Locus 3656

Sequence ID dm3.chr2R
Location 6,933,109 – 6,933,221
Length 112
Max. P 0.964798
window5014 window5015

overview

Window 4

Location 6,933,109 – 6,933,221
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 78.43
Shannon entropy 0.37299
G+C content 0.36489
Mean single sequence MFE -27.24
Consensus MFE -15.98
Energy contribution -16.58
Covariance contribution 0.60
Combinations/Pair 1.13
Mean z-score -2.29
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.45
SVM RNA-class probability 0.939260
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6933109 112 + 21146708
GUUGCAAUAAAGCCAGCUAAGAGUAAUAUAUAUGUGGUACUUACUUCGCUACAUGAAGUGCCCAUUUUUUUUAACGUGCAAAGAUCUUGGCUGGUAUUAAAAAUUUAUACCG
.......(((.(((((((((((.(((.....(((.(((((((.(..........))))))))))).....)))...........))))))))))).)))............. ( -26.60, z-score =  -1.83, R)
>droEre2.scaffold_4845 3726970 109 - 22589142
GUUGCCAUAAAGCCAGCUAAGAGUCGAAUAUUUGUGGUAUUUACUUCGAAACUUAAAGUGCUCAUUUUUUU-AGAGUGCAAAGACGUUGGCUGGC-UU-AAAAUGUAUAGCG
((((.(((.(((((((((((..(((.....((((.(((....))).)))).......(..(((........-.)))..)...))).)))))))))-))-...)))..)))). ( -31.90, z-score =  -2.73, R)
>droYak2.chr2R 18928510 109 - 21139217
GUGGCAAUAAAGCCAGCAAAGAGCUGAAUAUGUCAAGUAUUUACUUUGAUACUUGAAGUGAUCAUUUUUU--AGAGUGCAACGAUGUUGGCUGGC-UUUAAAAUUUAUACCG
.......((((((((((((((((.(((.(((.(((((((((......))))))))).))).)))))))))--......((((...))))))))))-))))............ ( -32.90, z-score =  -3.63, R)
>droSec1.super_1 4500512 97 + 14215200
UUUGCAAUAAAGCCAGCUAAGAGUA--------------UUUACUUCGCUACAUGAAGUGCCCAUUUUUUU-AACGUGCACAGAUCUUGGCUGGUAUUAAAAAUUUAUACCG
.......(((.(((((((((((...--------------.....((((.....))))((((.(.((.....-)).).))))...))))))))))).)))............. ( -22.70, z-score =  -2.13, R)
>droSim1.chr2R 5473600 97 + 19596830
GUUGCAAUAAAGCCAGCUAAGUGUA--------------UUUACUUCGCUACAUGAAGUGCCCAUUUUUUU-AACGUGCACAGAUCUUGGCUGGUAUUAAAAAUUUGUACCG
(.((((((((.(((((((((((((.--------------...((((((.....))))))((.(.((.....-)).).)))))...)))))))))).))).....))))).). ( -22.10, z-score =  -1.15, R)
>consensus
GUUGCAAUAAAGCCAGCUAAGAGUA__AUAU_U___GUAUUUACUUCGCUACAUGAAGUGCCCAUUUUUUU_AACGUGCAAAGAUCUUGGCUGGUAUUAAAAAUUUAUACCG
...........(((((((((((...................(((((((.....)))))))..(((.((....)).)))......)))))))))))................. (-15.98 = -16.58 +   0.60)

alignment

Postscript

secondary structure

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dotplot

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Window 5

Location 6,933,111 – 6,933,221
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 78.41
Shannon entropy 0.37320
G+C content 0.36436
Mean single sequence MFE -27.00
Consensus MFE -15.98
Energy contribution -16.58
Covariance contribution 0.60
Combinations/Pair 1.13
Mean z-score -2.45
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.74
SVM RNA-class probability 0.964798
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6933111 110 + 21146708
UGCAAUAAAGCCAGCUAAGAGUAAUAUAUAUGUGGUACUUACUUCGCUACAUGAAGUGCCCAUUUUUUUUAACGUGCAAAGAUCUUGGCUGGUAUUAAAAAUUUAUACCG
.....(((.(((((((((((.(((.....(((.(((((((.(..........))))))))))).....)))...........))))))))))).)))............. ( -26.60, z-score =  -2.06, R)
>droEre2.scaffold_4845 3726972 107 - 22589142
UGCCAUAAAGCCAGCUAAGAGUCGAAUAUUUGUGGUAUUUACUUCGAAACUUAAAGUGCUCAUUUUUUU-AGAGUGCAAAGACGUUGGCUGGC-UU-AAAAUGUAUAGCG
.((.((((((((((((((..(((.....((((.(((....))).)))).......(..(((........-.)))..)...))).)))))))))-))-......))).)). ( -31.30, z-score =  -2.78, R)
>droYak2.chr2R 18928512 107 - 21139217
GGCAAUAAAGCCAGCAAAGAGCUGAAUAUGUCAAGUAUUUACUUUGAUACUUGAAGUGAUCAUUUUUU--AGAGUGCAACGAUGUUGGCUGGC-UUUAAAAUUUAUACCG
.....((((((((((((((((.(((.(((.(((((((((......))))))))).))).)))))))))--......((((...))))))))))-))))............ ( -32.90, z-score =  -4.00, R)
>droSec1.super_1 4500514 95 + 14215200
UGCAAUAAAGCCAGCUAAGAGUA--------------UUUACUUCGCUACAUGAAGUGCCCAUUUUUUU-AACGUGCACAGAUCUUGGCUGGUAUUAAAAAUUUAUACCG
.....(((.(((((((((((...--------------.....((((.....))))((((.(.((.....-)).).))))...))))))))))).)))............. ( -22.70, z-score =  -2.19, R)
>droSim1.chr2R 5473602 95 + 19596830
UGCAAUAAAGCCAGCUAAGUGUA--------------UUUACUUCGCUACAUGAAGUGCCCAUUUUUUU-AACGUGCACAGAUCUUGGCUGGUAUUAAAAAUUUGUACCG
((((((((.(((((((((((((.--------------...((((((.....))))))((.(.((.....-)).).)))))...)))))))))).))).....)))))... ( -21.50, z-score =  -1.20, R)
>consensus
UGCAAUAAAGCCAGCUAAGAGUA__AUAU_U___GUAUUUACUUCGCUACAUGAAGUGCCCAUUUUUUU_AACGUGCAAAGAUCUUGGCUGGUAUUAAAAAUUUAUACCG
.........(((((((((((...................(((((((.....)))))))..(((.((....)).)))......)))))))))))................. (-15.98 = -16.58 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:14:17 2011