Locus 11022

Sequence ID	dm3.chr3R
Location	18,131,642 – 18,131,779
Length	137
Max. P	0.999218

overview

Window 4

Location	18,131,642 – 18,131,751
Length	109
Sequences	10
Columns	114
Reading direction	reverse
Mean pairwise identity	77.03
Shannon entropy	0.44337
G+C content	0.51524
Mean single sequence MFE	-32.66
Consensus MFE	-22.24
Energy contribution	-21.64
Covariance contribution	-0.60
Combinations/Pair	1.19
Mean z-score	-2.05
Structure conservation index	0.68
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	2.15
SVM RNA-class probability	0.983969
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18131642 109 - 27905053
---UGUCGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUUCUUGCGCCCAAUUCCACCCACUUUGCCGCAU
---..((((((.(((((..-.)))))))))))(((((((((((......)))))))))))........(((((((..-(((.....))).................))))))). ( -32.31, z-score =  -1.88, R)
>droPer1.super_0 3638689 95 + 11822988
------AGUCGUCGUCGUC-UGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUACUUGC-CGCACUUCGGCUCCU----------
------..((((((.(((.-...)))))))))(((((((((((......))))))))))).........(((((...-.)))))..((-((.....))))....---------- ( -30.80, z-score =  -1.58, R)
>dp4.chr2 12286650 101 - 30794189
AGUCGUCGUCGUCGUCGUC-UGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUACUUGC-CGCACUUCGGCUCCG----------
(((((((((((.((((...-..))))))))))(((((((((((......)))))))))))........(((((((..-.......)))-))))...)))))...---------- ( -33.80, z-score =  -1.76, R)
>droAna3.scaffold_13340 9113676 98 - 23697760
--UUUCUGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUACUUGCUGCCAAUCCCACCC------------
--...((((((.(((((..-.)))))))))))(((((((((((......)))))))))))..........(((((..-.((.....))))))).........------------ ( -28.70, z-score =  -2.43, R)
>droYak2.chr3R 18973530 109 - 28832112
---UGUCGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUUCUUGCGCCCAAUGCCACCCACUUUGCGGCAU
---(((((((((((.(((.-...)))))))).(((((((((((......))))))))))).........((((((..-(((.....))).....)))))).......)))))). ( -37.00, z-score =  -2.14, R)
>droSec1.super_0 18487141 109 - 21120651
---UGUCCUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC-CGCUUCUUGCGCCCAAUUCCACCCACUUUGCCGCAU
---.....((((((.(((.-...)))))))))(((((((((((......)))))))))))........(((((((..-(((.....))).................))))))). ( -30.11, z-score =  -1.67, R)
>droSim1.chr3R 17937023 109 - 27517382
---UGUCGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUAUUGUGGCACC-CGCUUCUUGCGCCCAAUUCCACCCACUUUGCCGCAU
---..((((((.(((((..-.)))))))))))(((((((((((......)))))))))))........(((((((..-(((.....))).................))))))). ( -32.31, z-score =  -2.28, R)
>droVir3.scaffold_13047 10872021 99 + 19223366
---CCUUGUUGUUGUCCUCCAGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCACC-CACAGCAACAGCCAACGUGCAACUC-----------
---....(((((.((((....))))(((.((((((((((((((......))))))))))......((((((((....-..)))))))))))).))))))))..----------- ( -34.90, z-score =  -3.26, R)
>droMoj3.scaffold_6540 27824024 98 - 34148556
---CCUUGUUGUUGUCCUCGAGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCACC-CACAGCCA-GGCAAACGUGUAACUC-----------
---(((.(((((.((((....))))((((((((((((((((((......)))))))))).)))))))).........-.))))).)-))..............----------- ( -29.20, z-score =  -1.38, R)
>droGri2.scaffold_15074 1267681 99 - 7742996
---CCUUGUUGUUGUCCUCCUGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCAUCGCGCAGCAA-GGCGAGCGUGCAUCGC-----------
---(((((((((.((((....))))((((((.(((((((((((......)))))))))))..((....))...)))))))))))))-))...(((.....)))----------- ( -37.50, z-score =  -2.10, R)
>consensus
___UGUCGUCGUCGUCGUC_UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC_CGCUUCUUGCGCCCAAUUCCACCCC___________
.......((((.(((((....)))))))))(((((((((((((......))))))))(((((....))))).)))))..................................... (-22.24 = -21.64 +  -0.60)

alignment

secondary structure

dotplot

Window 5

Location	18,131,678 – 18,131,779
Length	101
Sequences	10
Columns	110
Reading direction	reverse
Mean pairwise identity	75.11
Shannon entropy	0.48383
G+C content	0.50625
Mean single sequence MFE	-30.94
Consensus MFE	-22.04
Energy contribution	-21.44
Covariance contribution	-0.60
Combinations/Pair	1.19
Mean z-score	-2.96
Structure conservation index	0.71
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	3.72
SVM RNA-class probability	0.999218
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 18131678 101 - 27905053
CACCCGCCACCGCCCACUCUUCCAACGUUG--------UCGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC
.....(((((.((.................--------((((((.(((((..-.)))))))))))(((((((((((......)))))))))))......)).)))))... ( -32.50, z-score =  -2.94, R)
>droPer1.super_0 3638714 102 + 11822988
CACCGCCUUGCCACAUUC-UGCAAGCAUCCAGUA------GUCGUCGUCGUC-UGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC
........(((((((...-((....))..((((.------.((((((.(((.-...)))))))))(((((((((((......)))))))))))...)))).))))))).. ( -33.20, z-score =  -2.15, R)
>dp4.chr2 12286675 109 - 30794189
CACCGCCUUGCCACAUUCUUGCAAGCAUCCAGUAGUCGUCGUCGUCGUCGUC-UGGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC
........(((((((.........((..((((....((.((....)).)).)-)))..))(((..(((((((((((......)))))))))))))).....))))))).. ( -35.00, z-score =  -2.30, R)
>droAna3.scaffold_13340 9113700 100 - 23697760
-------ACCCGCCCUGUUUUCCGGCCCUCAGU--UUUCUGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC
-------.................((((.((((--...((((((.(((((..-.)))))))))))(((((((((((......)))))))))))...))))..).)))... ( -29.60, z-score =  -2.44, R)
>droYak2.chr3R 18973566 98 - 28832112
CACCCA--ACAG-CAACUCUGCCAACGUUG--------UCGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC
..((((--((((-......(((..(((..(--------(((.(((((.....-.)))))))))..)))((((((((......)))))))))))....)))))).)).... ( -31.90, z-score =  -2.68, R)
>droSec1.super_0 18487177 101 - 21120651
CACCCGCCACAGCCCACUCUUCCAACGUUG--------UCCUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC
.....((((((((.................--------...((((((.(((.-...)))))))))(((((((((((......)))))))))))......))))))))... ( -34.10, z-score =  -4.05, R)
>droSim1.chr3R 17937059 101 - 27517382
CACCCGCCACAGCCCACUCUUCCAACGUUG--------UCGUCGUCGUCGUC-UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUAUUGUGGCACC
.....(((((((..................--------((((((.(((((..-.)))))))))))(((((((((((......))))))))))).......)))))))... ( -33.30, z-score =  -3.81, R)
>droVir3.scaffold_13047 10872046 84 + 19223366
------------------UCUCCAUCGUCC--------UUGUUGUUGUCCUCCAGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCACC
------------------...(((((((((--------(((..(.....)..))))).)))))))(((((((((((......)))))))))))................. ( -25.40, z-score =  -3.16, R)
>droMoj3.scaffold_6540 27824048 84 - 34148556
------------------UCGCCAUCGUCC--------UUGUUGUUGUCCUCGAGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCACC
------------------.(((((((((((--------(((..(....)..)))))..))))))))).((((((((......))))))))((((.((....))))))... ( -28.30, z-score =  -3.06, R)
>droGri2.scaffold_15074 1267706 84 - 7742996
------------------UCGCCAUCGUCC--------UUGUUGUUGUCCUCCUGGGCGCGAUGGUGUGUUUUAUUAUCGCAAAUAAAGCGCAAUCAUUGUUGUUGCAUC
------------------.(((((((((..--------........((((....))))))))))))).((((((((......))))))))((((.((....))))))... ( -26.10, z-score =  -3.05, R)
>consensus
CACC____ACCG_CCACUUUGCCAACGUCC________UCGUCGUCGUCGUC_UCGGCGCGAUGGUGUGUUUUAUUAUCACAAAUAAAGCGCAAUCACUGUUGUGGCACC
........................................((((.(((((....)))))))))(((((((((((((......))))))))(((((....))))).))))) (-22.04 = -21.44 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:34:54 2011