Locus 11044

Sequence ID dm3.chr3R
Location 18,294,713 – 18,294,818
Length 105
Max. P 0.943232
window15173 window15174

overview

Window 3

Location 18,294,713 – 18,294,818
Length 105
Sequences 9
Columns 119
Reading direction forward
Mean pairwise identity 73.01
Shannon entropy 0.56148
G+C content 0.45274
Mean single sequence MFE -34.41
Consensus MFE -15.10
Energy contribution -15.81
Covariance contribution 0.71
Combinations/Pair 1.05
Mean z-score -1.98
Structure conservation index 0.44
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.49
SVM RNA-class probability 0.943232
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18294713 105 + 27905053
-----------CUGAACAUGCAUAUGUGUGUAUCCAUGUGAAUGUGGCAUCUAAUACGCUU-UAGUGGUGCAGGUUAUGAACCUGCGUGCUAUUCGCUUAUUACGCAUGUGUGAGUG--
-----------.....(((.((((((((((((.....((((..(((((((......(((..-..)))..((((((.....)))))))))))))))))....)))))))))))).)))-- ( -37.70, z-score =  -2.77, R)
>droVir3.scaffold_12822 3437640 84 - 4096053
----------------------------------UAUAUUC-UGUCCCUUCUAAUACGCUUCAAGUGGUGCAGGUUAUGAACCUGCGUGUUCAGCGCUCAUUACGCAUGUGUGUGAGUG
----------------------------------......(-((..((........(((.....)))..((((((.....))))))).)..)))(((((((.(((....)))))))))) ( -21.90, z-score =  -0.82, R)
>droWil1.scaffold_181089 2768693 106 + 12369635
-------GUGUAGGUGUUUAUGUAAAGGUAUUUGUGUGUACGUAUCCCAUCUAAU----UUCGAGUGGUGCAGGUUAUGAACCUGCGUGUUGUGCUCUUAUUACGCAUGUGUAAGAG--
-------...((((((..((((((.(.(....).)...))))))...))))))..----..........((((((.....))))))........(((((((.((....)))))))))-- ( -23.00, z-score =   0.16, R)
>droSim1.chr3R 18103238 105 + 27517382
-----------CUGAACAUGCAUAUGUGUGUAUCCAUGUGAAUGUGGCAUCUAAUACGCUU-UAGUGGUGCAGGUUAUGAACCUGCGUGCUAUUCGCUCAUUACGCAUGUGUGAGUG--
-----------.....(((.((((((((((((.....((((..(((((((......(((..-..)))..((((((.....)))))))))))))))))....)))))))))))).)))-- ( -37.70, z-score =  -2.50, R)
>droSec1.super_0 18649136 105 + 21120651
-----------CUGAACAUGCAUAUGUGUGUAUCCAUGUGAAUGUGGCAUCUAAUACGCUU-UAGUGGUGCAGGUUAUGAACCUGCGUGCUAUUCGCUCAUUACGCAUGUGUGAGUG--
-----------.....(((.((((((((((((.....((((..(((((((......(((..-..)))..((((((.....)))))))))))))))))....)))))))))))).)))-- ( -37.70, z-score =  -2.50, R)
>droYak2.chr3R 19140135 105 + 28832112
-----------CUGAACAAGCAUAUGUGUGUAUCCAUGUGAAUGUGGCAUCUAAUACGCUU-UAGUGGUGCAGGUUAUGAACCUGCGUGCUAUUCGCUCAUUACGCAUGUGUGAGUG--
-----------.....((..((((((((((((.....((((..(((((((......(((..-..)))..((((((.....)))))))))))))))))....))))))))))))..))-- ( -37.90, z-score =  -2.76, R)
>droEre2.scaffold_4820 687176 105 - 10470090
-----------CUAAACAAGCAUAUGUGUGUAUCCAUGUGAAUGUGGCAUCUAAUACGCUU-UAGUGGUGCAGGUUAUGAACCUGCGUGCUAUUCGCUCAUUACGCAUGUGUGAGUG--
-----------.....((..((((((((((((.....((((..(((((((......(((..-..)))..((((((.....)))))))))))))))))....))))))))))))..))-- ( -37.90, z-score =  -3.04, R)
>droAna3.scaffold_12911 5335513 111 + 5364042
-----GUGUAUCUGCAUUUGUGUGGGAGUGCGAGUGUAUGGGUGUCCCAUCUAAUACGCUUCGAGUGGUGCAGGUUAUGAACCUGCGUGAUAUGCGCACAUUACGCAUGUGUGGGU---
-----....(((..(((.(((((((..(((((((((((((((((...))))).)))))))....((..(((((((.....)))))))..))...))))).))))))).)))..)))--- ( -43.10, z-score =  -2.07, R)
>dp4.chr2 17008712 106 - 30794189
UGAACCAACACAUGCAGCGUCGUGUAUCUACAUAUGUGUCCGUGUCCCUUCUAAUACGCUUCUAGUGGUGCAGGUUAUGAACCUGCGU-----------AUUACGCAUGUGUGAGUG--
...((..((((((((.(((.((..(((....)))..))..)))........(((((((((......)))((((((.....))))))))-----------)))).))))))))..)).-- ( -32.80, z-score =  -1.53, R)
>consensus
___________CUGAACAUGCAUAUGUGUGUAUCCAUGUGAAUGUGGCAUCUAAUACGCUU_UAGUGGUGCAGGUUAUGAACCUGCGUGCUAUUCGCUCAUUACGCAUGUGUGAGUG__
......................................................(((((.....(((((((((((.....))))))(((.....)))..)))))....)))))...... (-15.10 = -15.81 +   0.71)

alignment

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secondary structure

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dotplot

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Window 4

Location 18,294,713 – 18,294,818
Length 105
Sequences 9
Columns 119
Reading direction reverse
Mean pairwise identity 73.01
Shannon entropy 0.56148
G+C content 0.45274
Mean single sequence MFE -24.55
Consensus MFE -10.93
Energy contribution -11.40
Covariance contribution 0.47
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.901783
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18294713 105 - 27905053
--CACUCACACAUGCGUAAUAAGCGAAUAGCACGCAGGUUCAUAACCUGCACCACUA-AAGCGUAUUAGAUGCCACAUUCACAUGGAUACACACAUAUGCAUGUUCAG-----------
--.......(((((((((....((...(((...((((((.....))))))....)))-..))(((((..(((.........))).))))).....)))))))))....----------- ( -26.30, z-score =  -2.55, R)
>droVir3.scaffold_12822 3437640 84 + 4096053
CACUCACACACAUGCGUAAUGAGCGCUGAACACGCAGGUUCAUAACCUGCACCACUUGAAGCGUAUUAGAAGGGACA-GAAUAUA----------------------------------
..(((.....(((.....))).(((((......((((((.....)))))).........))))).......)))...-.......---------------------------------- ( -17.76, z-score =  -0.67, R)
>droWil1.scaffold_181089 2768693 106 - 12369635
--CUCUUACACAUGCGUAAUAAGAGCACAACACGCAGGUUCAUAACCUGCACCACUCGAA----AUUAGAUGGGAUACGUACACACAAAUACCUUUACAUAAACACCUACAC-------
--..........((((((...............((((((.....)))))).(((.((...----....)))))..))))))...............................------- ( -18.70, z-score =  -2.46, R)
>droSim1.chr3R 18103238 105 - 27517382
--CACUCACACAUGCGUAAUGAGCGAAUAGCACGCAGGUUCAUAACCUGCACCACUA-AAGCGUAUUAGAUGCCACAUUCACAUGGAUACACACAUAUGCAUGUUCAG-----------
--.......(((((((((.((.((...(((...((((((.....))))))....)))-..))(((((..(((.........))).)))))...)))))))))))....----------- ( -26.70, z-score =  -2.12, R)
>droSec1.super_0 18649136 105 - 21120651
--CACUCACACAUGCGUAAUGAGCGAAUAGCACGCAGGUUCAUAACCUGCACCACUA-AAGCGUAUUAGAUGCCACAUUCACAUGGAUACACACAUAUGCAUGUUCAG-----------
--.......(((((((((.((.((...(((...((((((.....))))))....)))-..))(((((..(((.........))).)))))...)))))))))))....----------- ( -26.70, z-score =  -2.12, R)
>droYak2.chr3R 19140135 105 - 28832112
--CACUCACACAUGCGUAAUGAGCGAAUAGCACGCAGGUUCAUAACCUGCACCACUA-AAGCGUAUUAGAUGCCACAUUCACAUGGAUACACACAUAUGCUUGUUCAG-----------
--.................(((((.........((((((.....)))))).......-((((((((......(((........)))........))))))))))))).----------- ( -23.64, z-score =  -1.09, R)
>droEre2.scaffold_4820 687176 105 + 10470090
--CACUCACACAUGCGUAAUGAGCGAAUAGCACGCAGGUUCAUAACCUGCACCACUA-AAGCGUAUUAGAUGCCACAUUCACAUGGAUACACACAUAUGCUUGUUUAG-----------
--.......(((.(((((.((.((...(((...((((((.....))))))....)))-..))(((((..(((.........))).)))))...))))))).)))....----------- ( -22.40, z-score =  -0.75, R)
>droAna3.scaffold_12911 5335513 111 - 5364042
---ACCCACACAUGCGUAAUGUGCGCAUAUCACGCAGGUUCAUAACCUGCACCACUCGAAGCGUAUUAGAUGGGACACCCAUACACUCGCACUCCCACACAAAUGCAGAUACAC-----
---.....(((((.....))))).((((.....((((((.....))))))..........(((......(((((...))))).....)))............))))........----- ( -28.30, z-score =  -2.38, R)
>dp4.chr2 17008712 106 + 30794189
--CACUCACACAUGCGUAAU-----------ACGCAGGUUCAUAACCUGCACCACUAGAAGCGUAUUAGAAGGGACACGGACACAUAUGUAGAUACACGACGCUGCAUGUGUUGGUUCA
--.(((.((((((((.....-----------..((((((.....)))))).........(((((..........(((.(......).))).........))))))))))))).)))... ( -30.41, z-score =  -1.70, R)
>consensus
__CACUCACACAUGCGUAAUGAGCGAAUAGCACGCAGGUUCAUAACCUGCACCACUA_AAGCGUAUUAGAUGCCACAUUCACAUGGAUACACACAUAUGCAUGUUCAG___________
...........((((((.....(.......)..((((((.....))))))..........))))))..................................................... (-10.93 = -11.40 +   0.47)

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 00:35:19 2011