Locus 2735

Sequence ID dm3.chr2L
Location 21,738,294 – 21,738,397
Length 103
Max. P 0.999837
window3761 window3762 window3763 window3764

overview

Window 1

Location 21,738,294 – 21,738,393
Length 99
Sequences 3
Columns 101
Reading direction forward
Mean pairwise identity 60.87
Shannon entropy 0.54627
G+C content 0.37540
Mean single sequence MFE -23.80
Consensus MFE -13.42
Energy contribution -14.10
Covariance contribution 0.68
Combinations/Pair 1.41
Mean z-score -3.40
Structure conservation index 0.56
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.29
SVM RNA-class probability 0.999739
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21738294 99 + 23011544
CGACUUAAGCCGU--AAAAACCUUGUCUUAUUAUUGAUAUAAUUGCCGAGCCACAAGGCCGGUGAUUAGAGAGGAAGUAAACUCUCCAGCAUAAACGUCAU
.((((((.((...--........((((........))))((((..(((.(((....))))))..))))(((((........)))))..)).)))..))).. ( -27.70, z-score =  -3.40, R)
>droSim1.chrU 4996046 83 - 15797150
-----UAAAU------AAAACCUUG-CUUAUCAUUGAUAUAAUUACUGAGCUACAAGGCGUGCAAUUGGGGAGUAAAGUAACUCCCCAACGCACA------
-----.....------....(((((-....(((.((((...)))).)))....))))).((((..(((((((((......))))))))).)))).------ ( -28.70, z-score =  -5.26, R)
>droPer1.super_1039 3480 98 - 6997
--AUUUAAACACUUUAAGCACUUUGAAUUAUUAAUUCUAUA-CCACUGUACCACAAGGCCAGUGAUAAGAGAGACAGUUAUCUCUCCAACAUAAUCUUCAU
--.....................((((..((((........-.(((((..((....)).)))))....((((((......)))))).....)))).)))). ( -15.00, z-score =  -1.56, R)
>consensus
__A_UUAAAC__U__AAAAACCUUG_CUUAUUAUUGAUAUAAUUACUGAGCCACAAGGCCAGUGAUUAGAGAGAAAGUUAACUCUCCAACAUAAAC_UCAU
.......................................(((((((((.(((....))))))))))))(((((........)))))............... (-13.42 = -14.10 +   0.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,738,294 – 21,738,393
Length 99
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 60.87
Shannon entropy 0.54627
G+C content 0.37540
Mean single sequence MFE -27.64
Consensus MFE -15.64
Energy contribution -16.43
Covariance contribution 0.79
Combinations/Pair 1.44
Mean z-score -3.31
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.22
SVM RNA-class probability 0.999705
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21738294 99 - 23011544
AUGACGUUUAUGCUGGAGAGUUUACUUCCUCUCUAAUCACCGGCCUUGUGGCUCGGCAAUUAUAUCAAUAAUAAGACAAGGUUUUU--ACGGCUUAAGUCG
..(((......(((((((((........)))))((((..((((((....))).)))..))))........................--.))))....))). ( -24.70, z-score =  -1.57, R)
>droSim1.chrU 4996046 83 + 15797150
------UGUGCGUUGGGGAGUUACUUUACUCCCCAAUUGCACGCCUUGUAGCUCAGUAAUUAUAUCAAUGAUAAG-CAAGGUUUU------AUUUA-----
------.((((((((((((((......))))))))).)))))(((((((...(((.............)))...)-))))))...------.....----- ( -32.12, z-score =  -5.49, R)
>droPer1.super_1039 3480 98 + 6997
AUGAAGAUUAUGUUGGAGAGAUAACUGUCUCUCUUAUCACUGGCCUUGUGGUACAGUGG-UAUAGAAUUAAUAAUUCAAAGUGCUUAAAGUGUUUAAAU--
.((((......(((((((((((....))))))))(((((((((((....))).))))))-))...)))......))))(((..(.....)..)))....-- ( -26.10, z-score =  -2.86, R)
>consensus
AUGA_GUUUAUGUUGGAGAGUUAACUUACUCUCUAAUCACAGGCCUUGUGGCUCAGUAAUUAUAUCAAUAAUAAG_CAAGGUUUUU__A__GUUUAA_U__
..............(((((((......)))))))(((((((((((....))).))))))))........................................ (-15.64 = -16.43 +   0.79)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,738,298 – 21,738,397
Length 99
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 58.45
Shannon entropy 0.59351
G+C content 0.37461
Mean single sequence MFE -23.23
Consensus MFE -13.42
Energy contribution -14.10
Covariance contribution 0.68
Combinations/Pair 1.41
Mean z-score -3.29
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.53
SVM RNA-class probability 0.999837
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21738298 99 + 23011544
UUAAGCCGUAAAAACCUUGUCUUAUUAUUGAUAUAAUUGCCGAGCCACAAGGCCGGUGAUUAGAGAGGAAGUAAACUCUCCAGCAUAAACGUCAUAAGA
...................(((((....((((.((((..(((.(((....))))))..))))(((((........)))))..........))))))))) ( -26.00, z-score =  -3.04, R)
>droSim1.chrU 4996049 80 - 15797150
--------AUAAAACCUUG-CUUAUCAUUGAUAUAAUUACUGAGCUACAAGGCGUGCAAUUGGGGAGUAAAGUAACUCCCCAACGCACA----------
--------......(((((-....(((.((((...)))).)))....))))).((((..(((((((((......))))))))).)))).---------- ( -28.70, z-score =  -5.23, R)
>droPer1.super_1039 3484 97 - 6997
AAACACUUUAAGCACUUUGAAUUAUUAAUUCUAUA-CCACUGUACCACAAGGCCAGUGAUAAGAGAGACAGUUAUCUCUCCAACAUAAUCUUCAUAAA-
.................((((..((((........-.(((((..((....)).)))))....((((((......)))))).....)))).))))....- ( -15.00, z-score =  -1.61, R)
>consensus
__A__C__UAAAAACCUUG_CUUAUUAUUGAUAUAAUUACUGAGCCACAAGGCCAGUGAUUAGAGAGAAAGUUAACUCUCCAACAUAAAC_UCAUAA__
.................................(((((((((.(((....))))))))))))(((((........)))))................... (-13.42 = -14.10 +   0.68)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,738,298 – 21,738,397
Length 99
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 58.45
Shannon entropy 0.59351
G+C content 0.37461
Mean single sequence MFE -26.61
Consensus MFE -15.64
Energy contribution -16.43
Covariance contribution 0.79
Combinations/Pair 1.44
Mean z-score -3.07
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.33
SVM RNA-class probability 0.999762
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 21738298 99 - 23011544
UCUUAUGACGUUUAUGCUGGAGAGUUUACUUCCUCUCUAAUCACCGGCCUUGUGGCUCGGCAAUUAUAUCAAUAAUAAGACAAGGUUUUUACGGCUUAA
((((((......((((.(((((((........)))))))....((((((....))).)))....))))......))))))..(((((.....))))).. ( -22.30, z-score =  -1.09, R)
>droSim1.chrU 4996049 80 + 15797150
----------UGUGCGUUGGGGAGUUACUUUACUCCCCAAUUGCACGCCUUGUAGCUCAGUAAUUAUAUCAAUGAUAAG-CAAGGUUUUAU--------
----------.((((((((((((((......))))))))).)))))(((((((...(((.............)))...)-)))))).....-------- ( -32.12, z-score =  -5.59, R)
>droPer1.super_1039 3484 97 + 6997
-UUUAUGAAGAUUAUGUUGGAGAGAUAACUGUCUCUCUUAUCACUGGCCUUGUGGUACAGUGG-UAUAGAAUUAAUAAUUCAAAGUGCUUAAAGUGUUU
-....((((......(((((((((((....))))))))(((((((((((....))).))))))-))...)))......))))(((..(.....)..))) ( -25.40, z-score =  -2.51, R)
>consensus
__UUAUGA_GUUUAUGUUGGAGAGUUAACUUACUCUCUAAUCACAGGCCUUGUGGCUCAGUAAUUAUAUCAAUAAUAAG_CAAGGUUUUUA__G__U__
..................(((((((......)))))))(((((((((((....))).)))))))).................................. (-15.64 = -16.43 +   0.79)

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 Tue Apr 19 21:56:57 2011