Locus 1433

Sequence ID dm3.chr2L
Location 11,209,245 – 11,209,461
Length 216
Max. P 0.990922
window1952 window1953 window1954 window1955 window1956

overview

Window 2

Location 11,209,245 – 11,209,295
Length 50
Sequences 3
Columns 50
Reading direction forward
Mean pairwise identity 96.00
Shannon entropy 0.05510
G+C content 0.48000
Mean single sequence MFE -12.67
Consensus MFE -12.85
Energy contribution -12.63
Covariance contribution -0.22
Combinations/Pair 1.07
Mean z-score -2.10
Structure conservation index 1.01
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.19
SVM RNA-class probability 0.985042
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11209245 50 + 23011544
ACCCAUUGAGUUUGGGUAUGGAACUUUCCUCCGCCCAACCAAUUUCAUAC
....((((.(((.((((..(((....)))...)))))))))))....... ( -12.10, z-score =  -1.82, R)
>droSim1.chr2L 11010416 50 + 22036055
ACCCAUUGCGUUUGGGCAUGGAACUUUCCUCCGCCCAACCAAUUUCAUAC
....((((.(((.((((..(((....)))...)))))))))))....... ( -13.70, z-score =  -2.74, R)
>droSec1.super_3 6609779 50 + 7220098
AGCCAUUGCGUUUGGGUAUGGAACUUUCCUCCGCCCAACCAAUUUCAUAC
.(..((((.(((.((((..(((....)))...)))))))))))..).... ( -12.20, z-score =  -1.74, R)
>consensus
ACCCAUUGCGUUUGGGUAUGGAACUUUCCUCCGCCCAACCAAUUUCAUAC
....((((.(((.((((..(((....)))...)))))))))))....... (-12.85 = -12.63 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,209,295 – 11,209,398
Length 103
Sequences 9
Columns 115
Reading direction reverse
Mean pairwise identity 71.20
Shannon entropy 0.55520
G+C content 0.51841
Mean single sequence MFE -32.89
Consensus MFE -17.35
Energy contribution -17.57
Covariance contribution 0.21
Combinations/Pair 1.36
Mean z-score -2.13
Structure conservation index 0.53
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.45
SVM RNA-class probability 0.990922
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11209295 103 - 23011544
GCAGCUACAGCUUCCCAAAAAGGGAGCGCAAGUUGGUGGCAUGCGGCAGCU-AAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGAG-----------
(((((....)))..((((...((((((((.(((((.((.....)).)))))-..((((((.....)))))).(((.....)))..)))))))).)))).))...----------- ( -36.50, z-score =  -2.39, R)
>droMoj3.scaffold_6500 27518543 101 - 32352404
--------AUCUCCUC-CAAUGGAA-----GUCCGAUCACAUAGAGCGGCUAAAUGUAUCUAAUAGAUACACGACAGCAUGUCGAACGCUGCCAUCCGAGCAUAAAGUCUGAGAA
--------.((((.((-(...))).-----(..((.((.....))(((((....((((((.....))))))((((.....))))...)))))....))..).........)))). ( -24.60, z-score =  -1.20, R)
>droVir3.scaffold_12963 2294587 99 - 20206255
--------CCCUCCACACAAUGAGA-----GUCCGAUCACAUAGAGCGGCU-AAUGUAUCUAAUAGAUACACGACAGCAUGUCGAACUCUGCCAUCGGAGCAUAAA--CCGAGCG
--------..(((((.....)).))-----)..............(((((.-..((((((.....))))))((((.....))))......))).((((........--)))))). ( -23.90, z-score =  -1.56, R)
>droWil1.scaffold_180708 4560267 102 - 12563649
ACAGAGACAGAGCGAGGGAAUGAGA----GGGGAGAAUGCAGGCAGCGGCU-AAUGUAUCUAAUAGAUACACGACAGCAUGUCAAACGCUUCCAGCGGAGCAUUAAG--------
.........................----......(((((.((((...(((-..((((((.....))))))....))).))))...(((.....)))..)))))...-------- ( -22.20, z-score =  -0.51, R)
>droAna3.scaffold_12916 11936252 92 + 16180835
------GCAGUAUCU-----GGGGAUCUCUAGCCAGCGGCAUGCGGUAGCU-AAUGUAUCUAAUAGAUACACGACAGCAUGUCAAACGCUUCCAGUGGAGCGAG-----------
------((.....((-----(((....)))))...))(((((((.((....-..((((((.....))))))..)).)))))))...((((((....))))))..----------- ( -28.60, z-score =  -1.06, R)
>droEre2.scaffold_4929 12407285 102 + 26641161
GCAGCCGCAGCUUCC-AAAAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCU-AAUGUAUCUAAUAGAUACACGACAGCGCGUCAAGCGCUUCCAUUGGAGCGAG-----------
((.((((((((((((-.....))))))((......))....))))))..((-((((((((.....)))))..((.(((((.....))))))).))))).))...----------- ( -41.30, z-score =  -2.82, R)
>droYak2.chr2L 7607468 103 - 22324452
GCAGCUACAGCUUCCAAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCU-AAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGAG-----------
(((((....)))(((((....((((((((.(((((.((.....)).)))))-..((((((.....)))))).(((.....)))..)))))))).)))))))...----------- ( -39.50, z-score =  -3.33, R)
>droSec1.super_3 6609829 103 - 7220098
GCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCU-AAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGAG-----------
(((((....)))..((((...((((((((.(((((.((.....)).)))))-..((((((.....)))))).(((.....)))..)))))))).)))).))...----------- ( -39.70, z-score =  -3.13, R)
>droSim1.chr2L 11010466 103 - 22036055
GCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCU-AAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGAG-----------
(((((....)))..((((...((((((((.(((((.((.....)).)))))-..((((((.....)))))).(((.....)))..)))))))).)))).))...----------- ( -39.70, z-score =  -3.13, R)
>consensus
GCAGCUACAGCUUCCCAAAAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCU_AAUGUAUCUAAUAGAUACACGACAGCACGUCAAGCGCUUCCAUUGGAGCGAG___________
.........((((.................(((((.((.....)).)))))...((((((.....)))))).(((.....)))))))(((((....))))).............. (-17.35 = -17.57 +   0.21)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,209,321 – 11,209,436
Length 115
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 87.56
Shannon entropy 0.21882
G+C content 0.50307
Mean single sequence MFE -32.60
Consensus MFE -26.58
Energy contribution -26.66
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.56
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.42
SVM RNA-class probability 0.686929
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11209321 115 + 23011544
GCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCACCAACUUGCGCUCCCUUUUUGGGAAGCUGUAGCUGCAUCUACAGAUCGUUGCAUCCGAAACUCUGUGCAUUUGU--
((....(((((((.....))))))).((((((.((..((((......)).))((((.....)))).)).))))))))...(((((((((.......)))...)))))).......-- ( -32.40, z-score =  -1.27, R)
>droEre2.scaffold_4929 12407311 96 - 26641161
GCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUUUU-GGAAGCUGCGGCUGCAUCCACAGAUCGCUGCAUCC--------------------
((.((((((((((.....)))))))..((.((((((....((......))(((.((.....-)).))))))))).)).......))).)).......-------------------- ( -32.60, z-score =  -2.26, R)
>droYak2.chr2L 7607494 109 + 22324452
GCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUUGGAAGCUGUAGCUGCAUCUACAGAUCGUUGCAACCGAAACUCUCUGU--------
((((..(((((((.....)))))))))))(((.((.(((.((......))(((.((......)).))).))))).)))...(((((..(((........)))..)))))-------- ( -29.40, z-score =  -1.36, R)
>droSec1.super_3 6609855 117 + 7220098
GCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUGGGAAGCUGUAGCUGCAUCUACAGAUCGUUGCAUCCGAAACUUUGUGCAUCUGUUG
((....(((((((.....))))))).((((((.((..((.((......))))((((.....)))).)).))))))))....(((((....(((((..........)))))))))).. ( -34.30, z-score =  -1.49, R)
>droSim1.chr2L 11010492 117 + 22036055
GCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUGGGAAGCUGUAGCUGCAUCUACAGAUCGUUGCAUCCGAAACUCUGUGCAUCUGUUG
((....(((((((.....))))))).((((((.((..((.((......))))((((.....)))).)).))))))))....(((((....(((((..........)))))))))).. ( -34.30, z-score =  -1.42, R)
>consensus
GCUGUCGUGUAUCUAUUAGAUACAUUAGCUGCCGCAUGCCGCCAACUUGCGCUCCCUUCUUGGGAAGCUGUAGCUGCAUCUACAGAUCGUUGCAUCCGAAACUCUGUGCAU_UGU__
.((((.(((((((.....)))))))(((((((.(((...........)))((((((.....))).))).))))))).....))))................................ (-26.58 = -26.66 +   0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,209,321 – 11,209,436
Length 115
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 87.56
Shannon entropy 0.21882
G+C content 0.50307
Mean single sequence MFE -34.96
Consensus MFE -30.92
Energy contribution -30.68
Covariance contribution -0.24
Combinations/Pair 1.10
Mean z-score -1.58
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.94
SVM RNA-class probability 0.856590
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11209321 115 - 23011544
--ACAAAUGCACAGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAAAAGGGAGCGCAAGUUGGUGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGC
--.....((((((((...(((.......))))))))...(((((((((....((((.....))))((....))..))))).)))))))(((..((((((.....))))))....))) ( -35.10, z-score =  -1.61, R)
>droEre2.scaffold_4929 12407311 96 + 26641161
--------------------GGAUGCAGCGAUCUGUGGAUGCAGCCGCAGCUUCC-AAAAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGC
--------------------............((((.(..((.((((((((((((-.....))))))((......))....)))))).))...((((((.....))))))).)))). ( -35.30, z-score =  -1.91, R)
>droYak2.chr2L 7607494 109 - 22324452
--------ACAGAGAGUUUCGGUUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCAAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGC
--------.............((((.....(((((((((((((......((((((......))))))...(((((.((.....)).)))))..))))))).))))))...))))... ( -34.10, z-score =  -1.61, R)
>droSec1.super_3 6609855 117 - 7220098
CAACAGAUGCACAAAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGC
....(((((((...(((((((.((((..(.(((....))).(((((...((((((......))))))...))))))..)))).))).))))..)))))))................. ( -34.60, z-score =  -1.31, R)
>droSim1.chr2L 11010492 117 - 22036055
CAACAGAUGCACAGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGC
....(((((((...(((((((.((((..(.(((....))).(((((...((((((......))))))...))))))..)))).))).))))..)))))))................. ( -35.70, z-score =  -1.46, R)
>consensus
__ACA_AUGCACAGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCGGCAUGCGGCAGCUAAUGUAUCUAAUAGAUACACGACAGC
..................(((..(((.......(((((......)))))((((((......)))))))))(((((.((.....)).)))))..((((((.....))))))))).... (-30.92 = -30.68 +  -0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,209,360 – 11,209,461
Length 101
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 82.18
Shannon entropy 0.30414
G+C content 0.53325
Mean single sequence MFE -26.33
Consensus MFE -21.00
Energy contribution -20.36
Covariance contribution -0.64
Combinations/Pair 1.14
Mean z-score -1.24
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.27
SVM RNA-class probability 0.622474
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 11209360 101 - 23011544
---GCACCACCAAACAU--CCCAACGAUCC--ACAAAUGCACAGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAAAAGGGAGCGCAAGUUGGUG
---....((((((..((--((.(((.....--.............)))..))))((.......(((((......)))))((((((......))))))))...)))))) ( -25.17, z-score =  -1.00, R)
>droEre2.scaffold_4929 12407350 81 + 26641161
---GCACCACCGAACAU--CCCAACGA---------------------UCGGAUGCAGCGAUCUGUGGAUGCAGCCGCAGCUUCCAAA-AAGGGAGCGCAAGUUGGCG
---(((((((((..(((--((......---------------------..)))))...))....)))).))).(((((.((((((...-..)))))))).....))). ( -29.10, z-score =  -1.75, R)
>droYak2.chr2L 7607533 98 - 22324452
GCACCACCACCAAACAU--CCCAACGAUCC--------ACAGAGAGUUUCGGUUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCAAAGAAGGGAGCGCAAGUUGGCG
((...............--.......(((.--------(((((..(((........)))..))))).))).(((((...((((((......))))))...))))))). ( -26.70, z-score =  -1.60, R)
>droSec1.super_3 6609894 105 - 7220098
---GCACCACCAAACAUCACCAAACGAUCCCAACAGAUGCACAAAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCG
---..........................(((((...(((....((((.((..((((......))))..)).))))...((((((......))))))))).))))).. ( -24.20, z-score =  -0.65, R)
>droSim1.chr2L 11010531 105 - 22036055
---GCACCACCAAACAUCACCAAACGAUCCCAACAGAUGCACAGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCG
---((.........((((........(((......)))..(((((...(((.......)))))))).))))(((((...((((((......))))))...))))))). ( -26.50, z-score =  -1.18, R)
>consensus
___GCACCACCAAACAU__CCCAACGAUCC__ACA_AUGCACAGAGUUUCGGAUGCAACGAUCUGUAGAUGCAGCUACAGCUUCCCAAGAAGGGAGCGCAAGUUGGCG
.........((((...........(((.....................)))..(((.......(((((......)))))((((((......)))))))))..)))).. (-21.00 = -20.36 +  -0.64)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:31:51 2011