Locus 4239

Sequence ID dm3.chr2R
Location 11,616,685 – 11,616,781
Length 96
Max. P 0.999006
window5805 window5806

overview

Window 5

Location 11,616,685 – 11,616,781
Length 96
Sequences 9
Columns 101
Reading direction forward
Mean pairwise identity 88.11
Shannon entropy 0.23398
G+C content 0.38502
Mean single sequence MFE -22.18
Consensus MFE -17.66
Energy contribution -17.66
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.07
SVM RNA-class probability 0.886280
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11616685 96 + 21146708
AUGGCGGCGGGCGUUUG-----UCGAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
.......((((.((((.-----((....))...(((..(((.(((((((((...((((.......))))...))))))))).)))..)))..)))).)))) ( -22.10, z-score =  -1.09, R)
>droSim1.chr2R 10352419 93 + 19596830
---AUGGCGGGCGUUUG-----UCGAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
---....((((.((((.-----((....))...(((..(((.(((((((((...((((.......))))...))))))))).)))..)))..)))).)))) ( -22.10, z-score =  -1.66, R)
>droSec1.super_1 9109955 93 + 14215200
---AUGGCGGGCGUUUG-----UCGAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
---....((((.((((.-----((....))...(((..(((.(((((((((...((((.......))))...))))))))).)))..)))..)))).)))) ( -22.10, z-score =  -1.66, R)
>droYak2.chr2R 3767657 98 - 21139217
---GUGGCAGGCGUUUGGAAAGCCGAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGACACUCG
---......(((.........)))(((.(....(((..(((.(((((((((...((((.......))))...))))))))).)))..))).....).))). ( -22.80, z-score =  -1.70, R)
>droEre2.scaffold_4845 8343206 93 - 22589142
---AUGGCAGGCGUUUG-----CCGAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
---.((((((....)))-----))).((((...(((..(((.(((((((((...((((.......))))...))))))))).)))..))).....).))). ( -23.60, z-score =  -2.08, R)
>droAna3.scaffold_13266 7303241 82 - 19884421
-------------------AGGCCGAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
-------------------..(((..(((.........(((.(((((((((...((((.......))))...))))))))).))).)))....)))..... ( -18.80, z-score =  -2.15, R)
>dp4.chr3 207488 92 - 19779522
--GGUGGC--GCGUUUG-----CCAAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
--..((((--(....))-----))).((((...(((..(((.(((((((((...((((.......))))...))))))))).)))..))).....).))). ( -23.10, z-score =  -1.93, R)
>droPer1.super_37 186709 92 - 760358
--GGUGGC--GCGUUUG-----CCAAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
--..((((--(....))-----))).((((...(((..(((.(((((((((...((((.......))))...))))))))).)))..))).....).))). ( -23.10, z-score =  -1.93, R)
>droWil1.scaffold_180699 1599169 83 - 2593675
------------------GGAAGGGUGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
------------------....(((((......(((..(((.(((((((((...((((.......))))...))))))))).)))..))).....))))). ( -21.90, z-score =  -3.46, R)
>consensus
___GUGGC_GGCGUUUG_____CCGAGAGGAAAUGAAAUGUGUGUCAAUAUAUUGAUUGAAUAAUGGUCUACAUAUUGACAAACAACUCAAAAGGCACUCG
..........................((((...(((..(((.(((((((((...((((.......))))...))))))))).)))..))).....).))). (-17.66 = -17.66 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,616,685 – 11,616,781
Length 96
Sequences 9
Columns 101
Reading direction reverse
Mean pairwise identity 88.11
Shannon entropy 0.23398
G+C content 0.38502
Mean single sequence MFE -22.72
Consensus MFE -20.47
Energy contribution -20.52
Covariance contribution 0.05
Combinations/Pair 1.04
Mean z-score -3.95
Structure conservation index 0.90
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.59
SVM RNA-class probability 0.999006
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 11616685 96 - 21146708
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUCGA-----CAAACGCCCGCCGCCAU
((((.......((((.(((.(((((((((((.((...........)).))))))))))).))).))))......)))).-----................. ( -21.82, z-score =  -3.47, R)
>droSim1.chr2R 10352419 93 - 19596830
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUCGA-----CAAACGCCCGCCAU---
((((.......((((.(((.(((((((((((.((...........)).))))))))))).))).))))......)))).-----..............--- ( -21.82, z-score =  -3.88, R)
>droSec1.super_1 9109955 93 - 14215200
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUCGA-----CAAACGCCCGCCAU---
((((.......((((.(((.(((((((((((.((...........)).))))))))))).))).))))......)))).-----..............--- ( -21.82, z-score =  -3.88, R)
>droYak2.chr2R 3767657 98 + 21139217
CGAGUGUCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUCGGCUUUCCAAACGCCUGCCAC---
.(((.......((((.(((.(((((((((((.((...........)).))))))))))).))).))))......)))(((.............)))..--- ( -24.24, z-score =  -3.92, R)
>droEre2.scaffold_4845 8343206 93 + 22589142
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUCGG-----CAAACGCCUGCCAU---
.(((.......((((.(((.(((((((((((.((...........)).))))))))))).))).))))......)))((-----((......))))..--- ( -26.22, z-score =  -4.60, R)
>droAna3.scaffold_13266 7303241 82 + 19884421
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUCGGCCU-------------------
((((.......((((.(((.(((((((((((.((...........)).))))))))))).))).))))......))))....------------------- ( -22.02, z-score =  -4.26, R)
>dp4.chr3 207488 92 + 19779522
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUUGG-----CAAACGC--GCCACC--
.(((.(.....((((.(((.(((((((((((.((...........)).))))))))))).))).))))...)))).(((-----(......--))))..-- ( -23.70, z-score =  -3.67, R)
>droPer1.super_37 186709 92 + 760358
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUUGG-----CAAACGC--GCCACC--
.(((.(.....((((.(((.(((((((((((.((...........)).))))))))))).))).))))...)))).(((-----(......--))))..-- ( -23.70, z-score =  -3.67, R)
>droWil1.scaffold_180699 1599169 83 + 2593675
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCACCCUUCC------------------
.(((.(.....((((.(((.(((((((((((.((...........)).))))))))))).))).))))...))))........------------------ ( -19.10, z-score =  -4.18, R)
>consensus
CGAGUGCCUUUUGAGUUGUUUGUCAAUAUGUAGACCAUUAUUCAAUCAAUAUAUUGACACACAUUUCAUUUCCUCUCGG_____CAAACGCC_GCCAC___
((((.......((((.(((.(((((((((((.((...........)).))))))))))).))).))))......))))....................... (-20.47 = -20.52 +   0.05)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:25:20 2011