Locus 13643

Sequence ID dm3.chrX
Location 8,082,902 – 8,083,046
Length 144
Max. P 0.890252
window18775 window18776

overview

Window 5

Location 8,082,902 – 8,083,046
Length 144
Sequences 3
Columns 144
Reading direction forward
Mean pairwise identity 75.06
Shannon entropy 0.32348
G+C content 0.34871
Mean single sequence MFE -34.27
Consensus MFE -16.98
Energy contribution -16.43
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -2.35
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.684435
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8082902 144 + 22422827
GUUGCAUGGUAAACAAAAGUUGGGAUCAUAAUAGUAAUGGUGACCGAGAAGCGUUUACCAAAAUACAUGUGUGUGCUUUCAAAUGUUGCUGCAACUAAAAAGUACAUUUCGAGUGCCUAAAAGUAAAGCAGCAAACAACAAAUG
(((((.((((((((.....((((.(((((.......)))))..)))).....))))))))...(((...((.(..(((..((((((.(((..........))))))))).)))..).))...)))..)))))............ ( -34.20, z-score =  -1.20, R)
>droSec1.super_44 165980 116 + 251150
GUUGCAUGGUAAACAAAAGUUGGGAUCAUAAUAGUAGUAAUGUU---GCAGCGUUUACCAAAAUGCAUGUGUGU-UUU-UAAAUGUUACUGCAACUAAGAAAUUAGUUGCUGCAAC--AAAUG---------------------
((((((((((((((....((((.((.(((.((....)).)))))---.))))))))))))((((((....))))-)).-...........((((((((....))))))))))))))--.....--------------------- ( -34.30, z-score =  -2.92, R)
>droSim1.chrX 6443666 117 + 17042790
GUUGCAUGGUAAACAAAAGUUGGGAUCAUAAUAGUAGUAAUGUU---GCAGCGUUUACCAAAAUGCAUGUGUGU-UUUCUAAAUGUUACUGCAACUAAGAAAUUAGUUGCUGCAAC--AAAUG---------------------
((((((((((((((....((((.((.(((.((....)).)))))---.))))))))))))((((((....))))-)).............((((((((....))))))))))))))--.....--------------------- ( -34.30, z-score =  -2.93, R)
>consensus
GUUGCAUGGUAAACAAAAGUUGGGAUCAUAAUAGUAGUAAUGUU___GCAGCGUUUACCAAAAUGCAUGUGUGU_UUU_UAAAUGUUACUGCAACUAAGAAAUUAGUUGCUGCAAC__AAAUG_____________________
((((((((((((((....((((....(((.((....)).)))......))))))))))))....((((.((........)).))))...))))))................................................. (-16.98 = -16.43 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,082,902 – 8,083,046
Length 144
Sequences 3
Columns 144
Reading direction reverse
Mean pairwise identity 75.06
Shannon entropy 0.32348
G+C content 0.34871
Mean single sequence MFE -27.25
Consensus MFE -17.65
Energy contribution -18.99
Covariance contribution 1.34
Combinations/Pair 1.12
Mean z-score -2.13
Structure conservation index 0.65
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.09
SVM RNA-class probability 0.890252
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 8082902 144 - 22422827
CAUUUGUUGUUUGCUGCUUUACUUUUAGGCACUCGAAAUGUACUUUUUAGUUGCAGCAACAUUUGAAAGCACACACAUGUAUUUUGGUAAACGCUUCUCGGUCACCAUUACUAUUAUGAUCCCAACUUUUGUUUACCAUGCAAC
.....(((((.((((((...(((...(((.((.......)).)))...))).))))))((((.((........)).))))....(((((((((......(((((..((....))..)))))........))))))))).))))) ( -29.34, z-score =  -1.02, R)
>droSec1.super_44 165980 116 - 251150
---------------------CAUUU--GUUGCAGCAACUAAUUUCUUAGUUGCAGUAACAUUUA-AAA-ACACACAUGCAUUUUGGUAAACGCUGC---AACAUUACUACUAUUAUGAUCCCAACUUUUGUUUACCAUGCAAC
---------------------....(--(((((.((((((((....)))))))).))))))....-...-.......((((...(((((((((....---.............................))))))))))))).. ( -26.21, z-score =  -2.82, R)
>droSim1.chrX 6443666 117 - 17042790
---------------------CAUUU--GUUGCAGCAACUAAUUUCUUAGUUGCAGUAACAUUUAGAAA-ACACACAUGCAUUUUGGUAAACGCUGC---AACAUUACUACUAUUAUGAUCCCAACUUUUGUUUACCAUGCAAC
---------------------....(--(((((.((((((((....)))))))).))))))........-.......((((...(((((((((....---.............................))))))))))))).. ( -26.21, z-score =  -2.56, R)
>consensus
_____________________CAUUU__GUUGCAGCAACUAAUUUCUUAGUUGCAGUAACAUUUA_AAA_ACACACAUGCAUUUUGGUAAACGCUGC___AACAUUACUACUAUUAUGAUCCCAACUUUUGUUUACCAUGCAAC
............................(((((.((((((((....)))))))).))))).................((((...(((((((((....................................))))))))))))).. (-17.65 = -18.99 +   1.34)

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 01:25:09 2011