Locus 3144

Sequence ID dm3.chr2R
Location 2,835,782 – 2,835,865
Length 83
Max. P 0.994931
window4322 window4323

overview

Window 2

Location 2,835,782 – 2,835,865
Length 83
Sequences 12
Columns 85
Reading direction forward
Mean pairwise identity 82.10
Shannon entropy 0.40177
G+C content 0.56203
Mean single sequence MFE -28.82
Consensus MFE -26.37
Energy contribution -25.82
Covariance contribution -0.55
Combinations/Pair 1.32
Mean z-score -2.28
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.75
SVM RNA-class probability 0.994931
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2835782 83 + 21146708
--AUUGGUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGU
--.......((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).... ( -31.50, z-score =  -1.71, R)
>droSim1.chr2R 1652386 84 + 19596830
-AUUUGGUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGU
-........((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).... ( -31.50, z-score =  -1.71, R)
>droSec1.super_1 517707 84 + 14215200
-AUUUGGUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGU
-........((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).... ( -31.50, z-score =  -1.71, R)
>droYak2.chr2L 15567975 83 + 22324452
-AUUG-AUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAUGU
-....-...((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).... ( -31.50, z-score =  -2.91, R)
>droEre2.scaffold_4929 6926336 83 - 26641161
--AUGCAUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGU
--.......((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).... ( -31.50, z-score =  -2.10, R)
>droAna3.scaffold_13340 18293481 83 - 23697760
-GUCG-AUCGCCCGAGCAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUACCCGGGCAUUU
-....-...(((((..(((((.......))))).....((((((.....)))))).((((........))))....))))).... ( -29.10, z-score =  -2.83, R)
>dp4.chr3 1802541 82 - 19779522
--AUUUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCUGU-
--.......((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))...- ( -31.00, z-score =  -2.95, R)
>droPer1.super_73 78250 83 + 267513
--AAUUUGCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCUUGU
--.......((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).... ( -31.00, z-score =  -2.81, R)
>droWil1.scaffold_180700 5897142 80 + 6630534
--AUCUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCA---
--.......((((..((((((.......))))))....((((((.....)))))).((((........)))).....)))).--- ( -31.50, z-score =  -3.25, R)
>droVir3.scaffold_12875 15830063 81 - 20611582
GUAAUUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGC----
.........((((..((((((.......))))))....((((((.....)))))).((((........)))).....))))---- ( -29.80, z-score =  -2.86, R)
>droMoj3.scaffold_6496 25958194 68 - 26866924
--AUCCUCCAUCCAAAAUGUGACUCGCACCUACGACCUUGAGAUCAAAACUCUUAGGCCCUA---ACUGAGCU------------
--...(((..........(((.....))).......(((((((.......))))))).....---...)))..------------ (  -6.80, z-score =   0.26, R)
>droGri2.scaffold_14906 2742463 84 - 14172833
-AUUGUAUCGCCCGAGCAGGGACUUGAACCCUGGACCCUUGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCUACCCGGGCAUGU
-........(((((..(((((.......))))).....((((((.....)))))).((((........))))....))))).... ( -29.10, z-score =  -2.83, R)
>consensus
__AUUUUUCGCCCAACGUGGGGCUCGAACCCACGACCCUGAGAUUAAGAGUCUCAUGCUCUACCGACUGAGCUAGCCGGGCAGGU
.........((((...(((((.......))))).....((((((.....)))))).((((........)))).....)))).... (-26.37 = -25.82 +  -0.55)

alignment

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secondary structure

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dotplot

Postscript

Window 3

Location 2,835,782 – 2,835,865
Length 83
Sequences 12
Columns 85
Reading direction reverse
Mean pairwise identity 82.10
Shannon entropy 0.40177
G+C content 0.56203
Mean single sequence MFE -31.77
Consensus MFE -29.51
Energy contribution -29.01
Covariance contribution -0.50
Combinations/Pair 1.36
Mean z-score -2.14
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.61
SVM RNA-class probability 0.993424
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2835782 83 - 21146708
ACCUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGACCAAU--
...((((((((..((((........))))....((((((.......))))))(((((.......)))))))))))))......-- ( -32.80, z-score =  -1.64, R)
>droSim1.chr2R 1652386 84 - 19596830
ACCUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGACCAAAU-
...((((((((..((((........))))....((((((.......))))))(((((.......))))))))))))).......- ( -32.80, z-score =  -1.72, R)
>droSec1.super_1 517707 84 - 14215200
ACCUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGACCAAAU-
...((((((((..((((........))))....((((((.......))))))(((((.......))))))))))))).......- ( -32.80, z-score =  -1.72, R)
>droYak2.chr2L 15567975 83 - 22324452
ACAUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAU-CAAU-
...((((((((..((((........))))....((((((.......))))))(((((.......)))))))))))))..-....- ( -33.00, z-score =  -2.24, R)
>droEre2.scaffold_4929 6926336 83 + 26641161
ACCUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAUGCAU--
...((((((((..((((........))))....((((((.......))))))(((((.......)))))))))))))......-- ( -32.80, z-score =  -1.41, R)
>droAna3.scaffold_13340 18293481 83 + 23697760
AAAUGCCCGGGUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAU-CGAC-
...((((((((((((((........))))..(((((((((.....)))))))))(((.......)))))))))))))..-....- ( -35.50, z-score =  -3.49, R)
>dp4.chr3 1802541 82 + 19779522
-ACAGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAAAAU--
-...(((((((..((((........))))....((((((.......))))))(((((.......)))))))))))).......-- ( -32.90, z-score =  -2.58, R)
>droPer1.super_73 78250 83 - 267513
ACAAGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGCAAAUU--
....(((((((..((((........))))....((((((.......))))))(((((.......)))))))))))).......-- ( -32.90, z-score =  -2.48, R)
>droWil1.scaffold_180700 5897142 80 - 6630534
---UGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAAGAU--
---.(((((((..((((........))))....((((((.......))))))(((((.......)))))))))))).......-- ( -32.70, z-score =  -2.19, R)
>droVir3.scaffold_12875 15830063 81 + 20611582
----GCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAAAUUAC
----(((((((..((((........))))....((((((.......))))))(((((.......))))))))))))......... ( -32.70, z-score =  -2.64, R)
>droMoj3.scaffold_6496 25958194 68 + 26866924
------------AGCUCAGU---UAGGGCCUAAGAGUUUUGAUCUCAAGGUCGUAGGUGCGAGUCACAUUUUGGAUGGAGGAU--
------------..(((..(---((.(((((..(((.......))).))))).)))((.((((......)))).)).)))...-- ( -14.80, z-score =   0.20, R)
>droGri2.scaffold_14906 2742463 84 + 14172833
ACAUGCCCGGGUAGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCAAGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAUACAAU-
...((((((((((((((........))))..(((((((((.....)))))))))(((.......))))))))))))).......- ( -35.50, z-score =  -3.79, R)
>consensus
ACCUGCCCGGCUAGCUCAGUCGGUAGAGCAUGAGACUCUUAAUCUCAGGGUCGUGGGUUCGAGCCCCACGUUGGGCGAAAAAU__
....(((((((..((((........))))....((((((.......))))))(((((.......))))))))))))......... (-29.51 = -29.01 +  -0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:04:34 2011