Locus 3233

Sequence ID 2L_DroMel_CAF1
Location 9,278,344 – 9,278,441
Length 97
Max. P 0.889655
window5135 window5136

overview

Window 5

Location 9,278,344 – 9,278,441
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 89.00
Mean single sequence MFE -23.06
Consensus MFE -16.90
Energy contribution -19.03
Covariance contribution 2.13
Combinations/Pair 1.15
Mean z-score -2.14
Structure conservation index 0.73
SVM decision value 0.65
SVM RNA-class probability 0.812860
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9278344 97 + 22407834
UAAAUUCUUUCGAAGCCAACAUCUAAGUCAACUCUAUCGGCUUCAGAAUGCUUAGUUGCAGCUAAGAAUUCUAAGAAUGUCUGAGCUUCAAAGGAAA
....((((((.((((((((((((((((((.........))))).(((((.((((((....)))))).))))).)).)))).)).))))).)))))). ( -27.60)
>DroSec_CAF1 108377 97 + 1
UAAAUUCUUCCGAAGCCAACAUCUAAGUCAACUCUAUCGGCUUUAGAAUGCUUAGGUGCAGCUAAGAAUUCUAAGAAUGUCUGAGCCUCAAAGGAAA
....(((((..((.(((((((((((((((.........)))))((((((.(((((......))))).)))))))).)))).)).)).))..))))). ( -21.60)
>DroSim_CAF1 110490 97 + 1
UAAAUUCUUUCGUAGCCAACAUCUAAGUCAACUCUAUCGGCUUUAGAAUGCUUAGUUGCAGCUAAGAAUUCUAAGAAUGUCUGAGCCUCAAAGGAAA
....((((((.(..(((((((((((((((.........)))))((((((.((((((....)))))).)))))))).)))).)).))..).)))))). ( -23.70)
>DroYak_CAF1 115875 93 + 1
UACAUUUCUUCGAGGACAACAUCU----CAACUCUAUUUGCUGCGAAAUGCUUAGUUGCAGCUAAGAAUGCUAAGAAUGUCUGAGUCUCAAAGGAAA
....((((((.((((.((((((((----...........(((((((.........)))))))...........)).)))).))..)))).)))))). ( -19.35)
>consensus
UAAAUUCUUUCGAAGCCAACAUCUAAGUCAACUCUAUCGGCUUCAGAAUGCUUAGUUGCAGCUAAGAAUUCUAAGAAUGUCUGAGCCUCAAAGGAAA
....((((((.((((((((((((((((((.........))))).(((((.(((((......))))).))))).)).)))).)).))))).)))))). (-16.90 = -19.03 +   2.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 9,278,344 – 9,278,441
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 89.00
Mean single sequence MFE -25.75
Consensus MFE -19.12
Energy contribution -19.88
Covariance contribution 0.75
Combinations/Pair 1.15
Mean z-score -2.41
Structure conservation index 0.74
SVM decision value 0.96
SVM RNA-class probability 0.889655
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9278344 97 - 22407834
UUUCCUUUGAAGCUCAGACAUUCUUAGAAUUCUUAGCUGCAACUAAGCAUUCUGAAGCCGAUAGAGUUGACUUAGAUGUUGGCUUCGAAAGAAUUUA
.(((.(((((((((..((((((.(((((((.(((((......))))).)))))))........(((....))).))))))))))))))).))).... ( -26.90)
>DroSec_CAF1 108377 97 - 1
UUUCCUUUGAGGCUCAGACAUUCUUAGAAUUCUUAGCUGCACCUAAGCAUUCUAAAGCCGAUAGAGUUGACUUAGAUGUUGGCUUCGGAAGAAUUUA
(((((.....((((.........(((((((.(((((......))))).)))))))))))....((((..((......))..)))).)))))...... ( -26.10)
>DroSim_CAF1 110490 97 - 1
UUUCCUUUGAGGCUCAGACAUUCUUAGAAUUCUUAGCUGCAACUAAGCAUUCUAAAGCCGAUAGAGUUGACUUAGAUGUUGGCUACGAAAGAAUUUA
.(((.((((.((((.........(((((((.(((((......))))).))))))))))).....(((..((......))..))).)))).))).... ( -24.60)
>DroYak_CAF1 115875 93 - 1
UUUCCUUUGAGACUCAGACAUUCUUAGCAUUCUUAGCUGCAACUAAGCAUUUCGCAGCAAAUAGAGUUG----AGAUGUUGUCCUCGAAGAAAUGUA
....(((((((((...(((((.((((((..(((..(((((.............)))))....)))))))----))))))))).)))))))....... ( -25.42)
>consensus
UUUCCUUUGAGGCUCAGACAUUCUUAGAAUUCUUAGCUGCAACUAAGCAUUCUAAAGCCGAUAGAGUUGACUUAGAUGUUGGCUUCGAAAGAAUUUA
.(((.(((((((((..((((((.(((((((.(((((......))))).)))))))(((.......)))......))))))))))))))).))).... (-19.12 = -19.88 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:35 2006