Locus 2350

Sequence ID dm3.chr2L
Location 18,232,210 – 18,232,311
Length 101
Max. P 0.985180
window3237 window3238

overview

Window 7

Location 18,232,210 – 18,232,311
Length 101
Sequences 7
Columns 102
Reading direction forward
Mean pairwise identity 82.03
Shannon entropy 0.37065
G+C content 0.41067
Mean single sequence MFE -25.32
Consensus MFE -16.75
Energy contribution -19.30
Covariance contribution 2.55
Combinations/Pair 1.14
Mean z-score -2.50
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.19
SVM RNA-class probability 0.985180
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18232210 101 + 23011544
CCAGAGAAUAUGCAAUUAUUCAUUUUGCCG-AACUAAUGACGCAAUUAGUUGGGGCAACUGUACUCGCAGACAAAUGGAAGCGAUUACAGGUGAAUAUGAAU
................(((((((.(((((.-(((((((......))))))).).))))(((((.((((...(....)...)))).))))))))))))..... ( -27.80, z-score =  -3.14, R)
>droSim1.chr2L 17914697 101 + 22036055
CCAGAGAAUAUGCAAUUAUUCAUUUUGCCG-AACUAAUGACGCAAUUAGUUGGGGCAACUGUACUCGCAGACAAAUGGAAGCGAUUACAGGUGAAUAUGAAU
................(((((((.(((((.-(((((((......))))))).).))))(((((.((((...(....)...)))).))))))))))))..... ( -27.80, z-score =  -3.14, R)
>droSec1.super_7 1857920 101 + 3727775
CCAGAGAAUAUGCAAUUAUUCAUUUUGCCG-AACUAAUGACGCAAUUAGUUGGGGCAACUGUACUCGCAGACAAAUGGAAGCGAUUACAGGUGAAUAUGAAU
................(((((((.(((((.-(((((((......))))))).).))))(((((.((((...(....)...)))).))))))))))))..... ( -27.80, z-score =  -3.14, R)
>droYak2.chr2R 4742496 101 + 21139217
CCACAGAAUAUGCAAUUAUUCAUUUUGCCG-AACUAAUGACGCAAUUAGUUGGGGCAACUGUACUCGCAGACAAAUGGAAGCGAUUACAGGUGAAUAUGAAU
.(((.(((((......)))))...(((((.-(((((((......))))))).).))))(((((.((((...(....)...)))).))))))))......... ( -28.60, z-score =  -3.43, R)
>droEre2.scaffold_4845 16551484 101 - 22589142
CCAGAGAAUAUGCAAUUAUUCAUUUUGCCG-AACUAAUGACGCAAUUAGUUGGGGCAACUGUACUCGCAGACAAAUGGAAGCGAUUACAGGUGAAUAUGAAU
................(((((((.(((((.-(((((((......))))))).).))))(((((.((((...(....)...)))).))))))))))))..... ( -27.80, z-score =  -3.14, R)
>droAna3.scaffold_12916 2159299 92 + 16180835
---------GUGCAAUUAUUCAUCUUGCAG-AACUAAUGACGCAAUUAGUUGGGGCAACUGUACUCGGAGACAAAUGAAAGCGAUUACAGGUGAAUGGGAAU
---------......((((((((.((((..-(((((((......)))))))...))))(((((.(((..............))).))))))))))))).... ( -21.64, z-score =  -1.64, R)
>dp4.chr4_group3 7087216 81 - 11692001
-UCUGGAAUAUGCAAUUAUUCAUUUCAGAGCAACUAAUGAUGCAAUUAGAUGGGG-GCCAAUACA-GGGGGUGGGGGGCGGUGG------------------
-((((((((............)))))))).((.(((((......))))).))...-(((..(((.-....)))...))).....------------------ ( -15.80, z-score =   0.13, R)
>consensus
CCAGAGAAUAUGCAAUUAUUCAUUUUGCCG_AACUAAUGACGCAAUUAGUUGGGGCAACUGUACUCGCAGACAAAUGGAAGCGAUUACAGGUGAAUAUGAAU
................(((((((.(((((..(((((((......)))))))..)))))(((((.((((...(....)...)))).))))))))))))..... (-16.75 = -19.30 +   2.55)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,232,210 – 18,232,311
Length 101
Sequences 7
Columns 102
Reading direction reverse
Mean pairwise identity 82.03
Shannon entropy 0.37065
G+C content 0.41067
Mean single sequence MFE -20.97
Consensus MFE -13.76
Energy contribution -16.80
Covariance contribution 3.04
Combinations/Pair 1.04
Mean z-score -2.30
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.87
SVM RNA-class probability 0.972230
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 18232210 101 - 23011544
AUUCAUAUUCACCUGUAAUCGCUUCCAUUUGUCUGCGAGUACAGUUGCCCCAACUAAUUGCGUCAUUAGUU-CGGCAAAAUGAAUAAUUGCAUAUUCUCUGG
.....((((((.(((((.((((............)))).)))))(((((..(((((((......)))))))-.)))))..))))))................ ( -24.60, z-score =  -3.16, R)
>droSim1.chr2L 17914697 101 - 22036055
AUUCAUAUUCACCUGUAAUCGCUUCCAUUUGUCUGCGAGUACAGUUGCCCCAACUAAUUGCGUCAUUAGUU-CGGCAAAAUGAAUAAUUGCAUAUUCUCUGG
.....((((((.(((((.((((............)))).)))))(((((..(((((((......)))))))-.)))))..))))))................ ( -24.60, z-score =  -3.16, R)
>droSec1.super_7 1857920 101 - 3727775
AUUCAUAUUCACCUGUAAUCGCUUCCAUUUGUCUGCGAGUACAGUUGCCCCAACUAAUUGCGUCAUUAGUU-CGGCAAAAUGAAUAAUUGCAUAUUCUCUGG
.....((((((.(((((.((((............)))).)))))(((((..(((((((......)))))))-.)))))..))))))................ ( -24.60, z-score =  -3.16, R)
>droYak2.chr2R 4742496 101 - 21139217
AUUCAUAUUCACCUGUAAUCGCUUCCAUUUGUCUGCGAGUACAGUUGCCCCAACUAAUUGCGUCAUUAGUU-CGGCAAAAUGAAUAAUUGCAUAUUCUGUGG
.....((((((.(((((.((((............)))).)))))(((((..(((((((......)))))))-.)))))..)))))).(..((.....))..) ( -25.10, z-score =  -2.82, R)
>droEre2.scaffold_4845 16551484 101 + 22589142
AUUCAUAUUCACCUGUAAUCGCUUCCAUUUGUCUGCGAGUACAGUUGCCCCAACUAAUUGCGUCAUUAGUU-CGGCAAAAUGAAUAAUUGCAUAUUCUCUGG
.....((((((.(((((.((((............)))).)))))(((((..(((((((......)))))))-.)))))..))))))................ ( -24.60, z-score =  -3.16, R)
>droAna3.scaffold_12916 2159299 92 - 16180835
AUUCCCAUUCACCUGUAAUCGCUUUCAUUUGUCUCCGAGUACAGUUGCCCCAACUAAUUGCGUCAUUAGUU-CUGCAAGAUGAAUAAUUGCAC---------
......(((((.(((((.(((....(....)....))).)))))((((...(((((((......)))))))-..))))..)))))........--------- ( -16.10, z-score =  -1.57, R)
>dp4.chr4_group3 7087216 81 + 11692001
------------------CCACCGCCCCCCACCCCC-UGUAUUGGC-CCCCAUCUAAUUGCAUCAUUAGUUGCUCUGAAAUGAAUAAUUGCAUAUUCCAGA-
------------------.....(((...((.....-))....)))-............(((........)))((((....(((((......)))))))))- (  -7.20, z-score =   0.90, R)
>consensus
AUUCAUAUUCACCUGUAAUCGCUUCCAUUUGUCUGCGAGUACAGUUGCCCCAACUAAUUGCGUCAUUAGUU_CGGCAAAAUGAAUAAUUGCAUAUUCUCUGG
.....((((((.(((((.((((............)))).)))))(((((..(((((((......)))))))..)))))..))))))................ (-13.76 = -16.80 +   3.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:49:37 2011