Locus 12847

Sequence ID dm3.chrX
Location 2,597,910 – 2,598,087
Length 177
Max. P 0.917607
window17661 window17662 window17663 window17664

overview

Window 1

Location 2,597,910 – 2,598,028
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.67
Shannon entropy 0.42983
G+C content 0.41273
Mean single sequence MFE -34.72
Consensus MFE -14.89
Energy contribution -15.17
Covariance contribution 0.28
Combinations/Pair 1.42
Mean z-score -2.17
Structure conservation index 0.43
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.49
SVM RNA-class probability 0.716151
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2597910 118 - 22422827
AAUAGCAACAAAAGCUGCACGCCAUGGGCGUAGCUUGCUUUAAAAUGGGGAUCCAUCCCCCAGGAGCAUAUGUAAGGUGUAUUUA--CUUUACUGAAAUGCACAAUGCACUUUUAAAUUU
....(((...(((((.(((((((...))))).))..)))))....(((((.......)))))...((((..((((((((....))--))))))....))))....)))............ ( -36.40, z-score =  -2.47, R)
>droEre2.scaffold_4690 24446 116 - 18748788
AGCAGCAACAAAAGUUGCGGGCCAUGGGCGU-GCAUGGUAUAGAAAGGGGAUUU-UCCCCCAAGCGCAUAUUUAAGGUGUAGGUA--UUUUAGUGAAACACUCCAUGCGCCUUUGAACUU
.((.(((((....)))))..))((.((((..-((((((........((((....-..))))..............(((((...((--(....)))..))))))))))))))).))..... ( -35.60, z-score =  -0.93, R)
>droYak2.chrX 16018482 114 + 21770863
AGCAGCAACAAAAGUUGCAGGCCAUGGGCGUAGCCUGGUAUAGAAAAGGGAUAUUUCGCCCGAGAACAUAUUCAAGGAGUAUUUAUGUUUAAGUGAAAUAUGGAGUAUUCAUUU------
....(((((....))))).(..(.((((((...(((..(.....)..)))......)))))).)..).........((((((((((((((.....)))))).))))))))....------ ( -27.70, z-score =  -1.49, R)
>droSec1.super_10 2359485 118 - 3036183
AACAGCAACAAAAGUUGCAGGACAUGGGCGUAGUUUGCUAUAUGAUGGGGGUCCAUCCCCCAGAAGCAUAUGUAAGCUAUAUUUA--CUUUACUGAAAUUCACAAAGCACUUUUAAAUUU
....(((((....))))).........(((((((((((.(((((.((((((.....))))))....)))))))))))))).....--......((.....))....))............ ( -33.60, z-score =  -2.70, R)
>droSim1.chrX 1801030 118 - 17042790
AACAGCAACAAAAGUUGCAGGCCAUGGGCGUAGUUUGCUAUAUGAUGGGGGUCCAUCCCCCAGAAGCAUAUGUAAGCUAUAUUUA--CUUUACUGAAAUGCACAAUGCAGCUCUAAAUUU
....(((((....))))).......(((((((((((((.(((((.((((((.....))))))....)))))))))))))).....--...........(((.....)))))))....... ( -40.30, z-score =  -3.23, R)
>consensus
AACAGCAACAAAAGUUGCAGGCCAUGGGCGUAGCUUGCUAUAGAAUGGGGAUCCAUCCCCCAGGAGCAUAUGUAAGGUGUAUUUA__CUUUACUGAAAUACACAAUGCACCUUUAAAUUU
.((.(((((....)))))..(((...)))))...............((((.......))))............((((((((((....................))))))))))....... (-14.89 = -15.17 +   0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,597,948 – 2,598,068
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.50
Shannon entropy 0.30401
G+C content 0.49336
Mean single sequence MFE -40.92
Consensus MFE -23.57
Energy contribution -24.73
Covariance contribution 1.16
Combinations/Pair 1.20
Mean z-score -2.02
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.19
SVM RNA-class probability 0.584584
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2597948 120 - 22422827
CCAGCACUGUGACUAUCGAAAAGUCGGUCUCUGCUGCGAAAAUAGCAACAAAAGCUGCACGCCAUGGGCGUAGCUUGCUUUAAAAUGGGGAUCCAUCCCCCAGGAGCAUAUGUAAGGUGU
...(((((.(((((.......)))))((..(((.(((.......)))...(((((.(((((((...))))).))..))))).....(((((....))))))))..))........))))) ( -36.90, z-score =  -0.91, R)
>droEre2.scaffold_4690 24484 118 - 18748788
GCAUCACUGUGGCUAUCGAAAUGUCGGCUUCUGCCGCAAAAGCAGCAACAAAAGUUGCGGGCCAUGGGCGU-GCAUGGUAUAGAAAGGGGAU-UUUCCCCCAAGCGCAUAUUUAAGGUGU
(((((.((((((((.......((.((((....))))))......(((((....))))).))))))))..((-((.(((.........(((..-...)))))).))))........))))) ( -42.30, z-score =  -1.60, R)
>droYak2.chrX 16018516 120 + 21770863
GCAGCACUGUGGCUAUCGAAAAGUCGGCCUCUGCCACAAAAGCAGCAACAAAAGUUGCAGGCCAUGGGCGUAGCCUGGUAUAGAAAAGGGAUAUUUCGCCCGAGAACAUAUUCAAGGAGU
...((.((((((((........((.(((....))))).......(((((....))))).))))))))))....(((...(((.....(((........))).......)))...)))... ( -33.10, z-score =  -0.05, R)
>droSec1.super_10 2359523 120 - 3036183
UCAGCACUGUGGCUAUCGAAAAGUCGGUCUCUGCUGCGAAAACAGCAACAAAAGUUGCAGGACAUGGGCGUAGUUUGCUAUAUGAUGGGGGUCCAUCCCCCAGAAGCAUAUGUAAGCUAU
((((..(((..((((((((....)))))...(((((......))))).....)))..)))..).)))..(((((((((.(((((.((((((.....))))))....)))))))))))))) ( -45.00, z-score =  -3.36, R)
>droSim1.chrX 1801068 120 - 17042790
UCAGCACUGUGGUUAUCGAAAAGUCUGUCUCUGCUGCGAAAACAGCAACAAAAGUUGCAGGCCAUGGGCGUAGUUUGCUAUAUGAUGGGGGUCCAUCCCCCAGAAGCAUAUGUAAGCUAU
...((.((((((((.(((...(((........))).))).....(((((....))))).))))))))))(((((((((.(((((.((((((.....))))))....)))))))))))))) ( -47.30, z-score =  -4.17, R)
>consensus
GCAGCACUGUGGCUAUCGAAAAGUCGGUCUCUGCUGCGAAAACAGCAACAAAAGUUGCAGGCCAUGGGCGUAGCUUGCUAUAGAAUGGGGAUCCAUCCCCCAGGAGCAUAUGUAAGGUGU
...((.((((((((........(.((((....))))).......(((((....))))).))))))))))....(((((.......(((((.......))))).........))))).... (-23.57 = -24.73 +   1.16)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,597,967 – 2,598,087
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.33
Shannon entropy 0.27559
G+C content 0.54186
Mean single sequence MFE -44.00
Consensus MFE -31.00
Energy contribution -31.12
Covariance contribution 0.12
Combinations/Pair 1.21
Mean z-score -2.27
Structure conservation index 0.70
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.26
SVM RNA-class probability 0.917607
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2597967 120 + 22422827
GGGGGAUGGAUCCCCAUUUUAAAGCAAGCUACGCCCAUGGCGUGCAGCUUUUGUUGCUAUUUUCGCAGCAGAGACCGACUUUUCGAUAGUCACAGUGCUGGCAUUGUGGCGGAACUCGCG
.(((((....)))))........((((((((((((...)))))..))))).((((((.......))))))(((..(((....)))...(((((((((....)))))))))....))))). ( -45.30, z-score =  -2.29, R)
>droEre2.scaffold_4690 24503 118 + 18748788
-GGGGGAAAAUCCCCUUUCUAUACCAUGC-ACGCCCAUGGCCCGCAACUUUUGUUGCUGCUUUUGCGGCAGAAGCCGACAUUUCGAUAGCCACAGUGAUGCCAUUGUGGCGGGAGUCGCG
-(((((.....)))))...........((-((.(((..(((..(((((....))))).)))..((((((....)))).))........(((((((((....)))))))))))).)).)). ( -47.50, z-score =  -2.80, R)
>droYak2.chrX 16018535 120 - 21770863
GGGCGAAAUAUCCCUUUUCUAUACCAGGCUACGCCCAUGGCCUGCAACUUUUGUUGCUGCUUUUGUGGCAGAGGCCGACUUUUCGAUAGCCACAGUGCUGCCAUUGCAGCGGGACUUGCG
..((((....((((............(((((((....(((((((((((....)))))((((.....)))).))))))......)).))))).....(((((....))))))))).)))). ( -44.40, z-score =  -2.07, R)
>droSec1.super_10 2359542 120 + 3036183
GGGGGAUGGACCCCCAUCAUAUAGCAAACUACGCCCAUGUCCUGCAACUUUUGUUGCUGUUUUCGCAGCAGAGACCGACUUUUCGAUAGCCACAGUGCUGACAUUGUGGCGGGACUCGCG
(((((.....)))))................(((....(((((.....(((((((((.......)))))))))..(((....)))...(((((((((....))))))))))))))..))) ( -44.40, z-score =  -2.87, R)
>droSim1.chrX 1801087 120 + 17042790
GGGGGAUGGACCCCCAUCAUAUAGCAAACUACGCCCAUGGCCUGCAACUUUUGUUGCUGUUUUCGCAGCAGAGACAGACUUUUCGAUAACCACAGUGCUGACAUUGUGGCGGGACUCGCG
(((((.....)))))................(((....(((((((...(((((((((.......))))))))).................(((((((....)))))))))))).)).))) ( -38.40, z-score =  -1.31, R)
>consensus
GGGGGAUGGAUCCCCAUUAUAUAGCAAGCUACGCCCAUGGCCUGCAACUUUUGUUGCUGUUUUCGCAGCAGAGACCGACUUUUCGAUAGCCACAGUGCUGACAUUGUGGCGGGACUCGCG
(((((.....)))))................(((......(((((...(((((((((.......))))))))).................(((((((....))))))))))))....))) (-31.00 = -31.12 +   0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,597,967 – 2,598,087
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.33
Shannon entropy 0.27559
G+C content 0.54186
Mean single sequence MFE -42.22
Consensus MFE -32.64
Energy contribution -34.04
Covariance contribution 1.40
Combinations/Pair 1.25
Mean z-score -1.69
Structure conservation index 0.77
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.68
SVM RNA-class probability 0.784800
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2597967 120 - 22422827
CGCGAGUUCCGCCACAAUGCCAGCACUGUGACUAUCGAAAAGUCGGUCUCUGCUGCGAAAAUAGCAACAAAAGCUGCACGCCAUGGGCGUAGCUUGCUUUAAAAUGGGGAUCCAUCCCCC
.(((((((.((((.((..((((((...(.((((..(.....)..)))).)(((((......)))))......))))...))..)))))).)))))))........(((((....))))). ( -40.00, z-score =  -2.04, R)
>droEre2.scaffold_4690 24503 118 - 18748788
CGCGACUCCCGCCACAAUGGCAUCACUGUGGCUAUCGAAAUGUCGGCUUCUGCCGCAAAAGCAGCAACAAAAGUUGCGGGCCAUGGGCGU-GCAUGGUAUAGAAAGGGGAUUUUCCCCC-
.((.((.((((((.....)))......((((((.......((.((((....))))))......(((((....))))).))))))))).))-))............((((.....)))).- ( -44.80, z-score =  -1.71, R)
>droYak2.chrX 16018535 120 + 21770863
CGCAAGUCCCGCUGCAAUGGCAGCACUGUGGCUAUCGAAAAGUCGGCCUCUGCCACAAAAGCAGCAACAAAAGUUGCAGGCCAUGGGCGUAGCCUGGUAUAGAAAAGGGAUAUUUCGCCC
.....((((((((((....)))))((((.(((((.((....((.(((((.(((.......)))(((((....))))))))))))...)))))))))))........)))))......... ( -44.00, z-score =  -1.69, R)
>droSec1.super_10 2359542 120 - 3036183
CGCGAGUCCCGCCACAAUGUCAGCACUGUGGCUAUCGAAAAGUCGGUCUCUGCUGCGAAAACAGCAACAAAAGUUGCAGGACAUGGGCGUAGUUUGCUAUAUGAUGGGGGUCCAUCCCCC
.((((((..((((...(((((....(((..((((((((....)))))...(((((......))))).....)))..)))))))).))))..))))))........(((((.....))))) ( -44.30, z-score =  -2.24, R)
>droSim1.chrX 1801087 120 - 17042790
CGCGAGUCCCGCCACAAUGUCAGCACUGUGGUUAUCGAAAAGUCUGUCUCUGCUGCGAAAACAGCAACAAAAGUUGCAGGCCAUGGGCGUAGUUUGCUAUAUGAUGGGGGUCCAUCCCCC
.(((.....)))......((((((.((((((((.(((...(((........))).))).....(((((....))))).))))))))))((((....)))).))))(((((.....))))) ( -38.00, z-score =  -0.78, R)
>consensus
CGCGAGUCCCGCCACAAUGGCAGCACUGUGGCUAUCGAAAAGUCGGUCUCUGCUGCGAAAACAGCAACAAAAGUUGCAGGCCAUGGGCGUAGCUUGCUAUAGAAUGGGGAUCCAUCCCCC
.((((((..((((...(((((.....((((((.(((((....)))))....))))))......(((((....)))))..))))).))))..))))))........(((((....))))). (-32.64 = -34.04 +   1.40)

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 01:09:56 2011