Locus 12033

Sequence ID dm3.chr3R
Location 25,251,181 – 25,251,327
Length 146
Max. P 0.998335
window16541 window16542

overview

Window 1

Location 25,251,181 – 25,251,287
Length 106
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 71.25
Shannon entropy 0.49469
G+C content 0.46098
Mean single sequence MFE -26.47
Consensus MFE -15.56
Energy contribution -16.73
Covariance contribution 1.17
Combinations/Pair 1.10
Mean z-score -1.21
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.58
SVM RNA-class probability 0.749954
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25251181 106 + 27905053
-------GUGUGGCUGCCACAGACAAUGAUUAAUCGUACGCCGCUGCGUGUUCCACAUGUAGCAUAUACAUAUGUACAUAUGUAGCACCCCCACAUAUGUACAAUAUGUAUAA
-------.(((((...)))))....((((....)))).....((((((((.....)))))))).(((((((((((((((((((.(.....).)))))))))).))))))))). ( -37.10, z-score =  -3.13, R)
>droAna3.scaffold_12911 4940110 102 + 5364042
UCAGUUCCUGCUGCUGCCAGAGACAAUGAUUAAUCGUAUGACCGUGCGUGUCCCACAUGC-GUACAUCC-CAUAUCCAUAU---CCAUCCGCCCCUACAUACUAUAA------
...((..((((....).)))..))...........(((((...((((((((.....))))-))))....-.(((....)))---.............))))).....------ ( -15.70, z-score =  -0.12, R)
>droEre2.scaffold_4820 7712621 81 - 10470090
-------GUGCGGCUGCCACAGACAAUGAUUAAUCGUGCGCCGCUGCGUGUUCCACAUACAGCGAACA----------------GCACCCGCACAUAUGCAUAA---------
-------((((((.(((....(...((((....)))).)..(((((..((.....))..)))))....----------------))).))))))..........--------- ( -26.80, z-score =  -1.40, R)
>droYak2.chr3R 7597305 81 - 28832112
-------GUGUGGCUGCCACAGACAAUGAUUAAUCGUACGCCGCUGCGUGUUUCACAUGUAGUAUACA----------------GCACCCCCACAUAUGCAUAA---------
-------((((((.(((........((((....)))).....((((((((.....)))))))).....----------------)))...))))))........--------- ( -20.00, z-score =  -0.11, R)
>droSec1.super_4 4110298 102 + 6179234
-------GUGUGACUGCCACAGACAAUGAUUAAUCGUAAGCCGCUGCGUGUUCCACAUGUAGCAUAUACAUAUGU----AUGUAGCACCCCCACAUAUGUACAAUAUGUAUAA
-------.((((.....))))....((((....)))).....((((((((.....)))))))).(((((((((((----(((((...........))))))).))))))))). ( -27.60, z-score =  -1.49, R)
>droSim1.chr3R 24926878 106 + 27517382
-------GUGUGGCUGCCACAGACAAUGAUUAAUCGUACGCCGCUGCGUGUUCCACAUGUAGCAUAUAUGUACAUAUGUAUGUAGCACCCCCACAUAUGUACAAUAUGUAUAA
-------((((((.(((.(((.(((..((....))(((((..((((((((.....)))))))).....)))))...))).))).)))...)))))).(((((.....))))). ( -31.60, z-score =  -1.01, R)
>consensus
_______GUGUGGCUGCCACAGACAAUGAUUAAUCGUACGCCGCUGCGUGUUCCACAUGUAGCAUAUAC_UAU_U____AU___GCACCCCCACAUAUGUACAAUAU______
.......(((.((.(((........((((....)))).....((((((((.....)))))))).....................))).)).)))................... (-15.56 = -16.73 +   1.17)

alignment

Postscript

secondary structure

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dotplot

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Window 2

Location 25,251,210 – 25,251,327
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.76
Shannon entropy 0.43390
G+C content 0.42021
Mean single sequence MFE -27.85
Consensus MFE -16.10
Energy contribution -17.05
Covariance contribution 0.95
Combinations/Pair 1.12
Mean z-score -3.19
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.33
SVM RNA-class probability 0.998335
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 25251210 117 + 27905053
UACGCCGCUGCGUGUUCCACAUGUAGCAUAUACAUAUGUACAUAUGUAGCACCCCCACAUAUGUACAAUAUGUAUAAAUGGACUCCAAAAAGUCACAAAACUUUCCGUAGGCUUUAA
...(((((((((((.....)))))))).(((((((((((((((((((.(.....).)))))))))).)))))))))..((((((......)))).))............)))..... ( -41.00, z-score =  -6.44, R)
>droAna3.scaffold_12911 4940146 106 + 5364042
UAUGACCGUGCGUGUCCCACAU---GCGUACAUCCCAUAUC--CAUAUCCAUCCGCCCCUACAUAC------UAUAAAUGGACUCCAAAAAGUCACAAAACUUUCCGUAGGCUUUAA
.......((((((((.....))---))))))..........--..............(((((....------........((((......))))............)))))...... ( -16.95, z-score =  -1.38, R)
>droEre2.scaffold_4820 7712650 92 - 10470090
UGCGCCGCUGCGUGUUCCACAUACAGCGAACA----------------GCACCCGCACAUAUGCA---------UAAAUGGACUCCAAAAAGUCACAAAACUUUCCGUAGGCUUUAA
...(((((((..((.....))..)))).....----------------((....(((....))).---------....((((((......)))).)).........)).)))..... ( -20.10, z-score =  -0.64, R)
>droYak2.chr3R 7597334 92 - 28832112
UACGCCGCUGCGUGUUUCACAUGUAGUAUACA----------------GCACCCCCACAUAUGCA---------UAAAUGGACUCCAAAAAGUCACAAAACUUUCCAUAGGCUUUAA
...(((((((((((.....)))))))).....----------------(((..........))).---------...(((((.......((((......))))))))).)))..... ( -19.71, z-score =  -1.95, R)
>droSec1.super_4 4110327 113 + 6179234
UAAGCCGCUGCGUGUUCCACAUGUAGCAUAUACAUAUGU----AUGUAGCACCCCCACAUAUGUACAAUAUGUAUAAAUGGACUCCAAAAAGUCACAAAACUUUCCGUAGGCUUUAA
.(((((((((((((.....)))))))).(((((((((((----(((((...........))))))).)))))))))..((((((......)))).))............)))))... ( -34.50, z-score =  -4.75, R)
>droSim1.chr3R 24926907 117 + 27517382
UACGCCGCUGCGUGUUCCACAUGUAGCAUAUAUGUACAUAUGUAUGUAGCACCCCCACAUAUGUACAAUAUGUAUAAAUGGACUCCAAAAAGUCACAAAACUUUCCGUAGGCUUUAA
...(((((((((((.....))))))))((((((((((((((((.............)))))))))).)))))).....((((((......)))).))............)))..... ( -34.82, z-score =  -3.98, R)
>consensus
UACGCCGCUGCGUGUUCCACAUGUAGCAUACA__UA__U____AUGUAGCACCCCCACAUAUGUAC______UAUAAAUGGACUCCAAAAAGUCACAAAACUUUCCGUAGGCUUUAA
...(((((((((((.....))))))))...................................................((((((......)))).))............)))..... (-16.10 = -17.05 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:54:25 2011