Locus 9563

Sequence ID dm3.chr3R
Location 7,377,588 – 7,377,715
Length 127
Max. P 0.920856
window13122 window13123 window13124

overview

Window 2

Location 7,377,588 – 7,377,682
Length 94
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 90.71
Shannon entropy 0.16120
G+C content 0.37157
Mean single sequence MFE -18.30
Consensus MFE -13.29
Energy contribution -14.09
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.73
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.27
SVM RNA-class probability 0.919872
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7377588 94 + 27905053
CUAACAUAUUUCCAGUGAGUAGCAAAAGUACCUUGUAAAUUGUUUUU-AUCAGCUUACAAGCUACUUUGACUUAAAUCCCUCCAUGUGUCCCUGC
...((((((......(((((....((((((.(((((((.(((.....-..))).))))))).)))))).))))).........))))))...... ( -19.46, z-score =  -2.82, R)
>droEre2.scaffold_4770 3503431 95 - 17746568
CAAACAUAUUUCCAGAAAGCACCAAAAGUACCUUGUAAAUUGUUUUUUAUAAGCUUACAAGUUACUUUGACAUAAAUCCCUCCAUGUUUUCCUGC
............(((((((((...((((((.(((((((.((((.....))))..))))))).))))))((......))......)))))).))). ( -16.80, z-score =  -3.00, R)
>droYak2.chr3R 11417614 95 + 28832112
CAAACAUAUUUGCAGCCAGCACCAAAAGUACCUUGUAAAUUGUUUUUUAUCAGCUUACAAGCUACUUCGACUUAAAUCCCUCCAUGUGUCCCUGC
...........((((...((((...(((((.(((((((.(((........))).))))))).))))).((......)).......))))..)))) ( -17.50, z-score =  -2.41, R)
>droSec1.super_0 6533191 93 - 21120651
CUUACAUAUUUCCAGUGAGUAGCAAAAGUACCUUGUAAAUUGUUUUU-AUCAGCUUACAAGCUACUUUGACUCAAAUCCCUCCAUCUGUUC-UGC
...............(((((....((((((.(((((((.(((.....-..))).))))))).)))))).))))).................-... ( -19.20, z-score =  -2.86, R)
>droSim1.chr3R 13498939 94 - 27517382
CUUACAUAUUUCCAGUGAGCAGCAAAAGUACCUUGUAAAUUGUUUUU-AUCAGCUUACAAGCUACUUUGACUCAAAUCCCUCCAUGUGUCCCUGC
...((((((......((((...((((.(((.(((((((.(((.....-..))).))))))).))))))).)))).........))))))...... ( -18.56, z-score =  -2.23, R)
>consensus
CUAACAUAUUUCCAGUGAGCAGCAAAAGUACCUUGUAAAUUGUUUUU_AUCAGCUUACAAGCUACUUUGACUUAAAUCCCUCCAUGUGUCCCUGC
...((((((...............((((((.(((((((.(((........))).))))))).))))))...............))))))...... (-13.29 = -14.09 +   0.80)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,377,605 – 7,377,715
Length 110
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 76.47
Shannon entropy 0.43637
G+C content 0.36610
Mean single sequence MFE -22.17
Consensus MFE -10.15
Energy contribution -13.40
Covariance contribution 3.25
Combinations/Pair 1.19
Mean z-score -2.40
Structure conservation index 0.46
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.28
SVM RNA-class probability 0.920856
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7377605 110 + 27905053
AGUAGCAAAAGUACCUUGUAAAUUGUUUUU-AUCAGCUUACAAGCUACUUUGACUUAAAUCCCUCCAUGUGUCCCUGCUCAUUUGGAUUUUUAGCCAUUUUCCA--CGCUAUC-----
.(((((.((((((.(((((((.(((.....-..))).))))))).))))))(.((.((((((....(((.((....)).)))..))))))..)).)........--.))))).----- ( -24.40, z-score =  -3.60, R)
>droAna3.scaffold_13340 13821986 110 + 23697760
CGCCAUAAAAGUAUCU---AAAUUAUGGUUUUUCAGACUUUA--UAACUUAAAUUCAGAUGAAAUAAUAAGCU--UAGCAACUUAG-UUCUUAGACCUCAUCCAGUUGAGUUCAUUAG
.(((((((........---...))))))).............--.(((((((.....(((((.....((((..--.(((......)-))))))....)))))...)))))))...... ( -14.70, z-score =   0.13, R)
>droEre2.scaffold_4770 3503448 111 - 17746568
AGCACCAAAAGUACCUUGUAAAUUGUUUUUUAUAAGCUUACAAGUUACUUUGACAUAAAUCCCUCCAUGUUUUCCUGCUCAUUUGGAUUUUUCGGUAUUUUCCA--CGCAGUC-----
.((....((((((.(((((((.((((.....))))..))))))).))))))((...((((((......((......))......)))))).))((......)).--.))....----- ( -21.60, z-score =  -2.63, R)
>droYak2.chr3R 11417631 111 + 28832112
AGCACCAAAAGUACCUUGUAAAUUGUUUUUUAUCAGCUUACAAGCUACUUCGACUUAAAUCCCUCCAUGUGUCCCUGCUCAUUUGGAUUUUUGCGUAUUUUCCA--CGCCUUC-----
.((.....(((((.(((((((.(((........))).))))))).)))))((.(..((((((....(((.((....)).)))..))))))..))).........--.))....----- ( -21.20, z-score =  -2.92, R)
>droSec1.super_0 6533208 109 - 21120651
AGUAGCAAAAGUACCUUGUAAAUUGUUUUU-AUCAGCUUACAAGCUACUUUGACUCAAAUCCCUCCAUCUGUUC-UGCUCAUUUGGAUUUUUGGGCAUUUUCCA--CGCUUUC-----
...(((.((((((.(((((((.(((.....-..))).))))))).))))))(.((((((....((((..((...-....))..))))..)))))))........--.)))...----- ( -24.80, z-score =  -2.75, R)
>droSim1.chr3R 13498956 110 - 27517382
AGCAGCAAAAGUACCUUGUAAAUUGUUUUU-AUCAGCUUACAAGCUACUUUGACUCAAAUCCCUCCAUGUGUCCCUGCUCAUUUGGAUUUUUGGGCAUUUUCCA--CGCUUUC-----
...(((.((((((.(((((((.(((.....-..))).))))))).))))))(.((((((....((((.(((........))).))))..)))))))........--.)))...----- ( -26.30, z-score =  -2.62, R)
>consensus
AGCAGCAAAAGUACCUUGUAAAUUGUUUUU_AUCAGCUUACAAGCUACUUUGACUCAAAUCCCUCCAUGUGUCCCUGCUCAUUUGGAUUUUUGGGCAUUUUCCA__CGCUUUC_____
.((....((((((.(((((((.(((........))).))))))).))))))..((((((....((((.(((........))).))))..))))))............))......... (-10.15 = -13.40 +   3.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,377,605 – 7,377,715
Length 110
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 76.47
Shannon entropy 0.43637
G+C content 0.36610
Mean single sequence MFE -24.64
Consensus MFE -12.27
Energy contribution -14.33
Covariance contribution 2.06
Combinations/Pair 1.26
Mean z-score -1.63
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.09
SVM RNA-class probability 0.540911
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 7377605 110 - 27905053
-----GAUAGCG--UGGAAAAUGGCUAAAAAUCCAAAUGAGCAGGGACACAUGGAGGGAUUUAAGUCAAAGUAGCUUGUAAGCUGAU-AAAAACAAUUUACAAGGUACUUUUGCUACU
-----..(((((--.......(((((..((((((..(((.(......).)))....)))))).)))))(((((.((((((((.((..-.....)).)))))))).))))).))))).. ( -27.80, z-score =  -2.69, R)
>droAna3.scaffold_13340 13821986 110 - 23697760
CUAAUGAACUCAACUGGAUGAGGUCUAAGAA-CUAAGUUGCUA--AGCUUAUUAUUUCAUCUGAAUUUAAGUUA--UAAAGUCUGAAAAACCAUAAUUU---AGAUACUUUUAUGGCG
...............(((((((((.....((-.((((((....--)))))))))))))))))........((((--(((((((((((.........)))---))))...)))))))). ( -18.30, z-score =  -0.36, R)
>droEre2.scaffold_4770 3503448 111 + 17746568
-----GACUGCG--UGGAAAAUACCGAAAAAUCCAAAUGAGCAGGAAAACAUGGAGGGAUUUAUGUCAAAGUAACUUGUAAGCUUAUAAAAAACAAUUUACAAGGUACUUUUGGUGCU
-----..((((.--((((.............)))).....))))....(((((((....))))))).((((((.((((((((..............)))))))).))))))....... ( -21.36, z-score =  -0.92, R)
>droYak2.chr3R 11417631 111 - 28832112
-----GAAGGCG--UGGAAAAUACGCAAAAAUCCAAAUGAGCAGGGACACAUGGAGGGAUUUAAGUCGAAGUAGCUUGUAAGCUGAUAAAAAACAAUUUACAAGGUACUUUUGGUGCU
-----....(((--((.....)))))..((((((..(((.(......).)))....)))))).....((((((.((((((((.((........)).)))))))).))))))....... ( -26.80, z-score =  -2.34, R)
>droSec1.super_0 6533208 109 + 21120651
-----GAAAGCG--UGGAAAAUGCCCAAAAAUCCAAAUGAGCA-GAACAGAUGGAGGGAUUUGAGUCAAAGUAGCUUGUAAGCUGAU-AAAAACAAUUUACAAGGUACUUUUGCUACU
-----....(((--(.....))))((.....((((..((....-...))..)))).)).....(((.((((((.((((((((.((..-.....)).)))))))).)))))).)))... ( -26.40, z-score =  -2.14, R)
>droSim1.chr3R 13498956 110 + 27517382
-----GAAAGCG--UGGAAAAUGCCCAAAAAUCCAAAUGAGCAGGGACACAUGGAGGGAUUUGAGUCAAAGUAGCUUGUAAGCUGAU-AAAAACAAUUUACAAGGUACUUUUGCUGCU
-----...(((.--(((.......))).((((((..(((.(......).)))....)))))).(((.((((((.((((((((.((..-.....)).)))))))).)))))).)))))) ( -27.20, z-score =  -1.36, R)
>consensus
_____GAAAGCG__UGGAAAAUGCCCAAAAAUCCAAAUGAGCAGGAACACAUGGAGGGAUUUAAGUCAAAGUAGCUUGUAAGCUGAU_AAAAACAAUUUACAAGGUACUUUUGCUGCU
............................((((((..(((..........)))....)))))).(((.((((((.(((((((..((........))..))))))).)))))).)))... (-12.27 = -14.33 +   2.06)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:06:52 2011