Locus 12417

Sequence ID dm3.chr4
Location 954,350 – 954,476
Length 126
Max. P 0.999787
window17063 window17064

overview

Window 3

Location 954,350 – 954,476
Length 126
Sequences 5
Columns 132
Reading direction forward
Mean pairwise identity 52.15
Shannon entropy 0.78965
G+C content 0.43871
Mean single sequence MFE -30.22
Consensus MFE -10.68
Energy contribution -11.20
Covariance contribution 0.52
Combinations/Pair 1.72
Mean z-score -1.71
Structure conservation index 0.35
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.75
SVM RNA-class probability 0.965410
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 954350 126 + 1351857
------AGGAAGCCUACCACCAGCGGCUUUUUUGCGCUUUGGAGAUUCAUCUAAUAGCUUAAGGCCAUUAGACUGUGAAUUAAGUGCGGAAAGAAGAUCAUCGGCUCGACGAAAACUAUCUCUAGCUAUGCC
------..((((((..........))))))(((((((((....((((((((((((.((.....)).))))))...)))))))))))))))........(((.((((.((.((......)))).))))))).. ( -30.60, z-score =   0.38, R)
>droWil1.scaffold_181154 1898783 112 - 4610121
------AGAAACACCCCAAGGACUGGUCCUUUUACGUUUCGGAGACUCAUUCAUAAGCGAUAAACUUCUGAACUGAGUCUCCACCGCAGUAAACUCCGCUUGGAGUUUAUUAAAACCU--------------
------.(((((.....(((((....)))))....)))))(((((((((((((.(((.......))).)))).))))))))).....((((((((((....)))))))))).......-------------- ( -40.60, z-score =  -5.99, R)
>droPer1.super_3 489144 97 + 7375914
---------------------AGUAACCUUUUUACGCCUCGGAGACUCAUUCAGCAGUUGCAGGCUGCCAAAUUGAGACUCCAUGGCUAGGAGCCGAUCGUAUUGCUUUUUAAAGCCA--------------
---------------------.((((.....)))).....((((.((((....(((((.....))))).....)))).)))).(((((((((((..........))))))...)))))-------------- ( -27.40, z-score =  -1.14, R)
>dp4.Unknown_group_58 28531 97 - 69560
---------------------AGUGACCUUUUUGCACCUCGGAGACUCAUUCAGCAGUUUUAAACCGCUAAACUGAGCUUCUAUGGCUAGGAGCCGAAGGUAUUGUUUUUUAAAACCA--------------
---------------------....((((((.........((((.((((((.(((.((.....)).))).)).))))))))...(((.....))))))))).................-------------- ( -21.30, z-score =  -0.03, R)
>droVir3.scaffold_12958 1584457 118 - 3547706
AUGCAACGUCAAAUCACAAGAAGUGGACUUUUUAGGCCCAGGAGACUCAUUCAACAGUUUAAGGCUAUUAAAUUGGAUGUCCAGGGCUGUGAGCUGAUCGUUUAAUUUACGAAAAACC--------------
....(((((((..((((((((((....)))))).(((((.(((....((((((...((((((.....))))))))))))))).)))))))))..))).))))................-------------- ( -31.20, z-score =  -1.77, R)
>consensus
_______G__A_____C_A__AGUGGCCUUUUUACGCCUCGGAGACUCAUUCAACAGUUUAAGGCUACUAAACUGAGACUCCAGGGCUGGGAGCCGAUCGUAUAGUUUAUUAAAACCA______________
...................................(((..((((.((((((.((((((.....)))))).)).)))).))))..))).((((((..........))))))...................... (-10.68 = -11.20 +   0.52)

alignment

Postscript

secondary structure

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dotplot

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Window 4

Location 954,350 – 954,476
Length 126
Sequences 5
Columns 132
Reading direction reverse
Mean pairwise identity 52.15
Shannon entropy 0.78965
G+C content 0.43871
Mean single sequence MFE -33.70
Consensus MFE -16.92
Energy contribution -17.32
Covariance contribution 0.40
Combinations/Pair 1.71
Mean z-score -2.46
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.39
SVM RNA-class probability 0.999787
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr4 954350 126 - 1351857
GGCAUAGCUAGAGAUAGUUUUCGUCGAGCCGAUGAUCUUCUUUCCGCACUUAAUUCACAGUCUAAUGGCCUUAAGCUAUUAGAUGAAUCUCCAAAGCGCAAAAAAGCCGCUGGUGGUAGGCUUCCU------
((...(((((((((.((...((((((...)))))).)))))))((((.....(((((...(((((((((.....))))))))))))))......(((((......).)))).))))..)))).)).------ ( -34.00, z-score =  -0.64, R)
>droWil1.scaffold_181154 1898783 112 + 4610121
--------------AGGUUUUAAUAAACUCCAAGCGGAGUUUACUGCGGUGGAGACUCAGUUCAGAAGUUUAUCGCUUAUGAAUGAGUCUCCGAAACGUAAAAGGACCAGUCCUUGGGGUGUUUCU------
--------------.........((((((((....)))))))).......(((((((((.((((.((((.....)))).)))))))))))))(((((((..(((((....)))))...))))))).------ ( -42.10, z-score =  -4.25, R)
>droPer1.super_3 489144 97 - 7375914
--------------UGGCUUUAAAAAGCAAUACGAUCGGCUCCUAGCCAUGGAGUCUCAAUUUGGCAGCCUGCAACUGCUGAAUGAGUCUCCGAGGCGUAAAAAGGUUACU---------------------
--------------..((((....))))..((((.(((((.....)))..((((.((((.((..((((.......))))..)))))).))))))..))))...........--------------------- ( -34.00, z-score =  -2.80, R)
>dp4.Unknown_group_58 28531 97 + 69560
--------------UGGUUUUAAAAAACAAUACCUUCGGCUCCUAGCCAUAGAAGCUCAGUUUAGCGGUUUAAAACUGCUGAAUGAGUCUCCGAGGUGCAAAAAGGUCACU---------------------
--------------..((((....))))..((((((.(((.....)))...((..((((.(((((((((.....)))))))))))))..)).)))))).............--------------------- ( -28.30, z-score =  -2.35, R)
>droVir3.scaffold_12958 1584457 118 + 3547706
--------------GGUUUUUCGUAAAUUAAACGAUCAGCUCACAGCCCUGGACAUCCAAUUUAAUAGCCUUAAACUGUUGAAUGAGUCUCCUGGGCCUAAAAAGUCCACUUCUUGUGAUUUGACGUUGCAU
--------------................((((.((((.(((((((((.(((.(..((.((((((((.......))))))))))..).))).)))).....(((....)))..))))).)))))))).... ( -30.10, z-score =  -2.25, R)
>consensus
______________UGGUUUUAAUAAACAAUACGAUCAGCUCACAGCCAUGGAGACUCAGUUUAGCAGCCUAAAACUGCUGAAUGAGUCUCCGAGGCGUAAAAAGGCCACU__U_G_____U__C_______
.............................................(((.((((.(((((.(((((((((.....)))))))))))))).)))).)))................................... (-16.92 = -17.32 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:01:44 2011