Locus 11903

Sequence ID dm3.chr3R
Location 24,469,124 – 24,469,216
Length 92
Max. P 0.788279
window16358 window16359

overview

Window 8

Location 24,469,124 – 24,469,216
Length 92
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 58.85
Shannon entropy 0.68330
G+C content 0.44119
Mean single sequence MFE -21.60
Consensus MFE -11.16
Energy contribution -10.16
Covariance contribution -1.00
Combinations/Pair 1.50
Mean z-score -0.33
Structure conservation index 0.52
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.01
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>dm3.chr3R 24469124 92 + 27905053
AUUGAUUUUGUCCAUGUCCAGCUU------UACGUCCA------GUGGGCAAGAACAACUCGUUUUGCGGCUGAGAUUG--UGUUUGUUGCCCCAUCUAUAUGGCU
.........(.((((((...(((.------.......)------))(((((((((((.(((((......)).)))....--))))).)))))).....))))))). ( -19.50, z-score =   0.75, R)
>droSim1.chr3R 24166706 98 + 27517382
AUUGAUUUUGUCCAUGUCCAGCUC------CACGUCCACGUCCAGUGGGCAACAACAACUCGUGUUGUGGCUGAGAUUG--UGUUUGUUGCCUCAUCUAUAUGGGU
..........(((((((.(((((.------...((((((.....)))))).((((((.....)))))))))))((((..--.((.....))...))))))))))). ( -28.30, z-score =  -0.82, R)
>droSec1.super_4 3351504 70 + 6179234
----------------------AU------UGAUUCCA------GUAGGCAACAACAACUCGUGUUGUGGCCGAGAUUG--UGUUUGUUGCCUCAUCUAUAUGGCU
----------------------..------........------(.((((((((((((((((.((....)))))).)))--)...)))))))))............ ( -19.90, z-score =  -1.56, R)
>droEre2.scaffold_4820 6907030 106 - 10470090
AUUGAUUUUGUCCAUGUCCAGCUCAACAUCCACGUCCACUACCAGUGGGCAACAACAAGUUGUGUUGUGGCUGAGAUUGAGUGUUUGUUGCCCCAUCUGAAUGGCU
.........(.((((...(((..(((((..(((((((((.....)))))).((((((.....))))))............)))..)))))......))).))))). ( -28.40, z-score =  -0.06, R)
>droWil1.scaffold_181089 9175801 76 + 12369635
-----------------AUUGAUU------UUCGGUCAUGUUGGACAUGCCAUAACAACUCCAAUUACACUU----UUA---UUUUGUGGUCUCUGCUAGUUGAUU
-----------------.......------...((.((((.....))))))....(((((.((....(((..----...---....))).....))..)))))... ( -11.90, z-score =   0.03, R)
>consensus
AUUGAUUUUGUCCAUGUCCAGCUU______UACGUCCA______GUGGGCAACAACAACUCGUGUUGUGGCUGAGAUUG__UGUUUGUUGCCUCAUCUAUAUGGCU
...................................(((........(((((((((.............................)))))))))........))).. (-11.16 = -10.16 +  -1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 24,469,124 – 24,469,216
Length 92
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 58.85
Shannon entropy 0.68330
G+C content 0.44119
Mean single sequence MFE -20.72
Consensus MFE -10.45
Energy contribution -10.41
Covariance contribution -0.04
Combinations/Pair 1.38
Mean z-score -0.75
Structure conservation index 0.50
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.69
SVM RNA-class probability 0.788279
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 24469124 92 - 27905053
AGCCAUAUAGAUGGGGCAACAAACA--CAAUCUCAGCCGCAAAACGAGUUGUUCUUGCCCAC------UGGACGUA------AAGCUGGACAUGGACAAAAUCAAU
.(((((.......((((((.....(--(((.(((...........)))))))..)))))).(------..(.(...------..))..)..)))).)......... ( -18.50, z-score =   0.21, R)
>droSim1.chr3R 24166706 98 - 27517382
ACCCAUAUAGAUGAGGCAACAAACA--CAAUCUCAGCCACAACACGAGUUGUUGUUGCCCACUGGACGUGGACGUG------GAGCUGGACAUGGACAAAAUCAAU
..((((.(((.((.(((((((...(--(((.(((...........)))))))))))))))))))...)))).((((------........))))............ ( -24.60, z-score =  -0.47, R)
>droSec1.super_4 3351504 70 - 6179234
AGCCAUAUAGAUGAGGCAACAAACA--CAAUCUCGGCCACAACACGAGUUGUUGUUGCCUAC------UGGAAUCA------AU----------------------
.........(((.((((((((...(--(((.((((.........))))))))))))))))..------....))).------..---------------------- ( -19.90, z-score =  -2.81, R)
>droEre2.scaffold_4820 6907030 106 + 10470090
AGCCAUUCAGAUGGGGCAACAAACACUCAAUCUCAGCCACAACACAACUUGUUGUUGCCCACUGGUAGUGGACGUGGAUGUUGAGCUGGACAUGGACAAAAUCAAU
.(((((((((......(((((..(((.........((.((((((.....)))))).))((((.....))))..)))..)))))..)))))..))).)......... ( -28.90, z-score =  -0.25, R)
>droWil1.scaffold_181089 9175801 76 - 12369635
AAUCAACUAGCAGAGACCACAAAA---UAA----AAGUGUAAUUGGAGUUGUUAUGGCAUGUCCAACAUGACCGAA------AAUCAAU-----------------
...(((((..(((..((.((....---...----..))))..))).)))))...(((((((.....)))).)))..------.......----------------- ( -11.70, z-score =  -0.42, R)
>consensus
AGCCAUAUAGAUGAGGCAACAAACA__CAAUCUCAGCCACAACACGAGUUGUUGUUGCCCAC______UGGACGUA______AAGCUGGACAUGGACAAAAUCAAU
..(((........((((((((.................(((((....)))))))))))))........)))................................... (-10.45 = -10.41 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:51:52 2011