Locus 11375

Sequence ID dm3.chr3R
Location 20,740,555 – 20,740,635
Length 80
Max. P 0.915654
window15635 window15636

overview

Window 5

Location 20,740,555 – 20,740,635
Length 80
Sequences 12
Columns 84
Reading direction forward
Mean pairwise identity 91.01
Shannon entropy 0.19434
G+C content 0.57902
Mean single sequence MFE -29.79
Consensus MFE -29.23
Energy contribution -28.88
Covariance contribution -0.36
Combinations/Pair 1.24
Mean z-score -1.32
Structure conservation index 0.98
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.25
SVM RNA-class probability 0.915654
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20740555 80 + 27905053
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACCGAUAA---
((((((((........((((......(((((..-.....))))).))))((((.......)))))))))))).........--- ( -29.70, z-score =  -0.80, R)
>droAna3.scaffold_12916 5993929 75 - 16180835
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUG--------
((((((((........((((......(((((..-.....))))).))))((((.......))))))))))))....-------- ( -29.70, z-score =  -1.54, R)
>droEre2.scaffold_4820 3161050 80 - 10470090
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGACGUAAAG---
((((((((........((((......(((((..-.....))))).))))((((.......)))))))))))).........--- ( -29.70, z-score =  -1.35, R)
>droYak2.chr3R 3077535 80 - 28832112
UUCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAC-GAUAAA--
.((((((((.((.......)).))))(((.(((-(.....)))).(((.((((.......)))))))))))))).-......-- ( -27.90, z-score =  -0.72, R)
>droSec1.super_0 21088444 76 + 21120651
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCCCCCCGUCACGCGGGAGAUCGGGGUUCAAUUCCUUGUCGGGGAUACA--------
.((.(.........).))...((((((((..((((.....)))).(((.((((......)))).))))))))))).-------- ( -29.00, z-score =  -1.49, R)
>droSim1.chr3R 20575603 76 + 27517382
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUGU-------
((((((((........((((......(((((..-.....))))).))))((((.......)))))))))))).....------- ( -29.70, z-score =  -1.36, R)
>droPer1.super_5 1386587 79 - 6813705
UCCUCGAUAGUAUAGUGGUCAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAUGGAAA----
((((((((........((((......(((((..-.....))))).))))((((.......))))))))))))........---- ( -31.50, z-score =  -1.31, R)
>dp4.chr4_group5 1451821 72 - 2436548
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAG-----------
((((((((........((((......(((((..-.....))))).))))((((.......)))))))))))).----------- ( -29.70, z-score =  -1.83, R)
>droVir3.scaffold_12963 14518248 74 - 20206255
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAG---------
((((((((........((((......(((((..-.....))))).))))((((.......))))))))))))...--------- ( -29.70, z-score =  -1.65, R)
>droMoj3.scaffold_6500 7169186 74 - 32352404
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAU---------
((((((((........((((......(((((..-.....))))).))))((((.......))))))))))))...--------- ( -29.70, z-score =  -1.51, R)
>droGri2.scaffold_15252 7753518 74 + 17193109
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAC---------
((((((((........((((......(((((..-.....))))).))))((((.......))))))))))))...--------- ( -29.70, z-score =  -1.47, R)
>anoGam1.chr3L 4285096 81 + 41284009
UCCUCGAUAGUAUAGUGGUCAGUAUCCCCGCCU-GUCACGCGGGAGACCGGGGUUCGAUUCCCCGUCGGGGAG--GGAAAUUAA
((((((((........((((......(((((..-.....))))).))))((((.......)))))))))))).--......... ( -31.50, z-score =  -0.77, R)
>consensus
UCCUCGAUAGUAUAGUGGUUAGUAUCCCCGCCU_GUCACGCGGGAGACCGGGGUUCAAUUCCCCGUCGGGGAGAC_________
((((((((........((((......(((((........))))).))))((((.......))))))))))))............ (-29.23 = -28.88 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 20,740,555 – 20,740,635
Length 80
Sequences 12
Columns 84
Reading direction reverse
Mean pairwise identity 91.01
Shannon entropy 0.19434
G+C content 0.57902
Mean single sequence MFE -26.82
Consensus MFE -25.11
Energy contribution -25.37
Covariance contribution 0.26
Combinations/Pair 1.05
Mean z-score -0.87
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.13
SVM RNA-class probability 0.557089
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20740555 80 - 27905053
---UUAUCGGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
---.........(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -0.05, R)
>droAna3.scaffold_12916 5993929 75 + 16180835
--------CAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
--------....(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -1.18, R)
>droEre2.scaffold_4820 3161050 80 + 10470090
---CUUUACGUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
---.........(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -0.70, R)
>droYak2.chr3R 3077535 80 + 28832112
--UUUAUC-GUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGAA
--......-((.((((((.(((((.......)))))(((........)))-...)))))).))..................... ( -25.40, z-score =  -0.64, R)
>droSec1.super_0 21088444 76 - 21120651
--------UGUAUCCCCGACAAGGAAUUGAACCCCGAUCUCCCGCGUGACGGGGGGGGGAUACUAACCACUAUACUAUCGAGGA
--------.((((((((..(((....)))..(((((.((........))))))).))))))))..................... ( -26.60, z-score =  -0.87, R)
>droSim1.chr3R 20575603 76 - 27517382
-------ACAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
-------.....(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -1.15, R)
>droPer1.super_5 1386587 79 + 6813705
----UUUCCAUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUGACCACUAUACUAUCGAGGA
----........(((.(((.((((.......))))((((((((((.....-..)))))).....)))).........))).))) ( -27.60, z-score =  -0.82, R)
>dp4.chr4_group5 1451821 72 + 2436548
-----------CUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
-----------.(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -1.30, R)
>droVir3.scaffold_12963 14518248 74 + 20206255
---------CUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
---------...(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -1.14, R)
>droMoj3.scaffold_6500 7169186 74 + 32352404
---------AUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
---------...(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -1.10, R)
>droGri2.scaffold_15252 7753518 74 - 17193109
---------GUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
---------...(((.((((((((.......)))))(((.(((((.....-..))))))))................))).))) ( -26.80, z-score =  -0.88, R)
>anoGam1.chr3L 4285096 81 - 41284009
UUAAUUUCC--CUCCCCGACGGGGAAUCGAACCCCGGUCUCCCGCGUGAC-AGGCGGGGAUACUGACCACUAUACUAUCGAGGA
........(--(((......((((.......))))((((((((((.....-..)))))).....))))...........)))). ( -27.80, z-score =  -0.57, R)
>consensus
_________GUCUCCCCGACGGGGAAUUGAACCCCGGUCUCCCGCGUGAC_AGGCGGGGAUACUAACCACUAUACUAUCGAGGA
............(((.((((((((.......)))))(((.(((((........))))))))................))).))) (-25.11 = -25.37 +   0.26)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:41:46 2011