Locus 6177

Sequence ID dm3.chr3L
Location 4,385,784 – 4,385,835
Length 51
Max. P 0.998612
window8491 window8492

overview

Window 1

Location 4,385,784 – 4,385,835
Length 51
Sequences 8
Columns 54
Reading direction forward
Mean pairwise identity 78.63
Shannon entropy 0.41008
G+C content 0.53592
Mean single sequence MFE -20.58
Consensus MFE -17.41
Energy contribution -17.75
Covariance contribution 0.34
Combinations/Pair 1.13
Mean z-score -3.01
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.42
SVM RNA-class probability 0.998612
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4385784 51 + 24543557
AGUUUGGGGCACGAUCCGUGGAAA-GCGAUCGUGCCUUUCUGCGUAUCAUAG--
.((..(((((((((((.((.....-)))))))))))))...)).........-- ( -20.30, z-score =  -3.11, R)
>droPer1.super_24 981463 52 - 1556852
AGUCUAGGGCACGAUUCCGCCCUAUGCGAUCGUGCCUUUGCGCAUAUCAUAA--
.((..((((((((((..(((.....))))))))))))).))...........-- ( -18.90, z-score =  -2.91, R)
>dp4.chrXR_group8 2475175 52 + 9212921
AGUCUAGGGCACGAUUCGGCCCUAUGCGAUCGUGCCUUUGCGCAUGUCAUAA--
.((.((((((.((...)))))))).))((.(((((......)))))))....-- ( -18.90, z-score =  -2.04, R)
>droAna3.scaffold_13337 2465081 52 + 23293914
UGUCUUGGGCACGAUUCGUCCGAAUGCGAUCGUGCCUUCCUGCAUAUCAUAA--
(((...(((((((((.(((......))))))))))))....)))........-- ( -18.40, z-score =  -3.11, R)
>droEre2.scaffold_4784 7093486 52 + 25762168
AGUUUGGGGCACGAUCCGCAGAAAAGCGAUCGUGCCUUCCUGCAUAUCGUAA--
.((..(((((((((((.((......)))))))))))))...)).........-- ( -21.40, z-score =  -3.43, R)
>droYak2.chr3L 4961405 52 + 24197627
AGUUUGGGGCACGAUCCGCAGAAAAGCGAUCGUGCCUUCCUGCAUAUCGUAA--
.((..(((((((((((.((......)))))))))))))...)).........-- ( -21.40, z-score =  -3.43, R)
>droSec1.super_2 4375598 52 + 7591821
AGUUUGGG-CACGAUCCGUGGAAA-GCGAUCGUGCCUUCCUGCGUAUCGCGUAG
.....(((-(((((((.((.....-))))))))))))..(((((.....))))) ( -22.40, z-score =  -3.14, R)
>droSim1.chr3L 3922135 53 + 22553184
AGUUUGGGGCACGAUCCGUGGAAA-GCGAUCGUGCCUUCCUGCGUAUCGCGUAG
.....(((((((((((.((.....-))))))))))))).(((((.....))))) ( -22.90, z-score =  -2.89, R)
>consensus
AGUUUGGGGCACGAUCCGUCGAAA_GCGAUCGUGCCUUCCUGCAUAUCAUAA__
.((..((((((((((.(((......)))))))))))))...))........... (-17.41 = -17.75 +   0.34)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 4,385,784 – 4,385,835
Length 51
Sequences 8
Columns 54
Reading direction reverse
Mean pairwise identity 78.63
Shannon entropy 0.41008
G+C content 0.53592
Mean single sequence MFE -17.86
Consensus MFE -13.15
Energy contribution -13.40
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.71
Structure conservation index 0.74
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.04
SVM RNA-class probability 0.997134
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3L 4385784 51 - 24543557
--CUAUGAUACGCAGAAAGGCACGAUCGC-UUUCCACGGAUCGUGCCCCAAACU
--................(((((((((..-........)))))))))....... ( -15.40, z-score =  -2.79, R)
>droPer1.super_24 981463 52 + 1556852
--UUAUGAUAUGCGCAAAGGCACGAUCGCAUAGGGCGGAAUCGUGCCCUAGACU
--................(((((((((((.....)))..))))))))....... ( -16.20, z-score =  -1.52, R)
>dp4.chrXR_group8 2475175 52 - 9212921
--UUAUGACAUGCGCAAAGGCACGAUCGCAUAGGGCCGAAUCGUGCCCUAGACU
--................(((((((((((.....).)).))))))))....... ( -14.30, z-score =  -0.91, R)
>droAna3.scaffold_13337 2465081 52 - 23293914
--UUAUGAUAUGCAGGAAGGCACGAUCGCAUUCGGACGAAUCGUGCCCAAGACA
--................((((((((((........)).))))))))....... ( -14.40, z-score =  -1.66, R)
>droEre2.scaffold_4784 7093486 52 - 25762168
--UUACGAUAUGCAGGAAGGCACGAUCGCUUUUCUGCGGAUCGUGCCCCAAACU
--.((((((.(((((((((((......))))))))))).))))))......... ( -22.50, z-score =  -4.42, R)
>droYak2.chr3L 4961405 52 - 24197627
--UUACGAUAUGCAGGAAGGCACGAUCGCUUUUCUGCGGAUCGUGCCCCAAACU
--.((((((.(((((((((((......))))))))))).))))))......... ( -22.50, z-score =  -4.42, R)
>droSec1.super_2 4375598 52 - 7591821
CUACGCGAUACGCAGGAAGGCACGAUCGC-UUUCCACGGAUCGUG-CCCAAACU
...((((((.((..(((((((......))-))))).)).))))))-........ ( -18.70, z-score =  -2.98, R)
>droSim1.chr3L 3922135 53 - 22553184
CUACGCGAUACGCAGGAAGGCACGAUCGC-UUUCCACGGAUCGUGCCCCAAACU
....(((...))).((..(((((((((..-........)))))))))))..... ( -18.90, z-score =  -2.94, R)
>consensus
__UUACGAUAUGCAGGAAGGCACGAUCGC_UUUCCACGGAUCGUGCCCCAAACU
..................((((((((((........)).))))))))....... (-13.15 = -13.40 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:02:39 2011