Locus 12135

Sequence ID dm3.chr3R
Location 26,012,888 – 26,012,980
Length 92
Max. P 0.986877
window16685 window16686

overview

Window 5

Location 26,012,888 – 26,012,980
Length 92
Sequences 11
Columns 116
Reading direction forward
Mean pairwise identity 75.40
Shannon entropy 0.48368
G+C content 0.34935
Mean single sequence MFE -23.38
Consensus MFE -12.29
Energy contribution -12.61
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -2.06
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.67
SVM RNA-class probability 0.959488
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26012888 92 + 27905053
------------------GUUGGAAUUGUCAAUUUUACAGUUUGUCA-----GCCGCGACAGGCAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUUGCAUU-AUAGCCC
------------------....(((((((.......)))))))(((.-----.....))).(((..(((((......)))))((((((((((((....))))))))))-)).))). ( -24.50, z-score =  -2.64, R)
>droPer1.super_7 148833 95 - 4445127
---------------GUUUUCGGAAUUGUCAAUUUUACAGUUUGUCA-----GUCGCGAAAGGUAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUAAAUGGCAUU-ACAGCGG
---------------.((((((..((((.(((.........))).))-----))..)))))).((((((((......)))))))).(((...((((((.....)))))-)..))). ( -19.60, z-score =  -1.17, R)
>dp4.chr2 29300700 95 - 30794189
---------------GUUUUCGGAAUUGUCAAUUUUACAGUUUGUCA-----GUCGCGAAAGGUAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUGGCAUU-ACAGCGG
---------------.((((((..((((.(((.........))).))-----))..)))))).((((((((......)))))))).(((...((((((.....)))))-)..))). ( -19.60, z-score =  -1.18, R)
>droAna3.scaffold_13340 21047542 92 + 23697760
------------------GUUGGUAUUGUCAAUUUUACAGUUUUUCA-----GCCGCAACAGGCAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUUGCAUU-ACAGCCC
------------------(((((.(((((.......)))))...)))-----)).......((((((((((......)))))))((((((((((....))))))))))-...))). ( -23.90, z-score =  -2.77, R)
>droEre2.scaffold_4820 8484970 92 - 10470090
------------------GUUGGAAUUGUCAAUUUUACAGUUUGUCA-----GCCGCGACAGGCAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUUGCAUU-ACAGCCC
------------------((((.................(((((((.-----.....)))))))(((((((......)))))))((((((((((....))))))))))-.)))).. ( -24.80, z-score =  -2.61, R)
>droYak2.chr3R 26946402 92 + 28832112
------------------GUUGGAAUUGUCAAUUUUACAGUUUGUCA-----GCCGCGACAGGCAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUUGCAUU-ACAGCCC
------------------((((.................(((((((.-----.....)))))))(((((((......)))))))((((((((((....))))))))))-.)))).. ( -24.80, z-score =  -2.61, R)
>droSec1.super_4 4865644 92 + 6179234
------------------GUUGGAAUUGUCACUUUUACAGUUUGUCA-----GCCGCGACAGGCAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUUGCAUU-ACAGCCC
------------------((((.................(((((((.-----.....)))))))(((((((......)))))))((((((((((....))))))))))-.)))).. ( -24.80, z-score =  -2.48, R)
>droSim1.chr3R 25680346 92 + 27517382
------------------GUUGGAAUUGUCAAUUUUACAGUUUGUCA-----GCCGCGACAGGCAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUUGCAUU-ACAGCCC
------------------((((.................(((((((.-----.....)))))))(((((((......)))))))((((((((((....))))))))))-.)))).. ( -24.80, z-score =  -2.61, R)
>droWil1.scaffold_181130 9473999 78 + 16660200
---------------------------GUUCGUAUUGUUGCUU--CA-----AC----AAAAGCAUUAAGUUGUUAUAUUUAAUGAUGCAAUUAAUGUUAAUUGCAUUUACAACCC
---------------------------(((.(((((((((...--))-----))----))...((((((((......))))))))(((((((((....))))))))).)))))).. ( -16.70, z-score =  -2.20, R)
>droVir3.scaffold_12855 3080861 113 + 10161210
UGUUGUUGUCGCCGCCUUUUGUCAAUUUACAAUUUCGGCACAAGUCGCGCGGUGACAAAAAGGCAUUAAGCUGUUGUACUUAAUGACGCAAUUAAUGUUAAUUACAUU-ACGAC--
.((((((((((((((...((((......))))...((((....)))).)))))))))....((((((((..(((..(.....)..)))...)))))))).........-)))))-- ( -30.10, z-score =  -1.44, R)
>droGri2.scaffold_14906 5784838 106 + 14172833
-------GUUGACGGCUUUUGUUCAUUUACAGUUUCGGCGAUAGCGACAAAAAAAGAAAAAGGCAUUAAGUUGUCGUACUUAAUGAUGCAAUUAAUGCUAAUUGCAUU-ACGAC--
-------(((((((((((.((((..(((....(((..(((....)).)..)))...)))..))))..))))))))).))....(((((((((((....))))))))))-)....-- ( -23.60, z-score =  -0.98, R)
>consensus
__________________GUUGGAAUUGUCAAUUUUACAGUUUGUCA_____GCCGCGACAGGCAUUAAGUUGUUAUACUUAAUGAUGCAAUUAAUGUUAAUUGCAUU_ACAGCCC
...............................................................((((((((......))))))))(((((((((....)))))))))......... (-12.29 = -12.61 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 26,012,888 – 26,012,980
Length 92
Sequences 11
Columns 116
Reading direction reverse
Mean pairwise identity 75.40
Shannon entropy 0.48368
G+C content 0.34935
Mean single sequence MFE -20.31
Consensus MFE -11.52
Energy contribution -11.82
Covariance contribution 0.30
Combinations/Pair 1.18
Mean z-score -2.24
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.26
SVM RNA-class probability 0.986877
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 26012888 92 - 27905053
GGGCUAU-AAUGCAAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUGCCUGUCGCGGC-----UGACAAACUGUAAAAUUGACAAUUCCAAC------------------
((((...-.(((((((((....))))))))).(((((((......)))))))))))(((((((.-----.......))))......))).........------------------ ( -20.10, z-score =  -2.48, R)
>droPer1.super_7 148833 95 + 4445127
CCGCUGU-AAUGCCAUUUACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUACCUUUCGCGAC-----UGACAAACUGUAAAAUUGACAAUUCCGAAAAC---------------
..((..(-((((.......)))))...))...(((((((......)))))))...(((((.((.-----((.(((.........))).)).)).)))))..--------------- ( -12.60, z-score =  -1.39, R)
>dp4.chr2 29300700 95 + 30794189
CCGCUGU-AAUGCCAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUACCUUUCGCGAC-----UGACAAACUGUAAAAUUGACAAUUCCGAAAAC---------------
..((..(-((((.......)))))...))...(((((((......)))))))...(((((.((.-----((.(((.........))).)).)).)))))..--------------- ( -12.60, z-score =  -1.45, R)
>droAna3.scaffold_13340 21047542 92 - 23697760
GGGCUGU-AAUGCAAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUGCCUGUUGCGGC-----UGAAAAACUGUAAAAUUGACAAUACCAAC------------------
(((((((-((((((((((....)))))))..((((((((......))))))))...))))))))-----........(((.......)))...))...------------------ ( -23.60, z-score =  -3.30, R)
>droEre2.scaffold_4820 8484970 92 + 10470090
GGGCUGU-AAUGCAAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUGCCUGUCGCGGC-----UGACAAACUGUAAAAUUGACAAUUCCAAC------------------
.((((((-.(((((((((....)))))))))((((((((......))))))))......)))))-----)............................------------------ ( -21.70, z-score =  -2.57, R)
>droYak2.chr3R 26946402 92 - 28832112
GGGCUGU-AAUGCAAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUGCCUGUCGCGGC-----UGACAAACUGUAAAAUUGACAAUUCCAAC------------------
.((((((-.(((((((((....)))))))))((((((((......))))))))......)))))-----)............................------------------ ( -21.70, z-score =  -2.57, R)
>droSec1.super_4 4865644 92 - 6179234
GGGCUGU-AAUGCAAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUGCCUGUCGCGGC-----UGACAAACUGUAAAAGUGACAAUUCCAAC------------------
((((...-.(((((((((....))))))))).(((((((......)))))))))))(((((...-----..((.....))....))))).........------------------ ( -24.40, z-score =  -3.15, R)
>droSim1.chr3R 25680346 92 - 27517382
GGGCUGU-AAUGCAAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUGCCUGUCGCGGC-----UGACAAACUGUAAAAUUGACAAUUCCAAC------------------
.((((((-.(((((((((....)))))))))((((((((......))))))))......)))))-----)............................------------------ ( -21.70, z-score =  -2.57, R)
>droWil1.scaffold_181130 9473999 78 - 16660200
GGGUUGUAAAUGCAAUUAACAUUAAUUGCAUCAUUAAAUAUAACAACUUAAUGCUUUU----GU-----UG--AAGCAACAAUACGAAC---------------------------
(..((((..(((((((((....)))))))))....................((((((.----..-----.)--)))))))))..)....--------------------------- ( -16.40, z-score =  -2.48, R)
>droVir3.scaffold_12855 3080861 113 - 10161210
--GUCGU-AAUGUAAUUAACAUUAAUUGCGUCAUUAAGUACAACAGCUUAAUGCCUUUUUGUCACCGCGCGACUUGUGCCGAAAUUGUAAAUUGACAAAAGGCGGCGACAACAACA
--(((((-.(((((((((....))))))))).(((((((......)))))))(((((((.(((((.((((.....)))).)...........))))))))))).)))))....... ( -31.40, z-score =  -2.28, R)
>droGri2.scaffold_14906 5784838 106 - 14172833
--GUCGU-AAUGCAAUUAGCAUUAAUUGCAUCAUUAAGUACGACAACUUAAUGCCUUUUUCUUUUUUUGUCGCUAUCGCCGAAACUGUAAAUGAACAAAAGCCGUCAAC-------
--(((((-((((((((((....))))))))).......))))))......(((.(((((((.(((....((((....).)))......))).))..))))).)))....------- ( -17.21, z-score =  -0.36, R)
>consensus
GGGCUGU_AAUGCAAUUAACAUUAAUUGCAUCAUUAAGUAUAACAACUUAAUGCCUGUCGCGGC_____UGACAAACUGUAAAAUUGACAAUUCCAAC__________________
.........(((((((((....)))))))))((((((((......))))))))............................................................... (-11.52 = -11.82 +   0.30)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:56:26 2011