Locus 14550

Sequence ID dm3.chrX
Location 14,019,365 – 14,019,433
Length 68
Max. P 0.965280
window20032 window20033

overview

Window 2

Location 14,019,365 – 14,019,433
Length 68
Sequences 5
Columns 82
Reading direction forward
Mean pairwise identity 66.85
Shannon entropy 0.54303
G+C content 0.41225
Mean single sequence MFE -16.00
Consensus MFE -6.73
Energy contribution -6.29
Covariance contribution -0.44
Combinations/Pair 1.33
Mean z-score -2.31
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965280
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14019365 68 + 22422827
CACAAUUUUUCCGUUCACCUUCAUCAACGUG----------CAUUGAUUAGCAAUUCAAUGCAGAUGAAAACUGCAAU----
............((.....((((((....((----------((((((........))))))))))))))....))...---- ( -15.30, z-score =  -2.67, R)
>droSim1.chrX 10767675 68 + 17042790
CACAAUUUUUCCGUUCACCUUCAUCAACGUG----------CAUUGAUUAGCAAUUCAAUGCAGAUGAAAACUGCAAU----
............((.....((((((....((----------((((((........))))))))))))))....))...---- ( -15.30, z-score =  -2.67, R)
>droYak2.chrX 8278340 68 + 21770863
UACAAUUUUUCCGCUCACCUUCAUCCACGUG----------CAUUGAUUAGCAAUUCAAUGCAGAUGAAAGCUGCAAG----
............((...(.((((((....((----------((((((........)))))))))))))).)..))...---- ( -17.10, z-score =  -3.04, R)
>droEre2.scaffold_4690 5841020 57 - 18748788
-----------CACAAAGCUCCAUCAACGUG----------CAUUGAUUAGCAAUUCAAUGCAGAUGGAAACUGCAGG----
-----------......((((((((....((----------((((((........))))))))))))))....))...---- ( -18.00, z-score =  -3.36, R)
>droAna3.scaffold_13047 1529178 82 + 1816235
CGCCACCUUGCCACUUACCUUCUGCAAUCUGGAAUCUGCGGCAUUGAUUAGCAAUUCCAUGUAGCAAGUUGUCCUCUCCAUU
...((.(((((...........((((...((((((.(((...........)))))))))))))))))).))........... ( -14.30, z-score =   0.18, R)
>consensus
CACAAUUUUUCCGCUCACCUUCAUCAACGUG__________CAUUGAUUAGCAAUUCAAUGCAGAUGAAAACUGCAAG____
...................((((((................((((((........))))))..))))))............. ( -6.73 =  -6.29 +  -0.44) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 14,019,365 – 14,019,433
Length 68
Sequences 5
Columns 82
Reading direction reverse
Mean pairwise identity 66.85
Shannon entropy 0.54303
G+C content 0.41225
Mean single sequence MFE -20.16
Consensus MFE -8.23
Energy contribution -7.87
Covariance contribution -0.36
Combinations/Pair 1.40
Mean z-score -2.28
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.59
SVM RNA-class probability 0.953506
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14019365 68 - 22422827
----AUUGCAGUUUUCAUCUGCAUUGAAUUGCUAAUCAAUG----------CACGUUGAUGAAGGUGAACGGAAAAAUUGUG
----...(((((((((...((((((((........))))))----------))((((.((....)).))))).)))))))). ( -18.10, z-score =  -1.91, R)
>droSim1.chrX 10767675 68 - 17042790
----AUUGCAGUUUUCAUCUGCAUUGAAUUGCUAAUCAAUG----------CACGUUGAUGAAGGUGAACGGAAAAAUUGUG
----...(((((((((...((((((((........))))))----------))((((.((....)).))))).)))))))). ( -18.10, z-score =  -1.91, R)
>droYak2.chrX 8278340 68 - 21770863
----CUUGCAGCUUUCAUCUGCAUUGAAUUGCUAAUCAAUG----------CACGUGGAUGAAGGUGAGCGGAAAAAUUGUA
----.((((.(((((((((((((((((........))))))----------)....))))))))))..)))).......... ( -22.70, z-score =  -3.08, R)
>droEre2.scaffold_4690 5841020 57 + 18748788
----CCUGCAGUUUCCAUCUGCAUUGAAUUGCUAAUCAAUG----------CACGUUGAUGGAGCUUUGUG-----------
----...((((.(((((((((((((((........))))))----------))....)))))))..)))).----------- ( -19.40, z-score =  -3.31, R)
>droAna3.scaffold_13047 1529178 82 - 1816235
AAUGGAGAGGACAACUUGCUACAUGGAAUUGCUAAUCAAUGCCGCAGAUUCCAGAUUGCAGAAGGUAAGUGGCAAGGUGGCG
...........((.((((((((.(((((((((...........))).))))))..((((.....)))))))))))).))... ( -22.50, z-score =  -1.16, R)
>consensus
____AUUGCAGUUUUCAUCUGCAUUGAAUUGCUAAUCAAUG__________CACGUUGAUGAAGGUGAGCGGAAAAAUUGUG
..........(((((((((..((((((........))))))................)))))))))................ ( -8.23 =  -7.87 +  -0.36) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:42:14 2011