Locus 3894

Sequence ID 3L_DroMel_CAF1
Location 11,278,293 – 11,278,430
Length 137
Max. P 0.827365
window6064 window6065

overview

Window 4

Location 11,278,293 – 11,278,405
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.42
Mean single sequence MFE -32.12
Consensus MFE -22.09
Energy contribution -21.87
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.85
Structure conservation index 0.69
SVM decision value 0.70
SVM RNA-class probability 0.827365
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11278293 112 - 23771897
CAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCAGACUACG--------CGCUACCCGCUACUCCUUUUCCCAAAUGAAACG
.........(((((..............((((((.(((((((((((...........)))))))))))))))))....(--------((.....)))............)))))...... ( -32.40)
>DroPse_CAF1 3817 110 - 1
CAUUGAUUAAUUUGAAAUUUAUGAUGCGACUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUUG---GGAGCACCCCUGC-----ACCCUUGCG-CCCUCCACCCCAUGA-ACG
.................((((((.((.((..(((((((((((((((...........))))))))))))(---((.(((....)))-----.)))...))-)..))))...)))))-).. ( -34.10)
>DroSec_CAF1 2513 108 - 1
CAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAAGUUUUGCUCUGCGGUCGCUGGCAACUCCC------------CACUACCCCUUUUGCCAAAUGAAACG
((((...........................(((.(((((((((((...........))))))))))))))((((((.....------------...........))))))))))..... ( -28.59)
>DroSim_CAF1 4783 119 - 1
CAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCUGGCAACUCCCCUGCCCACCACCCACUACCCCU-UUGCCAAAUGAAACG
.................(((((...((....(((.(((((((((((...........)))))))))))))).((((.......)))).................-..))...)))))... ( -29.60)
>DroEre_CAF1 2621 116 - 1
CAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCUGGCACCAACCCG----GCUAACCGCUACCCCUUUCCAGAAGUGAAACG
(((.((((.......)))).)))..(((((((.(((((((((((((...........))))))))))))(((((.......)))----))................))))))))...... ( -36.40)
>DroPer_CAF1 3883 110 - 1
CAUUGAUUAAUUUGAAAUUUAUGAUGCGACUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUUG---GCAGCACCCCUGC-----ACCCUUGAG-CCCUCCACCCCAUGA-ACG
.................((((((....(.((((.((((((((((((...........)))))))))))).---)))))......((-----........)-).........)))))-).. ( -31.60)
>consensus
CAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCUGGCAACACCCCU_______ACCCACUACCCCUUUCACCAAAUGAAACG
(((.((((.......)))).))).(((....)))((((((((((((...........))))))))))))................................................... (-22.09 = -21.87 +  -0.22)

alignment

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secondary structure

Postscript

dotplot

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Window 5

Location 11,278,326 – 11,278,430
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.51
Mean single sequence MFE -40.27
Consensus MFE -25.08
Energy contribution -25.63
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.98
Structure conservation index 0.62
SVM decision value 0.42
SVM RNA-class probability 0.728044
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11278326 104 - 23771897
------------GCGAAGGACAUUGGGG---GCGUAAGCCCAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCAGACUACG-
------------.((((....((..(((---((....)))).)..))...))))..............((((((.(((((((((((...........))))))))))))))))).....- ( -40.50)
>DroPse_CAF1 3850 117 - 1
GGCAGCAGGACGGCCAAGGACUUUGUUGUCCUCAUAAGCCCAUUGAUUAAUUUGAAAUUUAUGAUGCGACUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUUG---GGAGCAC
....((((((((((.((....)).)))))))(((((((....(..(.....)..)..))))))))))(.((.(.((((((((((((...........)))))))))))).---).))).. ( -38.60)
>DroSec_CAF1 2541 104 - 1
------------GCGAAGAACAUUGG-G---GCGUAAGCCCAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAAGUUUUGCUCUGCGGUCGCUGGCAACUC
------------.((((...((...(-(---((....))))..)).....))))..........((((...(((.(((((((((((...........)))))))))))))).)))).... ( -38.60)
>DroSim_CAF1 4822 104 - 1
------------GCGAAGGACAUUGG-G---GCGUAAGCCCAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCUGGCAACUC
------------.((((...((...(-(---((....))))..)).....))))..........((((...(((.(((((((((((...........)))))))))))))).)))).... ( -38.60)
>DroEre_CAF1 2657 103 - 1
------------GCGAAGGACAUUG--G---GCGUAAGCCCAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCUGGCACCAA
------------.....((.((.((--(---((....))))).))...................((((...(((.(((((((((((...........)))))))))))))).)))))).. ( -42.20)
>DroPer_CAF1 3916 117 - 1
GGCAGCAGGACGGCCAAGGACUUUGUUGUCCUCAUAAGCCCAUUGAUUAAUUUGAAAUUUAUGAUGCGACUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUUG---GCAGCAC
....((((((((((.((....)).)))))))(((((((....(..(.....)..)..))))))))))(.((((.((((((((((((...........)))))))))))).---))))).. ( -43.10)
>consensus
____________GCGAAGGACAUUGG_G___GCGUAAGCCCAUUGAUUAAUUUGAAAUUUAUGAUGCUUCUGCGGAUCGCAGGGCAUCCAUAACUUUUGCUCUGCGGUCGCUGGCAACAC
...............................(((.((((.(((.((((.......)))).)))..)))).))).((((((((((((...........))))))))))))........... (-25.08 = -25.63 +   0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:25 2006