Locus 576

Sequence ID dm3.chr2L
Location 4,086,927 – 4,087,056
Length 129
Max. P 0.902246
window766 window767

overview

Window 6

Location 4,086,927 – 4,087,056
Length 129
Sequences 7
Columns 144
Reading direction forward
Mean pairwise identity 81.95
Shannon entropy 0.34590
G+C content 0.39878
Mean single sequence MFE -32.12
Consensus MFE -16.93
Energy contribution -17.93
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763633
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4086927 129 + 23011544
---CUCCCUCCCAUCUCGUUUUCGAGAG-----GAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAAGCCGCAC-CA----AAAAUUUUAUUUACAAAAUUUUCGUGCCAAA-UUUGACUUUUGCCAA-CGCACA
---....((((..(((((....))))))-----)))..(((..((((((((((((.....))))))).)))))((((..((((-..----((((((((......)))))))).))))....-))))...........-.))).. ( -35.40, z-score =  -3.16, R)
>droAna3.scaffold_12943 653560 133 - 5039921
-----CCCUAUAUCCUUGGCUUCCAGAGAGCUGGAGAAUGCCAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCAGAAGCCGCAC-CA----AAAAUUUUAUUUACAAAAUUUUCGUGCCAAA-UUUGACUUUUGCCAAACGCACC
-----...........((((((((((....))))))...))))((((((((((((.....))))))))).(((((((..((((-..----((((((((......)))))))).))))((..-..)).))))))).....))).. ( -37.00, z-score =  -2.76, R)
>droEre2.scaffold_4929 4144918 128 + 26641161
----CAUCUCCCAUCUCGUUUUCGAGCG-----GAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAAGCCGCAC-CA----AAAAUUUUAUUUACAAAAUUUUCGUGCCAAA-UUUGACUUUUGCCAA-CGCACA
----..(((((...((((....)))).)-----)))).(((..((((((((((((.....))))))).)))))((((..((((-..----((((((((......)))))))).))))....-))))...........-.))).. ( -35.20, z-score =  -2.64, R)
>droYak2.chr2L 4104051 124 + 22324452
--------UCCCAUCUCGUUUUCGAGAG-----GCGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAAGCCGCAC-CA----AAAAUUUUAUUUACAAAAUUUUCGUGCCAAA-UUUGACUUUUGCCAA-CGCACA
--------.....(((((....)))))(-----(((((..(((((((((((((((.....))))))).)))))......((((-..----((((((((......)))))))).))))....-.)))...))))))..-...... ( -36.20, z-score =  -2.94, R)
>droSec1.super_5 2186073 133 + 5866729
CUUCCUCCUCAAAUCUCGUUUUCGAGAG-----GAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAAGCCGCAC-CA----AAAAUUUUAUUUACAAAAUUUUCGUGCCAAAAUUUGACUUUUGCCAA-CGCACA
.......(((...(((((....))))).-----)))..(((..((((((((((((.....))))))).)))))......((((-..----((((((((......)))))))).))))....................-.))).. ( -33.80, z-score =  -2.35, R)
>droSim1.chr2L 4042087 121 + 22036055
-----------CAUCUCGUUUUCCAGAG-----GAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAAGCCGCAC-CA----AAAAUUUUAUUUACAAAAUUUUCGUGCCAAA-UUUGACUUUUGCCAA-CGCACA
-----------..((((.((.....)).-----)))).(((..((((((((((((.....))))))).)))))((((..((((-..----((((((((......)))))))).))))....-))))...........-.))).. ( -29.10, z-score =  -1.17, R)
>droWil1.scaffold_180703 2081315 116 + 3946847
-----------------------GAGAA-----GGUAACGCAAUGCAAUUUGCUCAAUGUGCACAAAUUUACACAAGCCGCACACAGCACAAAAUUUUAUUUACAAAAUUUUCCAUCGUACCGAAUAUUUUUGCCGACUUUUCG
-----------------------(((((-----(.....((((.......((((...(((((.................))))).)))).((((((((......))))))))..................))))...)))))). ( -18.13, z-score =  -0.54, R)
>consensus
_______CUCCCAUCUCGUUUUCGAGAG_____GAGAAUGCAAUGCAAUUUGCGCAAUGUGUGCAAAUUUGCACAAGCCGCAC_CA____AAAAUUUUAUUUACAAAAUUUUCGUGCCAAA_UUUGACUUUUGCCAA_CGCACA
.......................................((((((((((((((((.....))))))).)))))......((((.......((((((((......)))))))).)))).............)))).......... (-16.93 = -17.93 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,086,927 – 4,087,056
Length 129
Sequences 7
Columns 144
Reading direction reverse
Mean pairwise identity 81.95
Shannon entropy 0.34590
G+C content 0.39878
Mean single sequence MFE -39.06
Consensus MFE -22.92
Energy contribution -23.36
Covariance contribution 0.43
Combinations/Pair 1.15
Mean z-score -2.27
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.902246
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4086927 129 - 23011544
UGUGCG-UUGGCAAAAGUCAAA-UUUGGCACGAAAAUUUUGUAAAUAAAAUUUU----UG-GUGCGGCUUGUGCAAAUUUGCACACAUUGCGCAAAUUGCAUUGCAUUCUC-----CUCUCGAAAACGAGAUGGGAGGGAG---
.(((((-...((((..((((..-..)))).(((((((((((....)))))))))----))-((((((..((((((....))))))..))))))...))))..)))))((((-----((((((....)))))..)))))...--- ( -44.90, z-score =  -3.73, R)
>droAna3.scaffold_12943 653560 133 + 5039921
GGUGCGUUUGGCAAAAGUCAAA-UUUGGCACGAAAAUUUUGUAAAUAAAAUUUU----UG-GUGCGGCUUCUGCAAAUUUGCACACAUUGCGCAAAUUGCAUGGCAUUCUCCAGCUCUCUGGAAGCCAAGGAUAUAGGG-----
.(((((((((((....))))))-)...))))..................(((((----((-((...(((..(((((.(((((.(.....).)))))))))).)))....(((((....))))).)))))))))......----- ( -38.50, z-score =  -1.29, R)
>droEre2.scaffold_4929 4144918 128 - 26641161
UGUGCG-UUGGCAAAAGUCAAA-UUUGGCACGAAAAUUUUGUAAAUAAAAUUUU----UG-GUGCGGCUUGUGCAAAUUUGCACACAUUGCGCAAAUUGCAUUGCAUUCUC-----CGCUCGAAAACGAGAUGGGAGAUG----
.(((((-...((((..((((..-..)))).(((((((((((....)))))))))----))-((((((..((((((....))))))..))))))...))))..)))))((((-----(.((((....))))...)))))..---- ( -44.90, z-score =  -3.50, R)
>droYak2.chr2L 4104051 124 - 22324452
UGUGCG-UUGGCAAAAGUCAAA-UUUGGCACGAAAAUUUUGUAAAUAAAAUUUU----UG-GUGCGGCUUGUGCAAAUUUGCACACAUUGCGCAAAUUGCAUUGCAUUCGC-----CUCUCGAAAACGAGAUGGGA--------
.(((((-...((((..((((..-..)))).(((((((((((....)))))))))----))-((((((..((((((....))))))..))))))...))))..)))))((.(-----((((((....))))).))))-------- ( -41.60, z-score =  -2.68, R)
>droSec1.super_5 2186073 133 - 5866729
UGUGCG-UUGGCAAAAGUCAAAUUUUGGCACGAAAAUUUUGUAAAUAAAAUUUU----UG-GUGCGGCUUGUGCAAAUUUGCACACAUUGCGCAAAUUGCAUUGCAUUCUC-----CUCUCGAAAACGAGAUUUGAGGAGGAAG
..((((-...((((..((((.....)))).(((((((((((....)))))))))----))-((((((..((((((....))))))..))))))...))))..))))(((((-----((((((....))).....)))))))).. ( -44.20, z-score =  -3.36, R)
>droSim1.chr2L 4042087 121 - 22036055
UGUGCG-UUGGCAAAAGUCAAA-UUUGGCACGAAAAUUUUGUAAAUAAAAUUUU----UG-GUGCGGCUUGUGCAAAUUUGCACACAUUGCGCAAAUUGCAUUGCAUUCUC-----CUCUGGAAAACGAGAUG-----------
.(((((-...((((..((((..-..)))).(((((((((((....)))))))))----))-((((((..((((((....))))))..))))))...))))..)))))....-----(((........)))...----------- ( -35.30, z-score =  -1.66, R)
>droWil1.scaffold_180703 2081315 116 - 3946847
CGAAAAGUCGGCAAAAAUAUUCGGUACGAUGGAAAAUUUUGUAAAUAAAAUUUUGUGCUGUGUGCGGCUUGUGUAAAUUUGUGCACAUUGAGCAAAUUGCAUUGCGUUACC-----UUCUC-----------------------
(((....)))............((((((....(((((((((....)))))))))((((....(((....((((((......))))))....)))....))))..)).))))-----.....----------------------- ( -24.00, z-score =   0.32, R)
>consensus
UGUGCG_UUGGCAAAAGUCAAA_UUUGGCACGAAAAUUUUGUAAAUAAAAUUUU____UG_GUGCGGCUUGUGCAAAUUUGCACACAUUGCGCAAAUUGCAUUGCAUUCUC_____CUCUCGAAAACGAGAUGGGAG_______
.(((((....((((..((((.....))))...(((((((((....))))))))).......((((((..((((((....))))))..))))))...))))..)))))..................................... (-22.92 = -23.36 +   0.43)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:15:20 2011