Locus 4357

Sequence ID dm3.chr2R
Location 12,441,272 – 12,441,367
Length 95
Max. P 0.996694
window5974 window5975

overview

Window 4

Location 12,441,272 – 12,441,363
Length 91
Sequences 8
Columns 95
Reading direction reverse
Mean pairwise identity 87.22
Shannon entropy 0.24588
G+C content 0.38411
Mean single sequence MFE -20.45
Consensus MFE -16.00
Energy contribution -15.44
Covariance contribution -0.56
Combinations/Pair 1.11
Mean z-score -2.17
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.37
SVM RNA-class probability 0.932792
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12441272 91 - 21146708
--AUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGACGUUG
--.((((((((((..-..))))))))))....(((....((-...(((....(((.((....)).)))...)))...))......)))....... ( -19.20, z-score =  -1.98, R)
>droPer1.super_2 5146628 82 + 9036312
--AUGUUUUCCAUUAGGAGUGGAAAACAAAUAUGCAACCGGAAAACCAUGAUAUGAGUGAAAACACAUUGAAGUGGGCCCCCCG-----------
--.((((((((((.....))))))))))..........(((....((((...(((.((....)).)))....)))).....)))----------- ( -22.80, z-score =  -2.55, R)
>dp4.chr3 16076140 82 + 19779522
--AUGUUUUCCAUUAGGAGUGGAAAACAAAUAUGCAACCGGAAAACCAUGAUAUGAGUGAAAACACAUUGAAGUGGGCCCCCCG-----------
--.((((((((((.....))))))))))..........(((....((((...(((.((....)).)))....)))).....)))----------- ( -22.80, z-score =  -2.55, R)
>droAna3.scaffold_13266 15810044 94 - 19884421
AUAUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGGAAAAACCAAAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCUGGUGUUU
...((((((((((..-..))))))))))...((((((.((((...((((....)).)).....(((((....))))).....)))).)))))).. ( -19.90, z-score =  -1.74, R)
>droEre2.scaffold_4845 9168911 91 + 22589142
--AUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGACGUUG
--.((((((((((..-..))))))))))....(((....((-...(((....(((.((....)).)))...)))...))......)))....... ( -19.20, z-score =  -1.98, R)
>droYak2.chr2R 4594862 91 + 21139217
--AUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGACGUUG
--.((((((((((..-..))))))))))....(((....((-...(((....(((.((....)).)))...)))...))......)))....... ( -19.20, z-score =  -1.98, R)
>droSim1.chr2R 11174956 91 - 19596830
--AUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGACGUUG
--.((((((((((..-..))))))))))....(((....((-...(((....(((.((....)).)))...)))...))......)))....... ( -19.20, z-score =  -1.98, R)
>droSec1.super_1 9939451 91 - 14215200
--AUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCACACGUUG
--.((((((((((..-..)))))))))).............-..(((.....(((.((....)).)))....((((((.......))))))))). ( -21.30, z-score =  -2.56, R)
>consensus
__AUGUUUUCCAUUA_AAGUGGAAAAUAAAUAUGCUACCGG_AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGACGUUG
...((((((((((.....))))))))))...........((....((.....(((.((....)).)))......))...)).............. (-16.00 = -15.44 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,441,276 – 12,441,367
Length 91
Sequences 8
Columns 97
Reading direction reverse
Mean pairwise identity 88.53
Shannon entropy 0.21914
G+C content 0.38150
Mean single sequence MFE -23.16
Consensus MFE -19.86
Energy contribution -19.43
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -3.19
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.97
SVM RNA-class probability 0.996694
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 12441276 91 - 21146708
----GCAUAUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGAC
----(((((((((((((((..-..)))))))))..))))))....((-...(((....(((.((....)).)))...)))...))............ ( -21.80, z-score =  -2.99, R)
>droPer1.super_2 5146631 83 + 9036312
----GCAUAUGUUUUCCAUUAGGAGUGGAAAACAAAUAUGCAACCGGAAAACCAUGAUAUGAGUGAAAACACAUUGAAGUGGGCCCC----------
----(((((((((((((((.....))))))))))..)))))....((....((((...(((.((....)).)))....)))).))..---------- ( -27.10, z-score =  -4.25, R)
>dp4.chr3 16076143 83 + 19779522
----GCAUAUGUUUUCCAUUAGGAGUGGAAAACAAAUAUGCAACCGGAAAACCAUGAUAUGAGUGAAAACACAUUGAAGUGGGCCCC----------
----(((((((((((((((.....))))))))))..)))))....((....((((...(((.((....)).)))....)))).))..---------- ( -27.10, z-score =  -4.25, R)
>droAna3.scaffold_13266 15810048 96 - 19884421
ACAUCCAUAUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGGAAAAACCAAAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCUGGU
.((..((((((((((((((..-..)))))))))............((.....))..)))))..))....(((((....)))))..(((.....))). ( -20.00, z-score =  -1.50, R)
>droEre2.scaffold_4845 9168915 91 + 22589142
----GCAUAUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGAC
----(((((((((((((((..-..)))))))))..))))))....((-...(((....(((.((....)).)))...)))...))............ ( -21.80, z-score =  -2.99, R)
>droYak2.chr2R 4594866 91 + 21139217
----GCAUAUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGAC
----(((((((((((((((..-..)))))))))..))))))....((-...(((....(((.((....)).)))...)))...))............ ( -21.80, z-score =  -2.99, R)
>droSim1.chr2R 11174960 91 - 19596830
----GCAUAUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGAC
----(((((((((((((((..-..)))))))))..))))))....((-...(((....(((.((....)).)))...)))...))............ ( -21.80, z-score =  -2.99, R)
>droSec1.super_1 9939455 91 - 14215200
----GCAUAUGUUUUCCAUUA-AAGUGGAAAAUAAAUAUGCUACCGG-AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCACAC
----(((((((((((((((..-..)))))))))..))))))......-..........(((.((....)).)))....((((((.......)))))) ( -23.90, z-score =  -3.59, R)
>consensus
____GCAUAUGUUUUCCAUUA_AAGUGGAAAAUAAAUAUGCUACCGG_AAAACUAGAUAUGAGUGAAAACACAUUGAAGUGUGCCCCAUCUGCAGAC
....(((((((((((((((.....))))))))))..)))))....((....((.....(((.((....)).)))......))...)).......... (-19.86 = -19.43 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:27:39 2011