Locus 8856

Sequence ID dm3.chr3R
Location 2,150,123 – 2,150,175
Length 52
Max. P 0.971849
window12154 window12155

overview

Window 4

Location 2,150,123 – 2,150,175
Length 52
Sequences 4
Columns 58
Reading direction forward
Mean pairwise identity 76.90
Shannon entropy 0.37344
G+C content 0.46345
Mean single sequence MFE -12.47
Consensus MFE -9.99
Energy contribution -9.68
Covariance contribution -0.31
Combinations/Pair 1.36
Mean z-score -1.17
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.66
SVM RNA-class probability 0.776824
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2150123 52 + 27905053
GAUCUCUCUU--UUGGCCAUAAACGCCCGUGUCAGGCC----UUAUGGCUUUAUGUGA
....((.(..--..((((((((..(((.......))).----))))))))....).)) ( -13.70, z-score =  -1.72, R)
>droYak2.chr3R 18077594 54 + 28832112
GAUCUCCGUUCAUUGGUCAUAAACGUUUGAGUCAAGCUGGCUUUAUGGUUGUGG----
.....(((.....))).(((((.(((..(((((.....))))).))).))))).---- ( -10.30, z-score =  -0.33, R)
>droSec1.super_6 2235759 56 + 4358794
AAUCUCUCUU--UUGGUCAUAAACGCCCGAGUCGGGCUGUCUUUAUGGCUUUAUGUGG
.....(.(..--..(((((((((((((((...))))).))..))))))))....).). ( -15.30, z-score =  -2.44, R)
>droSim1.chr3R 2176014 56 + 27517382
GAUCUCUCUU--UUGGUCAUAAACGCCCGAGUCAGGCUGUCUUUAUGGCUUUAUGUGG
.....(.(..--..(((((((((.((((......))..)).)))))))))....).). ( -10.60, z-score =  -0.21, R)
>consensus
GAUCUCUCUU__UUGGUCAUAAACGCCCGAGUCAGGCUGUCUUUAUGGCUUUAUGUGG
..............(((((((((.(((((...)))))....)))))))))........ ( -9.99 =  -9.68 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 2,150,123 – 2,150,175
Length 52
Sequences 4
Columns 58
Reading direction reverse
Mean pairwise identity 76.90
Shannon entropy 0.37344
G+C content 0.46345
Mean single sequence MFE -11.30
Consensus MFE -7.80
Energy contribution -7.55
Covariance contribution -0.25
Combinations/Pair 1.27
Mean z-score -2.19
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.86
SVM RNA-class probability 0.971849
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 2150123 52 - 27905053
UCACAUAAAGCCAUAA----GGCCUGACACGGGCGUUUAUGGCCAA--AAGAGAGAUC
.........(((((((----((((((...))))).))))))))...--.......... ( -16.50, z-score =  -3.53, R)
>droYak2.chr3R 18077594 54 - 28832112
----CCACAACCAUAAAGCCAGCUUGACUCAAACGUUUAUGACCAAUGAACGGAGAUC
----...........(((....)))..(((...(((((((.....))))))))))... (  -7.90, z-score =  -1.33, R)
>droSec1.super_6 2235759 56 - 4358794
CCACAUAAAGCCAUAAAGACAGCCCGACUCGGGCGUUUAUGACCAA--AAGAGAGAUU
...........((((((....(((((...))))).)))))).....--.......... ( -11.50, z-score =  -2.77, R)
>droSim1.chr3R 2176014 56 - 27517382
CCACAUAAAGCCAUAAAGACAGCCUGACUCGGGCGUUUAUGACCAA--AAGAGAGAUC
...........((((((....(((((...))))).)))))).....--.......... (  -9.30, z-score =  -1.13, R)
>consensus
CCACAUAAAGCCAUAAAGACAGCCUGACUCGGGCGUUUAUGACCAA__AAGAGAGAUC
...........((((((....(((((...))))).))))))................. ( -7.80 =  -7.55 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 23:53:26 2011