Locus 2500

Sequence ID 2R_DroMel_CAF1
Location 8,917,319 – 8,917,434
Length 115
Max. P 0.999914
window4125 window4126 window4127

overview

Window 5

Location 8,917,319 – 8,917,418
Length 99
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.88
Mean single sequence MFE -19.84
Consensus MFE -18.00
Energy contribution -18.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.20
Structure conservation index 0.91
SVM decision value 0.15
SVM RNA-class probability 0.605339
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8917319 99 + 20766785
AUU---------------------GCCCACUUCCCGGACACUGGGCAACUAAAUUAAUUCGAUAAUUGACUUCCAUUGCCUUGCCCGGAACCAUUGUCAUACCUUCCGGAUCUCCAGCUA
...---------------------((.......(((((..((((((((...(((....((((...)))).....)))...)))))))).((....)).......))))).......)).. ( -18.44)
>DroSec_CAF1 162281 99 + 1
AUU---------------------GCCCACUUCCCGGACACUGGGCAACUAAAUUAAUUCGAUAAUUGACUUCCAUUGCCUUGCCCGGAUCCAUUGUCAUCCCUUCCGGAUCUCCAGCUA
...---------------------((.......(((((....((((((...(((....((((...)))).....)))...))))))((((........))))..))))).......)).. ( -20.14)
>DroSim_CAF1 162954 99 + 1
AUU---------------------GCCCACUUCCCGGACACUGGGCAACUAAAUUAAUUCGAUAAUUGACUUCCAUUGCCUUGCCCGGAACCAUUGUCAUCCCUUCCGGAUCUCCAGCUA
...---------------------((.......(((((..((((((((...(((....((((...)))).....)))...)))))))).((....)).......))))).......)).. ( -18.44)
>DroEre_CAF1 166504 99 + 1
AUU---------------------GCCCACUUCCCGGACACUGGGCAACUAAAUUAAUUCGAUAAUUGACUUCCAUUGCCUUGCCCGGAACCAUUGUCAUCCCUUCCGGAUCUCCAGCUC
...---------------------((.......(((((..((((((((...(((....((((...)))).....)))...)))))))).((....)).......))))).......)).. ( -18.44)
>DroYak_CAF1 168735 120 + 1
AUUGCCCAUUGCCCAUUGCCCAUUGCCCACUUCCCGGACACUGGGCAACUAAAUUAAUUCGAUAAUUGACUUCCAUUGCCUUGCCCGGAACCAUUGUCAUCCCUUCCGGAUCUCCAGCUC
...((.((..((...(((((((.((.((.......)).)).))))))).....((((((....))))))........))..)).((((((.............)))))).......)).. ( -23.72)
>consensus
AUU_____________________GCCCACUUCCCGGACACUGGGCAACUAAAUUAAUUCGAUAAUUGACUUCCAUUGCCUUGCCCGGAACCAUUGUCAUCCCUUCCGGAUCUCCAGCUA
........................((.......((((.((..((((((..((.((((((....)))))).))...)))))))).))))...................((....)).)).. (-18.00 = -18.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,917,319 – 8,917,418
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.88
Mean single sequence MFE -33.78
Consensus MFE -31.20
Energy contribution -31.60
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.75
Structure conservation index 0.92
SVM decision value 4.52
SVM RNA-class probability 0.999914
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8917319 99 - 20766785
UAGCUGGAGAUCCGGAAGGUAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAGUGUCCGGGAAGUGGGC---------------------AAU
..(((......((....)).....((....(((((((((.((((((..((((.((((....)))).)))).))))))...)))))))))..)))))---------------------... ( -32.60)
>DroSec_CAF1 162281 99 - 1
UAGCUGGAGAUCCGGAAGGGAUGACAAUGGAUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAGUGUCCGGGAAGUGGGC---------------------AAU
..(((.(...(((....)))...........((((((((.((((((..((((.((((....)))).)))).))))))...))))))))...).)))---------------------... ( -31.90)
>DroSim_CAF1 162954 99 - 1
UAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAGUGUCCGGGAAGUGGGC---------------------AAU
..(((.....(((....)))....((....(((((((((.((((((..((((.((((....)))).)))).))))))...)))))))))..)))))---------------------... ( -34.00)
>DroEre_CAF1 166504 99 - 1
GAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAGUGUCCGGGAAGUGGGC---------------------AAU
..(((.....(((....)))....((....(((((((((.((((((..((((.((((....)))).)))).))))))...)))))))))..)))))---------------------... ( -34.00)
>DroYak_CAF1 168735 120 - 1
GAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAGUGUCCGGGAAGUGGGCAAUGGGCAAUGGGCAAUGGGCAAU
..(((.(.(((((....))).((((..(.(((((......)).))).)..))))....))...........((((((((.((((((.....)))))).))))))))......).)))... ( -36.40)
>consensus
UAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAGUGUCCGGGAAGUGGGC_____________________AAU
..(((.....(((....)))....((....(((((((((.((((((..((((.((((....)))).)))).))))))...)))))))))..)))))........................ (-31.20 = -31.60 +   0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,917,338 – 8,917,434
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.05
Mean single sequence MFE -32.12
Consensus MFE -25.60
Energy contribution -26.04
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -1.69
Structure conservation index 0.80
SVM decision value 0.37
SVM RNA-class probability 0.709067
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8917338 96 - 20766785
UG------------------------UGGAACUGUAGCUGUAGCUGGAGAUCCGGAAGGUAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAG
..------------------------.(((((((((((....)))(.....((....)).....).))))))))(((((((((.......)))(((((......)))))...)))))).. ( -27.70)
>DroSec_CAF1 162300 96 - 1
GC------------------------UGGAGCUGUAGCUGUAGCUGGAGAUCCGGAAGGGAUGACAAUGGAUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAG
.(------------------------((((.((.((((....)))).)).)))))...((((........))))(((((((((.......)))(((((......)))))...)))))).. ( -30.30)
>DroSim_CAF1 162973 96 - 1
GC------------------------UGGAACUGUAGCUGUAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAG
.(------------------------((((.((.((((....)))).)).)))))..(((((.......)))))(((((((((.......)))(((((......)))))...)))))).. ( -30.50)
>DroEre_CAF1 166523 114 - 1
GCCGGAGCUGGAGCU------GGAGAUGGAGCUGGAGCUGGAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAG
(((..((((..((((------........))))..))))(((((((..(.(((....))).)..)...)))))).)))..((((((..((((.((((....)))).)))).))))))... ( -36.70)
>DroYak_CAF1 168775 120 - 1
GCUGGUGCUGUUGCUGUUACUGUUGCUGGAGCUGGAGGUGGAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAG
.((((.(((((((..((..((....(((((.(..(........)..)...))))).))..))..))))))).))))....((((((..((((.((((....)))).)))).))))))... ( -35.40)
>consensus
GC________________________UGGAGCUGUAGCUGUAGCUGGAGAUCCGGAAGGGAUGACAAUGGUUCCGGGCAAGGCAAUGGAAGUCAAUUAUCGAAUUAAUUUAGUUGCCCAG
...........................((((((..(((....)))(..(.(((....))).)..)...))))))(((((((((.......)))(((((......)))))...)))))).. (-25.60 = -26.04 +   0.44)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:31:38 2006