Locus 12836

Sequence ID	dm3.chrX
Location	2,545,982 – 2,546,097
Length	115
Max. P	0.536984

overview

Window 5

Location	2,545,982 – 2,546,074
Length	92
Sequences	3
Columns	92
Reading direction	reverse
Mean pairwise identity	88.19
Shannon entropy	0.15970
G+C content	0.56068
Mean single sequence MFE	-26.11
Consensus MFE	-24.71
Energy contribution	-23.17
Covariance contribution	-1.55
Combinations/Pair	1.17
Mean z-score	-0.87
Structure conservation index	0.95
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.09
SVM RNA-class probability	0.536984
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2545982 92 - 22422827
ACUGGAAGAUCGAUGCCAAGCAACUUGGGUCAAGUUGCGUCAGAUUCGGUUCAGACCAGAUGCCACCGGACCACCAGACCCACAAAAGUCUG
.((((..((((((......((((((((...)))))))).......))))))....))))...............(((((........))))) ( -24.72, z-score =  -0.50, R)
>droSim1.chrX_random 1321538 87 - 5698898
ACCGGAAGAUCGAUCCCAAGCAACUUGGGCCAAGUUGCGUCAGAUUCGGUUCAGACCAGACGCCACCGG-----UGGGCCCACAAAAGUCCG
(((((......((((....((((((((...))))))))....)))).(((((......)).))).))))-----)((((........)))). ( -27.40, z-score =  -0.96, R)
>droSec1.super_10 2311667 87 - 3036183
ACCGGAAGAUCGAUCCCAAGCAACUUUGGCAAAGUUGCGUCAGAUUCGGUUCAGUCCAGACGCCACCGG-----UGGGCCCACAAAAGUCCG
(((((..((((((((....(((((((.....)))))))....)).))))))..((....))....))))-----)((((........)))). ( -26.20, z-score =  -1.14, R)
>consensus
ACCGGAAGAUCGAUCCCAAGCAACUUGGGCCAAGUUGCGUCAGAUUCGGUUCAGACCAGACGCCACCGG_____UGGGCCCACAAAAGUCCG
.((((..(((((((.....((((((((...))))))))))).)))).(((((......)).))).)))).....(((((........))))) (-24.71 = -23.17 +  -1.55)

alignment

secondary structure

dotplot

Window 6

Location	2,546,002 – 2,546,097
Length	95
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	67.70
Shannon entropy	0.53664
G+C content	0.56795
Mean single sequence MFE	-33.40
Consensus MFE	-15.28
Energy contribution	-15.12
Covariance contribution	-0.16
Combinations/Pair	1.28
Mean z-score	-1.28
Structure conservation index	0.46
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.04
SVM RNA-class probability	0.513384
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chrX 2546002 95 + 22422827
GGUCCGGUGGCAUCUGGUCUGAACCGAAUCUGACGCAACUUG---ACCCAAGUUGCUUGGCAUCGAUCUUCCAGUGCACUAGCAC-----------CUUGGGCGAAAAG
.(((((((((((.((((...((..(((..(..(.((((((((---...)))))))))..)..))).))..))))))).....)))-----------)..))))...... ( -31.80, z-score =  -1.48, R)
>droSim1.chrX_random 1321556 92 + 5698898
---CCGGUGGCGUCUGGUCUGAACCGAAUCUGACGCAACUUG---GCCCAAGUUGCUUGGGAUCGAUCUUCCGGUGCACUAGCAC-----------CUAGGGCGAAAUG
---...((..(((((((...((..(((.((..(.((((((((---...)))))))))..)).))).))..))(((((....))))-----------)..)))))..)). ( -33.00, z-score =  -1.38, R)
>droSec1.super_10 2311685 92 + 3036183
---CCGGUGGCGUCUGGACUGAACCGAAUCUGACGCAACUUU---GCCAAAGUUGCUUGGGAUCGAUCUUCCGGUGCACUAGCAC-----------CUAGGGCGAAAUG
---...((..((((((((..((..(((.((..(.(((((((.---....))))))))..)).))).)).)))(((((....))))-----------)..)))))..)). ( -32.50, z-score =  -2.00, R)
>droYak2.chrX 15964571 99 - 21770863
---CCGGUGGCGUCUGGUCUGAACCGAAUCUGAGGCAACUUG---GCCCAACUUGCUUG----CCAUCUUCCGGUGCACUGGCACUAGCACUAGUACUUGGGUGAAAAG
---..(((((((..((((....))))...(..((....))..---)...........))----)))))....(((((....)))))..((((........))))..... ( -26.40, z-score =   1.22, R)
>dp4.chrXL_group1a 2866626 94 - 9151740
UCUCCGGUCUAGACUGGUCUUGUCCGGGUCUGGCCUGGUUCGAGUGCCAGUCCGGGGUACGGGCAUUGCGCAAGUGCAGCCGCAC------------UUGAACAAU---
..((((.((..(((((((((((.(((((.....)))))..)))).)))))))..))...)))).((((..(((((((....))))------------)))..))))--- ( -43.30, z-score =  -2.74, R)
>consensus
___CCGGUGGCGUCUGGUCUGAACCGAAUCUGACGCAACUUG___GCCCAAGUUGCUUGGGAUCGAUCUUCCGGUGCACUAGCAC___________CUUGGGCGAAAAG
...((((......))))......((.........((((((((......)))))))).................((((....))))..............))........ (-15.28 = -15.12 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:09:42 2011