Locus 4358

Sequence ID dm3.chr2R
Location 12,446,191 – 12,446,283
Length 92
Max. P 0.997617
window5976 window5977

overview

Window 6

Location 12,446,191 – 12,446,283
Length 92
Sequences 8
Columns 92
Reading direction forward
Mean pairwise identity 75.15
Shannon entropy 0.46992
G+C content 0.35679
Mean single sequence MFE -17.80
Consensus MFE -11.06
Energy contribution -10.28
Covariance contribution -0.78
Combinations/Pair 1.24
Mean z-score -1.31
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.73
SVM RNA-class probability 0.801812
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12446191 92 + 21146708
GAAAUGAGUUUAUAAAAGGGAAUGUAUUAUUUCGAUAACUCUCAAUUGUUUGCUUAAAAUGGCUGCUUUAAGCAAACAAUCGUAGUUUUUUU
(((((((...(((........)))..)))))))...((((..(.((((((((((((((........)))))))))))))).).))))..... ( -20.80, z-score =  -2.53, R)
>droSim1.chr2R 11180149 84 + 19596830
GAAAUGAGUUUUUAAAAGGGAAUGUGUU---UCGAUAACUCUCAGUUGUUUGCUCAAAAUGGCUGCUUUGAGCAAACAAUCGUAGUU-----
((((((.((((((....)))))).))))---))...((((..(.((((((((((((((........)))))))))))))).).))))----- ( -23.70, z-score =  -2.98, R)
>droSec1.super_1 9944282 84 + 14215200
GAAAUGAGUUUUUAAAAGGGAAUGUGUU---UCGAUAACUCUCAGUUGUUUGCUCAAAAUGGCUGCUUUGAGCAAACAAUCGUAGUU-----
((((((.((((((....)))))).))))---))...((((..(.((((((((((((((........)))))))))))))).).))))----- ( -23.70, z-score =  -2.98, R)
>droYak2.chr2R 4599781 83 - 21139217
GAAAUCAGUUUACAAACGGGAAUGCUG----UUG-UAACUCGCAAUUGAUUGCUUAAAAUGGCUGCUUUAAGCAAACAAUCGUAGUUU----
..........(((((.(((.....)))----)))-))(((.((.((((.(((((((((........))))))))).)))).)))))..---- ( -17.90, z-score =  -1.01, R)
>droEre2.scaffold_4845 9173760 83 - 22589142
GAAAUCAGUUUAUAAAAGGGAAUGCGG----UCGAUAACUGCCCAUUGAUUGCUUAAAAUGACUGCUUUAAGCAAGCAAUCGUAGUU-----
((.....((((........))))....----))...((((((..((((.(((((((((........))))))))).)))).))))))----- ( -16.10, z-score =  -0.32, R)
>droAna3.scaffold_13266 15814729 77 + 19884421
GAAAUAAUUAUUUAACAGGGAAU--------UC---AACUGCCCAUUGCUUACCUAAAAUGGCUGUUUUAGGCAAACAAUCGUAGUUU----
.......................--------..---((((((..((((.((.((((((((....)))))))).)).)))).)))))).---- ( -14.00, z-score =  -0.79, R)
>dp4.chr3 16080928 79 - 19779522
GAACUGAACACUGACUUGGGGAUG--------GUAUAACUUCCAAUUGAUGGUUUAAAAUGGCUGCUUUAAACGACCAAUCGUAGUU-----
.........((((..(((((((.(--------......).)))........(((((((........)))))))..))))...)))).----- ( -13.10, z-score =   0.06, R)
>droPer1.super_2 5151416 79 - 9036312
GAACUGAACACUGACUUGGGGAUG--------GUAUAACUUCCAAUUGAUGGUUUAAAAUGGCUGCUUUAAACGACCAAUCGUAGUU-----
.........((((..(((((((.(--------......).)))........(((((((........)))))))..))))...)))).----- ( -13.10, z-score =   0.06, R)
>consensus
GAAAUGAGUUUUUAAAAGGGAAUG_______UCGAUAACUCCCAAUUGAUUGCUUAAAAUGGCUGCUUUAAGCAAACAAUCGUAGUU_____
....................................((((....((((.(((((((((........))))))))).))))...))))..... (-11.06 = -10.28 +  -0.78)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,446,191 – 12,446,283
Length 92
Sequences 8
Columns 92
Reading direction reverse
Mean pairwise identity 75.15
Shannon entropy 0.46992
G+C content 0.35679
Mean single sequence MFE -18.61
Consensus MFE -18.82
Energy contribution -18.34
Covariance contribution -0.48
Combinations/Pair 1.33
Mean z-score -3.13
Structure conservation index 1.01
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.14
SVM RNA-class probability 0.997617
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12446191 92 - 21146708
AAAAAAACUACGAUUGUUUGCUUAAAGCAGCCAUUUUAAGCAAACAAUUGAGAGUUAUCGAAAUAAUACAUUCCCUUUUAUAAACUCAUUUC
..........(((((((((((((((((......))))))))))))))))).(((((...((((............))))...)))))..... ( -22.10, z-score =  -5.14, R)
>droSim1.chr2R 11180149 84 - 19596830
-----AACUACGAUUGUUUGCUCAAAGCAGCCAUUUUGAGCAAACAACUGAGAGUUAUCGA---AACACAUUCCCUUUUAAAAACUCAUUUC
-----.....((.((((((((((((((......)))))))))))))).)).(((((.(..(---((.........)))..).)))))..... ( -21.40, z-score =  -4.49, R)
>droSec1.super_1 9944282 84 - 14215200
-----AACUACGAUUGUUUGCUCAAAGCAGCCAUUUUGAGCAAACAACUGAGAGUUAUCGA---AACACAUUCCCUUUUAAAAACUCAUUUC
-----.....((.((((((((((((((......)))))))))))))).)).(((((.(..(---((.........)))..).)))))..... ( -21.40, z-score =  -4.49, R)
>droYak2.chr2R 4599781 83 + 21139217
----AAACUACGAUUGUUUGCUUAAAGCAGCCAUUUUAAGCAAUCAAUUGCGAGUUA-CAA----CAGCAUUCCCGUUUGUAAACUGAUUUC
----......((((((.((((((((((......)))))))))).))))))((..(((-(((----..((......))))))))..))..... ( -18.00, z-score =  -2.16, R)
>droEre2.scaffold_4845 9173760 83 + 22589142
-----AACUACGAUUGCUUGCUUAAAGCAGUCAUUUUAAGCAAUCAAUGGGCAGUUAUCGA----CCGCAUUCCCUUUUAUAAACUGAUUUC
-----((((.(.((((.((((((((((......)))))))))).)))).)..)))).....----........................... ( -15.80, z-score =  -1.34, R)
>droAna3.scaffold_13266 15814729 77 - 19884421
----AAACUACGAUUGUUUGCCUAAAACAGCCAUUUUAGGUAAGCAAUGGGCAGUU---GA--------AUUCCCUGUUAAAUAAUUAUUUC
----.((((.(.(((((((((((((((......))))))))))))))).)..))))---..--------....................... ( -21.00, z-score =  -3.34, R)
>dp4.chr3 16080928 79 + 19779522
-----AACUACGAUUGGUCGUUUAAAGCAGCCAUUUUAAACCAUCAAUUGGAAGUUAUAC--------CAUCCCCAAGUCAGUGUUCAGUUC
-----((((.((((((((.((((((((......)))))))).))))))))..))))....--------........................ ( -14.60, z-score =  -2.05, R)
>droPer1.super_2 5151416 79 + 9036312
-----AACUACGAUUGGUCGUUUAAAGCAGCCAUUUUAAACCAUCAAUUGGAAGUUAUAC--------CAUCCCCAAGUCAGUGUUCAGUUC
-----((((.((((((((.((((((((......)))))))).))))))))..))))....--------........................ ( -14.60, z-score =  -2.05, R)
>consensus
_____AACUACGAUUGUUUGCUUAAAGCAGCCAUUUUAAGCAAUCAAUUGGGAGUUAUCGA_______CAUUCCCUUUUAAAAACUCAUUUC
.....((((.(((((((((((((((((......)))))))))))))))))..)))).................................... (-18.82 = -18.34 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:27:41 2011