Locus 3739

Sequence ID 3L_DroMel_CAF1
Location 10,828,794 – 10,828,962
Length 168
Max. P 0.996874
window5839 window5840

overview

Window 9

Location 10,828,794 – 10,828,884
Length 90
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 90.53
Mean single sequence MFE -22.24
Consensus MFE -15.72
Energy contribution -15.94
Covariance contribution 0.22
Combinations/Pair 1.07
Mean z-score -2.08
Structure conservation index 0.71
SVM decision value 0.14
SVM RNA-class probability 0.602615
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10828794 90 + 23771897
GCUGCUGG--UUUGGGUUUUCGGUUUUUGUGAAAACCAGAUUUUUGUCGUUUUAUGCAUUAAAUUGUUUUUACAGCCGCUUUUGGCAGCCAG
(((((..(--...((.....((((...(((((((((..(((((.(((........)))..)))))))))))))))))))).)..)))))... ( -23.40)
>DroVir_CAF1 56701 80 + 1
---GGUGGCU-CUGGGU-UU-GG-UUUUGUGAAAACCAGAUUUUUGUCGUUUUAUGCAUUAAAUUGUUUUUACAGCCGCGUUUUAUA-----
---.((((((-..((((-((-((-(((.....))))))))))).....((.....(((......)))....))))))))........----- ( -19.50)
>DroSec_CAF1 37828 90 + 1
GUUGCUGG--UUUGGGUUUUCGGUUUUUGUGAAAACCAGAUUUUUGUCGUUUUAUGCAUUAAAUUGUUUUUACAGCCGCUUUUGGCAGCCAG
(((((..(--...((.....((((...(((((((((..(((((.(((........)))..)))))))))))))))))))).)..)))))... ( -21.00)
>DroSim_CAF1 38819 90 + 1
GCUGCUGG--UUUGGGUUUUCGGUUUUUGUGAAAACCAGAUUUUUGUCGUUUUAUGCAUUAAAUUGUUUUUACAGCCGCUUUUGGCAGCCAG
(((((..(--...((.....((((...(((((((((..(((((.(((........)))..)))))))))))))))))))).)..)))))... ( -23.40)
>DroYak_CAF1 38680 90 + 1
GCUGCUGG--UUUGGGUUUUUGGUUUUUGUGAAAACCAGAUUUUUGUCGUUUUAUGCAUUAAAUUGUUUUUACAGCCGCUUUUGGCAGCCAG
(((((..(--...((((((((((((((....)))))))))........((.....(((......)))....)))))).)..)..)))))... ( -23.90)
>consensus
GCUGCUGG__UUUGGGUUUUCGGUUUUUGUGAAAACCAGAUUUUUGUCGUUUUAUGCAUUAAAUUGUUUUUACAGCCGCUUUUGGCAGCCAG
(((((..(....(((...........((((((((((..(((((.(((........)))..))))))))))))))))))...)..)))))... (-15.72 = -15.94 +   0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,828,846 – 10,828,962
Length 116
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 96.72
Mean single sequence MFE -26.28
Consensus MFE -24.10
Energy contribution -24.14
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -2.06
Structure conservation index 0.92
SVM decision value 2.76
SVM RNA-class probability 0.996874
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10828846 116 - 23771897
GAUUAAAUGCAUAAAAACAGCAUAAAUCUAAAUUGUCAUCCAAGUUGUCAGUAUAACUGGCUUACGAAUCACCCUGUUCUGGCUGCCAAAAGCGGCUGUAAAAACAAUUUAAUGCA
((((..((((.........)))).))))((((((((..........(((((.....)))))((((((((......)))).((((((.....))))))))))..))))))))..... ( -25.10)
>DroSec_CAF1 37880 116 - 1
GAUUAAAUGCAUUAAAACUGCAUAAAUCUAAAUUGUCAUCCAAGUUGUCAGUAUAACUGGCUUACGAAUCACCCUGUUCUGGCUGCCAAAAGCGGCUGUAAAAACAAUUUAAUGCA
((((..(((((.......))))).))))((((((((..........(((((.....)))))((((((((......)))).((((((.....))))))))))..))))))))..... ( -26.50)
>DroSim_CAF1 38871 116 - 1
GAUUAAAUGCAUUAAAACAGCAUAAAUCUAAAUUGUCAUCCAAGUUGUCAGUAUAACUGGCUUACGAAUCACCCUGUUCUGGCUGCCAAAAGCGGCUGUAAAAACAAUUUAAUGCA
((((..((((.........)))).))))((((((((..........(((((.....)))))((((((((......)))).((((((.....))))))))))..))))))))..... ( -25.10)
>DroEre_CAF1 39310 116 - 1
GCUUAAGUGCAUUAAAGCCGCAUAAAUCUAAAUUGUCAUCCAAGUUGUCAGUAUAACUGGCUUGCGAAUCACCCUGUUCUGGCUGCCAAAAGCGGCUGUAAAAACAAUUUAAUGCA
.......((((((((((((((..........((((.((.......)).)))).....((((..((((((......))))..)).))))...)))))(((....))).))))))))) ( -29.70)
>DroYak_CAF1 38732 116 - 1
GCUUAAAUGCAUUAAAACCGCAUAAAUCUAAAUUGUCAUCGAAGUUGUCAGUAUAACUGGCUUACGUAUCACCCUGUUCUGGCUGCCAAAAGCGGCUGUAAAAACAAUUUAAUGCA
((......)).........((((.....((((((((....((.((.(((((.....)))))..))...))..........((((((.....))))))......)))))))))))). ( -25.00)
>consensus
GAUUAAAUGCAUUAAAACAGCAUAAAUCUAAAUUGUCAUCCAAGUUGUCAGUAUAACUGGCUUACGAAUCACCCUGUUCUGGCUGCCAAAAGCGGCUGUAAAAACAAUUUAAUGCA
...................((((.....((((((((..........(((((.....)))))((((((((......)))).((((((.....))))))))))..)))))))))))). (-24.10 = -24.14 +   0.04)

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 11:05:35 2006