). ( -27.40)
>DroYak_CAF1 9999 99 + 1
UUGACGCCAUCGCC------AGUGACAAAUGUUAAUGGAAACAUAGCACAGGCAGCAGCA------GCCACAACAGCUUCAGCGCCUAGAUUGCUGCUGCAACUGGACGCA
.....((.....((------(((......(((((.((....)))))))...(((((((((------..(......((....)).....)..))))))))).)))))..)). ( -33.90)
>consensus
UUGACGCCAUCGCC______AGUGACAAAUGUUAAUGGAAAUAUAGCACAGGCAGCAGCA_____________CAGCUUCAGCGCCUAGAUUGCUGCUGCAACUGGACGCA
.....................(((....(((((......)))))....(((((((((((.................................))))))))..)))..))). (-12.25 = -13.25 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,555,668 – 16,555,764
Length 96
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 70.40
Mean single sequence MFE -33.49
Consensus MFE -8.38
Energy contribution -9.06
Covariance contribution 0.68
Combinations/Pair 1.18
Mean z-score -2.12
Structure conservation index 0.25
SVM decision value 1.27
SVM RNA-class probability 0.938240
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16555668 96 - 22407834
UGCGUCCAGUUGCAGCAGCAAUCUAGGCGCUGAAGCUG---------CUGCUGCUGCUGCCUGUGCUAUAUUUCCAUUAACAUUUGUCACU------GGCGAUGGCGUCAA
.(((.(((...(((((((((.....(((......))).---------.)))))))))((((.((((...................).))).------)))).))))))... ( -32.71)
>DroVir_CAF1 8053 93 - 1
CGCGUCCAGUUGCAGCAGCAAUUGCGGCGCUGUUG------------------CCGCUGCCUGGCCGAUAUUUCCAUUAACAUUUGUCACAACGGCCACCGACGGUGUCAA
.((((((((((((....))))))).)))))((.((------------------(((.((..((((((.......((........))......)))))).)).))))).)). ( -32.32)
>DroEre_CAF1 10070 93 - 1
UGCGUCCAGUUGCAGCAGCAAUCUAGGCGCUGAAGCUGC------------UGCGGCUGCCUGUGCUAUGUUUCCAUUAACAUUUGUCACA------GGCGAUGGCGUCAA
.(((((.((((((((((((..((........)).)))))------------)))))))((((((((.(((((......)))))..).))))------)))...)))))... ( -42.30)
>DroWil_CAF1 12490 87 - 1
UGCGUCCAGUUGCAGCAAUAAACGAGGC--------UGCUGUG-UUGCUGCUUGCCCAGCCUGGACCAGAUUUCCAUUAACAUUUGUCACU------GCU---------GA
.(((..((((.((((((...........--------)))))).-..))))..))).((((...(((.((((..........)))))))...------)))---------). ( -21.80)
>DroYak_CAF1 9999 99 - 1
UGCGUCCAGUUGCAGCAGCAAUCUAGGCGCUGAAGCUGUUGUGGC------UGCUGCUGCCUGUGCUAUGUUUCCAUUAACAUUUGUCACU------GGCGAUGGCGUCAA
.(((.(((...((((((((......(((......)))......))------))))))((((.((((.(((((......)))))..).))).------)))).))))))... ( -38.30)
>consensus
UGCGUCCAGUUGCAGCAGCAAUCUAGGCGCUGAAGCUG_____________UGCCGCUGCCUGUGCUAUAUUUCCAUUAACAUUUGUCACU______GGCGAUGGCGUCAA
.(((((.((((((....)))).)).)))))................................................................................. ( -8.38 =  -9.06 +   0.68)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:11 2006