Locus 9806

Sequence ID	dm3.chr3R
Location	9,201,861 – 9,201,961
Length	100
Max. P	0.933161

overview

Window 4

Location	9,201,861 – 9,201,961
Length	100
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	63.92
Shannon entropy	0.53511
G+C content	0.39843
Mean single sequence MFE	-21.93
Consensus MFE	-9.06
Energy contribution	-11.12
Covariance contribution	2.06
Combinations/Pair	1.30
Mean z-score	-1.55
Structure conservation index	0.41
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.07
SVM RNA-class probability	0.526687
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9201861 100 + 27905053
-----UUAGUGUUUUAAAGGGGAUCAACUUACCGCAUGCAUUAAGCGCGGGUAGCUACCCGCAAUAAAUUAGUCAUAGAUUAUUCGAGUGGGAAUCGAAAACUGC
-----(((((((......((...........))....)))))))((((((((....))))))....................(((((.......)))))....)) ( -21.90, z-score =  -0.23, R)
>droSim1.chr2h_random 1478244 84 - 3178526
-------AUAUUUUCCAAGGGGAUCAGCUUUCCGUAUGCAUUAAGCGCGGGGAGCUGU--------------UUAUAAAUUAUUCAAGUGGGAAUCGAAAACUGC
-------....((((((...(((((((((..((((..((.....))))))..))))).--------------.........))))...))))))........... ( -24.80, z-score =  -2.55, R)
>droSec1.super_114 43131 84 + 67029
-------AUAUUUUCCAAGGGGAUCAGCUUUCCGUAUGCAUUAAGCGCGGGGAGCUGU--------------UUAUAAAUUAUUCAAGUGGGAAUCGAAAACUGA
-------....((((((...(((((((((..((((..((.....))))))..))))).--------------.........))))...))))))........... ( -24.80, z-score =  -2.49, R)
>droYak2.chrU 2918162 88 + 28119190
UCAGUUCAAUAGUUUCAGGGAAACUAUUUUUCCUUAGGCGAUAGGCACGAAUAUUUGU---------------CAUACUUUAUUUAAGGGGG--UUAAAAGCUUG
..((((.(((((((((...)))))))))(..(((((((..(..((((........)))---------------).....)..)))))))..)--.....)))).. ( -16.20, z-score =  -0.94, R)
>consensus
_______AUAUUUUCCAAGGGGAUCAGCUUUCCGUAUGCAUUAAGCGCGGGGAGCUGU______________UCAUAAAUUAUUCAAGUGGGAAUCGAAAACUGC
...........((((((...(((((((((((((((..((.....)))))))))))))........................))))...))))))........... ( -9.06 = -11.12 +   2.06)

alignment

secondary structure

dotplot

Window 5

Location	9,201,861 – 9,201,961
Length	100
Sequences	4
Columns	105
Reading direction	reverse
Mean pairwise identity	63.92
Shannon entropy	0.53511
G+C content	0.39843
Mean single sequence MFE	-17.66
Consensus MFE	-7.94
Energy contribution	-8.12
Covariance contribution	0.19
Combinations/Pair	1.44
Mean z-score	-2.00
Structure conservation index	0.45
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.38
SVM RNA-class probability	0.933161
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9201861 100 - 27905053
GCAGUUUUCGAUUCCCACUCGAAUAAUCUAUGACUAAUUUAUUGCGGGUAGCUACCCGCGCUUAAUGCAUGCGGUAAGUUGAUCCCCUUUAAAACACUAA-----
...((((((((.......)))).........((.(((((((((((((((....))))..((.....))..))))))))))).)).......)))).....----- ( -22.20, z-score =  -1.55, R)
>droSim1.chr2h_random 1478244 84 + 3178526
GCAGUUUUCGAUUCCCACUUGAAUAAUUUAUAA--------------ACAGCUCCCCGCGCUUAAUGCAUACGGAAAGCUGAUCCCCUUGGAAAAUAU-------
...((((((.((((......)))).........--------------.(((((..(((.((.....))...)))..))))).........))))))..------- ( -17.20, z-score =  -1.89, R)
>droSec1.super_114 43131 84 - 67029
UCAGUUUUCGAUUCCCACUUGAAUAAUUUAUAA--------------ACAGCUCCCCGCGCUUAAUGCAUACGGAAAGCUGAUCCCCUUGGAAAAUAU-------
...((((((.((((......)))).........--------------.(((((..(((.((.....))...)))..))))).........))))))..------- ( -17.20, z-score =  -2.12, R)
>droYak2.chrU 2918162 88 - 28119190
CAAGCUUUUAA--CCCCCUUAAAUAAAGUAUG---------------ACAAAUAUUCGUGCCUAUCGCCUAAGGAAAAAUAGUUUCCCUGAAACUAUUGAACUGA
...........--...(((((......(((((---------------(.......))))))........)))))...(((((((((...)))))))))....... ( -14.04, z-score =  -2.44, R)
>consensus
GCAGUUUUCGAUUCCCACUUGAAUAAUUUAUAA______________ACAGCUACCCGCGCUUAAUGCAUACGGAAAGCUGAUCCCCUUGAAAAAAAU_______
......(((((.......))))).........................(((((..((((((.....))..))))..)))))........................ ( -7.94 =  -8.12 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:11:31 2011