Locus 3011

Sequence ID dm3.chr2R
Location 1,318,229 – 1,318,328
Length 99
Max. P 0.999764
window4130 window4131 window4132 window4133

overview

Window 0

Location 1,318,229 – 1,318,323
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 59.03
Shannon entropy 0.65374
G+C content 0.43636
Mean single sequence MFE -23.57
Consensus MFE -9.18
Energy contribution -10.05
Covariance contribution 0.87
Combinations/Pair 1.58
Mean z-score -2.02
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.85
SVM RNA-class probability 0.971472
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1318229 94 + 21146708
GCGCUUUGGAGAUUCAUCUAAUAGCUUAAGGUCAUUAAACUGUGAAUUAAUCGCGGAAAGAAGAUCAUCGGCUCGACGAAAACUAUCUCUAGCU
..(((..((((((...((....((((...((((.((...((((((.....))))))...)).))))...))))....)).....))))))))). ( -20.90, z-score =  -0.52, R)
>dp4.Unknown_group_58 28543 85 - 69560
GCACCUCGGAGACUCAUUCAGCAGUUUUAAACCGCUAAACUGAGCUUCUAUGGCUAGGAGCCGAAGGUAUUGUUUUUUAAAACCA---------
..(((((((((.((((((.(((.((.....)).))).)).))))))))...(((.....)))).)))).................--------- ( -19.70, z-score =  -0.60, R)
>droPer1.super_2 225673 85 + 9036312
GCGCCUCGGAGACUCAUUCACCAGUUUUAAACAGCUAAACUGAGCCUCCAUGGCUAGGAGCCGAUCGUAUUGGUUUUUAAAACCA---------
..(((..((((.((((......((((......))))....)))).))))..)))(((((((((((...)))))))))))......--------- ( -24.50, z-score =  -2.32, R)
>droWil1.scaffold_181154 2082159 85 + 4610121
ACGUUUCGGAGACUCAUUCAUAAGCGAUAAACUUCUGAACUGAGUCUCCACCGCAGUAAACUCCGCUUGGAGUUUGUUAAAACCU---------
..((((.(((((((((((((.(((.......))).)))).))))))))).......((((((((....))))))))...))))..--------- ( -29.20, z-score =  -4.66, R)
>consensus
GCGCCUCGGAGACUCAUUCAACAGCUUUAAACCGCUAAACUGAGCCUCCAUCGCUAGAAGCCGAUCGUAGUGUUUUUUAAAACCA_________
..(((..((((.((((((((((.((.....)).)))))).)))).))))..)))........................................ ( -9.18 = -10.05 +   0.87)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,318,229 – 1,318,323
Length 94
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 59.03
Shannon entropy 0.65374
G+C content 0.43636
Mean single sequence MFE -27.00
Consensus MFE -17.52
Energy contribution -18.90
Covariance contribution 1.38
Combinations/Pair 1.55
Mean z-score -2.64
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.34
SVM RNA-class probability 0.999764
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1318229 94 - 21146708
AGCUAGAGAUAGUUUUCGUCGAGCCGAUGAUCUUCUUUCCGCGAUUAAUUCACAGUUUAAUGACCUUAAGCUAUUAGAUGAAUCUCCAAAGCGC
.(((.(((((.....((((((...))))))((.(((....(.((.....)).)(((((((.....)))))))...))).)))))))...))).. ( -17.90, z-score =   0.10, R)
>dp4.Unknown_group_58 28543 85 + 69560
---------UGGUUUUAAAAAACAAUACCUUCGGCUCCUAGCCAUAGAAGCUCAGUUUAGCGGUUUAAAACUGCUGAAUGAGUCUCCGAGGUGC
---------..((((....))))..((((((.(((.....)))...((..((((.(((((((((.....)))))))))))))..)).)))))). ( -28.30, z-score =  -3.34, R)
>droPer1.super_2 225673 85 - 9036312
---------UGGUUUUAAAAACCAAUACGAUCGGCUCCUAGCCAUGGAGGCUCAGUUUAGCUGUUUAAAACUGGUGAAUGAGUCUCCGAGGCGC
---------(((((.....)))))................(((.((((((((((.((((.(.((.....)).).)))))))))))))).))).. ( -28.80, z-score =  -2.73, R)
>droWil1.scaffold_181154 2082159 85 - 4610121
---------AGGUUUUAACAAACUCCAAGCGGAGUUUACUGCGGUGGAGACUCAGUUCAGAAGUUUAUCGCUUAUGAAUGAGUCUCCGAAACGU
---------..........(((((((....)))))))...(((.((((((((((.((((.((((.....)))).))))))))))))))...))) ( -33.00, z-score =  -4.59, R)
>consensus
_________UGGUUUUAAAAAACAAUACGAUCGGCUCCCAGCCAUGGAGGCUCAGUUUAGCGGUUUAAAACUGAUGAAUGAGUCUCCGAAGCGC
........................................(((.((((((((((.(((((((((.....))))))))))))))))))).))).. (-17.52 = -18.90 +   1.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,318,234 – 1,318,328
Length 94
Sequences 4
Columns 94
Reading direction forward
Mean pairwise identity 57.47
Shannon entropy 0.66036
G+C content 0.42294
Mean single sequence MFE -21.90
Consensus MFE -7.71
Energy contribution -8.03
Covariance contribution 0.31
Combinations/Pair 1.62
Mean z-score -2.07
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.55
SVM RNA-class probability 0.949362
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1318234 94 + 21146708
UUGGAGAUUCAUCUAAUAGCUUAAGGUCAUUAAACUGUGAAUUAAUCGCGGAAAGAAGAUCAUCGGCUCGACGAAAACUAUCUCUAGCUACGCC
((((((((...((....((((...((((.((...((((((.....))))))...)).))))...))))....)).....))))))))....... ( -19.30, z-score =  -0.39, R)
>dp4.Unknown_group_58 28548 80 - 69560
UCGGAGACUCAUUCAGCAGUUUUAAACCGCUAAACUGAGCUUCUAUGGCUAGGAGCCGAAGGUAUUGUUUUUUAAAACCA--------------
..((((.((((((.(((.((.....)).))).)).))))))))..((((.....))))..(((.(((.....))).))).-------------- ( -19.00, z-score =  -0.87, R)
>droPer1.super_2 225678 80 + 9036312
UCGGAGACUCAUUCACCAGUUUUAAACAGCUAAACUGAGCCUCCAUGGCUAGGAGCCGAUCGUAUUGGUUUUUAAAACCA--------------
..((((.((((......((((......))))....)))).)))).(((.(((((((((((...)))))))))))...)))-------------- ( -20.50, z-score =  -1.79, R)
>droWil1.scaffold_181154 2082164 80 + 4610121
UCGGAGACUCAUUCAUAAGCGAUAAACUUCUGAACUGAGUCUCCACCGCAGUAAACUCCGCUUGGAGUUUGUUAAAACCU--------------
..(((((((((((((.(((.......))).)))).))))))))).......((((((((....)))))))).........-------------- ( -28.80, z-score =  -5.22, R)
>consensus
UCGGAGACUCAUUCAACAGCUUUAAACCGCUAAACUGAGCCUCCAUCGCUAGAAGCCGAUCGUAGUGUUUUUUAAAACCA______________
..((((.((((((((((.((.....)).)))))).)))).)))).................................................. ( -7.71 =  -8.03 +   0.31)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,318,234 – 1,318,328
Length 94
Sequences 4
Columns 94
Reading direction reverse
Mean pairwise identity 57.47
Shannon entropy 0.66036
G+C content 0.42294
Mean single sequence MFE -24.18
Consensus MFE -15.25
Energy contribution -16.12
Covariance contribution 0.88
Combinations/Pair 1.59
Mean z-score -2.29
Structure conservation index 0.63
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.94
SVM RNA-class probability 0.999488
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1318234 94 - 21146708
GGCGUAGCUAGAGAUAGUUUUCGUCGAGCCGAUGAUCUUCUUUCCGCGAUUAAUUCACAGUUUAAUGACCUUAAGCUAUUAGAUGAAUCUCCAA
((....((.(((((.((...((((((...)))))).)))))))..))((((...((..(((((((.....)))))))....))..)))).)).. ( -16.80, z-score =   0.65, R)
>dp4.Unknown_group_58 28548 80 + 69560
--------------UGGUUUUAAAAAACAAUACCUUCGGCUCCUAGCCAUAGAAGCUCAGUUUAGCGGUUUAAAACUGCUGAAUGAGUCUCCGA
--------------.(((.............)))...(((.....)))...((..((((.(((((((((.....)))))))))))))..))... ( -23.12, z-score =  -2.70, R)
>droPer1.super_2 225678 80 - 9036312
--------------UGGUUUUAAAAACCAAUACGAUCGGCUCCUAGCCAUGGAGGCUCAGUUUAGCUGUUUAAAACUGGUGAAUGAGUCUCCGA
--------------(((((.....)))))........(((.....))).((((((((((.((((.(.((.....)).).)))))))))))))). ( -26.70, z-score =  -3.13, R)
>droWil1.scaffold_181154 2082164 80 - 4610121
--------------AGGUUUUAACAAACUCCAAGCGGAGUUUACUGCGGUGGAGACUCAGUUCAGAAGUUUAUCGCUUAUGAAUGAGUCUCCGA
--------------..........(((((((....))))))).......((((((((((.((((.((((.....)))).)))))))))))))). ( -30.10, z-score =  -3.98, R)
>consensus
______________UGGUUUUAAAAAACAAUACGAUCGGCUCCCAGCCAUGGAGGCUCAGUUUAGCGGUUUAAAACUGAUGAAUGAGUCUCCGA
.....................................(((.....))).((((((((((.(((((((((.....))))))))))))))))))). (-15.25 = -16.12 +   0.88)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:01:59 2011