Locus 11984

Sequence ID dm3.chr3R
Location 24,923,237 – 24,923,339
Length 102
Max. P 0.933313
window16465 window16466

overview

Window 5

Location 24,923,237 – 24,923,339
Length 102
Sequences 12
Columns 113
Reading direction forward
Mean pairwise identity 72.96
Shannon entropy 0.53806
G+C content 0.51143
Mean single sequence MFE -25.38
Consensus MFE -19.82
Energy contribution -19.90
Covariance contribution 0.08
Combinations/Pair 1.00
Mean z-score -0.93
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.933313
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24923237 102 + 27905053
-----------AAUAUUAAAUUUGAUCAAUUAAUUCAUCACUUUUAGGAGCGCAAGGCGGCGACGCCUGGCAGGAGACAGUCCAUCCACCAGUUCACCAAUGGCAGUCCCAAU
-----------....(((((..((((.((....)).))))..)))))((((((.(((((....))))).)).(((.........)))....)))).....(((.....))).. ( -24.10, z-score =  -1.21, R)
>droSim1.chr3R 24606574 102 + 27517382
-----------AAAAUUAAAUUUGGUCAAUUCAUUCUUCUGUUUCAGGAGCGCAAGGCGGCGACGCCUGGCAGGAGACAGUCCAUCCACCAGUUCACCAAUGGCAGUCCCAAU
-----------..........(((((.((((.......(((((((....((.((.((((....))))))))..)))))))..........)))).)))))(((.....))).. ( -26.03, z-score =  -0.63, R)
>droSec1.super_4 3787939 102 + 6179234
-----------AAAAUUAAAUUUGGUCAAUUCUUUCUUCUGUUGUAGGAGCGCAAGGCGGCGACGCCUGGCAGGAGACAGUCCAUCCACCAGUUCACCAAUGGCAGUCCCAAU
-----------..........((((.............((((..(..((((((.(((((....))))).)).(((.........)))....))))....)..))))..)))). ( -26.86, z-score =  -0.47, R)
>droEre2.scaffold_4820 7361693 101 - 10470090
-----------AAAAUUCAUUUUGUUCAAUUCAUU-UCCUCUUUUAGGAGCGCAAGGCGGCGACGCCUGGCAGGAGACAGUCCAUCCACCAGUUCACCAAUGGCAGUCCCAAU
-----------.......................(-((((.....))))).((.(((((....))))).)).((.(((.(.((((..............))))).)))))... ( -24.44, z-score =  -0.88, R)
>droYak2.chr3R 7257111 100 - 28832112
-------------UAUUAAUUGUGUUCAAUUCAUUGUACUUUCUUAGGAGCGCAAGGCGGCGACGCCUGGCAGGAGACAGUCCAUCCACCAGUUCACCAAUGGCAGUCCCAAU
-------------.....((((.(..(...((((((..((.....))((((((.(((((....))))).)).(((.........)))....))))..))))))..)..))))) ( -24.80, z-score =  -0.39, R)
>droAna3.scaffold_13340 4045074 93 - 23697760
-------------------UUUAUGCUUUUUUUUUUGCCAU-UUCAGGAGCGCAAGGCGGCGACGCCUGGCAGGAGACAGUCCAUCCAUCAGUUCACCAAUGGCAGCCCCAAC
-------------------...............(((((((-(....((((((.(((((....))))).)).(((.........)))....))))...))))))))....... ( -30.30, z-score =  -2.32, R)
>dp4.chr2 21031814 79 - 30794189
----------------------------------AAUAUUGAAAUAGGAGCGCAAGGCGGCGACGCCUGGCAGGCGACAGUCCAUCCAUCAGUUCGCAAAUGGCAGCCCCAAU
----------------------------------............((.((((.(((((....))))).)).(((....)))...((((..(....)..))))..)).))... ( -22.60, z-score =  -0.06, R)
>droPer1.super_0 10717354 79 + 11822988
----------------------------------AAUCUUGAAAUAGGAGCGCAAGGCGGCGACGCCUGGCAGGCGACAGUCCAUCCAUCAGUUCGCAAAUGGCAGCCCCAAU
----------------------------------............((.((((.(((((....))))).)).(((....)))...((((..(....)..))))..)).))... ( -22.60, z-score =   0.14, R)
>droWil1.scaffold_181108 4306573 87 - 4707319
--------------------------CAUUAUUUUUGCCACAAUCAGGAGCGCAAGGCGGCGACGCCUGGCAGGCGACAAUCUAUACAUCAGUUCACCAAUGGCAGUCCAAAU
--------------------------........((((((.......((((((.(((((....))))).)).(....).............)))).....))))))....... ( -25.30, z-score =  -2.04, R)
>droVir3.scaffold_12855 9264399 85 - 10161210
---------------------------AUCAUCUU-AUCCCAUACAGGAGCGCAAGGCGGCGACGCCUGGCAGGCGACAAUCCAUACAUCAGUUCACAAAUGGCAGUCCCAAU
---------------------------........-.(((......)))..((.(((((....))))).)).((.(((...((((..............))))..)))))... ( -22.84, z-score =  -1.38, R)
>droMoj3.scaffold_6540 7630286 85 + 34148556
-------------------------AUCAUUGAAU--CCUU-UGCAGGAGCGCAAGGCGGCGACGCCUGGCAGGCGACAAUCCAUACAUCAGUUCACAAAUGGCAGUCCCAAC
-------------------------.........(--(((.-...))))..((.(((((....))))).)).((.(((...((((..............))))..)))))... ( -23.84, z-score =  -0.73, R)
>droGri2.scaffold_14906 12185308 112 - 14172833
AUCAUAAAAUAACGAACAUCAUCCGCUCUUUGCUUUGCUUU-UGCAGGAGCGCAAGGCGGCGACGCCUGGCAGGCGACAAUCCAUACAUCAGUUCACAAAUGGCAGUCCCAAU
........................((((((.((........-.))))))))((.(((((....))))).)).((.(((...((((..............))))..)))))... ( -30.84, z-score =  -1.13, R)
>consensus
____________________UU___UCAAUUCAUU_UCCUCUUUCAGGAGCGCAAGGCGGCGACGCCUGGCAGGAGACAGUCCAUCCAUCAGUUCACCAAUGGCAGUCCCAAU
...............................................((((((.(((((....))))).)).(....).............)))).....(((.....))).. (-19.82 = -19.90 +   0.08)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 24,923,237 – 24,923,339
Length 102
Sequences 12
Columns 113
Reading direction reverse
Mean pairwise identity 72.96
Shannon entropy 0.53806
G+C content 0.51143
Mean single sequence MFE -26.98
Consensus MFE -20.01
Energy contribution -19.42
Covariance contribution -0.60
Combinations/Pair 1.17
Mean z-score -0.46
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.40
SVM RNA-class probability 0.679208
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24923237 102 - 27905053
AUUGGGACUGCCAUUGGUGAACUGGUGGAUGGACUGUCUCCUGCCAGGCGUCGCCGCCUUGCGCUCCUAAAAGUGAUGAAUUAAUUGAUCAAAUUUAAUAUU-----------
.((((((.(((...((((((.((((((((.((....))))).)))))...))))))....))).))))))...((((.((....)).))))...........----------- ( -29.70, z-score =  -1.66, R)
>droSim1.chr3R 24606574 102 - 27517382
AUUGGGACUGCCAUUGGUGAACUGGUGGAUGGACUGUCUCCUGCCAGGCGUCGCCGCCUUGCGCUCCUGAAACAGAAGAAUGAAUUGACCAAAUUUAAUUUU-----------
.(..(((.(((...((((((.((((((((.((....))))).)))))...))))))....))).)))..).....((((.((((((.....)))))).))))----------- ( -29.10, z-score =  -1.07, R)
>droSec1.super_4 3787939 102 - 6179234
AUUGGGACUGCCAUUGGUGAACUGGUGGAUGGACUGUCUCCUGCCAGGCGUCGCCGCCUUGCGCUCCUACAACAGAAGAAAGAAUUGACCAAAUUUAAUUUU-----------
..(((((.(((...((((((.((((((((.((....))))).)))))...))))))....))).)))))...........((((((((......))))))))----------- ( -28.00, z-score =  -0.58, R)
>droEre2.scaffold_4820 7361693 101 + 10470090
AUUGGGACUGCCAUUGGUGAACUGGUGGAUGGACUGUCUCCUGCCAGGCGUCGCCGCCUUGCGCUCCUAAAAGAGGA-AAUGAAUUGAACAAAAUGAAUUUU-----------
.((((((.(((...((((((.((((((((.((....))))).)))))...))))))....))).)))))).....((-(((..(((......)))..)))))----------- ( -29.00, z-score =  -1.15, R)
>droYak2.chr3R 7257111 100 + 28832112
AUUGGGACUGCCAUUGGUGAACUGGUGGAUGGACUGUCUCCUGCCAGGCGUCGCCGCCUUGCGCUCCUAAGAAAGUACAAUGAAUUGAACACAAUUAAUA-------------
.((((((.(((...((((((.((((((((.((....))))).)))))...))))))....))).))))))............(((((....)))))....------------- ( -28.70, z-score =  -0.96, R)
>droAna3.scaffold_13340 4045074 93 + 23697760
GUUGGGGCUGCCAUUGGUGAACUGAUGGAUGGACUGUCUCCUGCCAGGCGUCGCCGCCUUGCGCUCCUGAA-AUGGCAAAAAAAAAAGCAUAAA-------------------
...(((((..((((..(....)..))))..(((.....))).((.(((((....))))).)))))))....-...((..........)).....------------------- ( -29.30, z-score =  -0.81, R)
>dp4.chr2 21031814 79 + 30794189
AUUGGGGCUGCCAUUUGCGAACUGAUGGAUGGACUGUCGCCUGCCAGGCGUCGCCGCCUUGCGCUCCUAUUUCAAUAUU----------------------------------
...(((((..(((((........)))))..............((.(((((....))))).)))))))............---------------------------------- ( -23.30, z-score =   0.23, R)
>droPer1.super_0 10717354 79 - 11822988
AUUGGGGCUGCCAUUUGCGAACUGAUGGAUGGACUGUCGCCUGCCAGGCGUCGCCGCCUUGCGCUCCUAUUUCAAGAUU----------------------------------
...(((((..(((((........)))))..............((.(((((....))))).)))))))............---------------------------------- ( -23.30, z-score =   0.50, R)
>droWil1.scaffold_181108 4306573 87 + 4707319
AUUUGGACUGCCAUUGGUGAACUGAUGUAUAGAUUGUCGCCUGCCAGGCGUCGCCGCCUUGCGCUCCUGAUUGUGGCAAAAAUAAUG--------------------------
........((((((.(((((...(((......))).))))).((.(((((....))))).))..........)))))).........-------------------------- ( -24.00, z-score =  -0.62, R)
>droVir3.scaffold_12855 9264399 85 + 10161210
AUUGGGACUGCCAUUUGUGAACUGAUGUAUGGAUUGUCGCCUGCCAGGCGUCGCCGCCUUGCGCUCCUGUAUGGGAU-AAGAUGAU---------------------------
...(((((..((((.(((......))).))))...))).)).((.(((((....))))).))..((((....)))).-........--------------------------- ( -23.00, z-score =   0.34, R)
>droMoj3.scaffold_6540 7630286 85 - 34148556
GUUGGGACUGCCAUUUGUGAACUGAUGUAUGGAUUGUCGCCUGCCAGGCGUCGCCGCCUUGCGCUCCUGCA-AAGG--AUUCAAUGAU-------------------------
((((((((..((((.(((......))).))))...))).(((((.(((((....))))).))((....)).-.)))--..)))))...------------------------- ( -24.00, z-score =   0.31, R)
>droGri2.scaffold_14906 12185308 112 + 14172833
AUUGGGACUGCCAUUUGUGAACUGAUGUAUGGAUUGUCGCCUGCCAGGCGUCGCCGCCUUGCGCUCCUGCA-AAAGCAAAGCAAAGAGCGGAUGAUGUUCGUUAUUUUAUGAU
...(((((..((((.(((......))).))))...))).))...(..(((((((((((((..(((..(((.-...))).))).))).)))).))))))..)............ ( -32.30, z-score =  -0.04, R)
>consensus
AUUGGGACUGCCAUUGGUGAACUGAUGGAUGGACUGUCGCCUGCCAGGCGUCGCCGCCUUGCGCUCCUAAAAAAGGA_AAUGAAUUGA___AA____________________
..(((((..(((((..(....)..)))...............((.(((((....))))).)))))))))............................................ (-20.01 = -19.42 +  -0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:53:22 2011