Locus 3446

Sequence ID dm3.chr2R
Location 5,333,711 – 5,333,803
Length 92
Max. P 0.924536
window4733 window4734

overview

Window 3

Location 5,333,711 – 5,333,803
Length 92
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 83.93
Shannon entropy 0.27595
G+C content 0.48900
Mean single sequence MFE -32.75
Consensus MFE -21.68
Energy contribution -21.88
Covariance contribution 0.20
Combinations/Pair 1.32
Mean z-score -2.44
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.31
SVM RNA-class probability 0.924536
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5333711 92 + 21146708
----------UUGCGCACAGGGAGGCAGUGAAAAAGUUUUGUUUACCUUUUUUCGAUAUCCCAGAGUUCUGCGA--UUUCGG--UGUCGCUGUGUGCGUGUGCGAG-----
----------...((((((.(.(.((((((((((((..........))))).((((.(((.(((....))).))--).))))--..))))))).).).))))))..----- ( -32.80, z-score =  -2.75, R)
>droAna3.scaffold_13266 19594933 111 - 19884421
UAGCACGCAAAAUAGCAGUCGGAGGUGGUGAAAAAGUUUUGUUUACCUUUUUUCGAUAUCCGAGAAUUCUGCUGCGUUCUGGCCUGCUGGUGUGUGAGUGUGUGCCUUCGG
..(((((((..(((((((.(((((..((((((.........))))))..((((((.....)))))))))))))))......(((....))).)))...)))))))...... ( -33.50, z-score =  -1.33, R)
>droSim1.chr2R 3984316 92 + 19596830
----------UUGCGCACAGGGAGGCAGUGAAAAAGUUUUGUUUACCUUUUUUCGAUAUCCCAGAGUUCUGCGA--UUUCGG--UGUCGCUGUGUGCGUGUGCGAG-----
----------...((((((.(.(.((((((((((((..........))))).((((.(((.(((....))).))--).))))--..))))))).).).))))))..----- ( -32.80, z-score =  -2.75, R)
>droSec1.super_1 2959014 92 + 14215200
----------UAGCGCACAGGGAGGCAGUGAAAAAGUUUUGUUUACCUUUUUUCGAUAUCCCAGAGUUCUGCGA--UUUCGG--UGUCGCUGUGUGCGUGUGCGAG-----
----------...((((((.(.(.((((((((((((..........))))).((((.(((.(((....))).))--).))))--..))))))).).).))))))..----- ( -32.80, z-score =  -2.83, R)
>droYak2.chr2L 17989745 92 + 22324452
----------UUGUGCACAGGGAGGCAGUGAAAAGGUUUUGUUUACCUUUUUUCGAUAUCCCAGAGUUCUGCGA--UUUCGG--UGCCACUGUGUGCGUGUGCGAG-----
----------...((((((.(.(.(((((((((((((.......))))))).((((.(((.(((....))).))--).))))--...)))))).).).))))))..----- ( -35.90, z-score =  -3.82, R)
>droEre2.scaffold_4929 17623571 92 - 26641161
----------UGGCGCUCAGGGAGGCAGUGAAAAAGUUUUGUUUACCUUUUUUCGAUAUCCCAGAGUUCUGCGA--UUUCGG--UGCCACUGUGUGCGUGUGCGAG-----
----------...(((.((.(.(.((((((((((((..........))))))((((.(((.(((....))).))--).))))--...)))))).).).)).)))..----- ( -28.70, z-score =  -1.19, R)
>consensus
__________UUGCGCACAGGGAGGCAGUGAAAAAGUUUUGUUUACCUUUUUUCGAUAUCCCAGAGUUCUGCGA__UUUCGG__UGCCGCUGUGUGCGUGUGCGAG_____
.............((((((.(.(.((((((((((((..........)))))).(((..((.(((....))).))....)))......)))))).).).))))))....... (-21.68 = -21.88 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,333,711 – 5,333,803
Length 92
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 83.93
Shannon entropy 0.27595
G+C content 0.48900
Mean single sequence MFE -24.96
Consensus MFE -14.47
Energy contribution -14.77
Covariance contribution 0.31
Combinations/Pair 1.24
Mean z-score -2.68
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.21
SVM RNA-class probability 0.910309
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5333711 92 - 21146708
-----CUCGCACACGCACACAGCGACA--CCGAAA--UCGCAGAACUCUGGGAUAUCGAAAAAAGGUAAACAAAACUUUUUCACUGCCUCCCUGUGCGCAA----------
-----.........((.(((((.((..--.(((.(--((.(((....))).))).)))..(((((((.......))))))).......)).))))).))..---------- ( -24.20, z-score =  -2.76, R)
>droAna3.scaffold_13266 19594933 111 + 19884421
CCGAAGGCACACACUCACACACCAGCAGGCCAGAACGCAGCAGAAUUCUCGGAUAUCGAAAAAAGGUAAACAAAACUUUUUCACCACCUCCGACUGCUAUUUUGCGUGCUA
.....(((((..................((......)).(((((((..(((((.......(((((((.......))))))).......))))).....)))))))))))). ( -23.64, z-score =  -1.26, R)
>droSim1.chr2R 3984316 92 - 19596830
-----CUCGCACACGCACACAGCGACA--CCGAAA--UCGCAGAACUCUGGGAUAUCGAAAAAAGGUAAACAAAACUUUUUCACUGCCUCCCUGUGCGCAA----------
-----.........((.(((((.((..--.(((.(--((.(((....))).))).)))..(((((((.......))))))).......)).))))).))..---------- ( -24.20, z-score =  -2.76, R)
>droSec1.super_1 2959014 92 - 14215200
-----CUCGCACACGCACACAGCGACA--CCGAAA--UCGCAGAACUCUGGGAUAUCGAAAAAAGGUAAACAAAACUUUUUCACUGCCUCCCUGUGCGCUA----------
-----..(((((((((.....)))...--.(((.(--((.(((....))).))).))).....(((((................)))))...))))))...---------- ( -23.79, z-score =  -2.68, R)
>droYak2.chr2L 17989745 92 - 22324452
-----CUCGCACACGCACACAGUGGCA--CCGAAA--UCGCAGAACUCUGGGAUAUCGAAAAAAGGUAAACAAAACCUUUUCACUGCCUCCCUGUGCACAA----------
-----.........(((((..(.((((--.(((.(--((.(((....))).))).)))..(((((((.......)))))))...)))).)..)))))....---------- ( -30.00, z-score =  -4.61, R)
>droEre2.scaffold_4929 17623571 92 + 26641161
-----CUCGCACACGCACACAGUGGCA--CCGAAA--UCGCAGAACUCUGGGAUAUCGAAAAAAGGUAAACAAAACUUUUUCACUGCCUCCCUGAGCGCCA----------
-----........(((.((..(.((((--.(((.(--((.(((....))).))).)))..(((((((.......)))))))...)))).)..)).)))...---------- ( -23.90, z-score =  -2.02, R)
>consensus
_____CUCGCACACGCACACAGCGACA__CCGAAA__UCGCAGAACUCUGGGAUAUCGAAAAAAGGUAAACAAAACUUUUUCACUGCCUCCCUGUGCGCAA__________
.............((((((..((((............))))........((((.......(((((((.......))))))).......))))))))))............. (-14.47 = -14.77 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:10:22 2011