Locus 12563

Sequence ID dm3.chrX
Location 903,655 – 903,794
Length 139
Max. P 0.992634
window17275 window17276 window17277

overview

Window 5

Location 903,655 – 903,755
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.72
Shannon entropy 0.31628
G+C content 0.33011
Mean single sequence MFE -22.56
Consensus MFE -15.94
Energy contribution -16.50
Covariance contribution 0.56
Combinations/Pair 1.16
Mean z-score -2.04
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.24
SVM RNA-class probability 0.915526
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 903655 100 - 22422827
AGGGGAAA-UUUUGGGACUUACUCAAACUCAA-GUGAGUGAGUUUAUUGUGCAGAAUAAAAUC---------------AGAGUAAAACUCAGUAGGA-AUGCA--AAAAACUCACUCAAA
..(((...-.((((((.....)))))))))..-.(((((((((((....((((((......))---------------.(((.....))).......-.))))--..))))))))))).. ( -26.30, z-score =  -2.96, R)
>droSim1.chrX_random 847169 100 - 5698898
AGGGGAAA-UUUUGGGACUUACUCAAACUCAA-GUGAGUGAGUUGUUUGUGCAGAAUAAAAAC---------------AGAGUAAAACUCAGUUGAA-AAGCA--AAAAACUCACACAAA
........-.((((.((((((((((.......-.))))))))))...((((.((.........---------------.(((.....))).(((...-.))).--.....)))))))))) ( -22.10, z-score =  -1.22, R)
>droSec1.super_10 746718 99 - 3036183
AGGGGAAA-UUUUGGGAC-UACUCAAACUCAA-GUGAGUGAGUUGUUUGUGCAGAAUAAAAAC---------------AGAGUAAAACUCAGUUGAA-AAGCA--AAAAACUCACACAAA
..(((...-.((((((..-..)))))))))..-(((((((((((.(((((...........))---------------)))....))))).(((...-.))).--....))))))..... ( -22.00, z-score =  -1.40, R)
>droYak2.chrX 826249 97 - 21770863
AGGGGAAAUUUUUGGGACUUACUCAAACUCAAAGUGAGUAAGUAAA------AAAUUAAAAAU---------------AGAGUAAAACUCAGUUGAAUAGUGA--AAAAACUCACUCAAA
.(((..(((((((...(((((((((.........))))))))).))------)))))......---------------.((((.....(((.(.....).)))--....)))).)))... ( -20.50, z-score =  -2.60, R)
>droEre2.scaffold_4644 883960 120 - 2521924
AGGGGAAAUUUUUGGGACGUACUCAAACUCAAUGUGAGUGGGUUGUUGGUGCAAAAAAAAAACAAAGAAAUAAAAAAUAGAGUAAAACUCAGUAUAAUAUCUAACAAAAACUCACUCAAA
..(((.....((((((.....)))))))))....(((((((((((((((................(....)........(((.....)))..........))))))...))))))))).. ( -21.90, z-score =  -2.01, R)
>consensus
AGGGGAAA_UUUUGGGACUUACUCAAACUCAA_GUGAGUGAGUUGUUUGUGCAGAAUAAAAAC_______________AGAGUAAAACUCAGUUGAA_AAGCA__AAAAACUCACUCAAA
..(((.....((((((.....)))))))))....((((((((((...................................(((.....))).(((.....)))......)))))))))).. (-15.94 = -16.50 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 903,692 – 903,794
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 76.48
Shannon entropy 0.38555
G+C content 0.34162
Mean single sequence MFE -20.22
Consensus MFE -14.41
Energy contribution -14.53
Covariance contribution 0.12
Combinations/Pair 1.22
Mean z-score -2.51
Structure conservation index 0.71
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.53
SVM RNA-class probability 0.992301
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 903692 102 + 22422827
---------------CUGAUUUUAUUCUGCACAAUAAACUCACUCAC-UUGAGUUUGAGUAAGUCCCAAAA--UUUCCCCUUCUUUUAGGACAAUUUUUUUGCAGACGAAACUUAAAACG
---------------.(((.(((..((((((...((((((((.....-.)))))))).....((((.((((--..........)))).))))........))))))..))).)))..... ( -20.30, z-score =  -2.85, R)
>droSim1.chrX_random 847206 102 + 5698898
---------------CUGUUUUUAUUCUGCACAAACAACUCACUCAC-UUGAGUUUGAGUAAGUCCCAAAA--UUUCCCCUCCUUUUAGGACAAUAUUUUUGUAGACGAAAAUUAAAACA
---------------..((((((..((((((.(((..((((((((..-..))))..))))..((((.((((--..........)))).))))....))).)))))).))))))....... ( -19.40, z-score =  -2.22, R)
>droSec1.super_10 746755 101 + 3036183
---------------CUGUUUUUAUUCUGCACAAACAACUCACUCAC-UUGAGUUUGAGUA-GUCCCAAAA--UUUCCCCUCCUUUUAGGACAAUAUUUUUGCAGACCAAAAUUAAAACA
---------------..(((((.((((((((.(((..((((((((..-..))))..)))).-((((.((((--..........)))).))))....))).)))))).....)).))))). ( -20.80, z-score =  -3.30, R)
>droYak2.chrX 826287 99 + 21770863
---------------------CUAUUUUUAAUUUUUUACUUACUCACUUUGAGUUUGAGUAAGUCCCAAAAAUUUCCCCUCCUUCUUGGGACAAUUUUUUGGCGGACGCAAAUGAAAACA
---------------------...((((((.....((((((((((.....))))..))))))(((((.((((((..(((........)))..))))))...).)))).....)))))).. ( -21.60, z-score =  -2.17, R)
>droEre2.scaffold_4644 884000 120 + 2521924
CUAUUUUUUAUUUCUUUGUUUUUUUUUUGCACCAACAACCCACUCACAUUGAGUUUGAGUACGUCCCAAAAAUUUCCCCUCCCUCUUGGGACAAUUUUUUUGCAGACACAAAUUAAAACA
................((((((...((((......(((...((((.....))))))).....(((.((((((.......((((....)))).....))))))..))).))))..)))))) ( -19.00, z-score =  -2.02, R)
>consensus
_______________CUGUUUUUAUUCUGCACAAACAACUCACUCAC_UUGAGUUUGAGUAAGUCCCAAAA__UUUCCCCUCCUUUUAGGACAAUUUUUUUGCAGACGAAAAUUAAAACA
.........................((((((......((((((((.....))))..))))..((((......................))))........)))))).............. (-14.41 = -14.53 +   0.12)

alignment

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secondary structure

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dotplot

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Window 7

Location 903,692 – 903,794
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.48
Shannon entropy 0.38555
G+C content 0.34162
Mean single sequence MFE -26.40
Consensus MFE -17.42
Energy contribution -18.38
Covariance contribution 0.96
Combinations/Pair 1.13
Mean z-score -2.66
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.55
SVM RNA-class probability 0.992634
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 903692 102 - 22422827
CGUUUUAAGUUUCGUCUGCAAAAAAAUUGUCCUAAAAGAAGGGGAAA--UUUUGGGACUUACUCAAACUCAA-GUGAGUGAGUUUAUUGUGCAGAAUAAAAUCAG---------------
..............((((((..((((((.((((........))))))--)))).(((((((((((.......-.)))))))))))....))))))..........--------------- ( -26.10, z-score =  -2.79, R)
>droSim1.chrX_random 847206 102 - 5698898
UGUUUUAAUUUUCGUCUACAAAAAUAUUGUCCUAAAAGGAGGGGAAA--UUUUGGGACUUACUCAAACUCAA-GUGAGUGAGUUGUUUGUGCAGAAUAAAAACAG---------------
((((((.(((((.((..(((((....((.((((......)))).)).--......((((((((((.......-.)))))))))).)))))))))))).)))))).--------------- ( -24.50, z-score =  -2.05, R)
>droSec1.super_10 746755 101 - 3036183
UGUUUUAAUUUUGGUCUGCAAAAAUAUUGUCCUAAAAGGAGGGGAAA--UUUUGGGAC-UACUCAAACUCAA-GUGAGUGAGUUGUUUGUGCAGAAUAAAAACAG---------------
........(((((.((((((.(((((..(((((((((..........--)))))))))-.((((..((((..-..))))))))))))).)))))).)))))....--------------- ( -28.50, z-score =  -3.32, R)
>droYak2.chrX 826287 99 - 21770863
UGUUUUCAUUUGCGUCCGCCAAAAAAUUGUCCCAAGAAGGAGGGGAAAUUUUUGGGACUUACUCAAACUCAAAGUGAGUAAGUAAAAAAUUAAAAAUAG---------------------
........(((((((((....(((((((..(((........)))..))))))).))))(((((((.........)))))))))))).............--------------------- ( -23.00, z-score =  -2.04, R)
>droEre2.scaffold_4644 884000 120 - 2521924
UGUUUUAAUUUGUGUCUGCAAAAAAAUUGUCCCAAGAGGGAGGGGAAAUUUUUGGGACGUACUCAAACUCAAUGUGAGUGGGUUGUUGGUGCAAAAAAAAAACAAAGAAAUAAAAAAUAG
((((((..((((..((.((((.......((((((((((..........))))))))))...(((..((((.....))))))))))).))..))))...))))))................ ( -29.90, z-score =  -3.12, R)
>consensus
UGUUUUAAUUUUCGUCUGCAAAAAAAUUGUCCUAAAAGGAGGGGAAA__UUUUGGGACUUACUCAAACUCAA_GUGAGUGAGUUGUUUGUGCAGAAUAAAAACAG_______________
..............((((((........(((((((((............)))))))))..((((..((((.....))))))))......))))))......................... (-17.42 = -18.38 +   0.96)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:04:40 2011