Locus 7321

Sequence ID dm3.chr3L
Location 13,845,559 – 13,845,611
Length 52
Max. P 0.914858
window10076 window10077

overview

Window 6

Location 13,845,559 – 13,845,611
Length 52
Sequences 7
Columns 60
Reading direction forward
Mean pairwise identity 65.90
Shannon entropy 0.64296
G+C content 0.40744
Mean single sequence MFE -12.27
Consensus MFE -4.81
Energy contribution -5.10
Covariance contribution 0.29
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.39
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.914858
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13845559 52 + 24543557
AAUAUUCGCUGGAGAUCACAGCAUUUCUGCCGUGAGUAUAUAAUACUGACCU--------
.((((((((.(.(((..........))).).)))))))).............-------- ( -10.90, z-score =  -1.31, R)
>droSec1.super_0 5988721 52 + 21120651
AAUAUUCGCUGGAGAUCACAGCAUUUCUGCCGUGAGUAUUUAAUACUUACCU--------
.......((((.......)))).........((((((((...))))))))..-------- ( -12.20, z-score =  -2.42, R)
>droYak2.chr3L 13928298 56 + 24197627
AAUAUUCGCUGGAGAUCCCAGCAUUUUUGCCGUGAGUAGACAAAAAAUUCAUACCU----
.......(((((.....))))).((((((((....)..).))))))..........---- ( -11.50, z-score =  -2.05, R)
>droEre2.scaffold_4784 13836095 56 + 25762168
AAUAUUCGCUGGAGGUCCCAGCACUUUUGCCGUGAGUUCACUUAAGUAUCUUGCUU----
.......(((((.....))))).........(..((...((....))..))..)..---- ( -12.30, z-score =  -0.87, R)
>dp4.chrXR_group8 6391997 52 + 9212921
AAUAUACGCUGGAGAUCCCAGCAUUUCUGUCGUGAGUAGAGAAUUUAUAUCC--------
.(((((.(((((.....))))).((((((.(....)))))))...)))))..-------- ( -15.40, z-score =  -3.37, R)
>droPer1.super_45 528089 52 - 618639
AAUAUACGCUGGCGAUCCCAGCAUUUCUGUCGUGAGUAGAUAAUUUAUAUCC--------
.(((((.(((((.....)))))...((((.(....))))).....)))))..-------- ( -12.40, z-score =  -2.08, R)
>triCas2.ChLG9 9473649 60 + 15222296
CCGAUUAAGUGGCGAUCGCAAAAACUGUGUCGUAAGUAUCACAAUUUAUAGCACUGUGCU
..((((.......))))(((......((((..(((((......)))))..))))..))). ( -11.20, z-score =  -0.15, R)
>consensus
AAUAUUCGCUGGAGAUCCCAGCAUUUCUGCCGUGAGUAGAUAAUAUUUACCU________
.......((((.......))))...................................... ( -4.81 =  -5.10 +   0.29)

alignment

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secondary structure

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dotplot

Postscript

Window 7

Location 13,845,559 – 13,845,611
Length 52
Sequences 7
Columns 60
Reading direction reverse
Mean pairwise identity 65.90
Shannon entropy 0.64296
G+C content 0.40744
Mean single sequence MFE -12.40
Consensus MFE -4.60
Energy contribution -4.74
Covariance contribution 0.14
Combinations/Pair 1.29
Mean z-score -1.69
Structure conservation index 0.37
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.89
SVM RNA-class probability 0.845608
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 13845559 52 - 24543557
--------AGGUCAGUAUUAUAUACUCACGGCAGAAAUGCUGUGAUCUCCAGCGAAUAUU
--------.((...((((...))))((((((((....))))))))...)).......... ( -14.50, z-score =  -2.46, R)
>droSec1.super_0 5988721 52 - 21120651
--------AGGUAAGUAUUAAAUACUCACGGCAGAAAUGCUGUGAUCUCCAGCGAAUAUU
--------.((...((((...))))((((((((....))))))))...)).......... ( -14.50, z-score =  -2.95, R)
>droYak2.chr3L 13928298 56 - 24197627
----AGGUAUGAAUUUUUUGUCUACUCACGGCAAAAAUGCUGGGAUCUCCAGCGAAUAUU
----..........((((((((.......))))))))((((((.....))))))...... ( -14.00, z-score =  -2.03, R)
>droEre2.scaffold_4784 13836095 56 - 25762168
----AAGCAAGAUACUUAAGUGAACUCACGGCAAAAGUGCUGGGACCUCCAGCGAAUAUU
----.........((((..(((....))).....))))(((((.....)))))....... ( -11.30, z-score =  -0.66, R)
>dp4.chrXR_group8 6391997 52 - 9212921
--------GGAUAUAAAUUCUCUACUCACGACAGAAAUGCUGGGAUCUCCAGCGUAUAUU
--------............................(((((((.....)))))))..... (  -9.80, z-score =  -1.13, R)
>droPer1.super_45 528089 52 + 618639
--------GGAUAUAAAUUAUCUACUCACGACAGAAAUGCUGGGAUCGCCAGCGUAUAUU
--------(((((.....))))).............(((((((.....)))))))..... ( -12.60, z-score =  -2.30, R)
>triCas2.ChLG9 9473649 60 - 15222296
AGCACAGUGCUAUAAAUUGUGAUACUUACGACACAGUUUUUGCGAUCGCCACUUAAUCGG
.((....(((...((((((((..........))))))))..)))...))........... ( -10.10, z-score =  -0.28, R)
>consensus
________AGGUAAAUAUUAUAUACUCACGGCAGAAAUGCUGGGAUCUCCAGCGAAUAUU
.........................((.(((((....))))).))............... ( -4.60 =  -4.74 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:24:39 2011