Locus 10044

Sequence ID dm3.chr3R
Location 10,816,285 – 10,816,389
Length 104
Max. P 0.999859
window13801 window13802

overview

Window 1

Location 10,816,285 – 10,816,389
Length 104
Sequences 8
Columns 121
Reading direction forward
Mean pairwise identity 70.52
Shannon entropy 0.52998
G+C content 0.61304
Mean single sequence MFE -41.69
Consensus MFE -16.97
Energy contribution -18.33
Covariance contribution 1.36
Combinations/Pair 1.25
Mean z-score -2.23
Structure conservation index 0.41
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.38
SVM RNA-class probability 0.933727
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10816285 104 + 27905053
GUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGGGAAAAAGAGGGG-----------------
.((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....)))))))))))))))................----------------- ( -50.60, z-score =  -4.22, R)
>droSim1.chr3R 16875305 104 - 27517382
GUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGGGAAAAAGAGGGG-----------------
.((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....)))))))))))))))................----------------- ( -50.60, z-score =  -4.22, R)
>droSec1.super_0 10000152 104 - 21120651
GUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGGUGGGAAAAGGAGGGG-----------------
.((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....)))))))))))))))................----------------- ( -50.60, z-score =  -4.02, R)
>droYak2.chr3R 13223557 120 - 28832112
GUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGG-UGGUGUAACGUUGGUAAGGGGAGGGGAGGGG
.((((((((.(((((((.....((((((((((.......((((.......)))).....))))))))))....))))))))))))))).-............................... ( -50.60, z-score =  -2.32, R)
>droEre2.scaffold_4770 10353347 92 + 17746568
GUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGCGCCCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGGAGGGG-----------------------------
...(((((.((((((((.....((((((((((......(((.........)))......))))))))))....)))))))).))))).....----------------------------- ( -44.40, z-score =  -2.53, R)
>droAna3.scaffold_13340 5896040 101 + 23697760
GUGCCUCUAGUGGCCGGAGAGACUGUCAGAAGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGACCAAGGCCACAAAAGGGGGUAACACAAGGC--------------------
.(((((((.((((((.......(((((((..........((((.......))))........)))))))......))))))....))))))).........-------------------- ( -34.29, z-score =  -1.88, R)
>dp4.chr2 20773710 83 + 30794189
GUGCCG-UGGUGCCCCAGGGCAAUGUU----GCAACAUGGGCGCCAGAAUCGUCAAUUACUGCGGGCAGAGACAUAACCGGACUGUGG---------------------------------
.((((.-((((((((....(((....)----)).....))))))))....(((........)))))))....((((.......)))).--------------------------------- ( -26.20, z-score =   0.67, R)
>droPer1.super_3 3526186 83 + 7375914
GUGCCG-UGGUGCCCCAGGGCAAUGUU----GCAACAUGGGCGCCAGAAUCGUCAAUUACUGCGGGCAGAGACAUAACCGGACUGUGG---------------------------------
.((((.-((((((((....(((....)----)).....))))))))....(((........)))))))....((((.......)))).--------------------------------- ( -26.20, z-score =   0.67, R)
>consensus
GUGCCUCUGGUGGCCACUGGAACUGUCAGCGGCAACAUGGGCGCGAGAAUCGUCAAUUACCGCUGACAGGGGUGUGGCCACAGGGGCGG_GGG_A_AAG______________________
...(((...((((((.......(((((((..........((((.......))))........)))))))......))))))..)))................................... (-16.97 = -18.33 +   1.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,816,285 – 10,816,389
Length 104
Sequences 8
Columns 121
Reading direction reverse
Mean pairwise identity 70.52
Shannon entropy 0.52998
G+C content 0.61304
Mean single sequence MFE -39.67
Consensus MFE -18.68
Energy contribution -20.92
Covariance contribution 2.24
Combinations/Pair 1.19
Mean z-score -4.24
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.61
SVM RNA-class probability 0.999859
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 10816285 104 - 27905053
-----------------CCCCUCUUUUUCCCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCAC
-----------------.................(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).))).. ( -47.40, z-score =  -7.01, R)
>droSim1.chr3R 16875305 104 + 27517382
-----------------CCCCUCUUUUUCCCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCAC
-----------------.................(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).))).. ( -47.40, z-score =  -7.01, R)
>droSec1.super_0 10000152 104 + 21120651
-----------------CCCCUCCUUUUCCCACCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCAC
-----------------.................(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).))).. ( -47.40, z-score =  -7.00, R)
>droYak2.chr3R 13223557 120 + 28832112
CCCCUCCCCUCCCCUUACCAACGUUACACCA-CCGCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCAC
...............................-..(((.((((((((((....((((((((((((((((.((.......))..)).)))))))))))))).....))))))).))).))).. ( -47.40, z-score =  -6.43, R)
>droEre2.scaffold_4770 10353347 92 - 17746568
-----------------------------CCCCUCCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGGGCGCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCAC
-----------------------------..((((.....((((((((....((((((((((((((((.((.....))....)).)))))))))))))).....))))))))..))))... ( -45.10, z-score =  -4.88, R)
>droAna3.scaffold_13340 5896040 101 - 23697760
--------------------GCCUUGUGUUACCCCCUUUUGUGGCCUUGGUCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCUUCUGACAGUCUCUCCGGCCACUAGAGGCAC
--------------------..............(((((.((((((..((..(((((((.((((((((.((.......))..)).)))))).)))))))..))...)))))).)))))... ( -35.30, z-score =  -2.77, R)
>dp4.chr2 20773710 83 - 30794189
---------------------------------CCACAGUCCGGUUAUGUCUCUGCCCGCAGUAAUUGACGAUUCUGGCGCCCAUGUUGC----AACAUUGCCCUGGGGCACCA-CGGCAC
---------------------------------.....(.(((((((.....(((....)))....)))).....(((.((((.....((----(....)))....)))).)))-)))).. ( -23.70, z-score =   0.58, R)
>droPer1.super_3 3526186 83 - 7375914
---------------------------------CCACAGUCCGGUUAUGUCUCUGCCCGCAGUAAUUGACGAUUCUGGCGCCCAUGUUGC----AACAUUGCCCUGGGGCACCA-CGGCAC
---------------------------------.....(.(((((((.....(((....)))....)))).....(((.((((.....((----(....)))....)))).)))-)))).. ( -23.70, z-score =   0.58, R)
>consensus
______________________CUU_U_CCC_CCCCCCCUGUGGCCACACCCCUGUCAGCGGUAAUUGACGAUUCUCGCGCCCAUGUUGCCGCUGACAGUUCCAGUGGCCACCAGAGGCAC
...................................((.((((((((......(((((((.((((((((.((.......))..)).)))))).))))))).......)))))).)).))... (-18.68 = -20.92 +   2.24)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:16:17 2011