Locus 12204

Sequence ID	dm3.chr3R
Location	26,466,952 – 26,467,047
Length	95
Max. P	0.747465

overview

Window 3

Location	26,466,952 – 26,467,047
Length	95
Sequences	12
Columns	120
Reading direction	forward
Mean pairwise identity	86.15
Shannon entropy	0.25597
G+C content	0.34668
Mean single sequence MFE	-18.76
Consensus MFE	-16.11
Energy contribution	-16.11
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.32
Structure conservation index	0.86
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.54
SVM RNA-class probability	0.734870
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 26466952 95 + 27905053
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUCAUUGGCCGAGCUC-------------------------
.(((((.((((........))))...((((.(((((((.....))))))).))))))))).....(((..(((((....))....)))..)))..------------------------- ( -20.70, z-score =  -1.32, R)
>droSim1.chr3R 26112893 95 + 27517382
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUCAUUGGCCGAGCUC-------------------------
.(((((.((((........))))...((((.(((((((.....))))))).))))))))).....(((..(((((....))....)))..)))..------------------------- ( -20.70, z-score =  -1.32, R)
>droSec1.super_4 5293723 95 + 6179234
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUCAUUGGCCGAGCUC-------------------------
.(((((.((((........))))...((((.(((((((.....))))))).))))))))).....(((..(((((....))....)))..)))..------------------------- ( -20.70, z-score =  -1.32, R)
>droYak2.chr3R 27389139 120 + 28832112
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUCAUUGGCCCAGCUCUGUGCUCUGUGCUCUGUACUGUGUG
.(((((.((((........))))...((((.(((((((.....))))))).))))))))).....((.(((..((((..(.(((.(((...)))..))))...)))).))).))...... ( -24.60, z-score =  -0.25, R)
>droEre2.scaffold_4820 8939844 95 - 10470090
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUCAUUGGCCCAGCUC-------------------------
.(((((.((((........))))...((((.(((((((.....))))))).))))))))).........(((((.....((.....)).))))).------------------------- ( -19.70, z-score =  -1.31, R)
>droAna3.scaffold_12911 849303 95 - 5364042
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCCGCAUUUGUCAUUGGCUCGUAUC-------------------------
.(((((.((((........))))...((((.(((((((.....))))))).))))))))).........(((((..........)))))......------------------------- ( -19.30, z-score =  -1.60, R)
>dp4.chr2 30055138 83 - 30794189
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUCGGUC-------------------------------------
.(((((.((((........))))...((((.(((((((.....))))))).)))))))))..........((((....)))).------------------------------------- ( -16.40, z-score =  -1.56, R)
>droPer1.super_7 920038 83 - 4445127
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUCGGUC-------------------------------------
.(((((.((((........))))...((((.(((((((.....))))))).)))))))))..........((((....)))).------------------------------------- ( -16.40, z-score =  -1.56, R)
>droWil1.scaffold_181130 9983217 95 + 16660200
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUUGUCUGUCGUCGUC-------------------------
.(((....(((...(((((.(((........(((((((.....)))))))..((((((.......)))))).)))))))).)))....)))....------------------------- ( -17.40, z-score =  -0.95, R)
>droVir3.scaffold_13047 11246374 82 + 19223366
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUC--------------------------------------
(((((...((....(.(((((...((((((.(((((((.....))))))).))))))..))))).)....)).)))))....-------------------------------------- ( -16.20, z-score =  -1.67, R)
>droMoj3.scaffold_6540 3649623 82 - 34148556
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUC--------------------------------------
(((((...((....(.(((((...((((((.(((((((.....))))))).))))))..))))).)....)).)))))....-------------------------------------- ( -16.20, z-score =  -1.67, R)
>droGri2.scaffold_14624 1226668 87 + 4233967
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUCGUCGU---------------------------------
.......((((........))))...((((.(((((((.....))))))).))))(((((((...((......))..)))).)))..--------------------------------- ( -16.80, z-score =  -1.33, R)
>consensus
AAUGUUUUGCAUUUCAAAUUGCAUUUUAAUCGCAUUUCAACCUGAAAUGCCAUUAGACAUAAUUCGUUUAGCUGCAUUUGUCAUUGGCC____UC_________________________
(((((..((((........)))).((((((.(((((((.....))))))).))))))................))))).......................................... (-16.11 = -16.11 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	26,466,952 – 26,467,047
Length	95
Sequences	12
Columns	120
Reading direction	reverse
Mean pairwise identity	86.15
Shannon entropy	0.25597
G+C content	0.34668
Mean single sequence MFE	-18.91
Consensus MFE	-18.02
Energy contribution	-17.94
Covariance contribution	-0.08
Combinations/Pair	1.04
Mean z-score	-0.93
Structure conservation index	0.95
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.57
SVM RNA-class probability	0.747465
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 26466952 95 - 27905053
-------------------------GAGCUCGGCCAAUGACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------..((...((((..(((((((.(........).))).))))...))))(((((((((((................)))))))))))))........ ( -18.39, z-score =  -0.04, R)
>droSim1.chr3R 26112893 95 - 27517382
-------------------------GAGCUCGGCCAAUGACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------..((...((((..(((((((.(........).))).))))...))))(((((((((((................)))))))))))))........ ( -18.39, z-score =  -0.04, R)
>droSec1.super_4 5293723 95 - 6179234
-------------------------GAGCUCGGCCAAUGACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------..((...((((..(((((((.(........).))).))))...))))(((((((((((................)))))))))))))........ ( -18.39, z-score =  -0.04, R)
>droYak2.chr3R 27389139 120 - 28832112
CACACAGUACAGAGCACAGAGCACAGAGCUGGGCCAAUGACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
......((.((..((.(((..(...)..))).))...))))...((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... ( -23.70, z-score =   0.17, R)
>droEre2.scaffold_4820 8939844 95 + 10470090
-------------------------GAGCUGGGCCAAUGACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------.(((((.(...........).))))).........((((.((((.(((((((.....))))))).))))...((((........))))..)))). ( -19.90, z-score =  -0.51, R)
>droAna3.scaffold_12911 849303 95 + 5364042
-------------------------GAUACGAGCCAAUGACAAAUGCGGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------.......((((..(((((((.((......)).))).))))...))))(((((((((((................))))))))))).......... ( -20.19, z-score =  -1.28, R)
>dp4.chr2 30055138 83 + 30794189
-------------------------------------GACCGAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------------------.......((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... ( -18.00, z-score =  -1.62, R)
>droPer1.super_7 920038 83 + 4445127
-------------------------------------GACCGAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------------------.......((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... ( -18.00, z-score =  -1.62, R)
>droWil1.scaffold_181130 9983217 95 - 16660200
-------------------------GACGACGACAGACAACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
-------------------------...................((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... ( -18.00, z-score =  -1.20, R)
>droVir3.scaffold_13047 11246374 82 - 19223366
--------------------------------------GACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
--------------------------------------......((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... ( -18.00, z-score =  -1.77, R)
>droMoj3.scaffold_6540 3649623 82 + 34148556
--------------------------------------GACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
--------------------------------------......((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... ( -18.00, z-score =  -1.77, R)
>droGri2.scaffold_14624 1226668 87 - 4233967
---------------------------------ACGACGACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
---------------------------------...........((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... ( -18.00, z-score =  -1.41, R)
>consensus
_________________________GA____GGCCAAUGACAAAUGCAGCUAAACGAAUUAUGUCUAAUGGCAUUUCAGGUUGAAAUGCGAUUAAAAUGCAAUUUGAAAUGCAAAACAUU
............................................((((......((((((..((.((((.(((((((.....))))))).))))..))..))))))...))))....... (-18.02 = -17.94 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:57:46 2011