Locus 5489

Sequence ID	dm3.chr2R
Location	20,784,460 – 20,784,551
Length	91
Max. P	0.911012

overview

Window 9

Location	20,784,460 – 20,784,551
Length	91
Sequences	7
Columns	106
Reading direction	forward
Mean pairwise identity	61.39
Shannon entropy	0.68423
G+C content	0.66221
Mean single sequence MFE	-37.80
Consensus MFE	-14.83
Energy contribution	-14.73
Covariance contribution	-0.10
Combinations/Pair	1.21
Mean z-score	-1.26
Structure conservation index	0.39
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.58
SVM RNA-class probability	0.751182
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20784460 91 + 21146708
AUGGCGGCGGG-GGUUGUUGGGGCGUCCAGAUUGGUG-----GGUGGGUGAGUUGGAGGUGUUGGG---------UGGCCAGUGGCCAUGACCUCUCUCCGCUGCC
..(((((((((-((...(..(.((.(((((.(((.(.-----....).))).))))).)).)..)(---------(((((...))))))......))))))))))) ( -38.50, z-score =  -1.20, R)
>dp4.chr3 1872285 86 + 19779522
----------------AAAACAAUGGACAGGGAAGGGA----AGUGAGAGCGAACGAGACGCUGGGCGUCCAGUGCGGCCACUGGCCAUGACCUCGCCUCUCCGCU
----------------.............((..(((..----.((....))...((((.((((((....)))))).((((...)))).....)))))))..))... ( -29.50, z-score =  -0.17, R)
>droPer1.super_2 2055329 86 + 9036312
----------------AAAACAAUGGACAGGGAAGGGA----AGUGAGAGCGAACGAGACGCUGGGCGUCCAGUGCGGCCACUGGCCAUGACCUCGCCUCUCCGCU
----------------.............((..(((..----.((....))...((((.((((((....)))))).((((...)))).....)))))))..))... ( -29.50, z-score =  -0.17, R)
>droSim1.chr2R 19236985 91 + 19596830
AUGGCGGCGGG-GGUGGAUGGGGCGUGCAGAUUGGUG-----GGUGGGUGAGUUGGCGGUGUUGGG---------UGGCCAGUGGCCAUGACCUCUCUCCGCCGCC
..(((((((((-((.((((((.((.(((......)))-----.)).(((.(.(..((...))..).---------).))).....))))..)).).)))))))))) ( -38.60, z-score =  -0.46, R)
>droSec1.super_23 641475 90 + 989336
AUGGCGGCGGG-G-UGGAUGGGGCGUGCAGAUUGGUG-----GGUGGGUGAGUUGGCGGCGUUGGG---------UGGCCAGUGGCCAUGACCUCUCUCCGCCGCC
..(((((((((-(-.(((.((.((.(((......)))-----.)).(((.(.(((((.((.....)---------).)))))).)))....))))))))))))))) ( -42.80, z-score =  -1.67, R)
>droYak2.chr2R 20747447 104 + 21139217
AUGGCGGUGGGUGGAGGGAGGAGGGCGGAGGCGUAUGAGU--GGUGGGUGAGUUGGCGGUGUUGGGGCUGUUGGGUGGCCAGUGGCCAUGACCUCUCUCCGCCAGC
...((....((((((((((((...(((....)))....((--(((.(((.(.(..(((((......)))))..).).)))....)))))..)))))))))))).)) ( -46.80, z-score =  -3.57, R)
>droEre2.scaffold_4845 22154267 87 + 22589142
----------AUGGCGGAGGGGGCGUGCUGAGUGGUGGGUGAGAUGGCGGUGUUGGCGGUGUUGGG---------UGGCCAGUGGCCAUGACCUCUCUCCGCCAGC
----------.((((((((((((((((.(.(.((((.(.(.((((.((.......)).)).)).).---------).)))).).).)))).)).)))))))))).. ( -38.90, z-score =  -1.59, R)
>consensus
AUGGCGG_GGG_GGUGGAAGGGGCGUGCAGAGUGGUG_____GGUGGGUGAGUUGGCGGUGUUGGG_________UGGCCAGUGGCCAUGACCUCUCUCCGCCGCC
......................................................(((((.(..(((.........(((((...)))))...)))..).)))))... (-14.83 = -14.73 +  -0.10)

alignment

secondary structure

dotplot

Window 0

Location	20,784,460 – 20,784,551
Length	91
Sequences	7
Columns	106
Reading direction	reverse
Mean pairwise identity	61.39
Shannon entropy	0.68423
G+C content	0.66221
Mean single sequence MFE	-28.09
Consensus MFE	-11.09
Energy contribution	-10.30
Covariance contribution	-0.79
Combinations/Pair	1.25
Mean z-score	-1.57
Structure conservation index	0.39
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.22
SVM RNA-class probability	0.911012
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 20784460 91 - 21146708
GGCAGCGGAGAGAGGUCAUGGCCACUGGCCA---------CCCAACACCUCCAACUCACCCACC-----CACCAAUCUGGACGCCCCAACAACC-CCCGCCGCCAU
(((.((((.(.(((((..(((((...)))))---------......))))))............-----........(((.....)))......-.)))).))).. ( -27.70, z-score =  -2.51, R)
>dp4.chr3 1872285 86 - 19779522
AGCGGAGAGGCGAGGUCAUGGCCAGUGGCCGCACUGGACGCCCAGCGUCUCGUUCGCUCUCACU----UCCCUUCCCUGUCCAUUGUUUU----------------
...(((.(((.((((....((((...))))((((.((((((...)))))).))..)).......----..)))).))).)))........---------------- ( -30.90, z-score =  -0.85, R)
>droPer1.super_2 2055329 86 - 9036312
AGCGGAGAGGCGAGGUCAUGGCCAGUGGCCGCACUGGACGCCCAGCGUCUCGUUCGCUCUCACU----UCCCUUCCCUGUCCAUUGUUUU----------------
...(((.(((.((((....((((...))))((((.((((((...)))))).))..)).......----..)))).))).)))........---------------- ( -30.90, z-score =  -0.85, R)
>droSim1.chr2R 19236985 91 - 19596830
GGCGGCGGAGAGAGGUCAUGGCCACUGGCCA---------CCCAACACCGCCAACUCACCCACC-----CACCAAUCUGCACGCCCCAUCCACC-CCCGCCGCCAU
((((((((.(((.(((....)))..((((..---------.........)))).))).......-----((......))...............-.)))))))).. ( -28.30, z-score =  -1.97, R)
>droSec1.super_23 641475 90 - 989336
GGCGGCGGAGAGAGGUCAUGGCCACUGGCCA---------CCCAACGCCGCCAACUCACCCACC-----CACCAAUCUGCACGCCCCAUCCA-C-CCCGCCGCCAU
((((((((.(.(.((....(((....(((..---------......)))((.............-----.........))..)))....)).-)-))))))))).. ( -29.25, z-score =  -1.86, R)
>droYak2.chr2R 20747447 104 - 21139217
GCUGGCGGAGAGAGGUCAUGGCCACUGGCCACCCAACAGCCCCAACACCGCCAACUCACCCACC--ACUCAUACGCCUCCGCCCUCCUCCCUCCACCCACCGCCAU
..((((((.(((.(((..(((((...))))).......((.........))..........)))--.)))....((....)).................)))))). ( -23.90, z-score =  -1.18, R)
>droEre2.scaffold_4845 22154267 87 - 22589142
GCUGGCGGAGAGAGGUCAUGGCCACUGGCCA---------CCCAACACCGCCAACACCGCCAUCUCACCCACCACUCAGCACGCCCCCUCCGCCAU----------
..((((((((.(.(((..(((((...)))))---------.........((.......))......................))).))))))))).---------- ( -25.70, z-score =  -1.73, R)
>consensus
GGCGGCGGAGAGAGGUCAUGGCCACUGGCCA_________CCCAACACCGCCAACUCACCCACC_____CACCAAUCUGCACGCCCCAUCCACC_CCC_CCGCCAU
....((((.(...((...(((((...))))).........))...).))))....................................................... (-11.09 = -10.30 +  -0.79)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:49:18 2011