Locus 2652

Sequence ID dm3.chr2L
Location 20,719,297 – 20,719,404
Length 107
Max. P 0.946384
window3636 window3637

overview

Window 6

Location 20,719,297 – 20,719,388
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 72.73
Shannon entropy 0.42741
G+C content 0.49929
Mean single sequence MFE -17.23
Consensus MFE -14.00
Energy contribution -13.50
Covariance contribution -0.50
Combinations/Pair 1.25
Mean z-score -0.93
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.67
SVM RNA-class probability 0.782257
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20719297 91 - 23011544
CUUACCCAAAUCCACCACCCAUCACCACCCCAUGGAGCCGAAUGUUCUGUGUGUGACCGAGGUUCCUCCGACGUCAUAUACUCGCUUUAUA
...............................(((((((.((....)).(((((((((.(((....)))....)))))))))..))))))). ( -18.40, z-score =  -1.26, R)
>droYak2.chr2R 11302198 70 + 21139217
------------CUUGGU------CUUCCCCA-GAAAUGGAAUGUUUUGUGUGCGACUG-GGUUGCACCGACGUCAU-UAUACCCUUUAAA
------------...(((------.....(((-....)))((((..(((.(((((((..-.))))))))))...)))-)..)))....... ( -17.30, z-score =  -1.06, R)
>droSec1.super_18 638194 85 - 1342155
CUUACCCACACCCACCGC------CCACCUAAUGGAACCGAAUGUUCUGUGUGUGACCGAGGUGCCUCCGACGUCAUAUACUCACUUUAUA
..................------.........(((((.....)))))(((((((((.(((....)))....))))))))).......... ( -16.60, z-score =  -0.76, R)
>droSim1.chr2L 20332779 85 - 22036055
CUUACCCACACCCACCAC------CUACCUAAUGGAGCCGAAUGUUCUGUGUGUGACCGAGGUGCCUCCGACGUCAUAUACUCACUUUAUA
..................------.........(((((.....)))))(((((((((.(((....)))....))))))))).......... ( -16.60, z-score =  -0.62, R)
>consensus
CUUACCCACACCCACCAC______CCACCCAAUGGAACCGAAUGUUCUGUGUGUGACCGAGGUGCCUCCGACGUCAUAUACUCACUUUAUA
.................................(((((.....)))))(((((((((...((.....))...))))))))).......... (-14.00 = -13.50 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,719,307 – 20,719,404
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 71.91
Shannon entropy 0.46422
G+C content 0.56460
Mean single sequence MFE -24.38
Consensus MFE -17.45
Energy contribution -18.41
Covariance contribution 0.96
Combinations/Pair 1.17
Mean z-score -1.47
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.52
SVM RNA-class probability 0.946384
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 20719307 97 - 23011544
CACAGACCACCGGUUCCUUACCCAAAUCCACCACCCAUCACCACCCCAUGGAGCCGAAUGUUCUGUGUGUGACCGAGGUUCCUCCGACGUCAUAUAC
((((((.((.(((((((................................)))))))..)).))))))((((((.(((....)))....))))))... ( -26.05, z-score =  -2.21, R)
>droEre2.scaffold_4845 18844091 74 + 22589142
CACACCCCGCCGGUUCCUUGC----------------------CCCCCUGGAAGCGAGUGUUCUGUGUGUGACUG-GGUUGCACCGACGUCAUAUAC
.......(((((.((((....----------------------......)))).)).)))....((((((((((.-((.....)).).))))))))) ( -22.40, z-score =  -0.52, R)
>droYak2.chr2R 11302208 76 + 21139217
CACAGACCGCCGGCUACUUGGUC-------------------UUCCCCAGAAAUGGAAUGUUUUGUGUGCGACUG-GGUUGCACCGACGUCAU-UAU
...((((((.........)))))-------------------)...(((....)))((((..(((.(((((((..-.))))))))))...)))-).. ( -20.90, z-score =  -0.31, R)
>droSec1.super_18 638204 91 - 1342155
CACAGACCACCGGUUCCUUACCCACACCCACCGCCCA------CCUAAUGGAACCGAAUGUUCUGUGUGUGACCGAGGUGCCUCCGACGUCAUAUAC
((((((.((.(((((((....................------......)))))))..)).))))))((((((.(((....)))....))))))... ( -26.27, z-score =  -2.16, R)
>droSim1.chr2L 20332789 91 - 22036055
CACAGACCACCGGUUCCUUACCCACACCCACCACCUA------CCUAAUGGAGCCGAAUGUUCUGUGUGUGACCGAGGUGCCUCCGACGUCAUAUAC
((((((.((.(((((((....................------......)))))))..)).))))))((((((.(((....)))....))))))... ( -26.27, z-score =  -2.14, R)
>consensus
CACAGACCACCGGUUCCUUACCCA_A_CCACC_CC_A______CCCCAUGGAACCGAAUGUUCUGUGUGUGACCGAGGUUCCUCCGACGUCAUAUAC
((((((.((.(((((((................................)))))))..)).))))))((((((...((.....))...))))))... (-17.45 = -18.41 +   0.96)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:55:13 2011