Locus 11126

Sequence ID dm3.chr3R
Location 18,803,415 – 18,803,515
Length 100
Max. P 0.877159
window15288 window15289 window15290

overview

Window 8

Location 18,803,415 – 18,803,511
Length 96
Sequences 10
Columns 102
Reading direction forward
Mean pairwise identity 80.40
Shannon entropy 0.39984
G+C content 0.57086
Mean single sequence MFE -36.34
Consensus MFE -20.65
Energy contribution -20.34
Covariance contribution -0.31
Combinations/Pair 1.42
Mean z-score -2.00
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.03
SVM RNA-class probability 0.877159
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18803415 96 + 27905053
CACCGAGAAGACCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCCGGCUAUCUGCCCGACCAUCGUGGUCGCUGUCGGGAAAUCUGGUGAUU------
..((((.(.(((((((((((((((...((......))....))).....(((.....)))..))))))))))))..).))))..((((....))))------ ( -37.40, z-score =  -2.09, R)
>droSim1.chr3R 18616689 98 + 27517382
CACCGAGAAGCCCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGUUGUCGGGAAAUCUGGUGAUUCG----
..((((.(((.(((((((((((((...((......))....)))...(((((.....))))))))))))))).).)).))))(((.((....))))).---- ( -39.50, z-score =  -2.13, R)
>droSec1.super_0 19167546 98 + 21120651
CACCGAGAAGACCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGUUGUCGGGAAAUCUGGUGAUCCG----
..((((.(((((((((((((((((...((......))....)))...(((((.....))))))))))))))))).)).)))).......((....)).---- ( -44.30, z-score =  -3.50, R)
>droYak2.chr3R 19663077 96 + 28832112
CACCGAGAAGCCCAUGAUGGUGGCCAUGAUCGACUUUCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGCUGUCGGGAAAUCUGGUGAUU------
((((.(((..(((..(((((((((((((((.(.........(....)(((((.....))))).).))))))))))))))))))...)))))))...------ ( -42.30, z-score =  -3.08, R)
>droEre2.scaffold_4820 1203635 96 - 10470090
CACCGAGAAGCCCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGCGGUCGCUGUCGGGAAAUCUGGUGAUU------
(((((.((((.(.((.((((...)))).)).).)))).((((.((((.((((.....))))((((.....)))))))).)))).....)))))...------ ( -39.20, z-score =  -1.92, R)
>droAna3.scaffold_13340 11179480 102 - 23697760
UACCGAGAAAAUCAUGGAGGUGGCCAUGAUAGACUUCCCCUGCCAGCCGGGCUACCUGCCCGACCACCGUGGUCGGUGCCGGGAAAUCUGGUAAACGGCAAA
((((......(((((((......)))))))(((.(((((..((..(((((((.....))))((((.....))))))))).))))).)))))))......... ( -41.40, z-score =  -2.13, R)
>droWil1.scaffold_181089 11140380 94 - 12369635
UGAGAAAAAUAUUAUGCAGGUAGCCAUGAUUGAUUUCCCUUGCCAGCCUGGUUAUCUUCCCGACAGUCGUGGCCGUUGCCGUGAAAUCUGGUAG--------
..................((((((((((((((.........(((.....)))...........))))))))))...))))..............-------- ( -20.85, z-score =   0.01, R)
>droVir3.scaffold_12822 3991432 100 - 4096053
AACCGAAAAAAUUAUGGAGGUUGCUAUGAUUGAUUUUCCCUGUCAGCCAGGCUACCUGCCUGACAGCCGUGGACGCUGCCGUGAGAUAUGGUGAUCUGAU--
.((((......((((((.(((..(((((...(.....).(((((((.((((...)))).))))))).)))))..))).))))))....))))........-- ( -28.90, z-score =  -1.71, R)
>droMoj3.scaffold_6540 1343659 100 - 34148556
CACCGAGAAGAUCAUGGAGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUACCUGCCCGACAGUCGCGGACGGUGCCGCGAGAUAUGGUAAACCCCA--
....(((..((((((((......))))))))..)))....((((((.(((((.....))))).)..((((((......))))))....))))).......-- ( -39.80, z-score =  -2.06, R)
>droGri2.scaffold_15074 3608096 97 + 7742996
AACCGAGAAAAUUAUGGAGGUGGCCAUGAUUGAUUUUCCCUGUCAGCCCGGCUAUUUGCCCGACAGUCGUGGACGCUGCCGUGAGAUAUGGUGAUUC-----
.((((......((((((.((((.(((((((((.........(....)..(((.....)))...))))))))).)))).))))))....)))).....----- ( -29.80, z-score =  -1.38, R)
>consensus
CACCGAGAAGACCAUGAAGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGCUGCCGGGAAAUCUGGUGAUU______
(((((......((((((.(.((((...((......))....)))).)(((((.....)))))....))))))(((....)))......)))))......... (-20.65 = -20.34 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,803,415 – 18,803,511
Length 96
Sequences 10
Columns 102
Reading direction reverse
Mean pairwise identity 80.40
Shannon entropy 0.39984
G+C content 0.57086
Mean single sequence MFE -36.68
Consensus MFE -17.76
Energy contribution -17.97
Covariance contribution 0.21
Combinations/Pair 1.43
Mean z-score -1.89
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.07
SVM RNA-class probability 0.529280
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18803415 96 - 27905053
------AAUCACCAGAUUUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCGGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCUUCUCGGUG
------...((((.((((((((..((((((((.....)))).(((.....)))..))))....))))))))((((((((......)))))))).....)))) ( -42.80, z-score =  -3.12, R)
>droSim1.chr3R 18616689 98 - 27517382
----CGAAUCACCAGAUUUCCCGACAACGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGGCUUCUCGGUG
----.....((((.((((((((.....((....))..((((((((.....)))))))).....))))))))((....((((.........))))..)))))) ( -37.20, z-score =  -1.38, R)
>droSec1.super_0 19167546 98 - 21120651
----CGGAUCACCAGAUUUCCCGACAACGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGUCUUCUCGGUG
----.....((((.((((((((.....((....))..((((((((.....)))))))).....))))))))((((((((......)))))))).....)))) ( -41.00, z-score =  -2.27, R)
>droYak2.chr3R 19663077 96 - 28832112
------AAUCACCAGAUUUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGAAAGUCGAUCAUGGCCACCAUCAUGGGCUUCUCGGUG
------...(((((((((((((..((((((((.....))))((((.....)))).))))...))))))(((.((.((((...)))).)).))).))).)))) ( -42.80, z-score =  -3.29, R)
>droEre2.scaffold_4820 1203635 96 + 10470090
------AAUCACCAGAUUUCCCGACAGCGACCGCGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGGGCUUCUCGGUG
------...((((......(((..((((((((.....))))((((.....)))).))))...)))((((((.((.((((...)))).)).))))))..)))) ( -42.80, z-score =  -2.53, R)
>droAna3.scaffold_13340 11179480 102 + 23697760
UUUGCCGUUUACCAGAUUUCCCGGCACCGACCACGGUGGUCGGGCAGGUAGCCCGGCUGGCAGGGGAAGUCUAUCAUGGCCACCUCCAUGAUUUUCUCGGUA
..(((((......(((((((((.((((((....))))((((((((.....)))))))).))..)))))))))(((((((......))))))).....))))) ( -47.30, z-score =  -3.37, R)
>droWil1.scaffold_181089 11140380 94 + 12369635
--------CUACCAGAUUUCACGGCAACGGCCACGACUGUCGGGAAGAUAACCAGGCUGGCAAGGGAAAUCAAUCAUGGCUACCUGCAUAAUAUUUUUCUCA
--------......(((.((..(((....)))..))..)))(((((((....((((.((((....((......))...))))))))........))))))). ( -21.10, z-score =  -0.27, R)
>droVir3.scaffold_12822 3991432 100 + 4096053
--AUCAGAUCACCAUAUCUCACGGCAGCGUCCACGGCUGUCAGGCAGGUAGCCUGGCUGACAGGGAAAAUCAAUCAUAGCAACCUCCAUAAUUUUUUCGGUU
--........(((.........((((((.......)))))).((.((((..((((.....))))((.......))......))))))...........))). ( -23.70, z-score =  -0.51, R)
>droMoj3.scaffold_6540 1343659 100 + 34148556
--UGGGGUUUACCAUAUCUCGCGGCACCGUCCGCGACUGUCGGGCAGGUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCUCCAUGAUCUUCUCGGUG
--.(((((.......)))))....((((((((.(..(((((((((.....))))))).))..).)))((..((((((((......))))))))..))))))) ( -40.90, z-score =  -0.85, R)
>droGri2.scaffold_15074 3608096 97 - 7742996
-----GAAUCACCAUAUCUCACGGCAGCGUCCACGACUGUCGGGCAAAUAGCCGGGCUGACAGGGAAAAUCAAUCAUGGCCACCUCCAUAAUUUUCUCGGUU
-----.....(((....(((.((((((((....)).))))))(((.....))))))......((((((((.....((((......)))).))))))))))). ( -27.20, z-score =  -1.37, R)
>consensus
______AAUCACCAGAUUUCCCGACAGCGACCACGAUGGUCGGGCAGAUAGCCCGGCUGGCAGGGGAAGUCGAUCAUGGCCACCAUCAUGAUCUUCUCGGUG
.........((((.........................(((((((.....)))))))......((((((......((((......))))...)))))))))) (-17.76 = -17.97 +   0.21)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,803,419 – 18,803,515
Length 96
Sequences 10
Columns 104
Reading direction forward
Mean pairwise identity 79.19
Shannon entropy 0.41606
G+C content 0.56439
Mean single sequence MFE -34.72
Consensus MFE -19.33
Energy contribution -18.44
Covariance contribution -0.89
Combinations/Pair 1.42
Mean z-score -1.52
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.16
SVM RNA-class probability 0.571392
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18803419 96 + 27905053
GAGAAGACCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCCGGCUAUCUGCCCGACCAUCGUGGUCGCUGUCGGGAAAUCUGGUGAUUCGAU--------
.....(((((((((((((((...((......))....))).....(((.....)))..))))))))))))...(((((...(((....))))))))-------- ( -32.90, z-score =  -0.69, R)
>droSim1.chr3R 18616693 99 + 27517382
GAGAAGCCCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGUUGUCGGGAAAUCUGGUGAUUCGACGAU-----
.....(.(((((((((((((...((......))....)))...(((((.....))))))))))))))).)((((((((...(((....)))))))))))----- ( -38.90, z-score =  -1.70, R)
>droSec1.super_0 19167550 99 + 21120651
GAGAAGACCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGUUGUCGGGAAAUCUGGUGAUCCGACGAU-----
.....(((((((((((((((...((......))....)))...(((((.....)))))))))))))))))((((((((...(((....)))))))))))----- ( -46.20, z-score =  -3.81, R)
>droYak2.chr3R 19663081 96 + 28832112
GAGAAGCCCAUGAUGGUGGCCAUGAUCGACUUUCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGCUGUCGGGAAAUCUGGUGAUUCCGU--------
((..((((((((((((((((...((.......))...)))...(((((.....)))))))))))))))..))).)).((((.((....))))))..-------- ( -38.40, z-score =  -1.86, R)
>droEre2.scaffold_4820 1203639 96 - 10470090
GAGAAGCCCAUGAUGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGCGGUCGCUGUCGGGAAAUCUGGUGAUUCGAU--------
(((..(((((((........))))...((.(((((....((((.((((.....))))((((.....))))))))..))))).)).)))..)))...-------- ( -35.00, z-score =  -0.58, R)
>droAna3.scaffold_13340 11179484 104 - 23697760
GAGAAAAUCAUGGAGGUGGCCAUGAUAGACUUCCCCUGCCAGCCGGGCUACCUGCCCGACCACCGUGGUCGGUGCCGGGAAAUCUGGUAAACGGCAAAACCACU
..............(((.(((....((((.(((((..((..(((((((.....))))((((.....))))))))).))))).))))......)))...)))... ( -39.10, z-score =  -1.52, R)
>droWil1.scaffold_181089 11140384 95 - 12369635
AAAAAUAUUAUGCAGGUAGCCAUGAUUGAUUUCCCUUGCCAGCCUGGUUAUCUUCCCGACAGUCGUGGCCGUUGCCGUGAAAUCUGGUAGAAGAC---------
..............((((((((((((((.........(((.....)))...........))))))))))...))))......(((......))).--------- ( -21.65, z-score =  -0.18, R)
>droVir3.scaffold_12822 3991436 96 - 4096053
GAAAAAAUUAUGGAGGUUGCUAUGAUUGAUUUUCCCUGUCAGCCAGGCUACCUGCCUGACAGCCGUGGACGCUGCCGUGAGAUAUGGUGAUCUGAU--------
.............((((..(((((........((((((((((.((((...)))).)))))))....)))(((....)))...)))))..))))...-------- ( -28.70, z-score =  -1.80, R)
>droMoj3.scaffold_6540 1343663 96 - 34148556
GAGAAGAUCAUGGAGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUACCUGCCCGACAGUCGCGGACGGUGCCGCGAGAUAUGGUAAACCCCA--------
(((..((((((((......))))))))..)))....((((((.(((((.....))))).)..((((((......))))))....))))).......-------- ( -39.50, z-score =  -2.34, R)
>droGri2.scaffold_15074 3608100 93 + 7742996
GAGAAAAUUAUGGAGGUGGCCAUGAUUGAUUUUCCCUGUCAGCCCGGCUAUUUGCCCGACAGUCGUGGACGCUGCCGUGAGAUAUGGUGAUUC-----------
.......((((((.((((.(((((((((.........(....)..(((.....)))...))))))))).)))).)))))).............----------- ( -26.80, z-score =  -0.69, R)
>consensus
GAGAAGACCAUGAAGGUGGCCAUGAUCGACUUCCCCUGCCAGCCGGGCUAUCUGCCCGACCAUCGUGGUCGCUGCCGGGAAAUCUGGUGAUUCGAU________
.......((((((.(.((((...((......))....)))).)(((((.....)))))....))))))....((((((.....))))))............... (-19.33 = -18.44 +  -0.89)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:36:54 2011