Locus 5062

Sequence ID dm3.chr2R
Location 17,428,581 – 17,428,669
Length 88
Max. P 0.954557
window6947 window6948

overview

Window 7

Location 17,428,581 – 17,428,669
Length 88
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 62.57
Shannon entropy 0.68256
G+C content 0.48742
Mean single sequence MFE -25.64
Consensus MFE -9.16
Energy contribution -11.61
Covariance contribution 2.45
Combinations/Pair 1.40
Mean z-score -1.95
Structure conservation index 0.36
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.61
SVM RNA-class probability 0.954557
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17428581 88 + 21146708
-------GGUUGCGAGGAAUUUCGCUGGAGAUCGAAAGAGGGGAAUUGUGGUCCCACCACAAUCUCCAAGAAU--UCCCACUAUUUCUCUUCGUAUG
-------...((((((((.......(((.((((....))(((((.((((((.....)))))))))))......--))))).......)))))))).. ( -30.44, z-score =  -2.49, R)
>droPer1.super_4 3820552 95 - 7162766
AGAAUCGGGGUAUUCUGAAGGUCAGAGAUGCUUCCAACUGCAGCCUCCUUUUUCCUUCC--AUCAUCGAACAUCGUGCAUCUAAAAUUCUCCGUGCG
.(...(((((.(((..(((((...(((.(((........)))..)))......))))).--..((.((.....)))).......))).)))))..). ( -18.10, z-score =   0.51, R)
>droEre2.scaffold_4845 11573660 85 + 22589142
------AGCUUGC-AGGAAUUUCGCUGGCGAUCGAAGGAGGGGAAAUGUAGCCCCGC---AAUCUCCAAGAAU--UGCCCCUAUUUCCCCUCCGAUG
------.(((.((-.........)).))).......(((((((((..((((....((---((((.....).))--)))..))))))))))))).... ( -27.90, z-score =  -1.33, R)
>droYak2.chr2R 9390846 72 - 21139217
-------AAUUGAGAGGAAUUUCGCUAGCGAUCGAAAUAGGGGAA----------------AUCACCAAGAAU--UCCCCCUAUUUCCCCUUCAACG
-------..(((((.((....(((....)))..((((((((((((----------------.((.....)).)--).)))))))))))).))))).. ( -23.00, z-score =  -3.44, R)
>droSec1.super_9 756453 83 + 3197100
---------UUGCGAGGAAUUUCGCUGGCAAUCGAAAGAGGGGAAAUGUGACCCCAU---AAUUUCCAAGAAU--UCCCCCUAUUUCUCCUCGCGUG
---------..(((((((.............((....))((((((.((((....)))---)..(((...))))--))))).......)))))))... ( -25.20, z-score =  -2.05, R)
>droSim1.chr2R 16087849 83 + 19596830
---------UUGCGAGGAAUUUCGCUGGCGAUCGAAAGAGGGGAAAUGUGACCCCAC---AAUUUCCAAGAAU--UCCCCCUAUUUCUCCUCGCGUG
---------..(((((((...(((....)))..((((..((((((.((((....)))---)..(((...))))--)))))...)))))))))))... ( -29.20, z-score =  -2.92, R)
>consensus
_______G_UUGCGAGGAAUUUCGCUGGCGAUCGAAAGAGGGGAAAUGUGACCCCAC___AAUCUCCAAGAAU__UCCCCCUAUUUCUCCUCGCAUG
..........((((((((...(((....)))..((((.(((((..................................))))).)))))))))))).. ( -9.16 = -11.61 +   2.45)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 8

Location 17,428,581 – 17,428,669
Length 88
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 62.57
Shannon entropy 0.68256
G+C content 0.48742
Mean single sequence MFE -28.53
Consensus MFE -7.70
Energy contribution -9.53
Covariance contribution 1.84
Combinations/Pair 1.36
Mean z-score -1.96
Structure conservation index 0.27
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.50
SVM RNA-class probability 0.718802
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 17428581 88 - 21146708
CAUACGAAGAGAAAUAGUGGGA--AUUCUUGGAGAUUGUGGUGGGACCACAAUUCCCCUCUUUCGAUCUCCAGCGAAAUUCCUCGCAACC-------
................((((((--((((((((((((((.((.((((.......)))).))...)))))))))).).)))))).)))....------- ( -29.90, z-score =  -2.70, R)
>droPer1.super_4 3820552 95 + 7162766
CGCACGGAGAAUUUUAGAUGCACGAUGUUCGAUGAU--GGAAGGAAAAAGGAGGCUGCAGUUGGAAGCAUCUCUGACCUUCAGAAUACCCCGAUUCU
....(((.(.(((((.....((((.....)).))..--.(((((.....(((((.(((........))))))))..)))))))))).).)))..... ( -20.60, z-score =   0.70, R)
>droEre2.scaffold_4845 11573660 85 - 22589142
CAUCGGAGGGGAAAUAGGGGCA--AUUCUUGGAGAUU---GCGGGGCUACAUUUCCCCUCCUUCGAUCGCCAGCGAAAUUCCU-GCAAGCU------
....(((((((((((..(((((--(((......))))---))....))..))))))))))).......((..(((.......)-))..)).------ ( -28.00, z-score =  -0.30, R)
>droYak2.chr2R 9390846 72 + 21139217
CGUUGAAGGGGAAAUAGGGGGA--AUUCUUGGUGAU----------------UUCCCCUAUUUCGAUCGCUAGCGAAAUUCCUCUCAAUU-------
.(((((..((((((((((((((--(((......)))----------------))))))))))))..(((....)))....))..))))).------- ( -30.80, z-score =  -4.17, R)
>droSec1.super_9 756453 83 - 3197100
CACGCGAGGAGAAAUAGGGGGA--AUUCUUGGAAAUU---AUGGGGUCACAUUUCCCCUCUUUCGAUUGCCAGCGAAAUUCCUCGCAA---------
...(((((((((((.(((((((--(((((((......---.)))))....))))))))).))))..(((....)))...)))))))..--------- ( -29.40, z-score =  -2.39, R)
>droSim1.chr2R 16087849 83 - 19596830
CACGCGAGGAGAAAUAGGGGGA--AUUCUUGGAAAUU---GUGGGGUCACAUUUCCCCUCUUUCGAUCGCCAGCGAAAUUCCUCGCAA---------
...(((((((((((.(((((((--((((...)))..(---(((....)))))))))))).))))..(((....)))...)))))))..--------- ( -32.50, z-score =  -2.89, R)
>consensus
CACACGAGGAGAAAUAGGGGGA__AUUCUUGGAGAUU___GUGGGGCCACAUUUCCCCUCUUUCGAUCGCCAGCGAAAUUCCUCGCAA_C_______
......((((((((.(((((((....((((............))))......))))))).))))..(((....)))...)))).............. ( -7.70 =  -9.53 +   1.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:41:07 2011