Locus 11169

Sequence ID dm3.chr3R
Location 19,203,957 – 19,204,061
Length 104
Max. P 0.934159
window15343 window15344

overview

Window 3

Location 19,203,957 – 19,204,061
Length 104
Sequences 12
Columns 116
Reading direction forward
Mean pairwise identity 69.17
Shannon entropy 0.62032
G+C content 0.49268
Mean single sequence MFE -29.24
Consensus MFE -14.25
Energy contribution -13.82
Covariance contribution -0.43
Combinations/Pair 1.32
Mean z-score -1.41
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.934159
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19203957 104 + 27905053
----------UGAACCUUAGGAUCUACAAU--CGUUUGUAAACUUACUUGAACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGCGCCGAGUGGCGCCAUUCGGUGGUCCUAAG
----------.....(((((((((......--.....(((.((((......((.(((....))).))((((...)))).)))).)))((((((((....))))))))))))))))) ( -33.80, z-score =  -3.07, R)
>droSim1.chr3R 19022823 104 + 27517382
----------UGAACCGUAGGAUCUACAAU--CGUUUGUCAACUUACUUGAACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGCGCCGAGUGGCGCCAUUCGGUGGUCCUAAG
----------.......(((((((..((((--.((.((((((.((((.........)))))))))).))..)))).(((.....)))((((((((....))))))))))))))).. ( -30.80, z-score =  -1.58, R)
>droSec1.super_0 19567897 90 + 21120651
------------------------UAAGUA--GGGGAAGCAACUUACUUGAACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGCGCCGAGUGGCGCCAUUCGGUGGUCCUAAG
------------------------((((((--((........)))))))).(((..(((...(((.(((((...)))))..))))))((((((((....)))))))))))...... ( -28.50, z-score =  -1.25, R)
>droYak2.chr3R 20083334 105 + 28832112
------UAUCUAUACUAU---AUCUAUAAU--AAUUUGCAAACUUACUUGAACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGCGCCGAGUGGCGCCAUUCGGUGGUCCUAAG
------............---.........--.....(((.((((......((.(((....))).))((((...)))).)))).)))((((((((....))))))))......... ( -23.90, z-score =  -1.00, R)
>droEre2.scaffold_4820 1624152 114 - 10470090
UACGUUUACGUUUAACGCAGGAUAUACAAU--CGUUGGUAAGCUUACCUGAACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGCGCCGAGUGGCGCCAUUCGGUGGUCCUAAG
.........((((((((.((.((((.((((--((..(((.((.....))..))).))..)))))))).))))))))))........(((((((((....)))))))))........ ( -33.80, z-score =  -1.06, R)
>droAna3.scaffold_13340 3347014 106 - 23697760
----------GUUAUUAGAGCUUUUAUUGUUCAUUUUCGUAGCCUACCUGAACCCCGUAAUUAAUGUGCUCGUCGAGCAAAGUCUGCGCCGAGUGACGCCAUUCGGUGGUCCGUAU
----------.......((((.......)))).........((..(((........(((.......(((((...))))).....)))((((((((....)))))))))))..)).. ( -23.60, z-score =  -0.28, R)
>dp4.chr2 2685035 88 + 30794189
--------------------------GUCU--AGAGAGAAAACCUACCUGGACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGGGCCGAGUGGCGCCAUUCGGUGGUCCGGAG
--------------------------....--...............(((((((........(((.(((((...)))))..)))...((((((((....))))))))))))))).. ( -31.40, z-score =  -1.73, R)
>droPer1.super_7 2777864 88 - 4445127
--------------------------GUCU--AGAGAGAACACCUACCUGGACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGGGCCGAGUGGCGCCAUUCGGUGGUCCGGAG
--------------------------....--...............(((((((........(((.(((((...)))))..)))...((((((((....))))))))))))))).. ( -31.40, z-score =  -1.32, R)
>droWil1.scaffold_181130 9235616 90 + 16660200
--------------------------UAAAUUGUAUAAAAAACUUACCUGGACCUCGUAUUUAAUGUGCUCGUUGAGCAGAGUUUGGGCCGAAUGGCGCCAUUCGGUGGUGCGUAA
--------------------------......((((..........((..(((.((...(((((((....)))))))..)))))..))(((((((....)))))))..)))).... ( -25.40, z-score =  -1.25, R)
>droVir3.scaffold_13047 8838279 85 + 19223366
----------------------------AAAGUCA---UUCACUCACCUGGACCUCGUAUUUGAUGUGCUCAUCGAGCAGAGUUUGCGCCGAAUGACGCCAUUGGGUGGUGCGCAU
----------------------------.......---..(((.((((..(..(((...(((((((....)))))))..)))...(((........)))..)..)))))))..... ( -21.80, z-score =   0.80, R)
>droMoj3.scaffold_6540 2306664 101 - 34148556
---------------GAAAUUAUAUAUUGAGUUCAGCGUACACUCACCUGGACCUCGUAUUUGAUGUGCUCGUUAAGAAGAGUUUGUGCCGAGUGGCGCCACUGGGUGGUGCGCAU
---------------(((.(((.....))).))).((((((...((((..(..(((...(((((((....)))))))..)))...(((((....)))))..)..)))))))))).. ( -33.00, z-score =  -1.66, R)
>droGri2.scaffold_15074 6950172 85 - 7742996
----------------------------AAAACUG---UAGACUUACCUGAACCUCGUAUUUAAUGUGUUCAUUGAGUAGGGUUUGGGCCGAGUGGCGCCAUUGGGUGGUGCGCAG
----------------------------....(((---(..((((.((..(((((..(((((((((....))))))))))))))..))..)))).(((((((...))))))))))) ( -33.50, z-score =  -3.51, R)
>consensus
________________________UAUAAU__AGAUAGUAAACUUACCUGAACCUCGUAAUUGAUGUGCUCGUUGAGCAAAGUCUGCGCCGAGUGGCGCCAUUCGGUGGUCCGAAG
.................................................(.(((........(((.(((((...)))))..)))...(((.((((....)))).)))))).).... (-14.25 = -13.82 +  -0.43)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,203,957 – 19,204,061
Length 104
Sequences 12
Columns 116
Reading direction reverse
Mean pairwise identity 69.17
Shannon entropy 0.62032
G+C content 0.49268
Mean single sequence MFE -24.12
Consensus MFE -10.70
Energy contribution -10.73
Covariance contribution 0.04
Combinations/Pair 1.17
Mean z-score -1.01
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.08
SVM RNA-class probability 0.533167
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19203957 104 - 27905053
CUUAGGACCACCGAAUGGCGCCACUCGGCGCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUUCAAGUAAGUUUACAAACG--AUUGUAGAUCCUAAGGUUCA----------
(((((((..(((.....(((((....))))).((...(((((...)))))..))........))).........(((((((...--.)))))))))))))).....---------- ( -30.20, z-score =  -2.60, R)
>droSim1.chr3R 19022823 104 - 27517382
CUUAGGACCACCGAAUGGCGCCACUCGGCGCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUUCAAGUAAGUUGACAAACG--AUUGUAGAUCCUACGGUUCA----------
....(((((..((....(((((....)))))....((((.(((((((((...((......)).))))......)))))))))))--...((((...))))))))).---------- ( -28.50, z-score =  -1.49, R)
>droSec1.super_0 19567897 90 - 21120651
CUUAGGACCACCGAAUGGCGCCACUCGGCGCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUUCAAGUAAGUUGCUUCCCC--UACUUA------------------------
....(((((........(((((....))))).((...(((((...)))))..))........)))))(((((.(........).--))))).------------------------ ( -23.80, z-score =  -1.39, R)
>droYak2.chr3R 20083334 105 - 28832112
CUUAGGACCACCGAAUGGCGCCACUCGGCGCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUUCAAGUAAGUUUGCAAAUU--AUUAUAGAU---AUAGUAUAGAUA------
....(((((........(((((....))))).((...(((((...)))))..))........)))))..(((....)))....(--(((((....---))))))......------ ( -23.50, z-score =  -1.23, R)
>droEre2.scaffold_4820 1624152 114 + 10470090
CUUAGGACCACCGAAUGGCGCCACUCGGCGCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUUCAGGUAAGCUUACCAACG--AUUGUAUAUCCUGCGUUAAACGUAAACGUA
....(((((........(((((....))))).((...(((((...)))))..))........))))).((((....))))....--...........((((((.......)))))) ( -29.10, z-score =  -0.85, R)
>droAna3.scaffold_13340 3347014 106 + 23697760
AUACGGACCACCGAAUGGCGUCACUCGGCGCAGACUUUGCUCGACGAGCACAUUAAUUACGGGGUUCAGGUAGGCUACGAAAAUGAACAAUAAAAGCUCUAAUAAC----------
....(((((.(((....(((((....)))))......(((((...))))).........))))))))...((((((..................))).))).....---------- ( -26.67, z-score =  -1.65, R)
>dp4.chr2 2685035 88 - 30794189
CUCCGGACCACCGAAUGGCGCCACUCGGCCCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUCCAGGUAGGUUUUCUCUCU--AGAC--------------------------
(((((((((......(((.(((....))))))((...(((((...)))))..))........))))).)).))...........--....-------------------------- ( -25.40, z-score =  -1.27, R)
>droPer1.super_7 2777864 88 + 4445127
CUCCGGACCACCGAAUGGCGCCACUCGGCCCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUCCAGGUAGGUGUUCUCUCU--AGAC--------------------------
(((((((((......(((.(((....))))))((...(((((...)))))..))........))))).)).))...........--....-------------------------- ( -25.40, z-score =  -0.68, R)
>droWil1.scaffold_181130 9235616 90 - 16660200
UUACGCACCACCGAAUGGCGCCAUUCGGCCCAAACUCUGCUCAACGAGCACAUUAAAUACGAGGUCCAGGUAAGUUUUUUAUACAAUUUA--------------------------
..((..(((.(((((((....)))))))......((((((((...)))))..........))).....)))..))...............-------------------------- ( -19.40, z-score =  -1.46, R)
>droVir3.scaffold_13047 8838279 85 - 19223366
AUGCGCACCACCCAAUGGCGUCAUUCGGCGCAAACUCUGCUCGAUGAGCACAUCAAAUACGAGGUCCAGGUGAGUGAA---UGACUUU----------------------------
.....(((((((.....(((((....)))))...((((((((...)))))..........))).....)))).)))..---.......---------------------------- ( -21.70, z-score =   0.21, R)
>droMoj3.scaffold_6540 2306664 101 + 34148556
AUGCGCACCACCCAGUGGCGCCACUCGGCACAAACUCUUCUUAACGAGCACAUCAAAUACGAGGUCCAGGUGAGUGUACGCUGAACUCAAUAUAUAAUUUC---------------
..((((((((((...(((.(((.((((.................))))....((......)))))))))))).)))..)))....................--------------- ( -20.33, z-score =   0.23, R)
>droGri2.scaffold_15074 6950172 85 + 7742996
CUGCGCACCACCCAAUGGCGCCACUCGGCCCAAACCCUACUCAAUGAACACAUUAAAUACGAGGUUCAGGUAAGUCUA---CAGUUUU----------------------------
..((..(((......(((.(((....))))))............(((((...((......)).))))))))..))...---.......---------------------------- ( -15.40, z-score =   0.03, R)
>consensus
CUUCGGACCACCGAAUGGCGCCACUCGGCGCAGACUUUGCUCAACGAGCACAUCAAUUACGAGGUUCAGGUAAGUUUACAAACG__AUUAUA________________________
....(.(((..........(((....)))........(((((...)))))............))).)................................................. (-10.70 = -10.73 +   0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:37:40 2011