Locus 8315

Sequence ID dm3.chr3L
Location 21,954,927 – 21,955,075
Length 148
Max. P 0.671800
window11423 window11424

overview

Window 3

Location 21,954,927 – 21,955,035
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.67
Shannon entropy 0.19687
G+C content 0.34962
Mean single sequence MFE -24.90
Consensus MFE -18.77
Energy contribution -19.10
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.94
Structure conservation index 0.75
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.39
SVM RNA-class probability 0.671800
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21954927 108 + 24543557
UAGGACUUCAUAUUAAUUCAGUUUAGCCAUGAAUAAUGACACCAGUGUAAUCUGUUCAUGACGA------------ACUGCGUAAAUGUUCCGAUCAUUUAACUGAUCAAACAUACUUUA
..(((....(((((.((.((((((.(.((((((((...(((....)))....)))))))).)))------------)))).)).))))))))(((((......)))))............ ( -24.90, z-score =  -2.64, R)
>droSec1.super_11 1880391 116 + 2888827
-UAGACUUCAUAUUAAUUCCGUUCAGCCAUGAAU---GACACCAGUGUAAUCUGUUCAUGGCGAGAAGCACUUCAAACUGUGUAAAUGUAACGAUCAUUUAACUGAUCAAACACACUUUA
-...................((((((((((((((---.(((....))).....))))))))).....((((........))))...)).)))(((((......)))))............ ( -24.90, z-score =  -1.55, R)
>droSim1.chr3L 21294398 116 + 22553184
-UAGACUUCAUAUUAAUUCCGUUCAGCCAUGAAU---GACACCAGUGUAAUCUGUUCAUGGCGAGAAGCACUUUAAACUGUGUAAAUGUAACGAUCAUUUAACUGAUCAAACACACUUUA
-...................((((((((((((((---.(((....))).....))))))))).....((((........))))...)).)))(((((......)))))............ ( -24.90, z-score =  -1.64, R)
>consensus
_UAGACUUCAUAUUAAUUCCGUUCAGCCAUGAAU___GACACCAGUGUAAUCUGUUCAUGGCGAGAAGCACUU_AAACUGUGUAAAUGUAACGAUCAUUUAACUGAUCAAACACACUUUA
....................(((..(((((((((....(((....))).....)))))))))..............................(((((......))))).)))........ (-18.77 = -19.10 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,954,967 – 21,955,075
Length 108
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 83.19
Shannon entropy 0.27939
G+C content 0.37347
Mean single sequence MFE -30.06
Consensus MFE -21.44
Energy contribution -21.00
Covariance contribution -0.44
Combinations/Pair 1.19
Mean z-score -1.60
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.10
SVM RNA-class probability 0.544095
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 21954967 108 - 24543557
GGUGGGCUACUCGAGUUGACUACAAACAUUGAAUUGUUUGUAAAGUAUGUUUGAUCAGUUAAAUGAUCGGAACAUUUACGCAGU------------UCGUCAUGAACAGAUUACACUGGU
((((.((.............((((((((......))))))))..(((((((((((((......))))).)))))..))))).((------------((.....))))......))))... ( -25.90, z-score =  -0.89, R)
>droYak2.chr3L 22278342 118 - 24197627
GGUGGGCUACUCGAGCUUACUAC-AACAUUGAAUUGUUUGUGAAGUAUGUUUGAUCAGUUCAAUGAUCAUUACAUGCACGACCUUUUAAAUGUUUUUCGCCAUGAACAGAAAUAAUAUG-
((((((((.....))))))))..-.........(((((..((..((((((.((((((......))))))..)))))).(((...............))).))..)))))..........- ( -29.26, z-score =  -2.02, R)
>droSec1.super_11 1880427 120 - 2888827
GGUGGGCUACUCGAGUUCACUACAAACAUUGAAUUGUUUGUAAAGUGUGUUUGAUCAGUUAAAUGAUCGUUACAUUUACACAGUUUGAAGUGCUUCUCGCCAUGAACAGAUUACACUGGU
((((((.((((((((.....((((((((......))))))))(((((((..((((((......)))))).)))))))......)))).))))...)))))).....(((......))).. ( -32.60, z-score =  -1.59, R)
>droSim1.chr3L 21294434 120 - 22553184
GGUGGGCUACUCGAGUUCACUACAAACAUUGAAUUGUUUGUAAAGUGUGUUUGAUCAGUUAAAUGAUCGUUACAUUUACACAGUUUAAAGUGCUUCUCGCCAUGAACAGAUUACACUGGU
.(((((((.....)))))))((((((((......))))))))(((((((..((((((......)))))).)))))))...((((.(((..((.(((.......)))))..))).)))).. ( -32.50, z-score =  -1.91, R)
>consensus
GGUGGGCUACUCGAGUUCACUACAAACAUUGAAUUGUUUGUAAAGUAUGUUUGAUCAGUUAAAUGAUCGUUACAUUUACACAGUUU_AAGUGCUUCUCGCCAUGAACAGAUUACACUGGU
.(((((((.....)))))))((((((((......))))))))..((((((.((((((......))))))..))))..))......................................... (-21.44 = -21.00 +  -0.44)

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 23:43:21 2011