Locus 5413

Sequence ID	dm3.chr2R
Location	20,160,696 – 20,160,797
Length	101
Max. P	0.574242

overview

Window 3

Location	20,160,696 – 20,160,792
Length	96
Sequences	4
Columns	96
Reading direction	reverse
Mean pairwise identity	97.74
Shannon entropy	0.03577
G+C content	0.59896
Mean single sequence MFE	-36.12
Consensus MFE	-34.11
Energy contribution	-34.17
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.30
Structure conservation index	0.94
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.17
SVM RNA-class probability	0.574242
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20160696 96 - 21146708
AGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCCAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCAGG
.....((.((((((((((....((((..((((((........(((....)))..))))))))))..)))))))((((....))))..))).))... ( -37.10, z-score =  -1.36, R)
>droSec1.super_23 40354 96 - 989336
AGACAGCCGGAGACAGUUGCUCAGUGGUUGUCCUGUCCAGAGGCCAGGAGGCAAAGGACGCGAUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCAGG
...((((.(....).))))(((((.(((((((((((((....(((....)))...))))((((((....))))))....)).)))))))))).)). ( -35.80, z-score =  -1.69, R)
>droYak2.chr2R 20127117 96 - 21139217
AGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCGAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCAGCAGG
.....((.((((((((((....((((..((((((.(((........))).....))))))))))..)))))))((((....))))..))).))... ( -35.80, z-score =  -1.30, R)
>droEre2.scaffold_4845 21524515 96 - 22589142
AGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCGAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCAGG
.....((.((((((((((....((((..((((((.(((........))).....))))))))))..)))))))((((....))))..))).))... ( -35.80, z-score =  -0.87, R)
>consensus
AGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCCAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCAGG
.....((.((((((((((....((((..((((((.(((........))).....))))))))))..)))))))((((....))))..))).))... (-34.11 = -34.17 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	20,160,698 – 20,160,797
Length	99
Sequences	4
Columns	99
Reading direction	reverse
Mean pairwise identity	96.97
Shannon entropy	0.04984
G+C content	0.58478
Mean single sequence MFE	-35.95
Consensus MFE	-34.11
Energy contribution	-34.17
Covariance contribution	0.06
Combinations/Pair	1.03
Mean z-score	-1.16
Structure conservation index	0.95
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.12
SVM RNA-class probability	0.551648
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20160698 99 - 21146708
CUUCCAGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCCAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCA
..........((.((((((((((....((((..((((((........(((....)))..))))))))))..)))))))((((....))))..))).)). ( -37.10, z-score =  -1.19, R)
>droSec1.super_23 40356 98 - 989336
-UUCCAGACAGCCGGAGACAGUUGCUCAGUGGUUGUCCUGUCCAGAGGCCAGGAGGCAAAGGACGCGAUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCA
-.....(((((((.(((.(....))))...)))))))..((((....(((....)))...))))((((((....))))((((....))))......)). ( -35.10, z-score =  -1.40, R)
>droYak2.chr2R 20127119 99 - 21139217
UUUCCAGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCGAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCAGCA
..........((.((((((((((....((((..((((((.(((........))).....))))))))))..)))))))((((....))))..))).)). ( -35.80, z-score =  -1.20, R)
>droEre2.scaffold_4845 21524517 99 - 22589142
UUUCCAGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCGAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCA
..........((.((((((((((....((((..((((((.(((........))).....))))))))))..)))))))((((....))))..))).)). ( -35.80, z-score =  -0.83, R)
>consensus
UUUCCAGACAGCCGGAGACAGUUGCUCAGCGGUUGUCCUGUCCAGAGGCCAGGAGGCAAAGGACGCGCUAAAAUUGUCGCCGUCAGCGGCAAUCCUGCA
..........((.((((((((((....((((..((((((.(((........))).....))))))))))..)))))))((((....))))..))).)). (-34.11 = -34.17 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:47:49 2011