Locus 13581

Sequence ID	dm3.chrX
Location	7,573,871 – 7,574,023
Length	152
Max. P	0.748810

overview

Window 4

Location	7,573,871 – 7,573,983
Length	112
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	93.75
Shannon entropy	0.08794
G+C content	0.41071
Mean single sequence MFE	-29.47
Consensus MFE	-27.89
Energy contribution	-27.57
Covariance contribution	-0.33
Combinations/Pair	1.09
Mean z-score	-1.33
Structure conservation index	0.95
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.58
SVM RNA-class probability	0.748810
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7573871 112 - 22422827
AGGAAUGAAGUACCGUUUAAUUUACCGUUUUCGUGUAAAGUGUAUUUUUUUUAUGUGUUUAAGUGCAGUUUUAAUUUAGGGUCGACAGAUCCUUUGCGCUGGUGCGCAGGCG
..(((.(((((((.......(((((((....)).)))))..))))))).))).(((((...(((((((.........((((((....)))))))))))))...))))).... ( -28.50, z-score =  -1.53, R)
>droSim1.chrU 6826909 112 - 15797150
AGAAAUGAAGUACCGUUUGAUUUACCGUUUUCGUGUGAAGUGUAUUUUUUUUAUGUGCUUAAGUGCAGUUUAAAUUUUGGGUCGACAGAUCCUAUGCGCUGUUGCGCAGGCG
..(((.(((((((.......(((((((....)).)))))..))))))).))).(((((...((((((...........(((((....)))))..))))))...))))).... ( -28.22, z-score =  -1.07, R)
>droSec1.super_24 780657 112 - 912625
AGGAAUGAAGUACCGUUUGAUUUACCGUUUUCGUGUGAAGUGUAUUUUUUUUAUGUGCAUAAGUGCAGUUUCGAUUUUGGGUCGACAGAUCCUUUGCGCUGGUGCGCAGGCG
..(((.(((((((.......(((((((....)).)))))..))))))).))).(((((((.(((((((..........(((((....))))).))))))).))))))).... ( -31.70, z-score =  -1.40, R)
>consensus
AGGAAUGAAGUACCGUUUGAUUUACCGUUUUCGUGUGAAGUGUAUUUUUUUUAUGUGCUUAAGUGCAGUUUAAAUUUUGGGUCGACAGAUCCUUUGCGCUGGUGCGCAGGCG
..(((.(((((((.......(((((((....)).)))))..))))))).))).(((((...(((((((..........(((((....))))).)))))))...))))).... (-27.89 = -27.57 +  -0.33)

alignment

secondary structure

dotplot

Window 5

Location	7,573,911 – 7,574,023
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	81.03
Shannon entropy	0.29912
G+C content	0.40376
Mean single sequence MFE	-20.30
Consensus MFE	-13.15
Energy contribution	-13.96
Covariance contribution	0.81
Combinations/Pair	1.14
Mean z-score	-1.90
Structure conservation index	0.65
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.43
SVM RNA-class probability	0.692232
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 7573911 112 + 22422827
AAAACUGCACUUAAACACA-UAAAAAAAAUACACUU---UACACGAAAACGGUAAAUUAAACGGUACUUCAU----UCCUUACCGACAAGUGCAGCCAUUUCUCCGUGCUUUUGUACCUG
....((((((((.......-..............((---(((.((....))))))).....(((((......----....)))))..))))))))..........((((....))))... ( -22.30, z-score =  -3.41, R)
>droSim1.chrU 6826949 112 + 15797150
UAAACUGCACUUAAGCACA-UAAAAAAAAUACACUU---CACACGAAAACGGUAAAUCAAACGGUACUUCAU----UUCUUACCGACAAGUGCAGCCAUUUCUCCGGGCUUUUGUACCUG
....((((((((.......-.........(((..((---(....)))....))).......(((((......----....)))))..)))))))).........((((........)))) ( -19.50, z-score =  -1.69, R)
>droSec1.super_24 780697 112 + 912625
GAAACUGCACUUAUGCACA-UAAAAAAAAUACACUU---CACACGAAAACGGUAAAUCAAACGGUACUUCAU----UCCUUACCGACAAGUGCAGCCAUUUCUCCGGGCUUUUGUACCUG
((((((((((((.......-.........(((..((---(....)))....))).......(((((......----....)))))..))))))))...))))..((((........)))) ( -20.30, z-score =  -1.61, R)
>droEre2.scaffold_4690 16494479 119 + 18748788
GAAACAGCAUUCACACACAACAACAAAAAUACACAUUCCCGCACAAAAACGGUAGUUAAAACGGCACUUUUCAAUAUUCCCGCCGACAAAGGCAGC-ACUUUUCCGUGCUACUGUACGCG
......((..............................(((........)))........((((.................(((......)))(((-((......))))).))))..)). ( -19.10, z-score =  -0.89, R)
>consensus
GAAACUGCACUUAAACACA_UAAAAAAAAUACACUU___CACACGAAAACGGUAAAUCAAACGGUACUUCAU____UCCUUACCGACAAGUGCAGCCAUUUCUCCGGGCUUUUGUACCUG
....((((((((............................((.((....))))........(((((..............)))))..))))))))..........((((....))))... (-13.15 = -13.96 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:24:00 2011