Locus 5040

Sequence ID dm3.chr2R
Location 17,302,841 – 17,302,899
Length 58
Max. P 0.940549
window6922 window6923

overview

Window 2

Location 17,302,841 – 17,302,899
Length 58
Sequences 5
Columns 59
Reading direction forward
Mean pairwise identity 77.40
Shannon entropy 0.39267
G+C content 0.45507
Mean single sequence MFE -13.76
Consensus MFE -11.60
Energy contribution -11.52
Covariance contribution -0.08
Combinations/Pair 1.23
Mean z-score -1.46
Structure conservation index 0.84
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.46
SVM RNA-class probability 0.940549
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17302841 58 + 21146708
UGUCUGCACUGUCAUUAUGUUGAUGACAUGGCAGCCAUUUCUU-GUUUCCUCGAUUCCA
((.((((..(((((((.....)))))))..)))).))......-............... ( -13.80, z-score =  -1.61, R)
>droSec1.super_9 633808 50 + 3197100
UGUCUGCGCUGUCAUUAUGUUGAUGACAUGGCAGCCAUUUCUU-GGCUCCU--------
.........(((((((.....))))))).((.(((((.....)-)))))).-------- ( -15.80, z-score =  -1.98, R)
>droYak2.chr2R 9255292 51 - 21139217
UGUCUGCGCUGUCAUUAUGUUGAUGACACGGCAGCCAUUUCUUCGAUUCCU--------
((.((((..(((((((.....)))))))..)))).))..............-------- ( -13.40, z-score =  -1.66, R)
>droEre2.scaffold_4845 11447332 51 + 22589142
UGUCUGCGCUGUCAUUAUGUUGAUGACACGGCAGCCAUUUCUUCGGUUCCU--------
((.((((..(((((((.....)))))))..)))).))..............-------- ( -13.40, z-score =  -1.27, R)
>dp4.chr3 15575857 57 + 19779522
UGUUUGUGCCGUCAUUAUGUUGAUGACA-GGCAGCUUUUACUUCUAGAUUGGAAUCCA-
......((((((((((.....)))))).-))))........((((.....))))....- ( -12.40, z-score =  -0.78, R)
>consensus
UGUCUGCGCUGUCAUUAUGUUGAUGACACGGCAGCCAUUUCUUCGAUUCCU________
((.((((..(((((((.....)))))))..)))).))...................... (-11.60 = -11.52 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 17,302,841 – 17,302,899
Length 58
Sequences 5
Columns 59
Reading direction reverse
Mean pairwise identity 77.40
Shannon entropy 0.39267
G+C content 0.45507
Mean single sequence MFE -12.40
Consensus MFE -8.98
Energy contribution -9.22
Covariance contribution 0.24
Combinations/Pair 1.10
Mean z-score -1.38
Structure conservation index 0.72
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.806000
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17302841 58 - 21146708
UGGAAUCGAGGAAAC-AAGAAAUGGCUGCCAUGUCAUCAACAUAAUGACAGUGCAGACA
.....((..(....)-..))..((.((((..((((((.......))))))..)))).)) ( -14.00, z-score =  -1.75, R)
>droSec1.super_9 633808 50 - 3197100
--------AGGAGCC-AAGAAAUGGCUGCCAUGUCAUCAACAUAAUGACAGCGCAGACA
--------.((((((-(.....))))).)).((((((.......))))))......... ( -14.20, z-score =  -2.03, R)
>droYak2.chr2R 9255292 51 + 21139217
--------AGGAAUCGAAGAAAUGGCUGCCGUGUCAUCAACAUAAUGACAGCGCAGACA
--------..............((.((((..((((((.......))))))..)))).)) ( -11.20, z-score =  -0.75, R)
>droEre2.scaffold_4845 11447332 51 - 22589142
--------AGGAACCGAAGAAAUGGCUGCCGUGUCAUCAACAUAAUGACAGCGCAGACA
--------..............((.((((..((((((.......))))))..)))).)) ( -11.20, z-score =  -0.81, R)
>dp4.chr3 15575857 57 - 19779522
-UGGAUUCCAAUCUAGAAGUAAAAGCUGCC-UGUCAUCAACAUAAUGACGGCACAAACA
-(((((....))))).........(.((((-.(((((.......))))))))))..... ( -11.40, z-score =  -1.55, R)
>consensus
________AGGAACCGAAGAAAUGGCUGCCAUGUCAUCAACAUAAUGACAGCGCAGACA
.........................((((..((((((.......))))))..))))... ( -8.98 =  -9.22 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:40:46 2011