Locus 5166

Sequence ID dm3.chr2R
Location 18,259,450 – 18,259,571
Length 121
Max. P 0.956626
window7085 window7086 window7087

overview

Window 5

Location 18,259,450 – 18,259,548
Length 98
Sequences 7
Columns 110
Reading direction forward
Mean pairwise identity 75.34
Shannon entropy 0.47189
G+C content 0.39023
Mean single sequence MFE -24.24
Consensus MFE -11.98
Energy contribution -13.83
Covariance contribution 1.84
Combinations/Pair 1.39
Mean z-score -2.27
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.63
SVM RNA-class probability 0.956626
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18259450 98 + 21146708
-------AAACUCAACCACU--AAUUGUGCAAAUUAUUUGGAGUAAUUUCCUA---AUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAC
-------.............--....((((((((((...((((....))))))---))))))))....(((((((.(((((...(((...)))...))))).))))))). ( -26.40, z-score =  -3.31, R)
>droSim1.chr2R 16856979 98 + 19596830
-------AAACUCAACCACU--AAUUGCGCAAAUUAUUUGGAGUUAUUUCCUA---AUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAG
-------.............--......((((((((...((((....))))))---)))))).....((((((((.(((((...(((...)))...))))).)))))))) ( -26.80, z-score =  -3.54, R)
>droSec1.super_9 1567471 98 + 3197100
-------AAACUCAACCACU--AAUUGCGCAAAUUAUUUGGAGUAAUUUCCUA---AUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAG
-------.............--......((((((((...((((....))))))---)))))).....((((((((.(((((...(((...)))...))))).)))))))) ( -26.80, z-score =  -3.51, R)
>droYak2.chr2R 18008057 97 + 21139217
-------AAACUCAACCACU--AAUUGCGCAA-UUAUUUGGAGUAAUUUCCUA---AUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCUUUCAUUUUAGUCAGCAG
-------.............--......((((-......((((....))))..---..)))).....((((((((..((((.(..((...))..).))))..)))))))) ( -21.20, z-score =  -1.60, R)
>droEre2.scaffold_4845 12399490 97 + 22589142
-------AAACUCAACCACU--AAUUGCGCAA-UUAUUUGGAGUAAUUUCCUA---AUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCUUUCAUUUCAGUCAGCAG
-------.............--......((((-......((((....))))..---..)))).....((((((((.(((((.(..((...))..).))))).)))))))) ( -22.30, z-score =  -1.93, R)
>droAna3.scaffold_13266 12386568 98 - 19884421
-------CAGUUGAGUCACA--AAUUGUUCGAAUUAUUCGGAGUAAUUUGCUA---AUUUGUACUCUCCAUUGACCGAGAUAGUUGGCAGCCAUUCUUUUCUGUCAGCAG
-------((((.((((.(((--(((((..((((((((.....)))))))).))---))))))))))...)))).........((((((((..........)))))))).. ( -25.40, z-score =  -2.25, R)
>dp4.chr3 4905245 108 - 19779522
GGAUUUGGCACUAAAUUAUCGCAUCUGUAUUAUUUAGGAACUAUGUUUAUCUAUGCAUGUGCACACGCUUAUCCCUGGAACAGAUGCC--UCACACAACUCAGCAGAUGA
.((((((....))))))...((((((((....((((((...(((((........))))).((....)).....)))))))))))))).--.................... ( -20.80, z-score =   0.26, R)
>consensus
_______AAACUCAACCACU__AAUUGCGCAAAUUAUUUGGAGUAAUUUCCUA___AUUUGUAUUCUCUGCUGACCGAGAUAGUUGGCAGCCAUUCAUUUCAGUCAGCAG
............................((((.......((((....)))).......)))).....((((((((.(((((...((.....))...))))).)))))))) (-11.98 = -13.83 +   1.84)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,259,450 – 18,259,548
Length 98
Sequences 7
Columns 110
Reading direction reverse
Mean pairwise identity 75.34
Shannon entropy 0.47189
G+C content 0.39023
Mean single sequence MFE -24.54
Consensus MFE -13.32
Energy contribution -14.33
Covariance contribution 1.01
Combinations/Pair 1.45
Mean z-score -1.73
Structure conservation index 0.54
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.00
SVM RNA-class probability 0.871291
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18259450 98 - 21146708
GUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAU---UAGGAAAUUACUCCAAAUAAUUUGCACAAUU--AGUGGUUGAGUUU-------
.((((((((((.(((..(((...)))..))).)))))))))).......(((((---(((((......)))...)))))))(((....--.))).........------- ( -25.10, z-score =  -1.99, R)
>droSim1.chr2R 16856979 98 - 19596830
CUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAU---UAGGAAAUAACUCCAAAUAAUUUGCGCAAUU--AGUGGUUGAGUUU-------
(((((((((((.(((..(((...)))..))).)))))))))))......(((((---(((((......)))...)))))))(((....--.))).........------- ( -27.40, z-score =  -2.78, R)
>droSec1.super_9 1567471 98 - 3197100
CUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAU---UAGGAAAUUACUCCAAAUAAUUUGCGCAAUU--AGUGGUUGAGUUU-------
(((((((((((.(((..(((...)))..))).)))))))))))......(((((---(((((......)))...)))))))(((....--.))).........------- ( -27.40, z-score =  -2.67, R)
>droYak2.chr2R 18008057 97 - 21139217
CUGCUGACUAAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAU---UAGGAAAUUACUCCAAAUAA-UUGCGCAAUU--AGUGGUUGAGUUU-------
(((((((((.....((.((........)).))..)))))))))...........---..(((......)))...(((-(..(......--.)..)))).....------- ( -22.30, z-score =  -1.31, R)
>droEre2.scaffold_4845 12399490 97 - 22589142
CUGCUGACUGAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAU---UAGGAAAUUACUCCAAAUAA-UUGCGCAAUU--AGUGGUUGAGUUU-------
(((((((((((...((.((........)).)))))))))))))...........---..(((......)))...(((-(..(......--.)..)))).....------- ( -26.10, z-score =  -2.32, R)
>droAna3.scaffold_13266 12386568 98 + 19884421
CUGCUGACAGAAAAGAAUGGCUGCCAACUAUCUCGGUCAAUGGAGAGUACAAAU---UAGCAAAUUACUCCGAAUAAUUCGAACAAUU--UGUGACUCAACUG-------
((..((((.((......(((...)))......)).))))..)).((((((((((---(..(.(((((.......))))).)...))))--))).)))).....------- ( -16.00, z-score =   0.09, R)
>dp4.chr3 4905245 108 + 19779522
UCAUCUGCUGAGUUGUGUGA--GGCAUCUGUUCCAGGGAUAAGCGUGUGCACAUGCAUAGAUAAACAUAGUUCCUAAAUAAUACAGAUGCGAUAAUUUAGUGCCAAAUCC
......((((((((((....--.((((((((...((((((..(((((....)))))...(.....)...)))))).......)))))))).))))))))))......... ( -27.50, z-score =  -1.12, R)
>consensus
CUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAU___UAGGAAAUUACUCCAAAUAAUUUGCGCAAUU__AGUGGUUGAGUUU_______
(((((((((((.(((..((.....))..))).)))))))))))................(((......)))..........(((.......)))................ (-13.32 = -14.33 +   1.01)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,259,480 – 18,259,571
Length 91
Sequences 6
Columns 92
Reading direction reverse
Mean pairwise identity 93.21
Shannon entropy 0.13009
G+C content 0.42417
Mean single sequence MFE -25.72
Consensus MFE -21.57
Energy contribution -22.98
Covariance contribution 1.42
Combinations/Pair 1.10
Mean z-score -2.22
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.17
SVM RNA-class probability 0.903556
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 18259480 91 - 21146708
AUAUUAAUUGGCCUGGUUCGG-UGGUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCC
....(((((..(((((((..(-((.((((((((((.(((..(((...)))..))).)))))))))).....))).))))))).))))).... ( -26.60, z-score =  -2.33, R)
>droSim1.chr2R 16857009 91 - 19596830
AUAUUAAUUGGCCUGGUUCGG-UGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUAACUCC
...........(((((((..(-(.(((((((((((.(((..(((...)))..))).)))))))))))...))...))))))).......... ( -27.90, z-score =  -3.04, R)
>droSec1.super_9 1567501 91 - 3197100
AUAUUAAUUGGCCUGGUUCGG-CGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCC
....(((((..(((((((.(.-(.(((((((((((.(((..(((...)))..))).))))))))))).)....).))))))).))))).... ( -30.10, z-score =  -3.55, R)
>droYak2.chr2R 18008086 91 - 21139217
AUAUUAAUUGGCCUGGUUCGG-UGCUGCUGACUAAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCC
....(((((..(((((((..(-(.(((((((((.....((.((........)).))..)))))))))...))...))))))).))))).... ( -24.40, z-score =  -1.92, R)
>droEre2.scaffold_4845 12399519 91 - 22589142
AUAUUAAUUGGCCUGGUUCGG-UGCUGCUGACUGAAAUGAAAGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCC
....(((((..(((((((..(-(.(((((((((((...((.((........)).)))))))))))))...))...))))))).))))).... ( -28.20, z-score =  -2.96, R)
>droAna3.scaffold_13266 12386598 92 + 19884421
AUAUUAAUUGGUCCUAUUUGGCUGCUGCUGACAGAAAAGAAUGGCUGCCAACUAUCUCGGUCAAUGGAGAGUACAAAUUAGCAAAUUACUCC
......((((..(.((.(((((.(((.((........))...))).))))).))....)..))))...(((((.............))))). ( -17.12, z-score =   0.47, R)
>consensus
AUAUUAAUUGGCCUGGUUCGG_UGCUGCUGACUGAAAUGAAUGGCUGCCAACUAUCUCGGUCAGCAGAGAAUACAAAUUAGGAAAUUACUCC
....(((((..(((((((.(....(((((((((((.(((..(((...)))..))).)))))))))))......).))))))).))))).... (-21.57 = -22.98 +   1.42)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:43:04 2011