Locus 7036

Sequence ID dm3.chr3L
Location 11,653,880 – 11,654,067
Length 187
Max. P 0.734732
window9690 window9691 window9692 window9693

overview

Window 0

Location 11,653,880 – 11,653,992
Length 112
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 77.39
Shannon entropy 0.43660
G+C content 0.52331
Mean single sequence MFE -29.80
Consensus MFE -17.41
Energy contribution -17.17
Covariance contribution -0.24
Combinations/Pair 1.46
Mean z-score -1.32
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.12
SVM RNA-class probability 0.554387
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11653880 112 + 24543557
CAGCUGGAUUGCCGGCUAAUGGUCCCCGUGUGCUGGAUCCUUC-CACAAACCCCAAUGCUCUGUCAGCGAGAGUAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCA
..((((((...(((((..((((...))))..))))).......-..........((((.......((((.(((......))).)))).......)))).))))))........ ( -27.64, z-score =  -1.17, R)
>droEre2.scaffold_4784 11635879 112 + 25762168
CAGUUGGAUUGUCGGCUAAUGGUCCCCGUGUGCUGGAUCCUUC-CAUGAGCCGCUGUGCUCUGUCUGCGGGAGUAGUUUCUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCA
..((((((..(.(((((.((((...(((.....)))......)-))).))))))((((........(((((((......)))))))......))))...))))))........ ( -37.94, z-score =  -2.87, R)
>droYak2.chr3L 11682391 112 + 24197627
CAGUUGGAUUGUCGGCUAAUGGUCCCCGUGUGCUGGAUCCUUC-CAUAAGCCCCUGUGCUCUGUCUGCGAGAGUAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCA
..((((((.(((.((((.((((...(((.....)))......)-))).))))...(((......((((....)))).......))).......)))...))))))........ ( -27.32, z-score =  -1.24, R)
>droSec1.super_0 3840679 112 + 21120651
CAGCUGGAUUGUCGGCUAAUGGUCCCCGUGUGCUGGAUCCUUC-CACAAGCCCCAGUGCUCUGUCAGCGAGAGUAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCA
..((((((.(((.(((..((((...))))(..((((...(((.-...)))..))))..)...)))((((.(((......))).))))......)))...))))))........ ( -30.60, z-score =  -1.78, R)
>droSim1.chr3L 11023472 112 + 22553184
CAGCUGGAUUGUCGGCUAAUGGUCCCCGUGUGCUGGAUCCUUC-CACAAGCCCCAGUGCUCUGUCAGCGACAGUAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCA
..((((((.(((.((..(((((.......(..((((...(((.-...)))..))))..).(((((...))))).........))).))..)).)))...))))))........ ( -30.00, z-score =  -1.88, R)
>droMoj3.scaffold_6496 18811875 105 + 26866924
----AACAUUGCAAAAUUGUUUACUGUGCGCGCACAAACUUUGGUCCAGGCCGCCGCCCGUCAGCCACAAGUGGCGAUU----CGCUUCAGCAGCACCUGUGAGUAUAUUCCA
----...............(((((.((((..((.........(((....)))...((..(((.((((....))))))).----.))....)).))))..)))))......... ( -25.30, z-score =   1.01, R)
>consensus
CAGCUGGAUUGUCGGCUAAUGGUCCCCGUGUGCUGGAUCCUUC_CACAAGCCCCAGUGCUCUGUCAGCGAGAGUAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCA
.((((((....)))))).((((...))))((((((((..........((((.....((((((.......)))))).........))))...........))))))))...... (-17.41 = -17.17 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 1

Location 11,653,880 – 11,653,992
Length 112
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 77.39
Shannon entropy 0.43660
G+C content 0.52331
Mean single sequence MFE -33.94
Consensus MFE -20.96
Energy contribution -21.22
Covariance contribution 0.26
Combinations/Pair 1.46
Mean z-score -1.38
Structure conservation index 0.62
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.54
SVM RNA-class probability 0.734732
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11653880 112 - 24543557
UGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUCUCGCUGACAGAGCAUUGGGGUUUGUG-GAAGGAUCCAGCACACGGGGACCAUUAGCCGGCAAUCCAGCUG
((((...((((((..(((((......(((((((........)))))))......)))))((..((((((-(..(....)..).))))))..)).....)))))).)))).... ( -35.70, z-score =  -1.65, R)
>droEre2.scaffold_4784 11635879 112 - 25762168
UGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAGAAACUACUCCCGCAGACAGAGCACAGCGGCUCAUG-GAAGGAUCCAGCACACGGGGACCAUUAGCCGACAAUCCAACUG
((((...(((((((.............(((((((......)))))))...((((((......)))).))-......)))))))..(((..........)))....)))).... ( -38.60, z-score =  -3.19, R)
>droYak2.chr3L 11682391 112 - 24197627
UGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUCUCGCAGACAGAGCACAGGGGCUUAUG-GAAGGAUCCAGCACACGGGGACCAUUAGCCGACAAUCCAACUG
((((...(((((((.............((((((........))))))...((((((......)))).))-......)))))))..(((..........)))....)))).... ( -30.10, z-score =  -1.33, R)
>droSec1.super_0 3840679 112 - 21120651
UGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUCUCGCUGACAGAGCACUGGGGCUUGUG-GAAGGAUCCAGCACACGGGGACCAUUAGCCGACAAUCCAGCUG
........((((((...(((.((...(((((((........)))))))..........(((..((((((-(..(....)..).))))))..)))....)).))).)))))).. ( -36.20, z-score =  -2.03, R)
>droSim1.chr3L 11023472 112 - 22553184
UGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUGUCGCUGACAGAGCACUGGGGCUUGUG-GAAGGAUCCAGCACACGGGGACCAUUAGCCGACAAUCCAGCUG
........((((((...(((.((....((((......)).(((((...))))).))..(((..((((((-(..(....)..).))))))..)))....)).))).)))))).. ( -33.80, z-score =  -1.30, R)
>droMoj3.scaffold_6496 18811875 105 - 26866924
UGGAAUAUACUCACAGGUGCUGCUGAAGCG----AAUCGCCACUUGUGGCUGACGGGCGGCGGCCUGGACCAAAGUUUGUGCGCGCACAGUAAACAAUUUUGCAAUGUU----
(((.......((.(((((((((((((....----..))((((....)))).....)))))).)))))))))).....((((....))))(((((....)))))......---- ( -29.21, z-score =   1.20, R)
>consensus
UGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUCUCGCUGACAGAGCACUGGGGCUUGUG_GAAGGAUCCAGCACACGGGGACCAUUAGCCGACAAUCCAGCUG
((((...(((((((.............((((((........)))))).....((((......))))..........)))))))..(((..........)))....)))).... (-20.96 = -21.22 +   0.26)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,653,913 – 11,654,028
Length 115
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 71.40
Shannon entropy 0.50364
G+C content 0.53186
Mean single sequence MFE -36.34
Consensus MFE -17.42
Energy contribution -18.90
Covariance contribution 1.48
Combinations/Pair 1.38
Mean z-score -1.53
Structure conservation index 0.48
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.684398
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11653913 115 - 24543557
CACACACACACGGUGGUCUGCGCCACAUGUUGUGCGUGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUCUCGCUGACAGAGCAUUGGGGUUUGUGGAAGGAUCCA
..((((.((.(((((.(((((.((((((.....((((.....))))......))))))....(((((((........)))))))).)))).)))))..)).)))).......... ( -39.60, z-score =  -2.14, R)
>droEre2.scaffold_4784 11635912 113 - 25762168
--CACACACACGGUGGUCCGCGCCGAAUGUUGUGCGUGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAGAAACUACUCCCGCAGACAGAGCACAGCGGCUCAUGGAAGGAUCCA
--((((....(((((.((((((((((...))).)))))))...))))).....))))(((...(((((((......)))))))...((((((......)))).))......))). ( -44.40, z-score =  -2.96, R)
>droYak2.chr3L 11682424 109 - 24197627
------CACACGGUGGUCCGCGGCAAAUGUAGUGCGUGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUCUCGCAGACAGAGCACAGGGGCUUAUGGAAGGAUCCA
------(((((((((.((((((.((.......))))))))...))))).....))))(((...((((((........))))))...((((((......)))).))......))). ( -30.60, z-score =  -0.79, R)
>droSim1.chr3L 11023505 109 - 22553184
------CACACGGUGGUCUGCGCCAAAUGUUGUGCGUGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUGUCGCUGACAGAGCACUGGGGCUUGUGGAAGGAUCCA
------....(((((.(((((.(((....((..((((.....))))..)).....)))....(((((.(........).)))))).)))).)))))((((((.....))).))). ( -29.40, z-score =   0.14, R)
>droMoj3.scaffold_6496 18811905 105 - 26866924
------UGGACUUUGUACUUCAUCCGACUUUGUGGGUGGAAUAUACUCACAGGUGCUGCUGAAGCG----AAUCGCCACUUGUGGCUGACGGGCGGCGGCCUGGACCAAAGUUUG
------.((((((((...((((((((......))))))))......((.(((((((((((((....----..))((((....)))).....)))))).))))))).)))))))). ( -37.70, z-score =  -1.88, R)
>consensus
______CACACGGUGGUCUGCGCCAAAUGUUGUGCGUGGAAAAUGCUGGAAAAUGUGGGAAAAGCGGGAAAAACUACUCUCGCAGACAGAGCACAGGGGCUUGUGGAAGGAUCCA
......(((((((((.(((((((..........)))))))...))))).....))))(((...((((((........)))))).....((((......)))).........))). (-17.42 = -18.90 +   1.48)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,653,952 – 11,654,067
Length 115
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 75.64
Shannon entropy 0.42758
G+C content 0.48876
Mean single sequence MFE -31.40
Consensus MFE -16.56
Energy contribution -17.16
Covariance contribution 0.60
Combinations/Pair 1.30
Mean z-score -1.63
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.26
SVM RNA-class probability 0.618052
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 11653952 115 + 24543557
UAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCACGCACAACAUGUGGCGCAGACCACCGUGUGUGUGUGUGUGUGUGAAUUUGAUUGGCAGUGAGCCGUAGAGCUUCU
.((((((....((((...(((((..(((..((((....((((((((.(((((((......))).)))))))))))).))))..)))..))..)))....))))...))))))... ( -33.30, z-score =  -1.48, R)
>droEre2.scaffold_4784 11635951 113 + 25762168
UAGUUUCUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCACGCACAACAUUCGGCGCGGACCACCGUGUGUGUGUGUGUGUG--AAUUUGAUUGGCAGUGAGCCGGAGAGCUCCU
.((((.((((.(((.....(((.....((((((..(((((((((((.(((...((((((....))))))))))))))))).)--))..)).))))..)))))).))))))))... ( -41.50, z-score =  -3.42, R)
>droYak2.chr3L 11682463 109 + 24197627
UAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCACGCACUACAUUUGCCGCGGACCACCGUGUGUGUGUGUG------AAUUUGAUUGGCAGUGAGCCGUGGAGCUUCU
...........(((....((((.........((..((((((((((.........(((((....))))).))))))).)------))..))...(((.....)))))))))).... ( -30.60, z-score =  -1.72, R)
>droSim1.chr3L 11023544 109 + 22553184
UAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCACGCACAACAUUUGGCGCAGACCACCGUGUGUGUGUGUG------AAUUUGAUUGGCAGUGAGCCGUAGAGCUUCU
...........(((((...(.((((..((((((..(((((((((((.(((.(((......)))..))))))))))).)------))..)).)))).)))).)....))))).... ( -29.80, z-score =  -1.94, R)
>droMoj3.scaffold_6496 18811942 106 + 26866924
UGGCGAUU--CGCUUCAGCAGCACCUGUGAGUAUAUUCCACCCACAAAGUCGGAUGAAGUACAAAGUCCACGUUGCCA-----GAACCUGUUAAUUAG--AACUAUGGAGCUUCU
........--.(((((((((((...((((.((.......)).))))..((.((((..........)))))))))))..-----....(((.....)))--.....)))))).... ( -21.80, z-score =   0.41, R)
>consensus
UAGUUUUUCCCGCUUUUCCCACAUUUUCCAGCAUUUUCCACGCACAACAUUUGGCGCAGACCACCGUGUGUGUGUGUG______AAUUUGAUUGGCAGUGAGCCGUAGAGCUUCU
...........(((((......................(((((((.((((.(((.(.....).))).)))))))))))...............(((.....)))..))))).... (-16.56 = -17.16 +   0.60)

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 23:19:19 2011