Locus 9918

Sequence ID	dm3.chr3R
Location	9,804,123 – 9,804,220
Length	97
Max. P	0.977694

overview

Window 7

Location	9,804,123 – 9,804,218
Length	95
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	83.07
Shannon entropy	0.25107
G+C content	0.45721
Mean single sequence MFE	-18.30
Consensus MFE	-14.18
Energy contribution	-13.99
Covariance contribution	-0.19
Combinations/Pair	1.06
Mean z-score	-2.47
Structure conservation index	0.77
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.83
SVM RNA-class probability	0.970119
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9804123 95 - 27905053
--GGAACUUAAGUAAUUAAGUUCUCCCC----AUAUAUCAGCCACCCUUAAUAGCUGCCUCCCAACAUCGCACCGUCUCUUUCCACUGGCCGUAGGCUUUC
--(((((((((....)))))))))....----.......((((..........((..............))((.(((..........))).)).))))... ( -17.04, z-score =  -1.56, R)
>droEre2.scaffold_4770 9349782 94 - 17746568
---GAACUUAAGUAAUUAAGUUCUCCCUAUAUAUGUAUCAGCCACCCUUAAUAGCUGCCUC----CAUCGCCCCGUCUCUUUCCACUGGCAGCAGGCUUUC
---((((((((....))))))))................((((....(....)((((((..----......................)))))).))))... ( -21.26, z-score =  -3.19, R)
>droSec1.super_0 8914191 80 + 21120651
--AGAACUUAAGUAAUUAAGUUCUCCCC---UAUAUAUCAGCCACCCUUAAUAGCUGCC----------------UCUCUUUCCACUGGCCGUAGGCUUUC
--(((((((((....)))))))))..((---(((.....(((...........)))(((----------------............))).)))))..... ( -17.30, z-score =  -2.53, R)
>droSim1.chr3R 15894048 82 + 27517382
ACAGAACUUAAGUAAUUAAGUUCUCCCC---UAUAUAUCAGCCACCCUUAAUAGCUGCC----------------UCUCUUUCCACUGGCCGUAGGCUUUC
..(((((((((....)))))))))..((---(((.....(((...........)))(((----------------............))).)))))..... ( -17.60, z-score =  -2.60, R)
>consensus
__AGAACUUAAGUAAUUAAGUUCUCCCC___UAUAUAUCAGCCACCCUUAAUAGCUGCC________________UCUCUUUCCACUGGCCGUAGGCUUUC
...((((((((....))))))))................((((..........((.(((............................))).)).))))... (-14.18 = -13.99 +  -0.19)

alignment

secondary structure

dotplot

Window 8

Location	9,804,125 – 9,804,220
Length	95
Sequences	4
Columns	101
Reading direction	reverse
Mean pairwise identity	82.36
Shannon entropy	0.26031
G+C content	0.45578
Mean single sequence MFE	-18.58
Consensus MFE	-14.99
Energy contribution	-14.62
Covariance contribution	-0.37
Combinations/Pair	1.11
Mean z-score	-2.39
Structure conservation index	0.81
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.98
SVM RNA-class probability	0.977694
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9804125 95 - 27905053
--ACGGAACUUAAGUAAUUAAGUUCUCCCC----AUAUAUCAGCCACCCUUAAUAGCUGCCUCCCAACAUCGCACCGUCUCUUUCCACUGGCCGUAGGCUU
--..(((((((((....)))))))))....----.......((((..........((..............))((.(((..........))).)).)))). ( -17.34, z-score =  -1.40, R)
>droEre2.scaffold_4770 9349784 93 - 17746568
----AGAACUUAAGUAAUUAAGUUCUCCCUAUAUAUGUAUCAGCCACCCUUAAUAGCUGCCUC----CAUCGCCCCGUCUCUUUCCACUGGCAGCAGGCUU
----(((((((((....)))))))))...............((((....(....)((((((..----......................)))))).)))). ( -21.76, z-score =  -3.01, R)
>droSec1.super_0 8914193 80 + 21120651
--ACAGAACUUAAGUAAUUAAGUUCUCCCC---UAUAUAUCAGCCACCCUUAAUAGCUGCC----------------UCUCUUUCCACUGGCCGUAGGCUU
--..(((((((((....)))))))))..((---(((.....(((...........)))(((----------------............))).)))))... ( -17.60, z-score =  -2.59, R)
>droSim1.chr3R 15894050 82 + 27517382
ACACAGAACUUAAGUAAUUAAGUUCUCCCC---UAUAUAUCAGCCACCCUUAAUAGCUGCC----------------UCUCUUUCCACUGGCCGUAGGCUU
....(((((((((....)))))))))..((---(((.....(((...........)))(((----------------............))).)))))... ( -17.60, z-score =  -2.54, R)
>consensus
__ACAGAACUUAAGUAAUUAAGUUCUCCCC___UAUAUAUCAGCCACCCUUAAUAGCUGCC________________UCUCUUUCCACUGGCCGUAGGCUU
....(((((((((....)))))))))...............((((..........((.(((............................))).)).)))). (-14.99 = -14.62 +  -0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:13:53 2011