Locus 2335

Sequence ID dm3.chr2L
Location 18,123,589 – 18,123,694
Length 105
Max. P 0.820719
window3218 window3219

overview

Window 8

Location 18,123,589 – 18,123,694
Length 105
Sequences 7
Columns 109
Reading direction forward
Mean pairwise identity 66.46
Shannon entropy 0.62453
G+C content 0.51640
Mean single sequence MFE -30.10
Consensus MFE -16.97
Energy contribution -16.53
Covariance contribution -0.44
Combinations/Pair 1.38
Mean z-score -0.80
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.80
SVM RNA-class probability 0.820719
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18123589 105 + 23011544
----AACCGAAUCUCUCGAAUGUCGCGCAAAAUGUUGCAAGUGCCGGUAGCAACACUUGUGUUGCUGUCGCUGCUGCCGAUUGCCCAUGUUGCUGCUGCCUCAGCCACU
----...(((.....)))...(((((((((....)))).(((..((..(((((((....)))))))..))..)))).)))).......((.((((......)))).)). ( -29.00, z-score =   0.05, R)
>droAna3.scaffold_12916 13386358 102 - 16180835
GAGAAACCCAAAACC-CGAAUGUCGCGCAAAAUGUUGCAAGUGCCGCUGGCAACAUUCGUGUUGCUGUCGCUGGUGCU------CCAGAUUGCUGCUGCAGCUGCCGCA
............(((-(((..((.((((..((((((((.((.....)).)))))))).)))).))..)))..)))((.------.(((.((((....)))))))..)). ( -29.90, z-score =   0.78, R)
>dp4.chr4_group3 1428694 101 - 11692001
------CCGAAACUU--GAAUGUCGCGCAAAAUGUUGCAAGUGCCGGUGGCAACAUUUCUGUUGCUGCUGCUGCUGCAGAGUGCCUCGGCCUCUCCAGCUCCAGUUCCA
------(((..((((--((((((........))))).)))))..))).(((((((....)))))))((((..((((.((((.((....)))))).))))..)))).... ( -36.80, z-score =  -1.99, R)
>droPer1.super_8 2492884 101 - 3966273
------CCGAAACUU--GAAUGUCGCGCAAAAUGUUGCAAGUGCCGGUGGCAACAUUUCUGUUGCUGCUGCUGCUGCAGAGUGCCUCGGCCUCUCCAGCUCCAGUUCCA
------(((..((((--((((((........))))).)))))..))).(((((((....)))))))((((..((((.((((.((....)))))).))))..)))).... ( -36.80, z-score =  -1.99, R)
>droVir3.scaffold_12963 17214561 83 + 20206255
-----ACA-AAACUU--GAAUGUCACGCAAAAUGUUGCAAGUGCCGGCAGCAACAUUUUUGUUGCUGCUGCAGCUGGCUGCGACUGCGACU------------------
-----...-......--........((((....(((((((((..(((((((((((....)))))))))))..)))...))))))))))...------------------ ( -31.70, z-score =  -2.18, R)
>droMoj3.scaffold_6500 22255374 83 + 32352404
-----ACA-AAACUU--GAAUGUCACGCAAAAUGUUGCAAGUGCCGGCAGCAACAUUUUUAUUGCUGCUGCUGCUAACUGCGACGGCAACU------------------
-----...-..((((--((((((........))))).)))))((((((((((.((.......)).))))))(((.....))).))))....------------------ ( -24.50, z-score =  -1.11, R)
>droGri2.scaffold_15252 14640137 84 + 17193109
-----ACACAAACUU--GAAUGUCACACAAAAUGUUGCAAGUGCCGGGAGCAACAUUAUUGUUGUUGCUACUGUUGGCAGCAGCUGCAGCU------------------
-----..........--................((((((.(((((((.(((((((.......)))))))....)))))).)...)))))).------------------ ( -22.00, z-score =   0.88, R)
>consensus
_____ACCGAAACUU__GAAUGUCGCGCAAAAUGUUGCAAGUGCCGGUAGCAACAUUUUUGUUGCUGCUGCUGCUGCCGACUGCCGCGGCU_CU_C_GC__C_G___C_
....................(((.(((.....))).)))((((.(((((((((((....))))))))))).)))).................................. (-16.97 = -16.53 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,123,589 – 18,123,694
Length 105
Sequences 7
Columns 109
Reading direction reverse
Mean pairwise identity 66.46
Shannon entropy 0.62453
G+C content 0.51640
Mean single sequence MFE -33.17
Consensus MFE -11.86
Energy contribution -11.50
Covariance contribution -0.36
Combinations/Pair 1.36
Mean z-score -1.56
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.35
SVM RNA-class probability 0.655013
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18123589 105 - 23011544
AGUGGCUGAGGCAGCAGCAACAUGGGCAAUCGGCAGCAGCGACAGCAACACAAGUGUUGCUACCGGCACUUGCAACAUUUUGCGCGACAUUCGAGAGAUUCGGUU----
.((.((((..((....((.......)).....))..)))).))(((((((....)))))))(((((..(((((((....)))).((.....)).)))..))))).---- ( -32.10, z-score =  -0.18, R)
>droAna3.scaffold_12916 13386358 102 + 16180835
UGCGGCAGCUGCAGCAGCAAUCUGG------AGCACCAGCGACAGCAACACGAAUGUUGCCAGCGGCACUUGCAACAUUUUGCGCGACAUUCG-GGUUUUGGGUUUCUC
(((.((....)).)))(.((((..(------(((.((.((....)).....((((((((((((..((....))......))).))))))))))-)))))..)))).).. ( -33.80, z-score =  -0.29, R)
>dp4.chr4_group3 1428694 101 + 11692001
UGGAACUGGAGCUGGAGAGGCCGAGGCACUCUGCAGCAGCAGCAGCAACAGAAAUGUUGCCACCGGCACUUGCAACAUUUUGCGCGACAUUC--AAGUUUCGG------
.((((((.((((((.((((((....)).)))).)))).((.((.((((((....)))))).....))....((((....)))))).....))--.))))))..------ ( -40.20, z-score =  -2.73, R)
>droPer1.super_8 2492884 101 + 3966273
UGGAACUGGAGCUGGAGAGGCCGAGGCACUCUGCAGCAGCAGCAGCAACAGAAAUGUUGCCACCGGCACUUGCAACAUUUUGCGCGACAUUC--AAGUUUCGG------
.((((((.((((((.((((((....)).)))).)))).((.((.((((((....)))))).....))....((((....)))))).....))--.))))))..------ ( -40.20, z-score =  -2.73, R)
>droVir3.scaffold_12963 17214561 83 - 20206255
------------------AGUCGCAGUCGCAGCCAGCUGCAGCAGCAACAAAAAUGUUGCUGCCGGCACUUGCAACAUUUUGCGUGACAUUC--AAGUUU-UGU-----
------------------.(((((.(((((((....)))).(((((((((....))))))))).)))....((((....)))))))))....--......-...----- ( -34.20, z-score =  -3.13, R)
>droMoj3.scaffold_6500 22255374 83 - 32352404
------------------AGUUGCCGUCGCAGUUAGCAGCAGCAGCAAUAAAAAUGUUGCUGCCGGCACUUGCAACAUUUUGCGUGACAUUC--AAGUUU-UGU-----
------------------.......(((((.((..(((((((((..........)))))))))..))....((((....)))))))))....--......-...----- ( -28.80, z-score =  -2.01, R)
>droGri2.scaffold_15252 14640137 84 - 17193109
------------------AGCUGCAGCUGCUGCCAACAGUAGCAACAACAAUAAUGUUGCUCCCGGCACUUGCAACAUUUUGUGUGACAUUC--AAGUUUGUGU-----
------------------....((((((((((....))))))).(((.(((.((((((((...........)))))))))))))).......--.....)))..----- ( -22.90, z-score =   0.10, R)
>consensus
_G___C_G__GC_G_AG_AGCCGCGGCAGCCGGCAGCAGCAGCAGCAACAAAAAUGUUGCUACCGGCACUUGCAACAUUUUGCGCGACAUUC__AAGUUUCGGU_____
...................................((.((....((((((....)))))).....))....((((....))))))........................ (-11.86 = -11.50 +  -0.36)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:49:20 2011