Locus 3640

Sequence ID dm3.chr2R
Location 6,860,371 – 6,860,437
Length 66
Max. P 0.975929
window4990 window4991

overview

Window 0

Location 6,860,371 – 6,860,437
Length 66
Sequences 6
Columns 67
Reading direction forward
Mean pairwise identity 68.85
Shannon entropy 0.61727
G+C content 0.55063
Mean single sequence MFE -20.13
Consensus MFE -9.04
Energy contribution -10.07
Covariance contribution 1.03
Combinations/Pair 1.23
Mean z-score -1.38
Structure conservation index 0.45
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.92
SVM RNA-class probability 0.852014
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6860371 66 + 21146708
AACUGCGAAACUCAGGAGCCUGCAGUAUCAGCACAGUGUCCUGAA-ACCACAAGGAUCUGCGAGAAA
...(((((.((((((....))).))).)).)))(((.(((((...-......))))))))....... ( -16.30, z-score =  -0.58, R)
>droSim1.chr2R 5417457 63 + 19596830
AACUGCGGAGCUCAGGAGCCUGCAGUAUCGGCACAGUGUCCUGAA-ACCACAAGGAUCUGCAAU---
.(((((((.(((....)))))))))).......(((.(((((...-......))))))))....--- ( -21.40, z-score =  -1.62, R)
>droSec1.super_1 4442993 54 + 14215200
AACUGCGGAGCUCAGGAGCCUGCAGUAUCGGCACAGUGUCCUGAA-ACCGAUAGU------------
.(((((((.(((....))))))))))(((((..(((....)))..-.)))))...------------ ( -21.30, z-score =  -2.69, R)
>droYak2.chr2R 18868381 64 - 21139217
AACUGCGGAGCUCAGGAGCCUGCAGUAUC-GCACAGUGUCCUGAA-ACCACAAU-ACCUGCGGUAAU
.(((((((.(((....))))))))))(((-(((..((((..((..-..))..))-)).))))))... ( -23.20, z-score =  -2.72, R)
>droEre2.scaffold_4845 3667212 66 - 22589142
AACUGCGGAGCUCAGGAGCCUGCAGUAUCGGCACAGUGUCCUGAA-ACCACAAGGAUCUGCGGCAAU
.(((((((.(((....))))))))))...(.(.(((.(((((...-......)))))))).).)... ( -25.00, z-score =  -2.07, R)
>dp4.chr3 902910 60 - 19779522
-------CACUGGGGGAAGUCGAGGAGCCUGCACAGUGGCUUGAGUGCCGGCGAAAACUGGGGGAAA
-------..(..(.....((((.((((((........))))).....))))).....)..)...... ( -13.60, z-score =   1.40, R)
>consensus
AACUGCGGAGCUCAGGAGCCUGCAGUAUCGGCACAGUGUCCUGAA_ACCACAAGGAUCUGCGGGAA_
.(((((((.(((....)))))))))).......(((....)))........................ ( -9.04 = -10.07 +   1.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 6,860,371 – 6,860,437
Length 66
Sequences 6
Columns 67
Reading direction reverse
Mean pairwise identity 68.85
Shannon entropy 0.61727
G+C content 0.55063
Mean single sequence MFE -19.52
Consensus MFE -11.91
Energy contribution -13.92
Covariance contribution 2.00
Combinations/Pair 1.24
Mean z-score -1.26
Structure conservation index 0.61
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.94
SVM RNA-class probability 0.975929
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 6860371 66 - 21146708
UUUCUCGCAGAUCCUUGUGGU-UUCAGGACACUGUGCUGAUACUGCAGGCUCCUGAGUUUCGCAGUU
..............((((((.-(((((((..((((.........))))..)))))))..)))))).. ( -18.70, z-score =  -0.46, R)
>droSim1.chr2R 5417457 63 - 19596830
---AUUGCAGAUCCUUGUGGU-UUCAGGACACUGUGCCGAUACUGCAGGCUCCUGAGCUCCGCAGUU
---...........((((((.-(((((((..((((.........))))..)))))))..)))))).. ( -21.10, z-score =  -1.21, R)
>droSec1.super_1 4442993 54 - 14215200
------------ACUAUCGGU-UUCAGGACACUGUGCCGAUACUGCAGGCUCCUGAGCUCCGCAGUU
------------..(((((((-..(((....))).)))))))((((.((((....))))..)))).. ( -21.50, z-score =  -2.83, R)
>droYak2.chr2R 18868381 64 + 21139217
AUUACCGCAGGU-AUUGUGGU-UUCAGGACACUGUGC-GAUACUGCAGGCUCCUGAGCUCCGCAGUU
..((((...)))-)((((((.-(((((((..((((..-......))))..)))))))..)))))).. ( -23.50, z-score =  -2.01, R)
>droEre2.scaffold_4845 3667212 66 + 22589142
AUUGCCGCAGAUCCUUGUGGU-UUCAGGACACUGUGCCGAUACUGCAGGCUCCUGAGCUCCGCAGUU
((((.(((((.((((.(....-..)))))..))))).))))(((((.((((....))))..))))). ( -21.30, z-score =  -0.75, R)
>dp4.chr3 902910 60 + 19779522
UUUCCCCCAGUUUUCGCCGGCACUCAAGCCACUGUGCAGGCUCCUCGACUUCCCCCAGUG-------
...............(((.((((..........)))).)))...................------- ( -11.00, z-score =  -0.32, R)
>consensus
_UUACCGCAGAUCCUUGUGGU_UUCAGGACACUGUGCCGAUACUGCAGGCUCCUGAGCUCCGCAGUU
..............((((((...((((((..(((((.......)))))..))))))...)))))).. (-11.91 = -13.92 +   2.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:13:58 2011