Locus 3844

Sequence ID 3R_DroMel_CAF1
Location 10,482,780 – 10,482,913
Length 133
Max. P 0.999998
window6157 window6158 window6159

overview

Window 7

Location 10,482,780 – 10,482,882
Length 102
Sequences 3
Columns 113
Reading direction forward
Mean pairwise identity 79.76
Mean single sequence MFE -27.59
Consensus MFE -23.42
Energy contribution -23.10
Covariance contribution -0.32
Combinations/Pair 1.21
Mean z-score -2.57
Structure conservation index 0.85
SVM decision value 2.61
SVM RNA-class probability 0.995701
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10482780 102 + 27905053
UUCAACCCGGUCAUGGUUAAUUCACACCA-----------CAACUAAACGCCGAGAUGCCGAACAUAUGAGAGGCUCGACUUAAGAUGUUCGGCAUUCGAAUUUCUAACGUCU
........(((..((((........))))-----------..)))......((((.((((((((((....(((......)))...)))))))))))))).............. ( -26.50)
>DroSec_CAF1 29009 102 + 1
UUCAAACCAGUCUUGGUUCAUAGAUACCAUAU-----------AUAAACGCUGAGAUGCUGAAUAUCUAAGAGGCUCGACUUUAGAUGUUCGGCAUUCGAAUUCCUAAUGUCU
(((....((((..((((........))))...-----------......)))).(((((((((((((((.(((......)))))))))))))))))).)))............ ( -26.50)
>DroSim_CAF1 29683 113 + 1
UUCAAACCUGUCUUUGUUCAUAGAUACCAUAUUCAUACCACAAAUAAACGCUGAGAUGCCGAACAUCUAACAGGCUCGACUUUAGAUGUUCGGCAUUCGAAUUCCUAAUGUGU
........(((((........)))))............((((.........((((.((((((((((((((.((......)))))))))))))))))))).........)))). ( -29.77)
>consensus
UUCAAACCAGUCUUGGUUCAUAGAUACCAUAU________CAAAUAAACGCUGAGAUGCCGAACAUCUAAGAGGCUCGACUUUAGAUGUUCGGCAUUCGAAUUCCUAAUGUCU
.........((((........))))..........................((((.((((((((((((((.((......)))))))))))))))))))).............. (-23.42 = -23.10 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,482,809 – 10,482,913
Length 104
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 72.44
Mean single sequence MFE -28.66
Consensus MFE -22.26
Energy contribution -22.27
Covariance contribution 0.01
Combinations/Pair 1.15
Mean z-score -3.46
Structure conservation index 0.78
SVM decision value 6.42
SVM RNA-class probability 0.999998
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10482809 104 + 27905053
------CAACUAAACGCCGAGAUGCCGAACAUAUGAGAGGCUCGACUUAAGAUGUUCGGCAUUCGAAUUUCUAACGUCUCCAAAUGGGAGACUUUUAAAAUCACGAUCAG
------........((.((((.((((((((((....(((......)))...))))))))))))))..........((((((.....))))))...........))..... ( -31.70)
>DroSec_CAF1 29041 85 + 1
---------AUAAACGCUGAGAUGCUGAAUAUCUAAGAGGCUCGACUUUAGAUGUUCGGCAUUCGAAUUCCUAAUGUCU---AAU----A----UCAGAAUUAGC-----
---------......((((((((((((((((((((.(((......)))))))))))))))))).............(((---...----.----..))).)))))----- ( -25.10)
>DroSim_CAF1 29717 98 + 1
AUACCACAAAUAAACGCUGAGAUGCCGAACAUCUAACAGGCUCGACUUUAGAUGUUCGGCAUUCGAAUUCCUAAUGUGU---AAU----GACUUUUAAAGUUACG-----
....((((.........((((.((((((((((((((.((......)))))))))))))))))))).........)))).---..(----((((.....)))))..----- ( -29.17)
>consensus
______CAAAUAAACGCUGAGAUGCCGAACAUCUAAGAGGCUCGACUUUAGAUGUUCGGCAUUCGAAUUCCUAAUGUCU___AAU____GACUUUUAAAAUUACG_____
.................((((.((((((((((((((.((......))))))))))))))))))))............................................. (-22.26 = -22.27 +   0.01)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,482,809 – 10,482,913
Length 104
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 72.44
Mean single sequence MFE -27.13
Consensus MFE -17.10
Energy contribution -18.43
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.63
SVM decision value 4.19
SVM RNA-class probability 0.999832
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10482809 104 - 27905053
CUGAUCGUGAUUUUAAAAGUCUCCCAUUUGGAGACGUUAGAAAUUCGAAUGCCGAACAUCUUAAGUCGAGCCUCUCAUAUGUUCGGCAUCUCGGCGUUUAGUUG------
((((.(((((((((.((.((((((.....)))))).)).))))))((((((((((((((....((........))...))))))))))).)))))).))))...------ ( -34.10)
>DroSec_CAF1 29041 85 - 1
-----GCUAAUUCUGA----U----AUU---AGACAUUAGGAAUUCGAAUGCCGAACAUCUAAAGUCGAGCCUCUUAGAUAUUCAGCAUCUCAGCGUUUAU---------
-----(((..((((((----(----...---....)))))))....((((((.(((.((((((((......)).)))))).))).)))).)))))......--------- ( -18.30)
>DroSim_CAF1 29717 98 - 1
-----CGUAACUUUAAAAGUC----AUU---ACACAUUAGGAAUUCGAAUGCCGAACAUCUAAAGUCGAGCCUGUUAGAUGUUCGGCAUCUCAGCGUUUAUUUGUGGUAU
-----................----...---.((((....((((.((((((((((((((((((((......)).))))))))))))))).)).).))))...)))).... ( -29.00)
>consensus
_____CGUAAUUUUAAAAGUC____AUU___AGACAUUAGGAAUUCGAAUGCCGAACAUCUAAAGUCGAGCCUCUUAGAUGUUCGGCAUCUCAGCGUUUAUUUG______
..............................................(((((((((((((((((((......)).))))))))))))))).)).................. (-17.10 = -18.43 +   1.33)

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 11:11:28 2006