Locus 2240

Sequence ID dm3.chr2L
Location 17,247,455 – 17,247,587
Length 132
Max. P 0.651709
window3089 window3090

overview

Window 9

Location 17,247,455 – 17,247,551
Length 96
Sequences 8
Columns 114
Reading direction forward
Mean pairwise identity 64.27
Shannon entropy 0.66668
G+C content 0.44444
Mean single sequence MFE -28.84
Consensus MFE -8.96
Energy contribution -8.76
Covariance contribution -0.20
Combinations/Pair 1.56
Mean z-score -1.60
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.15
SVM RNA-class probability 0.569095
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17247455 96 + 23011544
-AGAUUGAAGGUAAAGGGAUAAAGA----AGUUUUCAUUGGUUUCGGCUGCGGGCUGAU------------GCAGCUGAAGCAGCU-UCAGGUAUUCGCUCAUCCUUUUUAUCC
-.(((.(((((...(((((((..((----((((.......((((((((((((......)------------)))))))))))))))-))...))))).))...)))))..))). ( -33.51, z-score =  -2.74, R)
>dp4.chr4_group4 153862 81 + 6586962
-AAAUGCAGAAUAAAAGGAUAAAGAUAAAGAUUUUCAUUGGUUUCGGCUGCAGGCAGGU---------------ACUAGGAUAUUUCUUAGCCAUUU-----------------
-...(((((...(((..(((.(((((....))))).)))..)))...)))))....((.---------------.((((((....))))))))....----------------- ( -15.60, z-score =  -0.77, R)
>droAna3.scaffold_12916 12573308 87 - 16180835
--------AAGCAA--GGAUAGGGA----AGUUUUCAUUGGUUUCGGCUGCGGACUGAU------------GAAGCUGAAAUGGCUGCCAGGUAUCCUUU-GUCCUUUGUAGCC
--------..((((--(((((((((----.....((((..(((.((....)))))..))------------))((((.....))))........))).))-)))).)))).... ( -25.20, z-score =  -0.37, R)
>droEre2.scaffold_4845 15589319 108 - 22589142
AAAUUUGAAGGUAAGGGGAUAAAGA----AGUUUUCAUUGGUUUCGGCUGCGGGCUGAUGCUGAUGCUGAUGCAGCCGAAGCAGCU-UCAGGUAUUUUCUCAUCCUUUU-AUCC
.........(((((((((((...((----((((.......(((((((((((((((..........)))..))))))))))))))))-))(((.....))).))))))))-))). ( -38.01, z-score =  -2.67, R)
>droYak2.chr2R 17282250 96 - 21139217
-AAAUUGAAGGUAAAGGGAUAAAGA----AGUUUUCAUUGGUUUCGGCUGCGGGCUGAU------------GCAGCCGAAGCAGCU-UCAGGUAUUUUCUCAUCCUUUUUAUCC
-........((.((((((((...((----((((.......((((((((((((......)------------)))))))))))))))-))(((.....))).))))))))...)) ( -33.01, z-score =  -3.11, R)
>droSec1.super_7 873701 96 + 3727775
-AGAUUGAAGUUAAAGGGAUAAAGA----AGUUUUCAUUGGUUUCGGCUGCGGGCUGAU------------GCAGCUGAAGCAGCU-UCAGGUAUUCGCUCAUCCUUUUUAUCC
-...........((((((((...((----((((.......((((((((((((......)------------)))))))))))))))-)).(((....))).))))))))..... ( -29.31, z-score =  -1.55, R)
>droSim1.chr2L 16946096 96 + 22036055
-AGAUUGAAGGUAAAGGGAUAAAGA----AGUUUUCAUUGGUUUCGGCUGCGGGCUGAU------------GCAGCUGAAGCAGCU-UCAGGUAUUCGCUCAUCCUUUUUAUCC
-.(((.(((((...(((((((..((----((((.......((((((((((((......)------------)))))))))))))))-))...))))).))...)))))..))). ( -33.51, z-score =  -2.74, R)
>droVir3.scaffold_13246 1902687 90 - 2672878
--------GGACAAACAUUUGCGAA---AGACUUUUAUUGGUUUAGGCUAAGAGCAGCAGCAGCCGCAGGAGCUGCUGAAACAGGUGCUGCGCCCAUUCCC-------------
--------(((..............---(((((......))))).(((.....((((((.((((.((....)).)))).......)))))))))...))).------------- ( -22.60, z-score =   1.14, R)
>consensus
_AAAUUGAAGGUAAAGGGAUAAAGA____AGUUUUCAUUGGUUUCGGCUGCGGGCUGAU____________GCAGCUGAAGCAGCU_UCAGGUAUUCUCUCAUCCUUUUUAUCC
........................................(((((((((........................)))))))))................................ ( -8.96 =  -8.76 +  -0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 17,247,490 – 17,247,587
Length 97
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 88.16
Shannon entropy 0.20898
G+C content 0.45860
Mean single sequence MFE -29.58
Consensus MFE -23.99
Energy contribution -24.32
Covariance contribution 0.33
Combinations/Pair 1.12
Mean z-score -1.60
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.34
SVM RNA-class probability 0.651709
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 17247490 97 + 23011544
GUUUCGGCUGCGGGC------------UGAUGCAGCUGAAGCAGCU-UCAGGUAUUCGCUCAUCCUUUUUAUCCAGGCUCAUCAAAAUCAUUCAUUUGCAUGAAGCCAAA
((((((((((((...------------...))))))))))))(((.-..........)))...............(((((((((((........)))).))).))))... ( -29.40, z-score =  -1.57, R)
>droAna3.scaffold_12916 12573334 97 - 16180835
GUUUCGGCUGCGGAC------------UGAUGAAGCUGAAAUGGCUGCCAGGUAUCCU-UUGUCCUUUGUAGCCCGUCUCAUAAAAAUCAUUCAUUUGCAAAAAGCCAAA
.....(((((((((.------------.(((((...(((.((((((((.(((((....-.)).)))..)))).)))).)))......)))))..)))))....))))... ( -24.40, z-score =  -0.95, R)
>droEre2.scaffold_4845 15589355 108 - 22589142
GUUUCGGCUGCGGGCUGAUGCUGAUGCUGAUGCAGCCGAAGCAGCU-UCAGGUAUUUUCUCAUCCUUUU-AUCCAGGCUCAUCAAAAUCAUUCAUUUGCAUGAAGCCAAA
(((((((((((((((..........)))..))))))))))))....-..(((...........)))...-.....(((((((((((........)))).))).))))... ( -33.30, z-score =  -1.06, R)
>droYak2.chr2R 17282285 97 - 21139217
GUUUCGGCUGCGGGC------------UGAUGCAGCCGAAGCAGCU-UCAGGUAUUUUCUCAUCCUUUUUAUCCAGGCUCAUCAAAAUCAUUCAUUUGCAUGAAGCCAAA
((((((((((((...------------...))))))))))))....-..(((...........))).........(((((((((((........)))).))).))))... ( -31.60, z-score =  -2.91, R)
>droSec1.super_7 873736 97 + 3727775
GUUUCGGCUGCGGGC------------UGAUGCAGCUGAAGCAGCU-UCAGGUAUUCGCUCAUCCUUUUUAUCCAGGCUCAUCAAAAUCAUUCAUUUGCAUGAAGCCAAA
((((((((((((...------------...))))))))))))(((.-..........)))...............(((((((((((........)))).))).))))... ( -29.40, z-score =  -1.57, R)
>droSim1.chr2L 16946131 97 + 22036055
GUUUCGGCUGCGGGC------------UGAUGCAGCUGAAGCAGCU-UCAGGUAUUCGCUCAUCCUUUUUAUCCAGGCUCAUCAAAAUCAUUCAUUUGCAUGAAGCCAAA
((((((((((((...------------...))))))))))))(((.-..........)))...............(((((((((((........)))).))).))))... ( -29.40, z-score =  -1.57, R)
>consensus
GUUUCGGCUGCGGGC____________UGAUGCAGCUGAAGCAGCU_UCAGGUAUUCGCUCAUCCUUUUUAUCCAGGCUCAUCAAAAUCAUUCAUUUGCAUGAAGCCAAA
((((((((((((..................)))))))))))).......(((...........))).........(((((((((((........)))).))).))))... (-23.99 = -24.32 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:47:32 2011