Locus 2527

Sequence ID dm3.chr2L
Location 19,770,056 – 19,770,186
Length 130
Max. P 0.693488
window3476 window3477

overview

Window 6

Location 19,770,056 – 19,770,186
Length 130
Sequences 11
Columns 141
Reading direction forward
Mean pairwise identity 87.07
Shannon entropy 0.27533
G+C content 0.38189
Mean single sequence MFE -27.16
Consensus MFE -22.45
Energy contribution -22.91
Covariance contribution 0.46
Combinations/Pair 1.04
Mean z-score -1.19
Structure conservation index 0.83
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.587812
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19770056 130 + 23011544
----------GAGAGAAAAAG-CAUAUGACGACGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAACUAAGUCGAACGUCAUUAUUAGGUUAAAGCCCUAAAAUGGGCGCAUUAG
----------..........(-(..((((((....(((.........))).(((...(((((....((((((.....))))))....)))))....)))...))))))............((((......))))))..... ( -27.90, z-score =  -2.02, R)
>droSec1.super_7 3375148 130 + 3727775
----------GAGAGAAAAAG-CAUAUGACGACGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAACUAAGUCGAACGUCAUUAUUAGGUUAAAGCCCUAAAACGGGCGCAUUAG
----------..........(-(..((((((....(((.........))).(((...(((((....((((((.....))))))....)))))....)))...))))))............((((......))))))..... ( -27.30, z-score =  -1.81, R)
>droSim1.chr2L 19426233 131 + 22036055
----------GAGAGAAAAAGGCAUAUGACGACGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAACUAAGUCGAACGUCAUUAUUAGGUUAAAGCCCUAAAACGGGCGCAUUAG
----------...........((..((((((....(((.........))).(((...(((((....((((((.....))))))....)))))....)))...))))))............((((......))))))..... ( -27.10, z-score =  -1.50, R)
>droYak2.chr2R 6232764 130 + 21139217
----------GAGAGAAAAAG-UAUAUCACGACGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAACUAAGUCGAACGUCAUUAUUAGGUUAAAGCCCUAAAACGGACGCAUUAG
----------...........-.......((((..((((.......((((((.....)))))).((((((....))))))......))))......))))..((((....(((((.......)))))....))))...... ( -22.10, z-score =  -0.77, R)
>droEre2.scaffold_4845 18033881 130 - 22589142
----------GAGAGAAAAAG-CAUAUGACGACGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAACUAAGUCGAACGUCAUUAUUAGGUUAAAGCCCUAAAACGGACGCAUUAG
----------..........(-(......((((..((((.......((((((.....)))))).((((((....))))))......))))......))))...(((....(((((.......)))))....)))))..... ( -23.50, z-score =  -1.05, R)
>droAna3.scaffold_12916 7141378 128 - 16180835
-------AAGAGAUGGAGCAGCCUGACGA------UGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAAGUAAGUCGAACAUAAUUAUUAGGUUAAAGCCCUAAAACGGGCGCAUUAG
-------..........(((((((((..(------(((.........))..(((...(((((....((((((.....))))))....)))))....))).......))..)))))))...((((......))))))..... ( -29.00, z-score =  -1.97, R)
>dp4.chr4_group5 99610 124 + 2436548
----------------GCGAG-UGAAUGUCGUGGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAAGUAAGUCGAACAUCAUUAUUAGGUUAAAGCCCUAAAGCGGGCGCAUUAG
----------------((.((-(((..(((((....)))))..........(((...(((((....((((((.....))))))....)))))....))).....)))))...........((((......))))))..... ( -27.80, z-score =  -1.03, R)
>droPer1.super_5 4600339 124 + 6813705
----------------GCGAG-UGAAUGUCGUGGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAAGUAAGUCGAACAUCAUUAUUAGGUUAAAGCCCUAAAGCGGGCGCAUUAG
----------------((.((-(((..(((((....)))))..........(((...(((((....((((((.....))))))....)))))....))).....)))))...........((((......))))))..... ( -27.80, z-score =  -1.03, R)
>droWil1.scaffold_180708 8546591 121 - 12563649
-----------------CGAG---UAUGCUGAGGAUGUGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAAGUAAGUCGAACAUCAUUAUUAGGUUAAAGCCCUAAAGCGGGCGCAUUAG
-----------------(((.---(.((((...(.((((((.....((((((.....)))))).((((((....))))))..)))))))..))))).)))....................((((......))))....... ( -25.30, z-score =  -0.95, R)
>droMoj3.scaffold_6500 3950607 141 - 32352404
GUGUGUAGUUGUGUGUGUGUGCCUGAAGAGAUGGCUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAAGUAAGUCGAACAUCAUUAUUAGGUUAAAGCCCUAAAGCGGGCGCAUUAG
................(((((((((...((..((((..((((.........(((...(((((....((((((.....))))))....)))))....)))(.....).......))))..))))))....)))))))))... ( -34.10, z-score =  -0.66, R)
>droGri2.scaffold_15126 7002529 130 + 8399593
----------GUGUGAAAGUG-UAUCUGCCUUGGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAAGUAAGUCGAACAUCAUUAUUAGGUUAAAGCCCUAAAGCGGGCGCAUUAG
----------((((......(-(((((.....))))))((((.........(((...(((((....((((((.....))))))....)))))....)))(.....).......))))...((((......))))))))... ( -26.90, z-score =  -0.30, R)
>consensus
__________GAGAGAAAAAG_CAUAUGACGACGAUGCGACCAAAAAGCAAGACAAAUUUGCUCGUUUUAUUAAUAAAAUAAGUCACGCAAAGUAAGUCGAACAUCAUUAUUAGGUUAAAGCCCUAAAACGGGCGCAUUAG
.................................(((((((((.........(((...(((((....((((((.....))))))....)))))....)))(.....).......))))...((((......))))))))).. (-22.45 = -22.91 +   0.46)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,770,056 – 19,770,186
Length 130
Sequences 11
Columns 141
Reading direction reverse
Mean pairwise identity 87.07
Shannon entropy 0.27533
G+C content 0.38189
Mean single sequence MFE -26.83
Consensus MFE -22.06
Energy contribution -22.25
Covariance contribution 0.19
Combinations/Pair 1.03
Mean z-score -1.36
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.43
SVM RNA-class probability 0.693488
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 19770056 130 - 23011544
CUAAUGCGCCCAUUUUAGGGCUUUAACCUAAUAAUGACGUUCGACUUAGUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCGUCGUCAUAUG-CUUUUUCUCUC----------
.....((((((......))))............((((((..(((....(....)((((((((((.....)))))...((((((.......))))))....))))).))).))))))..)-)..........---------- ( -29.00, z-score =  -2.13, R)
>droSec1.super_7 3375148 130 - 3727775
CUAAUGCGCCCGUUUUAGGGCUUUAACCUAAUAAUGACGUUCGACUUAGUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCGUCGUCAUAUG-CUUUUUCUCUC----------
.....((((((......))))............((((((..(((....(....)((((((((((.....)))))...((((((.......))))))....))))).))).))))))..)-)..........---------- ( -29.70, z-score =  -2.06, R)
>droSim1.chr2L 19426233 131 - 22036055
CUAAUGCGCCCGUUUUAGGGCUUUAACCUAAUAAUGACGUUCGACUUAGUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCGUCGUCAUAUGCCUUUUUCUCUC----------
.....((((((......))))............((((((..(((....(....)((((((((((.....)))))...((((((.......))))))....))))).))).))))))..))...........---------- ( -29.30, z-score =  -1.87, R)
>droYak2.chr2R 6232764 130 - 21139217
CUAAUGCGUCCGUUUUAGGGCUUUAACCUAAUAAUGACGUUCGACUUAGUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCGUCGUGAUAUA-CUUUUUCUCUC----------
...(((((.((((((((((.......)))))....)))((..(((..(((((((.((..(((((.....)))))..)).))))))).)))..)).....)).)))))............-...........---------- ( -27.40, z-score =  -1.43, R)
>droEre2.scaffold_4845 18033881 130 + 22589142
CUAAUGCGUCCGUUUUAGGGCUUUAACCUAAUAAUGACGUUCGACUUAGUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCGUCGUCAUAUG-CUUUUUCUCUC----------
...(((((.((((((((((.......)))))....)))((..(((..(((((((.((..(((((.....)))))..)).))))))).)))..)).....)).)))))............-...........---------- ( -27.40, z-score =  -1.49, R)
>droAna3.scaffold_12916 7141378 128 + 16180835
CUAAUGCGCCCGUUUUAGGGCUUUAACCUAAUAAUUAUGUUCGACUUACUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCA------UCGUCAGGCUGCUCCAUCUCUU-------
.....((((((......))))...............................((.(((((((((.....)))))..(((.((((...(.....)..)))).)))..------..)))).)).))..........------- ( -24.60, z-score =  -0.47, R)
>dp4.chr4_group5 99610 124 - 2436548
CUAAUGCGCCCGCUUUAGGGCUUUAACCUAAUAAUGAUGUUCGACUUACUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCCACGACAUUCA-CUCGC----------------
..(((((((((......))))..............((((..(((((......(((.(((..((((..((........))..))))..))).))).....)))))))))...).))))..-.....---------------- ( -23.90, z-score =  -0.71, R)
>droPer1.super_5 4600339 124 - 6813705
CUAAUGCGCCCGCUUUAGGGCUUUAACCUAAUAAUGAUGUUCGACUUACUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCCACGACAUUCA-CUCGC----------------
..(((((((((......))))..............((((..(((((......(((.(((..((((..((........))..))))..))).))).....)))))))))...).))))..-.....---------------- ( -23.90, z-score =  -0.71, R)
>droWil1.scaffold_180708 8546591 121 + 12563649
CUAAUGCGCCCGCUUUAGGGCUUUAACCUAAUAAUGAUGUUCGACUUACUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCACAUCCUCAGCAUA---CUCG-----------------
...((((((((......))))..............(((((..((((......(((.(((..((((..((........))..))))..))).))).....)))))))))....)))).---....----------------- ( -26.70, z-score =  -2.38, R)
>droMoj3.scaffold_6500 3950607 141 + 32352404
CUAAUGCGCCCGCUUUAGGGCUUUAACCUAAUAAUGAUGUUCGACUUACUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAGCCAUCUCUUCAGGCACACACACACAACUACACAC
....(((((((......))))..............(((((((((((......(((.(((..((((..((........))..))))..))).))).....))))).)).)))).......)))................... ( -27.00, z-score =  -0.89, R)
>droGri2.scaffold_15126 7002529 130 - 8399593
CUAAUGCGCCCGCUUUAGGGCUUUAACCUAAUAAUGAUGUUCGACUUACUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCCAAGGCAGAUA-CACUUUCACAC----------
....(((((((......))))..............((((..(((((......(((.(((..((((..((........))..))))..))).))).....)))))))))....)))....-...........---------- ( -26.20, z-score =  -0.86, R)
>consensus
CUAAUGCGCCCGUUUUAGGGCUUUAACCUAAUAAUGAUGUUCGACUUACUUUGCGUGACUUAUUUUAUUAAUAAAACGAGCAAAUUUGUCUUGCUUUUUGGUCGCAUCCUCGUCAUAUG_CUCUUUCUCUC__________
...(((((.(((..(((((.......))))).......((..(((....(((((.((..(((((.....)))))..)).)))))...)))..))....))).))))).................................. (-22.06 = -22.25 +   0.19)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:52:57 2011