Locus 11180

Sequence ID	dm3.chr3R
Location	19,259,740 – 19,259,872
Length	132
Max. P	0.762477

overview

Window 7

Location	19,259,740 – 19,259,815
Length	75
Sequences	5
Columns	77
Reading direction	forward
Mean pairwise identity	95.31
Shannon entropy	0.08147
G+C content	0.34212
Mean single sequence MFE	-11.23
Consensus MFE	-11.32
Energy contribution	-11.16
Covariance contribution	-0.16
Combinations/Pair	1.07
Mean z-score	-0.82
Structure conservation index	1.01
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.42
SVM RNA-class probability	0.688604
Prediction	RNA
WARNING	Out of training range. z-scores are NOT reliable.

Download alignment: ClustalW | MAF

>dm3.chr3R 19259740 75 + 27905053
ACUAAAGCCAAACA--ACAAUCGGCAAAUAAAUUAUGGCUAUGCACUAAGCGAAUAGAACUUAGAAAUUAUGGCUCC
......(((.....--......)))...........(((((((..(((((.........)))))....))))))).. ( -11.40, z-score =  -0.77, R)
>droSim1.chr3R 19077748 77 + 27517382
ACUAAAGCCAAACACAACAAUCGGCAAAUAAAUUAUGGCUAUGCACUAAGCAAAUAUAACUUAGAAAUUAUGGCUCC
......(((.............)))...........(((((((..(((((.........)))))....))))))).. ( -11.22, z-score =  -1.02, R)
>droSec1.super_0 19622634 76 + 21120651
-AUUAAGCCAAACACAACAAUCGGCAAAUAAAUUAUGGCUAUGCACUAAGCAAAUAUAACUUAGAAAUUAUGGCUCC
-.....(((.............)))...........(((((((..(((((.........)))))....))))))).. ( -11.22, z-score =  -0.85, R)
>droYak2.chr3R 20141582 77 + 28832112
ACUAAAGCCAAACACAACAAUCGGCAAAUAAAUUAUGGCUAUGCACUAAGCAAAUAUAACUUGGAAAUUAUGGCUCC
......(((.............)))...........(((((((..(((((.........)))))....))))))).. ( -10.92, z-score =  -0.49, R)
>droEre2.scaffold_4820 1680108 75 - 10470090
ACUAAAGCCAAACA--ACAAUCGGCAAAUAAAUUAUGGCUAUGCACUAAGCAAAUAUAACUUAGAAAUUAUGGCUCC
......(((.....--......)))...........(((((((..(((((.........)))))....))))))).. ( -11.40, z-score =  -0.97, R)
>consensus
ACUAAAGCCAAACACAACAAUCGGCAAAUAAAUUAUGGCUAUGCACUAAGCAAAUAUAACUUAGAAAUUAUGGCUCC
......(((.............)))...........(((((((..(((((.........)))))....))))))).. (-11.32 = -11.16 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	19,259,815 – 19,259,872
Length	57
Sequences	6
Columns	57
Reading direction	reverse
Mean pairwise identity	78.36
Shannon entropy	0.41969
G+C content	0.39059
Mean single sequence MFE	-10.32
Consensus MFE	-6.26
Energy contribution	-7.78
Covariance contribution	1.53
Combinations/Pair	1.10
Mean z-score	-1.54
Structure conservation index	0.61
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.61
SVM RNA-class probability	0.762477
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 19259815 57 - 27905053
GUAUAACAAAUGUGCGGCAAAUGAGCUGUCAUAGGUAAAUAAGGAAGACGAGAAGCU
.....((...((((((((......)))).)))).))..................... (  -8.60, z-score =  -0.60, R)
>droEre2.scaffold_4820 1680183 57 + 10470090
GUAUAACAAAUCUGCGGCAAAUGAGCUGUCGUAGGUAAAUAAGGAAGACGAGAAACC
.........((((((((((.......))))))))))..................... ( -12.10, z-score =  -2.09, R)
>droYak2.chr3R 20141659 57 - 28832112
GUAUAACAAAUCUGCGGCAAAUGAGCUGUCGUAGGUAAAUAAGGAAGACGAGAAACC
.........((((((((((.......))))))))))..................... ( -12.10, z-score =  -2.09, R)
>droSec1.super_0 19622710 57 - 21120651
UUAUAACAAAUCUGCGGCAAAUGAGCUGUCGUAGGUAAAUAAGGAAGACGAGAAACC
.........((((((((((.......))))))))))..................... ( -12.10, z-score =  -2.16, R)
>droSim1.chr3R 19077825 57 - 27517382
UUAUAACAAAUCUGCGGCAAAUGAGCUGUCGUAGGUAAAUAAGGAAGACGAGAAACC
.........((((((((((.......))))))))))..................... ( -12.10, z-score =  -2.16, R)
>droWil1.scaffold_181130 9299628 55 - 16660200
UAAAGACUGAACCUCAAAAAGAACACGGUCA-AAGUAAUUUAAAUGGAAUAGUAUU-
....(((((....((.....))...))))).-........................- (  -4.90, z-score =  -0.12, R)
>consensus
GUAUAACAAAUCUGCGGCAAAUGAGCUGUCGUAGGUAAAUAAGGAAGACGAGAAACC
.........((((((((((.......))))))))))..................... ( -6.26 =  -7.78 +   1.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:37:52 2011