Locus 9011

Sequence ID dm3.chr3R
Location 3,402,296 – 3,402,431
Length 135
Max. P 0.869475
window12371 window12372 window12373

overview

Window 1

Location 3,402,296 – 3,402,396
Length 100
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 62.45
Shannon entropy 0.63757
G+C content 0.46831
Mean single sequence MFE -27.68
Consensus MFE -12.86
Energy contribution -13.50
Covariance contribution 0.64
Combinations/Pair 1.41
Mean z-score -1.18
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.819253
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3402296 100 - 27905053
--UUUCUUAAUUCGUGGUAGACCGCACAGGUGGCC-----CUAACUUAUCGGAGCAACCUGCUCCUAGCAAUGGGUUAUCGGAUGGGGAAUCUGACACCUCUCGCAC--------
--.((((..((((((((....))))...(((((((-----(...((....(((((.....))))).))....))))))))))))..)))).................-------- ( -31.40, z-score =  -1.32, R)
>droSim1.chr3R 3450785 100 - 27517382
--UUUCUUAAUUCGUGGGAGACCACUCAGGUGGUC-----CUAACUUAUUGGAGCAACCUGCUCCUAGCAAUGGGUUAUCAAAUGGGAAAUCUGACACCUCUCGCAC--------
--...........(((((((.....((((((..((-----(((((((((((((((.....)))))....)))))))))......)))..))))))...)))))))..-------- ( -32.20, z-score =  -2.64, R)
>droSec1.super_6 3494190 100 - 4358794
--UUUCUUAAUUCGUGGGAGACCACUCAGGUGGUC-----CUAACUUAUUGGAGCAACCUGCUCCUAGCAAUGGGUUAUCAAAUGGGGAAUCUGACACCUCUCGCAC--------
--...........(((((((.....((((((..((-----(((((((((((((((.....)))))....)))))))))......)))..))))))...)))))))..-------- ( -31.70, z-score =  -2.07, R)
>droYak2.chr3R 21902494 87 + 28832112
--UUUCUUAAUUCGUGGGAGACCACU-GGGCUUCC-----CCAACUUAUCAGAAGAAUCUCCUCCUUCCAAUGAGUUAUCAAAUGUGGAACCUGA--------------------
--...........((((....)))).-(((.((((-----.((((((((..((((.........))))..)))))).......)).)))))))..-------------------- ( -22.41, z-score =  -1.08, R)
>droAna3.scaffold_13340 3174247 115 - 23697760
ACUUUCUGGGUUCAUAAAAAUCUUCCCCCAUCAUCUUAGUCUGAUUUAACUUAUCAGAGGGCUCCCAUCUGUGGCUCAGUGCUAACAGGGCCAGUUACACCUUACAUUUGUGCAU
......((((................)))).........((((((.......))))))((....)).....((((((.((....)).))))))...................... ( -20.69, z-score =   1.22, R)
>consensus
__UUUCUUAAUUCGUGGGAGACCACUCAGGUGGUC_____CUAACUUAUCGGAGCAACCUGCUCCUAGCAAUGGGUUAUCAAAUGGGGAAUCUGACACCUCUCGCAC________
...(((((.....((((....))))................((((((((.(((((.....))))).....)))))))).......)))))......................... (-12.86 = -13.50 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,402,328 – 3,402,423
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 75.34
Shannon entropy 0.45281
G+C content 0.49540
Mean single sequence MFE -27.58
Consensus MFE -14.77
Energy contribution -15.32
Covariance contribution 0.55
Combinations/Pair 1.22
Mean z-score -1.71
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.77
SVM RNA-class probability 0.811926
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3402328 95 - 27905053
GAGCACUUGACCAGCACCCUUGGUUUAUUUCUUAAUUCGUGGUAGACCGCACAGGUGGCCCUAACUUAUCGGAGCAACCUGCUCCUAGCAAUGGG
...(((((((((((.....)))))..............((((....)))).)))))).(((...((....(((((.....))))).))....))) ( -26.90, z-score =  -0.76, R)
>droSim1.chr3R 3450817 95 - 27517382
GAGCACUUGACCAGGACCCUUGGCUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGUCCUAACUUAUUGGAGCAACCUGCUCCUAGCAAUGGG
..((........(((((((((((.(((.....)))...((((....))))))))).))))))........(((((.....)))))..))...... ( -33.10, z-score =  -2.25, R)
>droSec1.super_6 3494222 95 - 4358794
GAGCACUUGACCAGGACCCUUGGUUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGUCCUAACUUAUUGGAGCAACCUGCUCCUAGCAAUGGG
..((........(((((((((((.(((.....)))...((((....))))))))).))))))........(((((.....)))))..))...... ( -33.30, z-score =  -2.30, R)
>droYak2.chr3R 21902514 78 + 28832112
----------------CCUUUGGUUUAUUUCUUAAUUCGUGGGAGACCACU-GGGCUUCCCCAACUUAUCAGAAGAAUCUCCUCCUUCCAAUGAG
----------------......................((((....))))(-(((....)))).(((((..((((.........))))..))))) ( -18.10, z-score =  -0.67, R)
>droEre2.scaffold_4770 3662221 80 - 17746568
GAGAACUUGACCAGUGCCCUUGGUUGACUUCUUAAUUCGUGGGAGACC---------------ACUUAUCGCAGGAACCUCCUCCUUGCAAUGGC
(((((.(..(((((.....)))))..).))))).....((((....))---------------)).....((((((......))).)))...... ( -26.50, z-score =  -2.58, R)
>consensus
GAGCACUUGACCAGGACCCUUGGUUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGCCCUAACUUAUCGGAGCAACCUGCUCCUAGCAAUGGG
................((((((................((((....))))..(((....)))........(((((.....)))))...))).))) (-14.77 = -15.32 +   0.55)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,402,336 – 3,402,431
Length 95
Sequences 5
Columns 95
Reading direction reverse
Mean pairwise identity 74.50
Shannon entropy 0.46801
G+C content 0.49899
Mean single sequence MFE -26.30
Consensus MFE -14.89
Energy contribution -15.64
Covariance contribution 0.75
Combinations/Pair 1.22
Mean z-score -1.63
Structure conservation index 0.57
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.99
SVM RNA-class probability 0.869475
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 3402336 95 - 27905053
GUCCGACAGAGCACUUGACCAGCACCCUUGGUUUAUUUCUUAAUUCGUGGUAGACCGCACAGGUGGCCCUAACUUAUCGGAGCAACCUGCUCCUA
.......((.((((((((((((.....)))))..............((((....)))).))))).)).))........(((((.....))))).. ( -25.20, z-score =  -0.85, R)
>droSim1.chr3R 3450825 95 - 27517382
GUCCGACAGAGCACUUGACCAGGACCCUUGGCUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGUCCUAACUUAUUGGAGCAACCUGCUCCUA
........((.((((((((((((...)))))...............((((....))))))))))).))..........(((((.....))))).. ( -32.20, z-score =  -2.33, R)
>droSec1.super_6 3494230 95 - 4358794
GUCCGACAGAGCACUUGACCAGGACCCUUGGUUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGUCCUAACUUAUUGGAGCAACCUGCUCCUA
........((.((((((((((((...)))))...............((((....))))))))))).))..........(((((.....))))).. ( -32.40, z-score =  -2.41, R)
>droYak2.chr3R 21902522 75 + 28832112
----------------GUCCG---CCUUUGGUUUAUUUCUUAAUUCGUGGGAGACCACU-GGGCUUCCCCAACUUAUCAGAAGAAUCUCCUCCUU
----------------.....---.....((.....(((((.....((((....))))(-(((....)))).........)))))......)).. ( -17.50, z-score =  -0.79, R)
>droEre2.scaffold_4770 3662229 80 - 17746568
GUCCGACAGAGAACUUGACCAGUGCCCUUGGUUGACUUCUUAAUUCGUGGGAGACC---------------ACUUAUCGCAGGAACCUCCUCCUU
.(((..(.(((((.(..(((((.....)))))..).))))).....((((....))---------------)).....)..)))........... ( -24.20, z-score =  -1.78, R)
>consensus
GUCCGACAGAGCACUUGACCAGGACCCUUGGUUUAUUUCUUAAUUCGUGGGAGACCACUCAGGUGGCCCUAACUUAUCGGAGCAACCUGCUCCUA
................((((((.....)))))).............((((....))))..(((....)))........(((((.....))))).. (-14.89 = -15.64 +   0.75)

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 23:56:28 2011