Locus 2925

Sequence ID 3R_DroMel_CAF1
Location 7,846,418 – 7,846,532
Length 114
Max. P 0.880843
window4708 window4709

overview

Window 8

Location 7,846,418 – 7,846,532
Length 114
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 88.84
Mean single sequence MFE -25.98
Consensus MFE -17.26
Energy contribution -18.57
Covariance contribution 1.31
Combinations/Pair 1.04
Mean z-score -2.24
Structure conservation index 0.66
SVM decision value 0.23
SVM RNA-class probability 0.646177
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7846418 114 + 27905053
---UAUUUACAUCUUGAGUUAGGAACGCAUGGAUGUGUGAUGAAAACAAGUUAUGCGUAUAUGAAUUGAGUGUUCUCAUUGAAAGUCGCAAGUUCAGCAGUAUGAUGAAGAUGUAAG-
---...(((((((((..((((...((((((((...(((.......)))..))))))))...((((((..((((((.....)))...))).))))))......)))).))))))))).- ( -28.50)
>DroSec_CAF1 9534 112 + 1
---UAUUUACAUCUUGAAUUAGGAACGCAUGGAUGUGUGAUGAAAACAAGUUAUGCGUAUAUGAAUUGAGUGUUCUCAUUGAAAGUCGUAAGUUAA---GUAUGCUGAAAAUGUAAGA
---..((((((((((((.(((.((((((((((...(((.......)))..))))))))........((((....)))).......)).))).))))---).))).))))......... ( -23.40)
>DroSim_CAF1 9620 112 + 1
---UAUUUACAUCUUGAAUUAGGAACGCAUGGAUGUGUGAUGAAAACAAGUUAUGCGUAUAUGAAUUGAGUGUUCUCAUUGAAAGUCUUAAGUUAA---GUAUGAUGAAGAUGUAAGA
---..((((((((((..((((...((((((((...(((.......)))..))))))))...(((.(((((..(((.....)))...))))).))).---...)))).)))))))))). ( -27.80)
>DroYak_CAF1 9747 115 + 1
ACAUAUUUGCAUCUUGAAUUCGGAACGCAAGGAUGUGUGAUGAAAACAAGUUAUGCAUAUAAGAAUUAAGAGUUCUAAUUGAAAGUCGAAACGUAA---GUAUGUUGAAAAUCUAAGA
((((((((((.((((((.(((....(....).(((((((((........)))))))))....))))))))).(((.....))).........))))---))))))............. ( -24.20)
>consensus
___UAUUUACAUCUUGAAUUAGGAACGCAUGGAUGUGUGAUGAAAACAAGUUAUGCGUAUAUGAAUUGAGUGUUCUCAUUGAAAGUCGUAAGUUAA___GUAUGAUGAAAAUGUAAGA
.....((((((((((.(.......((((((((...(((.......)))..))))))))........((((....))))...........................).)))))))))). (-17.26 = -18.57 +   1.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 7,846,418 – 7,846,532
Length 114
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 88.84
Mean single sequence MFE -16.05
Consensus MFE -12.09
Energy contribution -12.65
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -2.26
Structure conservation index 0.75
SVM decision value 0.91
SVM RNA-class probability 0.880843
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7846418 114 - 27905053
-CUUACAUCUUCAUCAUACUGCUGAACUUGCGACUUUCAAUGAGAACACUCAAUUCAUAUACGCAUAACUUGUUUUCAUCACACAUCCAUGCGUUCCUAACUCAAGAUGUAAAUA---
-.(((((((((.........((.......))((.......((((....))))........((((((....(((.........)))...)))))).......)))))))))))...--- ( -18.10)
>DroSec_CAF1 9534 112 - 1
UCUUACAUUUUCAGCAUAC---UUAACUUACGACUUUCAAUGAGAACACUCAAUUCAUAUACGCAUAACUUGUUUUCAUCACACAUCCAUGCGUUCCUAAUUCAAGAUGUAAAUA---
..(((((((((........---..................((((....))))........((((((....(((.........)))...)))))).........)))))))))...--- ( -14.40)
>DroSim_CAF1 9620 112 - 1
UCUUACAUCUUCAUCAUAC---UUAACUUAAGACUUUCAAUGAGAACACUCAAUUCAUAUACGCAUAACUUGUUUUCAUCACACAUCCAUGCGUUCCUAAUUCAAGAUGUAAAUA---
..(((((((((........---..................((((....))))........((((((....(((.........)))...)))))).........)))))))))...--- ( -17.00)
>DroYak_CAF1 9747 115 - 1
UCUUAGAUUUUCAACAUAC---UUACGUUUCGACUUUCAAUUAGAACUCUUAAUUCUUAUAUGCAUAACUUGUUUUCAUCACACAUCCUUGCGUUCCGAAUUCAAGAUGCAAAUAUGU
.............(((((.---....((((..(.......)..))))..............(((((..((((..(((...((.((....)).))...)))..)))))))))..))))) ( -14.70)
>consensus
UCUUACAUCUUCAUCAUAC___UUAACUUACGACUUUCAAUGAGAACACUCAAUUCAUAUACGCAUAACUUGUUUUCAUCACACAUCCAUGCGUUCCUAAUUCAAGAUGUAAAUA___
..(((((((((.............................((((....))))........((((((....(((.........)))...)))))).........)))))))))...... (-12.09 = -12.65 +   0.56)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:47:55 2006