Locus 13988

Sequence ID dm3.chrX
Location 10,431,446 – 10,431,578
Length 132
Max. P 0.988430
window19238 window19239 window19240

overview

Window 8

Location 10,431,446 – 10,431,565
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 75.56
Shannon entropy 0.39661
G+C content 0.38914
Mean single sequence MFE -31.20
Consensus MFE -19.62
Energy contribution -22.50
Covariance contribution 2.88
Combinations/Pair 1.10
Mean z-score -2.54
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.32
SVM RNA-class probability 0.988430
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10431446 119 - 22422827
AUACGUAUGUACAUAAGAUAUAUACGUGGGCUGAAAGACCGAUCGAUCGAUCGAUCUAUAGUUUUUGAGCAUGA-UUUCUCGUCUUUGGGAGAACUAAUUUGAAAGAUGUGCGUGCUUAG
.(((((((((((....).))))))))))(((((..(((.(((((....))))).))).)))))..((((((((.-.....(((((((.(((.......))).)))))))..)))))))). ( -36.30, z-score =  -3.02, R)
>droEre2.scaffold_4690 14048245 95 + 18748788
---------------------AUACGUGGGCUGAAAGACCGAUCGACCGAUCGAUC----GUUUUUGAGCAUGAUUUUCUCGUCUUUUAGAGAACUAAUUUGAAAGACGUGCGUGCUUAA
---------------------.(((((..(((.((((((.((((((....))))))----)))))).)))..........(((((((((((.......))))))))))).)))))..... ( -32.50, z-score =  -3.48, R)
>droSec1.super_15 1131256 110 - 1954846
AUACAUACAUAAGAUACAUACAUACGUGGGCUGAAAGAACGAUCGAUCGAUCGAUCUAUCGUUUUUGAGCAUGA----------UUUUUGAUGAUGAAUUUGAAAGAUGUGCGUGCUUAG
.........((((.(((.(((((......(((..(((((((((.((((....)))).))))))))).)))....----------((((..(........)..))))))))).))))))). ( -27.40, z-score =  -1.58, R)
>droSim1.chrX_random 2949833 109 - 5698898
AUACAUACAUAAGAUACAUACAUACGUGGGCUGAAAGAACGAUCGAUCGAUCGAUCUAUCGUUUUUGAGCAUGA-----------UUUGGAGAACUAAUCUGAAAGAUGUGCGUGCUUAG
.........((((.(((.(((((......(((..(((((((((.((((....)))).))))))))).)))....-----------((..((.......))..))..))))).))))))). ( -28.60, z-score =  -2.08, R)
>consensus
AUACAUACAUAAGAUACAUACAUACGUGGGCUGAAAGAACGAUCGAUCGAUCGAUCUAUCGUUUUUGAGCAUGA__________UUUUGGAGAACUAAUUUGAAAGAUGUGCGUGCUUAG
......................(((((..(((.((((((.((((((....))))))....)))))).)))..........(((((((((((.......))))))))))).)))))..... (-19.62 = -22.50 +   2.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,431,459 – 10,431,578
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 73.16
Shannon entropy 0.42986
G+C content 0.37195
Mean single sequence MFE -24.92
Consensus MFE -10.60
Energy contribution -11.85
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.63
SVM RNA-class probability 0.768312
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10431459 119 + 22422827
UCUUUCAAAUUAGUUCUCCCAAAGACGAGAAA-UCAUGCUCAAAAACUAUAGAUCGAUCGAUCGAUCGGUCUUUCAGCCCACGUAUAUAUCUUAUGUACAUACGUAUCUUCGGAACUGAA
.........((((((((....((((.(((...-.....))).....((..(((((((((....)))))))))...))...((((((.(((.....))).)))))).)))).)))))))). ( -28.00, z-score =  -2.54, R)
>droEre2.scaffold_4690 14048258 95 - 18748788
UCUUUCAAAUUAGUUCUCUAAAAGACGAGAAAAUCAUGCUCAAAAAC----GAUCGAUCGGUCGAUCGGUCUUUCAGCCCACGUAUCU-UUGAAACUAAA--------------------
..(((((((...((...((.(((((((((.........))).....(----((((((....))))))))))))).))...)).....)-)))))).....-------------------- ( -22.10, z-score =  -2.34, R)
>droSec1.super_15 1131269 110 + 1954846
UCUUUCAAAUUCAUCAUCAAAAA----------UCAUGCUCAAAAACGAUAGAUCGAUCGAUCGAUCGUUCUUUCAGCCCACGUAUGUAUGUAUCUUAUGUAUGUAUCUUCGGAACUGAA
................(((....----------....(((.(((((((((.((((....)))).)))))).))).)))..(((((((((.......))))))))).((....))..))). ( -22.20, z-score =  -1.51, R)
>droSim1.chrX_random 2949846 109 + 5698898
UCUUUCAGAUUAGUUCUCCAAA-----------UCAUGCUCAAAAACGAUAGAUCGAUCGAUCGAUCGUUCUUUCAGCCCACGUAUGUAUGUAUCUUAUGUAUGUAUCUUCGGAACUGAA
.........((((((((.....-----------....(((.(((((((((.((((....)))).)))))).))).)))..(((((((((.......)))))))))......)))))))). ( -27.40, z-score =  -2.58, R)
>consensus
UCUUUCAAAUUAGUUCUCCAAAA__________UCAUGCUCAAAAACGAUAGAUCGAUCGAUCGAUCGGUCUUUCAGCCCACGUAUGUAUGUAACUUAUAUAUGUAUCUUCGGAACUGAA
..................................(((((...........(((((((((....)))))))))..........)))))................................. (-10.60 = -11.85 +   1.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,431,459 – 10,431,578
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 73.16
Shannon entropy 0.42986
G+C content 0.37195
Mean single sequence MFE -28.78
Consensus MFE -14.06
Energy contribution -15.50
Covariance contribution 1.44
Combinations/Pair 1.09
Mean z-score -1.88
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.45
SVM RNA-class probability 0.701828
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 10431459 119 - 22422827
UUCAGUUCCGAAGAUACGUAUGUACAUAAGAUAUAUACGUGGGCUGAAAGACCGAUCGAUCGAUCGAUCUAUAGUUUUUGAGCAUGA-UUUCUCGUCUUUGGGAGAACUAAUUUGAAAGA
(((((((((((((((((((((((((....).)))))))))..(((.((((((.((((((....))))))....)))))).)))....-......))))))))))........)))))... ( -35.30, z-score =  -2.57, R)
>droEre2.scaffold_4690 14048258 95 + 18748788
--------------------UUUAGUUUCAA-AGAUACGUGGGCUGAAAGACCGAUCGACCGAUCGAUC----GUUUUUGAGCAUGAUUUUCUCGUCUUUUAGAGAACUAAUUUGAAAGA
--------------------.....((((((-(......((((((.((((((.((((((....))))))----)))))).)))......(((((........)))))))).))))))).. ( -26.90, z-score =  -2.07, R)
>droSec1.super_15 1131269 110 - 1954846
UUCAGUUCCGAAGAUACAUACAUAAGAUACAUACAUACGUGGGCUGAAAGAACGAUCGAUCGAUCGAUCUAUCGUUUUUGAGCAUGA----------UUUUUGAUGAUGAAUUUGAAAGA
((((....(((((((.(((..........(((......))).(((..(((((((((.((((....)))).))))))))).)))))))----------))))))....))))......... ( -26.00, z-score =  -1.25, R)
>droSim1.chrX_random 2949846 109 - 5698898
UUCAGUUCCGAAGAUACAUACAUAAGAUACAUACAUACGUGGGCUGAAAGAACGAUCGAUCGAUCGAUCUAUCGUUUUUGAGCAUGA-----------UUUGGAGAACUAAUCUGAAAGA
((((((((((((....(((..........(((......))).(((..(((((((((.((((....)))).))))))))).)))))).-----------))))))).......)))))... ( -26.91, z-score =  -1.62, R)
>consensus
UUCAGUUCCGAAGAUACAUACAUAAGAUACAUACAUACGUGGGCUGAAAGAACGAUCGAUCGAUCGAUCUAUCGUUUUUGAGCAUGA__________UUUUGGAGAACUAAUUUGAAAGA
..........................................(((.((((((.((((((....))))))....)))))).))).............((((((((.......)))))))). (-14.06 = -15.50 +   1.44)

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 01:31:32 2011