Locus 10550

Sequence ID dm3.chr3R
Location 14,656,242 – 14,656,357
Length 115
Max. P 0.967166
window14505 window14506 window14507

overview

Window 5

Location 14,656,242 – 14,656,332
Length 90
Sequences 7
Columns 108
Reading direction forward
Mean pairwise identity 67.12
Shannon entropy 0.57615
G+C content 0.50655
Mean single sequence MFE -24.10
Consensus MFE -13.82
Energy contribution -14.31
Covariance contribution 0.50
Combinations/Pair 1.52
Mean z-score -1.42
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956622
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14656242 90 + 27905053
--------UUGGACAAGACCAACUGAGCGAACUUUUCACCUGGUCAGGAUCC-GAAAGCUUGACACUUAUCCGCAUCGGGAAAGAUGUCAGAAAGUAAU---------
--------((((((..(((((..((((.......))))..)))))..).)))-))....(((((((((.((((...)))).))).))))))........--------- ( -24.90, z-score =  -1.79, R)
>droWil1.scaffold_181108 2891454 85 + 4707319
UUAGGCAGGCAAGCGAGGCCCCUUAAGUGAACUUUUUACCCGGUCAAGUCCACCAACACUUGACACUCAUCCGUGUCGCUUCGCU-----------------------
.......(((((((((.((.....(((....)))........(((((((........)))))))........)).)))))).)))----------------------- ( -22.90, z-score =  -1.33, R)
>droSim1.chr3R 20696991 90 - 27517382
--------UUGGACAAGACCAACCGAGCGAACUUUUCACCUGGUCAAGCCCC-AGAAGCUUGACACUUAUCCGCAUCGGGAAAGAUGCCAGAAGGUGAU---------
--------((((......)))).............((((((.(((((((...-....)))))))........(((((......)))))....)))))).--------- ( -27.10, z-score =  -2.28, R)
>droSec1.super_5 623137 90 - 5866729
--------UUGGACAAGACCAACCGAGCGAACUUUUCACCUGGUCAAGCCCC-AGAAGCUUGACACUUAUCCGCAUCGGGAAAGAUGCCAGAAGGUGAU---------
--------((((......)))).............((((((.(((((((...-....)))))))........(((((......)))))....)))))).--------- ( -27.10, z-score =  -2.28, R)
>droYak2.chr3R 3312903 99 + 28832112
--------UUGGACAGGACAAACCGAGCGAACUUUUCACCUGGUCAAGCCCC-AGAAGCCUGACACUUAUCUGCAUCGAAAAAGAUGCCAGAAAGCGAUGAUCAUGAU
--------((((..........)))).........(((..((((((.((..(-((....))).......((((((((......)))).))))..))..))))))))). ( -20.10, z-score =  -0.28, R)
>droEre2.scaffold_4770 10768095 90 - 17746568
--------UUGGACAGGAGCAACCGAGCGAACUUUUCACCUGUUCAGGCUCC-AGAAGCCUGACACUUAUCCGCAUCGGGAAAGAUGCCAGAAAGCGAU---------
--------..(((((((.((......))((.....)).)))).(((((((..-...)))))))......)))(((((......)))))...........--------- ( -26.30, z-score =  -1.38, R)
>droAna3.scaffold_12911 3009301 72 + 5364042
--------CCAGACGAGGCCAUUGGAGUGAACUUUUCACCUGGUCGAGUUCCGAAAAGCUUGACACUCAUCCUCGGCGAC----------------------------
--------.....(((((.....((.((((.....)))))).((((((((......))))))))......))))).....---------------------------- ( -20.30, z-score =  -0.59, R)
>consensus
________UUGGACAAGACCAACCGAGCGAACUUUUCACCUGGUCAAGCCCC_AGAAGCUUGACACUUAUCCGCAUCGGGAAAGAUGCCAGAAAGUGAU_________
..........(((.(((.......(((.......))).....(((((((........))))))).))).)))(((((......))))).................... (-13.82 = -14.31 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 14,656,242 – 14,656,332
Length 90
Sequences 7
Columns 108
Reading direction reverse
Mean pairwise identity 67.12
Shannon entropy 0.57615
G+C content 0.50655
Mean single sequence MFE -27.47
Consensus MFE -18.32
Energy contribution -18.39
Covariance contribution 0.07
Combinations/Pair 1.38
Mean z-score -1.20
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.78
SVM RNA-class probability 0.967166
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14656242 90 - 27905053
---------AUUACUUUCUGACAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUUC-GGAUCCUGACCAGGUGAAAAGUUCGCUCAGUUGGUCUUGUCCAA--------
---------..(((((((((.((((......)))))))).)))))..........-((((...((((((.(((.........))).))))))..))))..-------- ( -27.10, z-score =  -2.21, R)
>droWil1.scaffold_181108 2891454 85 - 4707319
-----------------------AGCGAAGCGACACGGAUGAGUGUCAAGUGUUGGUGGACUUGACCGGGUAAAAAGUUCACUUAAGGGGCCUCGCUUGCCUGCCUAA
-----------------------(((((.(((((((......))))).......(((((((((...........)))))))))......)).)))))........... ( -26.00, z-score =  -0.24, R)
>droSim1.chr3R 20696991 90 + 27517382
---------AUCACCUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUCU-GGGGCUUGACCAGGUGAAAAGUUCGCUCGGUUGGUCUUGUCCAA--------
---------...........(((((......)))))(((((((..(((((((...-..)))))))((..((((.....))))..)).....)))))))..-------- ( -30.60, z-score =  -1.84, R)
>droSec1.super_5 623137 90 + 5866729
---------AUCACCUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUCU-GGGGCUUGACCAGGUGAAAAGUUCGCUCGGUUGGUCUUGUCCAA--------
---------...........(((((......)))))(((((((..(((((((...-..)))))))((..((((.....))))..)).....)))))))..-------- ( -30.60, z-score =  -1.84, R)
>droYak2.chr3R 3312903 99 - 28832112
AUCAUGAUCAUCGCUUUCUGGCAUCUUUUUCGAUGCAGAUAAGUGUCAGGCUUCU-GGGGCUUGACCAGGUGAAAAGUUCGCUCGGUUUGUCCUGUCCAA--------
....(((....(((((((((.((((......)))))))).))))))))(((....-(((((..((((..((((.....))))..)))).))))))))...-------- ( -30.00, z-score =  -1.33, R)
>droEre2.scaffold_4770 10768095 90 + 17746568
---------AUCGCUUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAGGCUUCU-GGAGCCUGAACAGGUGAAAAGUUCGCUCGGUUGCUCCUGUCCAA--------
---------..(((((((((.((((......)))))))).)))))((((((((..-.))))))))(((((.((.....))((......)).)))))....-------- ( -28.80, z-score =  -1.12, R)
>droAna3.scaffold_12911 3009301 72 - 5364042
----------------------------GUCGCCGAGGAUGAGUGUCAAGCUUUUCGGAACUCGACCAGGUGAAAAGUUCACUCCAAUGGCCUCGUCUGG--------
----------------------------...(.(((((..(((((...(((((((((...((.....)).))))))))))))))......))))).)...-------- ( -19.20, z-score =   0.16, R)
>consensus
_________AUCACUUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUCU_GGGGCUUGACCAGGUGAAAAGUUCGCUCGGUUGGUCUUGUCCAA________
....................................(((((((.(((((((((....)))))))))..(((((.....)))))........))))))).......... (-18.32 = -18.39 +   0.07)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 14,656,259 – 14,656,357
Length 98
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 87.93
Shannon entropy 0.19175
G+C content 0.49767
Mean single sequence MFE -25.73
Consensus MFE -22.42
Energy contribution -22.05
Covariance contribution -0.37
Combinations/Pair 1.22
Mean z-score -1.32
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.25
SVM RNA-class probability 0.612229
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 14656259 98 - 27905053
CCCUUUCCCCAUCAACGUCAUCAUCAUUACUUUCUGACAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUUCGGAUCCUGACCAGGUGAAAAGUUCGCU
.........((((...((((..(((.........(((((.(((..(((...)))..))))))))........)))..))))..))))........... ( -17.83, z-score =   0.18, R)
>droSim1.chr3R 20697008 98 + 27517382
CCCUUUCACCAUCUUCGUCAUCAUCAUCACCUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUCUGGGGCUUGACCAGGUGAAAAGUUCGCU
...(((((((......................((((.((((......))))))))...(.((((((((.....))))))))).)))))))........ ( -28.50, z-score =  -1.93, R)
>droSec1.super_5 623154 98 + 5866729
CCCUUUCACCAUCUUCGUCAUCAUCAUCACCUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUCUGGGGCUUGACCAGGUGAAAAGUUCGCU
...(((((((......................((((.((((......))))))))...(.((((((((.....))))))))).)))))))........ ( -28.50, z-score =  -1.93, R)
>droEre2.scaffold_4770 10768112 94 + 17746568
----CACCCCAUCAUCCCCAUCAUCAUCGCUUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAGGCUUCUGGAGCCUGAACAGGUGAAAAGUUCGCU
----................(((((..(((((((((.((((......)))))))).)))))((((((((...))))))))...))))).......... ( -28.10, z-score =  -1.59, R)
>consensus
CCCUUUCACCAUCAUCGUCAUCAUCAUCACCUUCUGGCAUCUUUCCCGAUGCGGAUAAGUGUCAAGCUUCUGGAGCCUGACCAGGUGAAAAGUUCGCU
..........................((((((((((.((((......))))))))...(.((((((((.....))))))))))))))).......... (-22.42 = -22.05 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:26:04 2011