Locus 1577

Sequence ID 3L_DroMel_CAF1
Location 4,600,731 – 4,600,825
Length 94
Max. P 0.998756
window2444 window2445

overview

Window 4

Location 4,600,731 – 4,600,825
Length 94
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 90.10
Mean single sequence MFE -24.12
Consensus MFE -21.18
Energy contribution -21.74
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.46
Structure conservation index 0.88
SVM decision value 3.21
SVM RNA-class probability 0.998756
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4600731 94 + 23771897
AGGAGCUCAACAGGACACAACAAUGCAAAUGUUUGCAGUGUCCACAGAGAAAAUAUUGCACGAAACUCCCUUUAAUUUGUGCUAAUUAUACUCC----------
.(((((((....((((((.....(((((....)))))))))))...)))........(((((((...........)))))))........))))---------- ( -24.50)
>DroSec_CAF1 177291 94 + 1
AGGAGCUCAACAGGACACAACAAUGCAAAUGUUUGCAGUGUCCACAUGGAAAAUAUUGCACGAAACUUCCUUUAAUUUGUGCUAAUUAUACUCC----------
.((((.......((((((.....(((((....)))))))))))..............(((((((...........)))))))........))))---------- ( -23.30)
>DroSim_CAF1 177853 94 + 1
AGGAGCUCAACAGGACACAACAAUGCAAAUGUUUGCAGUGUCCACAGGGAAAAUAUUGCACGAAACUCCCUUUAAUUUGUGCUAAUUAUACUCC----------
.(((((((....((((((.....(((((....)))))))))))...)))........(((((((...........)))))))........))))---------- ( -23.60)
>DroEre_CAF1 185928 104 + 1
AGGAGCUCAACAGGACACAACAAUGCAAAUGUUUGCAGUGUCCACAGAGAAAAUAUUGCACGAAGCUCCCUUUAAUUUGUGCUAAUUAUACUCCGAUUCUGUAC
.(((((((....((((((.....(((((....)))))))))))...)))........(((((((...........)))))))........)))).......... ( -27.00)
>DroYak_CAF1 183157 104 + 1
ACGUGCUCAACAGGACACAGCAAUGCAAAUGUUUGCAGUGUCCACAGAGAAAAUAUUGCACGAAACUCCUUUUAAUUUUUGCUAAUUAUACUCCGAUUGUGUGC
..(..(.(((..((((((.((((.((....)))))).)))))).(.(((........(((.(((...........))).)))........))).).))).)..) ( -22.19)
>consensus
AGGAGCUCAACAGGACACAACAAUGCAAAUGUUUGCAGUGUCCACAGAGAAAAUAUUGCACGAAACUCCCUUUAAUUUGUGCUAAUUAUACUCC__________
.(((((((....((((((.....(((((....)))))))))))...)))........(((((((...........)))))))........)))).......... (-21.18 = -21.74 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,600,731 – 4,600,825
Length 94
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 90.10
Mean single sequence MFE -26.65
Consensus MFE -23.40
Energy contribution -24.04
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.01
Structure conservation index 0.88
SVM decision value 2.21
SVM RNA-class probability 0.990334
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4600731 94 - 23771897
----------GGAGUAUAAUUAGCACAAAUUAAAGGGAGUUUCGUGCAAUAUUUUCUCUGUGGACACUGCAAACAUUUGCAUUGUUGUGUCCUGUUGAGCUCCU
----------(((((.((((..(((((((((......))))).))))..............(((((((((((....))))).....)))))).)))).))))). ( -27.30)
>DroSec_CAF1 177291 94 - 1
----------GGAGUAUAAUUAGCACAAAUUAAAGGAAGUUUCGUGCAAUAUUUUCCAUGUGGACACUGCAAACAUUUGCAUUGUUGUGUCCUGUUGAGCUCCU
----------(((((.......(((((((((......))))).)))).........((...(((((((((((....))))).....))))))...)).))))). ( -27.30)
>DroSim_CAF1 177853 94 - 1
----------GGAGUAUAAUUAGCACAAAUUAAAGGGAGUUUCGUGCAAUAUUUUCCCUGUGGACACUGCAAACAUUUGCAUUGUUGUGUCCUGUUGAGCUCCU
----------(((((....((((((........((((((..............))))))..(((((((((((....))))).....))))))))))))))))). ( -28.44)
>DroEre_CAF1 185928 104 - 1
GUACAGAAUCGGAGUAUAAUUAGCACAAAUUAAAGGGAGCUUCGUGCAAUAUUUUCUCUGUGGACACUGCAAACAUUUGCAUUGUUGUGUCCUGUUGAGCUCCU
..........(((((....((((((........(((((((.....)).......)))))..(((((((((((....))))).....))))))))))))))))). ( -25.61)
>DroYak_CAF1 183157 104 - 1
GCACACAAUCGGAGUAUAAUUAGCAAAAAUUAAAAGGAGUUUCGUGCAAUAUUUUCUCUGUGGACACUGCAAACAUUUGCAUUGCUGUGUCCUGUUGAGCACGU
((.((((..(((((...(((..(((.(((((......)))))..)))...)))..))))).((((((.((((.........)))).)))))))).)).)).... ( -24.60)
>consensus
__________GGAGUAUAAUUAGCACAAAUUAAAGGGAGUUUCGUGCAAUAUUUUCUCUGUGGACACUGCAAACAUUUGCAUUGUUGUGUCCUGUUGAGCUCCU
..........(((((.((((..(((((((((......))))).))))..............((((((.((((.........)))).)))))).)))).))))). (-23.40 = -24.04 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:04 2006