Locus 4669

Sequence ID dm3.chr2R
Location 14,949,059 – 14,949,165
Length 106
Max. P 0.816420
window6411 window6412

overview

Window 1

Location 14,949,059 – 14,949,165
Length 106
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.96
Shannon entropy 0.34713
G+C content 0.46694
Mean single sequence MFE -34.22
Consensus MFE -22.84
Energy contribution -24.28
Covariance contribution 1.45
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.67
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.78
SVM RNA-class probability 0.816420
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14949059 106 + 21146708
AAGUGUGUGCCAUAGUAUGUGCAAGUGUACUGGCUGCACAUACAUAGACAUUAAAUGGGGCACAUAAUGUGCCGGG--AGUCAGGAAUCGAGAAUCAGAAUUCAGGCU----
...((((((((...(((((((((.((......))))))))))).....(((...))).))))))))....(((..(--(((...((........))...)))).))).---- ( -33.40, z-score =  -1.96, R)
>droSim1.chr2R 13648579 110 + 19596830
AAGUGUGUGCCAUAGUAUGUGCGAGUGUACUGGCUGCACAUACAUAGACAUUAAAUGGGGCACAUAAUGUGCUGGG--AGUCAGGAAUCGAGAAUCAGGAUUCAGGCUUCAG
...((((((((...((((((((.(((......))))))))))).....(((...))).))))))))........((--((((..(((((.........))))).)))))).. ( -37.00, z-score =  -2.51, R)
>droSec1.super_1 12455528 106 + 14215200
AAGUGUGUGCCAUAGUAUGUGCGAGUGUACUGGCUGCACAUACAUAGACAUUAAAUGGGGCACAUAAUGUGCUGGU--AGUCAGGAAUCGAGAAUCAGGAUUCAGGCU----
...((((((((...((((((((.(((......))))))))))).....(((...))).))))))))....(((.(.--((((..((........))..))))).))).---- ( -32.40, z-score =  -1.29, R)
>droYak2.chr2R 6904726 112 - 21139217
AAGUGUGUGCCAUAGUAUGUGCUAGUGUACUGGGUGCACAUACAUAGACAUUAAAUGGGGCACAUAAUGUGCCGGAGAAAUCAGGAAUCGAGAAUCAGGAAUCAGUACUAAG
..(((((..((.(((((..(....)..)))))))..)))))...(((((.........(((((.....))))).((....))......................)).))).. ( -31.30, z-score =  -1.79, R)
>droEre2.scaffold_4845 9146208 108 + 22589142
AAGUGUGUGCCAUAGUAUGUGCUAGUGUACUGGGUGCACAUACAUAGACAUUAAAUGGGGCACAUAAUGUGCCGGG--AGUCAGGAAUCGAGAAUCAGGAAUCAGGACAG--
..(((((..((.(((((..(....)..)))))))..))))).................(((((.....)))))...--.(((..((.((.........)).))..)))..-- ( -33.10, z-score =  -2.04, R)
>droAna3.scaffold_13266 2523024 98 - 19884421
AAGUGGGUGUUGUACUGUGUGUG------------GCACAUACACUGGCAUUAAAUGGGGCACAUAAUGUGCUGCG--AGUCAGGAGUCACUACCCAGUACCCGGCACCCGG
...((((((((((((((.(((((------------((.......(((((......((.(((((.....))))).))--.)))))..))))).)).))))))..)))))))). ( -38.10, z-score =  -1.10, R)
>consensus
AAGUGUGUGCCAUAGUAUGUGCGAGUGUACUGGCUGCACAUACAUAGACAUUAAAUGGGGCACAUAAUGUGCCGGG__AGUCAGGAAUCGAGAAUCAGGAUUCAGGAC____
..((((((((..(((((..(....)..)))))...))))))))...............(((((.....)))))...........(((((.........)))))......... (-22.84 = -24.28 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 14,949,059 – 14,949,165
Length 106
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 81.96
Shannon entropy 0.34713
G+C content 0.46694
Mean single sequence MFE -25.85
Consensus MFE -17.03
Energy contribution -17.95
Covariance contribution 0.92
Combinations/Pair 1.14
Mean z-score -1.44
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.04
SVM RNA-class probability 0.516618
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 14949059 106 - 21146708
----AGCCUGAAUUCUGAUUCUCGAUUCCUGACU--CCCGGCACAUUAUGUGCCCCAUUUAAUGUCUAUGUAUGUGCAGCCAGUACACUUGCACAUACUAUGGCACACACUU
----.(((.((((....)))).........(((.--...(((((.....))))).........)))...((((((((((.........))))))))))...)))........ ( -25.82, z-score =  -1.78, R)
>droSim1.chr2R 13648579 110 - 19596830
CUGAAGCCUGAAUCCUGAUUCUCGAUUCCUGACU--CCCAGCACAUUAUGUGCCCCAUUUAAUGUCUAUGUAUGUGCAGCCAGUACACUCGCACAUACUAUGGCACACACUU
..(((....((((....))))....)))......--....((((.....)))).........((((...((((((((((........)).))))))))...))))....... ( -23.90, z-score =  -1.26, R)
>droSec1.super_1 12455528 106 - 14215200
----AGCCUGAAUCCUGAUUCUCGAUUCCUGACU--ACCAGCACAUUAUGUGCCCCAUUUAAUGUCUAUGUAUGUGCAGCCAGUACACUCGCACAUACUAUGGCACACACUU
----.(((.(((((.........)))))..(((.--....((((.....))))..........)))...((((((((((........)).))))))))...)))........ ( -23.36, z-score =  -1.27, R)
>droYak2.chr2R 6904726 112 + 21139217
CUUAGUACUGAUUCCUGAUUCUCGAUUCCUGAUUUCUCCGGCACAUUAUGUGCCCCAUUUAAUGUCUAUGUAUGUGCACCCAGUACACUAGCACAUACUAUGGCACACACUU
.......................................(((((.....)))))........((((...((((((((.............))))))))...))))....... ( -23.22, z-score =  -1.35, R)
>droEre2.scaffold_4845 9146208 108 - 22589142
--CUGUCCUGAUUCCUGAUUCUCGAUUCCUGACU--CCCGGCACAUUAUGUGCCCCAUUUAAUGUCUAUGUAUGUGCACCCAGUACACUAGCACAUACUAUGGCACACACUU
--..(((..((.((.........)).))..))).--...(((((.....)))))........((((...((((((((.............))))))))...))))....... ( -25.72, z-score =  -2.16, R)
>droAna3.scaffold_13266 2523024 98 + 19884421
CCGGGUGCCGGGUACUGGGUAGUGACUCCUGACU--CGCAGCACAUUAUGUGCCCCAUUUAAUGCCAGUGUAUGUGC------------CACACACAGUACAACACCCACUU
..(((((....((((((((((((((........)--))).((((.....)))).........)))).((((......------------.)))).))))))..))))).... ( -33.10, z-score =  -0.85, R)
>consensus
____AGCCUGAAUCCUGAUUCUCGAUUCCUGACU__CCCAGCACAUUAUGUGCCCCAUUUAAUGUCUAUGUAUGUGCAGCCAGUACACUCGCACAUACUAUGGCACACACUU
.........(((((.........)))))............((((.....)))).........((((...((((((((.............))))))))...))))....... (-17.03 = -17.95 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:33:45 2011