Locus 7874

Sequence ID dm3.chr3L
Location 18,056,637 – 18,056,760
Length 123
Max. P 0.986091
window10835 window10836

overview

Window 5

Location 18,056,637 – 18,056,760
Length 123
Sequences 4
Columns 143
Reading direction forward
Mean pairwise identity 61.19
Shannon entropy 0.57566
G+C content 0.59458
Mean single sequence MFE -42.77
Consensus MFE -16.66
Energy contribution -16.22
Covariance contribution -0.44
Combinations/Pair 1.32
Mean z-score -1.58
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.30
SVM RNA-class probability 0.633854
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18056637 123 + 24543557
---------CUGUUUUCUUGGGGUCUCUGCAUUUCAGCGGAGUUGCCAG-GGGGCGUUGGGUGGUGGGGCUGCGUUCUGUUUGCAGGGGGUGUG----------GCUCGCCUCUAAUGAGGGUUGCAACUCCAGACGGAGUUU
---------....(..(((((.(.((((((......)))))).).))))-)..)(((((((.((((((.((((.(((((....))))).))).)----------.)))))))))))))........((((((....)))))). ( -51.00, z-score =  -2.12, R)
>droPer1.super_20 807794 110 + 1872136
----------GGAGUUGCUGG----UGGGCGAAUCUGUGGAGUUGCAG--CGCAGACAGGGCGGUAGGGGGGGGG--AGGCGGCCGACG---------------GACCGAUUCUAAUGAGGGUUGCAACUCCAGACGGAGUUU
----------....(((((..----..))))).(((((((((((((((--(.(....((((((((..(..((...--......))..).---------------.)))).)))).....).)))))))))))..))))).... ( -37.70, z-score =  -0.85, R)
>dp4.chrXR_group6 10898453 109 + 13314419
----------GGAGUUGCUGG----UGGGCGAAUCAGUGGAGUUGCAG--CGCAGACAAGGCGGUAGAGGGGGG---AGGCGGCGGACG---------------GAACGAUUCUAAUGAGGGUUGCAACUCCAGACGGAGUUU
----------...((((((((----(......))))))((((((((((--(.(.......((.((.........---..)).))....(---------------((.....))).....).))))))))))).)))....... ( -32.30, z-score =  -1.11, R)
>droAna3.scaffold_13337 18124994 137 - 23293914
UCGGGUUGUUGGGGUCGUUUC----UCUGCAUUUUUGUGGAGUUGCAGGCCGUCAGUGGGAGGUGGGCGGUGGGC--GGUUGGUUGGUGAUUUGUGGGGGUGUGGUCCGCCUCUAAUGAGGGUUGCAACUCCAGACGAAGUUU
(((...(((.((((.....))----)).)))....(.(((((((((((.((.(((...((((((((((..(.(((--.....))).)..(((......)))...))))))))))..))).))))))))))))).))))..... ( -50.10, z-score =  -2.26, R)
>consensus
__________GGAGUUGCUGG____UCGGCAAAUCAGUGGAGUUGCAG__CGCAGACAGGGCGGUAGGGGGGGG___AGGCGGCAGACG_______________GACCGACUCUAAUGAGGGUUGCAACUCCAGACGGAGUUU
.............(((............((......))((((((((((..(((..........................)))...........................((((....)))).)))))))))).)))....... (-16.66 = -16.22 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,056,637 – 18,056,760
Length 123
Sequences 4
Columns 143
Reading direction reverse
Mean pairwise identity 61.19
Shannon entropy 0.57566
G+C content 0.59458
Mean single sequence MFE -25.14
Consensus MFE -13.24
Energy contribution -14.80
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.22
SVM RNA-class probability 0.986091
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 18056637 123 - 24543557
AAACUCCGUCUGGAGUUGCAACCCUCAUUAGAGGCGAGC----------CACACCCCCUGCAAACAGAACGCAGCCCCACCACCCAACGCCCC-CUGGCAACUCCGCUGAAAUGCAGAGACCCCAAGAAAACAG---------
.......((((((((((((..(((((....)))).)...----------........((((.........))))...................-...))))))))((......))..)))).............--------- ( -29.20, z-score =  -2.38, R)
>droPer1.super_20 807794 110 - 1872136
AAACUCCGUCUGGAGUUGCAACCCUCAUUAGAAUCGGUC---------------CGUCGGCCGCCU--CCCCCCCCCUACCGCCCUGUCUGCG--CUGCAACUCCACAGAUUCGCCCA----CCAGCAACUCC----------
.......(((((((((((((..........((..(((((---------------....)))))..)--)...........(((.......)))--.)))))))))..))))..((...----...))......---------- ( -25.80, z-score =  -1.86, R)
>dp4.chrXR_group6 10898453 109 - 13314419
AAACUCCGUCUGGAGUUGCAACCCUCAUUAGAAUCGUUC---------------CGUCCGCCGCCU---CCCCCCUCUACCGCCUUGUCUGCG--CUGCAACUCCACUGAUUCGCCCA----CCAGCAACUCC----------
.......(((((((((((((........((((.......---------------.((.....))..---......)))).(((.......)))--.))))))))))..)))..((...----...))......---------- ( -18.49, z-score =  -1.07, R)
>droAna3.scaffold_13337 18124994 137 + 23293914
AAACUUCGUCUGGAGUUGCAACCCUCAUUAGAGGCGGACCACACCCCCACAAAUCACCAACCAACC--GCCCACCGCCCACCUCCCACUGACGGCCUGCAACUCCACAAAAAUGCAGA----GAAACGACCCCAACAACCCGA
.......(((((((((((((..(((((...((((.((.............................--.........)).))))....))).))..))))))))))((....))....----.....)))............. ( -27.06, z-score =  -2.30, R)
>consensus
AAACUCCGUCUGGAGUUGCAACCCUCAUUAGAAGCGGUC_______________CGCCAGCCAACU___CCCACCCCCACCGCCCUACCUGCG__CUGCAACUCCACAGAAACGCACA____CCAACAACUCC__________
..........(((((((((...((((....))))..............................................(((.......)))....)))))))))..................................... (-13.24 = -14.80 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:35:06 2011