Locus 7641

Sequence ID 3R_DroMel_CAF1
Location 20,467,169 – 20,467,298
Length 129
Max. P 0.980187
window12337 window12338 window12339

overview

Window 7

Location 20,467,169 – 20,467,274
Length 105
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.75
Mean single sequence MFE -24.65
Consensus MFE -17.81
Energy contribution -17.12
Covariance contribution -0.69
Combinations/Pair 1.29
Mean z-score -1.16
Structure conservation index 0.72
SVM decision value 0.50
SVM RNA-class probability 0.760276
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20467169 105 + 27905053
AUAA---C-------GA-----AUCUCACUUGAAAUAUGUGUGCUCGAAAAUGUUGCGAUCCUGCAGGAACUGUCGAUUGUCCUGCCAAAUCCAAUCCUCGAGCUCCUUGUUCAACAAUG
....---.-------..-----.......(((((....(.(.((((((....((((.(((...((((((.(........)))))))...)))))))..)))))).))...)))))..... ( -25.70)
>DroVir_CAF1 18901 108 + 1
AGAAUUUU------------UAUACCCACUUGAAGUAGGUGUGCUCGAAGAUAUUUCGAUCUUGCAAGAACUGUCGGUUAUCCUGCCAAAUCCAAUCUUCCAGCUCCUUACUCAACAAUG
........------------.........((((.(((((.(.(((.((((((.......(((....)))......(((......))).......)))))).))).))))))))))..... ( -22.00)
>DroGri_CAF1 23154 120 + 1
GAGAUUGUUUUUGCUUGUUGUCUGCUCACUUGAAGUAGGUGUGCUCGAAGAUGUUGCGAUCUUGCAGGAACUGUCUAUUGUCCUGCCAUAUCCAAUCCUCUAGCUCCUUGCUCAACAAUG
...((((((...((..(..((..((.((((((...)))))).))....(((.((((.(((...((((((.(........)))))))...)))))))..))).))..)..))..)))))). ( -27.80)
>DroWil_CAF1 19500 97 + 1
-----------------------GCUUACUUGAAAUAGGUGUGCUCGAAGAUAUUUCGAUCUUGGAGGAAUUGUCGAUUGUCCUGCCAGAUCCAAUCUUCAAGCUCUUUAUUCAAAAAUG
-----------------------......(((((..(((...(((.((((((.....(((((.((((((...........)))).)))))))..)))))).))).)))..)))))..... ( -23.80)
>DroMoj_CAF1 19966 108 + 1
AUAAAUAU------------UAAUCUCACUUAAAGUAUGUGUGCUCGAAGAUAUUUCGAUCUUGCAAGAACUGUCUGUUGUCUUGCCAAAUCCAAUCUUCCAGUUCCUUGCUUAACAAAG
........------------............(((((.(.(.(((.((((((.....(((...((((((((.....))..))))))...)))..)))))).))).)).)))))....... ( -18.80)
>DroAna_CAF1 17433 99 + 1
GU---------------------ACUUACUUGAAAUAAGUGUGCUCGAAGAUGUUGCGAUCUUGCAGGAACUGCCUGUUGUCCUGCCAGAUCCAAUCCUCCAGCUCCUUGUUCAACAAUG
..---------------------......(((((.((((.(.(((.((.(((..((.(((((.((((((((.....))..)))))).)))))))))).)).))).))))))))))..... ( -29.80)
>consensus
AUAA___U_______________ACUCACUUGAAAUAGGUGUGCUCGAAGAUAUUGCGAUCUUGCAGGAACUGUCGAUUGUCCUGCCAAAUCCAAUCCUCCAGCUCCUUGCUCAACAAUG
.............................((((.(((((.(.(((.((.(((.....(((...((((((.(........)))))))...)))..))).)).))).))))))))))..... (-17.81 = -17.12 +  -0.69)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,467,169 – 20,467,274
Length 105
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.75
Mean single sequence MFE -29.49
Consensus MFE -22.91
Energy contribution -21.83
Covariance contribution -1.08
Combinations/Pair 1.31
Mean z-score -2.25
Structure conservation index 0.78
SVM decision value 1.86
SVM RNA-class probability 0.980187
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20467169 105 - 27905053
CAUUGUUGAACAAGGAGCUCGAGGAUUGGAUUUGGCAGGACAAUCGACAGUUCCUGCAGGAUCGCAACAUUUUCGAGCACACAUAUUUCAAGUGAGAU-----UC-------G---UUAU
........(((.....((((((((((((((((..(((((((........).))))))..)))).))..))))))))))......(((((....)))))-----..-------)---)).. ( -30.80)
>DroVir_CAF1 18901 108 - 1
CAUUGUUGAGUAAGGAGCUGGAAGAUUGGAUUUGGCAGGAUAACCGACAGUUCUUGCAAGAUCGAAAUAUCUUCGAGCACACCUACUUCAAGUGGGUAUA------------AAAAUUCU
.......((((.....(((.(((((((.(((((.((((((...........)))))).))))).)...)))))).)))..((((((.....))))))...------------...)))). ( -32.40)
>DroGri_CAF1 23154 120 - 1
CAUUGUUGAGCAAGGAGCUAGAGGAUUGGAUAUGGCAGGACAAUAGACAGUUCCUGCAAGAUCGCAACAUCUUCGAGCACACCUACUUCAAGUGAGCAGACAACAAGCAAAAACAAUCUC
..((((((.((.....(((.(((((((((((...(((((((........).))))))...))).))..)))))).))).(((.........))).))...)))))).............. ( -30.60)
>DroWil_CAF1 19500 97 - 1
CAUUUUUGAAUAAAGAGCUUGAAGAUUGGAUCUGGCAGGACAAUCGACAAUUCCUCCAAGAUCGAAAUAUCUUCGAGCACACCUAUUUCAAGUAAGC-----------------------
....((((((......(((((((((((.(((((((.((((...........)))))).))))).)...))))))))))........)))))).....----------------------- ( -26.84)
>DroMoj_CAF1 19966 108 - 1
CUUUGUUAAGCAAGGAACUGGAAGAUUGGAUUUGGCAAGACAACAGACAGUUCUUGCAAGAUCGAAAUAUCUUCGAGCACACAUACUUUAAGUGAGAUUA------------AUAUUUAU
(((((.....)))))..((.(((((((.(((((.(((((((........).)))))).))))).)...)))))).))..(((.........)))......------------........ ( -23.60)
>DroAna_CAF1 17433 99 - 1
CAUUGUUGAACAAGGAGCUGGAGGAUUGGAUCUGGCAGGACAACAGGCAGUUCCUGCAAGAUCGCAACAUCUUCGAGCACACUUAUUUCAAGUAAGU---------------------AC
................(((.(((((((((((((.(((((((........).)))))).))))).))..)))))).)))..((((((.....))))))---------------------.. ( -32.70)
>consensus
CAUUGUUGAACAAGGAGCUGGAAGAUUGGAUUUGGCAGGACAACAGACAGUUCCUGCAAGAUCGAAACAUCUUCGAGCACACCUACUUCAAGUGAGA_______________A___UUAU
.....(((((....(.(((.((((((..(((((.((((((...........)))))).))))).....)))))).))).)......)))))............................. (-22.91 = -21.83 +  -1.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,467,194 – 20,467,298
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.07
Mean single sequence MFE -33.97
Consensus MFE -22.15
Energy contribution -21.99
Covariance contribution -0.16
Combinations/Pair 1.37
Mean z-score -2.03
Structure conservation index 0.65
SVM decision value 1.62
SVM RNA-class probability 0.967811
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20467194 104 - 27905053
-------C---------CCAGAAGCUACAACUAUUUCGUCCAUUGUUGAACAAGGAGCUCGAGGAUUGGAUUUGGCAGGACAAUCGACAGUUCCUGCAGGAUCGCAACAUUUUCGAGCAC
-------.---------.....................(((.(((.....))))))((((((((((((((((..(((((((........).))))))..)))).))..)))))))))).. ( -32.10)
>DroVir_CAF1 18929 120 - 1
GUGGAAGCAAAAGCGUCUAAUAAGCUACAACAGUUUCGUCCAUUGUUGAGUAAGGAGCUGGAAGAUUGGAUUUGGCAGGAUAACCGACAGUUCUUGCAAGAUCGAAAUAUCUUCGAGCAC
.((((.((....)).))))....(((.(((((((.......)))))))))).....(((.(((((((.(((((.((((((...........)))))).))))).)...)))))).))).. ( -34.90)
>DroGri_CAF1 23194 120 - 1
GCGGAAGCCAAAGUGUCCACAAAGCCACAACAGUUUCGUCCAUUGUUGAGCAAGGAGCUAGAGGAUUGGAUAUGGCAGGACAAUAGACAGUUCCUGCAAGAUCGCAACAUCUUCGAGCAC
(((((.((....)).))).........(((((((.......))))))).)).....(((.(((((((((((...(((((((........).))))))...))).))..)))))).))).. ( -34.70)
>DroWil_CAF1 19517 104 - 1
-------C---------UCAUAAAUUGCAGCUAUUUCGUCCAUUUUUGAAUAAAGAGCUUGAAGAUUGGAUCUGGCAGGACAAUCGACAAUUCCUCCAAGAUCGAAAUAUCUUCGAGCAC
-------.---------.............((..((((........))))...)).(((((((((((.(((((((.((((...........)))))).))))).)...)))))))))).. ( -26.00)
>DroAna_CAF1 17452 104 - 1
-------C---------CCAGAAGUUGCUACUAUUUCGUCCAUUGUUGAACAAGGAGCUGGAGGAUUGGAUCUGGCAGGACAACAGGCAGUUCCUGCAAGAUCGCAACAUCUUCGAGCAC
-------.---------...(((((.......))))).(((.(((.....))))))(((.(((((((((((((.(((((((........).)))))).))))).))..)))))).))).. ( -35.20)
>DroPer_CAF1 17635 110 - 1
-------C---UUCGUCCUUCAAGCUGCAGCUUCUUCGUCCUCUGCUGAACAAAGAGCUGGAGGACUGGAUCUGGCAGGACAACCGCCAGUUCCUGCAGGAGCGCAACAUCUUCGACCAC
-------.---...(((........(((.((((((.(((((((((((........))).))))))).(((.(((((.((....))))))).))).).)))))))))........)))... ( -40.89)
>consensus
_______C_________CCAGAAGCUACAACUAUUUCGUCCAUUGUUGAACAAGGAGCUGGAGGAUUGGAUCUGGCAGGACAACCGACAGUUCCUGCAAGAUCGCAACAUCUUCGAGCAC
.......................(((.((((.............))))))).....(((.((((((..(((((.((((((...........)))))).))))).....)))))).))).. (-22.15 = -21.99 +  -0.16)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:01 2006