Locus 2102

Sequence ID dm3.chr2L
Location 16,339,616 – 16,339,715
Length 99
Max. P 0.998914
window2890 window2891 window2892

overview

Window 0

Location 16,339,616 – 16,339,713
Length 97
Sequences 8
Columns 120
Reading direction reverse
Mean pairwise identity 59.21
Shannon entropy 0.71858
G+C content 0.61922
Mean single sequence MFE -48.36
Consensus MFE -9.89
Energy contribution -11.62
Covariance contribution 1.73
Combinations/Pair 1.45
Mean z-score -2.77
Structure conservation index 0.20
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.42
SVM RNA-class probability 0.938251
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16339616 97 - 23011544
------GACCCGGACCCAGAGGAUAUCCA---GGUCGUGGACCCAGGGGAUAUCCCGGUCCGGGACCCAGAGGAUAUCCUGGUCAGGGACCCAGAAGAUAUUCUUG--------------
------..(((.((((...(((((((((.---((((.((((((...(((....))))))))).))))....))))))))))))).)))....((((....))))..-------------- ( -47.90, z-score =  -2.88, R)
>droSim1.chr2L 16047289 97 - 22036055
------GUCCCGGACCCAGAGGAUAUCCA---GGUCAGGGACCCGGAGGAUAUCCUGGUCCGGGACCGAGAGGAUAUCCUGGUCCGGGACCGAGAGGAUGUCCUGG--------------
------((((((((((...(((((((((.---((((..(((((.(((.....))).)))))..))))....)))))))))))))))))))....(((....)))..-------------- ( -59.10, z-score =  -4.30, R)
>droSec1.super_5 5063394 97 - 5866729
------GUCCCGGACCCAGAGGAUAUCCA---GGUCAGGGACCCAGAGGAUAUCCUGGUCCGGGACCGAGAGGAUAUCCUGGUCCGGGACCGAGAGGAUGUCCUGG--------------
------((((((((((...(((((((((.---((((..(((((...(((....))))))))..))))....)))))))))))))))))))....(((....)))..-------------- ( -56.50, z-score =  -4.08, R)
>droYak2.chr2R 2794108 97 - 21139217
------GUUCAGGGCCCAGGGGAUAUCCA---GGUCCAGGAGCCAGGGGAUACCCAGGUCCUGGACCCAGGGGAUAUUCAGGCCCGGGAUCUAGAGGAUAUUCCGC--------------
------((((.(((((....((((((((.---(((((((((.((.(((....))).)))))))))))....)))))))).))))).)))).....((.....))..-------------- ( -51.10, z-score =  -3.58, R)
>droEre2.scaffold_4845 19405142 97 - 22589142
------GUCCGGGACCCAGGGGAUAUCCA---GGUCCGGGACCUAGGGGAUAUCCAGGUCCGGGAUCUAGAGGAUAUCCCGCUCCGGGAUCUAGAGGAUAUCCCGC--------------
------...((((((((((((((((((((---(((((.((((((.(((....))))))))).))))))...))))))))).))..)))(((.....))).))))).-------------- ( -52.90, z-score =  -2.61, R)
>droAna3.scaffold_13183 41606 111 + 43642
------GUCCUGACGCAGGAGCAAAAACA---GGUACGGGUCCAGGAGCAAAAGCAGUUCCUGGCGCAGAAGCAGGUACUGGCGCGGGAGCAGGUACUGGCCCAGGAGCAGGUCCUGGCG
------((((((..((....)).....))---)).))..(.((((((((....)).((((((((.((.......((((((...((....)).)))))).))))))))))...))))))). ( -43.60, z-score =  -0.90, R)
>dp4.chr4_group3 8039910 100 - 11692001
GACCUGGAUUUGGACUUGGACGAGGACCACCUGGCUAUGGACCUGGACCAGGACCA---CCUGGAUAUGGACGACCACCAGGACC---ACCAGGGUAUGGGCCUGG--------------
..((.((.......)).)).(.(((.((((((((...(((.(((((.(((((....---)))))...(((....)))))))).))---))))))...))).))).)-------------- ( -37.90, z-score =  -1.91, R)
>droPer1.super_1 9489342 100 - 10282868
GACCUGGAUUUGGACUUGGACGAGGACCACCUGGCUAUGGACCUGGACCAGGACCA---CCUGGAUAUGGACGACCACCAGGACC---ACCAGGGUAUGGGCCUGG--------------
..((.((.......)).)).(.(((.((((((((...(((.(((((.(((((....---)))))...(((....)))))))).))---))))))...))).))).)-------------- ( -37.90, z-score =  -1.91, R)
>consensus
______GUCCCGGACCCAGAGGAUAUCCA___GGUCAGGGACCCAGAGGAUAUCCAGGUCCGGGACCUAGAGGAUAUCCUGGUCCGGGACCAAGAGGAUGUCCUGG______________
........((.(((((...((((((.((....((.......))..........(((.....))).......)).))))))))))).))................................ ( -9.89 = -11.62 +   1.73)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 16,339,616 – 16,339,715
Length 99
Sequences 8
Columns 111
Reading direction forward
Mean pairwise identity 58.27
Shannon entropy 0.81562
G+C content 0.61603
Mean single sequence MFE -47.18
Consensus MFE -11.85
Energy contribution -11.54
Covariance contribution -0.31
Combinations/Pair 1.65
Mean z-score -2.76
Structure conservation index 0.25
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.67
SVM RNA-class probability 0.994116
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16339616 99 + 23011544
------------CAAGAAUAUCUUCUGGGUCCCUGACCAGGAUAUCCUCUGGGUCCCGGACCGGGAUAUCCCCUGGGUCCACGACCUGGAUAUCCUCUGGGUCCGGGUCCU
------------..((((....))))(((.(((.(((((((((((((...(((((..((((((((....)))...)))))..))))))))))))))...)))).))).))) ( -49.40, z-score =  -2.38, R)
>droSim1.chr2L 16047289 99 + 22036055
------------CCAGGACAUCCUCUCGGUCCCGGACCAGGAUAUCCUCUCGGUCCCGGACCAGGAUAUCCUCCGGGUCCCUGACCUGGAUAUCCUCUGGGUCCGGGACCU
------------..(((....)))...((((((((((((((((((((....((((..(((((.(((.....))).)))))..)))).)))))))))...))))))))))). ( -59.70, z-score =  -4.77, R)
>droSec1.super_5 5063394 99 + 5866729
------------CCAGGACAUCCUCUCGGUCCCGGACCAGGAUAUCCUCUCGGUCCCGGACCAGGAUAUCCUCUGGGUCCCUGACCUGGAUAUCCUCUGGGUCCGGGACCU
------------..(((....)))...((((((((((((((((((((....((((..((((((((....)))...)))))..)))).)))))))))...))))))))))). ( -57.90, z-score =  -4.39, R)
>droYak2.chr2R 2794108 99 + 21139217
------------GCGGAAUAUCCUCUAGAUCCCGGGCCUGAAUAUCCCCUGGGUCCAGGACCUGGGUAUCCCCUGGCUCCUGGACCUGGAUAUCCCCUGGGCCCUGAACCU
------------..((.....))..........(((((((.((((((...((((((((((((.(((....))).)).)))))))))))))))).)...))))))....... ( -45.40, z-score =  -2.68, R)
>droEre2.scaffold_4845 19405142 99 + 22589142
------------GCGGGAUAUCCUCUAGAUCCCGGAGCGGGAUAUCCUCUAGAUCCCGGACCUGGAUAUCCCCUAGGUCCCGGACCUGGAUAUCCCCUGGGUCCCGGACCU
------------..(((((((((...((.(((.(((...(((.....)))...))).))).)))))))))))..((((((.(((((..(.......)..))))).)))))) ( -49.20, z-score =  -2.17, R)
>droAna3.scaffold_13183 41608 111 - 43642
CCAGGACCUGCUCCUGGGCCAGUACCUGCUCCCGCGCCAGUACCUGCUUCUGCGCCAGGAACUGCUUUUGCUCCUGGACCCGUACCUGUUUUUGCUCCUGCGUCAGGACCU
((((((.....))))))((..((((..((......))..))))..))...((((((((((...((....))))))))...))))((((....(((....))).)))).... ( -36.20, z-score =  -0.80, R)
>dp4.chr4_group3 8039910 102 + 11692001
CCAGGCCCAUACCCUGGUGGUCCUGGUGGUCGUCCAUAUCCAGGUGGUCCUGGUCCAGGUCC---AUAGCCAGGUGGUCCUCGUCCAAGUCCAAAUCCAGGUCCA------
(((((.......)))))(((.((((((((.((.((((......)))).).(((.(.(((.((---((......)))).))).).))).).)))...))))).)))------ ( -39.80, z-score =  -2.46, R)
>droPer1.super_1 9489342 102 + 10282868
CCAGGCCCAUACCCUGGUGGUCCUGGUGGUCGUCCAUAUCCAGGUGGUCCUGGUCCAGGUCC---AUAGCCAGGUGGUCCUCGUCCAAGUCCAAAUCCAGGUCCA------
(((((.......)))))(((.((((((((.((.((((......)))).).(((.(.(((.((---((......)))).))).).))).).)))...))))).)))------ ( -39.80, z-score =  -2.46, R)
>consensus
____________CCAGGACAUCCUCUUGGUCCCGGACCAGGAUAUCCUCUUGGUCCAGGACCUGGAUAUCCCCUGGGUCCCCGACCUGGAUAUCCUCUGGGUCCAGGACCU
.................................(((........)))..((((.(((((....((...(((...(((.......))))))...)).))))).))))..... (-11.85 = -11.54 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 16,339,616 – 16,339,715
Length 99
Sequences 8
Columns 111
Reading direction reverse
Mean pairwise identity 58.27
Shannon entropy 0.81562
G+C content 0.61603
Mean single sequence MFE -50.94
Consensus MFE -13.45
Energy contribution -13.71
Covariance contribution 0.27
Combinations/Pair 1.60
Mean z-score -3.22
Structure conservation index 0.26
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.55
SVM RNA-class probability 0.998914
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 16339616 99 - 23011544
AGGACCCGGACCCAGAGGAUAUCCAGGUCGUGGACCCAGGGGAUAUCCCGGUCCGGGACCCAGAGGAUAUCCUGGUCAGGGACCCAGAAGAUAUUCUUG------------
.((.(((.((((...(((((((((.((((.((((((...(((....))))))))).))))....))))))))))))).))).)).((((....))))..------------ ( -49.80, z-score =  -3.02, R)
>droSim1.chr2L 16047289 99 - 22036055
AGGUCCCGGACCCAGAGGAUAUCCAGGUCAGGGACCCGGAGGAUAUCCUGGUCCGGGACCGAGAGGAUAUCCUGGUCCGGGACCGAGAGGAUGUCCUGG------------
.(((((((((((...(((((((((.((((..(((((.(((.....))).)))))..))))....))))))))))))))))))))...(((....)))..------------ ( -63.50, z-score =  -5.15, R)
>droSec1.super_5 5063394 99 - 5866729
AGGUCCCGGACCCAGAGGAUAUCCAGGUCAGGGACCCAGAGGAUAUCCUGGUCCGGGACCGAGAGGAUAUCCUGGUCCGGGACCGAGAGGAUGUCCUGG------------
.(((((((((((...(((((((((.((((..(((((...(((....))))))))..))))....))))))))))))))))))))...(((....)))..------------ ( -60.90, z-score =  -4.89, R)
>droYak2.chr2R 2794108 99 - 21139217
AGGUUCAGGGCCCAGGGGAUAUCCAGGUCCAGGAGCCAGGGGAUACCCAGGUCCUGGACCCAGGGGAUAUUCAGGCCCGGGAUCUAGAGGAUAUUCCGC------------
((((((.(((((....((((((((.(((((((((.((.(((....))).)))))))))))....)))))))).))))).))))))...((.....))..------------ ( -55.30, z-score =  -4.51, R)
>droEre2.scaffold_4845 19405142 99 - 22589142
AGGUCCGGGACCCAGGGGAUAUCCAGGUCCGGGACCUAGGGGAUAUCCAGGUCCGGGAUCUAGAGGAUAUCCCGCUCCGGGAUCUAGAGGAUAUCCCGC------------
((((((.(((((..(((....))).))))).))))))..(((((((((((((((.(((....(.((....)))..))).))))))...)))))))))..------------ ( -54.80, z-score =  -2.79, R)
>droAna3.scaffold_13183 41608 111 + 43642
AGGUCCUGACGCAGGAGCAAAAACAGGUACGGGUCCAGGAGCAAAAGCAGUUCCUGGCGCAGAAGCAGGUACUGGCGCGGGAGCAGGUACUGGCCCAGGAGCAGGUCCUGG
.(.(((((...))))).)...........((((.((....((....)).((((((((.((.......((((((...((....)).)))))).)))))))))).)).)))). ( -44.60, z-score =  -1.43, R)
>dp4.chr4_group3 8039910 102 - 11692001
------UGGACCUGGAUUUGGACUUGGACGAGGACCACCUGGCUAU---GGACCUGGACCAGGACCACCUGGAUAUGGACGACCACCAGGACCACCAGGGUAUGGGCCUGG
------.((.(((.....(((.(((....)))..)))(((((...(---((.(((((.(((((....)))))...(((....)))))))).))))))))....)))))... ( -39.30, z-score =  -1.98, R)
>droPer1.super_1 9489342 102 - 10282868
------UGGACCUGGAUUUGGACUUGGACGAGGACCACCUGGCUAU---GGACCUGGACCAGGACCACCUGGAUAUGGACGACCACCAGGACCACCAGGGUAUGGGCCUGG
------.((.(((.....(((.(((....)))..)))(((((...(---((.(((((.(((((....)))))...(((....)))))))).))))))))....)))))... ( -39.30, z-score =  -1.98, R)
>consensus
AGGUCCCGGACCCAGAGGAUAUCCAGGUCCGGGACCCAGAGGAUAUCCAGGUCCGGGACCAAGAGGAUAUCCUGGUCCGGGACCAAGAGGAUAUCCAGG____________
...............((.((((((.(((((.((.(((...((((......))))))).))....(((........))).)))))....)))))).)).............. (-13.45 = -13.71 +   0.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:44:48 2011