Locus 4720

Sequence ID	dm3.chr2R
Location	15,220,552 – 15,220,665
Length	113
Max. P	0.980458

overview

Window 7

Location	15,220,552 – 15,220,663
Length	111
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	68.97
Shannon entropy	0.55626
G+C content	0.40797
Mean single sequence MFE	-23.92
Consensus MFE	-10.12
Energy contribution	-10.72
Covariance contribution	0.60
Combinations/Pair	1.21
Mean z-score	-2.41
Structure conservation index	0.42
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.05
SVM RNA-class probability	0.980458
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15220552 111 + 21146708
UAAAAACAACAGAAUAAAAAACUAAAUGUAUAUGUAUGCUGUACAAAUUUCCACUUCUACUUCAUCGCUGCGUAUGUGGAAAACUGAGUAGAAGGCGGAAAAACUUCUGCC
.........(((((............((((((.(....)))))))..(((((.(((((((((.....(..(....)..)......)))))))))..)))))...))))).. ( -26.60, z-score =  -3.61, R)
>droEre2.scaffold_4845 9418237 88 + 22589142
----------AGAAUAAGAAACUAUAUGUAC-------------AAACUCCCACUUUUCCACCAUCCCUGUGUACGUGGCAGGCUGGUUGGUGGGCGGAGAAACUUCCGCC
----------.....................-------------......(((((.....((((..(((((.......))))).)))).)))))((((((....)))))). ( -23.70, z-score =  -0.39, R)
>droYak2.chr2R 7182692 109 - 21139217
AAAAAGAAACGGACUAAAAAACUACAUGUAC--AUAUGCCGUACAAAUUUCCACUCCUCCCACCACACUGUGCAUGUGAAAAAGUGAGUGGAAGGCGGAAAAACUUCGGCC
..........................(((((--.......)))))...((((((((((.....((((.......))))....)).))))))))(((.(((....))).))) ( -25.00, z-score =  -1.60, R)
>droSec1.super_1 12734132 92 + 14215200
-------UAAAAAAUAAAAAACUAUAUGUACCAAUAUGCUGUACAAAUUUCCACUUCUCCACCAACGCUGCGUAUGUGGAAA-----------GGCGGAAAAACUUCUGG-
-------...................(((((.........)))))..(((((.(((.(((((..(((...)))..))))).)-----------)).))))).........- ( -18.50, z-score =  -2.52, R)
>droSim1.chr2R 13931285 98 + 19596830
UGAAAACAACAGAAUAAAAAACUAUAUGUAC--AUAUGCUGUACAAAUUUCCACUUCUCCACCAACGCUGCGUAUGUGGAAA-----------GGCGGAAAAACUUCUGGC
.........(((((............(((((--(.....))))))..(((((.(((.(((((..(((...)))..))))).)-----------)).)))))...))))).. ( -25.80, z-score =  -3.95, R)
>consensus
__AAA__AACAGAAUAAAAAACUAUAUGUAC__AUAUGCUGUACAAAUUUCCACUUCUCCACCAACGCUGCGUAUGUGGAAA__UG__U_G__GGCGGAAAAACUUCUGCC
...............................................(((((((.....................)))))))...........(((((((....))))))) (-10.12 = -10.72 +   0.60)

alignment

secondary structure

dotplot

Window 8

Location	15,220,557 – 15,220,665
Length	108
Sequences	5
Columns	108
Reading direction	forward
Mean pairwise identity	70.04
Shannon entropy	0.53685
G+C content	0.42898
Mean single sequence MFE	-24.54
Consensus MFE	-10.76
Energy contribution	-11.36
Covariance contribution	0.60
Combinations/Pair	1.21
Mean z-score	-2.37
Structure conservation index	0.44
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.99
SVM RNA-class probability	0.978089
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15220557 108 + 21146708
ACAACAGAAUAAAAAACUAAAUGUAUAUGUAUGCUGUACAAAUUUCCACUUCUACUUCAUCGCUGCGUAUGUGGAAAACUGAGUAGAAGGCGGAAAAACUUCUGCCCC
....(((((............((((((.(....)))))))..(((((.(((((((((.....(..(....)..)......)))))))))..)))))...))))).... ( -26.60, z-score =  -3.27, R)
>droEre2.scaffold_4845 9418237 90 + 22589142
-----AGAAUAAGAAACUAUAUGUAC-------------AAACUCCCACUUUUCCACCAUCCCUGUGUACGUGGCAGGCUGGUUGGUGGGCGGAGAAACUUCCGCCCC
-----.....................-------------..............((((((..(((((.......))))).))).))).((((((((....)))))))). ( -26.00, z-score =  -0.85, R)
>droYak2.chr2R 7182697 106 - 21139217
GAAACGGACUAAAAAACUACAUGUAC--AUAUGCCGUACAAAUUUCCACUCCUCCCACCACACUGUGCAUGUGAAAAAGUGAGUGGAAGGCGGAAAAACUUCGGCCCU
.....................(((((--.......)))))...((((((((((.....((((.......))))....)).))))))))(((.(((....))).))).. ( -25.80, z-score =  -1.78, R)
>droSec1.super_1 12734137 87 + 14215200
-------AAUAAAAAACUAUAUGUACCAAUAUGCUGUACAAAUUUCCACUUCUCCACCAACGCUGCGUAUGUGGAAA-----------GGCGGAAAAACUUCUGG---
-------..............(((((.........)))))..(((((.(((.(((((..(((...)))..))))).)-----------)).))))).........--- ( -18.50, z-score =  -2.22, R)
>droSim1.chr2R 13931290 95 + 19596830
ACAACAGAAUAAAAAACUAUAUGUAC--AUAUGCUGUACAAAUUUCCACUUCUCCACCAACGCUGCGUAUGUGGAAA-----------GGCGGAAAAACUUCUGGCCC
....(((((............(((((--(.....))))))..(((((.(((.(((((..(((...)))..))))).)-----------)).)))))...))))).... ( -25.80, z-score =  -3.74, R)
>consensus
__AACAGAAUAAAAAACUAUAUGUAC__AUAUGCUGUACAAAUUUCCACUUCUCCACCAACGCUGCGUAUGUGGAAA__UG__U_G__GGCGGAAAAACUUCUGCCCC
..........................................(((((((.....................)))))))...........(((((((....))))))).. (-10.76 = -11.36 +   0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:34:39 2011