Locus 10076

Sequence ID dm3.chr3R
Location 11,119,925 – 11,120,081
Length 156
Max. P 0.975036
window13851 window13852 window13853 window13854

overview

Window 1

Location 11,119,925 – 11,120,021
Length 96
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 62.82
Shannon entropy 0.65214
G+C content 0.48094
Mean single sequence MFE -27.16
Consensus MFE -13.66
Energy contribution -12.58
Covariance contribution -1.08
Combinations/Pair 1.69
Mean z-score -1.12
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.18
SVM RNA-class probability 0.905004
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11119925 96 + 27905053
---CUAUAUCCAUCUCUAUCUCCAUGCCCGG---CACCAUAUCAGUCAUUGAGCAUGGAU-UUGGACAUGGACAUGGCAUGGAACUUAGAACUGGCACCGGAC
---(((..(((((..((((.((((((.((((---..((((.((((...))))..))))..-)))).)))))).)))).)))))...)))..(((....))).. ( -29.00, z-score =  -1.53, R)
>droSim1.chr3R 17171043 96 - 27517382
---CUAUAUCCAUCUCUAUCUCCAUGCCCGG---CACCAUAUCAGUCAUUGGACAUGGAU-UUGGACAUGGACACGGCAUGGAACUUAGAACUGGCACCGGAC
---......(((..((((..((((((((.((---(.........)))..((..((((...-.....))))..)).))))))))...))))..)))........ ( -28.70, z-score =  -1.80, R)
>droSec1.super_0 10288624 96 - 21120651
---CUAUAUCCAUCUCUAUCUCCAUGCCCGG---CACCAUAUCAGUCAUUGGACAUGGAU-UUGGACAUGGACAUGGCAUGGAACUUAGAACUGGCACCGGAC
---(((..(((((..((((.((((((.((((---..((((.((........)).))))..-)))).)))))).)))).)))))...)))..(((....))).. ( -28.70, z-score =  -1.46, R)
>droAna3.scaffold_13250 3401204 90 - 3535662
AUACUGUAUCUGUAUCUGUAUCUAUGCCCCGGCACACCAUAUCAGUCAUUGGACAUGGUU-UUGGACAUGGCACUGCCACCGGACCUGGAC------------
((((.......)))).....((((.(..((((....(((.(((((((....))).)))).-.)))...((((...))))))))..))))).------------ ( -20.20, z-score =   1.35, R)
>droGri2.scaffold_14906 882221 94 + 14172833
---UAGUAUUUGCAUUAGUGUAAAUGCAAUG-----CAAAAUUGGCAAUAUAGUUUAGCCAUCCAGCGUUGAGUGGACCUGGUCUACUGGACUGGAGUGGAC-
---..(((((((((....)))))))))..((-----(.......)))...........(((((((..(((.(((((((...))))))).))))))).)))..- ( -29.20, z-score =  -2.18, R)
>consensus
___CUAUAUCCAUCUCUAUCUCCAUGCCCGG___CACCAUAUCAGUCAUUGGACAUGGAU_UUGGACAUGGACAUGGCAUGGAACUUAGAACUGGCACCGGAC
...(((..(((((.((....((((((.((((.....((((.((........)).))))...)))).))))))...)).)))))...))).............. (-13.66 = -12.58 +  -1.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,119,925 – 11,120,021
Length 96
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 62.82
Shannon entropy 0.65214
G+C content 0.48094
Mean single sequence MFE -28.68
Consensus MFE -14.76
Energy contribution -14.76
Covariance contribution -0.00
Combinations/Pair 1.44
Mean z-score -1.46
Structure conservation index 0.51
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.92
SVM RNA-class probability 0.975036
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11119925 96 - 27905053
GUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUCCAA-AUCCAUGCUCAAUGACUGAUAUGGUG---CCGGGCAUGGAGAUAGAGAUGGAUAUAG---
.....((((((.(((((..(((((((((..(((((((((...-...(((.....)))...))))))).)---)..))))))))).))))).))).)))..--- ( -32.30, z-score =  -1.77, R)
>droSim1.chr3R 17171043 96 + 27517382
GUCCGGUGCCAGUUCUAAGUUCCAUGCCGUGUCCAUGUCCAA-AUCCAUGUCCAAUGACUGAUAUGGUG---CCGGGCAUGGAGAUAGAGAUGGAUAUAG---
.....((((((.(((((..(((((((((..(((((((((...-...(((.....)))...))))))).)---)..))))))))).))))).))).)))..--- ( -31.90, z-score =  -1.91, R)
>droSec1.super_0 10288624 96 + 21120651
GUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUCCAA-AUCCAUGUCCAAUGACUGAUAUGGUG---CCGGGCAUGGAGAUAGAGAUGGAUAUAG---
.....((((((.(((((..(((((((((..(((((((((...-...(((.....)))...))))))).)---)..))))))))).))))).))).)))..--- ( -32.30, z-score =  -1.98, R)
>droAna3.scaffold_13250 3401204 90 + 3535662
------------GUCCAGGUCCGGUGGCAGUGCCAUGUCCAA-AACCAUGUCCAAUGACUGAUAUGGUGUGCCGGGGCAUAGAUACAGAUACAGAUACAGUAU
------------((((.((..(.(((((...)))))......-.((((((((........)))))))))..)).))))..........((((.......)))) ( -25.30, z-score =   0.24, R)
>droGri2.scaffold_14906 882221 94 - 14172833
-GUCCACUCCAGUCCAGUAGACCAGGUCCACUCAACGCUGGAUGGCUAAACUAUAUUGCCAAUUUUG-----CAUUGCAUUUACACUAAUGCAAAUACUA---
-......((((((..(((.(((...))).)))....))))))((((...........))))......-----..(((((((......)))))))......--- ( -21.60, z-score =  -1.85, R)
>consensus
GUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUCCAA_AUCCAUGUCCAAUGACUGAUAUGGUG___CCGGGCAUGGAGAUAGAGAUGGAUAUAG___
...............................(((((((((.....(((((((........))))))).......))))))))).................... (-14.76 = -14.76 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,119,955 – 11,120,060
Length 105
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 70.01
Shannon entropy 0.54560
G+C content 0.47135
Mean single sequence MFE -29.10
Consensus MFE -11.78
Energy contribution -13.02
Covariance contribution 1.24
Combinations/Pair 1.33
Mean z-score -1.66
Structure conservation index 0.40
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.29
SVM RNA-class probability 0.629519
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11119955 105 - 27905053
UUUGAAUCG-UAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUCCAA-AUCCAUGCUCAAUGACUGAUAUGG
(((((..((-....))..)))))((((..((((((.((((....((.((.........)).)).)))).))))))))))...-..(((((.(((.....)))))))) ( -30.20, z-score =  -1.66, R)
>droSim1.chr3R 17171073 105 + 27517382
UUUGAAUCG-AAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCGUGUCCAUGUCCAA-AUCCAUGUCCAAUGACUGAUAUGG
(((((..((-....))..)))))((((..((((((.((((....((.((.........)).)).)))).))))))))))...-..(((((((........))))))) ( -31.40, z-score =  -1.96, R)
>droSec1.super_0 10288654 105 + 21120651
AUUGAAUCG-AAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUCCAA-AUCCAUGUCCAAUGACUGAUAUGG
.((((..((-....))..)))).((((..((((((.((((....((.((.........)).)).)))).))))))))))...-..(((((((........))))))) ( -30.80, z-score =  -1.80, R)
>droAna3.scaffold_13250 3401240 94 + 3535662
UUUAAAUCGAAAAAAGGCAGAAAAGCAAUUGGACAAGGCAGUCC------------AGGUCCGGUGGCAGUGCCAUGUCCAA-AACCAUGUCCAAUGACUGAUAUGG
................((......))..(((((((.((((.(((------------(.......))).).)))).)))))))-..(((((((........))))))) ( -28.20, z-score =  -2.29, R)
>droGri2.scaffold_14906 882251 98 - 14172833
CUUUGACCA-AAUGCGGC-----AUCGAUUGGACAAGGCAGUCCACU-CCAGUCCAGUAGACCAGGUCCACUCAACGCUGGAUGGCUAAACUAUAUUGCCAAUUU--
..(((.(((-(...((..-----..)).)))).)))(((((((((.(-(((((..(((.(((...))).)))....))))))))).........)))))).....-- ( -24.90, z-score =  -0.59, R)
>consensus
UUUGAAUCG_AAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUCCAA_AUCCAUGUCCAAUGACUGAUAUGG
.......................((((..((((((.((((........................)))).))))))))))......(((((((........))))))) (-11.78 = -13.02 +   1.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,119,982 – 11,120,081
Length 99
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 76.55
Shannon entropy 0.38008
G+C content 0.45382
Mean single sequence MFE -24.38
Consensus MFE -13.85
Energy contribution -15.72
Covariance contribution 1.87
Combinations/Pair 1.10
Mean z-score -1.65
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.556477
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 11119982 99 - 27905053
AAAAUUAGAGGCGAAUCAAACUUUGAAUCG-UAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUC
.........((((.......((((((..((-....))..)))))).....((((((.((((....((.((.........)).)).)))).)))))))))) ( -27.80, z-score =  -2.03, R)
>droSim1.chr3R 17171100 99 + 27517382
AAAAUUAGAGGCGAAUCAAACUUUGAAUCG-AAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCGUGUCCAUGUC
.........((((.......((((((..((-....))..)))))).....((((((.((((....((.((.........)).)).)))).)))))))))) ( -27.00, z-score =  -1.47, R)
>droSec1.super_0 10288681 99 + 21120651
AAAAUUAGAGGCGAAUCAAACAUUGAAUCG-AAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUC
.........(((((((..(((.((((..((-....))..)))).((((.((((((......)))))))))).)))....))))...)))........... ( -25.00, z-score =  -1.15, R)
>droAna3.scaffold_13250 3401267 77 + 3535662
-----------AAAGUAUAAGUUUAAAUCGAAAAAAGGCAGAAAAGCAAUUGGACAAGGCAGUCCAGGUCCGGUGGC-AGUGCCAUGUC-----------
-----------.........................((((.....((.(((((((..((....))..))))))).))-..)))).....----------- ( -17.70, z-score =  -1.96, R)
>consensus
AAAAUUAGAGGCGAAUCAAACUUUGAAUCG_AAAACGGCUCAAAGGCAAUUGGACAAGGCAGUCCGGUGCCAGUUCUAAGUUCCAUGCCAUGUCCAUGUC
.........((((........(((((.((.......)).)))))((((.((((((......))))))))))..............))))........... (-13.85 = -15.72 +   1.87)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:17:00 2011