Locus 4467

Sequence ID dm3.chr2R
Location 13,243,279 – 13,243,371
Length 92
Max. P 0.816399
window6116 window6117

overview

Window 6

Location 13,243,279 – 13,243,371
Length 92
Sequences 12
Columns 117
Reading direction forward
Mean pairwise identity 81.93
Shannon entropy 0.36930
G+C content 0.37986
Mean single sequence MFE -22.76
Consensus MFE -9.83
Energy contribution -11.17
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -2.52
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.60
SVM RNA-class probability 0.756282
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13243279 92 + 21146708
---------------------GUUGAAGCU-CACAUAAAACACGCCAUAAAUGUUGAUUUUCGUU-AGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCUG-
---------------------......(((-((........((((.(((((((((((((((.(..-...).)))))))))))))))......))))........))))-)......- ( -22.19, z-score =  -3.05, R)
>droSim1.chr2R 11977231 92 + 19596830
---------------------GUUGAAGCU-CACAUAAAACACGCCAUAAAUGUUGAUUUUCGUU-GGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((-((........((((.(((((((((((((((.(..-...).)))))))))))))))......))))........))))-)......- ( -22.19, z-score =  -2.70, R)
>droSec1.super_1 10744258 92 + 14215200
---------------------GUUGAAGCU-CACAUAAAACACGCCAUAAAUGUUGAUUUUCGUU-GGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((-((........((((.(((((((((((((((.(..-...).)))))))))))))))......))))........))))-)......- ( -22.19, z-score =  -2.70, R)
>droYak2.chr2R 2911233 92 - 21139217
---------------------GUUGAAGCU-CACAUAAAACACGCCAUAAAUGUUGAUUUUCGUU-GGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((-((........((((.(((((((((((((((.(..-...).)))))))))))))))......))))........))))-)......- ( -22.19, z-score =  -2.70, R)
>droEre2.scaffold_4845 9979122 92 - 22589142
---------------------GUUGAAGCU-CACAUAAAACACGCCAUAAAUGUUGAUUUUCGUU-GGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((-((........((((.(((((((((((((((.(..-...).)))))))))))))))......))))........))))-)......- ( -22.19, z-score =  -2.70, R)
>droAna3.scaffold_13266 6499079 92 - 19884421
---------------------GUUGAAGCU-CACAUAAAACACGCCAUAAAUGUUGAUUUUCGUC-GGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((-((........((((.(((((((((((((((.(..-...).)))))))))))))))......))))........))))-)......- ( -22.19, z-score =  -2.84, R)
>dp4.Unknown_group_205 12141 94 + 12543
---------------------GUUGAGGCU-CGCAUAAAACACGCCAUAAAUGUUGAUUUUCGUUCGGGCCAAAAUUAACAUUUAUUAUAACGCGUUAAAACCUUGAG-CACGCAGC
---------------------((((..(((-((........((((.(((((((((((((((.((....)).)))))))))))))))......))))........))))-)...)))) ( -25.59, z-score =  -2.63, R)
>droWil1.scaffold_181009 3060987 115 - 3585778
GUUGUAGCUGCUGCCCCGCCAUAUAUACAUAUAUAUAAAAUACGCCAUAAAUGUUGAUUUUCGUUGGGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
((((((((.((......)).((((((....)))))).......)).(((((((((((((((.((....)).)))))))))))))))))))))((((............-.))))..- ( -25.32, z-score =  -1.04, R)
>droVir3.scaffold_12875 7964004 92 + 20611582
---------------------GUUGAAGCUGCACAUAAAACACGCCAUAAAUGUUGAUUUUCGUUGGGG--AAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((((.((......((((.((((((((((((((((......)--)))))))))))))))......))))........)).)-)).))..- ( -24.04, z-score =  -2.95, R)
>droMoj3.scaffold_6496 7556764 92 - 26866924
---------------------GUUGAAGCUGCACAUAAAACACGCCAUAAAUGUUGAUUUUCGUUGGGG--AAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((((.((......((((.((((((((((((((((......)--)))))))))))))))......))))........)).)-)).))..- ( -24.04, z-score =  -2.95, R)
>droGri2.scaffold_15245 1460327 92 + 18325388
---------------------GUUGAAGCUGCGCAUAAAACACGCCAUAAAUGUUGAUUUUCGUUGGGG--AAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG-CACGCAG-
---------------------......(((((.((......((((.((((((((((((((((......)--)))))))))))))))......))))........)).)-)).))..- ( -24.54, z-score =  -2.56, R)
>anoGam1.chr3R 49087193 88 + 53272125
-----------------------------GAGAGGGCGAGAAAGCGAGAAAGGUAAAGAAUGUUUCGUUUGAAGGCGAAAGCAAGCGAAAAUGGUGUAAAGCAUAGAGACACACUGU
-----------------------------......((......))...........((..((((((.((((...((....))...))))....(((.....))).))))))..)).. ( -16.50, z-score =  -1.42, R)
>consensus
_____________________GUUGAAGCU_CACAUAAAACACGCCAUAAAUGUUGAUUUUCGUU_GGGCCAAAAUUAACAUUUAUUACAACGCGUUAAAACUUUGAG_CACGCAG_
..............................................(((((((((((((((..........)))))))))))))))......((((..............))))... ( -9.83 = -11.17 +   1.33)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,243,279 – 13,243,371
Length 92
Sequences 12
Columns 117
Reading direction reverse
Mean pairwise identity 81.93
Shannon entropy 0.36930
G+C content 0.37986
Mean single sequence MFE -23.98
Consensus MFE -11.65
Energy contribution -12.57
Covariance contribution 0.92
Combinations/Pair 1.23
Mean z-score -2.35
Structure conservation index 0.49
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.816399
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 13243279 92 - 21146708
-CAGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCU-AACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUG-AGCUUCAAC---------------------
-......(-((((.......(((((((....(((((((((.(((((.(...-..).))))).))))))))).))))))).....))-)))......--------------------- ( -25.30, z-score =  -2.71, R)
>droSim1.chr2R 11977231 92 - 19596830
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCC-AACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUG-AGCUUCAAC---------------------
-......(-((((.......(((((((....(((((((((.(((((.(...-..).))))).))))))))).))))))).....))-)))......--------------------- ( -25.30, z-score =  -2.62, R)
>droSec1.super_1 10744258 92 - 14215200
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCC-AACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUG-AGCUUCAAC---------------------
-......(-((((.......(((((((....(((((((((.(((((.(...-..).))))).))))))))).))))))).....))-)))......--------------------- ( -25.30, z-score =  -2.62, R)
>droYak2.chr2R 2911233 92 + 21139217
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCC-AACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUG-AGCUUCAAC---------------------
-......(-((((.......(((((((....(((((((((.(((((.(...-..).))))).))))))))).))))))).....))-)))......--------------------- ( -25.30, z-score =  -2.62, R)
>droEre2.scaffold_4845 9979122 92 + 22589142
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCC-AACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUG-AGCUUCAAC---------------------
-......(-((((.......(((((((....(((((((((.(((((.(...-..).))))).))))))))).))))))).....))-)))......--------------------- ( -25.30, z-score =  -2.62, R)
>droAna3.scaffold_13266 6499079 92 + 19884421
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCC-GACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUG-AGCUUCAAC---------------------
-......(-((((.......(((((((....(((((((((.(((((.(...-..).))))).))))))))).))))))).....))-)))......--------------------- ( -25.30, z-score =  -2.40, R)
>dp4.Unknown_group_205 12141 94 - 12543
GCUGCGUG-CUCAAGGUUUUAACGCGUUAUAAUAAAUGUUAAUUUUGGCCCGAACGAAAAUCAACAUUUAUGGCGUGUUUUAUGCG-AGCCUCAAC---------------------
..((.(.(-(((...((...((((((((((((...(((((.(((((.(......).))))).)))))))))))))))))....)))-)))).))..--------------------- ( -24.10, z-score =  -1.32, R)
>droWil1.scaffold_181009 3060987 115 + 3585778
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCCCAACGAAAAUCAACAUUUAUGGCGUAUUUUAUAUAUAUGUAUAUAUGGCGGGGCAGCAGCUACAAC
-((((.((-(((...((....)).(((..(((((((((((.(((((.(......).))))).))))))))).((((((.......))))))...))..))))))))))))....... ( -30.50, z-score =  -1.57, R)
>droVir3.scaffold_12875 7964004 92 - 20611582
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUU--CCCCAACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUGCAGCUUCAAC---------------------
-..((.((-(.((.......(((((((....(((((((((.(((((--(......)))))).))))))))).)))))))...)).)))))......--------------------- ( -24.40, z-score =  -3.06, R)
>droMoj3.scaffold_6496 7556764 92 + 26866924
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUU--CCCCAACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUGCAGCUUCAAC---------------------
-..((.((-(.((.......(((((((....(((((((((.(((((--(......)))))).))))))))).)))))))...)).)))))......--------------------- ( -24.40, z-score =  -3.06, R)
>droGri2.scaffold_15245 1460327 92 - 18325388
-CUGCGUG-CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUU--CCCCAACGAAAAUCAACAUUUAUGGCGUGUUUUAUGCGCAGCUUCAAC---------------------
-(((((((-(.....))...(((((((....(((((((((.(((((--(......)))))).))))))))).)))))))....)))))).......--------------------- ( -25.70, z-score =  -3.32, R)
>anoGam1.chr3R 49087193 88 - 53272125
ACAGUGUGUCUCUAUGCUUUACACCAUUUUCGCUUGCUUUCGCCUUCAAACGAAACAUUCUUUACCUUUCUCGCUUUCUCGCCCUCUC-----------------------------
...(((((...........))))).......(..((.(((((........)))))))..)............((......))......----------------------------- (  -6.80, z-score =  -0.33, R)
>consensus
_CUGCGUG_CUCAAAGUUUUAACGCGUUGUAAUAAAUGUUAAUUUUGGCCC_AACGAAAAUCAACAUUUAUGGCGUGUUUUAUGUG_AGCUUCAAC_____________________
...(((((............(((((((....(((((((((.(((((..........))))).))))))))).))))))).)))))................................ (-11.65 = -12.57 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:29:41 2011