Locus 597

Sequence ID dm3.chr2L
Location 4,221,928 – 4,221,982
Length 54
Max. P 0.998050
window793 window794

overview

Window 3

Location 4,221,928 – 4,221,982
Length 54
Sequences 8
Columns 54
Reading direction forward
Mean pairwise identity 94.11
Shannon entropy 0.11686
G+C content 0.34102
Mean single sequence MFE -9.20
Consensus MFE -6.45
Energy contribution -6.45
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.70
SVM RNA-class probability 0.791137
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 4221928 54 + 23011544
CUGCAACACAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUUCGGAA
((((((((...........))))))))(((((.....((......))..))))) ( -10.40, z-score =  -2.69, R)
>droSim1.chr2L_random 202837 54 + 909653
CUGCAACACAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUUCGGAA
((((((((...........))))))))(((((.....((......))..))))) ( -10.40, z-score =  -2.69, R)
>droSec1.super_5 2319234 54 + 5866729
CUGCAACACAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUUCGGAA
((((((((...........))))))))(((((.....((......))..))))) ( -10.40, z-score =  -2.69, R)
>dp4.chr4_group2 207929 54 + 1235136
CUGCAACACAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUUCGGAA
((((((((...........))))))))(((((.....((......))..))))) ( -10.40, z-score =  -2.69, R)
>droPer1.super_8 285716 54 - 3966273
CUGCAACACAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUUCGGAA
((((((((...........))))))))(((((.....((......))..))))) ( -10.40, z-score =  -2.69, R)
>droVir3.scaffold_13246 303664 54 + 2672878
CCGCAACAUAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUACUAAA
..((((((...........))))))............................. (  -7.20, z-score =  -2.60, R)
>droMoj3.scaffold_6500 298664 54 + 32352404
CCGCAACAUAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUACAGAA
..((((((...........))))))............................. (  -7.20, z-score =  -1.81, R)
>droGri2.scaffold_15252 215806 53 - 17193109
CCGCAACAUAUUUUUCACUUGUUGCAGUUUCAUUUUUCAUUUUCUUGUACCAA-
..((((((...........))))))............................- (  -7.20, z-score =  -3.37, R)
>consensus
CUGCAACACAUUUUUCACUUGUUGCAGUUUCGUUUUUCAUUUUCUUGUUCGGAA
..((((((...........))))))............................. ( -6.45 =  -6.45 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,221,928 – 4,221,982
Length 54
Sequences 8
Columns 54
Reading direction reverse
Mean pairwise identity 94.11
Shannon entropy 0.11686
G+C content 0.34102
Mean single sequence MFE -11.01
Consensus MFE -10.87
Energy contribution -10.64
Covariance contribution -0.23
Combinations/Pair 1.10
Mean z-score -3.23
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.24
SVM RNA-class probability 0.998050
Prediction RNA
WARNING Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr2L 4221928 54 - 23011544
UUCCGAACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUGUGUUGCAG
...........................((((((((..(....)...)))))))) ( -11.20, z-score =  -3.20, R)
>droSim1.chr2L_random 202837 54 - 909653
UUCCGAACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUGUGUUGCAG
...........................((((((((..(....)...)))))))) ( -11.20, z-score =  -3.20, R)
>droSec1.super_5 2319234 54 - 5866729
UUCCGAACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUGUGUUGCAG
...........................((((((((..(....)...)))))))) ( -11.20, z-score =  -3.20, R)
>dp4.chr4_group2 207929 54 - 1235136
UUCCGAACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUGUGUUGCAG
...........................((((((((..(....)...)))))))) ( -11.20, z-score =  -3.20, R)
>droPer1.super_8 285716 54 + 3966273
UUCCGAACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUGUGUUGCAG
...........................((((((((..(....)...)))))))) ( -11.20, z-score =  -3.20, R)
>droVir3.scaffold_13246 303664 54 - 2672878
UUUAGUACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUAUGUUGCGG
...........................((((((((.((.....)).)))))))) ( -10.20, z-score =  -2.99, R)
>droMoj3.scaffold_6500 298664 54 - 32352404
UUCUGUACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUAUGUUGCGG
((((.....))))..............((((((((.((.....)).)))))))) ( -11.70, z-score =  -3.48, R)
>droGri2.scaffold_15252 215806 53 + 17193109
-UUGGUACAAGAAAAUGAAAAAUGAAACUGCAACAAGUGAAAAAUAUGUUGCGG
-..........................((((((((.((.....)).)))))))) ( -10.20, z-score =  -3.33, R)
>consensus
UUCCGAACAAGAAAAUGAAAAACGAAACUGCAACAAGUGAAAAAUGUGUUGCAG
...........................((((((((.((.....)).)))))))) (-10.87 = -10.64 +  -0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:15:42 2011