Locus 1554

Sequence ID 2R_DroMel_CAF1
Location 5,888,682 – 5,888,837
Length 155
Max. P 0.742244
window2610 window2611

overview

Window 0

Location 5,888,682 – 5,888,797
Length 115
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 88.42
Mean single sequence MFE -39.67
Consensus MFE -30.18
Energy contribution -30.62
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -2.14
Structure conservation index 0.76
SVM decision value 0.14
SVM RNA-class probability 0.604748
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5888682 115 + 20766785
CCACAGGGCACUACGAUGGCCAUUGA-GCCAUGCCAAGGAAGCAGUGAAUCCUGCUACCGCUCAAAUGUCUCGAGUUGAUCGUCUGCCCAGUUAUGGGUAGAUCUGGG--UCCUUUAU
....((((((((.(((.(((..((((-((........((.(((((......))))).))))))))..))))))))).....(((((((((....)))))))))....)--)))).... ( -40.80)
>DroSec_CAF1 24826 118 + 1
CCACAGGGCACUACGAUGGACAUUGAUGCCAUUCCGAGGAAGCAGUGAAUCCUGCUCCCGCUCGAAUGUCUCGAGUUUAUCGUCUGCCCAGUUAUGGCCAGAUCUAUCUCUCCCCGAA
.....(((((..(((((((((.((((.(.(((((((.(((.((((......)))))))))...))))).)))))))))))))).))))).....(((..(((......)))..))).. ( -39.90)
>DroSim_CAF1 23471 118 + 1
CCACAGGGCACUACGAUGGACAUUGAUGCCAUUCCGAGGAAGCAGUGAAUCCUGCUCCCGCUCGCAUGUCUCGAGUUUAUCGUCUGUCCAGUUAUGGCCAGAUCUAUCUCUCCAUGAA
.....(((((..(((((((((.((((.(.(((..(((((.(((((......)))))..).)))).))).)))))))))))))).)))))..((((((..(((....)))..)))))). ( -38.30)
>consensus
CCACAGGGCACUACGAUGGACAUUGAUGCCAUUCCGAGGAAGCAGUGAAUCCUGCUCCCGCUCGAAUGUCUCGAGUUUAUCGUCUGCCCAGUUAUGGCCAGAUCUAUCUCUCCAUGAA
.....(((((..(((((((((.((((.((........((.(((((......))))).))........)).))))))))))))).)))))............................. (-30.18 = -30.62 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,888,721 – 5,888,837
Length 116
Sequences 3
Columns 118
Reading direction forward
Mean pairwise identity 87.29
Mean single sequence MFE -35.47
Consensus MFE -25.31
Energy contribution -25.53
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -2.53
Structure conservation index 0.71
SVM decision value 0.45
SVM RNA-class probability 0.742244
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5888721 116 + 20766785
AGCAGUGAAUCCUGCUACCGCUCAAAUGUCUCGAGUUGAUCGUCUGCCCAGUUAUGGGUAGAUCUGGG--UCCUUUAUGGGUCCUUUCGAUGAUUACCAUUUGCGACAUAUCUUCGUU
(((((......))))).........(((((.(((((((((((((((((((....))))))((...((.--.((.....))..))..))))))))))..))))).)))))......... ( -40.50)
>DroSec_CAF1 24866 118 + 1
AGCAGUGAAUCCUGCUCCCGCUCGAAUGUCUCGAGUUUAUCGUCUGCCCAGUUAUGGCCAGAUCUAUCUCUCCCCGAAGAGUCCUUUCGAUGAUUUCCAUUUGGGACAUUUCUUCGCU
(((((......)))))...((((((.....)))))).....(((((.(((....))).)))))...........(((((((((((...((((.....)))).)))))...)))))).. ( -34.10)
>DroSim_CAF1 23511 118 + 1
AGCAGUGAAUCCUGCUCCCGCUCGCAUGUCUCGAGUUUAUCGUCUGUCCAGUUAUGGCCAGAUCUAUCUCUCCAUGAAGAGUCCUUUCGAUGAUUUCUAUUUGGGACAUAUCUUCGCU
...((((((....((........))(((((((((((..((((((.......((((((..(((....)))..)))))).(((....)))))))))....)))))))))))...)))))) ( -31.80)
>consensus
AGCAGUGAAUCCUGCUCCCGCUCGAAUGUCUCGAGUUUAUCGUCUGCCCAGUUAUGGCCAGAUCUAUCUCUCCAUGAAGAGUCCUUUCGAUGAUUUCCAUUUGGGACAUAUCUUCGCU
(((((......))))).........(((((((((((((((((((((.(((....))).)))))...............(((....)))))))).....)))))))))))......... (-25.31 = -25.53 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:07:24 2006