Locus 1639

Sequence ID	X_DroMel_CAF1
Location	4,657,767 – 4,657,882
Length	115
Max. P	0.727000

overview

Window 9

Location	4,657,767 – 4,657,882
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.06
Mean single sequence MFE	-35.62
Consensus MFE	-23.71
Energy contribution	-24.48
Covariance contribution	0.77
Combinations/Pair	1.06
Mean z-score	-2.19
Structure conservation index	0.67
SVM decision value	-0.05
SVM RNA-class probability	0.506346
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4657767 115 + 22224390
---GAUAGAGGGCGAG--CGGAGCAAAGUGAAACUUUUCAAUAUCCGCAUCCGCUCAUGAAUAAUAAUUCAUAAUGGCCGUGGCCGCGUGUCAUAAAAACUCGAGCGGCAGGAGCCUCGA
---....((((.(..(--((((......((((....))))...)))))..((((((((((((....)))))).((((((((....))).)))))........)))))).....))))).. ( -39.20)
>DroSec_CAF1 19236 115 + 1
---GAUAGAGUGCGAG--CGGAGCAAAGUGAAACUUUUCAAUAUCCGCAUCCGCUCAUGAAUAAUAAUUUAUAAUGGCCGUGGCCGCGUGUCAUAAAAAGUCGAGCGGCAGGAGCCUCGA
---....(((.((..(--((((......((((....))))...)))))..((((((((((((....)))))).((((((((....))).)))))........)))))).....))))).. ( -37.00)
>DroSim_CAF1 7186 115 + 1
---GAUAGAGGGCGAG--CGGAGCAAAGUGAAACUUUUCAAUAUCCGCAUCCGCUCAUGAAUAAUAAUUUAUAAUGGCCGUGGCCGCGUGUCAUAAAAAGUCGAGCGGCAGGAGCCUCGA
---....(((((((((--((((((....((((....))))......)).)))))))((((((....))))))....)))((.(((((.((.(.......).)).)))))....))))).. ( -37.30)
>DroEre_CAF1 20039 114 + 1
----AGAGAGGGCGAG--CGGAGCAAAGUGAAACUUUUCAAUAUCCGCAUCCGCUCAUGAAUAAUAAUUUAUAAUGGCCGUGGCCGCGUGUCAUAAAAAGUCGAGCGGCAGCAGCCUCGA
----...(((((((((--((((((....((((....))))......)).)))))))((((((....))))))....)))((.(((((.((.(.......).)).))))).))...))).. ( -38.90)
>DroYak_CAF1 15752 102 + 1
AAGGAGAGAGAGCGAGCGCGGAGCAAAGUGAAACUUUUCAAUAUCCGCAUCCGCUCAUGAAUAAUAAUUUAUAAUGGCCAUGGCCGCGUGUCAUAAAAAGGC------------------
.........(((((...(((((......((((....))))...)))))...)))))((((((((....))))...(((....))).....))))........------------------ ( -25.70)
>consensus
___GAUAGAGGGCGAG__CGGAGCAAAGUGAAACUUUUCAAUAUCCGCAUCCGCUCAUGAAUAAUAAUUUAUAAUGGCCGUGGCCGCGUGUCAUAAAAAGUCGAGCGGCAGGAGCCUCGA
.........(((((....((((......((((....))))...))))....)))))((((((....)))))).((((((((....))).)))))......((((..(((....))))))) (-23.71 = -24.48 +   0.77)

alignment

secondary structure

dotplot

Window 0

Location	4,657,767 – 4,657,882
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.06
Mean single sequence MFE	-33.87
Consensus MFE	-23.59
Energy contribution	-24.24
Covariance contribution	0.65
Combinations/Pair	1.00
Mean z-score	-2.30
Structure conservation index	0.70
SVM decision value	0.41
SVM RNA-class probability	0.727000
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4657767 115 - 22224390
UCGAGGCUCCUGCCGCUCGAGUUUUUAUGACACGCGGCCACGGCCAUUAUGAAUUAUUAUUCAUGAGCGGAUGCGGAUAUUGAAAAGUUUCACUUUGCUCCG--CUCGCCCUCUAUC---
..(((......(((((....(((.....)))..)))))...(((....((((((....))))))(((((((.(((((...((((....)))).)))))))))--)))))))))....--- ( -38.10)
>DroSec_CAF1 19236 115 - 1
UCGAGGCUCCUGCCGCUCGACUUUUUAUGACACGCGGCCACGGCCAUUAUAAAUUAUUAUUCAUGAGCGGAUGCGGAUAUUGAAAAGUUUCACUUUGCUCCG--CUCGCACUCUAUC---
(((((((....)))..)))).............(((((....)))...................(((((((.(((((...((((....)))).)))))))))--)))))........--- ( -34.40)
>DroSim_CAF1 7186 115 - 1
UCGAGGCUCCUGCCGCUCGACUUUUUAUGACACGCGGCCACGGCCAUUAUAAAUUAUUAUUCAUGAGCGGAUGCGGAUAUUGAAAAGUUUCACUUUGCUCCG--CUCGCCCUCUAUC---
(((((((....)))..)))).............(((((....)))...................(((((((.(((((...((((....)))).)))))))))--)))))........--- ( -33.50)
>DroEre_CAF1 20039 114 - 1
UCGAGGCUGCUGCCGCUCGACUUUUUAUGACACGCGGCCACGGCCAUUAUAAAUUAUUAUUCAUGAGCGGAUGCGGAUAUUGAAAAGUUUCACUUUGCUCCG--CUCGCCCUCUCU----
....(((((..(((((.................)))))..)))))...................(((((((.(((((...((((....)))).)))))))))--))).........---- ( -36.33)
>DroYak_CAF1 15752 102 - 1
------------------GCCUUUUUAUGACACGCGGCCAUGGCCAUUAUAAAUUAUUAUUCAUGAGCGGAUGCGGAUAUUGAAAAGUUUCACUUUGCUCCGCGCUCGCUCUCUCUCCUU
------------------.....(((((((.....(((....))).)))))))...........(((((..((((((......((((.....))))..))))))..)))))......... ( -27.00)
>consensus
UCGAGGCUCCUGCCGCUCGACUUUUUAUGACACGCGGCCACGGCCAUUAUAAAUUAUUAUUCAUGAGCGGAUGCGGAUAUUGAAAAGUUUCACUUUGCUCCG__CUCGCCCUCUAUC___
(((((((....)))..)))).............(((((....)))...................(((((((.(((((...((((....)))).)))))))))..)))))........... (-23.59 = -24.24 +   0.65)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:26 2006