Locus 9544

Sequence ID dm3.chr3R
Location 7,303,051 – 7,303,184
Length 133
Max. P 0.888470
window13094 window13095 window13096

overview

Window 4

Location 7,303,051 – 7,303,157
Length 106
Sequences 12
Columns 120
Reading direction reverse
Mean pairwise identity 78.53
Shannon entropy 0.43607
G+C content 0.46595
Mean single sequence MFE -31.17
Consensus MFE -17.17
Energy contribution -16.70
Covariance contribution -0.47
Combinations/Pair 1.27
Mean z-score -1.46
Structure conservation index 0.55
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.17
SVM RNA-class probability 0.574933
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7303051 106 - 27905053
-------------AACUGAUUGCGAUGCCGGCCAAAGUUGCCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAGU-
-------------.(((..(((.(.((((((((...(((((((((((.((((((.....))))))...))))))))))).)))).........((........)).))))))))..)))- ( -35.80, z-score =  -2.03, R)
>droSim1.chr3R 13427765 106 + 27517382
-------------AACUGAUUGCGAUGCCGGCCAAAGUUGCCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAGU-
-------------.(((..(((.(.((((((((...(((((((((((.((((((.....))))))...))))))))))).)))).........((........)).))))))))..)))- ( -35.80, z-score =  -2.03, R)
>droSec1.super_0 6459663 106 + 21120651
-------------AACUGAUUGCGAUGCCGGCCAAAGUUGCCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAGU-
-------------.(((..(((.(.((((((((...(((((((((((.((((((.....))))))...))))))))))).)))).........((........)).))))))))..)))- ( -35.80, z-score =  -2.03, R)
>droYak2.chr3R 11337750 106 - 28832112
-------------AACUGAUUGCGAUGCCGGCCAAAGUUGCCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAGU-
-------------.(((..(((.(.((((((((...(((((((((((.((((((.....))))))...))))))))))).)))).........((........)).))))))))..)))- ( -35.80, z-score =  -2.03, R)
>droEre2.scaffold_4770 3429336 106 + 17746568
-------------AACUGAUUGCGAUGCCGGCCAAAGUUGCCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAGU-
-------------.(((..(((.(.((((((((...(((((((((((.((((((.....))))))...))))))))))).)))).........((........)).))))))))..)))- ( -35.80, z-score =  -2.03, R)
>droAna3.scaffold_13340 13737254 106 - 23697760
-------------AACUGAUUGCGAAACUGGCCAGAGUUUCCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAGU-
-------------..(((...(((...((((((...(((.(((((((.((((((.....))))))...))))))).))).)))...((.....)).........))).)))))).....- ( -27.60, z-score =  -0.25, R)
>dp4.chr2 25597699 106 - 30794189
------------UGAAGCACUGGGCCAGAGGCAGUGCUGGCCAUUAAAGGCGCGUUAAUUGCACUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAA--
------------.......(((((((...(((..(((((.(((((((.((.(((.....))).))...)))))))))))).))).........((........)).))).))))....-- ( -32.20, z-score =  -0.92, R)
>droPer1.super_6 926064 106 - 6141320
------------AGAAGCACUGGGCCAGAGGCAGUGCUGGCCAUUAAAGGCGCGUUAAUUGCACUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAA--
------------.......(((((((...(((..(((((.(((((((.((.(((.....))).))...)))))))))))).))).........((........)).))).))))....-- ( -32.20, z-score =  -1.05, R)
>droWil1.scaffold_181089 8191642 119 + 12369635
AACAAAAAUUGGACAUGAACACGGUCAGAGA-GUUGGCGCCCAUUAAAGGCGCGUUAAUUGCGCUCAAUUAAUGGCAGCAGGUUAAACGUUAAGUAAAAUUAAACAGACGCCAGGGACGG
.....................(.(((.....-.((((((((((((((.((((((.....))))))...)))))))..))..(((.....((((......))))...)))))))).))).) ( -25.70, z-score =   0.01, R)
>droVir3.scaffold_12855 9787712 93 - 10161210
--------------------------AUGGCCGGAGGGCAUCAUUAAAGGCGCGUUAAUUGCGCCCAAUUAAUGACAUCAGGUUAAACGUUAAGUGAAAUGAAACAGACGCCUGGGAAU-
--------------------------...(((....))).(((((((.((((((.....))))))...)))))))..(((((.....((((..((........)).)))))))))....- ( -25.70, z-score =  -1.39, R)
>droMoj3.scaffold_6540 24792704 93 - 34148556
--------------------------ACGACCGGAGGGCGUCAUUAAAGGCGCGUUAAUUGCGCUCAAUUAAUGACAUCAGGUUAAACGUUAAGUGAAAUUAAACAGACGCCCGGGACU-
--------------------------....((...(((((((.......(((((.....)))))(((.((((((.............)))))).))).........))))))).))...- ( -28.32, z-score =  -2.35, R)
>droGri2.scaffold_14830 2132601 91 - 6267026
--------------------------AUGACCAGAGGGCGUCAUUAAAGGCGCGUUAAUUGCGUCCAAUUAAUGGCAUCAGGUUAAACGUUAAGUGAAAUUAAACAGAUGCGUGGGG---
--------------------------.(((((.((....((((((((.((((((.....))))))...)))))))).)).))))).((((...((........))....))))....--- ( -23.30, z-score =  -1.39, R)
>consensus
_____________AACUGAUUGCGAUACCGGCCAAAGUUGCCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCAGGUUAAACGUUAAGUGAAAUUAAACAGGCGCCAGGGAGU_
....................................((..(((((((.((((((.....))))))...)))))))..)).(((......((((......))))......)))........ (-17.17 = -16.70 +  -0.47)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,303,090 – 7,303,184
Length 94
Sequences 7
Columns 105
Reading direction forward
Mean pairwise identity 65.54
Shannon entropy 0.64945
G+C content 0.48366
Mean single sequence MFE -24.54
Consensus MFE -10.32
Energy contribution -10.40
Covariance contribution 0.08
Combinations/Pair 1.09
Mean z-score -1.48
Structure conservation index 0.42
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.888470
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7303090 94 + 27905053
UGCUGCCAUUAAUCGAGCGCAAUUAACGCGCCUUUAAUGG----CAA--CUUUGGCCGGCAUCGCAAUCAGUUGGCUCACACACA-CACACACUUACUGGC----
.(((((((((((..(.((((.......))))).)))))))----)..--....(((((((..........)))))))........-............)))---- ( -25.80, z-score =  -1.61, R)
>droYak2.chr3R 11337789 98 + 28832112
UGCUGCCAUUAAUCGAGCGCAAUUAACGCGCCUUUAAUGG----CAA--CUUUGGCCGGCAUCGCAAUCAGUUGGCCAACACACA-CACACACGCAUUGACUGGC
((((((((((((..(.((((.......))))).)))))))----)).--..(((((((((..........)))))))))......-.......)))......... ( -32.40, z-score =  -2.65, R)
>droEre2.scaffold_4770 3429375 92 - 17746568
UGCUGCCAUUAAUCGAGCGCAAUUAACGCGCCUUUAAUGG----CAA--CUUUGGCCGGCAUCGCAAUCAGUUGGCUCACACACA-CACAUAG--ACUGGC----
.(((((((((((..(.((((.......))))).)))))))----)..--....(((((((..........)))))))........-.......--...)))---- ( -25.80, z-score =  -1.18, R)
>droAna3.scaffold_13340 13737293 94 + 23697760
UGCUGCCAUUAAUCGAGCGCAAUUAACGCGCCUUUAAUGG----AAA--CUCUGGCCAGUUUCGCAAUCAGUUUACCCUCACACA-CACACUACCACUCAC----
(((...((((((..(.((((.......))))).))))))(----(((--((......)))))))))...................-...............---- ( -17.30, z-score =  -1.40, R)
>droWil1.scaffold_181089 8191682 102 - 12369635
UGCUGCCAUUAAUUGAGCGCAAUUAACGCGCCUUUAAUGGGCGCCAACUCUCUGACCGUGUUCAUGUCCAAUUUUUGU-UGUAUUGUGUACACACACACACAC--
(((.((((.....)).)))))......((((((.....)))))).............((((.((((..((((....))-))...)))).))))..........-- ( -23.70, z-score =  -0.48, R)
>droVir3.scaffold_12855 9787751 76 + 10161210
UGAUGUCAUUAAUUGGGCGCAAUUAACGCGCCUUUAAUGA-UGCC----CUCCGGCCAUGUCCGGCGUGUAU----AUAUGUAUA--------------------
....((((((((..((((((.......)))))))))))))-)((.----(.((((......)))).).))..----.........-------------------- ( -23.40, z-score =  -1.28, R)
>droGri2.scaffold_14830 2132638 86 + 6267026
UGAUGCCAUUAAUUGGACGCAAUUAACGCGCCUUUAAUGA-CGCC----CUCUGGUCAUGUCCAGCAUAAACUUUGAUAUGCACAGGGUAC--------------
......((((((..((.(((.......))))).)))))).-.(((----((.(((......)))(((((........)))))..)))))..-------------- ( -23.40, z-score =  -1.74, R)
>consensus
UGCUGCCAUUAAUCGAGCGCAAUUAACGCGCCUUUAAUGG____CAA__CUCUGGCCGGCUUCGCAAUCAGUUGGCACACACACA_CACACAC__ACUGAC____
.....(((((((....((((.......))))..)))))))................................................................. (-10.32 = -10.40 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,303,090 – 7,303,184
Length 94
Sequences 7
Columns 105
Reading direction reverse
Mean pairwise identity 65.54
Shannon entropy 0.64945
G+C content 0.48366
Mean single sequence MFE -28.90
Consensus MFE -14.45
Energy contribution -13.80
Covariance contribution -0.65
Combinations/Pair 1.31
Mean z-score -1.04
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.870118
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7303090 94 - 27905053
----GCCAGUAAGUGUGUG-UGUGUGUGAGCCAACUGAUUGCGAUGCCGGCCAAAG--UUG----CCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCA
----(((.(((.(((....-((.((....))))......)))..))).)))....(--(((----(((((((.((((((.....))))))...))))))))))). ( -31.40, z-score =  -0.76, R)
>droYak2.chr3R 11337789 98 - 28832112
GCCAGUCAAUGCGUGUGUG-UGUGUGUUGGCCAACUGAUUGCGAUGCCGGCCAAAG--UUG----CCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCA
(((.(((((((((......-..))))))))).........((...)).)))....(--(((----(((((((.((((((.....))))))...))))))))))). ( -35.40, z-score =  -0.77, R)
>droEre2.scaffold_4770 3429375 92 + 17746568
----GCCAGU--CUAUGUG-UGUGUGUGAGCCAACUGAUUGCGAUGCCGGCCAAAG--UUG----CCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCA
----((((((--(....((-.((......))))...))))((...)).)))....(--(((----(((((((.((((((.....))))))...))))))))))). ( -30.40, z-score =  -0.64, R)
>droAna3.scaffold_13340 13737293 94 - 23697760
----GUGAGUGGUAGUGUG-UGUGUGAGGGUAAACUGAUUGCGAAACUGGCCAGAG--UUU----CCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCA
----.....(((((((...-((((...((.....))...))))..))).))))..(--((.----(((((((.((((((.....))))))...))))))).))). ( -26.90, z-score =  -0.66, R)
>droWil1.scaffold_181089 8191682 102 + 12369635
--GUGUGUGUGUGUGUACACAAUACA-ACAAAAAUUGGACAUGAACACGGUCAGAGAGUUGGCGCCCAUUAAAGGCGCGUUAAUUGCGCUCAAUUAAUGGCAGCA
--...(((((.(((((...((((...-......)))).))))).)))))(((((....)))))(((((((((.((((((.....))))))...)))))))..)). ( -28.50, z-score =  -0.26, R)
>droVir3.scaffold_12855 9787751 76 - 10161210
--------------------UAUACAUAU----AUACACGCCGGACAUGGCCGGAG----GGCA-UCAUUAAAGGCGCGUUAAUUGCGCCCAAUUAAUGACAUCA
--------------------.........----.....(.((((......)))).)----((..-(((((((.((((((.....))))))...)))))))..)). ( -22.40, z-score =  -2.15, R)
>droGri2.scaffold_14830 2132638 86 - 6267026
--------------GUACCCUGUGCAUAUCAAAGUUUAUGCUGGACAUGACCAGAG----GGCG-UCAUUAAAGGCGCGUUAAUUGCGUCCAAUUAAUGGCAUCA
--------------...((((..(((((........)))))(((......))).))----)).(-(((((((.((((((.....))))))...)))))))).... ( -27.30, z-score =  -2.08, R)
>consensus
____GUCAGU__GUGUGUG_UGUGUGUAAGCAAACUGAUUGCGAACCCGGCCAGAG__UUG____CCAUUAAAGGCGCGUUAAUUGCGCUCGAUUAAUGGCAGCA
.................................................................(((((((.((((((.....))))))...)))))))..... (-14.45 = -13.80 +  -0.65)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:06:30 2011