Locus 3018

Sequence ID dm3.chr2R
Location 1,483,315 – 1,483,607
Length 292
Max. P 0.995450
window4140 window4141 window4142

overview

Window 0

Location 1,483,315 – 1,483,382
Length 67
Sequences 3
Columns 67
Reading direction reverse
Mean pairwise identity 62.63
Shannon entropy 0.48966
G+C content 0.40609
Mean single sequence MFE -16.40
Consensus MFE -11.48
Energy contribution -9.93
Covariance contribution -1.54
Combinations/Pair 1.45
Mean z-score -2.20
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.80
SVM RNA-class probability 0.995450
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1483315 67 - 21146708
GUCGAUUUGCUUAUCUUUUGAAAUCUUUAAAAGUUGAUUAACGGUGUCGGUAAGUUCGUUGAUUCGA
((((((..(((((((((((((.....))))))...(((.......))))))))))..)))))).... ( -12.70, z-score =  -0.82, R)
>dp4.Unknown_group_54 46636 56 - 61718
-----------UCUUCCUGCUAACCUUCAACAAUUGGUUGACGGUUGCAGUGAGGGCAUUAAUCUGU
-----------(((((((((.((((.(((((.....))))).)))))))).)))))........... ( -20.70, z-score =  -3.71, R)
>droPer1.super_49 18114 56 + 569410
-----------UCUUCCUGCUAAACUUCAACAAUUGGUUGACGGUUGCAGUGAGGGCAUUAAUCUGU
-----------(((((((((..(((((((((.....))))).)))))))).)))))........... ( -15.80, z-score =  -2.08, R)
>consensus
___________UCUUCCUGCUAAACUUCAACAAUUGGUUGACGGUUGCAGUGAGGGCAUUAAUCUGU
............((((((((.((((.(((((.....))))).)))))))).))))(((......))) (-11.48 =  -9.93 +  -1.54)

alignment

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secondary structure

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dotplot

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Window 1

Location 1,483,382 – 1,483,501
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 54.08
Shannon entropy 0.58159
G+C content 0.36695
Mean single sequence MFE -25.90
Consensus MFE -11.86
Energy contribution -11.43
Covariance contribution -0.42
Combinations/Pair 1.46
Mean z-score -2.05
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.99
SVM RNA-class probability 0.978001
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1483382 119 - 21146708
GUCCAGAAAGACUGGACUAACUACGUUAAUUUUUGCGAGUGUGAUUGUAAGCAAAAGGUUCUAUGUUCCAUG-ACAAUGAUUCUAUUGCGUGUUAAUAGCAUUUCGUAAAGGUGGCCUGU
((((((.....)))))).......((((.(((((((((((((.((((...((((.((..((..((((....)-)))..))..)).))))....)))).))).)))))))))))))).... ( -32.10, z-score =  -2.07, R)
>dp4.Unknown_group_54 46692 91 - 61718
AUCAAUGAUAGACGGUUUGAUGGUGUUUAUUUUCGCCAAAGUGGUGGCUGUCAUUAUGUUUGGUAAUUCAAGCGUCAGAAUUAUAUUUCUU-----------------------------
...((((((((.((.(....(((((........)))))....).)).))))))))((((((((....)))))))).((((......)))).----------------------------- ( -21.80, z-score =  -1.92, R)
>droPer1.super_49 18170 91 + 569410
AUCAAUGAUAGACGGUUUGAUGGUGUUUAUUUGCGCCAAAGUGGUGGCUGUCAUUAUGUUUGGUAAUUCAAGCGUCAGAAUUAUAUUUCUU-----------------------------
...((((((((.((.(....((((((......))))))....).)).))))))))((((((((....)))))))).((((......)))).----------------------------- ( -23.80, z-score =  -2.15, R)
>consensus
AUCAAUGAUAGACGGUUUGAUGGUGUUUAUUUUCGCCAAAGUGGUGGCUGUCAUUAUGUUUGGUAAUUCAAGCGUCAGAAUUAUAUUUCUU_____________________________
........((((((...(((((((..((((((......))))))..)))))))...))))))(((((((........))))))).................................... (-11.86 = -11.43 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,483,497 – 1,483,607
Length 110
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 52.60
Shannon entropy 0.66773
G+C content 0.39877
Mean single sequence MFE -21.61
Consensus MFE -9.69
Energy contribution -7.71
Covariance contribution -1.99
Combinations/Pair 1.53
Mean z-score -1.18
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.95
SVM RNA-class probability 0.859358
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 1483497 110 - 21146708
GUAAAACGUUAAGGGAUUGUAAAACCUUUACGGACGCAACGGACAAAAUUUCCCUUAUGGGGGUGUUGGUGUGCUCCUCGCCCCAAACAUUCUCCAAGUCUGUAUGGUCC
.......((.((((..........)))).))((((.((((((((.........(....)((((((..((......)).)))))).............)))))).)))))) ( -30.80, z-score =  -0.71, R)
>dp4.Unknown_group_54 46779 90 - 61718
--------------------AAGGCACUCACAUUGGUAGCGUUCAUUAAUUGGAAUACGCUGAUACCGGUAGAACUUUAAUUCAAAAUCUCUUCCAAAUCAUCGCUAUCA
--------------------.............((((((((........((((((...((((....)))).(((......)))........)))))).....)))))))) ( -17.12, z-score =  -1.70, R)
>droPer1.super_49 18257 107 + 569410
-UUAAUUCUUUAUUAAC--UAAGGCACUCACAUUGGUAGCGUUCAUUAAUUGGGAUACGCUGAUACCGGUAGAACUUUUAUUCAAAAUCUCUUCCAAAUCAUCGCUAUCA
-......(((((.....--))))).........((((((((..........(((((..((((....)))).(((......)))...)))))...........)))))))) ( -16.90, z-score =  -1.13, R)
>consensus
_U_AA___UU_A___A___UAAGGCACUCACAUUGGUAGCGUUCAUUAAUUGGAAUACGCUGAUACCGGUAGAACUUUAAUUCAAAAUCUCUUCCAAAUCAUCGCUAUCA
..................................(((((((.......(((((......)))))...((.(((..............)))...)).......))))))). ( -9.69 =  -7.71 +  -1.99)

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 22:02:06 2011