Locus 6

Sequence ID dm3.chr2LHet
Location 258,180 – 258,250
Length 70
Max. P 0.999720
window9 window10

overview

Window 9

Location 258,180 – 258,250
Length 70
Sequences 5
Columns 70
Reading direction forward
Mean pairwise identity 58.35
Shannon entropy 0.74354
G+C content 0.43583
Mean single sequence MFE -11.24
Consensus MFE -6.58
Energy contribution -7.22
Covariance contribution 0.64
Combinations/Pair 1.50
Mean z-score -2.24
Structure conservation index 0.59
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 4.25
SVM RNA-class probability 0.999720
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2LHet 258180 70 + 368872
CAUGAUAGUUAGCGAAUUAUCACCACUAGACCGAGCUCGCCCCGUUAGCCUGAAAGGCUAACAACACACG
..((((((((....)))))))).....................(((((((.....)))))))........ ( -16.40, z-score =  -2.86, R)
>droSim1.chr2h_random 2530038 70 - 3178526
CACGAUAGUUCACGAAUUAUUACCUCUAGCCCGAGAUCGCCCCGUUAGCCAGGAAGAAUAACCUUACACG
...(((((((....))))))).((((((((.((....))....)))))..)))................. (  -8.50, z-score =  -0.28, R)
>droSec1.super_41 58351 70 + 296808
CAUGUAAGUUAGCAAACUAUCACCUCUACCCCAAGCUCGCCCCGUUAGCCAUUAAGGCUAACAACACACG
..(((..((.(((.....................))).))...(((((((.....))))))).))).... ( -13.10, z-score =  -3.12, R)
>droEre2.scaffold_4845 261897 57 + 22589142
UACGAUAGUUAGCGAAUUAUCACCAUUA-------------UUAUUAGCUUGGAAGGCUAACAACACACG
...(((((((....))))))).......-------------...((((((.....))))))......... (  -9.80, z-score =  -2.49, R)
>droPer1.super_120 50364 56 - 124538
---GCUAUUUACAAAAGGAUCACACCACAG-----------GAAUUUAUCCGUAAUAGUAGUCAUACAAA
---((((((.((....((......))...(-----------((.....)))))))))))........... (  -8.40, z-score =  -2.44, R)
>consensus
CACGAUAGUUAGCGAAUUAUCACCACUAGCCC_AG_UCGCCCCGUUAGCCAGGAAGGCUAACAACACACG
...(((((((....)))))))......................(((((((.....)))))))........ ( -6.58 =  -7.22 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 258,180 – 258,250
Length 70
Sequences 5
Columns 70
Reading direction reverse
Mean pairwise identity 58.35
Shannon entropy 0.74354
G+C content 0.43583
Mean single sequence MFE -16.89
Consensus MFE -5.28
Energy contribution -6.68
Covariance contribution 1.40
Combinations/Pair 1.64
Mean z-score -1.67
Structure conservation index 0.31
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.87
SVM RNA-class probability 0.840669
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2LHet 258180 70 - 368872
CGUGUGUUGUUAGCCUUUCAGGCUAACGGGGCGAGCUCGGUCUAGUGGUGAUAAUUCGCUAACUAUCAUG
..(((.(((((((((.....))))))))).))).........(((((((((....))))).))))..... ( -22.90, z-score =  -2.19, R)
>droSim1.chr2h_random 2530038 70 + 3178526
CGUGUAAGGUUAUUCUUCCUGGCUAACGGGGCGAUCUCGGGCUAGAGGUAAUAAUUCGUGAACUAUCGUG
.((....(((((((((((.(((((..((((.....))))))))))))).))))))).....))....... ( -15.50, z-score =   0.15, R)
>droSec1.super_41 58351 70 - 296808
CGUGUGUUGUUAGCCUUAAUGGCUAACGGGGCGAGCUUGGGGUAGAGGUGAUAGUUUGCUAACUUACAUG
(((((((((((((((.....)))))))))((((((((...............))))))))....)))))) ( -23.66, z-score =  -2.74, R)
>droEre2.scaffold_4845 261897 57 - 22589142
CGUGUGUUGUUAGCCUUCCAAGCUAAUAA-------------UAAUGGUGAUAAUUCGCUAACUAUCGUA
....((((((((((.......))))))))-------------)).((((((....))))))......... ( -14.50, z-score =  -3.12, R)
>droPer1.super_120 50364 56 + 124538
UUUGUAUGACUACUAUUACGGAUAAAUUC-----------CUGUGGUGUGAUCCUUUUGUAAAUAGC---
.......((.(((.((((((((.....))-----------).)))))))).))..............--- (  -7.90, z-score =  -0.43, R)
>consensus
CGUGUGUUGUUAGCCUUACAGGCUAACGGGGCGA_CU_GGGCUAGAGGUGAUAAUUCGCUAACUAUCAUG
...((.(((((((((.....))))))))).))...................................... ( -5.28 =  -6.68 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:04:48 2011