Locus 1307

Sequence ID dm3.chr2L
Location 10,007,777 – 10,007,836
Length 59
Max. P 0.571540
window1784 window1785

overview

Window 4

Location 10,007,777 – 10,007,836
Length 59
Sequences 8
Columns 63
Reading direction forward
Mean pairwise identity 86.09
Shannon entropy 0.26129
G+C content 0.32998
Mean single sequence MFE -7.75
Consensus MFE -5.32
Energy contribution -5.33
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.74
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.06
SVM RNA-class probability 0.526019
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10007777 59 + 23011544
CACGACUAACGUUUAAACUAUGUUUUAUCAAUUAGUUUAAAGCGUACACCGAACAGAAC----
..((....((((((((((((............)))))).))))))....))........---- (  -8.90, z-score =  -1.26, R)
>droEre2.scaffold_4929 10621395 58 + 26641161
CACGACUAACGUUUAAACUAUGUUUUAUCAAUUAGUUUAAAGCGUACACCGAACAGAA-----
..((....((((((((((((............)))))).))))))....)).......----- (  -8.90, z-score =  -1.32, R)
>droYak2.chr2L 12691378 58 + 22324452
CACGACUAACGUUUAAACUAUGUUUUAUCAAUUAGUUUAAAGCGUACACCGAACAGAA-----
..((....((((((((((((............)))))).))))))....)).......----- (  -8.90, z-score =  -1.32, R)
>droSec1.super_3 5447116 60 + 7220098
CACGACUAACGUUUAAACUAUGUUUUAUCAAUUAGUUUAAAGCGUACACCGAACAGAACC---
..((....((((((((((((............)))))).))))))....)).........--- (  -8.90, z-score =  -1.37, R)
>droSim1.chr2L 9792157 60 + 22036055
CACGACUAACGUUUAAACUAUGUUUUAUCAAUUAGUUUAAAGCGUACACCGAACAGAACC---
..((....((((((((((((............)))))).))))))....)).........--- (  -8.90, z-score =  -1.37, R)
>dp4.chr4_group3 11519191 59 - 11692001
CACAGCUACAAUUUAAACUAUACUUUAUCAUUUAGUUUAAACCGAACACCGAACAGAAC----
...........(((((((((............)))))))))..................---- (  -5.20, z-score =  -2.54, R)
>droPer1.super_1 8635185 59 - 10282868
CACAGCUACAAUUUAAACUAUACUUUAUCAUUUAGUUUAAACCGAACACCGAACAGAAC----
...........(((((((((............)))))))))..................---- (  -5.20, z-score =  -2.54, R)
>droMoj3.scaffold_6500 14797147 63 + 32352404
CACGACUACCAUUUAAACUAUACAUUAUCAUUUAGUUUAAACCGUACAUCAAACGAAUGAAAC
...((.(((..(((((((((............)))))))))..)))..))............. (  -7.10, z-score =  -2.19, R)
>consensus
CACGACUAACGUUUAAACUAUGUUUUAUCAAUUAGUUUAAAGCGUACACCGAACAGAAC____
...........(((((((((............)))))))))...................... ( -5.32 =  -5.33 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 10,007,777 – 10,007,836
Length 59
Sequences 8
Columns 63
Reading direction reverse
Mean pairwise identity 86.09
Shannon entropy 0.26129
G+C content 0.32998
Mean single sequence MFE -11.19
Consensus MFE -7.90
Energy contribution -7.14
Covariance contribution -0.76
Combinations/Pair 1.40
Mean z-score -1.71
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.571540
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 10007777 59 - 23011544
----GUUCUGUUCGGUGUACGCUUUAAACUAAUUGAUAAAACAUAGUUUAAACGUUAGUCGUG
----........(((...(((.(((((((((..((......))))))))))))))...))).. (  -9.40, z-score =  -0.55, R)
>droEre2.scaffold_4929 10621395 58 - 26641161
-----UUCUGUUCGGUGUACGCUUUAAACUAAUUGAUAAAACAUAGUUUAAACGUUAGUCGUG
-----.......(((...(((.(((((((((..((......))))))))))))))...))).. (  -9.40, z-score =  -0.70, R)
>droYak2.chr2L 12691378 58 - 22324452
-----UUCUGUUCGGUGUACGCUUUAAACUAAUUGAUAAAACAUAGUUUAAACGUUAGUCGUG
-----.......(((...(((.(((((((((..((......))))))))))))))...))).. (  -9.40, z-score =  -0.70, R)
>droSec1.super_3 5447116 60 - 7220098
---GGUUCUGUUCGGUGUACGCUUUAAACUAAUUGAUAAAACAUAGUUUAAACGUUAGUCGUG
---.........(((...(((.(((((((((..((......))))))))))))))...))).. (  -9.40, z-score =  -0.35, R)
>droSim1.chr2L 9792157 60 - 22036055
---GGUUCUGUUCGGUGUACGCUUUAAACUAAUUGAUAAAACAUAGUUUAAACGUUAGUCGUG
---.........(((...(((.(((((((((..((......))))))))))))))...))).. (  -9.40, z-score =  -0.35, R)
>dp4.chr4_group3 11519191 59 + 11692001
----GUUCUGUUCGGUGUUCGGUUUAAACUAAAUGAUAAAGUAUAGUUUAAAUUGUAGCUGUG
----........((((...((((((((((((.((......)).))))))))))))..)))).. ( -14.40, z-score =  -4.20, R)
>droPer1.super_1 8635185 59 + 10282868
----GUUCUGUUCGGUGUUCGGUUUAAACUAAAUGAUAAAGUAUAGUUUAAAUUGUAGCUGUG
----........((((...((((((((((((.((......)).))))))))))))..)))).. ( -14.40, z-score =  -4.20, R)
>droMoj3.scaffold_6500 14797147 63 - 32352404
GUUUCAUUCGUUUGAUGUACGGUUUAAACUAAAUGAUAAUGUAUAGUUUAAAUGGUAGUCGUG
.............(((.(((.((((((((((.((......)).)))))))))).))))))... ( -13.70, z-score =  -2.61, R)
>consensus
____GUUCUGUUCGGUGUACGCUUUAAACUAAUUGAUAAAACAUAGUUUAAACGUUAGUCGUG
............(((...(((.(((((((((............))))))))))))...))).. ( -7.90 =  -7.14 +  -0.76)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:29:28 2011